Query 025523
Match_columns 251
No_of_seqs 128 out of 189
Neff 4.1
Searched_HMMs 29240
Date Mon Mar 25 12:03:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025523.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/025523hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 4h61_A Mediator of RNA polymer 100.0 9.9E-58 3.4E-62 392.1 10.0 144 23-166 4-156 (175)
2 4gwp_G Mediator of RNA polymer 100.0 1.4E-58 4.9E-63 423.9 5.0 182 24-205 5-247 (295)
3 3mlq_A DNA-directed RNA polyme 35.6 68 0.0023 27.3 5.9 41 114-154 109-154 (188)
4 1txp_A HnRNP C, heterogeneous 15.6 91 0.0031 19.3 2.0 13 185-197 12-24 (28)
5 2dla_A 397AA long hypothetical 10.0 82 0.0028 27.7 0.8 16 111-126 150-165 (222)
6 1ufz_A Hypothetical protein BA 9.8 78 0.0027 24.0 0.5 28 124-151 21-48 (83)
7 2xfd_A VCBM60; sugar binding p 8.7 3.3E+02 0.011 21.6 3.8 20 109-128 59-78 (112)
8 3mce_A Nascent polypeptide-ass 8.5 2.1E+02 0.0073 20.3 2.4 41 78-122 13-53 (61)
9 3u4v_A Telomerase-associated p 8.0 1.9E+02 0.0064 22.5 2.0 34 92-125 47-94 (117)
10 3nf5_A Nucleoporin NUP116; nuc 7.9 3E+02 0.01 22.9 3.4 27 76-103 128-154 (164)
No 1
>4h61_A Mediator of RNA polymerase II transcription subun; mediator complex, nucleus; 2.70A {Schizosaccharomyces pombe} PDB: 4h63_F
Probab=100.00 E-value=9.9e-58 Score=392.08 Aligned_cols=144 Identities=33% Similarity=0.559 Sum_probs=124.1
Q ss_pred CCCCceeeeCchhhccC-CCCcchHHHhhhcCCCcccCCChHHHHhhhCCC-CC----hhhhhhcCCceeEEeeecCCce
Q 025523 23 TDMTGICFRDQLWLNTY-PLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHP-LD----ISQLSKMTGIEYMLSEVMEPHL 96 (251)
Q Consensus 23 ~d~~~i~wrDp~wL~~~-~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~-l~----~~~L~~m~GiEY~l~~~~ep~L 96 (251)
-|+++|+||||+||+.+ |||++||||||++||||||+||||+||||++++ ++ +++|++|+|+||+|+|++||+|
T Consensus 4 ~dl~~i~wr~p~wi~~~~~L~~~nvLdYF~~SPFyD~tsnNe~lrmQ~~~~~~~~~~~e~~L~~m~GiEy~l~~~~~p~l 83 (175)
T 4h61_A 4 MDLTSIQWRMPEWVQSMGGLRTENVLEYFSQSPFYSHKSNNEMLKMQSQFNALDLGDLNSQLKRLTGIQFVIIHERPPFL 83 (175)
T ss_dssp CCGGGCCBCCHHHHHHTTSCCTTTHHHHHHTSTTCCTTSHHHHHHHHHHHTTCCCCCHHHHHHTCCEEEEEEEEEETTTE
T ss_pred CCccccEEcCHHHHHhcCCCCccHHHHHhhcCCcccccchHHHHHHhhccCccchHHHHHHHhcCCCceEEEeecCCCce
Confidence 58999999999999997 799999999999999999999999999998643 32 4789999999999999999999
Q ss_pred EEEEEeeecCCCccccceeEEEEcCeEeeCCchhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCcCCCCC
Q 025523 97 FVIRKQKRDGPEKVTPMLTYYVLDGSIYQAPQLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYVDAEND 166 (251)
Q Consensus 97 fVIrKQ~R~s~~~v~pLa~YYIi~G~IYQAPsl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~~~~~~ 166 (251)
||||||+|+++++++||++||||||+|||||||++||++||++++++|++||+++.++.+ +.||+|....
T Consensus 84 fvI~Kq~R~~~~~~~~la~YyIi~g~IYqAP~l~~vl~sRl~s~~~~L~~a~~~~~~~~~~~ps~Gy~~~~~~ 156 (175)
T 4h61_A 84 WVIQKQNRLNENEVKPLTVYFVCNENIYMAPNAYTLLATRMLNATYCFQKALTKIEKFPQYNPQEGYTYPKLS 156 (175)
T ss_dssp EEEEEEEECSSSCEEEEEEEEEETTEEEECCHHHHHHHHHHHHHHHHHHHHHTTCC-----------------
T ss_pred EEEEEEEEcCCCcceEEEEEEEECCEEccCCCHHHHHHHHHHHHHHHHHHHHHHHHccCCccCcCCeeCCCCC
Confidence 999999999999999999999999999999999999999999999999999999998766 7999996444
No 2
>4gwp_G Mediator of RNA polymerase II transcription subun; binding sites, mediator complex, models, molecular, phosphor protein structure; 4.20A {Saccharomyces cerevisiae S288C} PDB: 3rj1_G 4gwq_G
Probab=100.00 E-value=1.4e-58 Score=423.90 Aligned_cols=182 Identities=23% Similarity=0.427 Sum_probs=123.7
Q ss_pred CCCceeeeCchhhccCCCCcchHHHhhhcCCCcccCCChHHHHhhhCCCC------------------------------
Q 025523 24 DMTGICFRDQLWLNTYPLDRNMIFDYFTLSLFYDRTCNNEQLRMRSIHPL------------------------------ 73 (251)
Q Consensus 24 d~~~i~wrDp~wL~~~~L~~~nvLdYFs~SPFYDrtsNNE~lrmQ~~~~l------------------------------ 73 (251)
-|.+|+||||+||+.+|||++||||||++||||||+||||+||||++++.
T Consensus 5 PLdEiqWr~P~wiq~~gL~s~NVLdYFa~SPFyDktSNNevlrmQ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 84 (295)
T 4gwp_G 5 PLDELQWKSPEWIQVFGLRTENVLDYFAESPFFDKTSNNQVIKMQRQFSQLNDPNAAVNMTQNIMTLPDGKNGNLEEEFA 84 (295)
T ss_dssp CSSCCBCCSTTTTTCCSSTHHHHHHHHHHSCCCSHHHHHHHHHHHCCSCCCCCSCC----------------------CC
T ss_pred CCcceeecCHHHHHhcCCCcchHHHHhhcCCccccccchHHHHHHHHhccccccccchhccccccccccccccchhhccc
Confidence 36789999999999999999999999999999999999999999986542
Q ss_pred ------------------ChhhhhhcCCceeEEeeecCCceEEEEEeeecCCC--------ccccceeEEEEcCeEeeCC
Q 025523 74 ------------------DISQLSKMTGIEYMLSEVMEPHLFVIRKQKRDGPE--------KVTPMLTYYVLDGSIYQAP 127 (251)
Q Consensus 74 ------------------~~~~L~~m~GiEY~l~~~~ep~LfVIrKQ~R~s~~--------~v~pLa~YYIi~G~IYQAP 127 (251)
.+++|++|.||||+|+|++||+|||||||+|++++ +++||++||||||+|||||
T Consensus 85 ~~~~~r~~i~~~~~~~~~~e~~L~~m~GiEyvl~~~~eP~lwVIrKQ~R~s~~~~~~~~~~ev~pLa~YYIig~~IYqAP 164 (295)
T 4gwp_G 85 YVDPARRQILFKYPMYMQLEEELMKLDGTEYVLSSVREPDFWVIRKQRRTNNSGVGSAKGPEIIPLQDYYIIGANIYQSP 164 (295)
T ss_dssp CCCCHHHHHHCCCSTHHHHHHHHHHHSCEEETTEEECSSEEEEEEETTEEEEEEEEECCCTTCCCEEEEEEEEETTEEEC
T ss_pred cccchhhhhhhhcchhhhhHHHHhhCCCeEEEEeecCCCceEEEEeeeccCCcccccccCcceeEeEEEEEECCEEecCC
Confidence 14789999999999999999999999999999864 7899999999999999999
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHhh---hcCCcCCCCCCCCCC--CCCCCCCCcchHHHhhHHHHHHHHHHhCCCC
Q 025523 128 QLCNVFSARIGRALHYIQKAFTTAASKLE---KIGYVDAENDGGTPL--HSKAGKETIDLKEVKRVDQILASLQRKLPPA 202 (251)
Q Consensus 128 sl~sVl~sRl~sa~~~L~kaf~~~~s~~~---~~GY~~~~~~~~~~~--~~k~~~e~~~~fQ~~RvD~lL~~L~~kfPp~ 202 (251)
+|++||++||+++++||+++|+.+.++.+ +.||+|.....+... ..+......+.+++.|++.....+.+++|.+
T Consensus 165 sl~~Vl~sRlls~~~~L~~a~~~~~~~~~f~Ps~G~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~ 244 (295)
T 4gwp_G 165 TIFKIVQSRLMSTSYHLNSTLESLYDLIEFQPSQGVHYKVPTDTSTTATAATNGNNAGGGSNKSSVRPTGGANMATVPST 244 (295)
T ss_dssp CCTTHHHHHHHHHHHHHHHHHHHHTCCC----------------------------------------------------
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHccCcccCCCCccccCCCCCccccccccCCCCCCccccccCCCCccccccccCCCC
Confidence 99999999999999999999999998766 899999644432222 2223345678999999999999999999887
Q ss_pred CCC
Q 025523 203 PPP 205 (251)
Q Consensus 203 ~~~ 205 (251)
.++
T Consensus 245 ~~~ 247 (295)
T 4gwp_G 245 TNV 247 (295)
T ss_dssp ---
T ss_pred CCc
Confidence 554
No 3
>3mlq_A DNA-directed RNA polymerase subunit beta; tudor, transferase-transcription complex; 2.91A {Thermus aquaticus}
Probab=35.60 E-value=68 Score=27.25 Aligned_cols=41 Identities=5% Similarity=0.125 Sum_probs=34.3
Q ss_pred eeEEEEcCeEe-----eCCchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025523 114 LTYYVLDGSIY-----QAPQLCNVFSARIGRALHYIQKAFTTAASK 154 (251)
Q Consensus 114 a~YYIi~G~IY-----QAPsl~sVl~sRl~sa~~~L~kaf~~~~s~ 154 (251)
.-||||||+-- .--+.+.+|++++...+..|+|...+-.+.
T Consensus 109 gGyFIING~ERVIVsQe~r~~gell~~q~r~gl~r~ek~~~e~~~~ 154 (188)
T 3mlq_A 109 DGSFIINGADRVIVSQGGRTVGELMADQFRVGLARLARGVRERMVM 154 (188)
T ss_dssp TSCEEETTEEEECCCCSSSCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCEEEECCEEEEEEEeecccCCeeeEEehhhHHHHHHHHHHhhhcc
Confidence 66999999753 346889999999999999999998876554
No 4
>1txp_A HnRNP C, heterogeneous nuclear ribonucleoprotein C protein; antiparallel four helix coiled coil tetramer HNRNPC, signaling protein; NMR {Homo sapiens}
Probab=15.59 E-value=91 Score=19.27 Aligned_cols=13 Identities=31% Similarity=0.690 Sum_probs=10.3
Q ss_pred HhhHHHHHHHHHH
Q 025523 185 VKRVDQILASLQR 197 (251)
Q Consensus 185 ~~RvD~lL~~L~~ 197 (251)
++.||.||..|-+
T Consensus 12 K~kvDsLLe~Le~ 24 (28)
T 1txp_A 12 KQKVDSLLENLEK 24 (28)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHh
Confidence 4579999998854
No 5
>2dla_A 397AA long hypothetical protein; helix bundle, twisted beta-sheet, replication; 2.90A {Pyrococcus horikoshii}
Probab=9.96 E-value=82 Score=27.66 Aligned_cols=16 Identities=25% Similarity=0.793 Sum_probs=14.1
Q ss_pred ccceeEEEEcCeEeeC
Q 025523 111 TPMLTYYVLDGSIYQA 126 (251)
Q Consensus 111 ~pLa~YYIi~G~IYQA 126 (251)
.-|..|||-+|++|.-
T Consensus 150 ~sLk~~YIr~G~vYLr 165 (222)
T 2dla_A 150 EKLANYYIYEGRVYLK 165 (222)
T ss_dssp SCGGGSEEETTEEEEC
T ss_pred cccceEEEEcCeEEec
Confidence 5689999999999974
No 6
>1ufz_A Hypothetical protein BAB28515; HBS1-like domain, structural genomics, riken structural genomics/proteomics initiative, RSGI, translatio; NMR {Mus musculus} SCOP: a.5.9.1
Probab=9.76 E-value=78 Score=24.01 Aligned_cols=28 Identities=21% Similarity=0.246 Sum_probs=23.6
Q ss_pred eeCCchhHHHHHHHHHHHHHHHHHHHHH
Q 025523 124 YQAPQLCNVFSARIGRALHYIQKAFTTA 151 (251)
Q Consensus 124 YQAPsl~sVl~sRl~sa~~~L~kaf~~~ 151 (251)
|+.|.|..+=..||.+|+.+|+.++-.+
T Consensus 21 ~~~~~Ls~~d~arL~SCLd~iR~VlGds 48 (83)
T 1ufz_A 21 LLNHQLSEIDQARLYSCLDHMREVLGDA 48 (83)
T ss_dssp HHHHHCCHHHHHHHHHHHHHHHHHTTTT
T ss_pred cccccCCHHHHHHHHHHHHHHHHHHccc
Confidence 5677788899999999999999887653
No 7
>2xfd_A VCBM60; sugar binding protein; HET: CBI; 1.19A {Escherichia coli} PDB: 2xfe_A* 2xhh_A 2xhj_A
Probab=8.74 E-value=3.3e+02 Score=21.63 Aligned_cols=20 Identities=25% Similarity=0.336 Sum_probs=16.6
Q ss_pred ccccceeEEEEcCeEeeCCc
Q 025523 109 KVTPMLTYYVLDGSIYQAPQ 128 (251)
Q Consensus 109 ~v~pLa~YYIi~G~IYQAPs 128 (251)
.-.+.-+|-.|||.++||=+
T Consensus 59 dRdV~vDyI~vnG~t~qaEd 78 (112)
T 2xfd_A 59 GRDVQVDYIVVNGQTRQAEN 78 (112)
T ss_dssp TCCEEEEEEEETTEEEEGGG
T ss_pred CcceEEEEEEECCEEEEccc
Confidence 45678899999999999854
No 8
>3mce_A Nascent polypeptide-associated complex subunit Al; beta-barrel like structure, NAC, homodimer, chaperone; 2.40A {Homo sapiens}
Probab=8.46 E-value=2.1e+02 Score=20.25 Aligned_cols=41 Identities=27% Similarity=0.378 Sum_probs=24.7
Q ss_pred hhhcCCceeEEeeecCCceEEEEEeeecCCCccccceeEEEEcCe
Q 025523 78 LSKMTGIEYMLSEVMEPHLFVIRKQKRDGPEKVTPMLTYYVLDGS 122 (251)
Q Consensus 78 L~~m~GiEY~l~~~~ep~LfVIrKQ~R~s~~~v~pLa~YYIi~G~ 122 (251)
|+.++||+=+-.--....+|||.+=.-.. .+-.+=|||-|.
T Consensus 13 lk~v~gI~rVtirK~~~~lf~i~~PdV~k----sp~snTyvVFGe 53 (61)
T 3mce_A 13 LRQVTGVTRVTIRKSKNILFVITKPDVYK----SPASDTYIVFGE 53 (61)
T ss_dssp CEECSSEEEEEEEETTTEEEEESSCEEEE----C---CEEEEESC
T ss_pred CeECCCEEEEEEEecCCEEEEECCCcEEE----cCCCCeEEEEcc
Confidence 56679988887766667788887643221 233445666664
No 9
>3u4v_A Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 1.80A {Tetrahymena thermophila}
Probab=7.96 E-value=1.9e+02 Score=22.52 Aligned_cols=34 Identities=21% Similarity=0.415 Sum_probs=22.3
Q ss_pred cCCceEEEEEeeecCC--------------CccccceeEEEEcCeEee
Q 025523 92 MEPHLFVIRKQKRDGP--------------EKVTPMLTYYVLDGSIYQ 125 (251)
Q Consensus 92 ~ep~LfVIrKQ~R~s~--------------~~v~pLa~YYIi~G~IYQ 125 (251)
++.-.|.|.-|.-... ....+=++||.|+|.|-|
T Consensus 47 qdskyffitaqdannqeinmsfwqkvdqsyqtlkvgqyyyfiggevkq 94 (117)
T 3u4v_A 47 QDSKYFFITAQDANNQEINMSFWQKVDQSYQTLKVGQYYYFIGGEVKQ 94 (117)
T ss_dssp TSCEEEEEEEECTTSCEEEEEEESSTHHHHTTCCTTCEEEEESCEEEE
T ss_pred ccccEEEEEeecCCCceechHHHHHhhhhhheEeeceEEEEEccchhh
Confidence 4455677777754432 113455889999999876
No 10
>3nf5_A Nucleoporin NUP116; nuclear pore complex, glebs domain, structural genom 2, protein structure initiative; 1.94A {Candida glabrata}
Probab=7.95 E-value=3e+02 Score=22.94 Aligned_cols=27 Identities=11% Similarity=0.134 Sum_probs=22.3
Q ss_pred hhhhhcCCceeEEeeecCCceEEEEEee
Q 025523 76 SQLSKMTGIEYMLSEVMEPHLFVIRKQK 103 (251)
Q Consensus 76 ~~L~~m~GiEY~l~~~~ep~LfVIrKQ~ 103 (251)
+.|+++.|.+|+ .|..+.|.|+.+=.+
T Consensus 128 ~rLk~~~g~~Fv-sYd~~tG~W~F~V~H 154 (164)
T 3nf5_A 128 EKLKKIPHTHFE-SYDPASGTYCFTVDH 154 (164)
T ss_dssp HHHHHCTTCEEE-EEETTTTEEEEEESS
T ss_pred HHHhccCCCEEE-EEeCCCcEEEEEEcc
Confidence 678999999998 677889999976554
Done!