Query 037910
Match_columns 235
No_of_seqs 165 out of 458
Neff 4.4
Searched_HMMs 29240
Date Mon Mar 25 09:07:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/037910.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/037910hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3po3_S Transcription elongatio 100.0 2.9E-29 9.8E-34 213.4 6.3 121 102-232 5-140 (178)
2 2lw4_A Transcription elongatio 100.0 1.2E-30 4.2E-35 208.0 -2.2 98 106-211 4-112 (113)
3 3ndq_A Transcription elongatio 99.9 4.1E-27 1.4E-31 186.2 5.1 90 106-203 8-108 (108)
4 2dme_A PHD finger protein 3; P 99.9 6.7E-28 2.3E-32 193.9 -0.9 99 109-212 7-116 (120)
5 1pqv_S STP-alpha, transcriptio 99.9 8.9E-26 3E-30 205.3 10.8 122 101-232 135-271 (309)
6 1kdx_A CBP; complex (transcrip 39.8 35 0.0012 25.3 4.1 50 111-164 11-60 (81)
7 2p6v_A Transcription initiatio 17.7 70 0.0024 25.3 2.4 15 117-131 21-35 (114)
8 2gut_A ARC/mediator, positive 10.8 3.4E+02 0.012 19.8 4.3 38 112-163 12-49 (77)
9 4ayb_Q DNA-directed RNA polyme 10.4 43 0.0015 25.7 -0.7 22 173-194 46-67 (104)
10 1iwp_G Glycerol dehydratase ga 7.6 1.2E+02 0.0042 24.7 0.8 22 178-200 34-55 (141)
No 1
>3po3_S Transcription elongation factor S-II; RNA polymerase II, mRNA, transcription, arrest, BACKTRACKING cleavage, transferase-DNA-RNA complex; HET: DNA BRU EPE PGE; 3.30A {Saccharomyces cerevisiae} PDB: 1y1v_S 1y1y_S 3gtm_S* 1enw_A
Probab=99.95 E-value=2.9e-29 Score=213.39 Aligned_cols=121 Identities=18% Similarity=0.224 Sum_probs=100.7
Q ss_pred ccccccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-------------ccC
Q 037910 102 TASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-------------LFN 168 (235)
Q Consensus 102 l~~~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-------------~fN 168 (235)
.+..+.+.++|++|++|+++||+||.....+.+. ++..+|.+||.+||..|++. +||
T Consensus 5 ~d~v~~~~~~d~vRdk~~~lL~~aL~~~~~~~~~----------~~~~~A~~IE~~if~~~~~~~~~k~Yk~k~Rsl~~N 74 (178)
T 3po3_S 5 NDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ----------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYSN 74 (178)
T ss_dssp ----------CHHHHHHHHHHHHHTTSSSSCSTT----------HHHHHHHHHHHHHHHHTSCSSSSTHHHHHHHHHHHH
T ss_pred CCCcCcCcCCChHHHHHHHHHHHHHhcCCCCchh----------hHHHHHHHHHHHHHHHhcCCCchhhhhhhhhHHHHH
Confidence 3444678899999999999999999997655543 34789999999999999861 999
Q ss_pred CCCCCChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccce--EEee
Q 037910 169 VKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEK--ELEC 232 (235)
Q Consensus 169 LKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~--~~~~ 232 (235)
|||++||+||++|++|+|+|.+||.||++||||+|+|++++++++++|+++|.++..|.. .+.|
T Consensus 75 LKd~~N~~Lr~~vl~g~isp~~lv~Ms~eElas~elk~~~e~~~~e~l~~~~~~~~~~~~t~~~~C 140 (178)
T 3po3_S 75 VISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTC 140 (178)
T ss_dssp HHSSSCSHHHHHHHHCCCTTHHHHCCTTTTSSCSHHHHHHHHHHHHHHHHTBCCCCCCCCBSSSCC
T ss_pred cCCCCCHHHHHHHhcCCCCHHHHHhcCchhhCCHHHHHHHHHHHHHHHHHhhhccccCCCcCCcCC
Confidence 999999999999999999999999999999999999999999999999999999988843 4555
No 2
>2lw4_A Transcription elongation factor A protein 2; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}
Probab=99.95 E-value=1.2e-30 Score=208.02 Aligned_cols=98 Identities=32% Similarity=0.437 Sum_probs=87.0
Q ss_pred ccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCC
Q 037910 106 VEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKN 174 (235)
Q Consensus 106 ~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KN 174 (235)
+.+.|+|++|++|+++||+||....... ....++..+|.+||.++|..|+++ +|||||++|
T Consensus 4 p~p~t~D~vRdk~~e~L~~aL~~~~~~~--------~~~~~~~~~A~~IE~~~f~~~~~~~~~Yk~k~Rsl~~NLkd~~N 75 (113)
T 2lw4_A 4 PVPVTCDAVRNKCREMLTAALQTDHDHV--------AIGADCERLSAQIEECIFRDVGNTDMKYKNRVRSRISNLKDAKN 75 (113)
T ss_dssp CSCCCCSTTHHHHHHHHHHHHHSSTHHH--------HHTCCHHHHHHHHHHHHHHHHTCTTTHHHHHHHHHHHHHHCSSS
T ss_pred CCCCCCcHHHHHHHHHHHHHHHcCCCcc--------cccchHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCC
Confidence 4688999999999999999998642111 124577899999999999999875 999999999
Q ss_pred hhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHH
Q 037910 175 PDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQI 211 (235)
Q Consensus 175 p~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki 211 (235)
|+||++||+|+|+|++||.||++||||+|||+||+++
T Consensus 76 p~Lr~~vl~G~i~p~~l~~Ms~eEmAs~elk~~r~~~ 112 (113)
T 2lw4_A 76 PDLRRNVLCGAITPQQIAVMTSEEMASDELKEIRKAM 112 (113)
T ss_dssp SHHHHHHHTTSSCHHHHHHSCHHHHHCTTTTTCSSSC
T ss_pred HHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHc
Confidence 9999999999999999999999999999999999865
No 3
>3ndq_A Transcription elongation factor A protein 1; helix bundle; 1.93A {Homo sapiens}
Probab=99.93 E-value=4.1e-27 Score=186.21 Aligned_cols=90 Identities=30% Similarity=0.436 Sum_probs=75.9
Q ss_pred ccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCC
Q 037910 106 VEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKN 174 (235)
Q Consensus 106 ~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KN 174 (235)
+.+.|+|++|++|+++||+||.......+ ...++..+|.+||.+||..|+++ +|||||++|
T Consensus 8 ~~~~t~d~vR~k~~~lL~~aL~~~~d~~~--------~~~~~~~lA~~IE~~if~~~~~~~~~Yk~k~Rsl~fNLKd~kN 79 (108)
T 3ndq_A 8 RAPSTSDSVRLKCREMLAAALRTGDDYIA--------IGADEEELGSQIEEAIYQEIRNTDMKYKNRVRSRISNLKDAKN 79 (108)
T ss_dssp CCCCCCCHHHHHHHHHHHHHTTGGGHHHH--------HTCCHHHHHHHHHHHHHHHHCSSSHHHHHHHHHHHHHHTCTTC
T ss_pred CCCCCCChHHHHHHHHHHHHHHcCCCCCc--------ccccHHHHHHHHHHHHHHHhcCCcHHHHHHHHHHHHHcCCCCC
Confidence 35779999999999999999998541111 13577899999999999999865 999999999
Q ss_pred hhhhhhhhcCCCCccccccCCcccCCcHH
Q 037910 175 PDFWRKVLLGEVKPETLVTALPEEMASDE 203 (235)
Q Consensus 175 p~Lr~~VL~GeIsP~~Lv~MSseEMASdE 203 (235)
|+||++|++|+|+|++||+||++||||+|
T Consensus 80 p~Lr~~vl~G~isp~~lv~Ms~eEmAS~E 108 (108)
T 3ndq_A 80 PNLRKNVLCGNIPPDLFARMTAEEMASDE 108 (108)
T ss_dssp HHHHHHHHHTSSCHHHHHHCCTTTC----
T ss_pred HHHHHHHHcCCcCHHHHhCCCHHHccCCC
Confidence 99999999999999999999999999997
No 4
>2dme_A PHD finger protein 3; PHF3, TFS2M, glioblastoma multiforme, brain tumor, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=99.93 E-value=6.7e-28 Score=193.85 Aligned_cols=99 Identities=31% Similarity=0.439 Sum_probs=85.8
Q ss_pred cCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-----------ccCCCCCCChhh
Q 037910 109 KCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-----------LFNVKDPKNPDF 177 (235)
Q Consensus 109 ~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-----------~fNLKD~KNp~L 177 (235)
.++|++|++|+++|+++|.....+.+... ..+++..+|.+||.+||..|+.+ +|||||++||+|
T Consensus 7 ~~~d~~Rd~~r~~L~eaL~~~~~~~~~~~-----~~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLKd~kNp~L 81 (120)
T 2dme_A 7 GSADQIRQSVRHSLKDILMKRLTDSNLKV-----PEEKAAKVATKIEKELFSFFRDTDAKYKNKYRSLMFNLKDPKNNIL 81 (120)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHTTTTCCC-----CHHHHHHHHHHHHHHHHHHHCSCSHHHHHHHHHHTHHHHSSSCCSH
T ss_pred CCCchHHHHHHHHHHHHHHHhcccccccc-----chhHHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCCCHHH
Confidence 35689999999999999998876543211 01345789999999999999875 999999999999
Q ss_pred hhhhhcCCCCccccccCCcccCCcHHHHHHHHHHH
Q 037910 178 WRKVLLGEVKPETLVTALPEEMASDERQSRNKQIR 212 (235)
Q Consensus 178 r~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~ 212 (235)
|++||+|+|+|++||.||++||||+|||+||+++.
T Consensus 82 r~~vl~G~i~p~~lv~Ms~eEmAS~elk~~r~~~~ 116 (120)
T 2dme_A 82 FKKVLKGEVTPDHLIRMSPEELASKELAAWRRRSG 116 (120)
T ss_dssp HHHHHHTSSCTTHHHHSCTTTTTTCCSTTTCTTCC
T ss_pred HHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHh
Confidence 99999999999999999999999999999998764
No 5
>1pqv_S STP-alpha, transcription elongation factor S-II, DNA; mRNA cleavage, proofreading, BACKTRACKING, gene expression, multiprotein complex; 3.80A {Saccharomyces cerevisiae} SCOP: i.8.1.1 PDB: 1eo0_A
Probab=99.93 E-value=8.9e-26 Score=205.30 Aligned_cols=122 Identities=19% Similarity=0.231 Sum_probs=105.7
Q ss_pred hccccccccCCchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCCc-------------cc
Q 037910 101 KTASAVEIKCSDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCPF-------------LF 167 (235)
Q Consensus 101 kl~~~~~~~t~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~s-------------~f 167 (235)
+.+.+....++|++|++|+++|++||.....+.+. ++..+|.+||.+||..|+++ +|
T Consensus 135 ~~~~~~~~~~~d~~R~k~r~~L~~aL~~~~~~~~~----------~~~~~A~~IE~al~~~~~~~~~~~~Yk~k~Rsl~~ 204 (309)
T 1pqv_S 135 KNDGVDTAIYHHKLRDQVLKALYDVLAKESEHPPQ----------SILHTAKAIESEMNKVNNCDTNEAAYKARYRIIYS 204 (309)
T ss_pred CCCCCCcCcCChHHHHHHHHHHHHHHhcCCCccch----------hHHHHHHHHHHHHHHHhCCCchhHHHHHHHHHHHH
Confidence 45555566889999999999999999875433322 45789999999999988643 99
Q ss_pred CCCCCCChhhhhhhhcCCCCccccccCCcccCCcHHHHHHHHHHHHHHHHHHhccccccce--EEee
Q 037910 168 NVKDPKNPDFWRKVLLGEVKPETLVTALPEEMASDERQSRNKQIREDALAKIRDHSVVGEK--ELEC 232 (235)
Q Consensus 168 NLKD~KNp~Lr~~VL~GeIsP~~Lv~MSseEMASdELK~ereki~eeAL~eaq~a~~~ge~--~~~~ 232 (235)
||||++||+||++||.|+|+|++||.||++||||+|+|++|+++++++|++||+++..+.. .+.|
T Consensus 205 NLKd~~N~~Lr~~vl~g~i~p~~lv~Ms~eElasde~k~~~~~~~~e~l~~~~~~~~~~~~~~~~~C 271 (309)
T 1pqv_S 205 NVISKNNPDLKHKIANGDITPEFLATCDAKDLAPAPLKQKIEEIAKQNLYNAQGATIERSVTDRFTC 271 (309)
T ss_pred HcCcCCChHHHHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhhccccccCcccccC
Confidence 9999999999999999999999999999999999999999999999999999999877643 4555
No 6
>1kdx_A CBP; complex (transcription activator/CO-activator), protein- protein interaction, phosphoserine recognition; HET: SEP; NMR {Mus musculus} SCOP: a.12.1.1 PDB: 1sb0_A 2agh_B 2kwf_A
Probab=39.78 E-value=35 Score=25.34 Aligned_cols=50 Identities=16% Similarity=0.170 Sum_probs=33.4
Q ss_pred CchHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhCC
Q 037910 111 SDATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMCP 164 (235)
Q Consensus 111 ~D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~~ 164 (235)
...+|+..+.-|..|+.... .|... .......+...|..+|..+|+.-..
T Consensus 11 t~~lR~hlv~Klv~aI~P~p--dp~a~--~d~rm~~l~~yArkvE~~~ye~A~s 60 (81)
T 1kdx_A 11 TQDLRSHLVHKLVQAIFPTP--DPAAL--KDRRMENLVAYAKKVEGDMYESANS 60 (81)
T ss_dssp CHHHHHHHHHHHHHHHSCCS--SGGGG--GSHHHHHHHHHHHHHHHHHHTTCSS
T ss_pred CHHHHHHHHHHHHHHhcCCC--Chhhh--hhHHHHHHHHHHHHHHHHHHHHhcc
Confidence 37899999999999998742 11111 0011123567899999999987543
No 7
>2p6v_A Transcription initiation factor TFIID subunit 4; alpha helix; HET: MLY; 2.00A {Homo sapiens} SCOP: a.277.1.1
Probab=17.72 E-value=70 Score=25.29 Aligned_cols=15 Identities=7% Similarity=0.020 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHhhhc
Q 037910 117 LIRERLAEAFSKVAG 131 (235)
Q Consensus 117 K~relL~~AL~~~~~ 131 (235)
||+.+|...+.-.+.
T Consensus 21 Kck~FL~tLi~las~ 35 (114)
T 2p6v_A 21 XCXNFLSTLIXLASS 35 (114)
T ss_dssp HHHHHHHHHHHHHTS
T ss_pred HHHHHHHHHHHHHhc
Confidence 999999988887654
No 8
>2gut_A ARC/mediator, positive cofactor 2 glutamine/Q- rich-associated protein; KIX, 3 helical bundle, transcription; NMR {Homo sapiens}
Probab=10.76 E-value=3.4e+02 Score=19.82 Aligned_cols=38 Identities=18% Similarity=0.171 Sum_probs=28.1
Q ss_pred chHHHHHHHHHHHHHHhhhccchhhHHhhhhhcCChHHHHHHHHHHHHHhhC
Q 037910 112 DATRTLIRERLAEAFSKVAGEVEEMEKKEQVRACDPVGVAVSVESVLFKNMC 163 (235)
Q Consensus 112 D~vRdK~relL~~AL~~~~~e~~d~ik~~~~~~~d~~~lA~eIE~aLF~~~~ 163 (235)
...|.+++..+-+|+....-.. -.=|.++|.++|.+-.
T Consensus 12 ~~FRq~vi~~i~~a~~~~G~~~--------------~k~a~emEnhvF~Ka~ 49 (77)
T 2gut_A 12 TAFRQKLVSQIEDAMRKAGVAH--------------SKSSKDMESHVFLKAK 49 (77)
T ss_dssp HHHHHHHHHHHHHHHHHHCCCC--------------SSCHHHHHHHHHHHCS
T ss_pred HHHHHHHHHhhHHHHHHhCCCC--------------CCCHHHHHHHHHhccC
Confidence 5789999999999998832111 1238899999997654
No 9
>4ayb_Q DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_J 4b1o_Q 4b1p_J 2y0s_J 2waq_Q
Probab=10.42 E-value=43 Score=25.74 Aligned_cols=22 Identities=23% Similarity=0.543 Sum_probs=18.6
Q ss_pred CChhhhhhhhcCCCCccccccC
Q 037910 173 KNPDFWRKVLLGEVKPETLVTA 194 (235)
Q Consensus 173 KNp~Lr~~VL~GeIsP~~Lv~M 194 (235)
||.+++.++|+|.|+.++--.|
T Consensus 46 KnTEIWd~Ll~gkISIeEAKK~ 67 (104)
T 4ayb_Q 46 KNTEIWDNLLNGKISVDEAKRL 67 (104)
T ss_dssp HHHHHHHHHHHCCSCHHHHHHH
T ss_pred hchHHHHHHHcCcccHHHHHHH
Confidence 7999999999999998765444
No 10
>1iwp_G Glycerol dehydratase gamma subunit; cobalamin, radical catalysis, lyase; HET: B12; 2.10A {Klebsiella pneumoniae} SCOP: a.23.2.1 PDB: 1mmf_G*
Probab=7.57 E-value=1.2e+02 Score=24.72 Aligned_cols=22 Identities=32% Similarity=0.489 Sum_probs=18.2
Q ss_pred hhhhhcCCCCccccccCCcccCC
Q 037910 178 WRKVLLGEVKPETLVTALPEEMA 200 (235)
Q Consensus 178 r~~VL~GeIsP~~Lv~MSseEMA 200 (235)
-.+|++|.|++++| ++|++=|.
T Consensus 34 le~V~~G~v~~~Dl-RIspetL~ 55 (141)
T 1iwp_G 34 LEKVLSGEVGPQDV-RISRQTLE 55 (141)
T ss_dssp HHHHHHTSSCGGGS-SCCHHHHH
T ss_pred HHHHHcCCCCHHHh-ccCHHHHH
Confidence 37999999999999 78877553
Done!