Query psy1016
Match_columns 718
No_of_seqs 200 out of 511
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 19:21:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1016.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1016hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2044|consensus 100.0 1E-218 3E-223 1804.9 40.5 571 1-718 1-661 (931)
2 COG5049 XRN1 5'-3' exonuclease 100.0 5E-188 1E-192 1541.3 37.5 541 1-718 1-696 (953)
3 KOG2045|consensus 100.0 2E-175 4E-180 1461.2 35.1 516 1-718 1-642 (1493)
4 PF03159 XRN_N: XRN 5'-3' exon 100.0 5.7E-86 1.2E-90 676.3 20.2 237 1-256 1-237 (237)
5 cd00128 XPG Xeroderma pigmento 98.8 8.7E-08 1.9E-12 102.7 14.6 243 1-366 1-245 (316)
6 PTZ00217 flap endonuclease-1; 98.3 6.5E-06 1.4E-10 91.5 13.1 234 1-352 1-245 (393)
7 PRK03980 flap endonuclease-1; 97.5 0.00092 2E-08 71.9 12.0 24 330-353 177-200 (292)
8 TIGR03674 fen_arch flap struct 97.5 0.0014 3.1E-08 71.7 13.5 66 50-119 23-96 (338)
9 smart00475 53EXOc 5'-3' exonuc 96.1 0.27 5.8E-06 52.3 16.8 140 51-252 4-146 (259)
10 smart00485 XPGN Xeroderma pigm 95.9 0.0075 1.6E-07 54.3 3.8 92 1-120 1-95 (99)
11 PF00752 XPG_N: XPG N-terminal 95.9 0.0093 2E-07 53.7 4.3 94 1-120 1-97 (101)
12 cd00008 53EXOc 5'-3' exonuclea 95.2 0.71 1.5E-05 48.4 15.7 56 51-107 4-62 (240)
13 PRK14976 5'-3' exonuclease; Pr 94.2 0.99 2.1E-05 48.6 14.1 57 50-107 5-67 (281)
14 KOG2044|consensus 93.0 0.09 2E-06 62.6 4.1 51 591-641 373-423 (931)
15 PF00867 XPG_I: XPG I-region; 92.7 0.22 4.7E-06 44.8 5.2 90 192-342 5-94 (94)
16 KOG2519|consensus 90.8 6.4 0.00014 45.1 15.2 35 329-365 216-250 (449)
17 KOG2518|consensus 84.9 4.2 9.1E-05 47.3 9.2 91 1-121 1-96 (556)
18 PRK05755 DNA polymerase I; Pro 82.7 26 0.00056 43.6 15.5 57 50-107 4-63 (880)
19 TIGR00593 pola DNA polymerase 78.2 50 0.0011 41.3 15.8 141 51-253 2-147 (887)
20 TIGR00600 rad2 DNA excision re 73.9 4.6 0.0001 50.7 5.4 39 191-242 785-823 (1034)
21 TIGR00600 rad2 DNA excision re 69.4 23 0.0005 44.8 10.0 90 1-120 1-94 (1034)
22 cd00080 HhH2_motif Helix-hairp 60.5 8.1 0.00018 33.6 2.8 33 330-364 8-42 (75)
23 PF00098 zf-CCHC: Zinc knuckle 54.2 9.6 0.00021 24.8 1.6 16 263-278 2-17 (18)
24 smart00484 XPGI Xeroderma pigm 47.7 11 0.00025 32.8 1.7 33 202-243 11-43 (73)
25 PF02739 5_3_exonuc_N: 5'-3' e 47.4 63 0.0014 32.3 7.1 56 51-107 4-63 (169)
26 COG0258 Exo 5'-3' exonuclease 34.3 1E+02 0.0023 33.4 6.8 65 50-115 13-82 (310)
27 smart00279 HhH2 Helix-hairpin- 34.0 26 0.00057 26.6 1.5 20 330-350 2-21 (36)
28 PF13696 zf-CCHC_2: Zinc knuck 31.6 19 0.00041 27.0 0.4 19 261-279 8-26 (32)
29 PHA02567 rnh RnaseH; Provision 31.3 59 0.0013 35.9 4.3 58 48-105 14-73 (304)
30 smart00292 BRCT breast cancer 25.6 89 0.0019 24.9 3.5 66 189-255 3-71 (80)
31 PF12387 Peptidase_C74: Pestiv 21.9 2.3E+02 0.005 29.1 6.1 89 161-275 79-189 (200)
32 cd00027 BRCT Breast Cancer Sup 20.7 1.9E+02 0.0042 22.3 4.5 47 191-238 1-49 (72)
33 PRK09482 flap endonuclease-lik 20.3 1.7E+02 0.0037 31.5 5.2 55 50-107 5-59 (256)
No 1
>KOG2044|consensus
Probab=100.00 E-value=1.2e-218 Score=1804.87 Aligned_cols=571 Identities=65% Similarity=1.135 Sum_probs=533.3
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCCCCCCCHHHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 80 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~~~~~teee~f~~ 80 (718)
||||+|||||++|||+++++|+|+++.+++|..||+|.|+|||||+||||||||||||||||+||+++|+|.||+|||..
T Consensus 1 MGVPaffRWLs~kyp~~I~~viEe~p~~~~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPEdkPaP~tedEm~~a 80 (931)
T KOG2044|consen 1 MGVPAFFRWLSRKYPKTISPVIEEEPVDVDGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPEDKPAPETEDEMFVA 80 (931)
T ss_pred CCchHHHHHHHHhcchhhhhhhhcCcccCCCcccccccCCCCCCcccccceeeecCcccccCCCCCCCCCCccHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCccccCCCCcccc
Q psy1016 81 IFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNC 160 (718)
Q Consensus 81 If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~~~~~~~~~~~~~l~~~g~~~p~~~~~~~~fDSN~ 160 (718)
||+||||||.+||||||||||||||||||||||||+||||||||++++.+++++++++++++|..+|++ .+.+.|||||
T Consensus 81 vFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~-~~~e~fDSNc 159 (931)
T KOG2044|consen 81 VFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPK-VKKETFDSNC 159 (931)
T ss_pred HHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCch-hhccccccCc
Confidence 999999999999999999999999999999999999999999999999999999999999999999887 5678999999
Q ss_pred ccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHH
Q psy1016 161 ITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIML 240 (718)
Q Consensus 161 ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLImL 240 (718)
|||||+||++|+.+|+|||+.||++||+|++++||+|||+||||||||||+|||+||++|+|||||+|||||+|||||||
T Consensus 160 ITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImL 239 (931)
T KOG2044|consen 160 ITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIML 239 (931)
T ss_pred cCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCcEEEeccccCCCCCCCCcccccCCcccccccCCCCCCCCC--ccccCCCCccEEEEEehhHHHHHHHHhCCCC
Q psy1016 241 GLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAEPNPE--SVITFGSEVEFIFVRLSVLREYLEKELAMPN 318 (718)
Q Consensus 241 ~LatHe~~f~ILRE~~~~~~~~~~~~c~q~g~~~~~c~~~~~~~~~~--~~~~~~~~~~f~ll~IsiLREyL~~E~~~~~ 318 (718)
||||||+||+||||+|.|+++++|.+|||.||+.++|.|+.+..... .+.. ..+++|+||||++|||||..||.+|+
T Consensus 240 gLATHE~hF~IlRE~~~P~~~~~C~~cgq~gh~~~dc~g~~~~~~~~~~~~~~-~~ek~fifl~I~vLREYLe~El~~p~ 318 (931)
T KOG2044|consen 240 GLATHEPHFSILREEFFPNKPRRCFLCGQTGHEAKDCEGKPRLGETNELADVP-GVEKPFIFLNISVLREYLERELRMPN 318 (931)
T ss_pred eccccCCceEEeeeeecCCCcccchhhcccCCcHhhcCCcCCcccccccccCc-ccccceEEEEHHHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999986522111 1122 46789999999999999999999999
Q ss_pred CCCCCCccchhhHHhhhhcccccccCCCCCCccccchhHHHHHHHHHHHhhhcCCcccccccC------------CCC--
Q psy1016 319 LPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGAVDRLVNLYKKTVYKTQEQLRQEENG------------GGG-- 384 (718)
Q Consensus 319 l~f~~d~ERiIDDFVfLcflvGNDFLPhlPsl~I~egaid~Li~~Yk~~l~~~~gYLt~~ek~------------g~~-- 384 (718)
+||++|+||+||||||||||||||||||||||+|++||||.|+++||+.+++++||||..++. |..
T Consensus 319 lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeIRegAId~L~~iyk~~~~~~kgYLT~~g~vNL~rve~~~~avg~~Ed 398 (931)
T KOG2044|consen 319 LPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEIREGAIDRLMEIYKKSFPKMKGYLTDSGKVNLDRVEMFMQAVGSVED 398 (931)
T ss_pred CCccccHHhhhcceEEEEeeecCccCCCCCchhhhhcHHHHHHHHHHHHHHhhcceeccCCcccHHHHHHHHHHHhhhcc
Confidence 999999999999999999999999999999999999999999999999999999999965320 000
Q ss_pred ------------CC-----------CC-----------CC-----------------CC-----------C---------
Q psy1016 385 ------------GR-----------GV-----------KR-----------------SF-----------D--------- 393 (718)
Q Consensus 385 ------------~~-----------~~-----------kr-----------------~~-----------~--------- 393 (718)
++ .. ++ ++ +
T Consensus 399 ~IFkkR~r~~e~frrrk~~rk~~~~~~~~sg~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~ 478 (931)
T KOG2044|consen 399 DIFKKRQRREERFRRRKAARKRQDRNAQDSGTNFSLAGSRELEASEPAQKALKVSLEKNESAANVERDNTEDLKTKLKHG 478 (931)
T ss_pred hHHHHhHhHHHHHHHhhhhhhhhhhhcccccccccccccccccccchhhhhhhhccccccchhhhcccchhhcccccccc
Confidence 00 00 00 00 0
Q ss_pred ---CCCCCCccccchhhhhhhhhhhHHHHHHhhcCCCCCcHHHHHHHHHHHHHhhHHHhhhhcCCCCCcccccCCCCCcc
Q psy1016 394 ---DVDESSEEEESNDEVRLWEDGFKDRYYESKFDVPKDDIAFRLMVGHEYVLGLCWVLKYYYQGCRSWKWYFPFHYAPF 470 (718)
Q Consensus 394 ---~~~~~~~~~~~~d~v~l~e~~~k~rYY~~Kf~~~~~d~e~~~~i~~~YleGL~WVL~YYy~GcpSW~WyYPYHYAPf 470 (718)
..+++..+++.+|+|+|||.|||+|||++||++++.+++++++||.+|+|||||||+|||+||+||+||||||||||
T Consensus 479 ~~~k~~~~~~~~~~~D~VkL~e~G~keRYY~~KF~v~~~eeq~R~~vv~~YveGLcWVl~YYyqGc~SW~WyYPYHYAPf 558 (931)
T KOG2044|consen 479 QRRKSEDSESEEENTDKVKLYEPGWKERYYEEKFDVTPDEEQIRKDVVLKYVEGLCWVLRYYYQGCASWNWYYPYHYAPF 558 (931)
T ss_pred ccccCccccCCCCCCcceeecCCchhhhhhhhhcCCCCHHHHHHHHHHHHHhcchhhhhhhhhccccccccccccccchh
Confidence 00122344566788999999999999999999999998899999999999999999999999999999999999999
Q ss_pred hhhhhhhccccccccCCCCCCCcHHHHHhhhhcccccchhcccccccccccccccccCCccccccchhhhhcchhHHHHH
Q psy1016 471 ASDFINIAEVDTNFETGTQPVNNNRILKFILYHFDNKMFFWNKSLINIAEVDTNFETGTQPVNNRILKFYVSDNIHLLIL 550 (718)
Q Consensus 471 aSDl~~i~~~~i~Fe~g~kPf~PfeQLl~Il~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 550 (718)
||||+++..++|+|++|+ ||+|||||
T Consensus 559 AsDf~~l~~ldikFe~g~-PFkP~eQL----------------------------------------------------- 584 (931)
T KOG2044|consen 559 ASDFKGLSDLDIKFELGK-PFKPLEQL----------------------------------------------------- 584 (931)
T ss_pred hhhhhcccccccccccCC-CCCcHHHH-----------------------------------------------------
Confidence 999999999999999995 99999999
Q ss_pred HHHHhhhhccceeeeeeeeeceeeecccccccccccccCCCCcCCccchhHHHHHHHHhhcccchHHHHHhhhhhHHHHH
Q psy1016 551 LVLRSWLVSLHVFTITYMIVSTMTLAGKASKLFSRMLTYPGFLTDSGDVKLERVQLIMQDLGMMEDEIFKKRQQTETMFK 630 (718)
Q Consensus 551 ~~~~~~~~~~~~~~~~~~~~~~m~vlp~~s~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 630 (718)
|+|||+||+++ || +.|
T Consensus 585 ----------------------mgVlPAAS~~~---------LP-------------------------------e~~-- 600 (931)
T KOG2044|consen 585 ----------------------MGVLPAASSHA---------LP-------------------------------EEW-- 600 (931)
T ss_pred ----------------------hhhcchhhcCC---------Cc-------------------------------HHH--
Confidence 99999999999 99 999
Q ss_pred HHHHHHHHHHHHHHHhhhcCCCCCcCCCCCCCCCCCCccccCCCCccccCCCCcccceeEEeccCCChhHHHHHHhhhhc
Q psy1016 631 MRNKMKKRRERQMKMAAQSTKAPSFIPGGQFAPQDSPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYE 710 (718)
Q Consensus 631 ~~~lm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Spi~dfyP~~f~~D~ngk~~~w~~v~llPfid~~~l~~~~~~~~~ 710 (718)
|+|| |||+|||+||||+||+||||||||+||||||||||||.|||+|++.++.
T Consensus 601 -r~LM--------------------------sdpdSpIiDFYPedF~iDmNGKk~aWQGIalLPFiDe~rLl~a~~~~y~ 653 (931)
T KOG2044|consen 601 -RKLM--------------------------SDPDSPIIDFYPEDFEIDMNGKKYAWQGIALLPFIDERRLLSAVAKVYP 653 (931)
T ss_pred -Hhhh--------------------------cCCCCcccccccccceeeccCceeeccccccccccchhhHHHHHHhhcc
Confidence 9999 9999999999999999999999999999999999999999999999999
Q ss_pred CCChhhhC
Q psy1016 711 KLSVEESE 718 (718)
Q Consensus 711 ~l~~~e~~ 718 (718)
.||+||++
T Consensus 654 ~Lt~EE~~ 661 (931)
T KOG2044|consen 654 TLTDEEKR 661 (931)
T ss_pred ccCHHHHh
Confidence 99999974
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=4.7e-188 Score=1541.27 Aligned_cols=541 Identities=51% Similarity=0.934 Sum_probs=476.1
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCCCCCCCHHHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 80 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~~~~~teee~f~~ 80 (718)
||||+|||||++|||+|++.+.|+ +|| ++||||||||||+|+|+||++++.|.+|+||+..
T Consensus 1 MGVPsfFRwlS~r~p~ii~~I~e~----------------~~P---~~DNLYLDMNgIlH~CtHp~d~~~petEeEm~~a 61 (953)
T COG5049 1 MGVPSFFRWLSERYPKIIQLIEEK----------------QIP---EFDNLYLDMNGILHNCTHPNDGSPPETEEEMYKA 61 (953)
T ss_pred CCchHHHHHHHhhhhHhhhhhhcc----------------CCC---CcceeEEecccccccCCCCCCCCCCCCHHHHHHH
Confidence 999999999999999998755432 234 6799999999999999999999999999999999
Q ss_pred HHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHH----hcCCCCCCccccCCCC
Q psy1016 81 IFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETAEKIAEVARIREKLL----ADGCILPPEKEKGSHF 156 (718)
Q Consensus 81 If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~~~~~~~~~~~~~l~----~~g~~~p~~~~~~~~f 156 (718)
||+|||+|+.++||||+||||||||||||||||||+||||+|+++..+....+...+++. ..|..+.....+.+.|
T Consensus 62 Vf~Yidhil~~irPrKllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~f 141 (953)
T COG5049 62 VFEYIDHILLKIRPRKLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKKF 141 (953)
T ss_pred HHHHHHHHHHhcCcceEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhccc
Confidence 999999999999999999999999999999999999999999986432221111112221 1233333334456789
Q ss_pred ccccccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChh
Q psy1016 157 DSNCITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADAD 236 (718)
Q Consensus 157 DSN~ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDAD 236 (718)
|||||||||+||++|+..|+|||+.||++||.|++++||+||+.||||||||||+|||+||++|+|+|||+|||||+|||
T Consensus 142 DSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDAD 221 (953)
T COG5049 142 DSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDAD 221 (953)
T ss_pred cccCCCCCChHHHHHHHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhhcCCCcEEEeccccCCC----CCCCCcccccCCcccccccCCCCCCCCCccccCCCCccEEEEEehhHHHHHHH
Q psy1016 237 LIMLGLATHEPNFTIIREEFKPN----QARPCDVCGQMGHEMKECVGLDAEPNPESVITFGSEVEFIFVRLSVLREYLEK 312 (718)
Q Consensus 237 LImL~LatHe~~f~ILRE~~~~~----~~~~~~~c~q~g~~~~~c~~~~~~~~~~~~~~~~~~~~f~ll~IsiLREyL~~ 312 (718)
||||||+||+|||.||||+|.++ ..+.|+.||..||...+|... ..++|.+||||+|||||..
T Consensus 222 LImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k~~-------------~~q~F~~LhiSlLREYLe~ 288 (953)
T COG5049 222 LIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKVL-------------THQPFYLLHISLLREYLER 288 (953)
T ss_pred ceeeecccCCCeeEEeechhccCcccccccccccccccccchhhhccc-------------ccCceEEEEHHHHHHHHHH
Confidence 99999999999999999998764 345899999999988888653 3678999999999999999
Q ss_pred HhCCCCCCCCCCccchhhHHhhhhcccccccCCCCCCccccchhHHHHHHHHHHHhhhcCCcccccccC-----------
Q psy1016 313 ELAMPNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGAVDRLVNLYKKTVYKTQEQLRQEENG----------- 381 (718)
Q Consensus 313 E~~~~~l~f~~d~ERiIDDFVfLcflvGNDFLPhlPsl~I~egaid~Li~~Yk~~l~~~~gYLt~~ek~----------- 381 (718)
||+.+++||+||+|||||||||||||||||||||||+|+|++||++.|+++||+.++.++||||..+..
T Consensus 289 Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldir~gai~~l~ei~k~~lp~~~gYit~~G~iNl~rle~~L~~ 368 (953)
T COG5049 289 EFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDIREGAIETLTEIWKKSLPHMKGYITCDGVINLARLEVILAI 368 (953)
T ss_pred HhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccccccchHHHHHHHHHHHhhhcCceeecCceecHHHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999999999999999844110
Q ss_pred --------------------------------------------------CCCC--------------------------
Q psy1016 382 --------------------------------------------------GGGG-------------------------- 385 (718)
Q Consensus 382 --------------------------------------------------g~~~-------------------------- 385 (718)
|+-.
T Consensus 369 L~~~E~~iFk~~~~qe~r~ne~~~~~~~~k~~~e~~~~~~~vv~eq~~~~gS~k~t~~d~~~~kk~~~l~~e~~id~~a~ 448 (953)
T COG5049 369 LGSFEDDIFKKDHIQEERKNESLERFSLRKERKEGLKGMPRVVYEQKKLIGSIKPTLMDQLQEKKSPDLPDEEFIDTLAL 448 (953)
T ss_pred HhhhhcchhhhhhhHhhhhccchhhHHHHhhhhhhhcccchhhhhhhhhcccccchhhhhhhhhccccCCCccccchhhc
Confidence 0000
Q ss_pred -------------------------CCCCCCCC------------CCC-C--------------------CCcc--ccch
Q psy1016 386 -------------------------RGVKRSFD------------DVD-E--------------------SSEE--EESN 405 (718)
Q Consensus 386 -------------------------~~~kr~~~------------~~~-~--------------------~~~~--~~~~ 405 (718)
...|.+.. ..+ | ..++ .+..
T Consensus 449 ~k~~d~kn~el~~~~~~ndl~ls~ska~ks~~n~~le~~iasds~~ed~ee~ese~d~i~~i~dk~vn~~v~ee~e~~~~ 528 (953)
T COG5049 449 PKDLDMKNHELFLKRFANDLGLSISKAIKSKGNYSLEMDIASDSPDEDEEEFESEVDSIRKIPDKYVNIIVEEEEENETE 528 (953)
T ss_pred hhhhhhhhhHHHHHHHHhhhhhhHHhhhhccCCchhhhhhhccccccchhhhhhccchhhhhhhhhhccccccchhcccc
Confidence 00000000 000 0 0000 1123
Q ss_pred hhhhhhhhhhHHHHHHhhcCCCCCcHHHHHHHHHHHHHhhHHHhhhhcCCCCCcccccCCCCCcchhhhhhhcccccccc
Q psy1016 406 DEVRLWEDGFKDRYYESKFDVPKDDIAFRLMVGHEYVLGLCWVLKYYYQGCRSWKWYFPFHYAPFASDFINIAEVDTNFE 485 (718)
Q Consensus 406 d~v~l~e~~~k~rYY~~Kf~~~~~d~e~~~~i~~~YleGL~WVL~YYy~GcpSW~WyYPYHYAPfaSDl~~i~~~~i~Fe 485 (718)
+.|++.+.||+++||.+||+++++++|.+++||++|||||||||.|||+|||||+|||||||||+|+|+.++++.+|+|+
T Consensus 529 ~Tv~l~~~g~~erYY~~K~~~t~~~~E~irdm~k~YVeGL~WVL~YYY~GC~SW~WyYpyHyAP~aaD~~k~~~~dIkFe 608 (953)
T COG5049 529 KTVNLRFPGWKERYYTSKLHFTTDSEEKIRDMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSDNDIKFE 608 (953)
T ss_pred cchhhcccchhhhhhhhhcCCCcCCHHHHHHHHHHHhhhhhhhhhhhhcCCCCcccccccccchhhhhhhhcccceeeec
Confidence 55778889999999999999999999989999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCCCcHHHHHhhhhcccccchhcccccccccccccccccCCccccccchhhhhcchhHHHHHHHHHhhhhccceeee
Q psy1016 486 TGTQPVNNNRILKFILYHFDNKMFFWNKSLINIAEVDTNFETGTQPVNNRILKFYVSDNIHLLILLVLRSWLVSLHVFTI 565 (718)
Q Consensus 486 ~g~kPf~PfeQLl~Il~~~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 565 (718)
+|+ ||+|||||
T Consensus 609 ~g~-PF~P~EQL-------------------------------------------------------------------- 619 (953)
T COG5049 609 LGT-PFRPFEQL-------------------------------------------------------------------- 619 (953)
T ss_pred CCC-CCCcHHHH--------------------------------------------------------------------
Confidence 997 99999999
Q ss_pred eeeeeceeeecccccccccccccCCCCcCCccchhHHHHHHHHhhcccchHHHHHhhhhhHHHHHHHHHHHHHHHHHHHH
Q psy1016 566 TYMIVSTMTLAGKASKLFSRMLTYPGFLTDSGDVKLERVQLIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRERQMKM 645 (718)
Q Consensus 566 ~~~~~~~m~vlp~~s~~~~~~~~~~~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lm~~~~~~~~~~ 645 (718)
|+|||++|+++ || +.| |.||
T Consensus 620 -------m~VLPa~Sk~~---------vP-------------------------------~~f---r~LM---------- 639 (953)
T COG5049 620 -------MAVLPARSKNL---------VP-------------------------------EGF---RPLM---------- 639 (953)
T ss_pred -------HhhcchhhcCc---------Cc-------------------------------hhh---hhhh----------
Confidence 99999999999 99 999 9999
Q ss_pred hhhcCCCCCcCCCCCCCCCCCCccccCCCCccccCCCCcccceeEEeccCCChhHHHHHHhhhhcCCChhhhC
Q psy1016 646 AAQSTKAPSFIPGGQFAPQDSPIIDFYPEDFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYEKLSVEESE 718 (718)
Q Consensus 646 ~~~~~~~~~~~~~~~~~~~~Spi~dfyP~~f~~D~ngk~~~w~~v~llPfid~~~l~~~~~~~~~~l~~~e~~ 718 (718)
+|++|||+||||++|++|||||++.||||||||||||.|||+|+++.+..||+||+.
T Consensus 640 ----------------~d~~S~IiDFYPe~f~lD~NGK~~~Wq~VvLlpFiDe~RLl~A~~~~~~~Ls~eE~~ 696 (953)
T COG5049 640 ----------------DDEKSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDERRLLSAVAVKYPTLSEEERK 696 (953)
T ss_pred ----------------cCCCCcccccchhhcccccCCceeeeeeeEEeeecchhHHHHHHHhhcccCCHHHHh
Confidence 999999999999999999999999999999999999999999999999999999974
No 3
>KOG2045|consensus
Probab=100.00 E-value=2.1e-175 Score=1461.22 Aligned_cols=516 Identities=47% Similarity=0.851 Sum_probs=455.2
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCC--CCCCCHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDK--PAPKDEDEMM 78 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~--~~~~teee~f 78 (718)
||||+||||+++|||++. .+ ++|.+|| ||||||||||||||+|+|++|. ..+.+|||||
T Consensus 1 MGvPKFfR~iSERyP~ls-el-------iee~qIP-----------EFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEif 61 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLS-EL-------IEEHQIP-----------EFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEIF 61 (1493)
T ss_pred CCchHHHHHhhhhchHHH-HH-------hhhccCC-----------cccceeeecccccccCCCCCCCccCcCCCHHHHH
Confidence 999999999999999875 33 4466787 9999999999999999999875 4578999999
Q ss_pred HHHHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCccccCCCCcc
Q psy1016 79 VAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDS 158 (718)
Q Consensus 79 ~~If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~~~~~~~~~~~~~l~~~g~~~p~~~~~~~~fDS 158 (718)
.+||+|||+||.+|||+|++|||||||||||||||||+||||+|+++.++ +.+.+++|+..|. ++|||
T Consensus 62 ~~IfnYIdhLf~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~q-------laKA~enGe~~p~-----erFDS 129 (1493)
T KOG2045|consen 62 QEIFNYIDHLFYLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQ-------LAKAAENGELRPH-----ERFDS 129 (1493)
T ss_pred HHHHHHHHHHHHhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHH-------HHHHHhccccCcc-----ccccc
Confidence 99999999999999999999999999999999999999999999987543 3345678888764 58999
Q ss_pred ccccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHH
Q psy1016 159 NCITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLI 238 (718)
Q Consensus 159 N~ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLI 238 (718)
|||||||+||.||++.|+|||+.|+++|+.||+++||+||++||||||||||+|||.++++|+|||||||||||+|||||
T Consensus 130 NcITPGTeFM~rl~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLI 209 (1493)
T KOG2045|consen 130 NCITPGTEFMVRLQEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLI 209 (1493)
T ss_pred CCCCCcHHHHHHHHHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcCCCcEEEeccccCCCCCCCCcccccCCcccccccCCCCCCCCCccccCCCCccEEEEEehhHHHHHHHHhCC--
Q psy1016 239 MLGLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAEPNPESVITFGSEVEFIFVRLSVLREYLEKELAM-- 316 (718)
Q Consensus 239 mL~LatHe~~f~ILRE~~~~~~~~~~~~c~q~g~~~~~c~~~~~~~~~~~~~~~~~~~~f~ll~IsiLREyL~~E~~~-- 316 (718)
||||+||+|||++|||+|+++.... .+....+.|.+||+++|||||+.||+-
T Consensus 210 mLGL~tHepHF~lLREEVtFgrrn~--------------------------~k~lehqkFyLLHLsLLREYlelEF~e~r 263 (1493)
T KOG2045|consen 210 MLGLCTHEPHFVLLREEVTFGRRNK--------------------------RKSLEHQKFYLLHLSLLREYLELEFDELR 263 (1493)
T ss_pred eeeeccCCcceeeeeeeeecccccc--------------------------cchhhhhhhhhhHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999862110 012356889999999999999999973
Q ss_pred CCCCCCCCccchhhHHhhhhcccccccCCCCCCccccchhHHHHHHHHHHHhhhcCCcccccccC---------------
Q psy1016 317 PNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGAVDRLVNLYKKTVYKTQEQLRQEENG--------------- 381 (718)
Q Consensus 317 ~~l~f~~d~ERiIDDFVfLcflvGNDFLPhlPsl~I~egaid~Li~~Yk~~l~~~~gYLt~~ek~--------------- 381 (718)
...+|+||+|||+||||+|+||||||||||||+|+|++||+..|+.+||+++|.+||||++.++.
T Consensus 264 dt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpllystykkvlpt~~GyINE~G~lNl~Rle~~L~eL~nf 343 (1493)
T KOG2045|consen 264 DTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLYSTYKKVLPTLGGYINENGKLNLRRLEIFLSELTNF 343 (1493)
T ss_pred hccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHHHHHHHHhccCCccccccceecHHHHHHHHHHHHhh
Confidence 36789999999999999999999999999999999999999999999999999999999865320
Q ss_pred --------------CCCC----------------------------CCCCCC---------CCCCC----------C-CC
Q psy1016 382 --------------GGGG----------------------------RGVKRS---------FDDVD----------E-SS 399 (718)
Q Consensus 382 --------------g~~~----------------------------~~~kr~---------~~~~~----------~-~~ 399 (718)
+... -..+.+ ..+.+ | ++
T Consensus 344 eke~Fke~led~k~~nskr~r~~~~~~~~~~~~dika~t~sq~~d~l~~~~~~~p~i~~~a~ld~dD~~Fl~~~~eDl~~ 423 (1493)
T KOG2045|consen 344 EKEHFKEHLEDLKYMNSKRERFDDPEQQELAEMDIKAITESQNLDSLLGEESKDPLINKSALLDDDDSAFLSDHEEDLSD 423 (1493)
T ss_pred hHHHHHHHHHhhhhccccccccccHHHHhhhcccHHhhhhhhhhhhhccccccccccccccccccchHHHHHHhhhhccc
Confidence 0000 000000 00000 0 00
Q ss_pred ---------------ccccchhh----------------------hhhhh--------hhhHHHHHHhhcCCCCCcHHHH
Q psy1016 400 ---------------EEEESNDE----------------------VRLWE--------DGFKDRYYESKFDVPKDDIAFR 434 (718)
Q Consensus 400 ---------------~~~~~~d~----------------------v~l~e--------~~~k~rYY~~Kf~~~~~d~e~~ 434 (718)
...+.+|+ --+|+ ..||..||+.|++.++.+++.+
T Consensus 424 ~~~~s~s~~~~ld~~~~de~EdEf~~~~~t~~ls~~~~~~~~n~eea~~eKti~n~~F~rwK~~yYrdKlkf~~~dee~l 503 (1493)
T KOG2045|consen 424 LEPGSGSDELLLDNLDADELEDEFAVELATLALSGMNDADFANDEEACWEKTILNKEFQRWKRNYYRDKLKFDPNDEELL 503 (1493)
T ss_pred cccccCccchhhccccchhhhHHHHHHHHHHHHhccccccccchHHHhhhhhhHHHHHHHHHHHHhhhhhcCCCccHHHH
Confidence 00001111 11222 3699999999999999999999
Q ss_pred HHHHHHHHHhhHHHhhhhcCCCCCcccccCCCCCcchhhhhhhccccccccCCCCCCCcHHHHHhhhhcccccchhcccc
Q psy1016 435 LMVGHEYVLGLCWVLKYYYQGCRSWKWYFPFHYAPFASDFINIAEVDTNFETGTQPVNNNRILKFILYHFDNKMFFWNKS 514 (718)
Q Consensus 435 ~~i~~~YleGL~WVL~YYy~GcpSW~WyYPYHYAPfaSDl~~i~~~~i~Fe~g~kPf~PfeQLl~Il~~~~n~~~~~~~~ 514 (718)
+++|++|||||||||.|||+||+||+||||||||||+||+.++.+++|.|++|+ ||+|||||
T Consensus 504 relae~YVeaLQWvL~YYYrGc~SWsWyYphHyaP~ISDl~kgldv~ieF~mgt-PF~PFqQL----------------- 565 (1493)
T KOG2045|consen 504 RELAEHYVEALQWVLDYYYRGCQSWSWYYPHHYAPFISDLKKGLDVEIEFHMGT-PFLPFQQL----------------- 565 (1493)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCccccccccccccchhHhHhcccceeEEEecCC-CCCcHHHH-----------------
Confidence 999999999999999999999999999999999999999999999999999998 99999999
Q ss_pred cccccccccccccCCccccccchhhhhcchhHHHHHHHHHhhhhccceeeeeeeeeceeeecccccccccccccCCCCcC
Q psy1016 515 LINIAEVDTNFETGTQPVNNRILKFYVSDNIHLLILLVLRSWLVSLHVFTITYMIVSTMTLAGKASKLFSRMLTYPGFLT 594 (718)
Q Consensus 515 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~m~vlp~~s~~~~~~~~~~~~lp 594 (718)
|||||++|+.+ ||
T Consensus 566 ----------------------------------------------------------lAVLPaaSa~l---------lP 578 (1493)
T KOG2045|consen 566 ----------------------------------------------------------LAVLPAASAKL---------LP 578 (1493)
T ss_pred ----------------------------------------------------------HHhchhhhhcc---------CC
Confidence 99999999999 99
Q ss_pred CccchhHHHHHHHHhhcccchHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhhhcCCCCCcCCCCCCCCCCCCccccCCC
Q psy1016 595 DSGDVKLERVQLIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRERQMKMAAQSTKAPSFIPGGQFAPQDSPIIDFYPE 674 (718)
Q Consensus 595 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lm~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Spi~dfyP~ 674 (718)
.+| |+|| .++.|||+||||.
T Consensus 579 -------------------------------p~f---rdLM--------------------------~~~~SPI~DFYPa 598 (1493)
T KOG2045|consen 579 -------------------------------PAF---RDLM--------------------------LLPTSPIADFYPA 598 (1493)
T ss_pred -------------------------------hhh---hHhh--------------------------cCCCCchhhcchh
Confidence 999 9999 9999999999999
Q ss_pred CccccCCCCcccceeEEeccCCChhHHHHHHhhhhcCCChhhhC
Q psy1016 675 DFKIDLNGKKFAWQGVALLPFVDEERLHKALAPYYEKLSVEESE 718 (718)
Q Consensus 675 ~f~~D~ngk~~~w~~v~llPfid~~~l~~~~~~~~~~l~~~e~~ 718 (718)
+|+.|+|||+..|++|||||||||.||++||.+.+..||.||++
T Consensus 599 efelD~NGKtadWEAVVLIpFIdEkRLleAm~pk~~~Ls~EEr~ 642 (1493)
T KOG2045|consen 599 EFELDLNGKTADWEAVVLIPFIDEKRLLEAMLPKEAQLSLEERE 642 (1493)
T ss_pred hheecccCCccceeEEEEEeecchHHHHHHHhhHhhhcCHHHhh
Confidence 99999999999999999999999999999999999999999985
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=5.7e-86 Score=676.31 Aligned_cols=237 Identities=62% Similarity=1.097 Sum_probs=189.0
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCCCCCCCHHHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 80 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~~~~~teee~f~~ 80 (718)
||||+||+||++|||.++..+.+.. ...+|||||||||||||+|+|+++.+.+.+++++|.+
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~------------------~~~~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~~ 62 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENS------------------IPSEFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQR 62 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTT------------------SEE-ESEEEEETHHHHHHHHS-SSS----SHHHHHHH
T ss_pred CCHHHHHHHHHHhCCcceeeccccC------------------CCCcCCEEEEEcchhhhHhcCCcccCCCccHHHHHHH
Confidence 9999999999999999987554311 1126999999999999999999888788899999999
Q ss_pred HHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCccccCCCCcccc
Q psy1016 81 IFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNC 160 (718)
Q Consensus 81 If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~~~~~~~~~~~~~l~~~g~~~p~~~~~~~~fDSN~ 160 (718)
||+|||+||++|||||+||||||||||||||||||+|||++++++...........++...+|...+.. .....|||||
T Consensus 63 i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~fdsn~ 141 (237)
T PF03159_consen 63 IFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPE-DQEEKFDSNC 141 (237)
T ss_dssp HHHHHHHHHHHH-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HH-HHS----GGG
T ss_pred HHHHHHHhheeecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhcccccccc-ccccccccce
Confidence 999999999999999999999999999999999999999999998776666556666666666555432 2347999999
Q ss_pred ccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHH
Q psy1016 161 ITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIML 240 (718)
Q Consensus 161 ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLImL 240 (718)
|||||+||.+|+++|++|+.+|+++||.|++++||+||++||||||||||+|||+++++|+|+||++|||||+|||||||
T Consensus 142 ITPGT~FM~~l~~~L~~~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll 221 (237)
T PF03159_consen 142 ITPGTEFMEKLSDALRYYIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILL 221 (237)
T ss_dssp SSTTSHHHHHHHHHHHHHHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHH
T ss_pred eccCCHHHHHHHHHHHHHHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCCcEEEecccc
Q psy1016 241 GLATHEPNFTIIREEF 256 (718)
Q Consensus 241 ~LatHe~~f~ILRE~~ 256 (718)
||++|++||+||||+|
T Consensus 222 ~L~~~~~~~~ilre~~ 237 (237)
T PF03159_consen 222 SLATHEPNIYILREEV 237 (237)
T ss_dssp HHHTT-SSEEEEEESS
T ss_pred HHccCCCeEEEEeccC
Confidence 9999999999999974
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=98.78 E-value=8.7e-08 Score=102.73 Aligned_cols=243 Identities=20% Similarity=0.317 Sum_probs=125.7
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCCC--CCCCHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKP--APKDEDEMM 78 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~~--~~~teee~f 78 (718)
|||+++..||...-+.+. +++ ..| --|=||.++.+|.+....... .........
T Consensus 1 MGI~gL~~~l~~~~~~~~---i~~----l~g-----------------k~laID~~~~l~r~~~a~~~~~~~~g~~~~~l 56 (316)
T cd00128 1 MGIKGLWPLLKPVARPVH---LEE----LRG-----------------KKVAIDASIWLYQFLKACRQELGSGGETTSHL 56 (316)
T ss_pred CchhhHHHHHHhhCCCCC---HHH----hCC-----------------cEEEecHHHHHHHHHHHhhhhccCCCCCcHHH
Confidence 999999999998876541 111 111 147899999999876432110 011122333
Q ss_pred HHHHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHHHHHHHHHHHHHHHHhcCCCCCCccccCCCCcc
Q psy1016 79 VAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDS 158 (718)
Q Consensus 79 ~~If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~~~~~~~~~~~~~l~~~g~~~p~~~~~~~~fDS 158 (718)
..++..+.+|... .. + ..+++||.+|-.|......||-+... +..+... ....|..-...+. .. .+
T Consensus 57 ~~~~~rl~~L~~~-~i-~-pvfVFDG~~~~~K~~~~~~R~~~r~~-~~~~~~~-------~~~~~~~~~~~~~-~~--~~ 122 (316)
T cd00128 57 QGFFYRTCRLLEL-GI-K-PVFVFDGKPPPLKAETLAKRRERREE-AEEEAKE-------ALEKGLEEEAKKL-ER--RA 122 (316)
T ss_pred HHHHHHHHHHHHC-CC-E-EEEEEcCCCchhhHHHHHHHHHHHHH-HHHHHHH-------HHHhCCHHHHHHH-Hh--cc
Confidence 4555555555531 22 3 34679999998887776655533221 1111110 0111100000000 00 01
Q ss_pred ccccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHH
Q psy1016 159 NCITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLI 238 (718)
Q Consensus 159 N~ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLI 238 (718)
..+||.. ...+.+.|+.+ ++.+|.+ |||+|-=+-..-++ .....|+|.|+|++
T Consensus 123 ~~~~~~~--~~~~~~lL~~~------------gi~~i~a----p~EAdaq~a~l~~~---------g~v~~i~S~DsD~l 175 (316)
T cd00128 123 VRVTPQM--IEEAKELLRLM------------GIPYIVA----PYEAEAQCAYLAKK---------GLVDAIITEDSDLL 175 (316)
T ss_pred CcCCHHH--HHHHHHHHHHc------------CCCEEEC----CcCHHHHHHHHHhC---------CCeeEEEecCCCee
Confidence 1244432 22233222221 5567764 89999765544322 13578999999998
Q ss_pred HHhhhcCCCcEEEeccccCCCCCCCCcccccCCcccccccCCCCCCCCCccccCCCCccEEEEEehhHHHHHHHHhCCCC
Q psy1016 239 MLGLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAEPNPESVITFGSEVEFIFVRLSVLREYLEKELAMPN 318 (718)
Q Consensus 239 mL~LatHe~~f~ILRE~~~~~~~~~~~~c~q~g~~~~~c~~~~~~~~~~~~~~~~~~~~f~ll~IsiLREyL~~E~~~~~ 318 (718)
+++- ++ ++|.-...+ ...+..++..-+.+ ++.+
T Consensus 176 ~fg~----~~--vi~~~~~~~-----------------------------------~~~~~~~~~~~~~~----~lgl-- 208 (316)
T cd00128 176 LFGA----PR--VYRNLFDSG-----------------------------------AKPVEEIDLEKILK----ELGL-- 208 (316)
T ss_pred eecC----ce--EEEecccCC-----------------------------------CCceEEEEHHHHHH----HcCC--
Confidence 8762 22 333210000 01234555444433 3322
Q ss_pred CCCCCCccchhhHHhhhhcccccccCCCCCCccccchhHHHHHHHHHH
Q psy1016 319 LPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEIREGAVDRLVNLYKK 366 (718)
Q Consensus 319 l~f~~d~ERiIDDFVfLcflvGNDFLPhlPsl~I~egaid~Li~~Yk~ 366 (718)
. -+.|+.+|.|+|+||+|.+|++-.. .|+ .|+..|..
T Consensus 209 -------~--~~q~id~~~L~G~Dy~~gv~giG~k-~A~-~li~~~~~ 245 (316)
T cd00128 209 -------T--REKLIDLAILLGCDYTEGIPGIGPV-TAL-KLIKKYGD 245 (316)
T ss_pred -------C--HHHHHHHHHhcCCCCCCCCCCccHH-HHH-HHHHHcCC
Confidence 2 2689999999999999999987542 233 35555653
No 6
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.29 E-value=6.5e-06 Score=91.52 Aligned_cols=234 Identities=20% Similarity=0.312 Sum_probs=123.2
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCC----CCCCCCCH--
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPE----DKPAPKDE-- 74 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~----~~~~~~te-- 74 (718)
|||.++...|....|.+++.. .-.+..|. -+-||....||.....- +.....+.
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~---~l~~l~gk-----------------~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G 60 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQ---ELKNYFGR-----------------VIAIDASMALYQFLIAIRDDSQGGNLTNEAG 60 (393)
T ss_pred CChhhHHHHHhhhcccccccc---CHHHhCCc-----------------EEEEeHHHHHHHHHHHcccccccccchhccC
Confidence 999999999999999876422 00111121 47899999999854211 10000110
Q ss_pred --HHHHHHHHHHHHHHHhh-hccceeEEEEecCCCcchhhHHHHHHh--hhhhHHHHHHHHHHHHHHHHHHhcCCCCCCc
Q psy1016 75 --DEMMVAIFECIDRLFRI-VRPRKLLYMAIDGVAPRAKMNQQRSRR--FRASKETAEKIAEVARIREKLLADGCILPPE 149 (718)
Q Consensus 75 --ee~f~~If~yId~L~~~-VrPrKllyiAIDGVAPrAKMnQQRsRR--Frsa~e~~~~~~~~~~~~~~l~~~g~~~p~~ 149 (718)
..-+.-++..+-+|+.. ++| .+++||.+|-.|...-..|| ...+.+..+ +....|..-
T Consensus 61 ~~t~~l~g~~~r~~~Ll~~gikP----v~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~----------~a~~~g~~~--- 123 (393)
T PTZ00217 61 EVTSHISGLFNRTIRLLEAGIKP----VYVFDGKPPELKSGELEKRRERREEAEEELE----------KAIEEGDDE--- 123 (393)
T ss_pred CccHHHHHHHHHHHHHHHCCCCE----EEEEcCCCchhhHHHHHHHHHHHHHhHHHHH----------HHHhcCCHH---
Confidence 12234556666667764 788 47999999976665443333 222222111 011122100
Q ss_pred cccCCCCccccccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEE
Q psy1016 150 KEKGSHFDSNCITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHC 229 (718)
Q Consensus 150 ~~~~~~fDSN~ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~Hc 229 (718)
....+-..++.--.+-+..+.+.|+. -++.+|.+ |||+|.=|-..- +. +....
T Consensus 124 --~a~k~~~r~~~vt~~~~~~~~~lL~~------------~Gip~i~A----P~EAdaq~A~L~-~~--------g~v~~ 176 (393)
T PTZ00217 124 --EIKKQSKRTVRVTKEQNEDAKKLLRL------------MGIPVIEA----PCEAEAQCAELV-KK--------GKVYA 176 (393)
T ss_pred --HHHHHHhhcccCCHHHHHHHHHHHHH------------cCCceEEC----CcCHHHHHHHHH-HC--------CCeEE
Confidence 00001111111111222222222221 24556754 899999544443 21 34578
Q ss_pred EEcCChhHHHHhhhcCCCcEEEeccccCCCCCCCCcccccCCcccccccCCCCCCCCCccccCCCCccEEEEEehhHHHH
Q psy1016 230 LCGADADLIMLGLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMKECVGLDAEPNPESVITFGSEVEFIFVRLSVLREY 309 (718)
Q Consensus 230 IYGlDADLImL~LatHe~~f~ILRE~~~~~~~~~~~~c~q~g~~~~~c~~~~~~~~~~~~~~~~~~~~f~ll~IsiLREy 309 (718)
|++-|.|+++++- + .++|.-...+ .....++.+++..+.+
T Consensus 177 ViS~D~D~l~fg~----~--~vi~~l~~~~---------------------------------~~~~~~~~~~~~~v~~- 216 (393)
T PTZ00217 177 VATEDMDALTFGT----P--VLLRNLNFSE---------------------------------AKKRPIQEINLSTVLE- 216 (393)
T ss_pred EeCCCcCeeecCC----c--EEEEcccccc---------------------------------cCCCCeEEEEHHHHHH-
Confidence 9999999998862 2 3344321000 0012344555554432
Q ss_pred HHHHhCCCCCCCCCCccchhhHHhhhhcccccccCCCCCCccc
Q psy1016 310 LEKELAMPNLPFPYSFERALDDWVFMCFFVGNDFLPHLPSLEI 352 (718)
Q Consensus 310 L~~E~~~~~l~f~~d~ERiIDDFVfLcflvGNDFLPhlPsl~I 352 (718)
++. +. -+.||-+|.|+|.||+|.+|++-.
T Consensus 217 ---~~g---------l~--~~q~id~~iL~G~Dy~pgi~GIG~ 245 (393)
T PTZ00217 217 ---ELG---------LS--MDQFIDLCILCGCDYCDTIKGIGP 245 (393)
T ss_pred ---HhC---------CC--HHHHHHHHHHhCCCCCCCCCCccH
Confidence 232 12 267888999999999999998754
No 7
>PRK03980 flap endonuclease-1; Provisional
Probab=97.49 E-value=0.00092 Score=71.89 Aligned_cols=24 Identities=17% Similarity=0.497 Sum_probs=20.9
Q ss_pred hHHhhhhcccccccCCCCCCcccc
Q psy1016 330 DDWVFMCFFVGNDFLPHLPSLEIR 353 (718)
Q Consensus 330 DDFVfLcflvGNDFLPhlPsl~I~ 353 (718)
+.||-+|.|+|.||+|.+|++-+.
T Consensus 177 ~q~id~~iL~G~Dy~~GI~GIG~k 200 (292)
T PRK03980 177 EQLIDIAILVGTDYNPGIKGIGPK 200 (292)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHH
Confidence 678889999999999999987553
No 8
>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=97.47 E-value=0.0014 Score=71.66 Aligned_cols=66 Identities=18% Similarity=0.210 Sum_probs=39.9
Q ss_pred eEEEecccccccccCCC---CCCCCCC----HHHHHHHHHHHHHHHHhh-hccceeEEEEecCCCcchhhHHHHHHhh
Q psy1016 50 NLYLDMNGIIHPCTHPE---DKPAPKD----EDEMMVAIFECIDRLFRI-VRPRKLLYMAIDGVAPRAKMNQQRSRRF 119 (718)
Q Consensus 50 nLYLDMNgIIH~c~h~~---~~~~~~t----eee~f~~If~yId~L~~~-VrPrKllyiAIDGVAPrAKMnQQRsRRF 119 (718)
-+-||....||.+...- +.....+ ...-+..++..+-+|+.. ++| .+++||.+|-.|..+-..||-
T Consensus 23 ~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P----v~VFDG~~p~~K~~~~~~R~~ 96 (338)
T TIGR03674 23 VVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKP----VYVFDGKPPELKAETLEERRE 96 (338)
T ss_pred EEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeE----EEEECCCChhhhHhhHHHHHH
Confidence 57799999999765421 1110011 112234444555556655 777 699999999877776666654
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=96.10 E-value=0.27 Score=52.31 Aligned_cols=140 Identities=18% Similarity=0.261 Sum_probs=79.2
Q ss_pred EEEecccccccccCCCCC--CCCCCHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHHHH
Q psy1016 51 LYLDMNGIIHPCTHPEDK--PAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETAEK 128 (718)
Q Consensus 51 LYLDMNgIIH~c~h~~~~--~~~~teee~f~~If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~~~ 128 (718)
|-||.|++||.+.|.-.. ...-........+++.+.+++...+|..+ .+|+||-.|-- |..-|-..|
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~-~~~fD~~~~~~-----R~~l~p~YK----- 72 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYV-AVVFDAKGKTF-----RHELYPEYK----- 72 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeE-EEEEeCCCCcc-----ccchhHHHH-----
Confidence 789999999998875311 00011123445566777777777889876 59999854421 211121111
Q ss_pred HHHHHHHHHHHHhcCCCCCCccccCCCCccccccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCC-chhh
Q psy1016 129 IAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPG-EGEH 207 (718)
Q Consensus 129 ~~~~~~~~~~l~~~g~~~p~~~~~~~~fDSN~ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPG-EGEH 207 (718)
++-...|. .|..++ .++++-+.. -++.+|- +|| |++=
T Consensus 73 ------------a~R~~~pe---------------------~L~~q~-~~~~~~l~~----~gi~~i~----~~g~EADD 110 (259)
T smart00475 73 ------------ANRPKTPD---------------------ELLEQI-PLIKELLDA----LGIPVLE----VEGYEADD 110 (259)
T ss_pred ------------hCCCCCCH---------------------HHHHHH-HHHHHHHHH----CCCCEEe----eCCcCHHH
Confidence 11111111 245555 445554432 1333432 689 9998
Q ss_pred HHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHHhhhcCCCcEEEe
Q psy1016 208 KIMDYIRKQRAQPDHDPNTQHCLCGADADLIMLGLATHEPNFTII 252 (718)
Q Consensus 208 KImdfIR~~r~~p~ydpNt~HcIYGlDADLImL~LatHe~~f~IL 252 (718)
=|--..++.... +...+|++.|-|+.-|. .+++.++
T Consensus 111 ~iatla~~~~~~-----g~~~~IvS~DkDl~ql~----~~~v~~~ 146 (259)
T smart00475 111 VIATLAKKAEAE-----GYEVRIVSGDKDLLQLV----SDKVSVL 146 (259)
T ss_pred HHHHHHHHHHhC-----CCeEEEEeCCCcHhhcC----CCCEEEE
Confidence 777666654432 24689999999998664 3455553
No 10
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=95.94 E-value=0.0075 Score=54.26 Aligned_cols=92 Identities=21% Similarity=0.321 Sum_probs=57.0
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCCC--CCCCHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKP--APKDEDEMM 78 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~~--~~~teee~f 78 (718)
|||+++..||...--.+ .+ .+..|. -+=||.+..||.+......+ .........
T Consensus 1 MGI~gL~~~l~~~~~~~---~i----~~l~g~-----------------~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l 56 (99)
T smart00485 1 MGIKGLWPLLKPVVREV---PL----EALRGK-----------------TLAIDASIWLYQFLTACREKLGTPLPNSKHL 56 (99)
T ss_pred CCHhHHHHHHHHhcccC---CH----HHhCCc-----------------eEeccHHHHHHHHHHHHhhhhcCCCCchHHH
Confidence 99999999999861110 01 112232 35688999999775432111 111122245
Q ss_pred HHHHHHHHHHH-hhhccceeEEEEecCCCcchhhHHHHHHhhh
Q psy1016 79 VAIFECIDRLF-RIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (718)
Q Consensus 79 ~~If~yId~L~-~~VrPrKllyiAIDGVAPrAKMnQQRsRRFr 120 (718)
..++..+.+|. .-|.| ++.+||.+|-+|...+..||-+
T Consensus 57 ~~~~~rl~~L~~~~I~P----ifVFDG~~~~~K~~t~~~R~~~ 95 (99)
T smart00485 57 MGLFYRTCRLLEFGIKP----IFVFDGKPPPLKSETLAKRRER 95 (99)
T ss_pred HHHHHHHHHHHHCCCeE----EEEECCCCchhhHHHHHHHHHH
Confidence 55666666554 33444 5889999999999999988854
No 11
>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=95.91 E-value=0.0093 Score=53.67 Aligned_cols=94 Identities=20% Similarity=0.355 Sum_probs=56.1
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccCCCCCCCC--CCHHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAP--KDEDEMM 78 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h~~~~~~~--~teee~f 78 (718)
|||+++..+|.... .+.... ..+..|. -|=||.+..||.+.+....... ......+
T Consensus 1 MGI~gL~~~l~~~~--~v~~~~---~~~l~g~-----------------~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~ 58 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA--AVRKVS---LSELRGK-----------------RVAIDASCWLHQFLFSCREELGQGVGTDSHL 58 (101)
T ss_dssp ---TTHHHHCHHHE--GEEEEE---GGGGTTC-----------------EEEEEHHHHHHHHHHHSBCTTSCB-BS-HHH
T ss_pred CCcccHHHHHHhhc--cCCccC---HHHhCCC-----------------EEEEEcHHHHHHHHHHhHHHhccccchHHHH
Confidence 99999999999987 221110 1112232 4779999999987554322111 1113556
Q ss_pred HHHHHHHHHHH-hhhccceeEEEEecCCCcchhhHHHHHHhhh
Q psy1016 79 VAIFECIDRLF-RIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (718)
Q Consensus 79 ~~If~yId~L~-~~VrPrKllyiAIDGVAPrAKMnQQRsRRFr 120 (718)
..++..+..|. .-|+| ++.+||.+|-+|......||-+
T Consensus 59 ~~~~~r~~~L~~~gI~P----ifVFDG~~~~~K~~~~~~R~~~ 97 (101)
T PF00752_consen 59 RGLFSRLCRLLEHGIKP----IFVFDGKPPPLKRETIQKRRKR 97 (101)
T ss_dssp HHHHHHHHHHHHTTEEE----EEEE--STTGGCHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCEE----EEEECCCCchhhHHHHHHHHHH
Confidence 67777777654 45665 6899999999999888877744
No 12
>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=95.18 E-value=0.71 Score=48.38 Aligned_cols=56 Identities=9% Similarity=0.096 Sum_probs=39.1
Q ss_pred EEEecccccccccCCCCCCC---CCCHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCc
Q psy1016 51 LYLDMNGIIHPCTHPEDKPA---PKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 107 (718)
Q Consensus 51 LYLDMNgIIH~c~h~~~~~~---~~teee~f~~If~yId~L~~~VrPrKllyiAIDGVAP 107 (718)
|.||.|+++|.+.|...... .-........++..+.+++...+|.+. .+|+||-+|
T Consensus 4 llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~-~~~fD~~~~ 62 (240)
T cd00008 4 LLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYV-AVVFDAGGK 62 (240)
T ss_pred EEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeE-EEEEeCCCC
Confidence 78999999999887642111 111223456677777888888899987 699999644
No 13
>PRK14976 5'-3' exonuclease; Provisional
Probab=94.18 E-value=0.99 Score=48.59 Aligned_cols=57 Identities=16% Similarity=0.211 Sum_probs=38.8
Q ss_pred eEEEecccccccccCCCC--CCCC----CCHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCc
Q psy1016 50 NLYLDMNGIIHPCTHPED--KPAP----KDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 107 (718)
Q Consensus 50 nLYLDMNgIIH~c~h~~~--~~~~----~teee~f~~If~yId~L~~~VrPrKllyiAIDGVAP 107 (718)
=|.||.|++|+.+.|... .+.. -........+++.+-+++...+|..+ -+|+||-.|
T Consensus 5 ~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~-~v~fD~~~~ 67 (281)
T PRK14976 5 ALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYI-LIAFDAGRK 67 (281)
T ss_pred EEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEE-EEEEECCCC
Confidence 468999999999887631 1111 11223445677777788888899886 589998544
No 14
>KOG2044|consensus
Probab=92.99 E-value=0.09 Score=62.63 Aligned_cols=51 Identities=53% Similarity=0.933 Sum_probs=42.6
Q ss_pred CCcCCccchhHHHHHHHHhhcccchHHHHHhhhhhHHHHHHHHHHHHHHHH
Q psy1016 591 GFLTDSGDVKLERVQLIMQDLGMMEDEIFKKRQQTETMFKMRNKMKKRRER 641 (718)
Q Consensus 591 ~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lm~~~~~~ 641 (718)
|.|.||+.|.+.+|+-|++.||+-||+|||||||.+.=|+=|+.-+||..+
T Consensus 373 gYLT~~g~vNL~rve~~~~avg~~Ed~IFkkR~r~~e~frrrk~~rk~~~~ 423 (931)
T KOG2044|consen 373 GYLTDSGKVNLDRVEMFMQAVGSVEDDIFKKRQRREERFRRRKAARKRQDR 423 (931)
T ss_pred ceeccCCcccHHHHHHHHHHHhhhcchHHHHhHhHHHHHHHhhhhhhhhhh
Confidence 348999999999999999999999999999998887766766665444444
No 15
>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=92.66 E-value=0.22 Score=44.77 Aligned_cols=90 Identities=23% Similarity=0.399 Sum_probs=53.3
Q ss_pred cEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHHhhhcCCCcEEEeccccCCCCCCCCcccccCC
Q psy1016 192 IKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIMLGLATHEPNFTIIREEFKPNQARPCDVCGQMG 271 (718)
Q Consensus 192 l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLImL~LatHe~~f~ILRE~~~~~~~~~~~~c~q~g 271 (718)
+.+|.+ |||+|.=+--.-|+ +..+.|++.|+|+++.|-- .|+|.-... ....
T Consensus 5 v~~i~A----P~EAeAq~A~L~~~---------g~vd~V~t~DsD~l~fG~~------~vi~~~~~~-~~~~-------- 56 (94)
T PF00867_consen 5 VPYIVA----PYEAEAQCAYLERN---------GLVDAVITEDSDLLLFGAP------KVIRKLSDK-SSGK-------- 56 (94)
T ss_dssp -EEEE-----SS-HHHHHHHHHHT---------TSSSEEE-SSSHHHHTT-S------EEEESST-C-SCCS--------
T ss_pred CeEEEc----CchHHHHHHHHHHh---------cceeEEEecCCCEEeeCCC------EEEEecccc-ccCC--------
Confidence 455553 89999988765544 3568999999999999644 566654200 0000
Q ss_pred cccccccCCCCCCCCCccccCCCCccEEEEEehhHHHHHHHHhCCCCCCCCCCccchhhHHhhhhcccccc
Q psy1016 272 HEMKECVGLDAEPNPESVITFGSEVEFIFVRLSVLREYLEKELAMPNLPFPYSFERALDDWVFMCFFVGND 342 (718)
Q Consensus 272 ~~~~~c~~~~~~~~~~~~~~~~~~~~f~ll~IsiLREyL~~E~~~~~l~f~~d~ERiIDDFVfLcflvGND 342 (718)
| .......+..++...+.+.+. + --+.|+.+|+|+|+|
T Consensus 57 -----~-------------~~~~~~~~~~~~~~~i~~~l~--l-------------~~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 57 -----C-------------SSKSEKEVEVIDLDDILKELG--L-------------TREQFIDLCILCGCD 94 (94)
T ss_dssp -----T-------------S-CCESEEEEEEHHHHHHHHT--T-------------SHHHHHHHHHHHHET
T ss_pred -----c-------------ccccccceEEEEHHHHHHHcC--C-------------CHHHHHHHheecCCC
Confidence 0 001234567777766655532 1 124799999999998
No 16
>KOG2519|consensus
Probab=90.85 E-value=6.4 Score=45.08 Aligned_cols=35 Identities=14% Similarity=0.449 Sum_probs=25.9
Q ss_pred hhHHhhhhcccccccCCCCCCccccchhHHHHHHHHH
Q psy1016 329 LDDWVFMCFFVGNDFLPHLPSLEIREGAVDRLVNLYK 365 (718)
Q Consensus 329 IDDFVfLcflvGNDFLPhlPsl~I~egaid~Li~~Yk 365 (718)
+.-||-||+|+|+||.|.+-++ +.+..=.|++.|+
T Consensus 216 ~~~fidL~lLlGCDYc~~I~Gi--g~~~al~lir~~~ 250 (449)
T KOG2519|consen 216 RESFIDLCLLLGCDYCPTIRGI--GPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHHhcCccccccccc--ChHHHHHHHHHhc
Confidence 3468889999999999997654 5544445666665
No 17
>KOG2518|consensus
Probab=84.87 E-value=4.2 Score=47.27 Aligned_cols=91 Identities=18% Similarity=0.232 Sum_probs=52.1
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccc----cCCCCCCCCCCHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPC----THPEDKPAPKDEDE 76 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c----~h~~~~~~~~teee 76 (718)
|||+||.-.+...--.+. +.+ .+.+-|=+|--+-+|.. .+.-.... .| +.
T Consensus 1 MGI~GLlp~~k~~~~~~h------------i~~------------~~g~tvavD~y~WLhrg~~~Ca~el~~~~-pT-~r 54 (556)
T KOG2518|consen 1 MGIQGLLPLLKPALKPIH------------ISE------------YKGKTVAVDGYCWLHRGALACAEKLAKGK-PT-DR 54 (556)
T ss_pred CCcchhHHHHHHHhhhhh------------HHH------------hcCceEEEehhhHHhhhHHhHHHHHhcCC-Ch-HH
Confidence 999999998877322211 111 13456778888888863 32211111 11 22
Q ss_pred HHHHHHHHHHHHH-hhhccceeEEEEecCCCcchhhHHHHHHhhhh
Q psy1016 77 MMVAIFECIDRLF-RIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRA 121 (718)
Q Consensus 77 ~f~~If~yId~L~-~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrs 121 (718)
-+.-..+++..|. .-|+| +|.+||=+=-+|--+-|.||-+.
T Consensus 55 yi~y~ik~v~lL~~~gikP----ilVFDG~~LP~K~~te~~Rr~~R 96 (556)
T KOG2518|consen 55 YIQFFIKRVKLLLSYGIKP----ILVFDGDPLPSKKETERKRRERR 96 (556)
T ss_pred HHHHHHHHHHHHHhcCCeE----EEEecCCCcccccccchHHHHHH
Confidence 2333334444333 33555 79999988888887777777543
No 18
>PRK05755 DNA polymerase I; Provisional
Probab=82.66 E-value=26 Score=43.55 Aligned_cols=57 Identities=11% Similarity=0.128 Sum_probs=36.8
Q ss_pred eEEEecccccccccCCCCCC---CCCCHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCc
Q psy1016 50 NLYLDMNGIIHPCTHPEDKP---APKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 107 (718)
Q Consensus 50 nLYLDMNgIIH~c~h~~~~~---~~~teee~f~~If~yId~L~~~VrPrKllyiAIDGVAP 107 (718)
-|.||.|.+++.+.|.-... ..-.........++.+-+++...+|..+ .+|+||-.|
T Consensus 4 ~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~-~v~fD~~~~ 63 (880)
T PRK05755 4 LLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHV-AVAFDAKGK 63 (880)
T ss_pred EEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEE-EEEEECCCC
Confidence 36899999999988864111 0111223344556667777778889775 599998433
No 19
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.22 E-value=50 Score=41.33 Aligned_cols=141 Identities=18% Similarity=0.305 Sum_probs=76.0
Q ss_pred EEEecccccccccCCCCC-CCCC---CHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCcchhhHHHHHHhhhhhHHHH
Q psy1016 51 LYLDMNGIIHPCTHPEDK-PAPK---DEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKETA 126 (718)
Q Consensus 51 LYLDMNgIIH~c~h~~~~-~~~~---teee~f~~If~yId~L~~~VrPrKllyiAIDGVAPrAKMnQQRsRRFrsa~e~~ 126 (718)
+.||-|++||.+.|.-.. +... .......-.++.+-+++...+|..+ .+|+||-.|- =|..-|-..|.
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i-~v~FD~~~~t-----fR~~~~~~YKa-- 73 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYV-AVAFDSGTPT-----FRHEAYAEYKA-- 73 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEE-EEEEcCCCCc-----chHHHHHHHHh--
Confidence 569999999998876421 1100 1112333455556666667789875 6999986542 12111211111
Q ss_pred HHHHHHHHHHHHHHhcCCCCCCccccCCCCccccccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEcCCCCCC-ch
Q psy1016 127 EKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMARLSACLHYYIHDRLNNDPGWKGIKVILSDANVPG-EG 205 (718)
Q Consensus 127 ~~~~~~~~~~~~l~~~g~~~p~~~~~~~~fDSN~ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~VIlSds~VPG-EG 205 (718)
+-...| +.|..++ .+|++-+.. - ++.++ .+|| |+
T Consensus 74 ---------------~R~~~P---------------------e~l~~Q~-~~i~~~l~~-~---gi~~i----~~~g~EA 108 (887)
T TIGR00593 74 ---------------NRAPTP---------------------EELIEQI-PLIKELLDA-L---GIPIL----EVEGYEA 108 (887)
T ss_pred ---------------CCCCCh---------------------HHHHHHH-HHHHHHHHH-C---CCcEE----eeCCccH
Confidence 101111 1223333 234443322 2 23344 3589 99
Q ss_pred hhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHHhhhcCCCcEEEec
Q psy1016 206 EHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIMLGLATHEPNFTIIR 253 (718)
Q Consensus 206 EHKImdfIR~~r~~p~ydpNt~HcIYGlDADLImL~LatHe~~f~ILR 253 (718)
+==|--..++.... ....+|++.|-|+.-|. .+|+.++.
T Consensus 109 DDiIatla~~~~~~-----g~~v~IvS~DkDllQLv----~~~v~~~~ 147 (887)
T TIGR00593 109 DDVIATLAKQAEKE-----GYEVRIISGDKDLLQLV----SDNVKVLI 147 (887)
T ss_pred HHHHHHHHHHHHhC-----CCcEEEEECCCChhhcC----CCCEEEEe
Confidence 98777776665432 23579999999997663 34677653
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=73.92 E-value=4.6 Score=50.70 Aligned_cols=39 Identities=23% Similarity=0.279 Sum_probs=29.5
Q ss_pred ccEEEEcCCCCCCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHHhh
Q psy1016 191 GIKVILSDANVPGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIMLGL 242 (718)
Q Consensus 191 ~l~VIlSds~VPGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLImL~L 242 (718)
++.+|.+ |||||.=+-...+. .....|++-|+|+++.|=
T Consensus 785 GIP~i~A----P~EAEAqcA~L~~~---------G~vd~V~TeDsD~llFGa 823 (1034)
T TIGR00600 785 GIPYIVA----PMEAEAQCAILDLL---------DQTSGTITDDSDIWLFGA 823 (1034)
T ss_pred CCCeeeC----CccHHHHHHHHHhC---------CCeEEEEccccceeccCC
Confidence 4556654 89999988776443 357899999999997763
No 21
>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=69.37 E-value=23 Score=44.76 Aligned_cols=90 Identities=24% Similarity=0.399 Sum_probs=50.1
Q ss_pred CcchhHHHHHHHhCCCceecccccCCcccCCccccCCCCCCCCCCcccceEEEecccccccccC---CCCCCCCCCHHHH
Q psy1016 1 MGVPAFFRWLSRKYPSVIVHCVEDKPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTH---PEDKPAPKDEDEM 77 (718)
Q Consensus 1 MGVP~FfrWL~~rYP~iv~~~~e~~~~~~~g~~ip~d~s~pnpn~~efDnLYLDMNgIIH~c~h---~~~~~~~~teee~ 77 (718)
|||.|++.+|...--.+- + ....|. -|=||...-||.+.. ........+ ..+
T Consensus 1 MGI~GLw~ll~~~~r~v~---l----e~l~Gk-----------------~vAIDasiWL~q~l~~vr~~~g~~l~n-~hl 55 (1034)
T TIGR00600 1 MGVQGLWKLLECSGRPVS---P----ETLEGK-----------------RLAVDISIWLNQALKGVRDREGNAIKN-SHL 55 (1034)
T ss_pred CChhHHHHHHHHhccccc---H----HHhCCe-----------------EEEechHHHHHHHHHHHHhccCCccCC-HHH
Confidence 999999999953211110 1 112333 456788888886532 111111122 222
Q ss_pred HHHHHHHHHHHH-hhhccceeEEEEecCCCcchhhHHHHHHhhh
Q psy1016 78 MVAIFECIDRLF-RIVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (718)
Q Consensus 78 f~~If~yId~L~-~~VrPrKllyiAIDGVAPrAKMnQQRsRRFr 120 (718)
..+|..|.+|+ .-|+| ++.+||.+|-.|...-..||-+
T Consensus 56 -~g~f~Ri~~Ll~~gI~P----VfVFDG~~p~lK~~t~~~R~~r 94 (1034)
T TIGR00600 56 -LTLFHRLCKLLFFRIRP----IFVFDGGAPLLKRQTLAKRRQR 94 (1034)
T ss_pred -HHHHHHHHHHHHCCCeE----EEEECCCCchHhHHHHHHHHHH
Confidence 34445455543 45565 6789999999888765444433
No 22
>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=60.54 E-value=8.1 Score=33.57 Aligned_cols=33 Identities=21% Similarity=0.552 Sum_probs=24.7
Q ss_pred hHHhhhhcccc--cccCCCCCCccccchhHHHHHHHH
Q psy1016 330 DDWVFMCFFVG--NDFLPHLPSLEIREGAVDRLVNLY 364 (718)
Q Consensus 330 DDFVfLcflvG--NDFLPhlPsl~I~egaid~Li~~Y 364 (718)
+-|+-+|.|+| .|++|.+|++ ..-....|+..|
T Consensus 8 ~q~~d~~~L~GD~~D~i~gv~gi--G~k~A~~ll~~~ 42 (75)
T cd00080 8 EQFIDLAILVGDKSDNIPGVPGI--GPKTALKLLKEY 42 (75)
T ss_pred HHHHHHHHHcCCccccCCCCCcc--cHHHHHHHHHHh
Confidence 56788999999 9999999985 554444455554
No 23
>PF00098 zf-CCHC: Zinc knuckle; InterPro: IPR001878 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the CysCysHisCys (CCHC) type zinc finger domains, and have the sequence: C-X2-C-X4-H-X4-C where X can be any amino acid, and number indicates the number of residues. These 18 residues CCHC zinc finger domains are mainly found in the nucleocapsid protein of retroviruses. It is required for viral genome packaging and for early infection process [, , ]. It is also found in eukaryotic proteins involved in RNA binding or single-stranded DNA binding []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 2L44_A 1A1T_A 1WWG_A 1U6P_A 1WWD_A 1WWE_A 1A6B_B 1F6U_A 1MFS_A 1NCP_C ....
Probab=54.15 E-value=9.6 Score=24.77 Aligned_cols=16 Identities=38% Similarity=0.955 Sum_probs=14.1
Q ss_pred CCcccccCCccccccc
Q psy1016 263 PCDVCGQMGHEMKECV 278 (718)
Q Consensus 263 ~~~~c~q~g~~~~~c~ 278 (718)
.|..||+.||...+|.
T Consensus 2 ~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 2 KCFNCGEPGHIARDCP 17 (18)
T ss_dssp BCTTTSCSSSCGCTSS
T ss_pred cCcCCCCcCcccccCc
Confidence 5889999999998885
No 24
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=47.72 E-value=11 Score=32.80 Aligned_cols=33 Identities=21% Similarity=0.368 Sum_probs=26.9
Q ss_pred CCchhhHHHHHHHHhhcCCCCCCCCcEEEEcCChhHHHHhhh
Q psy1016 202 PGEGEHKIMDYIRKQRAQPDHDPNTQHCLCGADADLIMLGLA 243 (718)
Q Consensus 202 PGEGEHKImdfIR~~r~~p~ydpNt~HcIYGlDADLImL~La 243 (718)
|||+|.-.--.-++ ..-+.|+|.|+|+++.|--
T Consensus 11 P~eAeAq~A~L~~~---------g~vdav~s~D~D~llfG~~ 43 (73)
T smart00484 11 PYEAEAQCAYLAKS---------GLVDAIITEDSDLLLFGAP 43 (73)
T ss_pred CCcHHHHHHHHHhC---------CCeeEEEcCccceEecCCc
Confidence 99999988777663 3578999999999998754
No 25
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=47.42 E-value=63 Score=32.28 Aligned_cols=56 Identities=18% Similarity=0.333 Sum_probs=39.3
Q ss_pred EEEecccccccccCCCCC-CCCCC---HHHHHHHHHHHHHHHHhhhccceeEEEEecCCCc
Q psy1016 51 LYLDMNGIIHPCTHPEDK-PAPKD---EDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 107 (718)
Q Consensus 51 LYLDMNgIIH~c~h~~~~-~~~~t---eee~f~~If~yId~L~~~VrPrKllyiAIDGVAP 107 (718)
|.||.|+++|.+.|.-.. +...+ .-......++.|.+++...+|..+ .+|+|+-+|
T Consensus 4 lLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~-vv~fD~~~~ 63 (169)
T PF02739_consen 4 LLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYV-VVAFDSKGP 63 (169)
T ss_dssp EEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEE-EEEEEBSSC
T ss_pred EEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceE-EEEecCCCc
Confidence 789999999999986431 11111 123445567777788888889874 599999987
No 26
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=34.33 E-value=1e+02 Score=33.44 Aligned_cols=65 Identities=20% Similarity=0.374 Sum_probs=44.6
Q ss_pred eEEEecccccccccCCCCCC---CCCCHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCc--chhhHHHH
Q psy1016 50 NLYLDMNGIIHPCTHPEDKP---APKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP--RAKMNQQR 115 (718)
Q Consensus 50 nLYLDMNgIIH~c~h~~~~~---~~~teee~f~~If~yId~L~~~VrPrKllyiAIDGVAP--rAKMnQQR 115 (718)
-+-||-+++++.+.|....+ ...........+...+.++++..+|.+. .+++||-+| |.++...|
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~-~~vFD~~~~tfR~~~~~~y 82 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHP-VVVFDGKPPTFRHELLEEY 82 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCCCcE-EEEEcCCCCcchHHHHHHH
Confidence 68899999999998864211 0011111556778889999999999664 699999666 44444443
No 27
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=33.98 E-value=26 Score=26.59 Aligned_cols=20 Identities=20% Similarity=0.594 Sum_probs=15.9
Q ss_pred hHHhhhhcccccccCCCCCCc
Q psy1016 330 DDWVFMCFFVGNDFLPHLPSL 350 (718)
Q Consensus 330 DDFVfLcflvGNDFLPhlPsl 350 (718)
+-|+-+|.|+| |+.+.+|++
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 999966654
No 28
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=31.57 E-value=19 Score=27.05 Aligned_cols=19 Identities=37% Similarity=0.873 Sum_probs=16.3
Q ss_pred CCCCcccccCCcccccccC
Q psy1016 261 ARPCDVCGQMGHEMKECVG 279 (718)
Q Consensus 261 ~~~~~~c~q~g~~~~~c~~ 279 (718)
...|.+|++.||...+|-.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 3579999999999999965
No 29
>PHA02567 rnh RnaseH; Provisional
Probab=31.30 E-value=59 Score=35.87 Aligned_cols=58 Identities=16% Similarity=0.139 Sum_probs=43.0
Q ss_pred cceEEEecccccccccCCCCCCC-CCCHHHHHHHHHHHHHHHHhhhccce-eEEEEecCC
Q psy1016 48 FDNLYLDMNGIIHPCTHPEDKPA-PKDEDEMMVAIFECIDRLFRIVRPRK-LLYMAIDGV 105 (718)
Q Consensus 48 fDnLYLDMNgIIH~c~h~~~~~~-~~teee~f~~If~yId~L~~~VrPrK-llyiAIDGV 105 (718)
-+-+.||++.|+..|.+.+-.+. ..++..+...+++.|..++..++|.- -+.+|+|+-
T Consensus 14 ~~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~ 73 (304)
T PHA02567 14 EGVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNS 73 (304)
T ss_pred CCEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence 45799999999999999865444 23444444558889999988877762 167999974
No 30
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=25.57 E-value=89 Score=24.87 Aligned_cols=66 Identities=14% Similarity=0.241 Sum_probs=43.4
Q ss_pred CCccEEEEcCCCCCCchhhHHHHHHHHhhcC--CCCCC-CCcEEEEcCChhHHHHhhhcCCCcEEEeccc
Q psy1016 189 WKGIKVILSDANVPGEGEHKIMDYIRKQRAQ--PDHDP-NTQHCLCGADADLIMLGLATHEPNFTIIREE 255 (718)
Q Consensus 189 W~~l~VIlSds~VPGEGEHKImdfIR~~r~~--p~ydp-Nt~HcIYGlDADLImL~LatHe~~f~ILRE~ 255 (718)
.+++.+.++| +.+++-=..+-+.|+..-.. ...++ ..+|+|.+....--.--......++.|++++
T Consensus 3 f~g~~~~~~g-~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~ 71 (80)
T smart00292 3 FKGKVFVITG-KFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTED 71 (80)
T ss_pred cCCeEEEEeC-CCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHH
Confidence 5678899998 66777778888888886554 45566 7899999876654321122223445555543
No 31
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=21.89 E-value=2.3e+02 Score=29.14 Aligned_cols=89 Identities=31% Similarity=0.499 Sum_probs=50.0
Q ss_pred ccCCcHHHHHHHHHHHHHHHHHHhcCCCCCccE--EEEcCC----------------CCCCchh----hHHHHHHHHhhc
Q psy1016 161 ITPGTPFMARLSACLHYYIHDRLNNDPGWKGIK--VILSDA----------------NVPGEGE----HKIMDYIRKQRA 218 (718)
Q Consensus 161 ITPGT~FM~kL~~~L~~yI~~kl~~dp~W~~l~--VIlSds----------------~VPGEGE----HKImdfIR~~r~ 218 (718)
|.=||-|+.|+-.+|.. +.--+. +..-+++| +++||. .--||+| -||+--||...-
T Consensus 79 iaGgtN~iSR~iAaliE-lNW~~d-~eE~kGlKKFflLS~R~r~LiiKHKVrNe~v~~Wf~EeEvyGmpKi~~iika~tL 156 (200)
T PF12387_consen 79 IAGGTNFISRLIAALIE-LNWAMD-EEESKGLKKFFLLSGRVRNLIIKHKVRNETVASWFGEEEVYGMPKIITIIKAATL 156 (200)
T ss_pred HcCcchHHHHHHHHHHH-hhcccc-chhhcCcceeeeehhHHHHHHHHhHhhhHHHHHHcccccccCcchhhhhhhHHhc
Confidence 56789999998888775 222222 22234543 445542 1135544 477777776543
Q ss_pred CCCCCCCCcEEEEcCChhHHHHhhhcCCCcEEEeccccCCCCCCCCcccccCCcccc
Q psy1016 219 QPDHDPNTQHCLCGADADLIMLGLATHEPNFTIIREEFKPNQARPCDVCGQMGHEMK 275 (718)
Q Consensus 219 ~p~ydpNt~HcIYGlDADLImL~LatHe~~f~ILRE~~~~~~~~~~~~c~q~g~~~~ 275 (718)
+ ..+|||.. | ++-=|++ +...|+.||+.|...+
T Consensus 157 s-----k~~hcilC-----------t----vCe~r~w----~g~~CPKCGr~G~pi~ 189 (200)
T PF12387_consen 157 S-----KSKHCILC-----------T----VCEGREW----KGGNCPKCGRHGKPIT 189 (200)
T ss_pred c-----CCCceEEE-----------e----eeecCcc----CCCCCCcccCCCCCee
Confidence 2 35677632 1 2223443 4457999999888653
No 32
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=20.66 E-value=1.9e+02 Score=22.26 Aligned_cols=47 Identities=21% Similarity=0.420 Sum_probs=34.3
Q ss_pred ccEEEEcCCCCCCchhhHHHHHHHHhhcC--CCCCCCCcEEEEcCChhHH
Q psy1016 191 GIKVILSDANVPGEGEHKIMDYIRKQRAQ--PDHDPNTQHCLCGADADLI 238 (718)
Q Consensus 191 ~l~VIlSds~VPGEGEHKImdfIR~~r~~--p~ydpNt~HcIYGlDADLI 238 (718)
++.|.++|.. +|+-...+-+.|+..-.. ...++.++|||.+-..+--
T Consensus 1 ~~~~~i~g~~-~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~ 49 (72)
T cd00027 1 GLTFVITGDL-PSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPK 49 (72)
T ss_pred CCEEEEEecC-CCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCch
Confidence 3567888763 388888888999886553 3555689999999776643
No 33
>PRK09482 flap endonuclease-like protein; Provisional
Probab=20.26 E-value=1.7e+02 Score=31.50 Aligned_cols=55 Identities=22% Similarity=0.314 Sum_probs=38.6
Q ss_pred eEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHhhhccceeEEEEecCCCc
Q psy1016 50 NLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 107 (718)
Q Consensus 50 nLYLDMNgIIH~c~h~~~~~~~~teee~f~~If~yId~L~~~VrPrKllyiAIDGVAP 107 (718)
=|.||-+++||-.+|.... +..........++.+.+|+...+|+.+ .+|+||-++
T Consensus 5 llLiDg~~l~~R~~~a~~~--~~g~t~av~gf~~~l~~ll~~~~p~~i-~v~fD~~~~ 59 (256)
T PRK09482 5 LLIIDALNLIRRIHAVQPS--PNDINACVETCQHALDKLIRHSQPTHA-VAVFDGDAR 59 (256)
T ss_pred EEEEeCcHHHHHHHhCCCC--CCCcchHHHHHHHHHHHHHHHcCCCEE-EEEEeCCCC
Confidence 4789999999998776321 111234445566777778888899886 599999655
Done!