Query T0590 MaR143A, , 137 residues
Match_columns 137
No_of_seqs 127 out of 1654
Neff 6.5
Searched_HMMs 11830
Date Mon Jul 5 08:58:28 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0590.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0590.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00801 PKD: PKD domain; Int 99.5 1.7E-14 1.4E-18 93.7 5.4 64 67-130 2-68 (69)
2 PF05048 NosD: Periplasmic cop 96.7 0.00028 2.4E-08 38.9 2.5 44 7-52 2-58 (61)
3 PF05345 He_PIG: Putative Ig d 76.9 0.61 5.2E-05 21.0 2.5 16 112-127 34-49 (49)
4 PF05895 DUF859: Siphovirus pr 59.6 3.6 0.00031 16.9 7.0 61 75-135 253-321 (624)
5 PF07532 Big_4: Bacterial Ig-l 55.1 3.5 0.00029 17.0 2.7 38 77-123 20-57 (59)
6 PF06092 DUF943: Enterobacteri 48.8 3.5 0.0003 16.9 1.9 12 89-100 83-94 (157)
7 PF11797 DUF3324: Protein of u 44.5 6.5 0.00055 15.5 3.0 27 110-136 102-130 (140)
8 PF02494 HYR: HYR domain; Int 44.2 6.6 0.00055 15.5 3.6 31 105-136 49-80 (81)
9 PF07523 Big_3: Bacterial Ig-l 32.6 10 0.00086 14.4 5.1 25 107-135 41-65 (67)
10 PF09624 DUF2393: Protein of u 29.0 12 0.001 14.1 3.3 26 110-135 42-67 (119)
11 PF01835 A2M_N: MG2 domain; I 27.9 12 0.001 14.0 3.1 60 75-134 35-97 (98)
12 PF08428 Rib: Rib/alpha-like r 26.3 13 0.0011 13.8 3.9 25 111-135 36-61 (65)
13 PF04234 CopC: Copper resistan 23.1 15 0.0013 13.5 2.3 26 111-136 93-121 (121)
No 1
>PF00801 PKD: PKD domain; InterPro: IPR000601 The PKD domain was first identified in the Polycystic kidney disease protein, polycystin-1 (PDK1 gene), and contains an Ig-like fold consisting of a beta-sandwich of seven strands in two sheets with a Greek key topology, although some members have additional strands . Polycystin-1 is a large cell-surface glycoprotein involved in adhesive protein-protein and protein-carbohydrate interactions; however it is not clear if the PKD domain mediates any of these interactions. PKD domains are also found in other proteins, usually in the extracellular parts of proteins involved in interactions with other proteins. For example, domains with a PKD-type fold are found in archaeal surface layer proteins that protect the cell from extreme environments , and in the human VPS10 domain-containing receptor SorCS2 .; PDB: 2c4x_A 2c26_A 1b4r_A 1wgo_A 1l0q_B.
Probab=99.47 E-value=1.7e-14 Score=93.68 Aligned_cols=64 Identities=36% Similarity=0.499 Sum_probs=57.0
Q ss_pred EEECCCCCCCCCEEEEECC--CCCEEEEEECCC-CCCCCCCCCCEEECCCCCEEEEEEEECCCCCEE
Q ss_conf 3311477548515743388--895069997289-840246874578748963579888877999500
Q T0590 67 TSDITEGFAPLSVRFKDFS--ENATSRLWMFGD-GNTSDSPSPLHTFFNEGEYIVSLIVSNENDSDS 130 (137)
Q Consensus 67 ~~~~~~g~~pl~v~Ftd~s--~~~~~~~WdFGD-G~~st~~np~htY~~~G~YtVtLtvtn~~Gs~t 130 (137)
++++...+.+..|+|.+.+ +.+.+|.|+||| +....+++++|+|.++|.|+|+|+|+|..|..+
T Consensus 2 ~as~~~~~~g~~v~f~a~~~~g~~~~y~W~fgd~~~~~~~~~~~hty~~~G~y~V~ltv~n~~g~~s 68 (69)
T PF00801_consen 2 SASPTTVPVGETVTFTASSPDGSIVTYSWDFGDGGTTSSGPSVTHTYTSPGTYTVTLTVTNDVGSTS 68 (69)
T ss_dssp -----SEBTT-EEEEEECT--CSECEEEEE---ECCEESSSEEEEE-S----EEEEEEEEE----EE
T ss_pred CCCCCEECCCCEEEEEEECCCCCCEEEEEEECCCCEEECCCCEEEEECCCEEEEEEEEEEECCCCCC
T ss_conf 7778448899889999995899968999996699823846767999689878999999998988728
No 2
>PF05048 NosD: Periplasmic copper-binding protein (NosD); InterPro: IPR007742 Bacterial nitrous oxide (N(2)O) reductase is the terminal oxidoreductase of a respiratory process that generates dinitrogen from N(2)O. To attain its functional state, the enzyme is subjected to a maturation process which involves the protein-driven synthesis of a unique copper-sulphur cluster and metallation of the binuclear Cu(A) site in the periplasm. NosD is a periplasmic protein which is thought to insert copper into the exported reductase apoenzyme .; GO: 0005507 copper ion binding, 0006825 copper ion transport, 0042597 periplasmic space
Probab=96.74 E-value=0.00028 Score=38.86 Aligned_cols=44 Identities=57% Similarity=1.273 Sum_probs=33.9
Q ss_pred CCCCCCCCC-------------CCEEECCCCCCCCCCCEEECCCCCCCCCCCCEEEEEE
Q ss_conf 861101775-------------4177378764567763132011221245752000000
Q T0590 7 KFNTWNDSR-------------GNYWSDYEGSDENGDGIGDSAYAVNPEAGSMDYMPLM 52 (137)
Q Consensus 7 ~~ntw~~s~-------------GNy~~~~~~td~~g~g~~~~~~~~~~~~~~~~~~~~~ 52 (137)
.-++|+.+. ||||..+.+.|.+++|+.+.+|.+... ..++.++.
T Consensus 2 ~~n~Wn~~~~~g~ni~gg~~~gGNyW~~~~G~D~d~DGi~D~pY~i~~~--~~D~~PL~ 58 (61)
T PF05048_consen 2 SNNTWNSPKTPGTNINGGPYIGGNYWSDYDGTDADGDGIGDTPYRINGG--NIDYLPLV 58 (61)
T ss_pred CCCEECCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCEEECCEECCCC--CCCCCCCC
T ss_conf 8678337886625663786576436689988338899757565285898--61234014
No 3
>PF05345 He_PIG: Putative Ig domain; InterPro: IPR008009 This alignment represents the conserved core region of a ~90 residue repeat found in several haemagglutinins and other cell surface proteins. Sequence similarities to Hyalin (IPR003410 from INTERPRO) and the PKD domain (IPR000601 from INTERPRO) suggest an Ig-like fold so this family may be similar in function to the (IPR003791 from INTERPRO) and (IPR003790 from INTERPRO) protein families.
Probab=76.92 E-value=0.61 Score=21.00 Aligned_cols=16 Identities=13% Similarity=0.432 Sum_probs=13.9
Q ss_pred CCCCEEEEEEEECCCC
Q ss_conf 8963579888877999
Q T0590 112 NEGEYIVSLIVSNEND 127 (137)
Q Consensus 112 ~~G~YtVtLtvtn~~G 127 (137)
++|.|+++++|+|..|
T Consensus 34 ~~G~y~~~v~atd~~G 49 (49)
T PF05345_consen 34 QPGTYTFTVTATDGSG 49 (49)
T ss_pred CCCEEEEEEEEECCCC
T ss_conf 5767999999986999
No 4
>PF05895 DUF859: Siphovirus protein of unknown function (DUF859); InterPro: IPR008577 This family consists of several uncharacterised proteins from a number of the Siphoviruses as well as some bacterial proteins from Streptococcus species. Some of the members of this family are described as putative minor structural proteins.
Probab=59.55 E-value=3.6 Score=16.85 Aligned_cols=61 Identities=20% Similarity=0.226 Sum_probs=39.9
Q ss_pred CCCCEEEEECCC--C--CEEEEEECCCCCCCCCCC--CCEEECCCCCEEEEEEEECCCC--CEEEEEEE
Q ss_conf 485157433888--9--506999728984024687--4578748963579888877999--50057887
Q T0590 75 APLSVRFKDFSE--N--ATSRLWMFGDGNTSDSPS--PLHTFFNEGEYIVSLIVSNEND--SDSASVTI 135 (137)
Q Consensus 75 ~pl~v~Ftd~s~--~--~~~~~WdFGDG~~st~~n--p~htY~~~G~YtVtLtvtn~~G--s~t~t~tV 135 (137)
-...|.|...++ + |.+|.=+.-+.+.+...+ ..-.....|..+|+-+|+|..| ++.++++|
T Consensus 253 SnikVtfn~A~g~yGSTI~~y~aEIvgk~~s~~~n~g~lg~ln~~G~~tira~VtDSRGr~S~~~~~~I 321 (624)
T PF05895_consen 253 SNIKVTFNGATGAYGSTIKSYYAEIVGKNNSTTSNGGTLGMLNFNGSATIRATVTDSRGRQSDPVTVKI 321 (624)
T ss_pred EEEEEEEECCCCCCCCEEEEEEEEEECCCCEEECCCCCCCCCCCCCEEEEEEEEEECCCCCCCCEEEEE
T ss_conf 026999823457777426899999945752070488512133678649999999938994278457799
No 5
>PF07532 Big_4: Bacterial Ig-like domain (group 4); InterPro: IPR011081 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.
Probab=55.10 E-value=3.5 Score=16.96 Aligned_cols=38 Identities=26% Similarity=0.418 Sum_probs=26.1
Q ss_pred CCEEEEECCCCCEEEEEECCCCCCCCCCCCCEEECCCCCEEEEEEEE
Q ss_conf 51574338889506999728984024687457874896357988887
Q T0590 77 LSVRFKDFSENATSRLWMFGDGNTSDSPSPLHTFFNEGEYIVSLIVS 123 (137)
Q Consensus 77 l~v~Ftd~s~~~~~~~WdFGDG~~st~~np~htY~~~G~YtVtLtvt 123 (137)
..+.|.|.+.......|+ ..+...+..+|+|+|+=++.
T Consensus 20 V~v~~~dGs~~~~~V~W~---------~~~~~~~~~~G~y~v~G~v~ 57 (59)
T PF07532_consen 20 VTVTYSDGSTEDVPVTWD---------PIPPYDLNKPGTYTVTGTVE 57 (59)
T ss_pred EEEEECCCCEEEEEEECC---------CCCCHHCCCCEEEEEEEEEE
T ss_conf 999986998968675849---------99813416973999999995
No 6
>PF06092 DUF943: Enterobacterial putative membrane protein (DUF943); InterPro: IPR010351 This family consists of several hypothetical proteins from Escherichia coli, Yersinia pestis and Salmonella typhi.
Probab=48.79 E-value=3.5 Score=16.91 Aligned_cols=12 Identities=42% Similarity=1.030 Sum_probs=9.3
Q ss_pred EEEEEECCCCCC
Q ss_conf 069997289840
Q T0590 89 TSRLWMFGDGNT 100 (137)
Q Consensus 89 ~~~~WdFGDG~~ 100 (137)
.-+.||||||-.
T Consensus 83 sI~iwDfGdGY~ 94 (157)
T PF06092_consen 83 SITIWDFGDGYK 94 (157)
T ss_pred EEEEEECCCCEE
T ss_conf 999997379747
No 7
>PF11797 DUF3324: Protein of unknown function C-terminal (DUF3324)
Probab=44.51 E-value=6.5 Score=15.49 Aligned_cols=27 Identities=15% Similarity=0.300 Sum_probs=19.6
Q ss_pred ECCCCCEEEEEEEECCCC--CEEEEEEEE
Q ss_conf 748963579888877999--500578876
Q T0590 110 FFNEGEYIVSLIVSNEND--SDSASVTIR 136 (137)
Q Consensus 110 Y~~~G~YtVtLtvtn~~G--s~t~t~tV~ 136 (137)
=-.||.|++.|++..... .-++..+|+
T Consensus 102 ~lkpG~Y~l~~~~~~~~~~W~f~k~FtIt 130 (140)
T PF11797_consen 102 RLKPGKYTLKVTAKSGKQTWTFTKDFTIT 130 (140)
T ss_pred CCCCCEEEEEEEEECCCEEEEEEEEEEEC
T ss_conf 20595889999997894389999979997
No 8
>PF02494 HYR: HYR domain; InterPro: IPR003410 This domain is known as the HYR (Hyalin Repeat) domain, after the protein hyalin that is composed exclusively of this repeat. This domain probably corresponds to a new superfamily in the immunoglobulin fold. The function of this domain is uncertain it may be involved in cell adhesion. In the Sushi repeat-containing protein (SrpX), this domain is found between two sushi repeats.
Probab=44.23 E-value=6.6 Score=15.47 Aligned_cols=31 Identities=19% Similarity=0.315 Sum_probs=22.1
Q ss_pred CCCEEECCCCCEEEEEEEECCCC-CEEEEEEEE
Q ss_conf 74578748963579888877999-500578876
Q T0590 105 SPLHTFFNEGEYIVSLIVSNEND-SDSASVTIR 136 (137)
Q Consensus 105 np~htY~~~G~YtVtLtvtn~~G-s~t~t~tV~ 136 (137)
.|-+.|. .|.|.|+.+|+|..| ..+-+..|+
T Consensus 49 ~~g~~f~-~G~t~VtytA~D~sgN~a~C~F~V~ 80 (81)
T PF02494_consen 49 PPGSTFP-VGTTTVTYTATDASGNSATCTFNVT 80 (81)
T ss_pred CCCCEEC-CCCEEEEEEEEECCCCEEEEEEEEE
T ss_conf 9988907-1378999999989999998999998
No 9
>PF07523 Big_3: Bacterial Ig-like domain (group 3); InterPro: IPR011080 This entry represents bacterial domains with an Ig-like fold. These domains are found in a variety of bacterial surface proteins.
Probab=32.61 E-value=10 Score=14.43 Aligned_cols=25 Identities=16% Similarity=0.181 Sum_probs=17.9
Q ss_pred CEEECCCCCEEEEEEEECCCCCEEEEEEE
Q ss_conf 57874896357988887799950057887
Q T0590 107 LHTFFNEGEYIVSLIVSNENDSDSASVTI 135 (137)
Q Consensus 107 ~htY~~~G~YtVtLtvtn~~Gs~t~t~tV 135 (137)
..--.++|.|.|+++..+ -+++.+|
T Consensus 41 ~vd~~~~G~y~Vt~ty~~----~t~t~~V 65 (67)
T PF07523_consen 41 NVDTSKPGTYTVTYTYGG----VTKTFTV 65 (67)
T ss_pred EECCCCCCEEEEEEEECC----EEEEEEE
T ss_conf 772689718999999998----9999999
No 10
>PF09624 DUF2393: Protein of unknown function (DUF2393)
Probab=28.98 E-value=12 Score=14.09 Aligned_cols=26 Identities=35% Similarity=0.520 Sum_probs=11.1
Q ss_pred ECCCCCEEEEEEEECCCCCEEEEEEE
Q ss_conf 74896357988887799950057887
Q T0590 110 FFNEGEYIVSLIVSNENDSDSASVTI 135 (137)
Q Consensus 110 Y~~~G~YtVtLtvtn~~Gs~t~t~tV 135 (137)
=...|-|-|-++|+|..|..-++..|
T Consensus 42 ~~~~gqyyVpF~V~N~g~~TAasV~V 67 (119)
T PF09624_consen 42 RQVEGQYYVPFTVTNDGGQTAASVQV 67 (119)
T ss_pred EEECCEEEEEEEEEECCCCEEEEEEE
T ss_conf 99777689999999788775778999
No 11
>PF01835 A2M_N: MG2 domain; InterPro: IPR002890 The proteinase-binding alpha-macroglobulins (A2M) are large glycoproteins found in the plasma of vertebrates, in the hemolymph of some invertebrates and in reptilian and avian egg white. A2M-like proteins are able to inhibit all four classes of proteinases by a 'trapping' mechanism. They have a peptide stretch, called the 'bait region', which contains specific cleavage sites for different proteinases. When a proteinase cleaves the bait region, a conformational change is induced in the protein, thus trapping the proteinase. The entrapped enzyme remains active against low molecular weight substrates, whilst its activity toward larger substrates is greatly reduced, due to steric hindrance. Following cleavage in the bait region, a thiol ester bond, formed between the side chains of a cysteine and a glutamine, is cleaved and mediates the covalent binding of the A2M-like protein to the proteinase. This family includes the N-terminal region of the alpha-2-macroglobulin family. The inhibitor domains belong to MEROPS inhibitor family I39.; GO: 0004866 endopeptidase inhibitor activity; PDB: 2wii_A 3g6j_C 2win_E 2a74_A 2icf_A 2hr0_A 2a73_A 2ice_D 2qki_D 2i07_A ....
Probab=27.95 E-value=12 Score=13.99 Aligned_cols=60 Identities=20% Similarity=0.209 Sum_probs=32.5
Q ss_pred CCCCEEEEECCCCCE-EEEE-ECCCCCCCCCCCCCEEECCCCCEEEEEEEECCCC-CEEEEEE
Q ss_conf 485157433888950-6999-7289840246874578748963579888877999-5005788
Q T0590 75 APLSVRFKDFSENAT-SRLW-MFGDGNTSDSPSPLHTFFNEGEYIVSLIVSNEND-SDSASVT 134 (137)
Q Consensus 75 ~pl~v~Ftd~s~~~~-~~~W-dFGDG~~st~~np~htY~~~G~YtVtLtvtn~~G-s~t~t~t 134 (137)
.++.+.+.|.++..+ .+.. .-.+.+.....=+.-.-...|.|+|.+...+..+ ..+.+..
T Consensus 35 ~~v~v~l~dp~G~~v~~~~~~~~~~~G~~~~~~~lp~~~~~G~y~l~~~~~~~~~~~~~~~F~ 97 (98)
T PF01835_consen 35 TPVTVELEDPNGNEVFRWTVSVTDDFGFFSGSFPLPDDAPTGTYTLEAYTDDAGGESASTSFQ 97 (98)
T ss_dssp EEEEEEEE-TT--EEEEEEEECTTT--TEEEEEE--SS-----EEEEEEETTECCCEEEEEEE
T ss_pred CCEEEEEECCCCCEEEEEEEECCCCCCEEEEEEECCCCCCCEEEEEEEEECCCCCCEEEEEEE
T ss_conf 758999996999999999930018998899998999988866179999985689979999998
No 12
>PF08428 Rib: Rib/alpha-like repeat; InterPro: IPR012706 This entry represents a region of about 79 amino acids found tandemly repeated up to fourteen times within the proteins that contain it. The repeats lack cysteines and are highly conserved, even at the DNA level, within and between proteins . Proteins containing these repeats include the Rib and alpha surface antigens of group B Streptococcus, Esp of Enterococcus faecalis, and related proteins of Lactobacillus. Most members of this protein family also have the cell wall anchor motif, LPXTG, shared by many staphyloccal and streptococcal surface antigens. These repeats are thought to define protective epitopes and may play a role in generating phenotypic and genotypic variation .
Probab=26.33 E-value=13 Score=13.82 Aligned_cols=25 Identities=24% Similarity=0.353 Sum_probs=18.9
Q ss_pred CCCCCEEEEEEEECCCCC-EEEEEEE
Q ss_conf 489635798888779995-0057887
Q T0590 111 FNEGEYIVSLIVSNENDS-DSASVTI 135 (137)
Q Consensus 111 ~~~G~YtVtLtvtn~~Gs-~t~t~tV 135 (137)
..+|.|.+..+|+-.+|+ +.....|
T Consensus 36 ~~~G~~~~~V~VTYpDgS~~~V~V~V 61 (65)
T PF08428_consen 36 STPGDKTGTVTVTYPDGSTDTVPVTV 61 (65)
T ss_pred CCCCEEEEEEEEEECCCCCEEEEEEE
T ss_conf 68860877999995999913988899
No 13
>PF04234 CopC: Copper resistance protein CopC; InterPro: IPR007348 CopC is a bacterial blue copper protein that binds 1 atom of copper per protein molecule. Along with CopA, CopC mediates copper resistance by sequestration of copper in the periplasm .; GO: 0005507 copper ion binding, 0046688 response to copper ion, 0042597 periplasmic space; PDB: 1lyq_A 1ix2_A 1ot4_A 1nm4_A 1m42_A 2c9q_A 2c9p_C 2c9r_A.
Probab=23.09 E-value=15 Score=13.47 Aligned_cols=26 Identities=31% Similarity=0.387 Sum_probs=18.9
Q ss_pred CCCCCEEEEEEEECCCC---CEEEEEEEE
Q ss_conf 48963579888877999---500578876
Q T0590 111 FNEGEYIVSLIVSNEND---SDSASVTIR 136 (137)
Q Consensus 111 ~~~G~YtVtLtvtn~~G---s~t~t~tV~ 136 (137)
-.+|+|+|.-.|.-.+| +.+-..+|+
T Consensus 93 l~~G~YtV~wrv~s~DGH~~~G~~~F~V~ 121 (121)
T PF04234_consen 93 LAPGTYTVEWRVVSADGHPMSGSFSFTVG 121 (121)
T ss_dssp -----EEEE--BEETTSCEB---EEEEE-
T ss_pred CCCEEEEEEEEEEECCCCCCCCEEEEEEC
T ss_conf 99832999999993679954886988869
Done!