Query T0625 YP_612324.1, SILICIBACTER SP. TM1040, 233 residues
Match_columns 233
No_of_seqs 102 out of 379
Neff 5.4
Searched_HMMs 11830
Date Thu Jul 22 15:03:17 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0625.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0625.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09347 DUF1989: Domain of un 100.0 0 0 452.5 9.1 166 35-201 1-167 (167)
2 PF06185 YecM: YecM protein; 36.6 5.1 0.00043 17.1 1.2 51 64-114 27-79 (185)
3 PF02408 CUB_2: CUB-like domai 35.2 10 0.00087 15.1 3.7 41 31-74 42-86 (119)
4 PF04151 PPC: Bacterial pre-pe 26.4 14 0.0012 14.2 2.9 31 43-73 4-34 (70)
5 PF02626 AHS2: Allophanate hyd 25.4 15 0.0013 14.1 4.8 64 38-102 62-131 (272)
6 PF11142 DUF2917: Protein of u 19.9 19 0.0016 13.4 2.9 37 35-77 1-37 (63)
7 PF01809 DUF37: Domain of unkn 16.6 23 0.0019 12.9 1.9 26 138-163 25-50 (68)
8 PF12148 DUF3590: Protein of u 16.1 17 0.0014 13.7 0.7 34 44-78 51-84 (85)
9 PF09261 Alpha-mann_mid: Alpha 16.0 21 0.0018 13.0 1.2 17 118-134 58-74 (78)
10 PF11172 DUF2959: Protein of u 15.5 24 0.0021 12.7 1.4 20 142-161 6-25 (201)
No 1
>PF09347 DUF1989: Domain of unknown function (DUF1989); PDB: 3di4_A.
Probab=100.00 E-value=0 Score=452.51 Aligned_cols=166 Identities=46% Similarity=0.742 Sum_probs=163.8
Q ss_pred EEEECCCCCEEEEECCCCEEEEEECCCCCEEEEEEECCCCCCCCCCHHHHHHHCCCEECCCCCEEEECCCCEEEEEEECC
Q ss_conf 47742898438997188789997378761144557634574223472689874120321468654506898489999457
Q T0625 35 TYTIPARQGRAIRMAQGEALMVINRDGSQIGDFWAFVEGDCGEYLSMEHLRPTLRRVSPRPGDVLVSNRRRPILTLLEDS 114 (233)
Q Consensus 35 ~~tip~g~~~a~~v~~G~~lrI~d~~G~q~~d~~~~na~d~~Erl~~~~T~~~~~~~~l~~G~~L~S~~~rpm~tIv~DT 114 (233)
+++||+|+||+++|++||.|||+|++|+||+|+|+||++|+.||||++||+|+||+++|++|++|||||+|||+|||+||
T Consensus 1 ~~~Ipag~~~a~~v~~Gq~lrI~d~~G~q~~d~~~~~a~d~~Er~s~~~T~~~~~~~~l~~G~~l~Sn~~r~m~tIveDT 80 (167)
T PF09347_consen 1 EETIPAGSGWAFRVKRGQILRIIDPEGGQVVDFLAFNADDPSERYSMGDTRKAQHSAYLTKGDVLYSNMGRPMLTIVEDT 80 (167)
T ss_dssp -EEE-CT------B----EEEEEE--------EEEEETTEEEEEB----HHHH----B-----EEEB-TT-EEEEEEEE-
T ss_pred CEEECCCCEEEEEECCCCEEEEEECCCCCEEEEEEECCCCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCEEEEEECCC
T ss_conf 96848998069998999989999689993778999857997444178898876434245789997828997369997567
Q ss_pred CCCCCCCCCCCCCHHHHHHHCCCCCC-CCCHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCCEEEEECCCCCCCCEEE
Q ss_conf 88704332478897998764167788-66578999999971788553465112442252178871787158889998799
Q T0625 115 SPGVHDTLVASCDVHRYAQLGHEGYH-DNCTDNLRMALGALGLRPTTVPCPLNLWMNTPVVEGGAMEWRPPVSRRGDHVL 193 (233)
Q Consensus 115 ~~G~HD~l~~~c~~~~y~~~~~~~~h-~nc~dNl~~al~k~Gl~~~di~~~lNlFm~v~v~~dG~l~~~~~~s~aGdyV~ 193 (233)
+ ||||+|+++|++++|+.+|++++| +||+|||+.||+||||+++|++++|||||||+|+++|+|+|++|+|+|||||+
T Consensus 81 ~-G~HD~l~~~c~~~~~~~~yg~~~~~~nc~dN~~~al~~~Gl~~~di~~~lN~Fmnv~vd~~G~l~~~~~~S~~GdyV~ 159 (167)
T PF09347_consen 81 V-GRHDTLGGACDAERYEELYGEGHHQRNCRDNFLLALAKYGLTPRDIPPPLNLFMNVPVDEDGQLSFDPPWSRPGDYVE 159 (167)
T ss_dssp ---EEE-------S-----------S--SHHHHHHHHHH-HHHHHCC----BEEEEE---------EEB--------EEE
T ss_pred C-CCHHCCCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCEEECCCCCCCCCEEE
T ss_conf 8-432004777898999862468888887699999999981999644677677058252889997897879999999899
Q ss_pred EEECCCEE
Q ss_conf 99724535
Q T0625 194 FRAELDVV 201 (233)
Q Consensus 194 LrAemDll 201 (233)
||||||||
T Consensus 160 LrAemDll 167 (167)
T PF09347_consen 160 LRAEMDLL 167 (167)
T ss_dssp EEESS-EE
T ss_pred EEEECCCC
T ss_conf 99954539
No 2
>PF06185 YecM: YecM protein; InterPro: IPR010393 This family consists of several bacterial YecM proteins of unknown function.; PDB: 1k4n_A.
Probab=36.58 E-value=5.1 Score=17.11 Aligned_cols=51 Identities=16% Similarity=0.072 Sum_probs=42.5
Q ss_pred EEEEEEECCCCCCCCCCHHHHHHHCCCEECCCCCEEEECC--CCEEEEEEECC
Q ss_conf 1445576345742234726898741203214686545068--98489999457
Q T0625 64 IGDFWAFVEGDCGEYLSMEHLRPTLRRVSPRPGDVLVSNR--RRPILTLLEDS 114 (233)
Q Consensus 64 ~~d~~~~na~d~~Erl~~~~T~~~~~~~~l~~G~~L~S~~--~rpm~tIv~DT 114 (233)
..|+-.|.+|..+=|.|...|-+.-+..++.-|..|-.|+ |||++.|-=|+
T Consensus 27 ~ldl~~~~~DHialRvn~~~~A~~w~~~l~q~G~llSen~INGRPI~l~~L~~ 79 (185)
T PF06185_consen 27 GLDLAQLEIDHIALRVNSNETAERWRQGLLQCGELLSENMINGRPICLFELNQ 79 (185)
T ss_dssp ----TT-EEEEEE---S-HHHHHHHH---TT---EEEEEE----EEEEEEEEE
T ss_pred CCCCCCCCCCEEEEEECCHHHHHHHHHHHHHHCHHHHHCCCCCEEEEEEECCC
T ss_conf 99711045768898618899999999999984544230634880589997488
No 3
>PF02408 CUB_2: CUB-like domain; InterPro: IPR003366 This domain is found in a family of hypothetical Caenorhabditis elegans proteins. The aligned region has no known function nor do any of the proteins which possess it. However, this domain is related to the CUB domain (IPR000859 from INTERPRO). The aligned region is approximately 130 amino acids long and contains two conserved cysteine residues.
Probab=35.19 E-value=10 Score=15.12 Aligned_cols=41 Identities=10% Similarity=0.120 Sum_probs=32.9
Q ss_pred CCCEEEEECCCCCEEEEECC----CCEEEEEECCCCCEEEEEEECCCC
Q ss_conf 45324774289843899718----878999737876114455763457
Q T0625 31 RPEATYTIPARQGRAIRMAQ----GEALMVINRDGSQIGDFWAFVEGD 74 (233)
Q Consensus 31 ~~~~~~tip~g~~~a~~v~~----G~~lrI~d~~G~q~~d~~~~na~d 74 (233)
.=.|...||-|.+..+++.. +..|.++|.-|.+ ....+.+.
T Consensus 42 ~C~~~i~IP~G~ya~v~~~~~~~~~~~i~v~Ds~g~~---~~~~~~~~ 86 (119)
T PF02408_consen 42 NCSYNINIPKGYYAKVTLSANLDDNDYITVTDSNGNS---EKITSSDN 86 (119)
T ss_pred CEEEEEEECCCEEEEEEEEEECCCCCEEEEEECCCCE---EEEEECCC
T ss_conf 6389999088479999999854889779999159969---99880788
No 4
>PF04151 PPC: Bacterial pre-peptidase C-terminal domain; InterPro: IPR007280 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. 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-, 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. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; 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. This domain is normally found at the C terminus of secreted archaeal and bacterial peptidases, the majority of which belong to MEROPS peptidase families M4 (vibriolysin, IPR001570 from INTERPRO), M9A amd M9B (microbial collangenase, IPR002169 from INTERPRO), M28 (aminopeptidase Ap1, IPR007484 from INTERPRO) and S8 (subtilisin family peptidases, IPR000209 from INTERPRO).; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 1wmf_A 1wme_A 1wmd_A 1nqd_B 2o8o_B 1nqj_B.
Probab=26.37 E-value=14 Score=14.17 Aligned_cols=31 Identities=13% Similarity=0.232 Sum_probs=22.8
Q ss_pred CEEEEECCCCEEEEEECCCCCEEEEEEECCC
Q ss_conf 4389971887899973787611445576345
Q T0625 43 GRAIRMAQGEALMVINRDGSQIGDFWAFVEG 73 (233)
Q Consensus 43 ~~a~~v~~G~~lrI~d~~G~q~~d~~~~na~ 73 (233)
.+++.|++|+.|+|.-..+..-.++.+++..
T Consensus 4 ~y~f~v~~g~~l~i~l~~~~~D~dl~l~~~~ 34 (70)
T PF04151_consen 4 YYSFEVPAGGTLTISLDGGGGDADLYLYDSN 34 (70)
T ss_dssp EEEE--S----EEEEEEESS-EEEEEEEEES
T ss_pred EEEEEECCCCEEEEEECCCCCCCEEEEECCC
T ss_conf 9999965999999999889756109996488
No 5
>PF02626 AHS2: Allophanate hydrolase subunit 2; InterPro: IPR003778 This domain represents subunit 2 of allophanate hydrolase (AHS2).
Probab=25.43 E-value=15 Score=14.06 Aligned_cols=64 Identities=22% Similarity=0.293 Sum_probs=36.7
Q ss_pred ECCCCCEEEEECCCCEEEEEECCCCCEEEEEEECCC-CCCCCCCHHH--HHHHCCCE---ECCCCCEEEEC
Q ss_conf 428984389971887899973787611445576345-7422347268--98741203---21468654506
Q T0625 38 IPARQGRAIRMAQGEALMVINRDGSQIGDFWAFVEG-DCGEYLSMEH--LRPTLRRV---SPRPGDVLVSN 102 (233)
Q Consensus 38 ip~g~~~a~~v~~G~~lrI~d~~G~q~~d~~~~na~-d~~Erl~~~~--T~~~~~~~---~l~~G~~L~S~ 102 (233)
.|.-.++++.|++||+|+|.-..-+.-+ -+++.-. +..+.|++-- ++...+-. .|++||+|--.
T Consensus 62 ~~v~~~~~~~v~~Gd~L~~g~~~~G~R~-YLAv~GG~~~~~vlGS~St~~~~~~Gg~~Gr~L~~GD~L~~~ 131 (272)
T PF02626_consen 62 EPVPMWQSIRVKAGDVLSFGQAKKGARA-YLAVAGGFDVPPVLGSRSTYLRAGIGGLEGRPLKAGDRLPIG 131 (272)
T ss_pred EECCCCEEEEECCCCEEEECCCCCCCEE-EEEECCCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEC
T ss_conf 8868980699799998982798984689-999716747811127843004533368678547889998606
No 6
>PF11142 DUF2917: Protein of unknown function (DUF2917)
Probab=19.86 E-value=19 Score=13.35 Aligned_cols=37 Identities=22% Similarity=0.430 Sum_probs=26.3
Q ss_pred EEEECCCCCEEEEECCCCEEEEEECCCCCEEEEEEECCCCCCC
Q ss_conf 4774289843899718878999737876114455763457422
Q T0625 35 TYTIPARQGRAIRMAQGEALMVINRDGSQIGDFWAFVEGDCGE 77 (233)
Q Consensus 35 ~~tip~g~~~a~~v~~G~~lrI~d~~G~q~~d~~~~na~d~~E 77 (233)
.+++..|...++++.+++.|++.+= .+|.-...++..
T Consensus 1 ~f~L~~g~~~~~r~~~~~~l~v~~G------~vWlT~~g~~~D 37 (63)
T PF11142_consen 1 VFELAPGETMSLRARRGTRLRVHEG------RVWLTREGDPDD 37 (63)
T ss_pred CEEECCCCEEEEECCCCCEEEECCC------CEEEECCCCCCC
T ss_conf 9891798717775378848999300------589967899888
No 7
>PF01809 DUF37: Domain of unknown function DUF37; InterPro: IPR002696 This is a family of short (70 amino acid) hypothetical proteins from various bacteria. They contain three conserved cysteine residues. Q44066 from SWISSPROT from Aeromonas hydrophila has been found to have hemolytic activity.
Probab=16.57 E-value=23 Score=12.87 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=20.1
Q ss_pred CCCCCCHHHHHHHHHHHCCCCCCCCC
Q ss_conf 78866578999999971788553465
Q T0625 138 GYHDNCTDNLRMALGALGLRPTTVPC 163 (233)
Q Consensus 138 ~~h~nc~dNl~~al~k~Gl~~~di~~ 163 (233)
.|+++|.+-...|+.+||+-+.-...
T Consensus 25 rf~PsCS~Ya~~ai~~~G~~~G~~l~ 50 (68)
T PF01809_consen 25 RFYPSCSEYALEAIRKHGLFKGSWLT 50 (68)
T ss_pred CCCCCHHHHHHHHHHHHCHHHHHHHH
T ss_conf 98878899999999995959999999
No 8
>PF12148 DUF3590: Protein of unknown function (DUF3590); PDB: 3db4_A 3db3_A.
Probab=16.13 E-value=17 Score=13.67 Aligned_cols=34 Identities=12% Similarity=0.050 Sum_probs=25.7
Q ss_pred EEEEECCCCEEEEEECCCCCEEEEEEECCCCCCCC
Q ss_conf 38997188789997378761144557634574223
Q T0625 44 RAIRMAQGEALMVINRDGSQIGDFWAFVEGDCGEY 78 (233)
Q Consensus 44 ~a~~v~~G~~lrI~d~~G~q~~d~~~~na~d~~Er 78 (233)
...+-++-.+|+--+++-+|++ |.-||.++|.||
T Consensus 51 kdvRpRARt~l~W~~l~vG~vV-MvNYN~d~PkeR 84 (85)
T PF12148_consen 51 KDVRPRARTLLPWNDLEVGDVV-MVNYNPDDPKER 84 (85)
T ss_dssp CCEEE----B--GGG-----EE-EEE--TTSTT--
T ss_pred CCCCCCCEEEEEHHHCCCCCEE-EEECCCCCCCCC
T ss_conf 3268212023005345625299-996488980307
No 9
>PF09261 Alpha-mann_mid: Alpha mannosidase, middle domain; InterPro: IPR015341 Members of this entry belong to the glycosyl hydrolase family 38, This domain, which is found in the central region adopts a structure consisting of three alpha helices, in an immunoglobulin/albumin-binding domain-like fold. The domain is predominantly found in the enzyme alpha-mannosidase . ; PDB: 3d50_A 1hty_A 2f7o_A 1tqw_A 3blb_A 1tqu_A 3bvv_A 3bvu_A 3czs_A 2f7p_A ....
Probab=16.02 E-value=21 Score=13.04 Aligned_cols=17 Identities=18% Similarity=0.288 Sum_probs=13.9
Q ss_pred CCCCCCCCCCHHHHHHH
Q ss_conf 04332478897998764
Q T0625 118 VHDTLVASCDVHRYAQL 134 (233)
Q Consensus 118 ~HD~l~~~c~~~~y~~~ 134 (233)
.||.|+|.|..+-|...
T Consensus 58 ~HD~i~Gts~~~V~~d~ 74 (78)
T PF09261_consen 58 FHDAIPGTSIDEVYDDY 74 (78)
T ss_dssp BTTT------HHHHHHH
T ss_pred CCCCCCCCCHHHHHHHH
T ss_conf 78677772669999999
No 10
>PF11172 DUF2959: Protein of unknown function (DUF2959)
Probab=15.46 E-value=24 Score=12.69 Aligned_cols=20 Identities=15% Similarity=0.434 Sum_probs=10.5
Q ss_pred CCHHHHHHHHHHHCCCCCCC
Q ss_conf 65789999999717885534
Q T0625 142 NCTDNLRMALGALGLRPTTV 161 (233)
Q Consensus 142 nc~dNl~~al~k~Gl~~~di 161 (233)
.|..-+..++.|.|+.+|||
T Consensus 6 gCqsaYY~aMEkvG~hKRDI 25 (201)
T PF11172_consen 6 GCQSAYYSAMEKVGVHKRDI 25 (201)
T ss_pred HHHHHHHHHHHHHCCCHHHH
T ss_conf 50688899999938743479
Done!