Query 024677
Match_columns 264
No_of_seqs 173 out of 628
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 06:32:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024677.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024677hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0439 VAMP-associated protei 100.0 6.2E-29 1.3E-33 218.6 14.3 186 72-262 4-217 (218)
2 COG5066 SCS2 VAMP-associated p 99.9 1.9E-25 4.2E-30 198.1 11.7 119 76-200 2-122 (242)
3 PF00635 Motile_Sperm: MSP (Ma 99.9 2.3E-22 5E-27 157.6 13.1 102 77-184 2-107 (109)
4 PF14874 PapD-like: Flagellar- 98.3 5.4E-06 1.2E-10 64.5 9.8 68 75-143 2-72 (102)
5 PF00345 PapD_N: Pili and flag 96.3 0.11 2.4E-06 41.6 11.9 62 77-142 2-72 (122)
6 PF14646 MYCBPAP: MYCBP-associ 94.3 1 2.2E-05 44.1 13.5 119 77-217 231-362 (426)
7 PRK09918 putative fimbrial cha 92.7 3.9 8.5E-05 37.0 13.4 64 76-143 25-93 (230)
8 PF07610 DUF1573: Protein of u 91.8 0.69 1.5E-05 31.6 5.8 42 99-141 2-44 (45)
9 PF11614 FixG_C: IG-like fold 89.8 1.3 2.9E-05 35.3 6.7 67 77-143 13-83 (118)
10 PRK15249 fimbrial chaperone pr 86.2 21 0.00045 32.9 12.9 64 76-143 29-103 (253)
11 PRK11385 putativi pili assembl 85.4 29 0.00064 31.7 13.5 64 76-143 27-102 (236)
12 PRK09926 putative chaperone pr 84.5 7.8 0.00017 35.5 9.2 65 75-143 25-99 (246)
13 PRK15299 fimbrial chaperone pr 84.1 21 0.00045 32.3 11.7 64 76-143 23-94 (227)
14 PF06280 DUF1034: Fn3-like dom 82.4 4.1 8.8E-05 32.3 5.8 52 92-143 7-79 (112)
15 PRK15211 fimbrial chaperone pr 81.9 25 0.00054 32.1 11.4 64 76-143 23-92 (229)
16 PRK15295 fimbrial assembly cha 81.8 12 0.00027 33.8 9.3 62 76-143 20-90 (226)
17 PRK15192 fimbrial chaperone Bc 81.5 43 0.00093 30.7 13.2 62 76-143 23-98 (234)
18 TIGR03079 CH4_NH3mon_ox_B meth 78.2 5.5 0.00012 39.2 6.1 53 91-143 280-353 (399)
19 PRK15208 long polar fimbrial c 76.9 23 0.00049 32.1 9.4 64 76-143 22-91 (228)
20 smart00809 Alpha_adaptinC2 Ada 76.5 18 0.00038 27.8 7.6 51 93-143 18-72 (104)
21 PF10633 NPCBM_assoc: NPCBM-as 76.3 5.3 0.00012 29.6 4.4 53 91-143 3-59 (78)
22 PRK15246 fimbrial assembly cha 75.0 67 0.0015 29.3 13.7 64 76-143 11-84 (233)
23 PF06030 DUF916: Bacterial pro 74.1 36 0.00079 27.9 9.2 60 84-143 18-102 (121)
24 PRK15195 fimbrial chaperone pr 70.6 34 0.00073 31.1 9.0 65 75-143 25-95 (229)
25 COG3121 FimC P pilus assembly 70.0 87 0.0019 28.5 13.5 112 76-203 28-147 (235)
26 PF02883 Alpha_adaptinC2: Adap 69.7 40 0.00087 26.4 8.3 53 91-143 22-78 (115)
27 PF00927 Transglut_C: Transglu 69.6 21 0.00046 27.8 6.6 53 91-143 13-75 (107)
28 PF11611 DUF4352: Domain of un 69.2 33 0.00072 26.7 7.7 54 90-143 33-100 (123)
29 PRK15188 fimbrial chaperone pr 67.7 99 0.0021 28.2 12.4 65 75-143 27-97 (228)
30 PF04744 Monooxygenase_B: Mono 66.2 18 0.00039 35.6 6.6 65 76-143 248-334 (381)
31 PRK15254 fimbrial chaperone pr 63.1 1.2E+02 0.0027 27.7 13.1 64 76-143 17-86 (239)
32 PRK15218 fimbrial chaperone pr 62.4 57 0.0012 29.7 8.7 62 76-143 19-92 (226)
33 PRK15224 pili assembly chapero 59.7 61 0.0013 29.8 8.5 62 76-143 29-97 (237)
34 PRK15290 lfpB fimbrial chapero 59.5 1.5E+02 0.0032 27.4 13.1 64 76-143 38-109 (243)
35 PF05506 DUF756: Domain of unk 57.6 40 0.00088 25.6 6.0 44 96-142 21-65 (89)
36 PF12690 BsuPI: Intracellular 54.4 60 0.0013 24.9 6.4 48 95-142 2-68 (82)
37 PRK15233 putative fimbrial cha 53.9 65 0.0014 29.9 7.7 62 76-143 41-109 (246)
38 PF13473 Cupredoxin_1: Cupredo 49.6 56 0.0012 25.3 5.8 54 77-143 30-83 (104)
39 PF02753 PapD_C: Pili assembly 47.9 21 0.00045 25.6 2.9 43 99-141 1-44 (68)
40 PF03173 CHB_HEX: Putative car 47.9 18 0.00039 31.5 2.9 51 83-143 51-103 (164)
41 PF14796 AP3B1_C: Clathrin-ada 46.6 1.9E+02 0.0041 24.8 9.7 51 92-142 84-138 (145)
42 PRK15285 putative fimbrial cha 45.7 1.4E+02 0.003 27.7 8.6 64 76-143 26-96 (250)
43 PF00553 CBM_2: Cellulose bind 44.0 63 0.0014 25.2 5.3 49 95-143 15-83 (101)
44 PRK15274 putative periplasmic 43.9 2.7E+02 0.0059 25.9 12.6 64 76-143 27-97 (257)
45 PF07705 CARDB: CARDB; InterP 43.0 76 0.0016 23.3 5.4 53 91-143 17-70 (101)
46 PRK15308 putative fimbrial pro 42.7 2.1E+02 0.0045 26.4 9.1 66 75-143 16-99 (234)
47 TIGR02745 ccoG_rdxA_fixG cytoc 39.7 2.3E+02 0.005 28.4 9.6 69 76-144 327-399 (434)
48 PF13205 Big_5: Bacterial Ig-l 39.4 1.4E+02 0.003 22.5 6.5 58 84-142 26-84 (107)
49 PF07233 DUF1425: Protein of u 39.3 1.5E+02 0.0032 23.1 6.7 51 92-142 23-80 (94)
50 smart00637 CBD_II CBD_II domai 37.8 1.4E+02 0.0029 22.6 6.2 24 119-142 50-75 (92)
51 PF05753 TRAP_beta: Translocon 35.0 2.1E+02 0.0046 25.1 7.7 52 91-143 36-96 (181)
52 PRK06655 flgD flagellar basal 33.0 1.7E+02 0.0036 26.7 6.9 82 61-142 91-178 (225)
53 PF07231 Hs1pro-1_N: Hs1pro-1 33.0 19 0.0004 32.0 0.7 18 244-261 109-126 (182)
54 PF11538 Snurportin1: Snurport 32.9 24 0.00051 24.1 1.0 17 242-258 13-29 (40)
55 PF08277 PAN_3: PAN-like domai 32.7 59 0.0013 23.2 3.2 30 81-113 42-71 (71)
56 PRK15253 putative fimbrial ass 31.2 4.2E+02 0.0091 24.3 11.5 62 76-143 34-107 (242)
57 PRK03879 ribonuclease P protei 29.0 29 0.00063 27.7 1.1 15 232-246 24-39 (96)
58 smart00538 POP4 A domain found 28.8 29 0.00063 27.4 1.1 15 232-246 22-37 (92)
59 smart00605 CW CW domain. 27.2 1.3E+02 0.0029 22.9 4.6 33 83-119 47-80 (94)
60 cd04094 selB_III This family r 27.1 2.8E+02 0.0061 21.2 6.4 32 127-167 54-85 (97)
61 COG3565 Predicted dioxygenase 26.8 71 0.0015 27.1 3.0 43 66-112 85-127 (138)
62 PF10453 NUFIP1: Nuclear fragi 26.4 16 0.00034 26.6 -0.7 17 242-258 22-40 (56)
63 PF08402 TOBE_2: TOBE domain; 24.7 2.4E+02 0.0051 19.4 7.2 65 77-142 1-69 (75)
64 COG3354 FlaG Putative archaeal 24.5 2.3E+02 0.005 24.7 5.8 67 73-142 50-128 (154)
65 PF06483 ChiC: Chitinase C; I 23.7 87 0.0019 28.0 3.2 26 107-143 116-141 (180)
66 PF01868 UPF0086: Domain of un 21.5 45 0.00097 26.0 0.9 15 232-246 23-38 (89)
67 PRK15249 fimbrial chaperone pr 20.4 2E+02 0.0043 26.5 5.0 42 98-140 177-219 (253)
68 PRK15295 fimbrial assembly cha 20.1 2.4E+02 0.0052 25.5 5.4 49 83-140 148-197 (226)
No 1
>KOG0439 consensus VAMP-associated protein involved in inositol metabolism [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.96 E-value=6.2e-29 Score=218.58 Aligned_cols=186 Identities=37% Similarity=0.482 Sum_probs=157.2
Q ss_pred CCCCcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEeeccCCCCcC
Q 024677 72 PPRRRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFKFVEAPENNE 151 (264)
Q Consensus 72 p~~~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtlq~e~P~~~E 151 (264)
..+.+|.++|..+|+|.+++.+++.+.|+|+|+++.+||||||||+|++|+|||+.|+|.||+++.|.|.++ |. ..
T Consensus 4 ~~~~~l~i~P~~~l~F~~~~~~~~~~~l~l~N~t~~~vaFKvktT~p~~y~VrP~~G~i~p~~t~~i~v~~q---~~-~~ 79 (218)
T KOG0439|consen 4 ETESLLEIEPSDELVFPLPLNEQVKCSLTLKNPTKLRVAFKVKTTAPKLYCVRPNGGVIDPGSTVEIEVTHQ---PF-EK 79 (218)
T ss_pred cccCccccCCCceEEeccCCCceEEEEEEEecCCCCceEEEEEcCCCCeEEEcCCcceECCCCcEEEEEEec---cC-cc
Confidence 466889999988999999999999999999999999999999999999999999999999999999999886 42 22
Q ss_pred CCCCCCCCCCeEEEEEEEeCCC-CCChhhhhhccC--CCcceEEEEEEEEecCCCCCchHHHH---HHhHHHHHHHHHhc
Q 024677 152 RQPLDQKSKDKFKIMSLKVKGG-IDYVPELFDEQK--DQVTVERILRVVFLNAERPSPALEKL---KLQLAEAEAALEAR 225 (264)
Q Consensus 152 ~pp~~~~~kDKFLVqS~~v~~~-~d~~~elfk~~~--~~~v~e~KLrV~fv~p~~pSp~~e~l---~~~~~ea~~~~ear 225 (264)
. |.+++|+|||+||++.++.+ ...+.++|+..+ +....+.+++|.|+.|..+....... ..+..+.++...+.
T Consensus 80 ~-P~d~~~r~kF~v~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 158 (218)
T KOG0439|consen 80 S-PPDFKSRHKFLIQSLKAPPPTTRDVVDLWKFQKETPKESFETKLRVVFVAPTETDSVVAKLQKAKKKEAEKEAFGEAT 158 (218)
T ss_pred C-chhhcccceEEEEEEecCCccccchhhhccccccccccccceeeEEEeeCCCCCcccccccccccccCCccccccccc
Confidence 2 77888999999999999986 677899999988 78899999999999987765555555 55556666777777
Q ss_pred CCCCCCC---CCceeccceeeehh-------------------hchHHHHHHhhhcccc
Q 024677 226 KRPPPDT---GPRVVGEGLVIDEW-------------------ERREKYLARQQVEAVD 262 (264)
Q Consensus 226 ~~~~~~~---~~~~~~~~~~~~~~-------------------~~~~~~~~~~~~~~~~ 262 (264)
....... .+...++.++++|| ++++++++.+|.+...
T Consensus 159 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (218)
T KOG0439|consen 159 KEASDGEVCVKSKEFGEKLELKEELKAFKLKANKVDEERLLKKKKEGRLLAELQAELVI 217 (218)
T ss_pred cccCcccccchhhhhhccccchhhhhccccccccccccchhhhhhhHHHHHhhhhhhcc
Confidence 6666654 46677888899888 5688888888877654
No 2
>COG5066 SCS2 VAMP-associated protein involved in inositol metabolism [Intracellular trafficking and secretion]
Probab=99.93 E-value=1.9e-25 Score=198.09 Aligned_cols=119 Identities=24% Similarity=0.355 Sum_probs=106.5
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEeeccCCCCcCCCCC
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFKFVEAPENNERQPL 155 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtlq~e~P~~~E~pp~ 155 (264)
.|.++| .+.|..++..+.++.+.|.|++..+|+||||||+|+.||||||.|+|.|++++.|.|+|+ ++..| |-+
T Consensus 2 aveisp--~~~fy~Plt~~ske~~sv~NnspepvgfKVKTTaPK~YcVRPN~g~Iep~stv~VeVilq---~l~eE-pap 75 (242)
T COG5066 2 AVEISP--QTTFYVPLTNKSKEMFSVQNNSPEPVGFKVKTTAPKDYCVRPNMGLIEPMSTVEVEVILQ---GLTEE-PAP 75 (242)
T ss_pred ceEecC--ceEEecccccccceeeEeecCCCCceeEEeeccCCcceeEcCCCceeccCCeeEEEEEee---ccccC-CCC
Confidence 367887 678888899999999999999999999999999999999999999999999999999997 54444 577
Q ss_pred CCCCCCeEEEEEEEeCCCC--CChhhhhhccCCCcceEEEEEEEEec
Q 024677 156 DQKSKDKFKIMSLKVKGGI--DYVPELFDEQKDQVTVERILRVVFLN 200 (264)
Q Consensus 156 ~~~~kDKFLVqS~~v~~~~--d~~~elfk~~~~~~v~e~KLrV~fv~ 200 (264)
+.+|+||||||++..+... .+++++|++..+.-++++||+|+|..
T Consensus 76 dfKCrdKFLiqs~~~~~~l~g~d~ad~wt~~sk~~i~~rkIrcvyse 122 (242)
T COG5066 76 DFKCRDKFLIQSYRFDWRLSGSDFADHWTSSSKKPIWTRKIRCVYSE 122 (242)
T ss_pred CccccceeEEEEeccChhhccchHHHHHHhhccccchhhheeEEeec
Confidence 9999999999999998753 45799999998888999999999984
No 3
>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=99.89 E-value=2.3e-22 Score=157.57 Aligned_cols=102 Identities=31% Similarity=0.508 Sum_probs=81.5
Q ss_pred EEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEeeccCCCCcCCCCCC
Q 024677 77 LRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFKFVEAPENNERQPLD 156 (264)
Q Consensus 77 L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtlq~e~P~~~E~pp~~ 156 (264)
|.|+|.+.|.|+++.++..++.|+|+|+++.+||||||||+|.+|+|+|+.|+|.||+++.|.|+++ |.... + .
T Consensus 2 l~v~P~~~i~F~~~~~~~~~~~l~l~N~s~~~i~fKiktt~~~~y~v~P~~G~i~p~~~~~i~I~~~---~~~~~--~-~ 75 (109)
T PF00635_consen 2 LSVEPSELIFFNAPFNKQQSCELTLTNPSDKPIAFKIKTTNPNRYRVKPSYGIIEPGESVEITITFQ---PFDFE--P-S 75 (109)
T ss_dssp CEEESSSEEEEESSTSS-EEEEEEEEE-SSSEEEEEEEES-TTTEEEESSEEEE-TTEEEEEEEEE----SSSTT--T-T
T ss_pred eEEeCCcceEEcCCCCceEEEEEEEECCCCCcEEEEEEcCCCceEEecCCCEEECCCCEEEEEEEEE---ecccC--C-C
Confidence 7899999999999999999999999999999999999999999999999999999999999999996 43322 1 1
Q ss_pred CCCCCeEEEEEEEeCCCCC----Chhhhhhcc
Q 024677 157 QKSKDKFKIMSLKVKGGID----YVPELFDEQ 184 (264)
Q Consensus 157 ~~~kDKFLVqS~~v~~~~d----~~~elfk~~ 184 (264)
...+|||+|+++.++++.. .+..+|++.
T Consensus 76 ~~~~dkf~I~~~~~~~~~~~~~~~~~~~~~~~ 107 (109)
T PF00635_consen 76 NKKKDKFLIQSIVVPDNATDPKKDFKQIWKNG 107 (109)
T ss_dssp STSSEEEEEEEEEE-TT-SSSHHHHHCCHHHS
T ss_pred CCCCCEEEEEEEEcCCCccchhhhHHHHHhcc
Confidence 2239999999999987753 356677654
No 4
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=98.33 E-value=5.4e-06 Score=64.45 Aligned_cols=68 Identities=29% Similarity=0.408 Sum_probs=59.4
Q ss_pred CcEEeeCCCceEeeC-CCCCeeEEEEEEEcCCCCeEEEEEeeCC--CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 75 RRLRLDPSNNLYFPY-EPGKQTRSAVRLKNTSKSHVAFKFQTTA--PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 75 ~~L~IdP~~eL~F~~-e~~k~vss~LtLtN~S~~~VAFKVKTTa--Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
..|.++|. +|.|-. ..|...+..|+|+|.+..+..|+|+.-. ...|.|.|..|+|+||++..+.|.+.
T Consensus 2 P~l~v~P~-~ldFG~v~~g~~~~~~v~l~N~s~~p~~f~v~~~~~~~~~~~v~~~~g~l~PG~~~~~~V~~~ 72 (102)
T PF14874_consen 2 PTLEVSPK-ELDFGNVFVGQTYSRTVTLTNTSSIPARFRVRQPESLSSFFSVEPPSGFLAPGESVELEVTFS 72 (102)
T ss_pred CEEEEeCC-EEEeeEEccCCEEEEEEEEEECCCCCEEEEEEeCCcCCCCEEEECCCCEECCCCEEEEEEEEE
Confidence 35899995 999976 4577888999999999999999998543 56799999999999999999999996
No 5
>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=96.30 E-value=0.11 Score=41.59 Aligned_cols=62 Identities=19% Similarity=0.367 Sum_probs=50.9
Q ss_pred EEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCC---C------cceEeeCCeeeeCCCCeEEEEEEe
Q 024677 77 LRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTA---P------KSCYMRPPGGVLAPGDSIIATVFK 142 (264)
Q Consensus 77 L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTa---P------k~Y~VRPn~GiL~Pgesi~V~Vtl 142 (264)
|.|+|. .+.|+.. +...+++|+|.++.++.+.+.... . .-|.|-|+.-.|+||++..|.|..
T Consensus 2 i~i~~t-rii~~~~---~~~~~i~v~N~~~~~~~vq~~v~~~~~~~~~~~~~~~~vsPp~~~L~pg~~q~vRv~~ 72 (122)
T PF00345_consen 2 IQISPT-RIIFNES---QRSASITVTNNSDQPYLVQVWVYDQDDEDEDEPTDPFIVSPPIFRLEPGESQTVRVYR 72 (122)
T ss_dssp EEESSS-EEEEETT---SSEEEEEEEESSSSEEEEEEEEEETTSTTSSSSSSSEEEESSEEEEETTEEEEEEEEE
T ss_pred EEEccE-EEEEeCC---CCEEEEEEEcCCCCcEEEEEEEEcCCCcccccccccEEEeCCceEeCCCCcEEEEEEe
Confidence 678885 7777752 236899999999999999987654 1 268999999999999999999954
No 6
>PF14646 MYCBPAP: MYCBP-associated protein family
Probab=94.35 E-value=1 Score=44.15 Aligned_cols=119 Identities=18% Similarity=0.277 Sum_probs=81.1
Q ss_pred EEeeCCCceEeeCCCCCeeEEEEE-EEcCCCCeEEEEEeeCC------------CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 77 LRLDPSNNLYFPYEPGKQTRSAVR-LKNTSKSHVAFKFQTTA------------PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 77 L~IdP~~eL~F~~e~~k~vss~Lt-LtN~S~~~VAFKVKTTa------------Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
..+.+.-.|.|.-.++......|. |.|.+..-|-|..+--. ...|+.....|+|.||++..|.|+.+
T Consensus 231 ~~~~~~~~l~Fe~~p~e~~~~~v~~l~N~Gt~~I~y~W~~~~~~~~~~~~~~~~~~~F~Fd~~~gvilPGe~~~~~~~F~ 310 (426)
T PF14646_consen 231 PEVSISIRLTFECHPGERVSKEVVRLENNGTTAIYYSWRRVPFFKNFGSLFRAQDQRFYFDTSSGVILPGETRNFPFMFK 310 (426)
T ss_pred CccCcceEEEEEcccCceeeEEEEEEecCCceEEEEEEEecccccccchhccccCCeEEEeCCCCEECCCceEEEEEEEe
Confidence 445555689999998887777777 99999999999866332 46789999999999999999999986
Q ss_pred ccCCCCcCCCCCCCCCCCeEEEEEEEeCCCCCChhhhhhccCCCcceEEEEEEEEecCCCCCchHHHHHHhHHH
Q 024677 144 VEAPENNERQPLDQKSKDKFKIMSLKVKGGIDYVPELFDEQKDQVTVERILRVVFLNAERPSPALEKLKLQLAE 217 (264)
Q Consensus 144 ~e~P~~~E~pp~~~~~kDKFLVqS~~v~~~~d~~~elfk~~~~~~v~e~KLrV~fv~p~~pSp~~e~l~~~~~e 217 (264)
...+ ...++...+..-+ .+|. ......+|+.+.+++..-.--++.+++.|+.
T Consensus 311 s~~~---------Gif~E~W~L~t~P---------~l~~----~~~l~v~L~G~~~~~~~~~~~~~~~~~~l~~ 362 (426)
T PF14646_consen 311 SRKV---------GIFKERWELRTFP---------PLFG----GASLTVRLHGVCTPPDEYLDKRKMLEEELAR 362 (426)
T ss_pred CCCc---------eEEEEEEEEEEec---------cccC----CCceEEEEEEEEcCchHhHHHHHHHHHHHHH
Confidence 2111 2345555555432 2333 2235677877777764444445555555533
No 7
>PRK09918 putative fimbrial chaperone protein; Provisional
Probab=92.71 E-value=3.9 Score=37.01 Aligned_cols=64 Identities=16% Similarity=0.175 Sum_probs=49.0
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCC-----cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAP-----KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaP-----k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++|. .+.|... +...+|+|+|.++.++......... .-|.|.|+.-.|+||++..|.|.+.
T Consensus 25 ~v~l~~t-Rvi~~~~---~~~~si~v~N~~~~p~lvQ~wv~~~~~~~~~~fivtPPl~rl~pg~~q~vRii~~ 93 (230)
T PRK09918 25 GMVPETS-VVIVEES---DGEGSINVKNTDSNPILLYTTLVDLPEDKSKLLLVTPPVARVEPGQSQQVRFILK 93 (230)
T ss_pred eEEEccE-EEEEECC---CCeEEEEEEcCCCCcEEEEEEEecCCCCCCCCEEEcCCeEEECCCCceEEEEEEC
Confidence 4788884 7777753 3357999999999876655543211 2599999999999999999999875
No 8
>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=91.84 E-value=0.69 Score=31.57 Aligned_cols=42 Identities=24% Similarity=0.171 Sum_probs=35.4
Q ss_pred EEEEcCCCCeE-EEEEeeCCCcceEeeCCeeeeCCCCeEEEEEE
Q 024677 99 VRLKNTSKSHV-AFKFQTTAPKSCYMRPPGGVLAPGDSIIATVF 141 (264)
Q Consensus 99 LtLtN~S~~~V-AFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vt 141 (264)
++|+|+++.++ ..+|+| +=+...+......|+||++..|.|+
T Consensus 2 F~~~N~g~~~L~I~~v~t-sCgCt~~~~~~~~i~PGes~~i~v~ 44 (45)
T PF07610_consen 2 FEFTNTGDSPLVITDVQT-SCGCTTAEYSKKPIAPGESGKIKVT 44 (45)
T ss_pred EEEEECCCCcEEEEEeeE-ccCCEEeeCCcceECCCCEEEEEEE
Confidence 68999999866 667776 4678888888899999999999886
No 9
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=89.83 E-value=1.3 Score=35.31 Aligned_cols=67 Identities=13% Similarity=0.303 Sum_probs=39.5
Q ss_pred EEeeCCCceEee-CCCCC-eeEEEEEEEcCCCCeEEEEEeeCCCcceEe-eCCeee-eCCCCeEEEEEEee
Q 024677 77 LRLDPSNNLYFP-YEPGK-QTRSAVRLKNTSKSHVAFKFQTTAPKSCYM-RPPGGV-LAPGDSIIATVFKF 143 (264)
Q Consensus 77 L~IdP~~eL~F~-~e~~k-~vss~LtLtN~S~~~VAFKVKTTaPk~Y~V-RPn~Gi-L~Pgesi~V~Vtlq 143 (264)
|.+-+.....|. ...|. +-..+|+|.|.+.++.-|.|+...+..+.+ .|...+ |.||++..+.|++.
T Consensus 13 ~~V~rdr~~ly~~~~dg~I~N~Y~lkl~Nkt~~~~~~~i~~~g~~~~~l~~~~~~i~v~~g~~~~~~v~v~ 83 (118)
T PF11614_consen 13 LNVLRDRGPLYRELSDGSIRNQYTLKLTNKTNQPRTYTISVEGLPGAELQGPENTITVPPGETREVPVFVT 83 (118)
T ss_dssp EEEEE-SS---------SEEEEEEEEEEE-SSS-EEEEEEEES-SS-EE-ES--EEEE-TT-EEEEEEEEE
T ss_pred EEEEecCCCcEEEcCCCeEEEEEEEEEEECCCCCEEEEEEEecCCCeEEECCCcceEECCCCEEEEEEEEE
Confidence 444444333343 33343 446899999999999999999988888888 675554 99999999998886
No 10
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=86.18 E-value=21 Score=32.93 Aligned_cols=64 Identities=17% Similarity=0.200 Sum_probs=47.6
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCC------C-----cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTA------P-----KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTa------P-----k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.|+|. .+.|+.. ....+|+|.|.++.++....-+.+ | .-|.|.|+.--|+||+...|.|...
T Consensus 29 ~l~l~~T-Rviy~~~---~~~~sl~l~N~~~~p~LvQsWv~~~~~~~~p~~~~~~pFivtPPlfrl~p~~~q~lRI~~~ 103 (253)
T PRK15249 29 SVTILGS-RIIYPST---ASSVDVQLKNNDAIPYIVQTWFDDGDMNTSPENSSAMPFIATPPVFRIQPKAGQVVRVIYN 103 (253)
T ss_pred EEEeCce-EEEEeCC---CcceeEEEEcCCCCcEEEEEEEeCCCCCCCccccccCcEEEcCCeEEecCCCceEEEEEEc
Confidence 4888884 7777643 234799999999886554442211 1 1399999999999999999999874
No 11
>PRK11385 putativi pili assembly chaperone; Provisional
Probab=85.44 E-value=29 Score=31.74 Aligned_cols=64 Identities=19% Similarity=0.300 Sum_probs=46.8
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeC------------CCcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTT------------APKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTT------------aPk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.+++. .+.|+. .....+|+|.|.++.+..-..... ...-|.|.|+.--|+||+...+.|+..
T Consensus 27 ~v~l~~T-RvIy~~---~~~~~sv~l~N~~~~p~LvQswv~~~~~~~~~~~~~~~~pFivtPPlfrl~p~~~q~lRIi~~ 102 (236)
T PRK11385 27 GVVVGGT-RFIFPA---DRESISILLTNTSQESWLINSKINRPTRWAGGEASTVPAPLLAAPPLILLKPGTTGTLRLLRT 102 (236)
T ss_pred eEEeCce-EEEEcC---CCceEEEEEEeCCCCcEEEEEEcccCccccCcccccccCCEEEcCCeEEECCCCceEEEEEEC
Confidence 5778884 777764 233579999999998643333211 112499999999999999999999885
No 12
>PRK09926 putative chaperone protein EcpD; Provisional
Probab=84.49 E-value=7.8 Score=35.47 Aligned_cols=65 Identities=12% Similarity=0.193 Sum_probs=49.7
Q ss_pred CcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCc----------ceEeeCCeeeeCCCCeEEEEEEee
Q 024677 75 RRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPK----------SCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 75 ~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk----------~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
--|.++|. .+.|+.. ....+|+|.|.++.++....-....+ -|.|-|+.--|+||+...|.|...
T Consensus 25 A~i~l~~T-RvI~~~~---~~~~sv~l~N~~~~p~LvQ~Wvd~~~~~~~p~~~~~pfivtPPl~rl~p~~~q~lRIi~~ 99 (246)
T PRK09926 25 ADIVISGT-RIIYKSD---QKDVNVRLENKGNNPLLVQSWLDTGDDNAEPGSIKVPFTATPPVSRIDPKRGQTIKLMYT 99 (246)
T ss_pred eeEEeCce-EEEEeCC---CceEEEEEEeCCCCcEEEEEEecCCCCccCccccCCCEEEcCCeEEECCCCccEEEEEeC
Confidence 35889984 7887752 33579999999998766555433211 299999999999999999999875
No 13
>PRK15299 fimbrial chaperone protein StiB; Provisional
Probab=84.15 E-value=21 Score=32.28 Aligned_cols=64 Identities=9% Similarity=0.198 Sum_probs=47.1
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCC--------CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTA--------PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTa--------Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++|. .+.|+.. .-..+|+|.|.++.++.-..-+.. ..-|.|.|+.--|+||+...|.|...
T Consensus 23 ~i~l~~T-Rvi~~~~---~~~~sl~l~N~~~~p~lvQsWv~~~~~~~~~~~~pfivtPPl~rl~p~~~q~lRI~~~ 94 (227)
T PRK15299 23 GINIGTT-RVIFHGD---AKDASISISNSDNVPYLIQSWAQSISETGASGDAPFMVTPPLFRLNGGQKNVLRIIRT 94 (227)
T ss_pred eEEECce-EEEEeCC---CcEEEEEEEeCCCCcEEEEEEeecCCCCCCcCCCCEEEcCCeEEECCCCccEEEEEEC
Confidence 5788884 7777643 235799999998876544432211 12399999999999999999999875
No 14
>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=82.35 E-value=4.1 Score=32.28 Aligned_cols=52 Identities=17% Similarity=0.225 Sum_probs=33.1
Q ss_pred CCeeEEEEEEEcCCCCeEEEEEeeC-----C---CcceEe-e------------CCeeeeCCCCeEEEEEEee
Q 024677 92 GKQTRSAVRLKNTSKSHVAFKFQTT-----A---PKSCYM-R------------PPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 92 ~k~vss~LtLtN~S~~~VAFKVKTT-----a---Pk~Y~V-R------------Pn~GiL~Pgesi~V~Vtlq 143 (264)
+...+.+|+|+|.+++.+-|+|.-. . .+.|.. . |..=.|+||++..|.|++.
T Consensus 7 ~~~~~~~itl~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV~ag~s~~v~vti~ 79 (112)
T PF06280_consen 7 GNKFSFTITLHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTVPAGQSKTVTVTIT 79 (112)
T ss_dssp -SEEEEEEEEEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE-TTEEEEEEEEEE
T ss_pred CCceEEEEEEEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEECCCCEEEEEEEEE
Confidence 3446789999999999999987644 1 122221 1 2223589999999999986
No 15
>PRK15211 fimbrial chaperone protein PefD; Provisional
Probab=81.92 E-value=25 Score=32.07 Aligned_cols=64 Identities=11% Similarity=0.116 Sum_probs=46.7
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeC--C----CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTT--A----PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTT--a----Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.+++. .+.|+.. ....+|+|+|.++.++.-..... . ..-|.|.|+.--|+||+...|.|...
T Consensus 23 ~v~l~~T-RvIy~~~---~~~~si~i~N~~~~p~LvQswv~~~~~~~~~~pFivtPPlfrl~p~~~q~lRI~~~ 92 (229)
T PRK15211 23 AFVLNGT-RFIYDEG---RKNISFEVTNQADQTYGGQVWIDNTTQGSSTVYMVPAPPFFKVRPKEKQIIRIMKT 92 (229)
T ss_pred EEEECce-EEEEcCC---CceEEEEEEeCCCCcEEEEEEEecCCCCCccCCEEEcCCeEEECCCCceEEEEEEC
Confidence 4778874 7777642 23589999999988644333221 1 12499999999999999999999885
No 16
>PRK15295 fimbrial assembly chaperone SthB; Provisional
Probab=81.79 E-value=12 Score=33.83 Aligned_cols=62 Identities=16% Similarity=0.229 Sum_probs=46.4
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEee--C--C-----CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQT--T--A-----PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKT--T--a-----Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.+++. .+.|+.. ....+|+|.|.++.++. |++ . . ..-|.|.|+.--|+||+...|.|...
T Consensus 20 ~i~l~~T-RvI~~~~---~~~~si~i~N~~~~p~L--vQsWv~~~~~~~~~~~pFivtPPl~rl~p~~~q~lRI~~~ 90 (226)
T PRK15295 20 SIVVGGT-RLVFDGN---NDESSINVENKDSKANL--VQSWLSVVDPQVTNKQAFIITPPLFRLDAGQKNSIRVIRS 90 (226)
T ss_pred cEEeCce-EEEEeCC---CceeEEEEEeCCCCcEE--EEEEEeCCCCCCCCCCCEEEcCCeEEECCCCceEEEEEEC
Confidence 4788884 7777653 23479999999987543 443 1 1 12499999999999999999999874
No 17
>PRK15192 fimbrial chaperone BcfG; Provisional
Probab=81.51 E-value=43 Score=30.69 Aligned_cols=62 Identities=13% Similarity=0.124 Sum_probs=46.3
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeC----------C----CcceEeeCCeeeeCCCCeEEEEEE
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTT----------A----PKSCYMRPPGGVLAPGDSIIATVF 141 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTT----------a----Pk~Y~VRPn~GiL~Pgesi~V~Vt 141 (264)
-|.++. ..+.|+.. ....+|+|.|.++.+ |=|++. . ..-|.|.|+.--|+||+...+.|.
T Consensus 23 gi~l~~-TRvIy~~~---~k~~sv~l~N~~~~p--~LvQswv~~~~~w~~~~~~~~~~PFivtPPlfrl~p~~~~~lRI~ 96 (234)
T PRK15192 23 GVVIGG-TRFIYHAG---APALSVPVSNHSEAS--WLIDTHILPGGRWPGTKNEGNITPFVVTPPLFMLSARQENSMRVV 96 (234)
T ss_pred eEEeCc-eEEEEcCC---CceEEEEEEeCCCCc--EEEEEEeccCccccccCCccccCCEEEcCCeEEECCCCceEEEEE
Confidence 467777 46777652 234799999999885 555551 1 113999999999999999999998
Q ss_pred ee
Q 024677 142 KF 143 (264)
Q Consensus 142 lq 143 (264)
..
T Consensus 97 ~~ 98 (234)
T PRK15192 97 YT 98 (234)
T ss_pred EC
Confidence 75
No 18
>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=78.17 E-value=5.5 Score=39.22 Aligned_cols=53 Identities=23% Similarity=0.374 Sum_probs=39.9
Q ss_pred CCCeeEEEEEEEcCCCCeEEEEEeeCCCcce-------EeeCCe-------ee-------eCCCCeEEEEEEee
Q 024677 91 PGKQTRSAVRLKNTSKSHVAFKFQTTAPKSC-------YMRPPG-------GV-------LAPGDSIIATVFKF 143 (264)
Q Consensus 91 ~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y-------~VRPn~-------Gi-------L~Pgesi~V~Vtlq 143 (264)
+|+..+-+|+|+|.++++|-.+==+|+.-+| ...|+. |+ |.|||+.+|.|..+
T Consensus 280 PGR~l~~~~~VTN~g~~~vrlgEF~TA~vRFlN~~~v~~~~~~yP~~lla~GL~v~d~~pI~PGETr~v~v~aq 353 (399)
T TIGR03079 280 PGRALRVTMEITNNGDQVISIGEFTTAGIRFMNANGVRVLDPDYPRELLAEGLEVDDQSAIAPGETVEVKMEAK 353 (399)
T ss_pred CCcEEEEEEEEEcCCCCceEEEeEeecceEeeCcccccccCCCChHHHhhccceeCCCCCcCCCcceEEEEEEe
Confidence 5888999999999999999887555554443 333333 22 89999999999886
No 19
>PRK15208 long polar fimbrial chaperone LpfB; Provisional
Probab=76.87 E-value=23 Score=32.09 Aligned_cols=64 Identities=13% Similarity=0.245 Sum_probs=45.9
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCC--eEEEEEeeC-CC---cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKS--HVAFKFQTT-AP---KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~--~VAFKVKTT-aP---k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++|. .+.|+.. ....+|+|+|.+++ .+.+..-.. .. .-|.|-|+.--|+||+...|.|...
T Consensus 22 gv~l~~T-RvI~~~~---~~~~si~i~N~~~~~~~LvQsWv~~~~~~~~~pfivtPPl~rl~p~~~q~lRIi~~ 91 (228)
T PRK15208 22 GVALSST-RVIYDGS---KKEASLTVNNKSKTEEFLIQSWIDDANGNKKTPFIITPPLFKLDPTKNNVLRIVNI 91 (228)
T ss_pred cEEeCce-EEEEeCC---CceEEEEEEeCCCCCcEEEEEEEECCCCCccCCEEECCCeEEECCCCccEEEEEEC
Confidence 4888884 7777753 23579999999864 333332222 11 1299999999999999999999874
No 20
>smart00809 Alpha_adaptinC2 Adaptin C-terminal domain. Adaptins are components of the adaptor complexes which link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. Gamma-adaptin is a subunit of the golgi adaptor. Alpha adaptin is a heterotetramer that regulates clathrin-bud formation. The carboxyl-terminal appendage of the alpha subunit regulates translocation of endocytic accessory proteins to the bud site. This Ig-fold domain is found in alpha, beta and gamma adaptins and consists of a beta-sandwich containing 7 strands in 2 beta-sheets in a greek-key topology PUBMED:10430869, PUBMED:12176391. The adaptor appendage contains an additional N-terminal strand.
Probab=76.49 E-value=18 Score=27.77 Aligned_cols=51 Identities=31% Similarity=0.490 Sum_probs=39.9
Q ss_pred CeeEEEEEEEcCCCCeEE-EEEeeCCCcceEee--CCe-eeeCCCCeEEEEEEee
Q 024677 93 KQTRSAVRLKNTSKSHVA-FKFQTTAPKSCYMR--PPG-GVLAPGDSIIATVFKF 143 (264)
Q Consensus 93 k~vss~LtLtN~S~~~VA-FKVKTTaPk~Y~VR--Pn~-GiL~Pgesi~V~Vtlq 143 (264)
....-.+...|.+..++- |.++-..|+.+.++ |.. ..|.||+.+...+.+.
T Consensus 18 ~~~~i~~~~~N~s~~~it~f~~~~avpk~~~l~l~~~s~~~l~p~~~i~q~~~i~ 72 (104)
T smart00809 18 GLIRITLTFTNKSPSPITNFSFQAAVPKSLKLQLQPPSSPTLPPGGQITQVLKVE 72 (104)
T ss_pred CeEEEEEEEEeCCCCeeeeEEEEEEcccceEEEEcCCCCCccCCCCCEEEEEEEE
Confidence 467789999999998774 88888888888776 554 4899998876666664
No 21
>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=76.25 E-value=5.3 Score=29.58 Aligned_cols=53 Identities=21% Similarity=0.389 Sum_probs=32.8
Q ss_pred CCCeeEEEEEEEcCCCCeE-EEEEeeCCCcceE--eeCCe-eeeCCCCeEEEEEEee
Q 024677 91 PGKQTRSAVRLKNTSKSHV-AFKFQTTAPKSCY--MRPPG-GVLAPGDSIIATVFKF 143 (264)
Q Consensus 91 ~~k~vss~LtLtN~S~~~V-AFKVKTTaPk~Y~--VRPn~-GiL~Pgesi~V~Vtlq 143 (264)
.|...+-.++|+|.....+ ..++.-..|.-+. ..|.. +-|.||++..+++.+.
T Consensus 3 ~G~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V~ 59 (78)
T PF10633_consen 3 PGETVTVTLTVTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTVT 59 (78)
T ss_dssp TTEEEEEEEEEE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEEE
T ss_pred CCCEEEEEEEEEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEEE
Confidence 4677888999999987643 3555555688877 55554 3699999999999886
No 22
>PRK15246 fimbrial assembly chaperone StbE; Provisional
Probab=75.02 E-value=67 Score=29.32 Aligned_cols=64 Identities=17% Similarity=0.305 Sum_probs=46.6
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCC------C----cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTA------P----KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTa------P----k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.|++. .+.|+.. ....+|+|.|.++.++.-..-... | .-|.|.|+.--|+||+...|.|...
T Consensus 11 ~v~l~~T-RvI~~~~---~~~~sv~l~N~~~~p~LvQsWvd~~~~~~~p~~~~~pFivtPPlfrl~~~~~~~lRI~~~ 84 (233)
T PRK15246 11 AVNIDRT-RIIFASD---DVAQSLTLSNDNTTPMLLQVWTDAGNIDASPDNSKTPLVALPPVFKMQPGELRTLRLLLS 84 (233)
T ss_pred EEEECce-EEEEcCC---CceEEEEEEeCCCCcEEEEEEEeCCCCccCcccccCcEEECCcceEECCCCceEEEEEEC
Confidence 4778884 7777752 335799999999886433331111 1 1499999999999999999999874
No 23
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=74.05 E-value=36 Score=27.93 Aligned_cols=60 Identities=22% Similarity=0.313 Sum_probs=41.4
Q ss_pred ceEeeCCCCCeeEEEEEEEcCCCCeEEEEEe-----eCCCcc--e-----------------Eee-CCeeeeCCCCeEEE
Q 024677 84 NLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQ-----TTAPKS--C-----------------YMR-PPGGVLAPGDSIIA 138 (264)
Q Consensus 84 eL~F~~e~~k~vss~LtLtN~S~~~VAFKVK-----TTaPk~--Y-----------------~VR-Pn~GiL~Pgesi~V 138 (264)
...+...++....-.|+|+|.+++.+-|+|. |+..+. | .|. |..-.|+|+++..|
T Consensus 18 YFdL~~~P~q~~~l~v~i~N~s~~~~tv~v~~~~A~Tn~nG~I~Y~~~~~~~d~sl~~~~~~~v~~~~~Vtl~~~~sk~V 97 (121)
T PF06030_consen 18 YFDLKVKPGQKQTLEVRITNNSDKEITVKVSANTATTNDNGVIDYSQNNPKKDKSLKYPFSDLVKIPKEVTLPPNESKTV 97 (121)
T ss_pred eEEEEeCCCCEEEEEEEEEeCCCCCEEEEEEEeeeEecCCEEEEECCCCcccCcccCcchHHhccCCcEEEECCCCEEEE
Confidence 3344456678888999999999999999976 333332 2 112 33345888888888
Q ss_pred EEEee
Q 024677 139 TVFKF 143 (264)
Q Consensus 139 ~Vtlq 143 (264)
.+.+.
T Consensus 98 ~~~i~ 102 (121)
T PF06030_consen 98 TFTIK 102 (121)
T ss_pred EEEEE
Confidence 88775
No 24
>PRK15195 fimbrial chaperone protein FimC; Provisional
Probab=70.59 E-value=34 Score=31.10 Aligned_cols=65 Identities=14% Similarity=0.280 Sum_probs=45.5
Q ss_pred CcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCC--eEEEE-EeeCC---CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 75 RRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKS--HVAFK-FQTTA---PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 75 ~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~--~VAFK-VKTTa---Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
--|.+++. .+.|+... ...+|+|.|.+++ .+... |.... ..-|.|.|+.--|+||+...|.|...
T Consensus 25 Agi~i~~T-RvIy~~~~---~~~si~l~N~~~~~~~LvQsWv~~~~~~~~~pfivtPPlfrl~p~~~q~lRIi~~ 95 (229)
T PRK15195 25 GGIALGAT-RVIYPADA---KQTSLAIRNSHTNERYLVNSWIENSSGVKEKSFIVTPPLFVSEPKSENTLRIIYA 95 (229)
T ss_pred eeEEECCe-EEEEeCCC---ceEEEEEEeCCCCccEEEEEEecCCCCCccCCEEEcCCeEEECCCCceEEEEEEC
Confidence 35788884 77776432 2389999999865 33332 11111 12499999999999999999999885
No 25
>COG3121 FimC P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=69.96 E-value=87 Score=28.47 Aligned_cols=112 Identities=13% Similarity=0.174 Sum_probs=71.4
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeC-------CCcceEeeCCeeeeCCCCeEEEEEEeeccCCC
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTT-------APKSCYMRPPGGVLAPGDSIIATVFKFVEAPE 148 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTT-------aPk~Y~VRPn~GiL~Pgesi~V~Vtlq~e~P~ 148 (264)
-+.+++. .+.|+.. .....|+|.|.++.++.-.+-.- ...-|.|-|+.-.|+||+...|.|.+... +
T Consensus 28 ~v~i~~T-RiI~~~~---~k~~sl~l~N~~~~p~LvQ~wvd~~~~~~~~~~pfvvtPPv~rl~p~~~q~vRi~~~~~-~- 101 (235)
T COG3121 28 GVVLGGT-RIIYPAG---DKETSLTLRNDGNQPYLVQSWVDDGLEPEKSTVPFVVTPPVFRLEPGQEQQLRILYTGN-K- 101 (235)
T ss_pred eEEecce-EEEEeCC---CceeEEEEEcCCCCCEEEEEEEcCCCCCccccCCEEecCCeEEECCCCccEEEEEecCC-C-
Confidence 4677774 6677643 23479999998888888875543 23458999999999999999999999631 1
Q ss_pred CcCCCCCCCCCCCeEEEEEEEeCCCCC-ChhhhhhccCCCcceEEEEEEEEecCCC
Q 024677 149 NNERQPLDQKSKDKFKIMSLKVKGGID-YVPELFDEQKDQVTVERILRVVFLNAER 203 (264)
Q Consensus 149 ~~E~pp~~~~~kDKFLVqS~~v~~~~d-~~~elfk~~~~~~v~e~KLrV~fv~p~~ 203 (264)
. |.| ...-|-+.-..++.... .-.. . .-.....++|++-|-++.-
T Consensus 102 ---l-P~d--rEslf~lnv~eIPp~~~~~~~~--n--~lq~a~r~riKlf~RP~~l 147 (235)
T COG3121 102 ---L-PAD--RESLFRLNVDEIPPKSKDDKGP--N--VLQLALRSRIKLFYRPAGL 147 (235)
T ss_pred ---C-CCC--ceeEEEEEeeecCCCCcccCCc--c--eEEEEeeeeeeEEECcccC
Confidence 1 332 22455555555655321 1000 0 0133457888888877544
No 26
>PF02883 Alpha_adaptinC2: Adaptin C-terminal domain; InterPro: IPR008152 Proteins synthesized 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. These vesicles have specific coat proteins (such as clathrin or coatomer) that are important for cargo selection and direction of transport []. Clathrin coats contain both clathrin (acts as a scaffold) and adaptor complexes that link clathrin to receptors in coated vesicles. Clathrin-associated protein complexes are believed to interact with the cytoplasmic tails of membrane proteins, leading to their selection and concentration. The two major types of clathrin adaptor complexes are the heterotetrameric adaptor protein (AP) complexes, and the monomeric GGA (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) adaptors [, ]. AP (adaptor protein) complexes are found in coated vesicles and clathrin-coated pits. AP complexes connect cargo proteins and lipids to clathrin at vesicle budding sites, as well as binding accessory proteins that regulate coat assembly and disassembly (such as AP180, epsins and auxilin). There are different AP complexes in mammals. AP1 is responsible for the transport of lysosomal hydrolases between the TGN and endosomes []. AP2 associates with the plasma membrane and is responsible for endocytosis []. AP3 is responsible for protein trafficking to lysosomes and other related organelles []. AP4 is less well characterised. AP complexes are heterotetramers composed of two large subunits (adaptins), a medium subunit (mu) and a small subunit (sigma). For example, in AP1 these subunits are gamma-1-adaptin, beta-1-adaptin, mu-1 and sigma-1, while in AP2 they are alpha-adaptin, beta-2-adaptin, mu-2 and sigma-2. Each subunit has a specific function. Adaptins recognise and bind to clathrin through their hinge region (clathrin box), and recruit accessory proteins that modulate AP function through their C-terminal ear (appendage) domains. Mu recognises tyrosine-based sorting signals within the cytoplasmic domains of transmembrane cargo proteins []. One function of clathrin and AP2 complex-mediated endocytosis is to regulate the number of GABA(A) receptors available at the cell surface []. GGAs (Golgi-localising, Gamma-adaptin ear domain homology, ARF-binding proteins) are a family of monomeric clathrin adaptor proteins that are conserved from yeasts to humans. GGAs regulate clathrin-mediated the transport of proteins (such as mannose 6-phosphate receptors) from the TGN to endosomes and lysosomes through interactions with TGN-sorting receptors, sometimes in conjunction with AP-1 [, ]. GGAs bind cargo, membranes, clathrin and accessory factors. GGA1, GGA2 and GGA3 all contain a domain homologous to the ear domain of gamma-adaptin. GGAs are composed of a single polypeptide with four domains: an N-terminal VHS (Vps27p/Hrs/Stam) domain, a GAT (GGA and Tom1) domain, a hinge region, and a C-terminal GAE (gamma-adaptin ear) domain. The VHS domain is responsible for endocytosis and signal transduction, recognising transmembrane cargo through the ACLL sequence in the cytoplasmic domains of sorting receptors []. The GAT domain (also found in Tom1 proteins) interacts with ARF (ADP-ribosylation factor) to regulate membrane trafficking [], and with ubiquitin for receptor sorting []. The hinge region contains a clathrin box for recognition and binding to clathrin, similar to that found in AP adaptins. The GAE domain is similar to the AP gamma-adaptin ear domain, and is responsible for the recruitment of accessory proteins that regulate clathrin-mediated endocytosis []. This entry represents a beta-sandwich structural motif found in the appendage (ear) domain of alpha-, beta- and gamma-adaptin from AP clathrin adaptor complexes, and the GAE (gamma-adaptin ear) domain of GGA adaptor proteins. These domains have an immunoglobulin-like beta-sandwich fold containing 7 or 8 strands in 2 beta-sheets in a Greek key topology [, ]. Although these domains share a similar fold, there is little sequence identity between the alpha/beta-adaptins and gamma-adaptin/GAE. More information about these proteins can be found at Protein of the Month: Clathrin [].; GO: 0006886 intracellular protein transport, 0016192 vesicle-mediated transport, 0030131 clathrin adaptor complex; PDB: 3MNM_B 3ZY7_B 1GYU_A 1GYW_B 2A7B_A 1GYV_A 2E9G_A 1E42_B 2G30_A 2IV9_B ....
Probab=69.71 E-value=40 Score=26.36 Aligned_cols=53 Identities=28% Similarity=0.493 Sum_probs=36.7
Q ss_pred CCCeeEEEEEEEcCCCCeEE-EEEeeCCCcceEe--eCC-eeeeCCCCeEEEEEEee
Q 024677 91 PGKQTRSAVRLKNTSKSHVA-FKFQTTAPKSCYM--RPP-GGVLAPGDSIIATVFKF 143 (264)
Q Consensus 91 ~~k~vss~LtLtN~S~~~VA-FKVKTTaPk~Y~V--RPn-~GiL~Pgesi~V~Vtlq 143 (264)
.+...+-.+++.|.+..++- |.++-..|+.|.+ .|. ...|.|+..+.-.+.+.
T Consensus 22 ~~~~~~i~~~f~N~s~~~it~f~~q~avpk~~~l~l~~~s~~~i~p~~~i~Q~~~v~ 78 (115)
T PF02883_consen 22 NPNQGRIKLTFGNKSSQPITNFSFQAAVPKSFKLQLQPPSSSTIPPGQQITQVIKVE 78 (115)
T ss_dssp ETTEEEEEEEEEE-SSS-BEEEEEEEEEBTTSEEEEEESS-SSB-TTTEEEEEEEEE
T ss_pred CCCEEEEEEEEEECCCCCcceEEEEEEeccccEEEEeCCCCCeeCCCCeEEEEEEEE
Confidence 35678889999999998775 7777766776655 465 56999999887766664
No 27
>PF00927 Transglut_C: Transglutaminase family, C-terminal ig like domain; InterPro: IPR008958 Synonym(s): Protein-glutamine gamma-glutamyltransferase, Fibrinoligase, TGase Transglutaminases catalyse the post-translational modification of proteins at glutamine residues, with formation of isopeptide bonds. Members of the transglutaminase family usually have three domains: N-terminal (IPR001102 from INTERPRO), middle (IPR013808 from INTERPRO) and C-terminal. The middle domain is usually well conserved, but family members can display major differences in their N- and C-terminal domains, although their overall structure is conserved []. This entry represents the C-terminal domain found in transglutaminases, which consists of an immunoglobulin-like beta-sandwich consisting of seven strands in two sheets with a Greek key topology. The best known transglutaminase is blood coagulation factor XIII, a plasma tetrameric protein composed of two catalytic A subunits and two non-catalytic B subunits. Factor XIII is responsible for cross-linking fibrin chains, thus stabilising the fibrin clot. Protein-glutamine gamma-glutamyltransferases (2.3.2.13 from EC) are calcium-dependent enzymes that catalyse the cross-linking of proteins by promoting the formation of isopeptide bonds between the gamma-carboxyl group of a glutamine in one polypeptide chain and the epsilon-amino group of a lysine in a second polypeptide chain. TGases also catalyse the conjugation of polyamines to proteins [, ].; GO: 0003810 protein-glutamine gamma-glutamyltransferase activity, 0018149 peptide cross-linking; PDB: 2XZZ_A 1GGY_B 1FIE_B 1GGU_B 1GGT_B 1F13_A 1QRK_B 1EVU_A 1EX0_B 1L9N_B ....
Probab=69.61 E-value=21 Score=27.79 Aligned_cols=53 Identities=21% Similarity=0.181 Sum_probs=39.1
Q ss_pred CCCeeEEEEEEEcCCCCe--------EEEEEeeCCCc--ceEeeCCeeeeCCCCeEEEEEEee
Q 024677 91 PGKQTRSAVRLKNTSKSH--------VAFKFQTTAPK--SCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 91 ~~k~vss~LtLtN~S~~~--------VAFKVKTTaPk--~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
.|+.....++++|+++.. .|+-|-=|.-. .+..+-..+.|.||++..+.+.+.
T Consensus 13 vG~d~~v~v~~~N~~~~~l~~v~~~l~~~~v~ytG~~~~~~~~~~~~~~l~p~~~~~~~~~i~ 75 (107)
T PF00927_consen 13 VGQDFTVSVSFTNPSSEPLRNVSLNLCAFTVEYTGLTRDQFKKEKFEVTLKPGETKSVEVTIT 75 (107)
T ss_dssp TTSEEEEEEEEEE-SSS-EECEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE-
T ss_pred CCCCEEEEEEEEeCCcCccccceeEEEEEEEEECCcccccEeEEEcceeeCCCCEEEEEEEEE
Confidence 578899999999999987 55666654333 256778889999999999999884
No 28
>PF11611 DUF4352: Domain of unknown function (DUF4352); InterPro: IPR021652 This entry is represented by Bacteriophage A118, Gp32. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a group of putative lipoproteins of unknown function.; PDB: 3CFU_A.
Probab=69.20 E-value=33 Score=26.65 Aligned_cols=54 Identities=19% Similarity=0.187 Sum_probs=33.7
Q ss_pred CCCCeeEEEEEEEcCCCCeEE-----EEEeeCCCcceEeeC---------CeeeeCCCCeEEEEEEee
Q 024677 90 EPGKQTRSAVRLKNTSKSHVA-----FKFQTTAPKSCYMRP---------PGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 90 e~~k~vss~LtLtN~S~~~VA-----FKVKTTaPk~Y~VRP---------n~GiL~Pgesi~V~Vtlq 143 (264)
+.++-+.-.++|+|.+++.+. |++.+..-+.|.... ..+-|.||+++...|...
T Consensus 33 ~g~~fv~v~v~v~N~~~~~~~~~~~~f~l~d~~g~~~~~~~~~~~~~~~~~~~~i~pG~~~~g~l~F~ 100 (123)
T PF11611_consen 33 EGNKFVVVDVTVKNNGDEPLDFSPSDFKLYDSDGNKYDPDFSASSNDNDLFSETIKPGESVTGKLVFE 100 (123)
T ss_dssp --SEEEEEEEEEEE-SSS-EEEEGGGEEEE-TT--B--EEE-CCCTTTB--EEEE-TT-EEEEEEEEE
T ss_pred CCCEEEEEEEEEEECCCCcEEecccceEEEeCCCCEEcccccchhccccccccEECCCCEEEEEEEEE
Confidence 345567789999999998775 788877777776443 458899999999988875
No 29
>PRK15188 fimbrial chaperone protein BcfB; Provisional
Probab=67.75 E-value=99 Score=28.24 Aligned_cols=65 Identities=15% Similarity=0.254 Sum_probs=45.9
Q ss_pred CcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCC-eEE-EE-EeeCCC---cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 75 RRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKS-HVA-FK-FQTTAP---KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 75 ~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~-~VA-FK-VKTTaP---k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
--|.+++. .+.|+.. ....+|+|+|.+++ +.. .. |..... .-|.|.|+.--|+||+...+.|...
T Consensus 27 Agi~l~~T-RvIy~~~---~~~~sv~i~N~~~~~p~LvQsWv~~~~~~~~~pFivtPPlfrl~~~~~~~lRI~~~ 97 (228)
T PRK15188 27 GGIALGAT-RVIYPQG---SKQTSLPIINSSASNVFLIQSWVANADGSRSTDFIITPPLFVIQPKKENILRIMYV 97 (228)
T ss_pred ceEEECcE-EEEEcCC---CceEEEEEEeCCCCccEEEEEEEecCCCCccCCEEEcCCeEEECCCCceEEEEEEC
Confidence 35888884 7777652 33579999999865 333 22 111111 2499999999999999999999874
No 30
>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=66.18 E-value=18 Score=35.65 Aligned_cols=65 Identities=18% Similarity=0.251 Sum_probs=43.4
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceE----------------------eeCCeeeeCCC
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCY----------------------MRPPGGVLAPG 133 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~----------------------VRPn~GiL~Pg 133 (264)
.+.++-. .-.|.- +++..+-+|+++|+++++|-..==+|+.-+|. |.|+ +=|+||
T Consensus 248 ~V~~~v~-~A~Y~v-pgR~l~~~l~VtN~g~~pv~LgeF~tA~vrFln~~v~~~~~~~P~~l~A~~gL~vs~~-~pI~PG 324 (381)
T PF04744_consen 248 SVKVKVT-DATYRV-PGRTLTMTLTVTNNGDSPVRLGEFNTANVRFLNPDVPTDDPDYPDELLAERGLSVSDN-SPIAPG 324 (381)
T ss_dssp SEEEEEE-EEEEES-SSSEEEEEEEEEEESSS-BEEEEEESSS-EEE-TTT-SS-S---TTTEETT-EEES---S-B-TT
T ss_pred ceEEEEe-ccEEec-CCcEEEEEEEEEcCCCCceEeeeEEeccEEEeCcccccCCCCCchhhhccCcceeCCC-CCcCCC
Confidence 4777763 566665 58889999999999999998775455555442 2222 348999
Q ss_pred CeEEEEEEee
Q 024677 134 DSIIATVFKF 143 (264)
Q Consensus 134 esi~V~Vtlq 143 (264)
|+.+++|.++
T Consensus 325 ETrtl~V~a~ 334 (381)
T PF04744_consen 325 ETRTLTVEAQ 334 (381)
T ss_dssp -EEEEEEEEE
T ss_pred ceEEEEEEee
Confidence 9999999986
No 31
>PRK15254 fimbrial chaperone protein StdC; Provisional
Probab=63.07 E-value=1.2e+02 Score=27.75 Aligned_cols=64 Identities=14% Similarity=0.179 Sum_probs=45.3
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEEEee--CCC---cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKS-HVAFKFQT--TAP---KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~-~VAFKVKT--TaP---k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-+.+++. .+.|+.. ....+|+|.|.+++ ++.-..-. ... .-|.|.|+.--|+||+...|.|+..
T Consensus 17 ~v~l~~T-RvIy~~~---~~~~sv~v~N~~~~~p~LvQsWv~d~~~~~~~pFivtPPlfrl~p~~~~~lRI~~~ 86 (239)
T PRK15254 17 AVNVDRT-RIIMDAP---QKTVAITLNNDDKTTPFLAQSWVTDADGVRTDALMALPPLQRIDAGQKSQVRITQV 86 (239)
T ss_pred eEEECce-EEEEeCC---CceEEEEEEeCCCCCcEEEEEEEecCCCCCcCCEEEcCCeEEECCCCceEEEEEEc
Confidence 4778874 7777742 33579999999864 54333221 111 2499999999999999999999874
No 32
>PRK15218 fimbrial chaperone protein PegB; Provisional
Probab=62.36 E-value=57 Score=29.70 Aligned_cols=62 Identities=18% Similarity=0.193 Sum_probs=44.5
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEee--CCC----------cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQT--TAP----------KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKT--TaP----------k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++- ..+.|+. + .-..+|+|.|.++.+ |-|++ ... .-|.|.|+.--|+||+...+.|...
T Consensus 19 gi~l~~-TRvIy~~--~-~~~~si~i~N~~~~p--yLvQsWvd~~~~~~~~~~~~~pFivtPPlfRl~p~~~~~lRI~~~ 92 (226)
T PRK15218 19 GIYIYG-TRIIYPA--Q-KKDITVQLMNDGKRS--SLIQAWIDNGDTSLPPEKLQVPFIMTPPVIRVAANSGQQLKIKKL 92 (226)
T ss_pred eEEeCc-eEEEEcC--C-CcEEEEEEEcCCCCc--EEEEEEEeCCCCCCCcccccCCEEECCCeEEECCCCceEEEEEEC
Confidence 355665 4667764 2 234799999999875 44443 111 1499999999999999999999974
No 33
>PRK15224 pili assembly chaperone protein SafB; Provisional
Probab=59.67 E-value=61 Score=29.81 Aligned_cols=62 Identities=11% Similarity=0.198 Sum_probs=45.4
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEee----CC---CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQT----TA---PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKT----Ta---Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++- ..+.|+.. .-..+|+|.|.++.+ |-|++ .. ..-|.|.|+.--|+|++...|.|...
T Consensus 29 gv~l~~-TRvIy~~~---~k~~sl~v~N~~~~p--yLvQsWvd~~~~~~~~pFivtPPlfRlep~~~~~lRI~~~ 97 (237)
T PRK15224 29 SVKLGA-TRVIYHAG---TAGATLSVSNPQNYP--ILVQSSVKAADKSSPAPFLVMPPLFRLEANQQSQLRIVRT 97 (237)
T ss_pred EEEeCc-eEEEEeCC---CcEEEEEEEcCCCCc--EEEEEEEeCCCCCccCCEEECCCeEEECCCCceEEEEEEC
Confidence 455664 46777642 234799999998875 66665 11 12399999999999999999999984
No 34
>PRK15290 lfpB fimbrial chaperone protein; Provisional
Probab=59.50 E-value=1.5e+02 Score=27.37 Aligned_cols=64 Identities=6% Similarity=0.119 Sum_probs=46.8
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCC-CeEEEEEeeC--C-C----cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSK-SHVAFKFQTT--A-P----KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~-~~VAFKVKTT--a-P----k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.+++ ..+.|+.. ....+|+|+|.++ .++.-..-.. + . .-|.|-|+.--|+||+...|.|...
T Consensus 38 gv~l~~-TRvIy~~~---~~~~sl~v~N~~~~~p~LvQsWvd~~~~~~~~~~pFivtPPlfrl~p~~~q~lRIi~~ 109 (243)
T PRK15290 38 GVVIGG-TRVVYLSN---NPDKSISVFSKEEKIPYLIQAWVDPFNKEDKSKAPFTVIPPVSRLEPSQEKVLRIIHT 109 (243)
T ss_pred eEEECc-eEEEEeCC---CceEEEEEEeCCCCCcEEEEEEEecCCCCCcccCCEEEcCCeEEECCCCceEEEEEEc
Confidence 478888 47777742 3347999999986 4555444332 1 1 1399999999999999999999875
No 35
>PF05506 DUF756: Domain of unknown function (DUF756); InterPro: IPR008475 This domain is found, normally as a tandem repeat, at the C terminus of bacterial phospholipase C proteins.; GO: 0004629 phospholipase C activity, 0016042 lipid catabolic process
Probab=57.64 E-value=40 Score=25.60 Aligned_cols=44 Identities=20% Similarity=0.127 Sum_probs=31.8
Q ss_pred EEEEEEEcCCCCeEEEEEeeCCCcceE-eeCCeeeeCCCCeEEEEEEe
Q 024677 96 RSAVRLKNTSKSHVAFKFQTTAPKSCY-MRPPGGVLAPGDSIIATVFK 142 (264)
Q Consensus 96 ss~LtLtN~S~~~VAFKVKTTaPk~Y~-VRPn~GiL~Pgesi~V~Vtl 142 (264)
.-.|+|.|.....+.|.|...+ |. -.|-.=.|.||++..+.+-+
T Consensus 21 ~l~l~l~N~g~~~~~~~v~~~~---y~~~~~~~~~v~ag~~~~~~w~l 65 (89)
T PF05506_consen 21 NLRLTLSNPGSAAVTFTVYDNA---YGGGGPWTYTVAAGQTVSLTWPL 65 (89)
T ss_pred EEEEEEEeCCCCcEEEEEEeCC---cCCCCCEEEEECCCCEEEEEEee
Confidence 4689999999999999999732 22 33444456678887777655
No 36
>PF12690 BsuPI: Intracellular proteinase inhibitor; InterPro: IPR020481 BsuPI is a intracellular proteinase inhibitor that directly regulates the major intracellular proteinase (ISP-1) activity in vivo. It inhibits ISP-1 in the early stages of sporulation and then may be inactivated by a membrane-bound proteinase [].; PDB: 3ISY_A.
Probab=54.37 E-value=60 Score=24.87 Aligned_cols=48 Identities=17% Similarity=0.234 Sum_probs=24.2
Q ss_pred eEEEEEEEcCCCCeEEEEEeeCCCcceEee-------------------CCeeeeCCCCeEEEEEEe
Q 024677 95 TRSAVRLKNTSKSHVAFKFQTTAPKSCYMR-------------------PPGGVLAPGDSIIATVFK 142 (264)
Q Consensus 95 vss~LtLtN~S~~~VAFKVKTTaPk~Y~VR-------------------Pn~GiL~Pgesi~V~Vtl 142 (264)
+.-.|+|+|.+++.|-+.+-|---=-|.|+ -..=.|.||++....+..
T Consensus 2 v~~~l~v~N~s~~~v~l~f~sgq~~D~~v~d~~g~~vwrwS~~~~FtQal~~~~l~pGe~~~~~~~~ 68 (82)
T PF12690_consen 2 VEFTLTVTNNSDEPVTLQFPSGQRYDFVVKDKEGKEVWRWSDGKMFTQALQEETLEPGESLTYEETW 68 (82)
T ss_dssp EEEEEEEEE-SSS-EEEEESSS--EEEEEE-TT--EEEETTTT-------EEEEE-TT-EEEEEEEE
T ss_pred EEEEEEEEeCCCCeEEEEeCCCCEEEEEEECCCCCEEEEecCCchhhheeeEEEECCCCEEEEEEEE
Confidence 345677777777776666544322222333 223357778877777776
No 37
>PRK15233 putative fimbrial chaperone protein SefB; Provisional
Probab=53.88 E-value=65 Score=29.89 Aligned_cols=62 Identities=15% Similarity=0.162 Sum_probs=43.8
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEee----CC---CcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQT----TA---PKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKT----Ta---Pk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++- ..+.|+.. + ...+|+|.|.++.+ |-|++ .. ..-|.|.|+.--|+||+...+.|...
T Consensus 41 gi~l~~-TRvIy~~~--~-~~~sl~i~N~~~~p--~LvQsWvd~~~~~~~~pFiVtPPLfRLep~~~~~lRIi~~ 109 (246)
T PRK15233 41 GLRLGT-TRVIYKED--A-PSTSFWIMNEKEYP--ILVQTQVYNDDKSSKAPFIVTPPILKVESNARTRLKVIPT 109 (246)
T ss_pred eEEeCc-eEEEEeCC--C-cEEEEEEEcCCCCc--EEEEEEEecCCCCccCCEEECCCeEEECCCCceEEEEEEC
Confidence 355554 35555532 2 34799999987766 55554 11 12499999999999999999999984
No 38
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=49.64 E-value=56 Score=25.27 Aligned_cols=54 Identities=19% Similarity=0.355 Sum_probs=35.1
Q ss_pred EEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 77 LRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 77 L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
..++|+ .|..+ .|+.+ +|+++|.....-.|-+.. +.+ ...|.||++..++++-.
T Consensus 30 ~~f~P~-~i~v~--~G~~v--~l~~~N~~~~~h~~~i~~-----~~~---~~~l~~g~~~~~~f~~~ 83 (104)
T PF13473_consen 30 FGFSPS-TITVK--AGQPV--TLTFTNNDSRPHEFVIPD-----LGI---SKVLPPGETATVTFTPL 83 (104)
T ss_dssp EEEES--EEEEE--TTCEE--EEEEEE-SSS-EEEEEGG-----GTE---EEEE-TT-EEEEEEEE-
T ss_pred CeEecC-EEEEc--CCCeE--EEEEEECCCCcEEEEECC-----Cce---EEEECCCCEEEEEEcCC
Confidence 588995 66655 46655 699999999888888776 111 16799999999988543
No 39
>PF02753 PapD_C: Pili assembly chaperone PapD, C-terminal domain; InterPro: IPR016148 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 C-terminal domain of pili assembly chaperone, and has a beta-sandwich fold consisting of eight strands in two sheets with a Greek key topology.; GO: 0007047 cellular cell wall organization, 0030288 outer membrane-bounded periplasmic space; PDB: 2UY7_C 2UY6_A 2W07_A 3GFU_A 3F65_F 3F6L_A 3F6I_A 3GEW_B 1PDK_A 2XG4_A ....
Probab=47.88 E-value=21 Score=25.64 Aligned_cols=43 Identities=16% Similarity=0.114 Sum_probs=27.1
Q ss_pred EEEEcCCCCeEEEE-EeeCCCcceEeeCCeeeeCCCCeEEEEEE
Q 024677 99 VRLKNTSKSHVAFK-FQTTAPKSCYMRPPGGVLAPGDSIIATVF 141 (264)
Q Consensus 99 LtLtN~S~~~VAFK-VKTTaPk~Y~VRPn~GiL~Pgesi~V~Vt 141 (264)
|+++|.|.-+|.|- ++....++=.--...+.|+|+++..+.+.
T Consensus 1 L~v~NpTPy~vtl~~~~~~~~~~~~~~~~~~mi~P~s~~~~~~~ 44 (68)
T PF02753_consen 1 LTVKNPTPYYVTLSSLKLNGGGKKKKIDNSGMIAPFSSKSFPLP 44 (68)
T ss_dssp EEEEE-SSS-EEEEEEEETHHHCCEECCCETEE-TTEEEEEETS
T ss_pred CEEECCCCcEEEEEeeeecccccccccCCceEECCCCceEEecc
Confidence 68999999999886 44443443333344459999999887544
No 40
>PF03173 CHB_HEX: Putative carbohydrate binding domain; InterPro: IPR004866 This domain represents the N-terminal domain in chitobiases and beta-hexosaminidases 3.2.1.52 from EC. Chitobiases degrade chitin, which forms the exoskeleton in insects and crustaceans, and which is one of the most abundant polysaccharides on earth []. Beta-hexosaminidases are composed of either a HexA/HexB heterodimer or a HexB homodimer, and can hydrolyse diverse substrates, including GM(2)-gangliosides; mutations in this enzyme are associated with Tay-Sachs disease []. HexB is structurally similar to chitobiase, consisting of a beta sandwich structure; this structure is similar to that found in the cellulose-binding domain of cellulase from Cellulomonas fimi (IPR001919 from INTERPRO), suggesting that it may function as a carbohydrate-binding domain.; GO: 0030246 carbohydrate binding; PDB: 1C7T_A 1QBA_A 1QBB_A 1C7S_A.
Probab=47.87 E-value=18 Score=31.51 Aligned_cols=51 Identities=24% Similarity=0.399 Sum_probs=33.9
Q ss_pred CceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceEeeCCeee--eCCCCeEEEEEEee
Q 024677 83 NNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGV--LAPGDSIIATVFKF 143 (264)
Q Consensus 83 ~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VRPn~Gi--L~Pgesi~V~Vtlq 143 (264)
-.|+|..- + -.++. .++. |+|.-=+-+.|++.|.-|+ |+||+++.|.+.-.
T Consensus 51 W~IYf~~i--r---~i~~~--~s~~---f~i~hinGDl~kl~Pt~~F~gl~~Ges~~I~~~~~ 103 (164)
T PF03173_consen 51 WAIYFSSI--R---PILQV--DSDQ---FKITHINGDLHKLTPTAGFKGLAPGESLEIPFVGE 103 (164)
T ss_dssp -EEEEE-S--S----EEEE--SSTT---EEEEE-STTEEEEEE-TT---B-TTEEEEEEEEEE
T ss_pred eEEEEecc--e---eeecc--CCCC---eEEEEEcCeEEEEeECCCCCccCCCCEEEEEEEcc
Confidence 57888742 2 23333 3333 8999889999999999998 89999999999864
No 41
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=46.62 E-value=1.9e+02 Score=24.85 Aligned_cols=51 Identities=16% Similarity=0.240 Sum_probs=35.3
Q ss_pred CCeeEEEEEEEcCCCCeEE-EEEeeCC-CcceEee--CCeeeeCCCCeEEEEEEe
Q 024677 92 GKQTRSAVRLKNTSKSHVA-FKFQTTA-PKSCYMR--PPGGVLAPGDSIIATVFK 142 (264)
Q Consensus 92 ~k~vss~LtLtN~S~~~VA-FKVKTTa-Pk~Y~VR--Pn~GiL~Pgesi~V~Vtl 142 (264)
...+.-.|+++|.++..+. -+|.... +.--+|+ |..+.|.||+++.+.+-.
T Consensus 84 ~~mvsIql~ftN~s~~~i~~I~i~~k~l~~g~~i~~F~~I~~L~pg~s~t~~lgI 138 (145)
T PF14796_consen 84 PSMVSIQLTFTNNSDEPIKNIHIGEKKLPAGMRIHEFPEIESLEPGASVTVSLGI 138 (145)
T ss_pred CCcEEEEEEEEecCCCeecceEECCCCCCCCcEeeccCcccccCCCCeEEEEEEE
Confidence 3567788999999997552 3343333 2244554 788999999998877765
No 42
>PRK15285 putative fimbrial chaperone protein StfD; Provisional
Probab=45.74 E-value=1.4e+02 Score=27.65 Aligned_cols=64 Identities=17% Similarity=0.156 Sum_probs=43.0
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEEE--eeCCCc----ceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKS-HVAFKF--QTTAPK----SCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~-~VAFKV--KTTaPk----~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-+.++- ..+.|+.. .-..+|+|+|.++. ++.-.. .....+ -|.|.|+.--|+||+...|.|...
T Consensus 26 gv~l~~-TRVIy~~~---~~~~sv~i~N~~~~~p~LvQsWvd~~~~~~~~~pFiVtPPlfRl~p~~~~~lRI~~~ 96 (250)
T PRK15285 26 AIAPDR-TRLVFRGE---DKSISVDLKNANSKLPYLAQSWVEDEKGVKITSPLIVVPPVQRIEPSAIGQVKIQGM 96 (250)
T ss_pred eEEeCc-cEEEEcCC---CceEEEEEEeCCCCCcEEEEEEeeCCCCCcccCCEEEcCCeEEECCCCceEEEEEEC
Confidence 355554 46777642 23479999999865 433222 111211 399999999999999999999874
No 43
>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=44.02 E-value=63 Score=25.22 Aligned_cols=49 Identities=22% Similarity=0.409 Sum_probs=33.0
Q ss_pred eEEEEEEEcCCCCeE-----EEEEe-------------eCCCcceEeeCCe--eeeCCCCeEEEEEEee
Q 024677 95 TRSAVRLKNTSKSHV-----AFKFQ-------------TTAPKSCYMRPPG--GVLAPGDSIIATVFKF 143 (264)
Q Consensus 95 vss~LtLtN~S~~~V-----AFKVK-------------TTaPk~Y~VRPn~--GiL~Pgesi~V~Vtlq 143 (264)
....|+|+|.++..+ .|.+. +..-..|.|+|.. +.|+||+++.+-+...
T Consensus 15 f~~~v~v~N~~~~~i~~W~v~~~~~~~~~i~~~Wna~~s~~g~~~~v~~~~wn~~i~~G~s~~~Gf~~~ 83 (101)
T PF00553_consen 15 FQGEVTVTNNGSSPINGWTVTFTFPSGQTITSSWNATVSQSGNTVTVTNPSWNGTIAPGGSVTFGFQAS 83 (101)
T ss_dssp EEEEEEEEESSSSTEESEEEEEEESTTEEEEEEESCEEEEETTEEEEEESSTCSEEEESEEEEEEEEEE
T ss_pred eEEEEEEEECCCCccCCEEEEEEeCCCCEEeeeeccEEEecCCEEEEEcCCcCcccCCCCeEEEEEEEe
Confidence 345788888877654 33322 1122578888765 7999999998877764
No 44
>PRK15274 putative periplasmic fimbrial chaperone protein SteC; Provisional
Probab=43.94 E-value=2.7e+02 Score=25.91 Aligned_cols=64 Identities=16% Similarity=0.113 Sum_probs=44.2
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEEEee--CC-C---cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKS-HVAFKFQT--TA-P---KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~-~VAFKVKT--Ta-P---k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++- ..+.|+.. ....+|+|+|.++. ++.-..-. .. . .-|.|.|+.--|+||+...|.|...
T Consensus 27 gi~l~~-TRvIy~e~---~~~~sv~v~N~~~~~p~LVQsWvdd~~~~~~~~pFivtPPLfRlep~~~q~lRI~~~ 97 (257)
T PRK15274 27 AIVPDR-TRVIFNGN---ENSITVTLKNGNATLPYLAQAWLEDDKFAKDTRYFTALPPLQRIEPKSDGQVKVQPL 97 (257)
T ss_pred eEEeCc-eEEEEeCC---CceEEEEEEeCCCCCcEEEEEEccCCCCCcccCCEEEcCCeEEECCCCceEEEEEEC
Confidence 466665 46777642 23479999999876 43332211 11 1 1499999999999999999999874
No 45
>PF07705 CARDB: CARDB; InterPro: IPR011635 The APHP (acidic peptide-dependent hydrolases/peptidase) domain is found in a variety of different proteins.; PDB: 2KUT_A 2L0D_A 3IDU_A 2KL6_A.
Probab=43.01 E-value=76 Score=23.31 Aligned_cols=53 Identities=21% Similarity=0.179 Sum_probs=34.3
Q ss_pred CCCeeEEEEEEEcCCCCe-EEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 91 PGKQTRSAVRLKNTSKSH-VAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 91 ~~k~vss~LtLtN~S~~~-VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
.|+..+-.++|+|..... =.|+|+-...+...-.-..+-|.||++..+.+...
T Consensus 17 ~g~~~~i~~~V~N~G~~~~~~~~v~~~~~~~~~~~~~i~~L~~g~~~~v~~~~~ 70 (101)
T PF07705_consen 17 PGEPVTITVTVKNNGTADAENVTVRLYLDGNSVSTVTIPSLAPGESETVTFTWT 70 (101)
T ss_dssp TTSEEEEEEEEEE-SSS-BEEEEEEEEETTEEEEEEEESEB-TTEEEEEEEEEE
T ss_pred CCCEEEEEEEEEECCCCCCCCEEEEEEECCceeccEEECCcCCCcEEEEEEEEE
Confidence 477888999999997753 45666533333322223337899999999999885
No 46
>PRK15308 putative fimbrial protein TcfA; Provisional
Probab=42.66 E-value=2.1e+02 Score=26.37 Aligned_cols=66 Identities=12% Similarity=0.172 Sum_probs=48.8
Q ss_pred CcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEee---CCC---------------cceEeeCCeeeeCCCCeE
Q 024677 75 RRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQT---TAP---------------KSCYMRPPGGVLAPGDSI 136 (264)
Q Consensus 75 ~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKT---TaP---------------k~Y~VRPn~GiL~Pgesi 136 (264)
--|.|.|- .+.+.. +.+....++|.|.++++..++|.. ++| ..-.+-|..-+|.||++-
T Consensus 16 a~l~V~Pi-~~~i~a--~~~~~~~v~V~N~g~~~~~vqV~v~r~~~PG~~~e~~~~~~~~~~~eLiaSP~~l~L~pg~~q 92 (234)
T PRK15308 16 ANMLVYPM-AAEIGA--GREEATSLFVYSKSDHTQYVRTRIKRIEHPATPQEKEVPAGNDIETGLVVSPEKFALPAGTTR 92 (234)
T ss_pred ceEEEEEe-EEEecC--CCcceEEEEEEeCCCCcEEEEEEEEEEcCCCCCCCcccccccCCCCcEEEcCceeEECCCCeE
Confidence 35888995 666543 334558999999999987776542 232 136788999999999999
Q ss_pred EEEEEee
Q 024677 137 IATVFKF 143 (264)
Q Consensus 137 ~V~Vtlq 143 (264)
.|.+...
T Consensus 93 ~IRli~l 99 (234)
T PRK15308 93 TVRVISL 99 (234)
T ss_pred EEEEEEc
Confidence 9998875
No 47
>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=39.66 E-value=2.3e+02 Score=28.35 Aligned_cols=69 Identities=14% Similarity=0.227 Sum_probs=47.1
Q ss_pred cEEeeCCCc-eEeeCCCCC-eeEEEEEEEcCCCCeEEEEEeeCCCcceEee-C-CeeeeCCCCeEEEEEEeec
Q 024677 76 RLRLDPSNN-LYFPYEPGK-QTRSAVRLKNTSKSHVAFKFQTTAPKSCYMR-P-PGGVLAPGDSIIATVFKFV 144 (264)
Q Consensus 76 ~L~IdP~~e-L~F~~e~~k-~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VR-P-n~GiL~Pgesi~V~Vtlq~ 144 (264)
.|.|..... |+...+.|. .-..+++|.|++.++..|.++........+. + +.=.|+||+..++.|++..
T Consensus 327 ~~~v~r~r~~l~~~~~~g~i~N~Y~~~i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v~~g~~~~~~v~v~~ 399 (434)
T TIGR02745 327 DLNVLRDRNLLYVRNSDGVVENTYTLKILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHVKAGEKVKLPVFLRT 399 (434)
T ss_pred EEEEEecCCcceEECCCCcEEEEEEEEEEECCCCCEEEEEEEecCCCcEEEcCCceEEECCCCEEEEEEEEEe
Confidence 455555433 444444443 5568999999999988888887655444443 2 2347999999999988863
No 48
>PF13205 Big_5: Bacterial Ig-like domain
Probab=39.44 E-value=1.4e+02 Score=22.45 Aligned_cols=58 Identities=19% Similarity=0.279 Sum_probs=35.1
Q ss_pred ceEeeCCCCC-eeEEEEEEEcCCCCeEEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEe
Q 024677 84 NLYFPYEPGK-QTRSAVRLKNTSKSHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFK 142 (264)
Q Consensus 84 eL~F~~e~~k-~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtl 142 (264)
.|.|.-+... .....+.+.+.....+.+.+.....+.+.++|. +-|.+|..+.|+|.-
T Consensus 26 ~i~Fs~~v~~~s~~~~~~~~~~~~~~~~v~~~~~~~~~~~i~p~-~~L~~~t~Y~v~i~~ 84 (107)
T PF13205_consen 26 VITFSEPVDPASVSSAITITDSNGSGVPVSFSSWDGNTLTITPS-QPLKPGTTYTVTIDS 84 (107)
T ss_pred EEEECCceecCccceEEEEEecCCCcEEEEEEEccCCEEEEEEC-CcCCCCCEEEEEECC
Confidence 4555554332 334555664433344344443344588999998 667899999998854
No 49
>PF07233 DUF1425: Protein of unknown function (DUF1425); InterPro: IPR010824 This family consists of several hypothetical bacterial proteins of around 125 residues in length. Several members of this family are described as putative lipoproteins and are often known as YcfL. The function of this family is unknown.; PDB: 3O0L_A.
Probab=39.28 E-value=1.5e+02 Score=23.05 Aligned_cols=51 Identities=16% Similarity=0.237 Sum_probs=32.8
Q ss_pred CCeeEEEEEEEcCCCCe--EEEEEeeCCCcceEeeCC-----eeeeCCCCeEEEEEEe
Q 024677 92 GKQTRSAVRLKNTSKSH--VAFKFQTTAPKSCYMRPP-----GGVLAPGDSIIATVFK 142 (264)
Q Consensus 92 ~k~vss~LtLtN~S~~~--VAFKVKTTaPk~Y~VRPn-----~GiL~Pgesi~V~Vtl 142 (264)
+......+.|+|+++.+ +.||+-==+.+-+-|.|. .=.|.++++..|.-+.
T Consensus 23 ~g~~~~~~~l~N~~~~~~~l~Yrf~WyD~~G~~v~~~~~~w~~~~l~~~~~~~l~~~a 80 (94)
T PF07233_consen 23 NGLLRAQATLSNKSSKPLTLQYRFYWYDKQGLEVDPEQSPWQSLTLPGGQTVTLSAVA 80 (94)
T ss_dssp CCEEEEEEEEEE-SSS-EEEEEEEEEE-TTS-EE--TT---EEEEE-TT-EEEEEEE-
T ss_pred CCeEEEEEEEEECCCCcEEEEEEEEEECCCCCCcCCCCCCCEEEEEcCCCEEEEEEEC
Confidence 66778999999999875 788887667777888877 4567888887776554
No 50
>smart00637 CBD_II CBD_II domain.
Probab=37.76 E-value=1.4e+02 Score=22.64 Aligned_cols=24 Identities=21% Similarity=0.256 Sum_probs=18.7
Q ss_pred cceEeeCCe--eeeCCCCeEEEEEEe
Q 024677 119 KSCYMRPPG--GVLAPGDSIIATVFK 142 (264)
Q Consensus 119 k~Y~VRPn~--GiL~Pgesi~V~Vtl 142 (264)
..|.++|.. +.|+||+++.+-+..
T Consensus 50 ~~~~~~~~~wn~~i~~G~s~~~gf~~ 75 (92)
T smart00637 50 GHVTATNASWNGTIAPGGSVSFGFQG 75 (92)
T ss_pred CEEEEecCccccccCCCCEEEEEEEe
Confidence 368888654 899999998876655
No 51
>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=34.95 E-value=2.1e+02 Score=25.13 Aligned_cols=52 Identities=15% Similarity=0.269 Sum_probs=39.2
Q ss_pred CCCeeEEEEEEEcCCCCeEEEEEeeCC----CcceEeeC-----CeeeeCCCCeEEEEEEee
Q 024677 91 PGKQTRSAVRLKNTSKSHVAFKFQTTA----PKSCYMRP-----PGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 91 ~~k~vss~LtLtN~S~~~VAFKVKTTa----Pk~Y~VRP-----n~GiL~Pgesi~V~Vtlq 143 (264)
.|+.+...++|.|..+. -||.|+-++ ++.|-+-- ....|+||+.+.-.+++.
T Consensus 36 ~g~~v~V~~~iyN~G~~-~A~dV~l~D~~fp~~~F~lvsG~~s~~~~~i~pg~~vsh~~vv~ 96 (181)
T PF05753_consen 36 EGEDVTVTYTIYNVGSS-AAYDVKLTDDSFPPEDFELVSGSLSASWERIPPGENVSHSYVVR 96 (181)
T ss_pred CCcEEEEEEEEEECCCC-eEEEEEEECCCCCccccEeccCceEEEEEEECCCCeEEEEEEEe
Confidence 47889999999999988 799999887 24444321 236688888888877774
No 52
>PRK06655 flgD flagellar basal body rod modification protein; Reviewed
Probab=32.98 E-value=1.7e+02 Score=26.69 Aligned_cols=82 Identities=13% Similarity=0.175 Sum_probs=58.3
Q ss_pred ccccceecccCCCCCcEEeeCCCceEeeCCCCCe-eEEEEEEEcCCCCeEE-EEEeeCCCcceEe----eCCeeeeCCCC
Q 024677 61 KTVSYVARSLLPPRRRLRLDPSNNLYFPYEPGKQ-TRSAVRLKNTSKSHVA-FKFQTTAPKSCYM----RPPGGVLAPGD 134 (264)
Q Consensus 61 ~~~~~~ak~~~p~~~~L~IdP~~eL~F~~e~~k~-vss~LtLtN~S~~~VA-FKVKTTaPk~Y~V----RPn~GiL~Pge 134 (264)
..++.|+|..+-.+..+.++......|.+.+... ...+|+|.|...+.|- +.+....++.+.+ +...|-..|..
T Consensus 91 ~a~~lIGk~V~~~~~~~~~~~~~~~~~~~~l~~~a~~vti~I~D~~G~~Vrt~~lg~~~aG~~~f~WDG~d~~G~~lp~G 170 (225)
T PRK06655 91 QASSLVGRGVLVPGDTVLVGTGGTTPFGVELPSAADNVTVTITDSAGQVVRTIDLGAQSAGVVSFTWDGTDTDGNALPDG 170 (225)
T ss_pred HHHHhcCCeEEEecceEEecCCCceEEEEEcCCCCcEEEEEEEcCCCCEEEEEecCCcCCCceeEEECCCCCCCCcCCCe
Confidence 3567888987777888888764466666665443 3589999999888774 7776667777776 34567766666
Q ss_pred eEEEEEEe
Q 024677 135 SIIATVFK 142 (264)
Q Consensus 135 si~V~Vtl 142 (264)
.+.|.|..
T Consensus 171 ~Yt~~V~A 178 (225)
T PRK06655 171 NYTIKASA 178 (225)
T ss_pred eEEEEEEE
Confidence 77777764
No 53
>PF07231 Hs1pro-1_N: Hs1pro-1 N-terminus; InterPro: IPR009869 This entry represents the N terminus (approximately 180 residues) of plant Hs1pro-1, which is believed to confer resistance to nematodes [].
Probab=32.98 E-value=19 Score=31.98 Aligned_cols=18 Identities=44% Similarity=0.767 Sum_probs=16.5
Q ss_pred ehhhchHHHHHHhhhccc
Q 024677 244 DEWERREKYLARQQVEAV 261 (264)
Q Consensus 244 ~~~~~~~~~~~~~~~~~~ 261 (264)
|||-||-+-||..|+|.+
T Consensus 109 rEw~RRlESLa~~qieii 126 (182)
T PF07231_consen 109 REWTRRLESLATSQIEII 126 (182)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 799999999999999865
No 54
>PF11538 Snurportin1: Snurportin1; InterPro: IPR024721 Snurportin-1 is a nuclear import receptor that contains an N-terminal importin beta binding domain which is essential for its function as an snRNP-specific nuclear import receptor []. Snurportin-1 interacts with m3G-cap where it enhances the m3G-cap dependent nuclear import of U snRNPs in Xenopus laevis oocytes and digitonin-permeabilized HeLa cells []. This entry represents the snurportin-1 N-terminal importin beta binding domain (IBB). The essential role of the IBB domain for snurportin-1 function suggests that snurportin-1 cooperates with importin beta in mediating nuclear import of snRNPs.; GO: 0005515 protein binding; PDB: 3LWW_D 3NC0_E 3NBZ_E 2Q5D_C 3NBY_B 3GB8_B 3GJX_B 2QNA_B 2P8Q_B.
Probab=32.85 E-value=24 Score=24.15 Aligned_cols=17 Identities=41% Similarity=0.694 Sum_probs=12.5
Q ss_pred eeehhhchHHHHHHhhh
Q 024677 242 VIDEWERREKYLARQQV 258 (264)
Q Consensus 242 ~~~~~~~~~~~~~~~~~ 258 (264)
..|-=|||+++|.+|-.
T Consensus 13 ~~~Q~eRR~~~Le~QK~ 29 (40)
T PF11538_consen 13 ALDQEERRREFLERQKN 29 (40)
T ss_dssp SCSHHHHHHHHHHHHHS
T ss_pred hHhHHHHHHHHHHHHHH
Confidence 33444999999998853
No 55
>PF08277 PAN_3: PAN-like domain; InterPro: IPR006583 PAN domains have significant functional versatility fulfilling diverse biological functions by mediating protein-protein or protein-carbohydrate interactions []. These domains contain a hair-pin loop like structure, similar to knottins, but the pattern of disulphide bonds differs The PAN-3 or CW is a domain associated with a number of Caenorhabditis elegans hypothetical proteins.
Probab=32.67 E-value=59 Score=23.16 Aligned_cols=30 Identities=23% Similarity=0.464 Sum_probs=18.8
Q ss_pred CCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEE
Q 024677 81 PSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKF 113 (264)
Q Consensus 81 P~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKV 113 (264)
+.....|.+ +. +...-++...+...||||+
T Consensus 42 ~~~C~~y~~--~~-i~~v~~~~~~~~~~VA~K~ 71 (71)
T PF08277_consen 42 SGKCYLYNY--GS-ISTVQKTDSSSGNKVAFKI 71 (71)
T ss_pred CCCEEEEEc--CC-EEEEEEeecCCCeEEEEEC
Confidence 334555554 43 5455556666778999996
No 56
>PRK15253 putative fimbrial assembly chaperone protein StcB; Provisional
Probab=31.19 E-value=4.2e+02 Score=24.35 Aligned_cols=62 Identities=18% Similarity=0.271 Sum_probs=45.0
Q ss_pred cEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEee---CC-----C----cceEeeCCeeeeCCCCeEEEEEEee
Q 024677 76 RLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQT---TA-----P----KSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 76 ~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKT---Ta-----P----k~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
-|.++- ..+.|+.. ....+|+|.|.++.+ |=|++ .. | .-|.|.|+.--|+|++...|.|...
T Consensus 34 gv~l~~-TRvIy~~~---~k~~sv~i~N~~~~p--yLvQsWvd~~~~~~~~~~~~~pFivtPPlfRl~p~~~~~lRI~~~ 107 (242)
T PRK15253 34 GIVIYG-TRVIYPAE---KKEVVVQLVNQGEQA--SLVQSWIDDGNTSLPPEKIQVPFMLTPPVARVAAESGQQIKIKKM 107 (242)
T ss_pred eEEeCc-eEEEEeCC---CceEEEEEEcCCCCc--EEEEEEEECCCCCCCcccccCCEEECCCeEEECCCCceEEEEEEC
Confidence 466665 46777642 234799999999875 44443 11 1 1499999999999999999999864
No 57
>PRK03879 ribonuclease P protein component 1; Validated
Probab=29.00 E-value=29 Score=27.70 Aligned_cols=15 Identities=53% Similarity=0.866 Sum_probs=12.7
Q ss_pred CCCceec-cceeeehh
Q 024677 232 TGPRVVG-EGLVIDEW 246 (264)
Q Consensus 232 ~~~~~~~-~~~~~~~~ 246 (264)
++|..|| +|.||||=
T Consensus 24 ~npslvGi~GiVv~ET 39 (96)
T PRK03879 24 TNPSLVGIKGRVVDET 39 (96)
T ss_pred CCCCcccceEEEEEec
Confidence 6788887 99999983
No 58
>smart00538 POP4 A domain found in a protein subunit of human RNase MRP and RNase P ribonucleoprotein complexes and archaeal proteins.
Probab=28.84 E-value=29 Score=27.37 Aligned_cols=15 Identities=53% Similarity=0.977 Sum_probs=12.7
Q ss_pred CCCceec-cceeeehh
Q 024677 232 TGPRVVG-EGLVIDEW 246 (264)
Q Consensus 232 ~~~~~~~-~~~~~~~~ 246 (264)
++|.++| +|+||||=
T Consensus 22 ~~ps~vGi~GiVv~ET 37 (92)
T smart00538 22 KNPSLVGIEGIVVDET 37 (92)
T ss_pred CCCCccCcEEEEEEee
Confidence 6788887 99999983
No 59
>smart00605 CW CW domain.
Probab=27.23 E-value=1.3e+02 Score=22.89 Aligned_cols=33 Identities=33% Similarity=0.521 Sum_probs=19.4
Q ss_pred CceEeeCCCCCeeEEEEEEEcC-CCCeEEEEEeeCCCc
Q 024677 83 NNLYFPYEPGKQTRSAVRLKNT-SKSHVAFKFQTTAPK 119 (264)
Q Consensus 83 ~eL~F~~e~~k~vss~LtLtN~-S~~~VAFKVKTTaPk 119 (264)
....|.+ +. + ..|+-.+. +...||||+.++.+.
T Consensus 47 ~C~~f~~--~~-~-~~v~~~~~~~~~~VAfK~~~~~~~ 80 (94)
T smart00605 47 TCYLFSY--GT-V-LTVKKLSSSSGKKVAFKVSTDQPS 80 (94)
T ss_pred ceEEEEc--CC-e-EEEEEccCCCCcEEEEEEeCCCCC
Confidence 4556665 32 2 34444444 457899999866544
No 60
>cd04094 selB_III This family represents the domain of elongation factor SelB, homologous to domain III of EF-Tu. SelB may function by replacing EF-Tu. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3' or 5' non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation.
Probab=27.09 E-value=2.8e+02 Score=21.15 Aligned_cols=32 Identities=28% Similarity=0.331 Sum_probs=23.9
Q ss_pred eeeeCCCCeEEEEEEeeccCCCCcCCCCCCCCCCCeEEEEE
Q 024677 127 GGVLAPGDSIIATVFKFVEAPENNERQPLDQKSKDKFKIMS 167 (264)
Q Consensus 127 ~GiL~Pgesi~V~Vtlq~e~P~~~E~pp~~~~~kDKFLVqS 167 (264)
...|.||++..+++.+. .|. -....|+|+|..
T Consensus 54 ~~~~~pg~~~~a~l~l~--~pl-------~~~~gdrfilR~ 85 (97)
T cd04094 54 RDELAPGEEALAQLRLE--EPL-------VALRGDRFILRS 85 (97)
T ss_pred ccccCCCCEEEEEEEEC--CcE-------eecCCCeEEEee
Confidence 44689999999999985 232 245679999964
No 61
>COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]
Probab=26.77 E-value=71 Score=27.08 Aligned_cols=43 Identities=28% Similarity=0.422 Sum_probs=34.0
Q ss_pred eecccCCCCCcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEE
Q 024677 66 VARSLLPPRRRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFK 112 (264)
Q Consensus 66 ~ak~~~p~~~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFK 112 (264)
+|.++...+-...|.| .++|.++++.+ .+|-|..++.+.+-||
T Consensus 85 laerlea~gi~~~i~P--~vRF~Ge~gEq--~TlFl~DP~gN~lEfK 127 (138)
T COG3565 85 LAERLEAAGIPFHIPP--KVRFKGEPGEQ--RTLFLFDPSGNALEFK 127 (138)
T ss_pred HHHHHHHcCCCcccCc--eEEecCCccce--EEEEEECCCCCeeeee
Confidence 4556554454555666 89999999986 5899999999999998
No 62
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=26.40 E-value=16 Score=26.61 Aligned_cols=17 Identities=35% Similarity=0.874 Sum_probs=13.0
Q ss_pred eeehh--hchHHHHHHhhh
Q 024677 242 VIDEW--ERREKYLARQQV 258 (264)
Q Consensus 242 ~~~~~--~~~~~~~~~~~~ 258 (264)
.|..| |||.+|.-++-+
T Consensus 22 eI~~W~eERrk~~PT~~~i 40 (56)
T PF10453_consen 22 EIAKWIEERRKNYPTKANI 40 (56)
T ss_pred HHHHHHHHHHHcCCcHHHH
Confidence 58899 999999765443
No 63
>PF08402 TOBE_2: TOBE domain; InterPro: IPR013611 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. Probably involved in the recognition of small ligands such as molybdenum (e.g. P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT). Found in ABC transporters immediately after the ATPase domain. A strong RPE motif is found at the presumed N terminus of the domain. ; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1Q12_A 1Q1B_C 2AWN_D 3RLF_B 3PUX_B 2R6G_B 3PUV_B 1Q1E_A 3PV0_B 2AWO_A ....
Probab=24.72 E-value=2.4e+02 Score=19.36 Aligned_cols=65 Identities=17% Similarity=0.227 Sum_probs=39.7
Q ss_pred EEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEeeCCCcceEee-CCee---eeCCCCeEEEEEEe
Q 024677 77 LRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFKFQTTAPKSCYMR-PPGG---VLAPGDSIIATVFK 142 (264)
Q Consensus 77 L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFKVKTTaPk~Y~VR-Pn~G---iL~Pgesi~V~Vtl 142 (264)
|.|-| +.|.+....+....++|.-.--....+-+.+++..-....+. ++.. .+.+|+.+.|.+-.
T Consensus 1 l~iRP-E~i~l~~~~~~~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~G~~v~l~~~~ 69 (75)
T PF08402_consen 1 LGIRP-EDIRLSPEGENRLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQRDSPLEPGDEVRLSWDP 69 (75)
T ss_dssp EEE-G-GGEEEESSTTTEEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG-TTT--TTSEEEEEEEG
T ss_pred CEECc-ceeEEECCCCCeEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccccCCCCCCCEEEEEECc
Confidence 45677 477775222336666666665566777778888777664443 4444 78899988887653
No 64
>COG3354 FlaG Putative archaeal flagellar protein G [Cell motility and secretion]
Probab=24.48 E-value=2.3e+02 Score=24.73 Aligned_cols=67 Identities=19% Similarity=0.166 Sum_probs=48.2
Q ss_pred CCCcEEeeCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEE-----------EeeCCCcceEeeCCeee-eCCCCeEEEEE
Q 024677 73 PRRRLRLDPSNNLYFPYEPGKQTRSAVRLKNTSKSHVAFK-----------FQTTAPKSCYMRPPGGV-LAPGDSIIATV 140 (264)
Q Consensus 73 ~~~~L~IdP~~eL~F~~e~~k~vss~LtLtN~S~~~VAFK-----------VKTTaPk~Y~VRPn~Gi-L~Pgesi~V~V 140 (264)
....+.=+|. .+...+.. ..-+-++-|||+.++.++|- +.|-+.-.|..-+..|+ |.||+--. .|
T Consensus 50 ~dFaIIndPg-~i~~~~~~-g~~t~t~yiKNtG~~~~~fd~~sitVliDG~iv~~a~~~~~~~~gs~i~l~PG~Vg~-ev 126 (154)
T COG3354 50 TDFAIINDPG-QIPYVGTD-GPYTYTFYIKNTGSDSIAFDNTSITVLIDGNIVTPAYVTFTSVNGSSIRLSPGQVGR-EV 126 (154)
T ss_pred ccEEEecCCC-CCccccCC-CceEEEEEEecCCCcccccCCCeEEEEEcCcEeccceEEEEecCCCeeEecCCceee-EE
Confidence 4445666784 66555532 34568999999999999985 45666677788888899 99999874 44
Q ss_pred Ee
Q 024677 141 FK 142 (264)
Q Consensus 141 tl 142 (264)
++
T Consensus 127 ~v 128 (154)
T COG3354 127 TV 128 (154)
T ss_pred Ee
Confidence 44
No 65
>PF06483 ChiC: Chitinase C; InterPro: IPR009470 This ~170 aa region is found at the C-terminal to the catalytic domain (IPR001223 from INTERPRO) found in members of glycoside hydrolase family 18.
Probab=23.66 E-value=87 Score=28.01 Aligned_cols=26 Identities=31% Similarity=0.543 Sum_probs=22.6
Q ss_pred CeEEEEEeeCCCcceEeeCCeeeeCCCCeEEEEEEee
Q 024677 107 SHVAFKFQTTAPKSCYMRPPGGVLAPGDSIIATVFKF 143 (264)
Q Consensus 107 ~~VAFKVKTTaPk~Y~VRPn~GiL~Pgesi~V~Vtlq 143 (264)
++|+||+ |....|+||+++++.+...
T Consensus 116 Hrvs~tl-----------p~wqslapG~s~~~~~~Yy 141 (180)
T PF06483_consen 116 HRVSFTL-----------PAWQSLAPGASVELDMVYY 141 (180)
T ss_pred EEEEEEC-----------CCccccCCCCEEEEeEEEE
Confidence 5888887 8889999999999998764
No 66
>PF01868 UPF0086: Domain of unknown function UPF0086; InterPro: IPR002730 The p29 subunit (also known as Rpp29 or Pop4) of the related ribonucleoproteins ribonuclease (RNase) P and RNase MRP can be found in both eukaryotes and arachea []. The structure of the RNase P subunit, Rpp29, from Methanobacterium thermoautotrophicum has been determined. Mth Rpp29 is a member of the oligonucleotide/oligosaccharide binding fold family. It contains a structured beta-barrel core and unstructured N- and C-terminal extensions bearing several highly conserved amino acid residues that could be involved in RNA contacts in the protein-RNA complex []. Rpp29 (3.1.26.5 from EC) catalyses the endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor. It interacts with the Rpp25 and Pop5 subunits. RNase P is a ubiquitous ribonucleoprotein enzyme primarily responsible for cleaving the 5' leader sequence during maturation of tRNAs in all three domains of life. In eubacteria, this enzyme is made up of two subunits: a large RNA (approximately 120 kDa) responsible for mediating catalysis, and a small protein cofactor (approximately 15 kDa) that modulates substrate recognition and is required for efficient in vivo catalysis. In contrast, multiple proteins are associated with eukaryotic and archaeal RNase P, and these proteins exhibit no recognizable homology to the conserved bacterial protein subunit. In reconstitution experiments with recombinantly expressed and purified protein subunits Mth Rpp29, a homologue of the Rpp29 protein subunit from eukaryotic RNase P, is an essential protein component of the archaeal holoenzyme []. In Saccharomyces cerevisiae (Baker's yeast), RNase P consists of 9 protein subunits (Pop1, Pop3-8, Rpr2 and Rpp1), while in humans there are 10 subunits (Rpp14, 20, 21, 25, 29, 30, 38, 40, hPop1, 5). RNase MRP (mitochondrial RNA processing) is an rRNA processing enzyme that cleaves a specific site within precursor rRNA to generate the mature 5'-end of 5.8S rRNA []. RNase MRP also cleaves primers for mitochondrial DNA replication and CLB2 mRNA. In yeast, RNase MRP possesses one putatively catalytic RNA and at least 9 protein subunits and is highly related to RNase P (Pop1, Pop3-Pop8, Rpp1, Snm1 and Rmp1).; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0006364 rRNA processing, 0006379 mRNA cleavage, 0008033 tRNA processing, 0000172 ribonuclease MRP complex, 0030677 ribonuclease P complex; PDB: 1V76_B 2ZAE_C 1OQK_A 2KI7_A 1TSF_A 1TS9_A 1PC0_A.
Probab=21.49 E-value=45 Score=26.00 Aligned_cols=15 Identities=53% Similarity=0.977 Sum_probs=12.0
Q ss_pred CCCceec-cceeeehh
Q 024677 232 TGPRVVG-EGLVIDEW 246 (264)
Q Consensus 232 ~~~~~~~-~~~~~~~~ 246 (264)
.+|..+| +|+||||=
T Consensus 23 ~~pslvG~~GiVV~ET 38 (89)
T PF01868_consen 23 KNPSLVGIEGIVVDET 38 (89)
T ss_dssp SSCCCTTEEEEEEEEE
T ss_pred CCCCccCCEEEEEEcc
Confidence 4678887 99999983
No 67
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=20.40 E-value=2e+02 Score=26.48 Aligned_cols=42 Identities=10% Similarity=0.066 Sum_probs=27.9
Q ss_pred EEEEEcCCCCeEEEE-EeeCCCcceEeeCCeeeeCCCCeEEEEE
Q 024677 98 AVRLKNTSKSHVAFK-FQTTAPKSCYMRPPGGVLAPGDSIIATV 140 (264)
Q Consensus 98 ~LtLtN~S~~~VAFK-VKTTaPk~Y~VRPn~GiL~Pgesi~V~V 140 (264)
.|+|+|.+..++.|- ++....++ .+....|.|.|+++..+.+
T Consensus 177 ~l~v~Nptpyyitl~~l~~~~~~~-~~~~~~~mv~P~s~~~~~l 219 (253)
T PRK15249 177 GIVIVNPQPWFASLSNLNVKVNGA-SYNLDADMIAPFSSQTWWL 219 (253)
T ss_pred EEEEECCCceEEEeeeeeeccCCe-ecCCCCceECCCCccEEEc
Confidence 499999999988775 33211221 1222457899999988854
No 68
>PRK15295 fimbrial assembly chaperone SthB; Provisional
Probab=20.08 E-value=2.4e+02 Score=25.49 Aligned_cols=49 Identities=10% Similarity=0.217 Sum_probs=32.7
Q ss_pred CceEeeCCCCCeeEEEEEEEcCCCCeEEEE-EeeCCCcceEeeCCeeeeCCCCeEEEEE
Q 024677 83 NNLYFPYEPGKQTRSAVRLKNTSKSHVAFK-FQTTAPKSCYMRPPGGVLAPGDSIIATV 140 (264)
Q Consensus 83 ~eL~F~~e~~k~vss~LtLtN~S~~~VAFK-VKTTaPk~Y~VRPn~GiL~Pgesi~V~V 140 (264)
..|.|.... ..|+|+|+|..++.|- ++... +. +. +.|.|+|+++..+.+
T Consensus 148 ~~L~~~~~~-----~~l~v~NptPyyitl~~l~~~~-~~--~~-~~~mI~P~s~~~~~~ 197 (226)
T PRK15295 148 QQLKWQTAG-----DVITVNNPTPYYMNFASVTLNS-HE--VK-SATFVPPKSSASFKL 197 (226)
T ss_pred hccEEEEcC-----CEEEEECCCceEEEEEEEEECC-cc--cC-CCceECCCCccEEEc
Confidence 355565322 2499999999999765 55432 22 22 358899999988864
Done!