Query 029067
Match_columns 199
No_of_seqs 153 out of 582
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 06:57:47 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029067.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029067hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0439 VAMP-associated protei 99.9 3.3E-24 7.1E-29 180.2 12.8 110 83-196 3-113 (218)
2 COG5066 SCS2 VAMP-associated p 99.9 4E-24 8.7E-29 182.8 10.9 104 88-196 2-107 (242)
3 PF00635 Motile_Sperm: MSP (Ma 99.9 1.4E-23 3E-28 157.2 11.9 102 89-195 2-107 (109)
4 PF14874 PapD-like: Flagellar- 98.5 1.8E-06 3.9E-11 64.2 10.1 66 88-154 3-71 (102)
5 PF00345 PapD_N: Pili and flag 96.5 0.036 7.9E-07 42.4 9.7 62 89-154 2-72 (122)
6 PRK09918 putative fimbrial cha 93.1 1.2 2.6E-05 38.5 10.3 63 88-154 25-92 (230)
7 PF14646 MYCBPAP: MYCBP-associ 92.7 0.54 1.2E-05 44.0 8.1 66 89-154 231-309 (426)
8 PF07610 DUF1573: Protein of u 92.6 0.5 1.1E-05 30.9 5.6 43 111-154 2-45 (45)
9 PF11614 FixG_C: IG-like fold 90.9 1 2.2E-05 34.4 6.6 48 108-155 34-83 (118)
10 PRK09926 putative chaperone pr 88.1 6.5 0.00014 34.4 10.2 65 87-155 25-99 (246)
11 PRK15249 fimbrial chaperone pr 86.0 9.2 0.0002 33.6 10.1 63 88-154 29-102 (253)
12 PRK15295 fimbrial assembly cha 85.5 12 0.00027 32.3 10.4 61 88-154 20-89 (226)
13 PRK15211 fimbrial chaperone pr 85.3 11 0.00024 32.8 10.1 63 88-154 23-91 (229)
14 PRK15299 fimbrial chaperone pr 84.5 13 0.00029 32.0 10.2 65 87-155 22-94 (227)
15 PRK11385 putativi pili assembl 83.2 17 0.00038 31.7 10.4 64 87-154 26-101 (236)
16 PF06280 DUF1034: Fn3-like dom 81.5 3.9 8.4E-05 30.9 5.1 51 104-154 7-78 (112)
17 PRK15208 long polar fimbrial c 81.1 21 0.00046 30.8 10.1 64 87-154 21-90 (228)
18 PRK15192 fimbrial chaperone Bc 79.1 23 0.00049 31.1 9.7 62 88-155 23-98 (234)
19 PRK15246 fimbrial assembly cha 78.3 45 0.00098 29.1 11.5 63 88-154 11-83 (233)
20 PRK15195 fimbrial chaperone pr 77.1 28 0.0006 30.2 9.7 64 87-154 25-94 (229)
21 PF10633 NPCBM_assoc: NPCBM-as 76.0 4.2 9E-05 28.8 3.6 52 103-154 3-58 (78)
22 smart00809 Alpha_adaptinC2 Ada 76.0 19 0.00041 26.3 7.3 51 104-154 17-71 (104)
23 PF06030 DUF916: Bacterial pro 75.2 33 0.00071 26.9 8.8 59 96-154 18-101 (121)
24 TIGR03079 CH4_NH3mon_ox_B meth 74.9 8.1 0.00018 36.5 6.1 52 103-154 280-352 (399)
25 PRK15188 fimbrial chaperone pr 74.5 46 0.00099 29.1 10.3 64 87-154 27-96 (228)
26 PF00927 Transglut_C: Transglu 73.8 12 0.00026 27.8 5.8 52 103-154 13-74 (107)
27 PRK15290 lfpB fimbrial chapero 71.6 51 0.0011 29.0 10.0 63 88-154 38-108 (243)
28 PF11611 DUF4352: Domain of un 71.4 24 0.00052 26.1 7.0 53 102-154 33-99 (123)
29 PRK15254 fimbrial chaperone pr 70.4 66 0.0014 28.2 10.4 63 88-154 17-85 (239)
30 PRK15218 fimbrial chaperone pr 70.2 70 0.0015 27.8 10.5 61 88-154 19-91 (226)
31 PF02883 Alpha_adaptinC2: Adap 69.2 14 0.00031 27.6 5.3 52 103-154 22-77 (115)
32 PRK15233 putative fimbrial cha 69.2 67 0.0014 28.5 10.2 61 88-154 41-108 (246)
33 PRK15224 pili assembly chapero 66.5 76 0.0016 27.9 10.0 61 88-154 29-96 (237)
34 COG3121 FimC P pilus assembly 65.9 90 0.0019 27.1 11.1 64 88-155 28-98 (235)
35 PF05506 DUF756: Domain of unk 64.6 26 0.00056 25.5 5.8 44 108-154 21-65 (89)
36 PF03173 CHB_HEX: Putative car 62.7 7.9 0.00017 32.2 3.0 50 95-154 51-102 (164)
37 PF04744 Monooxygenase_B: Mono 59.3 47 0.001 31.5 7.7 68 85-155 245-334 (381)
38 PRK15253 putative fimbrial ass 58.6 1.3E+02 0.0028 26.5 10.2 62 87-154 33-106 (242)
39 PRK15285 putative fimbrial cha 56.8 1.4E+02 0.0031 26.4 10.5 63 88-154 26-95 (250)
40 PRK15308 putative fimbrial pro 54.7 71 0.0015 28.1 7.7 66 86-154 15-98 (234)
41 PRK15274 putative periplasmic 54.1 1.6E+02 0.0035 26.2 10.2 63 88-154 27-96 (257)
42 PF02753 PapD_C: Pili assembly 50.1 16 0.00035 25.1 2.4 43 111-154 1-45 (68)
43 PF12690 BsuPI: Intracellular 49.6 90 0.002 22.8 6.5 48 107-154 2-68 (82)
44 PF13473 Cupredoxin_1: Cupredo 46.2 79 0.0017 23.3 5.9 53 89-154 30-82 (104)
45 PF00553 CBM_2: Cellulose bind 45.1 54 0.0012 24.4 4.8 49 106-154 14-82 (101)
46 cd04094 selB_III This family r 43.6 1.1E+02 0.0025 22.3 6.3 32 139-178 54-85 (97)
47 TIGR02745 ccoG_rdxA_fixG cytoc 43.0 2.6E+02 0.0057 26.7 10.1 68 88-155 327-398 (434)
48 PF05753 TRAP_beta: Translocon 42.2 1.2E+02 0.0025 25.6 6.9 51 103-154 36-95 (181)
49 smart00637 CBD_II CBD_II domai 38.6 1.4E+02 0.003 21.6 6.0 24 131-154 50-75 (92)
50 PF07705 CARDB: CARDB; InterP 37.8 1.1E+02 0.0024 21.3 5.4 52 103-154 17-69 (101)
51 PF07233 DUF1425: Protein of u 37.2 1.4E+02 0.0031 22.1 6.0 51 104-154 23-80 (94)
52 PF14796 AP3B1_C: Clathrin-ada 37.2 1.5E+02 0.0033 24.3 6.6 65 86-154 66-138 (145)
53 PF08402 TOBE_2: TOBE domain; 34.1 1.4E+02 0.003 19.6 7.0 65 89-154 1-69 (75)
54 PF13205 Big_5: Bacterial Ig-l 32.3 1.9E+02 0.0041 20.6 6.4 56 96-154 26-84 (107)
55 COG3354 FlaG Putative archaeal 31.7 1.2E+02 0.0027 25.3 5.2 64 88-154 53-128 (154)
56 PF08277 PAN_3: PAN-like domai 30.9 63 0.0014 21.9 3.0 28 95-125 44-71 (71)
57 PF11906 DUF3426: Protein of u 30.3 1.8E+02 0.0039 22.7 5.9 51 104-154 67-134 (149)
58 COG3565 Predicted dioxygenase 28.7 1E+02 0.0022 25.1 4.2 36 85-124 92-127 (138)
59 PF06483 ChiC: Chitinase C; I 27.0 74 0.0016 27.3 3.3 26 119-155 116-141 (180)
60 PRK15249 fimbrial chaperone pr 25.6 1.4E+02 0.003 26.2 4.9 42 110-152 177-219 (253)
61 PRK06655 flgD flagellar basal 24.9 3.7E+02 0.008 23.3 7.3 81 74-154 92-178 (225)
62 KOG3620 Uncharacterized conser 24.4 1.9E+02 0.0041 31.9 6.2 79 88-176 526-609 (1626)
63 smart00605 CW CW domain. 24.1 1.8E+02 0.004 21.1 4.6 32 95-130 47-79 (94)
64 PF06586 TraK: TraK protein; 23.6 2.8E+02 0.0061 23.4 6.3 75 72-152 157-234 (234)
65 PRK15295 fimbrial assembly cha 22.5 2E+02 0.0043 24.9 5.2 49 95-152 148-197 (226)
No 1
>KOG0439 consensus VAMP-associated protein involved in inositol metabolism [Intracellular trafficking, secretion, and vesicular transport]
Probab=99.91 E-value=3.3e-24 Score=180.19 Aligned_cols=110 Identities=38% Similarity=0.577 Sum_probs=98.9
Q ss_pred CCCCCcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceEecCCcceeCCCCeEEEEEEeecCCCCCC
Q 029067 83 LPTRRRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCYMRPPGGILAPGESLIATVFKFVEPPENN 162 (199)
Q Consensus 83 ~p~~~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl~~~qp~~~ 162 (199)
...+.+|.|+|..+|+|.+++.+++.+.|+|+|+++.+||||||||+|++|+|||+.|+|.||+++.|.|.+ +| ..
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---QP-FE 78 (218)
T ss_pred ccccCccccCCCceEEeccCCCceEEEEEEEecCCCCceEEEEEcCCCCeEEEcCCcceECCCCcEEEEEEe---cc-Cc
Confidence 356788999998899999999999999999999999999999999999999999999999999999999988 66 44
Q ss_pred CCCCCCCCCceEEEEEEEeCCC-CCchhhhhcccC
Q 029067 163 ERPTDQKSKVKFKIMSLKVKGE-MDYVPELVCIAS 196 (199)
Q Consensus 163 e~p~~~k~kDKFLVqSv~v~~~-~d~~~elFk~a~ 196 (199)
..|.+.+|+|||+||++.++.+ ...+.++|+..+
T Consensus 79 ~~P~d~~~r~kF~v~~~~~~~~~~~~~~~~~~~~k 113 (218)
T KOG0439|consen 79 KSPPDFKSRHKFLIQSLKAPPPTTRDVVDLWKFQK 113 (218)
T ss_pred cCchhhcccceEEEEEEecCCccccchhhhccccc
Confidence 5577888999999999999986 566678887654
No 2
>COG5066 SCS2 VAMP-associated protein involved in inositol metabolism [Intracellular trafficking and secretion]
Probab=99.91 E-value=4e-24 Score=182.80 Aligned_cols=104 Identities=25% Similarity=0.342 Sum_probs=93.3
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceEecCCcceeCCCCeEEEEEEeecCCCCCCCCCCC
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCYMRPPGGILAPGESLIATVFKFVEPPENNERPTD 167 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl~~~qp~~~e~p~~ 167 (199)
.|.|+| ++.|..++..+.++.+.|.|++.++|+||||||+|+.||||||.|+|+|++.+.|.|+| |+...|+.++
T Consensus 2 aveisp--~~~fy~Plt~~ske~~sv~NnspepvgfKVKTTaPK~YcVRPN~g~Iep~stv~VeVil---q~l~eEpapd 76 (242)
T COG5066 2 AVEISP--QTTFYVPLTNKSKEMFSVQNNSPEPVGFKVKTTAPKDYCVRPNMGLIEPMSTVEVEVIL---QGLTEEPAPD 76 (242)
T ss_pred ceEecC--ceEEecccccccceeeEeecCCCCceeEEeeccCCcceeEcCCCceeccCCeeEEEEEe---eccccCCCCC
Confidence 377888 67788789999999999999999999999999999999999999999999999999999 7888888889
Q ss_pred CCCCceEEEEEEEeCCCC--CchhhhhcccC
Q 029067 168 QKSKVKFKIMSLKVKGEM--DYVPELVCIAS 196 (199)
Q Consensus 168 ~k~kDKFLVqSv~v~~~~--d~~~elFk~a~ 196 (199)
.+||||||||++..+.+. .+.+++|...+
T Consensus 77 fKCrdKFLiqs~~~~~~l~g~d~ad~wt~~s 107 (242)
T COG5066 77 FKCRDKFLIQSYRFDWRLSGSDFADHWTSSS 107 (242)
T ss_pred ccccceeEEEEeccChhhccchHHHHHHhhc
Confidence 999999999999998753 33489997654
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=99.91 E-value=1.4e-23 Score=157.24 Aligned_cols=102 Identities=31% Similarity=0.429 Sum_probs=81.7
Q ss_pred EEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceEecCCcceeCCCCeEEEEEEeecCCCCCCCCCCCC
Q 029067 89 LRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCYMRPPGGILAPGESLIATVFKFVEPPENNERPTDQ 168 (199)
Q Consensus 89 L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl~~~qp~~~e~p~~~ 168 (199)
|.|+|.+.|.|.+++++...+.|+|+|+++.+||||||||+|.+|+|+|+.|+|+||+++.|.|++ +|...... .
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 789999999999999999999999999999999999999999999999999999999999999999 56543321 2
Q ss_pred CCCceEEEEEEEeCCCCCch----hhhhccc
Q 029067 169 KSKVKFKIMSLKVKGEMDYV----PELVCIA 195 (199)
Q Consensus 169 k~kDKFLVqSv~v~~~~d~~----~elFk~a 195 (199)
..+|||+|+++.++++.... ..+|+++
T Consensus 77 ~~~dkf~I~~~~~~~~~~~~~~~~~~~~~~~ 107 (109)
T PF00635_consen 77 KKKDKFLIQSIVVPDNATDPKKDFKQIWKNG 107 (109)
T ss_dssp TSSEEEEEEEEEE-TT-SSSHHHHHCCHHHS
T ss_pred CCCCEEEEEEEEcCCCccchhhhHHHHHhcc
Confidence 34999999999998776433 4455544
No 4
>PF14874 PapD-like: Flagellar-associated PapD-like
Probab=98.49 E-value=1.8e-06 Score=64.18 Aligned_cols=66 Identities=29% Similarity=0.449 Sum_probs=58.2
Q ss_pred cEEecCCCceEeeCC-CCCeeEEEEEEEcCCCCeEEEEEccCC--CCceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYE-PGKQVRSAISIKNTSKSHVAFKFQTTA--PKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e-~~k~v~s~L~LtN~S~~~VAFKVKTTa--P~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
.|.++|. +|.|-.- .+......|+|+|.+..++.|+|+.-. ...|.|.|..|+|+||+++.|.|.+
T Consensus 3 ~l~v~P~-~ldFG~v~~g~~~~~~v~l~N~s~~p~~f~v~~~~~~~~~~~v~~~~g~l~PG~~~~~~V~~ 71 (102)
T PF14874_consen 3 TLEVSPK-ELDFGNVFVGQTYSRTVTLTNTSSIPARFRVRQPESLSSFFSVEPPSGFLAPGESVELEVTF 71 (102)
T ss_pred EEEEeCC-EEEeeEEccCCEEEEEEEEEECCCCCEEEEEEeCCcCCCCEEEECCCCEECCCCEEEEEEEE
Confidence 5899996 9999763 477888999999999999999997433 5689999999999999999999999
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=96.49 E-value=0.036 Score=42.44 Aligned_cols=62 Identities=23% Similarity=0.403 Sum_probs=50.9
Q ss_pred EEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCC----C-----CceEecCCcceeCCCCeEEEEEEe
Q 029067 89 LRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTA----P-----KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 89 L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTa----P-----~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
|.|+|. .+.|.. ++....++|+|.++.++.+.+.... + ..+.|-|+.-.|+||++..|.|..
T Consensus 2 i~i~~t-rii~~~---~~~~~~i~v~N~~~~~~~vq~~v~~~~~~~~~~~~~~~~vsPp~~~L~pg~~q~vRv~~ 72 (122)
T PF00345_consen 2 IQISPT-RIIFNE---SQRSASITVTNNSDQPYLVQVWVYDQDDEDEDEPTDPFIVSPPIFRLEPGESQTVRVYR 72 (122)
T ss_dssp EEESSS-EEEEET---TSSEEEEEEEESSSSEEEEEEEEEETTSTTSSSSSSSEEEESSEEEEETTEEEEEEEEE
T ss_pred EEEccE-EEEEeC---CCCEEEEEEEcCCCCcEEEEEEEEcCCCcccccccccEEEeCCceEeCCCCcEEEEEEe
Confidence 678896 888875 2236899999999999999986543 1 268999999999999999999944
No 6
>PRK09918 putative fimbrial chaperone protein; Provisional
Probab=93.14 E-value=1.2 Score=38.48 Aligned_cols=63 Identities=17% Similarity=0.214 Sum_probs=48.8
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCC-----CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAP-----KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP-----~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.++|. .+.|... +-...++|+|.++.++...+..... .-|.|-|+.-.|+||++..|.|.+
T Consensus 25 ~v~l~~t-Rvi~~~~---~~~~si~v~N~~~~p~lvQ~wv~~~~~~~~~~fivtPPl~rl~pg~~q~vRii~ 92 (230)
T PRK09918 25 GMVPETS-VVIVEES---DGEGSINVKNTDSNPILLYTTLVDLPEDKSKLLLVTPPVARVEPGQSQQVRFIL 92 (230)
T ss_pred eEEEccE-EEEEECC---CCeEEEEEEcCCCCcEEEEEEEecCCCCCCCCEEEcCCeEEECCCCceEEEEEE
Confidence 5888885 7888753 3357999999999876655533211 359999999999999999999987
No 7
>PF14646 MYCBPAP: MYCBP-associated protein family
Probab=92.74 E-value=0.54 Score=43.97 Aligned_cols=66 Identities=18% Similarity=0.431 Sum_probs=54.6
Q ss_pred EEecCCCceEeeCCCCCeeEEEEE-EEcCCCCeEEEEEcc------------CCCCceEecCCcceeCCCCeEEEEEEe
Q 029067 89 LRLDPSTKLFFPYEPGKQVRSAIS-IKNTSKSHVAFKFQT------------TAPKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 89 L~IdP~~eL~F~~e~~k~v~s~L~-LtN~S~~~VAFKVKT------------TaP~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
..+.+.-.|.|...++..+...|. |.|.+..-|-|.-+- .....|......|+|.||++..|.|+.
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 445555689999999887777777 999999999998432 225678999999999999999999998
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=92.62 E-value=0.5 Score=30.87 Aligned_cols=43 Identities=28% Similarity=0.166 Sum_probs=35.4
Q ss_pred EEEEcCCCCe-EEEEEccCCCCceEecCCcceeCCCCeEEEEEEe
Q 029067 111 ISIKNTSKSH-VAFKFQTTAPKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 111 L~LtN~S~~~-VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
++|+|.++++ +..+|+|+ =+...+......|.||++..|.|+.
T Consensus 2 F~~~N~g~~~L~I~~v~ts-CgCt~~~~~~~~i~PGes~~i~v~y 45 (45)
T PF07610_consen 2 FEFTNTGDSPLVITDVQTS-CGCTTAEYSKKPIAPGESGKIKVTY 45 (45)
T ss_pred EEEEECCCCcEEEEEeeEc-cCCEEeeCCcceECCCCEEEEEEEC
Confidence 6899999986 45677765 5677888888999999999999863
No 9
>PF11614 FixG_C: IG-like fold at C-terminal of FixG, putative oxidoreductase; PDB: 2R39_A.
Probab=90.94 E-value=1 Score=34.40 Aligned_cols=48 Identities=17% Similarity=0.331 Sum_probs=34.2
Q ss_pred EEEEEEEcCCCCeEEEEEccCCCCceEe-cCCcce-eCCCCeEEEEEEee
Q 029067 108 RSAISIKNTSKSHVAFKFQTTAPKSCYM-RPPGGI-LAPGESLIATVFKF 155 (199)
Q Consensus 108 ~s~L~LtN~S~~~VAFKVKTTaP~~Y~V-RPn~Gi-L~Pgesi~I~Vtl~ 155 (199)
..+|+|.|.+.++..|.|+...+..+.+ .|...+ |+||+...+.|++.
T Consensus 34 ~Y~lkl~Nkt~~~~~~~i~~~g~~~~~l~~~~~~i~v~~g~~~~~~v~v~ 83 (118)
T PF11614_consen 34 QYTLKLTNKTNQPRTYTISVEGLPGAELQGPENTITVPPGETREVPVFVT 83 (118)
T ss_dssp EEEEEEEE-SSS-EEEEEEEES-SS-EE-ES--EEEE-TT-EEEEEEEEE
T ss_pred EEEEEEEECCCCCEEEEEEEecCCCeEEECCCcceEECCCCEEEEEEEEE
Confidence 4899999999999999999888778888 665554 99999998888873
No 10
>PRK09926 putative chaperone protein EcpD; Provisional
Probab=88.06 E-value=6.5 Score=34.36 Aligned_cols=65 Identities=8% Similarity=0.175 Sum_probs=49.7
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCC----------ceEecCCcceeCCCCeEEEEEEee
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPK----------SCYMRPPGGILAPGESLIATVFKF 155 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~----------~Y~VRPn~GiL~Pgesi~I~Vtl~ 155 (199)
--|.|+|. .+.|... +-...|.|.|.++.++.--.-....+ -|.|-|+.--|+||+...|.|.+.
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 45899995 8888752 23579999999998766554332211 399999999999999999999983
No 11
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=86.04 E-value=9.2 Score=33.64 Aligned_cols=63 Identities=14% Similarity=0.217 Sum_probs=47.4
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCC------C-----CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTA------P-----KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTa------P-----~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.|+|. .+.|.... -...|+|.|.++.++....-+.+ | .-|.|-|+.--|+||+...|.|.+
T Consensus 29 ~l~l~~T-Rviy~~~~---~~~sl~l~N~~~~p~LvQsWv~~~~~~~~p~~~~~~pFivtPPlfrl~p~~~q~lRI~~ 102 (253)
T PRK15249 29 SVTILGS-RIIYPSTA---SSVDVQLKNNDAIPYIVQTWFDDGDMNTSPENSSAMPFIATPPVFRIQPKAGQVVRVIY 102 (253)
T ss_pred EEEeCce-EEEEeCCC---cceeEEEEcCCCCcEEEEEEEeCCCCCCCccccccCcEEEcCCeEEecCCCceEEEEEE
Confidence 5889995 88886432 35799999999886554432211 1 139999999999999999999998
No 12
>PRK15295 fimbrial assembly chaperone SthB; Provisional
Probab=85.50 E-value=12 Score=32.30 Aligned_cols=61 Identities=18% Similarity=0.260 Sum_probs=46.5
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEcc----CC-----CCceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQT----TA-----PKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKT----Ta-----P~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.|++. .+.|... +-...|+|.|.++.++. |++ .. ..-|.|-|+.--|+||+...|.|..
T Consensus 20 ~i~l~~T-RvI~~~~---~~~~si~i~N~~~~p~L--vQsWv~~~~~~~~~~~pFivtPPl~rl~p~~~q~lRI~~ 89 (226)
T PRK15295 20 SIVVGGT-RLVFDGN---NDESSINVENKDSKANL--VQSWLSVVDPQVTNKQAFIITPPLFRLDAGQKNSIRVIR 89 (226)
T ss_pred cEEeCce-EEEEeCC---CceeEEEEEeCCCCcEE--EEEEEeCCCCCCCCCCCEEEcCCeEEECCCCceEEEEEE
Confidence 5888885 7888753 23579999999987533 442 11 2249999999999999999999988
No 13
>PRK15211 fimbrial chaperone protein PefD; Provisional
Probab=85.30 E-value=11 Score=32.79 Aligned_cols=63 Identities=13% Similarity=0.156 Sum_probs=46.9
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccC--C----CCceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTT--A----PKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTT--a----P~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
.|.+++. .+.|+.. .-..+|+|+|.++.++.-..... . ..-|.|-|+.--|+||+...|.|.+
T Consensus 23 ~v~l~~T-RvIy~~~---~~~~si~i~N~~~~p~LvQswv~~~~~~~~~~pFivtPPlfrl~p~~~q~lRI~~ 91 (229)
T PRK15211 23 AFVLNGT-RFIYDEG---RKNISFEVTNQADQTYGGQVWIDNTTQGSSTVYMVPAPPFFKVRPKEKQIIRIMK 91 (229)
T ss_pred EEEECce-EEEEcCC---CceEEEEEEeCCCCcEEEEEEEecCCCCCccCCEEEcCCeEEECCCCceEEEEEE
Confidence 4788885 7888742 23579999999988644333221 1 1249999999999999999999998
No 14
>PRK15299 fimbrial chaperone protein StiB; Provisional
Probab=84.55 E-value=13 Score=32.02 Aligned_cols=65 Identities=14% Similarity=0.227 Sum_probs=47.9
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCC--------CCceEecCCcceeCCCCeEEEEEEee
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTA--------PKSCYMRPPGGILAPGESLIATVFKF 155 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTa--------P~~Y~VRPn~GiL~Pgesi~I~Vtl~ 155 (199)
--|.|+|. .+.|... +-..+|+|+|.++.++.-..-+.. ..-|.|-|+.--|+||+...|.|...
T Consensus 22 a~i~l~~T-Rvi~~~~---~~~~sl~l~N~~~~p~lvQsWv~~~~~~~~~~~~pfivtPPl~rl~p~~~q~lRI~~~ 94 (227)
T PRK15299 22 AGINIGTT-RVIFHGD---AKDASISISNSDNVPYLIQSWAQSISETGASGDAPFMVTPPLFRLNGGQKNVLRIIRT 94 (227)
T ss_pred eeEEECce-EEEEeCC---CcEEEEEEEeCCCCcEEEEEEeecCCCCCCcCCCCEEEcCCeEEECCCCccEEEEEEC
Confidence 35889995 7888653 235799999998876544432111 12499999999999999999999983
No 15
>PRK11385 putativi pili assembly chaperone; Provisional
Probab=83.15 E-value=17 Score=31.75 Aligned_cols=64 Identities=19% Similarity=0.324 Sum_probs=47.3
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccC------------CCCceEecCCcceeCCCCeEEEEEEe
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTT------------APKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTT------------aP~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
--|.+++. .+.|.. ++-...|+|.|.++.++.=..... ...-|.|-|+.--|+||+...|.|.+
T Consensus 26 A~v~l~~T-RvIy~~---~~~~~sv~l~N~~~~p~LvQswv~~~~~~~~~~~~~~~~pFivtPPlfrl~p~~~q~lRIi~ 101 (236)
T PRK11385 26 AGVVVGGT-RFIFPA---DRESISILLTNTSQESWLINSKINRPTRWAGGEASTVPAPLLAAPPLILLKPGTTGTLRLLR 101 (236)
T ss_pred eeEEeCce-EEEEcC---CCceEEEEEEeCCCCcEEEEEEcccCccccCcccccccCCEEEcCCeEEECCCCceEEEEEE
Confidence 35888885 888874 233579999999998644333211 11249999999999999999999998
No 16
>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=81.50 E-value=3.9 Score=30.93 Aligned_cols=51 Identities=18% Similarity=0.271 Sum_probs=32.1
Q ss_pred CCeeEEEEEEEcCCCCeEEEEEccC-----C---CCceE--ec-----------CCcceeCCCCeEEEEEEe
Q 029067 104 GKQVRSAISIKNTSKSHVAFKFQTT-----A---PKSCY--MR-----------PPGGILAPGESLIATVFK 154 (199)
Q Consensus 104 ~k~v~s~L~LtN~S~~~VAFKVKTT-----a---P~~Y~--VR-----------Pn~GiL~Pgesi~I~Vtl 154 (199)
+...+.+|+|+|.+++.+.|+|.-. . .+.|. .. |..=.|+||++..|.|++
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 3446789999999999999997644 1 12222 11 112248999999999999
No 17
>PRK15208 long polar fimbrial chaperone LpfB; Provisional
Probab=81.06 E-value=21 Score=30.79 Aligned_cols=64 Identities=13% Similarity=0.264 Sum_probs=46.0
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEE-EE-EccCCC---CceEecCCcceeCCCCeEEEEEEe
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVA-FK-FQTTAP---KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VA-FK-VKTTaP---~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
--|.++|. .+.|... +-...|+|+|.+++ ++. +. |..... .-|.|-|+.--|+||+...|.|..
T Consensus 21 agv~l~~T-RvI~~~~---~~~~si~i~N~~~~~~~LvQsWv~~~~~~~~~pfivtPPl~rl~p~~~q~lRIi~ 90 (228)
T PRK15208 21 GGVALSST-RVIYDGS---KKEASLTVNNKSKTEEFLIQSWIDDANGNKKTPFIITPPLFKLDPTKNNVLRIVN 90 (228)
T ss_pred ccEEeCce-EEEEeCC---CceEEEEEEeCCCCCcEEEEEEEECCCCCccCCEEECCCeEEECCCCccEEEEEE
Confidence 35889995 8888753 23579999999864 333 22 211111 139999999999999999999987
No 18
>PRK15192 fimbrial chaperone BcfG; Provisional
Probab=79.09 E-value=23 Score=31.05 Aligned_cols=62 Identities=11% Similarity=0.160 Sum_probs=46.4
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccC----------C----CCceEecCCcceeCCCCeEEEEEE
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTT----------A----PKSCYMRPPGGILAPGESLIATVF 153 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTT----------a----P~~Y~VRPn~GiL~Pgesi~I~Vt 153 (199)
-|.|+.. .+.|+. ++-...|+|.|.++.+ |=|++. . ..-|.|-|+.--|+||+...|.|.
T Consensus 23 gi~l~~T-RvIy~~---~~k~~sv~l~N~~~~p--~LvQswv~~~~~w~~~~~~~~~~PFivtPPlfrl~p~~~~~lRI~ 96 (234)
T PRK15192 23 GVVIGGT-RFIYHA---GAPALSVPVSNHSEAS--WLIDTHILPGGRWPGTKNEGNITPFVVTPPLFMLSARQENSMRVV 96 (234)
T ss_pred eEEeCce-EEEEcC---CCceEEEEEEeCCCCc--EEEEEEeccCccccccCCccccCCEEEcCCeEEECCCCceEEEEE
Confidence 4777874 777865 2235799999999885 555541 1 113999999999999999999999
Q ss_pred ee
Q 029067 154 KF 155 (199)
Q Consensus 154 l~ 155 (199)
..
T Consensus 97 ~~ 98 (234)
T PRK15192 97 YT 98 (234)
T ss_pred EC
Confidence 83
No 19
>PRK15246 fimbrial assembly chaperone StbE; Provisional
Probab=78.33 E-value=45 Score=29.05 Aligned_cols=63 Identities=19% Similarity=0.376 Sum_probs=46.7
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCC------C----CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTA------P----KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTa------P----~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.|++. .+.|... +-...|+|.|.++.++.-.+-... | .-|.|-|+.--|+||+...|.|.+
T Consensus 11 ~v~l~~T-RvI~~~~---~~~~sv~l~N~~~~p~LvQsWvd~~~~~~~p~~~~~pFivtPPlfrl~~~~~~~lRI~~ 83 (233)
T PRK15246 11 AVNIDRT-RIIFASD---DVAQSLTLSNDNTTPMLLQVWTDAGNIDASPDNSKTPLVALPPVFKMQPGELRTLRLLL 83 (233)
T ss_pred EEEECce-EEEEcCC---CceEEEEEEeCCCCcEEEEEEEeCCCCccCcccccCcEEECCcceEECCCCceEEEEEE
Confidence 4788885 8888752 335799999999886433331111 1 149999999999999999999998
No 20
>PRK15195 fimbrial chaperone protein FimC; Provisional
Probab=77.11 E-value=28 Score=30.21 Aligned_cols=64 Identities=16% Similarity=0.342 Sum_probs=45.6
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEE-EE-EccCC---CCceEecCCcceeCCCCeEEEEEEe
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVA-FK-FQTTA---PKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VA-FK-VKTTa---P~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
--|.|++. .+.|.... + ...|+|+|.+++ +.. .. |.... ..-|.|-|+.--|+||+...|.|..
T Consensus 25 Agi~i~~T-RvIy~~~~-~--~~si~l~N~~~~~~~LvQsWv~~~~~~~~~pfivtPPlfrl~p~~~q~lRIi~ 94 (229)
T PRK15195 25 GGIALGAT-RVIYPADA-K--QTSLAIRNSHTNERYLVNSWIENSSGVKEKSFIVTPPLFVSEPKSENTLRIIY 94 (229)
T ss_pred eeEEECCe-EEEEeCCC-c--eEEEEEEeCCCCccEEEEEEecCCCCCccCCEEEcCCeEEECCCCceEEEEEE
Confidence 35888985 77786432 2 379999999865 333 21 21111 1259999999999999999999998
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=76.04 E-value=4.2 Score=28.81 Aligned_cols=52 Identities=25% Similarity=0.439 Sum_probs=31.8
Q ss_pred CCCeeEEEEEEEcCCCCeE-EEEEccCCCCceE--ecCCcc-eeCCCCeEEEEEEe
Q 029067 103 PGKQVRSAISIKNTSKSHV-AFKFQTTAPKSCY--MRPPGG-ILAPGESLIATVFK 154 (199)
Q Consensus 103 ~~k~v~s~L~LtN~S~~~V-AFKVKTTaP~~Y~--VRPn~G-iL~Pgesi~I~Vtl 154 (199)
.|....-.++|+|.....+ ..++.-..|.-+. +.|... -|.||++..+++.+
T Consensus 3 ~G~~~~~~~tv~N~g~~~~~~v~~~l~~P~GW~~~~~~~~~~~l~pG~s~~~~~~V 58 (78)
T PF10633_consen 3 PGETVTVTLTVTNTGTAPLTNVSLSLSLPEGWTVSASPASVPSLPPGESVTVTFTV 58 (78)
T ss_dssp TTEEEEEEEEEE--SSS-BSS-EEEEE--TTSE---EEEEE--B-TTSEEEEEEEE
T ss_pred CCCEEEEEEEEEECCCCceeeEEEEEeCCCCccccCCccccccCCCCCEEEEEEEE
Confidence 4677788999999987642 3444445588887 445443 69999999988888
No 22
>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=76.04 E-value=19 Score=26.29 Aligned_cols=51 Identities=29% Similarity=0.536 Sum_probs=38.9
Q ss_pred CCeeEEEEEEEcCCCCeEE-EEEccCCCCceEec--CCcc-eeCCCCeEEEEEEe
Q 029067 104 GKQVRSAISIKNTSKSHVA-FKFQTTAPKSCYMR--PPGG-ILAPGESLIATVFK 154 (199)
Q Consensus 104 ~k~v~s~L~LtN~S~~~VA-FKVKTTaP~~Y~VR--Pn~G-iL~Pgesi~I~Vtl 154 (199)
+..+.-.+...|.+..++. |.++-..|+.+.++ |..| .|+||+.+...+.+
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 3567889999999988765 88887778877665 5544 89999987766666
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=75.16 E-value=33 Score=26.95 Aligned_cols=59 Identities=22% Similarity=0.276 Sum_probs=39.3
Q ss_pred ceEeeCCCCCeeEEEEEEEcCCCCeEEEEEc-----cCCCCc--e-------------Ee----c-CCcceeCCCCeEEE
Q 029067 96 KLFFPYEPGKQVRSAISIKNTSKSHVAFKFQ-----TTAPKS--C-------------YM----R-PPGGILAPGESLIA 150 (199)
Q Consensus 96 eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVK-----TTaP~~--Y-------------~V----R-Pn~GiL~Pgesi~I 150 (199)
...+..+++....-.|+|+|.+++.+-|+|. |+..+. | .+ + |..-.|+|+++..|
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 3444455677777899999999999999974 333332 1 11 1 33345888888887
Q ss_pred EEEe
Q 029067 151 TVFK 154 (199)
Q Consensus 151 ~Vtl 154 (199)
.+.+
T Consensus 98 ~~~i 101 (121)
T PF06030_consen 98 TFTI 101 (121)
T ss_pred EEEE
Confidence 7776
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=74.95 E-value=8.1 Score=36.54 Aligned_cols=52 Identities=27% Similarity=0.424 Sum_probs=39.0
Q ss_pred CCCeeEEEEEEEcCCCCeEEEEEccCCCC-------ceEecCCc-------ce-------eCCCCeEEEEEEe
Q 029067 103 PGKQVRSAISIKNTSKSHVAFKFQTTAPK-------SCYMRPPG-------GI-------LAPGESLIATVFK 154 (199)
Q Consensus 103 ~~k~v~s~L~LtN~S~~~VAFKVKTTaP~-------~Y~VRPn~-------Gi-------L~Pgesi~I~Vtl 154 (199)
+++..+-+++|+|.++++|-.+==+|+.- .|..+|.. |+ |.|||+.+|.|..
T Consensus 280 PGR~l~~~~~VTN~g~~~vrlgEF~TA~vRFlN~~~v~~~~~~yP~~lla~GL~v~d~~pI~PGETr~v~v~a 352 (399)
T TIGR03079 280 PGRALRVTMEITNNGDQVISIGEFTTAGIRFMNANGVRVLDPDYPRELLAEGLEVDDQSAIAPGETVEVKMEA 352 (399)
T ss_pred CCcEEEEEEEEEcCCCCceEEEeEeecceEeeCcccccccCCCChHHHhhccceeCCCCCcCCCcceEEEEEE
Confidence 58889999999999999998774444433 34444433 22 8999999999998
No 25
>PRK15188 fimbrial chaperone protein BcfB; Provisional
Probab=74.47 E-value=46 Score=29.06 Aligned_cols=64 Identities=16% Similarity=0.288 Sum_probs=46.2
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEE-EE-EccCCC---CceEecCCcceeCCCCeEEEEEEe
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVA-FK-FQTTAP---KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VA-FK-VKTTaP---~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
--|.|++. .+.|... .-...++|+|.+++ +.. .. |..... .-|.|-|+.--|+||+...|.|..
T Consensus 27 Agi~l~~T-RvIy~~~---~~~~sv~i~N~~~~~p~LvQsWv~~~~~~~~~pFivtPPlfrl~~~~~~~lRI~~ 96 (228)
T PRK15188 27 GGIALGAT-RVIYPQG---SKQTSLPIINSSASNVFLIQSWVANADGSRSTDFIITPPLFVIQPKKENILRIMY 96 (228)
T ss_pred ceEEECcE-EEEEcCC---CceEEEEEEeCCCCccEEEEEEEecCCCCccCCEEEcCCeEEECCCCceEEEEEE
Confidence 45888985 8888752 23579999999865 333 22 211111 249999999999999999999998
No 26
>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=73.80 E-value=12 Score=27.80 Aligned_cols=52 Identities=23% Similarity=0.222 Sum_probs=39.3
Q ss_pred CCCeeEEEEEEEcCCCCe--------EEEEEccCCCC--ceEecCCcceeCCCCeEEEEEEe
Q 029067 103 PGKQVRSAISIKNTSKSH--------VAFKFQTTAPK--SCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 103 ~~k~v~s~L~LtN~S~~~--------VAFKVKTTaP~--~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|+.....++++|+++.+ .|+-|--|.-. ....+-..+-|.||++..+.+.+
T Consensus 13 vG~d~~v~v~~~N~~~~~l~~v~~~l~~~~v~ytG~~~~~~~~~~~~~~l~p~~~~~~~~~i 74 (107)
T PF00927_consen 13 VGQDFTVSVSFTNPSSEPLRNVSLNLCAFTVEYTGLTRDQFKKEKFEVTLKPGETKSVEVTI 74 (107)
T ss_dssp TTSEEEEEEEEEE-SSS-EECEEEEEEEEEEECTTTEEEEEEEEEEEEEE-TTEEEEEEEEE
T ss_pred CCCCEEEEEEEEeCCcCccccceeEEEEEEEEECCcccccEeEEEcceeeCCCCEEEEEEEE
Confidence 478899999999999987 66666655432 25677888899999999999998
No 27
>PRK15290 lfpB fimbrial chaperone protein; Provisional
Probab=71.60 E-value=51 Score=28.97 Aligned_cols=63 Identities=10% Similarity=0.182 Sum_probs=46.8
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEEEccC--C-C----CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVAFKFQTT--A-P----KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VAFKVKTT--a-P----~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.+++. .+.|+. ++-...|+|+|.+++ ++.-..-.. + . .-|.|-|+.--|+||+...|.|.+
T Consensus 38 gv~l~~T-RvIy~~---~~~~~sl~v~N~~~~~p~LvQsWvd~~~~~~~~~~pFivtPPlfrl~p~~~q~lRIi~ 108 (243)
T PRK15290 38 GVVIGGT-RVVYLS---NNPDKSISVFSKEEKIPYLIQAWVDPFNKEDKSKAPFTVIPPVSRLEPSQEKVLRIIH 108 (243)
T ss_pred eEEECce-EEEEeC---CCceEEEEEEeCCCCCcEEEEEEEecCCCCCcccCCEEEcCCeEEECCCCceEEEEEE
Confidence 5888885 888875 223469999999864 555444322 1 1 139999999999999999999998
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=71.41 E-value=24 Score=26.14 Aligned_cols=53 Identities=21% Similarity=0.247 Sum_probs=32.8
Q ss_pred CCCCeeEEEEEEEcCCCCeEE-----EEEccCCCCceEecC---------CcceeCCCCeEEEEEEe
Q 029067 102 EPGKQVRSAISIKNTSKSHVA-----FKFQTTAPKSCYMRP---------PGGILAPGESLIATVFK 154 (199)
Q Consensus 102 e~~k~v~s~L~LtN~S~~~VA-----FKVKTTaP~~Y~VRP---------n~GiL~Pgesi~I~Vtl 154 (199)
+.++-+.-.++|+|.+++.+. |++.+..-..|.... ..+-|.||+++...|..
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 345667789999999998776 678877767776443 35789999999988887
No 29
>PRK15254 fimbrial chaperone protein StdC; Provisional
Probab=70.35 E-value=66 Score=28.22 Aligned_cols=63 Identities=14% Similarity=0.201 Sum_probs=45.4
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEEEcc--CCC---CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVAFKFQT--TAP---KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VAFKVKT--TaP---~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.|++. .+.|.. ++-...|+|.|.+++ ++.-..-. ... .-|.|-|+.--|+||+...|.|.+
T Consensus 17 ~v~l~~T-RvIy~~---~~~~~sv~v~N~~~~~p~LvQsWv~d~~~~~~~pFivtPPlfrl~p~~~~~lRI~~ 85 (239)
T PRK15254 17 AVNVDRT-RIIMDA---PQKTVAITLNNDDKTTPFLAQSWVTDADGVRTDALMALPPLQRIDAGQKSQVRITQ 85 (239)
T ss_pred eEEECce-EEEEeC---CCceEEEEEEeCCCCCcEEEEEEEecCCCCCcCCEEEcCCeEEECCCCceEEEEEE
Confidence 4788885 888874 233579999999864 54333211 111 249999999999999999999987
No 30
>PRK15218 fimbrial chaperone protein PegB; Provisional
Probab=70.16 E-value=70 Score=27.79 Aligned_cols=61 Identities=15% Similarity=0.199 Sum_probs=44.4
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEcc--CCC----------CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQT--TAP----------KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKT--TaP----------~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.++-. .+.|+. +.-..+|+|.|.++.+ |-|++ ... .-|.|-|+.-.|+||+...|.|.+
T Consensus 19 gi~l~~T-RvIy~~---~~~~~si~i~N~~~~p--yLvQsWvd~~~~~~~~~~~~~pFivtPPlfRl~p~~~~~lRI~~ 91 (226)
T PRK15218 19 GIYIYGT-RIIYPA---QKKDITVQLMNDGKRS--SLIQAWIDNGDTSLPPEKLQVPFIMTPPVIRVAANSGQQLKIKK 91 (226)
T ss_pred eEEeCce-EEEEcC---CCcEEEEEEEcCCCCc--EEEEEEEeCCCCCCCcccccCCEEECCCeEEECCCCceEEEEEE
Confidence 4666664 777764 2234689999999875 44432 111 149999999999999999999998
No 31
>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=69.20 E-value=14 Score=27.62 Aligned_cols=52 Identities=27% Similarity=0.520 Sum_probs=35.6
Q ss_pred CCCeeEEEEEEEcCCCCeEE-EEEccCCCCce--EecCC-cceeCCCCeEEEEEEe
Q 029067 103 PGKQVRSAISIKNTSKSHVA-FKFQTTAPKSC--YMRPP-GGILAPGESLIATVFK 154 (199)
Q Consensus 103 ~~k~v~s~L~LtN~S~~~VA-FKVKTTaP~~Y--~VRPn-~GiL~Pgesi~I~Vtl 154 (199)
.+....-.+...|.+..++. |.++-..|+.| .+.|. ...|+|+..+.-.+.+
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 36778889999999988765 77766555655 55566 5599999988866666
No 32
>PRK15233 putative fimbrial chaperone protein SefB; Provisional
Probab=69.16 E-value=67 Score=28.48 Aligned_cols=61 Identities=16% Similarity=0.195 Sum_probs=43.5
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEcc----CC---CCceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQT----TA---PKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKT----Ta---P~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.++-. .+.|+... -..+|+|.|.++.+ |-|++ .. ..-|.|-|+.--|+||+...|.|.+
T Consensus 41 gi~l~~T-RvIy~~~~---~~~sl~i~N~~~~p--~LvQsWvd~~~~~~~~pFiVtPPLfRLep~~~~~lRIi~ 108 (246)
T PRK15233 41 GLRLGTT-RVIYKEDA---PSTSFWIMNEKEYP--ILVQTQVYNDDKSSKAPFIVTPPILKVESNARTRLKVIP 108 (246)
T ss_pred eEEeCce-EEEEeCCC---cEEEEEEEcCCCCc--EEEEEEEecCCCCccCCEEECCCeEEECCCCceEEEEEE
Confidence 3566653 66665422 35789999987765 44443 11 1249999999999999999999998
No 33
>PRK15224 pili assembly chaperone protein SafB; Provisional
Probab=66.47 E-value=76 Score=27.87 Aligned_cols=61 Identities=11% Similarity=0.220 Sum_probs=44.9
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEcc----CCC---CceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQT----TAP---KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKT----TaP---~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.|+-. .+.|+.. +-..+|+|.|.++.+ |-|++ ... .-|.|-|+.--|+|++...|.|.+
T Consensus 29 gv~l~~T-RvIy~~~---~k~~sl~v~N~~~~p--yLvQsWvd~~~~~~~~pFivtPPlfRlep~~~~~lRI~~ 96 (237)
T PRK15224 29 SVKLGAT-RVIYHAG---TAGATLSVSNPQNYP--ILVQSSVKAADKSSPAPFLVMPPLFRLEANQQSQLRIVR 96 (237)
T ss_pred EEEeCce-EEEEeCC---CcEEEEEEEcCCCCc--EEEEEEEeCCCCCccCCEEECCCeEEECCCCceEEEEEE
Confidence 4666663 7777642 234689999998775 55554 111 239999999999999999999998
No 34
>COG3121 FimC P pilus assembly protein, chaperone PapD [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=65.91 E-value=90 Score=27.09 Aligned_cols=64 Identities=13% Similarity=0.246 Sum_probs=50.2
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccC-------CCCceEecCCcceeCCCCeEEEEEEee
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTT-------APKSCYMRPPGGILAPGESLIATVFKF 155 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTT-------aP~~Y~VRPn~GiL~Pgesi~I~Vtl~ 155 (199)
-+.|++. .+.|+... -...|+|.|..+.++.-.+..- ...-|.|-|+.-.|+||+...|.|.+.
T Consensus 28 ~v~i~~T-RiI~~~~~---k~~sl~l~N~~~~p~LvQ~wvd~~~~~~~~~~pfvvtPPv~rl~p~~~q~vRi~~~ 98 (235)
T COG3121 28 GVVLGGT-RIIYPAGD---KETSLTLRNDGNQPYLVQSWVDDGLEPEKSTVPFVVTPPVFRLEPGQEQQLRILYT 98 (235)
T ss_pred eEEecce-EEEEeCCC---ceeEEEEEcCCCCCEEEEEEEcCCCCCccccCCEEecCCeEEECCCCccEEEEEec
Confidence 5778885 77776532 2579999998888888885443 234589999999999999999999993
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=64.56 E-value=26 Score=25.48 Aligned_cols=44 Identities=18% Similarity=0.130 Sum_probs=30.8
Q ss_pred EEEEEEEcCCCCeEEEEEccCCCCceE-ecCCcceeCCCCeEEEEEEe
Q 029067 108 RSAISIKNTSKSHVAFKFQTTAPKSCY-MRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 108 ~s~L~LtN~S~~~VAFKVKTTaP~~Y~-VRPn~GiL~Pgesi~I~Vtl 154 (199)
.-.|+|.|.....+.|.|...+ |. -.|-.=.|.||+++.+.+-+
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 4589999999999999998621 22 22333346668887777765
No 36
>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=62.71 E-value=7.9 Score=32.24 Aligned_cols=50 Identities=26% Similarity=0.434 Sum_probs=33.1
Q ss_pred CceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceEecCCcce--eCCCCeEEEEEEe
Q 029067 95 TKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCYMRPPGGI--LAPGESLIATVFK 154 (199)
Q Consensus 95 ~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VRPn~Gi--L~Pgesi~I~Vtl 154 (199)
..|+|..- +. .+.+ .++ .|+|.-=+-+.|++.|.-++ |.||+++.|.+.-
T Consensus 51 W~IYf~~i--r~---i~~~--~s~---~f~i~hinGDl~kl~Pt~~F~gl~~Ges~~I~~~~ 102 (164)
T PF03173_consen 51 WAIYFSSI--RP---ILQV--DSD---QFKITHINGDLHKLTPTAGFKGLAPGESLEIPFVG 102 (164)
T ss_dssp -EEEEE-S--S----EEEE--SST---TEEEEE-STTEEEEEE-TT---B-TTEEEEEEEEE
T ss_pred eEEEEecc--ee---eecc--CCC---CeEEEEEcCeEEEEeECCCCCccCCCCEEEEEEEc
Confidence 57888742 22 3333 333 38898888999999999998 9999999999986
No 37
>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=59.28 E-value=47 Score=31.48 Aligned_cols=68 Identities=19% Similarity=0.264 Sum_probs=44.4
Q ss_pred CCCcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceE----------------------ecCCccee
Q 029067 85 TRRRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCY----------------------MRPPGGIL 142 (199)
Q Consensus 85 ~~~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~----------------------VRPn~GiL 142 (199)
....+.++-. .-.|.- +++..+-+|+++|.++++|-..==+|+.-+|. |.|+ +=|
T Consensus 245 ~~~~V~~~v~-~A~Y~v-pgR~l~~~l~VtN~g~~pv~LgeF~tA~vrFln~~v~~~~~~~P~~l~A~~gL~vs~~-~pI 321 (381)
T PF04744_consen 245 PPNSVKVKVT-DATYRV-PGRTLTMTLTVTNNGDSPVRLGEFNTANVRFLNPDVPTDDPDYPDELLAERGLSVSDN-SPI 321 (381)
T ss_dssp S-SSEEEEEE-EEEEES-SSSEEEEEEEEEEESSS-BEEEEEESSS-EEE-TTT-SS-S---TTTEETT-EEES---S-B
T ss_pred CCCceEEEEe-ccEEec-CCcEEEEEEEEEcCCCCceEeeeEEeccEEEeCcccccCCCCCchhhhccCcceeCCC-CCc
Confidence 4445777774 677775 58899999999999999988774344444432 2333 248
Q ss_pred CCCCeEEEEEEee
Q 029067 143 APGESLIATVFKF 155 (199)
Q Consensus 143 ~Pgesi~I~Vtl~ 155 (199)
.|||+.+|+|...
T Consensus 322 ~PGETrtl~V~a~ 334 (381)
T PF04744_consen 322 APGETRTLTVEAQ 334 (381)
T ss_dssp -TT-EEEEEEEEE
T ss_pred CCCceEEEEEEee
Confidence 9999999999983
No 38
>PRK15253 putative fimbrial assembly chaperone protein StcB; Provisional
Probab=58.62 E-value=1.3e+02 Score=26.47 Aligned_cols=62 Identities=15% Similarity=0.260 Sum_probs=45.4
Q ss_pred CcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEcc---CC-----C----CceEecCCcceeCCCCeEEEEEEe
Q 029067 87 RRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQT---TA-----P----KSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 87 ~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKT---Ta-----P----~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
--|.++-. .+.|+.. .-..+|+|.|.++.+ |-|++ .. | .-|.|-|+.--|+||+...|.|..
T Consensus 33 Agv~l~~T-RvIy~~~---~k~~sv~i~N~~~~p--yLvQsWvd~~~~~~~~~~~~~pFivtPPlfRl~p~~~~~lRI~~ 106 (242)
T PRK15253 33 AGIVIYGT-RVIYPAE---KKEVVVQLVNQGEQA--SLVQSWIDDGNTSLPPEKIQVPFMLTPPVARVAAESGQQIKIKK 106 (242)
T ss_pred eeEEeCce-EEEEeCC---CceEEEEEEcCCCCc--EEEEEEEECCCCCCCcccccCCEEECCCeEEECCCCceEEEEEE
Confidence 35777764 7777642 234689999999875 44443 11 1 249999999999999999999987
No 39
>PRK15285 putative fimbrial chaperone protein StfD; Provisional
Probab=56.78 E-value=1.4e+02 Score=26.37 Aligned_cols=63 Identities=13% Similarity=0.163 Sum_probs=43.3
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEE--EccCCCC----ceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVAFK--FQTTAPK----SCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VAFK--VKTTaP~----~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-+.++-. .+.|+. +.-...|+|+|.++. ++.-. |.....+ -|.|-|+.--|+||+...|.|..
T Consensus 26 gv~l~~T-RVIy~~---~~~~~sv~i~N~~~~~p~LvQsWvd~~~~~~~~~pFiVtPPlfRl~p~~~~~lRI~~ 95 (250)
T PRK15285 26 AIAPDRT-RLVFRG---EDKSISVDLKNANSKLPYLAQSWVEDEKGVKITSPLIVVPPVQRIEPSAIGQVKIQG 95 (250)
T ss_pred eEEeCcc-EEEEcC---CCceEEEEEEeCCCCCcEEEEEEeeCCCCCcccCCEEEcCCeEEECCCCceEEEEEE
Confidence 4666663 777764 223469999999865 43322 2211211 39999999999999999999997
No 40
>PRK15308 putative fimbrial protein TcfA; Provisional
Probab=54.73 E-value=71 Score=28.09 Aligned_cols=66 Identities=14% Similarity=0.180 Sum_probs=49.2
Q ss_pred CCcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEcc---CCC---------------CceEecCCcceeCCCCe
Q 029067 86 RRRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQT---TAP---------------KSCYMRPPGGILAPGES 147 (199)
Q Consensus 86 ~~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKT---TaP---------------~~Y~VRPn~GiL~Pges 147 (199)
.--|.|.|- .+.+.. +.+....++|.|.++++..++|+. ++| ..-.+-|..-+|.||++
T Consensus 15 aa~l~V~Pi-~~~i~a--~~~~~~~v~V~N~g~~~~~vqV~v~r~~~PG~~~e~~~~~~~~~~~eLiaSP~~l~L~pg~~ 91 (234)
T PRK15308 15 RANMLVYPM-AAEIGA--GREEATSLFVYSKSDHTQYVRTRIKRIEHPATPQEKEVPAGNDIETGLVVSPEKFALPAGTT 91 (234)
T ss_pred hceEEEEEe-EEEecC--CCcceEEEEEEeCCCCcEEEEEEEEEEcCCCCCCCcccccccCCCCcEEEcCceeEECCCCe
Confidence 345889996 677653 334467999999999988777641 222 13677899999999999
Q ss_pred EEEEEEe
Q 029067 148 LIATVFK 154 (199)
Q Consensus 148 i~I~Vtl 154 (199)
..|.|..
T Consensus 92 q~IRli~ 98 (234)
T PRK15308 92 RTVRVIS 98 (234)
T ss_pred EEEEEEE
Confidence 9999887
No 41
>PRK15274 putative periplasmic fimbrial chaperone protein SteC; Provisional
Probab=54.06 E-value=1.6e+02 Score=26.19 Aligned_cols=63 Identities=13% Similarity=0.143 Sum_probs=44.3
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCC-eEEEEE--ccCC----CCceEecCCcceeCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKS-HVAFKF--QTTA----PKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~-~VAFKV--KTTa----P~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
-|.++-. .+.|.. ++-..+|+|.|.++. ++.-.. -... ..-|.|-|+.--|+||+...|.|..
T Consensus 27 gi~l~~T-RvIy~e---~~~~~sv~v~N~~~~~p~LVQsWvdd~~~~~~~~pFivtPPLfRlep~~~q~lRI~~ 96 (257)
T PRK15274 27 AIVPDRT-RVIFNG---NENSITVTLKNGNATLPYLAQAWLEDDKFAKDTRYFTALPPLQRIEPKSDGQVKVQP 96 (257)
T ss_pred eEEeCce-EEEEeC---CCceEEEEEEeCCCCCcEEEEEEccCCCCCcccCCEEEcCCeEEECCCCceEEEEEE
Confidence 4667764 777764 223569999999876 433332 1111 1149999999999999999999997
No 42
>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=50.06 E-value=16 Score=25.06 Aligned_cols=43 Identities=16% Similarity=0.196 Sum_probs=26.7
Q ss_pred EEEEcCCCCeEEEE-EccCCCC-ceEecCCcceeCCCCeEEEEEEe
Q 029067 111 ISIKNTSKSHVAFK-FQTTAPK-SCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 111 L~LtN~S~~~VAFK-VKTTaP~-~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
|+++|+|.-+|.|- ++....+ ...+ ...+.|+|+++..+.+.-
T Consensus 1 L~v~NpTPy~vtl~~~~~~~~~~~~~~-~~~~mi~P~s~~~~~~~~ 45 (68)
T PF02753_consen 1 LTVKNPTPYYVTLSSLKLNGGGKKKKI-DNSGMIAPFSSKSFPLPA 45 (68)
T ss_dssp EEEEE-SSS-EEEEEEEETHHHCCEEC-CCETEE-TTEEEEEETST
T ss_pred CEEECCCCcEEEEEeeeeccccccccc-CCceEECCCCceEEeccC
Confidence 68999999999886 4444333 3334 344499999998776553
No 43
>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=49.64 E-value=90 Score=22.81 Aligned_cols=48 Identities=23% Similarity=0.296 Sum_probs=25.4
Q ss_pred eEEEEEEEcCCCCeEEEEEccCCCCceEec-------------------CCcceeCCCCeEEEEEEe
Q 029067 107 VRSAISIKNTSKSHVAFKFQTTAPKSCYMR-------------------PPGGILAPGESLIATVFK 154 (199)
Q Consensus 107 v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VR-------------------Pn~GiL~Pgesi~I~Vtl 154 (199)
+.-.|+|+|.+++.|-+.+-+-.-=-|.|+ -..=.|+||++....+.+
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 445778888888777666544322222333 122248888888888887
No 44
>PF13473 Cupredoxin_1: Cupredoxin-like domain; PDB: 1IBZ_D 1IC0_E 1IBY_D.
Probab=46.15 E-value=79 Score=23.29 Aligned_cols=53 Identities=21% Similarity=0.375 Sum_probs=34.9
Q ss_pred EEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceEecCCcceeCCCCeEEEEEEe
Q 029067 89 LRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 89 L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
..++|+ ++..+ .|+++ +|.++|.....-.|-+..- .+. ..|.||++..++++-
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--TLTFTNNDSRPHEFVIPDL-----GIS---KVLPPGETATVTFTP 82 (104)
T ss_dssp EEEES--EEEEE--TTCEE--EEEEEE-SSS-EEEEEGGG-----TEE---EEE-TT-EEEEEEEE
T ss_pred CeEecC-EEEEc--CCCeE--EEEEEECCCCcEEEEECCC-----ceE---EEECCCCEEEEEEcC
Confidence 478896 66665 46655 5899999988888888761 111 569999999999854
No 45
>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=45.13 E-value=54 Score=24.45 Aligned_cols=49 Identities=20% Similarity=0.436 Sum_probs=32.3
Q ss_pred eeEEEEEEEcCCCCeE-----EEEEc-------------cCCCCceEecCCc--ceeCCCCeEEEEEEe
Q 029067 106 QVRSAISIKNTSKSHV-----AFKFQ-------------TTAPKSCYMRPPG--GILAPGESLIATVFK 154 (199)
Q Consensus 106 ~v~s~L~LtN~S~~~V-----AFKVK-------------TTaP~~Y~VRPn~--GiL~Pgesi~I~Vtl 154 (199)
-....|+|+|.++..| .|.+. +..-..|.|+|.. +.|+||+++.+-+..
T Consensus 14 Gf~~~v~v~N~~~~~i~~W~v~~~~~~~~~i~~~Wna~~s~~g~~~~v~~~~wn~~i~~G~s~~~Gf~~ 82 (101)
T PF00553_consen 14 GFQGEVTVTNNGSSPINGWTVTFTFPSGQTITSSWNATVSQSGNTVTVTNPSWNGTIAPGGSVTFGFQA 82 (101)
T ss_dssp EEEEEEEEEESSSSTEESEEEEEEESTTEEEEEEESCEEEEETTEEEEEESSTCSEEEESEEEEEEEEE
T ss_pred CeEEEEEEEECCCCccCCEEEEEEeCCCCEEeeeeccEEEecCCEEEEEcCCcCcccCCCCeEEEEEEE
Confidence 3456788888877653 33322 1112468888764 699999998877766
No 46
>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=43.59 E-value=1.1e+02 Score=22.29 Aligned_cols=32 Identities=31% Similarity=0.337 Sum_probs=23.6
Q ss_pred cceeCCCCeEEEEEEeecCCCCCCCCCCCCCCCceEEEEE
Q 029067 139 GGILAPGESLIATVFKFVEPPENNERPTDQKSKVKFKIMS 178 (199)
Q Consensus 139 ~GiL~Pgesi~I~Vtl~~~qp~~~e~p~~~k~kDKFLVqS 178 (199)
...+.||++..+++.+ +.| .-....|+|+|..
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 3468999999999998 222 2345679999965
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=42.97 E-value=2.6e+02 Score=26.73 Aligned_cols=68 Identities=15% Similarity=0.182 Sum_probs=44.1
Q ss_pred cEEecCCCc-eEeeCCCC-CeeEEEEEEEcCCCCeEEEEEccCCCCceEec-C-CcceeCCCCeEEEEEEee
Q 029067 88 RLRLDPSTK-LFFPYEPG-KQVRSAISIKNTSKSHVAFKFQTTAPKSCYMR-P-PGGILAPGESLIATVFKF 155 (199)
Q Consensus 88 ~L~IdP~~e-L~F~~e~~-k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~VR-P-n~GiL~Pgesi~I~Vtl~ 155 (199)
.|.|..... |+...+.+ -+-..+++|.|.+.++..|.++........+. + ..=.|+||+...+.|++.
T Consensus 327 ~~~v~r~r~~l~~~~~~g~i~N~Y~~~i~Nk~~~~~~~~l~v~g~~~~~~~~~~~~i~v~~g~~~~~~v~v~ 398 (434)
T TIGR02745 327 DLNVLRDRNLLYVRNSDGVVENTYTLKILNKTEQPHEYYLSVLGLPGIKIEGPGAPIHVKAGEKVKLPVFLR 398 (434)
T ss_pred EEEEEecCCcceEECCCCcEEEEEEEEEEECCCCCEEEEEEEecCCCcEEEcCCceEEECCCCEEEEEEEEE
Confidence 455555433 44443333 24458999999999988888776654443333 2 233799999998888873
No 48
>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=42.25 E-value=1.2e+02 Score=25.62 Aligned_cols=51 Identities=22% Similarity=0.333 Sum_probs=39.4
Q ss_pred CCCeeEEEEEEEcCCCCeEEEEEccCC----CCceEecC-----CcceeCCCCeEEEEEEe
Q 029067 103 PGKQVRSAISIKNTSKSHVAFKFQTTA----PKSCYMRP-----PGGILAPGESLIATVFK 154 (199)
Q Consensus 103 ~~k~v~s~L~LtN~S~~~VAFKVKTTa----P~~Y~VRP-----n~GiL~Pgesi~I~Vtl 154 (199)
.+++++-.++|.|..+. -||.|+-++ ++.|-+-- ....|+||+.+.-.+++
T Consensus 36 ~g~~v~V~~~iyN~G~~-~A~dV~l~D~~fp~~~F~lvsG~~s~~~~~i~pg~~vsh~~vv 95 (181)
T PF05753_consen 36 EGEDVTVTYTIYNVGSS-AAYDVKLTDDSFPPEDFELVSGSLSASWERIPPGENVSHSYVV 95 (181)
T ss_pred CCcEEEEEEEEEECCCC-eEEEEEEECCCCCccccEeccCceEEEEEEECCCCeEEEEEEE
Confidence 47889999999999988 799999777 34555431 13569999999888887
No 49
>smart00637 CBD_II CBD_II domain.
Probab=38.56 E-value=1.4e+02 Score=21.55 Aligned_cols=24 Identities=21% Similarity=0.217 Sum_probs=17.9
Q ss_pred CceEecCCc--ceeCCCCeEEEEEEe
Q 029067 131 KSCYMRPPG--GILAPGESLIATVFK 154 (199)
Q Consensus 131 ~~Y~VRPn~--GiL~Pgesi~I~Vtl 154 (199)
..|.|+|.. +.|+||+++.+-+..
T Consensus 50 ~~~~~~~~~wn~~i~~G~s~~~gf~~ 75 (92)
T smart00637 50 GHVTATNASWNGTIAPGGSVSFGFQG 75 (92)
T ss_pred CEEEEecCccccccCCCCEEEEEEEe
Confidence 368888644 799999988765554
No 50
>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=37.82 E-value=1.1e+02 Score=21.29 Aligned_cols=52 Identities=23% Similarity=0.236 Sum_probs=33.3
Q ss_pred CCCeeEEEEEEEcCCCCe-EEEEEccCCCCceEecCCcceeCCCCeEEEEEEe
Q 029067 103 PGKQVRSAISIKNTSKSH-VAFKFQTTAPKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 103 ~~k~v~s~L~LtN~S~~~-VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
.++..+-.++|+|..... =.|+|+-...+...-.-..+-|+||++..+.+..
T Consensus 17 ~g~~~~i~~~V~N~G~~~~~~~~v~~~~~~~~~~~~~i~~L~~g~~~~v~~~~ 69 (101)
T PF07705_consen 17 PGEPVTITVTVKNNGTADAENVTVRLYLDGNSVSTVTIPSLAPGESETVTFTW 69 (101)
T ss_dssp TTSEEEEEEEEEE-SSS-BEEEEEEEEETTEEEEEEEESEB-TTEEEEEEEEE
T ss_pred CCCEEEEEEEEEECCCCCCCCEEEEEEECCceeccEEECCcCCCcEEEEEEEE
Confidence 478888999999997753 4566653322222222223779999999999998
No 51
>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=37.23 E-value=1.4e+02 Score=22.09 Aligned_cols=51 Identities=14% Similarity=0.247 Sum_probs=32.1
Q ss_pred CCeeEEEEEEEcCCCCe--EEEEEccCCCCceEecCC-----cceeCCCCeEEEEEEe
Q 029067 104 GKQVRSAISIKNTSKSH--VAFKFQTTAPKSCYMRPP-----GGILAPGESLIATVFK 154 (199)
Q Consensus 104 ~k~v~s~L~LtN~S~~~--VAFKVKTTaP~~Y~VRPn-----~GiL~Pgesi~I~Vtl 154 (199)
++.....+.|+|.++.+ +.||+-==+.+-+.|.|. .=+|.+++++.|.-.-
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 67778999999999774 899987667777777776 2357777776666554
No 52
>PF14796 AP3B1_C: Clathrin-adaptor complex-3 beta-1 subunit C-terminal
Probab=37.15 E-value=1.5e+02 Score=24.29 Aligned_cols=65 Identities=18% Similarity=0.292 Sum_probs=40.9
Q ss_pred CCcEEecCCCceEeeCCC----CCeeEEEEEEEcCCCCeEE-EEEccCC-CCceEe--cCCcceeCCCCeEEEEEEe
Q 029067 86 RRRLRLDPSTKLFFPYEP----GKQVRSAISIKNTSKSHVA-FKFQTTA-PKSCYM--RPPGGILAPGESLIATVFK 154 (199)
Q Consensus 86 ~~~L~IdP~~eL~F~~e~----~k~v~s~L~LtN~S~~~VA-FKVKTTa-P~~Y~V--RPn~GiL~Pgesi~I~Vtl 154 (199)
+.-|.++ .+|..++ ...+.-.|+++|.++..+. -+|.... +.--+| -|..+.|+||+++.+.+-.
T Consensus 66 G~GL~v~----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 66 GKGLSVE----YRFSRQPSLYSPSMVSIQLTFTNNSDEPIKNIHIGEKKLPAGMRIHEFPEIESLEPGASVTVSLGI 138 (145)
T ss_pred CCceeEE----EEEccCCcCCCCCcEEEEEEEEecCCCeecceEECCCCCCCCcEeeccCcccccCCCCeEEEEEEE
Confidence 4445543 3466643 3677788999999997543 2232222 223334 4889999999998877655
No 53
>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=34.12 E-value=1.4e+02 Score=19.62 Aligned_cols=65 Identities=12% Similarity=0.174 Sum_probs=39.1
Q ss_pred EEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEccCCCCceEe-cCCcc---eeCCCCeEEEEEEe
Q 029067 89 LRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQTTAPKSCYM-RPPGG---ILAPGESLIATVFK 154 (199)
Q Consensus 89 L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVKTTaP~~Y~V-RPn~G---iL~Pgesi~I~Vtl 154 (199)
|-|-|+ .|.+.........+++.-.=-....+-+.|++-......+ .+... .+++|+.+.|.+--
T Consensus 1 l~iRPE-~i~l~~~~~~~~~g~V~~~~~~G~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~G~~v~l~~~~ 69 (75)
T PF08402_consen 1 LGIRPE-DIRLSPEGENRLPGTVVSVEFLGSETRYTVRLEGGEELVVRVPNSQRDSPLEPGDEVRLSWDP 69 (75)
T ss_dssp EEE-GG-GEEEESSTTTEEEEEEEEEEEESSEEEEEEEETTSSEEEEEEESSG-TTT--TTSEEEEEEEG
T ss_pred CEECcc-eeEEECCCCCeEEEEEEEEEECCCEEEEEEEECCCCEEEEEecCccccCCCCCCCEEEEEECc
Confidence 456675 7777422234666666666666677777788777666433 34444 68999988887653
No 54
>PF13205 Big_5: Bacterial Ig-like domain
Probab=32.27 E-value=1.9e+02 Score=20.65 Aligned_cols=56 Identities=25% Similarity=0.310 Sum_probs=34.8
Q ss_pred ceEeeCCCC-CeeEEEEEEEc--CCCCeEEEEEccCCCCceEecCCcceeCCCCeEEEEEEe
Q 029067 96 KLFFPYEPG-KQVRSAISIKN--TSKSHVAFKFQTTAPKSCYMRPPGGILAPGESLIATVFK 154 (199)
Q Consensus 96 eL~F~~e~~-k~v~s~L~LtN--~S~~~VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl 154 (199)
.|.|..+-+ ..+...+.+.. ....+|.+. ....+.+.++|. +-|.+|....|+|.-
T Consensus 26 ~i~Fs~~v~~~s~~~~~~~~~~~~~~~~v~~~--~~~~~~~~i~p~-~~L~~~t~Y~v~i~~ 84 (107)
T PF13205_consen 26 VITFSEPVDPASVSSAITITDSNGSGVPVSFS--SWDGNTLTITPS-QPLKPGTTYTVTIDS 84 (107)
T ss_pred EEEECCceecCccceEEEEEecCCCcEEEEEE--EccCCEEEEEEC-CcCCCCCEEEEEECC
Confidence 455655433 23344555643 333455555 334488899998 557899999999854
No 55
>COG3354 FlaG Putative archaeal flagellar protein G [Cell motility and secretion]
Probab=31.75 E-value=1.2e+02 Score=25.27 Aligned_cols=64 Identities=23% Similarity=0.219 Sum_probs=46.5
Q ss_pred cEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEE-----------EccCCCCceEecCCcce-eCCCCeEEEEEEe
Q 029067 88 RLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFK-----------FQTTAPKSCYMRPPGGI-LAPGESLIATVFK 154 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFK-----------VKTTaP~~Y~VRPn~Gi-L~Pgesi~I~Vtl 154 (199)
.+.=||. .+...+. +..-+-++-|+|+.++.++|- +.|-+.-.|..-+..++ |.||+--. +|++
T Consensus 53 aIIndPg-~i~~~~~-~g~~t~t~yiKNtG~~~~~fd~~sitVliDG~iv~~a~~~~~~~~gs~i~l~PG~Vg~-ev~v 128 (154)
T COG3354 53 AIINDPG-QIPYVGT-DGPYTYTFYIKNTGSDSIAFDNTSITVLIDGNIVTPAYVTFTSVNGSSIRLSPGQVGR-EVTV 128 (154)
T ss_pred EEecCCC-CCccccC-CCceEEEEEEecCCCcccccCCCeEEEEEcCcEeccceEEEEecCCCeeEecCCceee-EEEe
Confidence 4555775 5555442 245578999999999999996 45566667788889999 99999874 5554
No 56
>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=30.95 E-value=63 Score=21.93 Aligned_cols=28 Identities=25% Similarity=0.508 Sum_probs=17.5
Q ss_pred CceEeeCCCCCeeEEEEEEEcCCCCeEEEEE
Q 029067 95 TKLFFPYEPGKQVRSAISIKNTSKSHVAFKF 125 (199)
Q Consensus 95 ~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKV 125 (199)
.-..|.+ +. +...-++...+...||||+
T Consensus 44 ~C~~y~~--~~-i~~v~~~~~~~~~~VA~K~ 71 (71)
T PF08277_consen 44 KCYLYNY--GS-ISTVQKTDSSSGNKVAFKI 71 (71)
T ss_pred CEEEEEc--CC-EEEEEEeecCCCeEEEEEC
Confidence 4455544 33 5455556666678999996
No 57
>PF11906 DUF3426: Protein of unknown function (DUF3426); InterPro: IPR021834 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 262 to 463 amino acids in length.
Probab=30.32 E-value=1.8e+02 Score=22.69 Aligned_cols=51 Identities=18% Similarity=0.133 Sum_probs=31.5
Q ss_pred CCeeEEEEEEEcCCCCeEEEE---E------------ccCCCCceEecC--CcceeCCCCeEEEEEEe
Q 029067 104 GKQVRSAISIKNTSKSHVAFK---F------------QTTAPKSCYMRP--PGGILAPGESLIATVFK 154 (199)
Q Consensus 104 ~k~v~s~L~LtN~S~~~VAFK---V------------KTTaP~~Y~VRP--n~GiL~Pgesi~I~Vtl 154 (199)
.....-..+|.|.++.+++|= + |+-.|..|...+ ...-|.||+++.+.+.+
T Consensus 67 ~~~l~v~g~i~N~~~~~~~~P~l~l~L~D~~g~~l~~r~~~P~~yl~~~~~~~~~l~pg~~~~~~~~~ 134 (149)
T PF11906_consen 67 PGVLVVSGTIRNRADFPQALPALELSLLDAQGQPLARRVFTPADYLPPGLAAQAGLPPGESVPFRLRL 134 (149)
T ss_pred CCEEEEEEEEEeCCCCcccCceEEEEEECCCCCEEEEEEEChHHhcccccccccccCCCCeEEEEEEe
Confidence 455556667777776654441 1 122344454433 24459999999999998
No 58
>COG3565 Predicted dioxygenase of extradiol dioxygenase family [General function prediction only]
Probab=28.66 E-value=1e+02 Score=25.10 Aligned_cols=36 Identities=28% Similarity=0.463 Sum_probs=29.3
Q ss_pred CCCcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEE
Q 029067 85 TRRRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFK 124 (199)
Q Consensus 85 ~~~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFK 124 (199)
.+-...|.| .++|.++++.+ .+|-|..++.+.+-||
T Consensus 92 ~gi~~~i~P--~vRF~Ge~gEq--~TlFl~DP~gN~lEfK 127 (138)
T COG3565 92 AGIPFHIPP--KVRFKGEPGEQ--RTLFLFDPSGNALEFK 127 (138)
T ss_pred cCCCcccCc--eEEecCCccce--EEEEEECCCCCeeeee
Confidence 343455556 89999999987 5899999999999998
No 59
>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=27.01 E-value=74 Score=27.26 Aligned_cols=26 Identities=31% Similarity=0.520 Sum_probs=21.6
Q ss_pred CeEEEEEccCCCCceEecCCcceeCCCCeEEEEEEee
Q 029067 119 SHVAFKFQTTAPKSCYMRPPGGILAPGESLIATVFKF 155 (199)
Q Consensus 119 ~~VAFKVKTTaP~~Y~VRPn~GiL~Pgesi~I~Vtl~ 155 (199)
+||+||+ |...-|+||+++++.+...
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 4788887 6667799999999998884
No 60
>PRK15249 fimbrial chaperone protein StbB; Provisional
Probab=25.64 E-value=1.4e+02 Score=26.23 Aligned_cols=42 Identities=14% Similarity=0.093 Sum_probs=28.0
Q ss_pred EEEEEcCCCCeEEEE-EccCCCCceEecCCcceeCCCCeEEEEE
Q 029067 110 AISIKNTSKSHVAFK-FQTTAPKSCYMRPPGGILAPGESLIATV 152 (199)
Q Consensus 110 ~L~LtN~S~~~VAFK-VKTTaP~~Y~VRPn~GiL~Pgesi~I~V 152 (199)
.|+|+|++..++.|. ++....+ -.+....|+|.|+++..+.+
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 499999999988776 3321122 12223457899999987764
No 61
>PRK06655 flgD flagellar basal body rod modification protein; Reviewed
Probab=24.89 E-value=3.7e+02 Score=23.31 Aligned_cols=81 Identities=10% Similarity=0.097 Sum_probs=54.5
Q ss_pred ccccceeccCCCCCcEEecCCCceEeeCCCCCe-eEEEEEEEcCCCCeEE-EEEccCCCCceEe----cCCcceeCCCCe
Q 029067 74 NVSSMAKSLLPTRRRLRLDPSTKLFFPYEPGKQ-VRSAISIKNTSKSHVA-FKFQTTAPKSCYM----RPPGGILAPGES 147 (199)
Q Consensus 74 ~~~~~~ksl~p~~~~L~IdP~~eL~F~~e~~k~-v~s~L~LtN~S~~~VA-FKVKTTaP~~Y~V----RPn~GiL~Pges 147 (199)
.++.|+|..+-....+.++......|.+.+... ...+|+|+|...+.|. +.+....++.+.+ +...|-..|...
T Consensus 92 a~~lIGk~V~~~~~~~~~~~~~~~~~~~~l~~~a~~vti~I~D~~G~~Vrt~~lg~~~aG~~~f~WDG~d~~G~~lp~G~ 171 (225)
T PRK06655 92 ASSLVGRGVLVPGDTVLVGTGGTTPFGVELPSAADNVTVTITDSAGQVVRTIDLGAQSAGVVSFTWDGTDTDGNALPDGN 171 (225)
T ss_pred HHHhcCCeEEEecceEEecCCCceEEEEEcCCCCcEEEEEEEcCCCCEEEEEecCCcCCCceeEEECCCCCCCCcCCCee
Confidence 455677776667777877764356666655433 3578999999888775 6776666777765 455676555556
Q ss_pred EEEEEEe
Q 029067 148 LIATVFK 154 (199)
Q Consensus 148 i~I~Vtl 154 (199)
..+.|.-
T Consensus 172 Yt~~V~A 178 (225)
T PRK06655 172 YTIKASA 178 (225)
T ss_pred EEEEEEE
Confidence 7777765
No 62
>KOG3620 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.45 E-value=1.9e+02 Score=31.93 Aligned_cols=79 Identities=24% Similarity=0.265 Sum_probs=57.0
Q ss_pred cEEecCCCceEeeCCC-CCeeEEEEEEEcCCCCeEEEEE-ccCCCCceEec---CCcceeCCCCeEEEEEEeecCCCCCC
Q 029067 88 RLRLDPSTKLFFPYEP-GKQVRSAISIKNTSKSHVAFKF-QTTAPKSCYMR---PPGGILAPGESLIATVFKFVEPPENN 162 (199)
Q Consensus 88 ~L~IdP~~eL~F~~e~-~k~v~s~L~LtN~S~~~VAFKV-KTTaP~~Y~VR---Pn~GiL~Pgesi~I~Vtl~~~qp~~~ 162 (199)
.|.+.|+ +|+|..-+ +|.++.+|.|.|.=+++|.-|= .-..+-+|+-+ -+.+.|+||--..|-=.+| -|+
T Consensus 526 sL~~iPe-qi~f~ptFPgK~v~~~L~i~nSF~~~v~v~~i~l~edvrf~fk~f~~n~~~l~pg~ltk~griyF--dP~-- 600 (1626)
T KOG3620|consen 526 SLEIIPE-QISFKPTFPGKMVTAVLSIRNSFTHPVHVKGISLAEDVRFRFKDFNANGTTLAPGTLTKVGRIYF--DPA-- 600 (1626)
T ss_pred eeEechh-hhccCCCCCcceeeeeeehhcccCcceeeeeeeeccCcceeeecccCCccccccccccccceEEe--ccc--
Confidence 5889996 99998765 7999999999999988887663 33334455554 5778999999877766664 232
Q ss_pred CCCCCCCCCceEEE
Q 029067 163 ERPTDQKSKVKFKI 176 (199)
Q Consensus 163 e~p~~~k~kDKFLV 176 (199)
.+|.|.--|
T Consensus 601 -----a~CgdhCYi 609 (1626)
T KOG3620|consen 601 -----AVCGDHCYI 609 (1626)
T ss_pred -----ccccCeeEe
Confidence 467766543
No 63
>smart00605 CW CW domain.
Probab=24.06 E-value=1.8e+02 Score=21.09 Aligned_cols=32 Identities=38% Similarity=0.572 Sum_probs=17.8
Q ss_pred CceEeeCCCCCeeEEEEEEEcC-CCCeEEEEEccCCC
Q 029067 95 TKLFFPYEPGKQVRSAISIKNT-SKSHVAFKFQTTAP 130 (199)
Q Consensus 95 ~eL~F~~e~~k~v~s~L~LtN~-S~~~VAFKVKTTaP 130 (199)
....|.+ +. + ..|+-.+. +...||||+.++.+
T Consensus 47 ~C~~f~~--~~-~-~~v~~~~~~~~~~VAfK~~~~~~ 79 (94)
T smart00605 47 TCYLFSY--GT-V-LTVKKLSSSSGKKVAFKVSTDQP 79 (94)
T ss_pred ceEEEEc--CC-e-EEEEEccCCCCcEEEEEEeCCCC
Confidence 3455655 32 2 23444444 44689999986544
No 64
>PF06586 TraK: TraK protein; InterPro: IPR010563 This family consists of several TraK proteins from Escherichia coli, Salmonella typhi and Salmonella typhimurium. TraK is known to be essential for pilus assembly but its exact role in this process is unknown [].
Probab=23.60 E-value=2.8e+02 Score=23.39 Aligned_cols=75 Identities=27% Similarity=0.299 Sum_probs=43.8
Q ss_pred ccccccceeccCCCCCcEEecCCCceEeeCCCCCeeEEEEEEEcCCCCeEEEEEc-cCCCCceEe--cCCcceeCCCCeE
Q 029067 72 SSNVSSMAKSLLPTRRRLRLDPSTKLFFPYEPGKQVRSAISIKNTSKSHVAFKFQ-TTAPKSCYM--RPPGGILAPGESL 148 (199)
Q Consensus 72 ~~~~~~~~ksl~p~~~~L~IdP~~eL~F~~e~~k~v~s~L~LtN~S~~~VAFKVK-TTaP~~Y~V--RPn~GiL~Pgesi 148 (199)
+.++..+.+........|.+.|. -.|.+ ..-.-...+|+|.++.++.+.=+ +-.++..-| .|. .|.|||+.
T Consensus 157 gf~~~~~~~~~~~~~~~l~~~~~--~~~~G--~~l~~~~y~v~N~~~~~v~l~E~~f~~~~v~AVa~~~~--~L~PGe~t 230 (234)
T PF06586_consen 157 GFSVRPVDSEPPPLPKGLRLTPV--QRYEG--SGLRGEVYRVTNTSDQPVELDERDFYSPGVRAVALWPP--TLAPGEST 230 (234)
T ss_pred CcEEecccCCcccccccceEeee--eEEec--CceEEEEEEEEeCCCCCEEecHHHhCCCCcEEEEeccc--ccCCCCEE
Confidence 34444444444324445666663 34443 33334678899999999988744 223443333 344 78999987
Q ss_pred EEEE
Q 029067 149 IATV 152 (199)
Q Consensus 149 ~I~V 152 (199)
.|-|
T Consensus 231 ~vyV 234 (234)
T PF06586_consen 231 EVYV 234 (234)
T ss_pred EEEC
Confidence 7654
No 65
>PRK15295 fimbrial assembly chaperone SthB; Provisional
Probab=22.52 E-value=2e+02 Score=24.86 Aligned_cols=49 Identities=12% Similarity=0.234 Sum_probs=33.3
Q ss_pred CceEeeCCCCCeeEEEEEEEcCCCCeEEEE-EccCCCCceEecCCcceeCCCCeEEEEE
Q 029067 95 TKLFFPYEPGKQVRSAISIKNTSKSHVAFK-FQTTAPKSCYMRPPGGILAPGESLIATV 152 (199)
Q Consensus 95 ~eL~F~~e~~k~v~s~L~LtN~S~~~VAFK-VKTTaP~~Y~VRPn~GiL~Pgesi~I~V 152 (199)
..|.|....+ .|+|.|+|..+|.|- ++... +. +. ..|.|.|+++..+.+
T Consensus 148 ~~L~~~~~~~-----~l~v~NptPyyitl~~l~~~~-~~--~~-~~~mI~P~s~~~~~~ 197 (226)
T PRK15295 148 QQLKWQTAGD-----VITVNNPTPYYMNFASVTLNS-HE--VK-SATFVPPKSSASFKL 197 (226)
T ss_pred hccEEEEcCC-----EEEEECCCceEEEEEEEEECC-cc--cC-CCceECCCCccEEEc
Confidence 4666764322 499999999998775 55432 22 22 258999999987764
Done!