Query T0615 3NQW, , 179 residues
Match_columns 179
No_of_seqs 119 out of 1092
Neff 7.0
Searched_HMMs 11830
Date Mon Jul 5 09:02:46 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0615.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0615.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01966 HD: HD domain; Inter 96.9 0.00029 2.4E-08 43.3 3.7 92 33-128 1-118 (118)
2 PF05153 DUF706: Family of unk 66.6 1.5 0.00013 19.8 2.5 53 9-65 41-93 (251)
3 PF05082 DUF683: Protein of un 30.3 5.8 0.00049 16.1 0.6 23 130-152 27-52 (66)
4 PF06213 CobT: Cobalamin biosy 25.2 14 0.0012 13.7 2.1 20 4-23 7-26 (282)
5 PF08668 HDOD: HDOD domain; I 23.8 15 0.0013 13.5 2.5 14 163-176 180-193 (196)
6 PF01121 CoaE: Dephospho-CoA k 23.2 15 0.0013 13.5 1.9 42 39-84 15-57 (180)
7 PF11267 DUF3067: Protein of u 18.7 19 0.0016 12.9 2.3 42 19-64 34-75 (99)
8 PF00475 IGPD: Imidazoleglycer 16.1 2.7 0.00023 18.2 -3.4 42 29-74 1-46 (145)
9 PF11417 Inhibitor_G39P: Loade 15.0 19 0.0016 12.9 0.7 30 59-88 34-70 (71)
10 PF03469 XH: XH domain; Inter 11.5 30 0.0025 11.6 1.4 25 63-87 61-85 (135)
No 1
>PF01966 HD: HD domain; InterPro: IPR006674 This domain is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in the nucleic acid metabolism, signal transduction and possibly other functions in bacteria, archaea and eukaryotes. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins .; PDB: 2hek_B 2o6i_A 2q14_H 2cqz_D 1xx7_B 1ynb_B 1yoy_A 2par_B 2paq_B 2pau_B ....
Probab=96.93 E-value=0.00029 Score=43.26 Aligned_cols=92 Identities=26% Similarity=0.307 Sum_probs=51.4
Q ss_pred HHHHHHHHHHHHHHHCCC-----CCHHHHHHHHHHHHHHHCCCHHH---------------HHHHH---CCH---HHHHH
Q ss_conf 568889999999971036-----88999999999767751451288---------------99985---188---89999
Q T0615 33 YVNHVINVSTILSVEACI-----TDEGVLMAALLHDVVEDTDASFE---------------DVEKL---FGP---DVCGL 86 (179)
Q Consensus 33 Y~~H~~~Va~il~~~~~~-----~D~~~i~AalLHDvvEDt~~t~~---------------~l~~~---FG~---~Va~l 86 (179)
++.|.++|+.+....... ....+.+||+|||+-+....+.. .+... ++. .++.+
T Consensus 1 ~~~Hs~~V~~~a~~i~~~~~~~~~~~~l~~aallHDiGk~~~~~~~~~~~~~~~H~~~~~~~~~~~~~~~~~~~~~i~~~ 80 (118)
T PF01966_consen 1 RYEHSLRVAEIARAIAKRLGLEEDPELLEIAALLHDIGKYPEGDFQERKEEFRDHEIIGAEIAKEFLKRKGLDIEEIAHA 80 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHTTTTHCCHHCHHHHHTTTCHHHHHHHHHHHHHHHHCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHCHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf 98389999999999998858822199999999983568777875322110001189999999996101144439999999
Q ss_pred HHHHCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf 997014445783689999999987568899898999898688
Q T0615 87 VREVTDDKSLEKQERKRLQIENAAKSSCRAKLIKLADKLDNL 128 (179)
Q Consensus 87 V~~lT~~~~~~~~~~~~~~~~~~~~~d~~v~lIKLADrl~Nl 128 (179)
|..-+......... ........+..+.+|++||+++||
T Consensus 81 i~~h~~~~~~~~~~----~~~~~~~~~~~~~iv~~AD~l~~~ 118 (118)
T PF01966_consen 81 IRSHHEDWNGAGYP----EYLPKEPISLEAQIVKLADKLDAM 118 (118)
T ss_dssp HHHSCHCHHCHHC-----TCHHCHTHSHHHHHHHHHHHHHHH
T ss_pred HHHHHHCCCCCCHH----HHCCCCCCCHHHHHHHHHHHHHCC
T ss_conf 99973332432000----001346799999999999998587
No 2
>PF05153 DUF706: Family of unknown function (DUF706) ; InterPro: IPR007828 This is a family of uncharacterised eukaryotic proteins. Some members have a described putative function, but a common theme is not evident.; PDB: 2ibn_B 3bxd_A 2huo_A.
Probab=66.64 E-value=1.5 Score=19.83 Aligned_cols=53 Identities=13% Similarity=0.253 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf 999999999970267657888872568889999999971036889999999997677
Q T0615 9 FMECLQYAAFKHRQQRRKDPQETPYVNHVINVSTILSVEACITDEGVLMAALLHDVV 65 (179)
Q Consensus 9 ~~~A~~~A~~~H~gq~rk~g~~~PY~~H~~~Va~il~~~~~~~D~~~i~AalLHDvv 65 (179)
+.+|+++- ..--++-..+ .+.|=+.|++..|...... + ...-...+||+||+=
T Consensus 41 iwea~e~L-n~LvDESDPD-~~vsqi~H~LQTAE~iR~d-g-~~dW~~LtgLiHDLG 93 (251)
T PF05153_consen 41 IWEALEKL-NTLVDESDPD-TDVSQIQHALQTAEAIRRD-G-DPDWMQLTGLIHDLG 93 (251)
T ss_dssp HHHHHHHC-GG---TT-TT---S-HHHHHHHHH---TTT-T-T-HHHHH----TT--
T ss_pred HHHHHHHH-HHCCCCCCCC-CCHHHHHHHHHHHHHHHHC-C-CCCHHHHHHHHHHHH
T ss_conf 99999999-8613567888-8747999999999999867-9-971688999997369
No 3
>PF05082 DUF683: Protein of unknown function (DUF683); InterPro: IPR007774 This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons, so are likely to play a role in this process.; PDB: 3csx_B 2js5_B.
Probab=30.31 E-value=5.8 Score=16.10 Aligned_cols=23 Identities=30% Similarity=0.629 Sum_probs=10.4
Q ss_pred HHHHCCHHHHHH---HHHHHHHHHHH
Q ss_conf 887359678999---99999999999
Q T0615 130 DLQVNTPTGWTQ---ERRDQYFVWAK 152 (179)
Q Consensus 130 ~l~~~~~~~~~~---~a~e~~~~ya~ 152 (179)
++...-|..|.. .++.||..|+.
T Consensus 27 DLaEdLP~~w~~i~~vA~~t~~a~~~ 52 (66)
T PF05082_consen 27 DLAEDLPTDWEKIPEVAQKTYDAFAE 52 (66)
T ss_dssp HHHHTTTTTGCCHHHHHHHHHHHHHH
T ss_pred HHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf 88710411199889999999999999
No 4
>PF06213 CobT: Cobalamin biosynthesis protein CobT; InterPro: IPR006538 These proteins are CobT subunits of the aerobic cobalt chelatase (aerobic cobalamin biosynthesis pathway). Pseudomonas denitrificans CobT has been experimentally characterised , . Aerobic cobalt chelatase consists of three subunits, CobT, CobN (IPR003672 from INTERPRO) and CobS (IPR006537 from INTERPRO). Cobalamin (vitamin B12) can be complexed with metal via the ATP-dependent reactions (aerobic pathway) (e.g., in Pseudomonas denitrificans) or via ATP-independent reactions (anaerobic pathway) (e.g., in Salmonella typhimurium) , . The corresponding cobalt chelatases are not homologous. However, aerobic cobalt chelatase subunits CobN and CobS are homologous to Mg-chelatase subunits BchH and BchI, respectively . CobT, too, has been found to be remotely related to the third subunit of Mg-chelatase, BchD (involved in bacteriochlorophyll synthesis, e.g., in Rhodobacter capsulatus) . Nomenclature note: CobT of the aerobic pathway Pseudomonas denitrificans is not a homolog of CobT of the anaerobic pathway (Salmonella typhimurium, Escherichia coli). Therefore, annotation of any members of this family as nicotinate-mononucleotide--5,6-dimethylbenzimidazole phosphoribosyltransferases is erroneous.
Probab=25.23 E-value=14 Score=13.70 Aligned_cols=20 Identities=25% Similarity=0.190 Sum_probs=16.9
Q ss_pred CCHHHHHHHHHHHHHHHCCC
Q ss_conf 43689999999999970267
Q T0615 4 YPSAKFMECLQYAAFKHRQQ 23 (179)
Q Consensus 4 ~~~~~~~~A~~~A~~~H~gq 23 (179)
-+.+.|.+|+.-+.++-+|.
T Consensus 7 ~~~e~fK~Al~~~~rAia~~ 26 (282)
T PF06213_consen 7 NPAEPFKRALAGAARAIAGD 26 (282)
T ss_pred CCHHHHHHHHHHHHHHHCCC
T ss_conf 83789999999999997589
No 5
>PF08668 HDOD: HDOD domain; InterPro: IPR013976 This domain is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These members appear to be involved in the nucleic acid metabolism and signal transduction or possibly other functions and are restricted to bacteria, primarily the proteobacteria. The fact that all the highly conserved residues in the HD superfamily are histidines or aspartates suggests that coordination of divalent cations is essential for the activity of these proteins .; PDB: 3hc1_A.
Probab=23.76 E-value=15 Score=13.53 Aligned_cols=14 Identities=14% Similarity=0.171 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 88999999999962
Q T0615 163 ANLELKLDEIFRQR 176 (179)
Q Consensus 163 ~~L~~el~~~~~~~ 176 (179)
|.+-.++-+.+..|
T Consensus 180 W~lp~~i~~~i~~h 193 (196)
T PF08668_consen 180 WGLPEEIIDAIRHH 193 (196)
T ss_dssp TT--HHHHHHHHHT
T ss_pred CCCCHHHHHHHHHH
T ss_conf 79899999999998
No 6
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The cyrstal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases . ; GO: 0005524 ATP binding; PDB: 2f6r_A 2if2_C 1jjv_A 1viy_A 1n3b_A 1vht_C 1vhl_C 1t3h_A 2grj_F 1uf9_B ....
Probab=23.25 E-value=15 Score=13.46 Aligned_cols=42 Identities=21% Similarity=0.429 Sum_probs=28.1
Q ss_pred HHHHHHHHHCC-CCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCHHHH
Q ss_conf 99999997103-68899999999976775145128899985188899
Q T0615 39 NVSTILSVEAC-ITDEGVLMAALLHDVVEDTDASFEDVEKLFGPDVC 84 (179)
Q Consensus 39 ~Va~il~~~~~-~~D~~~i~AalLHDvvEDt~~t~~~l~~~FG~~Va 84 (179)
.|+.++...|. ..|.+.+ -|.+++........|.+.||+++.
T Consensus 15 tv~~~l~~~G~~vidaD~i----~~~l~~~~~~~~~~i~~~FG~~il 57 (180)
T PF01121_consen 15 TVAKILKELGAPVIDADEI----AHELYEPGSPVYKKIVERFGEDIL 57 (180)
T ss_dssp HHHHHHHH---EEEEHHHH----HHHTTHHTHHHHHHHHHH-GGTTB
T ss_pred HHHHHHHHCCCCEEEHHHH----HHHHHCCCHHHHHHHHHHHCHHHC
T ss_conf 9999999779969977789----999845982899999999486641
No 7
>PF11267 DUF3067: Protein of unknown function (DUF3067)
Probab=18.73 E-value=19 Score=12.87 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=25.4
Q ss_pred HHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf 7026765788887256888999999997103688999999999767
Q T0615 19 KHRQQRRKDPQETPYVNHVINVSTILSVEACITDEGVLMAALLHDV 64 (179)
Q Consensus 19 ~H~gq~rk~g~~~PY~~H~~~Va~il~~~~~~~D~~~i~AalLHDv 64 (179)
.|-+|.----++.-|..|+-+|+.+|..+|. .| .+ -.+|-.+
T Consensus 34 ~yLeQ~SFPltE~eY~~hL~~va~~L~~~G~-~~--~V-r~~l~~t 75 (99)
T PF11267_consen 34 KYLEQASFPLTEEEYLEHLDAVAEYLNAWGQ-AD--QV-RNFLEET 75 (99)
T ss_pred HHHCCCCCCCCHHHHHHHHHHHHHHHHHCCC-HH--HH-HHHHHHC
T ss_conf 6607788689999999999999999998253-99--99-9999867
No 8
>PF00475 IGPD: Imidazoleglycerol-phosphate dehydratase; InterPro: IPR000807 Imidazoleglycerol-phosphate dehydratase is the enzyme that catalyzes the seventh step in the biosynthesis of histidine in bacteria, fungi and plants. In most organisms it is a monofunctional protein of about 22 to 29 kD. In some bacteria such as Escherichia coli, it is the C-terminal domain of a bifunctional protein that include a histidinol-phosphatase domain .; GO: 0004424 imidazoleglycerol-phosphate dehydratase activity, 0000105 histidine biosynthetic process; PDB: 2f1d_K 1rhy_B 2ae8_E.
Probab=16.13 E-value=2.7 Score=18.15 Aligned_cols=42 Identities=17% Similarity=0.205 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHH----HHHHHHHCCCHHHH
Q ss_conf 88725688899999999710368899999999----97677514512889
Q T0615 29 QETPYVNHVINVSTILSVEACITDEGVLMAAL----LHDVVEDTDASFED 74 (179)
Q Consensus 29 ~~~PY~~H~~~Va~il~~~~~~~D~~~i~Aal----LHDvvEDt~~t~~~ 74 (179)
++.||+.|.+. .++.+++ .|-.+.+-+= -|-++||+.+++.+
T Consensus 1 TGi~FlDHML~---~~a~h~~-~dl~v~a~GDl~vD~HHtvEDvgI~LG~ 46 (145)
T PF00475_consen 1 TGIGFLDHMLE---QFAKHGG-FDLTVKAKGDLEVDDHHTVEDVGIVLGQ 46 (145)
T ss_dssp ---HHHHHHHH---HHHHH----EEEEEEE--TTT-CHHHHHHHHHH---
T ss_pred CCCCHHHHHHH---HHHHHCC-CCEEEEEECCCCCCCCCCHHHHHHHHHH
T ss_conf 98836889999---9999869-8769999679876686043169999999
No 9
>PF11417 Inhibitor_G39P: Loader and inhibitor of phage G40P; PDB: 1no1_B.
Probab=15.02 E-value=19 Score=12.86 Aligned_cols=30 Identities=23% Similarity=0.380 Sum_probs=18.5
Q ss_pred HHHHHHHHHCCCHHHH------H-HHHCCHHHHHHHH
Q ss_conf 9997677514512889------9-9851888999999
Q T0615 59 ALLHDVVEDTDASFED------V-EKLFGPDVCGLVR 88 (179)
Q Consensus 59 alLHDvvEDt~~t~~~------l-~~~FG~~Va~lV~ 88 (179)
-++|+++||.+..... + .+.|.|.|++++.
T Consensus 34 ~~W~~~L~d~~y~~v~~~lk~~ikt~kfPPsvaevi~ 70 (71)
T PF11417_consen 34 NLWHMMLEDYPYEEVQKALKKHIKTNKFPPSVAEVIK 70 (71)
T ss_dssp HHHHHHHTTS-HHHHHHHHHHHHHH-SS---GGGG--
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHCCCCCCHHHHHC
T ss_conf 9999999705679999999999985479989999830
No 10
>PF03469 XH: XH domain; InterPro: IPR005379 The XH (rice gene X Homology) domain is found in a family of plant proteins including Oryza sativa Q9SBW2 from SWISSPROT. The molecular function of these proteins is unknown, however these proteins usually contain an XS domain (IPR005380 from INTERPRO) that is also found in the PTGS protein SGS3. As the XS and XH domains are fused in most of these proteins, these two domains may interact. The XH domain is between 124 and 145 residues in length and contains a conserved glutamate residue that may be functionally important .
Probab=11.47 E-value=30 Score=11.65 Aligned_cols=25 Identities=20% Similarity=0.615 Sum_probs=0.0
Q ss_pred HHHHHCCCHHHHHHHHCCHHHHHHH
Q ss_conf 6775145128899985188899999
Q T0615 63 DVVEDTDASFEDVEKLFGPDVCGLV 87 (179)
Q Consensus 63 DvvEDt~~t~~~l~~~FG~~Va~lV 87 (179)
.+|...+..+..|....|++|...|
T Consensus 61 evI~edDekL~~Lk~e~GeeVy~aV 85 (135)
T PF03469_consen 61 EVIDEDDEKLKELKEEYGEEVYNAV 85 (135)
T ss_pred EEECCCHHHHHHHHHHHHHHHHHHH
T ss_conf 5326768999999999719999999
Done!