Query 030354
Match_columns 179
No_of_seqs 138 out of 643
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 12:27:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030354.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030354hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00635 Motile_Sperm: MSP (Ma 99.9 3.4E-23 7.4E-28 152.6 11.0 94 75-173 2-95 (109)
2 KOG0439 VAMP-associated protei 99.9 6.4E-23 1.4E-27 169.4 12.1 106 69-178 3-109 (218)
3 COG5066 SCS2 VAMP-associated p 99.9 4.5E-23 9.7E-28 172.9 9.4 98 75-178 3-103 (242)
4 PF14874 PapD-like: Flagellar- 98.6 6.2E-07 1.3E-11 65.5 9.8 67 73-140 2-71 (102)
5 PF00345 PapD_N: Pili and flag 96.5 0.042 9.1E-07 41.3 9.6 62 75-140 2-72 (122)
6 PF14646 MYCBPAP: MYCBP-associ 94.2 0.26 5.7E-06 45.1 8.5 66 75-140 231-309 (426)
7 PRK09918 putative fimbrial cha 93.7 0.58 1.3E-05 39.7 9.1 63 74-140 25-92 (230)
8 PF07610 DUF1573: Protein of u 92.4 0.51 1.1E-05 30.2 5.4 42 97-139 2-44 (45)
9 PF11614 FixG_C: IG-like fold 91.2 1.1 2.3E-05 33.6 6.8 67 75-141 13-83 (118)
10 PRK09926 putative chaperone pr 90.3 2.8 6.1E-05 35.9 9.4 64 73-140 25-98 (246)
11 PRK15249 fimbrial chaperone pr 89.3 4.4 9.6E-05 34.9 9.9 63 74-140 29-102 (253)
12 PRK15299 fimbrial chaperone pr 88.7 5.2 0.00011 33.8 9.7 63 74-140 23-93 (227)
13 PRK15295 fimbrial assembly cha 88.4 6.5 0.00014 33.3 10.1 61 74-140 20-89 (226)
14 PRK15211 fimbrial chaperone pr 88.2 6.3 0.00014 33.6 10.0 63 74-140 23-91 (229)
15 PRK11385 putativi pili assembl 86.0 5.7 0.00012 34.0 8.5 64 73-140 26-101 (236)
16 PRK15208 long polar fimbrial c 85.3 11 0.00024 31.8 10.0 63 74-140 22-90 (228)
17 PRK15246 fimbrial assembly cha 84.3 7 0.00015 33.4 8.3 63 74-140 11-83 (233)
18 PF06280 DUF1034: Fn3-like dom 84.0 3.2 6.9E-05 30.8 5.4 51 90-140 7-78 (112)
19 PF06030 DUF916: Bacterial pro 83.9 16 0.00036 28.0 9.5 63 82-146 18-105 (121)
20 PRK15192 fimbrial chaperone Bc 81.0 32 0.00069 29.5 11.1 60 75-140 24-97 (234)
21 PF10633 NPCBM_assoc: NPCBM-as 80.0 2.8 6.1E-05 29.1 3.6 53 88-140 2-58 (78)
22 PRK15195 fimbrial chaperone pr 80.0 18 0.00038 30.8 9.1 64 73-140 25-94 (229)
23 PRK15188 fimbrial chaperone pr 78.7 26 0.00057 29.9 9.8 64 73-140 27-96 (228)
24 TIGR03079 CH4_NH3mon_ox_B meth 78.5 5.6 0.00012 36.8 5.9 54 88-141 279-353 (399)
25 PF00927 Transglut_C: Transglu 78.4 11 0.00024 27.5 6.6 58 88-148 12-79 (107)
26 COG3121 FimC P pilus assembly 76.7 28 0.00061 29.6 9.5 63 74-140 28-97 (235)
27 PRK15254 fimbrial chaperone pr 76.7 37 0.0008 29.2 10.2 63 74-140 17-85 (239)
28 PF11611 DUF4352: Domain of un 75.0 22 0.00047 25.9 7.4 53 88-140 33-99 (123)
29 PRK15290 lfpB fimbrial chapero 74.8 22 0.00048 30.6 8.3 63 74-140 38-108 (243)
30 PRK15224 pili assembly chapero 74.7 21 0.00047 30.6 8.2 60 75-140 30-96 (237)
31 PRK15233 putative fimbrial cha 74.3 40 0.00086 29.3 9.8 60 75-140 42-108 (246)
32 PRK15218 fimbrial chaperone pr 74.3 25 0.00053 30.0 8.4 60 75-140 20-91 (226)
33 PF02883 Alpha_adaptinC2: Adap 73.2 16 0.00034 26.8 6.3 52 89-140 22-77 (115)
34 PF12690 BsuPI: Intracellular 70.7 26 0.00055 25.2 6.7 48 93-140 2-68 (82)
35 PF05506 DUF756: Domain of unk 66.6 25 0.00054 25.0 5.9 44 94-140 21-65 (89)
36 PRK15253 putative fimbrial ass 66.3 46 0.00099 28.7 8.4 61 74-140 34-106 (242)
37 smart00809 Alpha_adaptinC2 Ada 66.2 45 0.00098 23.8 9.0 51 90-140 17-71 (104)
38 PRK15285 putative fimbrial cha 66.1 86 0.0019 27.1 10.1 62 75-140 27-95 (250)
39 PRK15274 putative periplasmic 65.0 90 0.002 27.2 10.1 64 73-140 26-96 (257)
40 PF02753 PapD_C: Pili assembly 64.9 7 0.00015 26.3 2.6 43 97-139 1-44 (68)
41 PF04744 Monooxygenase_B: Mono 61.2 29 0.00062 32.2 6.5 67 72-141 246-334 (381)
42 PF03173 CHB_HEX: Putative car 60.4 7.5 0.00016 31.7 2.4 32 109-140 69-102 (164)
43 PRK15308 putative fimbrial pro 58.3 54 0.0012 28.2 7.4 65 73-140 16-98 (234)
44 PF05753 TRAP_beta: Translocon 55.5 67 0.0015 26.4 7.3 52 88-140 35-95 (181)
45 PF14796 AP3B1_C: Clathrin-ada 53.4 1.2E+02 0.0025 24.4 8.4 58 83-140 73-138 (145)
46 PF07233 DUF1425: Protein of u 48.9 86 0.0019 22.8 6.3 50 90-139 23-79 (94)
47 PF07705 CARDB: CARDB; InterP 48.6 53 0.0012 22.5 5.0 53 88-140 16-69 (101)
48 PF13473 Cupredoxin_1: Cupredo 48.2 1E+02 0.0022 22.2 6.8 53 75-140 30-82 (104)
49 PF00553 CBM_2: Cellulose bind 45.4 50 0.0011 24.1 4.6 48 93-140 15-82 (101)
50 COG3354 FlaG Putative archaeal 44.5 85 0.0018 25.6 6.0 63 75-140 54-128 (154)
51 TIGR02745 ccoG_rdxA_fixG cytoc 43.2 2.9E+02 0.0062 25.9 10.7 67 74-140 327-397 (434)
52 smart00637 CBD_II CBD_II domai 37.9 1.4E+02 0.003 21.1 5.8 24 117-140 50-75 (92)
53 PF08277 PAN_3: PAN-like domai 36.4 59 0.0013 21.6 3.5 28 81-111 44-71 (71)
54 COG3565 Predicted dioxygenase 35.3 63 0.0014 25.7 3.9 33 74-110 95-127 (138)
55 PRK15249 fimbrial chaperone pr 30.5 1E+02 0.0022 26.5 4.8 42 96-138 177-219 (253)
56 PRK15295 fimbrial assembly cha 29.8 1.3E+02 0.0028 25.4 5.3 50 81-139 148-198 (226)
57 cd04094 selB_III This family r 29.7 2.1E+02 0.0045 20.4 6.5 32 125-164 54-85 (97)
58 PF08402 TOBE_2: TOBE domain; 27.4 1.7E+02 0.0038 18.7 6.8 64 75-139 1-68 (75)
59 PRK15246 fimbrial assembly cha 25.8 1.5E+02 0.0033 25.2 5.0 49 81-138 144-192 (233)
60 PF09640 DUF2027: Domain of un 25.2 2.4E+02 0.0051 23.3 5.8 69 94-173 19-87 (162)
61 smart00605 CW CW domain. 24.7 1.8E+02 0.0038 20.7 4.5 33 81-117 47-80 (94)
62 COG3121 FimC P pilus assembly 24.7 1.8E+02 0.004 24.6 5.3 51 82-139 157-209 (235)
63 PRK09926 putative chaperone pr 22.9 2.3E+02 0.005 24.2 5.6 55 81-138 160-216 (246)
64 PF06483 ChiC: Chitinase C; I 22.8 1E+02 0.0022 25.8 3.3 26 105-141 116-141 (180)
65 PRK15192 fimbrial chaperone Bc 22.5 1.9E+02 0.0042 24.7 5.1 38 97-138 164-202 (234)
66 PRK09918 putative fimbrial cha 21.1 2.3E+02 0.0049 23.9 5.1 50 82-138 147-199 (230)
67 PRK06655 flgD flagellar basal 20.3 5.1E+02 0.011 22.0 7.2 82 59-140 91-178 (225)
No 1
>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=99.90 E-value=3.4e-23 Score=152.60 Aligned_cols=94 Identities=31% Similarity=0.475 Sum_probs=77.5
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEeeccCCCCCCCCCCC
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPMYQ 154 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l~~~~p~~~e~p~~~ 154 (179)
|.|+|.+.|.|.++.++...+.|+|+|.++.+||||||||+|.+|+|+|+.|+|.||+++.|.|++ +|...... .
T Consensus 2 l~v~P~~~i~F~~~~~~~~~~~l~l~N~s~~~i~fKiktt~~~~y~v~P~~G~i~p~~~~~i~I~~---~~~~~~~~--~ 76 (109)
T PF00635_consen 2 LSVEPSELIFFNAPFNKQQSCELTLTNPSDKPIAFKIKTTNPNRYRVKPSYGIIEPGESVEITITF---QPFDFEPS--N 76 (109)
T ss_dssp CEEESSSEEEEESSTSS-EEEEEEEEE-SSSEEEEEEEES-TTTEEEESSEEEE-TTEEEEEEEEE----SSSTTTT--S
T ss_pred eEEeCCcceEEcCCCCceEEEEEEEECCCCCcEEEEEEcCCCceEEecCCCEEECCCCEEEEEEEE---EecccCCC--C
Confidence 789999999999999999999999999999999999999999999999999999999999999998 66543321 2
Q ss_pred CCCCeEEEEEEEeCCCccc
Q 030354 155 KSRDKFKIISMKVKADVDY 173 (179)
Q Consensus 155 k~kDKFlVqs~~v~~~~d~ 173 (179)
..+|||+|+++.++++...
T Consensus 77 ~~~dkf~I~~~~~~~~~~~ 95 (109)
T PF00635_consen 77 KKKDKFLIQSIVVPDNATD 95 (109)
T ss_dssp TSSEEEEEEEEEE-TT-SS
T ss_pred CCCCEEEEEEEEcCCCccc
Confidence 2399999999999877644
No 2
>KOG0439 consensus VAMP-associated protein involved in inositol metabolism [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.89 E-value=6.4e-23 Score=169.39 Aligned_cols=106 Identities=36% Similarity=0.556 Sum_probs=93.2
Q ss_pred CCCCCcEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEeeccCCCCC
Q 030354 69 LPKRRRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENN 148 (179)
Q Consensus 69 ~p~~~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l~~~~p~~~ 148 (179)
+..+.+|.|+|..+|+|..+..+++++.|+|+|+++.++|||||||+|++|+|||+.|+|.||++++|.|.+ +|. .
T Consensus 3 ~~~~~~l~i~P~~~l~F~~~~~~~~~~~l~l~N~t~~~vaFKvktT~p~~y~VrP~~G~i~p~~t~~i~v~~---q~~-~ 78 (218)
T KOG0439|consen 3 LETESLLEIEPSDELVFPLPLNEQVKCSLTLKNPTKLRVAFKVKTTAPKLYCVRPNGGVIDPGSTVEIEVTH---QPF-E 78 (218)
T ss_pred ccccCccccCCCceEEeccCCCceEEEEEEEecCCCCceEEEEEcCCCCeEEEcCCcceECCCCcEEEEEEe---ccC-c
Confidence 346789999998899999999999999999999999999999999999999999999999999999999987 663 3
Q ss_pred CCCCCCCCCCeEEEEEEEeCCC-ccccCccC
Q 030354 149 EKPMYQKSRDKFKIISMKVKAD-VDYVPELV 178 (179)
Q Consensus 149 e~p~~~k~kDKFlVqs~~v~~~-~d~~~elF 178 (179)
..|.+.+++|||+||++.++.+ ...+.++|
T Consensus 79 ~~P~d~~~r~kF~v~~~~~~~~~~~~~~~~~ 109 (218)
T KOG0439|consen 79 KSPPDFKSRHKFLIQSLKAPPPTTRDVVDLW 109 (218)
T ss_pred cCchhhcccceEEEEEEecCCccccchhhhc
Confidence 5577888999999999999975 44444443
No 3
>COG5066 SCS2 VAMP-associated protein involved in inositol metabolism [Intracellular trafficking and secretion]
Probab=99.89 E-value=4.5e-23 Score=172.87 Aligned_cols=98 Identities=26% Similarity=0.358 Sum_probs=89.0
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEeeccCCCCCCCCCCC
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPMYQ 154 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l~~~~p~~~e~p~~~ 154 (179)
|.|+| ++.|+.+...+.++.+.|.|.+.++|+||||||+|+.|+||||.|.|.|++++.|+|+| +++.+|+..+.
T Consensus 3 veisp--~~~fy~Plt~~ske~~sv~NnspepvgfKVKTTaPK~YcVRPN~g~Iep~stv~VeVil---q~l~eEpapdf 77 (242)
T COG5066 3 VEISP--QTTFYVPLTNKSKEMFSVQNNSPEPVGFKVKTTAPKDYCVRPNMGLIEPMSTVEVEVIL---QGLTEEPAPDF 77 (242)
T ss_pred eEecC--ceEEecccccccceeeEeecCCCCceeEEeeccCCcceeEcCCCceeccCCeeEEEEEe---eccccCCCCCc
Confidence 67888 68888888999999999999999999999999999999999999999999999999998 88888998899
Q ss_pred CCCCeEEEEEEEeCCC---ccccCccC
Q 030354 155 KSRDKFKIISMKVKAD---VDYVPELV 178 (179)
Q Consensus 155 k~kDKFlVqs~~v~~~---~d~~~elF 178 (179)
+|+||||||++.++.+ +|| +|.|
T Consensus 78 KCrdKFLiqs~~~~~~l~g~d~-ad~w 103 (242)
T COG5066 78 KCRDKFLIQSYRFDWRLSGSDF-ADHW 103 (242)
T ss_pred cccceeEEEEeccChhhccchH-HHHH
Confidence 9999999999999844 466 5544
No 4
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=98.59 E-value=6.2e-07 Score=65.49 Aligned_cols=67 Identities=27% Similarity=0.416 Sum_probs=59.2
Q ss_pred CcEEEcCCCceEeecC-CCceEEEEEEEEcCCCCeEEEEeccCC--CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 73 RRLKLDPANKLYFPYE-AGKQVRSAIKIKNTSKSHVAFKFQTTA--PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~-~~k~~~s~LtL~N~s~~~VAFKVKTTa--P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
..|.++|. +|.|-.- .|......|+|+|.+..+..|+|+.-. ...|.|.|..|+|.||+++.|.|.+
T Consensus 2 P~l~v~P~-~ldFG~v~~g~~~~~~v~l~N~s~~p~~f~v~~~~~~~~~~~v~~~~g~l~PG~~~~~~V~~ 71 (102)
T PF14874_consen 2 PTLEVSPK-ELDFGNVFVGQTYSRTVTLTNTSSIPARFRVRQPESLSSFFSVEPPSGFLAPGESVELEVTF 71 (102)
T ss_pred CEEEEeCC-EEEeeEEccCCEEEEEEEEEECCCCCEEEEEEeCCcCCCCEEEECCCCEECCCCEEEEEEEE
Confidence 35899995 9999874 488889999999999999999998543 5789999999999999999999998
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=96.45 E-value=0.042 Score=41.30 Aligned_cols=62 Identities=21% Similarity=0.397 Sum_probs=50.6
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCC----C-----ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTA----P-----KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTa----P-----~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
|.|+|. -+.|..... ...++|+|.++.++.+.+.... + ..|.|-|+.-.|+||+...|.|..
T Consensus 2 i~i~~t-rii~~~~~~---~~~i~v~N~~~~~~~vq~~v~~~~~~~~~~~~~~~~vsPp~~~L~pg~~q~vRv~~ 72 (122)
T PF00345_consen 2 IQISPT-RIIFNESQR---SASITVTNNSDQPYLVQVWVYDQDDEDEDEPTDPFIVSPPIFRLEPGESQTVRVYR 72 (122)
T ss_dssp EEESSS-EEEEETTSS---EEEEEEEESSSSEEEEEEEEEETTSTTSSSSSSSEEEESSEEEEETTEEEEEEEEE
T ss_pred EEEccE-EEEEeCCCC---EEEEEEEcCCCCcEEEEEEEEcCCCcccccccccEEEeCCceEeCCCCcEEEEEEe
Confidence 678884 888875332 4899999999999999877553 1 278999999999999999999953
No 6
>PF14646 MYCBPAP: MYCBP-associated protein family
Probab=94.21 E-value=0.26 Score=45.13 Aligned_cols=66 Identities=12% Similarity=0.332 Sum_probs=55.5
Q ss_pred EEEcCCCceEeecCCCceEEEEEE-EEcCCCCeEEEEeccC------------CCceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIK-IKNTSKSHVAFKFQTT------------APKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~Lt-L~N~s~~~VAFKVKTT------------aP~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
..+.+.-.|.|...++......|. |.|.+..-|-|..+-- ....|......|+|.||++..|.|+.
T Consensus 231 ~~~~~~~~l~Fe~~p~e~~~~~v~~l~N~Gt~~I~y~W~~~~~~~~~~~~~~~~~~~F~Fd~~~gvilPGe~~~~~~~F 309 (426)
T PF14646_consen 231 PEVSISIRLTFECHPGERVSKEVVRLENNGTTAIYYSWRRVPFFKNFGSLFRAQDQRFYFDTSSGVILPGETRNFPFMF 309 (426)
T ss_pred CccCcceEEEEEcccCceeeEEEEEEecCCceEEEEEEEecccccccchhccccCCeEEEeCCCCEECCCceEEEEEEE
Confidence 344455589999999988888888 9999999999985532 25789999999999999999999987
No 7
>PRK09918 putative fimbrial chaperone protein; Provisional
Probab=93.73 E-value=0.58 Score=39.67 Aligned_cols=63 Identities=19% Similarity=0.285 Sum_probs=48.1
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCC-----CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTA-----PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTa-----P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.++|. .+.|...... ..|+|+|.++.++........ ..-|.|-|+.-.|+||++..|+|.+
T Consensus 25 ~v~l~~t-Rvi~~~~~~~---~si~v~N~~~~p~lvQ~wv~~~~~~~~~~fivtPPl~rl~pg~~q~vRii~ 92 (230)
T PRK09918 25 GMVPETS-VVIVEESDGE---GSINVKNTDSNPILLYTTLVDLPEDKSKLLLVTPPVARVEPGQSQQVRFIL 92 (230)
T ss_pred eEEEccE-EEEEECCCCe---EEEEEEcCCCCcEEEEEEEecCCCCCCCCEEEcCCeEEECCCCceEEEEEE
Confidence 4778884 7777754433 899999999887655543321 1359999999999999999999986
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=92.45 E-value=0.51 Score=30.17 Aligned_cols=42 Identities=26% Similarity=0.184 Sum_probs=34.2
Q ss_pred EEEEcCCCCeE-EEEeccCCCceeEecCCeeEeCCCCeEEEEEE
Q 030354 97 IKIKNTSKSHV-AFKFQTTAPKSCFMRPPGAILAPGESLIATVF 139 (179)
Q Consensus 97 LtL~N~s~~~V-AFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~ 139 (179)
++++|.++.++ ..+|+|+ =+-..+......|.||++..|.|+
T Consensus 2 F~~~N~g~~~L~I~~v~ts-CgCt~~~~~~~~i~PGes~~i~v~ 44 (45)
T PF07610_consen 2 FEFTNTGDSPLVITDVQTS-CGCTTAEYSKKPIAPGESGKIKVT 44 (45)
T ss_pred EEEEECCCCcEEEEEeeEc-cCCEEeeCCcceECCCCEEEEEEE
Confidence 68999999866 5667764 466778888899999999999986
No 9
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=91.18 E-value=1.1 Score=33.57 Aligned_cols=67 Identities=15% Similarity=0.274 Sum_probs=38.1
Q ss_pred EEEcCCCceEee-cCCCc-eEEEEEEEEcCCCCeEEEEeccCCCceeEe-cCCee-EeCCCCeEEEEEEee
Q 030354 75 LKLDPANKLYFP-YEAGK-QVRSAIKIKNTSKSHVAFKFQTTAPKSCFM-RPPGA-ILAPGESLIATVFKF 141 (179)
Q Consensus 75 L~I~P~~eL~F~-~~~~k-~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~V-rP~~G-iI~Pgesv~I~I~l~ 141 (179)
+.|-+..-..|. ...|. +=...|+|.|.+..+.-|.|+...+..+.+ .|... -|.||++..+.|++.
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 344443333333 34443 224899999999999999999888878888 66555 599999999888763
No 10
>PRK09926 putative chaperone protein EcpD; Provisional
Probab=90.34 E-value=2.8 Score=35.89 Aligned_cols=64 Identities=6% Similarity=0.186 Sum_probs=48.2
Q ss_pred CcEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCc----------eeEecCCeeEeCCCCeEEEEEEe
Q 030354 73 RRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPK----------SCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~----------~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
--|.|+|. -+.|...... ..|+|.|.++.++.--.-....+ -|.|-|+.--|+||+...|+|..
T Consensus 25 A~i~l~~T-RvI~~~~~~~---~sv~l~N~~~~p~LvQ~Wvd~~~~~~~p~~~~~pfivtPPl~rl~p~~~q~lRIi~ 98 (246)
T PRK09926 25 ADIVISGT-RIIYKSDQKD---VNVRLENKGNNPLLVQSWLDTGDDNAEPGSIKVPFTATPPVSRIDPKRGQTIKLMY 98 (246)
T ss_pred eeEEeCce-EEEEeCCCce---EEEEEEeCCCCcEEEEEEecCCCCccCccccCCCEEEcCCeEEECCCCccEEEEEe
Confidence 45888994 7887753333 89999999988765544332111 39999999999999999999986
No 11
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=89.32 E-value=4.4 Score=34.91 Aligned_cols=63 Identities=14% Similarity=0.262 Sum_probs=46.5
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccC------CC-----ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTT------AP-----KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTT------aP-----~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.|+|. -+.|+..... ..|+|.|.++.++.-..-+. .| .-|.|-|+.--|+||+...|+|..
T Consensus 29 ~l~l~~T-Rviy~~~~~~---~sl~l~N~~~~p~LvQsWv~~~~~~~~p~~~~~~pFivtPPlfrl~p~~~q~lRI~~ 102 (253)
T PRK15249 29 SVTILGS-RIIYPSTASS---VDVQLKNNDAIPYIVQTWFDDGDMNTSPENSSAMPFIATPPVFRIQPKAGQVVRVIY 102 (253)
T ss_pred EEEeCce-EEEEeCCCcc---eeEEEEcCCCCcEEEEEEEeCCCCCCCccccccCcEEEcCCeEEecCCCceEEEEEE
Confidence 4888884 7877644433 89999999987654443211 11 139999999999999999999986
No 12
>PRK15299 fimbrial chaperone protein StiB; Provisional
Probab=88.65 E-value=5.2 Score=33.83 Aligned_cols=63 Identities=14% Similarity=0.269 Sum_probs=45.8
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCC--------CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTA--------PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTa--------P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.|+|. -+.|..... ...|+|.|.++.++.-..-... ..-|.|-|+.--|+||+...|+|..
T Consensus 23 ~i~l~~T-Rvi~~~~~~---~~sl~l~N~~~~p~lvQsWv~~~~~~~~~~~~pfivtPPl~rl~p~~~q~lRI~~ 93 (227)
T PRK15299 23 GINIGTT-RVIFHGDAK---DASISISNSDNVPYLIQSWAQSISETGASGDAPFMVTPPLFRLNGGQKNVLRIIR 93 (227)
T ss_pred eEEECce-EEEEeCCCc---EEEEEEEeCCCCcEEEEEEeecCCCCCCcCCCCEEEcCCeEEECCCCccEEEEEE
Confidence 4788884 777765433 3899999998875443322111 1349999999999999999999986
No 13
>PRK15295 fimbrial assembly chaperone SthB; Provisional
Probab=88.39 E-value=6.5 Score=33.34 Aligned_cols=61 Identities=18% Similarity=0.285 Sum_probs=45.7
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc----CC-----CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT----TA-----PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT----Ta-----P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.+++. -+.|...... ..|+|.|.++.++ -|++ -+ ..-|.|-|+.--|+||+...|+|..
T Consensus 20 ~i~l~~T-RvI~~~~~~~---~si~i~N~~~~p~--LvQsWv~~~~~~~~~~~pFivtPPl~rl~p~~~q~lRI~~ 89 (226)
T PRK15295 20 SIVVGGT-RLVFDGNNDE---SSINVENKDSKAN--LVQSWLSVVDPQVTNKQAFIITPPLFRLDAGQKNSIRVIR 89 (226)
T ss_pred cEEeCce-EEEEeCCCce---eEEEEEeCCCCcE--EEEEEEeCCCCCCCCCCCEEEcCCeEEECCCCceEEEEEE
Confidence 4778884 7777754333 8999999998753 3442 11 2359999999999999999999986
No 14
>PRK15211 fimbrial chaperone protein PefD; Provisional
Probab=88.18 E-value=6.3 Score=33.62 Aligned_cols=63 Identities=13% Similarity=0.166 Sum_probs=45.7
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccC------CCceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTT------APKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTT------aP~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.+++. -+.|+.... ..+|+|+|.++.++.-..... ...-|.|-|+.--|+||+...|+|.+
T Consensus 23 ~v~l~~T-RvIy~~~~~---~~si~i~N~~~~p~LvQswv~~~~~~~~~~pFivtPPlfrl~p~~~q~lRI~~ 91 (229)
T PRK15211 23 AFVLNGT-RFIYDEGRK---NISFEVTNQADQTYGGQVWIDNTTQGSSTVYMVPAPPFFKVRPKEKQIIRIMK 91 (229)
T ss_pred EEEECce-EEEEcCCCc---eEEEEEEeCCCCcEEEEEEEecCCCCCccCCEEEcCCeEEECCCCceEEEEEE
Confidence 3777874 777774333 389999999987644332211 11249999999999999999999987
No 15
>PRK11385 putativi pili assembly chaperone; Provisional
Probab=85.96 E-value=5.7 Score=34.03 Aligned_cols=64 Identities=19% Similarity=0.348 Sum_probs=46.0
Q ss_pred CcEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccC------------CCceeEecCCeeEeCCCCeEEEEEEe
Q 030354 73 RRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTT------------APKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTT------------aP~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
--|.+++. -+.|+.... ...|+|.|.++.++.=..... ....|.|-|+.--|+||+...|+|.+
T Consensus 26 A~v~l~~T-RvIy~~~~~---~~sv~l~N~~~~p~LvQswv~~~~~~~~~~~~~~~~pFivtPPlfrl~p~~~q~lRIi~ 101 (236)
T PRK11385 26 AGVVVGGT-RFIFPADRE---SISILLTNTSQESWLINSKINRPTRWAGGEASTVPAPLLAAPPLILLKPGTTGTLRLLR 101 (236)
T ss_pred eeEEeCce-EEEEcCCCc---eEEEEEEeCCCCcEEEEEEcccCccccCcccccccCCEEEcCCeEEECCCCceEEEEEE
Confidence 34778884 777774333 389999999988643332111 11349999999999999999999987
No 16
>PRK15208 long polar fimbrial chaperone LpfB; Provisional
Probab=85.34 E-value=11 Score=31.83 Aligned_cols=63 Identities=13% Similarity=0.275 Sum_probs=45.4
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCC--eEEEEeccC-CC---ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKS--HVAFKFQTT-AP---KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~--~VAFKVKTT-aP---~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.++|. -+.|..... ...|+|+|.+++ .+.+..-.. .. .-|.|-|+.--|+||+...|.|..
T Consensus 22 gv~l~~T-RvI~~~~~~---~~si~i~N~~~~~~~LvQsWv~~~~~~~~~pfivtPPl~rl~p~~~q~lRIi~ 90 (228)
T PRK15208 22 GVALSST-RVIYDGSKK---EASLTVNNKSKTEEFLIQSWIDDANGNKKTPFIITPPLFKLDPTKNNVLRIVN 90 (228)
T ss_pred cEEeCce-EEEEeCCCc---eEEEEEEeCCCCCcEEEEEEEECCCCCccCCEEECCCeEEECCCCccEEEEEE
Confidence 4788884 777775433 389999999864 333332211 11 239999999999999999999986
No 17
>PRK15246 fimbrial assembly chaperone StbE; Provisional
Probab=84.28 E-value=7 Score=33.41 Aligned_cols=63 Identities=16% Similarity=0.334 Sum_probs=45.6
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc-C-----CC----ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT-T-----AP----KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT-T-----aP----~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.|++. -+.|..... ...|+|.|.++.++.-..-. . .| .-|.|-|+.--|+||+...|.|.+
T Consensus 11 ~v~l~~T-RvI~~~~~~---~~sv~l~N~~~~p~LvQsWvd~~~~~~~p~~~~~pFivtPPlfrl~~~~~~~lRI~~ 83 (233)
T PRK15246 11 AVNIDRT-RIIFASDDV---AQSLTLSNDNTTPMLLQVWTDAGNIDASPDNSKTPLVALPPVFKMQPGELRTLRLLL 83 (233)
T ss_pred EEEECce-EEEEcCCCc---eEEEEEEeCCCCcEEEEEEEeCCCCccCcccccCcEEECCcceEECCCCceEEEEEE
Confidence 3778884 777775333 38999999998754332211 1 11 159999999999999999999987
No 18
>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=83.98 E-value=3.2 Score=30.77 Aligned_cols=51 Identities=18% Similarity=0.278 Sum_probs=32.4
Q ss_pred CceEEEEEEEEcCCCCeEEEEeccC-----C---CceeE--ec-----------CCeeEeCCCCeEEEEEEe
Q 030354 90 GKQVRSAIKIKNTSKSHVAFKFQTT-----A---PKSCF--MR-----------PPGAILAPGESLIATVFK 140 (179)
Q Consensus 90 ~k~~~s~LtL~N~s~~~VAFKVKTT-----a---P~~Y~--Vr-----------P~~GiI~Pgesv~I~I~l 140 (179)
+...+..|+|+|.+++.+.|+|.-. . .+.|. .. |..=.|+||++..|.|++
T Consensus 7 ~~~~~~~itl~N~~~~~~ty~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~~~~~~~vTV~ag~s~~v~vti 78 (112)
T PF06280_consen 7 GNKFSFTITLHNYGDKPVTYTLSHVPVLTDKTDTEEGYSILVPPVPSISTVSFSPDTVTVPAGQSKTVTVTI 78 (112)
T ss_dssp -SEEEEEEEEEE-SSS-EEEEEEEE-EEEEEE--ETTEEEEEEEE----EEE---EEEEE-TTEEEEEEEEE
T ss_pred CCceEEEEEEEECCCCCEEEEEeeEEEEeeEeeccCCcccccccccceeeEEeCCCeEEECCCCEEEEEEEE
Confidence 4457799999999999999987644 0 11221 11 222368999999999997
No 19
>PF06030 DUF916: Bacterial protein of unknown function (DUF916); InterPro: IPR010317 This family consists of putative cell surface proteins, from Firmicutes, of unknown function.
Probab=83.94 E-value=16 Score=28.04 Aligned_cols=63 Identities=21% Similarity=0.296 Sum_probs=44.2
Q ss_pred ceEeecCCCceEEEEEEEEcCCCCeEEEEec-----cCCCceeE-------------------ec-CCeeEeCCCCeEEE
Q 030354 82 KLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQ-----TTAPKSCF-------------------MR-PPGAILAPGESLIA 136 (179)
Q Consensus 82 eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVK-----TTaP~~Y~-------------------Vr-P~~GiI~Pgesv~I 136 (179)
...+...+|....-.|+|+|.+++.+-|+|. |+..+..- |+ |..-.|+|+++..|
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 5555567888888999999999999999975 33333221 11 33357899999988
Q ss_pred EEEeeccCCC
Q 030354 137 TVFKFVELPE 146 (179)
Q Consensus 137 ~I~l~~~~p~ 146 (179)
.+.+. .|.
T Consensus 98 ~~~i~--~P~ 105 (121)
T PF06030_consen 98 TFTIK--MPK 105 (121)
T ss_pred EEEEE--cCC
Confidence 88763 554
No 20
>PRK15192 fimbrial chaperone BcfG; Provisional
Probab=81.03 E-value=32 Score=29.50 Aligned_cols=60 Identities=13% Similarity=0.204 Sum_probs=44.6
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccC----------C----CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTT----------A----PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTT----------a----P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
|.++. .-+.|+.... ...|+|.|.++.+ |=|++. . ..-|.|-|+.--|+||+...|.|..
T Consensus 24 i~l~~-TRvIy~~~~k---~~sv~l~N~~~~p--~LvQswv~~~~~w~~~~~~~~~~PFivtPPlfrl~p~~~~~lRI~~ 97 (234)
T PRK15192 24 VVIGG-TRFIYHAGAP---ALSVPVSNHSEAS--WLIDTHILPGGRWPGTKNEGNITPFVVTPPLFMLSARQENSMRVVY 97 (234)
T ss_pred EEeCc-eEEEEcCCCc---eEEEEEEeCCCCc--EEEEEEeccCccccccCCccccCCEEEcCCeEEECCCCceEEEEEE
Confidence 66676 3667664332 3899999999875 555551 1 1249999999999999999999987
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=80.01 E-value=2.8 Score=29.08 Aligned_cols=53 Identities=23% Similarity=0.396 Sum_probs=31.8
Q ss_pred CCCceEEEEEEEEcCCCCeE-EEEeccCCCceeE--ecCCe-eEeCCCCeEEEEEEe
Q 030354 88 EAGKQVRSAIKIKNTSKSHV-AFKFQTTAPKSCF--MRPPG-AILAPGESLIATVFK 140 (179)
Q Consensus 88 ~~~k~~~s~LtL~N~s~~~V-AFKVKTTaP~~Y~--VrP~~-GiI~Pgesv~I~I~l 140 (179)
..|+...-.++|+|....++ ..++.-..|.-.. ..|.. +-|.||++..+.+.+
T Consensus 2 ~~G~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V 58 (78)
T PF10633_consen 2 TPGETVTVTLTVTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTV 58 (78)
T ss_dssp -TTEEEEEEEEEE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEE
T ss_pred CCCCEEEEEEEEEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEE
Confidence 35778889999999987543 3555555687777 45543 379999999998887
No 22
>PRK15195 fimbrial chaperone protein FimC; Provisional
Probab=79.99 E-value=18 Score=30.81 Aligned_cols=64 Identities=16% Similarity=0.342 Sum_probs=45.6
Q ss_pred CcEEEcCCCceEeecCCCceEEEEEEEEcCCCC--eEEEE-eccCC---CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 73 RRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKS--HVAFK-FQTTA---PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~--~VAFK-VKTTa---P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
--|.|++. -+.|...... ..|+|.|.++. .+... |.... ...|.|-|+.=-|+||+...|+|..
T Consensus 25 Agi~i~~T-RvIy~~~~~~---~si~l~N~~~~~~~LvQsWv~~~~~~~~~pfivtPPlfrl~p~~~q~lRIi~ 94 (229)
T PRK15195 25 GGIALGAT-RVIYPADAKQ---TSLAIRNSHTNERYLVNSWIENSSGVKEKSFIVTPPLFVSEPKSENTLRIIY 94 (229)
T ss_pred eeEEECCe-EEEEeCCCce---EEEEEEeCCCCccEEEEEEecCCCCCccCCEEEcCCeEEECCCCceEEEEEE
Confidence 34788884 7777744333 89999999864 34332 21111 1359999999999999999999986
No 23
>PRK15188 fimbrial chaperone protein BcfB; Provisional
Probab=78.74 E-value=26 Score=29.91 Aligned_cols=64 Identities=16% Similarity=0.334 Sum_probs=45.4
Q ss_pred CcEEEcCCCceEeecCCCceEEEEEEEEcCCCC--eEEEE-eccCC---CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 73 RRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKS--HVAFK-FQTTA---PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~--~VAFK-VKTTa---P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
--|.+++. -+.|+.... ...|+|+|.++. .+... |...+ ..-|.|-|+.--|+||+...|.|..
T Consensus 27 Agi~l~~T-RvIy~~~~~---~~sv~i~N~~~~~p~LvQsWv~~~~~~~~~pFivtPPlfrl~~~~~~~lRI~~ 96 (228)
T PRK15188 27 GGIALGAT-RVIYPQGSK---QTSLPIINSSASNVFLIQSWVANADGSRSTDFIITPPLFVIQPKKENILRIMY 96 (228)
T ss_pred ceEEECcE-EEEEcCCCc---eEEEEEEeCCCCccEEEEEEEecCCCCccCCEEEcCCeEEECCCCceEEEEEE
Confidence 34788884 777775333 389999999864 33333 21111 1249999999999999999999986
No 24
>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=78.46 E-value=5.6 Score=36.79 Aligned_cols=54 Identities=22% Similarity=0.298 Sum_probs=40.9
Q ss_pred CCCceEEEEEEEEcCCCCeEEEEeccCCCcee-------EecCCe-------e-------EeCCCCeEEEEEEee
Q 030354 88 EAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSC-------FMRPPG-------A-------ILAPGESLIATVFKF 141 (179)
Q Consensus 88 ~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y-------~VrP~~-------G-------iI~Pgesv~I~I~l~ 141 (179)
-+|+..+-+++|+|.++++|-.+=-+|+.-+| ..+|.. | -|.|||+.+|.|...
T Consensus 279 VPGR~l~~~~~VTN~g~~~vrlgEF~TA~vRFlN~~~v~~~~~~yP~~lla~GL~v~d~~pI~PGETr~v~v~aq 353 (399)
T TIGR03079 279 VPGRALRVTMEITNNGDQVISIGEFTTAGIRFMNANGVRVLDPDYPRELLAEGLEVDDQSAIAPGETVEVKMEAK 353 (399)
T ss_pred cCCcEEEEEEEEEcCCCCceEEEeEeecceEeeCcccccccCCCChHHHhhccceeCCCCCcCCCcceEEEEEEe
Confidence 56899999999999999999888555555444 333332 2 389999999999864
No 25
>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=78.45 E-value=11 Score=27.49 Aligned_cols=58 Identities=21% Similarity=0.233 Sum_probs=42.4
Q ss_pred CCCceEEEEEEEEcCCCCe--------EEEEeccCCCc--eeEecCCeeEeCCCCeEEEEEEeeccCCCCC
Q 030354 88 EAGKQVRSAIKIKNTSKSH--------VAFKFQTTAPK--SCFMRPPGAILAPGESLIATVFKFVELPENN 148 (179)
Q Consensus 88 ~~~k~~~s~LtL~N~s~~~--------VAFKVKTTaP~--~Y~VrP~~GiI~Pgesv~I~I~l~~~~p~~~ 148 (179)
.-|+.....++++|++..+ .|+-|--|.-. .+..+-..+.|.||++..+.+.+ .|.++
T Consensus 12 ~vG~d~~v~v~~~N~~~~~l~~v~~~l~~~~v~ytG~~~~~~~~~~~~~~l~p~~~~~~~~~i---~p~~y 79 (107)
T PF00927_consen 12 VVGQDFTVSVSFTNPSSEPLRNVSLNLCAFTVEYTGLTRDQFKKEKFEVTLKPGETKSVEVTI---TPSQY 79 (107)
T ss_dssp BTTSEEEEEEEEEE-SSS-EECEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE----HHSH
T ss_pred cCCCCEEEEEEEEeCCcCccccceeEEEEEEEEECCcccccEeEEEcceeeCCCCEEEEEEEE---EceeE
Confidence 3589999999999999876 56666655443 36777889999999999999987 56543
No 26
>COG3121 FimC P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=76.72 E-value=28 Score=29.58 Aligned_cols=63 Identities=13% Similarity=0.274 Sum_probs=48.8
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccC-------CCceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTT-------APKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTT-------aP~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-+.|++. -+.|+..... ..|+|.|..+.++.-.+..- ....|.|-|+.=.|+||+...|.|.+
T Consensus 28 ~v~i~~T-RiI~~~~~k~---~sl~l~N~~~~p~LvQ~wvd~~~~~~~~~~pfvvtPPv~rl~p~~~q~vRi~~ 97 (235)
T COG3121 28 GVVLGGT-RIIYPAGDKE---TSLTLRNDGNQPYLVQSWVDDGLEPEKSTVPFVVTPPVFRLEPGQEQQLRILY 97 (235)
T ss_pred eEEecce-EEEEeCCCce---eEEEEEcCCCCCEEEEEEEcCCCCCccccCCEEecCCeEEECCCCccEEEEEe
Confidence 4667773 6666644444 89999997788888774433 34569999999999999999999997
No 27
>PRK15254 fimbrial chaperone protein StdC; Provisional
Probab=76.67 E-value=37 Score=29.16 Aligned_cols=63 Identities=13% Similarity=0.193 Sum_probs=44.3
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCC-eEEEEecc--CC---CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKS-HVAFKFQT--TA---PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~-~VAFKVKT--Ta---P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.+++ .-+.|..... ...|+|.|.++. ++.-..-. .. ..-|.|-|+.--|+||+...|.|.+
T Consensus 17 ~v~l~~-TRvIy~~~~~---~~sv~v~N~~~~~p~LvQsWv~d~~~~~~~pFivtPPlfrl~p~~~~~lRI~~ 85 (239)
T PRK15254 17 AVNVDR-TRIIMDAPQK---TVAITLNNDDKTTPFLAQSWVTDADGVRTDALMALPPLQRIDAGQKSQVRITQ 85 (239)
T ss_pred eEEECc-eEEEEeCCCc---eEEEEEEeCCCCCcEEEEEEEecCCCCCcCCEEEcCCeEEECCCCceEEEEEE
Confidence 367777 4777774333 389999999863 54322211 11 1359999999999999999999986
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=75.04 E-value=22 Score=25.85 Aligned_cols=53 Identities=21% Similarity=0.246 Sum_probs=32.8
Q ss_pred CCCceEEEEEEEEcCCCCeEE-----EEeccCCCceeEecC---------CeeEeCCCCeEEEEEEe
Q 030354 88 EAGKQVRSAIKIKNTSKSHVA-----FKFQTTAPKSCFMRP---------PGAILAPGESLIATVFK 140 (179)
Q Consensus 88 ~~~k~~~s~LtL~N~s~~~VA-----FKVKTTaP~~Y~VrP---------~~GiI~Pgesv~I~I~l 140 (179)
+.++-+.-.++|+|.+++.+. |++.+.+-..|.... ..+-|.||+++...|..
T Consensus 33 ~g~~fv~v~v~v~N~~~~~~~~~~~~f~l~d~~g~~~~~~~~~~~~~~~~~~~~i~pG~~~~g~l~F 99 (123)
T PF11611_consen 33 EGNKFVVVDVTVKNNGDEPLDFSPSDFKLYDSDGNKYDPDFSASSNDNDLFSETIKPGESVTGKLVF 99 (123)
T ss_dssp --SEEEEEEEEEEE-SSS-EEEEGGGEEEE-TT--B--EEE-CCCTTTB--EEEE-TT-EEEEEEEE
T ss_pred CCCEEEEEEEEEEECCCCcEEecccceEEEeCCCCEEcccccchhccccccccEECCCCEEEEEEEE
Confidence 445667799999999998765 778877766665433 46899999999998886
No 29
>PRK15290 lfpB fimbrial chaperone protein; Provisional
Probab=74.75 E-value=22 Score=30.62 Aligned_cols=63 Identities=8% Similarity=0.154 Sum_probs=45.7
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCC-CeEEEEeccC--C-C----ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSK-SHVAFKFQTT--A-P----KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~-~~VAFKVKTT--a-P----~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.+++. -+.|+..... ..|+|+|.++ .++.--.-.. + . .-|.|-|+.--|+||+...|+|.+
T Consensus 38 gv~l~~T-RvIy~~~~~~---~sl~v~N~~~~~p~LvQsWvd~~~~~~~~~~pFivtPPlfrl~p~~~q~lRIi~ 108 (243)
T PRK15290 38 GVVIGGT-RVVYLSNNPD---KSISVFSKEEKIPYLIQAWVDPFNKEDKSKAPFTVIPPVSRLEPSQEKVLRIIH 108 (243)
T ss_pred eEEECce-EEEEeCCCce---EEEEEEeCCCCCcEEEEEEEecCCCCCcccCCEEEcCCeEEECCCCceEEEEEE
Confidence 4778884 7777753333 7999999986 4554443222 1 1 149999999999999999999986
No 30
>PRK15224 pili assembly chaperone protein SafB; Provisional
Probab=74.69 E-value=21 Score=30.64 Aligned_cols=60 Identities=13% Similarity=0.278 Sum_probs=43.7
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc----CC---CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT----TA---PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT----Ta---P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
|.++- .-+.|+...+. ..|+|.|.++.+ |-|++ .+ ..-|.|-|+.=-|+|++...|+|.+
T Consensus 30 v~l~~-TRvIy~~~~k~---~sl~v~N~~~~p--yLvQsWvd~~~~~~~~pFivtPPlfRlep~~~~~lRI~~ 96 (237)
T PRK15224 30 VKLGA-TRVIYHAGTAG---ATLSVSNPQNYP--ILVQSSVKAADKSSPAPFLVMPPLFRLEANQQSQLRIVR 96 (237)
T ss_pred EEeCc-eEEEEeCCCcE---EEEEEEcCCCCc--EEEEEEEeCCCCCccCCEEECCCeEEECCCCceEEEEEE
Confidence 45554 35666643333 789999998765 66665 11 1249999999999999999999987
No 31
>PRK15233 putative fimbrial chaperone protein SefB; Provisional
Probab=74.27 E-value=40 Score=29.27 Aligned_cols=60 Identities=17% Similarity=0.217 Sum_probs=41.8
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc----CC---CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT----TA---PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT----Ta---P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
|.++- .-+.|+.... ...|+|.|.++.+ |-|++ .. ..-|.|-|+.--|+||+...|.|.+
T Consensus 42 i~l~~-TRvIy~~~~~---~~sl~i~N~~~~p--~LvQsWvd~~~~~~~~pFiVtPPLfRLep~~~~~lRIi~ 108 (246)
T PRK15233 42 LRLGT-TRVIYKEDAP---STSFWIMNEKEYP--ILVQTQVYNDDKSSKAPFIVTPPILKVESNARTRLKVIP 108 (246)
T ss_pred EEeCc-eEEEEeCCCc---EEEEEEEcCCCCc--EEEEEEEecCCCCccCCEEECCCeEEECCCCceEEEEEE
Confidence 44444 2455553332 3789999987665 55554 11 1249999999999999999999987
No 32
>PRK15218 fimbrial chaperone protein PegB; Provisional
Probab=74.26 E-value=25 Score=29.97 Aligned_cols=60 Identities=15% Similarity=0.239 Sum_probs=43.0
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc---CCC---------ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT---TAP---------KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT---TaP---------~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
|.++- .-+.|+..... .+|+|.|.++.+ |-|++ ... ..|.|-|+.=-|+||+...|+|.+
T Consensus 20 i~l~~-TRvIy~~~~~~---~si~i~N~~~~p--yLvQsWvd~~~~~~~~~~~~~pFivtPPlfRl~p~~~~~lRI~~ 91 (226)
T PRK15218 20 IYIYG-TRIIYPAQKKD---ITVQLMNDGKRS--SLIQAWIDNGDTSLPPEKLQVPFIMTPPVIRVAANSGQQLKIKK 91 (226)
T ss_pred EEeCc-eEEEEcCCCcE---EEEEEEcCCCCc--EEEEEEEeCCCCCCCcccccCCEEECCCeEEECCCCceEEEEEE
Confidence 55555 35666643222 789999999875 44443 111 259999999999999999999986
No 33
>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=73.21 E-value=16 Score=26.82 Aligned_cols=52 Identities=27% Similarity=0.514 Sum_probs=35.9
Q ss_pred CCceEEEEEEEEcCCCCeEE-EEeccCCCcee--EecCC-eeEeCCCCeEEEEEEe
Q 030354 89 AGKQVRSAIKIKNTSKSHVA-FKFQTTAPKSC--FMRPP-GAILAPGESLIATVFK 140 (179)
Q Consensus 89 ~~k~~~s~LtL~N~s~~~VA-FKVKTTaP~~Y--~VrP~-~GiI~Pgesv~I~I~l 140 (179)
.+...+-.++..|.+..+|. |.++-..|+.| .+.|. ...|.|+..+.-.+.+
T Consensus 22 ~~~~~~i~~~f~N~s~~~it~f~~q~avpk~~~l~l~~~s~~~i~p~~~i~Q~~~v 77 (115)
T PF02883_consen 22 NPNQGRIKLTFGNKSSQPITNFSFQAAVPKSFKLQLQPPSSSTIPPGQQITQVIKV 77 (115)
T ss_dssp ETTEEEEEEEEEE-SSS-BEEEEEEEEEBTTSEEEEEESS-SSB-TTTEEEEEEEE
T ss_pred CCCEEEEEEEEEECCCCCcceEEEEEEeccccEEEEeCCCCCeeCCCCeEEEEEEE
Confidence 46778899999999988774 77776555544 55566 5599999988877765
No 34
>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=70.74 E-value=26 Score=25.17 Aligned_cols=48 Identities=23% Similarity=0.300 Sum_probs=27.0
Q ss_pred EEEEEEEEcCCCCeEEEEeccCCCceeEec-------------------CCeeEeCCCCeEEEEEEe
Q 030354 93 VRSAIKIKNTSKSHVAFKFQTTAPKSCFMR-------------------PPGAILAPGESLIATVFK 140 (179)
Q Consensus 93 ~~s~LtL~N~s~~~VAFKVKTTaP~~Y~Vr-------------------P~~GiI~Pgesv~I~I~l 140 (179)
+.-.|+|+|.+++.|-+.+.+-.---|.|+ -..=.|+|||+....+.+
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 345677777777777666555444444444 223468899999888886
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=66.59 E-value=25 Score=25.00 Aligned_cols=44 Identities=18% Similarity=0.124 Sum_probs=31.2
Q ss_pred EEEEEEEcCCCCeEEEEeccCCCceeE-ecCCeeEeCCCCeEEEEEEe
Q 030354 94 RSAIKIKNTSKSHVAFKFQTTAPKSCF-MRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 94 ~s~LtL~N~s~~~VAFKVKTTaP~~Y~-VrP~~GiI~Pgesv~I~I~l 140 (179)
.-.|+|.|.....+.|.|...+ |. -.|-.=.|.||+++.+.+-+
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 3689999999999999998722 22 22334456668888877764
No 36
>PRK15253 putative fimbrial assembly chaperone protein StcB; Provisional
Probab=66.31 E-value=46 Score=28.67 Aligned_cols=61 Identities=16% Similarity=0.279 Sum_probs=44.1
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc---CC-----C----ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT---TA-----P----KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT---Ta-----P----~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
-|.++- .-+.|+..... ..|+|.|.++.+ |-|++ .. | .-|.|-|+.=-|+|++...|.|..
T Consensus 34 gv~l~~-TRvIy~~~~k~---~sv~i~N~~~~p--yLvQsWvd~~~~~~~~~~~~~pFivtPPlfRl~p~~~~~lRI~~ 106 (242)
T PRK15253 34 GIVIYG-TRVIYPAEKKE---VVVQLVNQGEQA--SLVQSWIDDGNTSLPPEKIQVPFMLTPPVARVAAESGQQIKIKK 106 (242)
T ss_pred eEEeCc-eEEEEeCCCce---EEEEEEcCCCCc--EEEEEEEECCCCCCCcccccCCEEECCCeEEECCCCceEEEEEE
Confidence 456665 36676643322 789999999875 44443 11 1 249999999999999999999986
No 37
>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=66.22 E-value=45 Score=23.76 Aligned_cols=51 Identities=29% Similarity=0.518 Sum_probs=39.2
Q ss_pred CceEEEEEEEEcCCCCeE-EEEeccCCCceeEec--CCee-EeCCCCeEEEEEEe
Q 030354 90 GKQVRSAIKIKNTSKSHV-AFKFQTTAPKSCFMR--PPGA-ILAPGESLIATVFK 140 (179)
Q Consensus 90 ~k~~~s~LtL~N~s~~~V-AFKVKTTaP~~Y~Vr--P~~G-iI~Pgesv~I~I~l 140 (179)
+....-.+...|.+..+| .|.++-..|+-+.++ |..| .|.||+.+...+.+
T Consensus 17 ~~~~~i~~~~~N~s~~~it~f~~~~avpk~~~l~l~~~s~~~l~p~~~i~q~~~i 71 (104)
T smart00809 17 PGLIRITLTFTNKSPSPITNFSFQAAVPKSLKLQLQPPSSPTLPPGGQITQVLKV 71 (104)
T ss_pred CCeEEEEEEEEeCCCCeeeeEEEEEEcccceEEEEcCCCCCccCCCCCEEEEEEE
Confidence 346778999999998877 488888788777655 6654 89999987766665
No 38
>PRK15285 putative fimbrial chaperone protein StfD; Provisional
Probab=66.15 E-value=86 Score=27.15 Aligned_cols=62 Identities=15% Similarity=0.193 Sum_probs=41.7
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCC-eEEEE--eccCCC----ceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKS-HVAFK--FQTTAP----KSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~-~VAFK--VKTTaP----~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
|.++- .-+.|+..... ..|+|+|.++. ++.-. |..... ..|.|-|+.--|+||+...|.|..
T Consensus 27 v~l~~-TRVIy~~~~~~---~sv~i~N~~~~~p~LvQsWvd~~~~~~~~~pFiVtPPlfRl~p~~~~~lRI~~ 95 (250)
T PRK15285 27 IAPDR-TRLVFRGEDKS---ISVDLKNANSKLPYLAQSWVEDEKGVKITSPLIVVPPVQRIEPSAIGQVKIQG 95 (250)
T ss_pred EEeCc-cEEEEcCCCce---EEEEEEeCCCCCcEEEEEEeeCCCCCcccCCEEEcCCeEEECCCCceEEEEEE
Confidence 44554 36666643333 78999999864 43222 211121 139999999999999999999986
No 39
>PRK15274 putative periplasmic fimbrial chaperone protein SteC; Provisional
Probab=64.97 E-value=90 Score=27.19 Aligned_cols=64 Identities=13% Similarity=0.105 Sum_probs=43.4
Q ss_pred CcEEEcCCCceEeecCCCceEEEEEEEEcCCCC-eEEEEec--cCC----CceeEecCCeeEeCCCCeEEEEEEe
Q 030354 73 RRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKS-HVAFKFQ--TTA----PKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~-~VAFKVK--TTa----P~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
--|.++= .-+.|+.... ...|+|.|.++. ++.-..- ... ..-|.|-|+.--|+||+...|.|..
T Consensus 26 Agi~l~~-TRvIy~e~~~---~~sv~v~N~~~~~p~LVQsWvdd~~~~~~~~pFivtPPLfRlep~~~q~lRI~~ 96 (257)
T PRK15274 26 SAIVPDR-TRVIFNGNEN---SITVTLKNGNATLPYLAQAWLEDDKFAKDTRYFTALPPLQRIEPKSDGQVKVQP 96 (257)
T ss_pred eeEEeCc-eEEEEeCCCc---eEEEEEEeCCCCCcEEEEEEccCCCCCcccCCEEEcCCeEEECCCCceEEEEEE
Confidence 3455665 3666664333 379999999865 4332221 111 1249999999999999999999986
No 40
>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=64.92 E-value=7 Score=26.33 Aligned_cols=43 Identities=14% Similarity=0.083 Sum_probs=27.5
Q ss_pred EEEEcCCCCeEEEE-eccCCCceeEecCCeeEeCCCCeEEEEEE
Q 030354 97 IKIKNTSKSHVAFK-FQTTAPKSCFMRPPGAILAPGESLIATVF 139 (179)
Q Consensus 97 LtL~N~s~~~VAFK-VKTTaP~~Y~VrP~~GiI~Pgesv~I~I~ 139 (179)
|+++|+|..+|.|- ++....++=.--...+.|.|.++..+.+.
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 44443443223344449999999988775
No 41
>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=61.20 E-value=29 Score=32.20 Aligned_cols=67 Identities=19% Similarity=0.234 Sum_probs=45.2
Q ss_pred CCcEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeE----------------------ecCCeeEeC
Q 030354 72 RRRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCF----------------------MRPPGAILA 129 (179)
Q Consensus 72 ~~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~----------------------VrP~~GiI~ 129 (179)
...++++-. .-+|. .+|+..+.+++++|.++++|-..=-+|+.-+|. |.|+ +=|.
T Consensus 246 ~~~V~~~v~-~A~Y~-vpgR~l~~~l~VtN~g~~pv~LgeF~tA~vrFln~~v~~~~~~~P~~l~A~~gL~vs~~-~pI~ 322 (381)
T PF04744_consen 246 PNSVKVKVT-DATYR-VPGRTLTMTLTVTNNGDSPVRLGEFNTANVRFLNPDVPTDDPDYPDELLAERGLSVSDN-SPIA 322 (381)
T ss_dssp -SSEEEEEE-EEEEE-SSSSEEEEEEEEEEESSS-BEEEEEESSS-EEE-TTT-SS-S---TTTEETT-EEES---S-B-
T ss_pred CCceEEEEe-ccEEe-cCCcEEEEEEEEEcCCCCceEeeeEEeccEEEeCcccccCCCCCchhhhccCcceeCCC-CCcC
Confidence 334777774 66666 678999999999999999998875555555553 2332 3589
Q ss_pred CCCeEEEEEEee
Q 030354 130 PGESLIATVFKF 141 (179)
Q Consensus 130 Pgesv~I~I~l~ 141 (179)
|||+.+|+|...
T Consensus 323 PGETrtl~V~a~ 334 (381)
T PF04744_consen 323 PGETRTLTVEAQ 334 (381)
T ss_dssp TT-EEEEEEEEE
T ss_pred CCceEEEEEEee
Confidence 999999999874
No 42
>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=60.39 E-value=7.5 Score=31.68 Aligned_cols=32 Identities=31% Similarity=0.424 Sum_probs=25.8
Q ss_pred EEeccCCCceeEecCCeeE--eCCCCeEEEEEEe
Q 030354 109 FKFQTTAPKSCFMRPPGAI--LAPGESLIATVFK 140 (179)
Q Consensus 109 FKVKTTaP~~Y~VrP~~Gi--I~Pgesv~I~I~l 140 (179)
|||.-=+-+.|++.|.-++ |.||+++.|.+.-
T Consensus 69 f~i~hinGDl~kl~Pt~~F~gl~~Ges~~I~~~~ 102 (164)
T PF03173_consen 69 FKITHINGDLHKLTPTAGFKGLAPGESLEIPFVG 102 (164)
T ss_dssp EEEEE-STTEEEEEE-TT---B-TTEEEEEEEEE
T ss_pred eEEEEEcCeEEEEeECCCCCccCCCCEEEEEEEc
Confidence 8899889999999999997 8999999999873
No 43
>PRK15308 putative fimbrial protein TcfA; Provisional
Probab=58.26 E-value=54 Score=28.24 Aligned_cols=65 Identities=12% Similarity=0.187 Sum_probs=46.9
Q ss_pred CcEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEecc---CCC---------------ceeEecCCeeEeCCCCeE
Q 030354 73 RRLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQT---TAP---------------KSCFMRPPGAILAPGESL 134 (179)
Q Consensus 73 ~lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKT---TaP---------------~~Y~VrP~~GiI~Pgesv 134 (179)
--|.|.|- .+.+.. +.+....++|+|.++++..++|+. ++| ..-.+-|+.-+|.||++.
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 34778884 665543 323348999999999877766542 121 246788999999999999
Q ss_pred EEEEEe
Q 030354 135 IATVFK 140 (179)
Q Consensus 135 ~I~I~l 140 (179)
.|.|..
T Consensus 93 ~IRli~ 98 (234)
T PRK15308 93 TVRVIS 98 (234)
T ss_pred EEEEEE
Confidence 999875
No 44
>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=55.55 E-value=67 Score=26.44 Aligned_cols=52 Identities=21% Similarity=0.294 Sum_probs=41.0
Q ss_pred CCCceEEEEEEEEcCCCCeEEEEeccCC----CceeEecCC-----eeEeCCCCeEEEEEEe
Q 030354 88 EAGKQVRSAIKIKNTSKSHVAFKFQTTA----PKSCFMRPP-----GAILAPGESLIATVFK 140 (179)
Q Consensus 88 ~~~k~~~s~LtL~N~s~~~VAFKVKTTa----P~~Y~VrP~-----~GiI~Pgesv~I~I~l 140 (179)
..|+++.-.++|.|..+. -||.|+-++ ++.|.+.-- ...|+||+.+.-.+++
T Consensus 35 v~g~~v~V~~~iyN~G~~-~A~dV~l~D~~fp~~~F~lvsG~~s~~~~~i~pg~~vsh~~vv 95 (181)
T PF05753_consen 35 VEGEDVTVTYTIYNVGSS-AAYDVKLTDDSFPPEDFELVSGSLSASWERIPPGENVSHSYVV 95 (181)
T ss_pred cCCcEEEEEEEEEECCCC-eEEEEEEECCCCCccccEeccCceEEEEEEECCCCeEEEEEEE
Confidence 468899999999999987 689999877 356654322 4689999999888776
No 45
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=53.39 E-value=1.2e+02 Score=24.42 Aligned_cols=58 Identities=17% Similarity=0.253 Sum_probs=38.3
Q ss_pred eEeecCC----CceEEEEEEEEcCCCCeE-EEEeccCC-CceeEec--CCeeEeCCCCeEEEEEEe
Q 030354 83 LYFPYEA----GKQVRSAIKIKNTSKSHV-AFKFQTTA-PKSCFMR--PPGAILAPGESLIATVFK 140 (179)
Q Consensus 83 L~F~~~~----~k~~~s~LtL~N~s~~~V-AFKVKTTa-P~~Y~Vr--P~~GiI~Pgesv~I~I~l 140 (179)
..|.+++ ...+.-.|+++|.++..+ --+|.... +.--+|+ |..+.|.||+++.+.+-.
T Consensus 73 Y~F~RqP~~~s~~mvsIql~ftN~s~~~i~~I~i~~k~l~~g~~i~~F~~I~~L~pg~s~t~~lgI 138 (145)
T PF14796_consen 73 YRFSRQPSLYSPSMVSIQLTFTNNSDEPIKNIHIGEKKLPAGMRIHEFPEIESLEPGASVTVSLGI 138 (145)
T ss_pred EEEccCCcCCCCCcEEEEEEEEecCCCeecceEECCCCCCCCcEeeccCcccccCCCCeEEEEEEE
Confidence 4555533 456778899999999755 23343333 2233444 889999999998877754
No 46
>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=48.86 E-value=86 Score=22.78 Aligned_cols=50 Identities=14% Similarity=0.264 Sum_probs=34.1
Q ss_pred CceEEEEEEEEcCCCC--eEEEEeccCCCceeEecCC-----eeEeCCCCeEEEEEE
Q 030354 90 GKQVRSAIKIKNTSKS--HVAFKFQTTAPKSCFMRPP-----GAILAPGESLIATVF 139 (179)
Q Consensus 90 ~k~~~s~LtL~N~s~~--~VAFKVKTTaP~~Y~VrP~-----~GiI~Pgesv~I~I~ 139 (179)
+......+.|+|.++. .+.||+-==+.+-+.|.|. .=+|.+++++.|.-.
T Consensus 23 ~g~~~~~~~l~N~~~~~~~l~Yrf~WyD~~G~~v~~~~~~w~~~~l~~~~~~~l~~~ 79 (94)
T PF07233_consen 23 NGLLRAQATLSNKSSKPLTLQYRFYWYDKQGLEVDPEQSPWQSLTLPGGQTVTLSAV 79 (94)
T ss_dssp CCEEEEEEEEEE-SSS-EEEEEEEEEE-TTS-EE--TT---EEEEE-TT-EEEEEEE
T ss_pred CCeEEEEEEEEECCCCcEEEEEEEEEECCCCCCcCCCCCCCEEEEEcCCCEEEEEEE
Confidence 7777899999999976 5889987767777788877 447888888877766
No 47
>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=48.61 E-value=53 Score=22.52 Aligned_cols=53 Identities=21% Similarity=0.177 Sum_probs=34.0
Q ss_pred CCCceEEEEEEEEcCCCC-eEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEe
Q 030354 88 EAGKQVRSAIKIKNTSKS-HVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 88 ~~~k~~~s~LtL~N~s~~-~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
..|+..+-.++|+|.... .=.|+|+-...+.-.-.-..+-|.||++..+.+.+
T Consensus 16 ~~g~~~~i~~~V~N~G~~~~~~~~v~~~~~~~~~~~~~i~~L~~g~~~~v~~~~ 69 (101)
T PF07705_consen 16 VPGEPVTITVTVKNNGTADAENVTVRLYLDGNSVSTVTIPSLAPGESETVTFTW 69 (101)
T ss_dssp ETTSEEEEEEEEEE-SSS-BEEEEEEEEETTEEEEEEEESEB-TTEEEEEEEEE
T ss_pred cCCCEEEEEEEEEECCCCCCCCEEEEEEECCceeccEEECCcCCCcEEEEEEEE
Confidence 358888899999999765 33566553322222222223789999999999987
No 48
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=48.22 E-value=1e+02 Score=22.20 Aligned_cols=53 Identities=21% Similarity=0.379 Sum_probs=34.4
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l 140 (179)
...+|. +|... .|+.+ .|+++|.....-.|-+..-. -...|.||++..++++-
T Consensus 30 ~~f~P~-~i~v~--~G~~v--~l~~~N~~~~~h~~~i~~~~--------~~~~l~~g~~~~~~f~~ 82 (104)
T PF13473_consen 30 FGFSPS-TITVK--AGQPV--TLTFTNNDSRPHEFVIPDLG--------ISKVLPPGETATVTFTP 82 (104)
T ss_dssp EEEES--EEEEE--TTCEE--EEEEEE-SSS-EEEEEGGGT--------EEEEE-TT-EEEEEEEE
T ss_pred CeEecC-EEEEc--CCCeE--EEEEEECCCCcEEEEECCCc--------eEEEECCCCEEEEEEcC
Confidence 378885 66654 67754 48899999888888877711 12579999999999853
No 49
>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=45.42 E-value=50 Score=24.09 Aligned_cols=48 Identities=19% Similarity=0.398 Sum_probs=31.7
Q ss_pred EEEEEEEEcCCCCeE-----EEEec-------------cCCCceeEecCC--eeEeCCCCeEEEEEEe
Q 030354 93 VRSAIKIKNTSKSHV-----AFKFQ-------------TTAPKSCFMRPP--GAILAPGESLIATVFK 140 (179)
Q Consensus 93 ~~s~LtL~N~s~~~V-----AFKVK-------------TTaP~~Y~VrP~--~GiI~Pgesv~I~I~l 140 (179)
....|+|+|.+...| .|.+. +..-..|.|+|. .+.|+||+++.+-+..
T Consensus 15 f~~~v~v~N~~~~~i~~W~v~~~~~~~~~i~~~Wna~~s~~g~~~~v~~~~wn~~i~~G~s~~~Gf~~ 82 (101)
T PF00553_consen 15 FQGEVTVTNNGSSPINGWTVTFTFPSGQTITSSWNATVSQSGNTVTVTNPSWNGTIAPGGSVTFGFQA 82 (101)
T ss_dssp EEEEEEEEESSSSTEESEEEEEEESTTEEEEEEESCEEEEETTEEEEEESSTCSEEEESEEEEEEEEE
T ss_pred eEEEEEEEECCCCccCCEEEEEEeCCCCEEeeeeccEEEecCCEEEEEcCCcCcccCCCCeEEEEEEE
Confidence 446788888776653 33322 112357888876 4799999999887765
No 50
>COG3354 FlaG Putative archaeal flagellar protein G [Cell motility and secretion]
Probab=44.49 E-value=85 Score=25.64 Aligned_cols=63 Identities=25% Similarity=0.271 Sum_probs=46.2
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEE-----------eccCCCceeEecCCeeE-eCCCCeEEEEEEe
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFK-----------FQTTAPKSCFMRPPGAI-LAPGESLIATVFK 140 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFK-----------VKTTaP~~Y~VrP~~Gi-I~Pgesv~I~I~l 140 (179)
+.=+| ..+...+..| ..+-++-|||+.++.++|- +.+-+.-.|..-+..++ |.||+--. +|++
T Consensus 54 IIndP-g~i~~~~~~g-~~t~t~yiKNtG~~~~~fd~~sitVliDG~iv~~a~~~~~~~~gs~i~l~PG~Vg~-ev~v 128 (154)
T COG3354 54 IINDP-GQIPYVGTDG-PYTYTFYIKNTGSDSIAFDNTSITVLIDGNIVTPAYVTFTSVNGSSIRLSPGQVGR-EVTV 128 (154)
T ss_pred EecCC-CCCccccCCC-ceEEEEEEecCCCcccccCCCeEEEEEcCcEeccceEEEEecCCCeeEecCCceee-EEEe
Confidence 44456 4665554433 3458899999999999996 56777778888899999 99999874 4443
No 51
>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=43.21 E-value=2.9e+02 Score=25.94 Aligned_cols=67 Identities=18% Similarity=0.244 Sum_probs=45.1
Q ss_pred cEEEcCCCc-eEeecCCCc-eEEEEEEEEcCCCCeEEEEeccCCCceeEec-C-CeeEeCCCCeEEEEEEe
Q 030354 74 RLKLDPANK-LYFPYEAGK-QVRSAIKIKNTSKSHVAFKFQTTAPKSCFMR-P-PGAILAPGESLIATVFK 140 (179)
Q Consensus 74 lL~I~P~~e-L~F~~~~~k-~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~Vr-P-~~GiI~Pgesv~I~I~l 140 (179)
.|.|..... |+...++|. +-..+++|.|.+..+..|.++........+. + +.=.|+||+..++.|++
T Consensus 327 ~~~v~r~r~~l~~~~~~g~i~N~Y~~~i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v~~g~~~~~~v~v 397 (434)
T TIGR02745 327 DLNVLRDRNLLYVRNSDGVVENTYTLKILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHVKAGEKVKLPVFL 397 (434)
T ss_pred EEEEEecCCcceEECCCCcEEEEEEEEEEECCCCCEEEEEEEecCCCcEEEcCCceEEECCCCEEEEEEEE
Confidence 455555433 554445553 3458999999999988888876654433332 2 24489999999988887
No 52
>smart00637 CBD_II CBD_II domain.
Probab=37.88 E-value=1.4e+02 Score=21.10 Aligned_cols=24 Identities=17% Similarity=0.129 Sum_probs=18.4
Q ss_pred ceeEecCC--eeEeCCCCeEEEEEEe
Q 030354 117 KSCFMRPP--GAILAPGESLIATVFK 140 (179)
Q Consensus 117 ~~Y~VrP~--~GiI~Pgesv~I~I~l 140 (179)
..|.++|. .+.|.||+++.+-+..
T Consensus 50 ~~~~~~~~~wn~~i~~G~s~~~gf~~ 75 (92)
T smart00637 50 GHVTATNASWNGTIAPGGSVSFGFQG 75 (92)
T ss_pred CEEEEecCccccccCCCCEEEEEEEe
Confidence 46888865 4799999998876653
No 53
>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=36.42 E-value=59 Score=21.58 Aligned_cols=28 Identities=25% Similarity=0.411 Sum_probs=16.6
Q ss_pred CceEeecCCCceEEEEEEEEcCCCCeEEEEe
Q 030354 81 NKLYFPYEAGKQVRSAIKIKNTSKSHVAFKF 111 (179)
Q Consensus 81 ~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKV 111 (179)
.-..|. .|. +...-++...++..||||+
T Consensus 44 ~C~~y~--~~~-i~~v~~~~~~~~~~VA~K~ 71 (71)
T PF08277_consen 44 KCYLYN--YGS-ISTVQKTDSSSGNKVAFKI 71 (71)
T ss_pred CEEEEE--cCC-EEEEEEeecCCCeEEEEEC
Confidence 344444 344 4344455555668999996
No 54
>COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]
Probab=35.34 E-value=63 Score=25.68 Aligned_cols=33 Identities=27% Similarity=0.469 Sum_probs=28.2
Q ss_pred cEEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEE
Q 030354 74 RLKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFK 110 (179)
Q Consensus 74 lL~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFK 110 (179)
-..|.| .++|.+++|++ .++-|..++.+.+-||
T Consensus 95 ~~~i~P--~vRF~Ge~gEq--~TlFl~DP~gN~lEfK 127 (138)
T COG3565 95 PFHIPP--KVRFKGEPGEQ--RTLFLFDPSGNALEFK 127 (138)
T ss_pred CcccCc--eEEecCCccce--EEEEEECCCCCeeeee
Confidence 344555 89999999997 7899999999999998
No 55
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=30.45 E-value=1e+02 Score=26.52 Aligned_cols=42 Identities=14% Similarity=0.077 Sum_probs=28.2
Q ss_pred EEEEEcCCCCeEEEE-eccCCCceeEecCCeeEeCCCCeEEEEE
Q 030354 96 AIKIKNTSKSHVAFK-FQTTAPKSCFMRPPGAILAPGESLIATV 138 (179)
Q Consensus 96 ~LtL~N~s~~~VAFK-VKTTaP~~Y~VrP~~GiI~Pgesv~I~I 138 (179)
.|+++|++..++.|- ++....+ -.+....|+|.|+++..+.+
T Consensus 177 ~l~v~Nptpyyitl~~l~~~~~~-~~~~~~~~mv~P~s~~~~~l 219 (253)
T PRK15249 177 GIVIVNPQPWFASLSNLNVKVNG-ASYNLDADMIAPFSSQTWWL 219 (253)
T ss_pred EEEEECCCceEEEeeeeeeccCC-eecCCCCceECCCCccEEEc
Confidence 499999999988775 3321122 12223457899999988865
No 56
>PRK15295 fimbrial assembly chaperone SthB; Provisional
Probab=29.84 E-value=1.3e+02 Score=25.42 Aligned_cols=50 Identities=12% Similarity=0.224 Sum_probs=33.8
Q ss_pred CceEeecCCCceEEEEEEEEcCCCCeEEEE-eccCCCceeEecCCeeEeCCCCeEEEEEE
Q 030354 81 NKLYFPYEAGKQVRSAIKIKNTSKSHVAFK-FQTTAPKSCFMRPPGAILAPGESLIATVF 139 (179)
Q Consensus 81 ~eL~F~~~~~k~~~s~LtL~N~s~~~VAFK-VKTTaP~~Y~VrP~~GiI~Pgesv~I~I~ 139 (179)
..|.|....+ .|+|+|++..+|.|- ++... +. +. ..|.|.|+++..+.+-
T Consensus 148 ~~L~~~~~~~-----~l~v~NptPyyitl~~l~~~~-~~--~~-~~~mI~P~s~~~~~~~ 198 (226)
T PRK15295 148 QQLKWQTAGD-----VITVNNPTPYYMNFASVTLNS-HE--VK-SATFVPPKSSASFKLG 198 (226)
T ss_pred hccEEEEcCC-----EEEEECCCceEEEEEEEEECC-cc--cC-CCceECCCCccEEEcc
Confidence 4666764322 399999999988764 55432 22 22 2589999999888753
No 57
>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=29.69 E-value=2.1e+02 Score=20.38 Aligned_cols=32 Identities=34% Similarity=0.443 Sum_probs=23.8
Q ss_pred eeEeCCCCeEEEEEEeeccCCCCCCCCCCCCCCCeEEEEE
Q 030354 125 GAILAPGESLIATVFKFVELPENNEKPMYQKSRDKFKIIS 164 (179)
Q Consensus 125 ~GiI~Pgesv~I~I~l~~~~p~~~e~p~~~k~kDKFlVqs 164 (179)
...|.||++..+++.+ +.| .-....|+|.|..
T Consensus 54 ~~~~~pg~~~~a~l~l--~~p------l~~~~gdrfilR~ 85 (97)
T cd04094 54 RDELAPGEEALAQLRL--EEP------LVALRGDRFILRS 85 (97)
T ss_pred ccccCCCCEEEEEEEE--CCc------EeecCCCeEEEee
Confidence 4578999999999997 233 3345679999964
No 58
>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=27.39 E-value=1.7e+02 Score=18.69 Aligned_cols=64 Identities=14% Similarity=0.238 Sum_probs=39.4
Q ss_pred EEEcCCCceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeEec-CCee---EeCCCCeEEEEEE
Q 030354 75 LKLDPANKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMR-PPGA---ILAPGESLIATVF 139 (179)
Q Consensus 75 L~I~P~~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~Vr-P~~G---iI~Pgesv~I~I~ 139 (179)
|-|-|+ .|.+....+....++|+-.=-....+-+.+++-.-....+. +... .+.+|+.+.|.+.
T Consensus 1 l~iRPE-~i~l~~~~~~~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~G~~v~l~~~ 68 (75)
T PF08402_consen 1 LGIRPE-DIRLSPEGENRLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQRDSPLEPGDEVRLSWD 68 (75)
T ss_dssp EEE-GG-GEEEESSTTTEEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG-TTT--TTSEEEEEEE
T ss_pred CEECcc-eeEEECCCCCeEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccccCCCCCCCEEEEEEC
Confidence 346674 77775323345666666655567788888888777664443 4444 7899999888875
No 59
>PRK15246 fimbrial assembly chaperone StbE; Provisional
Probab=25.79 E-value=1.5e+02 Score=25.24 Aligned_cols=49 Identities=22% Similarity=0.320 Sum_probs=31.7
Q ss_pred CceEeecCCCceEEEEEEEEcCCCCeEEEEeccCCCceeEecCCeeEeCCCCeEEEEE
Q 030354 81 NKLYFPYEAGKQVRSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATV 138 (179)
Q Consensus 81 ~eL~F~~~~~k~~~s~LtL~N~s~~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I 138 (179)
..|.|....+ .|++.|+|..+|.|---.-..+. + ...+|.|.++..+.+
T Consensus 144 ~~L~~~~~~~-----~l~v~NpTPyyvtl~~l~~~~~~--~--~~~mi~P~s~~~~~~ 192 (233)
T PRK15246 144 KKLRFIAKEN-----TIRIVNPTSWYMSLTLTMDNKKS--I--GDIMVAPKTALDVPL 192 (233)
T ss_pred hccEEEEcCC-----EEEEECCCCcEEEEEeEEECCcc--c--CcceECCCCccEEEc
Confidence 4677774322 39999999999988622222222 2 245899998887764
No 60
>PF09640 DUF2027: Domain of unknown function (DUF2027); InterPro: IPR018598 This protein domain is of unknown function. though putatively involved in DNA mismatch repair. It is associated with IPR002625 from INTERPRO. ; PDB: 2HUH_A.
Probab=25.16 E-value=2.4e+02 Score=23.30 Aligned_cols=69 Identities=17% Similarity=0.264 Sum_probs=48.8
Q ss_pred EEEEEEEcCCCCeEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEeeccCCCCCCCCCCCCCCCeEEEEEEEeCCCccc
Q 030354 94 RSAIKIKNTSKSHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKFVELPENNEKPMYQKSRDKFKIISMKVKADVDY 173 (179)
Q Consensus 94 ~s~LtL~N~s~~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l~~~~p~~~e~p~~~k~kDKFlVqs~~v~~~~d~ 173 (179)
+-..-|-|-|+..+.|-.-+...+.|.+| ..|.|+|+..+-|.-+- ... ...-.+.-||.+.-..++-|
T Consensus 19 ~fE~YlVNDSNYy~~y~y~~~~g~~w~lr-s~G~iEPNtKl~ieef~---~~e-------LN~~~~v~vQ~iAyK~~K~f 87 (162)
T PF09640_consen 19 RFECYLVNDSNYYLHYTYLTAEGNSWTLR-SAGEIEPNTKLFIEEFS---KEE-------LNDLERVAVQLIAYKKDKTF 87 (162)
T ss_dssp -EEEEEEE-SSSEEEEEEEEEETTEEEEE-EEEEE-TTEEEEEEEE----GGG-------GGG-SSEEEEEEEE-SSS--
T ss_pred ceEEEEEecCccEEEEEEEeccCCeEEEE-ecceECCCceeehhhcC---HHH-------hhccceeEEEEEEEcCCCcc
Confidence 46678999999999999999888899998 68999999999987763 111 22356778888877776644
No 61
>smart00605 CW CW domain.
Probab=24.71 E-value=1.8e+02 Score=20.71 Aligned_cols=33 Identities=36% Similarity=0.547 Sum_probs=18.6
Q ss_pred CceEeecCCCceEEEEEEEEcC-CCCeEEEEeccCCCc
Q 030354 81 NKLYFPYEAGKQVRSAIKIKNT-SKSHVAFKFQTTAPK 117 (179)
Q Consensus 81 ~eL~F~~~~~k~~~s~LtL~N~-s~~~VAFKVKTTaP~ 117 (179)
....|.+ |. + ..|+-.+. .+..||||+.++.+.
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 3445555 33 1 33444444 356899999865543
No 62
>COG3121 FimC P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=24.65 E-value=1.8e+02 Score=24.62 Aligned_cols=51 Identities=14% Similarity=0.102 Sum_probs=35.0
Q ss_pred ceEeecCCCceEEEEEEEEcCCCCeEEEE--eccCCCceeEecCCeeEeCCCCeEEEEEE
Q 030354 82 KLYFPYEAGKQVRSAIKIKNTSKSHVAFK--FQTTAPKSCFMRPPGAILAPGESLIATVF 139 (179)
Q Consensus 82 eL~F~~~~~k~~~s~LtL~N~s~~~VAFK--VKTTaP~~Y~VrP~~GiI~Pgesv~I~I~ 139 (179)
.|.|.... ..|+++|++..+|.|- .-...-++.- -..+.|.|+++..+.+-
T Consensus 157 ~L~~~~~~-----~~l~v~Nptpy~vtl~~~~l~~~~~~~~--~~~~mv~P~s~~~~~l~ 209 (235)
T COG3121 157 KLTWSRSG-----NLLTVKNPTPYYVTLANLTLNVGGRKLG--LNSGMVAPFSTRQFPLP 209 (235)
T ss_pred eEEEEEcC-----CEEEEECCCCcEEEEEEEEEeeCceecC--CCcceECCCccceeecC
Confidence 55555333 5799999999999887 3333333322 67889999999885543
No 63
>PRK09926 putative chaperone protein EcpD; Provisional
Probab=22.94 E-value=2.3e+02 Score=24.17 Aligned_cols=55 Identities=15% Similarity=0.216 Sum_probs=34.3
Q ss_pred CceEeecCCCceEEEEEEEEcCCCCeEEEE-eccC-CCceeEecCCeeEeCCCCeEEEEE
Q 030354 81 NKLYFPYEAGKQVRSAIKIKNTSKSHVAFK-FQTT-APKSCFMRPPGAILAPGESLIATV 138 (179)
Q Consensus 81 ~eL~F~~~~~k~~~s~LtL~N~s~~~VAFK-VKTT-aP~~Y~VrP~~GiI~Pgesv~I~I 138 (179)
..|.|....+.. ...|+++|++..++.|- ++-. +.+.+.+ ..+.|.|+++..+.+
T Consensus 160 ~~L~~~~~~~~~-~~~L~v~Nptpy~itl~~l~~~~~g~~~~~--~~~mi~P~s~~~~~l 216 (246)
T PRK09926 160 LALKWSWAGSEG-KASLRVTNPTPYYVSFSSGDLEAGGKRYPV--DSKMIAPFSDESMKV 216 (246)
T ss_pred hccEEEEecCCC-eEEEEEECCCceEEEEEeeeeecCCeeccc--CcceECCCCcceEec
Confidence 367776533221 24599999999988764 4322 2233333 347899999888765
No 64
>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=22.78 E-value=1e+02 Score=25.81 Aligned_cols=26 Identities=31% Similarity=0.530 Sum_probs=21.6
Q ss_pred CeEEEEeccCCCceeEecCCeeEeCCCCeEEEEEEee
Q 030354 105 SHVAFKFQTTAPKSCFMRPPGAILAPGESLIATVFKF 141 (179)
Q Consensus 105 ~~VAFKVKTTaP~~Y~VrP~~GiI~Pgesv~I~I~l~ 141 (179)
.+|+||+ |...-|.||+++++++...
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 4778877 7777899999999999764
No 65
>PRK15192 fimbrial chaperone BcfG; Provisional
Probab=22.45 E-value=1.9e+02 Score=24.69 Aligned_cols=38 Identities=11% Similarity=0.180 Sum_probs=26.3
Q ss_pred EEEEcCCCCeEEEE-eccCCCceeEecCCeeEeCCCCeEEEEE
Q 030354 97 IKIKNTSKSHVAFK-FQTTAPKSCFMRPPGAILAPGESLIATV 138 (179)
Q Consensus 97 LtL~N~s~~~VAFK-VKTTaP~~Y~VrP~~GiI~Pgesv~I~I 138 (179)
|++.|+|..+|.|. ++-. .+. +. ..+.|+|.++..+.+
T Consensus 164 l~v~NpTPyyvtl~~l~v~-~~~--~~-~~~miaPfs~~~~~~ 202 (234)
T PRK15192 164 ATVRNPTPYYVTLFLLRAN-ERA--QD-NAGVVAPFATRQTDW 202 (234)
T ss_pred EEEECCCCcEEEEEeEEEc-Ccc--cC-CCceECCCCccEEec
Confidence 99999999998775 3322 221 22 346899999887765
No 66
>PRK09918 putative fimbrial chaperone protein; Provisional
Probab=21.07 E-value=2.3e+02 Score=23.92 Aligned_cols=50 Identities=24% Similarity=0.342 Sum_probs=32.2
Q ss_pred ceEeecCCCceEEEEEEEEcCCCCeEEEE-e-ccC-CCceeEecCCeeEeCCCCeEEEEE
Q 030354 82 KLYFPYEAGKQVRSAIKIKNTSKSHVAFK-F-QTT-APKSCFMRPPGAILAPGESLIATV 138 (179)
Q Consensus 82 eL~F~~~~~k~~~s~LtL~N~s~~~VAFK-V-KTT-aP~~Y~VrP~~GiI~Pgesv~I~I 138 (179)
.|.|... | ..|+++|++..++-|- + +.. +.+.+.+ ..|.|.|+++..+.+
T Consensus 147 ~l~~~~~-~----~~l~v~N~~p~~i~l~~l~~~~~~g~~~~~--~~~~v~P~s~~~~~l 199 (230)
T PRK09918 147 LLVWSIS-G----NNLVVSNPSPYVVRLGQQVILLPSGKVVAL--PKPYILPGESLTVAI 199 (230)
T ss_pred ccEEEEe-C----CEEEEECCCCEEEEEeccEEEccCCceecc--CCceECCCceEEEEc
Confidence 4666543 2 2499999999988664 2 221 3333333 348999999998875
No 67
>PRK06655 flgD flagellar basal body rod modification protein; Reviewed
Probab=20.32 E-value=5.1e+02 Score=21.97 Aligned_cols=82 Identities=11% Similarity=0.107 Sum_probs=55.6
Q ss_pred CcccceeeecCCCCCcEEEcCCCceEeecCCCceE-EEEEEEEcCCCCeEE-EEeccCCCceeEe----cCCeeEeCCCC
Q 030354 59 SSVSSVARSLLPKRRRLKLDPANKLYFPYEAGKQV-RSAIKIKNTSKSHVA-FKFQTTAPKSCFM----RPPGAILAPGE 132 (179)
Q Consensus 59 ~~~~~~~~~~~p~~~lL~I~P~~eL~F~~~~~k~~-~s~LtL~N~s~~~VA-FKVKTTaP~~Y~V----rP~~GiI~Pge 132 (179)
..++.|+|.-+=.+..+.++......|.+...... ...|+|+|.....|. +.+....++.+.+ +...|-.-|..
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 45667888866567778887744677777655443 588999999888774 6776666777665 45566555555
Q ss_pred eEEEEEEe
Q 030354 133 SLIATVFK 140 (179)
Q Consensus 133 sv~I~I~l 140 (179)
...+.|.-
T Consensus 171 ~Yt~~V~A 178 (225)
T PRK06655 171 NYTIKASA 178 (225)
T ss_pred eEEEEEEE
Confidence 56666653
Done!