Query 005531
Match_columns 692
No_of_seqs 234 out of 535
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 00:56:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/005531.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/005531hhsearch_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-250 5E-255 2051.2 53.0 681 1-690 1-737 (931)
2 COG5049 XRN1 5'-3' exonuclease 100.0 8E-209 2E-213 1697.6 47.2 638 1-681 1-764 (953)
3 KOG2045 5'-3' exonuclease XRN1 100.0 9E-180 2E-184 1489.5 39.9 561 1-624 1-655 (1493)
4 PF03159 XRN_N: XRN 5'-3' exon 100.0 2.2E-87 4.8E-92 685.8 20.0 237 1-256 1-237 (237)
5 cd00128 XPG Xeroderma pigmento 98.7 2E-07 4.3E-12 100.3 15.9 237 1-369 1-244 (316)
6 PTZ00217 flap endonuclease-1; 98.4 4.4E-06 9.5E-11 92.7 15.3 231 1-357 1-246 (393)
7 TIGR03674 fen_arch flap struct 97.7 0.00098 2.1E-08 72.8 15.4 65 51-120 23-96 (338)
8 PRK03980 flap endonuclease-1; 97.6 0.0013 2.9E-08 70.4 15.3 25 334-358 177-201 (292)
9 smart00475 53EXOc 5'-3' exonuc 96.0 0.43 9.4E-06 50.5 17.8 133 52-241 4-139 (259)
10 cd00008 53EXOc 5'-3' exonuclea 95.7 0.43 9.4E-06 49.8 16.4 56 52-108 4-62 (240)
11 PF00752 XPG_N: XPG N-terminal 95.1 0.025 5.4E-07 50.8 4.1 95 1-122 1-98 (101)
12 smart00485 XPGN Xeroderma pigm 94.9 0.034 7.4E-07 49.8 4.3 93 1-122 1-96 (99)
13 PRK14976 5'-3' exonuclease; Pr 94.1 2 4.3E-05 46.1 16.2 57 51-108 5-67 (281)
14 PF00867 XPG_I: XPG I-region; 94.1 0.16 3.6E-06 45.3 6.8 90 192-346 5-94 (94)
15 PF00098 zf-CCHC: Zinc knuckle 92.6 0.071 1.5E-06 33.8 1.4 16 264-279 2-17 (18)
16 KOG2519 5'-3' exonuclease [Rep 90.7 7.1 0.00015 44.3 15.4 34 334-369 217-250 (449)
17 KOG2518 5'-3' exonuclease [Rep 89.8 2.7 5.9E-05 48.3 11.3 91 1-122 1-96 (556)
18 COG0258 Exo 5'-3' exonuclease 89.2 8.2 0.00018 41.8 14.3 62 51-116 13-82 (310)
19 PRK05755 DNA polymerase I; Pro 87.4 12 0.00026 46.4 15.8 56 52-108 5-63 (880)
20 TIGR00593 pola DNA polymerase 81.7 58 0.0012 40.7 17.9 56 52-108 2-61 (887)
21 PF13696 zf-CCHC_2: Zinc knuck 75.6 1.1 2.4E-05 32.7 0.5 20 261-280 7-26 (32)
22 TIGR00600 rad2 DNA excision re 74.7 3.9 8.5E-05 51.0 5.1 39 191-242 785-823 (1034)
23 TIGR00600 rad2 DNA excision re 71.8 16 0.00035 45.8 9.4 65 51-121 26-94 (1034)
24 cd00080 HhH2_motif Helix-hairp 68.7 5.6 0.00012 34.2 3.3 22 334-355 8-31 (75)
25 PF13917 zf-CCHC_3: Zinc knuck 51.2 8 0.00017 30.0 1.1 19 262-280 4-22 (42)
26 smart00343 ZnF_C2HC zinc finge 48.9 8 0.00017 26.3 0.7 16 264-279 1-16 (26)
27 smart00484 XPGI Xeroderma pigm 45.4 12 0.00026 32.2 1.5 34 201-243 10-43 (73)
28 smart00279 HhH2 Helix-hairpin- 43.0 21 0.00045 26.7 2.2 19 335-354 3-21 (36)
29 PF02739 5_3_exonuc_N: 5'-3' e 42.1 24 0.00052 35.0 3.2 56 52-108 4-63 (169)
30 PF14392 zf-CCHC_4: Zinc knuck 34.7 18 0.00038 28.6 0.7 20 260-279 29-48 (49)
31 COG5082 AIR1 Arginine methyltr 31.0 21 0.00045 36.4 0.7 45 225-279 68-114 (190)
32 PF14787 zf-CCHC_5: GAG-polypr 30.3 25 0.00055 26.5 0.9 20 263-282 3-22 (36)
33 PF15288 zf-CCHC_6: Zinc knuck 30.2 24 0.00052 27.2 0.8 14 263-276 2-15 (40)
34 PHA02567 rnh RnaseH; Provision 30.2 56 0.0012 35.8 3.8 57 50-106 15-73 (304)
35 COG5082 AIR1 Arginine methyltr 29.0 24 0.00052 35.9 0.8 18 262-279 60-77 (190)
36 PF12513 SUV3_C: Mitochondrial 25.7 37 0.00081 26.8 1.2 16 5-20 12-27 (49)
37 COG5350 Predicted protein tyro 23.9 88 0.0019 31.1 3.6 42 190-234 56-105 (172)
38 PRK09482 flap endonuclease-lik 23.4 1.3E+02 0.0027 32.2 5.0 55 51-108 5-59 (256)
No 1
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=100.00 E-value=2.1e-250 Score=2051.24 Aligned_cols=681 Identities=59% Similarity=1.025 Sum_probs=625.7
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCCCCCCCHHHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPTSYDDVFK 80 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~~~p~te~e~~~ 80 (692)
||||+|||||++|||++|++|+|++|.+. +|+.||+|.|+|||||+||||||||||||||||+||+++|+|+||+|||+
T Consensus 1 MGVPaffRWLs~kyp~~I~~viEe~p~~~-~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPEdkPaP~tedEm~~ 79 (931)
T KOG2044|consen 1 MGVPAFFRWLSRKYPKTISPVIEEEPVDV-DGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPEDKPAPETEDEMFV 79 (931)
T ss_pred CCchHHHHHHHHhcchhhhhhhhcCcccC-CCcccccccCCCCCCcccccceeeecCcccccCCCCCCCCCCccHHHHHH
Confidence 99999999999999999999999999887 88999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccceeEEEeecCCCchhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhCcccCCCCCCCCCCCcc
Q 005531 81 SIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFEEAGKLLSAKEKPETCDSNV 160 (692)
Q Consensus 81 ~If~yid~lv~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~e~~~~~~~~~~~~~~~~~eg~~~~~~~~~~~fDsN~ 160 (692)
+||+||||||.||||||||||||||||||||||||||||||||||++++++++++++++++++|..++++.++++|||||
T Consensus 80 avFeyiDrlf~mvRPRkLLymAIDGVAPRAKMNQQRsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~~~~e~fDSNc 159 (931)
T KOG2044|consen 80 AVFEYIDRLFSMVRPRKLLYMAIDGVAPRAKMNQQRSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPKVKKETFDSNC 159 (931)
T ss_pred HHHHHHHHHHHhccchheeEEeecccCchhhhhHHHHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCchhhccccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecChhHHHH
Q 005531 161 ITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIML 240 (692)
Q Consensus 161 ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DADLImL 240 (692)
|||||+||++|+.+|+|||+.||++||+|+||+||+|||+||||||||||+|||+||++|+|||||+|||||+|||||||
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 HhhcCCceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHHHHhhhCC
Q 005531 241 SLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREYLQYELDI 320 (692)
Q Consensus 241 ~Lathe~~f~ILRe~v~~~~~~~~c~~c~~~~h~~~~c~~~~~~~~~~~~~~~~~~~~~~~f~~l~i~~LREyL~~e~~~ 320 (692)
|||||||||+||||+++ |+++++|++|||+||.+++|.|+.... +.+.....+..+++|+||+||+|||||+.||.+
T Consensus 240 gLATHE~hF~IlRE~~~-P~~~~~C~~cgq~gh~~~dc~g~~~~~--~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~ 316 (931)
T KOG2044|consen 240 GLATHEPHFSILREEFF-PNKPRRCFLCGQTGHEAKDCEGKPRLG--ETNELADVPGVEKPFIFLNISVLREYLERELRM 316 (931)
T ss_pred eccccCCceEEeeeeec-CCCcccchhhcccCCcHhhcCCcCCcc--cccccccCcccccceEEEEHHHHHHHHHHHhcC
Confidence 99999999999999977 999999999999999999999986411 112222334678999999999999999999999
Q ss_pred CCCCCCCchhhhHHHHHHHhhhhcCCCCCCCCccccccchHHHHHHHHHHHhhhcCCccccCCeechHHHHHHHHHHHHh
Q 005531 321 PNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQSVAVY 400 (692)
Q Consensus 321 ~~~~f~~d~eriIDDfVfLcf~~GNDFLPhlpsl~I~egaid~Li~~Yk~~l~~~~gYLt~~g~inl~~l~~~l~~l~~~ 400 (692)
|++||+||+||+||||||||||||||||||||||+|||||||+|+++||+.+++|+||||++|.+||.||+.||+.||..
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 HHHHHHHHHHHHHHHHHHHHHHHhhhhcc-----------------------------------------hhhhh-----
Q 005531 401 EDQIFQKRTRIQQAYEYNEAMKLNARRES-----------------------------------------SEELL----- 434 (692)
Q Consensus 401 E~~if~~r~~~~~~~~~~~~~~~~~r~~~-----------------------------------------~~~~~----- 434 (692)
|++||++|.+.+.+++.....+.+.+++. .++.+
T Consensus 397 Ed~IFkkR~r~~e~frrrk~~rk~~~~~~~~sg~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~ 476 (931)
T KOG2044|consen 397 EDDIFKKRQRREERFRRRKAARKRQDRNAQDSGTNFSLAGSRELEASEPAQKALKVSLEKNESAANVERDNTEDLKTKLK 476 (931)
T ss_pred cchHHHHhHhHHHHHHHhhhhhhhhhhhcccccccccccccccccccchhhhhhhhccccccchhhhcccchhhcccccc
Confidence 99999999766655553322111111000 00000
Q ss_pred ----------cCccccccccccCCcchHHhHHHHhhCCCChhhHHHHHHHHHHHHHHHHHHHhhhhccCcCccccccCCC
Q 005531 435 ----------QAPVAVADTVKLGEPGYKERYYADKFEISNPEEIDKVKKDVVLKYVEGLCWVCRYYYQDVCSWQWFYPYH 504 (692)
Q Consensus 435 ----------~~~~~~~d~v~l~e~~~k~rYY~~Kf~~~~~~~~~~~~~~~~~~Y~eGl~Wvl~YYy~G~~SW~WyYPyH 504 (692)
.+..+..|+|+|+|+|||+|||++||++++++ +++|++||.+|||||||||+||||||+||+||||||
T Consensus 477 ~~~~~k~~~~~~~~~~~D~VkL~e~G~keRYY~~KF~v~~~e--eq~R~~vv~~YveGLcWVl~YYyqGc~SW~WyYPYH 554 (931)
T KOG2044|consen 477 HGQRRKSEDSESEEENTDKVKLYEPGWKERYYEEKFDVTPDE--EQIRKDVVLKYVEGLCWVLRYYYQGCASWNWYYPYH 554 (931)
T ss_pred ccccccCccccCCCCCCcceeecCCchhhhhhhhhcCCCCHH--HHHHHHHHHHHhcchhhhhhhhhccccccccccccc
Confidence 11235678999999999999999999998775 789999999999999999999999999999999999
Q ss_pred CCcchhchhcccCccccccCCCCCChHHHhhhcCCCCCCCCchHHhhhccCCCCCcccccCCCcccccCCCCccceeeee
Q 005531 505 YAPFASDLKDLSDLEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPSSPIYKFYPPDFQIDMNGKRFAWQGVV 584 (692)
Q Consensus 505 YAPfasDl~~l~~~~i~F~~g~P~~P~eQLm~VlP~~S~~~LP~~~~~Lm~~~~SpI~dfYP~df~iD~nGk~~~WqgV~ 584 (692)
||||||||.+|++++|+|++|+||+||||||+||||+|+|+||+.||.||+||+|||+||||+||+||||||+|+|||||
T Consensus 555 YAPfAsDf~~l~~ldikFe~g~PFkP~eQLmgVlPAAS~~~LPe~~r~LMsdpdSpIiDFYPedF~iDmNGKk~aWQGIa 634 (931)
T KOG2044|consen 555 YAPFASDFKGLSDLDIKFELGKPFKPLEQLMGVLPAASSHALPEEWRKLMSDPDSPIIDFYPEDFEIDMNGKKYAWQGIA 634 (931)
T ss_pred cchhhhhhhcccccccccccCCCCCcHHHHhhhcchhhcCCCcHHHHhhhcCCCCcccccccccceeeccCceeeccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCChHHHHHHHhhhccCCCHHHHhhccCCCcEEEEcCCCccHHHHHHHhhhccCCCCCCCcceeccCCccCCcceeE
Q 005531 585 KLPFIDEKLLLRQTKKLEVFLTEEELFRNSVMLDLLYVHPQHPLYQQITLYCQLYHQLPPQDRFAWEIDVNASGGMNGYI 664 (692)
Q Consensus 585 lLPFID~~~Ll~a~~~~~~~Lt~eE~~RN~~g~~~lf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~g~~ 664 (692)
|||||||+|||+|+++++++||+||++||+.|.|+||++++||+++.|.++|++..+ ++... +++-...+.|++|.+
T Consensus 635 lLPFiDe~rLl~a~~~~y~~Lt~EE~~RN~rg~d~Lfi~~~hp~~e~i~~lysk~k~-~~~~~--v~~~~~~~p~~~~~~ 711 (931)
T KOG2044|consen 635 LLPFIDERRLLSAVAKVYPTLTDEEKRRNSRGPDLLFISDKHPLFEFILQLYSKKKK-SNEKN--VKLAHGVDPGLNGAI 711 (931)
T ss_pred cccccchhhHHHHHHhhccccCHHHHhccccCCceEEecCCCchHHHHHHHHHhhcc-Ccccc--cccccccCcccceee
Confidence 999999999999999999999999999999999999999999999999999998654 22222 244556667999999
Q ss_pred ecccCCCCCcccCCCCCCCCCCccCC
Q 005531 665 WLCERNGLRSIIPSPVKGLPDIERNQ 690 (692)
Q Consensus 665 ~~~~~~~~~~~~~~p~~~~~~~~~~~ 690 (692)
.+++.......+.||..++-+...+.
T Consensus 712 ~~~~~~~~~~i~~~p~~~~~~~~~~~ 737 (931)
T KOG2044|consen 712 SKDPEGLESGISKSPPGGLSDYNTNT 737 (931)
T ss_pred ccCccccccccccCChhhcccCCccc
Confidence 99887766667888887766655543
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=8.2e-209 Score=1697.61 Aligned_cols=638 Identities=46% Similarity=0.829 Sum_probs=557.9
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCCCCCCCHHHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPTSYDDVFK 80 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~~~p~te~e~~~ 80 (692)
||||+|||||++|||+|++.|.|+ +||| +||||||||||||+|+||+++++|.||+||+.
T Consensus 1 MGVPsfFRwlS~r~p~ii~~I~e~-----------------~~P~---~DNLYLDMNgIlH~CtHp~d~~~petEeEm~~ 60 (953)
T COG5049 1 MGVPSFFRWLSERYPKIIQLIEEK-----------------QIPE---FDNLYLDMNGILHNCTHPNDGSPPETEEEMYK 60 (953)
T ss_pred CCchHHHHHHHhhhhHhhhhhhcc-----------------CCCC---cceeEEecccccccCCCCCCCCCCCCHHHHHH
Confidence 999999999999999999988653 2444 59999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccceeEEEeecCCCchhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHH----HhCcccCC-CCCCCC
Q 005531 81 SIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFE----EAGKLLSA-KEKPET 155 (692)
Q Consensus 81 ~If~yid~lv~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~e~~~~~~~~~~~~~~~~----~eg~~~~~-~~~~~~ 155 (692)
.||+|||||+.++||||+||||||||||||||||||+||||+|++|..+..+.+.-.+++. ..|..+.. ..+++.
T Consensus 61 aVf~Yidhil~~irPrKllymAVDGvAPRAKMNQQRaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~~~~~kk~ 140 (953)
T COG5049 61 AVFEYIDHILLKIRPRKLLYMAVDGVAPRAKMNQQRARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDTIDVEKKK 140 (953)
T ss_pred HHHHHHHHHHHhcCcceEEEEEecccCchhhhhHHHHHhhhhhhhhHHHHhhccccccccchhccccCCccchhhhhhcc
Confidence 9999999999999999999999999999999999999999999996654433332222222 22333322 235678
Q ss_pred CCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecCh
Q 005531 156 CDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDA 235 (692)
Q Consensus 156 fDsN~ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DA 235 (692)
||||||||||+||++|++.|+|||+.||++||.|+|++||+||+.||||||||||+|||+||++|+|+|||+|||||+||
T Consensus 141 fDSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDA 220 (953)
T COG5049 141 FDSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDA 220 (953)
T ss_pred ccccCCCCCChHHHHHHHHHHHHHHhhhcCCccceeEEEEEecCcCCCccHHHHHHHHHhcccCCCcCCCceeEEeccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHhhcCCceEEEeeccccCCC---CCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHH
Q 005531 236 DLIMLSLATHEIHFSILREVITLPG---QQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLRE 312 (692)
Q Consensus 236 DLImL~Lathe~~f~ILRe~v~~~~---~~~~c~~c~~~~h~~~~c~~~~~~~~~~~~~~~~~~~~~~~f~~l~i~~LRE 312 (692)
|||||||+||+|||.||||+|+++. +.++|..||.+||....|+.. ..++|.||||++|||
T Consensus 221 DLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k~~----------------~~q~F~~LhiSlLRE 284 (953)
T COG5049 221 DLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKVL----------------THQPFYLLHISLLRE 284 (953)
T ss_pred cceeeecccCCCeeEEeechhccCcccccccccccccccccchhhhccc----------------ccCceEEEEHHHHHH
Confidence 9999999999999999999999985 346899999999998888532 346899999999999
Q ss_pred HHHhhhCCCCCCCCCchhhhHHHHHHHhhhhcCCCCCCCCccccccchHHHHHHHHHHHhhhcCCccccCCeechHHHHH
Q 005531 313 YLQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEK 392 (692)
Q Consensus 313 yL~~e~~~~~~~f~~d~eriIDDfVfLcf~~GNDFLPhlpsl~I~egaid~Li~~Yk~~l~~~~gYLt~~g~inl~~l~~ 392 (692)
||+.||..|+.+|+||+|||||||||||||||||||||||+|+|++|||++|+++||+.++.|+||||++|.||+.||+.
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 HHHHHHHhHHHHHHHHHHHHHHHH----H---HHHHHH-----------h-----------------hhh-----cc---
Q 005531 393 FIQSVAVYEDQIFQKRTRIQQAYE----Y---NEAMKL-----------N-----------------ARR-----ES--- 429 (692)
Q Consensus 393 ~l~~l~~~E~~if~~r~~~~~~~~----~---~~~~~~-----------~-----------------~r~-----~~--- 429 (692)
++..|+..|+.||+++...+.+.. + .++++. + ++. +.
T Consensus 365 ~L~~L~~~E~~iFk~~~~qe~r~ne~~~~~~~~k~~~e~~~~~~~vv~eq~~~~gS~k~t~~d~~~~kk~~~l~~e~~id 444 (953)
T COG5049 365 ILAILGSFEDDIFKKDHIQEERKNESLERFSLRKERKEGLKGMPRVVYEQKKLIGSIKPTLMDQLQEKKSPDLPDEEFID 444 (953)
T ss_pred HHHHHhhhhcchhhhhhhHhhhhccchhhHHHHhhhhhhhcccchhhhhhhhhcccccchhhhhhhhhccccCCCccccc
Confidence 999999999999988764332110 0 000000 0 000 00
Q ss_pred ----------------------------hh-------hhh----------------c---------------------Cc
Q 005531 430 ----------------------------SE-------ELL----------------Q---------------------AP 437 (692)
Q Consensus 430 ----------------------------~~-------~~~----------------~---------------------~~ 437 (692)
+. .++ . ..
T Consensus 445 ~~a~~k~~d~kn~el~~~~~~ndl~ls~ska~ks~~n~~le~~iasds~~ed~ee~ese~d~i~~i~dk~vn~~v~ee~e 524 (953)
T COG5049 445 TLALPKDLDMKNHELFLKRFANDLGLSISKAIKSKGNYSLEMDIASDSPDEDEEEFESEVDSIRKIPDKYVNIIVEEEEE 524 (953)
T ss_pred hhhchhhhhhhhhHHHHHHHHhhhhhhHHhhhhccCCchhhhhhhccccccchhhhhhccchhhhhhhhhhccccccchh
Confidence 00 000 0 00
Q ss_pred cccccccccCCcchHHhHHHHhhCCCChhhHHHHHHHHHHHHHHHHHHHhhhhccCcCccccccCCCCCcchhchhcccC
Q 005531 438 VAVADTVKLGEPGYKERYYADKFEISNPEEIDKVKKDVVLKYVEGLCWVCRYYYQDVCSWQWFYPYHYAPFASDLKDLSD 517 (692)
Q Consensus 438 ~~~~d~v~l~e~~~k~rYY~~Kf~~~~~~~~~~~~~~~~~~Y~eGl~Wvl~YYy~G~~SW~WyYPyHYAPfasDl~~l~~ 517 (692)
.+..++|++-++||++|||.+||+++++ +.+++ ++||++|||||||||.|||+|||||+|||||||||+|+||.++.+
T Consensus 525 ~~~~~Tv~l~~~g~~erYY~~K~~~t~~-~~E~i-rdm~k~YVeGL~WVL~YYY~GC~SW~WyYpyHyAP~aaD~~k~~~ 602 (953)
T COG5049 525 NETEKTVNLRFPGWKERYYTSKLHFTTD-SEEKI-RDMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSD 602 (953)
T ss_pred cccccchhhcccchhhhhhhhhcCCCcC-CHHHH-HHHHHHHhhhhhhhhhhhhcCCCCcccccccccchhhhhhhhccc
Confidence 1234678888999999999999999765 34555 499999999999999999999999999999999999999999999
Q ss_pred ccccccCCCCCChHHHhhhcCCCCCCCCchHHhhhccCCCCCcccccCCCcccccCCCCccceeeeecccCCChHHHHHH
Q 005531 518 LEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPSSPIYKFYPPDFQIDMNGKRFAWQGVVKLPFIDEKLLLRQ 597 (692)
Q Consensus 518 ~~i~F~~g~P~~P~eQLm~VlP~~S~~~LP~~~~~Lm~~~~SpI~dfYP~df~iD~nGk~~~WqgV~lLPFID~~~Ll~a 597 (692)
.+|+|+.|+||+||||||+||||+|+++||+.||.||+|++|||+||||++|.+|||||+++|||||||||||++||++|
T Consensus 603 ~dIkFe~g~PF~P~EQLm~VLPa~Sk~~vP~~fr~LM~d~~S~IiDFYPe~f~lD~NGK~~~Wq~VvLlpFiDe~RLl~A 682 (953)
T COG5049 603 NDIKFELGTPFRPFEQLMAVLPARSKNLVPEGFRPLMDDEKSPIIDFYPEEFKLDMNGKTASWQAVVLLPFIDERRLLSA 682 (953)
T ss_pred ceeeecCCCCCCcHHHHHhhcchhhcCcCchhhhhhhcCCCCcccccchhhcccccCCceeeeeeeEEeeecchhHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhhccCCCHHHHhhccCCCcEEEEcCCCccHH-HHHHHhhhccCCCCCCCcceeccCCccC-CcceeEecc-cCCCCCc
Q 005531 598 TKKLEVFLTEEELFRNSVMLDLLYVHPQHPLYQ-QITLYCQLYHQLPPQDRFAWEIDVNASG-GMNGYIWLC-ERNGLRS 674 (692)
Q Consensus 598 ~~~~~~~Lt~eE~~RN~~g~~~lf~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~-g~~g~~~~~-~~~~~~~ 674 (692)
+++.+++||+||+.||.+|.++||.++.++.+. .+..+|.++. +...+.++...+. |+.|.|... +..+|+.
T Consensus 683 ~~~~~~~Ls~eE~~RN~~g~~llf~s~~~~~~~~l~~~lysk~~-----~~~~~~m~~~~~~~GL~g~v~~~ae~~~pn~ 757 (953)
T COG5049 683 VAVKYPTLSEEERKRNLRGLDLLFSSNKKSDLSELFKDLYSKCK-----QKEYITMCSKESPYGLFGTVKLGAEGLAPNL 757 (953)
T ss_pred HHhhcccCCHHHHhccccCCceeEeccCCccHHHHHHHHHHhhc-----cCCceeeeccccccccccccccccccccccc
Confidence 999999999999999999999999999988654 4557898763 2344567776666 999999986 6667777
Q ss_pred ccCCCCC
Q 005531 675 IIPSPVK 681 (692)
Q Consensus 675 ~~~~p~~ 681 (692)
.+.+|+.
T Consensus 758 ~~lcp~~ 764 (953)
T COG5049 758 LSLCPIS 764 (953)
T ss_pred cccCccc
Confidence 8888985
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=8.8e-180 Score=1489.51 Aligned_cols=561 Identities=46% Similarity=0.842 Sum_probs=489.8
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCC--CCCCCHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGK--PAPTSYDDV 78 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~--~~p~te~e~ 78 (692)
||||.||||+++|||.+ ++++|+ .+|| ||||||||||||||+|+||++. ..+.|||||
T Consensus 1 MGvPKFfR~iSERyP~l-seliee--------~qIP-----------EFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEi 60 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPCL-SELIEE--------HQIP-----------EFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEI 60 (1493)
T ss_pred CCchHHHHHhhhhchHH-HHHhhh--------ccCC-----------cccceeeecccccccCCCCCCCccCcCCCHHHH
Confidence 99999999999999986 456654 4455 8999999999999999999865 357899999
Q ss_pred HHHHHHHHHHHHhhcccceeEEEeecCCCchhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhCcccCCCCCCCCCCC
Q 005531 79 FKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFEEAGKLLSAKEKPETCDS 158 (692)
Q Consensus 79 ~~~If~yid~lv~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~e~~~~~~~~~~~~~~~~~eg~~~~~~~~~~~fDs 158 (692)
|.+||+|||+||.++||+|++|||||||||||||||||+||||+|++|..+... ....|+..+ .+.|||
T Consensus 61 f~~IfnYIdhLf~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaK-------A~enGe~~p----~erFDS 129 (1493)
T KOG2045|consen 61 FQEIFNYIDHLFYLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAK-------AAENGELRP----HERFDS 129 (1493)
T ss_pred HHHHHHHHHHHHHhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHH-------HHhccccCc----cccccc
Confidence 999999999999999999999999999999999999999999999998765332 223565443 378999
Q ss_pred cccccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecChhHH
Q 005531 159 NVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLI 238 (692)
Q Consensus 159 N~ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DADLI 238 (692)
|||||||+||.+|++.|+|||+.|+++|+.|++++||+||++||||||||||+|||.++++|+||||||||+||+|||||
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 HHHhhcCCceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHHHHhhh
Q 005531 239 MLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREYLQYEL 318 (692)
Q Consensus 239 mL~Lathe~~f~ILRe~v~~~~~~~~c~~c~~~~h~~~~c~~~~~~~~~~~~~~~~~~~~~~~f~~l~i~~LREyL~~e~ 318 (692)
||||.||+|||.+|||+|+|+.+.+ .+....++|.+||+++|||||+.||
T Consensus 210 mLGL~tHepHF~lLREEVtFgrrn~------------------------------~k~lehqkFyLLHLsLLREYlelEF 259 (1493)
T KOG2045|consen 210 MLGLCTHEPHFVLLREEVTFGRRNK------------------------------RKSLEHQKFYLLHLSLLREYLELEF 259 (1493)
T ss_pred eeeeccCCcceeeeeeeeecccccc------------------------------cchhhhhhhhhhHHHHHHHHHHHHH
Confidence 9999999999999999999863211 0112346799999999999999999
Q ss_pred CC--CCCCCCCchhhhHHHHHHHhhhhcCCCCCCCCccccccchHHHHHHHHHHHhhhcCCccccCCeechHHHHHHHHH
Q 005531 319 DI--PNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQS 396 (692)
Q Consensus 319 ~~--~~~~f~~d~eriIDDfVfLcf~~GNDFLPhlpsl~I~egaid~Li~~Yk~~l~~~~gYLt~~g~inl~~l~~~l~~ 396 (692)
.- ...+|++|+|||+||||+|.||||||||||||+|.|.+||+..|..+||+.++++||||.++|+||+.||+.||.+
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 72 3578999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhHHHHHHHHHHHHHHHHHHHH--------------HHH----hh----hhcchhhh---------------------
Q 005531 397 VAVYEDQIFQKRTRIQQAYEYNEA--------------MKL----NA----RRESSEEL--------------------- 433 (692)
Q Consensus 397 l~~~E~~if~~r~~~~~~~~~~~~--------------~~~----~~----r~~~~~~~--------------------- 433 (692)
|..+|.++|+++.+..+..++... .+. +. ..+.+..+
T Consensus 340 L~nfeke~Fke~led~k~~nskr~r~~~~~~~~~~~~dika~t~sq~~d~l~~~~~~~p~i~~~a~ld~dD~~Fl~~~~e 419 (1493)
T KOG2045|consen 340 LTNFEKEHFKEHLEDLKYMNSKRERFDDPEQQELAEMDIKAITESQNLDSLLGEESKDPLINKSALLDDDDSAFLSDHEE 419 (1493)
T ss_pred HHhhhHHHHHHHHHhhhhccccccccccHHHHhhhcccHHhhhhhhhhhhhccccccccccccccccccchHHHHHHhhh
Confidence 999999999988754432111000 000 00 00000000
Q ss_pred --------------h-c--Cccccccc---------------------c-ccCC--------cchHHhHHHHhhCCCChh
Q 005531 434 --------------L-Q--APVAVADT---------------------V-KLGE--------PGYKERYYADKFEISNPE 466 (692)
Q Consensus 434 --------------~-~--~~~~~~d~---------------------v-~l~e--------~~~k~rYY~~Kf~~~~~~ 466 (692)
+ . ...+.+|+ . -+|| ..||..||++|++.++.+
T Consensus 420 Dl~~~~~~s~s~~~~ld~~~~de~EdEf~~~~~t~~ls~~~~~~~~n~eea~~eKti~n~~F~rwK~~yYrdKlkf~~~d 499 (1493)
T KOG2045|consen 420 DLSDLEPGSGSDELLLDNLDADELEDEFAVELATLALSGMNDADFANDEEACWEKTILNKEFQRWKRNYYRDKLKFDPND 499 (1493)
T ss_pred hccccccccCccchhhccccchhhhHHHHHHHHHHHHhccccccccchHHHhhhhhhHHHHHHHHHHHHhhhhhcCCCcc
Confidence 0 0 00000011 0 0121 269999999999997653
Q ss_pred hHHHHHHHHHHHHHHHHHHHhhhhccCcCccccccCCCCCcchhchhcccCccccccCCCCCChHHHhhhcCCCCCCCCc
Q 005531 467 EIDKVKKDVVLKYVEGLCWVCRYYYQDVCSWQWFYPYHYAPFASDLKDLSDLEITFFLGEPFRPFDQLMGTLPAASSSAL 546 (692)
Q Consensus 467 ~~~~~~~~~~~~Y~eGl~Wvl~YYy~G~~SW~WyYPyHYAPfasDl~~l~~~~i~F~~g~P~~P~eQLm~VlP~~S~~~L 546 (692)
++..+++|..|||||||||.|||+||+||+||||||||||+||+++.-+++|.|+.|+||+||||||||||++|+.+|
T Consensus 500 --ee~lrelae~YVeaLQWvL~YYYrGc~SWsWyYphHyaP~ISDl~kgldv~ieF~mgtPF~PFqQLlAVLPaaSa~ll 577 (1493)
T KOG2045|consen 500 --EELLRELAEHYVEALQWVLDYYYRGCQSWSWYYPHHYAPFISDLKKGLDVEIEFHMGTPFLPFQQLLAVLPAASAKLL 577 (1493)
T ss_pred --HHHHHHHHHHHHHHHHHHHHHHhcCCccccccccccccchhHhHhcccceeEEEecCCCCCcHHHHHHhchhhhhccC
Confidence 456689999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHhhhccCCCCCcccccCCCcccccCCCCccceeeeecccCCChHHHHHHHhhhccCCCHHHHhhccCCCcEEEEcC
Q 005531 547 PEKYRNLMTDPSSPIYKFYPPDFQIDMNGKRFAWQGVVKLPFIDEKLLLRQTKKLEVFLTEEELFRNSVMLDLLYVHP 624 (692)
Q Consensus 547 P~~~~~Lm~~~~SpI~dfYP~df~iD~nGk~~~WqgV~lLPFID~~~Ll~a~~~~~~~Lt~eE~~RN~~g~~~lf~~~ 624 (692)
|.+||+||.++.|||+||||.+|+.|+|||+.+|++|||+|||||+||++||.+....||.||+.||++|.+++|.+.
T Consensus 578 Pp~frdLM~~~~SPI~DFYPaefelD~NGKtadWEAVVLIpFIdEkRLleAm~pk~~~Ls~EEr~RNs~g~~~vys~~ 655 (1493)
T KOG2045|consen 578 PPAFRDLMLLPTSPIADFYPAEFELDLNGKTADWEAVVLIPFIDEKRLLEAMLPKEAQLSLEERERNSHGPMYVYSYS 655 (1493)
T ss_pred ChhhhHhhcCCCCchhhcchhhheecccCCccceeEEEEEeecchHHHHHHHhhHhhhcCHHHhhhcccCCceeeecc
Confidence 999999999999999999999999999999999999999999999999999999999999999999999999999754
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=2.2e-87 Score=685.83 Aligned_cols=237 Identities=57% Similarity=1.028 Sum_probs=193.2
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCCCCCCCHHHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPTSYDDVFK 80 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~~~p~te~e~~~ 80 (692)
||||+|||||++|||.++..+.+... ..+|||||||||||||+|+|++..+.+.++++||+
T Consensus 1 MGVp~f~~wl~~ryp~~~~~~~~~~~-------------------~~~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~ 61 (237)
T PF03159_consen 1 MGVPGFFRWLSERYPLIVRPISENSI-------------------PSEFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQ 61 (237)
T ss_dssp --CCHHHHHHHHHSGGGEEEECTTTS-------------------EE-ESEEEEETHHHHHHHHS-SSS----SHHHHHH
T ss_pred CCHHHHHHHHHHhCCcceeeccccCC-------------------CCcCCEEEEEcchhhhHhcCCcccCCCccHHHHHH
Confidence 99999999999999999987754321 12699999999999999999998888999999999
Q ss_pred HHHHHHHHHHhhcccceeEEEeecCCCchhhhHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHhCcccCCCCCCCCCCCcc
Q 005531 81 SIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFEEAGKLLSAKEKPETCDSNV 160 (692)
Q Consensus 81 ~If~yid~lv~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~e~~~~~~~~~~~~~~~~~eg~~~~~~~~~~~fDsN~ 160 (692)
+||+|||+||++|||||+||||||||||||||||||+|||+++++++....+..+...+...+|...+.......||||+
T Consensus 62 ~i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~ 141 (237)
T PF03159_consen 62 RIFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPEDQEEKFDSNC 141 (237)
T ss_dssp HHHHHHHHHHHHH-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HHHHS----GGG
T ss_pred HHHHHHHHhheeecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchhHHHHHHHHhhhhhhccccccccccccccccce
Confidence 99999999999999999999999999999999999999999999998887777777777777776555444568999999
Q ss_pred cccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecChhHHHH
Q 005531 161 ITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIML 240 (692)
Q Consensus 161 ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DADLImL 240 (692)
|||||+||.+|+++|++|+++|+++||.|++++||+||++||||||||||+|||+++++|+|+||++|||||+|||||||
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 HhhcCCceEEEeeccc
Q 005531 241 SLATHEIHFSILREVI 256 (692)
Q Consensus 241 ~Lathe~~f~ILRe~v 256 (692)
||++|++||+||||+|
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=98.74 E-value=2e-07 Score=100.28 Aligned_cols=237 Identities=17% Similarity=0.239 Sum_probs=126.9
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCCC--CCCCHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKP--APTSYDDV 78 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~~--~p~te~e~ 78 (692)
|||++|..||...-+.+ ++ ++ . .| --|=||.++.+|.+....... ........
T Consensus 1 MGI~gL~~~l~~~~~~~--~i-~~--------------l-----~g---k~laID~~~~l~r~~~a~~~~~~~~g~~~~~ 55 (316)
T cd00128 1 MGIKGLWPLLKPVARPV--HL-EE--------------L-----RG---KKVAIDASIWLYQFLKACRQELGSGGETTSH 55 (316)
T ss_pred CchhhHHHHHHhhCCCC--CH-HH--------------h-----CC---cEEEecHHHHHHHHHHHhhhhccCCCCCcHH
Confidence 99999999999876653 11 10 0 01 147899999999875432110 11111233
Q ss_pred HHHHHHHHHHHHhhcccceeEEEeecCCCchhhhHHHHHhhhhhH--HHHHHHHHH---HHHHHHHHHHhCcccCCCCCC
Q 005531 79 FKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAA--KDAAEAEAE---EERLRKEFEEAGKLLSAKEKP 153 (692)
Q Consensus 79 ~~~If~yid~lv~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa--~e~~~~~~~---~~~~~~~~~~eg~~~~~~~~~ 153 (692)
...++..+.+|+.. .. + ..+++||.+|-.|......||-+.. +.......+ .++..+..
T Consensus 56 l~~~~~rl~~L~~~-~i-~-pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~------------- 119 (316)
T cd00128 56 LQGFFYRTCRLLEL-GI-K-PVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLE------------- 119 (316)
T ss_pred HHHHHHHHHHHHHC-CC-E-EEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHH-------------
Confidence 44555555555542 22 3 3467999999888777665554322 111111100 00111000
Q ss_pred CCCCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEec
Q 005531 154 ETCDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGL 233 (692)
Q Consensus 154 ~~fDsN~ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~ 233 (692)
. .+..+||.. ... ++..+.. -++.+|.+ |||+|-=+-..-+. .....|+|.
T Consensus 120 ~--~~~~~~~~~--~~~----~~~lL~~--------~gi~~i~a----p~EAdaq~a~l~~~---------g~v~~i~S~ 170 (316)
T cd00128 120 R--RAVRVTPQM--IEE----AKELLRL--------MGIPYIVA----PYEAEAQCAYLAKK---------GLVDAIITE 170 (316)
T ss_pred h--ccCcCCHHH--HHH----HHHHHHH--------cCCCEEEC----CcCHHHHHHHHHhC---------CCeeEEEec
Confidence 0 012345532 122 3332221 15677764 79999765544331 235789999
Q ss_pred ChhHHHHHhhcCCceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHH
Q 005531 234 DADLIMLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREY 313 (692)
Q Consensus 234 DADLImL~Lathe~~f~ILRe~v~~~~~~~~c~~c~~~~h~~~~c~~~~~~~~~~~~~~~~~~~~~~~f~~l~i~~LREy 313 (692)
|+|+++++- ++ ++|.- ... ....++.++..-+.+.
T Consensus 171 DsD~l~fg~----~~--vi~~~-~~~--------------------------------------~~~~~~~~~~~~~~~~ 205 (316)
T cd00128 171 DSDLLLFGA----PR--VYRNL-FDS--------------------------------------GAKPVEEIDLEKILKE 205 (316)
T ss_pred CCCeeeecC----ce--EEEec-ccC--------------------------------------CCCceEEEEHHHHHHH
Confidence 999988762 22 33321 000 0023556776555444
Q ss_pred HHhhhCCCCCCCCCchhhhHHHHHHHhhhhcCCCCCCCCccccccchHHHHHHHHH
Q 005531 314 LQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYR 369 (692)
Q Consensus 314 L~~e~~~~~~~f~~d~eriIDDfVfLcf~~GNDFLPhlpsl~I~egaid~Li~~Yk 369 (692)
+ . +. -+.|+.+|.|+|+||+|++|++-+.. |+. |+..|.
T Consensus 206 l----g---------l~--~~q~id~~~L~G~Dy~~gv~giG~k~-A~~-li~~~~ 244 (316)
T cd00128 206 L----G---------LT--REKLIDLAILLGCDYTEGIPGIGPVT-ALK-LIKKYG 244 (316)
T ss_pred c----C---------CC--HHHHHHHHHhcCCCCCCCCCCccHHH-HHH-HHHHcC
Confidence 3 2 12 24788999999999999999866542 333 444444
No 6
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.41 E-value=4.4e-06 Score=92.70 Aligned_cols=231 Identities=19% Similarity=0.287 Sum_probs=125.8
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCC-----CCCC----
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPD-----GKPA---- 71 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~-----~~~~---- 71 (692)
|||.++...|....|.+++.+- ...--| =-+-||....+|.....- +.+.
T Consensus 1 MGI~gL~~~l~~~~p~~~~~~~----l~~l~g-----------------k~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~ 59 (393)
T PTZ00217 1 MGIKGLSKFLADKAPNAIKEQE----LKNYFG-----------------RVIAIDASMALYQFLIAIRDDSQGGNLTNEA 59 (393)
T ss_pred CChhhHHHHHhhhccccccccC----HHHhCC-----------------cEEEEeHHHHHHHHHHHcccccccccchhcc
Confidence 9999999999999999875431 000011 147899999999854211 1110
Q ss_pred CCCHHHHHHHHHHHHHHHHhh-cccceeEEEeecCCCchhhhHHHHHhh--hhhHHHHHHHHHH---HHHHHHHHHHhCc
Q 005531 72 PTSYDDVFKSIFDYIDHIFLL-VRPRKLLYLAIDGVAPRAKMNQQRTRR--FRAAKDAAEAEAE---EERLRKEFEEAGK 145 (692)
Q Consensus 72 p~te~e~~~~If~yid~lv~~-vrPrkllyiAiDGVAPrAKmnQQRsRR--frsa~e~~~~~~~---~~~~~~~~~~eg~ 145 (692)
-... .-+.-+|..+-+|+.. ++| .+++||.+|-.|...-..|| ...+.+..+...+ .+++++...
T Consensus 60 G~~t-~~l~g~~~r~~~Ll~~gikP----v~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~---- 130 (393)
T PTZ00217 60 GEVT-SHISGLFNRTIRLLEAGIKP----VYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSK---- 130 (393)
T ss_pred CCcc-HHHHHHHHHHHHHHHCCCCE----EEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHh----
Confidence 0011 2234556666677764 788 47999999976665443333 3223221111000 011111110
Q ss_pred ccCCCCCCCCCCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCC
Q 005531 146 LLSAKEKPETCDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPN 225 (692)
Q Consensus 146 ~~~~~~~~~~fDsN~ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn 225 (692)
.+..||+- -+..+.+ .+.. -++.+|.+ |||+|.=|-..-+ .+
T Consensus 131 -----------r~~~vt~~--~~~~~~~----lL~~--------~Gip~i~A----P~EAdaq~A~L~~---------~g 172 (393)
T PTZ00217 131 -----------RTVRVTKE--QNEDAKK----LLRL--------MGIPVIEA----PCEAEAQCAELVK---------KG 172 (393)
T ss_pred -----------hcccCCHH--HHHHHHH----HHHH--------cCCceEEC----CcCHHHHHHHHHH---------CC
Confidence 01123321 2222222 2211 24667754 7999995544432 24
Q ss_pred CcEEEEecChhHHHHHhhcCCceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEE
Q 005531 226 TRHCLYGLDADLIMLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFL 305 (692)
Q Consensus 226 ~~H~IyG~DADLImL~Lathe~~f~ILRe~v~~~~~~~~c~~c~~~~h~~~~c~~~~~~~~~~~~~~~~~~~~~~~f~~l 305 (692)
....|++.|.|+++++- + .++|.- +..+ .....++.+
T Consensus 173 ~v~~ViS~D~D~l~fg~----~--~vi~~l-~~~~------------------------------------~~~~~~~~~ 209 (393)
T PTZ00217 173 KVYAVATEDMDALTFGT----P--VLLRNL-NFSE------------------------------------AKKRPIQEI 209 (393)
T ss_pred CeEEEeCCCcCeeecCC----c--EEEEcc-cccc------------------------------------cCCCCeEEE
Confidence 56789999999998872 2 334431 1000 011235667
Q ss_pred ehHHHHHHHHhhhCCCCCCCCCchhhhHHHHHHHhhhhcCCCCCCCCccccc
Q 005531 306 NIWVLREYLQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIR 357 (692)
Q Consensus 306 ~i~~LREyL~~e~~~~~~~f~~d~eriIDDfVfLcf~~GNDFLPhlpsl~I~ 357 (692)
+...+.+.+ . +. -+.||-+|.|+|.||+|.+|++-..
T Consensus 210 ~~~~v~~~~----g---------l~--~~q~id~~iL~G~Dy~pgi~GIG~k 246 (393)
T PTZ00217 210 NLSTVLEEL----G---------LS--MDQFIDLCILCGCDYCDTIKGIGPK 246 (393)
T ss_pred EHHHHHHHh----C---------CC--HHHHHHHHHHhCCCCCCCCCCccHH
Confidence 776554432 2 11 2578889999999999999986553
No 7
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=97.66 E-value=0.00098 Score=72.84 Aligned_cols=65 Identities=15% Similarity=0.211 Sum_probs=40.2
Q ss_pred eEEeeccccccccccCC---CCCCCCC-----HHHHHHHHHHHHHHHHhh-cccceeEEEeecCCCchhhhHHHHHhhh
Q 005531 51 NLYLDMNGIIHPCFHPD---GKPAPTS-----YDDVFKSIFDYIDHIFLL-VRPRKLLYLAIDGVAPRAKMNQQRTRRF 120 (692)
Q Consensus 51 nLYlDmNgIIH~c~h~~---~~~~p~t-----e~e~~~~If~yid~lv~~-vrPrkllyiAiDGVAPrAKmnQQRsRRf 120 (692)
-+-||....+|.+...- ++. +.+ ...-+..+|..+-+|+.. ++| .+++||.+|-.|..+-..||-
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 VVAVDAFNALYQFLSSIRQPDGT-PLMDSRGRITSHLSGLFYRTINLLENGIKP----VYVFDGKPPELKAETLEERRE 96 (338)
T ss_pred EEEEeHHHHHHHHHHHHhccccc-hhhhccCCCcHHHHHHHHHHHHHHHCCCeE----EEEECCCChhhhHhhHHHHHH
Confidence 47899999999765421 110 111 012234445555566665 778 799999999877776666654
No 8
>PRK03980 flap endonuclease-1; Provisional
Probab=97.61 E-value=0.0013 Score=70.43 Aligned_cols=25 Identities=16% Similarity=0.491 Sum_probs=21.5
Q ss_pred HHHHHHhhhhcCCCCCCCCcccccc
Q 005531 334 DDFVFLCFFVGNDFLPHMPTLEIRE 358 (692)
Q Consensus 334 DDfVfLcf~~GNDFLPhlpsl~I~e 358 (692)
+.|+-+|.|+|.||.|++|++-+..
T Consensus 177 ~q~id~~iL~G~Dy~~GI~GIG~kt 201 (292)
T PRK03980 177 EQLIDIAILVGTDYNPGIKGIGPKT 201 (292)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHHH
Confidence 4678899999999999999877653
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=95.99 E-value=0.43 Score=50.53 Aligned_cols=133 Identities=14% Similarity=0.188 Sum_probs=73.5
Q ss_pred EEeeccccccccccCCCC--CCCCCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCchhhhHHHHHhhhhhHHHHHHH
Q 005531 52 LYLDMNGIIHPCFHPDGK--PAPTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEA 129 (692)
Q Consensus 52 LYlDmNgIIH~c~h~~~~--~~p~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAPrAKmnQQRsRRfrsa~e~~~~ 129 (692)
|-||.|++||.++|.-.. ...-........++..+-+++...+|..+ .+|+||-.|.- |..-+-.
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~-~~~fD~~~~~~-----R~~l~p~------- 70 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYV-AVVFDAKGKTF-----RHELYPE------- 70 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeE-EEEEeCCCCcc-----ccchhHH-------
Confidence 689999999998885311 00001123344456666677777799875 59999854421 1111111
Q ss_pred HHHHHHHHHHHHHhCcccCCCCCCCCCCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCcccEEEEcCCCCCC-ChhhH
Q 005531 130 EAEEERLRKEFEEAGKLLSAKEKPETCDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPG-EGEHK 208 (692)
Q Consensus 130 ~~~~~~~~~~~~~eg~~~~~~~~~~~fDsN~ITPGT~FM~~L~~~L~~yi~~kl~~dp~w~~l~VI~Sds~vPG-EGEhK 208 (692)
+.+ +.. =+|. .|..++ .++++-+.. -++.+| .+|| |++==
T Consensus 71 ----------YKa-~R~--------------~~pe-----~L~~q~-~~~~~~l~~----~gi~~i----~~~g~EADD~ 111 (259)
T smart00475 71 ----------YKA-NRP--------------KTPD-----ELLEQI-PLIKELLDA----LGIPVL----EVEGYEADDV 111 (259)
T ss_pred ----------HHh-CCC--------------CCCH-----HHHHHH-HHHHHHHHH----CCCCEE----eeCCcCHHHH
Confidence 111 000 0111 144444 344443332 223444 2788 99987
Q ss_pred HHHHHHHhhcCCCCCCCCcEEEEecChhHHHHH
Q 005531 209 IMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLS 241 (692)
Q Consensus 209 Im~fIR~qr~~p~ydpn~~H~IyG~DADLImL~ 241 (692)
|-...++.... +...+|++.|-|+.-|.
T Consensus 112 iatla~~~~~~-----g~~~~IvS~DkDl~ql~ 139 (259)
T smart00475 112 IATLAKKAEAE-----GYEVRIVSGDKDLLQLV 139 (259)
T ss_pred HHHHHHHHHhC-----CCeEEEEeCCCcHhhcC
Confidence 77766654331 34689999999998764
No 10
>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=95.73 E-value=0.43 Score=49.81 Aligned_cols=56 Identities=7% Similarity=0.082 Sum_probs=38.4
Q ss_pred EEeeccccccccccCCCCCC---CCCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc
Q 005531 52 LYLDMNGIIHPCFHPDGKPA---PTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (692)
Q Consensus 52 LYlDmNgIIH~c~h~~~~~~---p~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP 108 (692)
|.||.|+++|.+.|...... .-........++..+-+++...+|.+. .+|+||-+|
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 68999999999888652111 011223445566677778888899997 699999644
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=95.11 E-value=0.025 Score=50.75 Aligned_cols=95 Identities=18% Similarity=0.350 Sum_probs=56.3
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCCCCCC--CHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPT--SYDDV 78 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~~~p~--te~e~ 78 (692)
|||++|..+|.... .+..+. .. +. +| --|=||.+..+|.+.+....+... .....
T Consensus 1 MGI~gL~~~l~~~~--~v~~~~----~~---------~l-----~g---~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~ 57 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA--AVRKVS----LS---------EL-----RG---KRVAIDASCWLHQFLFSCREELGQGVGTDSH 57 (101)
T ss_dssp ---TTHHHHCHHHE--GEEEEE----GG---------GG-----TT---CEEEEEHHHHHHHHHHHSBCTTSCB-BS-HH
T ss_pred CCcccHHHHHHhhc--cCCccC----HH---------Hh-----CC---CEEEEEcHHHHHHHHHHhHHHhccccchHHH
Confidence 99999999999976 222111 00 00 11 347899999999875544322111 11456
Q ss_pred HHHHHHHHHHHHh-hcccceeEEEeecCCCchhhhHHHHHhhhhh
Q 005531 79 FKSIFDYIDHIFL-LVRPRKLLYLAIDGVAPRAKMNQQRTRRFRA 122 (692)
Q Consensus 79 ~~~If~yid~lv~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfrs 122 (692)
+..++..+..|.. -|.| ++.+||.+|-+|..+...||-+.
T Consensus 58 ~~~~~~r~~~L~~~gI~P----ifVFDG~~~~~K~~~~~~R~~~r 98 (101)
T PF00752_consen 58 LRGLFSRLCRLLEHGIKP----IFVFDGKPPPLKRETIQKRRKRR 98 (101)
T ss_dssp HHHHHHHHHHHHHTTEEE----EEEE--STTGGCHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHCCCEE----EEEECCCCchhhHHHHHHHHHHH
Confidence 6677777776653 4555 68999999999998888776544
No 12
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=94.88 E-value=0.034 Score=49.82 Aligned_cols=93 Identities=18% Similarity=0.273 Sum_probs=56.9
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccccccCCCCC--CCCCHHHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKP--APTSYDDV 78 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~c~h~~~~~--~p~te~e~ 78 (692)
|||+++..||... ... .+...-.| --+=||.+..+|.+......+ ........
T Consensus 1 MGI~gL~~~l~~~----~~~----~~i~~l~g-----------------~~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~ 55 (99)
T smart00485 1 MGIKGLWPLLKPV----VRE----VPLEALRG-----------------KTLAIDASIWLYQFLTACREKLGTPLPNSKH 55 (99)
T ss_pred CCHhHHHHHHHHh----ccc----CCHHHhCC-----------------ceEeccHHHHHHHHHHHHhhhhcCCCCchHH
Confidence 9999999999875 111 11100012 135678888998765432110 11122225
Q ss_pred HHHHHHHHHHHHh-hcccceeEEEeecCCCchhhhHHHHHhhhhh
Q 005531 79 FKSIFDYIDHIFL-LVRPRKLLYLAIDGVAPRAKMNQQRTRRFRA 122 (692)
Q Consensus 79 ~~~If~yid~lv~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfrs 122 (692)
+..+|..+.+|++ -|.| ++.+||.+|-+|...+..||-+.
T Consensus 56 l~~~~~rl~~L~~~~I~P----ifVFDG~~~~~K~~t~~~R~~~r 96 (99)
T smart00485 56 LMGLFYRTCRLLEFGIKP----IFVFDGKPPPLKSETLAKRRERR 96 (99)
T ss_pred HHHHHHHHHHHHHCCCeE----EEEECCCCchhhHHHHHHHHHHH
Confidence 5666666666653 3444 58899999999999998887654
No 13
>PRK14976 5'-3' exonuclease; Provisional
Probab=94.10 E-value=2 Score=46.10 Aligned_cols=57 Identities=18% Similarity=0.243 Sum_probs=38.3
Q ss_pred eEEeeccccccccccCCC--CCCC----CCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc
Q 005531 51 NLYLDMNGIIHPCFHPDG--KPAP----TSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (692)
Q Consensus 51 nLYlDmNgIIH~c~h~~~--~~~p----~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP 108 (692)
=|.||.|++|+.++|... .+.- -.......-+++.+-+++...+|..+ .+|+||-.|
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 368999999999888741 1110 11123445567777778888899886 699998544
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=94.06 E-value=0.16 Score=45.26 Aligned_cols=90 Identities=20% Similarity=0.355 Sum_probs=54.7
Q ss_pred cEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhhcCCceEEEeeccccCCCCCccccccccc
Q 005531 192 TKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLSLATHEIHFSILREVITLPGQQEKCFVCGQV 271 (692)
Q Consensus 192 l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DADLImL~Lathe~~f~ILRe~v~~~~~~~~c~~c~~~ 271 (692)
+.+|+ -|||+|.=+--.-|+ +..+.|++.|+|+++.|-- .|+|... ......|
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--DKSSGKC------ 57 (94)
T ss_dssp -EEEE-----SS-HHHHHHHHHHT---------TSSSEEE-SSSHHHHTT-S------EEEESST---CSCCST------
T ss_pred CeEEE----cCchHHHHHHHHHHh---------cceeEEEecCCCEEeeCCC------EEEEecc--ccccCCc------
Confidence 45554 489999988866543 4578999999999999754 5666531 0000000
Q ss_pred CcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHHHHhhhCCCCCCCCCchhhhHHHHHHHhhhhcCC
Q 005531 272 GHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREYLQYELDIPNPPFPINFERIVDDFVFLCFFVGND 346 (692)
Q Consensus 272 ~h~~~~c~~~~~~~~~~~~~~~~~~~~~~~f~~l~i~~LREyL~~e~~~~~~~f~~d~eriIDDfVfLcf~~GND 346 (692)
.......+.+++...+.+.+.. . -+.|+.+|+|+|+|
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 0012345788888777666431 1 24799999999998
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=92.57 E-value=0.071 Score=33.84 Aligned_cols=16 Identities=56% Similarity=1.410 Sum_probs=14.8
Q ss_pred ccccccccCccccccc
Q 005531 264 KCFVCGQVGHLAAECH 279 (692)
Q Consensus 264 ~c~~c~~~~h~~~~c~ 279 (692)
.|+.||+.||++++|.
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 6999999999999985
No 16
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=90.70 E-value=7.1 Score=44.34 Aligned_cols=34 Identities=24% Similarity=0.476 Sum_probs=23.4
Q ss_pred HHHHHHhhhhcCCCCCCCCccccccchHHHHHHHHH
Q 005531 334 DDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYR 369 (692)
Q Consensus 334 DDfVfLcf~~GNDFLPhlpsl~I~egaid~Li~~Yk 369 (692)
.-||-||+|+|+||.|.+-+ |+.+..=.|++.|+
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 46788999999999999755 33333333555554
No 17
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=89.83 E-value=2.7 Score=48.33 Aligned_cols=91 Identities=22% Similarity=0.342 Sum_probs=51.4
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCcccCCCCCCCCCCCcccCeEEeeccccccc----cccCCCCCCCCCHH
Q 005531 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHP----CFHPDGKPAPTSYD 76 (692)
Q Consensus 1 MGVP~ffrWL~~rYP~i~~~~~e~~~~~~~~g~~~p~d~s~pn~n~~e~DnLYlDmNgIIH~----c~h~~~~~~p~te~ 76 (692)
|||++|+-.|.. +..++ .++ ..+.+-|=+|.-+-+|. |.+.-....|+ +
T Consensus 1 MGI~GLlp~~k~----~~~~~----------------hi~-----~~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT--~ 53 (556)
T KOG2518|consen 1 MGIQGLLPLLKP----ALKPI----------------HIS-----EYKGKTVAVDGYCWLHRGALACAEKLAKGKPT--D 53 (556)
T ss_pred CCcchhHHHHHH----Hhhhh----------------hHH-----HhcCceEEEehhhHHhhhHHhHHHHHhcCCCh--H
Confidence 999999998876 22211 010 02346778888888885 33322222232 3
Q ss_pred HHHHHHHHHHHHHHh-hcccceeEEEeecCCCchhhhHHHHHhhhhh
Q 005531 77 DVFKSIFDYIDHIFL-LVRPRKLLYLAIDGVAPRAKMNQQRTRRFRA 122 (692)
Q Consensus 77 e~~~~If~yid~lv~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfrs 122 (692)
.-++=+..++..|.. -|+| +|.+||=+=-+|--+-|.||-+.
T Consensus 54 ryi~y~ik~v~lL~~~gikP----ilVFDG~~LP~K~~te~~Rr~~R 96 (556)
T KOG2518|consen 54 RYIQFFIKRVKLLLSYGIKP----ILVFDGDPLPSKKETERKRRERR 96 (556)
T ss_pred HHHHHHHHHHHHHHhcCCeE----EEEecCCCcccccccchHHHHHH
Confidence 332333333333332 3455 79999988777777766666544
No 18
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=89.23 E-value=8.2 Score=41.77 Aligned_cols=62 Identities=18% Similarity=0.354 Sum_probs=44.2
Q ss_pred eEEeeccccccccccCCCC------CCCCCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc--hhhhHHHH
Q 005531 51 NLYLDMNGIIHPCFHPDGK------PAPTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP--RAKMNQQR 116 (692)
Q Consensus 51 nLYlDmNgIIH~c~h~~~~------~~p~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP--rAKmnQQR 116 (692)
-|-||.+++++.+.|.... ..++. ...-+...+.++++..+|.+ ..+++||-+| |.++...|
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~---~~~~~~~~l~~~~~~~~~~~-~~~vFD~~~~tfR~~~~~~y 82 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTG---AVSGFLGMLYRLIRLLEPTH-PVVVFDGKPPTFRHELLEEY 82 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCcc---HHHHHHHHHHHHHHhcCCCc-EEEEEcCCCCcchHHHHHHH
Confidence 4789999999999886521 12333 44556677789999999966 4699999777 55555544
No 19
>PRK05755 DNA polymerase I; Provisional
Probab=87.44 E-value=12 Score=46.35 Aligned_cols=56 Identities=11% Similarity=0.148 Sum_probs=36.1
Q ss_pred EEeeccccccccccCCCCC---CCCCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc
Q 005531 52 LYLDMNGIIHPCFHPDGKP---APTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (692)
Q Consensus 52 LYlDmNgIIH~c~h~~~~~---~p~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP 108 (692)
|.||.|.+++.+.|.-... ..-.......-++..+-+++...+|..+ .+|+||-.|
T Consensus 5 ~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~-~v~fD~~~~ 63 (880)
T PRK05755 5 LLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHV-AVAFDAKGK 63 (880)
T ss_pred EEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEE-EEEEECCCC
Confidence 6899999999988864110 0111223344455666677777899775 699998433
No 20
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=81.71 E-value=58 Score=40.67 Aligned_cols=56 Identities=13% Similarity=0.204 Sum_probs=34.3
Q ss_pred EEeeccccccccccCCCC-CC---CCCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc
Q 005531 52 LYLDMNGIIHPCFHPDGK-PA---PTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (692)
Q Consensus 52 LYlDmNgIIH~c~h~~~~-~~---p~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP 108 (692)
|.||.|++||-++|.-.. +- .-.......-++..+-+++...+|..+ .+|+||-.|
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 579999999998885421 00 001112233344555566666789875 699998654
No 21
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=75.61 E-value=1.1 Score=32.73 Aligned_cols=20 Identities=35% Similarity=0.763 Sum_probs=17.1
Q ss_pred CCcccccccccCcccccccC
Q 005531 261 QQEKCFVCGQVGHLAAECHG 280 (692)
Q Consensus 261 ~~~~c~~c~~~~h~~~~c~~ 280 (692)
....|.+|++.||+..+|-.
T Consensus 7 ~~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 7 PGYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCCEeecCCCCCccHhHCCC
Confidence 34679999999999999964
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=74.67 E-value=3.9 Score=51.04 Aligned_cols=39 Identities=18% Similarity=0.126 Sum_probs=30.4
Q ss_pred ccEEEEcCCCCCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHh
Q 005531 191 FTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLSL 242 (692)
Q Consensus 191 ~l~VI~Sds~vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DADLImL~L 242 (692)
++.+|.+ |||||.=+-...+. .....|++-|+|+++.|=
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 4667754 89999988877543 467999999999997764
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=71.81 E-value=16 Score=45.84 Aligned_cols=65 Identities=22% Similarity=0.355 Sum_probs=36.8
Q ss_pred eEEeeccccccccc---cCCCCCCCCCHHHHHHHHHHHHHHHHh-hcccceeEEEeecCCCchhhhHHHHHhhhh
Q 005531 51 NLYLDMNGIIHPCF---HPDGKPAPTSYDDVFKSIFDYIDHIFL-LVRPRKLLYLAIDGVAPRAKMNQQRTRRFR 121 (692)
Q Consensus 51 nLYlDmNgIIH~c~---h~~~~~~p~te~e~~~~If~yid~lv~-~vrPrkllyiAiDGVAPrAKmnQQRsRRfr 121 (692)
-|=||...-||.+. +........+ ..+ .-+|..|.+|+. -|+| ++.+||.+|-.|...-..||-|
T Consensus 26 ~vAIDasiWL~q~l~~vr~~~g~~l~n-~hl-~g~f~Ri~~Ll~~gI~P----VfVFDG~~p~lK~~t~~~R~~r 94 (1034)
T TIGR00600 26 RLAVDISIWLNQALKGVRDREGNAIKN-SHL-LTLFHRLCKLLFFRIRP----IFVFDGGAPLLKRQTLAKRRQR 94 (1034)
T ss_pred EEEechHHHHHHHHHHHHhccCCccCC-HHH-HHHHHHHHHHHHCCCeE----EEEECCCCchHhHHHHHHHHHH
Confidence 35667777777542 2222212222 232 445555556553 4555 6889999999888765555443
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=68.72 E-value=5.6 Score=34.22 Aligned_cols=22 Identities=32% Similarity=0.732 Sum_probs=18.7
Q ss_pred HHHHHHhhhhc--CCCCCCCCccc
Q 005531 334 DDFVFLCFFVG--NDFLPHMPTLE 355 (692)
Q Consensus 334 DDfVfLcf~~G--NDFLPhlpsl~ 355 (692)
+-|+-+|.|+| .|++|++|++-
T Consensus 8 ~q~~d~~~L~GD~~D~i~gv~giG 31 (75)
T cd00080 8 EQFIDLAILVGDKSDNIPGVPGIG 31 (75)
T ss_pred HHHHHHHHHcCCccccCCCCCccc
Confidence 46777999999 99999999843
No 25
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=51.23 E-value=8 Score=30.03 Aligned_cols=19 Identities=42% Similarity=0.935 Sum_probs=16.8
Q ss_pred CcccccccccCcccccccC
Q 005531 262 QEKCFVCGQVGHLAAECHG 280 (692)
Q Consensus 262 ~~~c~~c~~~~h~~~~c~~ 280 (692)
...|..|++.||...+|..
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 4579999999999999984
No 26
>smart00343 ZnF_C2HC zinc finger.
Probab=48.85 E-value=8 Score=26.30 Aligned_cols=16 Identities=50% Similarity=1.364 Sum_probs=14.3
Q ss_pred ccccccccCccccccc
Q 005531 264 KCFVCGQVGHLAAECH 279 (692)
Q Consensus 264 ~c~~c~~~~h~~~~c~ 279 (692)
.|..||+.||.+.+|.
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4889999999999985
No 27
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=45.44 E-value=12 Score=32.22 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=27.7
Q ss_pred CCCChhhHHHHHHHHhhcCCCCCCCCcEEEEecChhHHHHHhh
Q 005531 201 VPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLSLA 243 (692)
Q Consensus 201 vPGEGEhKIm~fIR~qr~~p~ydpn~~H~IyG~DADLImL~La 243 (692)
-|||+|.-.--.-++ ..-+.|+|.|+|+++.|--
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 489999988777652 4679999999999998763
No 28
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=42.98 E-value=21 Score=26.67 Aligned_cols=19 Identities=21% Similarity=0.597 Sum_probs=15.3
Q ss_pred HHHHHhhhhcCCCCCCCCcc
Q 005531 335 DFVFLCFFVGNDFLPHMPTL 354 (692)
Q Consensus 335 DfVfLcf~~GNDFLPhlpsl 354 (692)
-|+-+|.|+| |+.+.+|++
T Consensus 3 q~~~~~~L~G-D~~dni~Gv 21 (36)
T smart00279 3 QLIDYAILVG-DYSDNIPGV 21 (36)
T ss_pred HHHHHHHHhC-cCCCCCCCC
Confidence 5788999999 999955553
No 29
>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=42.15 E-value=24 Score=35.01 Aligned_cols=56 Identities=14% Similarity=0.234 Sum_probs=39.2
Q ss_pred EEeeccccccccccCCCCCCC----CCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc
Q 005531 52 LYLDMNGIIHPCFHPDGKPAP----TSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (692)
Q Consensus 52 LYlDmNgIIH~c~h~~~~~~p----~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP 108 (692)
|.||.|+++|.+.|.-....- -..-......++.|.+++...+|.. +.+|+|+-.+
T Consensus 4 lLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~-~vv~fD~~~~ 63 (169)
T PF02739_consen 4 LLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDY-VVVAFDSKGP 63 (169)
T ss_dssp EEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEE-EEEEEEBSSC
T ss_pred EEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCce-EEEEecCCCc
Confidence 689999999999886542110 0111344556777778888889987 4699999987
No 30
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=34.67 E-value=18 Score=28.61 Aligned_cols=20 Identities=40% Similarity=0.954 Sum_probs=17.0
Q ss_pred CCCcccccccccCccccccc
Q 005531 260 GQQEKCFVCGQVGHLAAECH 279 (692)
Q Consensus 260 ~~~~~c~~c~~~~h~~~~c~ 279 (692)
..+..|+.||..||...+|.
T Consensus 29 ~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 29 RLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred CcChhhcCCCCcCcCHhHcC
Confidence 34578999999999999985
No 31
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=31.00 E-value=21 Score=36.40 Aligned_cols=45 Identities=22% Similarity=0.527 Sum_probs=28.9
Q ss_pred CCcEEEEecChhHHHHHhhc--CCceEEEeeccccCCCCCcccccccccCccccccc
Q 005531 225 NTRHCLYGLDADLIMLSLAT--HEIHFSILREVITLPGQQEKCFVCGQVGHLAAECH 279 (692)
Q Consensus 225 n~~H~IyG~DADLImL~Lat--he~~f~ILRe~v~~~~~~~~c~~c~~~~h~~~~c~ 279 (692)
+.-|..+-..++|=... +. |..+=. .+..+|+.||+.||++.+|.
T Consensus 68 ~~GH~~~DCP~~iC~~C-~~~~H~s~~C---------~~~~~C~~Cg~~GH~~~dC~ 114 (190)
T COG5082 68 QNGHLRRDCPHSICYNC-SWDGHRSNHC---------PKPKKCYNCGETGHLSRDCN 114 (190)
T ss_pred ccCcccccCChhHhhhc-CCCCcccccC---------CcccccccccccCccccccC
Confidence 45677777777555555 21 311100 12368999999999999994
No 32
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=30.26 E-value=25 Score=26.48 Aligned_cols=20 Identities=40% Similarity=0.702 Sum_probs=12.6
Q ss_pred cccccccccCcccccccCCC
Q 005531 263 EKCFVCGQVGHLAAECHGKP 282 (692)
Q Consensus 263 ~~c~~c~~~~h~~~~c~~~~ 282 (692)
..|..|++-.|-+.+|+.+.
T Consensus 3 ~~CprC~kg~Hwa~~C~sk~ 22 (36)
T PF14787_consen 3 GLCPRCGKGFHWASECRSKT 22 (36)
T ss_dssp -C-TTTSSSCS-TTT---TC
T ss_pred ccCcccCCCcchhhhhhhhh
Confidence 36999999999999998764
No 33
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=30.22 E-value=24 Score=27.23 Aligned_cols=14 Identities=43% Similarity=0.968 Sum_probs=11.9
Q ss_pred cccccccccCcccc
Q 005531 263 EKCFVCGQVGHLAA 276 (692)
Q Consensus 263 ~~c~~c~~~~h~~~ 276 (692)
.+|..||+.||.+.
T Consensus 2 ~kC~~CG~~GH~~t 15 (40)
T PF15288_consen 2 VKCKNCGAFGHMRT 15 (40)
T ss_pred cccccccccccccc
Confidence 47999999999863
No 34
>PHA02567 rnh RnaseH; Provisional
Probab=30.20 E-value=56 Score=35.75 Aligned_cols=57 Identities=16% Similarity=0.158 Sum_probs=41.8
Q ss_pred CeEEeeccccccccccCCCCCCCCCHHHHH-HHHHHHHHHHHhhcccce-eEEEeecCC
Q 005531 50 DNLYLDMNGIIHPCFHPDGKPAPTSYDDVF-KSIFDYIDHIFLLVRPRK-LLYLAIDGV 106 (692)
Q Consensus 50 DnLYlDmNgIIH~c~h~~~~~~p~te~e~~-~~If~yid~lv~~vrPrk-llyiAiDGV 106 (692)
+-+.||++.|+-.|++..-.+.......|+ ..+++-|-.++..++|.- -+.+|+|+-
T Consensus 15 ~~~LiDgs~i~~~~~~a~l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~ 73 (304)
T PHA02567 15 GVNLIDFSQIIIATIMANFKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNS 73 (304)
T ss_pred CEEEEehHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCC
Confidence 568999999999999987544433334444 558888888888877662 167999974
No 35
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=29.02 E-value=24 Score=35.93 Aligned_cols=18 Identities=50% Similarity=1.145 Sum_probs=16.5
Q ss_pred CcccccccccCccccccc
Q 005531 262 QEKCFVCGQVGHLAAECH 279 (692)
Q Consensus 262 ~~~c~~c~~~~h~~~~c~ 279 (692)
...|+.|||.||.+.+|.
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 568999999999999996
No 36
>PF12513 SUV3_C: Mitochondrial degradasome RNA helicase subunit C terminal; InterPro: IPR022192 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF00271 from PFAM. The yeast mitochondrial degradosome (mtEXO) is an NTP-dependent exoribonuclease involved in mitochondrial RNA metabolism. mtEXO is made up of two subunits: an RNase (DSS1) and an RNA helicase (SUV3). These co-purify with mitochondrial ribosomes. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 3RC8_A 3RC3_A.
Probab=25.67 E-value=37 Score=26.78 Aligned_cols=16 Identities=38% Similarity=0.835 Sum_probs=12.2
Q ss_pred hHHHHHHhhCCCcccc
Q 005531 5 AFYRWLADRYPLSIVD 20 (692)
Q Consensus 5 ~ffrWL~~rYP~i~~~ 20 (692)
..|-||+.|||.+..+
T Consensus 12 ~lYlWLs~Rfp~~F~d 27 (49)
T PF12513_consen 12 DLYLWLSYRFPDVFPD 27 (49)
T ss_dssp HHHHHHHCC-TTTSTT
T ss_pred HHHHHHHHHcccccCC
Confidence 4799999999997643
No 37
>COG5350 Predicted protein tyrosine phosphatase [General function prediction only]
Probab=23.87 E-value=88 Score=31.14 Aligned_cols=42 Identities=24% Similarity=0.559 Sum_probs=34.7
Q ss_pred cccEEEEcCCCCCCCh--------hhHHHHHHHHhhcCCCCCCCCcEEEEecC
Q 005531 190 QFTKVILSDANVPGEG--------EHKIMSYIRLQRNLPGFDPNTRHCLYGLD 234 (692)
Q Consensus 190 ~~l~VI~Sds~vPGEG--------EhKIm~fIR~qr~~p~ydpn~~H~IyG~D 234 (692)
+.+.+.+.|-.+||+| =++|+||++ ..|.+.|=--||.-|.-
T Consensus 56 rhL~l~fnDI~~~~~g~~ap~e~Hv~~i~DF~~---~wp~~apllIHC~aGIS 105 (172)
T COG5350 56 RHLTLHFNDIAEPDDGWIAPGEAHVRAIIDFAD---EWPRFAPLLIHCYAGIS 105 (172)
T ss_pred hceeEeeccccCCCccccCCCHHHHHHHHHHHh---cCccccceeeeeccccc
Confidence 4589999999999999 368999998 46777777888887753
No 38
>PRK09482 flap endonuclease-like protein; Provisional
Probab=23.37 E-value=1.3e+02 Score=32.23 Aligned_cols=55 Identities=16% Similarity=0.229 Sum_probs=39.0
Q ss_pred eEEeeccccccccccCCCCCCCCCHHHHHHHHHHHHHHHHhhcccceeEEEeecCCCc
Q 005531 51 NLYLDMNGIIHPCFHPDGKPAPTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (692)
Q Consensus 51 nLYlDmNgIIH~c~h~~~~~~p~te~e~~~~If~yid~lv~~vrPrkllyiAiDGVAP 108 (692)
=|.||-+++||-.+|.... +.....+..-.++.|.+|+...+|..+ .+|+||-++
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 3789999999998876421 122234455566777788888899886 699999654
Done!