Query 003880
Match_columns 789
No_of_seqs 240 out of 557
Neff 5.7
Searched_HMMs 46136
Date Thu Mar 28 13:39:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003880.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003880hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2044 5'-3' exonuclease HKE1 100.0 2E-260 5E-265 2157.6 51.3 737 1-787 1-737 (931)
2 COG5049 XRN1 5'-3' exonuclease 100.0 2E-217 4E-222 1787.1 46.0 723 1-778 1-764 (953)
3 KOG2045 5'-3' exonuclease XRN1 100.0 2E-187 4E-192 1569.3 38.3 640 1-719 1-655 (1493)
4 PF03159 XRN_N: XRN 5'-3' exon 100.0 4.5E-87 9.8E-92 693.9 17.1 237 1-255 1-237 (237)
5 cd00128 XPG Xeroderma pigmento 98.6 4.7E-07 1E-11 99.1 13.5 231 1-357 1-234 (316)
6 PTZ00217 flap endonuclease-1; 98.2 9.6E-06 2.1E-10 91.5 13.1 233 1-357 1-246 (393)
7 PRK03980 flap endonuclease-1; 97.4 0.0032 7E-08 68.7 15.2 62 334-395 177-259 (292)
8 TIGR03674 fen_arch flap struct 97.1 0.0081 1.7E-07 66.9 14.1 67 50-120 23-97 (338)
9 smart00475 53EXOc 5'-3' exonuc 95.8 0.46 1E-05 51.2 17.5 56 51-107 4-61 (259)
10 PF00752 XPG_N: XPG N-terminal 94.9 0.021 4.5E-07 52.2 3.2 95 1-121 1-98 (101)
11 smart00485 XPGN Xeroderma pigm 94.9 0.025 5.3E-07 51.6 3.4 93 1-121 1-96 (99)
12 cd00008 53EXOc 5'-3' exonuclea 94.4 2.4 5.3E-05 45.1 17.7 57 50-107 3-62 (240)
13 PRK14976 5'-3' exonuclease; Pr 93.7 1.8 3.9E-05 47.3 15.3 57 50-107 5-67 (281)
14 PF00867 XPG_I: XPG I-region; 92.4 0.31 6.8E-06 44.2 6.1 90 191-346 5-94 (94)
15 PF00098 zf-CCHC: Zinc knuckle 92.3 0.08 1.7E-06 34.1 1.4 17 262-278 1-17 (18)
16 KOG2519 5'-3' exonuclease [Rep 89.9 6.9 0.00015 45.1 14.6 34 334-369 217-250 (449)
17 PRK05755 DNA polymerase I; Pro 88.7 9.6 0.00021 48.0 16.3 56 50-106 4-62 (880)
18 KOG2518 5'-3' exonuclease [Rep 88.6 1.8 3.9E-05 50.4 9.0 92 1-122 1-97 (556)
19 COG0258 Exo 5'-3' exonuclease 86.5 42 0.00092 37.0 18.0 62 50-115 13-82 (310)
20 PF13696 zf-CCHC_2: Zinc knuck 80.1 0.71 1.5E-05 34.2 0.6 18 262-279 9-26 (32)
21 TIGR00593 pola DNA polymerase 78.6 64 0.0014 41.0 17.2 56 51-107 2-61 (887)
22 TIGR00600 rad2 DNA excision re 68.6 5.8 0.00012 50.4 4.7 40 190-242 785-824 (1034)
23 TIGR00600 rad2 DNA excision re 66.9 19 0.00041 46.0 8.7 89 1-120 1-94 (1034)
24 cd00080 HhH2_motif Helix-hairp 60.0 9.3 0.0002 33.4 3.1 22 334-355 8-31 (75)
25 PF13917 zf-CCHC_3: Zinc knuck 46.2 11 0.00024 29.7 1.2 19 261-279 4-22 (42)
26 smart00343 ZnF_C2HC zinc finge 45.6 10 0.00022 26.2 0.9 16 263-278 1-16 (26)
27 PF15288 zf-CCHC_6: Zinc knuck 44.9 11 0.00024 29.5 1.0 15 262-276 2-16 (40)
28 smart00279 HhH2 Helix-hairpin- 42.9 19 0.00042 27.3 2.1 20 334-354 2-21 (36)
29 smart00484 XPGI Xeroderma pigm 40.1 15 0.00032 32.3 1.2 34 200-242 10-43 (73)
30 PF02739 5_3_exonuc_N: 5'-3' e 36.4 32 0.00069 34.8 3.1 56 51-107 4-63 (169)
31 COG1515 Nfi Deoxyinosine 3'end 30.8 21 0.00046 37.5 0.8 15 47-61 95-109 (212)
32 COG5082 AIR1 Arginine methyltr 29.3 26 0.00056 36.3 1.1 18 261-278 60-77 (190)
33 PF14392 zf-CCHC_4: Zinc knuck 28.9 25 0.00055 28.2 0.8 20 259-278 29-48 (49)
34 COG5082 AIR1 Arginine methyltr 26.5 29 0.00063 35.9 0.9 47 224-278 68-114 (190)
35 COG5350 Predicted protein tyro 23.0 88 0.0019 31.6 3.4 42 189-233 56-105 (172)
36 PHA02567 rnh RnaseH; Provision 20.7 1.2E+02 0.0026 33.8 4.3 58 48-105 14-73 (304)
No 1
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=100.00 E-value=2.4e-260 Score=2157.65 Aligned_cols=737 Identities=62% Similarity=1.037 Sum_probs=663.7
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQC 80 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~~p~t~~e~~~~ 80 (789)
||||+|||||++|||++|++|+|++|+++||+.||+|.|+|||||+||||||||||||||||+|||++|+|+||+|||.+
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 HHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccCcc
Q 003880 81 MFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSNVI 160 (789)
Q Consensus 81 if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~fDsn~I 160 (789)
||+||||||.||||||||||||||||||||||||||||||||+|+.++++++++++++++++|..||++.++++||||||
T Consensus 81 vFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fDSNcI 160 (931)
T KOG2044|consen 81 VFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFDSNCI 160 (931)
T ss_pred HHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhccccccCcc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 003880 161 TPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLA 240 (789)
Q Consensus 161 TPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~ 240 (789)
||||+||++|+.+|+|||+.||++||+|+||+||+|||+||||||||||+|||+||++|+|||||+|||||+||||||||
T Consensus 161 TPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLg 240 (931)
T KOG2044|consen 161 TPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLG 240 (931)
T ss_pred CCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceeee
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHhcC
Q 003880 241 LATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRI 320 (789)
Q Consensus 241 Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~~~ 320 (789)
||||||||+||||+|| |+++++|++|||.||.+.+|.|..+ .++.++..+.. ..+++|+|||||+|||||+.||.+
T Consensus 241 LATHE~hF~IlRE~~~-P~~~~~C~~cgq~gh~~~dc~g~~~--~~~~~~~~~~~-~~ek~fifl~I~vLREYLe~El~~ 316 (931)
T KOG2044|consen 241 LATHEPHFSILREEFF-PNKPRRCFLCGQTGHEAKDCEGKPR--LGETNELADVP-GVEKPFIFLNISVLREYLERELRM 316 (931)
T ss_pred ccccCCceEEeeeeec-CCCcccchhhcccCCcHhhcCCcCC--cccccccccCc-ccccceEEEEHHHHHHHHHHHhcC
Confidence 9999999999999976 9999999999999999999999866 45555554433 678999999999999999999999
Q ss_pred CCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHHHHhh
Q 003880 321 PNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQAVGSY 400 (789)
Q Consensus 321 ~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk~~l~~~~gYLt~~G~inl~rl~~fl~~l~~~ 400 (789)
|++||.||+||+||||||||||||||||||||||+||+||||+|+++||+.+++|+||||++|.+||.||+.||+.||.+
T Consensus 317 p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPsLeIRegAId~L~~iyk~~~~~~kgYLT~~g~vNL~rve~~~~avg~~ 396 (931)
T KOG2044|consen 317 PNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPSLEIREGAIDRLMEIYKKSFPKMKGYLTDSGKVNLDRVEMFMQAVGSV 396 (931)
T ss_pred CCCCccccHHhhhcceEEEEeeecCccCCCCCchhhhhcHHHHHHHHHHHHHHhhcceeccCCcccHHHHHHHHHHHhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccccCCCCCCCCCCCccccccccccccCCCCCCCCC
Q 003880 401 EDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPSPSPYQQSECVGRLDNGKGTSGRP 480 (789)
Q Consensus 401 E~~iF~~r~~~~~r~~e~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 480 (789)
||+||++|. |++|+++|+|+..++.+..+ +++| .+.+...+.... .+...
T Consensus 397 Ed~IFkkR~----r~~e~frrrk~~rk~~~~~~------------~~sg-~~~~~~~~~~~~-------------~~~p~ 446 (931)
T KOG2044|consen 397 EDDIFKKRQ----RREERFRRRKAARKRQDRNA------------QDSG-TNFSLAGSRELE-------------ASEPA 446 (931)
T ss_pred cchHHHHhH----hHHHHHHHhhhhhhhhhhhc------------cccc-cccccccccccc-------------ccchh
Confidence 999999994 45566665544322221111 1111 111111111000 12233
Q ss_pred CCccccCCCcchhhHHHhhhcCCCCCCcccHHHHHHHHHHHHhhhcccCCCCCcchhhcccCCCchhHHHHHHhcCCCCh
Q 003880 481 HKVPRLSSGATIGAAIVEAENSFETDPQENKEEFKAKLKELLRDKSDAFNSDNPEEDKVKLGEPGWKERYYEEKFNAKTP 560 (789)
Q Consensus 481 ~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~v~l~e~g~k~rYY~~Kf~~~~~ 560 (789)
+++.+++...+.++++++ .++.++++.+++...+++++.+.++....|+|+|||+|||+|||++||++++.
T Consensus 447 ~~~~~~~~~~~~~~~~~~---------~~~~e~~~~~~~~~~~~k~~~~~~~~~~~D~VkL~e~G~keRYY~~KF~v~~~ 517 (931)
T KOG2044|consen 447 QKALKVSLEKNESAANVE---------RDNTEDLKTKLKHGQRRKSEDSESEEENTDKVKLYEPGWKERYYEEKFDVTPD 517 (931)
T ss_pred hhhhhhccccccchhhhc---------ccchhhccccccccccccCccccCCCCCCcceeecCCchhhhhhhhhcCCCCH
Confidence 445555555566666552 23456677777777788888888888999999999999999999999999876
Q ss_pred hHHHHHHHHHHHHHHhHHHHHhhhhhcCcccccccccCCCCccccccccccCccccccCCCCCChhhhhhhcCCCCCCCC
Q 003880 561 EEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHA 640 (789)
Q Consensus 561 ~~~~~~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPyHYAPfasDl~~l~~~~i~F~~g~Pf~PfeQLm~VLP~~S~~~ 640 (789)
+ +++|++||.+|||||||||+||||||+||+||||||||||||||++|..++|+|++|+||+||||||+||||||+|+
T Consensus 518 e--eq~R~~vv~~YveGLcWVl~YYyqGc~SW~WyYPYHYAPfAsDf~~l~~ldikFe~g~PFkP~eQLmgVlPAAS~~~ 595 (931)
T KOG2044|consen 518 E--EQIRKDVVLKYVEGLCWVLRYYYQGCASWNWYYPYHYAPFASDFKGLSDLDIKFELGKPFKPLEQLMGVLPAASSHA 595 (931)
T ss_pred H--HHHHHHHHHHHhcchhhhhhhhhccccccccccccccchhhhhhhcccccccccccCCCCCcHHHHhhhcchhhcCC
Confidence 6 78999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCChHHHHHHHhhccCCCCHHHHhhccCCCceEEEecC
Q 003880 641 LPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLS 720 (789)
Q Consensus 641 LP~~~~~LM~d~~SpI~dfYP~~F~iD~nGkk~~WqgV~lLPFIDe~rLl~a~~~~~~~Lt~eE~~RN~~g~~~lf~~~~ 720 (789)
||+.||.||+||+|||+||||+||+||||||||+||||||||||||+|||+|++++|++||+||++||+.|.|+|||+++
T Consensus 596 LPe~~r~LMsdpdSpIiDFYPedF~iDmNGKk~aWQGIalLPFiDe~rLl~a~~~~y~~Lt~EE~~RN~rg~d~Lfi~~~ 675 (931)
T KOG2044|consen 596 LPEEWRKLMSDPDSPIIDFYPEDFEIDMNGKKYAWQGIALLPFIDERRLLSAVAKVYPTLTDEEKRRNSRGPDLLFISDK 675 (931)
T ss_pred CcHHHHhhhcCCCCcccccccccceeeccCceeeccccccccccchhhHHHHHHhhccccCHHHHhccccCCceEEecCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcchhhhhhhhhhhhhchhhhhhhccccCCCCCCCcceeeecCCCCCCCCccccCCCCCCCCCCCc
Q 003880 721 HPLSASIYTLDEHCKQLKIKERVEVKERLNPELSDGMNGYISPCAGDPHPPVFRSPVASMEDIMGNQ 787 (789)
Q Consensus 721 ~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~g~~g~v~~~~~~~~~~~~~~p~~~~~~i~~~~ 787 (789)
||+++++.+||..+++ ...++ +.+-..++.|++|.+++++.....+.+++|+.++.+...+.
T Consensus 676 hp~~e~i~~lysk~k~-~~~~~----v~~~~~~~p~~~~~~~~~~~~~~~~i~~~p~~~~~~~~~~~ 737 (931)
T KOG2044|consen 676 HPLFEFILQLYSKKKK-SNEKN----VKLAHGVDPGLNGAISKDPEGLESGISKSPPGGLSDYNTNT 737 (931)
T ss_pred CchHHHHHHHHHhhcc-Ccccc----cccccccCcccceeeccCccccccccccCChhhcccCCccc
Confidence 9999999999887765 22221 24555567799999999887766677888888777666554
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=2e-217 Score=1787.12 Aligned_cols=723 Identities=45% Similarity=0.819 Sum_probs=575.9
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQC 80 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~~p~t~~e~~~~ 80 (789)
||||+|||||++|||+|++.+.|+ +|| ++||||||||||||+|+||+++++|.||+||+..
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 999999999999999999987653 345 4699999999999999999999999999999999
Q ss_pred HHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHh----CCCCCCC-CCCCCC
Q 003880 81 MFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFERE----GRKLPPK-SDSQVF 155 (789)
Q Consensus 81 if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~----g~~~~~~-~~~~~f 155 (789)
||+|||||+.++|||||||||||||||||||||||+||||+|+||..++.+.+.-.+++..+ |..+... ..++.|
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 99999999999999999999999999999999999999999999777654444223333222 2222211 245789
Q ss_pred ccCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChh
Q 003880 156 DSNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDAD 235 (789)
Q Consensus 156 Dsn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DAD 235 (789)
|||||||||+||++|+..|+|||+.||++||.|+|++||+||+.||||||||||+|||+||++|+|+|||+|||||+|||
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 HHHHHhhcCCceEEEeecccccCCC---CccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHH
Q 003880 236 LIMLALATHEVHFSILREVVFTPGQ---QDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLRE 312 (789)
Q Consensus 236 LImL~Lathe~~f~ILRE~v~~~~~---~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LRe 312 (789)
||||||+||+|||.||||+|||+.. +++|..||.+||....|. ....++|.||||++|||
T Consensus 222 LImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k-----------------~~~~q~F~~LhiSlLRE 284 (953)
T COG5049 222 LIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECK-----------------VLTHQPFYLLHISLLRE 284 (953)
T ss_pred ceeeecccCCCeeEEeechhccCcccccccccccccccccchhhhc-----------------ccccCceEEEEHHHHHH
Confidence 9999999999999999999999853 468999999999888883 23457899999999999
Q ss_pred HHHHHhcCCCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHH
Q 003880 313 YLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEH 392 (789)
Q Consensus 313 yL~~e~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk~~l~~~~gYLt~~G~inl~rl~~ 392 (789)
||+.||..+++||.||+|||||||||||||||||||||||+|+|++|||++|+++||+.||.||||||++|.|||.||+.
T Consensus 285 YLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ldir~gai~~l~ei~k~~lp~~~gYit~~G~iNl~rle~ 364 (953)
T COG5049 285 YLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLDIREGAIETLTEIWKKSLPHMKGYITCDGVINLARLEV 364 (953)
T ss_pred HHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccccccchHHHHHHHHHHHhhhcCceeecCceecHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhc--CCCCCCC---CCCCCCccccc-----ccCCCCCCCCCCCccc
Q 003880 393 FIQAVGSYEDRIFQKRARLHQRHAERIKREKAQARR--GDDVEPL---AQPDSLVPVSR-----FHGSRLASGPSPSPYQ 462 (789)
Q Consensus 393 fl~~l~~~E~~iF~~r~~~~~r~~e~~k~~k~~~~~--~~~~~~~---~~~~~~~~~~~-----~~~~~l~~~~~~~~~~ 462 (789)
||..||.+|+.||+++..++.|..+...+.++++.+ +.+..+. .|...+..... +...+....+.+ ++.
T Consensus 365 ~L~~L~~~E~~iFk~~~~qe~r~ne~~~~~~~~k~~~e~~~~~~~vv~eq~~~~gS~k~t~~d~~~~kk~~~l~~e-~~i 443 (953)
T COG5049 365 ILAILGSFEDDIFKKDHIQEERKNESLERFSLRKERKEGLKGMPRVVYEQKKLIGSIKPTLMDQLQEKKSPDLPDE-EFI 443 (953)
T ss_pred HHHHHhhhhcchhhhhhhHhhhhccchhhHHHHhhhhhhhcccchhhhhhhhhcccccchhhhhhhhhccccCCCc-ccc
Confidence 999999999999999998888877766655444321 1111111 11000000000 000000000000 000
Q ss_pred cccccccccCCCCCCCCCCC----cc-ccCCCcchhhHHHhhhc---------CC-CCCCcccHHHHHH--H-HHHHHhh
Q 003880 463 QSECVGRLDNGKGTSGRPHK----VP-RLSSGATIGAAIVEAEN---------SF-ETDPQENKEEFKA--K-LKELLRD 524 (789)
Q Consensus 463 ~~~~~~~~~~~~~~~~~~~k----~~-~~~~~~~~~~~~~~~~~---------~~-~~~~~~~~~~~~~--~-~~~~~~~ 524 (789)
..... ......| .. +++ ..++.++..+.. .. .....+.+++.+. . ..++.+.
T Consensus 444 d~~a~--------~k~~d~kn~el~~~~~~--ndl~ls~ska~ks~~n~~le~~iasds~~ed~ee~ese~d~i~~i~dk 513 (953)
T COG5049 444 DTLAL--------PKDLDMKNHELFLKRFA--NDLGLSISKAIKSKGNYSLEMDIASDSPDEDEEEFESEVDSIRKIPDK 513 (953)
T ss_pred chhhc--------hhhhhhhhhHHHHHHHH--hhhhhhHHhhhhccCCchhhhhhhccccccchhhhhhccchhhhhhhh
Confidence 00000 0000000 00 000 000111111100 00 0001111111110 0 0111111
Q ss_pred hcc---cCCCCCcchhhcccCCCchhHHHHHHhcCCCChhHHHHHHHHHHHHHHhHHHHHhhhhhcCcccccccccCCCC
Q 003880 525 KSD---AFNSDNPEEDKVKLGEPGWKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYA 601 (789)
Q Consensus 525 ~~~---~~~~~~~~~d~v~l~e~g~k~rYY~~Kf~~~~~~~~~~~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPyHYA 601 (789)
... ....++..+++|++.++|||+|||.+|||+++ ++.+++| ++|++|||||||||.|||||||||+||||||||
T Consensus 514 ~vn~~v~ee~e~~~~~Tv~l~~~g~~erYY~~K~~~t~-~~~E~ir-dm~k~YVeGL~WVL~YYY~GC~SW~WyYpyHyA 591 (953)
T COG5049 514 YVNIIVEEEEENETEKTVNLRFPGWKERYYTSKLHFTT-DSEEKIR-DMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYA 591 (953)
T ss_pred hhccccccchhcccccchhhcccchhhhhhhhhcCCCc-CCHHHHH-HHHHHHhhhhhhhhhhhhcCCCCcccccccccc
Confidence 111 11123455789999999999999999999975 4456665 899999999999999999999999999999999
Q ss_pred ccccccccccCccccccCCCCCChhhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeec
Q 003880 602 PFASDLKDLDQFNISFELGHPFKPFNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKL 681 (789)
Q Consensus 602 PfasDl~~l~~~~i~F~~g~Pf~PfeQLm~VLP~~S~~~LP~~~~~LM~d~~SpI~dfYP~~F~iD~nGkk~~WqgV~lL 681 (789)
|+|+||.++...+|+|+.|+||+||||||+||||+|+++||+.||+||+|++|||+||||++|.+|||||+++|||||||
T Consensus 592 P~aaD~~k~~~~dIkFe~g~PF~P~EQLm~VLPa~Sk~~vP~~fr~LM~d~~S~IiDFYPe~f~lD~NGK~~~Wq~VvLl 671 (953)
T COG5049 592 PLAADLSKLSDNDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFRPLMDDEKSPIIDFYPEEFKLDMNGKTASWQAVVLL 671 (953)
T ss_pred hhhhhhhhcccceeeecCCCCCCcHHHHHhhcchhhcCcCchhhhhhhcCCCCcccccchhhcccccCCceeeeeeeEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCChHHHHHHHhhccCCCCHHHHhhccCCCceEEEecCCCcchhhhhhhhhhhhhchhhhhhhccccCCCCCC-Cccee
Q 003880 682 PFIDEARLLDEVKKIEHTLTEEEARRNSIMADMLFVLLSHPLSASIYTLDEHCKQLKIKERVEVKERLNPELSD-GMNGY 760 (789)
Q Consensus 682 PFIDe~rLl~a~~~~~~~Lt~eE~~RN~~g~~~lf~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~-g~~g~ 760 (789)
|||||+|||+|+++.+++||+||+.||.+|.++||+++.++-+. ..++++|++......+.++..-+. |+.|.
T Consensus 672 pFiDe~RLl~A~~~~~~~Ls~eE~~RN~~g~~llf~s~~~~~~~------~l~~~lysk~~~~~~~~m~~~~~~~GL~g~ 745 (953)
T COG5049 672 PFIDERRLLSAVAVKYPTLSEEERKRNLRGLDLLFSSNKKSDLS------ELFKDLYSKCKQKEYITMCSKESPYGLFGT 745 (953)
T ss_pred eecchhHHHHHHHhhcccCCHHHHhccccCCceeEeccCCccHH------HHHHHHHHhhccCCceeeeccccccccccc
Confidence 99999999999999999999999999999999999999887432 344455554433334456665554 99999
Q ss_pred eecC-CCCCCCCccccCCC
Q 003880 761 ISPC-AGDPHPPVFRSPVA 778 (789)
Q Consensus 761 v~~~-~~~~~~~~~~~p~~ 778 (789)
|... ++.+|..-..+|+.
T Consensus 746 v~~~ae~~~pn~~~lcp~~ 764 (953)
T COG5049 746 VKLGAEGLAPNLLSLCPIS 764 (953)
T ss_pred cccccccccccccccCccc
Confidence 9885 66666677778885
No 3
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=100.00 E-value=1.8e-187 Score=1569.33 Aligned_cols=640 Identities=44% Similarity=0.779 Sum_probs=502.4
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~--~p~t~~e~~ 78 (789)
||||.||||+|+|||++.+ ++ +|.+|| ||||||||||||||+|+||+|.. .+.||+|||
T Consensus 1 MGvPKFfR~iSERyP~lse-li-------ee~qIP-----------EFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEif 61 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCLSE-LI-------EEHQIP-----------EFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEIF 61 (1493)
T ss_pred CCchHHHHHhhhhchHHHH-Hh-------hhccCC-----------cccceeeecccccccCCCCCCCccCcCCCHHHHH
Confidence 9999999999999998864 44 456787 99999999999999999998753 478999999
Q ss_pred HHHHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccC
Q 003880 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSN 158 (789)
Q Consensus 79 ~~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~fDsn 158 (789)
.+||+|||+||.++||+|++|||||||||||||||||+||||+|++|+.+.. +....|+..|. +.||||
T Consensus 62 ~~IfnYIdhLf~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qla-------KA~enGe~~p~----erFDSN 130 (1493)
T KOG2045|consen 62 QEIFNYIDHLFYLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLA-------KAAENGELRPH----ERFDSN 130 (1493)
T ss_pred HHHHHHHHHHHHhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHH-------HHHhccccCcc----cccccC
Confidence 9999999999999999999999999999999999999999999999876543 23456776663 689999
Q ss_pred cccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHH
Q 003880 159 VITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIM 238 (789)
Q Consensus 159 ~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLIm 238 (789)
||||||+||.+|++.|+|||+.|+++|+.|++++||+||++||||||||||+|||.++++|+|||||||||||+||||||
T Consensus 131 cITPGTeFM~rl~~~L~yfIktKistDs~Wq~~~vIlSGhevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLIm 210 (1493)
T KOG2045|consen 131 CITPGTEFMVRLQEGLRYFIKTKISTDSLWQRCTVILSGHEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIM 210 (1493)
T ss_pred CCCCcHHHHHHHHHHHHHHHHhccccchhhcccEEEEeCCcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhhe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHh
Q 003880 239 LALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEF 318 (789)
Q Consensus 239 L~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~ 318 (789)
|||+||+|||++|||+|.|..+. ++| ....+.|.+||+++|||||+.||
T Consensus 211 LGL~tHepHF~lLREEVtFgrrn--------------------~~k-----------~lehqkFyLLHLsLLREYlelEF 259 (1493)
T KOG2045|consen 211 LGLCTHEPHFVLLREEVTFGRRN--------------------KRK-----------SLEHQKFYLLHLSLLREYLELEF 259 (1493)
T ss_pred eeeccCCcceeeeeeeeeccccc--------------------ccc-----------hhhhhhhhhhHHHHHHHHHHHHH
Confidence 99999999999999999885311 111 12345799999999999999999
Q ss_pred cC--CCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccccchHHHHHHHHHHHHHhcCCccccCCccCHHHHHHHHHH
Q 003880 319 RI--PNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYKKEFRALGGYLTDGSKPSLRRVEHFIQA 396 (789)
Q Consensus 319 ~~--~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk~~l~~~~gYLt~~G~inl~rl~~fl~~ 396 (789)
.- ...+|++|+|||+||||+|+||||||||||||+|+|.+||+.+|+.+||+.+|++||||+++|+|||.||+.||.+
T Consensus 260 ~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlpllystykkvlpt~~GyINE~G~lNl~Rle~~L~e 339 (1493)
T KOG2045|consen 260 DELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLYSTYKKVLPTLGGYINENGKLNLRRLEIFLSE 339 (1493)
T ss_pred HHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHHHHHHHHhccCCccccccceecHHHHHHHHHH
Confidence 84 3578999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCCCCCCCCcccccccCCCCCCCCC----CCccccccccccccC
Q 003880 397 VGSYEDRIFQKRARLHQRHAERIKREKAQARRGDDVEPLAQPDSLVPVSRFHGSRLASGPS----PSPYQQSECVGRLDN 472 (789)
Q Consensus 397 l~~~E~~iF~~r~~~~~r~~e~~k~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~----~~~~~~~~~~~~~~~ 472 (789)
|..+|.++|+.+.+..+ .- +.||.+- ++.. .+......+..+.++....... ..++-.... ...+
T Consensus 340 L~nfeke~Fke~led~k-~~-nskr~r~-----~~~~--~~~~~~~dika~t~sq~~d~l~~~~~~~p~i~~~a--~ld~ 408 (1493)
T KOG2045|consen 340 LTNFEKEHFKEHLEDLK-YM-NSKRERF-----DDPE--QQELAEMDIKAITESQNLDSLLGEESKDPLINKSA--LLDD 408 (1493)
T ss_pred HHhhhHHHHHHHHHhhh-hc-ccccccc-----ccHH--HHhhhcccHHhhhhhhhhhhhcccccccccccccc--cccc
Confidence 99999999998876543 11 1111000 0000 0000000011010000000000 000000000 0000
Q ss_pred CCCCCC-CCCCccccC-CCcchhhHHHhhhcCCCCCCcccHHHHHHHHHHHH-hhhccc-CCC--CCcchhhcccC-CCc
Q 003880 473 GKGTSG-RPHKVPRLS-SGATIGAAIVEAENSFETDPQENKEEFKAKLKELL-RDKSDA-FNS--DNPEEDKVKLG-EPG 545 (789)
Q Consensus 473 ~~~~~~-~~~k~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~-~~~--~~~~~d~v~l~-e~g 545 (789)
...... ......... .++......++. ...++.++|....+..+. ..+.+. +.. +...+.+|... ...
T Consensus 409 dD~~Fl~~~~eDl~~~~~~s~s~~~~ld~-----~~~de~EdEf~~~~~t~~ls~~~~~~~~n~eea~~eKti~n~~F~r 483 (1493)
T KOG2045|consen 409 DDSAFLSDHEEDLSDLEPGSGSDELLLDN-----LDADELEDEFAVELATLALSGMNDADFANDEEACWEKTILNKEFQR 483 (1493)
T ss_pred chHHHHHHhhhhccccccccCccchhhcc-----ccchhhhHHHHHHHHHHHHhccccccccchHHHhhhhhhHHHHHHH
Confidence 000000 000000000 000000000000 011122223322222221 111111 111 01112333322 357
Q ss_pred hhHHHHHHhcCCCChhHHHHHHHHHHHHHHhHHHHHhhhhhcCcccccccccCCCCccccccccccCccccccCCCCCCh
Q 003880 546 WKERYYEEKFNAKTPEEREETRKDVVLRYTEGLCWVMHYYYEGVCSWQWFYPYHYAPFASDLKDLDQFNISFELGHPFKP 625 (789)
Q Consensus 546 ~k~rYY~~Kf~~~~~~~~~~~~~~v~~~YveGL~WVL~YYy~Gc~SW~WyYPyHYAPfasDl~~l~~~~i~F~~g~Pf~P 625 (789)
||..||++|++.++.+ ++..+++|..|||||||||.|||+||+||+||||||||||+||+++..+++|.|++|+||+|
T Consensus 484 wK~~yYrdKlkf~~~d--ee~lrelae~YVeaLQWvL~YYYrGc~SWsWyYphHyaP~ISDl~kgldv~ieF~mgtPF~P 561 (1493)
T KOG2045|consen 484 WKRNYYRDKLKFDPND--EELLRELAEHYVEALQWVLDYYYRGCQSWSWYYPHHYAPFISDLKKGLDVEIEFHMGTPFLP 561 (1493)
T ss_pred HHHHHhhhhhcCCCcc--HHHHHHHHHHHHHHHHHHHHHHhcCCccccccccccccchhHhHhcccceeEEEecCCCCCc
Confidence 9999999999998655 35567899999999999999999999999999999999999999999999999999999999
Q ss_pred hhhhhhcCCCCCCCCCcHHHHhhhcCCCCCCcccCCCcccccCCCCccccceeeeccCCChHHHHHHHhhccCCCCHHHH
Q 003880 626 FNQLLGVFPSASSHALPEHYRKLMTDPNSPISDFYPTDFEVDMNGKRYSWQGIAKLPFIDEARLLDEVKKIEHTLTEEEA 705 (789)
Q Consensus 626 feQLm~VLP~~S~~~LP~~~~~LM~d~~SpI~dfYP~~F~iD~nGkk~~WqgV~lLPFIDe~rLl~a~~~~~~~Lt~eE~ 705 (789)
|||||||||++|+.+||.+||+||.++.|||+||||.+|+.|+|||+.+|++|||||||||+||++||.+....||+||+
T Consensus 562 FqQLlAVLPaaSa~llPp~frdLM~~~~SPI~DFYPaefelD~NGKtadWEAVVLIpFIdEkRLleAm~pk~~~Ls~EEr 641 (1493)
T KOG2045|consen 562 FQQLLAVLPAASAKLLPPAFRDLMLLPTSPIADFYPAEFELDLNGKTADWEAVVLIPFIDEKRLLEAMLPKEAQLSLEER 641 (1493)
T ss_pred HHHHHHhchhhhhccCChhhhHhhcCCCCchhhcchhhheecccCCccceeEEEEEeecchHHHHHHHhhHhhhcCHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhccCCCceEEEec
Q 003880 706 RRNSIMADMLFVLL 719 (789)
Q Consensus 706 ~RN~~g~~~lf~~~ 719 (789)
.||++|.+++|-+.
T Consensus 642 ~RNs~g~~~vys~~ 655 (1493)
T KOG2045|consen 642 ERNSHGPMYVYSYS 655 (1493)
T ss_pred hhcccCCceeeecc
Confidence 99999999998764
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=4.5e-87 Score=693.90 Aligned_cols=237 Identities=60% Similarity=1.088 Sum_probs=193.6
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCCHHHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTTFDEVFQC 80 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~~p~t~~e~~~~ 80 (789)
||||+|||||++|||.++..+.+.. ...+|||||||||||||+|+|++..+.+.++++||.+
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 9999999999999999998765421 1126999999999999999999988888999999999
Q ss_pred HHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHHHHHHHHHhCCCCCCCCCCCCCccCcc
Q 003880 81 MFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEERLRQEFEREGRKLPPKSDSQVFDSNVI 160 (789)
Q Consensus 81 if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~l~~~~~~~g~~~~~~~~~~~fDsn~I 160 (789)
||+|||+||.+|||||+||||||||||||||||||+|||+++++++....+.....++...+|...+.......||||+|
T Consensus 63 i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~I 142 (237)
T PF03159_consen 63 IFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSNCI 142 (237)
T ss_dssp HHHHHHHHHHHH-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GGGS
T ss_pred HHHHHHHhheeecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhcccccccccccccccccee
Confidence 99999999999999999999999999999999999999999999998887777777777777766654445578999999
Q ss_pred cCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 003880 161 TPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLA 240 (789)
Q Consensus 161 TPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~ 240 (789)
||||+||.+|+++|++|+..|+++||.|++++||+||++||||||||||+|||+++++|+|+||++|||||+||||||||
T Consensus 143 TPGT~FM~~l~~~L~~~~~~k~~~~~~~~~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 143 TPGTEFMEKLSDALRYYIKKKLNSDPKWQNLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp STTSHHHHHHHHHHHHHHHHHHHH-GGGCCSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred ccCCHHHHHHHHHHHHHHHHHhcCCCCcCceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcCCceEEEeeccc
Q 003880 241 LATHEVHFSILREVV 255 (789)
Q Consensus 241 Lathe~~f~ILRE~v 255 (789)
|++|++||+||||+|
T Consensus 223 L~~~~~~~~ilre~~ 237 (237)
T PF03159_consen 223 LATHEPNIYILREEV 237 (237)
T ss_dssp HHTT-SSEEEEEESS
T ss_pred HccCCCeEEEEeccC
Confidence 999999999999975
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=98.59 E-value=4.7e-07 Score=99.09 Aligned_cols=231 Identities=19% Similarity=0.295 Sum_probs=121.8
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~--~p~t~~e~~ 78 (789)
|||++|..||...-+.+ . +++ .. | --|=||.++.+|.+....... .........
T Consensus 1 MGI~gL~~~l~~~~~~~--~-i~~----l~--------------g---k~laID~~~~l~r~~~a~~~~~~~~g~~~~~l 56 (316)
T cd00128 1 MGIKGLWPLLKPVARPV--H-LEE----LR--------------G---KKVAIDASIWLYQFLKACRQELGSGGETTSHL 56 (316)
T ss_pred CchhhHHHHHHhhCCCC--C-HHH----hC--------------C---cEEEecHHHHHHHHHHHhhhhccCCCCCcHHH
Confidence 99999999999876654 1 110 00 1 157899999999865432110 001112233
Q ss_pred HHHHHHHHHHHhhccccceEEEeecCCCcchhhHHHhhhhccchhHHHhHHHHHHH-HHHHHHHhCCCCCCCCCCCCCcc
Q 003880 79 QCMFDYIDRLFVMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRASKDAADSAAEEER-LRQEFEREGRKLPPKSDSQVFDS 157 (789)
Q Consensus 79 ~~if~yid~l~~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~~~~~~~~~~~~-l~~~~~~~g~~~~~~~~~~~fDs 157 (789)
..++..+.+|+.. . -+ ..+++||.+|-.|......||-+.....+......++ -.++..+.. . .+
T Consensus 57 ~~~~~rl~~L~~~-~-i~-pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~---------~--~~ 122 (316)
T cd00128 57 QGFFYRTCRLLEL-G-IK-PVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLE---------R--RA 122 (316)
T ss_pred HHHHHHHHHHHHC-C-CE-EEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH---------h--cc
Confidence 4445555555532 2 23 3467999999888777665554332211111100000 000000000 0 11
Q ss_pred CcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHH
Q 003880 158 NVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLI 237 (789)
Q Consensus 158 n~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLI 237 (789)
..|||.+ ... ++..+... ++.+|.+ |||+|-=+-..-+. .....|+|.|+|++
T Consensus 123 ~~~~~~~--~~~----~~~lL~~~--------gi~~i~a----p~EAdaq~a~l~~~---------g~v~~i~S~DsD~l 175 (316)
T cd00128 123 VRVTPQM--IEE----AKELLRLM--------GIPYIVA----PYEAEAQCAYLAKK---------GLVDAIITEDSDLL 175 (316)
T ss_pred CcCCHHH--HHH----HHHHHHHc--------CCCEEEC----CcCHHHHHHHHHhC---------CCeeEEEecCCCee
Confidence 2344432 122 33333221 5667764 89999765544331 24578999999998
Q ss_pred HHHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHH
Q 003880 238 MLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYE 317 (789)
Q Consensus 238 mL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e 317 (789)
++|- ++ ++|-- +..+ ...+++++..-+.+.+
T Consensus 176 ~fg~----~~--vi~~~-~~~~---------------------------------------~~~~~~~~~~~~~~~l--- 206 (316)
T cd00128 176 LFGA----PR--VYRNL-FDSG---------------------------------------AKPVEEIDLEKILKEL--- 206 (316)
T ss_pred eecC----ce--EEEec-ccCC---------------------------------------CCceEEEEHHHHHHHc---
Confidence 8762 22 33321 0000 0135567765554443
Q ss_pred hcCCCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccc
Q 003880 318 FRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIR 357 (789)
Q Consensus 318 ~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~ 357 (789)
. ++. +.|+.+|.|+|+||+|.+|++-+.
T Consensus 207 -g-------l~~----~q~id~~~L~G~Dy~~gv~giG~k 234 (316)
T cd00128 207 -G-------LTR----EKLIDLAILLGCDYTEGIPGIGPV 234 (316)
T ss_pred -C-------CCH----HHHHHHHHhcCCCCCCCCCCccHH
Confidence 1 222 578889999999999999986643
No 6
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.24 E-value=9.6e-06 Score=91.51 Aligned_cols=233 Identities=21% Similarity=0.276 Sum_probs=124.8
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCC----CCCCCCCH--
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPE----DRPAPTTF-- 74 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~----~~~~p~t~-- 74 (789)
|||.++..+|....|.+++.+-= ...-| =-+=||....||.....- +...-.+.
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~l---~~l~g-----------------k~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G 60 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQEL---KNYFG-----------------RVIAIDASMALYQFLIAIRDDSQGGNLTNEAG 60 (393)
T ss_pred CChhhHHHHHhhhccccccccCH---HHhCC-----------------cEEEEeHHHHHHHHHHHcccccccccchhccC
Confidence 99999999999999988764310 00011 157889999998743211 00000000
Q ss_pred --HHHHHHHHHHHHHHHhh-ccccceEEEeecCCCcchhhHHHhhhh--ccchhHHHhHHHHHHHHHHHHHHhCCCCCCC
Q 003880 75 --DEVFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQQRSRR--FRASKDAADSAAEEERLRQEFEREGRKLPPK 149 (789)
Q Consensus 75 --~e~~~~if~yid~l~~~-vrPrkllyiAiDGVAPrAKmnQQRsRR--frsa~~~~~~~~~~~~l~~~~~~~g~~~~~~ 149 (789)
..-+.-+|..+-+|+.. ++| .+++||.+|-.|...-..|| -..+.+.... ....|.. +
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----VYVFDGKPPELKSGELEKRRERREEAEEELEK----------AIEEGDD--E- 123 (393)
T ss_pred CccHHHHHHHHHHHHHHHCCCCE----EEEEcCCCchhhHHHHHHHHHHHHHhHHHHHH----------HHhcCCH--H-
Confidence 01234455556667664 788 47999999976665443333 2222221110 0111110 0
Q ss_pred CCCCCCc--cCcccCCcHHHHHHHHHHHHHHHHHhcCCCCCcccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcE
Q 003880 150 SDSQVFD--SNVITPGTEFMAVLSIALQYYIHLRLNNDPGWEKIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRH 227 (789)
Q Consensus 150 ~~~~~fD--sn~ITPGT~FM~~L~~~L~~~i~~kl~~dp~w~~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H 227 (789)
....+- +..||+ +-+..+.+.|+ . -++.+|.+ |||+|.=|-..-+ .+...
T Consensus 124 -~a~k~~~r~~~vt~--~~~~~~~~lL~----~--------~Gip~i~A----P~EAdaq~A~L~~---------~g~v~ 175 (393)
T PTZ00217 124 -EIKKQSKRTVRVTK--EQNEDAKKLLR----L--------MGIPVIEA----PCEAEAQCAELVK---------KGKVY 175 (393)
T ss_pred -HHHHHHhhcccCCH--HHHHHHHHHHH----H--------cCCceEEC----CcCHHHHHHHHHH---------CCCeE
Confidence 000011 112332 22222333222 1 14566754 8999995544432 14567
Q ss_pred EEEecChhHHHHHhhcCCceEEEeecccccCCCCccccccCCCCCcccccccccccccCCCCcCCCccccCCCCceEeeH
Q 003880 228 CLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHI 307 (789)
Q Consensus 228 ~IyG~DADLImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i 307 (789)
.|++-|.|++++|- + .++|-- +..+ ....+++++++
T Consensus 176 ~ViS~D~D~l~fg~----~--~vi~~l-~~~~-------------------------------------~~~~~~~~~~~ 211 (393)
T PTZ00217 176 AVATEDMDALTFGT----P--VLLRNL-NFSE-------------------------------------AKKRPIQEINL 211 (393)
T ss_pred EEeCCCcCeeecCC----c--EEEEcc-cccc-------------------------------------cCCCCeEEEEH
Confidence 89999999998872 1 334431 0000 00124567777
Q ss_pred HHHHHHHHHHhcCCCCCCccchhhhhhHHHHHhhhccCCCCCCCCccccc
Q 003880 308 WTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGNDFLPHMPTLEIR 357 (789)
Q Consensus 308 ~~LReyL~~e~~~~~~~~~~d~eriIDDfVfLcf~vGNDFLPhlp~l~I~ 357 (789)
..+.+.+ .++ -+.||-+|.|+|.||+|.+|++-..
T Consensus 212 ~~v~~~~-----------gl~----~~q~id~~iL~G~Dy~pgi~GIG~k 246 (393)
T PTZ00217 212 STVLEEL-----------GLS----MDQFIDLCILCGCDYCDTIKGIGPK 246 (393)
T ss_pred HHHHHHh-----------CCC----HHHHHHHHHHhCCCCCCCCCCccHH
Confidence 6554432 122 2567889999999999999997654
No 7
>PRK03980 flap endonuclease-1; Provisional
Probab=97.41 E-value=0.0032 Score=68.65 Aligned_cols=62 Identities=16% Similarity=0.378 Sum_probs=38.2
Q ss_pred hHHHHHhhhccCCCCCCCCcccccc--------chHHHHHH-------HHHHHHH-----hc-CCccccCCccCHHHHHH
Q 003880 334 DDFIFMCFFVGNDFLPHMPTLEIRE--------GAINLLMA-------VYKKEFR-----AL-GGYLTDGSKPSLRRVEH 392 (789)
Q Consensus 334 DDfVfLcf~vGNDFLPhlp~l~I~~--------g~id~L~~-------~Yk~~l~-----~~-~gYLt~~G~inl~rl~~ 392 (789)
+.||-+|.|+|.||.|++|++-+.. |+|+.+++ -|.+... .. ..|--.=+.+|.+.|..
T Consensus 177 ~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~~~~~~~~~~r~~f~~p~v~~~~~~~~~~pd~~~l~~ 256 (292)
T PRK03980 177 EQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGFEIENYDEIREFFLNPPVTDDYELKWKEPDKEGIIE 256 (292)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhccCCCCCHHHHHHHhcCCCCCCCCCccCCCCCHHHHHH
Confidence 4677799999999999999876652 45555555 1222211 11 12222335677777777
Q ss_pred HHH
Q 003880 393 FIQ 395 (789)
Q Consensus 393 fl~ 395 (789)
||-
T Consensus 257 fl~ 259 (292)
T PRK03980 257 FLV 259 (292)
T ss_pred HHh
Confidence 774
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=97.07 E-value=0.0081 Score=66.89 Aligned_cols=67 Identities=16% Similarity=0.171 Sum_probs=39.6
Q ss_pred eEEEeccccccccccCC---CCCCCCCH----HHHHHHHHHHHHHHHhh-ccccceEEEeecCCCcchhhHHHhhhhcc
Q 003880 50 NLYLDMNGIIHPCFHPE---DRPAPTTF----DEVFQCMFDYIDRLFVM-VRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~---~~~~p~t~----~e~~~~if~yid~l~~~-vrPrkllyiAiDGVAPrAKmnQQRsRRfr 120 (789)
-+-||....||.+...- ++..-++. ..-+..+|..+-+|+.. ++| .+++||.+|-.|...-..||-+
T Consensus 23 ~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P----v~VFDG~~p~~K~~~~~~R~~~ 97 (338)
T TIGR03674 23 VVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKP----VYVFDGKPPELKAETLEERREI 97 (338)
T ss_pred EEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeE----EEEECCCChhhhHhhHHHHHHH
Confidence 57799999999754421 11100000 01233344455555555 777 6899999998777776666543
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=95.84 E-value=0.46 Score=51.19 Aligned_cols=56 Identities=9% Similarity=0.115 Sum_probs=35.3
Q ss_pred EEEeccccccccccCCCCC--CCCCHHHHHHHHHHHHHHHHhhccccceEEEeecCCCc
Q 003880 51 LYLDMNGIIHPCFHPEDRP--APTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (789)
Q Consensus 51 LYlDmNgIIH~c~h~~~~~--~p~t~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAP 107 (789)
|-||.|++||-+.|.-... ..-........++..+-+++...+|..+ .+|+||-.|
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~-~~~fD~~~~ 61 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYV-AVVFDAKGK 61 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeE-EEEEeCCCC
Confidence 7899999999988863110 0001112344455566677777789875 599998544
No 10
>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=94.94 E-value=0.021 Score=52.16 Aligned_cols=95 Identities=21% Similarity=0.336 Sum_probs=56.2
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCCCCCC--HHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRPAPTT--FDEVF 78 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~~p~t--~~e~~ 78 (789)
|||++|..+|.... .+..+.- ....| --|=||.+..||.+.+......... ....+
T Consensus 1 MGI~gL~~~l~~~~--~v~~~~~---~~l~g-----------------~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~ 58 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA--AVRKVSL---SELRG-----------------KRVAIDASCWLHQFLFSCREELGQGVGTDSHL 58 (101)
T ss_dssp ---TTHHHHCHHHE--GEEEEEG---GGGTT-----------------CEEEEEHHHHHHHHHHHSBCTTSCB-BS-HHH
T ss_pred CCcccHHHHHHhhc--cCCccCH---HHhCC-----------------CEEEEEcHHHHHHHHHHhHHHhccccchHHHH
Confidence 99999999999987 2221100 01112 2577999999998755433221111 13456
Q ss_pred HHHHHHHHHHHh-hccccceEEEeecCCCcchhhHHHhhhhccc
Q 003880 79 QCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRA 121 (789)
Q Consensus 79 ~~if~yid~l~~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfrs 121 (789)
..++..+..|.. -|+| ++.+||.+|-+|......||-+.
T Consensus 59 ~~~~~r~~~L~~~gI~P----ifVFDG~~~~~K~~~~~~R~~~r 98 (101)
T PF00752_consen 59 RGLFSRLCRLLEHGIKP----IFVFDGKPPPLKRETIQKRRKRR 98 (101)
T ss_dssp HHHHHHHHHHHHTTEEE----EEEE--STTGGCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCEE----EEEECCCCchhhHHHHHHHHHHH
Confidence 667777776654 4666 68999999999998888776543
No 11
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=94.87 E-value=0.025 Score=51.62 Aligned_cols=93 Identities=22% Similarity=0.301 Sum_probs=56.1
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccccccCCCCC--CCCCHHHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPCFHPEDRP--APTTFDEVF 78 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c~h~~~~~--~p~t~~e~~ 78 (789)
|||++|..||... ++.+ ......|. -+=||.+..+|.|......+ ........+
T Consensus 1 MGI~gL~~~l~~~----~~~~---~i~~l~g~-----------------~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~l 56 (99)
T smart00485 1 MGIKGLWPLLKPV----VREV---PLEALRGK-----------------TLAIDASIWLYQFLTACREKLGTPLPNSKHL 56 (99)
T ss_pred CCHhHHHHHHHHh----cccC---CHHHhCCc-----------------eEeccHHHHHHHHHHHHhhhhcCCCCchHHH
Confidence 9999999999876 1111 00011222 45578888888764322110 111112245
Q ss_pred HHHHHHHHHHHh-hccccceEEEeecCCCcchhhHHHhhhhccc
Q 003880 79 QCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRA 121 (789)
Q Consensus 79 ~~if~yid~l~~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfrs 121 (789)
..+|..+.+|++ -|.| ++.+||.+|-+|...+..||-+.
T Consensus 57 ~~~~~rl~~L~~~~I~P----ifVFDG~~~~~K~~t~~~R~~~r 96 (99)
T smart00485 57 MGLFYRTCRLLEFGIKP----IFVFDGKPPPLKSETLAKRRERR 96 (99)
T ss_pred HHHHHHHHHHHHCCCeE----EEEECCCCchhhHHHHHHHHHHH
Confidence 555666666554 3444 57899999999999998887654
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=94.44 E-value=2.4 Score=45.05 Aligned_cols=57 Identities=9% Similarity=0.083 Sum_probs=37.7
Q ss_pred eEEEeccccccccccCCCCCC---CCCHHHHHHHHHHHHHHHHhhccccceEEEeecCCCc
Q 003880 50 NLYLDMNGIIHPCFHPEDRPA---PTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~~~~~---p~t~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAP 107 (789)
-|.||.|++||-+.|...... ..........++..+-+++...+|.++ .+++||-.|
T Consensus 3 ~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~-~~~fD~~~~ 62 (240)
T cd00008 3 LLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYV-AVVFDAGGK 62 (240)
T ss_pred EEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeE-EEEEeCCCC
Confidence 378999999999887642111 011122445556667777778889987 699999643
No 13
>PRK14976 5'-3' exonuclease; Provisional
Probab=93.74 E-value=1.8 Score=47.27 Aligned_cols=57 Identities=16% Similarity=0.251 Sum_probs=37.5
Q ss_pred eEEEeccccccccccCCC--CCCCC----CHHHHHHHHHHHHHHHHhhccccceEEEeecCCCc
Q 003880 50 NLYLDMNGIIHPCFHPED--RPAPT----TFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~~--~~~p~----t~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAP 107 (789)
-|.||.|++|+-|+|... .+... .......-+++.+-+++...+|..+ -+|+||-.|
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 468999999999888731 11111 1123445556667777777889886 589998544
No 14
>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=92.44 E-value=0.31 Score=44.23 Aligned_cols=90 Identities=20% Similarity=0.371 Sum_probs=54.2
Q ss_pred cEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEeecccccCCCCccccccCCC
Q 003880 191 IKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQP 270 (789)
Q Consensus 191 l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~ 270 (789)
+.+|+ .|||+|.=+--.-|. +..+.|++.|+|+++.|-- .|+|... .. ....|
T Consensus 5 v~~i~----AP~EAeAq~A~L~~~---------g~vd~V~t~DsD~l~fG~~------~vi~~~~-~~-~~~~~------ 57 (94)
T PF00867_consen 5 VPYIV----APYEAEAQCAYLERN---------GLVDAVITEDSDLLLFGAP------KVIRKLS-DK-SSGKC------ 57 (94)
T ss_dssp -EEEE-----SS-HHHHHHHHHHT---------TSSSEEE-SSSHHHHTT-S------EEEESST--C-SCCST------
T ss_pred CeEEE----cCchHHHHHHHHHHh---------cceeEEEecCCCEEeeCCC------EEEEecc-cc-ccCCc------
Confidence 45555 389999988866553 5679999999999999654 5666531 00 00001
Q ss_pred CCcccccccccccccCCCCcCCCccccCCCCceEeeHHHHHHHHHHHhcCCCCCCccchhhhhhHHHHHhhhccCC
Q 003880 271 GHLAANCEGKAKRKAGEFDEKGDEVVVPKKPYQFLHIWTLREYLDYEFRIPNPPFEIDLECIVDDFIFMCFFVGND 346 (789)
Q Consensus 271 gh~~~~c~g~~k~k~~~~~~~~~~~~~~~~~f~~l~i~~LReyL~~e~~~~~~~~~~d~eriIDDfVfLcf~vGND 346 (789)
.......+.+++...+.+.+.. + -+.|+.+|+|+|+|
T Consensus 58 ------------------------~~~~~~~~~~~~~~~i~~~l~l-----------~----~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 58 ------------------------SSKSEKEVEVIDLDDILKELGL-----------T----REQFIDLCILCGCD 94 (94)
T ss_dssp ------------------------S-CCESEEEEEEHHHHHHHHTT-----------S----HHHHHHHHHHHHET
T ss_pred ------------------------ccccccceEEEEHHHHHHHcCC-----------C----HHHHHHHheecCCC
Confidence 0001235778888776666431 1 23699999999998
No 15
>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=92.34 E-value=0.08 Score=34.12 Aligned_cols=17 Identities=59% Similarity=1.491 Sum_probs=15.1
Q ss_pred ccccccCCCCCcccccc
Q 003880 262 DKCFLCGQPGHLAANCE 278 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~ 278 (789)
++|+.||+.||.+.+|.
T Consensus 1 ~~C~~C~~~GH~~~~Cp 17 (18)
T PF00098_consen 1 RKCFNCGEPGHIARDCP 17 (18)
T ss_dssp SBCTTTSCSSSCGCTSS
T ss_pred CcCcCCCCcCcccccCc
Confidence 36999999999999994
No 16
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=89.88 E-value=6.9 Score=45.11 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=22.3
Q ss_pred hHHHHHhhhccCCCCCCCCccccccchHHHHHHHHH
Q 003880 334 DDFIFMCFFVGNDFLPHMPTLEIREGAINLLMAVYK 369 (789)
Q Consensus 334 DDfVfLcf~vGNDFLPhlp~l~I~~g~id~L~~~Yk 369 (789)
.-||-||+|+|+||.|.+-+ |..+.-=.|++.|+
T Consensus 217 ~~fidL~lLlGCDYc~~I~G--ig~~~al~lir~~~ 250 (449)
T KOG2519|consen 217 ESFIDLCLLLGCDYCPTIRG--IGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHhcCcccccccc--cChHHHHHHHHHhc
Confidence 35777999999999999655 33333233455443
No 17
>PRK05755 DNA polymerase I; Provisional
Probab=88.70 E-value=9.6 Score=48.00 Aligned_cols=56 Identities=13% Similarity=0.154 Sum_probs=34.9
Q ss_pred eEEEeccccccccccCCCCC---CCCCHHHHHHHHHHHHHHHHhhccccceEEEeecCCC
Q 003880 50 NLYLDMNGIIHPCFHPEDRP---APTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVA 106 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~~~~---~p~t~~e~~~~if~yid~l~~~vrPrkllyiAiDGVA 106 (789)
-|.||.|.+++-+.|.-... ...........++..+-+++...+|..+ .+|+||-.
T Consensus 4 ~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~-~v~fD~~~ 62 (880)
T PRK05755 4 LLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHV-AVAFDAKG 62 (880)
T ss_pred EEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEE-EEEEECCC
Confidence 36899999999988864110 0011122333445556666677889775 59999843
No 18
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=88.60 E-value=1.8 Score=50.43 Aligned_cols=92 Identities=21% Similarity=0.313 Sum_probs=51.5
Q ss_pred CcchhHHHHHHhhCCcccccccccCccccCCccccCCCCCCCCCCCccCeEEEeccccccc----cccCCCCCCCCCHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADVIEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHP----CFHPEDRPAPTTFDE 76 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~----c~h~~~~~~p~t~~e 76 (789)
|||+||.-.+... .+++- +. .++.+-|=+|.-+-+|. |.+--....|+ +.
T Consensus 1 MGI~GLlp~~k~~----~~~~h--------i~------------~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT--~r 54 (556)
T KOG2518|consen 1 MGIQGLLPLLKPA----LKPIH--------IS------------EYKGKTVAVDGYCWLHRGALACAEKLAKGKPT--DR 54 (556)
T ss_pred CCcchhHHHHHHH----hhhhh--------HH------------HhcCceEEEehhhHHhhhHHhHHHHHhcCCCh--HH
Confidence 9999999888762 22210 00 12456778888888886 44322222222 22
Q ss_pred HHHHHHHHHHHHHh-hccccceEEEeecCCCcchhhHHHhhhhccch
Q 003880 77 VFQCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAS 122 (789)
Q Consensus 77 ~~~~if~yid~l~~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa 122 (789)
-+.=...++..|.. -|+| +|.+||=+=-+|--+-|.||-+..
T Consensus 55 yi~y~ik~v~lL~~~gikP----ilVFDG~~LP~K~~te~~Rr~~R~ 97 (556)
T KOG2518|consen 55 YIQFFIKRVKLLLSYGIKP----ILVFDGDPLPSKKETERKRRERRK 97 (556)
T ss_pred HHHHHHHHHHHHHhcCCeE----EEEecCCCcccccccchHHHHHHH
Confidence 22222233333332 3455 789999887778777666665443
No 19
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=86.51 E-value=42 Score=36.97 Aligned_cols=62 Identities=19% Similarity=0.370 Sum_probs=43.7
Q ss_pred eEEEeccccccccccCCCC------CCCCCHHHHHHHHHHHHHHHHhhccccceEEEeecCCCc--chhhHHHh
Q 003880 50 NLYLDMNGIIHPCFHPEDR------PAPTTFDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP--RAKMNQQR 115 (789)
Q Consensus 50 nLYlDmNgIIH~c~h~~~~------~~p~t~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAP--rAKmnQQR 115 (789)
-|-||-+++++.+.|.-.. ..++. ...-+...+.++++..+|.+. .+++||-.| |.++...|
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~---~~~~~~~~l~~~~~~~~~~~~-~~vFD~~~~tfR~~~~~~y 82 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTG---AVSGFLGMLYRLIRLLEPTHP-VVVFDGKPPTFRHELLEEY 82 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCcc---HHHHHHHHHHHHHHhcCCCcE-EEEEcCCCCcchHHHHHHH
Confidence 6889999999998887521 12333 344556678999999999664 599999777 55555443
No 20
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=80.09 E-value=0.71 Score=34.24 Aligned_cols=18 Identities=39% Similarity=0.887 Sum_probs=16.0
Q ss_pred ccccccCCCCCccccccc
Q 003880 262 DKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~c~g 279 (789)
-.|.+|+|.||+..+|--
T Consensus 9 Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 9 YVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CEeecCCCCCccHhHCCC
Confidence 479999999999999954
No 21
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=78.64 E-value=64 Score=40.95 Aligned_cols=56 Identities=14% Similarity=0.196 Sum_probs=33.6
Q ss_pred EEEeccccccccccCCCCCCCCC----HHHHHHHHHHHHHHHHhhccccceEEEeecCCCc
Q 003880 51 LYLDMNGIIHPCFHPEDRPAPTT----FDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (789)
Q Consensus 51 LYlDmNgIIH~c~h~~~~~~p~t----~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAP 107 (789)
|.||.|++|+-++|.-....-+| ......-.+..+-+++...+|..+ .+|+||-.|
T Consensus 2 ~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i-~v~FD~~~~ 61 (887)
T TIGR00593 2 LLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYV-AVAFDSGTP 61 (887)
T ss_pred EEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEE-EEEEcCCCC
Confidence 57999999999888642100001 111223334445566666789875 599998654
No 22
>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=68.60 E-value=5.8 Score=50.43 Aligned_cols=40 Identities=20% Similarity=0.199 Sum_probs=30.4
Q ss_pred ccEEEEcCCCCCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhh
Q 003880 190 KIKVILSDANVPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALA 242 (789)
Q Consensus 190 ~l~VI~Sds~vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~La 242 (789)
++-+|.+ |||||.=+-...+. +....|++-|+|+++.|=.
T Consensus 785 GIP~i~A----P~EAEAqcA~L~~~---------G~vd~V~TeDsD~llFGa~ 824 (1034)
T TIGR00600 785 GIPYIVA----PMEAEAQCAILDLL---------DQTSGTITDDSDIWLFGAR 824 (1034)
T ss_pred CCCeeeC----CccHHHHHHHHHhC---------CCeEEEEccccceeccCCc
Confidence 3556654 89999988777542 5779999999999976643
No 23
>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=66.95 E-value=19 Score=46.01 Aligned_cols=89 Identities=25% Similarity=0.383 Sum_probs=49.0
Q ss_pred CcchhHHHHHHhhCCcccccc-cccCccccCCccccCCCCCCCCCCCccCeEEEecccccccc---ccCCCCCCCCCHHH
Q 003880 1 MGVPAFYRWLAEKYPLVVADV-IEEEPVVIDGVKIPVDTSKPNPNGLEYDNLYLDMNGIIHPC---FHPEDRPAPTTFDE 76 (789)
Q Consensus 1 MGVP~ffrWL~~ryP~ii~~~-~e~~~~~~~g~~~p~d~s~pnpn~~e~DnLYlDmNgIIH~c---~h~~~~~~p~t~~e 76 (789)
|||.||+.||...= +++ ++ ...|. -|=||...-||.+ ++.......++ .
T Consensus 1 MGI~GLw~ll~~~~----r~v~le----~l~Gk-----------------~vAIDasiWL~q~l~~vr~~~g~~l~n-~- 53 (1034)
T TIGR00600 1 MGVQGLWKLLECSG----RPVSPE----TLEGK-----------------RLAVDISIWLNQALKGVRDREGNAIKN-S- 53 (1034)
T ss_pred CChhHHHHHHHHhc----ccccHH----HhCCe-----------------EEEechHHHHHHHHHHHHhccCCccCC-H-
Confidence 99999999995321 111 11 11233 4556777777753 22222211222 2
Q ss_pred HHHHHHHHHHHHHh-hccccceEEEeecCCCcchhhHHHhhhhcc
Q 003880 77 VFQCMFDYIDRLFV-MVRPRKLLYMAIDGVAPRAKMNQQRSRRFR 120 (789)
Q Consensus 77 ~~~~if~yid~l~~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfr 120 (789)
-+.-+|..|.+|+. -|+| ++.+||.+|-.|...-..||-|
T Consensus 54 hl~g~f~Ri~~Ll~~gI~P----VfVFDG~~p~lK~~t~~~R~~r 94 (1034)
T TIGR00600 54 HLLTLFHRLCKLLFFRIRP----IFVFDGGAPLLKRQTLAKRRQR 94 (1034)
T ss_pred HHHHHHHHHHHHHHCCCeE----EEEECCCCchHhHHHHHHHHHH
Confidence 22334444555544 4555 6789999999888765555443
No 24
>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=59.97 E-value=9.3 Score=33.43 Aligned_cols=22 Identities=32% Similarity=0.727 Sum_probs=18.6
Q ss_pred hHHHHHhhhcc--CCCCCCCCccc
Q 003880 334 DDFIFMCFFVG--NDFLPHMPTLE 355 (789)
Q Consensus 334 DDfVfLcf~vG--NDFLPhlp~l~ 355 (789)
+-|+-+|.|+| .|++|++|++-
T Consensus 8 ~q~~d~~~L~GD~~D~i~gv~giG 31 (75)
T cd00080 8 EQFIDLAILVGDKSDNIPGVPGIG 31 (75)
T ss_pred HHHHHHHHHcCCccccCCCCCccc
Confidence 35677999999 99999999844
No 25
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=46.23 E-value=11 Score=29.75 Aligned_cols=19 Identities=37% Similarity=0.893 Sum_probs=16.8
Q ss_pred CccccccCCCCCccccccc
Q 003880 261 QDKCFLCGQPGHLAANCEG 279 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~g 279 (789)
...|..|++.||.+.+|..
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4579999999999999974
No 26
>smart00343 ZnF_C2HC zinc finger.
Probab=45.62 E-value=10 Score=26.22 Aligned_cols=16 Identities=50% Similarity=1.379 Sum_probs=14.1
Q ss_pred cccccCCCCCcccccc
Q 003880 263 KCFLCGQPGHLAANCE 278 (789)
Q Consensus 263 ~c~~c~q~gh~~~~c~ 278 (789)
.|..||+.||.+.+|.
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4889999999999995
No 27
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=44.86 E-value=11 Score=29.50 Aligned_cols=15 Identities=47% Similarity=0.862 Sum_probs=12.6
Q ss_pred ccccccCCCCCcccc
Q 003880 262 DKCFLCGQPGHLAAN 276 (789)
Q Consensus 262 ~~c~~c~q~gh~~~~ 276 (789)
.+|..||+.||...+
T Consensus 2 ~kC~~CG~~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTN 16 (40)
T ss_pred ccccccccccccccC
Confidence 589999999998653
No 28
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=42.93 E-value=19 Score=27.26 Aligned_cols=20 Identities=25% Similarity=0.624 Sum_probs=15.9
Q ss_pred hHHHHHhhhccCCCCCCCCcc
Q 003880 334 DDFIFMCFFVGNDFLPHMPTL 354 (789)
Q Consensus 334 DDfVfLcf~vGNDFLPhlp~l 354 (789)
+-|+-+|.|+| |+.+.+|++
T Consensus 2 ~q~~~~~~L~G-D~~dni~Gv 21 (36)
T smart00279 2 EQLIDYAILVG-DYSDNIPGV 21 (36)
T ss_pred HHHHHHHHHhC-cCCCCCCCC
Confidence 35778999999 999966654
No 29
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=40.05 E-value=15 Score=32.26 Aligned_cols=34 Identities=18% Similarity=0.266 Sum_probs=27.7
Q ss_pred CCCChhhhHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhh
Q 003880 200 VPGEGEHKIMSYVRLQRNLPGYDPNTRHCLYGLDADLIMLALA 242 (789)
Q Consensus 200 vPGEGEHKIm~fIR~qr~~p~~dpn~~H~IyG~DADLImL~La 242 (789)
-|||+|.-.--.-++ +.-+.|+|.|+|+++.|--
T Consensus 10 AP~eAeAq~A~L~~~---------g~vdav~s~D~D~llfG~~ 43 (73)
T smart00484 10 APYEAEAQCAYLAKS---------GLVDAIITEDSDLLLFGAP 43 (73)
T ss_pred cCCcHHHHHHHHHhC---------CCeeEEEcCccceEecCCc
Confidence 399999988777662 4779999999999998754
No 30
>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=36.44 E-value=32 Score=34.78 Aligned_cols=56 Identities=14% Similarity=0.267 Sum_probs=38.5
Q ss_pred EEEeccccccccccCCCCCCC-CC---HHHHHHHHHHHHHHHHhhccccceEEEeecCCCc
Q 003880 51 LYLDMNGIIHPCFHPEDRPAP-TT---FDEVFQCMFDYIDRLFVMVRPRKLLYMAIDGVAP 107 (789)
Q Consensus 51 LYlDmNgIIH~c~h~~~~~~p-~t---~~e~~~~if~yid~l~~~vrPrkllyiAiDGVAP 107 (789)
|.||.|+++|-+.|.-....- .+ .-..+...++.|.+++...+|..+ .+|+||-.+
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 789999999999887531110 00 112444556677788888889874 599999887
No 31
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=30.84 E-value=21 Score=37.55 Aligned_cols=15 Identities=47% Similarity=0.698 Sum_probs=14.3
Q ss_pred ccCeEEEeccccccc
Q 003880 47 EYDNLYLDMNGIIHP 61 (789)
Q Consensus 47 e~DnLYlDmNgIIH~ 61 (789)
++|-+.+|-|||.||
T Consensus 95 ~~d~ilVDG~GiaHP 109 (212)
T COG1515 95 KPDLLLVDGHGIAHP 109 (212)
T ss_pred CCCEEEEcCcceecC
Confidence 589999999999999
No 32
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=29.32 E-value=26 Score=36.27 Aligned_cols=18 Identities=50% Similarity=1.152 Sum_probs=16.1
Q ss_pred CccccccCCCCCcccccc
Q 003880 261 QDKCFLCGQPGHLAANCE 278 (789)
Q Consensus 261 ~~~c~~c~q~gh~~~~c~ 278 (789)
...|..|||.||.+.+|.
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 468999999999999995
No 33
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=28.86 E-value=25 Score=28.21 Aligned_cols=20 Identities=35% Similarity=0.815 Sum_probs=16.9
Q ss_pred CCCccccccCCCCCcccccc
Q 003880 259 GQQDKCFLCGQPGHLAANCE 278 (789)
Q Consensus 259 ~~~~~c~~c~q~gh~~~~c~ 278 (789)
..+..|..||..||...+|.
T Consensus 29 ~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 29 RLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred CcChhhcCCCCcCcCHhHcC
Confidence 34578999999999999993
No 34
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=26.51 E-value=29 Score=35.92 Aligned_cols=47 Identities=23% Similarity=0.462 Sum_probs=29.0
Q ss_pred CCcEEEEecChhHHHHHhhcCCceEEEeecccccCCCCccccccCCCCCcccccc
Q 003880 224 NTRHCLYGLDADLIMLALATHEVHFSILREVVFTPGQQDKCFLCGQPGHLAANCE 278 (789)
Q Consensus 224 n~~H~IyG~DADLImL~Lathe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~ 278 (789)
+.-|..+--.++|=... +. .-|..+ . - .+..+|..||+.||++.+|.
T Consensus 68 ~~GH~~~DCP~~iC~~C-~~-~~H~s~--~---C-~~~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 68 QNGHLRRDCPHSICYNC-SW-DGHRSN--H---C-PKPKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccCcccccCChhHhhhc-CC-CCcccc--c---C-CcccccccccccCccccccC
Confidence 45677777776555444 21 112111 0 0 12368999999999999995
No 35
>COG5350 Predicted protein tyrosine phosphatase [General function prediction only]
Probab=22.95 E-value=88 Score=31.64 Aligned_cols=42 Identities=21% Similarity=0.551 Sum_probs=35.2
Q ss_pred cccEEEEcCCCCCCCh--------hhhHHHHHHHhhcCCCCCCCCcEEEEecC
Q 003880 189 EKIKVILSDANVPGEG--------EHKIMSYVRLQRNLPGYDPNTRHCLYGLD 233 (789)
Q Consensus 189 ~~l~VI~Sds~vPGEG--------EHKIm~fIR~qr~~p~~dpn~~H~IyG~D 233 (789)
+.|.+.+.|-.+||+| =++|+||++. .|.+.|=--||.-|.-
T Consensus 56 rhL~l~fnDI~~~~~g~~ap~e~Hv~~i~DF~~~---wp~~apllIHC~aGIS 105 (172)
T COG5350 56 RHLTLHFNDIAEPDDGWIAPGEAHVRAIIDFADE---WPRFAPLLIHCYAGIS 105 (172)
T ss_pred hceeEeeccccCCCccccCCCHHHHHHHHHHHhc---Cccccceeeeeccccc
Confidence 4589999999999999 3699999985 6788888889988753
No 36
>PHA02567 rnh RnaseH; Provisional
Probab=20.71 E-value=1.2e+02 Score=33.81 Aligned_cols=58 Identities=12% Similarity=0.131 Sum_probs=41.8
Q ss_pred cCeEEEeccccccccccCCCCCCCCCHHHHH-HHHHHHHHHHHhhccccc-eEEEeecCC
Q 003880 48 YDNLYLDMNGIIHPCFHPEDRPAPTTFDEVF-QCMFDYIDRLFVMVRPRK-LLYMAIDGV 105 (789)
Q Consensus 48 ~DnLYlDmNgIIH~c~h~~~~~~p~t~~e~~-~~if~yid~l~~~vrPrk-llyiAiDGV 105 (789)
-+-+.||++.|+-.|++..-.+.-.....|+ +.+++-|-.++..++|.- -+.+|+|+-
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 4689999999999999986544422223444 557888888888777662 167999974
Done!