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!