Query 000264
Match_columns 1764
No_of_seqs 352 out of 573
Neff 5.6
Searched_HMMs 29240
Date Tue Mar 26 22:37:50 2013
Command hhsearch -i /local_scratch/syshi/lefta3m2/000264.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H2_0-3//hhsearch_pdb/000264hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3ny3_A E3 ubiquitin-protein li 1.0 1 1 196.9 4.7 73 113-185 2-75 (75)
2 3nis_A E3 ubiquitin-protein li 1.0 1 1 193.1 5.7 74 112-185 5-81 (82)
3 2e5n_A RNA polymerase II elong 1.0 1 1 89.7 6.0 82 869-954 13-97 (100)
4 2doa_A RNA polymerase II elong 1.0 1 1 87.9 5.6 82 869-954 12-96 (104)
5 2ct0_A Non-SMC element 1 homol 1.0 1 1 31.7 0.7 40 1429-1488 32-71 (74)
6 1v87_A Deltex protein 2; ring- 1.0 1 1 31.1 2.8 41 1425-1482 55-95 (114)
7 2kiz_A E3 ubiquitin-protein li 1.0 1 1 30.6 2.8 40 1424-1485 28-67 (69)
8 3dpl_R Ring-box protein 1; ubi 1.0 1 1 30.5 1.6 35 1422-1478 64-98 (106)
9 1x4j_A Ring finger protein 38; 1.0 1 1 30.4 -0.0 33 1424-1478 37-69 (75)
10 2ct2_A Tripartite motif protei 1.0 1 1 30.2 1.5 35 1426-1479 32-66 (88)
No 1
>3ny3_A E3 ubiquitin-protein ligase UBR2; zinc finger-like, ubiquitin ligase, protein binding, lygase,; 1.60A {Homo sapiens} PDB: 3ny2_A 3ny1_A
Probab=1.00 E-value=1 Score=196.86 Aligned_cols=73 Identities=41% Similarity=1.090 Sum_probs=69.2
Q ss_pred CCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEC-CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 89875353224886259803578899820053335988999960599826-99412379921345667778788
Q 000264 113 GQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT-GGGCCDCGDVTAWKREGFCSRHK 185 (1764)
Q Consensus 113 ~~~~~Cg~v~~~ge~~y~C~~C~~d~tc~lC~~CF~~~~H~gH~y~~~~~-~gG~CDCGD~eawk~~~fC~~H~ 185 (1764)
.+.++||++|++||++|+|+||+.|+||+||.+||++++|+||+|+|..+ +||+|||||++|||+++||++|.
T Consensus 2 ~~g~~Cg~vf~~ge~~Y~C~~C~~d~tc~lC~~CF~~~~H~gH~~~~~~s~~gG~CDCGD~eawk~~~fC~~H~ 75 (75)
T 3ny3_A 2 PLGSLCGRVFKVGEPTYSCRDCAVDPTCVLCMECFLGSIHRDHRYRMTTSGGGGFCDCGDTEAWKEGPYCQKHE 75 (75)
T ss_dssp ----CCCCBCCTTCEEEEETTTBSSTTCCBCHHHHHTSGGGGSCEEEEECCSCBBCCTTCTTTBSSCCSCTTTC
T ss_pred CCCCCCCCCCCCCCEEEECCCCCCCCCEEECHHHCCCCCCCCCEEEEEECCCCCEECCCCHHHCCCCCCCCCCC
T ss_conf 88896688505998789794088999853876788998827845899976998780496999908898888888
No 2
>3nis_A E3 ubiquitin-protein ligase UBR1; E3 ubiquitin ligase, UBR BOX, zinc-binding protein, N-END RU ligase, metal binding protein; 1.68A {Saccharomyces cerevisiae} PDB: 3nii_A 3nij_A 3nih_A 3nik_A 3nim_A 3nin_A 3nil_A 3nit_A
Probab=1.00 E-value=1 Score=193.09 Aligned_cols=74 Identities=31% Similarity=0.750 Sum_probs=69.4
Q ss_pred CCCCCCCCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEC---CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 289875353224886259803578899820053335988999960599826---99412379921345667778788
Q 000264 112 IGQRGVCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYT---GGGCCDCGDVTAWKREGFCSRHK 185 (1764)
Q Consensus 112 ~~~~~~Cg~v~~~ge~~y~C~~C~~d~tc~lC~~CF~~~~H~gH~y~~~~~---~gG~CDCGD~eawk~~~fC~~H~ 185 (1764)
..+.++||++|++||++|+|+||+.|+||+||.+||++++|+||+|.|..+ +||+|||||++|||+++||+.+.
T Consensus 5 ~h~g~~Cg~vf~~ge~~Y~C~~C~~d~tcvlC~~CF~~s~H~gH~~~~~~s~~~~gG~CDCGD~eawk~~~fC~~~~ 81 (82)
T 3nis_A 5 KHTGRNCGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNHHVCTDICTEFTSGICDCGDEEAWNSPLHCKAEE 81 (82)
T ss_dssp CCTTSCCCCBCCTTCEEEEETTTBSSTTCCBCTTTCCGGGGTTSCEEEEECCSSEEEBCCTTCGGGBSSCCCCGGGC
T ss_pred CCCCCCCCCCCCCCCEEEEEECCCCCCCCEECHHHCCCCCCCCCEEEEEEECCCCCCEECCCCHHHHCCCCCCCCCC
T ss_conf 44899888705699778983156799984571566799885896599999528997380297999918898888876
No 3
>2e5n_A RNA polymerase II elongation factor ELL2; ELL_N2 domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=89.68 Aligned_cols=82 Identities=26% Similarity=0.309 Sum_probs=71.9
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHCCCCCCC---CCHHHHHHHHHHCCCCCCCCCCCEEEEHHHHHCCCCCCCCCCCCHHH
Q ss_conf 999999999802898869998619968789---20299999987044599988864057403121004655654482369
Q 000264 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (1764)
Q Consensus 869 ~lRrEIIh~Lc~~p~ThSeL~k~LPe~~~~---~~~fe~IL~eVA~fk~Psg~~~G~Y~LK~E~~~e~DPY~~hy~~~d~ 945 (1764)
-+|..|||.|+++|.+.+||...|..+... ...|+.||+|||++.++ +|.|+||+++|.|++..+++|+..|+
T Consensus 13 plReRvIHLLALkPykkpEL~~RL~kdGl~~~d~~~l~~iL~eVa~~~~~----~~~y~Lk~~~~~eVq~dWp~Yte~er 88 (100)
T 2e5n_A 13 PYRDRVIHLLALKAYKKPELLARLQKDGVNQKDKNSLGAILQQVANLNSK----DLSYTLKDYVFKELQRDWPGYSEIDR 88 (100)
T ss_dssp CHHHHHHHHHHHSCBCHHHHHHHHHHHCCCHHHHHHHHHHHHHHEEEETT----TTEEEECSTHHHHSCTTCTTCCTTHH
T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCC----CCEEEHHHHHHHHHCCCCCCCCHHHH
T ss_conf 69999999998277786999999998369777899999999999843776----77453059999875468899889999
Q ss_pred HHHHHHHHH
Q ss_conf 999999997
Q 000264 946 QVAEERYLR 954 (1764)
Q Consensus 946 q~Aeer~~k 954 (1764)
|....+..+
T Consensus 89 q~v~r~L~~ 97 (100)
T 2e5n_A 89 RSLESVLSR 97 (100)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
T ss_conf 999999987
No 4
>2doa_A RNA polymerase II elongation factor ELL; C19ORF17, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.5.81
Probab=1.00 E-value=1 Score=87.88 Aligned_cols=82 Identities=24% Similarity=0.351 Sum_probs=71.6
Q ss_pred HHHHHHHHHHHCCCCCHHHHHHHCCCCCCC---CCHHHHHHHHHHCCCCCCCCCCCEEEEHHHHHCCCCCCCCCCCCHHH
Q ss_conf 999999999802898869998619968789---20299999987044599988864057403121004655654482369
Q 000264 869 SLKRELVHRLAIGDATHSQLVKSLPRDLSK---FDQLQEILDAVAMYSHPSGFNQGMYSLRWSYWKELDIYHPRWSSRDL 945 (1764)
Q Consensus 869 ~lRrEIIh~Lc~~p~ThSeL~k~LPe~~~~---~~~fe~IL~eVA~fk~Psg~~~G~Y~LK~E~~~e~DPY~~hy~~~d~ 945 (1764)
-+|..|||.|+++|.+.+||...|..+... ...|+.||+|||++.++ +|.|+||+++|.|+|+-+++|+..|+
T Consensus 12 plReRvIHLLALkpykk~EL~~RL~kdGl~~~d~~~l~~iL~eVA~~~~~----~~~y~Lk~~~y~eVq~dWp~Yte~er 87 (104)
T 2doa_A 12 PFRDRVLHLLALRPYRKAELLLRLQKDGLTQADKDALDGLLQQVANMSAK----DGTCTLQDCMYKDVQKDWPGYSEGDQ 87 (104)
T ss_dssp CHHHHHHHHHHHSCEEHHHHHHHHHHHCCCHHHHHHHHHHHHHSSEECSS----SCEEECCSSGGGGCCSCCTTCCSHHH
T ss_pred CHHHHHHHHHHCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCC----CCEEEEHHHHHHHHCCCCCCCCHHHH
T ss_conf 68999999998277786999999998379777799999999999843776----77564149999875478899899999
Q ss_pred HHHHHHHHH
Q ss_conf 999999997
Q 000264 946 QVAEERYLR 954 (1764)
Q Consensus 946 q~Aeer~~k 954 (1764)
|....+..+
T Consensus 88 q~v~r~l~~ 96 (104)
T 2doa_A 88 QLLKRVLVR 96 (104)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
T ss_conf 999999998
No 5
>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=31.65 Aligned_cols=40 Identities=28% Similarity=0.586 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCC
Q ss_conf 256247658789999999998421011237886668989643461001001342246788
Q 000264 1429 SSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPALPW 1488 (1764)
Q Consensus 1429 ~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~N~~lP~~p~ 1488 (1764)
..|||.+|..|+.+|+++ + ..=.||+||+.=..-+|-+|+
T Consensus 32 ~~C~h~fH~~Ci~kWl~~---~-----------------~~~~CP~Cr~~w~~~~~~~~~ 71 (74)
T 2ct0_A 32 ETCGIRMHLPCVAKYFQS---N-----------------AEPRCPHCNDYWPHEIPKSGP 71 (74)
T ss_dssp SSSCCEECHHHHHHHSTT---C-----------------SSCCCTTTCSCCCSCCCCCCS
T ss_pred CCCCCHHHHHHHHHHHHH---C-----------------CCCCCCCCCCCCCCCCCCCCC
T ss_conf 887725659999999984---6-----------------899899984968788888799
No 6
>1v87_A Deltex protein 2; ring-H2 domain, zinc-binding domain, notch signaling, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Mus musculus} SCOP: g.44.1.1
Probab=1.00 E-value=1 Score=31.06 Aligned_cols=41 Identities=27% Similarity=0.574 Sum_probs=28.3
Q ss_pred CCEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCC
Q ss_conf 7367256247658789999999998421011237886668989643461001001342
Q 000264 1425 GIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSV 1482 (1764)
Q Consensus 1425 g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~N~~ 1482 (1764)
-+.+..|||..|..|+..++.. .. ......||+||+.-...
T Consensus 55 ~~~~~~C~H~Fh~~Ci~~wl~~-----~~------------~~~~~~CP~CR~~~~~~ 95 (114)
T 1v87_A 55 VGRLTKCSHAFHLLCLLAMYCN-----GN------------KDGSLQCPSCKTIYGEK 95 (114)
T ss_dssp CEEESSSCCEECHHHHHHHHHH-----TC------------CSSCCBCTTTCCBSSSC
T ss_pred CEECCCCCCCCCHHHHHHHHHC-----CC------------CCCCCCCCCCCCCCCCC
T ss_conf 3522997996049999999970-----36------------77898699999823777
No 7
>2kiz_A E3 ubiquitin-protein ligase arkadia; ring-H2 finger, E3 ligase, Zn binding domain, metal zinc, zinc-finger, metal binding protein; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=30.57 Aligned_cols=40 Identities=30% Similarity=0.718 Sum_probs=29.7
Q ss_pred CCCEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC
Q ss_conf 97367256247658789999999998421011237886668989643461001001342246
Q 000264 1424 DGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLANSVLPA 1485 (1764)
Q Consensus 1424 ~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~N~~lP~ 1485 (1764)
..+.+..|||..|..|+..++.. + ..||+||+--+..+|.
T Consensus 28 ~~~~~~~C~H~fc~~Ci~~~~~~------~----------------~~CP~Cr~~~~~~~~~ 67 (69)
T 2kiz_A 28 EDVRRLPCMHLFHQVCVDQWLIT------N----------------KKCPICRVDIEAQLPS 67 (69)
T ss_dssp SCEEECTTSCEEEHHHHHHHHHH------C----------------SBCTTTCSBSCSCCCC
T ss_pred CCEEEECCCCHHHHHHHHHHHHC------C----------------CCCCCCCCCCCCCCCC
T ss_conf 86898689989989999999985------9----------------9792809606476989
No 8
>3dpl_R Ring-box protein 1; ubiquitin, NEDD8, cullin, HOST-virus interaction, receptor, UBL conjugation, UBL conjugation pathway, acetylation, cytoplasm; 2.60A {Homo sapiens} SCOP: g.44.1.1 PDB: 3dqv_R 3rtr_B 4f52_B 1u6g_B 2hye_D* 4a0c_D 4a0l_F* 1ldj_B 1ldk_C 2lgv_A
Probab=1.00 E-value=1 Score=30.48 Aligned_cols=35 Identities=23% Similarity=0.592 Sum_probs=26.5
Q ss_pred CCCCCEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHC
Q ss_conf 889736725624765878999999999842101123788666898964346100100
Q 000264 1422 DCDGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQL 1478 (1764)
Q Consensus 1422 ~~~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l 1478 (1764)
+..-+....|||..|..|...++.. ...||+||+-
T Consensus 64 ~~~~~~~~~C~H~FH~~Ci~~Wl~~----------------------~~~CP~Cr~~ 98 (106)
T 3dpl_R 64 EECTVAWGVCNHAFHFHCISRWLKT----------------------RQVCPLDNRE 98 (106)
T ss_dssp -CCCEEEETTSCEEEHHHHHHHHTT----------------------CSBCSSSCSB
T ss_pred CCCEEEECCCCCEECHHHHHHHHHC----------------------CCCCCCCCCC
T ss_conf 6633761664867998999999976----------------------9858698982
No 9
>1x4j_A Ring finger protein 38; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=30.37 Aligned_cols=33 Identities=30% Similarity=0.848 Sum_probs=24.8
Q ss_pred CCCEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHC
Q ss_conf 9736725624765878999999999842101123788666898964346100100
Q 000264 1424 DGIHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQL 1478 (1764)
Q Consensus 1424 ~g~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l 1478 (1764)
..+.+..|||..|..|.+.++.. . ..||+||+-
T Consensus 37 ~~~~~l~C~H~fh~~Ci~~w~~~-----~-----------------~~CP~Cr~~ 69 (75)
T 1x4j_A 37 QLLRVLPCNHEFHAKCVDKWLKA-----N-----------------RTCPICRAD 69 (75)
T ss_dssp CEEEEETTTEEEETTHHHHHHHH-----C-----------------SSCTTTCCC
T ss_pred CEEEEECCCCHHHHHHHHHHHHC-----C-----------------CCCCCCCCC
T ss_conf 86998789987579999999974-----9-----------------939070880
No 10
>2ct2_A Tripartite motif protein 32; zinc-finger protein HT2A, TAT- interacting protein, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}
Probab=1.00 E-value=1 Score=30.16 Aligned_cols=35 Identities=29% Similarity=0.777 Sum_probs=27.5
Q ss_pred CEECCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHCC
Q ss_conf 367256247658789999999998421011237886668989643461001001
Q 000264 1426 IHLSSCGHAVHQGCLDRYVSSLKERYNRRIIFEGGHIVDPDQGEFLCPVCRQLA 1479 (1764)
Q Consensus 1426 ~~~~~CgH~~H~~C~~~y~~sl~~r~~~~~~~~~~~~~~~~~~Ef~CPlCr~l~ 1479 (1764)
+.+..|||..|..|++.++..- .+.+.||+||+.-
T Consensus 32 ~~~~~CgH~fC~~Ci~~~~~~~-------------------~~~~~CP~Cr~~~ 66 (88)
T 2ct2_A 32 PKLLHCGHTICRQCLEKLLASS-------------------INGVRCPFCSKIT 66 (88)
T ss_dssp EEECSSSCEEEHHHHHHHHHHC-------------------SSCBCCTTTCCCB
T ss_pred EEECCCCCHHHHHHHHHHHHCC-------------------CCCCCCCCCCCCC
T ss_conf 6878889854299999999829-------------------9972997899801
Done!