Query 039166
Match_columns 188
No_of_seqs 160 out of 895
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 06:58:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039166.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039166hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06280 DUF1034: Fn3-like dom 97.2 0.008 1.7E-07 44.8 11.2 87 94-183 3-111 (112)
2 PF10633 NPCBM_assoc: NPCBM-as 93.5 0.42 9.1E-06 33.2 6.7 53 100-152 6-59 (78)
3 PF14874 PapD-like: Flagellar- 90.9 4.5 9.7E-05 28.9 13.2 78 101-186 22-100 (102)
4 PF11614 FixG_C: IG-like fold 87.7 2.6 5.5E-05 31.4 6.5 51 101-152 33-83 (118)
5 smart00635 BID_2 Bacterial Ig- 84.1 4.7 0.0001 28.0 6.1 39 128-176 4-43 (81)
6 PF00345 PapD_N: Pili and flag 81.8 14 0.0003 27.4 8.2 52 99-152 14-72 (122)
7 PF07718 Coatamer_beta_C: Coat 76.6 14 0.0003 29.3 6.9 49 118-173 89-138 (140)
8 COG1470 Predicted membrane pro 75.0 16 0.00034 34.5 7.9 67 86-152 381-451 (513)
9 PF00635 Motile_Sperm: MSP (Ma 70.0 37 0.00079 24.2 7.6 50 100-152 19-68 (109)
10 TIGR02745 ccoG_rdxA_fixG cytoc 58.7 50 0.0011 30.7 7.8 50 102-152 349-398 (434)
11 cd00237 p23 p23 binds heat sho 44.5 81 0.0018 23.3 5.7 22 120-141 18-39 (106)
12 PF02368 Big_2: Bacterial Ig-l 43.9 18 0.00038 24.8 1.9 35 128-173 4-39 (79)
13 PF09244 DUF1964: Domain of un 43.4 36 0.00078 23.4 3.2 37 135-175 15-53 (68)
14 PLN03080 Probable beta-xylosid 40.1 1.1E+02 0.0023 30.6 7.3 52 100-152 685-743 (779)
15 PF00347 Ribosomal_L6: Ribosom 38.2 77 0.0017 21.3 4.4 22 124-145 2-23 (77)
16 PF08261 Carcinustatin: Carcin 36.6 17 0.00038 15.0 0.5 7 23-29 1-7 (8)
17 PF14874 PapD-like: Flagellar- 33.1 1.1E+02 0.0023 21.6 4.7 25 128-152 3-29 (102)
18 PRK15308 putative fimbrial pro 30.1 3.5E+02 0.0075 23.0 8.0 52 100-152 32-99 (234)
19 PF12970 DUF3858: Domain of Un 29.4 1E+02 0.0023 23.6 4.1 37 114-150 36-72 (116)
20 PRK13203 ureB urease subunit b 29.3 1.6E+02 0.0034 22.2 5.0 49 99-149 18-81 (102)
21 cd00407 Urease_beta Urease bet 25.5 2.1E+02 0.0045 21.5 5.0 49 99-149 18-81 (101)
22 COG1470 Predicted membrane pro 24.1 6.4E+02 0.014 24.1 9.4 66 86-152 270-342 (513)
23 PF07610 DUF1573: Protein of u 23.8 1.9E+02 0.004 17.8 4.8 19 132-151 27-45 (45)
24 PRK13205 ureB urease subunit b 23.7 2.1E+02 0.0046 23.1 5.1 51 98-150 17-82 (162)
25 PRK15098 beta-D-glucoside gluc 23.3 2.9E+02 0.0063 27.5 7.1 51 99-152 667-726 (765)
26 PF13195 DUF4011: Protein of u 22.8 1E+02 0.0022 24.6 3.3 22 165-186 120-144 (176)
27 PRK13201 ureB urease subunit b 22.5 2.4E+02 0.0051 22.3 5.1 50 99-150 18-82 (136)
28 TIGR00192 urease_beta urease, 21.8 2.7E+02 0.0059 20.8 5.1 49 99-149 18-81 (101)
29 cd06479 ACD_HspB7_like Alpha c 21.8 1.8E+02 0.0039 20.4 4.0 32 109-140 2-37 (81)
30 PF00699 Urease_beta: Urease b 21.8 2E+02 0.0043 21.5 4.3 17 98-114 16-32 (100)
31 PF00553 CBM_2: Cellulose bind 21.7 1.4E+02 0.003 21.5 3.5 35 102-136 16-52 (101)
32 PF12180 EABR: TSG101 and ALIX 20.9 8.9 0.00019 23.3 -2.4 16 43-58 15-30 (35)
33 KOG3316 Transport protein part 20.8 43 0.00094 27.0 0.7 50 35-104 106-157 (163)
No 1
>PF06280 DUF1034: Fn3-like domain (DUF1034); InterPro: IPR010435 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. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain of unknown function is present in bacterial and plant peptidases belonging to MEROPS peptidase family S8 (subfamily S8A subtilisin, clan SB). It is C-terminal to and adjacent to the S8 peptidase domain and can be found in conjunction with the PA (Protease associated) domain (IPR003137 from INTERPRO) and additionally in Gram-positive bacteria with the surface protein anchor domain (IPR001899 from INTERPRO).; GO: 0004252 serine-type endopeptidase activity, 0005618 cell wall, 0016020 membrane; PDB: 3EIF_A 1XF1_B.
Probab=97.24 E-value=0.008 Score=44.80 Aligned_cols=87 Identities=24% Similarity=0.397 Sum_probs=54.3
Q ss_pred EeecCccEEEEEEEEeecCCCceEEEEEEC--------CCCe-----------EEEEEcCEEEEeeCCeEEEEEEEEE-e
Q 039166 94 LTLGSGAQTYTRTVTNVGQPNSLYKSLIFV--------PQGV-----------EVEVTPSTLQFNEANQKASFAVTFK-R 153 (188)
Q Consensus 94 v~~~~~~~tv~RTVTNVg~~~~tY~a~v~~--------p~gv-----------~V~V~P~~l~f~~~ge~~sf~Vt~~-~ 153 (188)
+.......+++=+++|.|+..-+|+++... ..|. .+...|..++..+ ||++.++|+|+ .
T Consensus 3 L~d~~~~~~~~itl~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV~a-g~s~~v~vti~~p 81 (112)
T PF06280_consen 3 LKDTGNKFSFTITLHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTVPA-GQSKTVTVTITPP 81 (112)
T ss_dssp EEEE-SEEEEEEEEEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE-T-TEEEEEEEEEE--
T ss_pred ccccCCceEEEEEEEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEECC-CCEEEEEEEEEeh
Confidence 333444567777888888888888776541 1121 6778888999977 99999999999 4
Q ss_pred ccCCCCCCCCCeEEEEEEEEc-CCc-eEEeeE
Q 039166 154 TSYGGNRQDMPFAQGYIKWSS-DQH-SVRIPL 183 (188)
Q Consensus 154 ~~~~~~~~~~~~~fG~l~Wsd-~~h-~VrsPi 183 (188)
..... ....+..|.|.+++ ..+ .++.|.
T Consensus 82 ~~~~~--~~~~~~eG~I~~~~~~~~~~lsIPy 111 (112)
T PF06280_consen 82 SGLDA--SNGPFYEGFITFKSSDGEPDLSIPY 111 (112)
T ss_dssp GGGHH--TT-EEEEEEEEEESSTTSEEEEEEE
T ss_pred hcCCc--ccCCEEEEEEEEEcCCCCEEEEeee
Confidence 31100 13578999999995 344 788885
No 2
>PF10633 NPCBM_assoc: NPCBM-associated, NEW3 domain of alpha-galactosidase; InterPro: IPR018905 This domain has been named NEW3, but its function is not known. It is found on proteins which are bacterial galactosidases [].; PDB: 1EUT_A 2BZD_A 1WCQ_C 2BER_A 1W8O_A 1EUU_A 1W8N_A.
Probab=93.53 E-value=0.42 Score=33.16 Aligned_cols=53 Identities=23% Similarity=0.288 Sum_probs=34.7
Q ss_pred cEEEEEEEEeecCCC-ceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 100 AQTYTRTVTNVGQPN-SLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 100 ~~tv~RTVTNVg~~~-~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
..+++=+|+|-|... ...++++..|+|-.+.+.|..+.-=+.||+++++++++
T Consensus 6 ~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V~ 59 (78)
T PF10633_consen 6 TVTVTLTVTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTVT 59 (78)
T ss_dssp EEEEEEEEE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEEE
T ss_pred EEEEEEEEEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEEE
Confidence 567888999999754 56888899999999989999886334599999999998
No 3
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=90.93 E-value=4.5 Score=28.94 Aligned_cols=78 Identities=17% Similarity=0.130 Sum_probs=55.3
Q ss_pred EEEEEEEEeecCCCceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE-eccCCCCCCCCCeEEEEEEEEcCCceE
Q 039166 101 QTYTRTVTNVGQPNSLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK-RTSYGGNRQDMPFAQGYIKWSSDQHSV 179 (188)
Q Consensus 101 ~tv~RTVTNVg~~~~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~-~~~~~~~~~~~~~~fG~l~Wsd~~h~V 179 (188)
.+.+=+++|.|..+..|++.......-.++|+|..=.+.+ |++.++.|+|. ... . ...-+.|.-......+
T Consensus 22 ~~~~v~l~N~s~~p~~f~v~~~~~~~~~~~v~~~~g~l~P-G~~~~~~V~~~~~~~------~-g~~~~~l~i~~e~~~~ 93 (102)
T PF14874_consen 22 YSRTVTLTNTSSIPARFRVRQPESLSSFFSVEPPSGFLAP-GESVELEVTFSPTKP------L-GDYEGSLVITTEGGSF 93 (102)
T ss_pred EEEEEEEEECCCCCEEEEEEeCCcCCCCEEEECCCCEECC-CCEEEEEEEEEeCCC------C-ceEEEEEEEEECCeEE
Confidence 4445567999999999998764423455677887766766 99999999998 433 2 2345777776555677
Q ss_pred EeeEEEE
Q 039166 180 RIPLVVI 186 (188)
Q Consensus 180 rsPi~v~ 186 (188)
..||-+.
T Consensus 94 ~i~v~a~ 100 (102)
T PF14874_consen 94 EIPVKAE 100 (102)
T ss_pred EEEEEEE
Confidence 7777654
No 4
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=87.66 E-value=2.6 Score=31.40 Aligned_cols=51 Identities=18% Similarity=0.187 Sum_probs=37.2
Q ss_pred EEEEEEEEeecCCCceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 101 QTYTRTVTNVGQPNSLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 101 ~tv~RTVTNVg~~~~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
-.++=.++|-...+-.|+.++..++|+++......+...+ ||+..+.|.+.
T Consensus 33 N~Y~lkl~Nkt~~~~~~~i~~~g~~~~~l~~~~~~i~v~~-g~~~~~~v~v~ 83 (118)
T PF11614_consen 33 NQYTLKLTNKTNQPRTYTISVEGLPGAELQGPENTITVPP-GETREVPVFVT 83 (118)
T ss_dssp EEEEEEEEE-SSS-EEEEEEEES-SS-EE-ES--EEEE-T-T-EEEEEEEEE
T ss_pred EEEEEEEEECCCCCEEEEEEEecCCCeEEECCCcceEECC-CCEEEEEEEEE
Confidence 4577789999999999999999989999966558999977 99999999998
No 5
>smart00635 BID_2 Bacterial Ig-like domain 2.
Probab=84.10 E-value=4.7 Score=28.05 Aligned_cols=39 Identities=23% Similarity=0.440 Sum_probs=29.7
Q ss_pred EEEEEcCEEEEeeCCeEEEEEEEEE-eccCCCCCCCCCeEEEEEEEEcCC
Q 039166 128 EVEVTPSTLQFNEANQKASFAVTFK-RTSYGGNRQDMPFAQGYIKWSSDQ 176 (188)
Q Consensus 128 ~V~V~P~~l~f~~~ge~~sf~Vt~~-~~~~~~~~~~~~~~fG~l~Wsd~~ 176 (188)
.|++.|..+++.. |+++.|++++. ... .. ...+.|+...
T Consensus 4 ~i~i~p~~~~l~~-G~~~~l~a~~~~~~~-------~~--~~~v~w~Ssn 43 (81)
T smart00635 4 SVTVTPTTASVKK-GLTLQLTATVTPSSA-------KV--TGKVTWTSSN 43 (81)
T ss_pred EEEEeCCeeEEeC-CCeEEEEEEEECCCC-------Cc--cceEEEEECC
Confidence 6789999999976 99999999987 322 11 5678898543
No 6
>PF00345 PapD_N: Pili and flagellar-assembly chaperone, PapD N-terminal domain; InterPro: IPR016147 Most Gram-negative bacteria possess a supramolecular structure - the pili - on their surface, which mediates attachment to specific receptors. Many interactive subunits are required to assemble pili, but their assembly only takes place after translocation across the cytoplasmic membrane. Periplasmic chaperones assist pili assembly by binding to the subunits, thereby preventing premature aggregation [, ]. Pili chaperones are structurally, and possibly evolutionarily, related to the immunoglobulin superfamily [, ]: they contain two globular domains, with a topology identical to an immunoglobulin fold. This entry represents the N-terminal domain of pili assembly chaperone, and has a beta-sandwich fold consisting of seven strands in two sheets with a Greek key topology.; GO: 0007047 cellular cell wall organization, 0030288 outer membrane-bounded periplasmic space; PDB: 2CO6_B 2CO7_B 1L4I_B 3GFU_A 3F65_F 3F6L_A 3F6I_A 3GEW_B 3DSN_D 2OS7_B ....
Probab=81.81 E-value=14 Score=27.37 Aligned_cols=52 Identities=15% Similarity=0.273 Sum_probs=39.4
Q ss_pred ccEEEEEEEEeecCCCceEEEEEEC---CCC----eEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 99 GAQTYTRTVTNVGQPNSLYKSLIFV---PQG----VEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 99 ~~~tv~RTVTNVg~~~~tY~a~v~~---p~g----v~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
+..+..=+|+|-|+.+-.+.+.+.. ..+ -.+-|+|..+.+.+ |+++.+.| +.
T Consensus 14 ~~~~~~i~v~N~~~~~~~vq~~v~~~~~~~~~~~~~~~~vsPp~~~L~p-g~~q~vRv-~~ 72 (122)
T PF00345_consen 14 SQRSASITVTNNSDQPYLVQVWVYDQDDEDEDEPTDPFIVSPPIFRLEP-GESQTVRV-YR 72 (122)
T ss_dssp TSSEEEEEEEESSSSEEEEEEEEEETTSTTSSSSSSSEEEESSEEEEET-TEEEEEEE-EE
T ss_pred CCCEEEEEEEcCCCCcEEEEEEEEcCCCcccccccccEEEeCCceEeCC-CCcEEEEE-Ee
Confidence 3346677899999866777777764 111 15779999999988 99999999 76
No 7
>PF07718 Coatamer_beta_C: Coatomer beta C-terminal region; InterPro: IPR011710 Proteins synthesised on the ribosome and processed in the endoplasmic reticulum are transported from the Golgi apparatus to the trans-Golgi network (TGN), and from there via small carrier vesicles to their final destination compartment. This traffic is bidirectional, to ensure that proteins required to form vesicles are recycled. Vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transfer []. While clathrin mediates endocytic protein transport, and transport from ER to Golgi, coatomers primarily mediate intra-Golgi transport, as well as the reverse Golgi to ER transport of dilysine-tagged proteins []. For example, the coatomer COP1 (coat protein complex 1) is responsible for reverse transport of recycled proteins from Golgi and pre-Golgi compartments back to the ER, while COPII buds vesicles from the ER to the Golgi []. Coatomers reversibly associate with Golgi (non-clathrin-coated) vesicles to mediate protein transport and for budding from Golgi membranes []. Activated small guanine triphosphatases (GTPases) attract coat proteins to specific membrane export sites, thereby linking coatomers to export cargos. As coat proteins polymerise, vesicles are formed and budded from membrane-bound organelles. Coatomer complexes also influence Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors. In mammals, coatomer complexes can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins. Coatomer complexes are hetero-oligomers composed of at least an alpha, beta, beta', gamma, delta, epsilon and zeta subunits. This entry represents the C-terminal domain of the beta subunit from coatomer proteins (Beta-coat proteins). The C-terminal domain probably adapts the function of the N-terminal IPR002553 from INTERPRO domain. Coatomer protein complex I (COPI)-coated vesicles are involved in transport between the endoplasmic reticulum and the Golgi but also participate in transport from early to late endosomes within the endocytic pathway []. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0005198 structural molecule activity, 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030126 COPI vesicle coat
Probab=76.63 E-value=14 Score=29.31 Aligned_cols=49 Identities=12% Similarity=0.171 Sum_probs=39.1
Q ss_pred EEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE-eccCCCCCCCCCeEEEEEEEE
Q 039166 118 KSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK-RTSYGGNRQDMPFAQGYIKWS 173 (188)
Q Consensus 118 ~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~-~~~~~~~~~~~~~~fG~l~Ws 173 (188)
++....-.++++.=.|..+++.+ ++.+.++.+|+ ... .....||.|+|.
T Consensus 89 ~vElat~gdLklve~p~~~tL~P-~~~~~i~~~iKVsSt------etGvIfG~I~Yd 138 (140)
T PF07718_consen 89 TVELATLGDLKLVERPQPITLAP-HGFARIKATIKVSST------ETGVIFGNIVYD 138 (140)
T ss_pred EEEEEecCCcEEccCCCceeeCC-CcEEEEEEEEEEEec------cCCEEEEEEEEe
Confidence 34444445789999999999988 99999999998 554 457999999985
No 8
>COG1470 Predicted membrane protein [Function unknown]
Probab=74.96 E-value=16 Score=34.50 Aligned_cols=67 Identities=25% Similarity=0.364 Sum_probs=51.5
Q ss_pred ccCccc--eEEeecCc-cEEEEEEEEeecCCC-ceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 86 QLNYPS--FSLTLGSG-AQTYTRTVTNVGQPN-SLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 86 dLNyPS--i~v~~~~~-~~tv~RTVTNVg~~~-~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
.|+.++ +-+.-..| ..++.=.+.|-|+++ ..-+.+|..|.|-++.|.|.++---+.||+++..+|++
T Consensus 381 ~v~l~~g~~~lt~taGee~~i~i~I~NsGna~LtdIkl~v~~PqgWei~Vd~~~I~sL~pge~~tV~ltI~ 451 (513)
T COG1470 381 LVKLDNGPYRLTITAGEEKTIRISIENSGNAPLTDIKLTVNGPQGWEIEVDESTIPSLEPGESKTVSLTIT 451 (513)
T ss_pred eEEccCCcEEEEecCCccceEEEEEEecCCCccceeeEEecCCccceEEECcccccccCCCCcceEEEEEE
Confidence 555555 44444444 456777789999754 56788999999999999999876555699999999998
No 9
>PF00635 Motile_Sperm: MSP (Major sperm protein) domain; InterPro: IPR000535 Major sperm proteins (MSP) are central components in molecular interactions underlying sperm motility in Caenorhabditis elegans, whose sperm employ an amoebae-like crawling motion using a MSP-containing lamellipod, rather than the flagellar-based swimming motion associated with other sperm. These proteins oligomerise to form an extensive filament system that extends from sperm villipoda, along the leading edge of the pseudopod. About 30 MSP isoforms may exist in C. elegans. MSPs form a fibrous network, whereby MSP dimers form helical subfilaments that coil around one another to produce filaments, which in turn form supercoils to produce bundles. The crystal structure of MSP from C. elegans reveals an immunoglobulin (Ig)-like seven-stranded beta sandwich fold []. ; GO: 0005198 structural molecule activity; PDB: 1MSP_A 3MSP_B 2BVU_B 2MSP_C 1Z9O_F 1Z9L_A 3IKK_A 1WIC_A 2CRI_A 2RR3_A ....
Probab=70.03 E-value=37 Score=24.15 Aligned_cols=50 Identities=22% Similarity=0.252 Sum_probs=38.1
Q ss_pred cEEEEEEEEeecCCCceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 100 AQTYTRTVTNVGQPNSLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 100 ~~tv~RTVTNVg~~~~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
.....=+++|.++..-.|++....|..+. |.|..-.+.+ ||+..+.|++.
T Consensus 19 ~~~~~l~l~N~s~~~i~fKiktt~~~~y~--v~P~~G~i~p-~~~~~i~I~~~ 68 (109)
T PF00635_consen 19 QQSCELTLTNPSDKPIAFKIKTTNPNRYR--VKPSYGIIEP-GESVEITITFQ 68 (109)
T ss_dssp -EEEEEEEEE-SSSEEEEEEEES-TTTEE--EESSEEEE-T-TEEEEEEEEE-
T ss_pred eEEEEEEEECCCCCcEEEEEEcCCCceEE--ecCCCEEECC-CCEEEEEEEEE
Confidence 34555589999988889999988888765 6799988877 99999999998
No 10
>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=58.67 E-value=50 Score=30.71 Aligned_cols=50 Identities=18% Similarity=0.298 Sum_probs=43.2
Q ss_pred EEEEEEEeecCCCceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 102 TYTRTVTNVGQPNSLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 102 tv~RTVTNVg~~~~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
.++=.+.|-...+.+|+.+++..+|.++...++.++..+ ||+.++.|.+.
T Consensus 349 ~Y~~~i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v~~-g~~~~~~v~v~ 398 (434)
T TIGR02745 349 TYTLKILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHVKA-GEKVKLPVFLR 398 (434)
T ss_pred EEEEEEEECCCCCEEEEEEEecCCCcEEEcCCceEEECC-CCEEEEEEEEE
Confidence 566678998888899999999999999887656889987 99999999988
No 11
>cd00237 p23 p23 binds heat shock protein (Hsp)90 and participates in the folding of a number of Hsp90 clients, including the progesterone receptor. p23 also has a passive chaperoning activity and in addition may participate in prostaglandin synthesis.
Probab=44.46 E-value=81 Score=23.34 Aligned_cols=22 Identities=23% Similarity=0.258 Sum_probs=16.1
Q ss_pred EEECCCCeEEEEEcCEEEEeeC
Q 039166 120 LIFVPQGVEVEVTPSTLQFNEA 141 (188)
Q Consensus 120 ~v~~p~gv~V~V~P~~l~f~~~ 141 (188)
.+..+..+.|.++|..|.|+..
T Consensus 18 ~v~d~~d~~v~l~~~~l~f~~~ 39 (106)
T cd00237 18 CVEDSKDVKVDFEKSKLTFSCL 39 (106)
T ss_pred EeCCCCCcEEEEecCEEEEEEE
Confidence 3334567888888999988863
No 12
>PF02368 Big_2: Bacterial Ig-like domain (group 2); InterPro: IPR003343 Proteins that contain this domain are found in a variety of bacterial and phage surface proteins such as intimins as well as in some uncharacterised eukaryote proteins. Intimin is a bacterial cell-adhesion molecule that mediates the intimate bacterial host-cell interaction. It contains three domains; two immunoglobulin-like domains and a C-type lectin-like module implying that carbohydrate recognition may be important in intimin-mediated cell adhesion [].; PDB: 3NCX_B 3NCW_D 4AQ1_A 2ZQK_B 2ZWK_C 1F02_I 1E5U_I 1F00_I 2L04_A.
Probab=43.91 E-value=18 Score=24.79 Aligned_cols=35 Identities=17% Similarity=0.469 Sum_probs=27.3
Q ss_pred EEEEEcCEEEEeeCCeEEEEEEEEE-eccCCCCCCCCCeEEEEEEEE
Q 039166 128 EVEVTPSTLQFNEANQKASFAVTFK-RTSYGGNRQDMPFAQGYIKWS 173 (188)
Q Consensus 128 ~V~V~P~~l~f~~~ge~~sf~Vt~~-~~~~~~~~~~~~~~fG~l~Ws 173 (188)
+|++.|..+.+.. |+++.|++.+. .... . ..+.|+
T Consensus 4 ~I~i~~~~~~l~~-G~~~~l~~~~~~~~~~-----~-----~~v~w~ 39 (79)
T PF02368_consen 4 SITITPTSVTLKV-GQTQQLTATVTPSDGS-----N-----SKVTWS 39 (79)
T ss_dssp SEEETTTEEECET-TCEETTEEEEEEEEST-----T-----SCEEEE
T ss_pred EEEEECCEEEEEC-CCEEEEEEEEEECCCc-----E-----eEEEEE
Confidence 4778999999977 99999999998 5442 1 557887
No 13
>PF09244 DUF1964: Domain of unknown function (DUF1964); InterPro: IPR015325 This domain is C-terminal to the catalytic sucrose phosphorylase beta/alpha barrel domain. It adopts a beta-sandwich fold, with Greek-key topology and is functionally uncharacterised []. ; PDB: 1R7A_B 2GDU_A 2GDV_A.
Probab=43.39 E-value=36 Score=23.43 Aligned_cols=37 Identities=19% Similarity=0.316 Sum_probs=20.3
Q ss_pred EEEEeeCCeEEEEEEEEE--eccCCCCCCCCCeEEEEEEEEcC
Q 039166 135 TLQFNEANQKASFAVTFK--RTSYGGNRQDMPFAQGYIKWSSD 175 (188)
Q Consensus 135 ~l~f~~~ge~~sf~Vt~~--~~~~~~~~~~~~~~fG~l~Wsd~ 175 (188)
+++|.=.|+.-+-+++|+ ++.. ..+...-.+|.|+|.
T Consensus 15 Sitf~W~g~~t~atLtFePg~Glg----~~n~~pVatl~W~Ds 53 (68)
T PF09244_consen 15 SITFTWTGATTSATLTFEPGRGLG----VDNTTPVATLAWTDS 53 (68)
T ss_dssp EEEEEEE-SS-EEEEEE-GGGC-S----TT--S--EEEEEEET
T ss_pred EEEEEEeccccEEEEEEccCcccC----ccCCcceeEEEEecc
Confidence 466776678888888998 3332 123345689999984
No 14
>PLN03080 Probable beta-xylosidase; Provisional
Probab=40.12 E-value=1.1e+02 Score=30.64 Aligned_cols=52 Identities=15% Similarity=0.193 Sum_probs=32.0
Q ss_pred cEEEEEEEEeecCCCceEEEEE--ECCCCeEEEEEcCEEE-Ee----eCCeEEEEEEEEE
Q 039166 100 AQTYTRTVTNVGQPNSLYKSLI--FVPQGVEVEVTPSTLQ-FN----EANQKASFAVTFK 152 (188)
Q Consensus 100 ~~tv~RTVTNVg~~~~tY~a~v--~~p~gv~V~V~P~~l~-f~----~~ge~~sf~Vt~~ 152 (188)
..+++=+|||+|+..+.-.|.+ ..|.+ .+..-+++|. |+ +.||++..++++.
T Consensus 685 ~~~v~v~VtNtG~~~G~evvQlYv~~p~~-~~~~P~k~L~gF~kv~L~~Ges~~V~~~l~ 743 (779)
T PLN03080 685 RFNVHISVSNVGEMDGSHVVMLFSRSPPV-VPGVPEKQLVGFDRVHTASGRSTETEIVVD 743 (779)
T ss_pred eEEEEEEEEECCcccCcEEEEEEEecCcc-CCCCcchhccCcEeEeeCCCCEEEEEEEeC
Confidence 4789999999999776665544 44432 1111223333 33 2499988877775
No 15
>PF00347 Ribosomal_L6: Ribosomal protein L6; InterPro: IPR020040 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L6 is a protein from the large (50S) subunit. In Escherichia coli, it is located in the aminoacyl-tRNA binding site of the peptidyltransferase centre, and is known to bind directly to 23S rRNA. It belongs to a family of ribosomal proteins, including L6 from bacteria, cyanelles (structures that perform similar functions to chloroplasts, but have structural and biochemical characteristics of Cyanobacteria) and mitochondria; and L9 from mammals, Drosophila, plants and yeast. L6 contains two domains with almost identical folds, suggesting that is was derived by the duplication of an ancient RNA-binding protein gene. Analysis reveals several sites on the protein surface where interactions with other ribosome components may occur, the N terminus being involved in protein-protein interactions and the C terminus containing possible RNA-binding sites []. This entry represents the alpha-beta domain found duplicated in ribosomal L6 proteins. This domain consists of two beta-sheets and one alpha-helix packed around single core [].; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 2HGJ_H 2HGQ_H 2HGU_H 1S1I_H 3O5H_I 3O58_I 3J16_F 3IZS_F 2V47_H 2WDJ_H ....
Probab=38.20 E-value=77 Score=21.28 Aligned_cols=22 Identities=18% Similarity=0.436 Sum_probs=15.4
Q ss_pred CCCeEEEEEcCEEEEeeCCeEE
Q 039166 124 PQGVEVEVTPSTLQFNEANQKA 145 (188)
Q Consensus 124 p~gv~V~V~P~~l~f~~~ge~~ 145 (188)
|.|++|++....+.++....+.
T Consensus 2 P~gV~v~~~~~~i~v~G~~g~l 23 (77)
T PF00347_consen 2 PEGVKVTIKGNIITVKGPKGEL 23 (77)
T ss_dssp STTCEEEEETTEEEEESSSSEE
T ss_pred CCcEEEEEeCcEEEEECCCEeE
Confidence 7788888888877776433333
No 16
>PF08261 Carcinustatin: Carcinustatin peptide
Probab=36.57 E-value=17 Score=15.02 Aligned_cols=7 Identities=29% Similarity=0.653 Sum_probs=4.6
Q ss_pred CCccccC
Q 039166 23 ADIFAIG 29 (188)
Q Consensus 23 atpFd~G 29 (188)
|.|+.||
T Consensus 1 agpy~fg 7 (8)
T PF08261_consen 1 AGPYSFG 7 (8)
T ss_pred CCccccc
Confidence 4577776
No 17
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=33.10 E-value=1.1e+02 Score=21.58 Aligned_cols=25 Identities=36% Similarity=0.530 Sum_probs=20.5
Q ss_pred EEEEEcCEEEEee--CCeEEEEEEEEE
Q 039166 128 EVEVTPSTLQFNE--ANQKASFAVTFK 152 (188)
Q Consensus 128 ~V~V~P~~l~f~~--~ge~~sf~Vt~~ 152 (188)
.++++|+.|.|.. .|++.+.+|+++
T Consensus 3 ~l~v~P~~ldFG~v~~g~~~~~~v~l~ 29 (102)
T PF14874_consen 3 TLEVSPKELDFGNVFVGQTYSRTVTLT 29 (102)
T ss_pred EEEEeCCEEEeeEEccCCEEEEEEEEE
Confidence 5789999999986 478888888887
No 18
>PRK15308 putative fimbrial protein TcfA; Provisional
Probab=30.11 E-value=3.5e+02 Score=23.05 Aligned_cols=52 Identities=13% Similarity=0.142 Sum_probs=33.1
Q ss_pred cEEEEEEEEeecCCCceEEEEEE---CC---CC----------eEEEEEcCEEEEeeCCeEEEEEEEEE
Q 039166 100 AQTYTRTVTNVGQPNSLYKSLIF---VP---QG----------VEVEVTPSTLQFNEANQKASFAVTFK 152 (188)
Q Consensus 100 ~~tv~RTVTNVg~~~~tY~a~v~---~p---~g----------v~V~V~P~~l~f~~~ge~~sf~Vt~~ 152 (188)
.....-+|.|-|+....+++.+. .| ++ =++-++|..|.+.+ |+++.+.+.-.
T Consensus 32 ~~~~~v~V~N~g~~~~~vqV~v~r~~~PG~~~e~~~~~~~~~~~eLiaSP~~l~L~p-g~~q~IRli~l 99 (234)
T PRK15308 32 EEATSLFVYSKSDHTQYVRTRIKRIEHPATPQEKEVPAGNDIETGLVVSPEKFALPA-GTTRTVRVISL 99 (234)
T ss_pred cceEEEEEEeCCCCcEEEEEEEEEEcCCCCCCCcccccccCCCCcEEEcCceeEECC-CCeEEEEEEEc
Confidence 34456677888876666666542 22 11 15788999999977 77766655443
No 19
>PF12970 DUF3858: Domain of Unknown Function with PDB structure (DUF3858); InterPro: IPR024544 This domain of unknown function is structurally similar to part of neuropilin-2. The proteins it occurs in have not yet been functionally characterised.; PDB: 3KD4_A.
Probab=29.41 E-value=1e+02 Score=23.63 Aligned_cols=37 Identities=22% Similarity=0.399 Sum_probs=21.0
Q ss_pred CceEEEEEECCCCeEEEEEcCEEEEeeCCeEEEEEEE
Q 039166 114 NSLYKSLIFVPQGVEVEVTPSTLQFNEANQKASFAVT 150 (188)
Q Consensus 114 ~~tY~a~v~~p~gv~V~V~P~~l~f~~~ge~~sf~Vt 150 (188)
+++|+-.|..|+|+++...|..-..+..-.|.+++|+
T Consensus 36 ~E~ytyti~~pegm~l~t~~~~K~I~N~~Gk~~isv~ 72 (116)
T PF12970_consen 36 DETYTYTIELPEGMKLVTPPMEKKIDNPVGKVSISVK 72 (116)
T ss_dssp EEEEEEEEEE-TT-EE-S--S-EEEEETTEEEEEEEE
T ss_pred CcceEEEEEcCCCCeeecCccceeccCCcceEEEEEE
Confidence 4667777888999999888887777655555444443
No 20
>PRK13203 ureB urease subunit beta; Reviewed
Probab=29.34 E-value=1.6e+02 Score=22.18 Aligned_cols=49 Identities=27% Similarity=0.473 Sum_probs=27.5
Q ss_pred ccEEEEEEEEeecCCC----ceEEEEEEC---------CCCeEEEEEcC--EEEEeeCCeEEEEEE
Q 039166 99 GAQTYTRTVTNVGQPN----SLYKSLIFV---------PQGVEVEVTPS--TLQFNEANQKASFAV 149 (188)
Q Consensus 99 ~~~tv~RTVTNVg~~~----~tY~a~v~~---------p~gv~V~V~P~--~l~f~~~ge~~sf~V 149 (188)
+..+++-+|+|.|+.+ |-|+..-.. .-|..+.+ |+ .+.|.+ ||+++.++
T Consensus 18 gr~~~~l~V~NtGDRPIQVGSH~HF~E~N~aL~FDR~~A~G~RLdI-paGTavRFEP-G~~k~V~L 81 (102)
T PRK13203 18 GRETVTLTVANTGDRPIQVGSHYHFFEVNPALSFDREAARGMRLNI-PAGTAVRFEP-GQTREVEL 81 (102)
T ss_pred CCCEEEEEEEeCCCCceEEccccchhhcCcchhccHhhhcCccccc-CCCCeEeECC-CCeEEEEE
Confidence 5567788899999854 556532111 11333322 22 356766 88877554
No 21
>cd00407 Urease_beta Urease beta-subunit; Urease is a nickel-dependent metalloenzyme that catalyzes the hydrolysis of urea to form ammonia and carbon dioxide. Nickel-dependent ureases are found in bacteria, archaea, fungi and plants. Their primary role is to allow the use of external and internally-generated urea as a nitrogen source. The enzyme consists of three subunits, alpha, beta and gamma, which can exist as separate proteins or can be fused on a single protein chain. The alpha-beta-gamma heterotrimer forms multimers, mainly trimers. The large alpha subunit is the catalytic domain containing an active site with a bi-nickel center complexed by a carbamylated lysine. The beta and gamma subunits play a role in subunit association to form the higher order trimers.
Probab=25.52 E-value=2.1e+02 Score=21.49 Aligned_cols=49 Identities=22% Similarity=0.483 Sum_probs=27.7
Q ss_pred ccEEEEEEEEeecCCC----ceEEEEEECC---------CCeEEEEEcC--EEEEeeCCeEEEEEE
Q 039166 99 GAQTYTRTVTNVGQPN----SLYKSLIFVP---------QGVEVEVTPS--TLQFNEANQKASFAV 149 (188)
Q Consensus 99 ~~~tv~RTVTNVg~~~----~tY~a~v~~p---------~gv~V~V~P~--~l~f~~~ge~~sf~V 149 (188)
+..+++-+|+|.|+.+ |-|+..-..| -|..+.+ |+ .+.|.+ ||+++.++
T Consensus 18 gr~~~~l~V~NtGDRpIQVGSH~HF~E~N~aL~FDR~~A~G~RLdI-paGTavRFEP-G~~k~V~L 81 (101)
T cd00407 18 GREAVTLKVKNTGDRPIQVGSHYHFFEVNPALKFDREKAYGMRLDI-PAGTAVRFEP-GEEKEVEL 81 (101)
T ss_pred CCCEEEEEEEeCCCcceEEccccchhhcCccccccHHHcccceecc-cCCCeEEECC-CCeEEEEE
Confidence 5567778899999854 5565421111 2333332 22 456766 88877554
No 22
>COG1470 Predicted membrane protein [Function unknown]
Probab=24.10 E-value=6.4e+02 Score=24.12 Aligned_cols=66 Identities=17% Similarity=0.369 Sum_probs=48.8
Q ss_pred ccCccceEEeecCc-cEEEEEEEEeecCCCceEEEEEE-CCCCeEEEEEc-----CEEEEeeCCeEEEEEEEEE
Q 039166 86 QLNYPSFSLTLGSG-AQTYTRTVTNVGQPNSLYKSLIF-VPQGVEVEVTP-----STLQFNEANQKASFAVTFK 152 (188)
Q Consensus 86 dLNyPSi~v~~~~~-~~tv~RTVTNVg~~~~tY~a~v~-~p~gv~V~V~P-----~~l~f~~~ge~~sf~Vt~~ 152 (188)
.||--++..-...+ +..++=++.|-|..+-.|..++. .|+|....-.= +++.+++ ||++.++|.+.
T Consensus 270 El~~s~~~~~i~~~~t~sf~V~IeN~g~~~d~y~Le~~g~pe~w~~~Fteg~~~vt~vkL~~-gE~kdvtleV~ 342 (513)
T COG1470 270 ELNSSDIYLEISPSTTASFTVSIENRGKQDDEYALELSGLPEGWTAEFTEGELRVTSVKLKP-GEEKDVTLEVY 342 (513)
T ss_pred EeecccceeEEccCCceEEEEEEccCCCCCceeEEEeccCCCCcceEEeeCceEEEEEEecC-CCceEEEEEEe
Confidence 46665555444444 45788899999999999999998 78875443322 3566766 99999999998
No 23
>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=23.83 E-value=1.9e+02 Score=17.80 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=12.0
Q ss_pred EcCEEEEeeCCeEEEEEEEE
Q 039166 132 TPSTLQFNEANQKASFAVTF 151 (188)
Q Consensus 132 ~P~~l~f~~~ge~~sf~Vt~ 151 (188)
+.+.=.+.+ ||+..++|++
T Consensus 27 ~~~~~~i~P-Ges~~i~v~y 45 (45)
T PF07610_consen 27 EYSKKPIAP-GESGKIKVTY 45 (45)
T ss_pred eCCcceECC-CCEEEEEEEC
Confidence 333344555 8888888764
No 24
>PRK13205 ureB urease subunit beta; Reviewed
Probab=23.69 E-value=2.1e+02 Score=23.12 Aligned_cols=51 Identities=18% Similarity=0.358 Sum_probs=29.4
Q ss_pred CccEEEEEEEEeecCCC----ceEEEEEECC---------CCeEEEEEcC--EEEEeeCCeEEEEEEE
Q 039166 98 SGAQTYTRTVTNVGQPN----SLYKSLIFVP---------QGVEVEVTPS--TLQFNEANQKASFAVT 150 (188)
Q Consensus 98 ~~~~tv~RTVTNVg~~~----~tY~a~v~~p---------~gv~V~V~P~--~l~f~~~ge~~sf~Vt 150 (188)
.+..+++-+|+|.|+.+ |-|+..-..| -|..+.+ |+ .+.|.+ |++++.++-
T Consensus 17 ~GR~~i~L~V~NtGDRPIQVGSHyHF~EvN~AL~FDR~~A~G~RLdI-PAGTAVRFEP-Ge~ktV~LV 82 (162)
T PRK13205 17 VGREAKTIEIINTGDRPVQIGSHFHFAEVNPSISFDRSEGYGFRLDI-PSGTAVRLEP-GDARTVNLV 82 (162)
T ss_pred CCCcEEEEEEEeCCCCceEeccccchhhcCccccccHHHhcCccccc-CCCCeEeECC-CCeEEEEEE
Confidence 35667888999999854 5665431111 2333332 22 455766 887776553
No 25
>PRK15098 beta-D-glucoside glucohydrolase; Provisional
Probab=23.31 E-value=2.9e+02 Score=27.47 Aligned_cols=51 Identities=16% Similarity=0.208 Sum_probs=32.7
Q ss_pred ccEEEEEEEEeecCCCceEEEE--EECCCCeEEEEEcC-------EEEEeeCCeEEEEEEEEE
Q 039166 99 GAQTYTRTVTNVGQPNSLYKSL--IFVPQGVEVEVTPS-------TLQFNEANQKASFAVTFK 152 (188)
Q Consensus 99 ~~~tv~RTVTNVg~~~~tY~a~--v~~p~gv~V~V~P~-------~l~f~~~ge~~sf~Vt~~ 152 (188)
+..+++=+|||+|+..+.-.+. +..|.+ ++ ..|. +..+++ ||+++.++++.
T Consensus 667 ~~i~v~v~V~NtG~~~G~EVvQlYv~~~~~-~~-~~P~k~L~gF~Kv~L~p-Ges~~V~~~l~ 726 (765)
T PRK15098 667 GKVTASVTVTNTGKREGATVVQLYLQDVTA-SM-SRPVKELKGFEKIMLKP-GETQTVSFPID 726 (765)
T ss_pred CeEEEEEEEEECCCCCccEEEEEeccCCCC-CC-CCHHHhccCceeEeECC-CCeEEEEEeec
Confidence 3578999999999866544443 444432 11 1342 234444 99999999998
No 26
>PF13195 DUF4011: Protein of unknown function (DUF4011)
Probab=22.85 E-value=1e+02 Score=24.58 Aligned_cols=22 Identities=32% Similarity=0.810 Sum_probs=18.0
Q ss_pred eEEEEEEEEc---CCceEEeeEEEE
Q 039166 165 FAQGYIKWSS---DQHSVRIPLVVI 186 (188)
Q Consensus 165 ~~fG~l~Wsd---~~h~VrsPi~v~ 186 (188)
-+||.|.|.+ .....++|+...
T Consensus 120 La~G~L~W~~~~~~~~~~~APLlL~ 144 (176)
T PF13195_consen 120 LAFGFLEWYESDDSDKPRRAPLLLI 144 (176)
T ss_pred eeeeEEEeccCCCCCCEEECCEEEE
Confidence 3799999996 578899998764
No 27
>PRK13201 ureB urease subunit beta; Reviewed
Probab=22.47 E-value=2.4e+02 Score=22.26 Aligned_cols=50 Identities=16% Similarity=0.264 Sum_probs=28.2
Q ss_pred ccEEEEEEEEeecCCC----ceEEEEEECC---------CCeEEEEEcC--EEEEeeCCeEEEEEEE
Q 039166 99 GAQTYTRTVTNVGQPN----SLYKSLIFVP---------QGVEVEVTPS--TLQFNEANQKASFAVT 150 (188)
Q Consensus 99 ~~~tv~RTVTNVg~~~----~tY~a~v~~p---------~gv~V~V~P~--~l~f~~~ge~~sf~Vt 150 (188)
+..+++-+|+|.|+.+ |-|+..-..| -|..+.+ |+ .+.|.+ ||+++.++-
T Consensus 18 gr~~~~l~V~NtGDRPIQVGSHyHF~EvN~aL~FDR~~A~G~RLdI-PAGTAVRFEP-G~~k~V~LV 82 (136)
T PRK13201 18 HHPETVIEVENTGDRPIQVGSHFHFYEANAALDFEREMAYGKHLDI-PAGAAVRFEP-GDKKEVQLV 82 (136)
T ss_pred CCCEEEEEEEeCCCcceEeccccchhhcCccccccHhhhcCccccc-CCCCeEeECC-CCeEEEEEE
Confidence 5566788899999854 5665421111 2333332 22 456766 888776543
No 28
>TIGR00192 urease_beta urease, beta subunit. In a number of species, including B.subtilis, Synechocystis, and Haemophilus influenzae, urease subunits beta and gamma are encoded as separate polypeptides. In Helicobacter pylori UreA and in the fission yeast Schizosaccharomyces pombe, beta subunit-like sequence follows gamma subunit-like sequence in a single chain; the fission yeast protein contains additional C-terminal regions.
Probab=21.83 E-value=2.7e+02 Score=20.84 Aligned_cols=49 Identities=22% Similarity=0.436 Sum_probs=27.1
Q ss_pred ccEEEEEEEEeecCCC----ceEEEEEEC---------CCCeEEEEEcC--EEEEeeCCeEEEEEE
Q 039166 99 GAQTYTRTVTNVGQPN----SLYKSLIFV---------PQGVEVEVTPS--TLQFNEANQKASFAV 149 (188)
Q Consensus 99 ~~~tv~RTVTNVg~~~----~tY~a~v~~---------p~gv~V~V~P~--~l~f~~~ge~~sf~V 149 (188)
+..+++-.|+|.|+.+ |-|+..-.. ..|..+.+ |+ .+.|.+ ||+++.++
T Consensus 18 gr~~~~l~V~NtGDRPIQVGSHyHF~E~N~aL~FDR~~A~G~RLdI-paGTavRFEP-G~~k~V~L 81 (101)
T TIGR00192 18 GRKTVSVKVKNTGDRPIQVGSHFHFFEVNRALDFDRELAFGMRLDI-PSGTAVRFEP-GEEKSVEL 81 (101)
T ss_pred CCcEEEEEEEeCCCcceEEccccchhhcCcceeecHhhhcCccccc-CCCCeEeECC-CCeEEEEE
Confidence 4566777899999754 556532111 12333332 22 355766 88877554
No 29
>cd06479 ACD_HspB7_like Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB7, also known as cardiovascular small heat shock protein (cvHsp), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. HspB7 is a 25-kDa protein, preferentially expressed in heart and skeletal muscle. It binds the cytoskeleton protein alpha-filamin (also known as actin-binding protein 280). The expression of HspB7 is increased during rat muscle aging. Its expression is also modulated in obesity implicating this protein in this and related metabolic disorders. As the human gene encoding HspB7 is mapped to chromosome 1p36.23-p34.3 it is a positional candidate for several dystrophies and myopathies.
Probab=21.83 E-value=1.8e+02 Score=20.41 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=26.0
Q ss_pred eecCCCceEEEEEECC----CCeEEEEEcCEEEEee
Q 039166 109 NVGQPNSLYKSLIFVP----QGVEVEVTPSTLQFNE 140 (188)
Q Consensus 109 NVg~~~~tY~a~v~~p----~gv~V~V~P~~l~f~~ 140 (188)
||.+....|.+.++.| +.+.|+|....|+.+.
T Consensus 2 ~v~e~~~~~~v~~dlpG~~pedi~V~v~~~~L~I~g 37 (81)
T cd06479 2 NVKTLGDTYQFAVDVSDFSPEDIIVTTSNNQIEVHA 37 (81)
T ss_pred CccCcCCeEEEEEECCCCCHHHeEEEEECCEEEEEE
Confidence 5666778899999876 5789999999999864
No 30
>PF00699 Urease_beta: Urease beta subunit CAUTION: The Prosite patterns do not match this subunit of the enzyme; InterPro: IPR002019 Urease 3.5.1.5 from EC is a nickel-binding enzyme that catalyzes the hydrolysis of urea to carbon dioxide and ammonia []: Urea + H2O = CO2 + 2 NH3 Historically, it was the first enzyme to be crystallized (in 1926). It is mainly found in plant seeds and microorganisms. In plants, urease is a hexamer of identical chains. In bacteria [], it consists of either two or three different subunits (alpha IPR005847 from INTERPRO, beta, described in this entry, and gamma IPR002026 from INTERPRO). The structure of the urease complex is known []. This subunit does not appear to take part in the catalytic mechanism. This subunit is known (confusingly) as alpha in Helicobacter.; GO: 0009039 urease activity, 0016151 nickel ion binding, 0006807 nitrogen compound metabolic process; PDB: 1EJS_B 1EJW_B 1A5N_B 1A5K_B 1A5M_B 1EJR_B 1EJX_B 1A5L_B 1KRB_B 1FWA_B ....
Probab=21.75 E-value=2e+02 Score=21.52 Aligned_cols=17 Identities=35% Similarity=0.462 Sum_probs=11.6
Q ss_pred CccEEEEEEEEeecCCC
Q 039166 98 SGAQTYTRTVTNVGQPN 114 (188)
Q Consensus 98 ~~~~tv~RTVTNVg~~~ 114 (188)
.+..+++-+|+|.|+.+
T Consensus 16 ~gr~~~~l~V~N~GDRP 32 (100)
T PF00699_consen 16 AGRERITLEVTNTGDRP 32 (100)
T ss_dssp TTSEEEEEEEEE-SSS-
T ss_pred CCCcEEEEEEEeCCCcc
Confidence 35677888899999854
No 31
>PF00553 CBM_2: Cellulose binding domain; InterPro: IPR001919 The microbial degradation of cellulose and xylans requires several types of enzyme such as endoglucanases (3.2.1.4 from EC), cellobiohydrolases (3.2.1.91 from EC) (exoglucanases), or xylanases (3.2.1.8 from EC) []. Structurally, cellulases and xylanases generally consist of a catalytic domain joined to a cellulose-binding domain (CBD) by a short linker sequence rich in proline and/or hydroxy-amino acids. The CBD domain is found either at the N-terminal or at the C-terminal extremity of these enzymes. As it is shown in the following schematic representation, there are two conserved cysteines in this CBD domain - one at each extremity of the domain - which have been shown [] to be involved in a disulphide bond. There are also four conserved tryptophan, two are involved in cellulose binding. The CBD of a number of bacterial cellulases has been shown to consist of about 105 amino acid residues [, ]. +-------------------------------------------------+ | | xCxxxxWxxxxxNxxxWxxxxxxxWxxxxxxxxWNxxxxxGxxxxxxxxxxCx 'C': conserved cysteine involved in a disulphide bond. ; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0005975 carbohydrate metabolic process; PDB: 2CZN_A 2CWR_A 1HEH_C 1HEJ_C 3NDZ_E 3NDY_E 2XBD_A 1E5C_A 1XBD_A 1E5B_A ....
Probab=21.67 E-value=1.4e+02 Score=21.50 Aligned_cols=35 Identities=23% Similarity=0.224 Sum_probs=22.6
Q ss_pred EEEEEEEeecCCC-ceEEEEEECCCCeEEE-EEcCEE
Q 039166 102 TYTRTVTNVGQPN-SLYKSLIFVPQGVEVE-VTPSTL 136 (188)
Q Consensus 102 tv~RTVTNVg~~~-~tY~a~v~~p~gv~V~-V~P~~l 136 (188)
...=+|+|.++.. ..|++++.-|.|.+|. +.-..+
T Consensus 16 ~~~v~v~N~~~~~i~~W~v~~~~~~~~~i~~~Wna~~ 52 (101)
T PF00553_consen 16 QGEVTVTNNGSSPINGWTVTFTFPSGQTITSSWNATV 52 (101)
T ss_dssp EEEEEEEESSSSTEESEEEEEEESTTEEEEEEESCEE
T ss_pred EEEEEEEECCCCccCCEEEEEEeCCCCEEeeeeccEE
Confidence 3456788888755 4699988888666543 334444
No 32
>PF12180 EABR: TSG101 and ALIX binding domain of CEP55; InterPro: IPR022008 This domain family is found in eukaryotes, and is approximately 40 amino acids in length. This domain is the active domain of CEP55. CEP55 is a protein involved in cytokinesis, specifically in abscission of the plasma membrane at the midbody. To perform this function, CEP55 complexes with ESCRT-I (by a Proline rich sequence in its TSG101 domain) and ALIX. This is the domain on CEP55 which binds to both TSG101 and ALIX. It also acts as a hinge between the N and C termini. This domain is called EABR. ; PDB: 3E1R_A.
Probab=20.88 E-value=8.9 Score=23.33 Aligned_cols=16 Identities=25% Similarity=0.372 Sum_probs=14.2
Q ss_pred eeecCCccchhhhccc
Q 039166 43 LVFDIQPDDYIPYLCG 58 (188)
Q Consensus 43 LVyD~~~~DY~~fLC~ 58 (188)
|.||..-++|+.-||+
T Consensus 15 q~YD~qRE~YV~~L~~ 30 (35)
T PF12180_consen 15 QKYDQQREAYVRGLLA 30 (35)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHhHHHHHHHHHH
Confidence 5799999999999986
No 33
>KOG3316 consensus Transport protein particle (TRAPP) complex subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=20.78 E-value=43 Score=27.04 Aligned_cols=50 Identities=16% Similarity=0.256 Sum_probs=33.2
Q ss_pred CCCCCCCCeeecCCccchhhhcccCCCCcceeEEeecccceeccCCccCccccCccceEEeecCc--cEEEE
Q 039166 35 PSRANDPGLVFDIQPDDYIPYLCGLNYTDREIAILVQRKVKCSEISSIKEAQLNYPSFSLTLGSG--AQTYT 104 (188)
Q Consensus 35 p~~A~dPGLVyD~~~~DY~~fLC~~gy~~~~i~~it~~~~~C~~~~~~~~~dLNyPSi~v~~~~~--~~tv~ 104 (188)
+..-+.||.=|-.-.--|+.|=|++ | .+.-++|+|+||....+.. +|.|.
T Consensus 106 ~l~~~s~G~~~~~~a~~flaFpcGl---------i-----------RGvLs~LGi~siVtA~v~slPtckFh 157 (163)
T KOG3316|consen 106 WLTSMSPGTQYLEEAPKFLAFPCGL---------I-----------RGVLSNLGISSIVTASVSSLPTCKFH 157 (163)
T ss_pred eeeecCchhHHHHhcCCeEEeehhH---------H-----------HHHHhhCCCceEEeeecCCCCceEEE
Confidence 3444558888877777888888874 1 1234689999987776543 44444
Done!