Query T0565 ZP_02063661.1, Bacteroides ovatus, 326 residues
Match_columns 326
No_of_seqs 183 out of 2482
Neff 7.7
Searched_HMMs 11830
Date Tue Jun 1 15:17:23 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0565.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0565.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00877 NLPC_P60: NlpC/P60 fa 99.9 3.7E-27 3.1E-31 195.1 6.4 104 188-305 1-105 (105)
2 PF05382 Amidase_5: Bacterioph 98.8 1.4E-08 1.2E-12 72.5 10.2 79 198-279 26-112 (145)
3 PF08239 SH3_3: Bacterial SH3 98.7 6.7E-09 5.7E-13 74.6 5.0 51 39-90 1-52 (52)
4 PF06347 SH3_4: Bacterial SH3 98.5 3.7E-08 3.2E-12 69.7 5.0 52 38-90 2-54 (55)
5 PF06672 DUF1175: Protein of u 98.5 5.8E-07 4.9E-11 61.9 10.1 104 176-286 29-187 (216)
6 PF08239 SH3_3: Bacterial SH3 97.9 3.8E-06 3.2E-10 56.5 4.1 50 112-162 2-51 (52)
7 PF06347 SH3_4: Bacterial SH3 97.4 6.6E-05 5.6E-09 48.3 4.6 52 110-162 2-53 (55)
8 PF05708 DUF830: Orthopoxvirus 97.1 9.1E-05 7.7E-09 47.4 2.2 51 173-223 77-129 (155)
9 PF06940 DUF1287: Domain of un 95.3 0.018 1.5E-06 32.3 6.1 118 140-281 15-147 (164)
10 PF05257 CHAP: CHAP domain; I 94.9 0.0067 5.6E-07 35.1 2.8 69 198-270 15-88 (124)
11 PF08460 SH3_5: Bacterial SH3 94.4 0.015 1.2E-06 32.8 3.6 47 39-85 13-64 (65)
12 PF05708 DUF830: Orthopoxvirus 93.5 0.028 2.4E-06 30.9 3.7 60 240-306 1-72 (155)
13 PF07653 SH3_2: Variant SH3 do 92.4 0.027 2.3E-06 31.0 2.3 35 56-91 17-54 (55)
14 PF00018 SH3_1: SH3 domain; I 90.8 0.14 1.2E-05 26.4 4.5 31 56-86 15-48 (48)
15 PF07313 DUF1460: Protein of u 88.9 0.16 1.3E-05 26.0 3.6 41 238-281 151-194 (216)
16 PF07313 DUF1460: Protein of u 87.5 0.063 5.3E-06 28.7 0.8 34 181-214 1-46 (216)
17 PF11948 DUF3465: Protein of u 64.4 1.2 0.0001 20.2 1.7 16 1-16 1-16 (131)
18 PF11777 DUF3316: Protein of u 43.8 5.2 0.00044 16.0 2.2 19 1-20 1-19 (114)
19 PF02938 GAD: GAD domain; Int 42.0 3.7 0.00031 17.0 1.2 15 237-251 71-85 (95)
20 PF06551 DUF1120: Protein of u 38.1 8 0.00067 14.8 3.5 13 1-13 1-13 (145)
21 PF01878 DUF55: Protein of unk 37.2 4.1 0.00035 16.7 0.8 12 239-250 38-49 (143)
22 PF11153 DUF2931: Protein of u 35.4 8.3 0.0007 14.6 2.1 21 1-21 1-21 (216)
23 PF07203 DUF1412: Protein of u 34.8 9 0.00076 14.4 2.9 27 1-27 1-27 (74)
24 PF08007 Cupin_4: Cupin superf 31.5 10 0.00086 14.1 2.2 23 239-269 178-200 (319)
25 PF06097 DUF945: Bacterial pro 30.3 11 0.00089 14.0 2.1 23 1-23 1-23 (459)
26 PF04076 BOF: Bacterial OB fol 29.1 6.4 0.00054 15.4 0.7 20 1-21 1-20 (126)
27 PF03032 Brevenin: Brevenin/es 28.2 10 0.00086 14.1 1.6 22 1-23 3-24 (46)
28 PF02668 TauD: Taurine catabol 25.1 11 0.00097 13.7 1.4 11 240-250 221-231 (255)
29 PF00166 Cpn10: Chaperonin 10 24.6 3 0.00025 17.6 -1.7 39 213-251 21-68 (93)
30 PF10566 Glyco_hydro_97: Glyco 24.2 9.2 0.00077 14.4 0.7 45 177-222 313-373 (643)
31 PF01052 SpoA: Surface present 22.6 15 0.0012 13.1 2.8 34 236-276 24-57 (77)
32 PF12120 RNApol_Rpb2_rif: DNA/ 20.8 14 0.0012 13.2 1.1 28 237-264 6-33 (100)
No 1
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The Escherichia coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3h41_A 2fg0_B 2evr_A 2hbw_A 2k1g_A.
Probab=99.93 E-value=3.7e-27 Score=195.13 Aligned_cols=104 Identities=45% Similarity=0.730 Sum_probs=90.6
Q ss_pred CCCEECCCCCCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHCEECCCCCCHHHCCCCCEEEECCCCCCCCCCCCEEEEEE
Q ss_conf 98322158888960169999999997377689786999960702155566323588748985787787667762079999
Q T0565 188 GIPYLWAGTSSKGVDCSGLVRTVLFMHDIIIPRDASQQAYVGEHIDIAPDFSNVKRGDLVFFGRKATAERKEGISHVGIY 267 (326)
Q Consensus 188 G~pY~wGG~~~~g~DCSG~~~~~~~~~G~~lpr~s~~Q~~~g~~v~~~~~~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy 267 (326)
|+||+|||.++.|+|||||++++|+.+|+.||+++..|...+... ....+++||||||||.. .+.++|||||
T Consensus 1 G~pY~~Gg~~~~g~DCsglv~~~~~~~Gi~l~~~~~~~~~~~~~~--~~~~~~~~pGDlvf~~~------~~~~~HVgIy 72 (105)
T PF00877_consen 1 GKPYVWGGRSPDGFDCSGLVRWVYRQAGINLPRTSGAQYQAGTSK--WVSVDELQPGDLVFFKG------GGGPSHVGIY 72 (105)
T ss_dssp --B----------------HHHHHHTT-----SSHHHHCCHS-E----E-GGG-----EEEEES------TS-EEBEEEB
T ss_pred CCEECCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHCCCC--CCCHHHCCCCCEEEECC------CCCCCEEEEE
T ss_conf 973204885999964089999999983987996467876313534--58244189978899689------9898788999
Q ss_pred ECCCEEEECCC-CCEEEECCCCCCCCCCHHHCEEEEEEE
Q ss_conf 51987898179-955988112566544100071578887
Q T0565 268 LGNKQFIHALG-DVHVSSMNPADQNYDEFNTKRLLFAVR 305 (326)
Q Consensus 268 ~g~~~~iha~~-~~~~~~~~~~~~~~~~~~~~~~~~~~r 305 (326)
+|+++||||++ ++.+.+++ +.||.+||++++|
T Consensus 73 ~g~~~~iha~~~~v~~~~~~------~~~~~~~~~~~~r 105 (105)
T PF00877_consen 73 IGNGKMIHASGGGVSISSLN------SPYWKKRYVGARR 105 (105)
T ss_dssp ----EEEE--TSBSEEEETT------SHHHHHHEEEEE-
T ss_pred ECCCEEEEECCCCEEEEECC------CHHHHHHHHHEEC
T ss_conf 56998999899968999788------6789987575389
No 2
>PF05382 Amidase_5: Bacteriophage peptidoglycan hydrolase ; InterPro: IPR008044 At least one of the members of this domain, the Pal protein from the pneumococcal bacteriophage Dp-1 O03979 from SWISSPROT has been shown to be an N-acetylmuramoyl-L-alanine amidase . According to the known modular structure of this and other peptidoglycan hydrolases from the pneumococcal system, the active site should reside in the N-terminal domain whereas the C-terminal domain binds to the choline residues of the cell wall teichoic acids , .
Probab=98.83 E-value=1.4e-08 Score=72.50 Aligned_cols=79 Identities=23% Similarity=0.351 Sum_probs=54.8
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCC---CHHHHH----HHCE-ECCCCCCHHHCCCCCEEEECCCCCCCCCCCCEEEEEEEC
Q ss_conf 89601699999999973776897---869999----6070-215556632358874898578778766776207999951
Q T0565 198 SKGVDCSGLVRTVLFMHDIIIPR---DASQQA----YVGE-HIDIAPDFSNVKRGDLVFFGRKATAERKEGISHVGIYLG 269 (326)
Q Consensus 198 ~~g~DCSG~~~~~~~~~G~~lpr---~s~~Q~----~~g~-~v~~~~~~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g 269 (326)
+.+.|||+||.++++..|...+. ++..-. +.|. .|.. ....++|+||+++|...+. ..+-..|+||+++
T Consensus 26 ~~~~DCSs~V~~ALr~aG~~~~g~~~nT~tL~~~L~~~G~~~I~~-~~~~~~q~GDI~I~g~~g~--S~Ga~GHtgi~~~ 102 (145)
T PF05382_consen 26 PDSYDCSSFVYYALREAGFSISGWAGNTETLHQQLKKNGFKKISE-NEDWDLQRGDIVIWGKRGQ--SGGAGGHTGIFMD 102 (145)
T ss_pred CCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCEEECC-CCCCCCCCCCEEEECCCCC--CCCCCCEEEEEEC
T ss_conf 998850899999999839888887568899999997384399533-6767777789999827777--7898973799966
Q ss_pred CCEEEECCCC
Q ss_conf 9878981799
Q T0565 270 NKQFIHALGD 279 (326)
Q Consensus 270 ~~~~iha~~~ 279 (326)
..+|||....
T Consensus 103 ~~~~ihc~Y~ 112 (145)
T PF05382_consen 103 WDNIIHCNYG 112 (145)
T ss_pred CCEEEEECCC
T ss_conf 9808872355
No 3
>PF08239 SH3_3: Bacterial SH3 domain; InterPro: IPR013247 A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.
Probab=98.70 E-value=6.7e-09 Score=74.64 Aligned_cols=51 Identities=27% Similarity=0.458 Sum_probs=46.5
Q ss_pred CCCCCCCCCCCCCHHEEEECCCCEEEEEEE-CCEEEEECCCCCEEEEEHHHHC
Q ss_conf 403300378987100011217847999861-5648997278821544000102
Q T0565 39 SVCNLREEGKFTSGMSTQALLGMPVKVLQY-NGWYEIQTPDDYTGWVHRMVIT 90 (326)
Q Consensus 39 ~~lnvR~~Ps~~s~~vtql~~G~~v~Vl~~-~GW~kV~~~dG~~GWV~~~~i~ 90 (326)
+.||||++|++++++++++..|+.|+|+++ ++|++|++ +|..|||.++||+
T Consensus 1 ~~lnvR~~p~~~s~ii~~l~~g~~v~v~~~~~~W~~V~~-~g~~GwV~~~yl~ 52 (52)
T PF08239_consen 1 DNLNVRSGPSTSSKIIGTLPKGTRVTVLGESGGWYKVRY-NGKTGWVSSDYLK 52 (52)
T ss_pred CEEEEECCCCCCCHHHEEECCCCEEEEECCCCCEEEEEE-CCEEEEEEHHHCC
T ss_conf 979994899999846699939999999651296999998-9999999966585
No 4
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=98.53 E-value=3.7e-08 Score=69.72 Aligned_cols=52 Identities=37% Similarity=0.696 Sum_probs=46.6
Q ss_pred CCCCCCCCCCCCCCHHEEEECCCCEEEEEEEC-CEEEEECCCCCEEEEEHHHHC
Q ss_conf 24033003789871000112178479998615-648997278821544000102
Q T0565 38 ISVCNLREEGKFTSGMSTQALLGMPVKVLQYN-GWYEIQTPDDYTGWVHRMVIT 90 (326)
Q Consensus 38 ~~~lnvR~~Ps~~s~~vtql~~G~~v~Vl~~~-GW~kV~~~dG~~GWV~~~~i~ 90 (326)
.+.+|||++|+.+++++.++..|.+++|++.+ +|++|+ .||+.|||+...|.
T Consensus 2 ~~~~~lr~~P~~~s~v~~~l~~g~~~~v~~~~~~W~~V~-~~g~~GWi~~~~l~ 54 (55)
T PF06347_consen 2 KDEANLRSGPSTDSPVVAQLEPGVPVEVLECNGGWCRVR-ADGYEGWIHRSLLW 54 (55)
T ss_pred CCEEEEECCCCCCCCEEEEECCCCEEEEEEECCCEEEEE-ECCEEEEEECCCCC
T ss_conf 842588618899981349983997999999339889999-79908848901123
No 5
>PF06672 DUF1175: Protein of unknown function (DUF1175); InterPro: IPR009558 This family consists of several hypothetical bacterial proteins of around 210 residues in length. The function of this family is unknown.
Probab=98.49 E-value=5.8e-07 Score=61.85 Aligned_cols=104 Identities=21% Similarity=0.349 Sum_probs=61.0
Q ss_pred HHHHHHHHHHHCCCC-EECCCCCCCCCCHHHHHHHHHHHC-----CCCCCCCH-----------------HHHHH-----
Q ss_conf 478999999826983-221588889601699999999973-----77689786-----------------99996-----
Q T0565 176 VESIIETAYSMMGIP-YLWAGTSSKGVDCSGLVRTVLFMH-----DIIIPRDA-----------------SQQAY----- 227 (326)
Q Consensus 176 ~~~~i~~A~~~lG~p-Y~wGG~~~~g~DCSG~~~~~~~~~-----G~~lpr~s-----------------~~Q~~----- 227 (326)
++=++.+|+..+-.. =.| -....||+|||+++++.. +.|++++- ..|.-
T Consensus 29 R~Wfv~IA~~q~~~~~p~w---~~~~rDCAGlVRfa~~EALk~Hd~kW~~~~g~~~~d~~~y~~P~~pl~~~~~f~~~~w 105 (216)
T PF06672_consen 29 RAWFVRIALEQLRQGSPRW---REEQRDCAGLVRFAAREALKKHDKKWLQANGYSFEDVTKYLYPETPLSGAQIFRAQSW 105 (216)
T ss_pred HHHHHHHHHHHHHCCCCCC---CCCCCCHHHHHHHHHHHHHHHHCHHHHHHCCCCHHHHHHCCCCCCCCCHHHHEECCCC
T ss_conf 9999999999976479764---4414430799999999999875310586659985662330699887756661012132
Q ss_pred ---HC---EEC-----------CCCCCHHHCCCCCEEEECCCCCCCCCCCCEEEEEEECC----CEEEECC------CCC
Q ss_conf ---07---021-----------55566323588748985787787667762079999519----8789817------995
Q T0565 228 ---VG---EHI-----------DIAPDFSNVKRGDLVFFGRKATAERKEGISHVGIYLGN----KQFIHAL------GDV 280 (326)
Q Consensus 228 ---~g---~~v-----------~~~~~~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g~----~~~iha~------~~~ 280 (326)
.| ..+ .+..+.+.++||||+||.-.. ...+-|.|||+|+ .-.-|.- +++
T Consensus 106 ~~~~g~f~~ya~A~~Lv~~N~~fV~rd~~~A~PGDL~Ff~q~d----~~~pyHlMI~~g~~~~~~~vYHtG~~~~~~~~~ 181 (216)
T PF06672_consen 106 RQGDGKFGPYADAITLVQYNSRFVSRDVSQARPGDLLFFHQED----DQMPYHLMIWVGRDAENYIVYHTGPVGETDGEM 181 (216)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCC----CCCCEEEEEEEECCCCEEEEEECCCCCCCCCCE
T ss_conf 3279862257889999985001646567545987678864788----764137999960565136998337888998847
Q ss_pred EEEECC
Q ss_conf 598811
Q T0565 281 HVSSMN 286 (326)
Q Consensus 281 ~~~~~~ 286 (326)
+.+++.
T Consensus 182 R~v~~~ 187 (216)
T PF06672_consen 182 RAVRLS 187 (216)
T ss_pred EEEEHH
T ss_conf 787899
No 6
>PF08239 SH3_3: Bacterial SH3 domain; InterPro: IPR013247 A homologue of the SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.
Probab=97.90 E-value=3.8e-06 Score=56.51 Aligned_cols=50 Identities=24% Similarity=0.436 Sum_probs=46.8
Q ss_pred CEEEECCCCCCCCEEEEECCCCEEEEECCCCCEEEEEECCCCCCCCCCCCC
Q ss_conf 002310677654222332057501221157865898523632112211100
Q T0565 112 YGFAYEKPDESSQPVSDVVAGNRLKWEGSKGHFYQVSYPDGRKAYLSKSIS 162 (326)
Q Consensus 112 ~~~v~~~p~~~~~~i~~l~~G~~l~v~~~~~~wykV~~~~g~~g~i~~~~~ 162 (326)
.+++|++|++++++++.++.|+.+.++++.++|++|.+ +|..||++..++
T Consensus 2 ~lnvR~~p~~~s~ii~~l~~g~~v~v~~~~~~W~~V~~-~g~~GwV~~~yl 51 (52)
T PF08239_consen 2 NLNVRSGPSTSSKIIGTLPKGTRVTVLGESGGWYKVRY-NGKTGWVSSDYL 51 (52)
T ss_pred EEEEECCCCCCCHHHEEECCCCEEEEECCCCCEEEEEE-CCEEEEEEHHHC
T ss_conf 79994899999846699939999999651296999998-999999996658
No 7
>PF06347 SH3_4: Bacterial SH3 domain; InterPro: IPR010466 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=97.42 E-value=6.6e-05 Score=48.31 Aligned_cols=52 Identities=17% Similarity=0.281 Sum_probs=47.5
Q ss_pred ECCEEEECCCCCCCCEEEEECCCCEEEEECCCCCEEEEEECCCCCCCCCCCCC
Q ss_conf 21002310677654222332057501221157865898523632112211100
Q T0565 110 SHYGFAYEKPDESSQPVSDVVAGNRLKWEGSKGHFYQVSYPDGRKAYLSKSIS 162 (326)
Q Consensus 110 ~~~~~v~~~p~~~~~~i~~l~~G~~l~v~~~~~~wykV~~~~g~~g~i~~~~~ 162 (326)
.+.+++|+.|+.+++++..+..|..+.+++..++|++|. .+|..||+....+
T Consensus 2 ~~~~~lr~~P~~~s~v~~~l~~g~~~~v~~~~~~W~~V~-~~g~~GWi~~~~l 53 (55)
T PF06347_consen 2 KDEANLRSGPSTDSPVVAQLEPGVPVEVLECNGGWCRVR-ADGYEGWIHRSLL 53 (55)
T ss_pred CCEEEEECCCCCCCCEEEEECCCCEEEEEEECCCEEEEE-ECCEEEEEECCCC
T ss_conf 842588618899981349983997999999339889999-7990884890112
No 8
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); InterPro: IPR008548 This family contains the G6 protein from Vaccinia virus (strain Copenhagen) and related proteins from other Orthopoxvirus. The proteins are uncharacterised.; PDB: 2if6_A.
Probab=97.07 E-value=9.1e-05 Score=47.38 Aligned_cols=51 Identities=27% Similarity=0.352 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHHCCCCEECCCC-CCCCCCHHHHHHHHH-HHCCCCCCCCHH
Q ss_conf 330478999999826983221588-889601699999999-973776897869
Q T0565 173 KQDVESIIETAYSMMGIPYLWAGT-SSKGVDCSGLVRTVL-FMHDIIIPRDAS 223 (326)
Q Consensus 173 ~~~~~~~i~~A~~~lG~pY~wGG~-~~~g~DCSG~~~~~~-~~~G~~lpr~s~ 223 (326)
....+++++.|++++|.||-+... ....+=||-|+..+| ...|+.++....
T Consensus 77 ~~~~~~~~~~a~~~~g~~Y~~~~~~~~~~~yCSelV~~ay~~~~Gi~l~~~~~ 129 (155)
T PF05708_consen 77 DEQREKAIAYAKNYIGKPYDISFNLNDKKYYCSELVAQAYKKAAGIDLPKNSS 129 (155)
T ss_dssp HHHHHHHHHHHHCC----B-TT--SSSSSB-HHHHHHHHHHHH--------EE
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHCCCCCCCCC
T ss_conf 99999999999996499877654479997798999999999840997675211
No 9
>PF06940 DUF1287: Domain of unknown function (DUF1287); InterPro: IPR009706 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.
Probab=95.33 E-value=0.018 Score=32.26 Aligned_cols=118 Identities=16% Similarity=0.368 Sum_probs=67.6
Q ss_pred CCCCEEEEEECCCCC----CCCCCCCCCCCCCCCCCCCCCHHHHH--HHHHHHCCCCEECCCCCCC-CCCHH--HHHHHH
Q ss_conf 578658985236321----12211100112223443333047899--9999826983221588889-60169--999999
Q T0565 140 SKGHFYQVSYPDGRK----AYLSKSISQPEAGWRASLKQDVESII--ETAYSMMGIPYLWAGTSSK-GVDCS--GLVRTV 210 (326)
Q Consensus 140 ~~~~wykV~~~~g~~----g~i~~~~~~~~~~~~~~~~~~~~~~i--~~A~~~lG~pY~wGG~~~~-g~DCS--G~~~~~ 210 (326)
.+..++++.+|+|-. |.-......+... ....-+++| ++++.|--.|=.||...|+ ++|-- .=++..
T Consensus 15 Yd~aY~~~~YP~GDvp~~~GVCTDVViRA~R~----~g~DLQ~lVheDm~~nf~~Ypr~wgl~~pD~NIDhRRVpNL~vf 90 (164)
T PF06940_consen 15 YDPAYYSIGYPNGDVPDETGVCTDVVIRAYRA----AGYDLQKLVHEDMRANFSAYPRIWGLKRPDPNIDHRRVPNLEVF 90 (164)
T ss_pred CCCCEEECCCCCCCCCCCCCCCHHHHHHHHHH----CCCCHHHHHHHHHHHCHHHCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf 17770754799998876767528899999988----49768999999998798758710178888889763336449999
Q ss_pred HHHCCCCCCCCHHHHHHHCEECCCCCCHHHCCCCCEEEECCCCCCCCCCCCEEEEEEECC----C--EEEECCCCCE
Q ss_conf 997377689786999960702155566323588748985787787667762079999519----8--7898179955
Q T0565 211 LFMHDIIIPRDASQQAYVGEHIDIAPDFSNVKRGDLVFFGRKATAERKEGISHVGIYLGN----K--QFIHALGDVH 281 (326)
Q Consensus 211 ~~~~G~~lpr~s~~Q~~~g~~v~~~~~~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g~----~--~~iha~~~~~ 281 (326)
|...|..||-+..+ ++-||||+|-|...+ +..|+||.... | .+||-.|...
T Consensus 91 F~r~g~~l~~~~~~--------------~~~qpGDIVtw~L~~------~~~HIgIVSd~~~~~g~p~viHNig~g~ 147 (164)
T PF06940_consen 91 FKRHGQSLPTTVNA--------------EDWQPGDIVTWRLPG------NLPHIGIVSDKRNADGVPLVIHNIGPGQ 147 (164)
T ss_pred HHHCCEECCCCCCH--------------HHCCCCCEEEEECCC------CCCEEEEEECCCCCCCCEEEEEECCCCC
T ss_conf 97448435667887--------------676897879985699------9876899846657899858998268886
No 10
>PF05257 CHAP: CHAP domain; InterPro: IPR007921 The CHAP (cysteine, histidine-dependent amidohydrolases/peptidases) domain is a region between 110 and 140 amino acids that is found in proteins from bacteria, bacteriophages, archaea and eukaryotes of the Trypanosomidae family. Many of these proteins are uncharacterised, but it has been proposed that they may function mainly in peptidoglycan hydrolysis. The CHAP domain is found in a wide range of protein architectures; it is commonly associated with bacterial type SH3 domains and with several families of amidase domains. It has been suggested that CHAP domain containing proteins utilise a catalytic cysteine residue in a nucleophilic-attack mechanism , . The CHAP domain contains two invariant residues, a cysteine and a histidine. These residues form part of the putative active site of CHAP domain containing proteins. Secondary structure predictions show that the CHAP domain belongs to the alpha + beta structural class, with the N-terminal half largely containing predicted alpha helices and the C-terminal half principally composed of predicted beta strands , . Some proteins known to contain a CHAP domain are listed below: Bacterial and trypanosomal glutathionylspermidine amidases. A variety of bacterial autolysins. A Nocardia aerocolonigene putative esterase. Streptococcus pneumoniae choline-binding protein D. Methanosarcina mazei protein MM2478, a putative chloride channel. Several phage-encoded peptidoglycan hydrolases. Cysteine peptidases belonging to MEROPS peptidase family C51 (D-alanyl-glycyl endopeptidase, clan CA). ; PDB: 2vpm_B 2vps_A 2vob_A 2io8_B 2ioa_A 2iob_B 2io9_B 2io7_A 2k3a_A.
Probab=94.86 E-value=0.0067 Score=35.08 Aligned_cols=69 Identities=26% Similarity=0.207 Sum_probs=40.9
Q ss_pred CCCCCHHHHHHHHHHHCCCCCCCC---HHH-HHHHC-EECCCCCCHHHCCCCCEEEECCCCCCCCCCCCEEEEEEECC
Q ss_conf 896016999999999737768978---699-99607-02155566323588748985787787667762079999519
Q T0565 198 SKGVDCSGLVRTVLFMHDIIIPRD---ASQ-QAYVG-EHIDIAPDFSNVKRGDLVFFGRKATAERKEGISHVGIYLGN 270 (326)
Q Consensus 198 ~~g~DCSG~~~~~~~~~G~~lpr~---s~~-Q~~~g-~~v~~~~~~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g~ 270 (326)
..+..|--|+.+++...|..++.. +.+ -.... ........-+++||||+++|... ......||||....
T Consensus 15 ~~~~qC~~fv~~~~~~~g~~~~~~~gna~~~w~~~~~~~~~~~~~~~~P~~Gdivv~~~~----~~~~~GHVaiV~~v 88 (124)
T PF05257_consen 15 YYGGQCVDFVRWYLKQAGGPMPPGWGNAGDIWASSAGAQGYRNTTGSTPKPGDIVVFDSG----GSGGYGHVAIVEKV 88 (124)
T ss_dssp S-TT-HHHHHHHHHHHH---B----SSGGGGTCCEEECEE---EEES---SSBEEEBEEB----TTC----EEEEEEE
T ss_pred CCCCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCEECCCCCCCCCCCEEEEECCC----CCCCCCCEEEEEEE
T ss_conf 571716769998988759977897267889888642025271488999873669996367----89599868989998
No 11
>PF08460 SH3_5: Bacterial SH3 domain; InterPro: IPR013667 The SH3 domain has been found in a number of different bacterial proteins including glycyl-glycine endopeptidase, bacteriocin and some hypothetical proteins.; PDB: 1r77_B.
Probab=94.40 E-value=0.015 Score=32.84 Aligned_cols=47 Identities=21% Similarity=0.314 Sum_probs=37.4
Q ss_pred CCCCCCCCCCCCCHHEEEECCCCEEE---EEEECC--EEEEECCCCCEEEEE
Q ss_conf 40330037898710001121784799---986156--489972788215440
Q T0565 39 SVCNLREEGKFTSGMSTQALLGMPVK---VLQYNG--WYEIQTPDDYTGWVH 85 (326)
Q Consensus 39 ~~lnvR~~Ps~~s~~vtql~~G~~v~---Vl~~~G--W~kV~~~dG~~GWV~ 85 (326)
..+|||.+|++++++++++..|+.|. ++..+| |..-...+|..+||+
T Consensus 13 ~~~~Ir~~p~~~s~~~~~~~~G~~v~YD~~~~~dGy~Wi~y~~~sG~r~Yv~ 64 (65)
T PF08460_consen 13 TTTNIRTGPSTSSPVVGTYPAGQSVKYDQVIKADGYVWISYISYSGQRRYVP 64 (65)
T ss_dssp -SC-B-----TTS-B---B----EEEEEEEEE----EEE-EE-----EEEEE
T ss_pred CCEEEEECCCCCCCEEEEECCCCEEEECEEEEECCEEEEEEECCCCEEEEEE
T ss_conf 6105783887798368998999999879899979999999989899699998
No 12
>PF05708 DUF830: Orthopoxvirus protein of unknown function (DUF830); InterPro: IPR008548 This family contains the G6 protein from Vaccinia virus (strain Copenhagen) and related proteins from other Orthopoxvirus. The proteins are uncharacterised.; PDB: 2if6_A.
Probab=93.53 E-value=0.028 Score=30.93 Aligned_cols=60 Identities=28% Similarity=0.479 Sum_probs=38.7
Q ss_pred HCCCCCEEEECCCCCCC------CCCCCEEEEEEECCC----EEEECCC-CCEEEECCCCCCCCCCHHH-CEEEEEEEE
Q ss_conf 35887489857877876------677620799995198----7898179-9559881125665441000-715788875
Q T0565 240 NVKRGDLVFFGRKATAE------RKEGISHVGIYLGNK----QFIHALG-DVHVSSMNPADQNYDEFNT-KRLLFAVRF 306 (326)
Q Consensus 240 ~~~~GDlvff~~~~~~~------~~~~i~Hvgiy~g~~----~~iha~~-~~~~~~~~~~~~~~~~~~~-~~~~~~~r~ 306 (326)
++|+|||||+.+.+.-. .....+|||||+|.+ .+|||.+ +|...+++. |.. .+-+...|+
T Consensus 1 ~l~~GDIi~~~~~~~~s~~i~~~t~~~~sHvgI~~~~~~~~~~viea~~~Gv~~~~l~~-------~~~~~~~~~v~r~ 72 (155)
T PF05708_consen 1 QLQPGDIIFRRGKSRLSKAIRPVTSSPYSHVGIVVGEGGQEPYVIEAPGPGVRIEPLSD-------FLERNRKIAVYRL 72 (155)
T ss_dssp ------EEEB---STTHHHHHHHHTSS--B---EEEETTE-EEEEEE----EEEEEHHH-------HHH----EEEEEE
T ss_pred CCCCCCEEEEECCCCHHHHHHHHCCCCCCEEEEEEECCCCCEEEEEECCCCEEEEEHHH-------HHHCCCCEEEEEE
T ss_conf 99885189996797388899876089987799999338973699982379869978899-------9736896999993
No 13
>PF07653 SH3_2: Variant SH3 domain; InterPro: IPR011511 SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. These were first described in the Src cytoplasmic tyrosine kinase P12931 from SWISSPROT. The structure is a partly opened beta barrel.; PDB: 1k0x_A 1i1j_A 1hjd_A 2eyz_A 2eyx_A 2ggr_A 2bzx_A 2dbk_A 2bzy_B 2ebp_A ....
Probab=92.36 E-value=0.027 Score=31.05 Aligned_cols=35 Identities=26% Similarity=0.512 Sum_probs=29.2
Q ss_pred EECCCCEEEEE-EE--CCEEEEECCCCCEEEEEHHHHCC
Q ss_conf 12178479998-61--56489972788215440001022
Q T0565 56 QALLGMPVKVL-QY--NGWYEIQTPDDYTGWVHRMVITP 91 (326)
Q Consensus 56 ql~~G~~v~Vl-~~--~GW~kV~~~dG~~GWV~~~~i~~ 91 (326)
.+..|+.+.|+ ++ +||++.+. +|..||+++++|..
T Consensus 17 ~~~~Gdiv~V~~~~~~~~ww~g~~-~g~~G~~P~~~v~~ 54 (55)
T PF07653_consen 17 SFKKGDIVEVLGDKEDDGWWEGEN-NGKVGWFPSSYVEE 54 (55)
T ss_dssp -B-TT-EEEECEBCESSSEBBEEE-CTCS--BEGGGEEE
T ss_pred EEECCCEEEEEECCCCCCEEEEEE-CCCEEEECHHHEEE
T ss_conf 280899999911665899999998-99489976699897
No 14
>PF00018 SH3_1: SH3 domain; InterPro: IPR001452 SH3 (src Homology-3) domains are small protein modules containing approximately 50 amino acid residues , . They are found in a great variety of intracellular or membrane-associated proteins , , for example, in a variety of proteins with enzymatic activity, in adaptor proteins that lack catalytic sequences and in cytoskeletal proteins, such as fodrin and yeast actin binding protein ABP-1. The SH3 domain has a characteristic fold which consists of five or six beta-strands arranged as two tightly packed anti-parallel beta sheets. The linker regions may contain short helices . The surface of the SH2-domain bears a flat, hydrophobic ligand-binding pocket which consists of three shallow grooves defined by conservative aromatic residues in which the ligand adopts an extended left-handed helical arrangement. The ligand binds with low affinity but this may be enhanced by multiple interactions. The region bound by the SH3 domain is in all cases proline-rich and contains PXXP as a core-conserved binding motif. The function of the SH3 domain is not well understood but they may mediate many diverse processes such as increasing local concentration of proteins, altering their subcellular location and mediating the assembly of large multiprotein complexes .; PDB: 2ed1_A 2vge_A 1ycs_B 2cre_A 1wyx_A 2dil_A 1ugv_A 1yn8_F 2dl5_A 2enm_A ....
Probab=90.76 E-value=0.14 Score=26.37 Aligned_cols=31 Identities=26% Similarity=0.467 Sum_probs=25.2
Q ss_pred EECCCCEEEEEEE--CCEEEEECCC-CCEEEEEH
Q ss_conf 1217847999861--5648997278-82154400
Q T0565 56 QALLGMPVKVLQY--NGWYEIQTPD-DYTGWVHR 86 (326)
Q Consensus 56 ql~~G~~v~Vl~~--~GW~kV~~~d-G~~GWV~~ 86 (326)
.+..|+.+.|+++ ++|++++..+ |..|||++
T Consensus 15 s~~~Gd~i~vl~~~~~~W~~~~~~~~~~~G~vP~ 48 (48)
T PF00018_consen 15 SFKEGDIIIVLEKSDDGWWLGRNDRTGKQGWVPA 48 (48)
T ss_dssp EB-TTEEEEEEEESSSSEEEEEESTTTBSEEEEG
T ss_pred EECCCCEEEEEECCCCCEEEEEECCCCCEEEEEC
T ss_conf 5989999999782699958999999998998529
No 15
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2im9_A 2p1g_A.
Probab=88.93 E-value=0.16 Score=26.02 Aligned_cols=41 Identities=22% Similarity=0.314 Sum_probs=28.8
Q ss_pred HHHCCCCCEEEECCCCCCCCCCCCEEEEEEECCC---EEEECCCCCE
Q ss_conf 3235887489857877876677620799995198---7898179955
Q T0565 238 FSNVKRGDLVFFGRKATAERKEGISHVGIYLGNK---QFIHALGDVH 281 (326)
Q Consensus 238 ~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g~~---~~iha~~~~~ 281 (326)
.+.+|.||+|-+-+.- ..-.|+||||.+-.+ .|+|||...+
T Consensus 151 ~~~l~~GDiI~i~t~~---~GLDVtH~Gi~i~~~~~~~lrhASs~~~ 194 (216)
T PF07313_consen 151 LSQLQTGDIIGIYTND---PGLDVTHVGIAIRTNDGLHLRHASSLKG 194 (216)
T ss_dssp HTTS----EEEEEEEE-----EEEEE---EEEETTEEEEEEE-S---
T ss_pred HHHCCCCCEEEEEECC---CCCCEEEEEEEEEECCEEEEEECCCCCC
T ss_conf 9528999889998069---9973257889999799359995688678
No 16
>PF07313 DUF1460: Protein of unknown function (DUF1460); InterPro: IPR010846 This family consists of several hypothetical bacterial proteins of around 260 residues in length. The function of this family is unknown.; PDB: 2im9_A 2p1g_A.
Probab=87.54 E-value=0.063 Score=28.66 Aligned_cols=34 Identities=26% Similarity=0.489 Sum_probs=25.3
Q ss_pred HHHHHHCCCCEECCCC-----C-------CCCCCHHHHHHHHHHHC
Q ss_conf 9999826983221588-----8-------89601699999999973
Q T0565 181 ETAYSMMGIPYLWAGT-----S-------SKGVDCSGLVRTVLFMH 214 (326)
Q Consensus 181 ~~A~~~lG~pY~wGG~-----~-------~~g~DCSG~~~~~~~~~ 214 (326)
++++.|||+||+=|-. . ..||||=-|+-++....
T Consensus 1 ~is~~fLGtPY~a~tL~~~~~~~E~Lvi~~~~~DC~TfvE~vlALa 46 (216)
T PF07313_consen 1 QISRQFLGTPYVANTLGGSANEPEQLVINFDGFDCFTFVEYVLALA 46 (216)
T ss_dssp HHHHHTTT--B----T--TSSSS-S-SS-TTSB-HHHHHHHHHHHH
T ss_pred CCHHHHCCCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHHHHH
T ss_conf 9357667997657703578999852387788605130999999999
No 17
>PF11948 DUF3465: Protein of unknown function (DUF3465)
Probab=64.36 E-value=1.2 Score=20.19 Aligned_cols=16 Identities=31% Similarity=0.590 Sum_probs=9.7
Q ss_pred CCHHHHHHHHHHHHHH
Q ss_conf 9225789999999998
Q T0565 1 MKKNILLFYCFLATMA 16 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~ 16 (326)
||+.+.+|..++..++
T Consensus 1 ~k~~~~~~~~~l~~~~ 16 (131)
T PF11948_consen 1 MKRFLALFLSVLSAFS 16 (131)
T ss_pred CCCHHHHHHHHHHHCC
T ss_conf 9066999999998525
No 18
>PF11777 DUF3316: Protein of unknown function (DUF3316)
Probab=43.81 E-value=5.2 Score=16.00 Aligned_cols=19 Identities=37% Similarity=0.431 Sum_probs=12.1
Q ss_pred CCHHHHHHHHHHHHHHHHHC
Q ss_conf 92257899999999987503
Q T0565 1 MKKNILLFYCFLATMAASLK 20 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~~~l~ 20 (326)
|||.++|+ +++++++.+.+
T Consensus 1 MKkl~ll~-~~l~~s~~a~A 19 (114)
T PF11777_consen 1 MKKLILLA-SLLLLSSSAFA 19 (114)
T ss_pred CHHHHHHH-HHHHHHHHHHH
T ss_conf 90499999-99998667763
No 19
>PF02938 GAD: GAD domain; InterPro: IPR004115 This domain is found in some members of the GatB and aspartyl tRNA synthetases.; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0005737 cytoplasm; PDB: 1zq1_D 2d6f_D 1efw_B 1g51_B 1l0w_B 1eqr_C 1il2_A 1c0a_A.
Probab=41.96 E-value=3.7 Score=16.99 Aligned_cols=15 Identities=40% Similarity=0.612 Sum_probs=11.5
Q ss_pred CHHHCCCCCEEEECC
Q ss_conf 632358874898578
Q T0565 237 DFSNVKRGDLVFFGR 251 (326)
Q Consensus 237 ~~~~~~~GDlvff~~ 251 (326)
.+-++++||++||..
T Consensus 71 ~~~~~~~GD~i~f~A 85 (95)
T PF02938_consen 71 ERLGAKPGDLIFFIA 85 (95)
T ss_dssp HHCT--TT-EEEEEE
T ss_pred HHHCCCCCCEEEEEC
T ss_conf 994899899999976
No 20
>PF06551 DUF1120: Protein of unknown function (DUF1120); InterPro: IPR010546 This family consists of several bacterial proteins, at least one of which is involved in enzyme induction following nitrogen deprivation. The exact function of this family is unknown
Probab=38.12 E-value=8 Score=14.77 Aligned_cols=13 Identities=38% Similarity=0.470 Sum_probs=7.4
Q ss_pred CCHHHHHHHHHHH
Q ss_conf 9225789999999
Q T0565 1 MKKNILLFYCFLA 13 (326)
Q Consensus 1 mkk~i~l~~~~~~ 13 (326)
|||.++...+++.
T Consensus 1 MKK~l~~~~l~a~ 13 (145)
T PF06551_consen 1 MKKNLLATLLLAS 13 (145)
T ss_pred CCHHHHHHHHHHH
T ss_conf 9367999999999
No 21
>PF01878 DUF55: Protein of unknown function DUF55; InterPro: IPR002740 This family of prokaryotic proteins has no known function.; PDB: 2eve_A 2g2x_C 2ar1_A 2p5d_A 2zbn_A 1wmm_A 2hd9_A 2gbs_A.
Probab=37.16 E-value=4.1 Score=16.66 Aligned_cols=12 Identities=58% Similarity=0.908 Sum_probs=10.2
Q ss_pred HHCCCCCEEEEC
Q ss_conf 235887489857
Q T0565 239 SNVKRGDLVFFG 250 (326)
Q Consensus 239 ~~~~~GDlvff~ 250 (326)
.+|++||++||-
T Consensus 38 r~mk~GD~v~~Y 49 (143)
T PF01878_consen 38 RRMKPGDLVFFY 49 (143)
T ss_dssp CC-----EEEEE
T ss_pred HHCCCCCEEEEE
T ss_conf 855899989999
No 22
>PF11153 DUF2931: Protein of unknown function (DUF2931)
Probab=35.36 E-value=8.3 Score=14.64 Aligned_cols=21 Identities=29% Similarity=0.352 Sum_probs=13.9
Q ss_pred CCHHHHHHHHHHHHHHHHHCC
Q ss_conf 922578999999999875033
Q T0565 1 MKKNILLFYCFLATMAASLKA 21 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~~~l~~ 21 (326)
|||.++|+.|+++..|.+...
T Consensus 1 m~~i~~lll~lll~~Cs~~~~ 21 (216)
T PF11153_consen 1 MKKILLLLLLLLLAGCSTSPT 21 (216)
T ss_pred CCCHHHHHHHHHHHHCCCCCC
T ss_conf 900799999999975368864
No 23
>PF07203 DUF1412: Protein of unknown function (DUF1412); InterPro: IPR009853 This family consists of several Caenorhabditis elegans proteins of around 70-75 residues in length. The function of this family is unknown.
Probab=34.84 E-value=9 Score=14.44 Aligned_cols=27 Identities=26% Similarity=0.456 Sum_probs=14.8
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf 922578999999999875033100135
Q T0565 1 MKKNILLFYCFLATMAASLKAQEIRPM 27 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~~~l~~~~~~~~ 27 (326)
|-|+|++|.+++++.+.++.+..+|..
T Consensus 1 M~~~~~f~~~~~l~Ls~tVSagiiR~r 27 (74)
T PF07203_consen 1 MSKNLFFFLVLALLLSSTVSAGIIRDR 27 (74)
T ss_pred CCCCHHHHHHHHHHHHCCCCCCEEEEC
T ss_conf 942079999999998620001121100
No 24
>PF08007 Cupin_4: Cupin superfamily protein; InterPro: IPR013109 This family contains many hypothetical proteins that belong to the cupin superfamily.; PDB: 2ilm_A 1h2k_A 1h2m_A 1mze_A 2cgn_A 1yci_A 1mzf_A 1iz3_A 3d8c_A 1h2l_A ....
Probab=31.53 E-value=10 Score=14.09 Aligned_cols=23 Identities=26% Similarity=0.423 Sum_probs=17.7
Q ss_pred HHCCCCCEEEECCCCCCCCCCCCEEEEEEEC
Q ss_conf 2358874898578778766776207999951
Q T0565 239 SNVKRGDLVFFGRKATAERKEGISHVGIYLG 269 (326)
Q Consensus 239 ~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g 269 (326)
-.|+|||+||+.. +.-|-+..++
T Consensus 178 ~~L~pGD~LYiP~--------g~~H~~~~~~ 200 (319)
T PF08007_consen 178 VVLEPGDVLYIPR--------GWWHYAEALD 200 (319)
T ss_dssp EEE----EEEE-T--------T-EEEEEESS
T ss_pred EEECCCCEEEECC--------CCEEEEEECC
T ss_conf 9988998899789--------9659879889
No 25
>PF06097 DUF945: Bacterial protein of unknown function (DUF945); InterPro: IPR010352 This family consists of several hypothetical bacterial proteins of unknown function.
Probab=30.34 E-value=11 Score=13.96 Aligned_cols=23 Identities=35% Similarity=0.303 Sum_probs=17.0
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 92257899999999987503310
Q T0565 1 MKKNILLFYCFLATMAASLKAQE 23 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~~~l~~~~ 23 (326)
|||+.++..++++++++++....
T Consensus 1 MKK~~i~~~~iv~l~a~~~g~~w 23 (459)
T PF06097_consen 1 MKKSLIAIGVIVALVAAWLGAPW 23 (459)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHH
T ss_conf 97057689999999999988888
No 26
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 This family includes putative periplasmic proteins.; PDB: 1nnx_A.
Probab=29.13 E-value=6.4 Score=15.38 Aligned_cols=20 Identities=25% Similarity=0.311 Sum_probs=10.1
Q ss_pred CCHHHHHHHHHHHHHHHHHCC
Q ss_conf 922578999999999875033
Q T0565 1 MKKNILLFYCFLATMAASLKA 21 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~~~l~~ 21 (326)
|||.++++.+.+ +++.+++.
T Consensus 1 MKk~~i~~~~~L-~~~~a~A~ 20 (126)
T PF04076_consen 1 MKKTLIATAAAL-ASTPAFAA 20 (126)
T ss_dssp ---------------------
T ss_pred CCHHHHHHHHHH-HHHHHHHH
T ss_conf 957999999999-98899997
No 27
>PF03032 Brevenin: Brevenin/esculentin/gaegurin/rugosin family; InterPro: IPR004275 In addition to the highly specific cell-mediated immune system, vertebrates possess an efficient host-defense mechanism against invading microorganisms which involves the synthesis of highly potent antimicrobial peptides with a large spectrum of activity. This entry represents a number of these defence peptides secreted from the skin of amphibians, including the opiate-like dermorphins and deltorphins, and the antimicrobial dermoseptins and temporins.; GO: 0006952 defense response, 0042742 defense response to bacterium, 0005576 extracellular region
Probab=28.16 E-value=10 Score=14.07 Aligned_cols=22 Identities=41% Similarity=0.686 Sum_probs=12.9
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 92257899999999987503310
Q T0565 1 MKKNILLFYCFLATMAASLKAQE 23 (326)
Q Consensus 1 mkk~i~l~~~~~~~~~~~l~~~~ 23 (326)
|||+++|++. +-++++++--..
T Consensus 3 lKKSLlLlfF-LG~islSlCeee 24 (46)
T PF03032_consen 3 LKKSLLLLFF-LGTISLSLCEEE 24 (46)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHH
T ss_conf 2588999999-987211677776
No 28
>PF02668 TauD: Taurine catabolism dioxygenase TauD, TfdA family; InterPro: IPR003819 This family consists of TauD/TfdA taurine catabolism dioxygenases. The Escherichia coli tauD gene is required for the utilization of taurine (2-aminoethanesulphonic acid) as a sulphur source and is expressed only under conditions of sulphate starvation. TauD is an alpha-ketoglutarate-dependent dioxygenase catalyzing the oxygenolytic release of sulphite from taurine . The 2,4-dichlorophenoxyacetic acid/alpha-ketoglutarate dioxygenase from Burkholderia sp. (strain RASC) also belongs to this family . TfdA from Alcaligenes eutrophus is a 2,4-D monooxygenase .; GO: 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2wbp_A 2wbq_A 2wbo_A 1ds1_A 1dry_A 1gvg_A 1drt_A 1ds0_A 2og5_A 2og7_A ....
Probab=25.15 E-value=11 Score=13.74 Aligned_cols=11 Identities=27% Similarity=0.610 Sum_probs=9.2
Q ss_pred HCCCCCEEEEC
Q ss_conf 35887489857
Q T0565 240 NVKRGDLVFFG 250 (326)
Q Consensus 240 ~~~~GDlvff~ 250 (326)
.+||||||+|.
T Consensus 221 ~~~~GDlli~D 231 (255)
T PF02668_consen 221 RWQPGDLLIWD 231 (255)
T ss_dssp E--TTEEEEEE
T ss_pred CCCCCCEEEEE
T ss_conf 17899799993
No 29
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR001476 The chaperonins are 'helper' molecules required for correct folding and subsequent assembly of some proteins . These are required for normal cell growth , and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) . The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits . These ring structures assemble by self-stimulation in the presence of Mg^2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg^2+-ATP dependent manner . The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL . Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the 'Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0005524 ATP binding, 0006457 protein folding; PDB: 1p3h_B 1hx5_E 1p83_A 1wnr_E 1wf4_s 1we3_R 1aon_Q 1pcq_O 1svt_S 2c7d_T ....
Probab=24.65 E-value=3 Score=17.59 Aligned_cols=39 Identities=31% Similarity=0.522 Sum_probs=21.1
Q ss_pred HCCCCCCCCHHHHHHHCEECCCCC---------CHHHCCCCCEEEECC
Q ss_conf 737768978699996070215556---------632358874898578
Q T0565 213 MHDIIIPRDASQQAYVGEHIDIAP---------DFSNVKRGDLVFFGR 251 (326)
Q Consensus 213 ~~G~~lpr~s~~Q~~~g~~v~~~~---------~~~~~~~GDlvff~~ 251 (326)
..||.||+++.+-...|.-+..-. ...++++||.|+|..
T Consensus 21 ~gGI~Lp~~~~ek~~~G~VvavG~G~~~~~g~~~~~~vk~GD~Vl~~~ 68 (93)
T PF00166_consen 21 KGGIILPDSAKEKPNQGKVVAVGPGKRNENGEDVPMDVKVGDTVLFPK 68 (93)
T ss_dssp ----BE-CCCSSSEBEEEEEE-----BTT---BS--SS----EEEEE-
T ss_pred CCCEEECCCCCCCCCEEEEEEECCCEECCCCCEEEEEECCCCEEEECC
T ss_conf 230897675466730589999288406578869875261488998857
No 30
>PF10566 Glyco_hydro_97: Glycoside hydrolase 97 ; PDB: 2jkp_A 2zq0_A 2jke_B 2d73_B 2jka_B.
Probab=24.17 E-value=9.2 Score=14.37 Aligned_cols=45 Identities=29% Similarity=0.367 Sum_probs=25.8
Q ss_pred HHHHHHHHHHCCCCEE-----CCCCC----------CCCCCHHHHHHHHHHHC-CCCCCCCH
Q ss_conf 7899999982698322-----15888----------89601699999999973-77689786
Q T0565 177 ESIIETAYSMMGIPYL-----WAGTS----------SKGVDCSGLVRTVLFMH-DIIIPRDA 222 (326)
Q Consensus 177 ~~~i~~A~~~lG~pY~-----wGG~~----------~~g~DCSG~~~~~~~~~-G~~lpr~s 222 (326)
...|+.|.++ |.+|+ |-+.. --.+|--.|+.|.-... |++|=.++
T Consensus 313 K~yIDfAA~~-G~eyvLvD~gW~~~~~~~~~d~~~~~p~~di~elv~Ya~~KgV~i~lw~~~ 373 (643)
T PF10566_consen 313 KYYIDFAAEM-GIEYVLVDAGWDGNEWGNKFDFTKPIPDFDIKELVAYAKSKGVGIILWYNW 373 (643)
T ss_dssp HHHHHHHHH-----EEE--TT------SS---SS-B-TT--HHHHHHHHHH---EEEEETBH
T ss_pred HHHHHHHHHC-CCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEECC
T ss_conf 5546579873-997899725536766756676540468469899999997379769999521
No 31
>PF01052 SpoA: Surface presentation of antigens (SPOA); InterPro: IPR001543 Proteins in this group are involved in a secretory pathway responsible for the surface presentation of invasion plasmid antigen needed for the entry of Salmonella and other species into mammalian cells , .They could play a role in preserving the translocation competence of the IPA antigens and are required for secretion of the three IPA proteins .; PDB: 1yab_B 1o9y_B.
Probab=22.62 E-value=15 Score=13.05 Aligned_cols=34 Identities=21% Similarity=0.465 Sum_probs=24.7
Q ss_pred CCHHHCCCCCEEEECCCCCCCCCCCCEEEEEEECCCEEEEC
Q ss_conf 66323588748985787787667762079999519878981
Q T0565 236 PDFSNVKRGDLVFFGRKATAERKEGISHVGIYLGNKQFIHA 276 (326)
Q Consensus 236 ~~~~~~~~GDlvff~~~~~~~~~~~i~Hvgiy~g~~~~iha 276 (326)
.+..++++||++-+..... .+|-+|+++-.+-++
T Consensus 24 ~ell~L~~Gdvi~l~~~~~-------~~v~l~v~g~~~~~g 57 (77)
T PF01052_consen 24 GELLNLKVGDVIPLDKPAD-------EPVELYVNGRPIFRG 57 (77)
T ss_dssp CHHHC-----EEEESSB------------EEEE---EEEE-
T ss_pred HHHHCCCCCCEEEECCCCC-------CCEEEEECCEEEEEE
T ss_conf 9986689999999189899-------959999999999999
No 32
>PF12120 RNApol_Rpb2_rif: DNA/RNA tunnel of bacterial DNA dependent RNA polymerase; PDB: 2hw2_A.
Probab=20.79 E-value=14 Score=13.23 Aligned_cols=28 Identities=25% Similarity=0.400 Sum_probs=15.5
Q ss_pred CHHHCCCCCEEEECCCCCCCCCCCCEEE
Q ss_conf 6323588748985787787667762079
Q T0565 237 DFSNVKRGDLVFFGRKATAERKEGISHV 264 (326)
Q Consensus 237 ~~~~~~~GDlvff~~~~~~~~~~~i~Hv 264 (326)
.+.+|++||||--...++........||
T Consensus 6 TkAdL~~GdLl~pg~~sny~~~~~~nhv 33 (100)
T PF12120_consen 6 TKADLQVGDLLTPGRRSNYGDGRVMNHV 33 (100)
T ss_dssp --S------EE----B-SS----B-S-E
T ss_pred CCCCCCCCCEECCCCCCCCCCCCEEEEE
T ss_conf 5033776555047861445767456689
Done!