Query 025081
Match_columns 258
No_of_seqs 138 out of 187
Neff 5.5
Searched_HMMs 29240
Date Mon Mar 25 03:22:49 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025081.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/025081hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2krc_A DNA-directed RNA polyme 33.9 1.2E+02 0.0041 22.9 6.5 34 158-191 12-45 (99)
2 2dii_A TFIIH basal transcripti 29.9 48 0.0016 23.3 3.3 28 164-191 28-57 (61)
3 2yma_A YOS9P, protein OS-9 hom 18.7 89 0.0031 25.9 3.4 39 218-256 49-87 (161)
4 2fe3_A Peroxide operon regulat 17.7 2.7E+02 0.0091 21.4 6.0 54 157-241 20-73 (145)
5 1irz_A ARR10-B; helix-turn-hel 17.0 70 0.0024 22.5 2.1 17 218-234 9-25 (64)
6 3mwm_A ZUR, putative metal upt 16.6 2.3E+02 0.008 21.7 5.4 47 165-241 19-65 (139)
7 2xig_A Ferric uptake regulatio 14.9 3.5E+02 0.012 20.9 6.1 53 158-241 26-78 (150)
8 2o03_A Probable zinc uptake re 14.7 3.2E+02 0.011 20.5 5.7 47 165-241 16-62 (131)
9 1mzb_A Ferric uptake regulatio 14.1 3E+02 0.01 20.8 5.4 54 157-241 16-70 (136)
10 2w57_A Ferric uptake regulatio 11.9 3.4E+02 0.012 21.0 5.2 54 157-241 15-69 (150)
No 1
>2krc_A DNA-directed RNA polymerase subunit delta; delta subunit, GRAM-positive bacteria, nucleotidyltransferase, transcription, transferase; NMR {Bacillus subtilis}
Probab=33.94 E-value=1.2e+02 Score=22.92 Aligned_cols=34 Identities=15% Similarity=0.188 Sum_probs=30.3
Q ss_pred CcchHHHHHHHHHHhCCcccHHHHHHHHHhhhcC
Q 025081 158 SLHDTSILYNLAQEHGDHINLHDWYQSFKSKVCS 191 (258)
Q Consensus 158 s~Pd~silYkLY~EaG~lINlyDw~~AF~~~l~~ 191 (258)
.++-+-++|.+..+.|..++.+|.|....+..+-
T Consensus 12 e~SmiDvAy~iL~~~~~~~~F~dL~~eV~~~~~~ 45 (99)
T 2krc_A 12 EMALVEIAHELFEEHKKPVPFQELLNEIASLLGV 45 (99)
T ss_dssp TSCHHHHHHHHHHHHCSCEEHHHHHHHHHHHHTS
T ss_pred cCCHHHHHHHHHHHcCCcccHHHHHHHHHHHhCC
Confidence 3688999999999999999999999999887643
No 2
>2dii_A TFIIH basal transcription factor complex P62 subunit; BTF2-P62, general transcription factor IIH polypeptide 1, nuclear protein; NMR {Homo sapiens} SCOP: a.240.1.1
Probab=29.94 E-value=48 Score=23.27 Aligned_cols=28 Identities=11% Similarity=0.282 Sum_probs=22.1
Q ss_pred HHHHHHHH--hCCcccHHHHHHHHHhhhcC
Q 025081 164 ILYNLAQE--HGDHINLHDWYQSFKSKVCS 191 (258)
Q Consensus 164 ilYkLY~E--aG~lINlyDw~~AF~~~l~~ 191 (258)
.|++||++ .+.+|.-.|||...+..+..
T Consensus 28 ~L~qLyk~LV~s~vIse~eFW~~r~~ll~~ 57 (61)
T 2dii_A 28 VLFQLYKDLVVSQVISAEEFWANRLNVNSG 57 (61)
T ss_dssp HHHHHHHHHHTTTSSCHHHHHHHHCSSCCC
T ss_pred HHHHHHHHHHHhCcCCHHHHHHHHHHhhcC
Confidence 35677777 58899999999999886543
No 3
>2yma_A YOS9P, protein OS-9 homolog; carbohydrate binding protein, quality control, endoplasmic reticulum-associated protein degradation; 2.54A {Saccharomyces cerevisiae}
Probab=18.66 E-value=89 Score=25.86 Aligned_cols=39 Identities=10% Similarity=0.180 Sum_probs=28.8
Q ss_pred hhhHHHHHHHHHHHHHHHHcCcccCCCCCCcceeeeecc
Q 025081 218 PCEASIQARFCKAVTELQITGLIRMPTKRRPDFVQRVAF 256 (258)
Q Consensus 218 ~~e~~~qArF~rAv~EL~~lGfIK~~skrK~DhV~K~~W 256 (258)
+.+++.+-+|.-|+.+|-.+|||..|..+-.++=-..+|
T Consensus 49 ~~~~~~yk~~g~A~~kml~~~ll~~P~g~p~~~gD~ftW 87 (161)
T 2yma_A 49 EITETYYQKFGNAINKMLSLRLVSLPNGHILQPGDSCVW 87 (161)
T ss_dssp SCCHHHHHHHHHHHHHHHHTTCCBCTTSCBCCTTCEEEE
T ss_pred hHHHHHHHHHHHHHHHHHHhCcccCCCCCCCCCCCeEEE
Confidence 345789999999999999999999766443343333344
No 4
>2fe3_A Peroxide operon regulator; oxidative stress regulator, DNA binding protein; 1.75A {Bacillus subtilis} PDB: 3f8n_A 2rgv_A*
Probab=17.71 E-value=2.7e+02 Score=21.44 Aligned_cols=54 Identities=17% Similarity=0.217 Sum_probs=40.1
Q ss_pred CCcchHHHHHHHHHHhCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHHH
Q 025081 157 PSLHDTSILYNLAQEHGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQI 236 (258)
Q Consensus 157 ~s~Pd~silYkLY~EaG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~~ 236 (258)
.+.+-..||= +..+++.-++.+|.|+.++...+. ...+--||.+.-|.=
T Consensus 20 ~T~qR~~Il~-~L~~~~~~~sa~ei~~~l~~~~~~------------------------------is~aTVYR~L~~L~e 68 (145)
T 2fe3_A 20 ITPQRHAILE-YLVNSMAHPTADDIYKALEGKFPN------------------------------MSVATVYNNLRVFRE 68 (145)
T ss_dssp CCHHHHHHHH-HHHHCSSCCCHHHHHHHHGGGCTT------------------------------CCHHHHHHHHHHHHH
T ss_pred CCHHHHHHHH-HHHhCCCCCCHHHHHHHHHHhCCC------------------------------CChhhHHHHHHHHHH
Confidence 3455555554 445678889999999999764221 237889999999999
Q ss_pred cCccc
Q 025081 237 TGLIR 241 (258)
Q Consensus 237 lGfIK 241 (258)
.|+|+
T Consensus 69 ~Glv~ 73 (145)
T 2fe3_A 69 SGLVK 73 (145)
T ss_dssp TTSEE
T ss_pred CCCEE
Confidence 99997
No 5
>1irz_A ARR10-B; helix-turn-helix, DNA binding protein; NMR {Arabidopsis thaliana} SCOP: a.4.1.11
Probab=17.00 E-value=70 Score=22.48 Aligned_cols=17 Identities=24% Similarity=0.348 Sum_probs=15.3
Q ss_pred hhhHHHHHHHHHHHHHH
Q 025081 218 PCEASIQARFCKAVTEL 234 (258)
Q Consensus 218 ~~e~~~qArF~rAv~EL 234 (258)
.|..+++.+|..||..|
T Consensus 9 ~WT~elH~~Fv~Av~~L 25 (64)
T 1irz_A 9 LWTHELHNKFLAAVDHL 25 (64)
T ss_dssp SSCHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHh
Confidence 58889999999999976
No 6
>3mwm_A ZUR, putative metal uptake regulation protein; FUR, regulatory metal, graded transcription regulation, transcription; 2.40A {Streptomyces coelicolor}
Probab=16.57 E-value=2.3e+02 Score=21.70 Aligned_cols=47 Identities=13% Similarity=0.068 Sum_probs=36.3
Q ss_pred HHHHHHHhCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHHHcCccc
Q 025081 165 LYNLAQEHGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQITGLIR 241 (258)
Q Consensus 165 lYkLY~EaG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~~lGfIK 241 (258)
++++..+++.-++.+|.|..++...+. ...+--||.+..|.-.|+|+
T Consensus 19 Il~~L~~~~~h~sa~eI~~~l~~~~~~------------------------------is~aTVYR~L~~L~e~Glv~ 65 (139)
T 3mwm_A 19 VSAALQEVEEFRSAQELHDMLKHKGDA------------------------------VGLTTVYRTLQSLADAGEVD 65 (139)
T ss_dssp HHHHHTTCSSCEEHHHHHHHHHHTTCC------------------------------CCHHHHHHHHHHHHHTTSSE
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHhCCC------------------------------CCHHHHHHHHHHHHHCCCEE
Confidence 455666777789999999998763221 23788899999999999997
No 7
>2xig_A Ferric uptake regulation protein; hpfur, transcription, homeostasis; HET: CIT; 1.85A {Helicobacter pylori}
Probab=14.89 E-value=3.5e+02 Score=20.93 Aligned_cols=53 Identities=13% Similarity=0.194 Sum_probs=39.3
Q ss_pred CcchHHHHHHHHHHhCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHHHc
Q 025081 158 SLHDTSILYNLAQEHGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQIT 237 (258)
Q Consensus 158 s~Pd~silYkLY~EaG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~~l 237 (258)
+.+-..| +.+..+++.-++.+|.|+..+...+. ...+--||++.-|.=.
T Consensus 26 T~qR~~I-L~~l~~~~~~~sa~ei~~~l~~~~~~------------------------------is~aTVYR~L~~L~e~ 74 (150)
T 2xig_A 26 SKQREEV-VSVLYRSGTHLSPEEITHSIRQKDKN------------------------------TSISSVYRILNFLEKE 74 (150)
T ss_dssp HHHHHHH-HHHHHHCSSCBCHHHHHHHHHHHSTT------------------------------CCHHHHHHHHHHHHHT
T ss_pred CHHHHHH-HHHHHhCCCCCCHHHHHHHHHHhCCC------------------------------CCHhhHHHHHHHHHHC
Confidence 3444544 45555777789999999999874321 1268889999999999
Q ss_pred Cccc
Q 025081 238 GLIR 241 (258)
Q Consensus 238 GfIK 241 (258)
|+|+
T Consensus 75 Glv~ 78 (150)
T 2xig_A 75 NFIS 78 (150)
T ss_dssp TSEE
T ss_pred CcEE
Confidence 9997
No 8
>2o03_A Probable zinc uptake regulation protein FURB; DNA-binding, helix-turn-helix, zinc binding, GE regulation; 2.70A {Mycobacterium tuberculosis}
Probab=14.69 E-value=3.2e+02 Score=20.50 Aligned_cols=47 Identities=9% Similarity=0.164 Sum_probs=35.9
Q ss_pred HHHHHHHhCCcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHHHcCccc
Q 025081 165 LYNLAQEHGDHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQITGLIR 241 (258)
Q Consensus 165 lYkLY~EaG~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~~lGfIK 241 (258)
++.+..+++.-+..+|.|+..+...+. ...+--||.+..|.-.|+|+
T Consensus 16 Il~~l~~~~~~~sa~ei~~~l~~~~~~------------------------------is~~TVYR~L~~L~e~Glv~ 62 (131)
T 2o03_A 16 ISTLLETLDDFRSAQELHDELRRRGEN------------------------------IGLTTVYRTLQSMASSGLVD 62 (131)
T ss_dssp HHHHHHHCCSCEEHHHHHHHHHHTTCC------------------------------CCHHHHHHHHHHHHTTTSEE
T ss_pred HHHHHHhCCCCCCHHHHHHHHHHhCCC------------------------------CCHhhHHHHHHHHHHCCCEE
Confidence 345556777889999999998774221 13788899999999999997
No 9
>1mzb_A Ferric uptake regulation protein; ferric uptake regulator, iron, DTXR, gene regulation; 1.80A {Pseudomonas aeruginosa} SCOP: a.4.5.42
Probab=14.05 E-value=3e+02 Score=20.82 Aligned_cols=54 Identities=19% Similarity=0.273 Sum_probs=38.7
Q ss_pred CCcchHHHHHHHHHHhC-CcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHH
Q 025081 157 PSLHDTSILYNLAQEHG-DHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQ 235 (258)
Q Consensus 157 ~s~Pd~silYkLY~EaG-~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~ 235 (258)
.+.+-..||= +..+++ .-++.+|.|+.++...+. ...+--||.+.-|.
T Consensus 16 ~T~qR~~Il~-~L~~~~~~~~sa~ei~~~l~~~~~~------------------------------is~aTVYR~L~~L~ 64 (136)
T 1mzb_A 16 VTLPRVKILQ-MLDSAEQRHMSAEDVYKALMEAGED------------------------------VGLATVYRVLTQFE 64 (136)
T ss_dssp CCHHHHHHHH-HHHCC-CCSBCHHHHHHHHHHTTCC------------------------------CCHHHHHHHHHHHH
T ss_pred CCHHHHHHHH-HHHhCCCCCCCHHHHHHHHHhhCCC------------------------------CCHHHHHHHHHHHH
Confidence 3445555544 445666 789999999999874221 13788899999999
Q ss_pred HcCccc
Q 025081 236 ITGLIR 241 (258)
Q Consensus 236 ~lGfIK 241 (258)
=.|+|+
T Consensus 65 e~Glv~ 70 (136)
T 1mzb_A 65 AAGLVV 70 (136)
T ss_dssp HHTSEE
T ss_pred HCCcEE
Confidence 999997
No 10
>2w57_A Ferric uptake regulation protein; gene regulation, transcription regulation, transport, iron, repressor, DNA-binding, transcription; 2.60A {Vibrio cholerae}
Probab=11.89 E-value=3.4e+02 Score=21.03 Aligned_cols=54 Identities=19% Similarity=0.236 Sum_probs=39.4
Q ss_pred CCcchHHHHHHHHHHhC-CcccHHHHHHHHHhhhcCcccccCCCCCCCCCcccccCCCCCCChhhHHHHHHHHHHHHHHH
Q 025081 157 PSLHDTSILYNLAQEHG-DHINLHDWYQSFKSKVCSSRSKGKHKSKQSPLPKKRKDMNEPDKPCEASIQARFCKAVTELQ 235 (258)
Q Consensus 157 ~s~Pd~silYkLY~EaG-~lINlyDw~~AF~~~l~~~~~~~~~~~k~~~~~kK~k~~~e~~~~~e~~~qArF~rAv~EL~ 235 (258)
.+.+-..||--| .+++ .-++.+|.|+..+...+. ...+--||++.-|.
T Consensus 15 ~T~qR~~Il~~L-~~~~~~h~sa~ei~~~l~~~~~~------------------------------is~aTVYR~L~~L~ 63 (150)
T 2w57_A 15 VTLPRLKILEVL-QQPECQHISAEELYKKLIDLGEE------------------------------IGLATVYRVLNQFD 63 (150)
T ss_dssp CCHHHHHHHHHH-TSGGGSSEEHHHHHHHHHHTTCC------------------------------CCHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHH-HhCCCCCCCHHHHHHHHHHhCCC------------------------------CCHHHHHHHHHHHH
Confidence 345555555444 4666 789999999998874221 12788899999999
Q ss_pred HcCccc
Q 025081 236 ITGLIR 241 (258)
Q Consensus 236 ~lGfIK 241 (258)
=.|+|+
T Consensus 64 e~Glv~ 69 (150)
T 2w57_A 64 DAGIVT 69 (150)
T ss_dssp HTTSEE
T ss_pred HCCcEE
Confidence 999997
Done!