Query psy5725
Match_columns 117
No_of_seqs 169 out of 998
Neff 5.3
Searched_HMMs 29240
Date Sat Aug 17 01:00:33 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5725.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/5725hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_A DNA-directed RNA polyme 100.0 2.3E-31 7.8E-36 249.7 5.4 103 13-115 980-1082(1752)
2 1twf_A B220, DNA-directed RNA 99.9 4.4E-29 1.5E-33 234.2 5.3 104 14-117 978-1081(1733)
3 4ayb_C DNA-directed RNA polyme 99.8 1.1E-20 3.8E-25 154.6 1.4 75 41-115 11-85 (395)
4 3lu0_D DNA-directed RNA polyme 99.3 1.2E-13 4.3E-18 127.7 -3.6 72 35-115 857-930 (1407)
5 1hqm_D DNA-directed RNA polyme 99.1 1.9E-12 6.6E-17 119.5 -4.1 55 52-115 923-977 (1265)
6 2a6h_D DNA-directed RNA polyme 98.9 5.9E-11 2E-15 110.9 -1.5 55 52-115 1182-1236(1524)
7 2la2_A Cecropin, papiliocin; a 54.8 2.8 9.5E-05 23.9 0.1 25 85-109 11-36 (38)
8 2hh7_A Hypothetical protein CS 37.1 8.3 0.00028 26.9 0.3 54 52-113 56-109 (119)
9 2yfv_C SCM3, KLLA0F05115P; cel 19.3 83 0.0028 19.6 2.6 38 62-100 18-55 (63)
10 1sch_A PNP, peanut peroxidase, 17.8 57 0.002 25.5 1.9 29 82-110 145-173 (294)
No 1
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.96 E-value=2.3e-31 Score=249.72 Aligned_cols=103 Identities=45% Similarity=0.683 Sum_probs=100.7
Q ss_pred cCCCCChhhHHHHHHHhhhcceeEcCCCcccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhc
Q psy5725 13 SGSARRIIGLNIGVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQA 92 (117)
Q Consensus 13 ~~~~l~p~~vi~~v~~L~~~l~vv~g~D~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a 92 (117)
.+|+|+|.+|++.|++|+++|++++|+|.|++|+|+|||.||++++|+.|++|+++++++|++++|+||+++|+.||.++
T Consensus 980 ~~s~l~p~~~~~~v~~~~~~l~~~~g~d~l~~~~~~na~~l~~~~lr~~l~~k~~~~~~~l~~~~~~~~~~~~~~~y~~a 1059 (1752)
T 3h0g_A 980 KPTDLLPSDIINGLNELIAKLTIFRGSDRITRDVQNNATLLFQILLRSKFAVKRVIMEYRLNKVAFEWIMGEVEARFQQA 1059 (1752)
T ss_dssp SCCCCCHHHHHHHHHHHHTTCCCSCCCSTTTTHHHHTSSHHHHHHHTTSSSHHHHHHSSCCCHHHHHHHHHHHHHHHHTT
T ss_pred ccCCCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHHHhhhhhhhhhhhcCcCHHHHHHHHHHHHHHHHHh
Confidence 46899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCCchhhhhhhcccCcccCCC
Q psy5725 93 QCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 93 ~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
+|+||||||+|||||||||+||-
T Consensus 1060 ~v~pGe~VG~iaAQSIgEp~TQM 1082 (1752)
T 3h0g_A 1060 VVSPGEMVGTLAAQSIGEPATQM 1082 (1752)
T ss_dssp BCCSSCCHHHHHHHHHHHHHHHH
T ss_pred ccCcccchhhhhhcccCCchhhh
Confidence 99999999999999999999993
No 2
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription, mRNA, multiprotein complex; HET: UTP; 2.30A {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A 1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A* 1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A* 1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Probab=99.95 E-value=4.4e-29 Score=234.22 Aligned_cols=104 Identities=38% Similarity=0.684 Sum_probs=101.0
Q ss_pred CCCCChhhHHHHHHHhhhcceeEcCCCcccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcc
Q psy5725 14 GSARRIIGLNIGVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQ 93 (117)
Q Consensus 14 ~~~l~p~~vi~~v~~L~~~l~vv~g~D~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~ 93 (117)
+|+|+|.+++++|+++++++++++|.|.++.|+|+||++||++++||+|++|++++++++++++|+|++++|+.||.+++
T Consensus 978 ~s~l~p~~~~~~v~~~~~~~~~~~g~d~l~~~~~~n~~~l~~~~~rs~L~~k~~~~~~~l~~~~~~~~l~~i~~ky~~a~ 1057 (1733)
T 1twf_A 978 PSDLTIKDIVLGVKDLQENLLVLRGKNEIIQNAQRDAVTLFCCLLRSRLATRRVLQEYRLTKQAFDWVLSNIEAQFLRSV 1057 (1733)
T ss_dssp CBCCCHHHHHHHHHHHHTTCCSCCCCSHHHHHHHHHTTHHHHHHHHHHSCHHHHHHTSCCCHHHHHHHHHHHHHHHHHHB
T ss_pred cccCCHHHHHHHHHHHHHhhhcccCCcchhhhhhhchHHHHHHHhhhhhhhhhhhhhcCCCHHHHHHHHHHHHHHHHhcc
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCchhhhhhhcccCcccCCCCC
Q psy5725 94 CAPGEMVGALAAQSLGTSTYFPFL 117 (117)
Q Consensus 94 v~PGe~VG~iaAQSIGEP~TQ~~~ 117 (117)
|+||||||+|||||||||+||=-|
T Consensus 1058 v~pGe~VG~iaAQSigEp~TQMTL 1081 (1733)
T 1twf_A 1058 VHPGEMVGVLAAQSIGEPATQMTL 1081 (1733)
T ss_dssp CCTTCCHHHHHHHHHHHHHTTCCC
T ss_pred CCCCchhhhHhhhhcCCccccccc
Confidence 999999999999999999999543
No 3
>4ayb_C DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2y0s_C 4b1o_C 4b1p_Y 2waq_C 2wb1_C 3hkz_C 2pmz_C
Probab=99.79 E-value=1.1e-20 Score=154.64 Aligned_cols=75 Identities=16% Similarity=0.232 Sum_probs=63.4
Q ss_pred cccHHHHHhhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCC
Q psy5725 41 QLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 41 ~ls~Eaq~NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
....|.-..+..++...+...+..+.....+.+++.+++|+++.|..+|.+++|+||||||+|||||||||+||=
T Consensus 11 ~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~y~r~lv~pGEAVGiIAAQSIGEPgTQl 85 (395)
T 4ayb_C 11 SYLEEKVKQASNILPQKIVEDLKNLISNKEVLVTRDEIDKIFDLAIKEYSEGLIAPGEAIGIVAAQSVGEPGTQM 85 (395)
T ss_dssp HHHHHHHHHHHTTSCSHHHHHHHHHHHHSTTCCCHHHHHHHHHHHHHHHHHTBCCTTCCHHHHHHHHHHHHHHTC
T ss_pred hhHHHHHHhhcccccHHHHHHHHHHhccceeecCHHHHHHHHHHHHHHHHHhcCCCCchHhHHHHhhcCCchhhh
Confidence 344455556666777777777777666777889999999999999999999999999999999999999999994
No 4
>3lu0_D DNA-directed RNA polymerase subunit beta'; E. coli RNA polymerase, nucleotidyltransferase, transcription, transferase; 11.20A {Escherichia coli} PDB: 3iyd_D*
Probab=99.26 E-value=1.2e-13 Score=127.71 Aligned_cols=72 Identities=19% Similarity=0.259 Sum_probs=56.5
Q ss_pred eEcCCCcccHHHHH--hhhhhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCccc
Q psy5725 35 IVAGEDQLSKQANE--NATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTST 112 (117)
Q Consensus 35 vv~g~D~ls~Eaq~--NAt~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~ 112 (117)
++..+..|+++..+ .+..+-++.+||.|.|+. .+.++..|+.|-|. ...+|+.||+||+|||||||||+
T Consensus 857 i~~~n~~I~e~~a~~i~~~gi~~V~IRS~LTC~s---~~GVC~~CYGrdLa------~g~~V~iGEAVGiIAAQSIGEPG 927 (1407)
T 3lu0_D 857 LVPRNTLLHEQWCDLLEENSVDAVKVRSVVSCDT---DFGVCAHCYGRDLA------RGHIINKGEAIGVIAAQSIGEPG 927 (1407)
T ss_dssp CSSCBCCHHHHHHHHHTTTTCSEEEECCSSSCSC---SSSBCSTTTCSCSS------SSSCCCSSCCTTHHHHHHHHSGG
T ss_pred EEeCCCcCCHHHHHHHHHcCCCEEEEcCceeecC---CCcccHHHhCcccc------CCCCcccCceeeeeeeeccCCCc
Confidence 44444556665443 223456789999999984 67888889999876 46899999999999999999999
Q ss_pred CCC
Q psy5725 113 YFP 115 (117)
Q Consensus 113 TQ~ 115 (117)
||=
T Consensus 928 TQL 930 (1407)
T 3lu0_D 928 TQL 930 (1407)
T ss_dssp GSS
T ss_pred cee
Confidence 994
No 5
>1hqm_D DNA-directed RNA polymerase; transferase, transcription, 3D- structure; 3.30A {Thermus aquaticus} SCOP: i.8.1.1 PDB: 1i6v_D* 2gho_D
Probab=99.10 E-value=1.9e-12 Score=119.51 Aligned_cols=55 Identities=24% Similarity=0.333 Sum_probs=45.0
Q ss_pred hhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCC
Q psy5725 52 LLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 52 ~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
.+..+.+||.|+|+. .+.+...++.|.+. ..++|+|||+||+|||||||||+||=
T Consensus 923 gi~~v~iRs~ltc~s---~~gvc~~CYgr~La------~~~lV~~GEaVGiIAAQSIGEPGTQl 977 (1265)
T 1hqm_D 923 EVREVPVRSPLTCQT---RYGVCQKCYGYDLS------MARPVSIGEAVGVVAAESIGEPGTQL 977 (1265)
T ss_dssp SCSSCEEECGGGCSC---TTSCCSSSSCSCSS------SSSCCCTTCCHHHHHHHHHHGGGTTS
T ss_pred CCCEEEeecCcCHHH---HHHHHHHHhhhhhc------cCCEeccCceeeeeeccccCCCCcee
Confidence 445788999999975 45666667766553 57999999999999999999999994
No 6
>2a6h_D DNA-directed RNA polymerase beta' chain; RNA polymerase holoenzyme, streptolydigin, antibiotic, transcription regulation; HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.2 PDB: 1smy_D* 1zyr_D* 1iw7_D* 2a69_D* 2a6e_D 2a68_D* 2be5_D* 2cw0_D 2o5i_D 2o5j_D* 2ppb_D* 3aoh_D* 3aoi_D* 3dxj_D* 3eql_D* 1ynj_D* 1l9z_D 1l9u_D* 1ynn_D* 2auj_D
Probab=98.93 E-value=5.9e-11 Score=110.93 Aligned_cols=55 Identities=25% Similarity=0.343 Sum_probs=45.7
Q ss_pred hhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccCCC
Q psy5725 52 LLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFP 115 (117)
Q Consensus 52 ~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~TQ~ 115 (117)
.+..+.+||.|+|+. .+.++..++.|-+. ..++|+|||+||+|||||||||+||=
T Consensus 1182 gi~~v~iRS~ltC~s---~~gvc~~CYgr~La------~~~~v~~GeaVGiiaAQSIGEPgTQl 1236 (1524)
T 2a6h_D 1182 EIQEVPVRSPLTCQT---RYGVCQKCYGYDLS------MARPVSIGEAVGIVAAQSIGEPGTQL 1236 (1524)
T ss_dssp SCSEEEECCGGGCCC---SSCBCHHHHCSCSS------SSSSCCTTCCHHHHHHHHHHSGGGTC
T ss_pred CCCcccccccccHHH---HHHHHHHHhccccc------cCCccccccceeehhhhccCCCcccc
Confidence 345788999999975 45677777777654 57899999999999999999999995
No 7
>2la2_A Cecropin, papiliocin; antimicrobial peptide, cecropin-like peptide, AN inflammatory activity, antimicrobial protein; NMR {Papilio xuthus}
Probab=54.79 E-value=2.8 Score=23.94 Aligned_cols=25 Identities=12% Similarity=0.225 Sum_probs=20.1
Q ss_pred HHHHhhhcccCCCchhhhhh-hcccC
Q psy5725 85 IENRFQQAQCAPGEMVGALA-AQSLG 109 (117)
Q Consensus 85 i~~rf~~a~v~PGe~VG~ia-AQSIG 109 (117)
+-.+...+++..|-+|++++ |++||
T Consensus 11 vGq~iRd~ii~AgPAV~v~g~A~~ig 36 (38)
T 2la2_A 11 VGRNVRDGIIKAGPAVAVVGQAATVV 36 (38)
T ss_dssp HHHHHHHHHHHTCCSHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccHHHHHHHHHHhc
Confidence 34788889999999999987 66665
No 8
>2hh7_A Hypothetical protein CSOR; 4-helix bundle, unknown function; 2.55A {Mycobacterium tuberculosis}
Probab=37.08 E-value=8.3 Score=26.87 Aligned_cols=54 Identities=19% Similarity=0.374 Sum_probs=20.2
Q ss_pred hhhhcccccccchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchhhhhhhcccCcccC
Q psy5725 52 LLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTY 113 (117)
Q Consensus 52 ~Lf~i~lRS~LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~VG~iaAQSIGEP~T 113 (117)
.++..|++..+..-.--.. ..+.++.++..+ +|.+++-+|. |-+..--.|||.|
T Consensus 56 ~ILe~HL~~Cv~~a~~~~~---~~e~ieEl~~~i--k~~k~~~~~~---~~~~~~~~~~~~~ 109 (119)
T 2hh7_A 56 VMLHNHLETCFSTAVLDGH---GQAAIEELIDAV--KFTPALTGPH---ARLGGAAVGESAT 109 (119)
T ss_dssp HHHHHHHHTTTTTCSSTTH---HHHHHHHHHHTT--CC------------------------
T ss_pred HHHHHHHHHHHHhHhccCc---hHHHHHHHHHHH--HHHHhccCcc---ccccccccCCCCC
Confidence 6777778777753210000 235688888877 9999999885 4445556788876
No 9
>2yfv_C SCM3, KLLA0F05115P; cell cycle, kinetochore, centromere, histone chaperone, BUDD; 2.32A {Kluyveromyces lactis nrrl y-1140}
Probab=19.32 E-value=83 Score=19.56 Aligned_cols=38 Identities=16% Similarity=0.309 Sum_probs=29.7
Q ss_pred cchhhHHHhhcCCHHHHHHHHHHHHHHhhhcccCCCchh
Q psy5725 62 LCTKLVAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMV 100 (117)
Q Consensus 62 LasK~vl~~~~Lsk~af~~il~ei~~rf~~a~v~PGe~V 100 (117)
|+--.+++.|+.+.+-++.+...|-.||.+ +-.+|+.|
T Consensus 18 lsdeevme~hk~adermK~~w~~Ii~KY~~-~edqgD~I 55 (63)
T 2yfv_C 18 LSDEEVMERHKKADENMKRVWSQIIQKYES-IDNQGDVI 55 (63)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHHHHHHHHHS-GGGSSCCB
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHhc-ccCCCcee
Confidence 444567778888888888888899999995 88888765
No 10
>1sch_A PNP, peanut peroxidase, major cationic isozyme; calcium binding, glycosylation, oxidoreductase; HET: NAG HEM; 2.56A {Arachis hypogaea} SCOP: a.93.1.1
Probab=17.80 E-value=57 Score=25.54 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=24.1
Q ss_pred HHHHHHHhhhcccCCCchhhhhhhcccCc
Q psy5725 82 VGEIENRFQQAQCAPGEMVGALAAQSLGT 110 (117)
Q Consensus 82 l~ei~~rf~~a~v~PGe~VG~iaAQSIGE 110 (117)
+..+...|.+.=..+-|||-..+|++||-
T Consensus 145 ~~~l~~~F~~~Gl~~~d~VaLsGaHTiG~ 173 (294)
T 1sch_A 145 LSGLISAFSNKGFTTKELVTLSGAHTIGQ 173 (294)
T ss_dssp HHHHHHHHHTTTCCHHHHHHHHGGGGBCE
T ss_pred HHHHHHHHHHcCCCHHHhccccccceece
Confidence 45556788888889999999999999994
Done!