match no.	target id	target length	alignment length	probability	E-value	coverage	match description
1	COG1173	289	221	99.9	2.4E-29	[                  -------------------------------]	DppC	ABC-type dipeptide/oligopeptide/nickel transport system, permease component
2	PRK15406	302	220	99.9	2.4E-24	[                  -------------------------------]	PRK15406	oligopeptide ABC transporter permease OppC; Provisional
3	PRK15082	301	219	99.6	6.3E-17	[                  -------------------------------]	PRK15082	glutathione ABC transporter permease GsiD; Provisional
4	TIGR02790	258	218	99.6	3.5E-17	[                  -------------------------------]	nickel_nikC	nickel ABC transporter, permease subunit NikC. This family consists of the NikC family of nickel ABC transporter permeases. Operons that contain this protein also contain a homologous permease subunit NikB. Nickel is used in cells as part of urease or certain hydrogenases or superoxide dismutases.
5	PRK10417	272	216	99.3	2.5E-14	[                  -------------------------------]	nikC	nickel transporter permease NikC; Provisional
6	PRK10913	300	214	99.2	7.9E-14	[                  -------------------------------]	PRK10913	dipeptide transporter; Provisional
7	COG4239	341	212	99.2	6.5E-14	[                  -------------------------------]	YejE	ABC-type microcin C transport system, permease component YejE
8	PRK09881	296	218	99.1	3.5E-12	[                  -------------------------------]	PRK09881	D-ala-D-ala transporter subunit; Provisional
9	PRK15021	341	214	98.1	8E-08	[                  -------------------------------]	PRK15021	microcin C ABC transporter permease; Provisional
10	COG4171	296	213	97.9	7.6E-08	[                  -------------------------------]	SapC	ABC-type antimicrobial peptide transport system, permease component
11	PRK15111	296	210	97.4	8.4E-07	[                  -------------------------------]	PRK15111	antimicrobial peptide ABC transporter permease SapC; Provisional
12	pfam00528	183	173	96.7	3E-05	[                        -------------------------]	BPD_transp_1	Binding-protein-dependent transport system inner membrane component. The alignments cover the most conserved region of the proteins, which is thought to be located in a cytoplasmic loop between two transmembrane domains. The members of this family have a variable number of transmembrane helices.
13	cd06261	190	104	68.1	0.21	[                       ---------------           ]	TM_PBP2	Transmembrane subunit (TM) found in Periplasmic Binding Protein (PBP)-dependent ATP-Binding Cassette (ABC) transporters which generally bind type 2 PBPs. These types of transporters consist of a PBP, two TMs, and two cytoplasmic ABC ATPase subunits, and are mainly involved in importing solutes from the environment. The solute is captured by the PBP which delivers it to a gated translocation pathway formed by the two TMs. The two ABCs bind and hydrolyze ATP and drive the transport reaction. For these transporters the ABCs and TMs are on independent polypeptide chains. These systems transport a diverse range of substrates. Most are specific for a single substrate or a group of related substrates; however some transporters are more promiscuous, transporting structurally diverse substrates such as the histidine/lysine and arginine transporter in Enterobacteriaceae. In the latter case, this is achieved through binding different PBPs with different specificities to the TMs. For other promiscuous transporters such as the multiple-sugar transporter Msm of Streptococcus mutans, the PBP has a wide substrate specificity. These transporters include the maltose-maltodextrin, phosphate and sulfate transporters, among others.
14	COG0601	317	107	45.8	1.2	[                       ---------------           ]	DppB	ABC-type dipeptide/oligopeptide/nickel transport system, permease component
15	COG0555	274	100	37.6	5.8	[                          --------------         ]	CysU	ABC-type sulfate transport system, permease component
16	pfam04568	91	44	36.8	74	[           -------                               ]	IATP	Mitochondrial ATPase inhibitor, IATP. ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP. The minimum inhibitory region for bovine inhibitor is from residues 39 to 72. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH, the inhibitor forms a dimer via antiparallel coiled coil interactions between the C terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity.
17	PRK09390	202	67	34.0	31	[         ---------                               ]	fixJ	response regulator FixJ; Provisional
18	TIGR00135	93	76	31.9	45	[           -----------                           ]	gatC	aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, C subunit. Archaea, organelles, and many bacteria charge Gln-tRNA by first misacylating it with Glu and then amidating Glu to Gln. This small protein is part of the amidotransferase heterotrimer and appears to be important to the stability of the amidase subunit encode by gatA, but its function may not be required in every organism that expresses gatA and gatB. The seed alignment for this model does not include any eukaryotic sequence and is not guaranteed to find eukaryotic examples, although it does find some. Saccharomyces cerevisiae, which expresses the amidotransferase for mitochondrial protein translation, seems to lack a gatC ortholog. This model has been revised to remove the candidate sequence from Methanococcus jannaschii, now part of a related model.
19	PRK02292	188	44	28.9	1.3E+02	[            ------                               ]	PRK02292	V-type ATP synthase subunit E; Provisional
20	pfam12911	56	43	28.6	13	[   ------                                        ]	OppC_N	N-terminal TM domain of oligopeptide transport permease C. Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters. Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. Two integral highly hydrophobic membrane spanning proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. This N-terminal domain appears to be the first TM domain of the molecule.
21	COG3462	117	45	26.5	49	[         ------                                  ]	COG3462	Uncharacterized membrane protein
22	COG1390	194	23	23.3	2.3E+02	[              ---                                ]	NtpE	Archaeal/vacuolar-type H+-ATPase subunit E/Vma4
23	PRK00888	105	44	22.3	1.7E+02	[         -------                                 ]	ftsB	cell division protein FtsB; Reviewed
24	pfam13552	495	79	21.9	1.5E+02	[           -----------                           ]	DUF4127	Protein of unknown function (DUF4127). This family of uncharacterized bacterial proteins are about 500 amino acids in length.
25	pfam14607	147	60	21.4	57	[                                   ----------    ]	GxDLY	N-terminus of Esterase_SGNH_hydro-type. This domain lies upstream of SGNH hydrolase, but its function is not known. There is a highly conserved GxDLY sequence-motif.
26	TIGR00763	775	88	20.5	4.2E+02	[      -------------                              ]	lon	endopeptidase La. This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock.
27	TIGR00293	126	77	20.4	5.6E+02	[    -----------                                  ]	TIGR00293	prefoldin, archaeal alpha subunit/eukaryotic subunit 5. Members of this protein family, rich in coiled coil regions, are molecular chaperones in the class of the prefoldin (GimC) alpha subunit. Prefoldin is a hexamer of two alpha and four beta subunits. This protein appears universal in the archaea but is restricted to Aquifex aeolicus among bacteria so far. Eukaryotes have several related proteins; only prefoldin subunit 5, which appeared the most similar to archaeal prefoldin alpha, is included in this model. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and the model may have a significant number of hits to proteins that contain coiled coil regions.