Query 012485
Match_columns 462
No_of_seqs 110 out of 241
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 03:08:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012485.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012485hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2291 Oligosaccharyltransfer 100.0 6E-131 1E-135 1013.3 38.2 445 6-457 5-458 (602)
2 PF04597 Ribophorin_I: Ribopho 100.0 1E-125 3E-130 992.2 46.5 419 31-456 1-432 (432)
3 smart00609 VIT Vault protein I 91.8 3.6 7.9E-05 36.9 12.0 100 29-137 12-129 (130)
4 PF08487 VIT: Vault protein in 91.4 5.4 0.00012 34.8 12.5 94 34-137 5-117 (118)
5 PF09972 DUF2207: Predicted me 90.4 27 0.00059 37.1 21.5 184 229-434 3-190 (511)
6 TIGR03788 marine_srt_targ mari 80.8 17 0.00036 40.5 12.0 90 40-138 6-112 (596)
7 PF10989 DUF2808: Protein of u 43.5 2.5E+02 0.0054 25.4 10.5 28 112-139 87-114 (146)
8 TIGR02411 leuko_A4_hydro leuko 42.5 5.4E+02 0.012 28.9 14.2 92 32-139 13-104 (601)
9 COG2372 CopC Uncharacterized p 42.2 1.5E+02 0.0031 26.8 7.8 57 63-128 45-101 (127)
10 PF07610 DUF1573: Protein of u 40.8 34 0.00073 24.7 3.0 20 117-136 25-45 (45)
11 PF15240 Pro-rich: Proline-ric 38.1 19 0.0004 34.2 1.6 28 10-37 1-28 (179)
12 PRK10301 hypothetical protein; 36.8 2.5E+02 0.0053 24.9 8.5 63 63-137 44-106 (124)
13 TIGR03079 CH4_NH3mon_ox_B meth 34.7 1.7E+02 0.0037 31.0 8.0 22 116-137 332-353 (399)
14 PF09972 DUF2207: Predicted me 33.3 6E+02 0.013 26.8 20.0 126 35-181 5-141 (511)
15 PF05753 TRAP_beta: Translocon 32.0 1.3E+02 0.0028 28.6 6.2 20 49-68 39-58 (181)
16 PF04314 DUF461: Protein of un 27.8 1.7E+02 0.0038 25.0 5.9 82 53-136 19-101 (110)
17 PRK11901 hypothetical protein; 25.6 55 0.0012 33.9 2.7 12 37-48 75-86 (327)
18 PF03929 PepSY_TM: PepSY-assoc 25.4 43 0.00094 21.9 1.2 19 444-462 7-25 (27)
19 PRK10905 cell division protein 24.2 41 0.00089 34.8 1.5 14 34-47 31-44 (328)
20 PF09478 CBM49: Carbohydrate b 22.6 4.1E+02 0.0088 21.3 8.1 25 48-72 17-41 (80)
21 PF04744 Monooxygenase_B: Mono 22.0 8.9E+02 0.019 25.8 10.6 84 34-137 251-334 (381)
22 PF02102 Peptidase_M35: Deuter 22.0 30 0.00065 36.4 0.0 23 122-144 100-122 (359)
23 PHA02090 hypothetical protein 20.4 49 0.0011 26.3 0.9 20 318-341 41-61 (79)
No 1
>KOG2291 consensus Oligosaccharyltransferase, alpha subunit (ribophorin I) [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=6.2e-131 Score=1013.34 Aligned_cols=445 Identities=51% Similarity=0.815 Sum_probs=413.2
Q ss_pred hhhHHHHHHHHHHHHHHhhccCCCCCeEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCcccceeEEEEE
Q 012485 6 RPRIMLSLTIILIPIFLFISGASSHQIRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEAL 85 (462)
Q Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~n~~v~R~IdL~~~~vk~~~~i~ikN~g~~~~~~y~~~l~~~~~~~ls~~~a~ 85 (462)
+++||+..+++|..++..+++.+++.|+|.|++|||||++|++|++++++++|+|++|+++|.+++++....+||+++|.
T Consensus 5 ~~~~~~~l~l~l~aia~~~a~~a~~~w~n~nv~RTIDlsS~ivK~tt~l~i~N~g~ePatey~~a~~~~~~~~la~ls~~ 84 (602)
T KOG2291|consen 5 SASWALVLVLLLFAIASGAASSAEQDWVNVNVERTIDLSSQIVKVTTELSIENIGSEPATEYLLAFEKELGASLAFLSVA 84 (602)
T ss_pred hhHHHHHHHHHHHHHhhccccCCccccccccceEEEehhhhhhhheeEEEEEecCCCchheEEEeccCccccceeEEEEe
Confidence 66777666666665665557778899999999999999999999999999999999999999999999999999999998
Q ss_pred EcCCccccceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEEEcccccccCcccCcCCceeEEEEeCcee
Q 012485 86 AATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGETATLEILYILTHSLEPFPVEISQSESQLVYYRDSALI 165 (462)
Q Consensus 86 ~~~~~~k~~~~~~l~v~~~~~~~~~~~~~~~~I~Lp~pl~p~~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~l~~~~n~~~ 165 (462)
..+++++ +...+++.+.++.+ +++ .+|.|+||.|+.||++++|.|++++++.++|+|++|+|+|+|+|+|.+|+|+
T Consensus 85 ~~~g~~~--~~l~~s~~~~~~~~-~~~-~~y~v~lp~pl~pge~vTl~V~~~~t~vl~P~Pe~I~QsE~Q~vv~~tn~~~ 160 (602)
T KOG2291|consen 85 FTEGKKK--TLLKLSVNPPKKDG-ASE-RVYTVTLPNPLSPGEKVTLIVEAVLTHVLRPLPEEITQSEEQFVVYETNAYL 160 (602)
T ss_pred eccCccc--cccccccCCcccCC-Ccc-ceEEEeCCCCCCCCceEEEEEEeecccCcccChhhhCcCceeeEEEeccccc
Confidence 8776643 22445666655222 223 7999999999999999999999999999999999999999999999999999
Q ss_pred cCcceeceEEEEEEeCCCccceeeccCCccccCCeEEeccCCCCCCCCcCCeEEEEEcccceeEEeeeEEEEEEecccce
Q 012485 166 LSPYHIKQQTTFIKIPSNKVESFTRVEPTDRAGNELKYGPYEDRPPYSYSPLLVHFENNNPFSVVEELVREVEISHWGNL 245 (462)
Q Consensus 166 ~SpY~t~~q~t~i~~~s~~i~s~t~~~~~~~~g~~i~yGP~~~v~p~s~~~~~Vhye~n~P~~~v~~L~R~IeVSHWGni 245 (462)
+|||.|++|+|.+++||+++++||+.++.+++|+.++||||+|+++|+++|+.||||||.||+++++|+|+|||||||||
T Consensus 161 ~SpY~Tk~Q~t~ikl~Ss~ies~T~~~~~k~~gn~l~yGPyeni~afs~~pl~VhYEnnaPf~~v~~L~R~IevSHWgnI 240 (602)
T KOG2291|consen 161 LSPYDTKSQSTTIKLPSSKIESYTTVEPSKRSGNELKYGPYENIPAFSQEPLVVHYENNAPFVTVENLEREIEVSHWGNI 240 (602)
T ss_pred cCcccccceeEEEEcccccceeccccCcccccCceeeecCccccccccCCceEEEEecCCCcceeeeEEEEEEeecceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEEEEEEEEcCCCccCcccchhcccCCCCCCccceeeeeeecCCcccCeEEEeccceeeeeeeeecCCceEEEEEecCC
Q 012485 246 QITEQYKLAHAGARHKGIFSRVDYQSKPTFSGVSSFKHLLARLPPRVHSVYYRDEIGNISTSHLRADSWKISELEIEPRY 325 (462)
Q Consensus 246 ~veE~y~l~N~GA~Lkg~FSR~d~~~~~~~~~~~~~~~l~~~LP~~a~d~YY~D~IGNISTS~~r~~~~~~~~l~l~PRf 325 (462)
+|||+|+|+|+||+|||+|||+|||++...++.++++++.+.||++|+|+||||+||||||||+|.+.++ ++|+|+|||
T Consensus 241 qVeE~~~lth~gAkLkg~FSR~d~q~~~~~~g~sai~~l~~~LP~~A~dvYYrDeiGNISTShmr~~~~~-~eleirPRf 319 (602)
T KOG2291|consen 241 QVEENYELTHKGAKLKGPFSRLDYQKQRRTRGASAINSLKTVLPARAKDVYYRDEIGNISTSHMRIDPDK-TELEIRPRF 319 (602)
T ss_pred EEEEEEEEEecceeccCCcchHhhhhcCCcCcchHHHHHHhhCCCccCceeeecccCcEehhhhcccCcc-ceEEeccCC
Confidence 9999999999999999999999999886658899999999999999999999999999999999999999 999999999
Q ss_pred cccCCceeeEEEeecCCcccceeeccCCceE-EEEEecCCC-cceEEEEEEEEEEcCCCCcCCeeeCCccee-eeceeEE
Q 012485 326 PLFGGWRATFVIGYGLPLEDFLFESSDGRRY-LNFTFGCPL-VETVVDKLTIKVVLPEGAKGPSAVVPFPVE-QRLETKY 402 (462)
Q Consensus 326 PLfGGWk~~FtiGyn~pl~~~L~~~~~~~~y-L~vp~~~~~-~d~~vd~~~l~IiLPEGA~~i~v~~P~~v~-~~~~~~~ 402 (462)
||||||||+|++|||+|+++||+ .+|++| |+++|..++ +|++||+++++|+|||||+||++.+||+++ .+.++++
T Consensus 320 PlFGGWkt~ftiGy~lP~~eyl~--~~g~ry~L~~~~~~~~~d~~V~dkl~ikvvLPEGak~i~i~tP~~is~~p~e~~~ 397 (602)
T KOG2291|consen 320 PLFGGWKTNFTIGYNLPLEEYLF--SKGRRYALKIILIDHIFDDTVYDKLTIKVVLPEGAKDIEIDTPYEISRSPIELKY 397 (602)
T ss_pred ccccCceeeEEEecCCcHHHHhh--ccCceeEEccccccCCCccceeeeEEEEEEccCCCcccccccceeeccCchhhhh
Confidence 99999999999999999999998 478888 999998865 677999999999999999999999999986 6799999
Q ss_pred EecCCCCCeEEEEEeecCCcCCcceEEE--EeCCch----hHHHHHHHHHHHHHHHHHhhh
Q 012485 403 SYLDVVGRTVVVLEKKNVVPVHNIPFQV--TFSPVL----PLHFLSIDFIIFVSVLLGTFC 457 (462)
Q Consensus 403 tyLDt~GRpvv~l~~~Nlv~~h~~~~~V--~y~~~~----Pl~i~~~~f~~fl~~~~~~~~ 457 (462)
|||||.||||++++++|+|+.|+++|+| +|++.. ||+|+++||++|+++++|+|.
T Consensus 398 syLDt~GR~Vvv~ek~Nvv~~h~~~i~v~Y~f~~~sml~ePL~i~a~ffilf~~~i~y~~~ 458 (602)
T KOG2291|consen 398 SYLDTNGRPVVVLEKNNVVPDHNQDIVVHYTFSKSSMLQEPLLIIAAFFILFFAVIVYVRL 458 (602)
T ss_pred hhhhccCcEEEEEEccccCCCCCccEEEEEEechhHhhhccHHHHHHHHHHHHHHheeeec
Confidence 9999999999999999999999999999 777655 999999999999999999984
No 2
>PF04597 Ribophorin_I: Ribophorin I; InterPro: IPR007676 Ribophorin I is an essential subunit of oligosaccharyltransferase (OST), which is also known as dolichyl-diphosphooligosaccharide--protein glycosyltransferase, (2.4.1.119 from EC). OST catalyses the transfer of an oligosaccharide from dolichol pyrophosphate to selected asparagine residues of nascent polypeptides as they are translocated into the lumen of the rough endoplasmic reticulum. Ribophorin I and OST48 are thought to be responsible for OST catalytic activity []. Both yeast and mammalian proteins are glycosylated but the sites are not conserved. Glycosylation may contribute towards general solubility but is unlikely to be involved in a specific biochemical function []. Most family members are predicted to have a transmembrane helix at the C terminus of this region.; GO: 0004579 dolichyl-diphosphooligosaccharide-protein glycotransferase activity, 0006486 protein glycosylation, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=100.00 E-value=1.5e-125 Score=992.16 Aligned_cols=419 Identities=47% Similarity=0.796 Sum_probs=391.8
Q ss_pred CeEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecCCCCC
Q 012485 31 QIRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAP 110 (462)
Q Consensus 31 ~~~n~~v~R~IdL~~~~vk~~~~i~ikN~g~~~~~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~~~~~ 110 (462)
+|+|+++.|+|||++++|||+++++++|+|++|+++|+|++|.++.+++|+++|.+++++.+.. ...+..+ .+..
T Consensus 1 ~~~n~~~~R~idl~~~~vk~~~~i~i~N~g~~p~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~----~~~~~~~-~~~~ 75 (432)
T PF04597_consen 1 VWENTNVERTIDLSKSYVKETIEITIKNIGDEPVSEYYFALPNDEADHLSYVSAKDKDKKKKLK----VSKEITE-VNSG 75 (432)
T ss_pred CeEEeeEEEEEEccCcEEEEEEEEEEEECCCCCceEEEEEECchhhccEEEEEEEECCCccccc----ccccccc-ccCC
Confidence 5999999999999999999999999999999999999999999999999999999987663321 0111111 1122
Q ss_pred CCceEEEEEeCCCCCCCCeEEEEEEEEEcccccccCcccCcCCceeEEEEeCceecCcceeceEEEEEEeCCCccceeec
Q 012485 111 NETNYYTIVLANPLNTGETATLEILYILTHSLEPFPVEISQSESQLVYYRDSALILSPYHIKQQTTFIKIPSNKVESFTR 190 (462)
Q Consensus 111 ~~~~~~~I~Lp~pl~p~~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~l~~~~n~~~~SpY~t~~q~t~i~~~s~~i~s~t~ 190 (462)
....+|+|+||+||+||++++|.|+|++++++.|+|++|+|+|+|+|+|++|+|++|||+|++|+|+++++++++++||+
T Consensus 76 ~~~~~~~i~L~~pl~~~~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~v~~~~~~~~~SpY~t~~q~t~i~~~~~~i~s~t~ 155 (432)
T PF04597_consen 76 SEIKYYEITLPKPLAPGEKVTLTVEYVLTHALKPYPAEITQGEKQLVLFTGNAYPLSPYPTKKQKTKIKLPSSKIESYTK 155 (432)
T ss_pred CCcceEEEECCCCCCCCCEEEEEEEEEecccceEcCCcccCCCceEEEEEcCEEecCCccccEEEEEEEecCCceecccC
Confidence 34578999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cC---CccccCCeEEeccCCCCCCCCcCCeEEEEEcccceeEEeeeEEEEEEecccceEEEEEEEEEEcCCCccCcccch
Q 012485 191 VE---PTDRAGNELKYGPYEDRPPYSYSPLLVHFENNNPFSVVEELVREVEISHWGNLQITEQYKLAHAGARHKGIFSRV 267 (462)
Q Consensus 191 ~~---~~~~~g~~i~yGP~~~v~p~s~~~~~Vhye~n~P~~~v~~L~R~IeVSHWGni~veE~y~l~N~GA~Lkg~FSR~ 267 (462)
.. +.+++|++++||||+|++||+.+++.||||||.||++|++|+|+|||||||||+|||+|+|+|+||+|||+|||+
T Consensus 156 ~~~~~~~~~~~~~i~yGP~~~v~p~~~~~~~vhye~n~P~~~v~~l~R~IeVSHWgni~veE~y~l~N~GA~Lkg~FSR~ 235 (432)
T PF04597_consen 156 VEFEKPPKKKGNTITYGPYENVPPFSSQPLSVHYENNAPFLTVTSLERDIEVSHWGNIAVEEYYELRNDGAKLKGGFSRL 235 (432)
T ss_pred ccccCCceecCCeEEeccccccCCCCcccEEEEEECCCCceEEEEEEEEEEEcCCccEEEEEEEEEEEcCcccCCCcCHH
Confidence 87 899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcccCCC-CCCccceeeeeeecCCcccCeEEEeccceeeeeeeeecCCceEEEEEecCCcccCCceeeEEEeecCCcccc
Q 012485 268 DYQSKPT-FSGVSSFKHLLARLPPRVHSVYYRDEIGNISTSHLRADSWKISELEIEPRYPLFGGWRATFVIGYGLPLEDF 346 (462)
Q Consensus 268 d~~~~~~-~~~~~~~~~l~~~LP~~a~d~YY~D~IGNISTS~~r~~~~~~~~l~l~PRfPLfGGWk~~FtiGyn~pl~~~ 346 (462)
|||++++ +++++++++++++||++|+|+||||+||||||||+|.++++ ++|+|+|||||||||||+|++|||+|+++|
T Consensus 236 d~~~~~~~~~~~~~~~~l~~~LP~~a~d~YY~D~IGNISTS~~~~~~~~-~~l~l~PRfPLfGGWk~~FtiGyn~p~~~~ 314 (432)
T PF04597_consen 236 DYQKSQNSNRGSSALKSLETILPASASDVYYRDEIGNISTSHVRPNKDS-VELELKPRFPLFGGWKYNFTIGYNLPLSNF 314 (432)
T ss_pred HHHhhccCCCcChhheEEeccCCCccCCeEEEcCCccEEEEEEEeCCCc-eEEEEEcCCcccCCcceeEEEEccCChHHh
Confidence 9988765 46789999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred eeeccCCceE-EEEEecCCCcceEEEEEEEEEEcCCCCcCCeeeCCcce-eeeceeEEEecCCCCCeEEEEEeecCCcCC
Q 012485 347 LFESSDGRRY-LNFTFGCPLVETVVDKLTIKVVLPEGAKGPSAVVPFPV-EQRLETKYSYLDVVGRTVVVLEKKNVVPVH 424 (462)
Q Consensus 347 L~~~~~~~~y-L~vp~~~~~~d~~vd~~~l~IiLPEGA~~i~v~~P~~v-~~~~~~~~tyLDt~GRpvv~l~~~Nlv~~h 424 (462)
|++++++ +| |+|||++++.|++||+++++|+|||||+||+|.+|+++ +.+++.++||||++|||+|+++++||+|+|
T Consensus 315 l~~~~~~-~y~L~vp~~~~~~d~~~d~~~l~i~LPEGA~~i~v~~P~~~~~~~~~~~~tyLDt~GR~vv~l~~~nlvd~~ 393 (432)
T PF04597_consen 315 LRKSGDG-RYVLKVPFLPGIKDIVYDNVELRIILPEGAKNIKVSSPFPVDSVSVSTHKTYLDTTGRPVVVLEKKNLVDEH 393 (432)
T ss_pred EEECCCC-cEEEEEECcCCcCceEEEEEEEEEECCCCceeeeEeCCccceeeeccceeeeeeccCceEEEEEeccCCHhH
Confidence 9876555 88 99999999999999999999999999999999999996 578999999999999999999999999999
Q ss_pred c-ceEEE--EeCCch----hHHHHHHHHHHHHHHHHHhh
Q 012485 425 N-IPFQV--TFSPVL----PLHFLSIDFIIFVSVLLGTF 456 (462)
Q Consensus 425 ~-~~~~V--~y~~~~----Pl~i~~~~f~~fl~~~~~~~ 456 (462)
+ ++|+| +|+.++ ||+|++++|++|+++|+|.|
T Consensus 394 ~~~~~~v~Y~~~~~~~~~kPl~i~~~~f~~fl~~~~l~r 432 (432)
T PF04597_consen 394 NDQDFQVTYTYPSSAMLRKPLLIAGAFFILFLAFIVLRR 432 (432)
T ss_pred CCeeEEEEEEcCHHHHHHHHHHHHHHHHHHHHheeEEeC
Confidence 9 69999 777766 99999999999999999987
No 3
>smart00609 VIT Vault protein Inter-alpha-Trypsin domain.
Probab=91.81 E-value=3.6 Score=36.86 Aligned_cols=100 Identities=12% Similarity=0.197 Sum_probs=61.5
Q ss_pred CCCeEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCcccceeEEEEEEcCCc------cc----------
Q 012485 29 SHQIRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGK------KK---------- 92 (462)
Q Consensus 29 ~~~~~n~~v~R~IdL~~~~vk~~~~i~ikN~g~~~~~~y~~~l~~~~~~~ls~~~a~~~~~~------~k---------- 92 (462)
...+...++.=...+.+.+++++.+-+..|.++.+...|+|...+ ...-++.+...+++.. +|
T Consensus 12 ~~~~pL~s~~v~~~I~~~~a~t~vtq~f~N~~~~~~e~~~~~~lp-~~A~v~~~~~~i~~r~i~g~vkeK~~Ar~~Ye~A 90 (130)
T smart00609 12 VNGVPLYSLKVNSKVTSRFAHTVVTSRVVNRAVPAQEVTFDVELP-KTAFISNFAMTIDGKTYVGEIKEKEVAQKQYEKA 90 (130)
T ss_pred CCccceEEEEEEEEEECCEEEEEEEEEEECCCCCceEEEEEcCCC-CCcEEEeEEEEECCEEEEEEEeeHHHHHHHHHHH
Confidence 345666677777888999999999999999987666666554332 2233444554443321 00
Q ss_pred -c-ceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEE
Q 012485 93 -K-KTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGETATLEILYI 137 (462)
Q Consensus 93 -~-~~~~~l~v~~~~~~~~~~~~~~~~I~Lp~pl~p~~~~~l~v~~~ 137 (462)
. +....| ++. .......|++.+ +|.||+++++.+.|.
T Consensus 91 ~~~G~~a~L-~eq-----~~~~~~~F~~~V--NIppg~~v~v~l~Y~ 129 (130)
T smart00609 91 VSQGKTAGL-VRA-----SGRSMEQFTVSV--NVAPGSKVTFELTYE 129 (130)
T ss_pred HHcCCCeEE-EEe-----cCCccCcEEEEE--EeCCCCEEEEEEEEE
Confidence 0 000011 000 011125689998 899999999999885
No 4
>PF08487 VIT: Vault protein inter-alpha-trypsin domain; InterPro: IPR013694 Inter-alpha-trypsin inhibitors (ITIs) consist of one light chain and a variable set of heavy chains. ITIs play a role in extracellular matrix (ECM) stabilisation and tumour metastasis as well as in plasma protease inhibition []. The vault protein inter-alpha-trypsin (VIT) domain described here is found to the N terminus of a von Willebrand factor type A domain (IPR002035 from INTERPRO) in ITI heavy chains (ITIHs) and their precursors.
Probab=91.42 E-value=5.4 Score=34.79 Aligned_cols=94 Identities=12% Similarity=0.233 Sum_probs=59.0
Q ss_pred EeeEEEEEEcCCCeEEEEEEEEEEeCCCCCc-cEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecC------
Q 012485 34 INNAERRIDLSTHIVKVFLTLKVENTGKTSA-SEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQL------ 106 (462)
Q Consensus 34 n~~v~R~IdL~~~~vk~~~~i~ikN~g~~~~-~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~------ 106 (462)
..++.=...+.+.+.+.+++-++.|..+.+. -.|.|.||.+ .-++-+++..++.. -.+ .+.+.+.
T Consensus 5 l~s~~v~~~I~~~~a~t~v~q~f~N~~~~~~E~~y~fpLp~~--A~i~~f~~~i~g~~-i~g-----~v~ek~~A~~~y~ 76 (118)
T PF08487_consen 5 LKSVHVKVTIIDRFARTTVTQTFENPSSEPLEAVYSFPLPEG--AAISGFSMWIGGRT-IEG-----EVKEKEEAKQEYE 76 (118)
T ss_pred EEEEEEEEEEEccEEEEEEEEEEECCCCCcEEEEEEeECCCC--eEEEEEEEEECCEE-EEE-----EEecHHHHHHHHH
Confidence 3444455677889999999999999876654 3456777765 44566666665431 000 0110000
Q ss_pred -----------CCC-CCCceEEEEEeCCCCCCCCeEEEEEEEE
Q 012485 107 -----------PDA-PNETNYYTIVLANPLNTGETATLEILYI 137 (462)
Q Consensus 107 -----------~~~-~~~~~~~~I~Lp~pl~p~~~~~l~v~~~ 137 (462)
.+. ..+...|.+.+ ++.||+++++.+.|.
T Consensus 77 ~a~~~g~~a~lle~~~~~~~~F~~~v--ni~p~~~v~i~l~Y~ 117 (118)
T PF08487_consen 77 EAVAQGKSAALLEQSDPNVEVFTVSV--NIPPNEEVTIELTYV 117 (118)
T ss_pred HHHHcCCCchhhcccCCCCcEEEEEE--EeCCCCEEEEEEEEE
Confidence 010 11234599999 899999999999985
No 5
>PF09972 DUF2207: Predicted membrane protein (DUF2207); InterPro: IPR018702 This domain has no known function.
Probab=90.38 E-value=27 Score=37.08 Aligned_cols=184 Identities=18% Similarity=0.241 Sum_probs=96.9
Q ss_pred EEeeeEEEEEEecccceEEEEEEEEEEcCCCccCcccchhcccCCC-CCCccceeeeeeec--CCcccCeEEEeccceee
Q 012485 229 VVEELVREVEISHWGNLQITEQYKLAHAGARHKGIFSRVDYQSKPT-FSGVSSFKHLLARL--PPRVHSVYYRDEIGNIS 305 (462)
Q Consensus 229 ~v~~L~R~IeVSHWGni~veE~y~l~N~GA~Lkg~FSR~d~~~~~~-~~~~~~~~~l~~~L--P~~a~d~YY~D~IGNIS 305 (462)
.+.+++=+++|..=|.+.|+|.+...=+|. -.|-|-.++-..... ......++.+...- +.++...|-.
T Consensus 3 ~I~~~~v~~~v~~dG~~~V~E~ity~f~~~-~~giyr~i~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~------- 74 (511)
T PF09972_consen 3 SIDSYDVDATVQEDGSLDVTETITYDFDGS-FHGIYRTIPLKGTGQLGDDKQSIKNFSVSDDGSSGKPGTYGI------- 74 (511)
T ss_pred cceeeEEEEEECCCCcEEEEEEEEEEeccC-CceEEEEeccCCCCCCCcccccceeEEEEeCCCcCCCcceEE-------
Confidence 367788888898889999999999886665 222222232221110 00001222222222 1222222222
Q ss_pred eeeeeecCCceEEEEEecCCcccCCceeeEEEeecCCcccceeeccCCceEEEEEecCCCcceEEEEEEEEEEcCCCCcC
Q 012485 306 TSHLRADSWKISELEIEPRYPLFGGWRATFVIGYGLPLEDFLFESSDGRRYLNFTFGCPLVETVVDKLTIKVVLPEGAKG 385 (462)
Q Consensus 306 TS~~r~~~~~~~~l~l~PRfPLfGGWk~~FtiGyn~pl~~~L~~~~~~~~yL~vp~~~~~~d~~vd~~~l~IiLPEGA~~ 385 (462)
....+. .++++.-=.|--.|=...|++-|++. +.+..-+|.+. |.-.+...--++.+++++++|.||++...
T Consensus 75 ----~~~~~~-~~~~i~~~~~~~~~~~~~~~~~Y~v~--~~v~~~~D~~e-l~w~~~g~~~~~~i~~v~v~i~~P~~~~~ 146 (511)
T PF09972_consen 75 ----EETDDG-YEIRIGIYDPSKNGGTHTYTISYTVK--NAVTNYSDVAE-LYWNFIGSGWDVPIENVTVTITLPKPVDN 146 (511)
T ss_pred ----EecCCc-ceEEEEecCccccCCeEEEEEEEEEE--CceEEcCCeeE-EEEEEecCCCCCccceEEEEEECCCCCcc
Confidence 222222 34666665666654567889999964 55643344333 44455544358999999999999987777
Q ss_pred CeeeCC-cceeeeceeEEEecCCCCCeEEEEEeecCCcCCcceEEEEeCC
Q 012485 386 PSAVVP-FPVEQRLETKYSYLDVVGRTVVVLEKKNVVPVHNIPFQVTFSP 434 (462)
Q Consensus 386 i~v~~P-~~v~~~~~~~~tyLDt~GRpvv~l~~~Nlv~~h~~~~~V~y~~ 434 (462)
.++..= -+...... ++ ...-.|+++..|+-+...-.+.+.||.
T Consensus 147 ~~~~~~~g~~~~~~~-----~~-~~~~~v~~~~~~l~~~~~~~v~~~fP~ 190 (511)
T PF09972_consen 147 SKAWGHPGPYGGTVE-----ID-DDDGTVTFTTDNLPPNEGVEVRVSFPK 190 (511)
T ss_pred eEEEEeccCCCccce-----ee-ecCCEEEEEEeccCCCCeEEEEEEccc
Confidence 655331 11100000 22 233456667777433222256556655
No 6
>TIGR03788 marine_srt_targ marine proteobacterial sortase target protein. Members of this protein family are restricted to the Proteobacteria. Each contains a C-terminal sortase-recognition motif, transmembrane domain, and basic residues cluster at the the C-terminus, and is encoded adjacent to a sortase gene. This protein is frequently the only sortase target in its genome, which is as unusual its occurrence in Gram-negative rather than Gram-positive genomes. Many bacteria with this system are marine. In addition to the LPXTG signal, members carry a vault protein inter-alpha-trypsin inhibitor domain (pfam08487) and a von Willebrand factor type A domain (pfam00092).
Probab=80.79 E-value=17 Score=40.50 Aligned_cols=90 Identities=17% Similarity=0.207 Sum_probs=59.0
Q ss_pred EEEcCCCeEEEEEEEEEEeCCCCCcc-EEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecC------------
Q 012485 40 RIDLSTHIVKVFLTLKVENTGKTSAS-EILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQL------------ 106 (462)
Q Consensus 40 ~IdL~~~~vk~~~~i~ikN~g~~~~~-~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~------------ 106 (462)
.+++++.+++++++.+..|..+.+.. .|.|.||++ .-++-+++.+++.. ..-.+++.+.
T Consensus 6 ~~~V~g~~A~v~v~q~f~N~~~~~~E~~y~fPLp~~--aaV~~f~~~i~~r~------i~g~v~eKe~A~~~Ye~a~~~G 77 (596)
T TIGR03788 6 NITVTGLIARTEVTQTFRNPSQFWVEGRYVFPLPEN--AAVDSLTMHIGERV------IVGQIMPKAAARAIYEQAKAEG 77 (596)
T ss_pred EEEEEcceEEEEEEEEEECCCCCcEEEEEEeeCCCC--cEEEEEEEEECCEE------EEEEEeeHHHHHHHHHHHHHhc
Confidence 56789999999999999999877763 455667655 56666777765421 0011111110
Q ss_pred ----CCCCCCceEEEEEeCCCCCCCCeEEEEEEEEE
Q 012485 107 ----PDAPNETNYYTIVLANPLNTGETATLEILYIL 138 (462)
Q Consensus 107 ----~~~~~~~~~~~I~Lp~pl~p~~~~~l~v~~~~ 138 (462)
...+.....|++.+. ++.||++++|.++|.-
T Consensus 78 ~~a~Lleq~~~~~F~~~V~-nIpp~~~v~i~l~Y~q 112 (596)
T TIGR03788 78 KKAALVEQQRPNLFTNKVA-NIGPGETVVVTIEYQQ 112 (596)
T ss_pred cceeeeecccCCceeEEee-ccCCCCEEEEEEEEEE
Confidence 001122346888886 8999999999999873
No 7
>PF10989 DUF2808: Protein of unknown function (DUF2808); InterPro: IPR021256 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=43.54 E-value=2.5e+02 Score=25.36 Aligned_cols=28 Identities=21% Similarity=0.329 Sum_probs=23.4
Q ss_pred CceEEEEEeCCCCCCCCeEEEEEEEEEc
Q 012485 112 ETNYYTIVLANPLNTGETATLEILYILT 139 (462)
Q Consensus 112 ~~~~~~I~Lp~pl~p~~~~~l~v~~~~~ 139 (462)
+.....|.+..|+.||++++|.++-+.+
T Consensus 87 ~~~~i~I~f~~PV~pG~tv~V~l~~v~N 114 (146)
T PF10989_consen 87 DGRTITITFDEPVPPGTTVTVVLSPVRN 114 (146)
T ss_pred CCCEEEEEeCCCCCCCCEEEEEEEeeeC
Confidence 3467899999999999999999866643
No 8
>TIGR02411 leuko_A4_hydro leukotriene A-4 hydrolase/aminopeptidase. Members of this family represent a distinctive subset within the zinc metallopeptidase family M1 (pfam01433). The majority of the members of pfam01433 are aminopeptidases, but the sequences in this family for which the function is known are leukotriene A-4 hydrolase. A dual epoxide hydrolase and aminopeptidase activity at the same active site is indicated. The physiological substrate for aminopeptidase activity is not known.
Probab=42.50 E-value=5.4e+02 Score=28.94 Aligned_cols=92 Identities=11% Similarity=0.070 Sum_probs=55.6
Q ss_pred eEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecCCCCCC
Q 012485 32 IRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPN 111 (462)
Q Consensus 32 ~~n~~v~R~IdL~~~~vk~~~~i~ikN~g~~~~~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~~~~~~ 111 (462)
...-++.=++|+.++...-+++|+++... .+.++..+-. ..+..-+|.+.+.. ++.+... ..+.
T Consensus 13 ~~hy~L~L~vd~~~~~~~G~v~i~l~~~~-~~~~~i~Ld~-----~~L~I~~V~v~g~~--------~~~~~~~--~~~~ 76 (601)
T TIGR02411 13 TSHTDLNLSVDFTKRKLSGSVTFTLQSLT-DNLNSLVLDT-----SYLDIQKVTINGLP--------ADFAIGE--RKEP 76 (601)
T ss_pred EEEEEEEEEEeecCCEEEEEEEEEEEECC-CCCcEEEEEC-----CCCEEEEEEECCcc--------cceEecc--ccCC
Confidence 34455566788888888888888887642 2335555533 23444455444321 2221111 0111
Q ss_pred CceEEEEEeCCCCCCCCeEEEEEEEEEc
Q 012485 112 ETNYYTIVLANPLNTGETATLEILYILT 139 (462)
Q Consensus 112 ~~~~~~I~Lp~pl~p~~~~~l~v~~~~~ 139 (462)
....+.|.||.++++|+..+|.|.|.-.
T Consensus 77 ~g~~L~I~l~~~l~~g~~~~l~I~Y~~~ 104 (601)
T TIGR02411 77 LGSPLTISLPIATSKNKELVLNISFSTT 104 (601)
T ss_pred CCCeEEEEeCCccCCCceEEEEEEEeec
Confidence 3456899999999999999999988743
No 9
>COG2372 CopC Uncharacterized protein, homolog of Cu resistance protein CopC [General function prediction only]
Probab=42.16 E-value=1.5e+02 Score=26.78 Aligned_cols=57 Identities=19% Similarity=0.281 Sum_probs=30.7
Q ss_pred CccEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCC
Q 012485 63 SASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGE 128 (462)
Q Consensus 63 ~~~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~~~~~~~~~~~~I~Lp~pl~p~~ 128 (462)
....+.+.+.+....+-+.+.....++++ .+....... +.+...++|.||.||++|.
T Consensus 45 aP~~i~L~Fse~ve~~fs~~~l~~~d~~~-------v~t~~~~~~--~~~~~~l~v~l~~~L~aG~ 101 (127)
T COG2372 45 APAAITLEFSEGVEPGFSGAKLTGPDGEE-------VATAGTKLD--EQNHTQLEVPLPQPLKAGV 101 (127)
T ss_pred CceeEEEecCCccCCCcceeEEECCCCCc-------cccCccccc--ccCCcEEEecCcccCCCCc
Confidence 33444566666655555555555444331 222222211 1233568999999999983
No 10
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=40.84 E-value=34 Score=24.72 Aligned_cols=20 Identities=25% Similarity=0.630 Sum_probs=15.1
Q ss_pred EEEeC-CCCCCCCeEEEEEEE
Q 012485 117 TIVLA-NPLNTGETATLEILY 136 (462)
Q Consensus 117 ~I~Lp-~pl~p~~~~~l~v~~ 136 (462)
.++++ .+++||++..|.|.|
T Consensus 25 ~~~~~~~~i~PGes~~i~v~y 45 (45)
T PF07610_consen 25 TAEYSKKPIAPGESGKIKVTY 45 (45)
T ss_pred EeeCCcceECCCCEEEEEEEC
Confidence 34444 468999999999875
No 11
>PF15240 Pro-rich: Proline-rich
Probab=38.07 E-value=19 Score=34.21 Aligned_cols=28 Identities=11% Similarity=0.177 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHhhccCCCCCeEEeeE
Q 012485 10 MLSLTIILIPIFLFISGASSHQIRINNA 37 (462)
Q Consensus 10 ~~~~~~~l~~~~~~~~~~~~~~~~n~~v 37 (462)
||+.+|-++||||.+|-....++.+++.
T Consensus 1 MLlVLLSvALLALSSAQ~~dEdv~~e~~ 28 (179)
T PF15240_consen 1 MLLVLLSVALLALSSAQSTDEDVSQEES 28 (179)
T ss_pred ChhHHHHHHHHHhhhccccccccccccC
Confidence 6666666777777444444555555443
No 12
>PRK10301 hypothetical protein; Provisional
Probab=36.79 E-value=2.5e+02 Score=24.87 Aligned_cols=63 Identities=13% Similarity=0.206 Sum_probs=33.4
Q ss_pred CccEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEE
Q 012485 63 SASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGETATLEILYI 137 (462)
Q Consensus 63 ~~~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~~~~~~~~~~~~I~Lp~pl~p~~~~~l~v~~~ 137 (462)
+..+..+.|.+......+-+.....+++ .+...+.. . ...+...+.+.|+.+|.+| +-.|++-
T Consensus 44 ~P~~V~L~F~e~v~~~~s~i~v~~~~g~-------~v~~~~~~-~-~~~~~~~~~v~l~~~L~~G---~YtV~Wr 106 (124)
T PRK10301 44 APQALTLNFSEGIEPGFSGATITGPKQE-------NIKTLPAK-R-NEQDQKQLIVPLADSLKPG---TYTVDWH 106 (124)
T ss_pred CCCEEEEEcCCCccccccEEEEEcCCCC-------EeccCCcc-c-cCCCCcEEEEECCCCCCCc---cEEEEEE
Confidence 4455556666555555666666544332 11111111 0 1123456788998899998 4555554
No 13
>TIGR03079 CH4_NH3mon_ox_B methane monooxygenase/ammonia monooxygenase, subunit B. Both ammonia oxidizers such as Nitrosomonas europaea and methanotrophs (obligate methane oxidizers) such as Methylococcus capsulatus each can grow only on their own characteristic substrate. However, both groups have the ability to oxidize both substrates, and so the relevant enzymes must be named here according to their ability to oxidze both. The protein family represented here reflects subunit B of both the particulate methane monooxygenase of methylotrophs and the ammonia monooxygenase of nitrifying bacteria.
Probab=34.75 E-value=1.7e+02 Score=31.00 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=17.5
Q ss_pred EEEEeCCCCCCCCeEEEEEEEE
Q 012485 116 YTIVLANPLNTGETATLEILYI 137 (462)
Q Consensus 116 ~~I~Lp~pl~p~~~~~l~v~~~ 137 (462)
..|.=+.|++|||+.++.|+..
T Consensus 332 L~v~d~~pI~PGETr~v~v~aq 353 (399)
T TIGR03079 332 LEVDDQSAIAPGETVEVKMEAK 353 (399)
T ss_pred ceeCCCCCcCCCcceEEEEEEe
Confidence 3555567999999999998864
No 14
>PF09972 DUF2207: Predicted membrane protein (DUF2207); InterPro: IPR018702 This domain has no known function.
Probab=33.33 E-value=6e+02 Score=26.80 Aligned_cols=126 Identities=16% Similarity=0.212 Sum_probs=78.0
Q ss_pred eeEEEEEEc--CCC-eEEEEEEEEEEeCCCCCccEEEEEcCCCcc-------cceeEEEEEEcCCccccceeeeeeeeee
Q 012485 35 NNAERRIDL--STH-IVKVFLTLKVENTGKTSASEILLAFPPTQV-------DHLAFLEALAATGKKKKKTYVSLAVKPT 104 (462)
Q Consensus 35 ~~v~R~IdL--~~~-~vk~~~~i~ikN~g~~~~~~y~~~l~~~~~-------~~ls~~~a~~~~~~~k~~~~~~l~v~~~ 104 (462)
.+++=+++| .++ .|.|+.++++.. +-+..+..+|.... .++..+++...+..++. ....++.
T Consensus 5 ~~~~v~~~v~~dG~~~V~E~ity~f~~----~~~giyr~i~~~~~~~~~~~~~~~~~~~v~~~~~~~~~---~~~~~~~- 76 (511)
T PF09972_consen 5 DSYDVDATVQEDGSLDVTETITYDFDG----SFHGIYRTIPLKGTGQLGDDKQSIKNFSVSDDGSSGKP---GTYGIEE- 76 (511)
T ss_pred eeeEEEEEECCCCcEEEEEEEEEEecc----CCceEEEEeccCCCCCCCcccccceeEEEEeCCCcCCC---cceEEEe-
Confidence 334444444 344 366776666643 25666777776655 55666666655411111 1222222
Q ss_pred cCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEEEcccccccCcccCcCCceeEEEEeC-ceecCcceeceEEEEEEeC
Q 012485 105 QLPDAPNETNYYTIVLANPLNTGETATLEILYILTHSLEPFPVEISQSESQLVYYRDS-ALILSPYHIKQQTTFIKIP 181 (462)
Q Consensus 105 ~~~~~~~~~~~~~I~Lp~pl~p~~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~l~~~~n-~~~~SpY~t~~q~t~i~~~ 181 (462)
..+..-++|....+...+++.+++++|.+.+....+ +|.+.+.|+-- ...-.| .++-+.+|.+|
T Consensus 77 -----~~~~~~~~i~~~~~~~~~~~~~~~~~Y~v~~~v~~~------~D~~el~w~~~g~~~~~~--i~~v~v~i~~P 141 (511)
T PF09972_consen 77 -----TDDGYEIRIGIYDPSKNGGTHTYTISYTVKNAVTNY------SDVAELYWNFIGSGWDVP--IENVTVTITLP 141 (511)
T ss_pred -----cCCcceEEEEecCccccCCeEEEEEEEEEECceEEc------CCeeEEEEEEecCCCCCc--cceEEEEEECC
Confidence 122345788899998887999999999999999966 66677887743 333444 45567778888
No 15
>PF05753 TRAP_beta: Translocon-associated protein beta (TRAPB); InterPro: IPR008856 This family consists of several eukaryotic translocon-associated protein beta (TRAPB) or signal sequence receptor beta subunit (SSR-beta) proteins. The normal translocation of nascent polypeptides into the lumen of the endoplasmic reticulum (ER) is thought to be aided in part by a translocon-associated protein (TRAP) complex consisting of 4 protein subunits. The association of mature proteins with the ER and Golgi, or other intracellular locales, such as lysosomes, depends on the initial targeting of the nascent polypeptide to the ER membrane. A similar scenario must also exist for proteins destined for secretion [].; GO: 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=31.98 E-value=1.3e+02 Score=28.55 Aligned_cols=20 Identities=25% Similarity=0.398 Sum_probs=15.0
Q ss_pred EEEEEEEEEeCCCCCccEEE
Q 012485 49 KVFLTLKVENTGKTSASEIL 68 (462)
Q Consensus 49 k~~~~i~ikN~g~~~~~~y~ 68 (462)
..++++++.|.|++++..--
T Consensus 39 ~v~V~~~iyN~G~~~A~dV~ 58 (181)
T PF05753_consen 39 DVTVTYTIYNVGSSAAYDVK 58 (181)
T ss_pred EEEEEEEEEECCCCeEEEEE
Confidence 46778889999988766443
No 16
>PF04314 DUF461: Protein of unknown function (DUF461); InterPro: IPR007410 This entry represents a domain found in of proteins of unknown function, including DR1885 from Deinococcus radiodurans and CC3502 from Caulobacter crescentus (Caulobacter vibrioides), which share a potential metal binding motif H(M)X10MX21HXM. DR1885 was found to bind copper(I) through a histidine and three Mets in a cupredoxin-like fold []. The surface location of the copper-binding site as well as the type of coordination are well poised for metal transfer chemistry, suggesting that DR1885 might transfer copper, taking the role of Cox17 in bacteria (Cox17 being an accessory protein required for correct assembly of eukaryotic cyochrome c oxidase). ; PDB: 2K6W_A 2K6Z_A 2K6Y_A 2K70_A 1X9L_A 2JQA_A.
Probab=27.77 E-value=1.7e+02 Score=25.00 Aligned_cols=82 Identities=17% Similarity=0.338 Sum_probs=36.3
Q ss_pred EEEEEeCCCCCccEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecCCC-CCCCceEEEEEeCCCCCCCCeEE
Q 012485 53 TLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPD-APNETNYYTIVLANPLNTGETAT 131 (462)
Q Consensus 53 ~i~ikN~g~~~~~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~~~-~~~~~~~~~I~Lp~pl~p~~~~~ 131 (462)
-.+|+|.|+++.. ...+....+.+.-.-.....++.-+-.....+.+..-+... .+++...-...+..++++|+++.
T Consensus 19 y~ti~N~g~~~~~--L~~v~s~~a~~v~lh~~~~~~g~~~m~~v~~i~ipa~~~v~l~pgg~HlmL~g~~~~l~~G~~v~ 96 (110)
T PF04314_consen 19 YFTITNNGDQDDR--LVGVSSPAAARVELHETVMEDGVMKMRPVDSIPIPAGSTVELKPGGYHLMLMGLKRPLKPGDTVP 96 (110)
T ss_dssp EEEEE-CSSSEEE--EEEEE-TTCCEEEEEEECCCCCEEEECCSS-EEEETT-EEEE-CCCCEEEEECESS-B-TTEEEE
T ss_pred EEEEEeCCCCCeE--EEEEEcCCCceEEEEEEEccCCeEEEEECCCEEECCCCeEEecCCCEEEEEeCCcccCCCCCEEE
Confidence 3678887776554 55555555555444443322221000000112221100000 12233445567778999999888
Q ss_pred EEEEE
Q 012485 132 LEILY 136 (462)
Q Consensus 132 l~v~~ 136 (462)
+++.+
T Consensus 97 ltL~f 101 (110)
T PF04314_consen 97 LTLTF 101 (110)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 87754
No 17
>PRK11901 hypothetical protein; Reviewed
Probab=25.57 E-value=55 Score=33.91 Aligned_cols=12 Identities=50% Similarity=0.551 Sum_probs=9.6
Q ss_pred EEEEEEcCCCeE
Q 012485 37 AERRIDLSTHIV 48 (462)
Q Consensus 37 v~R~IdL~~~~v 48 (462)
-+|.|||+++-.
T Consensus 75 ~~knIdLS~sss 86 (327)
T PRK11901 75 AEKNIDLSGSSS 86 (327)
T ss_pred cccceecCCCCc
Confidence 379999998853
No 18
>PF03929 PepSY_TM: PepSY-associated TM helix; InterPro: IPR005625 This domain represents a conserved transmembrane (TM) helix that is found in bacterial proteins. Coil residues are significantly more conserved than other residues and are frequently found within channels and transporters, where they introduce the flexibility and polarity required for transport across the membrane []. This TM helix associates with PepSY (peptidase (M4) and YpeB of subtilis). PepSY is a repeated region first identified in Thermoanaerobacter tengcongensis. The PepSY domain functions in the control of M4 peptidases through their propeptide and in the germination of spores. It may also play a part in regulating protease activity [].
Probab=25.37 E-value=43 Score=21.95 Aligned_cols=19 Identities=21% Similarity=0.412 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHhhhccCCC
Q 012485 444 DFIIFVSVLLGTFCVSGMI 462 (462)
Q Consensus 444 ~f~~fl~~~~~~~~~~~~~ 462 (462)
.++.+.+.+.++.|++|++
T Consensus 7 w~~~i~al~~lv~~iTGl~ 25 (27)
T PF03929_consen 7 WFGDIFALFMLVFAITGLI 25 (27)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4566777778888888864
No 19
>PRK10905 cell division protein DamX; Validated
Probab=24.21 E-value=41 Score=34.76 Aligned_cols=14 Identities=29% Similarity=0.470 Sum_probs=11.0
Q ss_pred EeeEEEEEEcCCCe
Q 012485 34 INNAERRIDLSTHI 47 (462)
Q Consensus 34 n~~v~R~IdL~~~~ 47 (462)
...-+|.|||+++-
T Consensus 31 ~~~~eknIdLsgss 44 (328)
T PRK10905 31 TASGEKSIDLAGNA 44 (328)
T ss_pred ccccccceeccCCc
Confidence 44678999999873
No 20
>PF09478 CBM49: Carbohydrate binding domain CBM49; InterPro: IPR019028 A carbohydrate-binding module (CBM) is defined as a contiguous amino acid sequence within a carbohydrate-active enzyme with a discreet fold having carbohydrate-binding activity. A few exceptions are CBMs in cellulosomal scaffolding proteins and rare instances of independent putative CBMs. The requirement of CBMs existing as modules within larger enzymes sets this class of carbohydrate-binding protein apart from other non-catalytic sugar binding proteins such as lectins and sugar transport proteins. CBMs were previously classified as cellulose-binding domains (CBDs) based on the initial discovery of several modules that bound cellulose [, ]. However, additional modules in carbohydrate-active enzymes are continually being found that bind carbohydrates other than cellulose yet otherwise meet the CBM criteria, hence the need to reclassify these polypeptides using more inclusive terminology. Previous classification of cellulose-binding domains were based on amino acid similarity. Groupings of CBDs were called "Types" and numbered with roman numerals (e.g. Type I or Type II CBDs). In keeping with the glycoside hydrolase classification, these groupings are now called families and numbered with Arabic numerals. Families 1 to 13 are the same as Types I to XIII. For a detailed review on the structure and binding modes of CBMs see []. This domain is found at the C-terminal of cellulases and in vitro binding studies have shown it to binds to crystalline cellulose []. ; GO: 0030246 carbohydrate binding, 0005576 extracellular region
Probab=22.62 E-value=4.1e+02 Score=21.32 Aligned_cols=25 Identities=8% Similarity=0.217 Sum_probs=20.6
Q ss_pred EEEEEEEEEEeCCCCCccEEEEEcC
Q 012485 48 VKVFLTLKVENTGKTSASEILLAFP 72 (462)
Q Consensus 48 vk~~~~i~ikN~g~~~~~~y~~~l~ 72 (462)
.-...+++++|.|+.++....|.+.
T Consensus 17 ~y~qy~v~I~N~~~~~I~~~~i~~~ 41 (80)
T PF09478_consen 17 TYTQYDVTITNNGSKPIKSLKISID 41 (80)
T ss_pred EEEEEEEEEEECCCCeEEEEEEEEC
Confidence 4456778999999999998888776
No 21
>PF04744 Monooxygenase_B: Monooxygenase subunit B protein; InterPro: IPR006833 Ammonia monooxygenase and the particulate methane monooxygenase are both integral membrane proteins, occurring in ammonia oxidisers and methanotrophs respectively, which are thought to be evolutionarily related []. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons and aromatic molecules []. These enzymes are composed of 3 subunits - A (IPR003393 from INTERPRO), B (IPR006833 from INTERPRO) and C (IPR006980 from INTERPRO) - and contain various metal centres, including copper. Particulate methane monooxygenase from Methylococcus capsulatus str. Bath is an ABC homotrimer, which contains mononuclear and dinuclear copper metal centres, and a third metal centre containing a metal ion whose identity in vivo is not certain[]. The soluble regions of these enzymes derive primarily from the B subunit. This subunit forms two antiparallel beta-barrel-like structures and contains the mono- and di- nuclear copper metal centres [].; PDB: 3CHX_E 3RFR_A 3RGB_A 1YEW_A.
Probab=22.04 E-value=8.9e+02 Score=25.77 Aligned_cols=84 Identities=19% Similarity=0.258 Sum_probs=38.5
Q ss_pred EeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCcccceeEEEEEEcCCccccceeeeeeeeeecCCCCCCCc
Q 012485 34 INNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNET 113 (462)
Q Consensus 34 n~~v~R~IdL~~~~vk~~~~i~ikN~g~~~~~~y~~~l~~~~~~~ls~~~a~~~~~~~k~~~~~~l~v~~~~~~~~~~~~ 113 (462)
..-..-+.++-+.-.+ .+++++|.|++|+.==-| ...++.++.......+ .. .+ +..-..
T Consensus 251 ~~v~~A~Y~vpgR~l~--~~l~VtN~g~~pv~LgeF-----~tA~vrFln~~v~~~~-~~--------~P----~~l~A~ 310 (381)
T PF04744_consen 251 VKVTDATYRVPGRTLT--MTLTVTNNGDSPVRLGEF-----NTANVRFLNPDVPTDD-PD--------YP----DELLAE 310 (381)
T ss_dssp EEEEEEEEESSSSEEE--EEEEEEEESSS-BEEEEE-----ESSS-EEE-TTT-SS--S---------------TTTEET
T ss_pred EEEeccEEecCCcEEE--EEEEEEcCCCCceEeeeE-----EeccEEEeCcccccCC-CC--------Cc----hhhhcc
Confidence 3333456777777554 457889999998762222 1244544432111100 00 00 000000
Q ss_pred eEEEEEeCCCCCCCCeEEEEEEEE
Q 012485 114 NYYTIVLANPLNTGETATLEILYI 137 (462)
Q Consensus 114 ~~~~I~Lp~pl~p~~~~~l~v~~~ 137 (462)
.-..|.=+.|++|||+.+++|+..
T Consensus 311 ~gL~vs~~~pI~PGETrtl~V~a~ 334 (381)
T PF04744_consen 311 RGLSVSDNSPIAPGETRTLTVEAQ 334 (381)
T ss_dssp T-EEES--S-B-TT-EEEEEEEEE
T ss_pred CcceeCCCCCcCCCceEEEEEEee
Confidence 124566567999999999999874
No 22
>PF02102 Peptidase_M35: Deuterolysin metalloprotease (M35) family; InterPro: IPR001384 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M35 (deuterolysin family, clan MA(M)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Deuterolysin is a microbial zinc-containing metalloprotease that shows some similarity to thermolysin []. The protein is expressed with a possible 19-residue signal sequence, a 155-residue propeptide, and an active peptide of 177 residues []. The latter contains an HEXXH motif towards the C terminus, but the other zinc ligands are as yet undetermined [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 1EB6_A.
Probab=22.03 E-value=30 Score=36.40 Aligned_cols=23 Identities=30% Similarity=0.407 Sum_probs=0.0
Q ss_pred CCCCCCCeEEEEEEEEEcccccc
Q 012485 122 NPLNTGETATLEILYILTHSLEP 144 (462)
Q Consensus 122 ~pl~p~~~~~l~v~~~~~~~~~P 144 (462)
.+|+||++++..+...-++-+.+
T Consensus 100 ~~L~pG~sve~~fDiA~~~dLs~ 122 (359)
T PF02102_consen 100 QTLAPGESVEVEFDIAETHDLSS 122 (359)
T ss_dssp -----------------------
T ss_pred eecCCCCeEEEEEcchheeecCC
Confidence 37899999999999888888864
No 23
>PHA02090 hypothetical protein
Probab=20.44 E-value=49 Score=26.27 Aligned_cols=20 Identities=30% Similarity=0.871 Sum_probs=13.6
Q ss_pred EEEEecCCcccCCceeeEE-EeecC
Q 012485 318 ELEIEPRYPLFGGWRATFV-IGYGL 341 (462)
Q Consensus 318 ~l~l~PRfPLfGGWk~~Ft-iGyn~ 341 (462)
.++.-|- ||||++-+ +||+.
T Consensus 41 v~e~m~d----g~~ktna~flgy~i 61 (79)
T PHA02090 41 VIEVMED----GGWKTNAEFLGYAI 61 (79)
T ss_pred EEEeccC----CCccccceeeeeee
Confidence 3455553 99999875 57774
Done!