Query psy18235
Match_columns 232
No_of_seqs 97 out of 99
Neff 5.7
Searched_HMMs 46136
Date Fri Aug 16 17:08:29 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy18235.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/18235hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00128 XPG Xeroderma pigmento 96.5 0.0051 1.1E-07 56.2 5.5 82 19-106 162-246 (316)
2 PTZ00217 flap endonuclease-1; 96.0 0.01 2.2E-07 56.5 5.0 92 18-113 171-265 (393)
3 cd00008 53EXOc 5'-3' exonuclea 95.9 0.0081 1.7E-07 53.2 3.8 87 17-112 122-212 (240)
4 PRK03980 flap endonuclease-1; 95.7 0.033 7.3E-07 51.0 6.9 94 18-114 116-220 (292)
5 smart00475 53EXOc 5'-3' exonuc 95.2 0.023 5E-07 51.1 4.3 90 18-112 122-215 (259)
6 PRK14976 5'-3' exonuclease; Pr 95.2 0.027 5.8E-07 51.2 4.7 90 17-112 127-220 (281)
7 TIGR03674 fen_arch flap struct 94.9 0.046 9.9E-07 50.9 5.3 92 19-113 164-266 (338)
8 KOG2518|consensus 93.7 0.081 1.8E-06 52.1 4.4 101 6-111 150-253 (556)
9 COG0258 Exo 5'-3' exonuclease 92.9 0.11 2.3E-06 47.6 3.6 90 17-112 133-227 (310)
10 KOG2519|consensus 91.2 0.1 2.2E-06 50.4 1.5 92 18-112 165-258 (449)
11 cd00080 HhH2_motif Helix-hairp 90.0 0.28 6.1E-06 35.9 2.6 42 72-113 9-52 (75)
12 TIGR00600 rad2 DNA excision re 90.0 0.29 6.2E-06 52.0 3.6 81 18-104 805-887 (1034)
13 PRK05755 DNA polymerase I; Pro 87.7 0.57 1.2E-05 48.9 3.9 92 17-114 123-218 (880)
14 PRK09482 flap endonuclease-lik 87.3 0.79 1.7E-05 41.4 4.2 87 17-112 121-211 (256)
15 TIGR00593 pola DNA polymerase 85.3 1.1 2.4E-05 47.0 4.6 92 17-114 121-216 (887)
16 smart00279 HhH2 Helix-hairpin- 78.7 1.4 3.1E-05 28.0 1.6 30 73-103 4-36 (36)
17 KOG2520|consensus 45.6 15 0.00032 38.5 2.3 34 71-104 548-581 (815)
18 PF00867 XPG_I: XPG I-region; 41.5 4.4 9.5E-05 30.5 -1.7 18 19-36 25-42 (94)
19 cd04975 Ig4_SCFR_like Fourth i 27.2 1.5E+02 0.0032 22.4 4.8 40 12-51 2-43 (101)
20 PHA00439 exonuclease 26.9 83 0.0018 29.0 3.8 70 18-103 135-207 (286)
21 COG1393 ArsC Arsenate reductas 24.3 1.1E+02 0.0025 24.1 3.8 46 131-177 2-47 (117)
22 PF11105 CCAP: Arthropod cardi 22.4 23 0.0005 28.9 -0.5 15 71-85 43-57 (133)
23 cd00490 Met_repressor_MetJ Met 22.3 39 0.00084 26.1 0.6 14 67-82 55-68 (103)
24 PRK05264 transcriptional repre 21.9 40 0.00086 26.2 0.7 14 67-82 56-69 (105)
25 PF01340 MetJ: Met Apo-repress 21.0 39 0.00085 26.1 0.5 12 69-82 57-68 (104)
No 1
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=96.45 E-value=0.0051 Score=56.24 Aligned_cols=82 Identities=23% Similarity=0.281 Sum_probs=54.3
Q ss_pred CceEEEEeCCcceEEeeeccCCCccceeeecCC-ccccceEeccccccch-hh-HhHHHhhhhhcCCCcchhhhhcchhh
Q psy18235 19 DEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGR-GKVVPVLYHPQTTIDT-SL-AEHILFIRAISGCDSTSALFNQGKVK 95 (232)
Q Consensus 19 ~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~-g~~~~~i~~i~~~~~~-~~-~~~l~~~ha~tgcDtts~f~gkGK~k 95 (232)
|....|+|+|+|+|++..- .++..... ++.....++.+.+.+. .+ -..++.|=++.|||.+..+-|.|-++
T Consensus 162 g~v~~i~S~DsD~l~fg~~------~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~ 235 (316)
T cd00128 162 GLVDAIITEDSDLLLFGAP------RVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLGCDYTEGIPGIGPVT 235 (316)
T ss_pred CCeeEEEecCCCeeeecCc------eEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHH
Confidence 5555799999999886531 22222221 1111223444444331 12 24578888999999999999999999
Q ss_pred hhhhhccCcCh
Q psy18235 96 ALRTVVKNPDL 106 (232)
Q Consensus 96 alK~l~~n~~~ 106 (232)
|+++++++.++
T Consensus 236 A~~li~~~~~~ 246 (316)
T cd00128 236 ALKLIKKYGDI 246 (316)
T ss_pred HHHHHHHcCCh
Confidence 99999998765
No 2
>PTZ00217 flap endonuclease-1; Provisional
Probab=95.97 E-value=0.01 Score=56.53 Aligned_cols=92 Identities=16% Similarity=0.196 Sum_probs=59.9
Q ss_pred CCceEEEEeCCcceEEeeeccCCCccceeeec-CCccccceEeccccccch-hh-HhHHHhhhhhcCCCcchhhhhcchh
Q psy18235 18 EDEVVVLVGEDVDLLVILIGTRSPSNVYFLKP-GRGKVVPVLYHPQTTIDT-SL-AEHILFIRAISGCDSTSALFNQGKV 94 (232)
Q Consensus 18 ~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~-g~g~~~~~i~~i~~~~~~-~~-~~~l~~~ha~tgcDtts~f~gkGK~ 94 (232)
.|....|+|+|.|+|++..-. .+.-+.. |.++.....++.+.+.+. .+ -..+.-+=++.|||.+...-|+|-+
T Consensus 171 ~g~v~~ViS~D~D~l~fg~~~----vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~GIG~k 246 (393)
T PTZ00217 171 KGKVYAVATEDMDALTFGTPV----LLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPK 246 (393)
T ss_pred CCCeEEEeCCCcCeeecCCcE----EEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHH
Confidence 466677899999999776411 0000111 222222223444444431 12 2447778899999999999999999
Q ss_pred hhhhhhccCcChHHHHHHh
Q psy18235 95 KALRTVVKNPDLLPYIRRF 113 (232)
Q Consensus 95 kalK~l~~n~~~q~a~~~f 113 (232)
+|+++++++.++-+.+..+
T Consensus 247 tA~~Li~~~gsle~il~~~ 265 (393)
T PTZ00217 247 TAYKLIKKYKSIEEILEHL 265 (393)
T ss_pred HHHHHHHHcCCHHHHHHHH
Confidence 9999999998777666554
No 3
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=95.91 E-value=0.0081 Score=53.21 Aligned_cols=87 Identities=23% Similarity=0.318 Sum_probs=58.5
Q ss_pred cCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccch-hh-HhHHHhhhhhcC--CCcchhhhhcc
Q psy18235 17 EEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDT-SL-AEHILFIRAISG--CDSTSALFNQG 92 (232)
Q Consensus 17 ~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~-~~-~~~l~~~ha~tg--cDtts~f~gkG 92 (232)
..|..++|+|.|.|++-+.-. ...|..+++ ...++...+.++ .+ -..++-+.++.| ||..+..-|.|
T Consensus 122 ~~g~~~~I~S~DkD~~ql~~~-----~v~~~~~~~----~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG 192 (240)
T cd00008 122 AEGYKVVIVSGDKDLLQLVSD-----NVKVVSPMK----KKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIG 192 (240)
T ss_pred HcCCeEEEEeCCCChhhhCCC-----CEEEEeCCC----ceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccC
Confidence 346789999999999977621 122333332 122344333321 11 244777899999 89999999999
Q ss_pred hhhhhhhhccCcChHHHHHH
Q psy18235 93 KVKALRTVVKNPDLLPYIRR 112 (232)
Q Consensus 93 K~kalK~l~~n~~~q~a~~~ 112 (232)
.++|.+++.++..+.+.+..
T Consensus 193 ~ktA~~Ll~~~gsle~i~~~ 212 (240)
T cd00008 193 EKTAAKLLKEYGSLEGILEN 212 (240)
T ss_pred HHHHHHHHHHhCCHHHHHHh
Confidence 99999999988766555444
No 4
>PRK03980 flap endonuclease-1; Provisional
Probab=95.67 E-value=0.033 Score=50.97 Aligned_cols=94 Identities=18% Similarity=0.234 Sum_probs=59.2
Q ss_pred CCceEEEEeCCcceEEeeeccCCCccceeeecCCccc---------cceEeccccccch-hh-HhHHHhhhhhcCCCcch
Q psy18235 18 EDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKV---------VPVLYHPQTTIDT-SL-AEHILFIRAISGCDSTS 86 (232)
Q Consensus 18 ~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~---------~~~i~~i~~~~~~-~~-~~~l~~~ha~tgcDtts 86 (232)
.|....|+|+|.|+|.+..-.. .-++.+ .|.++. ....++.+.+.+. .+ -..++-+=++.|||...
T Consensus 116 ~g~vd~V~S~D~D~l~fg~~~v--ir~l~~-~~~~~~p~~~~~~~~~~e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~ 192 (292)
T PRK03980 116 KGDAWAVGSQDYDSLLFGAPRL--VRNLTI-SGKRKLPGKNVYVEVKPELIELEEVLKELGITREQLIDIAILVGTDYNP 192 (292)
T ss_pred CCCeEEEecCCcCeeeecCCEE--EEeecc-cccccCccccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCC
Confidence 3555678999999999875221 011111 222211 0112333333321 11 24467778899999999
Q ss_pred hhhhcchhhhhhhhccCcChHHHHHHhc
Q psy18235 87 ALFNQGKVKALRTVVKNPDLLPYIRRFL 114 (232)
Q Consensus 87 ~f~gkGK~kalK~l~~n~~~q~a~~~f~ 114 (232)
..-|.|-++|+++++++.++-+.+..+.
T Consensus 193 GI~GIG~ktA~kLi~~~~sle~i~~~~~ 220 (292)
T PRK03980 193 GIKGIGPKTALKLIKKHGDLEKVLEERG 220 (292)
T ss_pred CCCCccHHHHHHHHHHCCCHHHHHHhcc
Confidence 9999999999999999988777666543
No 5
>smart00475 53EXOc 5'-3' exonuclease.
Probab=95.24 E-value=0.023 Score=51.09 Aligned_cols=90 Identities=24% Similarity=0.318 Sum_probs=58.7
Q ss_pred CCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccch-hh-HhHHHhhhhhcC--CCcchhhhhcch
Q psy18235 18 EDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDT-SL-AEHILFIRAISG--CDSTSALFNQGK 93 (232)
Q Consensus 18 ~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~-~~-~~~l~~~ha~tg--cDtts~f~gkGK 93 (232)
.|..++|+|.|.|++-|.--. ..+|. +.++......++...+.+. .+ -..+.-+.++.| +|..+..-|.|.
T Consensus 122 ~g~~~~IvS~DkDl~ql~~~~----v~~~~-~~~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~ 196 (259)
T smart00475 122 EGYEVRIVSGDKDLLQLVSDK----VSVLD-PTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGE 196 (259)
T ss_pred CCCeEEEEeCCCcHhhcCCCC----EEEEe-ccCCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCH
Confidence 467899999999998775311 11222 2332221233444444321 01 134777889999 899999999999
Q ss_pred hhhhhhhccCcChHHHHHH
Q psy18235 94 VKALRTVVKNPDLLPYIRR 112 (232)
Q Consensus 94 ~kalK~l~~n~~~q~a~~~ 112 (232)
++|.+++.++..+-..+..
T Consensus 197 KtA~~Ll~~ygsle~i~~~ 215 (259)
T smart00475 197 KTAAKLLKEFGSLENILEN 215 (259)
T ss_pred HHHHHHHHHhCCHHHHHHH
Confidence 9999999998766555444
No 6
>PRK14976 5'-3' exonuclease; Provisional
Probab=95.21 E-value=0.027 Score=51.25 Aligned_cols=90 Identities=14% Similarity=0.249 Sum_probs=60.6
Q ss_pred cCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccchh-h-HhHHHhhhhhcC--CCcchhhhhcc
Q psy18235 17 EEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDTS-L-AEHILFIRAISG--CDSTSALFNQG 92 (232)
Q Consensus 17 ~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~~-~-~~~l~~~ha~tg--cDtts~f~gkG 92 (232)
..|..++|+|.|.|.+.|+--+ ..+..+.++.. .+.++...+.++- + -..++-+.|+.| +|..+..-|+|
T Consensus 127 ~~g~~v~IvS~DkDl~ql~~~~-----v~~~~~~~~~~-~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG 200 (281)
T PRK14976 127 KQNITVLIYSSDKDLLQLVNEN-----TDVLLKKKGTS-HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIG 200 (281)
T ss_pred HCCCeEEEEeCCCCcCccCCCC-----eEEEEecCCCC-cEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCccc
Confidence 3467899999999999886321 11222233322 2334444444311 1 234778899999 89999999999
Q ss_pred hhhhhhhhccCcChHHHHHH
Q psy18235 93 KVKALRTVVKNPDLLPYIRR 112 (232)
Q Consensus 93 K~kalK~l~~n~~~q~a~~~ 112 (232)
.++|.+++.++..+-..+..
T Consensus 201 ~KtA~~LL~~~gsle~i~~~ 220 (281)
T PRK14976 201 PKTAIKLLNKYGNIENIYEN 220 (281)
T ss_pred HHHHHHHHHHcCCHHHHHHh
Confidence 99999999999777665544
No 7
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=94.87 E-value=0.046 Score=50.94 Aligned_cols=92 Identities=18% Similarity=0.233 Sum_probs=57.1
Q ss_pred CceEEEEeCCcceEEeeeccCCCccceeeecCCcc----c-----cceEeccccccch-hh-HhHHHhhhhhcCCCcchh
Q psy18235 19 DEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGK----V-----VPVLYHPQTTIDT-SL-AEHILFIRAISGCDSTSA 87 (232)
Q Consensus 19 ~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~----~-----~~~i~~i~~~~~~-~~-~~~l~~~ha~tgcDtts~ 87 (232)
|....|+|+|.|+|.+..-.. + -++.. .|.++ . ...+++...+.+. .+ -..+.-+=++.|||....
T Consensus 164 g~vd~v~S~D~D~l~fg~~~v-i-~~~~~-~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~G 240 (338)
T TIGR03674 164 GDVDYVGSQDYDSLLFGAPRL-V-RNLTI-SGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGTDYNEG 240 (338)
T ss_pred CCeeEEecCCcCeeeecCCEE-E-Eeccc-ccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCC
Confidence 544478899999998865221 0 01111 12111 1 1112333333321 12 244677889999999999
Q ss_pred hhhcchhhhhhhhccCcChHHHHHHh
Q psy18235 88 LFNQGKVKALRTVVKNPDLLPYIRRF 113 (232)
Q Consensus 88 f~gkGK~kalK~l~~n~~~q~a~~~f 113 (232)
..|.|.++|+|+++++.++-..+...
T Consensus 241 v~GIG~ktA~kli~~~gsie~il~~~ 266 (338)
T TIGR03674 241 VKGIGPKTALKLIKEHGDLEKVLKAR 266 (338)
T ss_pred CCCccHHHHHHHHHHcCCHHHHHHhh
Confidence 99999999999999998776665543
No 8
>KOG2518|consensus
Probab=93.71 E-value=0.081 Score=52.05 Aligned_cols=101 Identities=21% Similarity=0.138 Sum_probs=58.7
Q ss_pred CCCCceeeeeccCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccc-h-hh-HhHHHhhhhhcCC
Q psy18235 6 PSSGRRSLASEEEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTID-T-SL-AEHILFIRAISGC 82 (232)
Q Consensus 6 ~~~t~~~lh~~~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~-~-~~-~~~l~~~ha~tgc 82 (232)
+.|.+|--=. .+|.-=-|+|||.|++|...-..-. =|=.+|.|--..+ ..+....+ . .. -..+..+=.++||
T Consensus 150 EADAQlayL~-~~~~i~~IITEDSDLl~fGc~~vif---K~d~~G~~le~~~-~~l~~~~~l~~~~~~ekfr~mciLSGC 224 (556)
T KOG2518|consen 150 EADAQLAYLE-REGIVDAIITEDSDLLVFGCKKVIF---KMDSFGNGLEINR-SKLPECKPLGDKFTEEKFRRMCILSGC 224 (556)
T ss_pred cccchhHHHH-hcCcceEEEeccccccccCchhhee---eccCCCCcccccH-hhhhhccccccccCHHHHHHHHHhcCC
Confidence 3455542222 3444455889999999988732100 0111444332110 11111111 1 11 1235556688999
Q ss_pred CcchhhhhcchhhhhhhhccCcChHHHHH
Q psy18235 83 DSTSALFNQGKVKALRTVVKNPDLLPYIR 111 (232)
Q Consensus 83 Dtts~f~gkGK~kalK~l~~n~~~q~a~~ 111 (232)
|.+++.-|.|=.+|.|++.++.+....+.
T Consensus 225 DYl~slpGvGl~tA~k~l~k~~~~d~vi~ 253 (556)
T KOG2518|consen 225 DYLSSLPGVGLATAHKLLSKYNTPDRVII 253 (556)
T ss_pred cccccCccccHHHHHHHHHhcCcHHHHHH
Confidence 99999999999999999999977766543
No 9
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=92.89 E-value=0.11 Score=47.61 Aligned_cols=90 Identities=19% Similarity=0.328 Sum_probs=58.5
Q ss_pred cCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccch--hh-HhHHHhhhhhcC--CCcchhhhhc
Q psy18235 17 EEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDT--SL-AEHILFIRAISG--CDSTSALFNQ 91 (232)
Q Consensus 17 ~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~--~~-~~~l~~~ha~tg--cDtts~f~gk 91 (232)
..|..+.|++.|.|.+.+..-+ +.....-+|.... .++...+.+. .+ -..|+-+=+++| ||.++--.|+
T Consensus 133 ~~g~~~~I~S~DkD~lql~~~~-----~~~~~~~~~~~~~-~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GI 206 (310)
T COG0258 133 KKGDVVLIISGDKDLLQLVSPN-----VLVINGKKGEPEK-FLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGI 206 (310)
T ss_pred hcCCeEEEEeCCcchhhhcCCC-----cEEEeccCCCCcc-cCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCc
Confidence 4578899999999999887744 2222222222211 1122211110 01 125788889999 9999999999
Q ss_pred chhhhhhhhccCcChHHHHHH
Q psy18235 92 GKVKALRTVVKNPDLLPYIRR 112 (232)
Q Consensus 92 GK~kalK~l~~n~~~q~a~~~ 112 (232)
|.++|+++++++..+-..+..
T Consensus 207 G~ktA~~Ll~~~gs~e~i~~~ 227 (310)
T COG0258 207 GPKTALKLLQEYGSLEGLYEN 227 (310)
T ss_pred CHHHHHHHHHHhCCHHHHHHh
Confidence 999999999998755444443
No 10
>KOG2519|consensus
Probab=91.19 E-value=0.1 Score=50.43 Aligned_cols=92 Identities=17% Similarity=0.188 Sum_probs=63.0
Q ss_pred CCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccc--hhhHhHHHhhhhhcCCCcchhhhhcchhh
Q psy18235 18 EDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTID--TSLAEHILFIRAISGCDSTSALFNQGKVK 95 (232)
Q Consensus 18 ~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~--~~~~~~l~~~ha~tgcDtts~f~gkGK~k 95 (232)
+|..--++++|.|.+-... ......+....++|.....| +.+.+.. ..-.+.+..+-.++|||.-+...|.|+.+
T Consensus 165 ~g~V~~~at~DsD~l~fg~--~~~lr~l~~s~~~~~pv~e~-~~~~il~~l~l~~~~fidL~lLlGCDYc~~I~Gig~~~ 241 (449)
T KOG2519|consen 165 AGKVYAVATEDSDALTFGA--PVKLRHLIHSLASGLPVSEY-DMSRILEGLGLSRESFIDLCLLLGCDYCPTIRGIGPKK 241 (449)
T ss_pred cCceeeeeccccchhhccC--HHHHHHhccchhcCCCeEEe-eHHHHHHHhcccHHHHHHHHHHhcCcccccccccChHH
Confidence 4677779999999543332 11123444557776665544 5554443 11234566677789999999999999999
Q ss_pred hhhhhccCcChHHHHHH
Q psy18235 96 ALRTVVKNPDLLPYIRR 112 (232)
Q Consensus 96 alK~l~~n~~~q~a~~~ 112 (232)
|+++++++.+..+.+..
T Consensus 242 al~lir~~~~i~~ile~ 258 (449)
T KOG2519|consen 242 ALKLIRQHGDIENILEI 258 (449)
T ss_pred HHHHHHHhcCHHHHhhh
Confidence 99999999877776663
No 11
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=90.04 E-value=0.28 Score=35.92 Aligned_cols=42 Identities=14% Similarity=0.237 Sum_probs=35.8
Q ss_pred HHHhhhhhcC--CCcchhhhhcchhhhhhhhccCcChHHHHHHh
Q psy18235 72 HILFIRAISG--CDSTSALFNQGKVKALRTVVKNPDLLPYIRRF 113 (232)
Q Consensus 72 ~l~~~ha~tg--cDtts~f~gkGK~kalK~l~~n~~~q~a~~~f 113 (232)
.+.-+-+++| ||.++..-|.|.++|.+++.++.++...+...
T Consensus 9 q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~ 52 (75)
T cd00080 9 QFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENL 52 (75)
T ss_pred HHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHH
Confidence 3566779999 99999999999999999999998777766553
No 12
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.98 E-value=0.29 Score=51.98 Aligned_cols=81 Identities=16% Similarity=0.203 Sum_probs=52.1
Q ss_pred CCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccc-hhh-HhHHHhhhhhcCCCcchhhhhcchhh
Q psy18235 18 EDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTID-TSL-AEHILFIRAISGCDSTSALFNQGKVK 95 (232)
Q Consensus 18 ~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~-~~~-~~~l~~~ha~tgcDtts~f~gkGK~k 95 (232)
.|..-.|+|+|.|+|+...-.. .-++ ++.++. .-++....+.. -.+ ...|..+-.+.|||.+....|.|-++
T Consensus 805 ~G~vd~V~TeDsD~llFGa~~v--~rn~---~~~~~~-ve~~~~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpkt 878 (1034)
T TIGR00600 805 LDQTSGTITDDSDIWLFGARHV--YKNF---FNQNKF-VEYYQYVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVS 878 (1034)
T ss_pred CCCeEEEEccccceeccCCcee--eecc---cCCCCc-eEEeeHHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHH
Confidence 4677779999999996544211 0011 123222 22232222222 112 24577888899999999999999999
Q ss_pred hhhhhccCc
Q psy18235 96 ALRTVVKNP 104 (232)
Q Consensus 96 alK~l~~n~ 104 (232)
|++++.++.
T Consensus 879 Al~li~~~~ 887 (1034)
T TIGR00600 879 AMEILNEFP 887 (1034)
T ss_pred HHHHHHHcC
Confidence 999999886
No 13
>PRK05755 DNA polymerase I; Provisional
Probab=87.72 E-value=0.57 Score=48.86 Aligned_cols=92 Identities=17% Similarity=0.177 Sum_probs=61.6
Q ss_pred cCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccchh-h-HhHHHhhhhhcC--CCcchhhhhcc
Q psy18235 17 EEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDTS-L-AEHILFIRAISG--CDSTSALFNQG 92 (232)
Q Consensus 17 ~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~~-~-~~~l~~~ha~tg--cDtts~f~gkG 92 (232)
..|..++|+|.|.|++-|.--+ ..+|...+ ++. ...++.+.+.+.- + -..++-+.|+.| +|.....-|+|
T Consensus 123 ~~~~~~~i~S~DkD~~ql~~~~----v~~~~~~~-~~~-~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG 196 (880)
T PRK05755 123 AAGYEVLIVTGDKDLLQLVDDN----VTLLDTMG-VSK-NEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIG 196 (880)
T ss_pred hCCCcEEEEcCCCChhhhCCCC----EEEeeccC-CCC-CeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCcc
Confidence 3467899999999999886321 11222221 111 2234444433311 1 245788999999 79999999999
Q ss_pred hhhhhhhhccCcChHHHHHHhc
Q psy18235 93 KVKALRTVVKNPDLLPYIRRFL 114 (232)
Q Consensus 93 K~kalK~l~~n~~~q~a~~~f~ 114 (232)
.++|.+++.++..+-+.+..+.
T Consensus 197 ~ktA~~Ll~~~gsle~i~~~~~ 218 (880)
T PRK05755 197 EKTAAKLLQEYGSLEGLYENLD 218 (880)
T ss_pred HHHHHHHHHHcCCHHHHHHhHH
Confidence 9999999999988877766553
No 14
>PRK09482 flap endonuclease-like protein; Provisional
Probab=87.33 E-value=0.79 Score=41.38 Aligned_cols=87 Identities=9% Similarity=0.005 Sum_probs=55.3
Q ss_pred cCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccch-hh-HhHHHhhhhhcC--CCcchhhhhcc
Q psy18235 17 EEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDT-SL-AEHILFIRAISG--CDSTSALFNQG 92 (232)
Q Consensus 17 ~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~-~~-~~~l~~~ha~tg--cDtts~f~gkG 92 (232)
+++..|+|+|.|.|.+-|.--+ ..+| .+.+ . ++++...+.+. .+ -..++-+.|+.| .|..+---|+|
T Consensus 121 ~~~~~v~I~S~DKDl~Qlv~~~----v~~~-~~~~--~--~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG 191 (256)
T PRK09482 121 QAGHQATIVSTDKGYCQLLSPT----IQIR-DYFQ--K--RWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIG 191 (256)
T ss_pred HCCCeEEEEECCCCccccCCCC----eEEE-eccc--c--ccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcC
Confidence 4567899999999987665311 1122 1221 1 12333333221 01 133566779999 78889999999
Q ss_pred hhhhhhhhccCcChHHHHHH
Q psy18235 93 KVKALRTVVKNPDLLPYIRR 112 (232)
Q Consensus 93 K~kalK~l~~n~~~q~a~~~ 112 (232)
.++|.++++++..+-..+..
T Consensus 192 ~KtA~~LL~~~gsle~i~~~ 211 (256)
T PRK09482 192 PKSAAELLNQFRSLENIYES 211 (256)
T ss_pred hHHHHHHHHHhCCHHHHHHh
Confidence 99999999998766655544
No 15
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.29 E-value=1.1 Score=47.03 Aligned_cols=92 Identities=18% Similarity=0.235 Sum_probs=61.1
Q ss_pred cCCceEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccchh-h-HhHHHhhhhhcCC--Ccchhhhhcc
Q psy18235 17 EEDEVVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDTS-L-AEHILFIRAISGC--DSTSALFNQG 92 (232)
Q Consensus 17 ~~~~~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~~-~-~~~l~~~ha~tgc--Dtts~f~gkG 92 (232)
+.|..++|+|.|.|.+-|.-- ...+..+.++.. ...++...+.++- + -.-++-+-|+.|. |..+..-|+|
T Consensus 121 ~~g~~v~IvS~DkDllQLv~~-----~v~~~~~~~~~~-~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG 194 (887)
T TIGR00593 121 KEGYEVRIISGDKDLLQLVSD-----NVKVLIPKGKTS-FTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIG 194 (887)
T ss_pred hCCCcEEEEECCCChhhcCCC-----CEEEEeccCCCC-ceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcC
Confidence 446789999999999887631 122222332211 1224444333310 1 2347778899994 9999999999
Q ss_pred hhhhhhhhccCcChHHHHHHhc
Q psy18235 93 KVKALRTVVKNPDLLPYIRRFL 114 (232)
Q Consensus 93 K~kalK~l~~n~~~q~a~~~f~ 114 (232)
.++|.|+++++.++-+.+....
T Consensus 195 ~KtA~kLL~~ygsle~i~~~~~ 216 (887)
T TIGR00593 195 EKTAAKLLQEFGSLENIYENLD 216 (887)
T ss_pred HHHHHHHHHHcCCHHHHHHHHH
Confidence 9999999999988877766553
No 16
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=78.74 E-value=1.4 Score=27.98 Aligned_cols=30 Identities=17% Similarity=0.222 Sum_probs=25.2
Q ss_pred HHhhhhhcCCCcch---hhhhcchhhhhhhhccC
Q psy18235 73 ILFIRAISGCDSTS---ALFNQGKVKALRTVVKN 103 (232)
Q Consensus 73 l~~~ha~tgcDtts---~f~gkGK~kalK~l~~n 103 (232)
+.-+-+++| |.+. ..-|.|.++|+++++++
T Consensus 4 ~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 4 LIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred HHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 455668999 9998 88999999999998754
No 17
>KOG2520|consensus
Probab=45.62 E-value=15 Score=38.51 Aligned_cols=34 Identities=26% Similarity=0.407 Sum_probs=30.3
Q ss_pred hHHHhhhhhcCCCcchhhhhcchhhhhhhhccCc
Q psy18235 71 EHILFIRAISGCDSTSALFNQGKVKALRTVVKNP 104 (232)
Q Consensus 71 ~~l~~~ha~tgcDtts~f~gkGK~kalK~l~~n~ 104 (232)
..|+-+--+.|+|.|.-..|+|=.+|+.++..+|
T Consensus 548 ~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp 581 (815)
T KOG2520|consen 548 PNLISLAQLLGSDYTEGLKGIGPVSALEILAEFP 581 (815)
T ss_pred hhhHHHHHhcccccccCCCcccchHHHHHHHHcC
Confidence 3466677789999999999999999999999998
No 18
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=41.49 E-value=4.4 Score=30.53 Aligned_cols=18 Identities=33% Similarity=0.359 Sum_probs=12.0
Q ss_pred CceEEEEeCCcceEEeee
Q psy18235 19 DEVVVLVGEDVDLLVILI 36 (232)
Q Consensus 19 ~~~~vv~~~DTDvlVl~~ 36 (232)
|..=.|.|+|+|+|+...
T Consensus 25 g~vd~V~t~DsD~l~fG~ 42 (94)
T PF00867_consen 25 GLVDAVITEDSDLLLFGA 42 (94)
T ss_dssp TSSSEEE-SSSHHHHTT-
T ss_pred cceeEEEecCCCEEeeCC
Confidence 444468899999988744
No 19
>cd04975 Ig4_SCFR_like Fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR) and similar proteins. Ig4_SCFR_like; fourth immunoglobulin (Ig)-like domain of stem cell factor receptor (SCFR). In addition to SCFR this group also includes the fourth Ig domain of platelet-derived growth factor receptors (PDGFR), alpha and beta, the fourth Ig domain of macrophage colony stimulating factor (M-CSF), and the Ig domain of the receptor tyrosine kinase KIT. SCFR and the PDGFR alpha and beta have similar organization: an extracellular component having five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. SCFR and its ligand SCF are critical for normal hematopoiesis, mast cell development, melanocytes and gametogenesis. SCF binds to the second and third Ig-like domains of SCFR, this fourth Ig-like domain participates in SCFR dimerization, which follows ligand binding. Deletion of this fourth SCFR_Ig-like domain abolishes
Probab=27.17 E-value=1.5e+02 Score=22.41 Aligned_cols=40 Identities=20% Similarity=0.391 Sum_probs=26.6
Q ss_pred eeeeccCCceEEEE--eCCcceEEeeeccCCCccceeeecCC
Q psy18235 12 SLASEEEDEVVVLV--GEDVDLLVILIGTRSPSNVYFLKPGR 51 (232)
Q Consensus 12 ~lh~~~~~~~~vv~--~~DTDvlVl~~~~~~~~~~~~~~~g~ 51 (232)
|++..+.+...+.+ |++..+-+.+-|+.+...+.|.+.|+
T Consensus 2 fi~~~~~~~~~~~v~~G~~v~L~c~v~g~~P~p~v~W~Kdg~ 43 (101)
T cd04975 2 FINLSPEQNTTIFVNLGENLNLVVEVEAYPPPPHINWTYDNR 43 (101)
T ss_pred eEEEecCCCceEEEECCCCEEEEEEEEecCCCCccEEEeCCe
Confidence 56777776444444 66665555555656667899999985
No 20
>PHA00439 exonuclease
Probab=26.89 E-value=83 Score=29.03 Aligned_cols=70 Identities=20% Similarity=0.180 Sum_probs=43.7
Q ss_pred CCc-eEEEEeCCcceEEeeeccCCCccceeeecCCccccceEeccccccchhhHhHHHhhhhhcC--CCcchhhhhcchh
Q psy18235 18 EDE-VVVLVGEDVDLLVILIGTRSPSNVYFLKPGRGKVVPVLYHPQTTIDTSLAEHILFIRAISG--CDSTSALFNQGKV 94 (232)
Q Consensus 18 ~~~-~~vv~~~DTDvlVl~~~~~~~~~~~~~~~g~g~~~~~i~~i~~~~~~~~~~~l~~~ha~tg--cDtts~f~gkGK~ 94 (232)
.|. .++|+|.|-|++=|.- ...+|.. .+.. +. ..++....++-+-|+.| .|..+-.-|+| +
T Consensus 135 ~g~~~vvIvS~DKDl~QLv~-----~~~~~~~--~~~~----~~----~~~~~p~~~~d~~AL~GDsSDNIPGVpGIG-K 198 (286)
T PHA00439 135 FGFKKAVLVSCDKDFKTIPN-----CDFLWCT--TGNI----LT----QTPETADRWHLFQTIKGDSTDGYSGIPGWG-D 198 (286)
T ss_pred CCCCeEEEEeCCCCHhhcCc-----ceEEEcc--CCce----EE----cCcccHHHHHhhhhcccccccCCCCCCCcC-H
Confidence 454 8999999999877631 1223332 1111 10 11222333555668887 57778899999 9
Q ss_pred hhhhhhccC
Q psy18235 95 KALRTVVKN 103 (232)
Q Consensus 95 kalK~l~~n 103 (232)
+|.+++.+-
T Consensus 199 TA~kLL~~~ 207 (286)
T PHA00439 199 TAEAFLENP 207 (286)
T ss_pred HHHHHHhCc
Confidence 999999883
No 21
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=24.34 E-value=1.1e+02 Score=24.11 Aligned_cols=46 Identities=11% Similarity=0.078 Sum_probs=33.1
Q ss_pred eeEEecCCCcccchhHHHHHHHHhhhcccccccccCCCchHHHHHHH
Q psy18235 131 LVVLYGGNHETTSLNKLRYKSYVTSALKVTSYIAALPPTESAASQHA 177 (232)
Q Consensus 131 v~~LY~~~~~~~sVn~~Ry~~F~~k~~~~~~~~~~LPPt~~al~qH~ 177 (232)
++.||+.+ +.++..++|-++....+.-.-++...=||+.+.|+.=+
T Consensus 2 ~itiy~~p-~C~t~rka~~~L~~~gi~~~~~~y~~~~~s~~eL~~~l 47 (117)
T COG1393 2 MITIYGNP-NCSTCRKALAWLEEHGIEYTFIDYLKTPPSREELKKIL 47 (117)
T ss_pred eEEEEeCC-CChHHHHHHHHHHHcCCCcEEEEeecCCCCHHHHHHHH
Confidence 47789987 47788888888877665333455677799988876544
No 22
>PF11105 CCAP: Arthropod cardioacceleratory peptide 2a; InterPro: IPR024276 Crustacean cardioactive peptide (CCAP), also known as cardioacceleratory peptide 2a, exerts a reversible and dose-dependent cardio-stimulatory effect on the semi-isolated heart of experimental beetles. CCAP also increases free hemolymph sugar concentration in young larvae and adults of the meal-worm beetle [].; PDB: 1Y49_A 1V46_A.
Probab=22.43 E-value=23 Score=28.94 Aligned_cols=15 Identities=27% Similarity=0.585 Sum_probs=4.9
Q ss_pred hHHHhhhhhcCCCcc
Q psy18235 71 EHILFIRAISGCDST 85 (232)
Q Consensus 71 ~~l~~~ha~tgcDtt 85 (232)
..=||..|||||--.
T Consensus 43 ~KRPFCNAFTGCGrK 57 (133)
T PF11105_consen 43 KKRPFCNAFTGCGRK 57 (133)
T ss_dssp -----SSSSS-----
T ss_pred ccCccchhhcccCcc
Confidence 346999999999654
No 23
>cd00490 Met_repressor_MetJ Met Repressor, MetJ. MetJ is a bacterial regulatory protein that uses S-adenosylmethionine (SAM) as a corepressor to regulate the production of Methionine. MetJ binds arrays of two to five adjacent copies of an eight base-pair 'metbox' sequence. MetJ forms sufficiently strong interactions with the sugar-phosphate backbone to accomodate sequence variation in natural operators. However, it is very sensitive to particular base changes in the operator. MetJ exists as a homodimer.
Probab=22.28 E-value=39 Score=26.15 Aligned_cols=14 Identities=36% Similarity=0.586 Sum_probs=9.7
Q ss_pred hhhHhHHHhhhhhcCC
Q psy18235 67 TSLAEHILFIRAISGC 82 (232)
Q Consensus 67 ~~~~~~l~~~ha~tgc 82 (232)
+-+|.| |+|||||.
T Consensus 55 ELLCEA--FLHAfTGQ 68 (103)
T cd00490 55 ELLCEA--FLHAFTGQ 68 (103)
T ss_pred HHHHHH--HHHHhcCC
Confidence 334554 78999985
No 24
>PRK05264 transcriptional repressor protein MetJ; Provisional
Probab=21.89 E-value=40 Score=26.23 Aligned_cols=14 Identities=36% Similarity=0.586 Sum_probs=9.8
Q ss_pred hhhHhHHHhhhhhcCC
Q psy18235 67 TSLAEHILFIRAISGC 82 (232)
Q Consensus 67 ~~~~~~l~~~ha~tgc 82 (232)
+-+|.| |+|||||.
T Consensus 56 ELLCEA--FLHA~TGQ 69 (105)
T PRK05264 56 ELLCEA--FLHAFTGQ 69 (105)
T ss_pred HHHHHH--HHHHHcCC
Confidence 334555 78999985
No 25
>PF01340 MetJ: Met Apo-repressor, MetJ; InterPro: IPR002084 Binding of a specific DNA fragment and S-adenosyl methionine (SAM) co-repressor molecules to the Escherichia coli methionine repressor (MetJ) leads to a significant reduction in dynamic flexibility of the ternary complex, with considerable entropy-enthalpy compensation, not necessarily involving any overall conformational change []. MetJ is a regulatory protein which when combined with S-adenosylmethionine (SAM) represses the expression of the methionine regulon and of enzymes involved in SAM synthesis. It is also autoregulated. The crystal structure of the met repressor-operator complex shows two dimeric repressor molecules bound to adjacent sites 8 base pairs apart on an 18-base-pair DNA fragment. Sequence specificity is achieved by insertion of double-stranded antiparallel protein beta-ribbons into the major groove of B-form DNA, with direct hydrogen-bonding between amino-acid side chains and the base pairs. The repressor also recognises sequence-dependent distortion or flexibility of the operator phosphate backbone, conferring specificity even for inaccessible base pairs [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006555 methionine metabolic process; PDB: 1MJO_D 1CMB_A 1MJQ_C 1CMC_B 1MJK_A 1MJ2_A 1MJP_A 1MJM_B 1CMA_B 1MJL_A ....
Probab=21.03 E-value=39 Score=26.14 Aligned_cols=12 Identities=42% Similarity=0.744 Sum_probs=7.4
Q ss_pred hHhHHHhhhhhcCC
Q psy18235 69 LAEHILFIRAISGC 82 (232)
Q Consensus 69 ~~~~l~~~ha~tgc 82 (232)
+|.| |+|||||.
T Consensus 57 LcEA--FLHAfTGQ 68 (104)
T PF01340_consen 57 LCEA--FLHAFTGQ 68 (104)
T ss_dssp HHHH--HHHHHH--
T ss_pred HHHH--HHHHhcCC
Confidence 4554 78999985
Done!