match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	pfam00575	74	63	83.9	1.8	[                                   ------------  ]	S1	S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
2	cd05691	73	62	79.2	2.9	[                                   ------------  ]	S1_RPS1_repeat_ec6	S1_RPS1_repeat_ec6: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
3	cd05694	74	67	74.9	4	[                                   ------------- ]	S1_Rrp5_repeat_hs2_sc2	S1_Rrp5_repeat_hs2_sc2: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 2 (hs2) and S. cerevisiae S1 repeat 2 (sc2). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
4	COG1098	129	64	74.9	3.6	[                                   ------------  ]	YabR	Predicted RNA-binding protein, contains ribosomal protein S1 (RPS1) domain
5	cd04455	67	58	71.2	4.4	[                                   -----------   ]	S1_NusA	S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
6	cd05706	73	66	67.6	13	[                                   -----------   ]	S1_Rrp5_repeat_sc10	S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
7	cd05692	69	22	59.5	7.4	[                                           ----  ]	S1_RPS1_repeat_hs4	S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
8	PRK06676	390	64	56.1	10	[                                   ------------  ]	rpsA	30S ribosomal protein S1; Reviewed
9	cd05789	86	69	55.9	25	[                                   ------------  ]	S1_Rrp4	S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure"td>
10	cd04472	68	27	54.5	11	[                                          -----  ]	S1_PNPase	S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
11	cd05702	70	62	53.0	17	[                                   -----------   ]	S1_Rrp5_repeat_hs11_sc8	S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
12	PRK05807	136	64	51.6	16	[                                   ------------  ]	PRK05807	hypothetical protein; Provisional
13	pfam11598	45	25	50.9	43	[    -----                                        ]	COMP	Cartilage oligomeric matrix protein. This family of proteins represents the five-stranded coiled-coil domain of cartilage oligomeric matrix protein (COMP). This region has a binding site between two internal rings formed by Leu37 and Thr40
14	PRK06676	390	67	50.7	16	[                                   -----------   ]	rpsA	30S ribosomal protein S1; Reviewed
15	pfam01843	105	74	49.5	27	[      ---------------                            ]	DIL	DIL domain. The DIL domain has no known function.
16	PRK06299	565	69	48.6	25	[                                   ------------  ]	rpsA	30S ribosomal protein S1; Reviewed
17	PRK07252	120	59	47.0	19	[                                   -----------   ]	PRK07252	hypothetical protein; Provisional
18	cd04454	82	67	46.7	34	[                                   ------------  ]	S1_Rrp4_like	S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure"td>
19	PRK14950	585	14	45.2	1.5E+02	[               --                                ]	PRK14950	DNA polymerase III subunits gamma and tau; Provisional
20	TIGR03591	688	70	45.0	24	[                                   ------------  ]	polynuc_phos	polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
21	cd00164	65	52	42.1	40	[                                    ----------   ]	S1_like	S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
22	PRK14954	620	15	41.7	4.1E+02	[ --                                              ]	PRK14954	DNA polymerase III subunits gamma and tau; Provisional
23	COG1327	156	68	40.7	45	[-------------                                    ]	NrdR	Transcriptional regulator NrdR, contains Zn-ribbon and ATP-cone domains
24	cd05687	70	55	39.4	52	[                                   -----------   ]	S1_RPS1_repeat_ec1_hs1	S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
25	cd05708	77	70	38.9	79	[                                   ------------- ]	S1_Rrp5_repeat_sc12	S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
26	TIGR00601	378	41	37.8	33	[                      -------                    ]	rad23	UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
27	cd04406	186	49	35.9	49	[        ---------                                ]	RhoGAP_myosin_IXA	RhoGAP_myosin_IXA: RhoGAP (GTPase-activator protein
28	PRK06299	565	64	35.3	43	[                                   ------------  ]	rpsA	30S ribosomal protein S1; Reviewed
29	COG4942	420	76	33.8	2.8E+02	[   --------------                                ]	EnvC	Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB
30	pfam00042	108	69	33.1	1.3E+02	[        -------------                            ]	Globin	Globin.
31	PRK11824	693	68	32.4	47	[                                   ------------  ]	PRK11824	polynucleotide phosphorylase/polyadenylase; Provisional
32	COG0539	541	71	31.9	49	[                                   ------------- ]	RpsA	Ribosomal protein S1
33	PRK14965	576	31	30.8	1.2E+02	[                                         -----   ]	PRK14965	DNA polymerase III subunits gamma and tau; Provisional
34	cd04465	67	59	30.7	58	[                                   ------------  ]	S1_RPS1_repeat_ec2_hs2	S1_RPS1_repeat_ec2_hs2: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain.While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
35	PRK13806	491	62	30.6	53	[                                   -----------   ]	rpsA	30S ribosomal protein S1; Provisional
36	cd04473	77	60	30.0	38	[                                   ------------  ]	S1_RecJ_like	S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
37	TIGR00717	516	64	28.8	59	[                                  ------------   ]	rpsA	ribosomal protein S1. This model describes ribosomal protein S1, RpsA. This protein is found in most bacterial genomes in a single copy, but is not present in the Mycoplasmas. It is heterogeneous with respect to the number of repeats of the S1 RNA binding domain described by pfam00575: six repeats in E. coli and most other bacteria, four in Bacillus subtilis and some other species. rpsA is an essential gene in E. coli but not in B. subtilis. It is associated with the cytidylate kinase gene cmk in many species, and fused to it in Treponema pallidum. RpsA is proposed (Medline:97323001) to assist in mRNA degradation. This model provides trusted hits to most long form (6 repeat) examples of RpsA. Among homologs with only four repeats are some to which other (perhaps secondary) functions have been assigned.
38	COG4046	368	70	27.2	2.2E+02	[          ------------                           ]	COG4046	Uncharacterized protein
39	PRK14965	576	22	26.9	66	[                                  ----           ]	PRK14965	DNA polymerase III subunits gamma and tau; Provisional
40	pfam07462	574	38	26.3	75	[                    ------                       ]	MSP1_C	Merozoite surface protein 1 (MSP1) C-terminus. This family represents the C-terminal region of merozoite surface protein 1 (MSP1) which are found in a number of Plasmodium species. MSP-1 is a 200-kDa protein expressed on the surface of the P. vivax merozoite. MSP-1 of Plasmodium species is synthesized as a high-molecular-weight precursor and then processed into several fragments. At the time of red cell invasion by the merozoite, only the 19-kDa C-terminal fragment (MSP-119), which contains two epidermal growth factor-like domains, remains on the surface. Antibodies against MSP-119 inhibit merozoite entry into red cells, and immunisation with MSP-119 protects monkeys from challenging infections. Hence, MSP-119 is considered a promising vaccine candidate.
41	cd04792	836	68	25.9	92	[        ------------                             ]	LanM-like	Cyclases involved in the biosynthesis of class II lantibiotics, and similar proteins. LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be unrelated to the dehydratase, LanB.
42	COG1428	216	42	25.7	2E+02	[          -------                                ]	Dck	Deoxyadenosine/deoxycytidine kinase
43	COG0539	541	68	25.5	77	[                                   ------------- ]	RpsA	Ribosomal protein S1
44	pfam01365	203	49	25.1	2.1E+02	[       ----------                                ]	RYDR_ITPR	RIH domain. The RIH (RyR and IP3R Homology) domain is an extracellular domain from two types of calcium channels. This region is found in the ryanodine receptor and the inositol-1,4,5- trisphosphate receptor. This domain may form a binding site for IP3.
45	pfam02865	125	55	24.7	2E+02	[          ----------                             ]	STAT_int	STAT protein, protein interaction domain. STAT proteins (Signal Transducers and Activators of Transcription) are a family of transcription factors that are specifically activated to regulate gene transcription when cells encounter cytokines and growth factors. STAT proteins also include an SH2 domain pfam00017.
46	PRK01712	64	23	24.1	28	[                                   ----          ]	PRK01712	carbon storage regulator; Provisional
47	COG1185	692	70	23.8	69	[                                   ------------  ]	Pnp	Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase)
48	TIGR04236	953	67	23.2	1.3E+02	[      -------------                              ]	seadorna_VP2	seadornavirus VP2 protein. This protein family occurs in the seadornavirus virus group, with the designation VP2 in Banna virus, Kadipiro virus, and Liao ning virus.
49	pfam11855	471	80	23.0	3.2E+02	[ ---------------                                 ]	DUF3375	Protein of unknown function (DUF3375). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 479 to 499 amino acids in length.
50	PRK07764	824	71	22.9	9.3E+02	[        ------------                             ]	PRK07764	DNA polymerase III subunits gamma and tau; Validated
51	TIGR01231	310	60	22.8	92	[      ----------                                 ]	lacC	tagatose-6-phosphate kinase. This enzyme is part of the tagatose-6-phosphate pathway of lactose degradation.
52	cd05046	275	65	22.6	40	[ -----------                                     ]	PTK_CCK4	Pseudokinase domain of the Protein Tyrosine Kinase, Colon Carcinoma Kinase 4. CCK4, also called protein tyrosine kinase 7 (PTK7), is an orphan receptor PTK (RTK) containing an extracellular region with seven immunoglobulin domains, a transmembrane segment, and an intracellular inactive pseudokinase domain, which shows similarity to tyr kinases but lacks crucial residues for catalytic activity and ATP binding. Studies in mice reveal that CCK4 is essential for neural development. Mouse embryos containing a truncated CCK4 die perinatally and display craniorachischisis, a severe form of neural tube defect. The mechanism of action of the CCK4 pseudokinase is still unknown. Other pseudokinases such as HER3 rely on the activity of partner RTKs. The CCK4 subfamily is part of a larger superfamily that includes other pseudokinases and the catalytic domains of active kinases including PTKs, protein serine/threonine kinases, RIO kinases, aminoglycoside phosphotransferase, choline kinase, and phosphoinositide 3-kinase.
53	TIGR00383	318	60	22.5	6.9E+02	[    -----------                                  ]	corA	magnesium Mg(2+) and cobalt Co(2+) transport protein (corA). The article in Microb Comp Genomics 1998;3(3):151-69 discusses this family and suggests that some members may have functions other than Mg2+ transport.
54	PRK00404	141	10	22.1	1.3E+02	[                -                                ]	tatB	sec-independent translocase; Provisional
55	COG5373	931	12	22.1	1.1E+02	[                      --                         ]	COG5373	Uncharacterized membrane protein
56	PRK08582	139	61	21.6	65	[                                   ------------  ]	PRK08582	hypothetical protein; Provisional
57	PRK00087	647	61	21.1	86	[                                   ------------  ]	PRK00087	4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
58	PRK14951	618	40	21.0	2.2E+02	[              -------                            ]	PRK14951	DNA polymerase III subunits gamma and tau; Provisional
59	pfam10597	136	43	21.0	79	[               -------                           ]	U5_2-snRNA_bdg	U5-snRNA binding site 2 of PrP8. The essential spliceosomal protein Prp8 interacts with U5 and U6 snRNAs and with specific pre-mRNA sequences that participate in catalysis. This close association with crucial RNA sequences, together with extensive genetic evidence, suggests that Prp8 could directly affect the function of the catalytic core, perhaps acting as a splicing cofactor.
60	PRK09202	470	59	21.0	89	[                                   -----------   ]	nusA	transcription elongation factor NusA; Validated