Query 015446
Match_columns 406
No_of_seqs 112 out of 236
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 06:23:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015446.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015446hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2291 Oligosaccharyltransfer 100.0 1E-117 3E-122 901.7 32.9 390 6-403 5-396 (602)
2 PF04597 Ribophorin_I: Ribopho 100.0 2E-111 5E-116 868.8 43.1 365 31-403 1-370 (432)
3 PF08487 VIT: Vault protein in 92.8 3.8 8.1E-05 35.1 12.9 95 33-137 4-117 (118)
4 smart00609 VIT Vault protein I 92.8 3.3 7.2E-05 36.4 12.8 100 29-137 12-129 (130)
5 TIGR03788 marine_srt_targ mari 82.2 16 0.00035 39.9 12.2 90 40-138 6-112 (596)
6 PF09972 DUF2207: Predicted me 50.6 3.1E+02 0.0067 28.4 15.2 146 229-389 3-149 (511)
7 PF10989 DUF2808: Protein of u 48.8 1.9E+02 0.0042 25.6 10.6 28 112-139 87-114 (146)
8 PF15240 Pro-rich: Proline-ric 47.1 11 0.00025 35.0 1.6 27 10-36 1-27 (179)
9 PF07610 DUF1573: Protein of u 44.9 28 0.00061 24.7 3.1 21 116-136 24-45 (45)
10 PRK10301 hypothetical protein; 44.2 1.8E+02 0.0038 25.3 8.6 63 63-137 44-106 (124)
11 TIGR02411 leuko_A4_hydro leuko 43.5 4.9E+02 0.011 28.7 14.4 92 32-139 13-104 (601)
12 PF09972 DUF2207: Predicted me 42.2 4.1E+02 0.0089 27.5 19.8 127 34-181 4-141 (511)
13 TIGR03079 CH4_NH3mon_ox_B meth 40.7 66 0.0014 33.4 6.0 22 116-137 332-353 (399)
14 PF05753 TRAP_beta: Translocon 38.7 90 0.002 29.0 6.3 20 49-68 39-58 (181)
15 PRK11901 hypothetical protein; 37.4 27 0.00058 35.5 2.7 12 37-48 75-86 (327)
16 PRK10905 cell division protein 35.9 20 0.00044 36.3 1.6 13 34-46 31-43 (328)
17 PF04314 DUF461: Protein of un 34.6 1.2E+02 0.0027 25.5 6.0 82 53-136 19-101 (110)
18 PF09478 CBM49: Carbohydrate b 32.5 2.4E+02 0.0052 22.2 7.1 25 48-72 17-41 (80)
19 COG2372 CopC Uncharacterized p 29.3 2.3E+02 0.0051 25.1 6.9 55 64-127 46-100 (127)
20 TIGR02745 ccoG_rdxA_fixG cytoc 24.3 8.7E+02 0.019 25.8 12.6 68 5-73 298-370 (434)
21 PF02102 Peptidase_M35: Deuter 22.7 28 0.00062 35.9 0.0 23 122-144 100-122 (359)
22 PHA02090 hypothetical protein 22.4 42 0.00091 26.3 0.9 20 318-341 41-61 (79)
23 PF08441 Integrin_alpha2: Inte 21.3 9.3E+02 0.02 24.9 11.7 86 41-140 185-271 (457)
24 PF01433 Peptidase_M1: Peptida 20.2 8.7E+02 0.019 24.2 11.9 85 40-138 16-100 (390)
No 1
>KOG2291 consensus Oligosaccharyltransferase, alpha subunit (ribophorin I) [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.2e-117 Score=901.68 Aligned_cols=390 Identities=49% Similarity=0.784 Sum_probs=360.1
Q ss_pred hhhhHHHHHHHHHHHHHhhccCCCCCeEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCCCcceEEEEEE
Q 015446 6 RPRIMLSLTIILIPIFLFISGASSHQIRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEAL 85 (406)
Q Consensus 6 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~n~~v~R~IDL~~~~vk~~~~i~vkN~g~~p~~~y~~~l~~~~~~~ls~~~a~ 85 (406)
+++||+..+++|..++..+++.+++.|+|.|++|||||++|++|++++|+++|+|++|+++|.+++++....+||++++.
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 56666666565555555456777899999999999999999999999999999999999999999999999999999998
Q ss_pred eccCccccceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEEEcccccccCcccCcCCceeEEEEeCcee
Q 015446 86 AATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGETATLEILYILTHSLEPFPVEISQSESQLVYYRDSALI 165 (406)
Q Consensus 86 ~~~~~~~~~~~~~L~v~~~~~~~~~~~~~~~~I~Lp~pl~~g~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~l~~~~n~~~ 165 (406)
..+++++ +...+++.+.+..+ .++ .+|.|+||.||.||++++|.|++++++.++|+|++|+|+|+|+|+|.+|+|+
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 7776533 23456666665333 233 7999999999999999999999999999999999999999999999999999
Q ss_pred cCcceeceEEEEEEeCCCccceeeccCCccccCCeEEeccCCCCCCCCcCCeEEEEEccccceEEeeeEEEEEEecccce
Q 015446 166 LSPYHIKQQTTFIKIPSNKVESFTRVEPTDRAGNELKYGPYEDRPPYSYSPLLVHFENNNPFSVVEELVREVEISHWGNL 245 (406)
Q Consensus 166 ~SpY~t~~q~t~v~~~s~~i~s~t~~~~~~~~g~~i~yGP~~~v~p~s~~~~~Vhye~n~P~~~v~~L~R~IeVSHWGni 245 (406)
+|||.|++|+|.+++||++|++||+.++.+++|+.++||||+|+++|+++|+.||||||.||+++++|+|+|||||||||
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 EEEEEEEEEEcCCCCCCCcchhhhccCCCCCCccceeEEeeecCCCccCeEEEeccceeeeeeeeecCCceEEEEEecCC
Q 015446 246 QITEQYKLAHAGARHKGIFSRVDYQSKPTFSGVSSFKHLLARLPPRVHSVYYRDEIGNISTSHLRADSWKISELEIEPRY 325 (406)
Q Consensus 246 ~veE~y~l~N~GA~Lkg~FSR~d~~~~~~~~~~~~~~~l~~~LP~~a~d~YY~D~IGNISTS~~r~~~~~~~~l~l~PRf 325 (406)
||||+|+|+|.||+|||+|||+|||++...++.++++++.+.||++|+|+||||+||||||||+|.+.++ ++|+|+|||
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 9999999999999999999999999886668899999999999999999999999999999999999999 999999999
Q ss_pred cccCCceeeEEEeecCCcccceeeccCCceE-EEEEccCCC-cceEEEEEEEEEEecCCCcccceeecCcceeeeccceE
Q 015446 326 PLFGGWRATFVIGYGLPLEDFLFESSDGRRY-LNFTFGCPL-VETVVDKLTIKVSCVAGRSKRPFCCCSFSCRATSRDQV 403 (406)
Q Consensus 326 PLfGGWk~~FtiGyn~pl~~~L~~~~~~~~y-L~vp~~~~~-~d~~~d~~~l~IiLPEG~A~~i~v~~P~~v~~~s~~~~ 403 (406)
||||||||+|+||||+|+++||+ .+|++| |+++|..++ +|++||+++++|+|||| |+||++.+||++++.+.+.+
T Consensus 320 PlFGGWkt~ftiGy~lP~~eyl~--~~g~ry~L~~~~~~~~~d~~V~dkl~ikvvLPEG-ak~i~i~tP~~is~~p~e~~ 396 (602)
T KOG2291|consen 320 PLFGGWKTNFTIGYNLPLEEYLF--SKGRRYALKIILIDHIFDDTVYDKLTIKVVLPEG-AKDIEIDTPYEISRSPIELK 396 (602)
T ss_pred ccccCceeeEEEecCCcHHHHhh--ccCceeEEccccccCCCccceeeeEEEEEEccCC-CcccccccceeeccCchhhh
Confidence 99999999999999999999998 478888 999998864 77799999999999999 99999999999998876653
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=2.4e-111 Score=868.83 Aligned_cols=365 Identities=45% Similarity=0.770 Sum_probs=340.2
Q ss_pred CeEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCCCC
Q 015446 31 QIRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAP 110 (406)
Q Consensus 31 ~~~n~~v~R~IDL~~~~vk~~~~i~vkN~g~~p~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~~~ 110 (406)
+|+|+++.|+|||+++||||+++|+++|+|++|+++|+|++|.++.+++|+++|.+++++.+.. ...+..+ .+..
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 1112112 1122
Q ss_pred CCceEEEEEeCCCCCCCCeEEEEEEEEEcccccccCcccCcCCceeEEEEeCceecCcceeceEEEEEEeCCCccceeec
Q 015446 111 NETNYYTIVLANPLNTGETATLEILYILTHSLEPFPVEISQSESQLVYYRDSALILSPYHIKQQTTFIKIPSNKVESFTR 190 (406)
Q Consensus 111 ~~~~~~~I~Lp~pl~~g~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~l~~~~n~~~~SpY~t~~q~t~v~~~s~~i~s~t~ 190 (406)
....+|+|+||.||+||++++|.|+|++++++.|+|++|+|+|+|+|+|++|+|++|||+|++|+|+++++++++++||+
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---CccccCCeEEeccCCCCCCCCcCCeEEEEEccccceEEeeeEEEEEEecccceEEEEEEEEEEcCCCCCCCcchh
Q 015446 191 VE---PTDRAGNELKYGPYEDRPPYSYSPLLVHFENNNPFSVVEELVREVEISHWGNLQITEQYKLAHAGARHKGIFSRV 267 (406)
Q Consensus 191 ~~---~~~~~g~~i~yGP~~~v~p~s~~~~~Vhye~n~P~~~v~~L~R~IeVSHWGni~veE~y~l~N~GA~Lkg~FSR~ 267 (406)
.. +.+++|++++||||+|++||+.+++.||||||.||++|++|+|+|||||||||+|||+|+|+|+||+|||+|||+
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 hhccCCC-CCCccceeEEeeecCCCccCeEEEeccceeeeeeeeecCCceEEEEEecCCcccCCceeeEEEeecCCcccc
Q 015446 268 DYQSKPT-FSGVSSFKHLLARLPPRVHSVYYRDEIGNISTSHLRADSWKISELEIEPRYPLFGGWRATFVIGYGLPLEDF 346 (406)
Q Consensus 268 d~~~~~~-~~~~~~~~~l~~~LP~~a~d~YY~D~IGNISTS~~r~~~~~~~~l~l~PRfPLfGGWk~~FtiGyn~pl~~~ 346 (406)
|||++++ .++++++++|+++||++|+|+||||+||||||||+|.++++ ++|+|+|||||||||||+|++|||+|+++|
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 36789999999999999999999999999999999999999 999999999999999999999999999999
Q ss_pred eeeccCCceE-EEEEccCCCcceEEEEEEEEEEecCCCcccceeecCcceeeeccceE
Q 015446 347 LFESSDGRRY-LNFTFGCPLVETVVDKLTIKVSCVAGRSKRPFCCCSFSCRATSRDQV 403 (406)
Q Consensus 347 L~~~~~~~~y-L~vp~~~~~~d~~~d~~~l~IiLPEG~A~~i~v~~P~~v~~~s~~~~ 403 (406)
|++++++ +| |+|||++++.|++||+++++|+|||| |+||+|.+|+++++.+++.-
T Consensus 315 l~~~~~~-~y~L~vp~~~~~~d~~~d~~~l~i~LPEG-A~~i~v~~P~~~~~~~~~~~ 370 (432)
T PF04597_consen 315 LRKSGDG-RYVLKVPFLPGIKDIVYDNVELRIILPEG-AKNIKVSSPFPVDSVSVSTH 370 (432)
T ss_pred EEECCCC-cEEEEEECcCCcCceEEEEEEEEEECCCC-ceeeeEeCCccceeeeccce
Confidence 9976555 88 99999999999999999999999999 99999999999999887754
No 3
>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=92.78 E-value=3.8 Score=35.11 Aligned_cols=95 Identities=13% Similarity=0.241 Sum_probs=60.0
Q ss_pred EEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCc-cEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeee-------
Q 015446 33 RINNAERRIDLSTHIVKVFLTLKVENTGKTSA-SEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPT------- 104 (406)
Q Consensus 33 ~n~~v~R~IDL~~~~vk~~~~i~vkN~g~~p~-~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~------- 104 (406)
....+.=...+.+.+.+.+++-++.|..+.+. -.|.|.||.+ .-++-+++.+++..-+ + .+.+-
T Consensus 4 ~l~s~~v~~~I~~~~a~t~v~q~f~N~~~~~~E~~y~fpLp~~--A~i~~f~~~i~g~~i~-g-----~v~ek~~A~~~y 75 (118)
T PF08487_consen 4 PLKSVHVKVTIIDRFARTTVTQTFENPSSEPLEAVYSFPLPEG--AAISGFSMWIGGRTIE-G-----EVKEKEEAKQEY 75 (118)
T ss_pred eEEEEEEEEEEEccEEEEEEEEEEECCCCCcEEEEEEeECCCC--eEEEEEEEEECCEEEE-E-----EEecHHHHHHHH
Confidence 34445556677899999999999999876654 3456777765 4566666666543100 0 00000
Q ss_pred ------c----CCCC-CCCceEEEEEeCCCCCCCCeEEEEEEEE
Q 015446 105 ------Q----LPDA-PNETNYYTIVLANPLNTGETATLEILYI 137 (406)
Q Consensus 105 ------~----~~~~-~~~~~~~~I~Lp~pl~~g~~~~l~v~~~ 137 (406)
+ ..+. ..+...|.+.+ ++.||+++++.+.|.
T Consensus 76 ~~a~~~g~~a~lle~~~~~~~~F~~~v--ni~p~~~v~i~l~Y~ 117 (118)
T PF08487_consen 76 EEAVAQGKSAALLEQSDPNVEVFTVSV--NIPPNEEVTIELTYV 117 (118)
T ss_pred HHHHHcCCCchhhcccCCCCcEEEEEE--EeCCCCEEEEEEEEE
Confidence 0 0000 11334699999 899999999999985
No 4
>smart00609 VIT Vault protein Inter-alpha-Trypsin domain.
Probab=92.78 E-value=3.3 Score=36.42 Aligned_cols=100 Identities=11% Similarity=0.184 Sum_probs=61.9
Q ss_pred CCCeEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCCCcceEEEEEEeccCc------cc----------
Q 015446 29 SHQIRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGK------KK---------- 92 (406)
Q Consensus 29 ~~~~~n~~v~R~IDL~~~~vk~~~~i~vkN~g~~p~~~y~~~l~~~~~~~ls~~~a~~~~~~------~~---------- 92 (406)
...+...++.=...+.+.+++++++.+..|.++.+..-|||...+ ...-++.+...+++.. +|
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 345667777777888999999999999999986666665554332 2334444554443321 00
Q ss_pred -c-ceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEE
Q 015446 93 -K-KTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGETATLEILYI 137 (406)
Q Consensus 93 -~-~~~~~L~v~~~~~~~~~~~~~~~~I~Lp~pl~~g~~~~l~v~~~ 137 (406)
. +....|. +. + ......|++.+ +|.||+++++.+.|.
T Consensus 91 ~~~G~~a~L~-eq----~-~~~~~~F~~~V--NIppg~~v~v~l~Y~ 129 (130)
T smart00609 91 VSQGKTAGLV-RA----S-GRSMEQFTVSV--NVAPGSKVTFELTYE 129 (130)
T ss_pred HHcCCCeEEE-Ee----c-CCccCcEEEEE--EeCCCCEEEEEEEEE
Confidence 0 0001111 00 0 11125799999 899999999999885
No 5
>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=82.19 E-value=16 Score=39.88 Aligned_cols=90 Identities=17% Similarity=0.226 Sum_probs=58.8
Q ss_pred EEEcCCCeEEEEEEEEEEeCCCCCcc-EEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecC------------
Q 015446 40 RIDLSTHIVKVFLTLKVENTGKTSAS-EILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQL------------ 106 (406)
Q Consensus 40 ~IDL~~~~vk~~~~i~vkN~g~~p~~-~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~------------ 106 (406)
.+++++.+++++++.+..|..+.+.. .|.|.||++ .-+.-+++.+++.. ..-.+.+-+.
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 57789999999999999999877663 455666655 56777777765421 0001111000
Q ss_pred CC----CCCCceEEEEEeCCCCCCCCeEEEEEEEEE
Q 015446 107 PD----APNETNYYTIVLANPLNTGETATLEILYIL 138 (406)
Q Consensus 107 ~~----~~~~~~~~~I~Lp~pl~~g~~~~l~v~~~~ 138 (406)
.+ .......|++.+. ++.||+++++.++|.-
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 00 0112346899986 8999999999999873
No 6
>PF09972 DUF2207: Predicted membrane protein (DUF2207); InterPro: IPR018702 This domain has no known function.
Probab=50.55 E-value=3.1e+02 Score=28.41 Aligned_cols=146 Identities=16% Similarity=0.190 Sum_probs=81.6
Q ss_pred EEeeeEEEEEEecccceEEEEEEEEEEcCCCCCCCcchhhhccCCC-CCCccceeEEeeecCCCccCeEEEeccceeeee
Q 015446 229 VVEELVREVEISHWGNLQITEQYKLAHAGARHKGIFSRVDYQSKPT-FSGVSSFKHLLARLPPRVHSVYYRDEIGNISTS 307 (406)
Q Consensus 229 ~v~~L~R~IeVSHWGni~veE~y~l~N~GA~Lkg~FSR~d~~~~~~-~~~~~~~~~l~~~LP~~a~d~YY~D~IGNISTS 307 (406)
++.+++=+++|..=|.+.|+|.+...=+|. -.|-|-.++-..... ......++.+...-.. .-|.-.+-
T Consensus 3 ~I~~~~v~~~v~~dG~~~V~E~ity~f~~~-~~giyr~i~~~~~~~~~~~~~~~~~~~v~~~~---------~~~~~~~~ 72 (511)
T PF09972_consen 3 SIDSYDVDATVQEDGSLDVTETITYDFDGS-FHGIYRTIPLKGTGQLGDDKQSIKNFSVSDDG---------SSGKPGTY 72 (511)
T ss_pred cceeeEEEEEECCCCcEEEEEEEEEEeccC-CceEEEEeccCCCCCCCcccccceeEEEEeCC---------CcCCCcce
Confidence 467788888998889999999999886665 222222233221110 0000122222222211 11122222
Q ss_pred eeeecCCceEEEEEecCCcccCCceeeEEEeecCCcccceeeccCCceEEEEEccCCCcceEEEEEEEEEEecCCCcccc
Q 015446 308 HLRADSWKISELEIEPRYPLFGGWRATFVIGYGLPLEDFLFESSDGRRYLNFTFGCPLVETVVDKLTIKVSCVAGRSKRP 387 (406)
Q Consensus 308 ~~r~~~~~~~~l~l~PRfPLfGGWk~~FtiGyn~pl~~~L~~~~~~~~yL~vp~~~~~~d~~~d~~~l~IiLPEG~A~~i 387 (406)
.+....+. .++.+.-=.|--.|=...|++-|++. +.+..-+|... |.-.+...--++-+++++++|.||++ ...+
T Consensus 73 ~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~Y~v~--~~v~~~~D~~e-l~w~~~g~~~~~~i~~v~v~i~~P~~-~~~~ 147 (511)
T PF09972_consen 73 GIEETDDG-YEIRIGIYDPSKNGGTHTYTISYTVK--NAVTNYSDVAE-LYWNFIGSGWDVPIENVTVTITLPKP-VDNS 147 (511)
T ss_pred EEEecCCc-ceEEEEecCccccCCeEEEEEEEEEE--CceEEcCCeeE-EEEEEecCCCCCccceEEEEEECCCC-Ccce
Confidence 22222222 34666655666654567899999955 66643344333 44455544458999999999999987 6666
Q ss_pred ee
Q 015446 388 FC 389 (406)
Q Consensus 388 ~v 389 (406)
++
T Consensus 148 ~~ 149 (511)
T PF09972_consen 148 KA 149 (511)
T ss_pred EE
Confidence 65
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=48.81 E-value=1.9e+02 Score=25.58 Aligned_cols=28 Identities=21% Similarity=0.329 Sum_probs=23.6
Q ss_pred CceEEEEEeCCCCCCCCeEEEEEEEEEc
Q 015446 112 ETNYYTIVLANPLNTGETATLEILYILT 139 (406)
Q Consensus 112 ~~~~~~I~Lp~pl~~g~~~~l~v~~~~~ 139 (406)
+.....|.+..|+.||++++|.++-+.+
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 3467899999999999999999876654
No 8
>PF15240 Pro-rich: Proline-rich
Probab=47.07 E-value=11 Score=35.04 Aligned_cols=27 Identities=11% Similarity=0.170 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHhhccCCCCCeEEee
Q 015446 10 MLSLTIILIPIFLFISGASSHQIRINN 36 (406)
Q Consensus 10 ~~~~~~~l~~~~~~~~~~~~~~~~n~~ 36 (406)
||+.+|-++||||.+|-....++.+++
T Consensus 1 MLlVLLSvALLALSSAQ~~dEdv~~e~ 27 (179)
T PF15240_consen 1 MLLVLLSVALLALSSAQSTDEDVSQEE 27 (179)
T ss_pred ChhHHHHHHHHHhhhcccccccccccc
Confidence 677777777777744444444555544
No 9
>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=44.88 E-value=28 Score=24.67 Aligned_cols=21 Identities=24% Similarity=0.570 Sum_probs=15.8
Q ss_pred EEEEeC-CCCCCCCeEEEEEEE
Q 015446 116 YTIVLA-NPLNTGETATLEILY 136 (406)
Q Consensus 116 ~~I~Lp-~pl~~g~~~~l~v~~ 136 (406)
..++++ .+++||++..|.|.|
T Consensus 24 t~~~~~~~~i~PGes~~i~v~y 45 (45)
T PF07610_consen 24 TTAEYSKKPIAPGESGKIKVTY 45 (45)
T ss_pred EEeeCCcceECCCCEEEEEEEC
Confidence 444454 468999999999875
No 10
>PRK10301 hypothetical protein; Provisional
Probab=44.18 E-value=1.8e+02 Score=25.31 Aligned_cols=63 Identities=13% Similarity=0.219 Sum_probs=33.4
Q ss_pred CccEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEE
Q 015446 63 SASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTGETATLEILYI 137 (406)
Q Consensus 63 p~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~~~~~~~~~~I~Lp~pl~~g~~~~l~v~~~ 137 (406)
+..+.-+.|.+......+-+.....+++. +...+.. .+ ..+...+.+.|+.+|.+| +-.|+|-
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 APQALTLNFSEGIEPGFSGATITGPKQEN-------IKTLPAK-RN-EQDQKQLIVPLADSLKPG---TYTVDWH 106 (124)
T ss_pred CCCEEEEEcCCCccccccEEEEEcCCCCE-------eccCCcc-cc-CCCCcEEEEECCCCCCCc---cEEEEEE
Confidence 44555666666655566666665443331 1111111 00 123356788998899998 4455554
No 11
>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=43.54 E-value=4.9e+02 Score=28.71 Aligned_cols=92 Identities=11% Similarity=0.070 Sum_probs=55.8
Q ss_pred eEEeeEEEEEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCCCCC
Q 015446 32 IRINNAERRIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPN 111 (406)
Q Consensus 32 ~~n~~v~R~IDL~~~~vk~~~~i~vkN~g~~p~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~~~~ 111 (406)
...-++.=++|+.+....-+++|+++... .+.++..+-. ..|..-++.+.+.. +..+... ..+.
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 33455566788888888888888887642 2335555544 23444455443321 2221111 0011
Q ss_pred CceEEEEEeCCCCCCCCeEEEEEEEEEc
Q 015446 112 ETNYYTIVLANPLNTGETATLEILYILT 139 (406)
Q Consensus 112 ~~~~~~I~Lp~pl~~g~~~~l~v~~~~~ 139 (406)
....+.|.||.++++|+..+|.|.|.-+
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 2356899999999999999999988754
No 12
>PF09972 DUF2207: Predicted membrane protein (DUF2207); InterPro: IPR018702 This domain has no known function.
Probab=42.22 E-value=4.1e+02 Score=27.47 Aligned_cols=127 Identities=16% Similarity=0.210 Sum_probs=77.7
Q ss_pred EeeEEEEEEcCC--C-eEEEEEEEEEEeCCCCCccEEEEEcCCCCC-------cceEEEEEEeccCccccceeeeeeeee
Q 015446 34 INNAERRIDLST--H-IVKVFLTLKVENTGKTSASEILLAFPPTQV-------DHLAFLEALAATGKKKKKTYVSLAVKP 103 (406)
Q Consensus 34 n~~v~R~IDL~~--~-~vk~~~~i~vkN~g~~p~~~y~~~l~~~~~-------~~ls~~~a~~~~~~~~~~~~~~L~v~~ 103 (406)
+.+++=+++|.. + .|.|+.++++.. + -+..+..+|.... .++..+++...+...+ .....+..
T Consensus 4 I~~~~v~~~v~~dG~~~V~E~ity~f~~--~--~~giyr~i~~~~~~~~~~~~~~~~~~~v~~~~~~~~---~~~~~~~~ 76 (511)
T PF09972_consen 4 IDSYDVDATVQEDGSLDVTETITYDFDG--S--FHGIYRTIPLKGTGQLGDDKQSIKNFSVSDDGSSGK---PGTYGIEE 76 (511)
T ss_pred ceeeEEEEEECCCCcEEEEEEEEEEecc--C--CceEEEEeccCCCCCCCcccccceeEEEEeCCCcCC---CcceEEEe
Confidence 344444555533 3 356666655543 2 6777888886665 5555666655441101 11222222
Q ss_pred ecCCCCCCCceEEEEEeCCCCCCCCeEEEEEEEEEcccccccCcccCcCCceeEEEEeC-ceecCcceeceEEEEEEeC
Q 015446 104 TQLPDAPNETNYYTIVLANPLNTGETATLEILYILTHSLEPFPVEISQSESQLVYYRDS-ALILSPYHIKQQTTFIKIP 181 (406)
Q Consensus 104 ~~~~~~~~~~~~~~I~Lp~pl~~g~~~~l~v~~~~~~~~~P~P~~I~q~e~Q~l~~~~n-~~~~SpY~t~~q~t~v~~~ 181 (406)
..+..-++|....+...+++.+++++|.+.+....+ +|.+.+.|+-- ...-.| .++-+.+|.+|
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 112234788888998887899999999999999977 56677877743 333344 45557778888
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=40.72 E-value=66 Score=33.38 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=17.4
Q ss_pred EEEEeCCCCCCCCeEEEEEEEE
Q 015446 116 YTIVLANPLNTGETATLEILYI 137 (406)
Q Consensus 116 ~~I~Lp~pl~~g~~~~l~v~~~ 137 (406)
..|.=+.|++|||+.++.|+..
T Consensus 332 L~v~d~~pI~PGETr~v~v~aq 353 (399)
T TIGR03079 332 LEVDDQSAIAPGETVEVKMEAK 353 (399)
T ss_pred ceeCCCCCcCCCcceEEEEEEe
Confidence 3455567999999999998864
No 14
>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=38.69 E-value=90 Score=29.05 Aligned_cols=20 Identities=25% Similarity=0.398 Sum_probs=15.4
Q ss_pred EEEEEEEEEeCCCCCccEEE
Q 015446 49 KVFLTLKVENTGKTSASEIL 68 (406)
Q Consensus 49 k~~~~i~vkN~g~~p~~~y~ 68 (406)
..++++++.|.|+.++...-
T Consensus 39 ~v~V~~~iyN~G~~~A~dV~ 58 (181)
T PF05753_consen 39 DVTVTYTIYNVGSSAAYDVK 58 (181)
T ss_pred EEEEEEEEEECCCCeEEEEE
Confidence 57788899999998776533
No 15
>PRK11901 hypothetical protein; Reviewed
Probab=37.40 E-value=27 Score=35.52 Aligned_cols=12 Identities=50% Similarity=0.551 Sum_probs=9.6
Q ss_pred EEEEEEcCCCeE
Q 015446 37 AERRIDLSTHIV 48 (406)
Q Consensus 37 v~R~IDL~~~~v 48 (406)
-+|.|||+++-.
T Consensus 75 ~~knIdLS~sss 86 (327)
T PRK11901 75 AEKNIDLSGSSS 86 (327)
T ss_pred cccceecCCCCc
Confidence 379999998843
No 16
>PRK10905 cell division protein DamX; Validated
Probab=35.90 E-value=20 Score=36.34 Aligned_cols=13 Identities=31% Similarity=0.526 Sum_probs=10.6
Q ss_pred EeeEEEEEEcCCC
Q 015446 34 INNAERRIDLSTH 46 (406)
Q Consensus 34 n~~v~R~IDL~~~ 46 (406)
...-+|.|||+++
T Consensus 31 ~~~~eknIdLsgs 43 (328)
T PRK10905 31 TASGEKSIDLAGN 43 (328)
T ss_pred ccccccceeccCC
Confidence 4467899999987
No 17
>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=34.62 E-value=1.2e+02 Score=25.46 Aligned_cols=82 Identities=17% Similarity=0.338 Sum_probs=37.6
Q ss_pred EEEEEeCCCCCccEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCC-CCCCceEEEEEeCCCCCCCCeEE
Q 015446 53 TLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPD-APNETNYYTIVLANPLNTGETAT 131 (406)
Q Consensus 53 ~i~vkN~g~~p~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~-~~~~~~~~~I~Lp~pl~~g~~~~ 131 (406)
-.+|+|.|+++.. +..+....+.+.-.-.....++.-+-.....+.+..-+... .+.+...-...+..++++|+++.
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 66666555565555443332221000000112221100000 12234455567778999999888
Q ss_pred EEEEE
Q 015446 132 LEILY 136 (406)
Q Consensus 132 l~v~~ 136 (406)
+++.+
T Consensus 97 ltL~f 101 (110)
T PF04314_consen 97 LTLTF 101 (110)
T ss_dssp EEEEE
T ss_pred EEEEE
Confidence 88764
No 18
>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=32.49 E-value=2.4e+02 Score=22.23 Aligned_cols=25 Identities=8% Similarity=0.217 Sum_probs=20.6
Q ss_pred EEEEEEEEEEeCCCCCccEEEEEcC
Q 015446 48 VKVFLTLKVENTGKTSASEILLAFP 72 (406)
Q Consensus 48 vk~~~~i~vkN~g~~p~~~y~~~l~ 72 (406)
.-...+++++|.|+.++....|.+.
T Consensus 17 ~y~qy~v~I~N~~~~~I~~~~i~~~ 41 (80)
T PF09478_consen 17 TYTQYDVTITNNGSKPIKSLKISID 41 (80)
T ss_pred EEEEEEEEEEECCCCeEEEEEEEEC
Confidence 4456778999999999999888776
No 19
>COG2372 CopC Uncharacterized protein, homolog of Cu resistance protein CopC [General function prediction only]
Probab=29.33 E-value=2.3e+02 Score=25.05 Aligned_cols=55 Identities=20% Similarity=0.315 Sum_probs=29.5
Q ss_pred ccEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCCCCCCceEEEEEeCCCCCCC
Q 015446 64 ASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIVLANPLNTG 127 (406)
Q Consensus 64 ~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~~~~~~~~~~I~Lp~pl~~g 127 (406)
...+.+.|.+....+-+.+.....++++ +........+ .+...++|.|+.||++|
T Consensus 46 P~~i~L~Fse~ve~~fs~~~l~~~d~~~-------v~t~~~~~~~--~~~~~l~v~l~~~L~aG 100 (127)
T COG2372 46 PAAITLEFSEGVEPGFSGAKLTGPDGEE-------VATAGTKLDE--QNHTQLEVPLPQPLKAG 100 (127)
T ss_pred ceeEEEecCCccCCCcceeEEECCCCCc-------cccCcccccc--cCCcEEEecCcccCCCC
Confidence 3444555665555555555555444331 1222222111 22356899999999998
No 20
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=24.31 E-value=8.7e+02 Score=25.76 Aligned_cols=68 Identities=26% Similarity=0.233 Sum_probs=36.5
Q ss_pred chhhhHHHHHHHHHHHHHhhccCCCCCeEEeeEEEE-----EEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCC
Q 015446 5 LRPRIMLSLTIILIPIFLFISGASSHQIRINNAERR-----IDLSTHIVKVFLTLKVENTGKTSASEILLAFPP 73 (406)
Q Consensus 5 ~~~~~~~~~~~~l~~~~~~~~~~~~~~~~n~~v~R~-----IDL~~~~vk~~~~i~vkN~g~~p~~~y~~~l~~ 73 (406)
+|+|...-+.++++++++++..-..-.=...++.|. +-++...+.-..++++.|.+.++ .+|.+.+..
T Consensus 298 ~R~r~~~Y~~~l~~~~~~~~~~l~~r~~~~~~v~r~r~~l~~~~~~g~i~N~Y~~~i~Nk~~~~-~~~~l~v~g 370 (434)
T TIGR02745 298 LRPRTIGYAAVLAIVIGLLAIALSTREPMDLNVLRDRNLLYVRNSDGVVENTYTLKILNKTEQP-HEYYLSVLG 370 (434)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhCCCceEEEEEecCCcceEECCCCcEEEEEEEEEEECCCCC-EEEEEEEec
Confidence 788877555554443333222221111112222222 23466678888888899976555 566776553
No 21
>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=22.66 E-value=28 Score=35.91 Aligned_cols=23 Identities=30% Similarity=0.407 Sum_probs=0.0
Q ss_pred CCCCCCCeEEEEEEEEEcccccc
Q 015446 122 NPLNTGETATLEILYILTHSLEP 144 (406)
Q Consensus 122 ~pl~~g~~~~l~v~~~~~~~~~P 144 (406)
.+|+||++++..+...-++-|.+
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 37899999999999888888865
No 22
>PHA02090 hypothetical protein
Probab=22.39 E-value=42 Score=26.26 Aligned_cols=20 Identities=30% Similarity=0.871 Sum_probs=13.4
Q ss_pred EEEEecCCcccCCceeeEE-EeecC
Q 015446 318 ELEIEPRYPLFGGWRATFV-IGYGL 341 (406)
Q Consensus 318 ~l~l~PRfPLfGGWk~~Ft-iGyn~ 341 (406)
.++.-|- ||||++-+ +||+.
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 3455453 99999875 57764
No 23
>PF08441 Integrin_alpha2: Integrin alpha; InterPro: IPR013649 This domain is found in integrin alpha and integrin alpha precursors to the C terminus of a number of IPR013517 from INTERPRO repeats and to the N terminus of the IPR013513 from INTERPRO cytoplasmic region. ; PDB: 1M1X_A 1U8C_A 1L5G_A 3IJE_A 1JV2_A 2VDN_A 2VC2_A 3NIF_A 3NIG_C 2VDM_A ....
Probab=21.29 E-value=9.3e+02 Score=24.95 Aligned_cols=86 Identities=16% Similarity=0.327 Sum_probs=52.3
Q ss_pred EEcCCCeEEEEEEEEEEeCCCCCc-cEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCCCCCCceEEEEE
Q 015446 41 IDLSTHIVKVFLTLKVENTGKTSA-SEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIV 119 (406)
Q Consensus 41 IDL~~~~vk~~~~i~vkN~g~~p~-~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~~~~~~~~~~I~ 119 (406)
+-|+ +--...++++|+|.|+.+= ...++.+|+ .|.|..+...... ...+.+.... ..+.....-.
T Consensus 185 l~lg-~~~~l~l~v~v~N~GE~AY~a~l~v~~P~----~l~~~~v~~~~~~-----~~~~~C~~~~----~~~~~~~~C~ 250 (457)
T PF08441_consen 185 LVLG-SDNTLNLNVTVTNKGEDAYEAKLTVTYPS----GLSYSKVEKKQNS-----DSPISCSQPE----SNSSSTVSCS 250 (457)
T ss_dssp EECS-S-EEEEEEEEEEESSS-BSSEEEEEEEET----TEEEEEEE-SSSS-----SC--EEEEEE----SSSSCEEEEE
T ss_pred EEEC-CCCEEEEEEEEEECCCCCCceeEEEECCC----Ccccccccccccc-----ccceecccCC----CCCceEEEEE
Confidence 5566 4478889999999986543 344566774 4777666521111 1234555443 1111266778
Q ss_pred eCCCCCCCCeEEEEEEEEEcc
Q 015446 120 LANPLNTGETATLEILYILTH 140 (406)
Q Consensus 120 Lp~pl~~g~~~~l~v~~~~~~ 140 (406)
|..|+.+|+++++.+.+-...
T Consensus 251 lgnPl~~~~~~~~~l~f~~~~ 271 (457)
T PF08441_consen 251 LGNPLKRGSQVTFSLRFDVSS 271 (457)
T ss_dssp EETSBBTTEEEEEEEEEEE-T
T ss_pred CChhhhcCCcceEEEEeeccc
Confidence 999999999899988887654
No 24
>PF01433 Peptidase_M1: Peptidase family M1 This is family M1 in the peptidase classification.; InterPro: IPR014782 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 the MEROPS peptidase family M1 (clan MA(E)), the type example being aminopeptidase N from Homo sapiens (Human). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. Membrane alanine aminopeptidase (3.4.11.2 from EC) is part of the HEXXH+E group; it consists entirely of aminopeptidases, spread across a wide variety of species []. Functional studies show that CD13/APN catalyzes the removal of single amino acids from the amino terminus of small peptides and probably plays a role in their final digestion; one family member (leukotriene-A4 hydrolase) is known to hydrolyse the epoxide leukotriene-A4 to form an inflammatory mediator []. This hydrolase has been shown to have aminopeptidase activity [], and the zinc ligands of the M1 family were identified by site-directed mutagenesis on this enzyme [] CD13 participates in trimming peptides bound to MHC class II molecules [] and cleaves MIP-1 chemokine, which alters target cell specificity from basophils to eosinophils []. CD13 acts as a receptor for specific strains of RNA viruses (coronaviruses) which cause a relatively large percentage of upper respiratory trace infections. CD molecules are leucocyte antigens on cell surfaces. CD antigens nomenclature is updated at Protein Reviews On The Web (http://prow.nci.nih.gov/). ; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding; PDB: 2XQ0_A 2XPY_A 2XPZ_A 3SE6_B 3EBH_A 3EBG_A 3T8V_A 3Q44_A 3Q43_A 3EBI_A ....
Probab=20.18 E-value=8.7e+02 Score=24.19 Aligned_cols=85 Identities=22% Similarity=0.266 Sum_probs=51.6
Q ss_pred EEEcCCCeEEEEEEEEEEeCCCCCccEEEEEcCCCCCcceEEEEEEeccCccccceeeeeeeeeecCCCCCCCceEEEEE
Q 015446 40 RIDLSTHIVKVFLTLKVENTGKTSASEILLAFPPTQVDHLAFLEALAATGKKKKKTYVSLAVKPTQLPDAPNETNYYTIV 119 (406)
Q Consensus 40 ~IDL~~~~vk~~~~i~vkN~g~~p~~~y~~~l~~~~~~~ls~~~a~~~~~~~~~~~~~~L~v~~~~~~~~~~~~~~~~I~ 119 (406)
++|+.+....-+++|+++-.. +.+...+... ++..-++.+.+...... ........ ........|.
T Consensus 16 ~~~~~~~~f~G~v~I~~~~~~--~~~~I~L~~~-----~l~I~~v~~~~~~~~~~----~~~~~~~~---~~~~~~l~I~ 81 (390)
T PF01433_consen 16 TPDFEKRTFSGTVTITFEVTE--PTNSIVLHAK-----DLSISSVSLNGNDSSSE----YKSSPFEY---DDENEKLTIT 81 (390)
T ss_dssp EEETTTTEEEEEEEEEEEESS--TECEEEEEES-----SEEEEEEEETTEECSCT----ECCEEEEE---ECCBTEEEEE
T ss_pred EEeCCCCEEEEEEEEEEEEec--CCCEEEEEee-----ccEEEEEeecCcccccc----ccccceee---ccccceeehh
Confidence 377888888888888888743 6776666542 24444555544321110 00000110 1123468999
Q ss_pred eCCCCCCCCeEEEEEEEEE
Q 015446 120 LANPLNTGETATLEILYIL 138 (406)
Q Consensus 120 Lp~pl~~g~~~~l~v~~~~ 138 (406)
|+.++.+|+..+|.|.|.-
T Consensus 82 l~~~l~~g~~~~L~I~y~g 100 (390)
T PF01433_consen 82 LPKPLPPGSNYTLRIEYSG 100 (390)
T ss_dssp EEEECSTTEEEEEEEEEEE
T ss_pred hhhhcccCcEEEEEEEEee
Confidence 9999999998888888764
Done!