Query psy12450
Match_columns 168
No_of_seqs 156 out of 1276
Neff 6.6
Searched_HMMs 29240
Date Fri Aug 16 19:37:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12450.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/12450hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3iay_A DNA polymerase delta ca 100.0 1.2E-35 4.2E-40 280.4 8.8 165 2-167 447-627 (919)
2 3qex_A DNA polymerase, GP43; d 100.0 1.8E-30 6.1E-35 244.2 9.1 114 41-158 371-492 (903)
3 1qht_A Protein (DNA polymerase 100.0 5.4E-30 1.8E-34 238.4 6.5 155 2-167 308-479 (775)
4 2gv9_A DNA polymerase; polymer 99.9 1.1E-28 3.7E-33 237.8 7.5 105 61-167 653-761 (1193)
5 3k59_A POL II, DNA polymerase 99.9 3.7E-28 1.3E-32 226.3 7.8 108 41-157 382-489 (786)
6 1s5j_A DNA polymerase I; repli 99.9 1.3E-27 4.6E-32 224.1 5.9 158 2-167 371-560 (847)
7 2py5_A DNA polymerase; protein 98.3 3.5E-07 1.2E-11 82.6 4.1 43 59-102 223-270 (575)
8 3k59_A POL II, DNA polymerase 95.1 0.011 3.7E-07 55.3 3.3 32 8-39 634-665 (786)
9 3iay_A DNA polymerase delta ca 95.0 0.012 4.1E-07 55.8 3.1 33 8-40 766-798 (919)
10 1qht_A Protein (DNA polymerase 94.3 0.019 6.6E-07 53.3 2.6 33 8-40 605-637 (775)
11 2gv9_A DNA polymerase; polymer 91.9 0.051 1.8E-06 52.9 1.6 32 8-39 910-941 (1193)
12 3qex_A DNA polymerase, GP43; d 91.3 0.11 3.8E-06 49.2 3.2 31 8-38 727-757 (903)
13 1s5j_A DNA polymerase I; repli 91.0 0.041 1.4E-06 51.7 -0.1 32 8-39 678-709 (847)
14 1noy_A Protein (DNA polymerase 68.8 0.37 1.3E-05 40.9 -2.7 53 2-54 317-381 (388)
15 2lnu_A Uncharacterized protein 27.2 81 0.0028 24.2 4.5 50 45-96 105-157 (190)
16 3c01_A Surface presentation of 21.8 47 0.0016 19.9 1.8 18 148-165 3-21 (48)
17 3zqu_A Probable aromatic acid 21.2 34 0.0012 26.5 1.3 16 63-78 157-172 (209)
No 1
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae}
Probab=100.00 E-value=1.2e-35 Score=280.38 Aligned_cols=165 Identities=43% Similarity=0.701 Sum_probs=130.0
Q ss_pred ccccchhhhhhhhhccC----cHHHHHHHHHH---HHHHHhccCC--------CccccccceeeeeCCCCCCCcccCccE
Q psy12450 2 LRHVTWRDGLETVRRDN----SPLVANMINTC---LQKLLINRDP--------DGAVTQKNFIIPTYHGGQGEDQFEGAT 66 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~----c~Lv~~i~~~~---L~~lli~r~~--------~~A~~~~~~liP~~~~~~~~~~y~Gg~ 66 (168)
|++|.++|...+.++.. .+....+-..+ +..++ .|.. .++++++|+++|++......++|+||+
T Consensus 447 L~~Y~~~Da~l~~~L~~kl~~l~~~~elArl~Gi~~~~vl-~rG~qi~ves~Llr~a~~~~~ilP~~~~~~~~~~y~Gg~ 525 (919)
T 3iay_A 447 LAVYCLKDAYLPLRLMEKLMALVNYTEMARVTGVPFSYLL-ARGQQIKVVSQLFRKCLEIDTVIPNMQSQASDDQYEGAT 525 (919)
T ss_dssp HHHHHHHHHHHHHHHHHHTTHHHHHHHHHHHHCCCHHHHH-HSCHHHHHHHHHHHHHHHTTEECBCCCCCCCSSCCCCCC
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHcCCCHHHhh-cccchHHHHHHHHHHHhhCCeeCCCcccccccccCCCCE
Confidence 45677777777777633 22222332222 33332 2221 267899999999986445568899999
Q ss_pred eecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCC-CCceeeCCCceEEeecCCCCcchHHHHHHHH
Q psy12450 67 VIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELT-PDQYSKTPCGNFFLKSSLRKGLLPEILENLL 145 (168)
Q Consensus 67 VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~-~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll 145 (168)
|++|++|+|++||++|||+|||||||++|||||||++++.+.++.++. .+++..+|+|.+|++++.++||+|++|++|+
T Consensus 526 V~eP~~G~y~~pV~~lDF~SLYPSIi~~~Nlc~~Tl~~~~~~~~~~~~~~~~~~~~p~g~~f~~~~~~~gilp~~l~~ll 605 (919)
T 3iay_A 526 VIEPIRGYYDVPIATLDFNSLYPSIMMAHNLCYTTLCNKATVERLNLKIDEDYVITPNGDYFVTTKRRRGILPIILDELI 605 (919)
T ss_dssp BCCCCCEEECSCEEEEEETTHHHHHHHHTTCSGGGEECHHHHHHTTCCBTTTEEECTTSCEEECTTTCCCHHHHHHHHHH
T ss_pred EecCCCCceeccEEEEEecccchHHHHhcCcCcccccccchhhhcCCCCCcceeeCCCCcEEeccCCCCCchHHHHHHHH
Confidence 999999999999999999999999999999999999987643334433 3488899999999998889999999999999
Q ss_pred HHHHHHHHHhccCCChhhhhcc
Q psy12450 146 SARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 146 ~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
+.|+++|++||+++||+++++|
T Consensus 606 ~~R~~~K~~mk~~~d~~~~~~l 627 (919)
T 3iay_A 606 SARKRAKKDLRDEKDPFKRDVL 627 (919)
T ss_dssp HHHHHHHHHHHTCCCHHHHHHH
T ss_pred HHHHHHHHHHhhcCChHHHHHH
Confidence 9999999999999999988765
No 2
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ...
Probab=99.96 E-value=1.8e-30 Score=244.24 Aligned_cols=114 Identities=27% Similarity=0.457 Sum_probs=99.6
Q ss_pred ccccccceeeeeCCCCCCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCcccccccccccc--------CC
Q psy12450 41 GAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITK--------LE 112 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~--------~~ 112 (168)
+.++++|+++|++. .....+|+||+|++|.+|+|++ |++|||+|||||||++|||||+|+++..+.++ ..
T Consensus 371 r~a~~~~~iiP~~~-~~~~~~y~Gg~V~~p~~G~y~~-v~~lDf~SLYPsIi~~~ni~~~T~~~~~~~~~~~~~i~~~~~ 448 (903)
T 3qex_A 371 NSLKEQNKVIPQGR-SHPVQPYPGAFVKEPIPNRYKY-VMSFDLTSLYPSIIRQVNISPETIAGTFKVAPLHDYINAVAE 448 (903)
T ss_dssp HHHHTTTEECCCCC-CCCCCCCCCCCBCCCCCEECSS-EEEEEETTHHHHHHHHHTCCGGGEEEECCCCCHHHHHTTCSC
T ss_pred HHHHHCCEeccCCc-ccccCCCCCCEEecccCCceEE-EEEEehhhhchHHHHHhCcChhhccccccccchhcccccccC
Confidence 56789999999984 5567789999999999999997 99999999999999999999999998765321 12
Q ss_pred CCCCceeeCCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhccC
Q psy12450 113 LTPDQYSKTPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKKE 158 (168)
Q Consensus 113 ~~~~~~~~~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~~ 158 (168)
.+.+++..+|+|++|++ .++||+|++|++|++.|+++|++|+++
T Consensus 449 ~p~~~~~~~p~g~~F~k--~~~GiLP~iL~~Ll~~R~~~K~~mk~~ 492 (903)
T 3qex_A 449 RPSDVYSCSPNGMMYYK--DRDGVVPTEITKVFNQRKEHKGYMLAA 492 (903)
T ss_dssp CSCSSSEECTTSEEECC--SSCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCceeeCCCCceEec--CCCcchHHHHHHHHHHHHHHHHHHhhc
Confidence 34567888999999987 589999999999999999999999864
No 3
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
Probab=99.96 E-value=5.4e-30 Score=238.40 Aligned_cols=155 Identities=27% Similarity=0.436 Sum_probs=115.0
Q ss_pred ccccchhhhhhhhhccC--cHHHHHHHHHH-HHHHHhccC---C------CccccccceeeeeCCCCC----CCcccCcc
Q psy12450 2 LRHVTWRDGLETVRRDN--SPLVANMINTC-LQKLLINRD---P------DGAVTQKNFIIPTYHGGQ----GEDQFEGA 65 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~--c~Lv~~i~~~~-L~~lli~r~---~------~~A~~~~~~liP~~~~~~----~~~~y~Gg 65 (168)
|++|..+|...+.++.. .|+...+.+.+ +....+.|. . .+.++++|+++|+..... ..++|+||
T Consensus 308 l~~Y~~~Da~lt~~L~~~~~~~~~~la~i~g~~~~~v~r~~~~~~ve~~Ll~~~~~~~~i~P~~~~~~~~~~~~~~y~Gg 387 (775)
T 1qht_A 308 VARYSMEDAKVTYELGREFFPMEAQLSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKPDERELARRRGGYAGG 387 (775)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTSCHHHHTTCCHHHHHHHHHHHHHHHTTBCCCCCCCHHHHHHTTTCCCCC
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHhCCCchhceecccHHHHHHHHhHHHHhCCEeCCCCCchhhhhccccccCCc
Confidence 45677777777777643 23322222222 000111111 1 267889999999974211 14689999
Q ss_pred EeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCC-CceEEeecCCCCcchHHHHHHH
Q psy12450 66 TVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTP-CGNFFLKSSLRKGLLPEILENL 144 (168)
Q Consensus 66 ~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p-~~~~f~~~~~~~Gilp~~L~~l 144 (168)
+|++|++|+|++ |++|||+|||||||++|||||+|+++..+. ++...| .|++|++. ++|++|++|++|
T Consensus 388 ~V~eP~~G~y~~-v~~lDF~SLYPSIi~~~nl~~~t~~~~~~~--------~~~~~~~~~~~f~~~--~~g~lp~~l~~l 456 (775)
T 1qht_A 388 YVKEPERGLWDN-IVYLDFRSLYPSIIITHNVSPDTLNREGCK--------EYDVAPEVGHKFCKD--FPGFIPSLLGDL 456 (775)
T ss_dssp CBCCCCCSCEEE-EEEEECSSHHHHHHHHTTCSTTTBTCTTCS--------CEEECTTTCCEEECS--SCCHHHHHHHHH
T ss_pred eEecccCCcccc-eeecchhcccHHHHHhcCCCcccccccccc--------ccccCCccCcccccc--cCCCchHHHHHH
Confidence 999999999999 999999999999999999999999876652 233333 57889874 899999999999
Q ss_pred HHHHHHHHHHhccCCChhhhhcc
Q psy12450 145 LSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 145 l~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
+++|+++|++|++++||.++++|
T Consensus 457 ~~~R~~~K~~~k~~~~~~~~~~~ 479 (775)
T 1qht_A 457 LEERQKIKRKMKATVDPLEKKLL 479 (775)
T ss_dssp HHHHHHHHHHHHTCCCHHHHHHH
T ss_pred HHHHHHHHHHhhcCCCHHHHHHH
Confidence 99999999999999999988765
No 4
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B*
Probab=99.95 E-value=1.1e-28 Score=237.78 Aligned_cols=105 Identities=34% Similarity=0.644 Sum_probs=81.5
Q ss_pred ccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCC-CCceee---CCCceEEeecCCCCcc
Q psy12450 61 QFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELT-PDQYSK---TPCGNFFLKSSLRKGL 136 (168)
Q Consensus 61 ~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~-~~~~~~---~p~~~~f~~~~~~~Gi 136 (168)
+|+||+|++|.+|+|++||++|||+|||||||++|||||+|++...... .++. .+++.. .+...+|++++.++|+
T Consensus 653 ~Y~Gg~VleP~~Gly~~pV~vLDF~SLYPSII~a~Nlc~sTl~~~~~~~-~~l~~~~dy~~~~~~~~~~~fvk~~~~~gi 731 (1193)
T 2gv9_A 653 GYQGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAV-AHLEAGKDYLEIEVGGRRLFFVKAHVRESL 731 (1193)
T ss_dssp ------CCCCCCEEECSCEEEEEEETHHHHHHHHTTCCTTTEESCSTTS-TTCCTTTTEEEEECSSSEEEEECTTTSCCH
T ss_pred ccCCCEEeecCCCeeeCcEEEEeccccchHHHHHhcCCcceeccCchhh-ccCCCccceeEecCCCCceeeccCccccch
Confidence 7999999999999999999999999999999999999999999764321 1222 234432 2233689998899999
Q ss_pred hHHHHHHHHHHHHHHHHHhccCCChhhhhcc
Q psy12450 137 LPEILENLLSARKQAKNDLKKETDELTQVLY 167 (168)
Q Consensus 137 lp~~L~~ll~~R~~~K~~mk~~~Dp~~k~~l 167 (168)
+|++|++|++.|+++|++||++ |+.++.+|
T Consensus 732 lp~lL~~ll~~Rk~~K~~mk~~-~~~~~~ll 761 (1193)
T 2gv9_A 732 LSILLRDWLAMRKQIRSRIPQS-SPEEAVLL 761 (1193)
T ss_dssp HHHHHHHHHHHHHHHHHHGGGS-CHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhcccC-CHHHHHHH
Confidence 9999999999999999999987 78877654
No 5
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Probab=99.94 E-value=3.7e-28 Score=226.32 Aligned_cols=108 Identities=24% Similarity=0.419 Sum_probs=92.4
Q ss_pred ccccccceeeeeCCCCCCCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceee
Q psy12450 41 GAVTQKNFIIPTYHGGQGEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSK 120 (168)
Q Consensus 41 ~A~~~~~~liP~~~~~~~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~ 120 (168)
++++++|+++|++. ....++|+||+|++|++|+|++ |++|||+|||||||++|||||+|++...+.. ..++...
T Consensus 382 ~~~~~~~~i~P~~~-~~~~~~y~Gg~V~eP~~G~y~~-V~~lDF~SLYPSIi~~~ni~~~t~~~~~~~~----~~~~~~~ 455 (786)
T 3k59_A 382 PRMHRAGYVAPNLG-EVPPHASPGGYVMDSRPGLYDS-VLVLDYKSLYPSIIRTFLIDPVGLVEGMAQP----DPEHSTE 455 (786)
T ss_dssp HHHHHTTBCCCCTT-SSCCCCCCCCCBCCCCCEEESC-EEEEEETTHHHHHHHHHCCCHHHHHHHHHSC----STTTEEE
T ss_pred HHHHHcCeeCCCcc-ccccccCCCcEEeeccCCceee-EEEEEhhhccHHHHHHhCCCccccccccCCc----ccccccc
Confidence 56888999999984 4456789999999999999998 9999999999999999999999997544311 1245566
Q ss_pred CCCceEEeecCCCCcchHHHHHHHHHHHHHHHHHhcc
Q psy12450 121 TPCGNFFLKSSLRKGLLPEILENLLSARKQAKNDLKK 157 (168)
Q Consensus 121 ~p~~~~f~~~~~~~Gilp~~L~~ll~~R~~~K~~mk~ 157 (168)
+|++++|++ ++|++|++|++|++.|+++|++|++
T Consensus 456 ~~~g~~f~~---~~g~lp~~l~~l~~~R~~~K~~~~~ 489 (786)
T 3k59_A 456 GFLDAWFSR---EKHCLPEIVTNIWHGRDEAKRQGNK 489 (786)
T ss_dssp CSTTCEEES---SCCSHHHHHHHHHHHHHHHHHTTCH
T ss_pred CCCCceEee---cCCchHHHHHHHHHHHHHHHHhcch
Confidence 789999987 7999999999999999999998764
No 6
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1
Probab=99.94 E-value=1.3e-27 Score=224.13 Aligned_cols=158 Identities=26% Similarity=0.347 Sum_probs=108.4
Q ss_pred ccccchhhhhhhhhccC------cHHHHHHHHHH---HHHHHhccCC---------CccccccceeeeeCCC-----CC-
Q psy12450 2 LRHVTWRDGLETVRRDN------SPLVANMINTC---LQKLLINRDP---------DGAVTQKNFIIPTYHG-----GQ- 57 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~------c~Lv~~i~~~~---L~~lli~r~~---------~~A~~~~~~liP~~~~-----~~- 57 (168)
|++|..+|...+.++.. .++...+...+ +..+ .|.. .+.++++|+++|++.. ..
T Consensus 371 l~~Ycl~Da~lt~~L~~~~~~~~~~~~~~la~i~~lp~~~l--~r~~~~~~v~slll~~~~~~~~i~P~~~~~~~~~~~~ 448 (847)
T 1s5j_A 371 LIEYNFRDAEITLQLTTFNNDLTMKLIVLFSRISRLGIEEL--TRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSSNI 448 (847)
T ss_dssp HHHHHHHHHHHHHHTTTHHHHHHHHHHHHHHHHHCCCHHHH--TTSCHHHHHHHHHHHHHHHHTBCCCCHHHHHHTTCC-
T ss_pred HHHHHHHHHHHHHHHHHHHhHhHHHHHHHHHHHhCCCchhh--cccchhhhhHHHHHHHHHhcCcccCCchhhhhhcccc
Confidence 56788889998888854 12222222222 2222 2221 1578899999999731 11
Q ss_pred ------CCcccCccEeecccCccccCCeEEeecCCcChhHHHhhcCCccccccccccccCCCCCCceeeCCCceEEeecC
Q psy12450 58 ------GEDQFEGATVIEPKKGYYADPIATLDFSSLYPSIMMAHNLCYTTLLTPQTITKLELTPDQYSKTPCGNFFLKSS 131 (168)
Q Consensus 58 ------~~~~y~Gg~VleP~~G~y~~pV~~lDF~SLYPSIm~~~Ni~p~Tl~~~~~~~~~~~~~~~~~~~p~~~~f~~~~ 131 (168)
..++|+||+|++|++|+|++ |++|||+|||||||++|||||||++...+... .+.....|...+|+++
T Consensus 449 ~~~~~~~~~~y~Gg~V~eP~~G~y~~-v~~lDf~SLYPSIi~~~Nl~~~T~~~~~~~~~----~~~~~~~~~~~~~~~~- 522 (847)
T 1s5j_A 449 RTSALIKGKGYKGAVVIDPPAGIFFN-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKP----YEVKDETGEVLHIVCM- 522 (847)
T ss_dssp -------------CCCCCCCSEEEEE-EEEEEETTHHHHHHHHTTCCTTTBSCSCCSSC----CEECCSSSCCCEEBCC-
T ss_pred cchhccccccccCCcccCCCCCcccc-eeEeehhhhchHHHHHcCCCcceecccccccc----ccccccCCCCceeEec-
Confidence 23579999999999999998 99999999999999999999999997544211 1112234666667664
Q ss_pred CCCcchHHHHHHHHHHHHHHHHHhccC--CChhhhhcc
Q psy12450 132 LRKGLLPEILENLLSARKQAKNDLKKE--TDELTQVLY 167 (168)
Q Consensus 132 ~~~Gilp~~L~~ll~~R~~~K~~mk~~--~Dp~~k~~l 167 (168)
.++|++|.+|+.|++.|+++|++|++. .||.++++|
T Consensus 523 ~~~g~~p~~l~~l~~~R~~~kk~~~k~~~~~~~~~~~~ 560 (847)
T 1s5j_A 523 DRPGITAVITGLLRDFRVKIYKKKAKNPNNSEEQKLLY 560 (847)
T ss_dssp SSCCHHHHHHHHHHHHHHHTHHHHHTCTTSCHHHHHHH
T ss_pred cCCcccHHHHHHHHHHHHHHHHHHHhccCCCHHHHHHH
Confidence 689999999999999999998888653 488876654
No 7
>2py5_A DNA polymerase; protein-DNA complex, replication, transferase/DNA complex; HET: DNA; 1.60A {Bacillus phage PHI29} SCOP: c.55.3.5 e.8.1.1 PDB: 1xhz_A* 1xhx_A* 2ex3_A* 1xi1_A* 2pyj_A* 2pyl_A* 2pzs_A*
Probab=98.30 E-value=3.5e-07 Score=82.65 Aligned_cols=43 Identities=16% Similarity=0.214 Sum_probs=33.6
Q ss_pred CcccCccEeec-cc--CccccCCeEEeecCCcChhHHHh--hcCCcccc
Q psy12450 59 EDQFEGATVIE-PK--KGYYADPIATLDFSSLYPSIMMA--HNLCYTTL 102 (168)
Q Consensus 59 ~~~y~Gg~Vle-P~--~G~y~~pV~~lDF~SLYPSIm~~--~Ni~p~Tl 102 (168)
.++|.||.|+. |. .|++++ |+++||+|||||+|.. ++++.-+.
T Consensus 223 r~~y~GGr~~~~p~y~~~~~~~-i~~~D~~SLYPs~m~~~~~P~g~p~~ 270 (575)
T 2py5_A 223 RYAYRGGFTWLNDRFKEKEIGE-GMVFDVNSLYPAQMYSRLLPYGEPIV 270 (575)
T ss_dssp HTTCCCCCEEECGGGBTCEECS-EEEEEETTHHHHHHHHSCEEEEEEEE
T ss_pred HHcCCCccccccccccccCCCc-eEEEecCCchHHHHcCCCCCCCCcee
Confidence 36789999974 55 567887 9999999999999997 55554343
No 8
>3k59_A POL II, DNA polymerase II; protein-DNA complex, DNA damage, DNA repair, DNA-binding; HET: DNA DOC DCP; 1.92A {Escherichia coli} PDB: 3k57_A* 3k58_A* 3k5l_A* 3k5m_A* 3k5n_A* 3k5o_A* 3maq_A* 1q8i_A*
Probab=95.15 E-value=0.011 Score=55.28 Aligned_cols=32 Identities=31% Similarity=0.412 Sum_probs=30.0
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||+|+||||+|||+.++.+.++..+|.++++
T Consensus 634 ~KGle~vRrD~~~l~k~~~~~~l~~il~~~~v 665 (786)
T 3k59_A 634 FKGLETVRTDWTPLAQQFQQELYLRIFRNEPY 665 (786)
T ss_dssp EESSGGGCTTSCHHHHHHHHHHHHHHHTTCCC
T ss_pred EEeeEEEcCCccHHHHHHHHHHHHHHHcCCCH
Confidence 47999999999999999999999999998876
No 9
>3iay_A DNA polymerase delta catalytic subunit; protein-DNA complex, DNA replication, DNA-BI DNA-directed DNA polymerase, exonuclease, hydrolase; HET: DNA DOC DCP; 2.00A {Saccharomyces cerevisiae}
Probab=94.98 E-value=0.012 Score=55.79 Aligned_cols=33 Identities=45% Similarity=0.777 Sum_probs=30.5
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPD 40 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~ 40 (168)
.||+++||||+|+|++++.++++..+|.++++.
T Consensus 766 ~KGie~vRrD~~~~~k~~~~~~l~~ll~~~~~~ 798 (919)
T 3iay_A 766 QKGLASVRRDSCSLVSIVMNKVLKKILIERNVD 798 (919)
T ss_dssp EESSGGGCTTSCHHHHHHHHHHHHHHHTTCCHH
T ss_pred EEeEEEEeCCchHHHHHHHHHHHHHHHcCCCHH
Confidence 579999999999999999999999999988853
No 10
>1qht_A Protein (DNA polymerase); archaea, hyperthermostable, family B polymer alpha family polymerase, transferase; 2.10A {Thermococcus SP} SCOP: c.55.3.5 e.8.1.1 PDB: 1tgo_A 2xhb_A* 2vwj_A* 2vwk_A* 1wns_A* 1wn7_A 1qqc_A* 4ahc_A* 4ail_C* 3a2f_A* 2jgu_A* 1d5a_A
Probab=94.25 E-value=0.019 Score=53.33 Aligned_cols=33 Identities=33% Similarity=0.455 Sum_probs=30.4
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDPD 40 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~~ 40 (168)
.||+|+||||+|+|+.++.+.++..+|.+++..
T Consensus 605 ~KG~e~vRrd~~~l~k~~~~~vl~~ll~~~d~~ 637 (775)
T 1qht_A 605 TRGLEIVRRDWSEIAKETQARVLEAILKHGDVE 637 (775)
T ss_dssp EESCSCCCSCCCHHHHHHHHHHHHHHHHHCCHH
T ss_pred EEeeEEEeCCcHHHHHHHHHHHHHHHhcCCCHH
Confidence 589999999999999999999999999888753
No 11
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B*
Probab=91.88 E-value=0.051 Score=52.90 Aligned_cols=32 Identities=16% Similarity=0.347 Sum_probs=29.3
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||+++||||+|+|+.++.+.++..+|.++++
T Consensus 910 ~KG~e~vRRD~~~lvk~~~~~vl~~ll~~~d~ 941 (1193)
T 2gv9_A 910 IKGVDLVRKNNCAFINRTSRALVDLLFYDDTV 941 (1193)
T ss_dssp EESCCSCCTTSCHHHHHHHHHHHHHHHHCHHH
T ss_pred EECCeeecCchHHHHHHHHHHHHHHHHcCCCH
Confidence 58999999999999999999999999987764
No 12
>3qex_A DNA polymerase, GP43; difluorotoluene nucleoside; HET: DNA DOC DGT; 1.73A {Enterobacteria phage RB69} PDB: 3qei_A* 3qer_A* 3qes_A* 3qet_A* 3qep_A* 3qew_A* 3qev_A* 3s9h_A* 3sq0_A* 4dtn_A* 4dto_A* 4dtp_A* 4dtr_A* 4dts_A* 4dtu_A* 4dtx_A* 4e3s_A* 4fjm_A* 4fjl_A* 3spz_A* ...
Probab=91.28 E-value=0.11 Score=49.24 Aligned_cols=31 Identities=23% Similarity=0.482 Sum_probs=28.4
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRD 38 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~ 38 (168)
.||+|+||||+||+++++...++..++-+.+
T Consensus 727 ~kGlE~vRrd~~~~~k~~~~~~l~~ll~~~~ 757 (903)
T 3qex_A 727 IMGLETQKSSTPKAVQKALKECIRRMLQEGE 757 (903)
T ss_dssp EESSGGGCTTSCHHHHHHHHHHHHHHHHTCH
T ss_pred EeceEEEeccchHHHHHHHHHHHHHHHhcCc
Confidence 5899999999999999999999999988754
No 13
>1s5j_A DNA polymerase I; replication, disulfide bonds, transferase; HET: DNA; 2.40A {Sulfolobus solfataricus} SCOP: c.55.3.5 e.8.1.1
Probab=91.02 E-value=0.041 Score=51.70 Aligned_cols=32 Identities=16% Similarity=0.335 Sum_probs=21.0
Q ss_pred hhhhhhhhccCcHHHHHHHHHHHHHHHhccCC
Q psy12450 8 RDGLETVRRDNSPLVANMINTCLQKLLINRDP 39 (168)
Q Consensus 8 ~~~~~~~r~~~c~Lv~~i~~~~L~~lli~r~~ 39 (168)
.||+++||||+|+|+.++.+.++..++..+++
T Consensus 678 ~KG~e~vRrd~~~l~k~~~~~~l~~ll~~~~~ 709 (847)
T 1s5j_A 678 IKGMLVKKRNTPEFVKKVFNEVKELMISINSP 709 (847)
T ss_dssp EESCCC--------CCSHHHHHHHHHHTTCCS
T ss_pred eeeeEEeeCCcHHHHHHHHHHHHHHHHhcCCh
Confidence 58999999999999999999999999876653
No 14
>1noy_A Protein (DNA polymerase (E.C.2.7.7.7)); exonuclease, DNA-binding, complex (nucleotidyltransferase/DNA); HET: DNA; 2.20A {Enterobacteria phage T4} SCOP: c.55.3.5 PDB: 1noz_A*
Probab=68.80 E-value=0.37 Score=40.92 Aligned_cols=53 Identities=13% Similarity=0.043 Sum_probs=26.7
Q ss_pred ccccchhhhhhhhhccC----cHHHHHHHHHH---HHHHHhccCC-----CccccccceeeeeCC
Q psy12450 2 LRHVTWRDGLETVRRDN----SPLVANMINTC---LQKLLINRDP-----DGAVTQKNFIIPTYH 54 (168)
Q Consensus 2 ~~~~~~~~~~~~~r~~~----c~Lv~~i~~~~---L~~lli~r~~-----~~A~~~~~~liP~~~ 54 (168)
|++|..+|...+.++.. .++..++.+.+ +..++.++.+ .++++++|+++|++.
T Consensus 317 l~~Y~~~D~~l~~~L~~kl~~l~~~~ela~i~g~~~~~vl~q~~~~~~lll~~~~~~~~i~P~~~ 381 (388)
T 1noy_A 317 YISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVMSPIKTWDAIIFNSLKGEHKVIPQQG 381 (388)
T ss_dssp HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCCGGGGGCHHHHHHHHHHHHTTCC--------
T ss_pred HHHHHHHHHHHHHHHHHHHChHHHHHHHhCccCCCHHHhCccHHHHHHHHHHHHHhCCEEcccCC
Confidence 45677778777777733 45555555555 3333333322 278999999999984
No 15
>2lnu_A Uncharacterized protein; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Haloarcula marismortui}
Probab=27.15 E-value=81 Score=24.21 Aligned_cols=50 Identities=22% Similarity=0.407 Sum_probs=30.0
Q ss_pred ccceeeeeCCCCCCCcccCccEeec-ccCccc--cCCeEEeecCCcChhHHHhhc
Q psy12450 45 QKNFIIPTYHGGQGEDQFEGATVIE-PKKGYY--ADPIATLDFSSLYPSIMMAHN 96 (168)
Q Consensus 45 ~~~~liP~~~~~~~~~~y~Gg~Vle-P~~G~y--~~pV~~lDF~SLYPSIm~~~N 96 (168)
..+..+|-.......+.|.||..|+ +.+... .. -++||||=-|= --+|||
T Consensus 105 ~~~LflpF~D~TsG~~TYg~GRyL~~~~p~~~~~~g-~vvLDFNrAyN-PpCAys 157 (190)
T 2lnu_A 105 SRTLFVPFRDKTTGQQSYDGGRYMELEPDRDLSDGD-EITLDFNLAYS-PFCAYS 157 (190)
T ss_dssp SCCEEEEEBCSSBTTTBCTTCEEEEECCSSCCCTTC-EEEEEGGGCBC-CHHHHC
T ss_pred CCeEEEEEEcCCCCCcccCCccEEeccCCCccCCCC-eEEEEccCccC-CccccC
Confidence 3456788875445567898886664 334321 23 57999997662 223555
No 16
>3c01_A Surface presentation of antigens protein SPAS; auto cleavage protein, flagella, ESCU, YSCU, intein, T3SS, M inner membrane, transmembrane; 2.60A {Salmonella typhimurium} SCOP: d.367.1.1
Probab=21.77 E-value=47 Score=19.89 Aligned_cols=18 Identities=17% Similarity=0.390 Sum_probs=13.4
Q ss_pred HHHHHHHhcc-CCChhhhh
Q psy12450 148 RKQAKNDLKK-ETDELTQV 165 (168)
Q Consensus 148 R~~~K~~mk~-~~Dp~~k~ 165 (168)
+.++|+++|+ ++||..|.
T Consensus 3 kqEvK~E~Ke~EGdP~iK~ 21 (48)
T 3c01_A 3 KEEVKREMKEQEGNPEVKS 21 (48)
T ss_pred HHHHHHHHHhccCCHHHHH
Confidence 5678888886 57888764
No 17
>3zqu_A Probable aromatic acid decarboxylase; lyase; HET: FNR; 1.50A {Pseudomonas aeruginosa} SCOP: c.34.1.0
Probab=21.22 E-value=34 Score=26.53 Aligned_cols=16 Identities=31% Similarity=0.794 Sum_probs=14.0
Q ss_pred CccEeecccCccccCC
Q psy12450 63 EGATVIEPKKGYYADP 78 (168)
Q Consensus 63 ~Gg~VleP~~G~y~~p 78 (168)
.|+.|+.|.+|+|..|
T Consensus 157 ~G~~iipp~~g~ya~p 172 (209)
T 3zqu_A 157 LGAVILPAAPGFYHQP 172 (209)
T ss_dssp HTCEECCSCCCCTTCC
T ss_pred CCCEEeCCCcccccCC
Confidence 4999999999999764
Done!