Query psy8052
Match_columns 67
No_of_seqs 38 out of 40
Neff 3.7
Searched_HMMs 29240
Date Fri Aug 16 17:10:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8052.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/8052hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 2ba3_A NIKA; dimer, bacterial 84.4 0.73 2.5E-05 24.6 2.4 23 14-36 27-49 (51)
2 2k9i_A Plasmid PRN1, complete 80.5 1.4 4.6E-05 23.1 2.5 23 15-37 22-44 (55)
3 2cpg_A REPA protein, transcrip 74.9 2.6 8.7E-05 21.3 2.5 24 14-37 14-37 (45)
4 1p94_A Plasmid partition prote 67.2 2.6 9E-05 25.1 1.6 30 14-45 46-75 (76)
5 2gpe_A Bifunctional protein PU 59.7 7.1 0.00024 20.4 2.3 24 14-37 15-38 (52)
6 3m91_B Prokaryotic ubiquitin-l 53.0 3.6 0.00012 23.1 0.4 22 5-26 23-44 (44)
7 2k5j_A Uncharacterized protein 39.1 19 0.00066 20.9 2.1 27 15-43 22-48 (80)
8 2ay0_A Bifunctional PUTA prote 36.0 22 0.00074 19.6 1.9 30 13-44 14-43 (58)
9 1y9b_A Conserved hypothetical 31.9 32 0.0011 20.6 2.4 24 13-36 16-40 (90)
10 3m9d_G Prokaryotic ubiquitin-l 27.5 9.1 0.00031 23.1 -0.7 21 6-26 48-68 (68)
11 2kel_A SVTR protein, uncharact 27.1 31 0.0011 19.0 1.6 23 15-37 26-48 (56)
12 2yru_A Steroid receptor RNA ac 25.2 1.1E+02 0.0039 19.2 4.2 37 19-64 76-112 (118)
13 2bj7_A Nickel responsive regul 24.8 36 0.0012 21.4 1.7 22 15-36 16-38 (138)
14 3if8_A Hzwilch, protein zwilch 24.1 83 0.0028 23.8 3.9 39 26-66 278-316 (339)
15 2wvf_A Hpnikr, putative nickel 22.9 46 0.0016 21.4 2.0 29 15-43 23-56 (148)
16 2qsb_A UPF0147 protein TA0600; 21.7 51 0.0017 20.6 2.0 19 44-62 26-44 (89)
17 2byc_A Blue-light receptor of 21.2 62 0.0021 20.8 2.4 23 43-65 114-136 (137)
18 2qzg_A Conserved uncharacteriz 20.4 48 0.0016 20.9 1.6 19 44-62 30-48 (94)
19 2hza_A Nickel-responsive regul 20.1 68 0.0023 20.0 2.3 22 15-36 14-36 (133)
No 1
>2ba3_A NIKA; dimer, bacterial conjugation, relaxase, DNA binding, ribbon- helix-helix, DNA binding protein; NMR {Plasmid R64}
Probab=84.43 E-value=0.73 Score=24.59 Aligned_cols=23 Identities=17% Similarity=-0.010 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHH
Q psy8052 14 DFLGVVVLEIERSIISQMLRKSV 36 (67)
Q Consensus 14 q~Ll~~yv~~qG~~lsqmlrkSV 36 (67)
..+|..|++..|..+|+.||+.+
T Consensus 27 ~~~l~~~A~~~g~s~SeyiR~~~ 49 (51)
T 2ba3_A 27 DETIRKKAEDSGLTVSAYIRNAA 49 (51)
T ss_dssp HHHHHHHHHHHTCCHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Confidence 46899999999999999999975
No 2
>2k9i_A Plasmid PRN1, complete sequence; plasmid COPY control protein, ribbon helix helix protein, DNA binding protein; NMR {Sulfolobus islandicus} PDB: 3ft7_A
Probab=80.49 E-value=1.4 Score=23.12 Aligned_cols=23 Identities=9% Similarity=0.028 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
.-++.|++..|...|+.||..++
T Consensus 22 ~~l~~~a~~~g~s~s~~ir~ai~ 44 (55)
T 2k9i_A 22 DRLMEIAKEKNLTLSDVCRLAIK 44 (55)
T ss_dssp HHHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH
Confidence 46889999999999999999854
No 3
>2cpg_A REPA protein, transcriptional repressor COPG; DNA-binding protein, plasmid, gene regulation; 1.60A {Streptococcus agalactiae} SCOP: a.43.1.3 PDB: 1b01_A* 1ea4_A*
Probab=74.90 E-value=2.6 Score=21.33 Aligned_cols=24 Identities=13% Similarity=-0.220 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 14 DFLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 14 q~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
-.-|+.|++..|..-|+.||++++
T Consensus 14 ~~~Ld~~a~~~g~srS~~ir~ai~ 37 (45)
T 2cpg_A 14 LENLEKMAREMGLSKSAMISVALE 37 (45)
T ss_dssp HHHHHHHHHHHTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHH
Confidence 356889999999999999999864
No 4
>1p94_A Plasmid partition protein PArg; ribbon-helix-helix, dimer, DNA binding, cell cycle; NMR {Salmonella enterica} SCOP: a.43.1.3
Probab=67.17 E-value=2.6 Score=25.14 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHhhccccccC
Q psy8052 14 DFLGVVVLEIERSIISQMLRKSVEAKDWLHGI 45 (67)
Q Consensus 14 q~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~~ 45 (67)
-..+..|...+|..++++||..| ++||...
T Consensus 46 h~rlK~~Aa~~g~Smsdvvreli--~~~L~~~ 75 (76)
T 1p94_A 46 HTRFKAACARKGTSITDVVNQLV--DNWLKEN 75 (76)
T ss_dssp HHHHHHHHHHHTCCHHHHHHHHH--HHHHHHC
T ss_pred HHHHHHHHHHcCCCHHHHHHHHH--HHHHHhc
Confidence 35688999999999999999985 5676543
No 5
>2gpe_A Bifunctional protein PUTA; ribbon-helix-helix, DNA-binding domain, proline catabo proline utilization A, DNA binding protein; 1.90A {Escherichia coli} PDB: 2rbf_A* 2jxg_A 2jxh_A 2jxi_A*
Probab=59.71 E-value=7.1 Score=20.43 Aligned_cols=24 Identities=0% Similarity=-0.224 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 14 DFLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 14 q~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
..-|+.|++..|+.-|..||.+++
T Consensus 15 ~~~l~~lA~~~~rs~s~lir~Ai~ 38 (52)
T 2gpe_A 15 RERIKSAATRIDRTPHWLIKQAIF 38 (52)
T ss_dssp HHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHH
Confidence 456899999999999999999854
No 6
>3m91_B Prokaryotic ubiquitin-like protein PUP; coil COIL alpha helix, ATP-binding, chaperone, nucleotide-BI proteasome, S-nitrosylation; 1.80A {Mycobacterium tuberculosis}
Probab=52.97 E-value=3.6 Score=23.08 Aligned_cols=22 Identities=0% Similarity=-0.037 Sum_probs=6.6
Q ss_pred HHHHhhchHHHHHHHHHHHHhH
Q psy8052 5 LSLLFGSSPDFLGVVVLEIERS 26 (67)
Q Consensus 5 ~~~~~~~aaq~Ll~~yv~~qG~ 26 (67)
+.++.+.-|+.+++.||++.|.
T Consensus 23 Id~vLE~NAeeFV~~fVQKGGq 44 (44)
T 3m91_B 23 IDDVLEENAEDFVRAYVQKGGE 44 (44)
T ss_dssp HHHHHHHTC-------------
T ss_pred HHHHHHHhHHHHHHHHHHccCC
Confidence 4567788899999999998874
No 7
>2k5j_A Uncharacterized protein YIIF; structure, NESG, structural genomics, PSI-2, protein structure initiative; NMR {Shigella flexneri 5 str}
Probab=39.14 E-value=19 Score=20.92 Aligned_cols=27 Identities=15% Similarity=0.005 Sum_probs=21.9
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHhhccccc
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVEAKDWLH 43 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~ 43 (67)
.-|+.+++.+|..-|+.||.+| ++++.
T Consensus 22 ~~Ld~la~~~g~srselireAi--~~yl~ 48 (80)
T 2k5j_A 22 KQLDDLEVQRNLPRADLLREAV--DQYLI 48 (80)
T ss_dssp HHHHHHHHHHTCCHHHHHHHHH--HHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHH--HHHHH
Confidence 4578899999999999999985 34554
No 8
>2ay0_A Bifunctional PUTA protein; ribbon-helix-helix, DNA-binding domain, proline catabo proline utilization A, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.43.1.11
Probab=36.00 E-value=22 Score=19.63 Aligned_cols=30 Identities=3% Similarity=-0.089 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHhhcccccc
Q psy8052 13 PDFLGVVVLEIERSIISQMLRKSVEAKDWLHG 44 (67)
Q Consensus 13 aq~Ll~~yv~~qG~~lsqmlrkSVe~rDWl~~ 44 (67)
-..-|+.+++..|+.-|..||..++ +|+..
T Consensus 14 l~~rL~~lA~~~~rs~s~lireAi~--~yl~~ 43 (58)
T 2ay0_A 14 TRERIKSAATRIDRTPHWLIKQAIF--SYLEQ 43 (58)
T ss_dssp HHHHHHHHHHHTTCCHHHHHHHHHH--HHHHH
T ss_pred HHHHHHHHHHHHCcCHHHHHHHHHH--HHHHH
Confidence 3456889999999999999999854 34443
No 9
>1y9b_A Conserved hypothetical protein; MCSG, structural genomics, conserved hypoth protein, PSI, protein structure initiative; 2.20A {Vibrio cholerae o1 biovar eltor} SCOP: a.43.1.9
Probab=31.93 E-value=32 Score=20.58 Aligned_cols=24 Identities=13% Similarity=0.056 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHh-HHHHHHHHHHH
Q psy8052 13 PDFLGVVVLEIER-SIISQMLRKSV 36 (67)
Q Consensus 13 aq~Ll~~yv~~qG-~~lsqmlrkSV 36 (67)
-..+++......| .++|+.++.++
T Consensus 16 ~k~lI~~AA~~~G~~s~s~Fv~~aa 40 (90)
T 1y9b_A 16 TQDLLAKAAALAGMSSINSFVLNAA 40 (90)
T ss_dssp HHHHHHHHHHHTTCSCHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 4578999999999 79999998774
No 10
>3m9d_G Prokaryotic ubiquitin-like protein PUP; alpha helix coil COIL, 5 beta-strand barrel, ATP-binding, CH nucleotide-binding, proteasome; 4.50A {Mycobacterium tuberculosis}
Probab=27.48 E-value=9.1 Score=23.10 Aligned_cols=21 Identities=0% Similarity=-0.083 Sum_probs=5.7
Q ss_pred HHHhhchHHHHHHHHHHHHhH
Q psy8052 6 SLLFGSSPDFLGVVVLEIERS 26 (67)
Q Consensus 6 ~~~~~~aaq~Ll~~yv~~qG~ 26 (67)
.++.+.-|+.+|+.||++.|.
T Consensus 48 d~vLe~NAeefV~~fVQKGGq 68 (68)
T 3m9d_G 48 DDVLEENAEDFVRAYVQKGGE 68 (68)
T ss_dssp TTTSSSCC-------------
T ss_pred HHHHHHhHHHHHHHHHHhcCC
Confidence 456778899999999998873
No 11
>2kel_A SVTR protein, uncharacterized protein 56B; homodimer, ribbon-helix-helix, transcription repres; NMR {Sulfolobus islandicus rod-shaped virus}
Probab=27.06 E-value=31 Score=19.05 Aligned_cols=23 Identities=9% Similarity=0.024 Sum_probs=19.0
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHh
Q psy8052 15 FLGVVVLEIERSIISQMLRKSVE 37 (67)
Q Consensus 15 ~Ll~~yv~~qG~~lsqmlrkSVe 37 (67)
+-+..|+..+|..+++.|+..++
T Consensus 26 ~rlk~~Aa~~g~Sln~~i~eAL~ 48 (56)
T 2kel_A 26 TRLKVYCAKNNLQLTQAIEEAIK 48 (56)
T ss_dssp HHHHHHHHHSCCCHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHH
Confidence 34678999999999999988865
No 12
>2yru_A Steroid receptor RNA activator 1; SRAP, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}
Probab=25.22 E-value=1.1e+02 Score=19.15 Aligned_cols=37 Identities=22% Similarity=0.265 Sum_probs=24.7
Q ss_pred HHHHHHhHHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHHhhh
Q psy8052 19 VVLEIERSIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEELTLV 64 (67)
Q Consensus 19 ~yv~~qG~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel~ai 64 (67)
-|.......+.-+--..=|+.+|| +.+||++....+.
T Consensus 76 dy~~A~~ih~~l~t~~~~E~~~Wm---------~GlKrLI~~a~~~ 112 (118)
T 2yru_A 76 QWDAADDIHRSLMVDHVTEVSQWM---------VGVKRLIAEKKSL 112 (118)
T ss_dssp CHHHHHHHHHHHHHSTHHHHTTTH---------HHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHCcHHHHHhHH---------HHHHHHHHHHHHc
Confidence 355566666666655556778888 6788888766554
No 13
>2bj7_A Nickel responsive regulator; transcription, repressor, NIKR, DNA- binding, metal-binding, transcription regulation; HET: PG4; 2.1A {Pyrococcus horikoshii} SCOP: a.43.1.3 d.58.18.4 PDB: 2bj1_A 2bj3_A* 2bj8_A* 2bj9_A*
Probab=24.76 E-value=36 Score=21.44 Aligned_cols=22 Identities=14% Similarity=-0.078 Sum_probs=17.8
Q ss_pred HHHHHHHHHHh-HHHHHHHHHHH
Q psy8052 15 FLGVVVLEIER-SIISQMLRKSV 36 (67)
Q Consensus 15 ~Ll~~yv~~qG-~~lsqmlrkSV 36 (67)
..++.|++..| .+=|+.||.++
T Consensus 16 ~~ld~~v~~~~y~sRSe~Ir~ai 38 (138)
T 2bj7_A 16 EKFDQIIEEIGYENRSEAIRDLI 38 (138)
T ss_dssp HHHHHHHHHHTCSSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHH
Confidence 56889999999 78888888764
No 14
>3if8_A Hzwilch, protein zwilch homolog; incomplete beta-barrel, alternative splicing, cell cycle, CE division, kinetochore, mitosis, polymorphism; 2.55A {Homo sapiens}
Probab=24.12 E-value=83 Score=23.81 Aligned_cols=39 Identities=18% Similarity=0.529 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHhhccccccCCCchHHHHHHHHHHHHhhhhc
Q psy8052 26 SIISQMLRKSVEAKDWLHGIEPRNVRAVMKRIIEELTLVDN 66 (67)
Q Consensus 26 ~~lsqmlrkSVe~rDWl~~~EPR~VRav~krvveel~aiD~ 66 (67)
+.||..||.+ -..|....|-.+-=..+..+++||+..|+
T Consensus 278 lvLAdGLrTG--vTEWpEplE~kSAveLvqefLndLnkldg 316 (339)
T 3if8_A 278 LVLADGLRTG--VTEWLEPLEAKSAVELVQEFLNDLNKLDG 316 (339)
T ss_dssp HHHHHHHHHS--CCCCCCCSCSSCHHHHHHHHHHHHHCC--
T ss_pred HHHHhhhhcC--CeeCCCchhhhhHHHHHHHHHHHhhcccC
Confidence 5689999999 57899999988877888889999988774
No 15
>2wvf_A Hpnikr, putative nickel-responsive regulator; transcription factor, transcription regulation, RHH, DNA-binding, transcription, metal-binding; 1.60A {Helicobacter pylori} PDB: 2wvc_A 3pht_A 2ca9_A 2cad_A* 2caj_A 3lgh_A 2wvd_A 2wve_A* 2wvb_A 2y3y_A* 3qsi_B
Probab=22.93 E-value=46 Score=21.43 Aligned_cols=29 Identities=14% Similarity=0.079 Sum_probs=20.9
Q ss_pred HHHHHHHHHHh-HHHHHHHHHHH----hhccccc
Q psy8052 15 FLGVVVLEIER-SIISQMLRKSV----EAKDWLH 43 (67)
Q Consensus 15 ~Ll~~yv~~qG-~~lsqmlrkSV----e~rDWl~ 43 (67)
..++.|++..| .+=|+.||.++ +...|..
T Consensus 23 ~~lD~~v~~~~y~sRSe~Ir~Air~~l~~~~~~~ 56 (148)
T 2wvf_A 23 DELDNRIIKNGYSSRSELVRDMIREKLVEDNWAE 56 (148)
T ss_dssp HHHHHHHHHHTCSCHHHHHHHHHHHHHHCSSCTT
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHHHHHHhhhh
Confidence 46889999999 78888888764 3445543
No 16
>2qsb_A UPF0147 protein TA0600; structural genomics, four-helix bundle, PSI-2, protein structure initiative; HET: MSE; 1.30A {Thermoplasma acidophilum dsm 1728} SCOP: a.29.14.1
Probab=21.75 E-value=51 Score=20.56 Aligned_cols=19 Identities=32% Similarity=0.378 Sum_probs=16.5
Q ss_pred cCCCchHHHHHHHHHHHHh
Q psy8052 44 GIEPRNVRAVMKRIIEELT 62 (67)
Q Consensus 44 ~~EPR~VRav~krvveel~ 62 (67)
..-||+.|.+.....+.|.
T Consensus 26 ~sVPRNIRraA~ea~~~L~ 44 (89)
T 2qsb_A 26 ITVPKNVRKVAQDSKAKLS 44 (89)
T ss_dssp TTSCHHHHHHHHHHHHHHT
T ss_pred CCCChHHHHHHHHHHHHHh
Confidence 7789999999998888774
No 17
>2byc_A Blue-light receptor of the BLUF-family; signaling protein, photoreceptor, flavin; HET: FMN; 1.9A {Rhodobacter sphaeroides} SCOP: d.58.10.2
Probab=21.17 E-value=62 Score=20.77 Aligned_cols=23 Identities=22% Similarity=0.255 Sum_probs=20.2
Q ss_pred ccCCCchHHHHHHHHHHHHhhhh
Q psy8052 43 HGIEPRNVRAVMKRIIEELTLVD 65 (67)
Q Consensus 43 ~~~EPR~VRav~krvveel~aiD 65 (67)
....|.++-...++|+++|++=|
T Consensus 114 ~~~~~~~i~~l~~~~~~~~~~~~ 136 (137)
T 2byc_A 114 DLSGPEDVAELHRTIAASLSRGD 136 (137)
T ss_dssp CCCSTTHHHHHHHHHHHHTTTTC
T ss_pred CCCCHHHHHHHHHHHHHHHhccC
Confidence 36799999999999999998755
No 18
>2qzg_A Conserved uncharacterized archaeal protein; unknown function protein, structu genomics, PSI-2, protein structure initiative; 2.09A {Methanococcus maripaludis S2} SCOP: a.29.14.1
Probab=20.44 E-value=48 Score=20.88 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=16.3
Q ss_pred cCCCchHHHHHHHHHHHHh
Q psy8052 44 GIEPRNVRAVMKRIIEELT 62 (67)
Q Consensus 44 ~~EPR~VRav~krvveel~ 62 (67)
+.-||++|.+.....+.|.
T Consensus 30 ~sVPRNIRraA~ea~~~L~ 48 (94)
T 2qzg_A 30 TTVPRNIRAAADNAKNALH 48 (94)
T ss_dssp TTSCHHHHHHHHHHHHHTT
T ss_pred CCCChHHHHHHHHHHHHHh
Confidence 6789999999998888774
No 19
>2hza_A Nickel-responsive regulator; nickel-binding, ribbon-helix-helix, transcription factor, ME binding protein; HET: 3CM; 2.10A {Escherichia coli} SCOP: a.43.1.3 d.58.18.4 PDB: 1q5v_A* 2hzv_A 3od2_A*
Probab=20.06 E-value=68 Score=19.99 Aligned_cols=22 Identities=9% Similarity=-0.121 Sum_probs=18.2
Q ss_pred HHHHHHHHHHh-HHHHHHHHHHH
Q psy8052 15 FLGVVVLEIER-SIISQMLRKSV 36 (67)
Q Consensus 15 ~Ll~~yv~~qG-~~lsqmlrkSV 36 (67)
..++.|++..| .+=|+.||.++
T Consensus 14 ~~lD~~v~~~~y~sRSe~Ir~ai 36 (133)
T 2hza_A 14 ETLDSLSQRRGYNNRSEAIRDIL 36 (133)
T ss_dssp HHHHHHHHHTTCCSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHH
Confidence 46889999999 78888888874
Done!