Query 030872
Match_columns 170
No_of_seqs 53 out of 55
Neff 3.0
Searched_HMMs 29240
Date Mon Mar 25 08:56:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030872.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/030872hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3h0g_D DNA-directed RNA polyme 99.9 2.7E-22 9.2E-27 155.7 6.4 76 91-168 4-79 (135)
2 2c35_A Human RPB4, DNA-directe 99.8 1E-20 3.4E-25 148.7 7.0 78 88-168 18-95 (152)
3 1go3_F DNA-directed RNA polyme 99.2 2.6E-11 8.9E-16 90.6 5.2 56 102-168 2-57 (107)
4 3hou_D DNA-directed RNA polyme 98.7 2.1E-08 7.1E-13 84.4 6.8 30 139-168 136-165 (221)
5 1y14_A B32, RPB4, DNA-directed 98.4 1.8E-07 6.1E-12 76.8 5.3 49 109-168 83-131 (187)
6 4ayb_F DNA-directed RNA polyme 97.8 1.7E-06 5.8E-11 64.9 -1.5 48 111-168 10-57 (113)
7 3ayh_A DNA-directed RNA polyme 97.5 6.2E-05 2.1E-09 57.7 3.8 61 108-168 13-82 (136)
8 2ckz_A DNA-directed RNA polyme 96.0 0.0028 9.4E-08 50.3 2.3 50 108-157 6-72 (161)
9 2llh_A Nucleophosmin; nucleola 36.9 10 0.00036 27.1 0.0 45 122-167 24-68 (74)
10 3m62_A Ubiquitin conjugation f 14.5 2.1E+02 0.007 28.5 5.2 71 91-167 793-865 (968)
No 1
>3h0g_D DNA-directed RNA polymerase II subunit RPB4; transcription, multi-protein complex, DNA- binding, magnesium; 3.65A {Schizosaccharomyces pombe}
Probab=99.86 E-value=2.7e-22 Score=155.68 Aligned_cols=76 Identities=20% Similarity=0.237 Sum_probs=67.2
Q ss_pred ccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 91 VVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 91 a~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
+..||||++|+||+||+ ||+||+||||++||+.+++|... .....++++.||.|||+|+++|+||+|+++|++||+
T Consensus 4 ~~~ee~a~~L~lg~eF~-~a~~Ls~sEv~~lL~~~~~~r~~-~~~~~~~~~~v~~kTl~Yl~~Fsk~~~~e~~~~v~~ 79 (135)
T 3h0g_D 4 AIFEEDAAQLKLGPEFE-NEDMLTVSEAKILIETVLAQRAR-ETNGEIPMTDVMKKTVAYFNVFARFKTAEATYACER 79 (135)
T ss_dssp --CCCCCTTTCSCHHHH-HSCBCCHHHHHHHHHHHHHHHHT-TCCSCCCCTTHHHHHHHHHHTTCTTCSHHHHHHHHH
T ss_pred hHHHHhHHhhCCCHhhc-CcccccHHHHHHHHHHHHHHHHh-cccCCcchhHHHHHHHHHHHHccCCCCHHHHHHHHH
Confidence 67899999999999998 89999999999999999877652 234568899999999999999999999999999986
No 2
>2c35_A Human RPB4, DNA-directed RNA polymerase II 16 kDa polypeptide; transcription, nucleotidyltransferase; 2.70A {Homo sapiens} SCOP: a.60.8.2
Probab=99.82 E-value=1e-20 Score=148.72 Aligned_cols=78 Identities=23% Similarity=0.260 Sum_probs=68.1
Q ss_pred CccccccCCccccccCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhh
Q 030872 88 KVSVVKEALPLELRVEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167 (170)
Q Consensus 88 kssa~~eEdAaELkf~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR 167 (170)
......||||++|+|++||. |++||+||||+.||++|+++.. +.|+..+++.+|.|||+|+++|++|+|+++|++||
T Consensus 18 ~~~~~~ee~a~~l~~gkef~-~~~~Lt~sEV~~lL~~~~~~~~--~~~~~~els~v~~kTl~Yl~~F~k~k~~e~~~~l~ 94 (152)
T 2c35_A 18 PRAGDVEEDASQLIFPKEFE-TAETLLNSEVHMLLEHRKQQNE--SAEDEQELSEVFMKTLNYTARFSRFKNRETIASVR 94 (152)
T ss_dssp ------CCBGGGTBCCSSSS-SCEECCHHHHHHHHHHHHHHHH--SSCSSCCCCHHHHHHHHHHHHTCSCCSHHHHHHHH
T ss_pred CCCCCccccHHHHhcchhhc-ccccccHHHHHHHHHHHHHhhc--ccccccchHHHHHHHHHHHHHccCCCCHHHHHHHH
Confidence 55667899999999999997 7999999999999999999875 57788999999999999999999999999999998
Q ss_pred c
Q 030872 168 Q 168 (170)
Q Consensus 168 ~ 168 (170)
+
T Consensus 95 e 95 (152)
T 2c35_A 95 S 95 (152)
T ss_dssp H
T ss_pred H
Confidence 5
No 3
>1go3_F DNA-directed RNA polymerase subunit F; transferase, transferase, transcription; 1.75A {Methanococcus jannaschii} SCOP: a.60.8.2
Probab=99.16 E-value=2.6e-11 Score=90.57 Aligned_cols=56 Identities=14% Similarity=0.206 Sum_probs=49.7
Q ss_pred cCcccccchhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 102 VEQELPKNAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 102 f~~EF~~NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
++++|. +++||++|||+.||++|.+. .+++.+|.|||+|+++|++| +++.++++++
T Consensus 2 i~kei~-~~~~lt~sEa~~iL~~~~~~---------~e~s~~~~ktl~y~~kFsk~-~~e~a~~l~e 57 (107)
T 1go3_F 2 IGKKIL-GERYVTVSEAAEIMYNRAQI---------GELSYEQGCALDYLQKFAKL-DKEEAKKLVE 57 (107)
T ss_dssp CSSEEE-EEEEECHHHHHHHHHHHHHH---------SCCCHHHHHHHHHHHHHCCS-CHHHHHHHHH
T ss_pred chHHHh-cccccCHHHHHHHHHHHHhc---------ccccHHHHHHHHHHHHHhCC-CHHHHHHHHH
Confidence 567887 69999999999999999772 68999999999999999999 7888887764
No 4
>3hou_D DNA-directed RNA polymerase II subunit RPB4; RNA polymerase II, metal-binding, transcription bubble; HET: BRU; 3.20A {Saccharomyces cerevisiae} PDB: 1nt9_D 1y1w_D 1y1y_D 1y77_D* 2b63_D* 2b8k_D 2ja5_D* 2ja6_D* 2ja7_D* 2ja8_D* 2r7z_D 2r92_D 2r93_D 1y1v_D* 3fki_D 3h3v_E 2vum_D* 3hov_D* 3how_D* 3hox_D* ...
Probab=98.71 E-value=2.1e-08 Score=84.39 Aligned_cols=30 Identities=17% Similarity=0.298 Sum_probs=28.2
Q ss_pred cchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 139 KIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 139 eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
..++||+|||+|+++|+||+|+++|+.||+
T Consensus 136 ~~seVf~KTLdYl~rFSKfkn~EAv~aVrE 165 (221)
T 3hou_D 136 GNNKDLKNTMQYLTNFSRFRDQETVGAVIQ 165 (221)
T ss_dssp SCCHHHHHHHHHHHHSCSCCCHHHHHHHHH
T ss_pred CccHHHHHHHHHHHHhcCCCcHHHHHHHHH
Confidence 368999999999999999999999999996
No 5
>1y14_A B32, RPB4, DNA-directed RNA polymerase II 32 kDa polypeptide; transferase; 2.30A {Saccharomyces cerevisiae} SCOP: a.60.8.2
Probab=98.44 E-value=1.8e-07 Score=76.81 Aligned_cols=49 Identities=16% Similarity=0.143 Sum_probs=41.9
Q ss_pred chhhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 109 NAKCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 109 NAkcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
|.+-.-++||+.||+.+ ..+++.+|.|||+|+.+|++|+||++|++||+
T Consensus 83 ~~~~~~i~~v~~lle~~-----------~~~ls~v~~KTLeYl~rFsk~kn~Esa~elre 131 (187)
T 1y14_A 83 ETREKELESIDVLLEQT-----------TGGNNKDLKNTMQYLTNFSRFRDQETVGAVIQ 131 (187)
T ss_dssp -CHHHHHHHHHHHHHHH-----------SCSCCHHHHHHHHHHHHHCSCCSHHHHHHHHH
T ss_pred chhhhhHHHHHHHHhhc-----------cccccHHHHHHHHHHHHccCCCCHHHHHHHHH
Confidence 34455679999999954 35899999999999999999999999999985
No 6
>4ayb_F DNA-directed RNA polymerase; transferase, multi-subunit, transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_F 2y0s_F 2waq_F 4b1o_F 4b1p_U 2pmz_F 3hkz_F
Probab=97.78 E-value=1.7e-06 Score=64.92 Aligned_cols=48 Identities=6% Similarity=0.089 Sum_probs=38.3
Q ss_pred hhhhhHHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhhc
Q 030872 111 KCLMDCEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLFQ 168 (170)
Q Consensus 111 kcLmnsEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR~ 168 (170)
+-+.++||..||+.+ .++.+++++|.|||+|+++|++| +++.++++|+
T Consensus 10 ~~it~~eakeiL~~~---------~~~~~~s~~~~ktl~y~~~Fsk~-~~e~a~~l~e 57 (113)
T 4ayb_F 10 HYIPYSVAKKLLSDV---------IKSGSSSNLLQRTYDYLNSVEKC-DAESAQKVVE 57 (113)
T ss_dssp EEECTTGGGGTTTTT---------SSSSCCCTTHHHHHHHTTTTCSS-CHHHHHHHHH
T ss_pred cccCHHHHHHHHHHH---------HhcccccHHHHHHHHHHHHHcCC-CHHHHHHHHH
Confidence 456688888888654 23468899999999999999999 7777777764
No 7
>3ayh_A DNA-directed RNA polymerase III subunit RPC9; transcription; 2.19A {Schizosaccharomyces pombe}
Probab=97.52 E-value=6.2e-05 Score=57.69 Aligned_cols=61 Identities=8% Similarity=-0.024 Sum_probs=47.9
Q ss_pred cchhhhhhHHHHHHHHHHHHHHHhh--hc-----CCCCcchHHHHHHHHHHHhc--CCCCCHHHHHhhhc
Q 030872 108 KNAKCLMDCEAAHILEGIQEQMALL--SA-----DPTIKIPVSFDKGLLYAKTH--SHFTNPQAVKGLFQ 168 (170)
Q Consensus 108 ~NAkcLmnsEVa~ILE~rkeq~~~l--Se-----Dp~~eiseVF~KTL~YakrF--SrfkN~eSVr~VR~ 168 (170)
.|+.+|.|.||..+|++++.+...- .+ .....+..|+.+|++|..++ ..+.|+++|+++++
T Consensus 13 ~~~a~LsN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~l~ti~~e~l~YL~~~p~~~~q~~e~i~~l~~ 82 (136)
T 3ayh_A 13 ARDAYLTNAEVFFHLKEMENEQNARTQERGAAQALVCENLRTIQFEILKYLSSQGNCEGLTKERFLDCIA 82 (136)
T ss_dssp EEEEEECHHHHHHHHHHHHHHHHHHHHHHGGGGCCCCHHHHHHHHHHHHHHHTTTCCTTCCHHHHHHHHH
T ss_pred cccccccHHHHHHHHHHHHhhhcccccccCCccccccchHHHHHHHHHHHHHhCCCccccCHHHHHHHHH
Confidence 4688999999999999998654311 11 12366899999999999999 56689999999874
No 8
>2ckz_A DNA-directed RNA polymerase III 18 KD polypeptide; multiprotein complex, nucleotidyltransferase, nuclear protein, hypothetical protein; 3.2A {Saccharomyces cerevisiae}
Probab=96.01 E-value=0.0028 Score=50.29 Aligned_cols=50 Identities=12% Similarity=0.140 Sum_probs=34.0
Q ss_pred cchhhhhhHHHHHHHHHHHHHHHh---------------hhcC--CCCcchHHHHHHHHHHHhcCCC
Q 030872 108 KNAKCLMDCEAAHILEGIQEQMAL---------------LSAD--PTIKIPVSFDKGLLYAKTHSHF 157 (170)
Q Consensus 108 ~NAkcLmnsEVa~ILE~rkeq~~~---------------lSeD--p~~eiseVF~KTL~YakrFSrf 157 (170)
.++.+|.|.||..+|++++.+... -.+. +...+..|+.++++|..++++|
T Consensus 6 ~~~a~LSN~EVl~~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~ti~~e~~~YL~~~p~~ 72 (161)
T 2ckz_A 6 ERNAFLSDYEVLKFLTDLEKKHLWDQKSLAALKKSRSKGKQNRPYNHPELQGITRNVVNYLSINKNF 72 (161)
T ss_dssp EEEEEECHHHHHHHHHHHHHHTTCSHHHHHCC----------CCCCCHHHHHHHHHHHHHHTC----
T ss_pred hhhhhhhHHHHHHHHHHhhhhccccccchhhhhcccccccccCCCCCccHHHHHHHHHHHHHhCCcc
Confidence 357899999999999999875320 0011 1245788999999999999984
No 9
>2llh_A Nucleophosmin; nucleolar, chaperone, oncoprotein, DNA binding protein; NMR {Homo sapiens} PDB: 2vxd_A
Probab=36.90 E-value=10 Score=27.10 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=33.4
Q ss_pred HHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhh
Q 030872 122 LEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167 (170)
Q Consensus 122 LE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR 167 (170)
+|.++.-|+ .|-+...-+|.|=.|-.+||+.+=|.++.++|..+-
T Consensus 24 vedIKaKmq-asieKg~slPKvE~KF~NyvKn~F~mtdqe~IqdLW 68 (74)
T 2llh_A 24 VEDIKAKMQ-ASIEKGGSLPKVEAKFINYVKNCFRMTDQEAIQDLW 68 (74)
Confidence 344444443 244455779999999999999999999999998653
No 10
>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL conjugation pathway, DNA damage, nucleus, phosphoprotein; HET: 1PE; 2.40A {Saccharomyces cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A
Probab=14.50 E-value=2.1e+02 Score=28.52 Aligned_cols=71 Identities=14% Similarity=0.118 Sum_probs=50.4
Q ss_pred ccccCCccccccCcccccchhhhhh--HHHHHHHHHHHHHHHhhhcCCCCcchHHHHHHHHHHHhcCCCCCHHHHHhhh
Q 030872 91 VVKEALPLELRVEQELPKNAKCLMD--CEAAHILEGIQEQMALLSADPTIKIPVSFDKGLLYAKTHSHFTNPQAVKGLF 167 (170)
Q Consensus 91 a~~eEdAaELkf~~EF~~NAkcLmn--sEVa~ILE~rkeq~~~lSeDp~~eiseVF~KTL~YakrFSrfkN~eSVr~VR 167 (170)
.-+++|+.+.. |. .+-|+. |+|.+=|-...+-...++.|...==++.|+++.....|-...++++-|.+.+
T Consensus 793 ~LKVknpekY~----F~--Pk~lL~~i~~IYlnL~~~~~F~~aVa~DgRSy~~elF~~a~~il~~~~~l~~~~~i~~~~ 865 (968)
T 3m62_A 793 ELKVKDPQSYS----FN--PKDLLKALTTVYINLSEQSEFISAVAKDERSFNRNLFVRAVDILGRKTGLASPEFIEKLL 865 (968)
T ss_dssp TCCCSCGGGGT----CC--HHHHHHHHHHHHHHTTTCHHHHHHHHHCTTTCCHHHHHHHHHHHTTSTTSSCHHHHHHHH
T ss_pred ccccCCHhhcC----CC--HHHHHHHHHHHHhhccCChHHHHHHHhcCCCCCHHHHHHHHHHHHHhhcCCCHHHHHHHH
Confidence 34445555544 33 444443 7777777665666667788987777999999999998888899999887654
Done!