Query T0538 NsR143, , 54 residues
Match_columns 54
No_of_seqs 103 out of 193
Neff 4.4
Searched_HMMs 11830
Date Fri May 21 18:05:26 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0538.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/hhm/T0538.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF08369 PCP_red: Proto-chloro 99.6 9.4E-17 7.9E-21 111.4 4.9 45 5-49 1-45 (45)
2 PF11084 DUF2621: Protein of u 88.0 0.29 2.4E-05 26.2 4.4 44 4-47 58-109 (141)
3 PF05016 Plasmid_stabil: Plasm 30.9 9.7 0.00082 17.8 1.9 31 3-33 1-37 (88)
4 PF03938 OmpH: Outer membrane 22.7 23 0.002 15.7 2.6 22 19-40 113-134 (158)
5 PF07750 GcrA: GcrA cell cycle 20.6 17 0.0015 16.4 1.6 14 3-16 1-14 (162)
6 PF12559 Inhibitor_I10: Serine 18.8 9.9 0.00084 17.8 0.0 19 10-28 7-25 (56)
7 PF00926 DHBP_synthase: 3,4-di 18.1 32 0.0027 15.0 2.7 25 25-49 170-194 (194)
8 PF10163 EnY2: Transcription f 13.3 43 0.0036 14.3 3.7 28 21-48 33-60 (86)
9 PF02797 Chal_sti_synt_C: Chal 12.0 47 0.004 14.1 3.2 28 14-41 32-59 (151)
10 PF00570 HRDC: HRDC domain Blo 10.7 40 0.0034 14.4 1.3 25 7-31 40-64 (68)
No 1
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase 57 kDa subunit of the cyanobacterium Synechocystis. ; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process
Probab=99.63 E-value=9.4e-17 Score=111.44 Aligned_cols=45 Identities=40% Similarity=0.717 Sum_probs=44.4
Q ss_pred CCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 688899998608801237899999999987699813889899999
Q T0538 5 WTSEAKTKLKNIPFFARSQAKARIEQLARQAEQDIVTPELVEQAR 49 (54)
Q Consensus 5 Wt~eA~~~L~kIP~FvR~kvr~~~E~~A~e~g~~~IT~ev~~~Ak 49 (54)
||+||+++|++||||||+++|+++|+||+++|++.||++++++||
T Consensus 1 W~~eA~~~L~~iP~fvR~~~r~~~E~~A~~~G~~~IT~e~v~~Ak 45 (45)
T PF08369_consen 1 WTDEAEAELKKIPFFVRKKVRDNAEKYARENGYTEITVEVVDAAK 45 (45)
T ss_pred CCHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCEECHHHHHHHC
T ss_conf 988999999879877799999999999998599837799998639
No 2
>PF11084 DUF2621: Protein of unknown function (DUF2621)
Probab=87.97 E-value=0.29 Score=26.24 Aligned_cols=44 Identities=32% Similarity=0.491 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHC----CCCHHHHHHH----HHHHHHHHHCCCCCCCHHHHHH
Q ss_conf 768889999860----8801237899----9999999876998138898999
Q T0538 4 RWTSEAKTKLKN----IPFFARSQAK----ARIEQLARQAEQDIVTPELVEQ 47 (54)
Q Consensus 4 ~Wt~eA~~~L~k----IP~FvR~kvr----~~~E~~A~e~g~~~IT~ev~~~ 47 (54)
-|++|+.+.|+. ||--.|.-+| .++.+.|.+.|-++||.+.+-.
T Consensus 58 lW~de~k~lL~eLV~PVPelFRdvAk~kIAgkIgelAl~e~a~~it~dliI~ 109 (141)
T PF11084_consen 58 LWTDEEKELLNELVSPVPELFRDVAKEKIAGKIGELALEEGATEITRDLIIR 109 (141)
T ss_pred CCCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf 1488899999999751609889999998777898999871863320888888
No 3
>PF05016 Plasmid_stabil: Plasmid stabilisation system protein; InterPro: IPR007712 Members of this family are involved in plasmid stabilisation. The exact molecular function of this protein is not known.; PDB: 2kc9_A 2kc8_A 1wmi_A 3bpq_D 3g5o_B 1z8m_A 2otr_A.
Probab=30.87 E-value=9.7 Score=17.83 Aligned_cols=31 Identities=29% Similarity=0.451 Sum_probs=22.4
Q ss_pred CCCCHHHHHHHHCCCCHH------HHHHHHHHHHHHH
Q ss_conf 876888999986088012------3789999999998
Q T0538 3 LRWTSEAKTKLKNIPFFA------RSQAKARIEQLAR 33 (54)
Q Consensus 3 l~Wt~eA~~~L~kIP~Fv------R~kvr~~~E~~A~ 33 (54)
+.||+.|+..|+++.-|. ..++...+++...
T Consensus 1 v~~t~~A~~dl~~i~~~~~~~~~~a~~~~~~i~~~~~ 37 (88)
T PF05016_consen 1 VRWTPSAEKDLKEIIDYIAQFGPAAERFLDEIEEAIE 37 (88)
T ss_dssp EEEEHHHHHHHHCHHCHH------HHHHHHHHHHHHH
T ss_pred CEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999899999999998875537889999999999997
No 4
>PF03938 OmpH: Outer membrane protein (OmpH-like); InterPro: IPR005632 This family contains proteins annotated as OmpH (outer membrane protein H). OmpH is a major structural protein of the outer membrane. In Pasteurella multocida it acts as a channel-forming transmembrane porin . Porins act as molecular sieves to allow the diffusion of small hydrophilic solutes through the outer membrane and also acts as a receptor for bacteriophages and bacteriocins. Porins are highly immunogenic and are conserved in bacterial families, making them attractive vaccine candidates . The 17-kDa protein (Skp, OmpH) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesised outer-membrane proteins, the X-ray structure of which has been reported at resolutions of 2.35 A and 2.30 A , . Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerisation domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forcep'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin (IPR009053 from INTERPRO), although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm. The ability of Skp to prevent the aggregation of model substrates in vitro is independent of ATP. Skp can interact directly with membrane lipids and lipopolysaccharide. These interactions are needed for efficient Skp-assisted folding of membrane proteins .; GO: 0005515 protein binding; PDB: 1sg2_A 1u2m_C.
Probab=22.74 E-value=23 Score=15.73 Aligned_cols=22 Identities=18% Similarity=0.327 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHCCCCCC
Q ss_conf 1237899999999987699813
Q T0538 19 FARSQAKARIEQLARQAEQDIV 40 (54)
Q Consensus 19 FvR~kvr~~~E~~A~e~g~~~I 40 (54)
=+..++..-+.++|.++|++.|
T Consensus 113 ~i~~~i~~~i~~vak~~g~~~V 134 (158)
T PF03938_consen 113 PIQDKINKAIKEVAKENGYDLV 134 (158)
T ss_dssp -HHHHHHHHHHHHHHHTT-SEE
T ss_pred HHHHHHHHHHHHHHHHCCCEEE
T ss_conf 9999999999999998799399
No 5
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis . During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes . More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery .
Probab=20.57 E-value=17 Score=16.44 Aligned_cols=14 Identities=36% Similarity=0.821 Sum_probs=12.1
Q ss_pred CCCCHHHHHHHHCC
Q ss_conf 87688899998608
Q T0538 3 LRWTSEAKTKLKNI 16 (54)
Q Consensus 3 l~Wt~eA~~~L~kI 16 (54)
|.||+|--+.|++.
T Consensus 1 MsWTderve~Lk~l 14 (162)
T PF07750_consen 1 MSWTDERVERLKKL 14 (162)
T ss_pred CCCCHHHHHHHHHH
T ss_conf 98878999999999
No 6
>PF12559 Inhibitor_I10: Serine endopeptidase inhibitors; PDB: 1ixu_A.
Probab=18.76 E-value=9.9 Score=17.79 Aligned_cols=19 Identities=32% Similarity=0.508 Sum_probs=12.9
Q ss_pred HHHHHCCCCHHHHHHHHHH
Q ss_conf 9998608801237899999
Q T0538 10 KTKLKNIPFFARSQAKARI 28 (54)
Q Consensus 10 ~~~L~kIP~FvR~kvr~~~ 28 (54)
...-+.+|||.|=-.....
T Consensus 7 ~~~~ka~PFFArFLe~Q~~ 25 (56)
T PF12559_consen 7 DKNSKAVPFFARFLEEQEK 25 (56)
T ss_dssp -------------------
T ss_pred CCCCCCCCHHHHHHHHHHC
T ss_conf 3212224389999987311
No 7
>PF00926 DHBP_synthase: 3,4-dihydroxy-2-butanone 4-phosphate synthase; InterPro: IPR000422 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin . It is sometimes found as a bifunctional enzyme with GTP cyclohydrolase II that catalyses the first committed step in the biosynthesis of riboflavin (IPR000926 from INTERPRO). No sequences with significant homology to DHBP synthase are found in the metazoa.; GO: 0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity, 0009231 riboflavin biosynthetic process; PDB: 1pvw_C 1pvy_A 1snn_B 1tks_B 1tku_A 2ris_A 2riu_A 1k49_A 1k4o_A 1k4p_A ....
Probab=18.09 E-value=32 Score=14.98 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=20.8
Q ss_pred HHHHHHHHHHCCCCCCCHHHHHHHH
Q ss_conf 9999999987699813889899999
Q T0538 25 KARIEQLARQAEQDIVTPELVEQAR 49 (54)
Q Consensus 25 r~~~E~~A~e~g~~~IT~ev~~~Ak 49 (54)
+.-.++||+++|++.||.+.+.+-|
T Consensus 170 ~~~~~~fA~~h~l~~i~i~dli~yr 194 (194)
T PF00926_consen 170 RDELEEFAKKHGLPIISIEDLIAYR 194 (194)
T ss_dssp HHHHHHHHHHTT-EEEEHHHHHHHH
T ss_pred HHHHHHHHHHCCCCEEEHHHHHHHC
T ss_conf 9999999998399699899999659
No 8
>PF10163 EnY2: Transcription factor e(y)2; PDB: 3fwc_G 3fwb_C.
Probab=13.29 E-value=43 Score=14.27 Aligned_cols=28 Identities=11% Similarity=0.125 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHH
Q ss_conf 3789999999998769981388989999
Q T0538 21 RSQAKARIEQLARQAEQDIVTPELVEQA 48 (54)
Q Consensus 21 R~kvr~~~E~~A~e~g~~~IT~ev~~~A 48 (54)
|..+|..+....++.|...+|.+-+++.
T Consensus 33 ~devr~~~r~~i~~~~~~~~t~~dl~~~ 60 (86)
T PF10163_consen 33 RDEVRQLCREIIKERGIENLTFEDLIAE 60 (86)
T ss_dssp HHHHHHHHHHHHHH--SSSS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf 9999999999999860479999999999
No 9
>PF02797 Chal_sti_synt_C: Chalcone and stilbene synthases, C-terminal domain; InterPro: IPR012328 Synonym(s): Chalcone synthase, Flavonone synthase, 6'-deoxychalcone synthase Naringenin-chalcone synthases () and stilbene synthases (STS) (formerly known as resveratrol synthases) are related plant enzymes. CHS is an important enzyme in flavanoid biosynthesis and STS is a key enzyme in stilbene-type phyloalexin biosynthesis. Both enzymes catalyze the addition of three molecules of malonyl-CoA to a starter CoA ester (a typical example is 4-coumaroyl-CoA), producing either a chalcone (with CHS) or stilbene (with STS) . These enzymes have a conserved cysteine residue, located in the central section of the protein sequence, which is essential for the catalytic activity of both enzymes and probably represents the binding site for the 4-coumaryl-CoA group . This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. ; GO: 0008415 acyltransferase activity; PDB: 1z1f_A 1z1e_A 2p0u_A 1ted_A 1tee_D 1u0m_B 2h84_B 3euq_C 3e1h_B 3eut_D ....
Probab=12.05 E-value=47 Score=14.05 Aligned_cols=28 Identities=11% Similarity=0.169 Sum_probs=24.9
Q ss_pred HCCCCHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf 6088012378999999999876998138
Q T0538 14 KNIPFFARSQAKARIEQLARQAEQDIVT 41 (54)
Q Consensus 14 ~kIP~FvR~kvr~~~E~~A~e~g~~~IT 41 (54)
+.||.+|+..++...+.+-...|++..+
T Consensus 32 ~~VP~~i~~~i~~~~~~~l~~~g~~~~n 59 (151)
T PF02797_consen 32 KDVPALISDNIEPCLEEFLAPHGLSDWN 59 (151)
T ss_dssp TTHHHHHHHHHHHHHHHHHHTCTCCSGG
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf 1516999999999999999763897543
No 10
>PF00570 HRDC: HRDC domain Bloom syndrome. Werner syndrome.; InterPro: IPR002121 The HRDC (Helicase and RNase D C-terminal) domain has a putative role in nucleic acid binding. Mutations in the HRDC domain associated with the human BLM gene result in Bloom Syndrome (BS), an autosomal recessive disorder characterised by proportionate pre- and postnatal growth deficiency; sun-sensitive, telangiectatic, hypo- and hyperpigmented skin; predisposition to malignancy; and chromosomal instability .; GO: 0003676 nucleic acid binding, 0005622 intracellular; PDB: 2rhf_A 2dgz_A 2e1f_A 2e1e_A 1yt3_A 3cym_A 2cpr_A 2hbl_A 2hbj_A 2hbk_A ....
Probab=10.71 E-value=40 Score=14.43 Aligned_cols=25 Identities=12% Similarity=0.182 Sum_probs=18.9
Q ss_pred HHHHHHHHCCCCHHHHHHHHHHHHH
Q ss_conf 8899998608801237899999999
Q T0538 7 SEAKTKLKNIPFFARSQAKARIEQL 31 (54)
Q Consensus 7 ~eA~~~L~kIP~FvR~kvr~~~E~~ 31 (54)
|....+|.+||+|-++++++-.+.+
T Consensus 40 P~t~~eL~~i~g~~~~~~~~yg~~i 64 (68)
T PF00570_consen 40 PTTIEELLQIPGMGPKKVEKYGDEI 64 (68)
T ss_dssp -SSHHHHTTTSCCGSHHHHHTHHHH
T ss_pred CCCHHHHHHCCCCCHHHHHHHHHHH
T ss_conf 8999999652398999999999999
Done!