Query 005854
Match_columns 673
No_of_seqs 67 out of 69
Neff 4.2
Searched_HMMs 46136
Date Thu Mar 28 14:43:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09577 Spore_YpjB: Sporulati 86.5 3.1 6.8E-05 43.5 8.5 129 541-671 95-230 (232)
2 TIGR02878 spore_ypjB sporulati 81.5 5.3 0.00011 41.9 7.6 119 541-671 96-231 (233)
3 COG5074 t-SNARE complex subuni 53.7 38 0.00082 36.1 6.7 117 531-653 126-265 (280)
4 PF05545 FixQ: Cbb3-type cytoc 49.2 11 0.00025 29.9 1.7 22 642-663 13-34 (49)
5 PRK10404 hypothetical protein; 46.0 82 0.0018 29.1 7.0 38 623-662 64-101 (101)
6 cd01324 cbb3_Oxidase_CcoQ Cyto 39.0 19 0.00042 29.1 1.6 23 642-664 14-36 (48)
7 PF05957 DUF883: Bacterial pro 38.0 60 0.0013 28.8 4.7 40 623-662 53-94 (94)
8 PRK10132 hypothetical protein; 37.1 1.5E+02 0.0033 27.8 7.4 23 640-662 85-107 (108)
9 PHA02416 hypothetical protein 35.1 61 0.0013 31.2 4.5 30 227-256 130-159 (167)
10 COG4736 CcoQ Cbb3-type cytochr 33.8 26 0.00057 29.8 1.7 24 641-664 12-35 (60)
11 PF08261 Carcinustatin: Carcin 33.5 20 0.00043 19.5 0.6 7 238-244 1-7 (8)
12 PF12729 4HB_MCP_1: Four helix 30.7 3.3E+02 0.0071 24.7 8.6 36 575-610 112-147 (181)
13 PF08693 SKG6: Transmembrane a 27.8 32 0.00068 27.3 1.1 18 647-664 23-40 (40)
14 PF10510 PIG-S: Phosphatidylin 27.2 7.3E+02 0.016 28.8 12.3 89 524-624 381-472 (517)
15 PF03908 Sec20: Sec20; InterP 26.9 1.1E+02 0.0023 27.3 4.5 60 603-662 27-91 (92)
16 KOG4433 Tweety transmembrane/c 26.7 3.9E+02 0.0084 31.5 9.6 135 521-659 110-254 (526)
17 COG4575 ElaB Uncharacterized c 26.5 2.9E+02 0.0064 26.1 7.3 32 631-662 71-104 (104)
18 PRK10947 global DNA-binding tr 25.4 45 0.00097 32.4 1.9 8 223-230 107-114 (135)
19 COG2916 Hns DNA-binding protei 25.0 47 0.001 32.2 1.9 20 202-230 88-107 (128)
20 KOG0810 SNARE protein Syntaxin 24.2 2.3E+02 0.0049 31.1 7.1 29 575-604 199-227 (297)
21 KOG2500 Uncharacterized conser 23.6 92 0.002 33.1 3.8 50 188-237 14-96 (253)
22 PF07087 DUF1353: Protein of u 22.0 37 0.0008 30.9 0.6 46 488-543 34-80 (95)
23 PF11844 DUF3364: Domain of un 20.3 45 0.00097 28.2 0.7 11 663-673 21-31 (56)
No 1
>PF09577 Spore_YpjB: Sporulation protein YpjB (SpoYpjB); InterPro: IPR014231 Proteins in thie entry, typified by YpjB, are restricted to a subset of the endospore-forming bacteria which includes Bacillus species, but not species. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon []. Sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect, but this gene is not, however, a part of the endospore formation minimal gene set.
Probab=86.54 E-value=3.1 Score=43.52 Aligned_cols=129 Identities=17% Similarity=0.303 Sum_probs=69.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccccchhcccchhHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHhccc---chhhH
Q 005854 541 LLTSLNYSISSAVDVLESIAAHGGERRLLKQNRYLDFVQRWNLFKYKLDKAVTALSHMDFEMALYYLRSSDH---DLYTM 617 (673)
Q Consensus 541 i~t~Ld~SI~sai~~L~s~~~~~~~~~ll~~~~~~e~~~r~n~v~~kl~r~~sa~s~ldf~~Al~~l~~a~~---d~~a~ 617 (673)
+-...+.+|...++.|+.....|+. +.++ ..-.+|.+.|..+.=.+.-....-..-+.+.-+.|+....- +-...
T Consensus 95 LW~~~e~~i~~~~~~mk~a~~~~~~-~~f~-~~~n~f~~~y~~I~Psl~I~~~~~~v~~v~s~i~yl~~~~~~~~~~~~~ 172 (232)
T PF09577_consen 95 LWLQYEKPIMEDFQRMKQAAQKGDK-EAFR-ASLNEFLSHYELIRPSLTIDRPPEQVQRVDSHISYLERLRFQQLDQKEV 172 (232)
T ss_pred cHHHHHHHHHHHHHHHHHHHHhCCH-HHHH-HHHHHHHHHHHHhcchhhccCCHHHHHHHHHHHHHHHHhhhcccChHHH
Confidence 4556677777888888877776654 2234 44567777777664222111111001111111333333211 11112
Q ss_pred hHHHHHhhHhhhhcccccc----ccCCCcchhhhHHHHHHHHHHhhhchhhHhhhhhc
Q 005854 618 HSLVHHATQELEASLVCFK----DPPVPWASISMSAVVFLALSYVYTKRDQLFRNKRK 671 (673)
Q Consensus 618 ~~~~~~a~~~lea~l~C~~----d~~~~w~~v~~~~v~~~~~~~~~~~~~~~~~~~~~ 671 (673)
..-..+..+.+...+.-.+ ||++-|.+++++++.+++|.||=+|.=|==+.|||
T Consensus 173 ~~~l~~le~~l~~lF~~~k~d~~dpsl~Wv~l~iG~iIi~tLtYvGwRKYrgek~~~k 230 (232)
T PF09577_consen 173 QEALEQLEEDLQKLFDGVKEDEADPSLIWVMLSIGGIIIATLTYVGWRKYRGEKEKRK 230 (232)
T ss_pred HHHHHHHHHHHHHHhCcccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 2222333333333332222 68999999999999999999998877666566665
No 2
>TIGR02878 spore_ypjB sporulation protein YpjB. Members of this protein, YpjB, family are restricted to a subset of endospore-forming bacteria, including Bacillus species but not CLostridium or some others. In Bacillus subtilis, ypjB was found to be part of the sigma-E regulon, where sigma-E is a sporulation sigma factor that regulates expression in the mother cell compartment. Null mutants of ypjB show a sporulation defect. This protein family is not, however, a part of the endospore formation minimal gene set.
Probab=81.46 E-value=5.3 Score=41.94 Aligned_cols=119 Identities=22% Similarity=0.329 Sum_probs=75.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccccchhcccchhHHHHHHHHHHH------------HHHHHHHHHhccCCHHHH-----
Q 005854 541 LLTSLNYSISSAVDVLESIAAHGGERRLLKQNRYLDFVQRWNLFK------------YKLDKAVTALSHMDFEMA----- 603 (673)
Q Consensus 541 i~t~Ld~SI~sai~~L~s~~~~~~~~~ll~~~~~~e~~~r~n~v~------------~kl~r~~sa~s~ldf~~A----- 603 (673)
+-...+.+|-.+++.|+.....|+. ..|+ ..-++|++.|..+. .+.+..++.+.+++|...
T Consensus 96 LW~~~e~~im~~f~~mk~a~~~~~~-~~f~-~~ln~Fl~~Y~~I~PSl~Idl~~~~~q~v~~~i~~l~~~r~~~~~~~~~ 173 (233)
T TIGR02878 96 LWGSLEKPVMEAFTELEKAAQKEDS-QAFQ-EKLNEFLSLYDLIYPSLTIDVPEDQVQRVDSHLSYLENFRFQQRSEDEK 173 (233)
T ss_pred hHHHHHHHHHHHHHHHHHHHHcCCH-HHHH-HHHHHHHHHhhhcccceeeecCHHHHHHHHHHHHHHHhhhhhccChHHH
Confidence 3445566666777777766655554 3344 45678888888764 344555555556655532
Q ss_pred HHHHHhcccchhhHhHHHHHhhHhhhhccccccccCCCcchhhhHHHHHHHHHHhhhchhhHhhhhhc
Q 005854 604 LYYLRSSDHDLYTMHSLVHHATQELEASLVCFKDPPVPWASISMSAVVFLALSYVYTKRDQLFRNKRK 671 (673)
Q Consensus 604 l~~l~~a~~d~~a~~~~~~~a~~~lea~l~C~~d~~~~w~~v~~~~v~~~~~~~~~~~~~~~~~~~~~ 671 (673)
+.-|+.++.|+. .+|..+.+. --||.+=|.+++..++.|+.|-||=+|.=|==+.|||
T Consensus 174 ~~~L~~~~~dl~---~lF~~vkkD-------~aDPSLiWvmistGg~IvltLTYVGwRKYkgEKek~k 231 (233)
T TIGR02878 174 EEQLSLMRGDLK---ALFDGVKED-------EADPSLLWVMISTGGIIVATLTYVGWRKYKGEKEKVK 231 (233)
T ss_pred HHHHHHHHHHHH---HHHcccccC-------CCCcHHHHHHHHhhHHHHHHHhhhhhhhhhhHhhhhc
Confidence 555666666644 222222111 2268899999999999999999998887666555555
No 3
>COG5074 t-SNARE complex subunit, syntaxin [Intracellular trafficking and secretion]
Probab=53.73 E-value=38 Score=36.08 Aligned_cols=117 Identities=15% Similarity=0.236 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHHHH-------HHHHHHH------HHHHHHHHHhccccchhcccchhHHHHHHHHHHHHHHHHHHHHhcc
Q 005854 531 VQKDAARRNVLLTS-------LNYSISS------AVDVLESIAAHGGERRLLKQNRYLDFVQRWNLFKYKLDKAVTALSH 597 (673)
Q Consensus 531 ~q~Daa~RN~i~t~-------Ld~SI~s------ai~~L~s~~~~~~~~~ll~~~~~~e~~~r~n~v~~kl~r~~sa~s~ 597 (673)
--.|-++|-|+++- +++.|+. ..+.|......|..+..|+ |.-+|++.+. |+++.++-+..
T Consensus 126 e~~e~~rrQy~Ia~P~ATEdeve~aInd~nG~qvfsqalL~anr~geAktaL~-----Evq~Rh~~ik-kiEkt~ael~q 199 (280)
T COG5074 126 EEKEQARRQYIIAQPEATEDEVEAAINDVNGQQVFSQALLNANRRGEAKTALA-----EVQARHQEIK-KIEKTMAELTQ 199 (280)
T ss_pred HHHHHHHHhhhhcCCccchHHHHHHhcccchHHHHHHHHHhcCccchHHHHHH-----HHHHHHHHHH-HHHHHHHHHHH
Confidence 34678899999864 4444531 2233333344555555666 8889999999 99999999988
Q ss_pred CCHHHHHHHHHhc------ccchhhHhHHHHHhhHhhhhcccccc----ccCCCcchhhhHHHHHH
Q 005854 598 MDFEMALYYLRSS------DHDLYTMHSLVHHATQELEASLVCFK----DPPVPWASISMSAVVFL 653 (673)
Q Consensus 598 ldf~~Al~~l~~a------~~d~~a~~~~~~~a~~~lea~l~C~~----d~~~~w~~v~~~~v~~~ 653 (673)
|=.+++---.+.- .+++.-...-+.++...++..+..-+ .--+-|+++.++++++|
T Consensus 200 Lfndm~~~V~eq~e~Vd~I~~~~~~~~~n~~~g~~h~d~AvksaRaaRkkki~c~gI~~iii~viv 265 (280)
T COG5074 200 LFNDMEELVIEQQENVDVIDKNVEDAQENVEQGVGHTDKAVKSARAARKKKIRCYGICFIIIIVIV 265 (280)
T ss_pred HHHHHHHHHHhhcchHHHHHhhHhhHHhhHHHhhhhHHHHHHHHHHHHhcceehhhhHHHHHHHHH
Confidence 8777663222222 22333233334455555554443222 22355666644443333
No 4
>PF05545 FixQ: Cbb3-type cytochrome oxidase component FixQ; InterPro: IPR008621 This family consists of several Cbb3-type cytochrome oxidase components (FixQ/CcoQ). FixQ is found in nitrogen fixing bacteria. Since nitrogen fixation is an energy-consuming process, effective symbioses depend on operation of a respiratory chain with a high affinity for O2, closely coupled to ATP production. This requirement is fulfilled by a special three-subunit terminal oxidase (cytochrome terminal oxidase cbb3), which was first identified in Bradyrhizobium japonicum as the product of the fixNOQP operon [].
Probab=49.18 E-value=11 Score=29.91 Aligned_cols=22 Identities=9% Similarity=0.217 Sum_probs=18.1
Q ss_pred cchhhhHHHHHHHHHHhhhchh
Q 005854 642 WASISMSAVVFLALSYVYTKRD 663 (673)
Q Consensus 642 w~~v~~~~v~~~~~~~~~~~~~ 663 (673)
|+++.++++.++.++|+|+||.
T Consensus 13 ~~~v~~~~~F~gi~~w~~~~~~ 34 (49)
T PF05545_consen 13 IGTVLFFVFFIGIVIWAYRPRN 34 (49)
T ss_pred HHHHHHHHHHHHHHHHHHcccc
Confidence 6677888888888999999874
No 5
>PRK10404 hypothetical protein; Provisional
Probab=46.05 E-value=82 Score=29.14 Aligned_cols=38 Identities=26% Similarity=0.414 Sum_probs=24.7
Q ss_pred HhhHhhhhccccccccCCCcchhhhHHHHHHHHHHhhhch
Q 005854 623 HATQELEASLVCFKDPPVPWASISMSAVVFLALSYVYTKR 662 (673)
Q Consensus 623 ~a~~~lea~l~C~~d~~~~w~~v~~~~v~~~~~~~~~~~~ 662 (673)
++.+..+..=.|-++ -||.+|++.+.+-|++.+.++||
T Consensus 64 ~~k~aa~~td~yV~e--~Pw~avGiaagvGlllG~Ll~RR 101 (101)
T PRK10404 64 RAKQAVYRADDYVHE--KPWQGIGVGAAVGLVLGLLLARR 101 (101)
T ss_pred HHHHHHHHHHHHHHh--CcHHHHHHHHHHHHHHHHHHhcC
Confidence 343434333455555 46999988877777777777776
No 6
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ. Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I. Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center. ccoQ, the fourth subunit, is a single transmembrane helix protein. It has been shown to protect the core complex from proteolytic degradation by serine proteases. See cd00919, cd01322
Probab=39.04 E-value=19 Score=29.08 Aligned_cols=23 Identities=4% Similarity=0.343 Sum_probs=18.5
Q ss_pred cchhhhHHHHHHHHHHhhhchhh
Q 005854 642 WASISMSAVVFLALSYVYTKRDQ 664 (673)
Q Consensus 642 w~~v~~~~v~~~~~~~~~~~~~~ 664 (673)
|+.+.+.++.++.++|+++||.|
T Consensus 14 ~~l~~~~~~Figiv~wa~~p~~k 36 (48)
T cd01324 14 WGLLYLALFFLGVVVWAFRPGRK 36 (48)
T ss_pred HHHHHHHHHHHHHHHHHhCCCcc
Confidence 66677778888899999998753
No 7
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=38.04 E-value=60 Score=28.81 Aligned_cols=40 Identities=23% Similarity=0.369 Sum_probs=25.9
Q ss_pred HhhHhhhhccccccc--cCCCcchhhhHHHHHHHHHHhhhch
Q 005854 623 HATQELEASLVCFKD--PPVPWASISMSAVVFLALSYVYTKR 662 (673)
Q Consensus 623 ~a~~~lea~l~C~~d--~~~~w~~v~~~~v~~~~~~~~~~~~ 662 (673)
++.+.......|+.+ -.-||.+|.+.+.+-|++.++++||
T Consensus 53 ~~~~~~~~~~~~~~~~V~e~P~~svgiAagvG~llG~Ll~RR 94 (94)
T PF05957_consen 53 QAREQAREAAEQTEDYVRENPWQSVGIAAGVGFLLGLLLRRR 94 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHhCC
Confidence 333444444445543 2356999988888888888888876
No 8
>PRK10132 hypothetical protein; Provisional
Probab=37.11 E-value=1.5e+02 Score=27.79 Aligned_cols=23 Identities=26% Similarity=0.502 Sum_probs=17.5
Q ss_pred CCcchhhhHHHHHHHHHHhhhch
Q 005854 640 VPWASISMSAVVFLALSYVYTKR 662 (673)
Q Consensus 640 ~~w~~v~~~~v~~~~~~~~~~~~ 662 (673)
-||.+|++.+.+-|++.++++||
T Consensus 85 ~Pw~svgiaagvG~llG~Ll~RR 107 (108)
T PRK10132 85 RPWCSVGTAAAVGIFIGALLSLR 107 (108)
T ss_pred CcHHHHHHHHHHHHHHHHHHhcc
Confidence 56999988777777777777765
No 9
>PHA02416 hypothetical protein
Probab=35.11 E-value=61 Score=31.22 Aligned_cols=30 Identities=30% Similarity=0.450 Sum_probs=28.0
Q ss_pred cCccEEEEEcCCCCccccCCCCCCccCCCc
Q 005854 227 GKERYVWIDLGAGPVDYGPALSGDGVLPKG 256 (673)
Q Consensus 227 G~~RyawIDLsAGP~sYGPa~gGeG~LPr~ 256 (673)
|-|-|.++|--|.-+.|.-..|-||++|+-
T Consensus 130 gvgvysvvdphasdvkyagwtgtegvipnr 159 (167)
T PHA02416 130 GVGVYSVVDPHASDVKYAGWTGTEGVIPNR 159 (167)
T ss_pred ceeEEEeeCCCcccceecccccccccccCC
Confidence 668899999999999999999999999985
No 10
>COG4736 CcoQ Cbb3-type cytochrome oxidase, subunit 3 [Posttranslational modification, protein turnover, chaperones]
Probab=33.84 E-value=26 Score=29.83 Aligned_cols=24 Identities=13% Similarity=0.524 Sum_probs=20.8
Q ss_pred CcchhhhHHHHHHHHHHhhhchhh
Q 005854 641 PWASISMSAVVFLALSYVYTKRDQ 664 (673)
Q Consensus 641 ~w~~v~~~~v~~~~~~~~~~~~~~ 664 (673)
-|+++.++++.+..++|+|||+.|
T Consensus 12 a~~t~~~~l~fiavi~~ayr~~~K 35 (60)
T COG4736 12 AWGTIAFTLFFIAVIYFAYRPGKK 35 (60)
T ss_pred HHHHHHHHHHHHHHHHHHhcccch
Confidence 488999999999999999998754
No 11
>PF08261 Carcinustatin: Carcinustatin peptide
Probab=33.53 E-value=20 Score=19.48 Aligned_cols=7 Identities=57% Similarity=1.317 Sum_probs=5.7
Q ss_pred CCCcccc
Q 005854 238 AGPVDYG 244 (673)
Q Consensus 238 AGP~sYG 244 (673)
|||.++|
T Consensus 1 agpy~fg 7 (8)
T PF08261_consen 1 AGPYSFG 7 (8)
T ss_pred CCccccc
Confidence 7888887
No 12
>PF12729 4HB_MCP_1: Four helix bundle sensory module for signal transduction; InterPro: IPR024478 This entry represents a four-helix bundle that operates as a ubiquitous sensory module in prokaryotic signal-transduction, which is known as four-helix bundles methyl-accepting chemotaxis protein (4HB_MCP) domain. The 4HB_MCP is always found between two predicted transmembrane helices indicating that it detects only extracellular signals. In many cases the domain is associated with a cytoplasmic HAMP domain suggesting that most proteins carrying the bundle might share the mechanism of transmembrane signalling which is well-characterised in E coli chemoreceptors [].
Probab=30.75 E-value=3.3e+02 Score=24.72 Aligned_cols=36 Identities=17% Similarity=0.273 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHhc
Q 005854 575 LDFVQRWNLFKYKLDKAVTALSHMDFEMALYYLRSS 610 (673)
Q Consensus 575 ~e~~~r~n~v~~kl~r~~sa~s~ldf~~Al~~l~~a 610 (673)
.++...|+.......+.+......+.++|..++..-
T Consensus 112 ~~~~~~~~~y~~~~~~~~~~~~~~~~~~a~~~~~~~ 147 (181)
T PF12729_consen 112 EEFKEAWKAYRKLRDQVIELAKSGDNDEARAILNGE 147 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHh
Confidence 477888888877777777777789999886665543
No 13
>PF08693 SKG6: Transmembrane alpha-helix domain; InterPro: IPR014805 SKG6 and AXL2 are membrane proteins that show polarised intracellular localisation [, ]. This entry represents the highly conserved transmembrane alpha-helical domain found in these proteins [, ]. The full-length AXL2 protein has a negative regulatory function in cytokinesis [].
Probab=27.77 E-value=32 Score=27.25 Aligned_cols=18 Identities=17% Similarity=0.412 Sum_probs=9.5
Q ss_pred hHHHHHHHHHHhhhchhh
Q 005854 647 MSAVVFLALSYVYTKRDQ 664 (673)
Q Consensus 647 ~~~v~~~~~~~~~~~~~~ 664 (673)
.+++++.+++|+++||+|
T Consensus 23 vI~~vl~~~l~~~~rR~k 40 (40)
T PF08693_consen 23 VIIIVLGAFLFFWYRRKK 40 (40)
T ss_pred HHHHHHHHHhheEEeccC
Confidence 334444445565677654
No 14
>PF10510 PIG-S: Phosphatidylinositol-glycan biosynthesis class S protein; InterPro: IPR019540 Phosphatidylinositol-glycan biosynthesis class S protein (PIG-S) is one of several key, core components of the glycosylphosphatidylinositol (GPI) trans-amidase complex that mediates GPI anchoring in the endoplasmic reticulum. Anchoring occurs when a protein's C-terminal GPI attachment signal peptide is replaced with a pre-assembled GPI []. Mammalian GPI transamidase consists of at least five components: Gaa1, Gpi8, PIG-S, PIG-T, and PIG-U, all five of which are required for its function. It is possible that Gaa1, Gpi8, PIG-S, and PIG-T form a tightly associated core that is only weakly associated with PIG-U. The exact function of PIG-S is unclear [].
Probab=27.23 E-value=7.3e+02 Score=28.80 Aligned_cols=89 Identities=20% Similarity=0.144 Sum_probs=57.0
Q ss_pred CCcchhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhccccchhcccchhHHHHHHHHHHHHHHHHHHHHhccCCH
Q 005854 524 EISSLSFVQKDAARRNVLLTSLNYSIS---SAVDVLESIAAHGGERRLLKQNRYLDFVQRWNLFKYKLDKAVTALSHMDF 600 (673)
Q Consensus 524 ~~~~lS~~q~Daa~RN~i~t~Ld~SI~---sai~~L~s~~~~~~~~~ll~~~~~~e~~~r~n~v~~kl~r~~sa~s~ldf 600 (673)
....+....-|...|-.++.-+..++. +-++.++++. +. .++ .+.-.+=+.....++++...+...++
T Consensus 381 ~~~~~~~~eld~l~r~r~~~~l~~a~~TL~SL~~L~~~i~---~i--~I~----~~V~~~v~~al~~l~~a~~~l~~~~~ 451 (517)
T PF10510_consen 381 SSTGSPPWELDSLLRRRTVENLASASSTLQSLAKLLDSIP---NI--VIP----DEVAERVQQALEALEQAIDALNNGDL 451 (517)
T ss_pred cccCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC---CC--ccc----HHHHHHHHHHHHHHHHHHHHHhCCCH
Confidence 444568888899999988876665543 2333333222 11 112 23334444455688899999999999
Q ss_pred HHHHHHHHhcccchhhHhHHHHHh
Q 005854 601 EMALYYLRSSDHDLYTMHSLVHHA 624 (673)
Q Consensus 601 ~~Al~~l~~a~~d~~a~~~~~~~a 624 (673)
+.|+..++.|..- .++.|++-
T Consensus 452 ~~al~~a~~a~~~---ae~AFfd~ 472 (517)
T PF10510_consen 452 EEALAHAREAFAL---AERAFFDP 472 (517)
T ss_pred HHHHHHHHHHHHH---HHHHhCCH
Confidence 9999999888773 45566654
No 15
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=26.90 E-value=1.1e+02 Score=27.26 Aligned_cols=60 Identities=18% Similarity=0.145 Sum_probs=29.2
Q ss_pred HHHHHHhcccchhhHhHHHHHhhHhhhhc---ccccc--ccCCCcchhhhHHHHHHHHHHhhhch
Q 005854 603 ALYYLRSSDHDLYTMHSLVHHATQELEAS---LVCFK--DPPVPWASISMSAVVFLALSYVYTKR 662 (673)
Q Consensus 603 Al~~l~~a~~d~~a~~~~~~~a~~~lea~---l~C~~--d~~~~w~~v~~~~v~~~~~~~~~~~~ 662 (673)
++..|.+....+..++.-...-...|..+ +...+ +..=.|-...+++++++++.|+++||
T Consensus 27 t~~~L~~Ss~~L~~~~~e~~~~~~~l~~s~~ll~~l~r~~~~D~~li~~~~~~f~~~v~yI~~rR 91 (92)
T PF03908_consen 27 TLQTLEESSATLRSTNDEYDGQSSLLKKSRKLLKKLERRDKTDRILIFFAFLFFLLVVLYILWRR 91 (92)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHhhhc
Confidence 35555555554444444444444444444 22222 11112444456666666667888877
No 16
>KOG4433 consensus Tweety transmembrane/cell surface protein [General function prediction only]
Probab=26.65 E-value=3.9e+02 Score=31.47 Aligned_cols=135 Identities=18% Similarity=0.137 Sum_probs=72.4
Q ss_pred CCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccchhcccchhHHHHHHHHHHHHHHHHHHHHhccCCH
Q 005854 521 PFSEISSLSFVQKDAARRNVLLTSLNYSISSAVDVLESIAAHGGERRLLKQNRYLDFVQRWNLFKYKLDKAVTALSHMDF 600 (673)
Q Consensus 521 pfS~~~~lS~~q~Daa~RN~i~t~Ld~SI~sai~~L~s~~~~~~~~~ll~~~~~~e~~~r~n~v~~kl~r~~sa~s~ldf 600 (673)
.+++| +++....-..=|-.++.++..+..-.+.|.......-++..-.+....|++|--+.+....+.++.+.+.+.|
T Consensus 110 e~~~G--~~q~~~Sl~~an~tv~ti~~qv~~~~~~l~~~~~~~l~~~~~n~t~~~~l~~~l~~vq~~~~~a~~~l~~~~~ 187 (526)
T KOG4433|consen 110 ETSDG--LLQATYSLRHANHTVSTIDAQVSDTAEGLNNTAEQLLETLEENLTARPELLQALRRVQGNAETAVGQLSGLPF 187 (526)
T ss_pred cccch--HHHHHHhhhhhcchhhHHHHHHHHHHHHHHHHHHHHhhhHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCcc
Confidence 34444 4554444444455666677776654444444333222322112255689999999999999999999985443
Q ss_pred --HHHHHHHHhcc-cchhhHhHHHHHhhHhhhhccccc-------cccCCCcchhhhHHHHHHHHHHhh
Q 005854 601 --EMALYYLRSSD-HDLYTMHSLVHHATQELEASLVCF-------KDPPVPWASISMSAVVFLALSYVY 659 (673)
Q Consensus 601 --~~Al~~l~~a~-~d~~a~~~~~~~a~~~lea~l~C~-------~d~~~~w~~v~~~~v~~~~~~~~~ 659 (673)
.+|+....-++ .|+|...|-..-+-=-+--.+.|+ |+-+ |+.|.+++..++++...|
T Consensus 188 ~~~~~~sl~~l~~~~~~yE~~RW~~~v~lL~l~LvvC~v~vlglak~Sk--c~li~fsv~Gll~lvisW 254 (526)
T KOG4433|consen 188 WRMVAVSLEKLAEQVDFYESYRWLAYVLLLTLLLVVCLVLVLGLAKRSK--CLLIVFSVCGLLALVISW 254 (526)
T ss_pred cccCcccHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc--hhhhHHHHHHHHHHHHHH
Confidence 45533332222 245544442111110111114777 2333 777777777666665544
No 17
>COG4575 ElaB Uncharacterized conserved protein [Function unknown]
Probab=26.51 E-value=2.9e+02 Score=26.10 Aligned_cols=32 Identities=25% Similarity=0.456 Sum_probs=23.7
Q ss_pred ccccccc--cCCCcchhhhHHHHHHHHHHhhhch
Q 005854 631 SLVCFKD--PPVPWASISMSAVVFLALSYVYTKR 662 (673)
Q Consensus 631 ~l~C~~d--~~~~w~~v~~~~v~~~~~~~~~~~~ 662 (673)
...|+.+ -.-||-+|++.+.+=+++...++||
T Consensus 71 a~~~tD~yV~e~PWq~VGvaAaVGlllGlLlsRR 104 (104)
T COG4575 71 AADATDDYVRENPWQGVGVAAAVGLLLGLLLSRR 104 (104)
T ss_pred HHHHHHHHHHcCCchHHHHHHHHHHHHHHHHhcC
Confidence 3567764 3467999988888777777788776
No 18
>PRK10947 global DNA-binding transcriptional dual regulator H-NS; Provisional
Probab=25.36 E-value=45 Score=32.45 Aligned_cols=8 Identities=50% Similarity=1.174 Sum_probs=7.3
Q ss_pred ceeecCcc
Q 005854 223 SIWTGKER 230 (673)
Q Consensus 223 ~~WiG~~R 230 (673)
++|+|+||
T Consensus 107 ~TWTGrGR 114 (135)
T PRK10947 107 KTWTGQGR 114 (135)
T ss_pred CcccCCCC
Confidence 79999998
No 19
>COG2916 Hns DNA-binding protein H-NS [General function prediction only]
Probab=24.99 E-value=47 Score=32.25 Aligned_cols=20 Identities=40% Similarity=0.836 Sum_probs=15.9
Q ss_pred CcceeeCCCCCCCCCccccccceeecCcc
Q 005854 202 KNYAYSYSPGESSPGFTKCLGSIWTGKER 230 (673)
Q Consensus 202 ~~Y~Y~y~~~~~~~~~~~Cl~~~WiG~~R 230 (673)
..|.|.+.+|.. ++|+|.||
T Consensus 88 a~~~~~~~n~eg---------~TWTGrGR 107 (128)
T COG2916 88 AKYKYYDENGEG---------KTWTGRGR 107 (128)
T ss_pred CCCCeecCCCCC---------CcccCCCC
Confidence 478888877776 78999987
No 20
>KOG0810 consensus SNARE protein Syntaxin 1 and related proteins [Intracellular trafficking, secretion, and vesicular transport]
Probab=24.18 E-value=2.3e+02 Score=31.06 Aligned_cols=29 Identities=28% Similarity=0.504 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhccCCHHHHH
Q 005854 575 LDFVQRWNLFKYKLDKAVTALSHMDFEMAL 604 (673)
Q Consensus 575 ~e~~~r~n~v~~kl~r~~sa~s~ldf~~Al 604 (673)
.|.-.|++.+. +|++.+.-+..+=.++|.
T Consensus 199 ~Eiq~Rh~~ik-~LEksi~ELhqlFlDMa~ 227 (297)
T KOG0810|consen 199 AEIQERHDEIK-KLEKSIRELHQLFLDMAV 227 (297)
T ss_pred HHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Confidence 68888999998 999988888877667763
No 21
>KOG2500 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.57 E-value=92 Score=33.09 Aligned_cols=50 Identities=16% Similarity=0.339 Sum_probs=32.7
Q ss_pred CceEEEEeeCCCCCCcce---eeCC----------------------CCCCCCCccccccceee--------cCccEEEE
Q 005854 188 NGIYIYLLNLGSKAKNYA---YSYS----------------------PGESSPGFTKCLGSIWT--------GKERYVWI 234 (673)
Q Consensus 188 ~~~~Iy~iN~~~q~~~Y~---Y~y~----------------------~~~~~~~~~~Cl~~~Wi--------G~~RyawI 234 (673)
+.+.||.|-|++..++|. +..+ ++++...|.+|..+..- -+.||.+|
T Consensus 14 pev~VY~IPPr~t~~gyra~eW~l~~~~WtGrlrvvakg~~~~ikLeD~tsg~LfA~c~id~~~~~avEav~DSSRYFVi 93 (253)
T KOG2500|consen 14 PEVFVYKIPPRATSRGYRAGEWNLDKPAWTGRLRVVAKGERCEIKLEDKTSGELFAQCPIDEGPGNAVEAVSDSSRYFVI 93 (253)
T ss_pred ccEEEEECCCcccCCCccccccccCCccccceeEEEEcCcEEEEEeccCCchhhhhhCcccCCCCccceeecccceEEEE
Confidence 589999999998777765 2222 23344557888887773 34666666
Q ss_pred EcC
Q 005854 235 DLG 237 (673)
Q Consensus 235 DLs 237 (673)
-+-
T Consensus 94 Rv~ 96 (253)
T KOG2500|consen 94 RVE 96 (253)
T ss_pred EEe
Confidence 554
No 22
>PF07087 DUF1353: Protein of unknown function (DUF1353); InterPro: IPR010767 This entry is represented by Campylobacter phage CGC-2007, Cje0229. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical phage and bacterial proteins of around 100 residues in length. The function of this family is unknown.
Probab=22.00 E-value=37 Score=30.91 Aligned_cols=46 Identities=20% Similarity=0.255 Sum_probs=37.9
Q ss_pred hhcCCCCcc-cccccccccccccceeccCCCCCCCCCCCcchhHHHHHHHHHHHHHH
Q 005854 488 SMWGVSPTH-LLWSSMHNNTLVDYTWSIGQTPFGPFSEISSLSFVQKDAARRNVLLT 543 (673)
Q Consensus 488 ~l~Gv~Pth-l~yS~ah~~~~~dwlWSvG~~PfgpfS~~~~lS~~q~Daa~RN~i~t 543 (673)
-+|++.|++ =.|..+ ++++||+...| +....+.-+.|.+.|..+.+
T Consensus 34 ~~~~~~~p~~g~y~~A--avvHD~l~~~~--------~~~~~~r~~aD~iF~~am~~ 80 (95)
T PF07087_consen 34 ILWWLIPPFDGKYLKA--AVVHDYLYSRG--------NDRGRSRKEADRIFREAMRE 80 (95)
T ss_pred HHhheeCCCccchhhH--HHHHHHHHhCC--------CcCCCCHHHHHHHHHHHHHH
Confidence 367888998 788888 69999999999 56667889999998887754
No 23
>PF11844 DUF3364: Domain of unknown function (DUF3364); InterPro: IPR024564 The enzyme responsible for nitrogen fixation, the nitrogenase, shows a high degree of conservation of structure, function, and amino acid sequence across wide phylogenetic ranges. All known Mo-nitrogenases consist of two components, component I (also called dinitrogenase, or Fe-Mo protein), an alpha2beta2 tetramer encoded by the nifD and nifK genes, and component II (dinitrogenase reductase, or Fe protein) a homodimer encoded by the nifH gene [, ]. Nitrogenase contains two unusual rare metal clusters; one of them is the iron molybdenum cofactor (FeMo-co), which is considered to be the site of dinitrogen reduction and whose biosynthesis requires the products of nifNE operon and of some other nif genes []. It has been proposed that NifNE might serve as a scaffold upon which FeMo-co is built and then inserted into component I []. This entry represents the uncharacterised N-terminal domain of the molybdenum-iron protein beta chain, which is part of the nitrogenase complex that catalyses the key enzymatic reactions in nitrogen fixation. ; PDB: 3U7Q_B 3MIN_D 1M34_D 2AFI_D 2MIN_B 1G21_B 2AFK_D 1FP4_B 1M1Y_L 1G20_D ....
Probab=20.26 E-value=45 Score=28.19 Aligned_cols=11 Identities=55% Similarity=1.047 Sum_probs=9.4
Q ss_pred hhHhhhhhccC
Q 005854 663 DQLFRNKRKQF 673 (673)
Q Consensus 663 ~~~~~~~~~~~ 673 (673)
.++|.||||+|
T Consensus 21 qe~f~~Kk~~f 31 (56)
T PF11844_consen 21 QELFANKKKEF 31 (56)
T ss_dssp HHHHHHHHHCC
T ss_pred HHHHHHHHHHh
Confidence 47899999988
Done!