Query psy14280
Match_columns 1891
No_of_seqs 267 out of 606
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 15:50:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14280.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14280hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2045|consensus 100.0 1E-304 3E-309 2677.6 82.7 1139 1-1233 1-1209(1493)
2 COG5049 XRN1 5'-3' exonuclease 100.0 3E-208 7E-213 1828.4 46.7 843 1-935 1-945 (953)
3 KOG2044|consensus 100.0 3E-186 6E-191 1663.3 45.1 614 1-683 1-679 (931)
4 PF03159 XRN_N: XRN 5'-3' exon 100.0 4.6E-77 1E-81 668.5 17.8 233 1-298 1-237 (237)
5 cd00128 XPG Xeroderma pigmento 98.4 3.6E-06 7.8E-11 100.1 16.7 95 1-103 1-95 (316)
6 KOG2044|consensus 98.3 1.9E-07 4.1E-12 117.4 2.4 39 135-173 91-129 (931)
7 PTZ00217 flap endonuclease-1; 98.1 2.3E-05 5.1E-10 96.1 14.3 92 1-101 1-103 (393)
8 PF03159 XRN_N: XRN 5'-3' exon 98.1 1.6E-06 3.6E-11 99.6 2.5 40 135-174 73-112 (237)
9 COG5049 XRN1 5'-3' exonuclease 97.7 1.3E-05 2.7E-10 100.4 2.4 52 136-187 73-124 (953)
10 KOG2045|consensus 97.5 3.9E-05 8.5E-10 97.8 2.9 35 136-173 75-109 (1493)
11 PRK03980 flap endonuclease-1; 97.3 0.0052 1.1E-07 73.3 16.7 104 234-378 97-200 (292)
12 TIGR03674 fen_arch flap struct 97.2 0.0019 4.1E-08 78.4 11.6 91 1-103 1-97 (338)
13 PF00752 XPG_N: XPG N-terminal 95.3 0.016 3.4E-07 58.4 3.8 97 1-105 1-99 (101)
14 smart00485 XPGN Xeroderma pigm 95.1 0.029 6.2E-07 56.5 4.8 96 1-105 1-97 (99)
15 KOG2518|consensus 94.6 0.23 4.9E-06 62.8 11.8 96 1-105 1-97 (556)
16 smart00475 53EXOc 5'-3' exonuc 92.9 3.2 7E-05 49.3 16.7 90 243-376 103-195 (259)
17 PF00867 XPG_I: XPG I-region; 88.9 1.2 2.6E-05 44.9 7.0 89 234-367 5-94 (94)
18 cd00008 53EXOc 5'-3' exonuclea 86.8 14 0.00031 43.4 15.1 56 32-88 4-60 (240)
19 TIGR00600 rad2 DNA excision re 58.8 13 0.00029 51.7 5.7 91 234-377 786-876 (1034)
20 TIGR00600 rad2 DNA excision re 49.8 29 0.00064 48.5 6.7 92 1-103 1-94 (1034)
21 COG0258 Exo 5'-3' exonuclease 45.9 3.2E+02 0.007 33.5 14.0 57 31-91 13-73 (310)
22 cd00552 RaiA RaiA ("ribosome-a 42.8 81 0.0017 31.3 7.0 74 1744-1824 10-85 (93)
23 PRK05755 DNA polymerase I; Pro 42.3 3.7E+02 0.0081 37.7 15.4 89 243-376 105-196 (880)
24 PF01302 CAP_GLY: CAP-Gly doma 39.2 92 0.002 30.3 6.5 58 1156-1220 1-68 (69)
25 KOG0971|consensus 31.5 1.6E+02 0.0034 40.8 8.6 69 1152-1226 4-79 (1243)
26 cd00080 HhH2_motif Helix-hairp 30.1 33 0.00073 33.7 2.0 22 355-376 8-31 (75)
27 PF02482 Ribosomal_S30AE: Sigm 29.6 1E+02 0.0022 30.8 5.3 74 1744-1824 10-85 (97)
28 COG1515 Nfi Deoxyinosine 3'end 29.2 29 0.00062 40.6 1.6 37 3-42 73-109 (212)
29 cd00048 DSRM Double-stranded R 27.7 1.4E+02 0.0029 27.2 5.4 61 1758-1822 4-68 (68)
30 COG4003 Uncharacterized protei 26.8 2.5E+02 0.0054 28.9 7.2 60 1043-1118 5-76 (98)
31 KOG2519|consensus 25.4 1.8E+02 0.0039 37.7 7.5 102 1-110 1-105 (449)
32 smart00422 HTH_MERR helix_turn 24.8 1E+02 0.0023 28.7 4.2 51 970-1048 2-52 (70)
33 smart00279 HhH2 Helix-hairpin- 24.5 54 0.0012 28.3 2.0 20 355-375 2-21 (36)
34 PRK14976 5'-3' exonuclease; Pr 22.7 3.3E+02 0.0072 33.3 8.8 101 242-389 108-211 (281)
35 smart00484 XPGI Xeroderma pigm 20.9 73 0.0016 31.5 2.4 35 243-286 10-44 (73)
36 COG2451 Ribosomal protein L35A 20.6 1.1E+02 0.0024 31.8 3.6 45 1150-1201 39-84 (100)
No 1
>KOG2045|consensus
Probab=100.00 E-value=1.4e-304 Score=2677.64 Aligned_cols=1139 Identities=46% Similarity=0.803 Sum_probs=1024.8
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHhhcccceE
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILFRMIQPKKL 80 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~~iVrPrKl 80 (1891)
||||+||||++|||||+++++++.+||||||||||||||||+|+|+||+++++|++|||||.+||+|||+||.+|||+|+
T Consensus 1 MGvPKFfR~iSERyP~lseliee~qIPEFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEif~~IfnYIdhLf~~IkPqKl 80 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLSELIEEHQIPEFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEIFQEIFNYIDHLFYLIKPQKL 80 (1493)
T ss_pred CCchHHHHHhhhhchHHHHHhhhccCCcccceeeecccccccCCCCCCCccCcCCCHHHHHHHHHHHHHHHHHhhCcceE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeecCCCcchhhhHHHhhhhhhhhHHHHHHHHHhhhCCCCCcccccccccccccCcccceeeeccCCCchhhhhhhhh
Q psy14280 81 FFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQKAKEKGERLPTEKRFDFITLKFCFPKKLFFMAIDGVAPRAKMNQQRG 160 (1891)
Q Consensus 81 lyiAIDGVAPRAKMnQQRsRRFrsa~ea~~~~~~~k~~g~~l~~e~~fd~~~l~~~~p~k~~~~aiDGvaP~aKmnqQr~ 160 (1891)
||||||||||||||||||+||||+|
T Consensus 81 ffMAVDGvAPRAKMNQQRsRRFrTA------------------------------------------------------- 105 (1493)
T KOG2045|consen 81 FFMAVDGVAPRAKMNQQRSRRFRTA------------------------------------------------------- 105 (1493)
T ss_pred EEEeecccCchhhhhHHHHHhhhhh-------------------------------------------------------
Confidence 9999999999999999999999998
Q ss_pred ccccchHHHHHHHHHHHHhCCCCCCcccCCCCcccCCchHHHHHHHHHHHHHHHhhcCCcccccccccccccceEEEEcC
Q psy14280 161 RRFRSAKEAEVLEQKAKEKGERLPTEKRFDSNCITPGTPFMCRLHQQLRYFVKLKITTDKLWKDTLSLWVWKDVCVILSG 240 (1891)
Q Consensus 161 rrf~s~keae~~~~ka~~~G~~lp~e~~FDSN~ITPGTeFM~kL~~~Lk~fI~~KistDp~W~~~~~~~~~~~lkVIlSg 240 (1891)
++|+.++.||.++|+.+|. ++||||||||||+||.||++.|+|||+.|+++|+.|++ ++|||||
T Consensus 106 ------rdAe~qlaKA~enGe~~p~-erFDSNcITPGTeFM~rl~~~L~yfIktKistDs~Wq~---------~~vIlSG 169 (1493)
T KOG2045|consen 106 ------RDAEQQLAKAAENGELRPH-ERFDSNCITPGTEFMVRLQEGLRYFIKTKISTDSLWQR---------CTVILSG 169 (1493)
T ss_pred ------hhHHHHHHHHHhccccCcc-cccccCCCCCcHHHHHHHHHHHHHHHHhccccchhhcc---------cEEEEeC
Confidence 4567778889999999997 89999999999999999999999999999999999999 9999999
Q ss_pred CCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCCCCcccCCCCcceE
Q psy14280 241 HETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKGGSQIVTPEETKFF 320 (1891)
Q Consensus 241 s~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~~~~~~~~~~~~F~ 320 (1891)
|+||||||||||||||.+|+||+|||||||||||+|||||||||+||+|||++|||||+|+++.+++ ..+.++|+
T Consensus 170 hevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn~~k-----~lehqkFy 244 (1493)
T KOG2045|consen 170 HEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRNKRK-----SLEHQKFY 244 (1493)
T ss_pred CcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeecccccccc-----hhhhhhhh
Confidence 9999999999999999999999999999999999999999999999999999999999999765554 35778999
Q ss_pred EEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhccCCCCCCCCccccCCcHHHHHHHHHHHcccCCCcc
Q psy14280 321 LLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIGNDFIPNLPDLHIINGALPLLYKVYQEVLPTLDGYI 400 (1891)
Q Consensus 321 llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvGNDFLPhLP~L~I~eGald~L~~~Yk~~Lp~l~gYL 400 (1891)
|||||+|||||++||..+++ .+.|+||+|||+||||||+||+|||||||||+|||++|||++|+.+|++++|++||||
T Consensus 245 LLHLsLLREYlelEF~e~rd--t~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpllystykkvlpt~~GyI 322 (1493)
T KOG2045|consen 245 LLHLSLLREYLELEFDELRD--TDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLYSTYKKVLPTLGGYI 322 (1493)
T ss_pred hhHHHHHHHHHHHHHHHhhh--ccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHHHHHHHHhccCCccc
Confidence 99999999999999999988 8999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCeecHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhhhCCCcc----h--------hh--hh------hccccC--C-
Q psy14280 401 NEGGYLNLKRFEKFLTKLASFDFEQFREKYADIQYLEGKMGKKFS----D--------VF--HK------EKSKEM--D- 457 (1891)
Q Consensus 401 te~G~INl~rL~~fL~~Ls~~E~~~F~~~~~d~~~~e~k~~~k~~----e--------~~--k~------~~~k~~--~- 457 (1891)
||+|.|||.||+.||.+|..+|.++|.++.+|+++.++|..+--. + .. +. ++.+.. +
T Consensus 323 NE~G~lNl~Rle~~L~eL~nfeke~Fke~led~k~~nskr~r~~~~~~~~~~~~dika~t~sq~~d~l~~~~~~~p~i~~ 402 (1493)
T KOG2045|consen 323 NENGKLNLRRLEIFLSELTNFEKEHFKEHLEDLKYMNSKRERFDDPEQQELAEMDIKAITESQNLDSLLGEESKDPLINK 402 (1493)
T ss_pred cccceecHHHHHHHHHHHHhhhHHHHHHHHHhhhhccccccccccHHHHhhhcccHHhhhhhhhhhhhcccccccccccc
Confidence 999999999999999999999999999999999988877543210 0 00 00 000000 0
Q ss_pred -----ccHHHHHhhcC------------------CCCCCChhhh----------hcccccccccCCCcchhhh-cccccc
Q psy14280 458 -----PDLAALIKATD------------------DDYDDGTEEV----------LNYANYEEYYYSDEDEEWR-TNFFSE 503 (1891)
Q Consensus 458 -----~~l~~l~k~~~------------------~~~~d~~~~~----------~~~~~~~~i~~~~d~ee~~-~~~~~~ 503 (1891)
.+-+++++... .++.|+.|++ ..++.++.. .+.+..|+ .++.++
T Consensus 403 ~a~ld~dD~~Fl~~~~eDl~~~~~~s~s~~~~ld~~~~de~EdEf~~~~~t~~ls~~~~~~~~--n~eea~~eKti~n~~ 480 (1493)
T KOG2045|consen 403 SALLDDDDSAFLSDHEEDLSDLEPGSGSDELLLDNLDADELEDEFAVELATLALSGMNDADFA--NDEEACWEKTILNKE 480 (1493)
T ss_pred ccccccchHHHHHHhhhhccccccccCccchhhccccchhhhHHHHHHHHHHHHhcccccccc--chHHHhhhhhhHHHH
Confidence 00001111000 0011111111 011111111 01111233 345677
Q ss_pred ccchHHHHhhhhcCCCCCCHHHHHHHHHHHHHhhhhhhcccccccCcCCCCCccccCCCccccccccccccccccCCCCC
Q psy14280 504 FGQHKTDYYHYKLDYAKVTNEVLRDQAECYIRAIQWNLHYYYNGCVSWSWYYPHHYAPYISDIKDFSHLNLKYEMGEPFL 583 (1891)
Q Consensus 504 ~~~~K~~YY~~Kf~~~~~~~e~l~~i~~~YveGLqWVL~YYy~GcpSW~WyYPYHYAP~iSDl~~~~~~~i~Fe~g~Pf~ 583 (1891)
|+.||+.||++|+++++.|+|.++++|++|||||||||+|||+||+||+|||||||||||||++++.+++|+|++|+||+
T Consensus 481 F~rwK~~yYrdKlkf~~~dee~lrelae~YVeaLQWvL~YYYrGc~SWsWyYphHyaP~ISDl~kgldv~ieF~mgtPF~ 560 (1493)
T KOG2045|consen 481 FQRWKRNYYRDKLKFDPNDEELLRELAEHYVEALQWVLDYYYRGCQSWSWYYPHHYAPFISDLKKGLDVEIEFHMGTPFL 560 (1493)
T ss_pred HHHHHHHHhhhhhcCCCccHHHHHHHHHHHHHHHHHHHHHHhcCCccccccccccccchhHhHhcccceeEEEecCCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHhHhhhccCCcccCCCCHhhHhhhcCCCCcccccCCCcceecCCCCccceeeEEecCCcChHHHHHHHHhhcCCCCHHH
Q psy14280 584 PFQQLLAVLPAASKELLPEPYQNLMTLENSPILEYYPEEFATDLNGKKQDWEAVVLIPFIDEVKLIKAMDAVEHLLTDEE 663 (1891)
Q Consensus 584 PfeQLmaVLPp~Sk~LLP~~yr~LMtdp~SPI~dFYP~~FeiDlNGKk~~WegVVLLPFIDe~rLl~Am~~~~~~LT~EE 663 (1891)
||||||||||++|+.|||.+||+||.++.|||+||||.+|++|+|||+++||||||||||||+||++||.+++..||.||
T Consensus 561 PFqQLlAVLPaaSa~llPp~frdLM~~~~SPI~DFYPaefelD~NGKtadWEAVVLIpFIdEkRLleAm~pk~~~Ls~EE 640 (1493)
T KOG2045|consen 561 PFQQLLAVLPAASAKLLPPAFRDLMLLPTSPIADFYPAEFELDLNGKTADWEAVVLIPFIDEKRLLEAMLPKEAQLSLEE 640 (1493)
T ss_pred cHHHHHHhchhhhhccCChhhhHhhcCCCCchhhcchhhheecccCCccceeEEEEEeecchHHHHHHHhhHhhhcCHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhccCCCcEEEEecCCCCccccC--CCCCCCcccccceeecccCCccccCCccccccCCccccccccccCCCccccccc
Q psy14280 664 RSRNRHGPMLVYTYSNVNLGTALA--PDYFPAINENHAVEKPLYRDDIYVHPNKLRKGLCQDVNLKLYVTHFPTLKHVQF 741 (1891)
Q Consensus 664 k~RN~~G~~llF~yd~~~~~~~~S--p~~Fpdi~~~~~~~~~~~~~~~~~p~~~l~~gL~~gv~~~~~~~GFPTL~~Lp~ 741 (1891)
+.||+||++++|.|+......|+| |+.|+++.+|||+.+.+.... ++....++||||||+++++++|||||+||||
T Consensus 641 r~RNs~g~~~vys~~~~~~s~yps~l~g~f~dv~~~~~v~K~y~~~~--~~~se~~~gllPnaklgvff~GFPTm~~L~~ 718 (1493)
T KOG2045|consen 641 RERNSHGPMYVYSYSTVAQSPYPSYLPGRFLDVLYCTEVAKWYHEIA--VNLSESVCGLLPNAKLGVFFPGFPTMQHLPF 718 (1493)
T ss_pred hhhcccCCceeeecchhhcCCCCCCCccccccccccccccccccccc--ccCceeEEEEcCCchhceeccCCcchhcCCc
Confidence 999999999999999999999998 899999999999987765543 4667889999999999999999999999999
Q ss_pred eeeeecceeEEecCCCCCCcEEEEeccCCCc-cHHHHHHHHcCCEEEecCCccceEEEEEEecCCeeEEEecCCCCccc-
Q psy14280 742 THKIENAKVKVFQQPSRNESIIIVQDKVQVP-SLKQVADQILGKTIFINYPHLIEIRVQAVATKDSRISFDKNSGPVFE- 819 (1891)
Q Consensus 742 t~~L~~~gV~VFq~pSR~eSMiL~I~~~~~~-sl~eiAk~LLGK~VyVgWP~L~EAKVVsVSD~~~ky~l~~~~g~~~~- 819 (1891)
+++|++++|+||||+||++||||.+.+.... +++++|+++|||+|||+||||+||+||+|+|++..|...+. +...
T Consensus 719 ~~eLry~~~nVFgq~SrnqsmVlkved~~~~~tle~~asq~l~k~I~vdWPyLreAkv~s~~dgd~i~~~~~s--ti~kk 796 (1493)
T KOG2045|consen 719 DFELRYDRVNVFGQVSRNQSMVLKVEDRQLEDTLEAVASQYLGKVIHVDWPYLREAKVVSVADGDQIVDSEGS--TINKK 796 (1493)
T ss_pred cceeeecceeeecccccCcceEechhhhhccchHHHHHHHhcCceEEccCchhheeeeeeecCCCeEEeccCC--chhhh
Confidence 9999999999999999999999999998755 68999999999999999999999999999999988776532 2221
Q ss_pred ccchhHHHHHHHHHHHHHHHHhcccceeecCeeEEEEEEeecceeEEecCCCceeEEeeccccccceecchhcccccccc
Q psy14280 820 RAAKDMQDAFQLSKKSITDGYYTKLGVDIGNTEVLVYGQPVESRKYFFGPRGKVTQQRTFIRSTVTYAYQSAVLNLQQAR 899 (1891)
Q Consensus 820 ~~~~~e~~~w~k~~~~I~e~Y~KR~GI~IGev~VLVhVrpL~Glkyv~~~~Gav~lvK~fS~~e~~YPlQlIV~DV~~~D 899 (1891)
.....|+++|.++|+.+.++|.||+||.+|+.++|++|||++|+.|.+...|.+..-++||+..+.||+|+||+||.++|
T Consensus 797 d~~e~eKrq~~s~~n~l~e~y~krfgi~~a~~~ala~Vrp~tGlvye~~ggg~lk~f~~wss~~~~yPaqlVVedv~~ed 876 (1493)
T KOG2045|consen 797 DMSEEEKRQFDSECNALQEHYIKRFGIQFANYDALAYVRPFTGLVYEFRGGGALKVFDSWSSSVTGYPAQLVVEDVTVED 876 (1493)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHhhhhhcccceeeEEEEeeccceEeccCCcEEEeeccccCcccccchhhhhhhhhccc
Confidence 13457889999999999999999999999999999999999999998766667777789999999999999999999999
Q ss_pred ccC-ccCCcccccCCCCEEEEeCCCC-CCCcEEEeccc-cccCcEEEEEEEecCCCChhhhhhhcccccccccChHHHHH
Q psy14280 900 ESL-EYKTIDEIFYPGCQCFALSNPH-YGSGGCVISTV-KEENSFIKLSFKVQQEPDLSDLVHLQDDTVYNYLPSYTVAS 976 (1891)
Q Consensus 900 ~Rf-~~~pIeEeFPiGSkVffLG~~~-YGs~G~Vvg~~-~~~~~rlkVsv~v~~EP~~~~~~~~~~~~~~~Y~Ps~~VAk 976 (1891)
+|+ +.+|+|++||+||+||+||+++ ||++|+|.|++ ....+.+.+++-+..||.++++++++++...+|||+|+||+
T Consensus 877 ~r~kerlpve~efP~~Skv~~lg~ya~yG~~~tv~g~s~~k~~~~~~e~~gld~epk~ga~r~~me~~~~kyypsyivak 956 (1493)
T KOG2045|consen 877 RRRKERLPVEHEFPVGSKVFLLGPYAYYGSEGTVQGPSLAKTNGRIQESIGLDPEPKVGAARQLMEERDRKYYPSYIVAK 956 (1493)
T ss_pred hhhhccCCceeecCCCCeEEEecCccccCCcccccCccchhhcceEEEeeccCCchhHHHHHHhhhhhhhhhccHHHHhh
Confidence 999 8899999999999999999876 99999999998 34445566666688999999999999999999999999999
Q ss_pred HcCCCHhhHhhhcceEEEecCCccCcceeeeeeeeeeccCCceecCceeccCCCCceEecHHHHHHHHHHHHhChHHHHH
Q psy14280 977 KLSISPLLLSRFTGSIFIIDSTEEGAKRHNIGLNIKFSRKNEEVVGFTRRDETTKKWFYTEQVVTLIKNYMKQFPEVFGF 1056 (1891)
Q Consensus 977 ~LGIspl~LSRITGS~~V~~gsr~~~~KiNIGLNLKF~~RnqkVlGYTRk~~~~~~WEYS~kAV~LI~eY~~kFPeLF~~ 1056 (1891)
.|+|+|++||||||+|+|..++ ++++||||+|||.+|++||+||||| +.++|+||++||+|+++|+++||+||.+
T Consensus 957 ~l~ihp~llsrITgtf~i~n~~---rkr~niGlqlkfdar~qkvlgysrR--~~~gweySn~tv~l~key~qtfpdff~~ 1031 (1493)
T KOG2045|consen 957 LLRIHPRLLSRITGTFWIVNGP---RKRHNIGLQLKFDARNQKVLGYSRR--TNNGWEYSNLTVDLMKEYCQTFPDFFDF 1031 (1493)
T ss_pred hhccchHHHhhhcceEEEEcCC---ccceecccccccchhhhhhhhhccc--cCccccchhhHHHHHHHHHhhchHHHHH
Confidence 9999999999999999999986 5899999999999999999999999 9999999999999999999999999999
Q ss_pred hhcCCCCCccccCCCCCc-chHHHHHHHHHHHhhCCCCccccccCCccccCHHHHHHHHHHHHHhhhcc-ccEe--eecC
Q psy14280 1057 LKDHSSDDIYLRDDVFPH-QGEQRVAQIVSWLKEQPHAKAEVRPCGAAVVDAKVVSLIEHAVDTCEKVE-KQIT--LFVK 1132 (1891)
Q Consensus 1057 L~~~~~~d~~~~~DIFp~-~~~~kLkEIkaWLKe~~~~~le~Vscgse~Ldke~IkaIE~~idk~~k~~-K~v~--l~Vk 1132 (1891)
|..+...++....|+||+ ++..+|++|+.|||++++.++++|+|+++.|++++|+.+|++++++.+.+ +.++ +.|+
T Consensus 1032 l~~~~t~d~~~~~d~FP~kd~~~~l~~vk~wlk~~g~~~~~rVsl~sd~l~~e~Ik~~e~~~~~~~s~~~~~~k~l~~vp 1111 (1493)
T KOG2045|consen 1032 LGDNDTADFVFEQDVFPNKDGHRRLEEVKNWLKQQGHMKVERVSLGSDTLCRETIKLLEAAVDDLRSLPVKHVKLLVKVP 1111 (1493)
T ss_pred hcccccccchhhHhhCCCchhhhHHHHHHHHHHhcCcceeeeEeecccchhHHHHHHHHHHHHhhhhccchhhhhhcCcc
Confidence 998888899999999997 88899999999999999999999999999999999999999999988544 3222 3466
Q ss_pred CCccccccCCCCCcCCCCCCCcccCCeEEEEeCCCCccccCceEEEEEecCCCCccceEEEEeecccCCCCccc--cCCC
Q psy14280 1133 PNKLYIPKPTLDKLCPDPDTKFKLFDRVVNIRDCYTVPLGYRGTIIGIVQGETSYDAMYDVVFDKPFPHGVKIR--CSES 1210 (1891)
Q Consensus 1133 p~~L~kP~~~~~~L~PD~~q~F~LGDRVV~VrdsG~VPfG~kGTVVGI~~~~~~~d~~vDVLFDepF~GGttL~--cs~~ 1210 (1891)
+.++..|......+ ..|.|+||||||||+|+|+||+|++||||||+..++ +++++||||.|+++|++|+ |+++
T Consensus 1112 r~a~lnp~~~~v~l---~sq~f~lgdrVvyvqdsgkvPv~~kGTVvG~m~~~~--~~~~~vlFd~~~~ngnn~~Gr~~~~ 1186 (1493)
T KOG2045|consen 1112 RLAKLNPTLPDVYL---SSQPFRLGDRVVYVQDSGKVPVGTKGTVVGIMPVTD--DTFCKVLFDSPVPNGNNIHGRAEDR 1186 (1493)
T ss_pred hhhhcCCCCcceee---ccccccccceEEEeeccCccccccccceEEEEeccc--ccccceeecccccCCCccCceeccc
Confidence 66656555543333 699999999999999999999999999999999864 7899999999999999998 9999
Q ss_pred ccccccCcceeecCccccccCCC
Q psy14280 1211 RGYRMPAQAMINLSYGERLCGNS 1233 (1891)
Q Consensus 1211 RG~~Vp~ssLLNLT~gqr~~~~s 1233 (1891)
||..+..+.+||+|.++.+....
T Consensus 1187 ~g~~~e~a~vlnitdrqfv~~s~ 1209 (1493)
T KOG2045|consen 1187 VGKVPEIALVLNITDRQFVTASG 1209 (1493)
T ss_pred ccccccceeeeeecchhheeecC
Confidence 99999999999999998755433
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=3.2e-208 Score=1828.42 Aligned_cols=843 Identities=39% Similarity=0.681 Sum_probs=702.7
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHhhcccceE
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILFRMIQPKKL 80 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~~iVrPrKl 80 (1891)
||||+|||||++|||.+.+.|.+.++|+|||||||||||||+|+||++. +.+.+|+||+.+||.|||+|+.++|||||
T Consensus 1 MGVPsfFRwlS~r~p~ii~~I~e~~~P~~DNLYLDMNgIlH~CtHp~d~--~~petEeEm~~aVf~Yidhil~~irPrKl 78 (953)
T COG5049 1 MGVPSFFRWLSERYPKIIQLIEEKQIPEFDNLYLDMNGILHNCTHPNDG--SPPETEEEMYKAVFEYIDHILLKIRPRKL 78 (953)
T ss_pred CCchHHHHHHHhhhhHhhhhhhccCCCCcceeEEecccccccCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHhcCcceE
Confidence 9999999999999999999999999999999999999999999999984 45789999999999999999999999999
Q ss_pred EEEeecCCCcchhhhHHHhhhhhhhhHHHHHHHHHhhhCCCCCcccccccccccccCcccceeeeccCCCchhhhhhhhh
Q psy14280 81 FFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQKAKEKGERLPTEKRFDFITLKFCFPKKLFFMAIDGVAPRAKMNQQRG 160 (1891)
Q Consensus 81 lyiAIDGVAPRAKMnQQRsRRFrsa~ea~~~~~~~k~~g~~l~~e~~fd~~~l~~~~p~k~~~~aiDGvaP~aKmnqQr~ 160 (1891)
||||||||||||||||||+||||||++|..+..+|+..|+.++.|++-
T Consensus 79 lymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e-------------------------------- 126 (953)
T COG5049 79 LYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDE-------------------------------- 126 (953)
T ss_pred EEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccc--------------------------------
Confidence 999999999999999999999999998765444444445544322100
Q ss_pred ccccchHHHHHHHHHHHHhCCCC----CCcccCCCCcccCCchHHHHHHHHHHHHHHHhhcCCcccccccccccccceEE
Q psy14280 161 RRFRSAKEAEVLEQKAKEKGERL----PTEKRFDSNCITPGTPFMCRLHQQLRYFVKLKITTDKLWKDTLSLWVWKDVCV 236 (1891)
Q Consensus 161 rrf~s~keae~~~~ka~~~G~~l----p~e~~FDSN~ITPGTeFM~kL~~~Lk~fI~~KistDp~W~~~~~~~~~~~lkV 236 (1891)
-|..+ .+.+.||||||||||+||++|++.|+|||+.||++||.|++ ++|
T Consensus 127 ------------------~g~~id~~~~~kk~fDSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrn---------l~i 179 (953)
T COG5049 127 ------------------IGNEIDTIDVEKKKFDSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRN---------LRI 179 (953)
T ss_pred ------------------cCCccchhhhhhccccccCCCCCChHHHHHHHHHHHHHHhhhcCCcccee---------EEE
Confidence 01111 12467999999999999999999999999999999999999 999
Q ss_pred EEcCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCC--CCcc---
Q psy14280 237 ILSGHETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKG--GSQI--- 311 (1891)
Q Consensus 237 IlSgs~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~--~~~~--- 311 (1891)
|||||.||||||||||+|||+||+||+|||||+|||||+|||||||||+||+|||+||||+|.|+.+.+++ |.++
T Consensus 180 I~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t 259 (953)
T COG5049 180 IFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRT 259 (953)
T ss_pred EEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCccccccccccccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999998765433 2111
Q ss_pred -------cCCCCcceEEEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhccCCCCCCCCccccCCcHHH
Q psy14280 312 -------VTPEETKFFLLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIGNDFIPNLPDLHIINGALPL 384 (1891)
Q Consensus 312 -------~~~~~~~F~llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvGNDFLPhLP~L~I~eGald~ 384 (1891)
.....++|+|||||+|||||+.||... .++|.||+|||||||||||||+|||||||||+|||++||+++
T Consensus 260 ~~~~e~~k~~~~q~F~~LhiSlLREYLe~Ef~~~----~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldir~gai~~ 335 (953)
T COG5049 260 GHSDEECKVLTHQPFYLLHISLLREYLEREFREP----TLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDIREGAIET 335 (953)
T ss_pred ccchhhhcccccCceEEEEHHHHHHHHHHHhhcc----CCCccccHHHhhhhheeeeeeeccccCCCCCccccccchHHH
Confidence 134567899999999999999999876 468999999999999999999999999999999999999999
Q ss_pred HHHHHHHHcccCCCccccCCeecHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhhhCCC-cc----h--------hhhh-
Q psy14280 385 LYKVYQEVLPTLDGYINEGGYLNLKRFEKFLTKLASFDFEQFREKYADIQYLEGKMGKK-FS----D--------VFHK- 450 (1891)
Q Consensus 385 L~~~Yk~~Lp~l~gYLte~G~INl~rL~~fL~~Ls~~E~~~F~~~~~d~~~~e~k~~~k-~~----e--------~~k~- 450 (1891)
|+++|+++||+++||||++|.||+.||+.||..|+.+|.++|+....+..|.++...+. +. + +..+
T Consensus 336 l~ei~k~~lp~~~gYit~~G~iNl~rle~~L~~L~~~E~~iFk~~~~qe~r~ne~~~~~~~~k~~~e~~~~~~~vv~eq~ 415 (953)
T COG5049 336 LTEIWKKSLPHMKGYITCDGVINLARLEVILAILGSFEDDIFKKDHIQEERKNESLERFSLRKERKEGLKGMPRVVYEQK 415 (953)
T ss_pred HHHHHHHHhhhcCceeecCceecHHHHHHHHHHHhhhhcchhhhhhhHhhhhccchhhHHHHhhhhhhhcccchhhhhhh
Confidence 99999999999999999999999999999999999999999987654444432210000 00 0 0000
Q ss_pred --------------hcccc---CCc---cH---------------------------HHHHhhcC---------CC--CC
Q psy14280 451 --------------EKSKE---MDP---DL---------------------------AALIKATD---------DD--YD 472 (1891)
Q Consensus 451 --------------~~~k~---~~~---~l---------------------------~~l~k~~~---------~~--~~ 472 (1891)
..+|. .+. ++ ...+++.. ++ +.
T Consensus 416 ~~~gS~k~t~~d~~~~kk~~~l~~e~~id~~a~~k~~d~kn~el~~~~~~ndl~ls~ska~ks~~n~~le~~iasds~~e 495 (953)
T COG5049 416 KLIGSIKPTLMDQLQEKKSPDLPDEEFIDTLALPKDLDMKNHELFLKRFANDLGLSISKAIKSKGNYSLEMDIASDSPDE 495 (953)
T ss_pred hhcccccchhhhhhhhhccccCCCccccchhhchhhhhhhhhHHHHHHHHhhhhhhHHhhhhccCCchhhhhhhcccccc
Confidence 00000 000 00 00111110 00 11
Q ss_pred CChhhhhcccccccc----cC--CCcchhh--hccccccccchHHHHhhhhcCCCCCCHHHHHHHHHHHHHhhhhhhccc
Q psy14280 473 DGTEEVLNYANYEEY----YY--SDEDEEW--RTNFFSEFGQHKTDYYHYKLDYAKVTNEVLRDQAECYIRAIQWNLHYY 544 (1891)
Q Consensus 473 d~~~~~~~~~~~~~i----~~--~~d~ee~--~~~~~~~~~~~K~~YY~~Kf~~~~~~~e~l~~i~~~YveGLqWVL~YY 544 (1891)
++++.+++......+ .. ..++++. .+.+...+.+||.+||.+||+++..++|.++++|++|||||||||.||
T Consensus 496 d~ee~ese~d~i~~i~dk~vn~~v~ee~e~~~~~Tv~l~~~g~~erYY~~K~~~t~~~~E~irdm~k~YVeGL~WVL~YY 575 (953)
T COG5049 496 DEEEFESEVDSIRKIPDKYVNIIVEEEEENETEKTVNLRFPGWKERYYTSKLHFTTDSEEKIRDMAKEYVEGLQWVLSYY 575 (953)
T ss_pred chhhhhhccchhhhhhhhhhccccccchhcccccchhhcccchhhhhhhhhcCCCcCCHHHHHHHHHHHhhhhhhhhhhh
Confidence 111111111000000 00 0111111 234556688999999999999999999999999999999999999999
Q ss_pred ccccCcCCCCCccccCCCccccccccccccccccCCCCChHhHhhhccCCcccCCCCHhhHhhhcCCCCcccccCCCcce
Q psy14280 545 YNGCVSWSWYYPHHYAPYISDIKDFSHLNLKYEMGEPFLPFQQLLAVLPAASKELLPEPYQNLMTLENSPILEYYPEEFA 624 (1891)
Q Consensus 545 y~GcpSW~WyYPYHYAP~iSDl~~~~~~~i~Fe~g~Pf~PfeQLmaVLPp~Sk~LLP~~yr~LMtdp~SPI~dFYP~~Fe 624 (1891)
|+|||||+|||||||||+|+|+.++.+.+|+|++|+||+||||||+|||++|+++||++||+||+|++|||+||||++|.
T Consensus 576 Y~GC~SW~WyYpyHyAP~aaD~~k~~~~dIkFe~g~PF~P~EQLm~VLPa~Sk~~vP~~fr~LM~d~~S~IiDFYPe~f~ 655 (953)
T COG5049 576 YRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFRPLMDDEKSPIIDFYPEEFK 655 (953)
T ss_pred hcCCCCcccccccccchhhhhhhhcccceeeecCCCCCCcHHHHHhhcchhhcCcCchhhhhhhcCCCCcccccchhhcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCccceeeEEecCCcChHHHHHHHHhhcCCCCHHHHhhccCCCcEEEEecCCCCccccCCCCCCCcccccceeecc
Q psy14280 625 TDLNGKKQDWEAVVLIPFIDEVKLIKAMDAVEHLLTDEERSRNRHGPMLVYTYSNVNLGTALAPDYFPAINENHAVEKPL 704 (1891)
Q Consensus 625 iDlNGKk~~WegVVLLPFIDe~rLl~Am~~~~~~LT~EEk~RN~~G~~llF~yd~~~~~~~~Sp~~Fpdi~~~~~~~~~~ 704 (1891)
+|||||+++|||||||||||++|||+||++....||+||++||.+|.+++|..+++.. -+++|++|.+ +|+.+++
T Consensus 656 lD~NGK~~~Wq~VvLlpFiDe~RLl~A~~~~~~~Ls~eE~~RN~~g~~llf~s~~~~~----~~~l~~~lys-k~~~~~~ 730 (953)
T COG5049 656 LDMNGKTASWQAVVLLPFIDERRLLSAVAVKYPTLSEEERKRNLRGLDLLFSSNKKSD----LSELFKDLYS-KCKQKEY 730 (953)
T ss_pred cccCCceeeeeeeEEeeecchhHHHHHHHhhcccCCHHHHhccccCCceeEeccCCcc----HHHHHHHHHH-hhccCCc
Confidence 9999999999999999999999999999999999999999999999999999887644 2567888885 6766543
Q ss_pred cCCccccCCccccccCCcccccccc-ccCCCccccccceeeeecceeEEecCCCCCCcEEEEeccCCCc-cHHHHHHHHc
Q psy14280 705 YRDDIYVHPNKLRKGLCQDVNLKLY-VTHFPTLKHVQFTHKIENAKVKVFQQPSRNESIIIVQDKVQVP-SLKQVADQIL 782 (1891)
Q Consensus 705 ~~~~~~~p~~~l~~gL~~gv~~~~~-~~GFPTL~~Lp~t~~L~~~gV~VFq~pSR~eSMiL~I~~~~~~-sl~eiAk~LL 782 (1891)
.. +....+..||+++|+++.. ++ |++.+|++...+...++.||+..|+++||+|.+.+.... +.++++.+.+
T Consensus 731 ~~----m~~~~~~~GL~g~v~~~ae~~~--pn~~~lcp~~~~s~~~l~~~~~~~~n~S~~lv~~~pks~~~~ksi~~rg~ 804 (953)
T COG5049 731 IT----MCSKESPYGLFGTVKLGAEGLA--PNLLSLCPISFLSYPGLMVFLEYSKNQSARLVIEDPKSTVTNKSIVLRGF 804 (953)
T ss_pred ee----eecccccccccccccccccccc--ccccccCccccccccchhhhcccccCCceEEEeeccccccchHHHHHHhc
Confidence 32 3345566799999999864 33 999999999999999999999999999999998876654 5788999999
Q ss_pred CCEEEecCCccceEEEEEEecCCeeEEEecC-CCCcccccchhHHHHHHHHHHHHHHHHhcccceeecCeeEEEEEEeec
Q psy14280 783 GKTIFINYPHLIEIRVQAVATKDSRISFDKN-SGPVFERAAKDMQDAFQLSKKSITDGYYTKLGVDIGNTEVLVYGQPVE 861 (1891)
Q Consensus 783 GK~VyVgWP~L~EAKVVsVSD~~~ky~l~~~-~g~~~~~~~~~e~~~w~k~~~~I~e~Y~KR~GI~IGev~VLVhVrpL~ 861 (1891)
++.++|.|||++|+++++..|+...|...+. +.+ +.. ......+....+.|++|+|+.+ +..|.+..
T Consensus 805 ~~~~~vl~py~~es~~~s~~d~sys~r~n~~nd~k--~~~-----~~~g~k~s~q~r~ys~r~~~~~-----~~~~~~~~ 872 (953)
T COG5049 805 IKPINVLWPYLRESKLVSLTDGSYSYRYNNSNDKK--KFG-----FITGSKKSSQLRMYSKRKAVKF-----IATVFPVT 872 (953)
T ss_pred CCccccCCHHHHHHHHHHhcccchhhhhhcCcccc--cCc-----eeeccccchhhhhhhccccEEE-----EEEecccC
Confidence 9999999999999999999999887766431 111 000 1124455566788999999655 88999999
Q ss_pred ceeEEecCCCceeEEeeccccccceecchhccccccccccC---ccCCcccccCCCCEEEEeCCCCCCCcEEEeccc
Q psy14280 862 SRKYFFGPRGKVTQQRTFIRSTVTYAYQSAVLNLQQARESL---EYKTIDEIFYPGCQCFALSNPHYGSGGCVISTV 935 (1891)
Q Consensus 862 Glkyv~~~~Gav~lvK~fS~~e~~YPlQlIV~DV~~~D~Rf---~~~pIeEeFPiGSkVffLG~~~YGs~G~Vvg~~ 935 (1891)
|++. +.+|+ +.|.|+..-..||.|++|..+.+.|+|+ .+.|++.+||.|+++++||++.||....+.|+.
T Consensus 873 glqp--~~~ga--~n~~~s~syns~pg~~vv~sr~~g~~r~y~rn~~p~~n~y~~nr~~g~l~~~n~~~~nn~~g~y 945 (953)
T COG5049 873 GLQP--DSDGA--YNKTFSPSYNSYPGQLVVESRVNGDERYYERNPPPIENEYPLNRKVGFLGDYNYGGENNIDGYY 945 (953)
T ss_pred Cccc--CCCCC--ccccCCCCccccccccccceeecCCccccccCCCcccccCCCCCcceeccccccCCcccccccc
Confidence 9974 67887 7899998778999999999999999998 688999999999999999999999999999975
No 3
>KOG2044|consensus
Probab=100.00 E-value=2.9e-186 Score=1663.26 Aligned_cols=614 Identities=45% Similarity=0.824 Sum_probs=509.1
Q ss_pred CChhHHHHHHHhhcCCc-hhhhccc-------CC-----------CCCCEEEEecCCcccccccCCCCCCCCCCCHHHHH
Q psy14280 1 MGVPKFFRYISERYPCL-SEVVREY-------QI-----------PEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIF 61 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i-~~~v~e~-------~i-----------pefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif 61 (1891)
||||+|||||+++||.+ +.++++. .| -||||||||||||||+|+||++... +.||+|||
T Consensus 1 MGVPaffRWLs~kyp~~I~~viEe~p~~~~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPEdkPa--P~tedEm~ 78 (931)
T KOG2044|consen 1 MGVPAFFRWLSRKYPKTISPVIEEEPVDVDGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPEDKPA--PETEDEMF 78 (931)
T ss_pred CCchHHHHHHHHhcchhhhhhhhcCcccCCCcccccccCCCCCCcccccceeeecCcccccCCCCCCCCC--CccHHHHH
Confidence 99999999999999975 4444421 11 2899999999999999999998654 57999999
Q ss_pred HHHHHHHHHHHhhcccceEEEEeecCCCcchhhhHHHhhhhhhhhHHHHHHHHHhhhCCCCCcccccccccccccCcccc
Q psy14280 62 QDIFHYIEILFRMIQPKKLFFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQKAKEKGERLPTEKRFDFITLKFCFPKKL 141 (1891)
Q Consensus 62 ~~If~yID~L~~iVrPrKllyiAIDGVAPRAKMnQQRsRRFrsa~ea~~~~~~~k~~g~~l~~e~~fd~~~l~~~~p~k~ 141 (1891)
..||+|||+||.+||||||||||||||||||||||||+||||+|+|+.+.++
T Consensus 79 ~avFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~---------------------------- 130 (931)
T KOG2044|consen 79 VAVFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEA---------------------------- 130 (931)
T ss_pred HHHHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHH----------------------------
Confidence 9999999999999999999999999999999999999999999998865432
Q ss_pred eeeeccCCCchhhhhhhhhccccchHHHHHHHHHHHHhCCCCCC---cccCCCCcccCCchHHHHHHHHHHHHHHHhhcC
Q psy14280 142 FFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQKAKEKGERLPT---EKRFDSNCITPGTPFMCRLHQQLRYFVKLKITT 218 (1891)
Q Consensus 142 ~~~aiDGvaP~aKmnqQr~rrf~s~keae~~~~ka~~~G~~lp~---e~~FDSN~ITPGTeFM~kL~~~Lk~fI~~Kist 218 (1891)
|.|..+++..+.|..||. .+.||||||||||+||++|+.+|+|||+.||++
T Consensus 131 --------------------------e~e~~ree~~~~G~~lpp~~~~e~fDSNcITPGTpFM~~La~aLrYyI~~rLn~ 184 (931)
T KOG2044|consen 131 --------------------------EIERLREEFEAEGKFLPPKVKKETFDSNCITPGTPFMDRLAKALRYYIHDRLNS 184 (931)
T ss_pred --------------------------HHHHHHHHHHhcCCcCCchhhccccccCccCCCChHHHHHHHHHHHHHHHhhcC
Confidence 223345566677888865 468999999999999999999999999999999
Q ss_pred CcccccccccccccceEEEEcCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccc
Q psy14280 219 DKLWKDTLSLWVWKDVCVILSGHETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEV 298 (1891)
Q Consensus 219 Dp~W~~~~~~~~~~~lkVIlSgs~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV 298 (1891)
||.|++ ++|||||++||||||||||+|||+||++|+|||||+|||||+||||||||||||||||.||||+|
T Consensus 185 DPgWkN---------ikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLgLATHE~hF~IlRE~~ 255 (931)
T KOG2044|consen 185 DPGWKN---------IKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLGLATHEPHFSILREEF 255 (931)
T ss_pred Cccccc---------eEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceeeeccccCCceEEeeeee
Confidence 999999 99999999999999999999999999999999999999999999999999999999999999998
Q ss_pred cccccCC-----------CCCCcc----------cCC-CCcceEEEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHH
Q psy14280 299 KFNTKSN-----------KGGSQI----------VTP-EETKFFLLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDD 356 (1891)
Q Consensus 299 ~f~~~~~-----------k~~~~~----------~~~-~~~~F~llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDD 356 (1891)
.-++.++ +.|..+ ..+ -++.|++|||++|||||+.|+... .++|.+|+||+|||
T Consensus 256 ~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p----~lPf~fd~ER~iDD 331 (931)
T KOG2044|consen 256 FPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMP----NLPFTFDLERAIDD 331 (931)
T ss_pred cCCCcccchhhcccCCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCC----CCCccccHHhhhcc
Confidence 7332211 011001 011 246899999999999999999864 58999999999999
Q ss_pred HHHhhhhhccCCCCCCCCccccCCcHHHHHHHHHHHcccCCCccccCCeecHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
Q psy14280 357 WVLMGFLIGNDFIPNLPDLHIINGALPLLYKVYQEVLPTLDGYINEGGYLNLKRFEKFLTKLASFDFEQFREKYADIQYL 436 (1891)
Q Consensus 357 FVfL~fLvGNDFLPhLP~L~I~eGald~L~~~Yk~~Lp~l~gYLte~G~INl~rL~~fL~~Ls~~E~~~F~~~~~d~~~~ 436 (1891)
|||||||||||||||||+|+|++|||++|+++|++.+++++||||++|.+||+|++.||+.|+..|.++|+.+..+...|
T Consensus 332 wVF~CFFvGNDFLPHlPsLeIRegAId~L~~iyk~~~~~~kgYLT~~g~vNL~rve~~~~avg~~Ed~IFkkR~r~~e~f 411 (931)
T KOG2044|consen 332 WVFLCFFVGNDFLPHLPSLEIREGAIDRLMEIYKKSFPKMKGYLTDSGKVNLDRVEMFMQAVGSVEDDIFKKRQRREERF 411 (931)
T ss_pred eEEEEeeecCccCCCCCchhhhhcHHHHHHHHHHHHHHhhcceeccCCcccHHHHHHHHHHHhhhcchHHHHhHhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999886666666
Q ss_pred HhhhC-CCcch-hhhhhc-------cc-cCCccHH-HHHhhcCCC-------CCCChhhhhccccc---ccccCCCcchh
Q psy14280 437 EGKMG-KKFSD-VFHKEK-------SK-EMDPDLA-ALIKATDDD-------YDDGTEEVLNYANY---EEYYYSDEDEE 495 (1891)
Q Consensus 437 e~k~~-~k~~e-~~k~~~-------~k-~~~~~l~-~l~k~~~~~-------~~d~~~~~~~~~~~---~~i~~~~d~ee 495 (1891)
+.+.. ++-.+ ..+... .. ......+ ...+..... ..+..++...+... +.-...+++++
T Consensus 412 rrrk~~rk~~~~~~~~sg~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~k~~~~~~~~~ 491 (931)
T KOG2044|consen 412 RRRKAARKRQDRNAQDSGTNFSLAGSRELEASEPAQKALKVSLEKNESAANVERDNTEDLKTKLKHGQRRKSEDSESEEE 491 (931)
T ss_pred HHhhhhhhhhhhhcccccccccccccccccccchhhhhhhhccccccchhhhcccchhhccccccccccccCccccCCCC
Confidence 53211 00000 000000 00 0000000 000000000 00000110000000 00000112223
Q ss_pred hhccccccccchHHHHhhhhcCCCCCCHHHHHHHHHHHHHhhhhhhcccccccCcCCCCCccccCCCccccccccccccc
Q psy14280 496 WRTNFFSEFGQHKTDYYHYKLDYAKVTNEVLRDQAECYIRAIQWNLHYYYNGCVSWSWYYPHHYAPYISDIKDFSHLNLK 575 (1891)
Q Consensus 496 ~~~~~~~~~~~~K~~YY~~Kf~~~~~~~e~l~~i~~~YveGLqWVL~YYy~GcpSW~WyYPYHYAP~iSDl~~~~~~~i~ 575 (1891)
..|+......+||++||.+||++...++.+.+++|.+|||||||||+|||+||+||.||||||||||+|||+++.++.|+
T Consensus 492 ~~D~VkL~e~G~keRYY~~KF~v~~~eeq~R~~vv~~YveGLcWVl~YYyqGc~SW~WyYPYHYAPfAsDf~~l~~ldik 571 (931)
T KOG2044|consen 492 NTDKVKLYEPGWKERYYEEKFDVTPDEEQIRKDVVLKYVEGLCWVLRYYYQGCASWNWYYPYHYAPFASDFKGLSDLDIK 571 (931)
T ss_pred CCcceeecCCchhhhhhhhhcCCCCHHHHHHHHHHHHHhcchhhhhhhhhccccccccccccccchhhhhhhcccccccc
Confidence 33444444579999999999999987655667899999999999999999999999999999999999999999999999
Q ss_pred cccCCCCChHhHhhhccCCcccCCCCHhhHhhhcCCCCcccccCCCcceecCCCCccceeeEEecCCcChHHHHHHHHhh
Q psy14280 576 YEMGEPFLPFQQLLAVLPAASKELLPEPYQNLMTLENSPILEYYPEEFATDLNGKKQDWEAVVLIPFIDEVKLIKAMDAV 655 (1891)
Q Consensus 576 Fe~g~Pf~PfeQLmaVLPp~Sk~LLP~~yr~LMtdp~SPI~dFYP~~FeiDlNGKk~~WegVVLLPFIDe~rLl~Am~~~ 655 (1891)
|++|+||+||||||+|||++|++.||+.||.||++|+|||+||||+||+||||||+++|+||+|||||||+|||+|++.+
T Consensus 572 Fe~g~PFkP~eQLmgVlPAAS~~~LPe~~r~LMsdpdSpIiDFYPedF~iDmNGKk~aWQGIalLPFiDe~rLl~a~~~~ 651 (931)
T KOG2044|consen 572 FELGKPFKPLEQLMGVLPAASSHALPEEWRKLMSDPDSPIIDFYPEDFEIDMNGKKYAWQGIALLPFIDERRLLSAVAKV 651 (931)
T ss_pred cccCCCCCcHHHHhhhcchhhcCCCcHHHHhhhcCCCCcccccccccceeeccCceeeccccccccccchhhHHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCCCHHHHhhccCCCcEEEEecCCCCc
Q psy14280 656 EHLLTDEERSRNRHGPMLVYTYSNVNLG 683 (1891)
Q Consensus 656 ~~~LT~EEk~RN~~G~~llF~yd~~~~~ 683 (1891)
+..||+||++||+.|.++||..+.+..+
T Consensus 652 y~~Lt~EE~~RN~rg~d~Lfi~~~hp~~ 679 (931)
T KOG2044|consen 652 YPTLTDEEKRRNSRGPDLLFISDKHPLF 679 (931)
T ss_pred ccccCHHHHhccccCCceEEecCCCchH
Confidence 9999999999999999999998887655
No 4
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=100.00 E-value=4.6e-77 Score=668.49 Aligned_cols=233 Identities=60% Similarity=1.090 Sum_probs=181.9
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCC-CCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHhhcccce
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIP-EFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILFRMIQPKK 79 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ip-efDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~~iVrPrK 79 (1891)
|||||||+||++|||++.+.+.+...+ +|||||||||||||+|+|++.. ..+.+++++|.+||+|||+||++|||||
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~~~~~D~LYiDmN~IIH~~~~~~~~--~~~~~~~~~~~~i~~~id~l~~~v~P~k 78 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSIPSEFDNLYIDMNGIIHNCIHPNDS--SIPKTEEEIFQRIFNYIDRLVRIVRPRK 78 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTSEE-ESEEEEETHHHHHHHHS-SSS------SHHHHHHHHHHHHHHHHHHH-ESS
T ss_pred CCHHHHHHHHHHhCCcceeeccccCCCCcCCEEEEEcchhhhHhcCCccc--CCCccHHHHHHHHHHHHHHhheeecCce
Confidence 999999999999999988777777666 8999999999999999999875 3456899999999999999999999999
Q ss_pred EEEEeecCCCcchhhhHHHhhhhhhhhHHHHHHHHHhhhCCCCCcccccccccccccCcccceeeeccCCCchhhhhhhh
Q psy14280 80 LFFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQKAKEKGERLPTEKRFDFITLKFCFPKKLFFMAIDGVAPRAKMNQQR 159 (1891)
Q Consensus 80 llyiAIDGVAPRAKMnQQRsRRFrsa~ea~~~~~~~k~~g~~l~~e~~fd~~~l~~~~p~k~~~~aiDGvaP~aKmnqQr 159 (1891)
+||||||||||||||||||+|||++++++........+
T Consensus 79 ~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~------------------------------------------ 116 (237)
T PF03159_consen 79 LLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESE------------------------------------------ 116 (237)
T ss_dssp EEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHH------------------------------------------
T ss_pred EEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHH------------------------------------------
Confidence 99999999999999999999999999876543221110
Q ss_pred hccccchHHHHHHHHHHHHhCCCCCC---cccCCCCcccCCchHHHHHHHHHHHHHHHhhcCCcccccccccccccceEE
Q psy14280 160 GRRFRSAKEAEVLEQKAKEKGERLPT---EKRFDSNCITPGTPFMCRLHQQLRYFVKLKITTDKLWKDTLSLWVWKDVCV 236 (1891)
Q Consensus 160 ~rrf~s~keae~~~~ka~~~G~~lp~---e~~FDSN~ITPGTeFM~kL~~~Lk~fI~~KistDp~W~~~~~~~~~~~lkV 236 (1891)
...+....|...+. ...||||||||||+||.+|+++|++||.+|+++|+.|++ ++|
T Consensus 117 ------------~~~~~~~~~~~~~~~~~~~~fdsn~ITPGT~FM~~l~~~L~~~~~~k~~~~~~~~~---------~~v 175 (237)
T PF03159_consen 117 ------------IKEEIDEEGEQLPPEDQEEKFDSNCITPGTEFMEKLSDALRYYIKKKLNSDPKWQN---------LKV 175 (237)
T ss_dssp ------------HHHHHHHHT--B-HHHHS----GGGSSTTSHHHHHHHHHHHHHHHHHHHH-GGGCC---------SEE
T ss_pred ------------HhhhhhhccccccccccccccccceeccCCHHHHHHHHHHHHHHHHHhcCCCCcCc---------eEE
Confidence 11111122222221 368999999999999999999999999999999999999 999
Q ss_pred EEcCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccc
Q psy14280 237 ILSGHETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEV 298 (1891)
Q Consensus 237 IlSgs~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV 298 (1891)
||||++||||||||||+|||+++++|+|+||++|||||+|||||||||++|++||+||||+|
T Consensus 176 i~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L~~~~~~~~ilre~~ 237 (237)
T PF03159_consen 176 IFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSLATHEPNIYILREEV 237 (237)
T ss_dssp EEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHHHTT-SSEEEEEESS
T ss_pred EEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHHccCCCeEEEEeccC
Confidence 99999999999999999999999999999999999999999999999999999999999975
No 5
>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=98.44 E-value=3.6e-06 Score=100.07 Aligned_cols=95 Identities=16% Similarity=0.139 Sum_probs=57.6
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHhhcccceE
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILFRMIQPKKL 80 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~~iVrPrKl 80 (1891)
|||+||+.||...-+.+ .+++..- --|=||.++.||.+...........-........+|..+..|... .. +
T Consensus 1 MGI~gL~~~l~~~~~~~--~i~~l~g---k~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~~-~i-~- 72 (316)
T cd00128 1 MGIKGLWPLLKPVARPV--HLEELRG---KKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLEL-GI-K- 72 (316)
T ss_pred CchhhHHHHHHhhCCCC--CHHHhCC---cEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHHC-CC-E-
Confidence 99999999999887743 2222221 247899999999876432111000011123445566666666542 22 2
Q ss_pred EEEeecCCCcchhhhHHHhhhhh
Q psy14280 81 FFMAIDGVAPRAKMNQQRGRRFR 103 (1891)
Q Consensus 81 lyiAIDGVAPRAKMnQQRsRRFr 103 (1891)
..++.||..|-.|......||-+
T Consensus 73 pvfVFDG~~~~~K~~~~~~R~~~ 95 (316)
T cd00128 73 PVFVFDGKPPPLKAETLAKRRER 95 (316)
T ss_pred EEEEEcCCCchhhHHHHHHHHHH
Confidence 34579999999988776555544
No 6
>KOG2044|consensus
Probab=98.33 E-value=1.9e-07 Score=117.45 Aligned_cols=39 Identities=72% Similarity=1.031 Sum_probs=35.6
Q ss_pred ccCcccceeeeccCCCchhhhhhhhhccccchHHHHHHH
Q psy14280 135 FCFPKKLFFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLE 173 (1891)
Q Consensus 135 ~~~p~k~~~~aiDGvaP~aKmnqQr~rrf~s~keae~~~ 173 (1891)
.++|+|++|||||||||||||||||.|||+++||+.+.+
T Consensus 91 mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~ 129 (931)
T KOG2044|consen 91 MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKE 129 (931)
T ss_pred hccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHH
Confidence 468999999999999999999999999999999985543
No 7
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.13 E-value=2.3e-05 Score=96.12 Aligned_cols=92 Identities=17% Similarity=0.291 Sum_probs=58.0
Q ss_pred CChhHHHHHHHhhcCCchhh--hcccCCCCCCEEEEecCCcccccccCCC-----CCCC---CCCCHHHHHHHHHHHHHH
Q psy14280 1 MGVPKFFRYISERYPCLSEV--VREYQIPEFDNLYLDMNGIIHNCSHPND-----NDPH---FRITEKQIFQDIFHYIEI 70 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~--v~e~~ipefDnLYLDMNGIIH~Csh~~~-----~d~~---~~~seeeif~~If~yID~ 70 (1891)
|||.|+..+|.+..|...+. +++.. ==-|-||....||....... .... -..| .-+.-+|..+-+
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l~~l~---gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t--~~l~g~~~r~~~ 75 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQELKNYF---GRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVT--SHISGLFNRTIR 75 (393)
T ss_pred CChhhHHHHHhhhccccccccCHHHhC---CcEEEEeHHHHHHHHHHHcccccccccchhccCCcc--HHHHHHHHHHHH
Confidence 99999999999998854321 22221 12478999999998532111 0000 0111 234566777777
Q ss_pred HHhh-cccceEEEEeecCCCcchhhhHHHhhh
Q psy14280 71 LFRM-IQPKKLFFMAIDGVAPRAKMNQQRGRR 101 (1891)
Q Consensus 71 L~~i-VrPrKllyiAIDGVAPRAKMnQQRsRR 101 (1891)
|+.. |+| .+++||..|-.|...-..||
T Consensus 76 Ll~~gikP----v~VFDG~~p~~K~~~~~~Rk 103 (393)
T PTZ00217 76 LLEAGIKP----VYVFDGKPPELKSGELEKRR 103 (393)
T ss_pred HHHCCCCE----EEEEcCCCchhhHHHHHHHH
Confidence 7774 888 37999999988776644444
No 8
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=98.06 E-value=1.6e-06 Score=99.59 Aligned_cols=40 Identities=63% Similarity=0.972 Sum_probs=30.1
Q ss_pred ccCcccceeeeccCCCchhhhhhhhhccccchHHHHHHHH
Q psy14280 135 FCFPKKLFFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQ 174 (1891)
Q Consensus 135 ~~~p~k~~~~aiDGvaP~aKmnqQr~rrf~s~keae~~~~ 174 (1891)
.++|++++|+|+|||||+|||+|||.|||+++++.+....
T Consensus 73 ~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~ 112 (237)
T PF03159_consen 73 IVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNK 112 (237)
T ss_dssp HH-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred eecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHH
Confidence 4789999999999999999999999999999988766544
No 9
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=97.74 E-value=1.3e-05 Score=100.44 Aligned_cols=52 Identities=63% Similarity=0.961 Sum_probs=47.5
Q ss_pred cCcccceeeeccCCCchhhhhhhhhccccchHHHHHHHHHHHHhCCCCCCcc
Q psy14280 136 CFPKKLFFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLEQKAKEKGERLPTEK 187 (1891)
Q Consensus 136 ~~p~k~~~~aiDGvaP~aKmnqQr~rrf~s~keae~~~~ka~~~G~~lp~e~ 187 (1891)
.+|+|++|||+|||||||||||||.|||++|+||+.+..||...|+.+|++.
T Consensus 73 irPrKllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~ 124 (953)
T COG5049 73 IRPRKLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEK 124 (953)
T ss_pred cCcceEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhc
Confidence 4799999999999999999999999999999999998888887888887654
No 10
>KOG2045|consensus
Probab=97.55 E-value=3.9e-05 Score=97.77 Aligned_cols=35 Identities=71% Similarity=1.052 Sum_probs=30.8
Q ss_pred cCcccceeeeccCCCchhhhhhhhhccccchHHHHHHH
Q psy14280 136 CFPKKLFFMAIDGVAPRAKMNQQRGRRFRSAKEAEVLE 173 (1891)
Q Consensus 136 ~~p~k~~~~aiDGvaP~aKmnqQr~rrf~s~keae~~~ 173 (1891)
.+|+|++|||+|||||||||||||.||| +.|.+++
T Consensus 75 IkPqKlffMAVDGvAPRAKMNQQRsRRF---rTArdAe 109 (1493)
T KOG2045|consen 75 IKPQKLFFMAVDGVAPRAKMNQQRSRRF---RTARDAE 109 (1493)
T ss_pred hCcceEEEEeecccCchhhhhHHHHHhh---hhhhhHH
Confidence 4799999999999999999999999999 6655443
No 11
>PRK03980 flap endonuclease-1; Provisional
Probab=97.32 E-value=0.0052 Score=73.34 Aligned_cols=104 Identities=21% Similarity=0.324 Sum_probs=57.1
Q ss_pred eEEEEcCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCCCCcccC
Q psy14280 234 VCVILSGHETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKGGSQIVT 313 (1891)
Q Consensus 234 lkVIlSgs~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~~~~~~~ 313 (1891)
+.+|.+ |||+|-= +.|+-+. +.-.+|++.|.|++++|- +++ +|.- .+..++ +.... ..
T Consensus 97 Ip~i~A----P~EAEAq-~A~L~~~--------g~vd~V~S~D~D~l~fg~----~~v--ir~l-~~~~~~-~~p~~-~~ 154 (292)
T PRK03980 97 IPYVQA----PSEGEAQ-AAYMAKK--------GDAWAVGSQDYDSLLFGA----PRL--VRNL-TISGKR-KLPGK-NV 154 (292)
T ss_pred CCEEec----CchHHHH-HHHHHHC--------CCeEEEecCCcCeeeecC----CEE--EEee-cccccc-cCccc-cc
Confidence 666665 8999976 3343321 245679999999999973 332 3321 111111 00000 00
Q ss_pred CCCcceEEEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhccCCCCCCCCcccc
Q psy14280 314 PEETKFFLLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIGNDFIPNLPDLHII 378 (1891)
Q Consensus 314 ~~~~~F~llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvGNDFLPhLP~L~I~ 378 (1891)
.-...+..++...+.+. +. +.+ +.||-+|+|+|.||+|.+|++.+.
T Consensus 155 ~~~~~~e~~~~~~vl~~----lg-------------l~~--~q~id~~iL~G~Dy~~GI~GIG~k 200 (292)
T PRK03980 155 YVEVKPELIELEEVLKE----LG-------------ITR--EQLIDIAILVGTDYNPGIKGIGPK 200 (292)
T ss_pred cccccceeeeHHHHHHH----hC-------------CCH--HHHHHHHHhcCCCCCCCCCCccHH
Confidence 00012334554433221 11 111 678999999999999999998754
No 12
>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=97.21 E-value=0.0019 Score=78.38 Aligned_cols=91 Identities=18% Similarity=0.201 Sum_probs=53.5
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccccccCC---CCCCCC-C-CCHHHHHHHHHHHHHHHHhh-
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPN---DNDPHF-R-ITEKQIFQDIFHYIEILFRM- 74 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~---~~d~~~-~-~seeeif~~If~yID~L~~i- 74 (1891)
||| +|+..|..+--. +++.. . --|-||....||.+.... ++.... . -....-+..+|..+-+|+..
T Consensus 1 MGi-~l~~~~~~~~~~----l~~~~-g--k~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~ 72 (338)
T TIGR03674 1 MGV-DLRDLLAKEEIE----LEDLS-G--KVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENG 72 (338)
T ss_pred CCC-ChHHHhccCccC----HHHhC-C--CEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCC
Confidence 999 999999822111 11111 1 257799999999864421 100000 0 00012234455566666666
Q ss_pred cccceEEEEeecCCCcchhhhHHHhhhhh
Q psy14280 75 IQPKKLFFMAIDGVAPRAKMNQQRGRRFR 103 (1891)
Q Consensus 75 VrPrKllyiAIDGVAPRAKMnQQRsRRFr 103 (1891)
++| .+++||.+|-.|...-..||-+
T Consensus 73 i~P----v~VFDG~~p~~K~~~~~~R~~~ 97 (338)
T TIGR03674 73 IKP----VYVFDGKPPELKAETLEERREI 97 (338)
T ss_pred CeE----EEEECCCChhhhHhhHHHHHHH
Confidence 888 6899999998887776666554
No 13
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=95.32 E-value=0.016 Score=58.40 Aligned_cols=97 Identities=16% Similarity=0.293 Sum_probs=58.9
Q ss_pred CChhHHHHHHHhhcCCchh-hhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHH-hhcccc
Q psy14280 1 MGVPKFFRYISERYPCLSE-VVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILF-RMIQPK 78 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~-~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~-~iVrPr 78 (1891)
|||+||+.+|.+.. .+.. .+.+..- --|=||.+..||.|.+...............+..+|..+..|. .-|+|
T Consensus 1 MGI~gL~~~l~~~~-~v~~~~~~~l~g---~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~P- 75 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA-AVRKVSLSELRG---KRVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKP- 75 (101)
T ss_dssp ---TTHHHHCHHHE-GEEEEEGGGGTT---CEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEE-
T ss_pred CCcccHHHHHHhhc-cCCccCHHHhCC---CEEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEE-
Confidence 99999999999987 2111 1222221 4478999999999755433222222222466777887777755 45765
Q ss_pred eEEEEeecCCCcchhhhHHHhhhhhhh
Q psy14280 79 KLFFMAIDGVAPRAKMNQQRGRRFRSA 105 (1891)
Q Consensus 79 KllyiAIDGVAPRAKMnQQRsRRFrsa 105 (1891)
++.+||..|-+|......||-+.+
T Consensus 76 ---ifVFDG~~~~~K~~~~~~R~~~r~ 99 (101)
T PF00752_consen 76 ---IFVFDGKPPPLKRETIQKRRKRRE 99 (101)
T ss_dssp ---EEEE--STTGGCHHHHHHHHHHHH
T ss_pred ---EEEECCCCchhhHHHHHHHHHHHh
Confidence 578899999999999877765543
No 14
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=95.06 E-value=0.029 Score=56.48 Aligned_cols=96 Identities=16% Similarity=0.194 Sum_probs=60.5
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHHh-hcccce
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILFR-MIQPKK 79 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~~-iVrPrK 79 (1891)
|||+||+.||...--.+ .+.+..- --+=||.+..||.|....................+|..|..|.+ -|.|
T Consensus 1 MGI~gL~~~l~~~~~~~--~i~~l~g---~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l~~~~~rl~~L~~~~I~P-- 73 (99)
T smart00485 1 MGIKGLWPLLKPVVREV--PLEALRG---KTLAIDASIWLYQFLTACREKLGTPLPNSKHLMGLFYRTCRLLEFGIKP-- 73 (99)
T ss_pred CCHhHHHHHHHHhcccC--CHHHhCC---ceEeccHHHHHHHHHHHHhhhhcCCCCchHHHHHHHHHHHHHHHCCCeE--
Confidence 99999999999862111 1112111 23567999999987543211111112223366667777766653 3554
Q ss_pred EEEEeecCCCcchhhhHHHhhhhhhh
Q psy14280 80 LFFMAIDGVAPRAKMNQQRGRRFRSA 105 (1891)
Q Consensus 80 llyiAIDGVAPRAKMnQQRsRRFrsa 105 (1891)
.+.+||.+|-+|...+..||-+..
T Consensus 74 --ifVFDG~~~~~K~~t~~~R~~~r~ 97 (99)
T smart00485 74 --IFVFDGKPPPLKSETLAKRRERRE 97 (99)
T ss_pred --EEEECCCCchhhHHHHHHHHHHHh
Confidence 578899999999999988887653
No 15
>KOG2518|consensus
Probab=94.63 E-value=0.23 Score=62.80 Aligned_cols=96 Identities=18% Similarity=0.249 Sum_probs=56.1
Q ss_pred CChhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHH-hhcccce
Q psy14280 1 MGVPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILF-RMIQPKK 79 (1891)
Q Consensus 1 MGVP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~-~iVrPrK 79 (1891)
|||.||.-.+...--.+ .+++. +-+-|=+|--+-+|...-.+.....+....+.-+.-..+++-.|. .-|+|
T Consensus 1 MGI~GLlp~~k~~~~~~--hi~~~---~g~tvavD~y~WLhrg~~~Ca~el~~~~pT~ryi~y~ik~v~lL~~~gikP-- 73 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPI--HISEY---KGKTVAVDGYCWLHRGALACAEKLAKGKPTDRYIQFFIKRVKLLLSYGIKP-- 73 (556)
T ss_pred CCcchhHHHHHHHhhhh--hHHHh---cCceEEEehhhHHhhhHHhHHHHHhcCCChHHHHHHHHHHHHHHHhcCCeE--
Confidence 99999999887732111 12222 357788899999997332221111111112333333334443333 23554
Q ss_pred EEEEeecCCCcchhhhHHHhhhhhhh
Q psy14280 80 LFFMAIDGVAPRAKMNQQRGRRFRSA 105 (1891)
Q Consensus 80 llyiAIDGVAPRAKMnQQRsRRFrsa 105 (1891)
+|..||-.==+|-.+-|.||-+..
T Consensus 74 --ilVFDG~~LP~K~~te~~Rr~~R~ 97 (556)
T KOG2518|consen 74 --ILVFDGDPLPSKKETERKRRERRK 97 (556)
T ss_pred --EEEecCCCcccccccchHHHHHHH
Confidence 788999988888888777777655
No 16
>smart00475 53EXOc 5'-3' exonuclease.
Probab=92.93 E-value=3.2 Score=49.35 Aligned_cols=90 Identities=21% Similarity=0.289 Sum_probs=54.8
Q ss_pred CCC-chhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCCCCcccCCCCcceEE
Q psy14280 243 TPG-EGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKGGSQIVTPEETKFFL 321 (1891)
Q Consensus 243 VPG-EGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~~~~~~~~~~~~F~l 321 (1891)
+|| |++==|--+.++.... +...+|++.|-|+.-|. .+++.++.- + +.. ..+.+
T Consensus 103 ~~g~EADD~iatla~~~~~~-----g~~~~IvS~DkDl~ql~----~~~v~~~~~---~---~~~----------~~~~~ 157 (259)
T smart00475 103 VEGYEADDVIATLAKKAEAE-----GYEVRIVSGDKDLLQLV----SDKVSVLDP---T---KGI----------KEFEL 157 (259)
T ss_pred eCCcCHHHHHHHHHHHHHhC-----CCeEEEEeCCCcHhhcC----CCCEEEEec---c---CCC----------CccEE
Confidence 788 9998776666654432 35789999999998764 344554431 0 000 01234
Q ss_pred EehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhc--cCCCCCCCCcc
Q psy14280 322 LHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIG--NDFIPNLPDLH 376 (1891)
Q Consensus 322 lhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvG--NDFLPhLP~L~ 376 (1891)
++..-+. .+|. ...++ |+-++.|+| .|++|.+|++.
T Consensus 158 ~~~~~v~----~~~G-----------v~p~q----~~d~~aL~GD~sDnipGV~GIG 195 (259)
T smart00475 158 YTPENVI----EKYG-----------LTPEQ----IIDYKALMGDSSDNIPGVPGIG 195 (259)
T ss_pred EcHHHHH----HHhC-----------cCHHH----HHHHHHHhCCcccCCCCCCCCC
Confidence 4443332 2232 22344 566899999 79999999975
No 17
>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=88.86 E-value=1.2 Score=44.91 Aligned_cols=89 Identities=21% Similarity=0.291 Sum_probs=52.5
Q ss_pred eEEEEcCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccc-cccccCCCCCCccc
Q psy14280 234 VCVILSGHETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEV-KFNTKSNKGGSQIV 312 (1891)
Q Consensus 234 lkVIlSgs~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV-~f~~~~~k~~~~~~ 312 (1891)
+.+|+ .|||+|.=+--.-|+ +.-+.|++.|+|++++|-- .|+|.-. ...++. .
T Consensus 5 v~~i~----AP~EAeAq~A~L~~~---------g~vd~V~t~DsD~l~fG~~------~vi~~~~~~~~~~~-------~ 58 (94)
T PF00867_consen 5 VPYIV----APYEAEAQCAYLERN---------GLVDAVITEDSDLLLFGAP------KVIRKLSDKSSGKC-------S 58 (94)
T ss_dssp -EEEE-----SS-HHHHHHHHHHT---------TSSSEEE-SSSHHHHTT-S------EEEESST-CSCCST-------S
T ss_pred CeEEE----cCchHHHHHHHHHHh---------cceeEEEecCCCEEeeCCC------EEEEeccccccCCc-------c
Confidence 55555 489999988755433 3568999999999999654 4566432 110100 0
Q ss_pred CCCCcceEEEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhccC
Q psy14280 313 TPEETKFFLLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIGND 367 (1891)
Q Consensus 313 ~~~~~~F~llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvGND 367 (1891)
......+..++..-+.+.+. + + -+.|+.+|+|+|.|
T Consensus 59 ~~~~~~~~~~~~~~i~~~l~--l-------------~----~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 59 SKSEKEVEVIDLDDILKELG--L-------------T----REQFIDLCILCGCD 94 (94)
T ss_dssp -CCESEEEEEEHHHHHHHHT--T-------------S----HHHHHHHHHHHHET
T ss_pred cccccceEEEEHHHHHHHcC--C-------------C----HHHHHHHheecCCC
Confidence 01123567788866655532 1 1 15699999999998
No 18
>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=86.83 E-value=14 Score=43.40 Aligned_cols=56 Identities=9% Similarity=0.064 Sum_probs=36.5
Q ss_pred EEEecCCcccccccCCCCCCCC-CCCHHHHHHHHHHHHHHHHhhcccceEEEEeecCC
Q psy14280 32 LYLDMNGIIHNCSHPNDNDPHF-RITEKQIFQDIFHYIEILFRMIQPKKLFFMAIDGV 88 (1891)
Q Consensus 32 LYLDMNGIIH~Csh~~~~d~~~-~~seeeif~~If~yID~L~~iVrPrKllyiAIDGV 88 (1891)
|.||.|.+||.+.|........ .-........++..|.+++...+|.++ .++.||.
T Consensus 4 llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~-~~~fD~~ 60 (240)
T cd00008 4 LLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYV-AVVFDAG 60 (240)
T ss_pred EEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeE-EEEEeCC
Confidence 6799999999987754211100 001123345566677778888889886 7899995
No 19
>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=58.84 E-value=13 Score=51.70 Aligned_cols=91 Identities=14% Similarity=0.265 Sum_probs=56.6
Q ss_pred eEEEEcCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCCCCcccC
Q psy14280 234 VCVILSGHETPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKGGSQIVT 313 (1891)
Q Consensus 234 lkVIlSgs~VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~~~~~~~ 313 (1891)
+-+|.+ |||||.=+-...+. +....|++-|+|+++.|=.. |+|.- |+. +
T Consensus 786 IP~i~A----P~EAEAqcA~L~~~---------G~vd~V~TeDsD~llFGa~~------v~rn~--~~~---~------- 834 (1034)
T TIGR00600 786 IPYIVA----PMEAEAQCAILDLL---------DQTSGTITDDSDIWLFGARH------VYKNF--FNQ---N------- 834 (1034)
T ss_pred CCeeeC----CccHHHHHHHHHhC---------CCeEEEEccccceeccCCce------eeecc--cCC---C-------
Confidence 566654 89999987766333 35789999999999776442 34421 111 0
Q ss_pred CCCcceEEEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhccCCCCCCCCccc
Q psy14280 314 PEETKFFLLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIGNDFIPNLPDLHI 377 (1891)
Q Consensus 314 ~~~~~F~llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvGNDFLPhLP~L~I 377 (1891)
....++...-+ ..++ .+.| +.||.||+|+|-||.+.||++.+
T Consensus 835 ---~~ve~~~~~~i----~~~l-------------glt~--~qli~laiL~G~DY~~GI~GIGp 876 (1034)
T TIGR00600 835 ---KFVEYYQYVDI----HNQL-------------GLDR--NKLINLAYLLGSDYTEGIPTVGP 876 (1034)
T ss_pred ---CceEEeeHHHH----HHHh-------------CCCH--HHHHHHHHeeCCCCCCCCCcccH
Confidence 01112222211 1111 1222 78999999999999999999853
No 20
>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=49.79 E-value=29 Score=48.55 Aligned_cols=92 Identities=23% Similarity=0.320 Sum_probs=52.9
Q ss_pred CChhHHHHHHHhhc-CCchhhhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHH-hhcccc
Q psy14280 1 MGVPKFFRYISERY-PCLSEVVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILF-RMIQPK 78 (1891)
Q Consensus 1 MGVP~FfrWL~erY-P~i~~~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~-~iVrPr 78 (1891)
|||.||+.+|...- |.-.+.+.. --|=||.-.-||.+...........++ ..-+..+|..|.+|+ .-|+|
T Consensus 1 MGI~GLw~ll~~~~r~v~le~l~G------k~vAIDasiWL~q~l~~vr~~~g~~l~-n~hl~g~f~Ri~~Ll~~gI~P- 72 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVSPETLEG------KRLAVDISIWLNQALKGVRDREGNAIK-NSHLLTLFHRLCKLLFFRIRP- 72 (1034)
T ss_pred CChhHHHHHHHHhcccccHHHhCC------eEEEechHHHHHHHHHHHHhccCCccC-CHHHHHHHHHHHHHHHCCCeE-
Confidence 99999999995321 111111111 256778888889753321100001111 233455666666655 44665
Q ss_pred eEEEEeecCCCcchhhhHHHhhhhh
Q psy14280 79 KLFFMAIDGVAPRAKMNQQRGRRFR 103 (1891)
Q Consensus 79 KllyiAIDGVAPRAKMnQQRsRRFr 103 (1891)
++.+||.+|-.|...-..||-|
T Consensus 73 ---VfVFDG~~p~lK~~t~~~R~~r 94 (1034)
T TIGR00600 73 ---IFVFDGGAPLLKRQTLAKRRQR 94 (1034)
T ss_pred ---EEEECCCCchHhHHHHHHHHHH
Confidence 6778999999998875444443
No 21
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=45.89 E-value=3.2e+02 Score=33.48 Aligned_cols=57 Identities=18% Similarity=0.257 Sum_probs=38.7
Q ss_pred EEEEecCCcccccccCCC----CCCCCCCCHHHHHHHHHHHHHHHHhhcccceEEEEeecCCCcc
Q psy14280 31 NLYLDMNGIIHNCSHPND----NDPHFRITEKQIFQDIFHYIEILFRMIQPKKLFFMAIDGVAPR 91 (1891)
Q Consensus 31 nLYLDMNGIIH~Csh~~~----~d~~~~~seeeif~~If~yID~L~~iVrPrKllyiAIDGVAPR 91 (1891)
-|-||-++++|.+.|.-. .+...+.. ....+...|.++++..+|.+ ..++.||-.|-
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~---~~~~~~~~l~~~~~~~~~~~-~~~vFD~~~~t 73 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTG---AVSGFLGMLYRLIRLLEPTH-PVVVFDGKPPT 73 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCcc---HHHHHHHHHHHHHHhcCCCc-EEEEEcCCCCc
Confidence 477899999999877541 11122222 45566677889999999955 56799995543
No 22
>cd00552 RaiA RaiA ("ribosome-associated inhibitor A", also known as Protein Y (PY), YfiA, and SpotY, is a stress-response protein that binds the ribosomal subunit interface and arrests translation by interfering with aminoacyl-tRNA binding to the ribosomal A site. RaiA is also thought to counteract miscoding at the A site thus reducing translation errors. The RaiA fold structurally resembles the double-stranded RNA-binding domain (dsRBD).
Probab=42.82 E-value=81 Score=31.34 Aligned_cols=74 Identities=19% Similarity=0.271 Sum_probs=52.3
Q ss_pred CChhhHHHhHHHHHHHHHhHhhcccCCCCCceeecccc--ceEEEEEeeecCCcceeeeCcccccccchHHHHHHhhhhh
Q psy14280 1744 DTTEDLEERADSYLAKLLRLTRAHNLGAPDYTFSMDAS--KLYVATVRICHPHSDIVVRGKPCAKKADSVEICARRAFNE 1821 (1891)
Q Consensus 1744 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1821 (1891)
+.++.|++.+.+-+.+|-|+. ..+-.-.-+++-+.. ..|.+.+++.-|+..+++. ..++.+..+...||..
T Consensus 10 ~~t~al~~~i~~k~~kl~r~~--~~i~~~~V~l~~~~~~~~~~~v~i~v~~~g~~~~a~-----~~~~d~~~Aid~a~~k 82 (93)
T cd00552 10 EVTDALREYVEEKLEKLEKYF--DRIISVDVVLSVEKNHGKRFKVEITIHLPGGVLRAE-----ASAEDLYAAIDLAVDK 82 (93)
T ss_pred cCCHHHHHHHHHHHHHHHHhc--CCCceEEEEEEEecCCCCceEEEEEEEeCCCEEEEE-----EccCCHHHHHHHHHHH
Confidence 457888888888888766664 233334455655442 5899999999998888886 4567788888888877
Q ss_pred hhh
Q psy14280 1822 LTQ 1824 (1891)
Q Consensus 1822 ~~~ 1824 (1891)
|..
T Consensus 83 l~r 85 (93)
T cd00552 83 LER 85 (93)
T ss_pred HHH
Confidence 653
No 23
>PRK05755 DNA polymerase I; Provisional
Probab=42.34 E-value=3.7e+02 Score=37.71 Aligned_cols=89 Identities=21% Similarity=0.256 Sum_probs=54.8
Q ss_pred CCC-chhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCCCCcccCCCCcceEE
Q psy14280 243 TPG-EGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKGGSQIVTPEETKFFL 321 (1891)
Q Consensus 243 VPG-EGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~~~~~~~~~~~~F~l 321 (1891)
.|| |++==|--+.++.... +...+|++.|-||.-|. .+++.++.- +.. + .+..
T Consensus 105 ~~g~EADD~ia~la~~~~~~-----~~~~~i~S~DkD~~ql~----~~~v~~~~~---~~~---~-----------~~~~ 158 (880)
T PRK05755 105 LEGYEADDVIGTLAKQAEAA-----GYEVLIVTGDKDLLQLV----DDNVTLLDT---MGV---S-----------KNEE 158 (880)
T ss_pred eCCccHHHHHHHHHHHHHhC-----CCcEEEEcCCCChhhhC----CCCEEEeec---cCC---C-----------CCeE
Confidence 388 9998777777765432 25799999999998764 346666542 100 0 1222
Q ss_pred EehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhc--cCCCCCCCCcc
Q psy14280 322 LHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIG--NDFIPNLPDLH 376 (1891)
Q Consensus 322 lhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvG--NDFLPhLP~L~ 376 (1891)
++..-+ ...+. ...+ =|+-++.|+| .|++|.+|++.
T Consensus 159 ~~~~~v----~~~~g-----------~~p~----q~~d~~~L~GD~sDnipGv~GiG 196 (880)
T PRK05755 159 LDPEEV----VEKYG-----------VTPE----QIIDYLALMGDSSDNIPGVPGIG 196 (880)
T ss_pred EcHHHH----HHHHC-----------cCHH----HHHHHHHHhCCccCCCCCCCCcc
Confidence 333322 22222 1223 3577899999 79999999975
No 24
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=39.21 E-value=92 Score=30.32 Aligned_cols=58 Identities=28% Similarity=0.377 Sum_probs=35.8
Q ss_pred cCCeEEEEeCCCCccccCceEEE--EEecCCCCccceEEEEeecccCCCCc--c------ccCCCccccccCcce
Q psy14280 1156 LFDRVVNIRDCYTVPLGYRGTII--GIVQGETSYDAMYDVVFDKPFPHGVK--I------RCSESRGYRMPAQAM 1220 (1891)
Q Consensus 1156 LGDRVV~VrdsG~VPfG~kGTVV--GI~~~~~~~d~~vDVLFDepF~GGtt--L------~cs~~RG~~Vp~ssL 1220 (1891)
+||||.. .-+-..+|||- |-... ......+-|-||++ .|.++ + .|.+.+|..|+.+.|
T Consensus 1 VG~rV~v-----~~~~~~~G~vryiG~~~~-~~~g~~vGVEld~~-~G~~dGt~~G~rYF~c~~~~G~Fv~~~~v 68 (69)
T PF01302_consen 1 VGDRVRV-----DDPGGRRGTVRYIGPVPG-FKSGIWVGVELDEP-RGKNDGTVKGKRYFECPPNHGIFVRPSKV 68 (69)
T ss_dssp TTSEEEE-----SSTTTEEEEEEEEEE-SS-SSSSEEEEEEESSS-TSSBSSEETTEESS-SSTTTEEEEEGGGE
T ss_pred CCCEEEE-----eeCCCCEEEEEEEeeCCC-CCCCEEEEEEEcCC-CCCCCcEECCEEEeeeCCCCEEEecHHHC
Confidence 5899988 22345567763 33331 11235677777998 44432 2 299999999998765
No 25
>KOG0971|consensus
Probab=31.48 E-value=1.6e+02 Score=40.76 Aligned_cols=69 Identities=22% Similarity=0.248 Sum_probs=47.9
Q ss_pred CCcccCCeEEEEeCCCCccccCceEEEEEecCCCCccceEEEEeecccC--CCCccc-----cCCCccccccCcceeecC
Q psy14280 1152 TKFKLFDRVVNIRDCYTVPLGYRGTIIGIVQGETSYDAMYDVVFDKPFP--HGVKIR-----CSESRGYRMPAQAMINLS 1224 (1891)
Q Consensus 1152 q~F~LGDRVV~VrdsG~VPfG~kGTVVGI~~~~~~~d~~vDVLFDepF~--GGttL~-----cs~~RG~~Vp~ssLLNLT 1224 (1891)
..|++|-||=.... +++|||+=+-.+.=....-|.||.|+|-= +|+-=| |.++.|..|-++.|--+-
T Consensus 4 r~lkvG~RVevtgk------nl~G~VayvG~T~FA~G~WvGVvLDep~GKNnGsVqg~qYF~Cd~ncG~FVr~sq~r~lE 77 (1243)
T KOG0971|consen 4 RSLKVGTRVEVTGK------NLQGTVAYVGQTQFAEGKWVGVVLDEPKGKNNGSVQGVQYFECDENCGVFVRSSQVRELE 77 (1243)
T ss_pred ccccccceEEeccC------CccceEEEecccccccCceEEEEeccccCCCCCcccceeeEecCCCcceEeehhhhHHhh
Confidence 46889999977642 57899876655433345689999999852 122112 999999999999855443
Q ss_pred cc
Q psy14280 1225 YG 1226 (1891)
Q Consensus 1225 ~g 1226 (1891)
.+
T Consensus 78 da 79 (1243)
T KOG0971|consen 78 DA 79 (1243)
T ss_pred cc
Confidence 33
No 26
>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=30.09 E-value=33 Score=33.65 Aligned_cols=22 Identities=27% Similarity=0.753 Sum_probs=19.7
Q ss_pred HHHHHhhhhhc--cCCCCCCCCcc
Q psy14280 355 DDWVLMGFLIG--NDFIPNLPDLH 376 (1891)
Q Consensus 355 DDFVfL~fLvG--NDFLPhLP~L~ 376 (1891)
+-|+-+|.|+| .||+|++|++-
T Consensus 8 ~q~~d~~~L~GD~~D~i~gv~giG 31 (75)
T cd00080 8 EQFIDLAILVGDKSDNIPGVPGIG 31 (75)
T ss_pred HHHHHHHHHcCCccccCCCCCccc
Confidence 56888999999 99999999965
No 27
>PF02482 Ribosomal_S30AE: Sigma 54 modulation protein / S30EA ribosomal protein; InterPro: IPR003489 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the sigma-54 modulation protein family and the S30Ae family of ribosomal proteins which includes the light-repressed protein (lrtA) [].; GO: 0005488 binding, 0044238 primary metabolic process; PDB: 1L4S_A 1VOX_a 1VOV_a 3V2E_Y 3V2C_Y 1N3G_A 1VOS_a 1VOZ_a 1VOQ_a 1IMU_A ....
Probab=29.59 E-value=1e+02 Score=30.80 Aligned_cols=74 Identities=24% Similarity=0.329 Sum_probs=53.7
Q ss_pred CChhhHHHhHHHHHHHHHhHhhcccCCCCCceeecc--ccceEEEEEeeecCCcceeeeCcccccccchHHHHHHhhhhh
Q psy14280 1744 DTTEDLEERADSYLAKLLRLTRAHNLGAPDYTFSMD--ASKLYVATVRICHPHSDIVVRGKPCAKKADSVEICARRAFNE 1821 (1891)
Q Consensus 1744 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1821 (1891)
+.++.|++.+.+.+.+|-|+.. ..-..+.+++.+ ....|.+.+++.-|+..+++.+ .++.+.-+...||..
T Consensus 10 ~~t~~l~~~i~~kl~kl~~~~~--~i~~~~V~l~~~~~~~~~~~v~i~i~~~~~~l~a~~-----~~~d~~~Aid~a~dk 82 (97)
T PF02482_consen 10 ELTDALREYIEEKLEKLERFFD--DIIEAHVTLSKEKSEGKGYRVEITIHVPGHVLVAEE-----SAEDLYAAIDEAFDK 82 (97)
T ss_dssp ---HHHHHHHHHHHHHHHTTSS--C-SEEEEEEEEE--ETTEEEEEEEEEETTEEEEEEE-----EESSHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHHHHhhcC--CCeeEEEEEEEeeccCCCEEEEEEEEeCCceEEEEE-----ecCCHHHHHHHHHHH
Confidence 4678899999999999766542 233456777775 5688999999988888888776 367788888888887
Q ss_pred hhh
Q psy14280 1822 LTQ 1824 (1891)
Q Consensus 1822 ~~~ 1824 (1891)
|..
T Consensus 83 l~r 85 (97)
T PF02482_consen 83 LER 85 (97)
T ss_dssp HHH
T ss_pred HHH
Confidence 754
No 28
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=29.23 E-value=29 Score=40.61 Aligned_cols=37 Identities=27% Similarity=0.516 Sum_probs=27.7
Q ss_pred hhHHHHHHHhhcCCchhhhcccCCCCCCEEEEecCCcccc
Q psy14280 3 VPKFFRYISERYPCLSEVVREYQIPEFDNLYLDMNGIIHN 42 (1891)
Q Consensus 3 VP~FfrWL~erYP~i~~~v~e~~ipefDnLYLDMNGIIH~ 42 (1891)
||||+.+ +.+|++.+.++... -++|-|.+|-|||.|+
T Consensus 73 IPGfLaF--RE~p~~l~a~~~l~-~~~d~ilVDG~GiaHP 109 (212)
T COG1515 73 IPGFLAF--RELPLLLKALEKLS-VKPDLLLVDGHGIAHP 109 (212)
T ss_pred ccchhhh--hhhHHHHHHHHhcC-CCCCEEEEcCcceecC
Confidence 6888765 56777655554433 2689999999999998
No 29
>cd00048 DSRM Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
Probab=27.68 E-value=1.4e+02 Score=27.17 Aligned_cols=61 Identities=18% Similarity=0.302 Sum_probs=43.2
Q ss_pred HHHHhHhhcccCCCCCcee-ecccc---ceEEEEEeeecCCcceeeeCcccccccchHHHHHHhhhhhh
Q psy14280 1758 AKLLRLTRAHNLGAPDYTF-SMDAS---KLYVATVRICHPHSDIVVRGKPCAKKADSVEICARRAFNEL 1822 (1891)
Q Consensus 1758 ~~~~~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 1822 (1891)
..|-.+...|+...|.|.+ +.+.. +.|.++|.|.- -++..|.-+ .|-++-..+|+.|+..|
T Consensus 4 ~~L~e~~~~~~~~~~~y~~~~~~g~~~~~~f~~~v~i~~---~~~~~g~g~-sKk~Ak~~AA~~al~~L 68 (68)
T cd00048 4 SLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGG---KITGEGEGS-SKKEAKQNAAEAALRKL 68 (68)
T ss_pred HHHHHHHHHcCCCCCeEEEeeeeCCCCCCeEEEEEEECC---EEEEEeecC-CHHHHHHHHHHHHHHhC
Confidence 3456667778899999998 44332 78999999943 366667665 55567778888887654
No 30
>COG4003 Uncharacterized protein conserved in archaea [Function unknown]
Probab=26.79 E-value=2.5e+02 Score=28.93 Aligned_cols=60 Identities=13% Similarity=0.273 Sum_probs=38.9
Q ss_pred HHHHHHhChHHHHHhhcCCCCCccccCCCCCc------------chHHHHHHHHHHHhhCCCCccccccCCccccCHHHH
Q psy14280 1043 IKNYMKQFPEVFGFLKDHSSDDIYLRDDVFPH------------QGEQRVAQIVSWLKEQPHAKAEVRPCGAAVVDAKVV 1110 (1891)
Q Consensus 1043 I~eY~~kFPeLF~~L~~~~~~d~~~~~DIFp~------------~~~~kLkEIkaWLKe~~~~~le~Vscgse~Ldke~I 1110 (1891)
..+++++||.|+.-|+... .-. ++=|.+ +.++..-||.+||..++. ++++.-
T Consensus 5 ~~~fkk~fp~l~~eleg~~---l~~-~~~~~gy~PtV~D~L~rCdT~EEAlEii~yleKrGE------------i~~E~A 68 (98)
T COG4003 5 KEEFKKKFPALAKELEGIR---LEP-KIDFSGYNPTVIDFLRRCDTEEEALEIINYLEKRGE------------ITPEMA 68 (98)
T ss_pred HHHHHHHhHHHHHHhhccc---ccc-cCCcCCCCchHHHHHHHhCcHHHHHHHHHHHHHhCC------------CCHHHH
Confidence 4689999999999998431 111 111222 234556788899988875 666776
Q ss_pred HHHHHHHH
Q psy14280 1111 SLIEHAVD 1118 (1891)
Q Consensus 1111 kaIE~~id 1118 (1891)
++|+..+.
T Consensus 69 ~~L~~~~~ 76 (98)
T COG4003 69 KALRVTLV 76 (98)
T ss_pred HHHHhhHH
Confidence 67766553
No 31
>KOG2519|consensus
Probab=25.42 E-value=1.8e+02 Score=37.67 Aligned_cols=102 Identities=18% Similarity=0.215 Sum_probs=55.7
Q ss_pred CChhHHHHHHHhhcC-Cchh-hhcccCCCCCCEEEEecCCcccccccCCCCCCCCCCCHHHHHHHHHHHHHHHH-hhccc
Q psy14280 1 MGVPKFFRYISERYP-CLSE-VVREYQIPEFDNLYLDMNGIIHNCSHPNDNDPHFRITEKQIFQDIFHYIEILF-RMIQP 77 (1891)
Q Consensus 1 MGVP~FfrWL~erYP-~i~~-~v~e~~ipefDnLYLDMNGIIH~Csh~~~~d~~~~~seeeif~~If~yID~L~-~iVrP 77 (1891)
|||-|++.-+.+.=| ++.. .++..... -+-||.|.-++.--.........--....-+..+|...-+|+ +-|+|
T Consensus 1 MGIkgL~~v~~d~a~~~ir~~~~~~f~~k---kVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt~~l~~~gi~P 77 (449)
T KOG2519|consen 1 MGIKGLSKVIADVAPPCIRKNPIKFFFGK---KVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRTIRLIENGIKP 77 (449)
T ss_pred CCchhHHHHHHHhchHHhhhccHHHhcCc---eEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHHHHHHHcCCcE
Confidence 999999877766665 3322 11111111 178999999987432221100001123344555565544444 34554
Q ss_pred ceEEEEeecCCCcchhhhHHHhhhhhhhhHHHH
Q psy14280 78 KKLFFMAIDGVAPRAKMNQQRGRRFRSAKEAEV 110 (1891)
Q Consensus 78 rKllyiAIDGVAPRAKMnQQRsRRFrsa~ea~~ 110 (1891)
-..+||++|--|.-.--.|-.|++ ++..
T Consensus 78 ----v~VfDG~pP~lKs~e~~kR~~rr~-~a~~ 105 (449)
T KOG2519|consen 78 ----VYVFDGKPPDLKSQELAKRSERRS-EADK 105 (449)
T ss_pred ----EEEECCCCCCcchHHHHHHHHHhh-hhhh
Confidence 457899999777665545545554 5544
No 32
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.77 E-value=1e+02 Score=28.73 Aligned_cols=51 Identities=12% Similarity=0.081 Sum_probs=35.6
Q ss_pred ChHHHHHHcCCCHhhHhhhcceEEEecCCccCcceeeeeeeeeeccCCceecCceeccCCCCceEecHHHHHHHHHHHH
Q psy14280 970 PSYTVASKLSISPLLLSRFTGSIFIIDSTEEGAKRHNIGLNIKFSRKNEEVVGFTRRDETTKKWFYTEQVVTLIKNYMK 1048 (1891)
Q Consensus 970 Ps~~VAk~LGIspl~LSRITGS~~V~~gsr~~~~KiNIGLNLKF~~RnqkVlGYTRk~~~~~~WEYS~kAV~LI~eY~~ 1048 (1891)
..-+||+.+||++.+|.+....-.+.. . -|. .++.|.||...|..|+..+.
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~gli~~-----------------~---------~~~--~~g~r~y~~~dl~~l~~i~~ 52 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIGLLPP-----------------P---------IRT--EGGYRLYSDEDLERLRFIKR 52 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCC-----------------C---------ccC--CCCCEecCHHHHHHHHHHHH
Confidence 456899999999999998853211110 0 012 56779999999998887663
No 33
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=24.55 E-value=54 Score=28.33 Aligned_cols=20 Identities=25% Similarity=0.674 Sum_probs=16.5
Q ss_pred HHHHHhhhhhccCCCCCCCCc
Q psy14280 355 DDWVLMGFLIGNDFIPNLPDL 375 (1891)
Q Consensus 355 DDFVfL~fLvGNDFLPhLP~L 375 (1891)
+-|+-+|.|+| |+.+++|++
T Consensus 2 ~q~~~~~~L~G-D~~dni~Gv 21 (36)
T smart00279 2 EQLIDYAILVG-DYSDNIPGV 21 (36)
T ss_pred HHHHHHHHHhC-cCCCCCCCC
Confidence 35788999999 999977765
No 34
>PRK14976 5'-3' exonuclease; Provisional
Probab=22.73 E-value=3.3e+02 Score=33.25 Aligned_cols=101 Identities=25% Similarity=0.364 Sum_probs=0.0
Q ss_pred CCCC-chhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhcccCCCcEEEecccccccccCCCCCCcccCCCCcceE
Q psy14280 242 ETPG-EGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCTHEPYFSLLREEVKFNTKSNKGGSQIVTPEETKFF 320 (1891)
Q Consensus 242 ~VPG-EGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLatHep~f~ILREeV~f~~~~~k~~~~~~~~~~~~F~ 320 (1891)
..|| |+.==|--+.++.... +..++|++.|-|+..|. .+++.++ .......+.
T Consensus 108 ~~~g~EADDviatla~~~~~~-----g~~v~IvS~DkDl~ql~----~~~v~~~-----------------~~~~~~~~~ 161 (281)
T PRK14976 108 EQPGYEADDLIGSLAKKLSKQ-----NITVLIYSSDKDLLQLV----NENTDVL-----------------LKKKGTSHF 161 (281)
T ss_pred ecCCcCHHHHHHHHHHHHHHC-----CCeEEEEeCCCCcCccC----CCCeEEE-----------------EecCCCCcE
Q ss_pred EEehHHHHHHHHHHhcCCCCCCCCCCcCcchhhHHHHHHhhhhhc--cCCCCCCCCccccCCcHHHHHHHH
Q psy14280 321 LLHLSLMRDYLELEFGKLKEPGVLSFPFSIENIIDDWVLMGFLIG--NDFIPNLPDLHIINGALPLLYKVY 389 (1891)
Q Consensus 321 llhIslLREYL~~Ef~~lk~~~~l~f~~D~ERIIDDFVfL~fLvG--NDFLPhLP~L~I~eGald~L~~~Y 389 (1891)
+++..-+.+. +....++++| ++.|+| .|.+|.+|+ |.....-.|+..|
T Consensus 162 ~~~~~~v~~~---------------~gv~p~q~~d----~~aL~GD~sDnipGVpG--IG~KtA~~LL~~~ 211 (281)
T PRK14976 162 ILNTNNFFEL---------------YGIEPKQIID----YKGLVGDSSDNIKGVKG--IGPKTAIKLLNKY 211 (281)
T ss_pred EEcHHHHHHH---------------hCcCHHHHHH----HHHHhCCccCCCCCCCc--ccHHHHHHHHHHc
No 35
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=20.88 E-value=73 Score=31.49 Aligned_cols=35 Identities=20% Similarity=0.311 Sum_probs=27.3
Q ss_pred CCCchhHHHHHHHHHhhcCCCCCCCCcEEEEccCchhhhhhccc
Q psy14280 243 TPGEGEHKIMDYIRYMKSKPDYNPNMRHCLYGLDADLIMLGLCT 286 (1891)
Q Consensus 243 VPGEGEHKImdfIR~~r~qp~ydpN~rHcIYGlDADLImLgLat 286 (1891)
.|||+|.-+--.-++ +.-+.|+|.|+|+++.|--.
T Consensus 10 AP~eAeAq~A~L~~~---------g~vdav~s~D~D~llfG~~~ 44 (73)
T smart00484 10 APYEAEAQCAYLAKS---------GLVDAIITEDSDLLLFGAPR 44 (73)
T ss_pred cCCcHHHHHHHHHhC---------CCeeEEEcCccceEecCCcE
Confidence 489999987766552 35789999999999987543
No 36
>COG2451 Ribosomal protein L35AE/L33A [Translation, ribosomal structure and biogenesis]
Probab=20.59 E-value=1.1e+02 Score=31.85 Aligned_cols=45 Identities=18% Similarity=0.279 Sum_probs=36.2
Q ss_pred CCCCcccCCeEEEEeCC-CCccccCceEEEEEecCCCCccceEEEEeecccCC
Q psy14280 1150 PDTKFKLFDRVVNIRDC-YTVPLGYRGTIIGIVQGETSYDAMYDVVFDKPFPH 1201 (1891)
Q Consensus 1150 ~~q~F~LGDRVV~Vrds-G~VPfG~kGTVVGI~~~~~~~d~~vDVLFDepF~G 1201 (1891)
..+.|-||-||+|+-.+ |.| .+|+|+.+|..+ --|-+=|-...+|
T Consensus 39 ~eA~~y~gk~v~yk~~~~G~V---i~G~V~R~HGns----GaVrarF~~~LP~ 84 (100)
T COG2451 39 EEAQFYLGKRVCYKYRSSGRV---IKGKVVRTHGNS----GAVRARFERNLPG 84 (100)
T ss_pred HHHHhhhccEEEEEeCCCCcE---EEEEEEEecCCc----ceEEEEecCCCCc
Confidence 36789999999999887 755 899999999764 2467788887765
Done!