Query 002216
Match_columns 952
No_of_seqs 254 out of 441
Neff 5.1
Searched_HMMs 29240
Date Mon Mar 25 17:20:12 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002216.a3m -d /work/01045/syshi/HHdatabase/pdb70.hhm -o /work/01045/syshi/hhsearch_pdb/002216hhsearch_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 1E-185 4E-190 1667.2 50.2 737 166-949 19-816 (883)
2 3spa_A Mtrpol, DNA-directed RN 100.0 7E-175 2E-179 1574.8 54.6 726 171-948 296-1058(1134)
3 3q23_A Virion RNA polymerase; 97.8 8.6E-05 2.9E-09 88.6 12.5 304 487-809 338-703 (1118)
4 2kfn_A Klenow fragment of DNA 33.1 17 0.00057 43.1 2.2 133 691-873 365-497 (605)
5 4dfk_A DNA polymerase I, therm 23.6 30 0.001 40.5 2.2 192 691-950 301-498 (540)
6 1bgx_T TAQ DNA polymerase; DNA 22.4 37 0.0013 41.9 2.7 114 708-863 605-718 (832)
7 3pv8_A DNA polymerase I; DNA p 19.6 40 0.0014 40.0 2.1 113 708-862 364-476 (592)
8 1iv0_A Hypothetical protein; r 14.3 66 0.0023 29.2 1.7 36 691-726 42-81 (98)
9 1d2v_A Myeloperoxidase; heme-p 11.5 51 0.0017 30.3 0.0 11 711-721 9-19 (104)
10 4fjo_A DNA repair protein REV1 10.6 5E+02 0.017 23.3 6.3 50 804-857 15-64 (97)
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=1.2e-185 Score=1667.24 Aligned_cols=737 Identities=27% Similarity=0.436 Sum_probs=632.7
Q ss_pred HHhhhhHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHHh-hccC
Q 002216 166 EYREMKKRKFN-LLRRRQVKQETEAWERMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQR-TKKQ 243 (952)
Q Consensus 166 ~~~~~~~~~~~-~l~~RQ~~LE~~~~~~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~~-~~~~ 243 (952)
+-++.-...|+ .|++||++||++++++|++||++++++++++|+++++|++++++.+|+++|+++|+++++..+ +.|.
T Consensus 19 ~~~~~~~~~~~~~l~~rQ~~lE~e~~~~a~~r~~~~~~~~~~~g~~~~~~~~~~l~~~~~~~l~~~i~~~~~~~~~~~g~ 98 (883)
T 1msw_D 19 IPFNTLADHYGERLAREQLALEHESYEMGEARFRKMFERQLKAGEVADNAAAKPLITTLLPKMIARINDWFEEVKAKRGK 98 (883)
T ss_dssp HHHHHHTTTTCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTTCGGGSTTTHHHHHHHHHHHHHHHHHHHHHHHHSCSC
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccCChhhHHHHHHHHHHHHHHHHHHHHHHhcccCc
Confidence 34455556677 678999999999999999999999999999999999999999999999999999999988776 3567
Q ss_pred ccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhhhhHHHHH
Q 002216 244 KAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIADTEEVLS 323 (952)
Q Consensus 244 r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~k~~~~~~~~~~~~~~~ 323 (952)
++.|+|||++|+||++|+|||+++|+++++ .+++++++++.+||++||+|++++++.++.++++.+.
T Consensus 99 ~~~~~~~L~~l~~e~lA~iti~~~l~~~~~---~~~~~~~~~~~~iG~ave~E~~~~~~~~~~~~~~~~~---------- 165 (883)
T 1msw_D 99 RPTAFQFLQEIKPEAVAYITIKTTLACLTS---ADNTTVQAVASAIGRAIEDEARFGRIRDLEAKHFKKN---------- 165 (883)
T ss_dssp CCTTTTTTTSSCHHHHHHHHHHHHHHHHHH---CSCCBHHHHHHHHHHHHHHHHHHHHHHHSSCSSHHHH----------
T ss_pred chHHHHHHHhCCHHHHHHHHHHHHHHHhcc---cCCccHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHH----------
Confidence 899999999999999999999999999987 4578999999999999999999999987665543221
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHhh-c-----CCCCCCCCHHHHHHHHHHHHHHHHHh-ccccCCCCCCCCCCCCccCc
Q 002216 324 KEKELLRKRVNSLIKSKRVMEAQKLL-K-----NEETKPWGRDTQAKLGSRLVELLIET-AYVQHPVNPADYSPPDVRPA 396 (952)
Q Consensus 324 ~~~~~~~~~~~~~~~~~~~~~~~~~~-~-----~~~~~~W~~~~~~kvG~~Ll~~L~e~-~~i~~~~~~~~~~~~~~~pa 396 (952)
..+.++++.+...++...+.+.... + ++++.+|+..++++||++|+++|+++ +.|++....
T Consensus 166 -~~~~l~~~~~~~~k~~~~~~~~~~~~~~g~~~~~~~~~W~~~~~~~vG~~Li~~l~~~~~~~~~~~~~----------- 233 (883)
T 1msw_D 166 -VEEQLNKRVGHVYKKAFMQVVEADMLSKGLLGGEAWSSWHKEDSIHVGVRCIEMLIESTGMVSLHRQN----------- 233 (883)
T ss_dssp -TSHHHHHSCSHHHHHHHHHHHHHHSTTTTTTTTCCCCCCCTTHHHHHHHHHHHHHHHHCTTEEEECC------------
T ss_pred -HHHHHHhcccHHHHHHHHHHHHHHhhhccccccCCCCCCCHHHHHHHHHHHHHHHHHhhCCcceeccc-----------
Confidence 1123333333333333333333311 1 26689999999999999999999995 666653221
Q ss_pred eEEEEEeeecCCCCccceeEEEEecCHHHHHHHHhhh---hcccCCCCceeeCCCCCcCCCCcccccC---CccceecCC
Q 002216 397 FRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSA---KHMLIPYVPMLVPPKKWKGYNKGGYLFL---PSYVMRTHG 470 (952)
Q Consensus 397 F~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~---~~~~~~~LPMlvpPkpW~~~~~GGYL~~---~s~~~R~~~ 470 (952)
.|.. ++++|+|++||++++.+.+.. ..+.+.+|||||||+||+++.+||||+. +..++|+..
T Consensus 234 -----------~~~~-~k~~~~i~~~~~~~~~l~~~~~~~~~~~~~~lPMlvpP~pW~~~~~GGYl~~~~~~~~~ir~~~ 301 (883)
T 1msw_D 234 -----------AGVV-GQDSETIELAPEYAEAIATRAGALAGISPMFQPCVVPPKPWTGITGGGYWANGRRPLALVRTHS 301 (883)
T ss_dssp -------------------CCEEEECHHHHHHHHHHHHHHTTSCCCCCCBSSCCBCCSSSBSCBSSSCCSSCCBSEECSS
T ss_pred -----------cCCC-CceeeEEEeCHHHHHHHhhcccchhhcCCCCCceeeCCccCCCCCCCCccCCCcccchhhcccC
Confidence 1211 367899999999999998643 2345569999999999999999999974 345677653
Q ss_pred cHHHHHHHHhccccChHHHHHHHHhhcCceeEEcHHHHHHHHHHHH-cCCCCCCCCCCCCCCCCCCCCCCC--HHHHHHH
Q 002216 471 SRKQQEALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWV-SGGNIAGLVDRNDVLIPEKPLSED--MTEVQKW 547 (952)
Q Consensus 471 ~~~q~~~l~~~~~~~l~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~-~g~~i~~l~~~~~~p~P~~p~~~d--~~~~~~w 547 (952)
. .++++..+++++.||++||+||+|||+||++||+||+++|+ +|+++++||+..+.|+|++|++.| ++++++|
T Consensus 302 ~----~~~~~~~~~~l~~v~~aLN~L~~t~w~IN~~vL~vi~~~~~~~g~~~~~ip~~~~~~~P~~p~~~d~~~~~~~~~ 377 (883)
T 1msw_D 302 K----KALMRYEDVYMPEVYKAINIAQNTAWKINKKVLAVANVITKWKHCPVEDIPAIEREELPMKPEDIDMNPEALTAW 377 (883)
T ss_dssp T----THHHHTTTCCCHHHHHHHHHHHTCCEEECHHHHHHHHHHTTCSSCSSTTCCCSSCCCCCCC-----------CCT
T ss_pred H----HHHHhccccchHHHHHHHHHhccCCeEecHHHHHHHHHHHhhcCCcccCCCCcCcCCCCCCCCccccCHHHHHHH
Confidence 2 45666677899999999999999999999999999999999 999999999988899999987543 6788999
Q ss_pred HHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccCccCCcch
Q 002216 548 KWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEGRPLGKSG 627 (952)
Q Consensus 548 k~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~FaegkpLG~~G 627 (952)
++.++++++.++++||+||+++++|++|++|+|++.||||||+|||||+||+| ||||||+|+|||||+||+|+|||++|
T Consensus 378 k~~~~~~~~~~~~~~S~r~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~p-~Ln~~GsDl~RsLL~FaegkpLG~~G 456 (883)
T 1msw_D 378 KRAAAAVYRKDKARKSRRISLEFMLEQANKFANHKAIWFPYNMDWRGRVYAVS-MFNPQGNDMTKGLLTLAKGKPIGKEG 456 (883)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHTTTSSSSSCSCBBCCEEEETTSCEEESS-SSCTTSCHHHHHHEEESSCEECHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeEEeecccCCCCcCCCCC-CCCCCcchHHHHHHHhccCCccChhH
Confidence 99999999999999999999999999999999988999999999999999995 99999999999999999999999999
Q ss_pred hHHHHHHHhhhhCCCCCCCCHHHHHHHHHHhHHHHHHhccCCCCCchhhhhCCChHHHHHHHHHHHHHHhcCCCCcceec
Q 002216 628 LRWLKIHLANLFSGGVEKLSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALKSSSPHSVISH 707 (952)
Q Consensus 628 l~WLKIhlAN~yG~G~DK~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLA~C~El~~al~s~~P~~y~S~ 707 (952)
|+|||||+||+| |+||+||+||++||++|+++|++||+|||+ .+||++||+||||||+|+||++|+++|+ +|+||
T Consensus 457 l~WLkIhlAN~~--G~dK~s~~eRi~wv~~n~~~I~dsA~~Pl~-~~wW~~Ad~PwQfLA~C~El~~a~~~~~--~y~S~ 531 (883)
T 1msw_D 457 YYWLKIHGANCA--GVDKVPFPERIKFIEENHENIMACAKSPLE-NTWWAEQDSPFCFLAFCFEYAGVQHHGL--SYNCS 531 (883)
T ss_dssp HHHHHHHHHHHT--TCCSSCHHHHHHHHHHTHHHHHHHHHCHHH-HCGGGGSSSHHHHHHHHHHHHHHHHHCT--TCEEC
T ss_pred HHHHHHHHHHhc--CCCcCCHHHHHHHHHHHHHHHHHHhcCccc-chHHHcCCcHHHHHHHHHHHHHHHhCCC--ccccc
Confidence 999999999999 899999999999999999999999999999 5899999999999999999999999876 89999
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCC------C------------
Q 002216 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSK------H------------ 769 (952)
Q Consensus 708 lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~------~------------ 769 (952)
|||||||||||||||||||||.+||++|||+|+|+|||||+.||+.|.+.+++|+.+|.+. +
T Consensus 532 lPVhqDgSCnGLQHyAALgrD~~ga~~VNL~psd~PqDvYs~Va~~v~~~~~~da~~g~~~~~~~~~d~~~g~i~e~~~~ 611 (883)
T 1msw_D 532 LPLAFDGSCSGIQHFSAMLRDEVGGRAVNLLPSETVQDIYGIVAKKVNEILQADAINGTDNEVVTVTDENTGEISEKVKL 611 (883)
T ss_dssp CCEEEECSCHHHHHHHHHHTCTTHHHHTTCSCCSSCCCHHHHHHHHHHHHHHHHHTTSCCCCCCCSSSSSSCCSSCCCCC
T ss_pred cccccCCCCcHHHHHHHHhcChhhhhHhCCCCCCCCcchHHHHHHHHHHHHHHHHhcccccccccccccccccchhhccc
Confidence 9999999999999999999999999999999999999999999999999999998765321 0
Q ss_pred -hhHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCCh----hhHHHHHHHHHHHHHHHHHHHHHH
Q 002216 770 -PQALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDD----RQLFAAACYAAKVTLTALGEIFEA 844 (952)
Q Consensus 770 -~~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~----~~~~~~a~Ylak~v~~ai~e~f~~ 844 (952)
.....+++|.++|+||+|||||||+|||||++|+++||.++|+++++..++ .....+|+|+|++||+||+++|++
T Consensus 612 ~~~~l~~~~l~~~i~RKvvKqtVMT~vYGvT~~Ga~~qI~~~l~~~~~~~~~~~~~~~~~~~a~yla~~i~~ai~~~f~~ 691 (883)
T 1msw_D 612 GTKALAGQWLAYGVTRSVTKRSVMTLAYGSKEFGFRQQVLEDTIQPAIDSGKGLMFTQPNQAAGYMAKLIWESVSVTVVA 691 (883)
T ss_dssp CHHHHHHHHHTTCCCHHHHHHHHHGGGGTCCHHHHHHHHHHHTHHHHHHTSCCCSCSSHHHHHHHHHHHHHHHHHHHCHH
T ss_pred chhHHHHHHHhcCCCHHHhccceeeeeeCCcchhhHHHHHHHHhhhhccccccccccchhHHHHHHHHHHHHHHHHHHHH
Confidence 112346788999999999999999999999999999999999874321111 123488999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHcC------------CCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEE---EecCC---CCCCh
Q 002216 845 ARSIMGWLGDCAKVIASE------------NQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLA---LQREG---NLVKI 906 (952)
Q Consensus 845 A~~im~WL~~~A~~i~~~------------~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~---l~~~~---d~vd~ 906 (952)
|+.||+||++||++|+++ +.||.||||+||||+|||++.++++|+|.+|.++ +..+. +++|+
T Consensus 692 a~~im~wL~~~a~~i~~~v~~~~~~~~~~~~~pv~W~TPlGlpV~Q~Y~~~~~~~V~t~l~~~~~i~l~~~~~~~~~~d~ 771 (883)
T 1msw_D 692 AVEAMNWLKSAAKLLAAEVKDKKTGEILRKRCAVHWVTPDGFPVWQEYKKPIQTRLNLMFLGQFRLQPTINTNKDSEIDA 771 (883)
T ss_dssp HHHHHHHHHHHHHHHHSCEECTTTCCEEECCCCEEEECTTSCEEEECCBCCSSCCEECSSSCEECCCCSCSSCCSCCBCH
T ss_pred HHHHHHHHHHHHHHHHhhcccccccccccCCCeEEEECCCCCEEEEEecCCCceEEEEeecceeeEeeecccccccccch
Confidence 999999999999999998 9999999999999999999999999999998653 23332 35999
Q ss_pred hhhhcCCCCcchhhhhHHHHHHHHHHHhHc-CC-cEEEeeccccc
Q 002216 907 RKQRTAFPPNFVHSLDGSHMMMTAVACRDA-GL-HFAGLSFQSAL 949 (952)
Q Consensus 907 rKQ~~Af~PNFIHSLDAsHmmlTa~~c~~~-Gi-~FaaVHDn~~~ 949 (952)
+||++|||||||||||||||||||++|.++ || +||+|||||.-
T Consensus 772 ~Kq~~af~PNFIHSLDAsHmmlta~~~~~~~gl~~fa~VHDsfwT 816 (883)
T 1msw_D 772 HKQESGIAPNFVHSQDGSHLRKTVVWAHEKYGIESFALIHDSFGT 816 (883)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTCCCCCEECSSEEEE
T ss_pred HHHhcCCCchhHhhHHHHHHHHHHHHHHHhcCCCceEEEeccccC
Confidence 999999999999999999999999999998 99 69999999963
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=6.9e-175 Score=1574.84 Aligned_cols=726 Identities=33% Similarity=0.584 Sum_probs=575.7
Q ss_pred hHHHHHHHHHHHHHHHHHH------HH------HHHHHHHHHHHHHHHcccCCCChhHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 171 KKRKFNLLRRRQVKQETEA------WE------RMVDEYKELEAKMIEKRLAPNLPHIKGLFLGWFGPLSEAIEREQKMQ 238 (952)
Q Consensus 171 ~~~~~~~l~~RQ~~LE~~~------~~------~a~~r~r~~~~~~~~~g~a~~~~~~~~ll~~w~~~L~~~I~~e~~~~ 238 (952)
+....+.+.+.|+.+|..+ ++ ..+.++|+. +.++..+|...|..+|+++....
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 3445677788899999762 11 122234444 35566889999999999877654
Q ss_pred hh--ccCccchhhhhccCChhHHHHHHHHHHHHHHhcCCCCCcchHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhhh
Q 002216 239 RT--KKQKAAYAPHIELLPADKVAVIVMHKMMGLVMAGHEDRCVQVVQAAVHIGMAIEQEIRIHSFLEKTKNYKRKKIIA 316 (952)
Q Consensus 239 ~~--~~~r~~y~p~L~~l~~e~lA~Iti~~~l~~~~~~~~~~~~~~~~~a~~IG~aVe~E~~~~~~~~k~~k~~~~~~~~ 316 (952)
.. ...+..++|||+.|+.+.++.|.|.++..+..+ |..++.++..||..|++++.+++-...+.
T Consensus 361 ~~~~~~~~~~~~p~l~~l~~~~~~~~~~~~~~~l~~~-----g~~~~~~~~~lg~~~~~~~~~~~~~~~~~--------- 426 (1134)
T 3spa_A 361 EREVYEGRFSLYPFLCLLDEREVVRMLLQVLQALPAQ-----GESFTTLARELSARTFSRHVVQRQRVSGQ--------- 426 (1134)
T ss_dssp HHHHHTTCCCSTGGGGSSCHHHHHHHHHHHHHHCCTT-----CEEHHHHHHHHHHHHHHHHHHHHHHHHTH---------
T ss_pred HHhhccCCCccccceeeCCHHHHHHHHHHHHHHhccc-----CccHHHHHHHHHHHHHHHHHHHHHHhhhH---------
Confidence 32 456889999999999999999777777664332 34688899999999999998865322110
Q ss_pred hhHHHHHHHHHHHHHHHHhHHHH-------HHHHHHHHhhcC--CCCCCCCHHHHHHHHHHHHHHHHHhccccCCCCCCC
Q 002216 317 DTEEVLSKEKELLRKRVNSLIKS-------KRVMEAQKLLKN--EETKPWGRDTQAKLGSRLVELLIETAYVQHPVNPAD 387 (952)
Q Consensus 317 ~~~~~~~~~~~~~~~~~~~~~~~-------~~~~~~~~~~~~--~~~~~W~~~~~~kvG~~Ll~~L~e~~~i~~~~~~~~ 387 (952)
+.+..+...+...-+... .-.+.|+.+... ..+.+|+..++++||++|+++|+++++|.+...++
T Consensus 427 -----~~~~~~~y~~y~~~~~~~~~~~~~~~~r~~w~~l~~~~~~~~~~W~~~~~~kvG~~Ll~~L~~~~~i~~~~~~~- 500 (1134)
T 3spa_A 427 -----VQALQNHYRKYLCLLASDAEVPEPCLPRQYWEALGAPEALREQPWPLPVQMELGKLLAEMLVQATQMPCSLDKP- 500 (1134)
T ss_dssp -----HHHHHHHHHHHGGGTCSSCCCSSCCCHHHHHHHHHCCCCGGGCCCCHHHHHHHHHHHHHHHHHHCBCCC------
T ss_pred -----HHHHHHHHHHHHHHHhcCCccCCCCChHHHHHHhCCcccCCCCCCCHHHHHHHHHHHHHHHHhhccCCccccCC-
Confidence 011111111111111100 012334444433 45789999999999999999999999998765543
Q ss_pred CCCCCccCceEEEEEeeecCCCCccceeEEEEecCHHHHHHHHhhhhc---ccCCCCceeeCCCCCcCCCCcccccCCcc
Q 002216 388 YSPPDVRPAFRHRFKTILKHPGQKTTKRYGVVECDPLVLEGLDRSAKH---MLIPYVPMLVPPKKWKGYNKGGYLFLPSY 464 (952)
Q Consensus 388 ~~~~~~~paF~h~~~~~~~~~g~~~~k~~gvi~~~~~~~~~l~~~~~~---~~~~~LPMlvpPkpW~~~~~GGYL~~~s~ 464 (952)
++....+|||+|+|++. . ++++|+|++||.+++.+++.... +.+.+|||||||+||+++++||||+.++.
T Consensus 501 ~~~~~~~paf~h~y~~~---~----~~~~G~i~~hp~~~~~l~~~~~~~~~~~~~~lPMlvpP~pW~~~~~GGYl~~~t~ 573 (1134)
T 3spa_A 501 HRSSRLVPVLYHVYSFR---N----VQQIGILKPHPAYVQLLEKAAEPTLTFEAVDVPMLCPPLPWTSPHSGAFLLSPTK 573 (1134)
T ss_dssp ------CBSEEEEEC-----------CCCEEEEECHHHHHHHHHHTCSEEEEEGGGSCBSSCCEEEEETTEEESSSSCCC
T ss_pred CCCcccccceEEEEEEE---c----CcEEEEEEECHHHHHHHHhccccccccCcCCCCcccCCCCCCCCCCceeEecCcc
Confidence 34456799999999764 3 36799999999999999875432 33459999999999999999999999999
Q ss_pred ceecCCcHHHH-HHHHhccccChHHHHHHHHhhcCceeEEcHHHHHHHHHHHHc-CCCCCCCCCCC-CCCCCC---CCCC
Q 002216 465 VMRTHGSRKQQ-EALKSVTGNCMKKVFEALDTLGSTKWRVNKQVLSVLESIWVS-GGNIAGLVDRN-DVLIPE---KPLS 538 (952)
Q Consensus 465 ~~R~~~~~~q~-~~l~~~~~~~l~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~-g~~i~~l~~~~-~~p~P~---~p~~ 538 (952)
+||+++...|. ..+++..+++|+.||++||+||+|||+||++||+|+.++|++ |+++.++|+.. +.|.|+ .|.+
T Consensus 574 ~mR~~~~~~q~~~~l~~~~~~~l~~v~~aLN~Lg~t~W~IN~~VLdVv~~vw~~~G~~~~~iP~~~~~~p~~p~~~~~~~ 653 (1134)
T 3spa_A 574 LMRTVEGATQHQELLETCPPTALHGALDALTQLGNCAWRVNGRVLDLVLQLFQAKGCPQLGVPAPPSEAPQPPEAHLPHS 653 (1134)
T ss_dssp SBCCCTTHHHHHHHHHSSCGGGGHHHHHHHHHHHTCEEEECHHHHHHHHHHHTTTCBGGGTBCCCC--------------
T ss_pred eeecCCChHHHHHHHHhccccccHHHHHHHHHHhCCCcEecHHHHHHHHHHHHhcCCCcCCCCCCccccCCCCCCCCCCC
Confidence 99997655444 445556678999999999999999999999999999999986 55678888753 345444 2345
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcc
Q 002216 539 EDMTEVQKWKWSVRKAKKINQERHSQRCDTELKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFA 618 (952)
Q Consensus 539 ~d~~~~~~wk~~~~~~~~~~~~~~S~R~~~~~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~Fa 618 (952)
.++++.++|++++++.++.++++||+||+++++|+||++|+|+ .||||||+|||||+||+||||||||+|+|||||+||
T Consensus 654 ~~~~~~~~~kr~~~~~~~~~~~~~S~Rc~~~~kL~iA~~f~~~-~fYfPhnlDFRGR~Yp~~p~LnhqGsDl~RsLL~Fa 732 (1134)
T 3spa_A 654 AAPARKAELRRELAHCQKVAREMHSLRAEALYRLSLAQHLRDR-VFWLPHNMDFRGRTYPCPPHFNHLGSDVARALLEFA 732 (1134)
T ss_dssp --------------------CTHHHHHHHHHHHHHHHHHHTTS-CEECCEEECTTCCEEESCSSSCSCSSHHHHHTEEES
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHhcCC-eeecccccCCCCcCcCCCCCcCcccchHHHHHHHhc
Confidence 5677888999999888899999999999999999999999996 999999999999999999999999999999999999
Q ss_pred cCccCCcchhHHHHHHHhhhhCCCCCC-CCHHHHHHHHHHhHHHHHHhccCCCCCchhhhhCCChHHHHHHHHHHHHHHh
Q 002216 619 EGRPLGKSGLRWLKIHLANLFSGGVEK-LSHDGRLAFVENHLYEIFDSAENPINGSRWWLTAEDPFQCLAACINLSEALK 697 (952)
Q Consensus 619 egkpLG~~Gl~WLKIhlAN~yG~G~DK-~S~deRi~wv~~n~~~I~dsA~dPL~g~~wW~~AD~PwQfLA~C~El~~al~ 697 (952)
+|+|||++|++|||||+||+| |+|| .||+||++|+++|+++|++||+|||+|.+||++||+||||||+||||++|++
T Consensus 733 egkpLG~~Gl~WLkIhlAN~~--G~dKk~s~~eRi~wv~~n~~~I~dsA~~Pl~g~~wW~~Ad~PwQfLA~C~El~~a~~ 810 (1134)
T 3spa_A 733 QGRPLGPHGLDWLKIHLVNLT--GLKKREPLRKRLAFAEEVMDDILDSADQPLTGRKWWMGAEEPWQTLACCMEVANAVR 810 (1134)
T ss_dssp SCEECTTTHHHHHHHHHHHHH--SCCTTSCHHHHHHHHHHHHHHHHHHHHCTTTSCCGGGGSSSHHHHHHHHHHHHHHHT
T ss_pred cCCcCCcchHHHHHHHHHHhc--CCCcCCCHHHHHHHHHHHHHHHHHHHhCcccchhHHHhCCCHHHHHHHHHHHHHHHh
Confidence 999999999999999999999 7998 7999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHH
Q 002216 698 SSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKI 777 (952)
Q Consensus 698 s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~ 777 (952)
++||++|+|||||||||||||||||||||||.+||++|||+|+|+|||||+.||+.|++.+++|++++ ..+|++
T Consensus 811 ~~dp~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNL~psd~PqDvYs~Va~~V~~~~~~Da~~~------~~~a~~ 884 (1134)
T 3spa_A 811 ASDPAAYVSHLPVHQDGSCNGLQHYAALGRDSVGAASVNLEPSDVPQDVYSGVAAQVEVFRRQDAQRG------MRVAQV 884 (1134)
T ss_dssp SSSGGGCEECCEEEECCSSHHHHHHHHHTTCHHHHHHTTCSCCSSCCCHHHHHHHHHHHHHHHHHHTT------CHHHHH
T ss_pred cCCCccccccCccccCCCCcHHHHHHHHccChhhHHHhCCCCCCCcccHHHHHHHHHHHHHHhhhhcC------hHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999998766 378999
Q ss_pred hhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 778 LIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAK 857 (952)
Q Consensus 778 l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~ 857 (952)
|.++|+||+|||||||+|||||++|+++||.++|++.+.++++ .++.+++|+|++||+||+++|++|+.||+||++||+
T Consensus 885 l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~e~~~~~~~-~~~~~a~Yla~~i~~si~e~f~~a~~im~WL~~~A~ 963 (1134)
T 3spa_A 885 LEGFITRKVVKQTVMTVVYGVTRYGGRLQIEKRLRELSDFPQE-FVWEASHYLVRQVFKSLQEMFSGTRAIQHWLTESAR 963 (1134)
T ss_dssp TTTCCCHHHHHHHHHHHHHCCSSSHHHHHHHHHHHTCTTSCTT-THHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_pred hhCCCChhhcccceEEeeecceehhHHHHHHHHHHhcccCchH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999999999999999999999999988666654 678999999999999999999999999999999999
Q ss_pred HHHcCCCcEEEEcCCCCeEEeeeccCcce-eEEeeeEEEEEecCCC---CCChhhhhcCCCCcchhhhhHHHHHHHHHHH
Q 002216 858 VIASENQPVRWTTPLGLPVVQPYCKNERH-LIRTSLQVLALQREGN---LVKIRKQRTAFPPNFVHSLDGSHMMMTAVAC 933 (952)
Q Consensus 858 ~i~~~~~pV~WtTPlGlpVvQpY~k~~~~-~I~t~lq~v~l~~~~d---~vd~rKQ~~Af~PNFIHSLDAsHmmlTa~~c 933 (952)
+|++++.||.||||+||||+|||++..+. .|.|.+|++++..+++ ++|++||++|||||||||||||||||||++|
T Consensus 964 ~i~~~~~pV~WtTPlGlpVvQpY~k~~k~~~i~~~~q~v~~~~~~d~~~~~d~~KQ~~afpPNFIHSLDAsHmmlTa~~c 1043 (1134)
T 3spa_A 964 LISHMGSVVEWVTPLGVPVIQPYRLDSKVKQIGGGIQSITYTHNGDISRKPNTRKQKNGFPPNFIHSLDSSHMMLTALHC 1043 (1134)
T ss_dssp HHHHTTCCCEEECTTSCEEECCCBCC-----------------------CBCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhcCCCCEEEECCCCCEEEEeccCCCceeEecCCceEEEEeccCCcccCCCHHHHhccCCchHHhhHHHHHHHHHHHHH
Confidence 99999999999999999999999997655 7889999998886543 6999999999999999999999999999999
Q ss_pred hHcCCcEEEeecccc
Q 002216 934 RDAGLHFAGLSFQSA 948 (952)
Q Consensus 934 ~~~Gi~FaaVHDn~~ 948 (952)
.+.||+||+|||||.
T Consensus 1044 ~~~gi~FasVHDSfw 1058 (1134)
T 3spa_A 1044 YRKGLTFVSVHDCYW 1058 (1134)
T ss_dssp HHTTCCCEEETTEEE
T ss_pred HhCCCCEEEeecccc
Confidence 999999999999985
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=97.81 E-value=8.6e-05 Score=88.62 Aligned_cols=304 Identities=15% Similarity=0.153 Sum_probs=176.5
Q ss_pred HHHHHHHHhhcCceeEEcHHHHHHHHHHHHcC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhh
Q 002216 487 KKVFEALDTLGSTKWRVNKQVLSVLESIWVSG-GNIAGLVDRNDVLIPEKPLSEDMTEVQKWKWSVRKAKKINQERHSQR 565 (952)
Q Consensus 487 ~~v~~aLN~Lqst~WrIN~~VL~vi~~~w~~g-~~i~~l~~~~~~p~P~~p~~~d~~~~~~wk~~~~~~~~~~~~~~S~R 565 (952)
+.+-.+|...|.+|++||..+..+...+=+.+ ..+.|.- ++..|. -..+..+. +.-+ ..+.+
T Consensus 338 ~lqakalkkaQ~q~hrvn~~m~~~~e~LgEDalltmlGa~---~l~~e~----ln~~~RkS-------lEGK---N~sV~ 400 (1118)
T 3q23_A 338 PEQKAALKAEQATEFYVHTPMVQFYETLGKDRILELMGAG---TLNKEL----LNDNHAKS-------LEGK---NRSVE 400 (1118)
T ss_dssp HHHHHHHHHHHHCCBEECHHHHHHHHHHHHHHHHHHHSCC---SCCTTS----SCHHHHHH-------HHHH---HHHHH
T ss_pred HHHHHHHHHhhccCceecccHHHHHHHhchhHHHHHhCcc---cccccc----cchhHHhh-------hhcc---cHHHH
Confidence 44667788899999999999999977764433 1222321 111121 11111111 1111 11112
Q ss_pred hhhh-------HHHHHHHhhcCCCceeecccCCCCCcccCCCCCCCCCCccchhhhhhcccC-ccCC---cchhHHHHHH
Q 002216 566 CDTE-------LKLSVARRMKDEEGFYYPHNLDFRGRAYPMHPHLNHLSSDVCRGVLEFAEG-RPLG---KSGLRWLKIH 634 (952)
Q Consensus 566 ~~~~-------~~L~iA~~f~~~~~fYfPhnlDFRGR~Yp~~~~Ln~qGsDl~RsLL~Faeg-kpLG---~~Gl~WLKIh 634 (952)
.+++ ..-+++... +.-.+|||++|+==||.=-. .-+|||.+=|-|-++.=++. -.|+ ...++-|+.+
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 1211 111222211 11279999999555554322 67899999999999876553 2455 3468888888
Q ss_pred HhhhhCCCCCCCCHHHHHHHHHH-----------hHHHHHHhccCCCCC---chhhhhCCChHHHHHHHHHHHHHHhcCC
Q 002216 635 LANLFSGGVEKLSHDGRLAFVEN-----------HLYEIFDSAENPING---SRWWLTAEDPFQCLAACINLSEALKSSS 700 (952)
Q Consensus 635 lAN~yG~G~DK~S~deRi~wv~~-----------n~~~I~dsA~dPL~g---~~wW~~AD~PwQfLA~C~El~~al~s~~ 700 (952)
+|-.+|=.+||.+-++-++=+.+ -+.+|+....=|-+- ..=-+.+++||-.+-+-+|+++++....
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 99999656678876655544433 223444433322110 0011678999654448899998877555
Q ss_pred CCcceeccccccCCCcchhhHHHHh-hCChh----------h-------hcccccCCC-CCCcchhhHHHHHHHHHHHhh
Q 002216 701 PHSVISHLPIHQDGSCNGLQHYAAL-GRNTL----------E-------AAAVNLVAG-EKPADVYSEIAVRVHEIMKRD 761 (952)
Q Consensus 701 P~~y~S~lPVhqDGSCNGLQHyAAL-grD~~----------G-------a~~VNLip~-d~PqDvYs~Va~~V~~~i~~d 761 (952)
-+.|.+.|-+-.||--||=-..=-+ |.-.. | |+.+|=.-+ ..--|.|..+++.+...+...
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 22111 1 122222211 123799999999999998865
Q ss_pred cCCCCCCCh------hH-HHHHHh----------hccCcccccccceeeeecccchhhHHHHHHH
Q 002216 762 SNKDPSKHP------QA-LLAKIL----------IDQVDRKLVKQTVMTSVYGVTFVGAREQIKR 809 (952)
Q Consensus 762 a~~~~~~~~------~~-~~ak~l----------~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~ 809 (952)
..+=..+.| .. .++..+ .-.++|++.|.|+=..+||+...|+..-|-+
T Consensus 639 ~~~~~~n~Pwq~q~~~l~sl~s~f~gd~~~~Eng~~~l~R~~aKnPlT~~~YGSg~rgia~gva~ 703 (1118)
T 3q23_A 639 RSNYASNMPIQSQIDSLLSLMDLFLPDINLGENGALELKRGIAKNPLTITIYGSGARGIAGKLVS 703 (1118)
T ss_dssp HHTTTTCHHHHHHHHHHHHHHHHHCTTEEECTTCCEEECTHHHHHHHHHHHTTCCHHHHHHHHHH
T ss_pred hhhcccCCchHHHHHHHHHHHHHhhcccccCCCcchhhhhhhhhCCceeeeecCchHHHHHHHHH
Confidence 321111112 01 122222 1268999999999999999988877655443
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=33.05 E-value=17 Score=43.11 Aligned_cols=133 Identities=17% Similarity=0.207 Sum_probs=87.6
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
++++++.. |.++ .-|.-|-|-==|-.+|.|.+|....++.+ .-.|||+..|..+-..-.++
T Consensus 365 ~iR~~f~~--~~g~---~lv~aDysqiElRilA~ls~d~~l~~af~-----~g~Dih~~tA~~~f~~~~e~--------- 425 (605)
T 2kfn_A 365 RIRQAFIA--PEDY---VIVSADYSQIELRIMAHLSRDKGLLTAFA-----EGKDIHRATAAEVFGLPLET--------- 425 (605)
T ss_dssp HHHHTBBC--CTTE---EEEEEEETTHHHHHHHHHTTCHHHHHHHH-----TTCCHHHHHHHHHTTCCGGG---------
T ss_pred hHhheeeC--CCCC---EEEEechhhhHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHhCCChhh---------
Confidence 56676653 2343 46888999999999999999999877765 45799999887652210000
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 850 (952)
...-.|+..|...--.+||.+.+|...++ |+-.++ |+.+.+...+.||+ +.+
T Consensus 426 --------vt~~~R~~aK~~~fg~~YG~~~~~la~~l-------~i~~~e----------a~~~i~~~~~~~p~---v~~ 477 (605)
T 2kfn_A 426 --------VTSEQRRSAKAINFGLIYGMSAFGLARQL-------NIPRKE----------AQKYMDLYFERYPG---VLE 477 (605)
T ss_dssp --------CCHHHHHHHHHHHHHHHTTCCTTHHHHHH-------TCCTTT----------HHHHHHHHHHHCHH---HHH
T ss_pred --------cCHHHHhhhhhhhccccccCCHHHHHHHc-------CCCHHH----------HHHHHHHHHHHCcc---HHH
Confidence 01124899999999999999999988765 432222 23444555566776 566
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCC
Q 002216 851 WLGDCAKVIASENQPVRWTTPLG 873 (952)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlG 873 (952)
|+.++.+...+.| .| +|.+|
T Consensus 478 ~~~~~~~~a~~~g-~v--~tl~G 497 (605)
T 2kfn_A 478 YMERTRAQAKEQG-YV--ETLDG 497 (605)
T ss_dssp HHHHHHHHHHHHS-EE--ECTTC
T ss_pred HHHHHHHHHHHcC-cE--ECCCC
Confidence 7776666544433 22 55555
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=23.63 E-value=30 Score=40.52 Aligned_cols=192 Identities=15% Similarity=0.164 Sum_probs=112.1
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCCh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHP 770 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~ 770 (952)
+++.++..+ .++ .=|.-|-|-==|-.+|.|.+|...-++.+ .-.|||+..|..+-..-.++
T Consensus 301 ~iR~~f~a~--~G~---~lv~aDySqiElRvlAhls~D~~l~~af~-----~g~Dih~~tA~~~fg~~~~~--------- 361 (540)
T 4dfk_A 301 RIRRAFIAE--EGW---LLVALDYSQIELRVLAHLSGDENLIRVFQ-----EGRDIHTETASWMFGVPREA--------- 361 (540)
T ss_dssp HHHTTEECC--TTE---EEEEEEETTHHHHHHHHHHCCHHHHHHHH-----TTCCHHHHHHHHHHTCCGGG---------
T ss_pred hhhheEeCC--CCC---EEEEecHHHHHHHHHHHHcCCHHHHHHHh-----cCCCHHHHHHHHHcCCChhh---------
Confidence 556665432 243 46888999999999999999998776655 35799999887663321000
Q ss_pred hHHHHHHhhccCcccccccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 771 QALLAKILIDQVDRKLVKQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMG 850 (952)
Q Consensus 771 ~~~~ak~l~~~I~RKvVKqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~ 850 (952)
...-.|+..|...--.+||.+.+|..+++ |+ +.+ -|+.+.+...+.||+ +.+
T Consensus 362 --------v~~~~R~~aK~~~fg~~YG~~~~~La~~l-------gi-s~~---------eA~~~i~~~~~~~p~---v~~ 413 (540)
T 4dfk_A 362 --------VDPLMRRAAKTINFGVLYGMSAHRLSQEL-------AI-PYE---------EAQAFIERYFQSFPK---VRA 413 (540)
T ss_dssp --------CCHHHHHHHHHHHHHHHTTCCHHHHHHHH-------TC-CHH---------HHHHHHHHHHHHSTH---HHH
T ss_pred --------cCHHHHhHHHHHHHhhhhCCchhHHHHHc-------CC-CHH---------HHHHHHHHHHHhChh---HHH
Confidence 01125899999999999999999988765 33 222 234455555667776 566
Q ss_pred HHHHHHHHHHcCCCcEEEEcCCCCeEEeeeccCcceeEEeeeEEEEEecCCCCCChhhhhcCCCCcchhhhhHHHHHHHH
Q 002216 851 WLGDCAKVIASENQPVRWTTPLGLPVVQPYCKNERHLIRTSLQVLALQREGNLVKIRKQRTAFPPNFVHSLDGSHMMMTA 930 (952)
Q Consensus 851 WL~~~A~~i~~~~~pV~WtTPlGlpVvQpY~k~~~~~I~t~lq~v~l~~~~d~vd~rKQ~~Af~PNFIHSLDAsHmmlTa 930 (952)
|+.++.....+.| .| +|..|-...-|--. +.....|.+.--.+-|++=+==|+=++..|
T Consensus 414 ~~~~~~~~a~~~G-yv--~Tl~GRrr~~p~~~------------------s~~~~~r~~aeR~a~N~~iQGsaAdi~K~a 472 (540)
T 4dfk_A 414 WIEKTLEEGRRRG-YV--ETLFGRRRYVPDLE------------------ARVKSVREAAERMAFNMPVQGTAADLMKLA 472 (540)
T ss_dssp HHHHHHHHHHHHS-EE--ECTTCCEEECGGGG------------------CSSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCC-cE--ECCCCCeecCCccc------------------cccHHHHhhhhhhHhhhhhHhHHHHHHHHH
Confidence 6666655544433 12 45655422211100 111111111112346665555555433332
Q ss_pred -----HHHhHcCC-cEEEeecccccc
Q 002216 931 -----VACRDAGL-HFAGLSFQSALE 950 (952)
Q Consensus 931 -----~~c~~~Gi-~FaaVHDn~~~~ 950 (952)
....+.|. -..-|||..-+|
T Consensus 473 mi~~~~~l~~~~~~l~lqVHDElv~e 498 (540)
T 4dfk_A 473 MVKLFPRLEEMGARMLLQVHDELVLE 498 (540)
T ss_dssp HHHHHHHHHHHTCEEEEECSSEEEEE
T ss_pred HHHHHHHHHhcCCeEEEEEcceEEEE
Confidence 12344565 457899988765
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=22.36 E-value=37 Score=41.88 Aligned_cols=114 Identities=15% Similarity=0.179 Sum_probs=76.5
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCccccc
Q 002216 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (952)
Q Consensus 708 lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKvV 787 (952)
.-|.-|-|-==|-.+|.|.+|...-++.+ .-.|||+..|..+-..- .+ + ...-.|+..
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 46777888888889999999988766655 34799998876653211 00 0 012358889
Q ss_pred ccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCC
Q 002216 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASEN 863 (952)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~~ 863 (952)
|...--.+||.+.+|.++++ |+ +.+ -|+.+.+...+.||+ +.+|+.++.....+.|
T Consensus 663 K~~nfgi~YG~~~~gLa~~l-------gi-s~~---------eA~~~i~~~~~~~p~---v~~~~~~~~~~a~~~G 718 (832)
T 1bgx_T 663 KTINFGVLYGMSAHRLSQEL-------AI-PYE---------EAQAFIERYFQSFPK---VRAWIEKTLEEGRRRG 718 (832)
T ss_dssp HHHHHHTTSCCCHHHHHHHS-------SC-CHH---------HHHHHHHHHHHHCHH---HHHHHHHHTHHHHTTS
T ss_pred HHHHHhhhcCCchhHHHHHc-------CC-CHH---------HHHHHHHHHHHHCcc---HHHHHHHHHHHHHHCC
Confidence 99999999999999887654 43 222 234455556667776 6677777766655543
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=19.59 E-value=40 Score=39.96 Aligned_cols=113 Identities=15% Similarity=0.193 Sum_probs=77.2
Q ss_pred cccccCCCcchhhHHHHhhCChhhhcccccCCCCCCcchhhHHHHHHHHHHHhhcCCCCCCChhHHHHHHhhccCccccc
Q 002216 708 LPIHQDGSCNGLQHYAALGRNTLEAAAVNLVAGEKPADVYSEIAVRVHEIMKRDSNKDPSKHPQALLAKILIDQVDRKLV 787 (952)
Q Consensus 708 lPVhqDGSCNGLQHyAALgrD~~Ga~~VNLip~d~PqDvYs~Va~~V~~~i~~da~~~~~~~~~~~~ak~l~~~I~RKvV 787 (952)
.=|.-|-|-==|-.+|.|.+|...-.+.+ ...|||+..|..+-..- .+. ...-.|+..
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 46788999999999999999998776655 35799999887763210 000 011248899
Q ss_pred ccceeeeecccchhhHHHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Q 002216 788 KQTVMTSVYGVTFVGAREQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAKVIASE 862 (952)
Q Consensus 788 KqtVMT~vYGvT~~Gar~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~~i~~~ 862 (952)
|...--.+||.+.+|...++ |+ +.+ -|+.+.+...+.||+ +.+|+.++.....+.
T Consensus 422 K~~~fg~~YG~~~~~La~~l-------~i-~~~---------eA~~~i~~~~~~~p~---v~~~~~~~~~~a~~~ 476 (592)
T 3pv8_A 422 KAVNYGIVYGISDYGLAQNL-------NI-SRK---------EAAEFIERYFESFPG---VKRYMENIVQEAKQK 476 (592)
T ss_dssp HHHHHHHHTTCCHHHHHHHH-------TC-CHH---------HHHHHHHHHHHHCHH---HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhcCChHHHHHHc-------CC-CHH---------HHHHHHHHHHHHChh---HHHHHHHHHHHHHHc
Confidence 99999999999999988765 33 222 134455556667776 556666665554443
No 8
>1iv0_A Hypothetical protein; rnaseh-like, YQGF, structural genomics, riken structural genomics/proteomics initiative, RSGI, unknown function; NMR {Thermus thermophilus} SCOP: c.55.3.8
Probab=14.33 E-value=66 Score=29.20 Aligned_cols=36 Identities=11% Similarity=0.124 Sum_probs=25.4
Q ss_pred HHHHHHhcCCCCcceeccccccCCCcch----hhHHHHhh
Q 002216 691 NLSEALKSSSPHSVISHLPIHQDGSCNG----LQHYAALG 726 (952)
Q Consensus 691 El~~al~s~~P~~y~S~lPVhqDGSCNG----LQHyAALg 726 (952)
++.+.++.-+|+..+-.+|.++|||-+- .++|+..+
T Consensus 42 ~l~~li~e~~v~~iVvGlP~~mdGt~~~~~~~~~~f~~~L 81 (98)
T 1iv0_A 42 ALLDFVRREGLGKLVVGLPLRTDLKESAQAGKVLPLVEAL 81 (98)
T ss_dssp HHHHHHHHHTCCEEEEECCCCCCSSSCCCSSTTHHHHHHH
T ss_pred HHHHHHHHcCCCEEEEeeccCCCCCcCHHHHHHHHHHHHH
Confidence 4445454446889999999999999765 33565544
No 9
>1d2v_A Myeloperoxidase; heme-protein, oxidoreductase, peroxidase-bromide; HET: NAG BMA MAN FUC HEM; 1.75A {Homo sapiens} SCOP: a.93.1.2 PDB: 1cxp_A* 1d5l_A* 1d7w_A* 1dnu_A* 1dnw_A* 4dl1_A* 3zs1_A* 3f9p_A* 1mhl_A* 1myp_A* 3zs0_A*
Probab=11.52 E-value=51 Score=30.27 Aligned_cols=11 Identities=27% Similarity=0.540 Sum_probs=9.8
Q ss_pred ccCCCcchhhH
Q 002216 711 HQDGSCNGLQH 721 (952)
Q Consensus 711 hqDGSCNGLQH 721 (952)
..||+||-|+|
T Consensus 9 t~DG~cNNl~~ 19 (104)
T 1d2v_A 9 TITGMCNNRRS 19 (104)
T ss_dssp CSSCTTSSSSS
T ss_pred CCCCCccCCCC
Confidence 47999999997
No 10
>4fjo_A DNA repair protein REV1; translesion synthesis, transferase -DNA binding protein COMP transferase-DNA binding protein complex; HET: DNA; 2.72A {Mus musculus} PDB: 2lsg_A* 2lsk_A* 2lsy_A*
Probab=10.55 E-value=5e+02 Score=23.34 Aligned_cols=50 Identities=6% Similarity=0.146 Sum_probs=33.0
Q ss_pred HHHHHHHHHHcCCCCChhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 002216 804 REQIKRRLEEKGHITDDRQLFAAACYAAKVTLTALGEIFEAARSIMGWLGDCAK 857 (952)
Q Consensus 804 r~QI~~~L~~~~~~~d~~~~~~~a~Ylak~v~~ai~e~f~~A~~im~WL~~~A~ 857 (952)
++.|.+.... ...|.+.++-.++.||.+++ + ..-...+..+|+||..+.+
T Consensus 15 r~~l~~Wv~~-~~~P~~~DV~~l~~yL~~lv-~--~~~lek~~~vlk~l~rlv~ 64 (97)
T 4fjo_A 15 KTLLKEWITT-ISDPMEEDILQVVRYCTDLI-E--EKDLEKLDLVIKYMKRLMQ 64 (97)
T ss_dssp HHHHHHHHHH-CSSCCHHHHHHHHHHHHHHH-H--TTCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHc-CCCCCHHHHHHHHHHHHHHh-h--ccCHHHHHHHHHHHHHHHh
Confidence 3344444443 23466667777889999887 3 3456788899999976554
Done!