Query 001982
Match_columns 986
No_of_seqs 254 out of 439
Neff 5.1
Searched_HMMs 29240
Date Mon Mar 25 07:21:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001982.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/001982hhsearch_pdb -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 1msw_D DNA-directed RNA polyme 100.0 7E-198 2E-202 1779.9 53.2 774 168-986 21-883 (883)
2 3spa_A Mtrpol, DNA-directed RN 100.0 4E-189 2E-193 1704.1 55.0 763 171-986 296-1134(1134)
3 3q23_A Virion RNA polymerase; 97.3 0.00066 2.3E-08 81.5 10.7 277 487-782 338-702 (1118)
4 2kfn_A Klenow fragment of DNA 67.3 5.8 0.0002 47.2 6.1 210 664-942 364-584 (605)
5 4dfk_A DNA polymerase I, therm 32.5 21 0.00072 42.1 3.0 210 664-941 300-517 (540)
6 1bgx_T TAQ DNA polymerase; DNA 28.7 29 0.00099 43.0 3.4 196 682-941 605-809 (832)
7 3pv8_A DNA polymerase I; DNA p 27.7 28 0.00095 41.5 2.9 197 682-942 364-571 (592)
8 1x9m_A DNA polymerase; DNA plo 25.4 74 0.0025 38.5 6.1 107 664-822 443-559 (698)
9 1gdt_A GD resolvase, protein ( 14.6 2.5E+02 0.0084 27.5 6.2 60 897-957 73-132 (183)
10 3g13_A Putative conjugative tr 12.8 3.3E+02 0.011 26.1 6.4 62 897-959 91-152 (169)
No 1
>1msw_D DNA-directed RNA polymerase, bacteriophage T7 RNA; T7RNAP elongation complex, transcription/DNA/RNA complex; 2.10A {Enterobacteria phage T7} SCOP: e.8.1.3 PDB: 1h38_A 1cez_A 1qln_A* 1s0v_A* 1s76_D* 1s77_D* 4rnp_A 3e2e_A* 3e3j_C* 1aro_P 2pi4_A* 2pi5_A
Probab=100.00 E-value=7.2e-198 Score=1779.93 Aligned_cols=774 Identities=28% Similarity=0.461 Sum_probs=669.1
Q ss_pred hhhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHh-hccCcc
Q 001982 168 REMKKRKFN-LLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR-TKKQKA 245 (986)
Q Consensus 168 ~~~~~~~~~-~l~~RQ~~lE~~~~~~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~-~~~~r~ 245 (986)
.+.-...|+ .|++||++||++++++|++||++++++++++|+++++|++++++.+|+++|+++|+++++..+ +.|.++
T Consensus 21 ~~~~~~~~~~~l~~rQ~~lE~e~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~~~~~l~~~i~~~~~~~~~~~g~~~ 100 (883)
T 1msw_D 21 FNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGKRP 100 (883)
T ss_dssp HHHHTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCGGGSTTTHHHHHHHHHHHHHHHHHHHHHHHHSCSCCC
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCChhhHHHHHHHHHHHHHHHHHHHHHHhcccCcch
Confidence 344456676 678999999999999999999999999999999999999999999999999999999988776 356789
Q ss_pred chhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHHHH
Q 001982 246 AYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLSKE 325 (986)
Q Consensus 246 ~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~~~~~~~~~~ 325 (986)
.|+|||++|+||++|+|||+++|+++++ ++++++++++.+||++||+|++++++.++.++++.+..
T Consensus 101 ~~~~~L~~l~~e~lA~iti~~~l~~~~~---~~~~~~~~~~~~iG~ave~E~~~~~~~~~~~~~~~~~~----------- 166 (883)
T 1msw_D 101 TAFQFLQEIKPEAVAYITIKTTLACLTS---ADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKNV----------- 166 (883)
T ss_dssp TTTTTTTSSCHHHHHHHHHHHHHHHHHH---CSCCBHHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHHT-----------
T ss_pred HHHHHHHhCCHHHHHHHHHHHHHHHhcc---cCCccHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHH-----------
Confidence 9999999999999999999999999987 35789999999999999999999998877655433211
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhh-c-----CCCCCCCCHHHHHHHHHHHHHHHHHH-ccccCCCCCCCCCCCCccCcee
Q 001982 326 KELLRKRVNSLIKSKRVMEAQKLL-K-----NEETKPWGRDTQAKLGSRLVELLIET-AYVQHPVNPADYSPPDVRPAFR 398 (986)
Q Consensus 326 ~~~~~~~~~~~~~~~~~~~~~~~~-~-----~~~~~~W~~~~~~kvG~~Li~~L~e~-~~i~~~~~~~~~~~~~~~paF~ 398 (986)
.+.++++.+...++...+.+.... + ++++.+|+..++++||++|+++|+++ +.|++....
T Consensus 167 ~~~l~~~~~~~~k~~~~~~~~~~~~~~g~~~~~~~~~W~~~~~~~vG~~Li~~l~~~~~~~~~~~~~------------- 233 (883)
T 1msw_D 167 EEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQN------------- 233 (883)
T ss_dssp SHHHHHSCSHHHHHHHHHHHHHHSTTTTTTTTCCCCCCCTTHHHHHHHHHHHHHHHHCTTEEEECC--------------
T ss_pred HHHHHhcccHHHHHHHHHHHHHHhhhccccccCCCCCCCHHHHHHHHHHHHHHHHHhhCCcceeccc-------------
Confidence 123333333333333333333311 1 26788999999999999999999995 666653211
Q ss_pred EeeeeeecCCCCCcceeEEEEecCHHHHHHHHhhh---hcccCCCCcceeCCCCCcCCCCcccccC---CccceecCCcH
Q 001982 399 HRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSA---KHMLIPYVPMLVPPKKWKGYNKGGYLFL---PSYVMRTHGSR 472 (986)
Q Consensus 399 h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~---~~~~~~~lPMlvpP~pW~~~~~GGYl~~---~s~l~R~~~~~ 472 (986)
.|. .++++|+|++||++++.+.+.. ..+.+.+|||||||+||+++.+||||+. +..++|+..
T Consensus 234 ---------~~~-~~k~~~~i~~~~~~~~~l~~~~~~~~~~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~~~ir~~~-- 301 (883)
T 1msw_D 234 ---------AGV-VGQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS-- 301 (883)
T ss_dssp -----------------CCEEEECHHHHHHHHHHHHHHTTSCCCCCCBSSCCBCCSSSBSCBSSSCCSSCCBSEECSS--
T ss_pred ---------cCC-CCceeeEEEeCHHHHHHHhhcccchhhcCCCCCceeeCCccCCCCCCCCccCCCcccchhhcccC--
Confidence 121 1367899999999999997643 2345569999999999999999999974 345667653
Q ss_pred HHHHHHHhccccChHHHHHHHHhhcCcceEEcHHHHHHHHHHHH-cCCCCCCCCCCCCCCCCCCCCCCC--HHHHHHHHH
Q 001982 473 KQQEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWV-SGGNIAGLVDRNDVLIPEKPLSED--MTEVQKWKW 549 (986)
Q Consensus 473 ~q~~~l~~~~~~~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~-~g~~i~~l~~~~~~p~P~~p~~~d--~~~~~~wk~ 549 (986)
+.++++..+++++.||++||+||+|||+||++||+||+++|+ +|+++++||+..+.|+|++|++.+ ++++++|++
T Consensus 302 --~~~~~~~~~~~l~~v~~aLN~L~~t~w~IN~~vL~vi~~~~~~~g~~~~~ip~~~~~~~P~~p~~~d~~~~~~~~~k~ 379 (883)
T 1msw_D 302 --KKALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAWKR 379 (883)
T ss_dssp --TTHHHHTTTCCCHHHHHHHHHHHTCCEEECHHHHHHHHHHTTCSSCSSTTCCCSSCCCCCCC-----------CCTTH
T ss_pred --HHHHHhccccchHHHHHHHHHhccCCeEecHHHHHHHHHHHhhcCCcccCCCCcCcCCCCCCCCccccCHHHHHHHHH
Confidence 244666677899999999999999999999999999999999 999999999988899999986543 678899999
Q ss_pred HHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCchhhhhhhhcccCccCCcchhh
Q 001982 550 SVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSGLR 629 (986)
Q Consensus 550 ~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~Gl~ 629 (986)
.++++++.++++||+||+++++|++|++|+|++.||||||+|||||+||+| ||||||+|+|||||+||+|+|||++||+
T Consensus 380 ~~~~~~~~~~~~~S~r~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~p-~Ln~~GsDl~RsLL~FaegkpLG~~Gl~ 458 (883)
T 1msw_D 380 AAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVS-MFNPQGNDMTKGLLTLAKGKPIGKEGYY 458 (883)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSCSCBBCCEEEETTSCEEESS-SSCTTSCHHHHHHEEESSCEECHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEEeecccCCCCcCCCCC-CCCCCcchHHHHHHHhccCCccChhHHH
Confidence 999999999999999999999999999999988999999999999999995 9999999999999999999999999999
Q ss_pred HHHHHHHhhcC------------------------CCCCCCchhhhcCCChHHHHHHHHHHHHHHhcCCCCcceeccccc
Q 001982 630 WLKIHLANLFS------------------------ENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISHLPIH 685 (986)
Q Consensus 630 WLKIhlANl~G------------------------~dPl~~~~wW~~AD~PwQfLA~C~El~~a~~s~~P~~y~S~lPV~ 685 (986)
|||||+||+|| +||++ .+||++||+||||||+|+||++|+++|+ +|+||+|||
T Consensus 459 WLkIhlAN~~G~dK~s~~eRi~wv~~n~~~I~dsA~~Pl~-~~wW~~Ad~PwQfLA~C~El~~a~~~~~--~y~S~lPVh 535 (883)
T 1msw_D 459 WLKIHGANCAGVDKVPFPERIKFIEENHENIMACAKSPLE-NTWWAEQDSPFCFLAFCFEYAGVQHHGL--SYNCSLPLA 535 (883)
T ss_dssp HHHHHHHHHTTCCSSCHHHHHHHHHHTHHHHHHHHHCHHH-HCGGGGSSSHHHHHHHHHHHHHHHHHCT--TCEECCCEE
T ss_pred HHHHHHHHhcCCCcCCHHHHHHHHHHHHHHHHHHhcCccc-chHHHcCCcHHHHHHHHHHHHHHHhCCC--ccccccccc
Confidence 99999999999 78998 5899999999999999999999999876 899999999
Q ss_pred ccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCC------C-------------hhH
Q 001982 686 QDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSK------H-------------PQA 746 (986)
Q Consensus 686 qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~------~-------------~~~ 746 (986)
|||||||||||||||||.+||++|||+|+|+|||||+.||+.|.+.+++|+.+|.+. + ...
T Consensus 536 qDgSCnGLQHyAALgrD~~ga~~VNL~psd~PqDvYs~Va~~v~~~~~~da~~g~~~~~~~~~d~~~g~i~e~~~~~~~~ 615 (883)
T 1msw_D 536 FDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKLGTKA 615 (883)
T ss_dssp EECSCHHHHHHHHHHTCTTHHHHTTCSCCSSCCCHHHHHHHHHHHHHHHHHTTSCCCCCCCSSSSSSCCSSCCCCCCHHH
T ss_pred cCCCCcHHHHHHHHhcChhhhhHhCCCCCCCCcchHHHHHHHHHHHHHHHHhcccccccccccccccccchhhcccchhH
Confidence 999999999999999999999999999999999999999999999999998765321 0 112
Q ss_pred HHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCCh----hhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 747 LLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDD----RQLFAAACYAAKVTLTALGEIFEAARSI 822 (986)
Q Consensus 747 ~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~----~~~~~~a~Ylak~v~~ai~e~f~~A~~i 822 (986)
..+++|.++|+||+|||||||+|||||++|+++||+++|+++++..++ .....+|+|+|++||+||+++|++|+.|
T Consensus 616 l~~~~l~~~i~RKvvKqtVMT~vYGvT~~Ga~~qI~~~l~~~~~~~~~~~~~~~~~~~a~yla~~i~~ai~~~f~~a~~i 695 (883)
T 1msw_D 616 LAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVAAVEA 695 (883)
T ss_dssp HHHHHHTTCCCHHHHHHHHHGGGGTCCHHHHHHHHHHHTHHHHHHTSCCCSCSSHHHHHHHHHHHHHHHHHHHCHHHHHH
T ss_pred HHHHHHhcCCCHHHhccceeeeeeCCcchhhHHHHHHHHhhhhccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999999999999999999999874321111 1234889999999999999999999999
Q ss_pred HHHHHHHHHHHHcC------------CCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEE---EecCC---CcCchhhhh
Q 001982 823 MGWLGDCAKVIASE------------NQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLA---LQREG---NLVEIRKQR 884 (986)
Q Consensus 823 m~WL~~~A~~i~~~------------~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~---l~~~~---d~vd~rKQ~ 884 (986)
|+||++||++|+++ +.||.|+||+||||+|||++.++++|+|.+|.++ +..+. +++|++||+
T Consensus 696 m~wL~~~a~~i~~~v~~~~~~~~~~~~~pv~W~TPlGlpV~Q~Y~~~~~~~V~t~l~~~~~i~l~~~~~~~~~~d~~Kq~ 775 (883)
T 1msw_D 696 MNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDAHKQE 775 (883)
T ss_dssp HHHHHHHHHHHHSCEECTTTCCEEECCCCEEEECTTSCEEEECCBCCSSCCEECSSSCEECCCCSCSSCCSCCBCHHHHH
T ss_pred HHHHHHHHHHHHhhcccccccccccCCCeEEEECCCCCEEEEEecCCCceEEEEeecceeeEeeecccccccccchHHHh
Confidence 99999999999998 9999999999999999999999999999998653 23332 359999999
Q ss_pred ccCCCcchhhhhhHHHHHHHHHHhhc-CC-cEEEeeccccCCCCChhHHHHHHHHHHHHhcCc-chHHHHHHHHHHhCCC
Q 001982 885 TAFPPNFVHSLDGSHMMMTAVACRDA-GL-HFAGVHDSFWTHACDVDEMNQILRKKFVELYNM-PMLENLLESFQTSYPT 961 (986)
Q Consensus 885 ~Af~PNFIHSLDAsHmmlta~~~~~~-Gi-~FasVHDSFwThA~dvd~m~~ilRe~FV~Lys~-~il~~l~e~f~~~~~~ 961 (986)
+|||||||||||||||||||++|.+. |+ +|++|||||||||||||.|+++|||+||+||++ |+|++|.++|..+|+.
T Consensus 776 ~af~PNFIHSLDAsHmmlta~~~~~~~gl~~fa~VHDsfwTha~dvd~m~~~lRe~FV~lys~~~~L~~l~~~~~~~~~~ 855 (883)
T 1msw_D 776 SGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGTIPADAANLFKAVRETMVDTYESCDVLADFYDQFADQLHE 855 (883)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCEECSSEEEECGGGHHHHHHHHHHHHHHHHHHCCHHHHHHHHHSSTTTC
T ss_pred cCCCchhHhhHHHHHHHHHHHHHHHhcCCCceEEEeccccCCHhhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhcch
Confidence 99999999999999999999999998 99 799999999999999999999999999999999 9999999999999985
Q ss_pred ---CCCCCCCCCCCCChhhhccCCCCCC
Q 001982 962 ---LSFPPLPERGNFDLEEVLESPYFFN 986 (986)
Q Consensus 962 ---~~~p~~P~~G~LDL~~Vl~S~YFF~ 986 (986)
.+||++|++|+|||++|++|+|||+
T Consensus 856 ~~~~~~p~~P~~G~ldl~~Vl~S~YfFs 883 (883)
T 1msw_D 856 SQLDKMPALPAKGNLNLRDILESDFAFA 883 (883)
T ss_dssp TTCCCCCCCCCCCSCCGGGGGTCSSCCC
T ss_pred hhhhcCCCCCCCCCCCHHHHhcCCCCCC
Confidence 5899999999999999999999997
No 2
>3spa_A Mtrpol, DNA-directed RNA polymerase, mitochondrial; single-subunit DNA-dependent RNA polymerase in mitochondria, transferase; 2.50A {Homo sapiens}
Probab=100.00 E-value=4.5e-189 Score=1704.11 Aligned_cols=763 Identities=34% Similarity=0.616 Sum_probs=615.6
Q ss_pred hHHHHHHHHHHHHHHHHHH------HH------HHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 171 KKRKFNLLRRRQVKQETEA------WE------RMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQ 238 (986)
Q Consensus 171 ~~~~~~~l~~RQ~~lE~~~------~~------~a~~r~~~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~ 238 (986)
+....+.+.+.|+.+|..+ ++ ..+.++|+. +.++..+|...|..+|+++....
T Consensus 296 ~~~~L~~~~~~Ql~~E~~~~v~v~sve~~~~~t~~~~~~r~~---------------l~~~~~~w~~~l~~~~~~~~~~~ 360 (1134)
T 3spa_A 296 PLKTLQCLFEKQLHMELASRVCVVSVEKPTLPSKEVKHARKT---------------LKTLRDQWEKALCRALRETKNRL 360 (1134)
T ss_dssp CHHHHHHHHHHHHHHHHHCEEEEECCSCCCCCCTTHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHcCeeEEeecccCCCCCHHHHHHHHH---------------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445777888999999662 11 112234443 45667889999999999877644
Q ss_pred h--hccCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhh
Q 001982 239 R--TKKQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIA 316 (986)
Q Consensus 239 ~--~~~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~~~~IG~aVe~E~~~~~~~~k~~~~~~~~~~~ 316 (986)
. ....+..++|||+.|+.+.++.|.|.++..+..+ |..++.++..||..|++++.+++-....
T Consensus 361 ~~~~~~~~~~~~p~l~~l~~~~~~~~~~~~~~~l~~~-----g~~~~~~~~~lg~~~~~~~~~~~~~~~~---------- 425 (1134)
T 3spa_A 361 EREVYEGRFSLYPFLCLLDEREVVRMLLQVLQALPAQ-----GESFTTLARELSARTFSRHVVQRQRVSG---------- 425 (1134)
T ss_dssp HHHHHTTCCCSTGGGGSSCHHHHHHHHHHHHHHCCTT-----CEEHHHHHHHHHHHHHHHHHHHHHHHHT----------
T ss_pred HHhhccCCCccccceeeCCHHHHHHHHHHHHHHhccc-----CccHHHHHHHHHHHHHHHHHHHHHHhhh----------
Confidence 3 2456789999999999999999777777665432 3468889999999999999886532210
Q ss_pred hhHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHhhcC--CCCCCCCHHHHHHHHHHHHHHHHHHccccCCCC
Q 001982 317 DTEEVLSKEKELLRKRVNSL----------IKSKRVMEAQKLLKN--EETKPWGRDTQAKLGSRLVELLIETAYVQHPVN 384 (986)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~--~~~~~W~~~~~~kvG~~Li~~L~e~~~i~~~~~ 384 (986)
.+.+..+...+...-+ ..| +.|+.+... ..+.+|+..++++||++|+++|+++++|.+...
T Consensus 426 ----~~~~~~~~y~~y~~~~~~~~~~~~~~~~r---~~w~~l~~~~~~~~~~W~~~~~~kvG~~Ll~~L~~~~~i~~~~~ 498 (1134)
T 3spa_A 426 ----QVQALQNHYRKYLCLLASDAEVPEPCLPR---QYWEALGAPEALREQPWPLPVQMELGKLLAEMLVQATQMPCSLD 498 (1134)
T ss_dssp ----HHHHHHHHHHHHGGGTCSSCCCSSCCCHH---HHHHHHHCCCCGGGCCCCHHHHHHHHHHHHHHHHHHCBCCC---
T ss_pred ----HHHHHHHHHHHHHHHHhcCCccCCCCChH---HHHHHhCCcccCCCCCCCHHHHHHHHHHHHHHHHhhccCCcccc
Confidence 0011111111111111 122 335554433 457899999999999999999999999987655
Q ss_pred CCCCCCCCccCceeEeeeeeecCCCCCcceeEEEEecCHHHHHHHHhhhhc---ccCCCCcceeCCCCCcCCCCcccccC
Q 001982 385 PADYSPPDVRPAFRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKH---MLIPYVPMLVPPKKWKGYNKGGYLFL 461 (986)
Q Consensus 385 ~~~~~~~~~~paF~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~~~---~~~~~lPMlvpP~pW~~~~~GGYl~~ 461 (986)
++ .+..+.+|||+|+|++. + ++++|+|++||.+++.+++.... +.+.+|||||||+||+++++||||+.
T Consensus 499 ~~-~~~~~~~paf~h~y~~~---~----~~~~G~i~~hp~~~~~l~~~~~~~~~~~~~~lPMlvpP~pW~~~~~GGYl~~ 570 (1134)
T 3spa_A 499 KP-HRSSRLVPVLYHVYSFR---N----VQQIGILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLS 570 (1134)
T ss_dssp ---------CBSEEEEEC-----------CCCEEEEECHHHHHHHHHHTCSEEEEEGGGSCBSSCCEEEEETTEEESSSS
T ss_pred CC-CCCcccccceEEEEEEE---c----CcEEEEEEECHHHHHHHHhccccccccCcCCCCcccCCCCCCCCCCceeEec
Confidence 43 34456799999999865 3 46899999999999999875432 33459999999999999999999999
Q ss_pred CccceecCCcHHH-HHHHHhccccChHHHHHHHHhhcCcceEEcHHHHHHHHHHHHc-CCCCCCCCCCC-CCCCCC---C
Q 001982 462 PSYVMRTHGSRKQ-QEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVS-GGNIAGLVDRN-DVLIPE---K 535 (986)
Q Consensus 462 ~s~l~R~~~~~~q-~~~l~~~~~~~l~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~-g~~i~~l~~~~-~~p~P~---~ 535 (986)
++.+||+++...| ...+++..+++|+.||++||+||+|||+||++||+|+.++|++ |+++.++|+.. +.|.|+ .
T Consensus 571 ~t~~mR~~~~~~q~~~~l~~~~~~~l~~v~~aLN~Lg~t~W~IN~~VLdVv~~vw~~~G~~~~~iP~~~~~~p~~p~~~~ 650 (1134)
T 3spa_A 571 PTKLMRTVEGATQHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQLFQAKGCPQLGVPAPPSEAPQPPEAHL 650 (1134)
T ss_dssp CCCSBCCCTTHHHHHHHHHSSCGGGGHHHHHHHHHHHTCEEEECHHHHHHHHHHHTTTCBGGGTBCCCC-----------
T ss_pred CcceeecCCChHHHHHHHHhccccccHHHHHHHHHHhCCCcEecHHHHHHHHHHHHhcCCCcCCCCCCccccCCCCCCCC
Confidence 9999999765544 4455666678999999999999999999999999999999986 55678888753 344443 2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCchhhhhhh
Q 001982 536 PLSEDMTEVQKWKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVL 615 (986)
Q Consensus 536 p~~~d~~~~~~wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL 615 (986)
|.+.++++.++|+++.++.++.++++||+||+++++|+||++|+|+ .||||||+|||||+||+||||||||+|+|||||
T Consensus 651 ~~~~~~~~~~~~kr~~~~~~~~~~~~~S~Rc~~~~kL~iA~~f~~~-~fYfPhnlDFRGR~Yp~~p~LnhqGsDl~RsLL 729 (1134)
T 3spa_A 651 PHSAAPARKAELRRELAHCQKVAREMHSLRAEALYRLSLAQHLRDR-VFWLPHNMDFRGRTYPCPPHFNHLGSDVARALL 729 (1134)
T ss_dssp -----------------------CTHHHHHHHHHHHHHHHHHHTTS-CEECCEEECTTCCEEESCSSSCSCSSHHHHHTE
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCC-eeecccccCCCCcCcCCCCCcCcccchHHHHHH
Confidence 3455677888999999888899999999999999999999999996 999999999999999999999999999999999
Q ss_pred hcccCccCCcchhhHHHHHHHhhcC-------------------------CCCCCCchhhhcCCChHHHHHHHHHHHHHH
Q 001982 616 EFAEGRPLGKSGLRWLKIHLANLFS-------------------------ENPINGSRWWLTAEDPFQCLAACINLSEAL 670 (986)
Q Consensus 616 ~FaegkpLG~~Gl~WLKIhlANl~G-------------------------~dPl~~~~wW~~AD~PwQfLA~C~El~~a~ 670 (986)
+||+|+|||++|++|||||+||+|| +||++|++||++||+||||||+|+||++|+
T Consensus 730 ~FaegkpLG~~Gl~WLkIhlAN~~G~dKk~s~~eRi~wv~~n~~~I~dsA~~Pl~g~~wW~~Ad~PwQfLA~C~El~~a~ 809 (1134)
T 3spa_A 730 EFAQGRPLGPHGLDWLKIHLVNLTGLKKREPLRKRLAFAEEVMDDILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAV 809 (1134)
T ss_dssp EESSCEECTTTHHHHHHHHHHHHHSCCTTSCHHHHHHHHHHHHHHHHHHHHCTTTSCCGGGGSSSHHHHHHHHHHHHHHH
T ss_pred HhccCCcCCcchHHHHHHHHHHhcCCCcCCCHHHHHHHHHHHHHHHHHHHhCcccchhHHHhCCCHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999 689999999999999999999999999999
Q ss_pred hcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHH
Q 001982 671 KSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAK 750 (986)
Q Consensus 671 ~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak 750 (986)
+++||++|+|||||||||||||||||||||||.+||++|||+|+|+|||||+.||+.|.+.+++|++++ ..+|+
T Consensus 810 ~~~dp~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNL~psd~PqDvYs~Va~~V~~~~~~Da~~~------~~~a~ 883 (1134)
T 3spa_A 810 RASDPAAYVSHLPVHQDGSCNGLQHYAALGRDSVGAASVNLEPSDVPQDVYSGVAAQVEVFRRQDAQRG------MRVAQ 883 (1134)
T ss_dssp TSSSGGGCEECCEEEECCSSHHHHHHHHHTTCHHHHHHTTCSCCSSCCCHHHHHHHHHHHHHHHHHHTT------CHHHH
T ss_pred hcCCCccccccCccccCCCCcHHHHHHHHccChhhHHHhCCCCCCCcccHHHHHHHHHHHHHHhhhhcC------hHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999998766 46899
Q ss_pred HhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 751 ILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCA 830 (986)
Q Consensus 751 ~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A 830 (986)
+|.++|+||+|||||||+|||||++|+++||+++|++.+.++++ .++.+|.|+|++||+||+++|++|+.||+||++||
T Consensus 884 ~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~e~~~~~~~-~~~~~a~Yla~~i~~si~e~f~~a~~im~WL~~~A 962 (1134)
T 3spa_A 884 VLEGFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRELSDFPQE-FVWEASHYLVRQVFKSLQEMFSGTRAIQHWLTESA 962 (1134)
T ss_dssp HTTTCCCHHHHHHHHHHHHHCCSSSHHHHHHHHHHHTCTTSCTT-THHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_pred HhhCCCChhhcccceEEeeecceehhHHHHHHHHHHhcccCchH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999998766654 68899999999999999999999999999999999
Q ss_pred HHHHcCCCcEEEEcCCCCeEEEeeccCCce-eEEeeeEEEEEecCCC---cCchhhhhccCCCcchhhhhhHHHHHHHHH
Q 001982 831 KVIASENQPVRWTTPLGLPVVQPYCKNERH-LIRTSLQVLALQREGN---LVEIRKQRTAFPPNFVHSLDGSHMMMTAVA 906 (986)
Q Consensus 831 ~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~-~I~t~lq~~~l~~~~d---~vd~rKQ~~Af~PNFIHSLDAsHmmlta~~ 906 (986)
++|++++.||.|+||+||||+|||++..+. .|.|.+|++++..+++ ++|++||++|||||||||||||||||||++
T Consensus 963 ~~i~~~~~pV~WtTPlGlpVvQpY~k~~k~~~i~~~~q~v~~~~~~d~~~~~d~~KQ~~afpPNFIHSLDAsHmmlTa~~ 1042 (1134)
T 3spa_A 963 RLISHMGSVVEWVTPLGVPVIQPYRLDSKVKQIGGGIQSITYTHNGDISRKPNTRKQKNGFPPNFIHSLDSSHMMLTALH 1042 (1134)
T ss_dssp HHHHHTTCCCEEECTTSCEEECCCBCC-----------------------CBCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhcCCCCEEEECCCCCEEEEeccCCCceeEecCCceEEEEeccCCcccCCCHHHHhccCCchHHhhHHHHHHHHHHHH
Confidence 999999999999999999999999997655 7889999998876543 699999999999999999999999999999
Q ss_pred HhhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhCCCCC------------CCCCCCCCCCC
Q 001982 907 CRDAGLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSYPTLS------------FPPLPERGNFD 974 (986)
Q Consensus 907 ~~~~Gi~FasVHDSFwThA~dvd~m~~ilRe~FV~Lys~~il~~l~e~f~~~~~~~~------------~p~~P~~G~LD 974 (986)
|.+.|++|++|||||||||||||.|+++|||+||+|||+|||++|.++|.++|+... ||++|++|+||
T Consensus 1043 c~~~gi~FasVHDSfwTHA~dvd~M~~ilRe~FV~L~s~~il~~L~~~~~~~~~~~~~~~~~~~~~~~~~p~~P~~G~lD 1122 (1134)
T 3spa_A 1043 CYRKGLTFVSVHDCYWTHAADVSVMNQVCREQFVRLHSEPILQDLSRFLVKRFCSEPQKILEASQLKETLQAVPKPGAFD 1122 (1134)
T ss_dssp HHHTTCCCEEETTEEEEEGGGHHHHHHHHHHHHHHHHHSCHHHHHHHHHHHHHSCCTTSHHHHHHHHHHHHSCCCCCSCC
T ss_pred HHhCCCCEEEeecccccCcccHHHHHHHHHHHHHHHccchHHHHHHHHHHHHcccchhhhhhhhHHHhhCCCCCCCCCcc
Confidence 999999999999999999999999999999999999999999999999999999764 99999999999
Q ss_pred hhhhccCCCCCC
Q 001982 975 LEEVLESPYFFN 986 (986)
Q Consensus 975 L~~Vl~S~YFF~ 986 (986)
|++|++|+||||
T Consensus 1123 L~~Vl~S~YFFs 1134 (1134)
T 3spa_A 1123 LEQVKRSTYFFS 1134 (1134)
T ss_dssp GGGGGGCTTSCC
T ss_pred HHHHhcCCCCCC
Confidence 999999999997
No 3
>3q23_A Virion RNA polymerase; protein-DNA complex; HET: DNA G2P; 1.80A {Enterobacteria phage N4} PDB: 3q0a_A* 3q22_A* 4ff1_A 4ff2_A* 4ff3_A* 4ff4_A* 3q24_A* 3c3l_A 3c46_A 3c2p_A* 2po4_A
Probab=97.30 E-value=0.00066 Score=81.51 Aligned_cols=277 Identities=16% Similarity=0.172 Sum_probs=162.8
Q ss_pred HHHHHHHHhhcCcceEEcHHHHHHHHHHHHcC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 001982 487 KKVFEALDTLGSTKWRVNKQVLSVLESIWVSG-GNIAGLVDRNDVLIPEKPLSEDMTEVQKWKWSVRKAKKINQERHSQR 565 (986)
Q Consensus 487 ~~v~~aLN~Lqst~wrIN~~VL~vi~~~w~~g-~~i~~l~~~~~~p~P~~p~~~d~~~~~~wk~~~~~~~~~~~~~~S~R 565 (986)
+.+-.+|...|.+|++||..+..+...+=+.+ ..+.|.- ++..|. -..+..+. +.-+| .+.+
T Consensus 338 ~lqakalkkaQ~q~hrvn~~m~~~~e~LgEDalltmlGa~---~l~~e~----ln~~~RkS-------lEGKN---~sV~ 400 (1118)
T 3q23_A 338 PEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAG---TLNKEL----LNDNHAKS-------LEGKN---RSVE 400 (1118)
T ss_dssp HHHHHHHHHHHHCCBEECHHHHHHHHHHHHHHHHHHHSCC---SCCTTS----SCHHHHHH-------HHHHH---HHHH
T ss_pred HHHHHHHHHhhccCceecccHHHHHHHhchhHHHHHhCcc---cccccc----cchhHHhh-------hhccc---HHHH
Confidence 45667788999999999999999977664433 1222321 111111 11111111 11111 1111
Q ss_pred hhhhH-------HHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCchhhhhhhhcccC-ccCC---cchhhHHHHH
Q 001982 566 CDTEL-------KLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEG-RPLG---KSGLRWLKIH 634 (986)
Q Consensus 566 ~~~~~-------~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~Faeg-kpLG---~~Gl~WLKIh 634 (986)
.+++- .-+++... +.-.+|||++|+==||.=-. .-+|||.+=|-|-++.=++. -.|+ ...++-|+.+
T Consensus 401 rdi~~~~d~iN~i~e~~~~~-~~vpIyf~y~mtrVGR~qm~-g~~NPQSsKLhRemv~pt~StV~L~~~N~~dm~~FqLg 478 (1118)
T 3q23_A 401 DSYNQLFSVIEQVRAQSEDI-STVPIHYAYNMTRVGRMQML-GKYNPQSAKLVREAILPTKATLDLSNQNNEDFSAFQLG 478 (1118)
T ss_dssp HHHHHHHHHHHHHHHHCSCG-GGCCEECCEEECTTSCEEES-SSSSTTTCHHHHTTEESCCEEECCSSTTSHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhhhccc-ccCceeeeechhhhhhhhhc-CCCCchhHHHHHHHhcCCceEeecCCCCHHHHHHHHHH
Confidence 11111 11222211 11279999999555554422 67899999999999876553 2455 4568888889
Q ss_pred HHhhcC-------------------CCCCCC------------------c---hhhhcCCChHHHHHHHHHHHHHHhcCC
Q 001982 635 LANLFS-------------------ENPING------------------S---RWWLTAEDPFQCLAACINLSEALKSSS 674 (986)
Q Consensus 635 lANl~G-------------------~dPl~~------------------~---~wW~~AD~PwQfLA~C~El~~a~~s~~ 674 (986)
+|-.+| +.||.. . .--+.+++||-.+-+-+|+++++...+
T Consensus 479 vaQslGiKVeK~~~e~~~~~~~~~l~t~lkpaVdmm~eiLt~G~~d~~~~dtl~~alg~~k~fvaamA~~e~Ary~la~G 558 (1118)
T 3q23_A 479 LAQALDIKVHTMTREVMSDELTKLLEGNLKPAIDMMVEFNTTGSLPENAVDVLNTALGDRKSFVALMALMEYSRYLVAED 558 (1118)
T ss_dssp HHHHTTCCGGGSCHHHHHHHHHHHHHTTTHHHHHHHHHHHHHSCCCTTHHHHHHHHHGGGCSHHHHHHHHHHHHHHHCSC
T ss_pred HHHHcCcchhcccHHHHHHHHHHHhcccccHHHHHHHHHhccCCCChhHHHHHHHHhcCCchHHHHHHHHHHHHHHHhcC
Confidence 999999 112210 0 012578899554448899999877555
Q ss_pred CCcceecccccccCCcchhHHHHHh-cCChhhh-----------------hhcccCCC-CCCcchhhHHHHHHHHHHHhh
Q 001982 675 PHSVISHLPIHQDGSCNGLQHYAAL-GRNTLEA-----------------AAVNLVAG-EKPADVYSEIAVRVHEIMKRD 735 (986)
Q Consensus 675 P~~y~S~lPV~qDGSCNGLQHyAAL-~rD~~Ga-----------------~~VNLip~-d~PqDvYs~Va~~V~~~i~~d 735 (986)
-+.|.+.|-+-.||--||=-..=-+ |.-.... +.+|=.-+ ..=-|.|..+++.+...+...
T Consensus 559 ~asF~T~L~~ElDGVTNGP~Namv~~G~g~~t~~~~~nl~KgG~F~G~~g~t~N~~~~~~~n~DLYE~ts~~l~~aLg~~ 638 (1118)
T 3q23_A 559 KSAFVTPLYVEADGVTNGPINAMMLMTGGLFTPDWIRNIAKGGLFIGSPNKTMNEHRSTADNNDLYQASTNALMESLGKL 638 (1118)
T ss_dssp GGGEEECCEEEEEETTHHHHHHHHHHCCSCCCHHHHHHHHTTTEEESCTTCCHHHHHHHTCCCCHHHHHHHHHHHHHHHH
T ss_pred CccceeeeEEEecCccccHHHHHHHhcCCcCCHHHHHHhhccceeecCCCchhhhhhcccCCchHHHHHHHHHHHHHHHh
Confidence 5789999999999999995433222 2211111 22222111 123699999999999988755
Q ss_pred cCCCCCCCh------hH-HHHHHh----------hcccccccccccceeeecccchhhHHHHHH
Q 001982 736 SNKDPSKHP------QA-LLAKIL----------IDQVDRKLVKQTVMTSVYGVTFVGAREQIK 782 (986)
Q Consensus 736 a~~~~~~~~------~~-~~ak~l----------~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~ 782 (986)
..+=....+ .. .++..+ .-.++|++.|.++=..+||+...|+..-|-
T Consensus 639 ~~~~~~n~Pwq~q~~~l~sl~s~f~gd~~~~Eng~~~l~R~~aKnPlT~~~YGSg~rgia~gva 702 (1118)
T 3q23_A 639 RSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLV 702 (1118)
T ss_dssp HHTTTTCHHHHHHHHHHHHHHHHHCTTEEECTTCCEEECTHHHHHHHHHHHTTCCHHHHHHHHH
T ss_pred hhhcccCCchHHHHHHHHHHHHHhhcccccCCCcchhhhhhhhhCCceeeeecCchHHHHHHHH
Confidence 321111112 01 122222 126899999999999999998877765443
No 4
>2kfn_A Klenow fragment of DNA polymerase I; complex (polymerase/DNA), exonuclease, transferase, transferase/DNA complex; HET: US1; 2.03A {Escherichia coli} SCOP: c.55.3.5 e.8.1.1 PDB: 1d9f_A* 1d9d_A* 1krp_A* 1ksp_A* 1qsl_A* 1kfs_A* 2kfz_A* 2kzm_A* 2kzz_A* 1dpi_A* 1kfd_A* 1kln_A* 1d8y_A*
Probab=67.30 E-value=5.8 Score=47.21 Aligned_cols=210 Identities=17% Similarity=0.152 Sum_probs=125.1
Q ss_pred HHHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCC
Q 001982 664 INLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKH 743 (986)
Q Consensus 664 ~El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~ 743 (986)
.++++++.. |.++ .-|.-|-|-==|-.+|.|.+|....++.+ .-.|||+..|..+-..-.++
T Consensus 364 ~~iR~~f~~--~~g~---~lv~aDysqiElRilA~ls~d~~l~~af~-----~g~Dih~~tA~~~f~~~~e~-------- 425 (605)
T 2kfn_A 364 RRIRQAFIA--PEDY---VIVSADYSQIELRIMAHLSRDKGLLTAFA-----EGKDIHRATAAEVFGLPLET-------- 425 (605)
T ss_dssp HHHHHTBBC--CTTE---EEEEEEETTHHHHHHHHHTTCHHHHHHHH-----TTCCHHHHHHHHHTTCCGGG--------
T ss_pred HhHhheeeC--CCCC---EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCCChhh--------
Confidence 467777763 3343 47889999999999999999999887776 45799999887663210000
Q ss_pred hhHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 744 PQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIM 823 (986)
Q Consensus 744 ~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im 823 (986)
...-.|+..|...--.+||.+.+|...++ |+-.++ |+.+.+...+.||+ +.
T Consensus 426 ---------vt~~~R~~aK~~~fg~~YG~~~~~la~~l-------~i~~~e----------a~~~i~~~~~~~p~---v~ 476 (605)
T 2kfn_A 426 ---------VTSEQRRSAKAINFGLIYGMSAFGLARQL-------NIPRKE----------AQKYMDLYFERYPG---VL 476 (605)
T ss_dssp ---------CCHHHHHHHHHHHHHHHTTCCTTHHHHHH-------TCCTTT----------HHHHHHHHHHHCHH---HH
T ss_pred ---------cCHHHHhhhhhhhccccccCCHHHHHHHc-------CCCHHH----------HHHHHHHHHHHCcc---HH
Confidence 01125899999999999999999988765 443222 24455556667777 55
Q ss_pred HHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecC-CCcCchhhhhccCCCcchhhhhhH---H
Q 001982 824 GWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGS---H 899 (986)
Q Consensus 824 ~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~-~d~vd~rKQ~~Af~PNFIHSLDAs---H 899 (986)
+|+.++.+...+.| .| +|.+|-... +..- +.....|.+.--.+-|++=+==|+ .
T Consensus 477 ~~~~~~~~~a~~~g-~v--~tl~GRrr~-------------------~p~~~s~~~~~r~~~~r~a~N~~iQgsaaDi~k 534 (605)
T 2kfn_A 477 EYMERTRAQAKEQG-YV--ETLDGRRLY-------------------LPDIKSSNGARRAAAERAAINAPMQGTAADIIK 534 (605)
T ss_dssp HHHHHHHHHHHHHS-EE--ECTTCCEEE-------------------CTTTTCSSHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHcC-cE--ECCCCCeEE-------------------CCcccCCCchhhhhhhhhHhhHHhHHHHHHHHH
Confidence 67666665544433 22 555653221 1110 011111111111344555443333 3
Q ss_pred HHHHHH--HHhhcCCc---EEEeeccccC--CCCChhHHHHHHHHHHHHh
Q 001982 900 MMMTAV--ACRDAGLH---FAGVHDSFWT--HACDVDEMNQILRKKFVEL 942 (986)
Q Consensus 900 mmlta~--~~~~~Gi~---FasVHDSFwT--hA~dvd~m~~ilRe~FV~L 942 (986)
+.|..+ .+.+.|+. ...|||.... +...++.+..++++.+-.-
T Consensus 535 ~am~~~~~~l~~~~~~~~~~l~vHDEl~~ev~~~~~~~~~~~v~~~M~~~ 584 (605)
T 2kfn_A 535 RAMIAVDAWLQAEQPRVRMIMQVHDELVFEVHKDDVDAVAKQIHQLMENC 584 (605)
T ss_dssp HHHHHHHHHHHHHCCSEEEEEEETTEEEEEEETTTHHHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHhcCCCceeeEEeccEEEEEcCHHHHHHHHHHHHHHHhcc
Confidence 333322 23445752 3569998776 4567888888888876554
No 5
>4dfk_A DNA polymerase I, thermostable; DNA polymerase, transferase-DNA complex; HET: DNA DOC 0L5; 1.65A {Thermus aquaticus} PDB: 1jxe_A* 3ktq_A* 3lwl_A* 3lwm_A* 3m8s_A* 3m8r_A* 3oju_A* 3rr7_A* 3rr8_A* 3rrg_A* 3ojs_A* 3rtv_A* 3sv3_A* 3sv4_A* 3syz_A* 3sz2_A* 3t3f_A* 4df4_A* 4df8_A* 4dfj_A* ...
Probab=32.49 E-value=21 Score=42.05 Aligned_cols=210 Identities=14% Similarity=0.168 Sum_probs=126.8
Q ss_pred HHHHHHHhcCCCCcceecccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCC
Q 001982 664 INLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKH 743 (986)
Q Consensus 664 ~El~~a~~s~~P~~y~S~lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~ 743 (986)
.+++.++..+ .++ .=|.-|-|-==|-.+|.|.+|....++.+ .-.|||+..|..+-..-.++
T Consensus 300 ~~iR~~f~a~--~G~---~lv~aDySqiElRvlAhls~D~~l~~af~-----~g~Dih~~tA~~~fg~~~~~-------- 361 (540)
T 4dfk_A 300 QRIRRAFIAE--EGW---LLVALDYSQIELRVLAHLSGDENLIRVFQ-----EGRDIHTETASWMFGVPREA-------- 361 (540)
T ss_dssp HHHHTTEECC--TTE---EEEEEEETTHHHHHHHHHHCCHHHHHHHH-----TTCCHHHHHHHHHHTCCGGG--------
T ss_pred HhhhheEeCC--CCC---EEEEecHHHHHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHcCCChhh--------
Confidence 4566766532 344 57889999999999999999998777765 35799999887664321000
Q ss_pred hhHHHHHHhhcccccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 001982 744 PQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIM 823 (986)
Q Consensus 744 ~~~~~ak~l~~~i~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im 823 (986)
...-.|+..|...--.+||.+.+|..+++ |+ +.+ -|+.+.+...+.||+ +.
T Consensus 362 ---------v~~~~R~~aK~~~fg~~YG~~~~~La~~l-------gi-s~~---------eA~~~i~~~~~~~p~---v~ 412 (540)
T 4dfk_A 362 ---------VDPLMRRAAKTINFGVLYGMSAHRLSQEL-------AI-PYE---------EAQAFIERYFQSFPK---VR 412 (540)
T ss_dssp ---------CCHHHHHHHHHHHHHHHTTCCHHHHHHHH-------TC-CHH---------HHHHHHHHHHHHSTH---HH
T ss_pred ---------cCHHHHhHHHHHHHhhhhCCchhHHHHHc-------CC-CHH---------HHHHHHHHHHHhChh---HH
Confidence 01236999999999999999999988765 33 222 234555666667777 55
Q ss_pred HHHHHHHHHHHcCCCcEEEEcCCCCeEEEeeccCCceeEEeeeEEEEEecCCCcCchhhhhccCCCcchhhhhhHHHHHH
Q 001982 824 GWLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVEIRKQRTAFPPNFVHSLDGSHMMMT 903 (986)
Q Consensus 824 ~WL~~~A~~i~~~~~pV~WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlt 903 (986)
+|+.++.....+.| .| +|..|-...-|--. +.....|.+.--.+-|++=+==|+=++..
T Consensus 413 ~~~~~~~~~a~~~G-yv--~Tl~GRrr~~p~~~------------------s~~~~~r~~aeR~a~N~~iQGsaAdi~K~ 471 (540)
T 4dfk_A 413 AWIEKTLEEGRRRG-YV--ETLFGRRRYVPDLE------------------ARVKSVREAAERMAFNMPVQGTAADLMKL 471 (540)
T ss_dssp HHHHHHHHHHHHHS-EE--ECTTCCEEECGGGG------------------CSSHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhCC-cE--ECCCCCeecCCccc------------------cccHHHHhhhhhhHhhhhhHhHHHHHHHH
Confidence 66666655544443 12 46665432211110 11111111112234566555455544433
Q ss_pred H-----HHHhhcCCc-EEEeeccccC--CCCChhHHHHHHHHHHHH
Q 001982 904 A-----VACRDAGLH-FAGVHDSFWT--HACDVDEMNQILRKKFVE 941 (986)
Q Consensus 904 a-----~~~~~~Gi~-FasVHDSFwT--hA~dvd~m~~ilRe~FV~ 941 (986)
| ....+.|.. ...|||.... +...++.+.+++++.+-.
T Consensus 472 ami~~~~~l~~~~~~l~lqVHDElv~ev~~~~~~~~~~~v~~~Me~ 517 (540)
T 4dfk_A 472 AMVKLFPRLEEMGARMLLQVHDELVLEAPKERAEAVARLAKEVMEG 517 (540)
T ss_dssp HHHHHHHHHHHHTCEEEEECSSEEEEEEEGGGHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHhcCCeEEEEEcceEEEEeCHHHHHHHHHHHHHHHhc
Confidence 2 123445664 4569999765 567788899999987754
No 6
>1bgx_T TAQ DNA polymerase; DNA polymerase, FAB, PCR, inhibition, helix-coil dynamics, inhibitor design, complex (polymerase/inhibitor); 2.30A {Thermus aquaticus} SCOP: a.60.7.1 c.120.1.2 c.55.3.5 e.8.1.1 PDB: 1cmw_A 1tau_A* 1taq_A*
Probab=28.71 E-value=29 Score=43.01 Aligned_cols=196 Identities=14% Similarity=0.178 Sum_probs=113.0
Q ss_pred ccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001982 682 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 761 (986)
Q Consensus 682 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvV 761 (986)
.-|.-|-|-==|-.+|.|.+|....++.+ .-.|||+..|..+-..- .+ + ...-.|+..
T Consensus 605 ~lv~aDySqiElRilAhls~D~~l~~af~-----~g~Dih~~tA~~~fg~~---~e-~-------------vt~~~R~~a 662 (832)
T 1bgx_T 605 LLVALDYSQIELRVLAHLSGDENLIRVFQ-----EGRDIHTETASWMFGVP---RE-A-------------VDPLMRRAA 662 (832)
T ss_dssp CEEEEEESSHHHHHHHHTTTCTTHHHHHH-----HTCCHHHHHHHHHHTCC---TT-S-------------CCTTHHHHH
T ss_pred EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCCC---hh-h-------------cCHHHHHHH
Confidence 46788888888899999999998777765 35799998887653211 00 0 012358889
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 001982 762 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPVR 841 (986)
Q Consensus 762 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV~ 841 (986)
|...--.+||.+.+|...++ |+ +.+ -|+.+.+...+.||+ +.+|+.++.+...+.|- |
T Consensus 663 K~~nfgi~YG~~~~gLa~~l-------gi-s~~---------eA~~~i~~~~~~~p~---v~~~~~~~~~~a~~~Gy-v- 720 (832)
T 1bgx_T 663 KTINFGVLYGMSAHRLSQEL-------AI-PYE---------EAQAFIERYFQSFPK---VRAWIEKTLEEGRRRGY-V- 720 (832)
T ss_dssp HHHHHHTTSCCCHHHHHHHS-------SC-CHH---------HHHHHHHHHHHHCHH---HHHHHHHHTHHHHTTSS-C-
T ss_pred HHHHHhhhcCCchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHHHHHHHHHHHHHCCe-E-
Confidence 99999999999999887654 43 222 234455666677777 56777777666554432 2
Q ss_pred EEcCCCCeEEEeeccCCceeEEeeeEEEEEec-CCCcCchhhhhccCCCcchhhhhhHHH---HHHHHH--HhhcCCc-E
Q 001982 842 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQR-EGNLVEIRKQRTAFPPNFVHSLDGSHM---MMTAVA--CRDAGLH-F 914 (986)
Q Consensus 842 WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~-~~d~vd~rKQ~~Af~PNFIHSLDAsHm---mlta~~--~~~~Gi~-F 914 (986)
+|..|-... +.+ .+.....|...--.+-|++=+==|+=+ .|..+. ..+.+.. .
T Consensus 721 -~Tl~GRrr~-------------------~p~i~s~~~~~r~~~eR~a~N~~iQGsAADiik~Ami~~~~~l~~~~~~lv 780 (832)
T 1bgx_T 721 -ETLFGRRRY-------------------VPDLEARVKSVREAAERMAFNMPVQGTAADLMKLAMVKLFPRLEEMGARML 780 (832)
T ss_dssp -CCSSCCCCC-------------------CGGGSCSSHHHHHHHHHHHTTHHHHTHHHHHHHTHHHHHHHHHHHHTCEEE
T ss_pred -EecCCCEEE-------------------CCcccCCCcchhhhhhhhhccHhhHHHHHHHHHHHHHHHHHHHHhCCCeEE
Confidence 344442110 110 011111122212245675544333322 233221 1223553 4
Q ss_pred EEeeccccC--CCCChhHHHHHHHHHHHH
Q 001982 915 AGVHDSFWT--HACDVDEMNQILRKKFVE 941 (986)
Q Consensus 915 asVHDSFwT--hA~dvd~m~~ilRe~FV~ 941 (986)
..|||.... +...++.+..++++.+-.
T Consensus 781 lqVHDElv~evp~~~~~~~~~~v~~~M~~ 809 (832)
T 1bgx_T 781 LQVHDELVLEAPKERAEAVARLAKEVMEG 809 (832)
T ss_dssp EEETTEEEEEC----CHHHHHHHHHHHHS
T ss_pred EEeccEEEEEcCHHHHHHHHHHHHHHHhc
Confidence 569998776 456788888888887654
No 7
>3pv8_A DNA polymerase I; DNA polymerase I, protein-DNA complex, thymine-adenine, CLOS conformation; HET: DNA 2DT D3T; 1.52A {Geobacillus kaustophilus} PDB: 3px0_A* 3px4_A* 3px6_A* 3thv_A* 3ti0_A* 4dse_A* 4dsf_A* 4ds4_A* 4dqp_A* 4dqi_A* 4ds5_A* 4e0d_A* 4dqr_A* 4dqq_A* 3tan_A* 3tap_A* 3taq_A* 3tar_A* 4dqs_A* 3hp6_A* ...
Probab=27.72 E-value=28 Score=41.52 Aligned_cols=197 Identities=15% Similarity=0.170 Sum_probs=118.4
Q ss_pred ccccccCCcchhHHHHHhcCChhhhhhcccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhcccccccc
Q 001982 682 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 761 (986)
Q Consensus 682 lPV~qDGSCNGLQHyAAL~rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~i~RKvV 761 (986)
.=|.-|-|-==|-.+|.|.+|...-.+.+ ...|||+..|..+-..- .+. ...-.|+..
T Consensus 364 ~lv~aDySqiElRilAhls~D~~l~~af~-----~g~Dih~~tA~~~fg~~-------~~~----------vt~~~R~~a 421 (592)
T 3pv8_A 364 LIFAADYSQIELRVLAHIAEDDNLMEAFR-----RDLDIHTKTAMDIFQVS-------EDE----------VTPNMRRQA 421 (592)
T ss_dssp EEEEEEETTHHHHHHHHHHTCHHHHHHHH-----TTCCHHHHHHHHHHSCC-------TTT----------CCHHHHHHH
T ss_pred EEEEechhhHHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCCC-------hhh----------CCHHHHHHH
Confidence 46888999999999999999998877765 35799999987763210 000 011248999
Q ss_pred cccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcEE
Q 001982 762 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASENQPVR 841 (986)
Q Consensus 762 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~~pV~ 841 (986)
|...--.+||.+.+|...++ |+ +.+ -|+.+.+...+.||+ +.+|+.++.+...+.| .|
T Consensus 422 K~~~fg~~YG~~~~~La~~l-------~i-~~~---------eA~~~i~~~~~~~p~---v~~~~~~~~~~a~~~G-yv- 479 (592)
T 3pv8_A 422 KAVNYGIVYGISDYGLAQNL-------NI-SRK---------EAAEFIERYFESFPG---VKRYMENIVQEAKQKG-YV- 479 (592)
T ss_dssp HHHHHHHHTTCCHHHHHHHH-------TC-CHH---------HHHHHHHHHHHHCHH---HHHHHHHHHHHHHHHS-EE-
T ss_pred HHHHHHHHhcCChHHHHHHc-------CC-CHH---------HHHHHHHHHHHHChh---HHHHHHHHHHHHHHcC-CE-
Confidence 99999999999999988765 33 222 134455666677777 5566666655544433 12
Q ss_pred EEcCCCCeEEEeeccCCceeEEeeeEEEEEecC-CCcCchhhhhccCCCcchhhhhhHHHHHHH---H--HHhhcCC---
Q 001982 842 WTTPLGLPVVQPYCKNERHLIRTSLQVLALQRE-GNLVEIRKQRTAFPPNFVHSLDGSHMMMTA---V--ACRDAGL--- 912 (986)
Q Consensus 842 WtTPlGlpVvQ~Y~k~~~~~I~t~lq~~~l~~~-~d~vd~rKQ~~Af~PNFIHSLDAsHmmlta---~--~~~~~Gi--- 912 (986)
+|..|-... +.+- +.....|.+.--.+-|++=+==|+=++..| + ...+.|+
T Consensus 480 -~Tl~GRrr~-------------------~p~i~s~n~~~r~~~eR~a~N~~iQGsaAdi~k~ami~i~~~l~~~~~~~~ 539 (592)
T 3pv8_A 480 -TTLLHRRRY-------------------LPDITSRNFNVRSFAERMAMNTPIQGSAADIIKKAMIDLNARLKEERLQAH 539 (592)
T ss_dssp -ECTTCCEEE-------------------CGGGGCSSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTCCCE
T ss_pred -ECCCCCeee-------------------CCCccccchhhhhhhhhhhhchhhhhHHHHHHHHHHHHHHHHHHhcCCCce
Confidence 355552211 1110 111111211111345775444444333222 2 2345675
Q ss_pred cEEEeecccc--CCCCChhHHHHHHHHHHHHh
Q 001982 913 HFAGVHDSFW--THACDVDEMNQILRKKFVEL 942 (986)
Q Consensus 913 ~FasVHDSFw--ThA~dvd~m~~ilRe~FV~L 942 (986)
=...|||... ++...++.+..++++.+-.-
T Consensus 540 l~lqVHDElv~ev~~~~~~~~~~~v~~~Me~a 571 (592)
T 3pv8_A 540 LLLQVHDELILEAPKEEMERLCRLVPEVMEQA 571 (592)
T ss_dssp EEEECSSEEEEEEEGGGHHHHHHHHHHHHHTS
T ss_pred EEEEEcceeEEEeCHHHHHHHHHHHHHHHhhc
Confidence 2556999875 56678888899998887543
No 8
>1x9m_A DNA polymerase; DNA ploymerase, N-2-acetylaminofluorene, replication block, mutagenesis, transferase/electron transport/DNA complex; HET: DNA 2DT 8FG; 2.10A {Enterobacteria phage T7} SCOP: c.55.3.5 e.8.1.1 PDB: 1skr_A* 1skw_A* 1sl0_A* 1sks_A* 1sl2_A* 1t7p_A* 1t8e_A* 1tk0_A* 1tk5_A* 1tk8_A* 1tkd_A* 1sl1_A* 1x9s_A* 1x9w_A* 1zyq_A* 2ajq_A*
Probab=25.44 E-value=74 Score=38.48 Aligned_cols=107 Identities=16% Similarity=0.114 Sum_probs=72.8
Q ss_pred HHHHHHHhcC------CCCcceecccccccCCcchhHHHHHhc---CChhhhhhcccCCCCCCcchhhHHHHHHHHHHHh
Q 001982 664 INLSEALKSS------SPHSVISHLPIHQDGSCNGLQHYAALG---RNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKR 734 (986)
Q Consensus 664 ~El~~a~~s~------~P~~y~S~lPV~qDGSCNGLQHyAAL~---rD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~ 734 (986)
.+++.++..+ -|.++ .-|.-|-|-==|=.+|.|. +|.....+.+ .+ |||+..|. +-
T Consensus 443 ~~iR~~F~a~~~~~~~~~~G~---~lv~aDySqiElRilAhls~~~~D~~l~~af~--~g----DiH~~tA~-~~----- 507 (698)
T 1x9m_A 443 EQCRAAFGAEHHLDGITGKPW---VQAGIDASGLELRCLAHFMARFDNGEYAHEIL--NG----DIHTKNQI-AA----- 507 (698)
T ss_dssp HHHHHTBSGGGSBCTTTCCBC---EEEEEEETTHHHHHHHHHHHHHHTTHHHHHHH--HS----CHHHHHHH-HS-----
T ss_pred hhhhheeecCcccccCCCCCC---EEEEEehhhhHHHHHHHHhhhcCcHHHHHHHh--CC----CHhHHHHH-Hh-----
Confidence 4666666531 13344 4788899988888899999 9999887765 12 99998765 21
Q ss_pred hcCCCCCCChhHHHHHHhhccc-ccccccccceeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHH
Q 001982 735 DSNKDPSKHPQALLAKILIDQV-DRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALG 813 (986)
Q Consensus 735 da~~~~~~~~~~~~ak~l~~~i-~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~ 813 (986)
++ .|+..|...--..||.+..|...++ |+ +.+ -|+.+.+...
T Consensus 508 --------------------gv~~R~~aK~~nfg~~YG~g~~~La~~l-------gi-s~~---------eA~~~i~~~~ 550 (698)
T 1x9m_A 508 --------------------ELPTRDNAKTFIYGFLYGAGDEKIGQIV-------GA-GKE---------RGKELKKKFL 550 (698)
T ss_dssp --------------------CCSSHHHHHHHHHHHHTTCCHHHHHTTT-------TC-CHH---------HHHHHHHHHH
T ss_pred --------------------CCchHhhhHHHHHccccCCCHHHHHHHc-------CC-CHH---------HHHHHHHHHH
Confidence 12 2999999999999999999888543 32 221 2344555666
Q ss_pred HHHHHHHHH
Q 001982 814 EIFEAARSI 822 (986)
Q Consensus 814 e~f~~A~~i 822 (986)
+.||+.+..
T Consensus 551 ~~~p~v~~~ 559 (698)
T 1x9m_A 551 ENTPAIAAL 559 (698)
T ss_dssp HTCHHHHHH
T ss_pred HHCcCHHHH
Confidence 677775544
No 9
>1gdt_A GD resolvase, protein (gamma delta resolvase); protein-DNA complex, double helix, overhanging base, DNA binding protein/DNA complex; 3.00A {Escherichia coli} SCOP: a.4.1.2 c.53.1.1 PDB: 1zr4_A 1zr2_A 2gm4_A 1res_A 1ret_A
Probab=14.59 E-value=2.5e+02 Score=27.47 Aligned_cols=60 Identities=15% Similarity=0.127 Sum_probs=43.9
Q ss_pred hHHHHHHHHHHhhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHH
Q 001982 897 GSHMMMTAVACRDAGLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQT 957 (986)
Q Consensus 897 AsHmmlta~~~~~~Gi~FasVHDSFwThA~dvd~m~~ilRe~FV~Lys~~il~~l~e~f~~ 957 (986)
..+++.....|.+.|+.|.++.|.+-| ...++.|.-.+...|-+++++.+-++..+-...
T Consensus 73 ~~~~~~~~~~l~~~gv~l~~~~~~~d~-~~~~~~~~~~i~~~~ae~E~~~i~~R~~~g~~~ 132 (183)
T 1gdt_A 73 TADMIQLIKEFDAQGVSIRFIDDGIST-DGEMGKMVVTILSAVAQAERQRILERTNEGRQE 132 (183)
T ss_dssp HHHHHHHHHHHHHTTCEEEEGGGCCBC-TTHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCEEEEecCCccC-CChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666666788999999999999854 344566666677788888888777777665543
No 10
>3g13_A Putative conjugative transposon recombinase; resolvase, PSI-II, target 11223F, structural genomics, prote structure initiative; 2.00A {Clostridium difficile}
Probab=12.82 E-value=3.3e+02 Score=26.14 Aligned_cols=62 Identities=5% Similarity=-0.049 Sum_probs=47.2
Q ss_pred hHHHHHHHHHHhhcCCcEEEeeccccCCCCChhHHHHHHHHHHHHhcCcchHHHHHHHHHHhC
Q 001982 897 GSHMMMTAVACRDAGLHFAGVHDSFWTHACDVDEMNQILRKKFVELYNMPMLENLLESFQTSY 959 (986)
Q Consensus 897 AsHmmlta~~~~~~Gi~FasVHDSFwThA~dvd~m~~ilRe~FV~Lys~~il~~l~e~f~~~~ 959 (986)
..+++.....|.+.|+.|.++.|.+-|. ...+.|...+...|-+++++.+-++..+-+..+-
T Consensus 91 ~~~~~~~~~~l~~~gv~l~~~~~~~d~~-~~~~~~~~~i~~~~ae~E~~~~~~R~~~g~~~~~ 152 (169)
T 3g13_A 91 TLDTLKYVRMLKERNIAVYFEDEKINTL-TMDGELLLVVLSSVAQQEVENISANVKKGLKMKM 152 (169)
T ss_dssp HHHHHHHHHHHHTTTCEEEETTTTEETT-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHSC
T ss_pred hHHHHHHHHHHHHcCCEEEEecCCcCCC-CcchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566666667889999999999987653 3456677778888999988888888877776543
Done!