Query T0623 3NKH, , 220 residues
Match_columns 220
No_of_seqs 108 out of 7094
Neff 9.9
Searched_HMMs 11830
Date Thu Jul 22 15:12:17 2010
Command /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0623.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0623.hhr
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00589 Phage_integrase: Phag 100.0 8.3E-30 7E-34 190.2 9.9 171 1-205 2-172 (173)
2 PF11917 DUF3435: Protein of u 98.9 3.2E-09 2.7E-13 70.2 8.4 193 5-201 2-236 (417)
3 PF01028 Topoisom_I: Eukaryoti 97.3 0.00067 5.6E-08 39.2 8.4 134 31-202 43-211 (234)
4 PF07900 DUF1670: Protein of u 63.0 3.4 0.00029 17.6 5.5 67 138-206 117-190 (220)
5 PF01191 RNA_pol_Rpb5_C: RNA p 26.4 6.7 0.00057 15.8 0.4 44 2-54 15-58 (74)
6 PF06217 GAGA_bind: GAGA bindi 17.3 21 0.0018 12.9 1.8 34 135-168 255-291 (299)
7 PF12554 DUF3743: Protein of u 15.2 24 0.0021 12.6 2.7 27 159-187 19-45 (51)
8 PF10905 DUF2695: Protein of u 14.6 25 0.0021 12.5 2.5 26 162-188 15-40 (53)
9 PF10188 Oscp1: Organic solute 13.3 27 0.0023 12.3 4.8 58 2-59 46-104 (173)
10 PF02796 HTH_7: Helix-turn-hel 12.9 28 0.0024 12.2 3.4 41 155-198 1-41 (45)
No 1
>PF00589 Phage_integrase: Phage integrase family; InterPro: IPR002104 Phage integrase proteins cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment , . The catalytic site residues in CRE recombinase (P06956 from SWISSPROT) are Arg-173, His-289, Arg-292 and Tyr-324.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration; PDB: 1a0p_A 2hof_A 1ouq_B 1xo0_B 5crx_B 2hoi_H 3crx_A 1q3u_A 1crx_A 1pvq_B ....
Probab=99.96 E-value=8.3e-30 Score=190.18 Aligned_cols=171 Identities=32% Similarity=0.481 Sum_probs=145.4
Q ss_pred CCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCCCCCCEEEEEEECCCCCCCCC
Q ss_conf 98888999999986310111001002467899999999998617666888417532310247807872101023323465
Q T0623 1 YLELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDFDNKSLNINGTIHWFHDESGG 80 (220)
Q Consensus 1 yl~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~~~~~i~i~~~~~~~~~~~~~ 80 (220)
||+.+|++++++.+... ......+++.+++.||+|++|+++|+|+||+++++.+.+.
T Consensus 2 ~lt~~e~~~l~~~~~~~-----------~~~~~~~~~~l~~~tG~R~~El~~l~~~~i~~~~~~~~i~------------ 58 (173)
T PF00589_consen 2 ALTPEEIKALLNALKEN-----------QNLRDRLIFLLLLYTGLRPGELLNLKWDDIDLENGEIYIP------------ 58 (173)
T ss_dssp HHHHHHHHHHHHHSCTH-----------CHCHHHHHHHHHHHHT--HHHHHT-BGGGBESTTEEEEEE------------
T ss_pred CCCHHHHHHHHHHHHHC-----------CCHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCC------------
T ss_conf 89999999999975441-----------6989999999999987699998640442101322333223------------
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCC
Q ss_conf 20124666876110256608999999999876422100245567887067123333323013455555556533886544
Q T0623 81 FGVKDTTKTESSYRTIGLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDKEV 160 (220)
Q Consensus 81 ~~~~~~~k~~~~~R~vpi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~~~~ 160 (220)
...+|++.. |.+|+++.+.+.++++.... .....+.+++|.+..+.+++.+.+++.|+++++.+|++..+
T Consensus 59 ---~~~~K~~~~-~~~~i~~~~~~~l~~~~~~~------~~~~~~~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (173)
T PF00589_consen 59 ---IPRTKTGKS-RIIPISPELIKLLKEYIERR------QKKNEDDEYLFPSPKGKPLSRNTINRIFKRAGKKAGIPKNF 128 (173)
T ss_dssp ----ECSSSSCE-EEEECTCHHHHHHHHHHHHH------HHHHCCCCBSSBETTSSB--HHHHHHHHHHHHHHTT--SC-
T ss_pred ---CCCCCCCCC-CCCCCCCCCCCCCCCCCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf ---222112233-32222222222222222322------22245544332211222222222222222222222222222
Q ss_pred CHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHH
Q ss_conf 202455565434664389989999985899878999984123788
Q T0623 161 SSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQ 205 (220)
Q Consensus 161 ~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~~~~ 205 (220)
++|+||||+||.|+..|+|+..|+.++||+|+++| ++|.+.+++
T Consensus 129 ~~h~lR~t~~t~l~~~g~~~~~i~~~~gH~~~~~t-~~Y~~~~~~ 172 (173)
T PF00589_consen 129 SPHDLRHTFATRLANSGVSLEEIARLLGHSSISTT-RHYIKASEE 172 (173)
T ss_dssp HHHHHHHHHHHHHHHHHT-HHHHHHH----SCHHH-HHHHHHCHH
T ss_pred CCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCHHHH-HHCCCCCCC
T ss_conf 23334333333223478997899998389988897-540473747
No 2
>PF11917 DUF3435: Protein of unknown function (DUF3435)
Probab=98.89 E-value=3.2e-09 Score=70.21 Aligned_cols=193 Identities=18% Similarity=0.191 Sum_probs=105.0
Q ss_pred HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCCC------CCCCEEEEEEECCCCCCC
Q ss_conf 89999999863101110010024678999999999986176668884175323102------478078721010233234
Q T0623 5 NEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDIDF------DNKSLNINGTIHWFHDES 78 (220)
Q Consensus 5 ~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~~------~~~~i~i~~~~~~~~~~~ 78 (220)
+++-.++..+.......+. .....+...++..++.+||.|+|++..|.|.||.+ +.+.....-.++ ....
T Consensus 2 ~Dl~~~~~~~~~~~~~~f~--~~~~rvql~~~~~l~~~T~~Rpgal~~l~y~~i~l~l~r~p~~~~~~l~~~~~--~~~~ 77 (417)
T PF11917_consen 2 EDLAELLRHLWTTDEKRFP--HGRQRVQLALFLLLAAFTSARPGALLELCYKDIELTLVRDPEGGPPMLVVELT--PEFT 77 (417)
T ss_pred HHHHHHHHHHHCCCCEECC--CCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCEEEEEEECCCCCCCEEEEEEE--HHHH
T ss_conf 2589999997204642257--74459999999999988557806898721326799999899999755589975--6663
Q ss_pred CCCCCCCCCCCCCCCCCCC----CHH---HHHHHHHH--------------HHHHH-HHH----HCCCCCCCCCCEEEEC
Q ss_conf 6520124666876110256----608---99999999--------------98764-221----0024556788706712
Q T0623 79 GGFGVKDTTKTESSYRTIG----LSS---RSCEILKK--------------AILEN-KKD----SKWNDGYLNRNFVFTN 132 (220)
Q Consensus 79 ~~~~~~~~~k~~~~~R~vp----i~~---~~~~~L~~--------------~~~~~-~~~----~~~~~~~~~~~~if~~ 132 (220)
+++...+.+.+-.-..++. +-. .++.++.. .+... ..- ...-.....+-+||..
T Consensus 78 K~~~~~~~~~~~~~peiif~~~L~l~p~~~ll~l~f~d~AF~~~~i~s~e~l~~~~vp~~~~~~~L~~K~e~~d~pvFr~ 157 (417)
T PF11917_consen 78 KGFRGKKKPNTFKLPEIIFDPSLILSPHVFLLGLAFADDAFKAPNITSPEDLYRLKVPDGRQSLPLKLKPEMLDIPVFRQ 157 (417)
T ss_pred CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCEEEEECCHHHCCCCEECC
T ss_conf 56778777764213687328960434899999999874400264438999995065899865246646645468887336
Q ss_pred C----------CCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHC
Q ss_conf 3----------33332301345555555653388654420245556543466438998999998589987899998412
Q T0623 133 H----------KGNPMQTERFNKILREAAKDVGIDKEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSH 201 (220)
Q Consensus 133 ~----------~g~~l~~~~i~~~l~~~~~~~gi~~~~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~ 201 (220)
. ...||++.+++..++++.+.+|....+++|++|.+.|..+-+-.++...-+..|||+|+.|-.++|.+
T Consensus 158 ~~~~~~g~~i~~~~~l~~~t~~~~~~~lg~~aGf~~~~~~y~~R~g~~~~~n~~~~s~a~rn~il~H~~~~tF~k~Y~~ 236 (417)
T PF11917_consen 158 VERTDGGVRISPERPLTYSTFRSYLKRLGEIAGFEDPLTPYCLRRGAANALNNGKVSEAERNQILGHASSRTFLKYYLP 236 (417)
T ss_pred CEECCCCEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCEEEHHHHHHHHHCCCCCCCHHHHHHHHCCCCCHHHHHHHHH
T ss_conf 4202785165136676766799999998886476534501002256785225200697887787368970789997666
No 3
>PF01028 Topoisom_I: Eukaryotic DNA topoisomerase I, catalytic core; InterPro: IPR013500 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA . Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the catalytic core of eukaryotic and viral topoisomerase I (type IB) enzymes, which occurs near the C-terminal region of the protein. Human topoisomerase I has been shown to be inhibited by camptothecin (CPT), a plant alkaloid with antitumour activity . The crystal structures of human topoisomerase I comprising the core and carboxyl-terminal domains in covalent and noncovalent complexes with 22-base pair DNA duplexes reveal an enzyme that "clamps" around essentially B-form DNA. The core domain and the first eight residues of the carboxyl-terminal domain of the enzyme, including the active-site nucleophile tyrosine-723, share significant structural similarity with the bacteriophage family of DNA integrases. A binding mode for the anticancer drug camptothecin has been proposed on the basis of chemical and biochemical information combined with the three-dimensional structures of topoisomerase I-DNA complexes . Vaccinia virus, a cytoplasmically-replicating poxvirus, encodes a type I DNA topoisomerase that is biochemically similar to eukaryotic-like DNA topoisomerases I, and which has been widely studied as a model topoisomerase. It is the smallest topoisomerase known and is unusual in that it is resistant to the potent chemotherapeutic agent camptothecin. The crystal structure of an amino-terminal fragment of vaccinia virus DNA topoisomerase I shows that the fragment forms a five-stranded, antiparallel beta-sheet with two short alpha-helices and connecting loops. Residues that are conserved between all eukaryotic-like type I topoisomerases are not clustered in particular regions of the structure . More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 2b9s_A 2f4q_A 1a41_A 1vcc_A 2h7f_X 2h7g_X 1sc7_A 1r49_A 1t8i_A 1a35_A ....
Probab=97.28 E-value=0.00067 Score=39.18 Aligned_cols=134 Identities=15% Similarity=0.274 Sum_probs=86.1
Q ss_pred HHHHHHHHHHHHCCCCHH-H-----------HHCCCHHHCCCCCC-CEEEEEEECCCCCCCCCCCCCCCCCCCCC-CCCC
Q ss_conf 999999999986176668-8-----------84175323102478-07872101023323465201246668761-1025
Q T0623 31 LFVALMTEFQALNGMRIG-E-----------MLAIQNEDIDFDNK-SLNINGTIHWFHDESGGFGVKDTTKTESS-YRTI 96 (220)
Q Consensus 31 ~~~~~~~~~~~~tGlR~~-E-----------l~~L~~~di~~~~~-~i~i~~~~~~~~~~~~~~~~~~~~k~~~~-~R~v 96 (220)
...++++.++-.+-+|+| | ++.|+..+|.+..+ .+.+. -.+|.+.. ...|
T Consensus 43 ~~lA~~~~LlD~~~iRvGne~Ya~~n~dT~GltTLr~~Hv~v~~~~~i~f~----------------F~GK~g~~~~~~v 106 (234)
T PF01028_consen 43 RVLAAAVRLLDRTAIRVGNEKYAEENGDTYGLTTLRVRHVTVSGDNVIRFD----------------FRGKSGQRHEREV 106 (234)
T ss_dssp HHHHHHHHHHHHH------HHHHHHCTST---TT-BGGGEEEETTCEEEEE----------------E---TT--EEEEE
T ss_pred HHHHHHHHHHHHHHEECCCCCCCCCCCCCEEECCCCHHHEEECCCCEEEEE----------------EECCCCEEEEEEE
T ss_conf 799999999997511058822341258866234341866366599769999----------------7579973999986
Q ss_pred CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf 66089999999998764221002455678870671233333230134555555565338865442024555654346643
Q T0623 97 GLSSRSCEILKKAILENKKDSKWNDGYLNRNFVFTNHKGNPMQTERFNKILREAAKDVGIDKEVSSHILRHSHISLLSQQ 176 (220)
Q Consensus 97 pi~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~if~~~~g~~l~~~~i~~~l~~~~~~~gi~~~~~~H~lRht~at~l~~~ 176 (220)
.+++.+...|...+.... +...+| .+++...+|..|+.++ ..+|...||=+.||.++..
T Consensus 107 ~~d~~l~~~l~~~~~~~~----------pg~~LF-----~~v~s~~vN~yl~~~~------~~~TaKdFRTw~as~~a~~ 165 (234)
T PF01028_consen 107 RVDPRLARNLRRLLKRKL----------PGQRLF-----HPVDSSDVNAYLREIM------EGFTAKDFRTWNASVTAAE 165 (234)
T ss_dssp ETTHHHHHHHHHHHTTT-----------TTSBTT-----TT--HHHHHHHHHHH-----------HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCCC----------CHHHHC-----CCCCHHHHHHHHHHHC------CCCCHHHHCCCHHHHHHHH
T ss_conf 689899999999971789----------803531-----4589999999999980------8986011003439999999
Q ss_pred -----C-----C-----------CHHHHHHHHCCCCHHHHHHHHHCC
Q ss_conf -----8-----9-----------989999985899878999984123
Q T0623 177 -----G-----V-----------SLKAIMDRVGHSDHRTTLSIYSHV 202 (220)
Q Consensus 177 -----G-----~-----------~~~~i~~~lGH~s~~~t~~~Y~~~ 202 (220)
+ . -+..++..+||+ +.+.-+.|+|-
T Consensus 166 ~L~~~~~~~~~~~~~~~~~~i~~a~~~vA~~lgnT-paV~r~sYi~p 211 (234)
T PF01028_consen 166 ALAEAPEEEPPESEKERKKAINAAIKEVAELLGNT-PAVCRKSYIHP 211 (234)
T ss_dssp HHHHHH--HHSSSHHHHHHHHHHHHHHHHHHCT-E-CCHHHHHTSHH
T ss_pred HHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCC-CCCCHHHCCCH
T ss_conf 99866477888888999999999999999985898-53535540087
No 4
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=62.96 E-value=3.4 Score=17.57 Aligned_cols=67 Identities=16% Similarity=0.204 Sum_probs=47.9
Q ss_pred CCCHHHHHHHHHHHHHCCC-------CCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHCCCHHH
Q ss_conf 2301345555555653388-------65442024555654346643899899999858998789999841237889
Q T0623 138 MQTERFNKILREAAKDVGI-------DKEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSIYSHVTEQM 206 (220)
Q Consensus 138 l~~~~i~~~l~~~~~~~gi-------~~~~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~Y~~~~~~~ 206 (220)
.|+.+|++.++.+-++.|. -..+.|----.+.|-.+.-+|.+...|++.+.|+ ++-. +.|+....+.
T Consensus 117 ~S~~TI~~~vk~ye~~~g~vvPtRG~i~DiGp~lTHK~iii~~~lkg~~~~eiAr~t~HS-~eAv-~RYik~f~rV 190 (220)
T PF07900_consen 117 VSPKTISRDVKEYEEEHGEVVPTRGTIKDIGPGLTHKTIIIELYLKGKSTSEIARETYHS-PEAV-DRYIKDFKRV 190 (220)
T ss_pred CCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCC-HHHH-HHHHHHHHHH
T ss_conf 898889999999999619652357621335765107999999998279989999984168-9999-9999863766
No 5
>PF01191 RNA_pol_Rpb5_C: RNA polymerase Rpb5, C-terminal domain; InterPro: IPR000783 Prokaryotes contain a single DNA-dependent RNA polymerase (RNAP; 2.7.7.6 from EC) that is responsible for the transcription of all genes, while eukaryotes have three classes of RNAPs (I-III) that transcribe different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. Certain subunits of RNAPs, including RPB5 (POLR2E in mammals), are common to all three eukaryotic polymerases. RPB5 plays a role in the transcription activation process. Eukaryotic RPB5 has a bipartite structure consisting of a unique N-terminal region (IPR005571 from INTERPRO), plus a C-terminal region that is structurally homologous to the prokaryotic RPB5 homologue, subunit H (gene rpoH) , , , . This entry represents prokaryotic subunit H and the C-terminal domain of eukaryotic RPB5, which share a two-layer alpha/beta fold, with a core structure of beta/alpha/beta/alpha/beta(2). ; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription; PDB: 3gtj_E 1y1v_E 3gtk_E 1r5u_E 2b63_E 3gtm_E 3gtg_E 1k83_E 1twh_E 2e2i_E ....
Probab=26.39 E-value=6.7 Score=15.83 Aligned_cols=44 Identities=16% Similarity=0.269 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCC
Q ss_conf 88889999999863101110010024678999999999986176668884175
Q T0623 2 LELNEIESIIKDINTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQ 54 (220)
Q Consensus 2 l~~~E~~~il~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~ 54 (220)
|+.+|.+.+|+...........-...+.. .-+.|+.+|++..+.
T Consensus 15 ls~eE~~~lL~~y~i~~~qLP~I~~~DPv---------~r~~g~k~GdVVkI~ 58 (74)
T PF01191_consen 15 LSEEEKKELLKKYKIKPEQLPRILSSDPV---------ARYYGAKPGDVVKIT 58 (74)
T ss_dssp E-HHHHHHHHHHTT--TTCSSEEBTTSHH---------HHCTT-----EEEEE
T ss_pred CCHHHHHHHHHHHCCCHHHCCCEECCCHH---------HHHCCCCCCCEEEEE
T ss_conf 79999999999809996578825155824---------676199989899997
No 6
>PF06217 GAGA_bind: GAGA binding protein-like family; InterPro: IPR010409 This family includes gbp a protein from Soybean that binds to GAGA element dinucleotide repeat DNA . It seems likely that the region which defines this family mediates DNA binding. This putative domain contains several conserved cysteines and a histidine suggesting this may be a zinc-binding DNA interaction domain.
Probab=17.30 E-value=21 Score=12.90 Aligned_cols=34 Identities=24% Similarity=0.458 Sum_probs=19.7
Q ss_pred CCCCCCHHHHHHHHHHHHH-CCC--CCCCCHHHHHHH
Q ss_conf 3332301345555555653-388--654420245556
Q T0623 135 GNPMQTERFNKILREAAKD-VGI--DKEVSSHILRHS 168 (220)
Q Consensus 135 g~~l~~~~i~~~l~~~~~~-~gi--~~~~~~H~lRht 168 (220)
|+.||..+|.+.|.+++.+ .++ +..+..|+.||.
T Consensus 255 GRKMS~gAF~KlL~rLAaEGydlsnPiDLK~hWAkHG 291 (299)
T PF06217_consen 255 GRKMSGGAFKKLLERLAAEGYDLSNPIDLKDHWAKHG 291 (299)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHCC
T ss_conf 5532356999999998754567688521677887526
No 7
>PF12554 DUF3743: Protein of unknown function (DUF3743)
Probab=15.15 E-value=24 Score=12.58 Aligned_cols=27 Identities=22% Similarity=0.224 Sum_probs=19.1
Q ss_pred CCCHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf 44202455565434664389989999985
Q T0623 159 EVSSHILRHSHISLLSQQGVSLKAIMDRV 187 (220)
Q Consensus 159 ~~~~H~lRht~at~l~~~G~~~~~i~~~l 187 (220)
+++.+.++ .+-.|.++|++++.++...
T Consensus 19 gLdre~L~--ici~L~e~GVnPeaLA~vV 45 (51)
T PF12554_consen 19 GLDRETLS--ICIELCEAGVNPEALAAVV 45 (51)
T ss_pred CCCHHHHH--HHHHHHHCCCCHHHHHHHH
T ss_conf 99999999--9999998699989999999
No 8
>PF10905 DUF2695: Protein of unknown function (DUF2695)
Probab=14.65 E-value=25 Score=12.49 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHCCCCHHHHHHHHC
Q ss_conf 024555654346643899899999858
Q T0623 162 SHILRHSHISLLSQQGVSLKAIMDRVG 188 (220)
Q Consensus 162 ~H~lRht~at~l~~~G~~~~~i~~~lG 188 (220)
-|++|+| ...+...+++...|-.++|
T Consensus 15 DHTlr~~-~~fl~~~~l~~~~v~~wL~ 40 (53)
T PF10905_consen 15 DHTLRFA-QRFLAQRKLDWEDVLDWLG 40 (53)
T ss_pred CCHHHHH-HHHHHHCCCCHHHHHHHHH
T ss_conf 7469999-9999984999899999998
No 9
>PF10188 Oscp1: Organic solute transport protein 1
Probab=13.34 E-value=27 Score=12.28 Aligned_cols=58 Identities=9% Similarity=0.221 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHH-HHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHCC
Q ss_conf 8888999999986-310111001002467899999999998617666888417532310
Q T0623 2 LELNEIESIIKDI-NTKAQKMHSGIHKRFYLFVALMTEFQALNGMRIGEMLAIQNEDID 59 (220)
Q Consensus 2 l~~~E~~~il~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~tGlR~~El~~L~~~di~ 59 (220)
+|.+.++.+++.+ ....-+....--...+-.....+-+...+..+|.|+..+++.++|
T Consensus 46 ys~~~~r~~f~~lah~SIMRLne~SM~KL~DLM~M~~KyQl~~~~~p~ell~iT~nHld 104 (173)
T PF10188_consen 46 YSKSALRTVFTRLAHCSIMRLNENSMDKLFDLMTMGFKYQLFLCRHPLELLEITLNHLD 104 (173)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf 46999999999988607660499889999999999999999967988999999999999
No 10
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known . The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second , called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1jko_C 1jkp_C 1jj8_C 1hcr_A 1jkq_C 1jj6_C 1ijw_C 1jkr_C 1zr4_B 2gm4_A ....
Probab=12.92 E-value=28 Score=12.20 Aligned_cols=41 Identities=27% Similarity=0.363 Sum_probs=0.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHH
Q ss_conf 88654420245556543466438998999998589987899998
Q T0623 155 GIDKEVSSHILRHSHISLLSQQGVSLKAIMDRVGHSDHRTTLSI 198 (220)
Q Consensus 155 gi~~~~~~H~lRht~at~l~~~G~~~~~i~~~lGH~s~~~t~~~ 198 (220)
|=++.++++ ..-.+-.|+++|.++..|++.+|=+ .+|..++
T Consensus 1 GRp~~~~~~--~~~~i~~l~~~G~s~~~IAk~~gvs-r~TvyR~ 41 (45)
T PF02796_consen 1 GRPPKLTDE--QIEEIRELYAQGMSISEIAKRFGVS-RSTVYRY 41 (45)
T ss_dssp ---SSSSHC--CHHHHHHHHH----HHHHHHHCTS--HHHHHHH
T ss_pred CCCCCCCHH--HHHHHHHHHHCCCCHHHHHHHHCCC-HHHHHHH
T ss_conf 969989999--9999999999799999999998919-9999999
Done!