Query 029410
Match_columns 194
No_of_seqs 86 out of 88
Neff 4.1
Searched_HMMs 29240
Date Mon Mar 25 20:30:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029410.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/029410hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1f3u_A Transcription initiatio 100.0 2.5E-31 8.5E-36 207.6 9.8 92 1-110 17-118 (118)
2 4emo_A Sharpin; pleckstrin hom 25.4 1.1E+02 0.0039 23.9 5.0 25 30-66 43-67 (129)
3 1psb_C NDR Ser/Thr kinase-like 17.9 63 0.0022 18.0 1.7 12 115-126 13-24 (26)
4 3nfg_B DNA-directed RNA polyme 15.0 29 0.001 26.9 -0.4 12 1-12 32-43 (123)
5 2oyn_A Hypothetical protein MJ 11.6 1.4E+02 0.0048 23.6 2.7 40 93-153 5-46 (146)
6 1ois_A DNA topoisomerase I; DN 11.5 59 0.002 27.7 0.4 27 148-174 187-216 (223)
7 3u4z_A Telomerase-associated p 11.2 51 0.0018 24.5 -0.0 13 174-186 50-62 (109)
8 2k0q_A Putative uncharacterize 10.6 1.1E+02 0.0037 21.9 1.5 28 79-109 13-40 (74)
9 2k0n_A Mediator of RNA polymer 10.0 1.2E+02 0.004 22.2 1.5 24 111-135 55-78 (85)
10 2arp_A Inhibin beta A chain; c 9.2 4.2E+02 0.015 19.3 4.5 26 83-108 88-116 (116)
No 1
>1f3u_A Transcription initiation factor IIF, beta subunit; general transcription initiation and elongation factor, RNA polymerase II; 1.70A {Homo sapiens} SCOP: b.65.1.1
Probab=99.97 E-value=2.5e-31 Score=207.58 Aligned_cols=92 Identities=27% Similarity=0.430 Sum_probs=79.0
Q ss_pred CeeeeccHHHHHhhCCCCCCCCCCCCCCceeEEEEeeCCCCCCCCCCCCCCCCccEEEEE--e-c------CCCCCCCCc
Q 029410 1 MWLMKCPALVSRSLKIPSSDNDDDDSARPVAKVILSIDPLQSNEDSSSSSSSSSTRFTME--L-I------STESGNAPK 71 (194)
Q Consensus 1 VWLVKVPkyvS~~W~ka~~~~~~~d~~~~VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLe--l-~------~~e~~~iPK 71 (194)
|||||||+||+++|+++++ +..+|||+|..++++ .+++|+|+ + . ..++.++||
T Consensus 17 VWLvKvPk~L~e~W~~~~~-------~~~vGkvri~~~~g~-----------~~v~l~L~~~~~~~~~~~~~~~~~~iPk 78 (118)
T 1f3u_A 17 VWLVKVPKYLSQQWAKASG-------RGEVGKLRIAKTQGR-----------TEVSFTLNEDLANIHDIGGKPASVSAPR 78 (118)
T ss_dssp EEEEEEEHHHHHHHTTCCT-------TCEEEEEEEEEETTE-----------EEEEEEECHHHHTCCCTTCCCSTTCSCC
T ss_pred EEEEECCHHHHHHHHhCCC-------CCceEEEEEecCCCc-----------eeEEEEeChhHhhhccccccccccCCCh
Confidence 7999999999999986643 235999999998764 45888887 2 2 124689999
Q ss_pred ceecccccC-CceeEEEeeecCCceEEEEEeeeeeeeecC
Q 029410 72 RYSMDMSKD-LIPMSVFAESSNGKISVEGKIKNKFDMRPH 110 (194)
Q Consensus 72 ey~L~m~~~-~qpm~VFSe~~~gklalEGkVv~K~dcRP~ 110 (194)
+|+|+|++. +|||+||||+++|+++|||+|+|||||||+
T Consensus 79 eY~l~~~~~~~~~~~VFSE~~~~~~a~EG~V~~k~d~rP~ 118 (118)
T 1f3u_A 79 EHPFVLQSVGGQTLTVFTESSSDKLSLEGIVVQRAECRPA 118 (118)
T ss_dssp EEEEEEECCTTSEEEEEEEETTCCEEEEEEEEEEEEECCC
T ss_pred hceEEeeccCCceeEEEeccCCCcEEEEEEEEEEEEeecC
Confidence 999999995 999999999999999999999999999994
No 2
>4emo_A Sharpin; pleckstrin homology (PH) domain, lubac, SIPL1, linear ubiqui HOIL-1L, HOIP, protein binding; 2.00A {Homo sapiens}
Probab=25.35 E-value=1.1e+02 Score=23.92 Aligned_cols=25 Identities=32% Similarity=0.618 Sum_probs=18.3
Q ss_pred eeEEEEeeCCCCCCCCCCCCCCCCccEEEEEecCCCC
Q 029410 30 VAKVILSIDPLQSNEDSSSSSSSSSTRFTMELISTES 66 (194)
Q Consensus 30 VgKv~I~~dp~~~~d~~~~~~~~~~v~ftLel~~~e~ 66 (194)
+-+|.++.||.++- .|+|+|.+++.
T Consensus 43 l~RLQLSadp~RpG------------~FRL~L~gsg~ 67 (129)
T 4emo_A 43 LRRLQLSADPERPG------------RFRLELLGAGP 67 (129)
T ss_dssp EEEEEEEECTTSTT------------CEEEEECCSST
T ss_pred heeeeeccCCCCCc------------cEEEEEecCCC
Confidence 78888888887642 58888766543
No 3
>1psb_C NDR Ser/Thr kinase-like protein; helix-loop-helix, protein-peptide complex, metal binding protein; NMR {Bos taurus}
Probab=17.89 E-value=63 Score=17.96 Aligned_cols=12 Identities=25% Similarity=0.385 Sum_probs=10.2
Q ss_pred HHHHHHHHHHhh
Q 029410 115 ENYGKLCRERTN 126 (194)
Q Consensus 115 ~~YmkLkr~ri~ 126 (194)
.+|++++|.++.
T Consensus 13 te~lRl~R~Kl~ 24 (26)
T 1psb_C 13 TEFLRLKRTRLG 24 (26)
T ss_dssp HHHHHHHHHHHH
T ss_pred HHHHHHhhcccC
Confidence 579999999875
No 4
>3nfg_B DNA-directed RNA polymerase I subunit RPA34; triple barrel, transcription, dimerization; 2.51A {Candida glabrata} PDB: 3nff_B
Probab=15.01 E-value=29 Score=26.92 Aligned_cols=12 Identities=50% Similarity=1.018 Sum_probs=10.2
Q ss_pred CeeeeccHHHHH
Q 029410 1 MWLMKCPALVSR 12 (194)
Q Consensus 1 VWLVKVPkyvS~ 12 (194)
|||.|.|+.|-=
T Consensus 32 vWlIkaP~~~pl 43 (123)
T 3nfg_B 32 LWLMKVPANIDI 43 (123)
T ss_dssp EEEEEEETTCCG
T ss_pred EEEEeCCCCCCH
Confidence 699999998754
No 5
>2oyn_A Hypothetical protein MJ0056; structural genomics, unknown function, PSI-2, protein structure initiative; HET: CDP; 1.85A {Methanocaldococcus jannaschii DSM2661} SCOP: b.43.5.2 PDB: 2p3m_A 2vbs_A 2vbt_A* 2vbu_A* 2vbv_A*
Probab=11.60 E-value=1.4e+02 Score=23.59 Aligned_cols=40 Identities=20% Similarity=0.358 Sum_probs=24.8
Q ss_pred CceEEEEEeeeeeeeecCCCChHHHHHH--HHHHhhhhhccccceEEeccCCCCccccCCCce
Q 029410 93 GKISVEGKIKNKFDMRPHHENMENYGKL--CRERTNKYMTKSRQIQVIDNDNGSHMRPMPGMM 153 (194)
Q Consensus 93 gklalEGkVv~K~dcRP~~~~~~~YmkL--kr~ri~kas~ptRqvQ~Ld~~v~~~~kP~pg~~ 153 (194)
..+.|+|+|+-=+. + -.-||.+ -|+|+++.. -|.|-||++
T Consensus 5 ~~i~l~G~VvSGlG-----E-G~~y~sl~~Y~~qf~~~L---------------GF~PfPGTL 46 (146)
T 2oyn_A 5 KLMIIEGEVVSGLG-----E-GRYFLSLPPYKEIFKKIL---------------GFEPYEGTL 46 (146)
T ss_dssp CEEEEEEEEECCSS-----H-HHHHTTSHHHHHHHHHHH---------------SSCCCSSCE
T ss_pred eEEEEEEEEEcccc-----c-eEEEEeCHHHHHHHHHHh---------------CCcCCCCcE
Confidence 45789999982221 1 1235555 455555433 399999999
No 6
>1ois_A DNA topoisomerase I; DNA-binding protein; HET: DNA; 1.90A {Saccharomyces cerevisiae} SCOP: e.15.1.1
Probab=11.53 E-value=59 Score=27.68 Aligned_cols=27 Identities=26% Similarity=0.324 Sum_probs=20.3
Q ss_pred cCCCce---ecccccccccccceechhhhh
Q 029410 148 PMPGMM---ISTGFTVLWLTSFLCSVELCF 174 (194)
Q Consensus 148 P~pg~~---~~s~~~~~~~~~~~~~~~~~~ 174 (194)
|.||.- |....|++||+++-.|+.-.+
T Consensus 187 pp~Gh~WkeV~HDntvtWLA~W~enI~~~~ 216 (223)
T 1ois_A 187 APEGHKWGEIRHDNTVQWLAMWRENIFNSF 216 (223)
T ss_dssp CSTTCCCSEEECCTTCCCSEEEECTTTCCE
T ss_pred cCCCCCcceeecCCCceEEEEeeeccCCce
Confidence 455655 667789999999998886544
No 7
>3u4z_A Telomerase-associated protein 82; TEB1, processivity factor, DNA BIND protein; 2.30A {Tetrahymena thermophila}
Probab=11.24 E-value=51 Score=24.54 Aligned_cols=13 Identities=46% Similarity=1.122 Sum_probs=10.9
Q ss_pred hhhhhhhcCceeE
Q 029410 174 FALCYFWENPFSV 186 (194)
Q Consensus 174 ~~~~~~~~~~~~~ 186 (194)
-.|||-|.+-||+
T Consensus 50 pdlcyewrdkfsi 62 (109)
T 3u4z_A 50 PDLCYEWRDKFSI 62 (109)
T ss_dssp TTHHHHHTTTCCT
T ss_pred hhHHHHHHhhcch
Confidence 3689999999984
No 8
>2k0q_A Putative uncharacterized protein COPK; copper, heavy metal resistance, open barrel, plasmid- encoded, metal binding protein; NMR {Cupriavidus metallidurans} PDB: 2km0_A 2lel_A 3dso_A 3dsp_A 3n7d_A 3n7e_A
Probab=10.57 E-value=1.1e+02 Score=21.93 Aligned_cols=28 Identities=29% Similarity=0.501 Sum_probs=21.3
Q ss_pred cCCceeEEEeeecCCceEEEEEeeeeeeeec
Q 029410 79 KDLIPMSVFAESSNGKISVEGKIKNKFDMRP 109 (194)
Q Consensus 79 ~~~qpm~VFSe~~~gklalEGkVv~K~dcRP 109 (194)
+|+-+++||- .||.++|.|-.+-.-+.|
T Consensus 13 kDGstvyiFK---DGKMamEdk~Gra~~m~~ 40 (74)
T 2k0q_A 13 QDGSKVHVFK---DGKMGMENKFGKSMNMPE 40 (74)
T ss_dssp TTSCEEEEET---TSCEEEECTTSCEECCCB
T ss_pred CCCcEEEEEc---CCceehhhhcCceEEcCC
Confidence 4688999996 599999988766555544
No 9
>2k0n_A Mediator of RNA polymerase II transcription subunit 15; protein, activator, nucleus, phosphoprotein, transcription regulation; NMR {Saccharomyces cerevisiae}
Probab=9.97 E-value=1.2e+02 Score=22.21 Aligned_cols=24 Identities=13% Similarity=0.187 Sum_probs=18.2
Q ss_pred CCChHHHHHHHHHHhhhhhccccce
Q 029410 111 HENMENYGKLCRERTNKYMTKSRQI 135 (194)
Q Consensus 111 ~~~~~~YmkLkr~ri~kas~ptRqv 135 (194)
++.-+.||.-+|++|. +|.-||+.
T Consensus 55 sSSK~eYmdsMr~ki~-aMr~t~~~ 78 (85)
T 2k0n_A 55 SSSKKEYMDSMNEKVA-VMRNTYNT 78 (85)
T ss_dssp CCSHHHHHHHHHHHHH-HHHHHHHH
T ss_pred cccHHHHHHHHHHHHH-HHHHHHHH
Confidence 3455789999999997 77666653
No 10
>2arp_A Inhibin beta A chain; cystine knot, disulfide rich, EGF domain, kazal domain, PROT complex, hormone-growth factor complex; HET: 1PG; 2.00A {Homo sapiens} SCOP: g.17.1.2 PDB: 1nyu_B 1nys_B 1s4y_B* 2arv_A* 2b0u_A 2p6a_A 3b4v_A*
Probab=9.23 E-value=4.2e+02 Score=19.29 Aligned_cols=26 Identities=19% Similarity=0.321 Sum_probs=18.1
Q ss_pred eeEEEeeecCCce---EEEEEeeeeeeee
Q 029410 83 PMSVFAESSNGKI---SVEGKIKNKFDMR 108 (194)
Q Consensus 83 pm~VFSe~~~gkl---alEGkVv~K~dcR 108 (194)
||.+..-+..+.+ .+++.|+.+|.||
T Consensus 88 ~ls~ly~d~~~~v~~~~~~~Mvv~~CgC~ 116 (116)
T 2arp_A 88 PMSMLYYDDGQNIIKKDIQNMIVEECGCS 116 (116)
T ss_dssp EEEEEEECTTCCEEEEEEEEEEEEEEEEC
T ss_pred cEEEEEEeCCCCEEEEEcCCeEEeecccC
Confidence 5555554444544 4889999999996
Done!