Query 000502
Match_columns 1459
No_of_seqs 387 out of 1985
Neff 5.0
Searched_HMMs 29240
Date Tue Mar 26 16:28:31 2013
Command hhsearch -i /local_scratch/syshi/lefta3m/000502.a3m -d /local_scratch/syshi/pdb70.hhm -v 0 -o /local_scratch/syshi/H1_276-280//hhsearch_pdb/000502hhsearch_pdb
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 3iay_A DNA polymerase delta ca 1.0 1 1 883.2 46.1 542 824-1459 139-704 (919)
2 2gv9_A DNA polymerase; polymer 1.0 1 1 800.7 44.3 544 824-1459 219-852 (1193)
3 3qex_A DNA polymerase, GP43; d 1.0 1 1 727.6 42.6 457 939-1459 92-629 (903)
4 1qht_A Protein (DNA polymerase 1.0 1 1 722.2 42.0 472 820-1459 71-548 (775)
5 3k59_A POL II, DNA polymerase 1.0 1 1 709.6 39.4 474 825-1459 75-556 (786)
6 1s5j_A DNA polymerase I; repli 1.0 1 1 684.7 32.0 517 824-1459 88-628 (847)
7 1noy_A Protein (DNA polymerase 1.0 1 1 319.2 24.2 256 955-1255 104-382 (388)
8 2py5_A DNA polymerase; protein 1.0 1 1 242.9 12.1 373 958-1458 7-463 (575)
9 3iay_A DNA polymerase delta ca 1.0 1 1 200.9 11.0 134 18-167 28-214 (919)
10 2gv9_A DNA polymerase; polymer 1.0 1 1 147.7 11.8 118 39-162 132-279 (1193)
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=1.00 E-value=1 Score=883.22 Aligned_cols=542 Identities=25% Similarity=0.415 Sum_probs=455.8
Q ss_pred EC-CCCCEEEEECCCCCCCHHHHHHHHHHC-------------CCCCCCCCCCCCEEECCCCCCCCCEECCHHHHH---C
Q ss_conf 01-699457964189999705889774402-------------997654555554342289865562444125331---0
Q 000502 824 YL-NDGSCLYMLRPPFSPPSVDSVHKWLLH-------------DDKGASGDMDKASVEHSSLKGSDIRPVLEEMHQ---E 886 (1459)
Q Consensus 824 y~-~d~s~~~~lt~~~sp~s~~~v~~wL~~-------------~~~~~~v~~~~r~~~d~~~s~~~~~~~~~~~~~---~ 886 (1459)
|+ +....++++++ .+|-.+..+.+-|.. +-++ ||+...||++|+++.+++|+.+..+..+ .
T Consensus 139 y~~~~~~~~lKI~~-~~p~~v~~~r~~l~~g~~~~~~~~~~~~~~yE-dI~~~~RfliD~~I~g~~W~~i~~~~~~~~~~ 216 (919)
T 3iay_A 139 YSGDTKLPFWKIYV-TYPHMVNKLRTAFERGHLSFNSWFSNGTTTYD-NIAYTLRLMVDCGIVGMSWITLPKGKYSMIEP 216 (919)
T ss_dssp CSCSCCEEEEEEEE-SSTTHHHHHHHHHHHSCCCGGGSSTTCCCCBC-CCCHHHHHHHHHTCCTTCEEEECTTSEEECCG
T ss_pred CCCCCCEEEEEEEE-CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-CCCHHHHHEEECCCCCCEEEEEECCCCEECCC
T ss_conf 78898347999998-19999999999987066543433556742035-87767664044588653699995574011146
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEE
Q ss_conf 02468888788998543212356664587743234666444358999999997766785788777989882599999994
Q 000502 887 ADEMISTEPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQA 966 (1459)
Q Consensus 887 ~~~~s~~e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~k~~~~~~~~~~LtiLsIEIet 966 (1459)
..+.|+|++|++|+..+++.|. .+ ..| ...+++++|+|||||
T Consensus 217 ~~~~S~c~~Ev~v~~~~l~~~~------------------------~~--------~~~------~~~PplrilSfDIEt 258 (919)
T 3iay_A 217 NNRVSSCQLEVSINYRNLIAHP------------------------AE--------GDW------SHTAPLRIMSFDIEC 258 (919)
T ss_dssp GGCCBCCSEEEEEETTTCEEEC------------------------SS--------GGG------SCCCCCEEEEEEEEE
T ss_pred CCCCCCEEEEEEEECCCCCCCC------------------------CC--------CCC------CCCCCCEEEEEEEEE
T ss_conf 6785310389996133334365------------------------54--------445------679984699999998
Q ss_pred CCCCCCCCCCCCCCEEEEEEEEECCCCCE-EEEEEEEECCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCE
Q ss_conf 76999999988894899999950599760-89999992179764454579899289971899999999999985219998
Q 000502 967 ESRGDLRPDPRYDSINVVALAFENDSDHA-VEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDI 1045 (1459)
Q Consensus 967 ~srg~~fPDPe~DpI~~Isl~i~~d~d~~-~ev~vLi~~~~~~~~~~~~~i~g~~V~~f~sEkELL~aFidlIre~DPDI 1045 (1459)
.++++.||+|++|+|++|++.+...+... ....++... .+..+.++.|..|++|++||.+|+++|+++||||
T Consensus 259 ~~~~g~fP~~~~D~Ii~IS~~v~~~g~~~~~~r~~f~l~-------~~~~~~~~~V~~~~sE~eLL~~F~~~i~~~DPDI 331 (919)
T 3iay_A 259 AGRIGVFPEPEYDPVIQIANVVSIAGAKKPFIRNVFTLN-------TCSPITGSMIFSHATEEEMLSNWRNFIIKVDPDV 331 (919)
T ss_dssp CCCTTSCCCTTTCCEEEEEEEEEETTCSSCSEEEEEEES-------CCCCBTTBEEEEESSHHHHHHHHHHHHHHHCCSE
T ss_pred CCCCCCCCCCCCCCEEEEEEEEECCCCCCCCEEEEEEEC-------CCCCCCCCEEEECCCHHHHHHHHHHHHHHHCCCE
T ss_conf 778998989887828999999852798643225799725-------8777799869977999999999999988719999
Q ss_pred EEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf 98036777659999999999299976677889853334579963101233445566225677654333110012245445
Q 000502 1046 LMGWDIQGGSLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHA 1125 (1459)
Q Consensus 1046 ItGYNi~~FDLpYLieRAk~Lgidl~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~vk~~~~~d~~G~~~~ 1125 (1459)
|+|||+++||||||++||+.+|++.+..+||.+...... +...+ ..+.||.++.
T Consensus 332 IvGyNi~~FDlpyL~~Ra~~lgi~~~~~lGR~~~~~~~~-~~~~~-------------------------~~~~~g~~~~ 385 (919)
T 3iay_A 332 IIGYNTTNFDIPYLLNRAKALKVNDFPYFGRLKTVKQEI-KESVF-------------------------SSKAYGTRET 385 (919)
T ss_dssp EEESSTTTTHHHHHHHHHHHTTCTTCSCCSSBTTCCCCB-CCEEE-------------------------EETTTEEEEE
T ss_pred EEECCCCCCCHHHHHHHHHHCCCCCHHHHCCCCCCCCCC-CCCCC-------------------------CCCCCCCCCC
T ss_conf 996078667899999999980998256526456766553-34544-------------------------5331145555
Q ss_pred CCEEECCEEEEEHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 55022271885169998400289988989999998168989989350679984599257999999998987999999986
Q 000502 1126 SGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQ 1205 (1459)
Q Consensus 1126 s~i~I~GRivIDL~rv~Rke~kL~sYSLenVA~~vLgekK~dis~k~L~k~y~~g~~~~r~rii~YcikDa~Lvl~Ll~k 1205 (1459)
+.+.+.||+++|+|+++++++++.+|+|++||+++||++|++++++.|++||..++ ..+.+++.||++|+.++++|+.+
T Consensus 386 ~~~~i~GR~~lDl~~~~k~~~~l~sysL~~Va~~~Lg~~K~dv~~~~I~~l~~~~~-~~~~~L~~Y~~~Da~l~~~L~~k 464 (919)
T 3iay_A 386 KNVNIDGRLQLDLLQFIQREYKLRSYTLNAVSAHFLGEQKEDVHYSIISDLQNGDS-ETRRRLAVYCLKDAYLPLRLMEK 464 (919)
T ss_dssp CCBCCTTCEEEEHHHHHHHHCCCSCCCHHHHHHHHHCCC------CCHHHHHTSCH-HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CEEEECCEEEEEHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCH-HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 23687684998819999753687889999999996566888899899999985090-55999999999999999999999
Q ss_pred CCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEE
Q ss_conf 03302589999984756210023774235689988873217978638999855566532469845505677445884795
Q 000502 1206 LDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVL 1285 (1459)
Q Consensus 1206 L~iI~~t~ElAri~GIp~~sVlsRGSq~rVESlLLR~ak~enfIlPsPsk~qv~~q~a~E~GglVlEP~sGlY~nPVvVL 1285 (1459)
++++.++.|+|+++|+++.++++||+|++||++|+|+|+++||++|++... ..+.+++ ||+||||++|+|++||++|
T Consensus 465 l~~l~~~~elArl~Gi~~~~vl~rG~qi~ves~Llr~a~~~~~ilP~~~~~--~~~~~y~-Gg~V~eP~~G~y~~pV~~l 541 (919)
T 3iay_A 465 LMALVNYTEMARVTGVPFSYLLARGQQIKVVSQLFRKCLEIDTVIPNMQSQ--ASDDQYE-GATVIEPIRGYYDVPIATL 541 (919)
T ss_dssp TTHHHHHHHHHHHHCCCHHHHHHSCHHHHHHHHHHHHHHHTTEECBCCCCC--CCSSCCC-CCCBCCCCCEEECSCEEEE
T ss_pred HHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHHHCCEECCCCCCC--CCCCCCC-CCEEECCCCCCEECCEEEE
T ss_conf 733677999988709987996406663999999999874077457786444--6655677-8788547887365658998
Q ss_pred ECCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHHH
Q ss_conf 21440066886327540233466678765558975568892000156765213899810038987677749999999999
Q 000502 1286 DFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILST 1365 (1459)
Q Consensus 1286 DFqSLYPSIIIAyNICpSTivg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPnG~~Fvk~~vrkGILP~lL~eLL~~ 1365 (1459)
||+||||||||||||||||+++.... +.++ .. ..+++.++|+|.+|+++++++||||++|++||+.
T Consensus 542 DF~SLYPSIi~~~Nlc~~Tl~~~~~~---~~~~-----~~------~~~~~~~~p~g~~f~~~~~~~gilp~~l~~ll~~ 607 (919)
T 3iay_A 542 DFNSLYPSIMMAHNLCYTTLCNKATV---ERLN-----LK------IDEDYVITPNGDYFVTTKRRRGILPIILDELISA 607 (919)
T ss_dssp EETTHHHHHHHHTTCSGGGEECHHHH---HHTT-----CC------BTTTEEECTTSCEEECTTTCCCHHHHHHHHHHHH
T ss_pred EECCCCHHHHHHCCCCCCCCCCCCHH---HHCC-----CC------CCCCEEECCCCCEEECCCCCCCCHHHHHHHHHHH
T ss_conf 73320347898607485421364106---4337-----99------8766465799857843677787239999999999
Q ss_pred HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC-----
Q ss_conf 999999998409816899999999997710103330243356666767897779799999899999999998623-----
Q 000502 1366 RIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNEN----- 1440 (1459)
Q Consensus 1366 R~~vKk~MKk~~~~d~~l~~iLD~rQlALKIlANS~YGytGa~fSGRmpc~eIAdSIT~~GRe~Le~ai~~Ie~~----- 1440 (1459)
|+++|+.||+.. ++.++++||.+|+|+|++|||+|||||+++ |||||.++|++||++||++|++++++|++.
T Consensus 608 R~~~K~~mk~~~--d~~~~~~ld~~Q~AlKi~~NS~YG~~G~~~-~r~~~~~iA~siT~~GR~~l~~t~~~ie~~~~~~~ 684 (919)
T 3iay_A 608 RKRAKKDLRDEK--DPFKRDVLNGRQLALKISANSVYGFTGATV-GKLPCLAISSSVTAYGRTMILKTKTAVQEKYCIKN 684 (919)
T ss_dssp HHHHHHHHHTCC--CHHHHHHHHHHHHHHHHHHHHHHHHHTCSS-SSCCCHHHHHHHHHHHHHHHHHHHHHHHHHSSGGG
T ss_pred HHHHHHHHHHCC--CHHHHHHHHHHHHHHCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 999999875367--868999889999863410134344135426-75679889999999989999999999998631013
Q ss_pred -CCCCCEEEEECCCEEEEEC
Q ss_conf -8898199996264347999
Q 000502 1441 -EKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1441 -~~~GakVIYGDTDSiFV~l 1459 (1459)
+.||++||||||||+||++
T Consensus 685 g~~~~~~ViYGDTDSvfv~~ 704 (919)
T 3iay_A 685 GYKHDAVVVYGDTDSVMVKF 704 (919)
T ss_dssp TCSSCCEEEECBSSEEEEEC
T ss_pred CCCCCEEEEEECCCEEEEEC
T ss_conf 78788499998377069971
No 2
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B*
Probab=1.00 E-value=1 Score=800.67 Aligned_cols=544 Identities=22% Similarity=0.321 Sum_probs=425.0
Q ss_pred ECCCCCEEEEECCCCCCCHHHHHHHHHHC--CCCCCCCCCCCCEEECC-CCCCCCCEECCHH------HHH-CCCCCCCC
Q ss_conf 01699457964189999705889774402--99765455555434228-9865562444125------331-00246888
Q 000502 824 YLNDGSCLYMLRPPFSPPSVDSVHKWLLH--DDKGASGDMDKASVEHS-SLKGSDIRPVLEE------MHQ-EADEMIST 893 (1459)
Q Consensus 824 y~~d~s~~~~lt~~~sp~s~~~v~~wL~~--~~~~~~v~~~~r~~~d~-~~s~~~~~~~~~~------~~~-~~~~~s~~ 893 (1459)
|++....+++++. .+|-.+..+.+.+.. +-++.+|+...||++|+ ++.+++||.+..+ ..+ ...+.|+|
T Consensus 219 ~~~~~~~~~ki~~-~~p~~v~~lr~~~~~~~~~~E~dI~~~~RfliD~~~i~~~~W~~i~~~~~g~~~~~r~~~~~~s~c 297 (1193)
T 2gv9_A 219 YETRPALFYRVYV-RSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNPGFVTFGWYRLKPGRNNTLAQPRAPMAFGTSS 297 (1193)
T ss_dssp SSCCCEEEEEEEE-SCHHHHHHHHHHTCSSSCEESTTCCHHHHHHHHSTTCCSSEEEEECCBTTTBCCEECCGGGCSBSC
T ss_pred CCCCCCEEEEEEC-CCHHHHHHHHHHCCCCCEEEECCCCHHHEEEEECCCCCCCCEEEEECCCCCCEEEECCCCCCCCCC
T ss_conf 6777642899960-189999999860457743775367525157677489887533997225666401220432457777
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCC---
Q ss_conf 87889985432123566645877432346664443589999999977667857887779898825999999947699---
Q 000502 894 EPTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRG--- 970 (1459)
Q Consensus 894 e~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~k~~~~~~~~~~LtiLsIEIet~srg--- 970 (1459)
++|++|...+++.+. .+ ...+++++++|||||.+.|
T Consensus 298 ~~E~~~~~~~~~~~~------------------------~~-----------------~~~P~lrvlsfDIE~~~~g~~~ 336 (1193)
T 2gv9_A 298 DVEFNCTADNLAIEG------------------------GM-----------------SDLPAYKLMCFDIECKAGGEDE 336 (1193)
T ss_dssp SEEEEEEGGGEEECC------------------------SC-----------------CCCCCCEEEEEEEEEECCSSCT
T ss_pred CEEEEEECCCCEECC------------------------CC-----------------CCCCCCEEEEEEEEECCCCCCC
T ss_conf 558999746536746------------------------65-----------------7899855999998973567777
Q ss_pred CCCCCCC--CCCEEEEEEEEECCCCCEEEEE-EEEECCCC-C-C-CC--CCCCCCCCEEEEECCHHHHHHHHHHHHHHCC
Q ss_conf 9999988--8948999999505997608999-99921797-6-4-45--4579899289971899999999999985219
Q 000502 971 DLRPDPR--YDSINVVALAFENDSDHAVEIY-VLLYCKSE-S-H-QR--SLVGIPDCKVFVCSKEIHLFSHFIKILCSFD 1042 (1459)
Q Consensus 971 ~~fPDPe--~DpI~~Isl~i~~d~d~~~ev~-vLi~~~~~-~-~-~~--~~~~i~g~~V~~f~sEkELL~aFidlIre~D 1042 (1459)
..||+|+ .|+|++|++.++..+....... ++..+.-. + . .. ...+..+..|..|++|++||.+|+++|+++|
T Consensus 337 ~~FP~a~~~~D~Ii~IS~~~~~~~~~~~~~~~v~~l~~~~~~~~f~~~~k~~~~~~~~V~~~~sE~eLL~~F~~~I~~~D 416 (1193)
T 2gv9_A 337 LAFPVAGHPEDLVIQISCLLYDLSTTALEHVLLFSLGSCDLPESHLNELAARGLPTPVVLEFDSEFEMLLAFMTLVKQYG 416 (1193)
T ss_dssp TSCCCTTSTTSEEEEEEEEEEETTTCCEEEEEEEEESCCCCCHHHHHHHHHTTCCCCEEEEESSHHHHHHHHHHHHHHHC
T ss_pred CCCCCCCCCCCCEEEEEEEEEECCCCCCCEEEEEECCCCCCCCHHHHHCCCCCCCCCEEEECCCHHHHHHHHHHHHHHCC
T ss_conf 78998655678558898899742677764699997798678503332011136788559965999999999999988529
Q ss_pred CCEEEECCCCCCCHHHHHHHH-HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf 998980367776599999999-9929997667788985333457996310123344556622567765433311001224
Q 000502 1043 PDILMGWDIQGGSLGFLAERA-AHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWG 1121 (1459)
Q Consensus 1043 PDIItGYNi~~FDLpYLieRA-k~Lgidl~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~vk~~~~~d~~G 1121 (1459)
||||+|||+++||||||++|+ ..+++++. .+||.+......... ...++
T Consensus 417 PDIIvGyNi~~FDlpyL~~Ra~~~~gl~l~-~~GRl~r~~~~k~~~-----------------------------~~~~~ 466 (1193)
T 2gv9_A 417 PEFVTGYNIINFDWPFLLAKLTDIYKVPLD-GYGRMNGRGVFRVWD-----------------------------IGQSH 466 (1193)
T ss_dssp CSEEEESSTTTTHHHHHHHHHHHTTCCCCT-TTSSBSSSCCEEECC----------------------------------
T ss_pred CCEEEECCCCCCCHHHHHHHHHHHCCCCHH-HHCCCCCCCCCEEEC-----------------------------CCCCC
T ss_conf 989997488676289999999997398857-726335677510442-----------------------------66655
Q ss_pred CCCCCCEEECCEEEEEHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf 54455502227188516999840028998898999999816898998935067998459925799999999898799999
Q 000502 1122 RTHASGLHVGGRIVLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLE 1201 (1459)
Q Consensus 1122 ~~~~s~i~I~GRivIDL~rv~Rke~kL~sYSLenVA~~vLgekK~dis~k~L~k~y~~g~~~~r~rii~YcikDa~Lvl~ 1201 (1459)
+.+.+.+.+.||+++|+|++++++.++.+|+|++||+++||++|+++++++|.+||.+++. .+.+++.||++|+.++++
T Consensus 467 f~~~~~~~i~GRv~lDl~~~~~~~~kl~sYsL~~Va~~~Lg~~K~dv~~~eI~~~~~~~~~-~r~~L~~Ycl~Da~lt~~ 545 (1193)
T 2gv9_A 467 FQKRSKIKVNGMVNIDMYGIITDKIKLSSYKLNAVAEAVLKDKKKDLSYRDIPAYYATGPA-QRGVIGEYCIQDSLLVGQ 545 (1193)
T ss_dssp -----CEEETTBEEEEHHHHHTTTCCCSCCCHHHHHHHTSCCCCCCCCTTTHHHHHHHCHH-HHHHHHHHHHHHHHHHHH
T ss_pred CCCCCEEEECCEEEEHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCCH-HHHHHHHHHHHHHHHHHH
T ss_conf 4666338871757626999999873568889899999983668788999999999972974-689999997899999999
Q ss_pred HHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECCCCCCC-----------------------
Q ss_conf 998603302589999984756210023774235689988873217978638999855-----------------------
Q 000502 1202 IMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQV----------------------- 1258 (1459)
Q Consensus 1202 Ll~kL~iI~~t~ElAri~GIp~~sVlsRGSq~rVESlLLR~ak~enfIlPsPsk~qv----------------------- 1258 (1459)
|+.++..+..++++|+++|+++.+|+++|+|.++|++|+++++++||++|++.....
T Consensus 546 L~~kl~~~lel~elarl~gi~~~~vl~~G~~irves~Ll~~a~~~~~ilP~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 625 (1193)
T 2gv9_A 546 LFFKFLPHLELSAVARLAGINITRTIYDGQQIRVFTCLLRLADQKGFILPDTQGRFRGAGGEAPKRPAAAREDEERPEEE 625 (1193)
T ss_dssp HHHHHCHHHHHHHHHHHHTSCGGGTTSSCSTHHHHHHHHHHHHHHTEECBCCC---------------------------
T ss_pred HHHHHHHHHHHHHHHHHCCCCHHHHHCCCCHHHHHHHHHHHHHHCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 99999999989999998198889974076389999999999997998078766432223333334432234444332224
Q ss_pred -----------------------CCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCHHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf -----------------------566532469845505677445884795214400668863275402334666787655
Q 000502 1259 -----------------------ASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKEN 1315 (1459)
Q Consensus 1259 -----------------------~~q~a~E~GglVlEP~sGlY~nPVvVLDFqSLYPSIIIAyNICpSTivg~~~~~~~n 1315 (1459)
+....+ .||+||||++|||++||++|||+||||||||+|||||+|+++......
T Consensus 626 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Y-~Gg~VleP~~Gly~~pV~vLDF~SLYPSII~a~Nlc~sTl~~~~~~~~-- 702 (1193)
T 2gv9_A 626 GEDEDEREEGGGEREPEGARETAGRHVGY-QGAKVLDPTSGFHVNPVVVFDFASLYPSIIQAHNLCFSTLSLRADAVA-- 702 (1193)
T ss_dssp ----------------------------------CCCCCCEEECSCEEEEEEETHHHHHHHHTTCCTTTEESCSTTST--
T ss_pred CCCCCCCCCCCCCCCCCHHHHCCCCCCCC-CCCEEEECCCCEEECCEEEEECCCCCHHHHHHHCCCCCEECCCCHHHC--
T ss_conf 64310113444445620121001323455-787786057880667589886123141899973578521335710100--
Q ss_pred CCCCCCCCCCCHHHCCCCCCCCCCCC--CCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf 58975568892000156765213899--8100389876777499999999999999999984098168999999999977
Q 000502 1316 TLGVSSFRPDLHVLRDLKDELLIPPN--GVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPSQQILHRIFNARQLA 1393 (1459)
Q Consensus 1316 ~~Gv~~~~~d~~~l~~Lkd~i~isPn--G~~Fvk~~vrkGILP~lL~eLL~~R~~vKk~MKk~~~~d~~l~~iLD~rQlA 1393 (1459)
+ +..+ .+...+.++ +.+|+++++++|+||++|++|+++|+++|+.||+++ +.++.+||.+|+|
T Consensus 703 --~---l~~~-------~dy~~~~~~~~~~~fvk~~~~~gilp~lL~~ll~~Rk~~K~~mk~~~---~~~~~llD~~QlA 767 (1193)
T 2gv9_A 703 --H---LEAG-------KDYLEIEVGGRRLFFVKAHVRESLLSILLRDWLAMRKQIRSRIPQSS---PEEAVLLDKQQAA 767 (1193)
T ss_dssp --T---CCTT-------TTEEEEECSSSEEEEECTTTSCCHHHHHHHHHHHHHHHHHHHGGGSC---HHHHHHHHHHHHH
T ss_pred --C---CCCC-------CCEEEECCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCC---HHHHHHHHHHHHH
T ss_conf --4---7875-------55367557998213115766564689999999999999997662389---8899999999999
Q ss_pred HHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHC--------------------CCCCCEEEEECCC
Q ss_conf 10103330243356666767897779799999899999999998623--------------------8898199996264
Q 000502 1394 LKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNEN--------------------EKWKAKVIYGDTD 1453 (1459)
Q Consensus 1394 LKIlANS~YGytGa~fSGRmpc~eIAdSIT~~GRe~Le~ai~~Ie~~--------------------~~~GakVIYGDTD 1453 (1459)
+|++|||+|||+|+. +|||||.++|++||++||++|++|+++|++. ..+|++|||||||
T Consensus 768 lKi~aNS~YG~~G~~-~grlpc~~iA~sVT~~GR~~L~~tk~~IE~~~~~~~~l~~~f~~~~~~~~~~~~g~~VIYGDTD 846 (1193)
T 2gv9_A 768 IKVVCNSVYGFTGVQ-HGLLPCLHVAATVTTIGREMLLATREYVHARWAAFEQLLADFPEAADMRAPGPYSMRIIYGDTD 846 (1193)
T ss_dssp HHHHHHHHHHHHHCT-TSSSCCHHHHHHHHHHHHHHHHHHHHHHHHHHSSHHHHHHHCGGGGGGBCSSCCEEEEEEECSS
T ss_pred HHHHHCCEECCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCCCCCCCCCCCCCEEECCCC
T ss_conf 887542211336440-5435687889999999899999999999865100234444212211234552311110340677
Q ss_pred EEEEEC
Q ss_conf 347999
Q 000502 1454 RYTVCI 1459 (1459)
Q Consensus 1454 SiFV~l 1459 (1459)
|+||++
T Consensus 847 SvfV~~ 852 (1193)
T 2gv9_A 847 SIFVLC 852 (1193)
T ss_dssp EEEEEE
T ss_pred CEEEEC
T ss_conf 327864
No 3
>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=1.00 E-value=1 Score=727.59 Aligned_cols=457 Identities=20% Similarity=0.227 Sum_probs=359.7
Q ss_pred CCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCC--CCCEEEEEEEEECCCCCEEEEEEEEECC----CCCCC--
Q ss_conf 776678578877798988259999999476999999988--8948999999505997608999999217----97644--
Q 000502 939 PLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPR--YDSINVVALAFENDSDHAVEIYVLLYCK----SESHQ-- 1010 (1459)
Q Consensus 939 p~~~~~~k~~~~~~~~~~LtiLsIEIet~srg~~fPDPe--~DpI~~Isl~i~~d~d~~~ev~vLi~~~----~~~~~-- 1010 (1459)
++++. |+++...+. +.++++.+|||+..++ .||||+ .+||++|+++...+ ..+.++.++... ..+..
T Consensus 92 y~~~~-~~~~i~~~~-~~ir~~~~DIEv~~~~-~fPd~~~~~~~Ii~It~~d~~~--~~~~~~~l~~~~~~~~~~~~~~~ 166 (903)
T 3qex_A 92 YLSDT-YNYEIKYDH-TKIRVANFDIEVTSPD-GFPEPSQAKHPIDAITHYDSID--DRFYVFDLLNSPYGNVEEWSIEI 166 (903)
T ss_dssp HHHHH-CCSCCCCCG-GGSCEEEEEEECCCTT-SSCCTTTCCSCCCEEEEEETTT--TEEEEEEECEETTEECCCCCHHH
T ss_pred HHHHH-CCCCCCCCC-CCCCEEEEEEEECCCC-CCCCCCCCCCCEEEEEEEECCC--CEEEEEEEECCCCCCCCCCCCCC
T ss_conf 99987-544533576-6462899967867899-9988434777779999996799--97999986225445655544210
Q ss_pred ------CCCC-----CCCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHH-HCCCCC---CCCC
Q ss_conf ------5457-----989928997189999999999998521999898036777659999999999-299976---6778
Q 000502 1011 ------RSLV-----GIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAH-LGIGLL---NDIS 1075 (1459)
Q Consensus 1011 ------~~~~-----~i~g~~V~~f~sEkELL~aFidlIre~DPDIItGYNi~~FDLpYLieRAk~-Lgidl~---~~LS 1075 (1459)
+... .++++.|..|++|++||.+|+++|+++|||||+|||+++||||||++||.. +|++.. ..+|
T Consensus 167 ~~~~~~~~~~~~~~~~~~~v~v~~f~sE~eLL~~F~~~I~~~DPDIItGyN~~~FDlPYL~~RA~~l~gi~~~~~ls~~g 246 (903)
T 3qex_A 167 AAKLQEQGGDEVPSEIIDKIIYMPFDNEKELLMEYLNFWQQKTPVILTGWNVESFAIPYVYNRIKNIFGESTAKRLSPHR 246 (903)
T ss_dssp HHSCGGGTCCCCCHHHHTTEEEEEESSHHHHHHHHHHHHHHTCCSEEECSSTTTTHHHHHHHHHHHHHCHHHHGGGSTTS
T ss_pred CCCCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf 01224566666654467971899749999999999999998399989962775577999999999973985000001026
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEECCEEEEEHHHHHHH--CCCCCCCCH
Q ss_conf 898533345799631012334455662256776543331100122454455502227188516999840--028998898
Q 000502 1076 RTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRG--EVKLNMYTV 1153 (1459)
Q Consensus 1076 R~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~vk~~~~~d~~G~~~~s~i~I~GRivIDL~rv~Rk--e~kL~sYSL 1153 (1459)
|.+... ..+.||+++ .+.+.||+++|+|+++|+ +.++.+|+|
T Consensus 247 R~~~~~----------------------------------~~~~~G~~~--~~~i~GRv~lDl~~~~k~~~~~~l~SYsL 290 (903)
T 3qex_A 247 KTRVKV----------------------------------IENMYGSRE--IITLFGISVLDYIDLYKKFSFTNQPSYSL 290 (903)
T ss_dssp CEEEEE----------------------------------EEETTEEEE--EEEETTCEECCHHHHHHHHSCCCCSCCCH
T ss_pred CCCCCC----------------------------------HHHHCCCCE--EEEEECEEEEEHHHHHHHHCCCCCCCCCH
T ss_conf 544432----------------------------------033228731--69871768753999998737167677899
Q ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHH
Q ss_conf 99999981689899893506799845992579999999989879999999860330258999998475621002377423
Q 000502 1154 EAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQY 1233 (1459)
Q Consensus 1154 enVA~~vLgekK~dis~k~L~k~y~~g~~~~r~rii~YcikDa~Lvl~Ll~kL~iI~~t~ElAri~GIp~~sVlsRGSq~ 1233 (1459)
++||+++||++|++++ ..|.+||.. .+.+++.||++||.++++|+.++++++++.|+||++|+++.+|++ |.
T Consensus 291 d~VA~~lLg~~K~d~~-~~I~~~~~~----d~~~L~~Ycl~Da~Lt~~L~~Kl~li~~~~elArl~Gi~~~~vls---q~ 362 (903)
T 3qex_A 291 DYISEFELNVGKLKYD-GPISKLRES----NHQRYISYNIIAVYRVLQIDAKRQFINLSLDMGYYAKIQIQSVFS---PI 362 (903)
T ss_dssp HHHHHHHHCCCCCCCS-SCGGGHHHH----HHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTSCGGGGGC---HH
T ss_pred HHHHHHHCCCCCCCCH-HHHHHHHHC----CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHCC---HH
T ss_conf 9999997399966527-799999953----989999999988899999999975179999999984988799334---17
Q ss_pred HH-HHHHHHHHHHCCEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCHHHHHHCCCCCCCCCCCCCCC
Q ss_conf 56-89988873217978638999855566532469845505677445884795214400668863275402334666787
Q 000502 1234 RV-ESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPS 1312 (1459)
Q Consensus 1234 rV-ESlLLR~ak~enfIlPsPsk~qv~~q~a~E~GglVlEP~sGlY~nPVvVLDFqSLYPSIIIAyNICpSTivg~~~~~ 1312 (1459)
++ |++|+|+++++||++|++. +... ..++ ||+|++|++|+|+ +|++|||+||||||||+|||||+|+++.....
T Consensus 363 ~v~e~LLlr~a~~~~~iiP~~~--~~~~-~~y~-Gg~V~~p~~G~y~-~v~~lDf~SLYPsIi~~~ni~~~T~~~~~~~~ 437 (903)
T 3qex_A 363 KTWDAIIFNSLKEQNKVIPQGR--SHPV-QPYP-GAFVKEPIPNRYK-YVMSFDLTSLYPSIIRQVNISPETIAGTFKVA 437 (903)
T ss_dssp HHHHHHHHHHHHTTTEECCCCC--CCCC-CCCC-CCCBCCCCCEECS-SEEEEEETTHHHHHHHHHTCCGGGEEEECCCC
T ss_pred HHHHHHHHHHHHHCCEECCCCC--CCCC-CCCC-CCEEECCCCCCEE-EEEEEEHHHHCHHHHHHHCCCHHHCCCCCCCC
T ss_conf 8899999999987898266775--5556-7888-8778556678668-99997623435489998585943304654432
Q ss_pred CCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-------------
Q ss_conf 6555897556889200015676521389981003898767774999999999999999999840981-------------
Q 000502 1313 KENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKLAPS------------- 1379 (1459)
Q Consensus 1313 ~~n~~Gv~~~~~d~~~l~~Lkd~i~isPnG~~Fvk~~vrkGILP~lL~eLL~~R~~vKk~MKk~~~~------------- 1379 (1459)
+.. .+ ++ +......+++.++|||++|++ .++||||+||++||++|+++|+.||+.+..
T Consensus 438 ~~~-----~~-i~-~~~~~p~~~~~~~p~g~~F~k--~~~GiLP~iL~~Ll~~R~~~K~~mk~~~~~~~~~k~~L~~~~~ 508 (903)
T 3qex_A 438 PLH-----DY-IN-AVAERPSDVYSCSPNGMMYYK--DRDGVVPTEITKVFNQRKEHKGYMLAAQRNGEIIKEALHNPNL 508 (903)
T ss_dssp CHH-----HH-HT-TCSCCSCSSSEECTTSEEECC--SSCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSCCS
T ss_pred CHH-----CC-CC-CCCCCCCCCEEECCCCCEEEC--CCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCCCCC
T ss_conf 100-----00-11-245798775466799856735--7882559999999999999999976453553012210023344
Q ss_pred ---HH---------------------------------HHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHH
Q ss_conf ---68---------------------------------999999999977101033302433566667678977797999
Q 000502 1380 ---QQ---------------------------------ILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIV 1423 (1459)
Q Consensus 1380 ---d~---------------------------------~l~~iLD~rQlALKIlANS~YGytGa~fSGRmpc~eIAdSIT 1423 (1459)
|+ .++++||.+|+|+|++|||+|||||+.+ |||||.++|++||
T Consensus 509 ~~~dp~~~~~~~~~~~~~~~~~~~~~~~~L~~~l~~~~~~~~~~d~rQ~AlKi~~NS~YG~~G~~~-~r~~~~~~A~sIT 587 (903)
T 3qex_A 509 SVDEPLDVDYRFDFSDEIKEKIKKLSAKSLNEMLFRAQRTEVAGMTAQINRKALINGLAGALGNVW-FRYYDLRNATAIT 587 (903)
T ss_dssp SCCCCCCCCTTSCCCHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSTT-STTCCHHHHHHHH
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHH
T ss_conf 556731000012332345444310115666555433467888878999878888887777656856-6668999999999
Q ss_pred HHHHHHHHHHHHHHHHC------CCCCCEEEEECCCEEEEEC
Q ss_conf 99899999999998623------8898199996264347999
Q 000502 1424 QCGRSTLEKAISFVNEN------EKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1424 ~~GRe~Le~ai~~Ie~~------~~~GakVIYGDTDSiFV~l 1459 (1459)
++||++|+.+++.+++. ..++++||||||||+||++
T Consensus 588 ~~GR~~i~~~~~~v~~~~~~~~~~~~~~~VIYGDTDSvfV~~ 629 (903)
T 3qex_A 588 TFGQMALQWIERKVNEYLNEVCGTEGEAFVLYGDTDSIYVSA 629 (903)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTCSSCCCEEEEETTEEEEEC
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEECCCEEEEE
T ss_conf 971599999999999998753177797189999688069984
No 4
>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=1.00 E-value=1 Score=722.19 Aligned_cols=472 Identities=25% Similarity=0.371 Sum_probs=390.7
Q ss_pred CCCEECCCCCEEEEECCCCCCCHHHHHHHHHHCCC-----CCCCCCCCCCEEECCCCCCCCCEECCHHHHHCCCCCCCCC
Q ss_conf 77100169945796418999970588977440299-----7654555554342289865562444125331002468888
Q 000502 820 VPTLYLNDGSCLYMLRPPFSPPSVDSVHKWLLHDD-----KGASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTE 894 (1459)
Q Consensus 820 ~p~~y~~d~s~~~~lt~~~sp~s~~~v~~wL~~~~-----~~~~v~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e 894 (1459)
+..++......+++++. .+|..+..+.++|...+ ++.+++.+.||++|+++..+.|
T Consensus 71 v~k~~~g~~~~~~ki~~-~~~~~~~~~r~~l~~~~~~~~~~E~dI~~~~r~lid~~i~~~~~------------------ 131 (775)
T 1qht_A 71 VQKKFLGRPIEVWKLYF-NHPQDVPAIRDRIRAHPAVVDIYEYDIPFAKRYLIDKGLIPMEG------------------ 131 (775)
T ss_dssp EEEEETTEEEEEEEEEC-SCTTHHHHHHHHHHTSTTEEEEESCSSCHHHHHHHHTTCCTTCS------------------
T ss_pred EEEEECCCCCEEEEEEE-CCHHHHHHHHHHHHHCCCCEEEEECCCCHHHEEEEECCCCCCCC------------------
T ss_conf 97556488835999998-69999999999997489840157436774751457758455688------------------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCC
Q ss_conf 78899854321235666458774323466644435899999999776678578877798988259999999476999999
Q 000502 895 PTPDLNGVTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRP 974 (1459)
Q Consensus 895 ~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~k~~~~~~~~~~LtiLsIEIet~srg~~fP 974 (1459)
.+++++++|||||.+. .+|
T Consensus 132 -----------------------------------------------------------~~~l~ilsfDIEt~~~--~~p 150 (775)
T 1qht_A 132 -----------------------------------------------------------DEELTMLAFAIATLYH--EGE 150 (775)
T ss_dssp -----------------------------------------------------------CCCCCEEEEEEEECCC--TTC
T ss_pred -----------------------------------------------------------CCCCEEEEEEEEECCC--CCC
T ss_conf -----------------------------------------------------------8886799999998679--999
Q ss_pred CCCCCCEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf 98889489999995059976089999992179764454579899289971899999999999985219998980367776
Q 000502 975 DPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGG 1054 (1459)
Q Consensus 975 DPe~DpI~~Isl~i~~d~d~~~ev~vLi~~~~~~~~~~~~~i~g~~V~~f~sEkELL~aFidlIre~DPDIItGYNi~~F 1054 (1459)
+|..|+|++|+++..+.. .+ +.+ ..+....|..|++|++||.+|+++|+++|||||+|||+++|
T Consensus 151 ~~~~d~Ii~Is~~~~~~~----~~--~t~----------~~i~~~~v~~~~~E~~LL~~f~~~i~~~dPDiivGyN~~~F 214 (775)
T 1qht_A 151 EFGTGPILMISYADGSEA----RV--ITW----------KKIDLPYVDVVSTEKEMIKRFLRVVREKDPDVLITYNGDNF 214 (775)
T ss_dssp CTTCSCEEEEEEECSSCE----EE--EES----------SCCCCSSEEECSCHHHHHHHHHHHHHHHCCSEEEESSTTTT
T ss_pred CCCCCCEEEEEEEECCCC----EE--EEE----------CCCCCCCEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf 877781899999846997----46--751----------25566653875999999999999998639999999678876
Q ss_pred CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEECCEE
Q ss_conf 59999999999299976677889853334579963101233445566225677654333110012245445550222718
Q 000502 1055 SLGFLAERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRI 1134 (1459)
Q Consensus 1055 DLpYLieRAk~Lgidl~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~vk~~~~~d~~G~~~~s~i~I~GRi 1134 (1459)
|||||.+||..+|+++ .+||.+..... ..+|. ...+.+.||+
T Consensus 215 DlpyL~~Ra~~~gi~~--~lgR~~~~~~~----------------------------------~~~g~--~~~~~i~Gr~ 256 (775)
T 1qht_A 215 DFAYLKKRCEELGIKF--TLGRDGSEPKI----------------------------------QRMGD--RFAVEVKGRI 256 (775)
T ss_dssp HHHHHHHHHHHTTCCC--CCSTTSCCCEE----------------------------------EEETT--EEEEECTTSE
T ss_pred CHHHHHHHHHHCCCCC--CCCCCCCCCCE----------------------------------EECCC--EEEEEECCEE
T ss_conf 3899999999809993--01567776734----------------------------------10584--3567766749
Q ss_pred EEEHHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf 85169998400289988989999998168989989350679984599257999999998987999999986033025899
Q 000502 1135 VLNVWRLMRGEVKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSE 1214 (1459)
Q Consensus 1135 vIDL~rv~Rke~kL~sYSLenVA~~vLgekK~dis~k~L~k~y~~g~~~~r~rii~YcikDa~Lvl~Ll~kL~iI~~t~E 1214 (1459)
++|+|++++++.++++|+|++||+++||.+|+++++.++.+||.+++ .+.++++||++|+.++++|+.++ ++.+.+
T Consensus 257 ~lDl~~~~k~~~~l~sysL~~Va~~~Lg~~K~dv~~~~i~~~~~~~~--~l~~l~~Y~~~Da~lt~~L~~~~--~~~~~~ 332 (775)
T 1qht_A 257 HFDLYPVIRRTINLPTYTLEAVYEAVFGKPKEKVYAEEIAQAWESGE--GLERVARYSMEDAKVTYELGREF--FPMEAQ 332 (775)
T ss_dssp EEEHHHHHHHHSCCSCCCHHHHHHHHHCCCCCCCCHHHHHHHHTTTC--SHHHHHHHHHHHHHHHHHHHHHH--HHHHHH
T ss_pred EEEHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCC--CHHHHHHHHHHHHHHHHHHHHHH--HHHHHH
T ss_conf 98789999875576768899999998399977659999999986593--18899999999999999998743--189999
Q ss_pred HHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECC-CCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCHH
Q ss_conf 999847562100237742356899888732179786389-9985556653246984550567744588479521440066
Q 000502 1215 LARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISP-GNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPS 1293 (1459)
Q Consensus 1215 lAri~GIp~~sVlsRGSq~rVESlLLR~ak~enfIlPsP-sk~qv~~q~a~E~GglVlEP~sGlY~nPVvVLDFqSLYPS 1293 (1459)
+|+++|++++++..+|++.+||++|+++++++||++|+. +..+...+...+.||+|+||++|+|++ |++|||+|||||
T Consensus 333 la~i~g~~~~~v~r~~~~~~ve~~Ll~~~~~~~~i~P~~~~~~~~~~~~~~y~Gg~V~eP~~G~y~~-v~~lDF~SLYPS 411 (775)
T 1qht_A 333 LSRLIGQSLWDVSRSSTGNLVEWFLLRKAYKRNELAPNKPDERELARRRGGYAGGYVKEPERGLWDN-IVYLDFRSLYPS 411 (775)
T ss_dssp HHHHHTSCHHHHTTCCHHHHHHHHHHHHHHHTTBCCCCCCCHHHHHHTTTCCCCCCBCCCCCSCEEE-EEEEECSSHHHH
T ss_pred HHHHHCCCCHHCEECCCHHHHHHHHHHHHHHCCEECCCCCCHHHHHCCCCCCCCCEEECCCCCCCCC-EEECCHHCCCHH
T ss_conf 9998689804404324289999997688975988377787434430444456785575166784334-254122013178
Q ss_pred HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf 88632754023346667876555897556889200015676521389981003898767774999999999999999999
Q 000502 1294 MMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAI 1373 (1459)
Q Consensus 1294 IIIAyNICpSTivg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPnG~~Fvk~~vrkGILP~lL~eLL~~R~~vKk~M 1373 (1459)
||++|||||+|+++.... +.......|..|++ .++|++|++|++|+++|+++|+.|
T Consensus 412 Ii~~~nl~~~t~~~~~~~----------------------~~~~~~~~~~~f~~--~~~g~lp~~l~~l~~~R~~~K~~~ 467 (775)
T 1qht_A 412 IIITHNVSPDTLNREGCK----------------------EYDVAPEVGHKFCK--DFPGFIPSLLGDLLEERQKIKRKM 467 (775)
T ss_dssp HHHHTTCSTTTBTCTTCS----------------------CEEECTTTCCEEEC--SSCCHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHCCCCCCCCCCCCCC----------------------CCCCCCCCCCCCCC--CCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf 998608995103456521----------------------25568866741225--568876499999999999999986
Q ss_pred HHHCCCHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCC
Q ss_conf 84098168999999999977101033302433566667678977797999998999999999986238898199996264
Q 000502 1374 KKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTD 1453 (1459)
Q Consensus 1374 Kk~~~~d~~l~~iLD~rQlALKIlANS~YGytGa~fSGRmpc~eIAdSIT~~GRe~Le~ai~~Ie~~~~~GakVIYGDTD 1453 (1459)
|+.. ++.++++||.+|+|+|++|||+|||+|+. +|||||.++|++||++||++|+.++++|++. +|++|||||||
T Consensus 468 k~~~--~~~~~~~~d~~Q~A~Ki~~NS~YG~~g~~-~~r~~~~~~A~~vT~~Gr~~i~~~~~~i~~~--~g~~ViygDTD 542 (775)
T 1qht_A 468 KATV--DPLEKKLLDYRQRAIKILANSFYGYYGYA-KARWYCKECAESVTAWGREYIEMVIRELEEK--FGFKVLYADTD 542 (775)
T ss_dssp HTCC--CHHHHHHHHHHHHHHHHHHTTHHHHHHCT-TCSSCCHHHHHHHHHHHHHHHHHHHHHHHHH--HCCEEEEEETT
T ss_pred HCCC--CHHHHHHHHHHHHHHHEEECCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH--CCCEEEEEECC
T ss_conf 3289--97999999999875425210230314444-6676788899998999999999999999986--39768996055
Q ss_pred EEEEEC
Q ss_conf 347999
Q 000502 1454 RYTVCI 1459 (1459)
Q Consensus 1454 SiFV~l 1459 (1459)
|+||++
T Consensus 543 Si~v~~ 548 (775)
T 1qht_A 543 GLHATI 548 (775)
T ss_dssp EEEEEC
T ss_pred CEEEEC
T ss_conf 327875
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=1.00 E-value=1 Score=709.63 Aligned_cols=474 Identities=19% Similarity=0.244 Sum_probs=378.7
Q ss_pred CCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCC---CCCCCCCEEECCCCCCCCCEECCHHHHHCCCCCCCCCCCCCCCC
Q ss_conf 169945796418999970588977440299765---45555543422898655624441253310024688887889985
Q 000502 825 LNDGSCLYMLRPPFSPPSVDSVHKWLLHDDKGA---SGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLNG 901 (1459)
Q Consensus 825 ~~d~s~~~~lt~~~sp~s~~~v~~wL~~~~~~~---~v~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~~ 901 (1459)
.-++..++++++ .+|..+..+.+.|.+.|+++ +++...||++|+++.+|+|++..... ...++++
T Consensus 75 ~~~~~~~~~i~~-~~~~~~~~~r~~l~~~g~~v~EadI~~~~RfliD~~i~~~~w~~~~~~~----~~~~~~~------- 142 (786)
T 3k59_A 75 DFHRQPVYGLYC-RAHRQLMNYEKRLREGGVTVYEADVRPPERYLMERFITSPVWVEGDMHN----GTIVNAR------- 142 (786)
T ss_dssp CTTCCEEEEEEE-SSHHHHHHHHHHHHHTTCCCBSTTCCHHHHHHHHTTCSSEEEEEEEEET----TEEEEEE-------
T ss_pred EECCCEEEEEEE-CCHHHHHHHHHHHHHCCCCEEECCCCHHHEEEEECCCCCCEEEEEECCC----CCEECCE-------
T ss_conf 126956999998-7999999999999975983632468835515576586650699973347----8152115-------
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCE
Q ss_conf 43212356664587743234666444358999999997766785788777989882599999994769999999888948
Q 000502 902 VTAIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAESRGDLRPDPRYDSI 981 (1459)
Q Consensus 902 ~~~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~k~~~~~~~~~~LtiLsIEIet~srg~~fPDPe~DpI 981 (1459)
+. | . .+..+++++++|||||..+| +|
T Consensus 143 --------------------------~~-~--------~----------~~~~p~lrilsfDIE~~~~g---------~i 168 (786)
T 3k59_A 143 --------------------------LK-P--------H----------PDYRPPLKWVSIDIETTRHG---------EL 168 (786)
T ss_dssp --------------------------EE-E--------C----------SSCCCCCCEEEEEEEECTTS---------CE
T ss_pred --------------------------EE-E--------C----------CCCCCCCEEEEEEEEECCCC---------CE
T ss_conf --------------------------74-5--------7----------88888870899999976899---------88
Q ss_pred EEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHH
Q ss_conf 99999950599760899999921797644545798992899718999999999999852199989803677765999999
Q 000502 982 NVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAE 1061 (1459)
Q Consensus 982 ~~Isl~i~~d~d~~~ev~vLi~~~~~~~~~~~~~i~g~~V~~f~sEkELL~aFidlIre~DPDIItGYNi~~FDLpYLie 1061 (1459)
++|++. +.. ...+ ++.+..... ..+.+..|..|++|++||.+|+++|+++|||||+|||+.+||||||.+
T Consensus 169 ~~I~~~--~~~--~~~v--~~l~~~~~~----~~~~~~~V~~f~~E~~lL~~f~~~i~~~dPDii~g~N~~~FD~pyL~~ 238 (786)
T 3k59_A 169 YCIGLE--GCG--QRIV--YMLGPENGD----ASSLDFELEYVASRPQLLEKLNAWFANYDPDVIIGWNVVQFDLRMLQK 238 (786)
T ss_dssp EEEEEE--ETT--EEEE--EEESSCCSC----CTTCSSEEEEESSHHHHHHHHHHHHHHHCCSEEEESSTTTTHHHHHHH
T ss_pred EEEEEC--CCC--CCEE--EEEECCCCC----CCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHH
T ss_conf 999823--899--8869--999668877----778884499969999999999999987099999961776676899999
Q ss_pred HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEECCEEEEEHHHH
Q ss_conf 99992999766778898533345799631012334455662256776543331100122454455502227188516999
Q 000502 1062 RAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRL 1141 (1459)
Q Consensus 1062 RAk~Lgidl~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~vk~~~~~d~~G~~~~s~i~I~GRivIDL~rv 1141 (1459)
||..||+++ .+||.+.....+ ...++ .....+.+.||+++|+|++
T Consensus 239 Ra~~~~i~~--~lGR~~~~~~~~--------------------------------~~~~~-~~~~~~~i~GRv~lDl~~~ 283 (786)
T 3k59_A 239 HAERYRLPL--RLGRDNSELEWR--------------------------------EHGFK-NGVFFAQAKGRLIIDGIEA 283 (786)
T ss_dssp HHHHHTCCC--CCBTTTBCCEEE--------------------------------ECSSS-TTCEEEECTTCEEEEHHHH
T ss_pred HHHHHCCCC--EECCCCCCCCCC--------------------------------CCCCC-CCCEEEEECCEEEEEHHHH
T ss_conf 999849994--014478865323--------------------------------56667-7731688758799981998
Q ss_pred HHH-CCCCCCCCHHHHHHHHHCCCCCCCC----HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
Q ss_conf 840-0289988989999998168989989----35067998459925799999999898799999998603302589999
Q 000502 1142 MRG-EVKLNMYTVEAVAETVLRRKIPSIP----FRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELA 1216 (1459)
Q Consensus 1142 ~Rk-e~kL~sYSLenVA~~vLgekK~dis----~k~L~k~y~~g~~~~r~rii~YcikDa~Lvl~Ll~kL~iI~~t~ElA 1216 (1459)
+++ .+++.+|+|++||+++||++|++.. +++|++||.++ +.+++.||++||.++++|+.++++++++.|+|
T Consensus 284 lk~~~~~l~SysL~~Va~~~Lg~~K~~~~~~~~~~eI~~~~~~~----~~~L~~Y~l~Da~L~~~L~~kl~ll~~~~ela 359 (786)
T 3k59_A 284 LKSAFWNFSSFSLETVAQELLGEGKSIDNPWDRMDEIDRRFAED----KPALATYNLKNCELVTQIFHKTEIMPFLLERA 359 (786)
T ss_dssp HHHTTCCCSCCSHHHHHHHHHCCCCC-CCHHHHHHHHHHHHHHC----HHHHHHHHHHHHHHHHHHHHHHTHHHHHHHHH
T ss_pred HHHCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHCC----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 97603787888889999998089875657423599999999629----79999999999999999998750899999999
Q ss_pred HHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCCCEEEEECCCCCHHHHH
Q ss_conf 98475621002377423568998887321797863899985556653246984550567744588479521440066886
Q 000502 1217 RVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVASQPAMECLPLVMEPESGFYADPVVVLDFQSLYPSMMI 1296 (1459)
Q Consensus 1217 ri~GIp~~sVlsRGSq~rVESlLLR~ak~enfIlPsPsk~qv~~q~a~E~GglVlEP~sGlY~nPVvVLDFqSLYPSIII 1296 (1459)
+++|+++.++ +||+.++++++++.++++||++|++.. ... ..++ ||+||||++|+|++ |++|||+||||||||
T Consensus 360 rl~Gi~~~~~--ggs~~~~~~lll~~~~~~~~i~P~~~~--~~~-~~y~-Gg~V~eP~~G~y~~-V~~lDF~SLYPSIi~ 432 (786)
T 3k59_A 360 TVNGLPVDRH--GGSVAAFGHLYFPRMHRAGYVAPNLGE--VPP-HASP-GGYVMDSRPGLYDS-VLVLDYKSLYPSIIR 432 (786)
T ss_dssp HHHCSCTTCC--CCHHHHHHHHHHHHHHHTTBCCCCTTS--SCC-CCCC-CCCBCCCCCEEESC-EEEEEETTHHHHHHH
T ss_pred HHHCCCHHHC--CCHHHHHHHHHHHHHHHCCEECCCCCC--CCC-CCCC-CCEEEECCCCCEEE-EEEEEHHHCCHHHHH
T ss_conf 9969897880--557999999999998775900777665--566-6688-85796045774326-999980110478999
Q ss_pred HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 32754023346667876555897556889200015676521389981003898767774999999999999999999840
Q 000502 1297 AYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKL 1376 (1459)
Q Consensus 1297 AyNICpSTivg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPnG~~Fvk~~vrkGILP~lL~eLL~~R~~vKk~MKk~ 1376 (1459)
+|||||+|++...... ..++...+|+|.+|++ ++|+||+||++|++.|+++|+.|++
T Consensus 433 ~~ni~~~t~~~~~~~~-------------------~~~~~~~~~~g~~f~~---~~g~lp~~l~~l~~~R~~~K~~~~~- 489 (786)
T 3k59_A 433 TFLIDPVGLVEGMAQP-------------------DPEHSTEGFLDAWFSR---EKHCLPEIVTNIWHGRDEAKRQGNK- 489 (786)
T ss_dssp HHCCCHHHHHHHHHSC-------------------STTTEEECSTTCEEES---SCCSHHHHHHHHHHHHHHHHHTTCH-
T ss_pred HHCCCCCCCCCCCCCC-------------------CCCCCCCCCCCCEEEE---CCCCHHHHHHHHHHHHHHHHHHCCH-
T ss_conf 8578964333456775-------------------4455236899845752---6874399999999999999984415-
Q ss_pred CCCHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCEEE
Q ss_conf 98168999999999977101033302433566667678977797999998999999999986238898199996264347
Q 000502 1377 APSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNENEKWKAKVIYGDTDRYT 1456 (1459)
Q Consensus 1377 ~~~d~~l~~iLD~rQlALKIlANS~YGytGa~fSGRmpc~eIAdSIT~~GRe~Le~ai~~Ie~~~~~GakVIYGDTDSiF 1456 (1459)
.+|+|+|++|||+|||+|++ +|||||.++|++||++||++|++++++|++ +|++||||||||+|
T Consensus 490 ------------~~q~AlKi~~Ns~YG~~G~~-~~~~~~~~~A~~iT~~GR~~l~~~~~~ie~---~g~~ViYGDTDSvf 553 (786)
T 3k59_A 490 ------------PLSQALKIIMNAFYGVLGTT-ACRFFDPRLASSITMRGHQIMRQTKALIEA---QGYDVIYGDTDSTF 553 (786)
T ss_dssp ------------HHHHHHHHHHHHHHHGGGST-TSTTCCHHHHHHHHHHHHHHHHHHHHHHHH---TTCEEEECBSSEEE
T ss_pred ------------HHHHHHHEEEECCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH---CCCEEEEEECCCEE
T ss_conf ------------78874530002132402355-777777789999999999999999999998---69889999556049
Q ss_pred EEC
Q ss_conf 999
Q 000502 1457 VCI 1459 (1459)
Q Consensus 1457 V~l 1459 (1459)
|++
T Consensus 554 v~~ 556 (786)
T 3k59_A 554 VWL 556 (786)
T ss_dssp EEC
T ss_pred EEC
T ss_conf 971
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=1.00 E-value=1 Score=684.70 Aligned_cols=517 Identities=17% Similarity=0.180 Sum_probs=384.3
Q ss_pred ECCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCCEECCHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf 01699457964189999705889774402997654555554342289865562444125331002468888788998543
Q 000502 824 YLNDGSCLYMLRPPFSPPSVDSVHKWLLHDDKGASGDMDKASVEHSSLKGSDIRPVLEEMHQEADEMISTEPTPDLNGVT 903 (1459)
Q Consensus 824 y~~d~s~~~~lt~~~sp~s~~~v~~wL~~~~~~~~v~~~~r~~~d~~~s~~~~~~~~~~~~~~~~~~s~~e~e~~~~~~~ 903 (1459)
|......++++|. .+|..+..+-+.|. +-++.++..+.||++|+++.+++||.+.....+.... ....|.+|.+.+
T Consensus 88 ~~~~~~~~~ki~~-~~p~~v~~~r~~l~-~~~EadI~~~~RfliD~~i~~~~w~~~~~~~~~~~~~--~~~~~~~~~~~~ 163 (847)
T 1s5j_A 88 YTWNKFKLTKIVV-RDPLAVRRLRNDVP-KAYEAHIKYFNNYMYDIGLIPGMPYVVKNGKLESVYL--SLDEKDVEEIKK 163 (847)
T ss_dssp TTCCEEEEEEEEE-SSHHHHHHHTTSSS-CEESCSSCHHHHHHHHHTCCTTSEEEEETTEEEECCC--CCCHHHHHHHHH
T ss_pred CCCCCEEEEEEEE-ECHHHHHHHHHHHH-HHEECCCCHHHHHHEECCCCCEEEEEEECCCCCCCCC--CCCHHHCCCHHH
T ss_conf 5787436999999-57899999999856-6600377668651112486640799985465533565--455211010233
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECC-CCCCCCCCCC--CC
Q ss_conf 21235666458774323466644435899999999776678578877798988259999999476-9999999888--94
Q 000502 904 AIMHNEGHIAEPNACADCLQDISQISGPDGRSKPTPLSQIGFQDPASAGAGEQLTLLSIEVQAES-RGDLRPDPRY--DS 980 (1459)
Q Consensus 904 ~~~~~~~~~~~~~~~~~~~~~~sqi~g~~~~~~~~p~~~~~~k~~~~~~~~~~LtiLsIEIet~s-rg~~fPDPe~--Dp 980 (1459)
+..|.-..+...+ ..|.+. .....+++++++|||||.+ ++++||+|+. |+
T Consensus 164 ~~~~~~~~~~~~~--------------------------~~~~~~-~~~~~p~l~ilsfDIEt~s~~~g~fP~~~~~~d~ 216 (847)
T 1s5j_A 164 AFADSDEMTRQMA--------------------------VDWLPI-FETEIPKIKRVAIDIEVYTPVKGRIPDSQKAEFP 216 (847)
T ss_dssp HTTTSCHHHHHHH--------------------------HHHTHH-HHSCCCCCCEEEEEEEECCSSSSCCCCTTTCCSC
T ss_pred HHCCCHHHHCCCC--------------------------CCCCHH-CCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCC
T ss_conf 3306503310110--------------------------110100-0157998549999778676888999995446771
Q ss_pred EEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHH
Q ss_conf 89999995059976089999992179764454579899289971899999999999985219998980367776599999
Q 000502 981 INVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLA 1060 (1459)
Q Consensus 981 I~~Isl~i~~d~d~~~ev~vLi~~~~~~~~~~~~~i~g~~V~~f~sEkELL~aFidlIre~DPDIItGYNi~~FDLpYLi 1060 (1459)
|++|++.. .+++ ..++ +....... ....++.+..|..|++|++||.+|+++|.+. |+|+|||+.+||||||.
T Consensus 217 Ii~Is~~~-~~g~--~~~~--~~~~~~~~-~~~~~i~~~~v~~~~~E~~LL~~f~~~i~~~--diivgyN~~~FDlPyL~ 288 (847)
T 1s5j_A 217 IISIALAG-SDGL--KKVL--VLNRNDVN-EGSVKLDGISVERFNTEYELLGRFFDILLEY--PIVLTFNGDDFDLPYIY 288 (847)
T ss_dssp EEEEEEEE-TTSC--EEEE--EECSSCCC-CCCEEETTEEEEEESSHHHHHHHHHHHHTTC--SEEEESSTTTTHHHHHH
T ss_pred EEEEEEEC-CCCC--CEEE--EEECCCCC-CCCCCCCCCEEEEECCHHHHHHHHHHHHCCC--CEEEEECCCCCHHHHHH
T ss_conf 89999980-6897--3899--99277455-5666779976998099999999999984449--97999578775699999
Q ss_pred HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCC-CCCCCCCEEECCEEEEEHH
Q ss_conf 999992999766778898533345799631012334455662256776543331100122-4544555022271885169
Q 000502 1061 ERAAHLGIGLLNDISRTPLESKIAAGDSEISERGITDNMLAEPVVAESLLAKDAIIEDEW-GRTHASGLHVGGRIVLNVW 1139 (1459)
Q Consensus 1061 eRAk~Lgidl~~~LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~~~vk~~~~~d~~-G~~~~s~i~I~GRivIDL~ 1139 (1459)
+||..+|+... +.+. .+ |+. .+.+.||+++|+|
T Consensus 289 ~Ra~~lgi~~~----~~p~---------------------------------------~~~gr~---~~~i~gr~~~Dl~ 322 (847)
T 1s5j_A 289 FRALKLGYFPE----EIPI---------------------------------------DVAGKD---EAKYLAGLHIDLY 322 (847)
T ss_dssp HHHHTTTCCGG----GCSE---------------------------------------ECCSTT---CCEETTSEEEEHH
T ss_pred HHHHHCCCCCC----CCCE---------------------------------------EECCCC---CEEECCEEEEEHH
T ss_conf 99987299733----3780---------------------------------------005998---3686457870317
Q ss_pred HHHHHC--------CCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH--HCCCC
Q ss_conf 998400--------28998898999999816898998935067998459925799999999898799999998--60330
Q 000502 1140 RLMRGE--------VKLNMYTVEAVAETVLRRKIPSIPFRVLTKWFASGPGRARYRCVEYVVGRAKLNLEIMN--QLDMI 1209 (1459)
Q Consensus 1140 rv~Rke--------~kL~sYSLenVA~~vLgekK~dis~k~L~k~y~~g~~~~r~rii~YcikDa~Lvl~Ll~--kL~iI 1209 (1459)
++++.+ .++.+|+|++||+++||++|.+++ ..+ ... .+.++++||++||.++++|+. +..++
T Consensus 323 ~~~~~~~~~~y~f~~kl~sysL~~Va~~~Lg~~K~dv~-~~i----~~~---~~~~l~~Ycl~Da~lt~~L~~~~~~~~~ 394 (847)
T 1s5j_A 323 KFFFNKAVRNYAFEGKYNEYNLDAVAKALLGTSKVKVD-TLI----SFL---DVEKLIEYNFRDAEITLQLTTFNNDLTM 394 (847)
T ss_dssp HHHTSHHHHHHTSTTCCSSCSHHHHHHHHHCCCCC--S-SCT----TTC---CHHHHHHHHHHHHHHHHHTTTHHHHHHH
T ss_pred HHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCHH-HHH----HHC---CHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 88755334430024554656689999998099986545-755----221---4999999988879999999998767677
Q ss_pred HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECCCC-----CCCC-----CCCCCCCCCEEEECCCCCCC
Q ss_conf 2589999984756210023774235689988873217978638999-----8555-----66532469845505677445
Q 000502 1210 NRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGN-----HQVA-----SQPAMECLPLVMEPESGFYA 1279 (1459)
Q Consensus 1210 ~~t~ElAri~GIp~~sVlsRGSq~rVESlLLR~ak~enfIlPsPsk-----~qv~-----~q~a~E~GglVlEP~sGlY~ 1279 (1459)
....++|+++|+|+..+...|++.+|+++|+++++++||++|++.. .+.. ....+ .||+|+||++|+|+
T Consensus 395 ~~~~~la~i~~lp~~~l~r~~~~~~v~slll~~~~~~~~i~P~~~~~~~~~~~~~~~~~~~~~~y-~Gg~V~eP~~G~y~ 473 (847)
T 1s5j_A 395 KLIVLFSRISRLGIEELTRTEISTWVKNLYYWEHRKRNWLIPLKEEILAKSSNIRTSALIKGKGY-KGAVVIDPPAGIFF 473 (847)
T ss_dssp HHHHHHHHHHCCCHHHHTTSCHHHHHHHHHHHHHHHHTBCCCCHHHHHHTTCC---------------CCCCCCCSEEEE
T ss_pred HHHHHHHHHHCCCCHHHCCCCHHHHHHHHHHHHHHHCCCCCCCCHHHHHHCCCCCCHHCCCCCCC-CCCCCCCCCCCCCC
T ss_conf 99999998838890551664243666878899998669516781465432034441000356545-67711177778604
Q ss_pred CCEEEEECCCCCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCCCCCEECCCCCCCCCHHHHH
Q ss_conf 88479521440066886327540233466678765558975568892000156765213899810038987677749999
Q 000502 1280 DPVVVLDFQSLYPSMMIAYNLCFCTCLGKILPSKENTLGVSSFRPDLHVLRDLKDELLIPPNGVMYVPPKVRKGVLPRLL 1359 (1459)
Q Consensus 1280 nPVvVLDFqSLYPSIIIAyNICpSTivg~~~~~~~n~~Gv~~~~~d~~~l~~Lkd~i~isPnG~~Fvk~~vrkGILP~lL 1359 (1459)
+ |++|||+||||||||+|||||+|+++...... .+.....|++.+|++ ..++|++|.+|
T Consensus 474 ~-v~~lDf~SLYPSIi~~~Nl~~~T~~~~~~~~~-------------------~~~~~~~~~~~~~~~-~~~~g~~p~~l 532 (847)
T 1s5j_A 474 N-ITVLDFASLYPSIIRTWNLSYETVDIQQCKKP-------------------YEVKDETGEVLHIVC-MDRPGITAVIT 532 (847)
T ss_dssp E-EEEEEETTHHHHHHHHTTCCTTTBSCSCCSSC-------------------CEECCSSSCCCEEBC-CSSCCHHHHHH
T ss_pred C-EEEEEHHHHCHHHHHHCCCCCCEECCCCCCCC-------------------CCCCCCCCCCCEEEE-CCCCCCCHHHH
T ss_conf 2-46764121363889870798310114555654-------------------444212798760575-05776667999
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf 99999999999999840981689999999999771010333024335666676789777979999989999999999862
Q 000502 1360 EEILSTRIMVKQAIKKLAPSQQILHRIFNARQLALKLIANVTYGYTAAGFSGRMPCAELADSIVQCGRSTLEKAISFVNE 1439 (1459)
Q Consensus 1360 ~eLL~~R~~vKk~MKk~~~~d~~l~~iLD~rQlALKIlANS~YGytGa~fSGRmpc~eIAdSIT~~GRe~Le~ai~~Ie~ 1439 (1459)
++|++.|+++|+.|++....++.++.+||.+|+|+|++|||+|||||+. +|||||.++|++||++||++|+++++++++
T Consensus 533 ~~l~~~R~~~kk~~~k~~~~~~~~~~~~d~~Q~AlKi~~NS~YG~~g~~-~~~~~~~~~A~~iT~~GR~~l~~t~~~ve~ 611 (847)
T 1s5j_A 533 GLLRDFRVKIYKKKAKNPNNSEEQKLLYDVVQRAMKVFINATYGVFGAE-TFPLYAPRVAESVTALGRYVITSTVKKARE 611 (847)
T ss_dssp HHHHHHHHHTHHHHHTCTTSCHHHHHHHHHHHHHHHHHHHHHHHHHHST-TSTTCCHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf 9999999999999875657998999998999999999862232101454-566668889999999999999999999985
Q ss_pred CCCCCCEEEEECCCEEEEEC
Q ss_conf 38898199996264347999
Q 000502 1440 NEKWKAKVIYGDTDRYTVCI 1459 (1459)
Q Consensus 1440 ~~~~GakVIYGDTDSiFV~l 1459 (1459)
+|++||||||||+||++
T Consensus 612 ---~g~~ViYGDTDSi~v~~ 628 (847)
T 1s5j_A 612 ---EGLTVLYGDTDSLFLLN 628 (847)
T ss_dssp ---TTCCEEEEETTEEEEES
T ss_pred ---CCCEEECCCCCCEEEEC
T ss_conf ---89689617875348954
No 7
>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=1.00 E-value=1 Score=319.24 Aligned_cols=256 Identities=14% Similarity=0.237 Sum_probs=200.3
Q ss_pred CCCEEEEEEEEECCCCCCCCCCCC--CCEEEEEEEEECCCCCEEEEEEEEECCC-C--C-CC-----------CCCCC--
Q ss_conf 882599999994769999999888--9489999995059976089999992179-7--6-44-----------54579--
Q 000502 955 EQLTLLSIEVQAESRGDLRPDPRY--DSINVVALAFENDSDHAVEIYVLLYCKS-E--S-HQ-----------RSLVG-- 1015 (1459)
Q Consensus 955 ~~LtiLsIEIet~srg~~fPDPe~--DpI~~Isl~i~~d~d~~~ev~vLi~~~~-~--~-~~-----------~~~~~-- 1015 (1459)
+++++++|||||.+ ++||+|+. |+|++|++....+. .+.+++++..+. . + .. ..+..
T Consensus 104 p~l~vlsfDIEt~~--~~fP~~~~~~d~Ii~Is~~~~~~~--~~~~~~l~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~ 179 (388)
T 1noy_A 104 KFVRVANCDIEVTG--DKFPDPMKAEYEIDAITHYDSIDD--RFYVFDLLNSMYGSVSKWDAKLAAKLDCEGGDEVPQEI 179 (388)
T ss_dssp GGCCEEEEEEEECC--SSCCCTTTCCSCEEEEEEEETTTT--EEEEEEECCCSSCCCCCCCHHHHHSCGGGTCCCCCHHH
T ss_pred CCEEEEEEEEEECC--CCCCCCCCCCCEEEEEEEEEECCC--EEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf 87479999888688--999997789984999999996487--07999875046788775201222222212346666556
Q ss_pred CCCCEEEEECCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHH-HCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf 89928997189999999999998521999898036777659999999999-29997667788985333457996310123
Q 000502 1016 IPDCKVFVCSKEIHLFSHFIKILCSFDPDILMGWDIQGGSLGFLAERAAH-LGIGLLNDISRTPLESKIAAGDSEISERG 1094 (1459)
Q Consensus 1016 i~g~~V~~f~sEkELL~aFidlIre~DPDIItGYNi~~FDLpYLieRAk~-Lgidl~~~LSR~~~~~~~~~~~~~f~~k~ 1094 (1459)
..++.|..|++|++||.+|+++|+++|||||+|||+++||||||.+||.. +|+++...+++.+.....
T Consensus 180 ~~~v~v~~~~~E~~LL~~f~~~i~~~dPDii~GyN~~~FDlpyL~~Ra~~~lg~~l~~~~s~~~r~~~~----------- 248 (388)
T 1noy_A 180 LDRVIYMPFDNERDMLMEYINLWEQKRPAIFTGWNIEGFDVPYIMNRVKMILGERSMKRFSPIGRVKSK----------- 248 (388)
T ss_dssp HTTEEEEEESCHHHHHHHHHHHHHHSCCSEEECSSTTTTHHHHHHHHHHHHHHHHHHGGGSTTSCEEEE-----------
T ss_pred CCCEEEEECCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC-----------
T ss_conf 897589975999999999999998719969995377776199999999987497310014755500455-----------
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEECCEEEEEHHHHHHH-CCC-CCCCCHHHHHHHHHCCCCCCCCHHH
Q ss_conf 34455662256776543331100122454455502227188516999840-028-9988989999998168989989350
Q 000502 1095 ITDNMLAEPVVAESLLAKDAIIEDEWGRTHASGLHVGGRIVLNVWRLMRG-EVK-LNMYTVEAVAETVLRRKIPSIPFRV 1172 (1459)
Q Consensus 1095 ~~~~~l~~p~~~g~~~vk~~~~~d~~G~~~~s~i~I~GRivIDL~rv~Rk-e~k-L~sYSLenVA~~vLgekK~dis~k~ 1172 (1459)
...+.||... .+.+.||+++|+|+++|+ +++ +.+|+|++||+++||++|.+++ ++
T Consensus 249 --------------------~~~~~~g~~~--~~~i~GR~~lD~~~~~k~~~~~~l~sysL~~Va~~~Lg~~K~d~~-~~ 305 (388)
T 1noy_A 249 --------------------LLQNMYGSKE--IYSIDGVSILDYLDLYKKFAFTNLPSFSLESVAQHETKKGKLPYD-GP 305 (388)
T ss_dssp --------------------ECCGGGCSCE--EEEETTSEECCHHHHHHHHTCCCCSCCSHHHHHHHHHSCCCCCCS-SC
T ss_pred --------------------CCHHHHCCCC--EEEECCEEEEEHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCCH-HH
T ss_conf --------------------6745628754--189737698577999865374756679999999999699977827-99
Q ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHH-HHHHHHHHHHCCEEEE
Q ss_conf 679984599257999999998987999999986033025899999847562100237742356-8998887321797863
Q 000502 1173 LTKWFASGPGRARYRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRV-ESMLLRLAHTQNYLAI 1251 (1459)
Q Consensus 1173 L~k~y~~g~~~~r~rii~YcikDa~Lvl~Ll~kL~iI~~t~ElAri~GIp~~sVlsRGSq~rV-ESlLLR~ak~enfIlP 1251 (1459)
+.+||. ..+.++++||++||.++++|+.++++++++.|+|+++|+++.+|+ | |.++ +++|+++|+++||++|
T Consensus 306 i~~~~~----~~~~~l~~Y~~~D~~l~~~L~~kl~~l~~~~ela~i~g~~~~~vl--~-q~~~~~~lll~~~~~~~~i~P 378 (388)
T 1noy_A 306 INKLRE----TNHQRYISYNIIDVESVQAIDKIRGFIDLVLSMSYYAKMPFSGVM--S-PIKTWDAIIFNSLKGEHKVIP 378 (388)
T ss_dssp GGGHHH----HHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHTCCGGGGG--C-HHHHHHHHHHHHTTCC-----
T ss_pred HHHHHH----HCHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCCCCHHHHC--C-CHHHHHHHHHHHHHHCCEECC
T ss_conf 999998----689999999999999999999987768889999675598979957--1-699999999999976899843
Q ss_pred CCCC
Q ss_conf 8999
Q 000502 1252 SPGN 1255 (1459)
Q Consensus 1252 sPsk 1255 (1459)
++..
T Consensus 379 ~~~~ 382 (388)
T 1noy_A 379 QQGS 382 (388)
T ss_dssp ----
T ss_pred CCCC
T ss_conf 6876
No 8
>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=1.00 E-value=1 Score=242.89 Aligned_cols=373 Identities=14% Similarity=0.120 Sum_probs=207.9
Q ss_pred EEEEEEEEECCCCCCCCCCCCCCEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCCCCCEEEEECCHHHHHHHHHHH
Q ss_conf 59999999476999999988894899999950599760899999921797644545798992899718999999999999
Q 000502 958 TLLSIEVQAESRGDLRPDPRYDSINVVALAFENDSDHAVEIYVLLYCKSESHQRSLVGIPDCKVFVCSKEIHLFSHFIKI 1037 (1459)
Q Consensus 958 tiLsIEIet~srg~~fPDPe~DpI~~Isl~i~~d~d~~~ev~vLi~~~~~~~~~~~~~i~g~~V~~f~sEkELL~aFidl 1037 (1459)
+++++|+|| ++|+..+++.+|+|..... .. .+ . ...+ |.+|+++
T Consensus 7 ~i~~~D~Et------~~d~~~~~~~~i~~~~~~~-~~---~~--------------------~--~~~~----l~~fi~~ 50 (575)
T 2py5_A 7 KMYSCAFET------TTKVEDCRVWAYGYMNIED-HS---EY--------------------K--IGNS----LDEFMAW 50 (575)
T ss_dssp CEEEEEEEE------CCBTTBCCEEEEEEEESSC-TT---CE--------------------E--EESC----HHHHHHH
T ss_pred EEEEEEEEE------ECCCCCCCEEEEEEEECCC-EE---EE--------------------E--ECHH----HHHHHHH
T ss_conf 479999874------1477788508999991880-28---99--------------------8--0200----9999999
Q ss_pred HHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCC-----CC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf 8521999898036777659999999999299976-----67----78898533345799631012334455662256776
Q 000502 1038 LCSFDPDILMGWDIQGGSLGFLAERAAHLGIGLL-----ND----ISRTPLESKIAAGDSEISERGITDNMLAEPVVAES 1108 (1459)
Q Consensus 1038 Ire~DPDIItGYNi~~FDLpYLieRAk~Lgidl~-----~~----LSR~~~~~~~~~~~~~f~~k~~~~~~l~~p~~~g~ 1108 (1459)
+...||||+ +||+ +||+.||+.|+...|+..- .. ++|.+..-.. +
T Consensus 51 ~~~~~~~i~-~hNl-~FD~~~l~~~~~~~~~~~~~~~~p~~~~~~i~r~~~~~~~---------~--------------- 104 (575)
T 2py5_A 51 VLKVQADLY-FHNL-KFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMI---------D--------------- 104 (575)
T ss_dssp HHHHCCEEE-ETTH-HHHHHHHHHHHHHTTCEECTTCCTTEEEEEEBTTCCEEEE---------E---------------
T ss_pred HHHCCCEEE-EECH-HHHHHHHHHHHHHHCCCCCCCCCCCCCCCEECCCCEEEEE---------E---------------
T ss_conf 987199799-9874-4349999999997376543223641101034269848999---------9---------------
Q ss_pred HHHHHHHHCCCCCCCCCCCEEECC--EEEEEHHHHHHHCCCCCCCCHHHHHHHHHCC-CCCCCCHHHHHHHHHCCCHHHH
Q ss_conf 543331100122454455502227--1885169998400289988989999998168-9899893506799845992579
Q 000502 1109 LLAKDAIIEDEWGRTHASGLHVGG--RIVLNVWRLMRGEVKLNMYTVEAVAETVLRR-KIPSIPFRVLTKWFASGPGRAR 1185 (1459)
Q Consensus 1109 ~~vk~~~~~d~~G~~~~s~i~I~G--RivIDL~rv~Rke~kL~sYSLenVA~~vLge-kK~dis~k~L~k~y~~g~~~~r 1185 (1459)
+ .+ ...| ++.++++..++. -.++|+++|+.+... .|..++|..+... +. ..+
T Consensus 105 ------i---~~--------~~~~k~~~~i~~~Ds~~~----~~~SL~~~a~~f~~~~~K~~~py~~~~~~---~~-~~~ 159 (575)
T 2py5_A 105 ------I---CL--------GYKGKRKIHTVIYDSLKK----LPFPVKKIAKDFKLTVLKGDIDYHKERPV---GY-KIT 159 (575)
T ss_dssp ------E---EE--------EEETTEEEEEEEEEHHHH----SCSCHHHHHHHTTCCCCSSCCCTTSCCCT---TC-CCC
T ss_pred ------E---EE--------ECCCCCEEEEEEEEHHHH----HHHHHHHHHHHHCCCCCCCCCCCCCCCCC---CC-HHH
T ss_conf ------9---98--------028874699999984865----25509999998289654776573004765---51-115
Q ss_pred HHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECCCCCCCCC-CCCC
Q ss_conf 999999989879999999860330258999998475621002377423568998887321797863899985556-6532
Q 000502 1186 YRCVEYVVGRAKLNLEIMNQLDMINRTSELARVFGIDFFSVLSRGSQYRVESMLLRLAHTQNYLAISPGNHQVAS-QPAM 1264 (1459)
Q Consensus 1186 ~rii~YcikDa~Lvl~Ll~kL~iI~~t~ElAri~GIp~~sVlsRGSq~rVESlLLR~ak~enfIlPsPsk~qv~~-q~a~ 1264 (1459)
..++.||++||.++.+++.+. +.. . +..+...|-.+.+.--.+ ..+..+.++|.++..-... ..++
T Consensus 160 ~~~~~Y~~~Dv~ll~~i~~~~--f~~--------~--~~~~Tissla~~~f~~~~-~~~~~~~~~p~~~~~~~~~ir~~y 226 (575)
T 2py5_A 160 PEEYAYIKNDIQIIAEALLIQ--FKQ--------G--LDRMTAGSDSLKGFKDII-TTKKFKKVFPTLSLGLDKEVRYAY 226 (575)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH--HHT--------T--CCSSSHHHHHHHHHHHHH-CHHHHHHHSCCCCHHHHHHHHTTC
T ss_pred HHHHHHHHHHHHHHHHHHHHH--HHH--------H--HHHCCCCCHHHHHHHHHH-HHCCCHHHCCCCCCHHHHHHHHCC
T ss_conf 999999999999999999999--876--------4--443201308999998674-100010214667821778899717
Q ss_pred CCCCEEEE-CC--CCCCCCCEEEEECCCCCHHHHHH--CCCCCCCCCCCCCCC---CCCCCCCCC--CCCCCHHHCCC--
Q ss_conf 46984550-56--77445884795214400668863--275402334666787---655589755--68892000156--
Q 000502 1265 ECLPLVME-PE--SGFYADPVVVLDFQSLYPSMMIA--YNLCFCTCLGKILPS---KENTLGVSS--FRPDLHVLRDL-- 1332 (1459)
Q Consensus 1265 E~GglVlE-P~--sGlY~nPVvVLDFqSLYPSIIIA--yNICpSTivg~~~~~---~~n~~Gv~~--~~~d~~~l~~L-- 1332 (1459)
. ||.|+. |. .+++++ |+++||+|||||+|.. +++..-+.+...... .....|+-. ..+|++.++-+
T Consensus 227 ~-GGr~~~~p~y~~~~~~~-i~~~D~~SLYPs~m~~~~~P~g~p~~~~~~~~~~~~~~~~~g~v~~~v~~p~~~~P~lpp 304 (575)
T 2py5_A 227 R-GGFTWLNDRFKEKEIGE-GMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQI 304 (575)
T ss_dssp C-CCCEEECGGGBTCEECS-EEEEEETTHHHHHHHHSCEEEEEEEEEESSCCCCTTSCEEEEEEEEEEEECTTCCCCCCC
T ss_pred C-CCCCCCCCCCCCCCCCC-EEEEECCCCHHHHHCCCCCCCCCCEECCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCC
T ss_conf 8-85300011435667773-499866786488971799899984332441013457865228999999677002874565
Q ss_pred ------CCCCCCCC------------------------------CCCEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf ------76521389------------------------------981003898767774999999999999999999840
Q 000502 1333 ------KDELLIPP------------------------------NGVMYVPPKVRKGVLPRLLEEILSTRIMVKQAIKKL 1376 (1459)
Q Consensus 1333 ------kd~i~isP------------------------------nG~~Fvk~~vrkGILP~lL~eLL~~R~~vKk~MKk~ 1376 (1459)
+.+-.+.| .|.+|. ...|++++.++.+++.|...|
T Consensus 305 ~~~~~~~~~~li~~~~~~~~g~~~t~vd~eL~~a~~g~ki~~i~~~~~f~---~~~~~f~~~i~~l~~~k~~~~------ 375 (575)
T 2py5_A 305 KRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFK---ATTGLFKDFIDKWTYIKTTSE------ 375 (575)
T ss_dssp -------CCSCCSBCTTSCEEEEEEHHHHHHHHHHEEEEEEEEEEEEEEE---EESCTTHHHHHHHHHHHHHCC------
T ss_pred CCCCCCCCCCCCCCCCCCCCEEEEECCCHHHHHCCCCCEEEEEEEEEEEC---CCCCCHHHHHHHHHHHHHHCC------
T ss_conf 34666678853267776542089956628888605785788877889990---688844999999999765275------
Q ss_pred CCCHHHHHHHHHHHHHHHHHEEEEECCCCCCCCC-------------CCC---------C-CHHHHHHHHHHHHHHHHHH
Q ss_conf 9816899999999997710103330243356666-------------767---------8-9777979999989999999
Q 000502 1377 APSQQILHRIFNARQLALKLIANVTYGYTAAGFS-------------GRM---------P-CAELADSIVQCGRSTLEKA 1433 (1459)
Q Consensus 1377 ~~~d~~l~~iLD~rQlALKIlANS~YGytGa~fS-------------GRm---------p-c~eIAdSIT~~GRe~Le~a 1433 (1459)
+ ..+| +.|+++||+||.+|++.. -+| | ++.+|.+||+.||..|..+
T Consensus 376 ----~------~~~~-~~Kl~lNS~YGk~g~~~~~~~~~~~~~~~~~~~f~~~e~~~~~p~~v~ia~~iTa~aR~~m~~~ 444 (575)
T 2py5_A 376 ----G------AIKQ-LAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITA 444 (575)
T ss_dssp ----H------HHHH-HHHHHHHSSHHHHTCCSBCCBEEEEECTTSSEEEEECCCCBCCCCCHHHHHHHHHHHHHHHHHH
T ss_pred ----H------HHHH-HHHHHHHHHHHHHCCCCCCCCEEEEECCCCEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf ----8------8999-9999877676662347555532898645310232037622268620468999999999999999
Q ss_pred HHHHHHCCCCCCEEEEECCCEEEEE
Q ss_conf 9998623889819999626434799
Q 000502 1434 ISFVNENEKWKAKVIYGDTDRYTVC 1458 (1459)
Q Consensus 1434 i~~Ie~~~~~GakVIYGDTDSiFV~ 1458 (1459)
++.+ |.+|+||||||+||.
T Consensus 445 ~~~~------~~~v~Y~DTDSi~~~ 463 (575)
T 2py5_A 445 AQAC------YDRIIYCDTDSIHLT 463 (575)
T ss_dssp HHHT------TTTEEEEETTEEEEE
T ss_pred HHHC------CCCEEEECCCCCEEC
T ss_conf 9974------793899608760434
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=1.00 E-value=1 Score=200.93 Aligned_cols=134 Identities=20% Similarity=0.425 Sum_probs=102.8
Q ss_pred EEECCCCCCCC-C-----CCCCCCCCCCCCC--------CCCEEEEEEECCCCCEEEEEECCCCCEEEEECCCC---CCC
Q ss_conf 10016999999-9-----9641012375117--------93489999657999879999947411596107998---532
Q 000502 18 IDHYMAPPIPG-Y-----DICYSSLQGGKVN--------EVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCADI---PVQ 80 (1459)
Q Consensus 18 iD~y~rpPip~-l-----d~~fq~ld~~~~~--------~vPVIRIFG~T~~G~SVCvHVHGf~PYFYV~~p~~---~~~ 80 (1459)
...|.|||+|+ + +++||++|.++.. .+|||||||+|++|+|||||||||.|||||++|++ +..
T Consensus 28 ~~~~~~~~~~~~~~~~~~~~~f~~ld~~~~~~~~~~~~~~~~virlfg~t~~G~sv~v~V~gf~PYFYv~~~~~~~~~~~ 107 (919)
T 3iay_A 28 LSSFERKKLPTDFDPSLYDISFQQIDAEQSVLNGIKDENTSTVVRFFGVTSEGHSVLCNVTGFKNYLYVPAPNSSDANDQ 107 (919)
T ss_dssp -CCCCCCCCCTTCCTTTCCEEEEEEEEEEEECSSSCBTTBCEEEEEEEEETTSCEEEEEEESCCCEEEEECCSSGGGGCH
T ss_pred CCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCCEEEEEEEEEECCCCEEEEEECCCCCEEEEECCCCCCCCCH
T ss_conf 56767999986568887843799984234444565465982699999880899989999878388799976786443456
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEECCC-------------------------------CC-CCC
Q ss_conf 2223124899999999999883289999870466899974035-------------------------------87-546
Q 000502 81 LRQEDDGYMHAISLALEKALKVKGSAGSKRQHVHECSLVRAKK-------------------------------GG-AVF 128 (1459)
Q Consensus 81 ~~~~~~~~i~~L~~~Le~al~~~~~~~~~~~~V~~V~iV~~~s-------------------------------~G-~v~ 128 (1459)
.. +..+...|++.+ ...+..|++|.+++ .| ..+
T Consensus 108 ~~------~~~~~~~L~~~~---------~~~v~~ve~v~K~~l~gy~~~~~~~~lKI~~~~p~~v~~~r~~l~~g~~~~ 172 (919)
T 3iay_A 108 EQ------INKFVHYLNETF---------DHAIDSIEVVSKQSIWGYSGDTKLPFWKIYVTYPHMVNKLRTAFERGHLSF 172 (919)
T ss_dssp HH------HHHHHHHHHTTT---------TTCEEEEEEEEEEESSCCSCSCCEEEEEEEESSTTHHHHHHHHHHHSCCCG
T ss_pred HH------HHHHHHHHHHHH---------CCCCEEEEEEEEECCCCCCCCCCEEEEEEEECCHHHHHHHHHHHHCCCCCC
T ss_conf 67------999999998750---------477107999964446457889834799999819999999999987066543
Q ss_pred C----CCCCCCCCCHHHHHHHHHCCCCCCCEEEEECCCCCCCC
Q ss_conf 8----98773004823465653306865303479278630147
Q 000502 129 D----KSLQPHESHIPFLLQFLVDYNLYGMGHLHLSKLKFRHP 167 (1459)
Q Consensus 129 ~----~~~q~YESnIpy~LRFMID~nL~Gm~WI~l~~~kfR~p 167 (1459)
+ ..+++|| ||||.+|||||.+|.||+|++++++.|+..
T Consensus 173 ~~~~~~~~~~yE-dI~~~~RfliD~~I~g~~W~~i~~~~~~~~ 214 (919)
T 3iay_A 173 NSWFSNGTTTYD-NIAYTLRLMVDCGIVGMSWITLPKGKYSMI 214 (919)
T ss_dssp GGSSTTCCCCBC-CCCHHHHHHHHHTCCTTCEEEECTTSEEEC
T ss_pred CCCCCCCCCCCC-CCCHHHHHEEECCCCCCEEEEEECCCCEEC
T ss_conf 433556742035-877676640445886536999955740111
No 10
>2gv9_A DNA polymerase; polymerase alpha fold, transferase; HET: DNA; 2.68A {Human herpesvirus 1} PDB: 1dml_B*
Probab=1.00 E-value=1 Score=147.65 Aligned_cols=118 Identities=16% Similarity=0.222 Sum_probs=85.9
Q ss_pred CCCCCCCEEEEEEECCCCCEEEEEECCCCCEEEEECCCC---CCCCCCCCHHHHHHHHHHHHHHHHHCCC--CCCCCEEE
Q ss_conf 511793489999657999879999947411596107998---5322223124899999999999883289--99987046
Q 000502 39 GKVNEVPVIRVYGSTPAGQKTCLHIHRALPYLYVPCADI---PVQLRQEDDGYMHAISLALEKALKVKGS--AGSKRQHV 113 (1459)
Q Consensus 39 ~~~~~vPVIRIFG~T~~G~SVCvHVHGf~PYFYV~~p~~---~~~~~~~~~~~i~~L~~~Le~al~~~~~--~~~~~~~V 113 (1459)
+..+.+|||||||+|++|+|||||||||.|||||+++++ +.... +..+...|++++..... .......+
T Consensus 132 ~i~p~g~vi~l~g~t~~G~sv~v~v~~f~pYFYv~~~~~~~~~~~~~------~~~~~~~l~~~l~~~~~~~~~~~~~~~ 205 (1193)
T 2gv9_A 132 AITPTGTVITLLGLTPEGHRVAVHVYGTRQYFYMNKEEVDRHLQCRA------PRDLCERMAAALRESPGASFRGISADH 205 (1193)
T ss_dssp HTSSCEEEEEEEEECSSCCEEEEEEECCCEEEEEEHHHHHHTTCCCS------HHHHHHHHHHHHHHSSSCCTTCCCGGG
T ss_pred CCCCCCCEEEEEEECCCCCEEEEEECCCCEEEEEECCCCCCCCCCCC------HHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf 64789878999998389997999987877499997787421013321------789999999999752034445656675
Q ss_pred EEEEEEECCCC-------C--------------C---CCCCCCCCCCCCHHHHHHHHHCC-CCCCCEEEEECCC
Q ss_conf 68999740358-------7--------------5---46898773004823465653306-8653034792786
Q 000502 114 HECSLVRAKKG-------G--------------A---VFDKSLQPHESHIPFLLQFLVDY-NLYGMGHLHLSKL 162 (1459)
Q Consensus 114 ~~V~iV~~~s~-------G--------------~---v~~~~~q~YESnIpy~LRFMID~-nL~Gm~WI~l~~~ 162 (1459)
+.+++|.+..- . . .+...+.+||+||+|..|||||. +|.||+|++++.+
T Consensus 206 ~~ve~V~k~~l~~~~~~~~~~~ki~~~~p~~v~~lr~~~~~~~~~~E~dI~~~~RfliD~~~i~~~~W~~i~~~ 279 (1193)
T 2gv9_A 206 FEAEVVERTDVYYYETRPALFYRVYVRSGRVLSYLCDNFCPAIKKYEGGVDATTRFILDNPGFVTFGWYRLKPG 279 (1193)
T ss_dssp CEEEEEEEEESSCSSCCCEEEEEEEESCHHHHHHHHHHTCSSSCEESTTCCHHHHHHHHSTTCCSSEEEEECCB
T ss_pred CEEEEEEEEECCCCCCCCCEEEEEECCCHHHHHHHHHHCCCCCEEEECCCCHHHEEEEECCCCCCCCEEEEECC
T ss_conf 04899997603556777642899960189999999860457743775367525157677489887533997225
Done!