Query 002147
Match_columns 959
No_of_seqs 261 out of 552
Neff 4.7
Searched_HMMs 46136
Date Thu Mar 28 17:34:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/002147.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/002147hhsearch_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 5E-257 1E-261 2166.3 65.2 744 1-764 1-805 (931)
2 COG5049 XRN1 5'-3' exonuclease 100.0 4E-210 9E-215 1758.8 48.0 684 1-727 1-819 (953)
3 KOG2045 5'-3' exonuclease XRN1 100.0 9E-182 2E-186 1548.2 43.7 561 1-624 1-655 (1493)
4 PF03159 XRN_N: XRN 5'-3' exon 100.0 2.1E-85 4.5E-90 692.2 19.4 237 1-256 1-237 (237)
5 cd00128 XPG Xeroderma pigmento 98.6 7.9E-07 1.7E-11 98.6 14.7 237 1-369 1-244 (316)
6 PTZ00217 flap endonuclease-1; 98.2 2.8E-05 6.1E-10 89.3 17.4 230 1-356 1-245 (393)
7 PRK03980 flap endonuclease-1; 97.6 0.0033 7.1E-08 70.0 19.2 33 334-366 177-217 (292)
8 TIGR03674 fen_arch flap struct 97.2 0.015 3.2E-07 66.1 17.2 67 51-121 23-97 (338)
9 smart00475 53EXOc 5'-3' exonuc 95.2 1 2.3E-05 49.5 17.7 133 52-241 4-139 (259)
10 cd00008 53EXOc 5'-3' exonuclea 94.7 1.4 2.9E-05 48.0 16.7 57 51-108 3-62 (240)
11 smart00485 XPGN Xeroderma pigm 94.5 0.042 9.2E-07 51.2 4.1 93 1-122 1-96 (99)
12 PF00752 XPG_N: XPG N-terminal 94.3 0.053 1.1E-06 50.6 4.3 95 1-122 1-98 (101)
13 PF00867 XPG_I: XPG I-region; 91.9 0.71 1.5E-05 43.0 7.9 89 192-346 5-94 (94)
14 KOG2518 5'-3' exonuclease [Rep 89.8 2.8 6.1E-05 50.2 11.8 92 1-123 1-97 (556)
15 PF00098 zf-CCHC: Zinc knuckle 89.8 0.19 4.1E-06 33.9 1.4 16 264-279 2-17 (18)
16 PRK14976 5'-3' exonuclease; Pr 89.5 7.3 0.00016 43.5 14.3 57 51-108 5-67 (281)
17 PRK05755 DNA polymerase I; Pro 86.7 14 0.0003 47.5 16.1 56 51-107 4-62 (880)
18 COG0258 Exo 5'-3' exonuclease 83.2 29 0.00062 39.1 14.9 62 51-116 13-82 (310)
19 KOG2519 5'-3' exonuclease [Rep 81.2 70 0.0015 38.3 17.3 35 333-369 216-250 (449)
20 TIGR00593 pola DNA polymerase 76.4 78 0.0017 41.1 17.2 56 52-108 2-61 (887)
21 KOG2044 5'-3' exonuclease HKE1 66.8 55 0.0012 41.5 12.2 153 683-844 699-855 (931)
22 TIGR00600 rad2 DNA excision re 62.0 12 0.00026 48.7 5.8 39 191-242 785-823 (1034)
23 TIGR00600 rad2 DNA excision re 61.1 29 0.00064 45.4 9.0 66 51-122 26-95 (1034)
24 PF13696 zf-CCHC_2: Zinc knuck 59.7 3.8 8.2E-05 31.9 0.5 19 262-280 8-26 (32)
25 cd00080 HhH2_motif Helix-hairp 52.8 13 0.00028 33.6 2.9 21 334-354 8-30 (75)
26 smart00279 HhH2 Helix-hairpin- 35.2 30 0.00066 27.3 2.1 20 334-354 2-21 (36)
27 PF02739 5_3_exonuc_N: 5'-3' e 35.1 1.3E+02 0.0029 31.2 7.4 56 52-108 4-63 (169)
28 KOG0921 Dosage compensation co 34.3 1E+02 0.0023 39.9 7.4 27 521-547 835-861 (1282)
29 smart00484 XPGI Xeroderma pigm 33.5 32 0.00069 31.2 2.3 34 201-243 10-43 (73)
30 smart00343 ZnF_C2HC zinc finge 31.2 23 0.00049 25.6 0.8 16 264-279 1-16 (26)
31 PHA02567 rnh RnaseH; Provision 25.2 80 0.0017 36.2 4.1 58 49-106 14-73 (304)
32 PF14392 zf-CCHC_4: Zinc knuck 24.6 34 0.00073 28.5 0.8 21 259-279 28-48 (49)
33 PF13917 zf-CCHC_3: Zinc knuck 23.4 43 0.00094 27.6 1.2 19 262-280 4-22 (42)
34 COG5082 AIR1 Arginine methyltr 22.8 36 0.00078 36.4 0.8 45 225-279 68-114 (190)
35 COG5082 AIR1 Arginine methyltr 21.4 40 0.00086 36.1 0.8 18 262-279 60-77 (190)
36 COG5350 Predicted protein tyro 20.6 1.1E+02 0.0023 32.2 3.5 42 190-234 56-105 (172)
No 1
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=100.00 E-value=5.3e-257 Score=2166.31 Aligned_cols=744 Identities=57% Similarity=0.978 Sum_probs=668.2
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCCCCCCCHHHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPTSYDDVFK 80 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~p~p~te~em~~ 80 (959)
||||+|||||++|||++|++|+|++|.+ .+|+.||+|.|+|||||+||||||||||||||||+||+++|+|+||||||.
T Consensus 1 MGVPaffRWLs~kyp~~I~~viEe~p~~-~~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPEdkPaP~tedEm~~ 79 (931)
T KOG2044|consen 1 MGVPAFFRWLSRKYPKTISPVIEEEPVD-VDGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPEDKPAPETEDEMFV 79 (931)
T ss_pred CCchHHHHHHHHhcchhhhhhhhcCccc-CCCcccccccCCCCCCcccccceeeecCcccccCCCCCCCCCCccHHHHHH
Confidence 9999999999999999999999999975 488999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccceEEEEEecCCCchhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHcCCccCCCCCCCccCCcc
Q 002147 81 SIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFEEAGKLLSAKEKPETCDSNV 160 (959)
Q Consensus 81 ~If~yID~L~~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsakea~~~~~e~~~l~~e~~~~G~~l~~~~~~~~fDSN~ 160 (959)
+||+||||||.||||||||||||||||||||||||||||||||||++++++|+|++++|++++|..|+++.+.++|||||
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 cccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCchhHHh
Q 002147 161 ITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIML 240 (959)
Q Consensus 161 ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL 240 (959)
|||||+||++|+.+|+|||+.||++||+|+||+||+|||+||||||||||+|||+||++|+|||||+|||||+|||||||
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 hhccccceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHHHHhhcCC
Q 002147 241 SLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREYLQYELDI 320 (959)
Q Consensus 241 ~LatHe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~~~~~~d~~~~~~~~~~~~~f~~l~I~vLREYL~~E~~~ 320 (959)
||||||+||+||||+|+ |+++++|++|||+||.+++|.|++.. .+.+...+.+..+++|+|||||||||||+.||.+
T Consensus 240 gLATHE~hF~IlRE~~~-P~~~~~C~~cgq~gh~~~dc~g~~~~--~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~ 316 (931)
T KOG2044|consen 240 GLATHEPHFSILREEFF-PNKPRRCFLCGQTGHEAKDCEGKPRL--GETNELADVPGVEKPFIFLNISVLREYLERELRM 316 (931)
T ss_pred eccccCCceEEeeeeec-CCCcccchhhcccCCcHhhcCCcCCc--ccccccccCcccccceEEEEHHHHHHHHHHHhcC
Confidence 99999999999999986 99999999999999999999999662 2223333445788999999999999999999999
Q ss_pred CCCCCCCchhhhHhHHHHHhhhhcCCCCCCCCccccCcChHHHHHHHHHHHHhhcCCccccCCeechHHHHHHHHHHHHH
Q 002147 321 PNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQSVAVY 400 (959)
Q Consensus 321 ~~~pf~~dlERiIDDFVFLcffvGNDFLPhLPsl~I~eGaid~Li~~Yk~~l~~~~gYLT~~G~Inl~rl~~fl~~L~~~ 400 (959)
|++||+||+||+||||||||||||||||||||||+|||||||+|+++||+.|++|+||||++|.|||.||+.||+.|+..
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 HHHHHHHHHHHHHHHHHHHHHHHhhh----------------------------c---cc----------hhhhh-----
Q 002147 401 EDQIFQKRTRIQQAYEYNEAMKLNAR----------------------------R---ES----------SEELL----- 434 (959)
Q Consensus 401 E~~iF~kr~~~~~~~~~ne~~~~~~r----------------------------~---~~----------~~~~l----- 434 (959)
|++||++|.+.+.++......+++.+ + ++ ..+.+
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 99999999654443331111100000 0 00 00000
Q ss_pred ----------ccccccccccccCCcchHHhHHHHhhCCCChhHHHHHHHHHHHHHHHhHHhhhcccccccCccccccccC
Q 002147 435 ----------QAPVAVADTVKLGEPGYKERYYADKFEISNPEEIDKVKKDVVLKYVEGLCWVCRYYYQDVCSWQWFYPYH 504 (959)
Q Consensus 435 ----------~~~~~~~D~vkl~e~gyk~rYY~~KF~~~~~~d~~~~~~~vv~~YveGL~WVL~YYy~GcpSW~WyYPYH 504 (959)
..+....|+|+|+|+|||+|||++||++++++ ++||++||++|||||||||+||||||+||+||||||
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 12234678999999999999999999997766 789999999999999999999999999999999999
Q ss_pred CCccccchhcccCcccccccCCCCChHhHhhhccCCCCCCCCcHHHHhhhCCCCCCCcccCCCCccccCCCCccceeeec
Q 002147 505 YAPFASDLKDLSDLEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPSSPIYKFYPPDFQIDMNGKRFAWQGVV 584 (959)
Q Consensus 505 YAPfasDl~~l~~~~i~F~~g~Pf~PfeQLM~VLP~~S~~~LP~~~~~LM~dp~SpI~dfYP~dF~iD~nGKk~~WqgVv 584 (959)
||||||||++|.+++|+|++|+||+||||||+||||+|+++||+.||.||+||+|||+||||+||+||||||||+|||||
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 cccCCCHHHHHHHHHhhhcCCCHHHHhhcCCCCcEEEecCCCcchHHHHHHHhhccCCCCCCCCcccccccccCCCccce
Q 002147 585 KLPFIDEKLLLRQTKKLEVFLTEEELFRNSVMLDLLYVHPQHPLYQQITLYCQLYHQLPPQDRFAWEIDVNASGGMNGYI 664 (959)
Q Consensus 585 lLPFIDe~rLl~a~~~~~~~Lt~eE~~RN~~g~d~lf~~~~~~l~~~i~~~~~~~~~~~~~~~~~~~id~~~~~g~~G~v 664 (959)
|||||||+|||+|+++++++||+||++||+.|.|+||++++||+++.|.++|+++++ +.... ..+-...+.|++|.+
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 999999999999999999999999999999999999999999999999999987764 22221 134445566899999
Q ss_pred eecccCCCCcccCCCCCCCCCCCCCcEEEEEeeCCCCCCC---CCCCCCCCCCCCCcCCCCCCCCCCcccccCCccccCC
Q 002147 665 WLCERNGLRSIIPSPVKGLPDIERNQAINVTYLNPQKHRH---IPEPPKGATIPAKTLKPIDIKPFPTLWHEDNSRRQQG 741 (959)
Q Consensus 665 ~~~~~~~~~~~~~sP~~~l~di~~n~~~~~~y~~P~~~~~---~~~ll~g~~~p~~~l~~~d~~~~~~lw~~~~~~r~~~ 741 (959)
.+++......++.||..++.+...+..++++|..|..+.. .++.++|++.|+++|++ -||... +.+
T Consensus 712 ~~~~~~~~~~i~~~p~~~~~~~~~~~~v~~~~~~~~~~ed~~~~a~~l~G~~~p~~~lkP-------~dwn~s----R~~ 780 (931)
T KOG2044|consen 712 SKDPEGLESGISKSPPGGLSDYNTNTGVCLKYVDPEYPEDYIFPAIRLDGAKEPEKVLKP-------DDWNDR----RDG 780 (931)
T ss_pred ccCccccccccccCChhhcccCCccceeeecccCccccccccchhhhcCCCCCCccccCc-------chhhhh----hhh
Confidence 9987766677889999999999999999999999987532 36889999999999973 355533 256
Q ss_pred CCCCCCCCCC--CCCCCChhHHHHH
Q 002147 742 RERPQVPGAI--AGPVLGEAAHRLI 764 (959)
Q Consensus 742 ~~r~~~~~~~--~~~~~~~~~~r~~ 764 (959)
++++|++... .+..+..++||.|
T Consensus 781 ~~~~~~~~~~~~~~~~~~~~~~~~v 805 (931)
T KOG2044|consen 781 RYQPQAGFNRNAPRGSLPQSGHRQV 805 (931)
T ss_pred hcCcccccccCCCCCcCCccccccc
Confidence 6677666222 2334555555544
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=4.1e-210 Score=1758.82 Aligned_cols=684 Identities=45% Similarity=0.796 Sum_probs=589.6
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCCCCCCCHHHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPTSYDDVFK 80 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~p~p~te~em~~ 80 (959)
||||+|||||++|||+||+.+.|+ +||| |||||||||||||+|+||+++++|.||+||+.
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 999999999999999999877654 2444 69999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhcccceEEEEEecCCCchhhhHHHHHhhhhHHHHHHHHHHHHH----HHHHHHHHcCCccCC-CCCCCc
Q 002147 81 SIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEE----RLRKEFEEAGKLLSA-KEKPET 155 (959)
Q Consensus 81 ~If~yID~L~~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsakea~~~~~e~~----~l~~e~~~~G~~l~~-~~~~~~ 155 (959)
+||+|||||+.++|||||||||||||||||||||||+||||+|+||..+..+.+ ++-++-+..|..+.. ..+.++
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 999999999999999999999999999999999999999999999665433322 122222223333322 224578
Q ss_pred cCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCc
Q 002147 156 CDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDA 235 (959)
Q Consensus 156 fDSN~ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDA 235 (959)
||||||||||+||++|+..|+|||+.||++||.|++++||+||+.||||||||||+|||+||++|+|||||+|||||+||
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 hhHHhhhccccceEEEeeccccCCCC---CcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHH
Q 002147 236 DLIMLSLATHEIHFSILREVITLPGQ---QEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLRE 312 (959)
Q Consensus 236 DLImL~LatHe~~f~ILRE~v~~~~~---~~~c~~c~q~gh~~~~c~g~~~~~~~d~~~~~~~~~~~~~f~~l~I~vLRE 312 (959)
|||||||+||+|||.||||+|+|+.. .++|..||.++|....|.. ...++|.||||++|||
T Consensus 221 DLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~~k~----------------~~~q~F~~LhiSlLRE 284 (953)
T COG5049 221 DLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEECKV----------------LTHQPFYLLHISLLRE 284 (953)
T ss_pred cceeeecccCCCeeEEeechhccCcccccccccccccccccchhhhcc----------------cccCceEEEEHHHHHH
Confidence 99999999999999999999999743 5689999999999888853 2347899999999999
Q ss_pred HHHhhcCCCCCCCCCchhhhHhHHHHHhhhhcCCCCCCCCccccCcChHHHHHHHHHHHHhhcCCccccCCeechHHHHH
Q 002147 313 YLQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEK 392 (959)
Q Consensus 313 YL~~E~~~~~~pf~~dlERiIDDFVFLcffvGNDFLPhLPsl~I~eGaid~Li~~Yk~~l~~~~gYLT~~G~Inl~rl~~ 392 (959)
||+.||..+..||.||+|||||||||||||||||||||||+|+|++|||++|+++||+.|+.|+||||++|.||+.||+.
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 HHHHHHHHHHHHHHHHHHHHHH----HH---------------------H------------------------------
Q 002147 393 FIQSVAVYEDQIFQKRTRIQQA----YE---------------------Y------------------------------ 417 (959)
Q Consensus 393 fl~~L~~~E~~iF~kr~~~~~~----~~---------------------~------------------------------ 417 (959)
||..|+.+|+.||+++...+.. ++ .
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 9999999999999865421100 00 0
Q ss_pred ------------HHHHHHhh------------h--c--------------cchhh----------hh----------ccc
Q 002147 418 ------------NEAMKLNA------------R--R--------------ESSEE----------LL----------QAP 437 (959)
Q Consensus 418 ------------ne~~~~~~------------r--~--------------~~~~~----------~l----------~~~ 437 (959)
++.+..+. + . +..++ +. ...
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 00000000 0 0 00000 00 001
Q ss_pred cccccccccCCcchHHhHHHHhhCCCChhHHHHHHHHHHHHHHHhHHhhhcccccccCccccccccCCCccccchhcccC
Q 002147 438 VAVADTVKLGEPGYKERYYADKFEISNPEEIDKVKKDVVLKYVEGLCWVCRYYYQDVCSWQWFYPYHYAPFASDLKDLSD 517 (959)
Q Consensus 438 ~~~~D~vkl~e~gyk~rYY~~KF~~~~~~d~~~~~~~vv~~YveGL~WVL~YYy~GcpSW~WyYPYHYAPfasDl~~l~~ 517 (959)
....|+|++.++|||+|||.+||++++. +.+++| ++|++|||||||||.|||+|||||+|||||||||+|+||.++.+
T Consensus 525 ~~~~~Tv~l~~~g~~erYY~~K~~~t~~-~~E~ir-dm~k~YVeGL~WVL~YYY~GC~SW~WyYpyHyAP~aaD~~k~~~ 602 (953)
T COG5049 525 NETEKTVNLRFPGWKERYYTSKLHFTTD-SEEKIR-DMAKEYVEGLQWVLSYYYRGCPSWDWYYPYHYAPLAADLSKLSD 602 (953)
T ss_pred cccccchhhcccchhhhhhhhhcCCCcC-CHHHHH-HHHHHHhhhhhhhhhhhhcCCCCcccccccccchhhhhhhhccc
Confidence 1235778889999999999999999654 456775 99999999999999999999999999999999999999999999
Q ss_pred cccccccCCCCChHhHhhhccCCCCCCCCcHHHHhhhCCCCCCCcccCCCCccccCCCCccceeeeccccCCCHHHHHHH
Q 002147 518 LEITFFLGEPFRPFDQLMGTLPAASSSALPEKYRNLMTDPSSPIYKFYPPDFQIDMNGKRFAWQGVVKLPFIDEKLLLRQ 597 (959)
Q Consensus 518 ~~i~F~~g~Pf~PfeQLM~VLP~~S~~~LP~~~~~LM~dp~SpI~dfYP~dF~iD~nGKk~~WqgVvlLPFIDe~rLl~a 597 (959)
.+|+|+.|+||+||||||+||||+|+++||+.||.||+|++|||+||||++|.+|||||+++||||||||||||+|||.|
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 HHhhhcCCCHHHHhhcCCCCcEEEecCCCc-chHHHHHHHhhccCCCCCCCCcccccccccC-CCccceeec-ccCCCCc
Q 002147 598 TKKLEVFLTEEELFRNSVMLDLLYVHPQHP-LYQQITLYCQLYHQLPPQDRFAWEIDVNASG-GMNGYIWLC-ERNGLRS 674 (959)
Q Consensus 598 ~~~~~~~Lt~eE~~RN~~g~d~lf~~~~~~-l~~~i~~~~~~~~~~~~~~~~~~~id~~~~~-g~~G~v~~~-~~~~~~~ 674 (959)
+++.+++||+||+.||.+|.|+||+.+.|+ +...+..+|..+.+ ...+.++...+. |+.|.|.+. +...+..
T Consensus 683 ~~~~~~~Ls~eE~~RN~~g~~llf~s~~~~~~~~l~~~lysk~~~-----~~~~~m~~~~~~~GL~g~v~~~ae~~~pn~ 757 (953)
T COG5049 683 VAVKYPTLSEEERKRNLRGLDLLFSSNKKSDLSELFKDLYSKCKQ-----KEYITMCSKESPYGLFGTVKLGAEGLAPNL 757 (953)
T ss_pred HHhhcccCCHHHHhccccCCceeEeccCCccHHHHHHHHHHhhcc-----CCceeeeccccccccccccccccccccccc
Confidence 999999999999999999999999999887 45566668865543 233446665555 999999886 4445556
Q ss_pred ccCCCCCC--------CCCCCCCcEEEEEeeCCCC-CCCCCCCCCCCCCCCCcCCCCCCCCC
Q 002147 675 IIPSPVKG--------LPDIERNQAINVTYLNPQK-HRHIPEPPKGATIPAKTLKPIDIKPF 727 (959)
Q Consensus 675 ~~~sP~~~--------l~di~~n~~~~~~y~~P~~-~~~~~~ll~g~~~p~~~l~~~d~~~~ 727 (959)
.+.+|+.. +..+..|+++.+.+.+|.. ..+++.++.|++.|..+|++.|++..
T Consensus 758 ~~lcp~~~~s~~~l~~~~~~~~n~S~~lv~~~pks~~~~ksi~~rg~~~~~~vl~py~~es~ 819 (953)
T COG5049 758 LSLCPISFLSYPGLMVFLEYSKNQSARLVIEDPKSTVTNKSIVLRGFIKPINVLWPYLRESK 819 (953)
T ss_pred cccCccccccccchhhhcccccCCceEEEeeccccccchHHHHHHhcCCccccCCHHHHHHH
Confidence 66677643 2346788999999999974 47889999999999999999888753
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=9e-182 Score=1548.17 Aligned_cols=561 Identities=46% Similarity=0.838 Sum_probs=491.2
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCC--CCCCCHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGK--PAPTSYDDV 78 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~--p~p~te~em 78 (959)
||||+||||+++|||. ++++||+.+ || ||||||||||||||+|+|+++. ..+.|||||
T Consensus 1 MGvPKFfR~iSERyP~-lseliee~q--------IP-----------EFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEi 60 (1493)
T KOG2045|consen 1 MGVPKFFRYISERYPC-LSELIEEHQ--------IP-----------EFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEI 60 (1493)
T ss_pred CCchHHHHHhhhhchH-HHHHhhhcc--------CC-----------cccceeeecccccccCCCCCCCccCcCCCHHHH
Confidence 9999999999999999 678887653 56 8999999999999999999975 357899999
Q ss_pred HHHHHHHHHHHHhhcccceEEEEEecCCCchhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHcCCccCCCCCCCccCC
Q 002147 79 FKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFEEAGKLLSAKEKPETCDS 158 (959)
Q Consensus 79 ~~~If~yID~L~~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsakea~~~~~e~~~l~~e~~~~G~~l~~~~~~~~fDS 158 (959)
|.+||+|||+||.++||+|++|||||||||||||||||+||||+|++|+.+.+. ...+|+..+. +.|||
T Consensus 61 f~~IfnYIdhLf~~IkPqKlffMAVDGvAPRAKMNQQRsRRFrTArdAe~qlaK-------A~enGe~~p~----erFDS 129 (1493)
T KOG2045|consen 61 FQEIFNYIDHLFYLIKPQKLFFMAVDGVAPRAKMNQQRSRRFRTARDAEQQLAK-------AAENGELRPH----ERFDS 129 (1493)
T ss_pred HHHHHHHHHHHHHhhCcceEEEEeecccCchhhhhHHHHHhhhhhhhHHHHHHH-------HHhccccCcc----ccccc
Confidence 999999999999999999999999999999999999999999999998764322 2236776652 78999
Q ss_pred cccccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCchhH
Q 002147 159 NVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLI 238 (959)
Q Consensus 159 N~ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLI 238 (959)
|||||||+||.+|++.|+|||+.|+++|+.|++++||+||++||||||||||+|||.++++|+|||||||||||||||||
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 HhhhccccceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHHHHhhc
Q 002147 239 MLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREYLQYEL 318 (959)
Q Consensus 239 mL~LatHe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~~~~~~d~~~~~~~~~~~~~f~~l~I~vLREYL~~E~ 318 (959)
||||+||+|||++|||+|+|+...+ .+.+..++|.+||+++|||||+.||
T Consensus 210 mLGL~tHepHF~lLREEVtFgrrn~------------------------------~k~lehqkFyLLHLsLLREYlelEF 259 (1493)
T KOG2045|consen 210 MLGLCTHEPHFVLLREEVTFGRRNK------------------------------RKSLEHQKFYLLHLSLLREYLELEF 259 (1493)
T ss_pred eeeeccCCcceeeeeeeeecccccc------------------------------cchhhhhhhhhhHHHHHHHHHHHHH
Confidence 9999999999999999999963211 0113446899999999999999999
Q ss_pred CCC--CCCCCCchhhhHhHHHHHhhhhcCCCCCCCCccccCcChHHHHHHHHHHHHhhcCCccccCCeechHHHHHHHHH
Q 002147 319 DIP--NPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYRREFTAMGGYLTDAGEVLLDRVEKFIQS 396 (959)
Q Consensus 319 ~~~--~~pf~~dlERiIDDFVFLcffvGNDFLPhLPsl~I~eGaid~Li~~Yk~~l~~~~gYLT~~G~Inl~rl~~fl~~ 396 (959)
..- ..+|++|+|||+||||+|.||||||||||||+|+|.+||+.+|..+||+.++.+||||.++|.|||.||+.||.+
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 743 478999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHH--------------------------HHHHHHHh-hh-------cc---chh-------h
Q 002147 397 VAVYEDQIFQKRTRIQQAYE--------------------------YNEAMKLN-AR-------RE---SSE-------E 432 (959)
Q Consensus 397 L~~~E~~iF~kr~~~~~~~~--------------------------~ne~~~~~-~r-------~~---~~~-------~ 432 (959)
|..+|.++|+++....+..+ +++.+... .+ .. .+. +
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 99999999998754222100 00000000 00 00 000 0
Q ss_pred h--------------hcc--cc---------------------cc-ccccccCC--------cchHHhHHHHhhCCCChh
Q 002147 433 L--------------LQA--PV---------------------AV-ADTVKLGE--------PGYKERYYADKFEISNPE 466 (959)
Q Consensus 433 ~--------------l~~--~~---------------------~~-~D~vkl~e--------~gyk~rYY~~KF~~~~~~ 466 (959)
. +.+ .. +. .|+--+|| ..||..||++|++.+..+
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 0 000 00 00 01111222 259999999999997654
Q ss_pred HHHHHHHHHHHHHHHhHHhhhcccccccCccccccccCCCccccchhcccCcccccccCCCCChHhHhhhccCCCCCCCC
Q 002147 467 EIDKVKKDVVLKYVEGLCWVCRYYYQDVCSWQWFYPYHYAPFASDLKDLSDLEITFFLGEPFRPFDQLMGTLPAASSSAL 546 (959)
Q Consensus 467 d~~~~~~~vv~~YveGL~WVL~YYy~GcpSW~WyYPYHYAPfasDl~~l~~~~i~F~~g~Pf~PfeQLM~VLP~~S~~~L 546 (959)
++..+++|..|||||+|||.|||+||+||+||||||||||+||+++..+++|.|++|+||+||||||||||++|+.+|
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 345579999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHhhhCCCCCCCcccCCCCccccCCCCccceeeeccccCCCHHHHHHHHHhhhcCCCHHHHhhcCCCCcEEEecC
Q 002147 547 PEKYRNLMTDPSSPIYKFYPPDFQIDMNGKRFAWQGVVKLPFIDEKLLLRQTKKLEVFLTEEELFRNSVMLDLLYVHP 624 (959)
Q Consensus 547 P~~~~~LM~dp~SpI~dfYP~dF~iD~nGKk~~WqgVvlLPFIDe~rLl~a~~~~~~~Lt~eE~~RN~~g~d~lf~~~ 624 (959)
|.+||+||.+++|||+||||.+|+.|+|||+.+|++|||||||||+||++||.+.+..||+||+.||++|.+++|.+.
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=2.1e-85 Score=692.21 Aligned_cols=237 Identities=57% Similarity=1.028 Sum_probs=193.6
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCCCCCCCHHHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPTSYDDVFK 80 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~p~p~te~em~~ 80 (959)
||||+|||||++|||.++..+.+... ..+|||||||||||||+|+|++..+.+.++++||.
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 99999999999999998877654321 12699999999999999999998888899999999
Q ss_pred HHHHHHHHHHhhcccceEEEEEecCCCchhhhHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHcCCccCCCCCCCccCCcc
Q 002147 81 SIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEEERLRKEFEEAGKLLSAKEKPETCDSNV 160 (959)
Q Consensus 81 ~If~yID~L~~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsakea~~~~~e~~~l~~e~~~~G~~l~~~~~~~~fDSN~ 160 (959)
+||+|||+||.+|||||+||||||||||||||||||+|||+++++++....+..+..++...+|..+........|||||
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 99999999999999999999999999999999999999999999998887777777778777776665444557999999
Q ss_pred cccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCchhHHh
Q 002147 161 ITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIML 240 (959)
Q Consensus 161 ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL 240 (959)
|||||+||.+|+++|++||.+|+++||.|++++||+||++||||||||||+|||+++++|+|+||++|||||+|||||||
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 hhccccceEEEeeccc
Q 002147 241 SLATHEIHFSILREVI 256 (959)
Q Consensus 241 ~LatHe~~f~ILRE~v 256 (959)
||++|+++|+||||+|
T Consensus 222 ~L~~~~~~~~ilre~~ 237 (237)
T PF03159_consen 222 SLATHEPNIYILREEV 237 (237)
T ss_dssp HHHTT-SSEEEEEESS
T ss_pred HHccCCCeEEEEeccC
Confidence 9999999999999975
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=98.57 E-value=7.9e-07 Score=98.58 Aligned_cols=237 Identities=17% Similarity=0.238 Sum_probs=126.7
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCCC--CCCCHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKP--APTSYDDV 78 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~p--~p~te~em 78 (959)
|||++|..||...-+.+ .+ ++ . .| --|=||.++.||.+....... ........
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 157899999999866432110 11112234
Q ss_pred HHHHHHHHHHHHhhcccceEEEEEecCCCchhhhHHHHHhhhhHHHHHHHHHHHH-----HHHHHHHHHcCCccCCCCCC
Q 002147 79 FKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEAEAEE-----ERLRKEFEEAGKLLSAKEKP 153 (959)
Q Consensus 79 ~~~If~yID~L~~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsakea~~~~~e~-----~~l~~e~~~~G~~l~~~~~~ 153 (959)
...++..+.+|+.. . -+ ..+++||.+|-.|......||-+.....+...... ++..+...
T Consensus 56 l~~~~~rl~~L~~~-~-i~-pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~------------ 120 (316)
T cd00128 56 LQGFFYRTCRLLEL-G-IK-PVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLER------------ 120 (316)
T ss_pred HHHHHHHHHHHHHC-C-CE-EEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHh------------
Confidence 45555555555532 2 23 34679999998887776655543322111110000 11111000
Q ss_pred CccCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEec
Q 002147 154 ETCDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGL 233 (959)
Q Consensus 154 ~~fDSN~ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGl 233 (959)
.+..|||.+ ... ++..+... ++.+|.+ |+|+|-=+-.+-+. .....|++.
T Consensus 121 ---~~~~~~~~~--~~~----~~~lL~~~--------gi~~i~a----p~EAdaq~a~l~~~---------g~v~~i~S~ 170 (316)
T cd00128 121 ---RAVRVTPQM--IEE----AKELLRLM--------GIPYIVA----PYEAEAQCAYLAKK---------GLVDAIITE 170 (316)
T ss_pred ---ccCcCCHHH--HHH----HHHHHHHc--------CCCEEEC----CcCHHHHHHHHHhC---------CCeeEEEec
Confidence 012244433 122 23322221 5777764 79999765544331 236789999
Q ss_pred CchhHHhhhccccceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHH
Q 002147 234 DADLIMLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREY 313 (959)
Q Consensus 234 DADLImL~LatHe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~~~~~~d~~~~~~~~~~~~~f~~l~I~vLREY 313 (959)
|+|+++++- ++ ++|-- ...+ ...+..++..-+.+.
T Consensus 171 DsD~l~fg~----~~--vi~~~-~~~~--------------------------------------~~~~~~~~~~~~~~~ 205 (316)
T cd00128 171 DSDLLLFGA----PR--VYRNL-FDSG--------------------------------------AKPVEEIDLEKILKE 205 (316)
T ss_pred CCCeeeecC----ce--EEEec-ccCC--------------------------------------CCceEEEEHHHHHHH
Confidence 999988762 22 23321 0000 013455665555444
Q ss_pred HHhhcCCCCCCCCCchhhhHhHHHHHhhhhcCCCCCCCCccccCcChHHHHHHHHH
Q 002147 314 LQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYR 369 (959)
Q Consensus 314 L~~E~~~~~~pf~~dlERiIDDFVFLcffvGNDFLPhLPsl~I~eGaid~Li~~Yk 369 (959)
| . +. -+.|+.+|.|+|+||+|++|.+-+.. |+. |+..|.
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 26889999999999999999875442 333 444444
No 6
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.25 E-value=2.8e-05 Score=89.29 Aligned_cols=230 Identities=19% Similarity=0.281 Sum_probs=124.5
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCC-----CCCC----
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPD-----GKPA---- 71 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~-----~~p~---- 71 (959)
|||.++..+|....|.++..+- ...-.| =-|-||....||.....- +.+.
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 9999999999999998765421 000011 157899999999744211 1110
Q ss_pred CCCHHHHHHHHHHHHHHHHhh-cccceEEEEEecCCCchhhhHHHHHhh--hhHHHHHHH-HHH--HHHHHHHHHHHcCC
Q 002147 72 PTSYDDVFKSIFDYIDHIFLL-VRPRKLLYLAIDGVAPRAKMNQQRTRR--FRAAKDAAE-AEA--EEERLRKEFEEAGK 145 (959)
Q Consensus 72 p~te~em~~~If~yID~L~~~-VrPrKlLyiAIDGVAPrAKMNQQRsRR--Frsakea~~-~~~--e~~~l~~e~~~~G~ 145 (959)
-... .-+.-+|..+-+|+.. ++| .+++||..|-.|...-..|| ...+.+..+ +.+ ..+++++.+.+
T Consensus 60 G~~t-~~l~g~~~r~~~Ll~~gikP----v~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r--- 131 (393)
T PTZ00217 60 GEVT-SHISGLFNRTIRLLEAGIKP----VYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKR--- 131 (393)
T ss_pred CCcc-HHHHHHHHHHHHHHHCCCCE----EEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhh---
Confidence 0011 2334556666677764 788 47999999976665443333 222222111 000 01111111100
Q ss_pred ccCCCCCCCccCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCC
Q 002147 146 LLSAKEKPETCDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPN 225 (959)
Q Consensus 146 ~l~~~~~~~~fDSN~ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpN 225 (959)
+..||+ +-+..+.+. +.. -++.+|.+ |||+|.=|-..-+ .+
T Consensus 132 ------------~~~vt~--~~~~~~~~l----L~~--------~Gip~i~A----P~EAdaq~A~L~~---------~g 172 (393)
T PTZ00217 132 ------------TVRVTK--EQNEDAKKL----LRL--------MGIPVIEA----PCEAEAQCAELVK---------KG 172 (393)
T ss_pred ------------cccCCH--HHHHHHHHH----HHH--------cCCceEEC----CcCHHHHHHHHHH---------CC
Confidence 112332 122222222 221 14677765 7999995544432 24
Q ss_pred CcEEEEecCchhHHhhhccccceEEEeeccccCCCCCcccccccccCcccccccCCCCCCCCCCCCCCCCccccCceEEE
Q 002147 226 TRHCLYGLDADLIMLSLATHEIHFSILREVITLPGQQEKCFVCGQVGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFL 305 (959)
Q Consensus 226 t~HcIYGlDADLImL~LatHe~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~g~~~~~~~d~~~~~~~~~~~~~f~~l 305 (959)
....|++-|.|+++++- + .++|--. ..+ + .+..++.+
T Consensus 173 ~v~~ViS~D~D~l~fg~----~--~vi~~l~-~~~-----------------------------~-------~~~~~~~~ 209 (393)
T PTZ00217 173 KVYAVATEDMDALTFGT----P--VLLRNLN-FSE-----------------------------A-------KKRPIQEI 209 (393)
T ss_pred CeEEEeCCCcCeeecCC----c--EEEEccc-ccc-----------------------------c-------CCCCeEEE
Confidence 56789999999998872 1 2343311 000 0 01235666
Q ss_pred ehHHHHHHHHhhcCCCCCCCCCchhhhHhHHHHHhhhhcCCCCCCCCcccc
Q 002147 306 NIWVLREYLQYELDIPNPPFPINFERIVDDFVFLCFFVGNDFLPHMPTLEI 356 (959)
Q Consensus 306 ~I~vLREYL~~E~~~~~~pf~~dlERiIDDFVFLcffvGNDFLPhLPsl~I 356 (959)
+..-+.+.+ . + . -+.||-+|.|+|.||+|.+|.+-.
T Consensus 210 ~~~~v~~~~----g-------l--~--~~q~id~~iL~G~Dy~pgi~GIG~ 245 (393)
T PTZ00217 210 NLSTVLEEL----G-------L--S--MDQFIDLCILCGCDYCDTIKGIGP 245 (393)
T ss_pred EHHHHHHHh----C-------C--C--HHHHHHHHHHhCCCCCCCCCCccH
Confidence 766554432 1 1 2 267888999999999999998744
No 7
>PRK03980 flap endonuclease-1; Provisional
Probab=97.64 E-value=0.0033 Score=69.97 Aligned_cols=33 Identities=15% Similarity=0.503 Sum_probs=26.1
Q ss_pred hHHHHHhhhhcCCCCCCCCccccCc--------ChHHHHHH
Q 002147 334 DDFVFLCFFVGNDFLPHMPTLEIRE--------GAINLLMH 366 (959)
Q Consensus 334 DDFVFLcffvGNDFLPhLPsl~I~e--------Gaid~Li~ 366 (959)
+.||-+|.|+|.||+|++|.+-+.. |+|+.+++
T Consensus 177 ~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~ 217 (292)
T PRK03980 177 EQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLE 217 (292)
T ss_pred HHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHH
Confidence 5788899999999999999877653 45555554
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=97.15 E-value=0.015 Score=66.07 Aligned_cols=67 Identities=15% Similarity=0.189 Sum_probs=40.3
Q ss_pred eEEEeccccccccccCCC--CCCCCC-----HHHHHHHHHHHHHHHHhh-cccceEEEEEecCCCchhhhHHHHHhhhh
Q 002147 51 NLYLDMNGIIHPCFHPDG--KPAPTS-----YDDVFKSIFDYIDHIFLL-VRPRKLLYLAIDGVAPRAKMNQQRTRRFR 121 (959)
Q Consensus 51 nLYLDMNgIIH~C~H~~~--~p~p~t-----e~em~~~If~yID~L~~~-VrPrKlLyiAIDGVAPrAKMNQQRsRRFr 121 (959)
-|-||....||.+...-. ...+.+ ...-+..+|..+-+|+.. ++| .+++||-+|-.|..+-..||-+
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 577999999997654210 000111 012234445555566655 777 7999999998777766666543
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=95.19 E-value=1 Score=49.55 Aligned_cols=133 Identities=15% Similarity=0.180 Sum_probs=73.2
Q ss_pred EEEeccccccccccCCCC--CCCCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCCchhhhHHHHHhhhhHHHHHHHH
Q 002147 52 LYLDMNGIIHPCFHPDGK--PAPTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAAKDAAEA 129 (959)
Q Consensus 52 LYLDMNgIIH~C~H~~~~--p~p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsakea~~~ 129 (959)
|.||.|++||-+.|.-.. ...-........++..+.+++...+|..+ .+|+||-.|-- |..-+
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~-~~~fD~~~~~~-----R~~l~--------- 68 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYV-AVVFDAKGKTF-----RHELY--------- 68 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeE-EEEEeCCCCcc-----ccchh---------
Confidence 789999999998885311 00011123344566666677777789875 59999854411 21111
Q ss_pred HHHHHHHHHHHHHcCCccCCCCCCCccCCcccccccHHHHHHHHHHHHHHHHHHhcCCCCCccEEEEeCCCCCC-chhHH
Q 002147 130 EAEEERLRKEFEEAGKLLSAKEKPETCDSNVITPGTQFMAVLSAALQYFIQARLNQIPGWQFTKVILSDANVPG-EGEHK 208 (959)
Q Consensus 130 ~~e~~~l~~e~~~~G~~l~~~~~~~~fDSN~ITPGT~FM~~Ls~~L~~yI~~kl~~dp~W~~lkVIlSds~VPG-EGEHK 208 (959)
.++++.-.. +|. .|..++ .++++-|.. - ++.+|- +|| |++==
T Consensus 69 --------p~YKa~R~~---------------~pe-----~L~~q~-~~~~~~l~~-~---gi~~i~----~~g~EADD~ 111 (259)
T smart00475 69 --------PEYKANRPK---------------TPD-----ELLEQI-PLIKELLDA-L---GIPVLE----VEGYEADDV 111 (259)
T ss_pred --------HHHHhCCCC---------------CCH-----HHHHHH-HHHHHHHHH-C---CCCEEe----eCCcCHHHH
Confidence 112211110 111 133343 334433322 1 344443 788 99987
Q ss_pred HHHHHHHhhcCCCCCCCCcEEEEecCchhHHhh
Q 002147 209 IMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLS 241 (959)
Q Consensus 209 ImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~ 241 (959)
|-...++.... +...+|++.|-|+.-|.
T Consensus 112 iatla~~~~~~-----g~~~~IvS~DkDl~ql~ 139 (259)
T smart00475 112 IATLAKKAEAE-----GYEVRIVSGDKDLLQLV 139 (259)
T ss_pred HHHHHHHHHhC-----CCeEEEEeCCCcHhhcC
Confidence 76666654321 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=94.69 E-value=1.4 Score=47.96 Aligned_cols=57 Identities=7% Similarity=0.063 Sum_probs=39.0
Q ss_pred eEEEeccccccccccCCCCCC---CCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCCc
Q 002147 51 NLYLDMNGIIHPCFHPDGKPA---PTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (959)
Q Consensus 51 nLYLDMNgIIH~C~H~~~~p~---p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVAP 108 (959)
-|.||.|.+||-+.|...... .-........++..|.+++...+|.++ .+|+||-.|
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 378999999999888652211 011223445666677778888899987 699999643
No 11
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=94.50 E-value=0.042 Score=51.20 Aligned_cols=93 Identities=19% Similarity=0.268 Sum_probs=56.2
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCCC--CCCCHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKP--APTSYDDV 78 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~p--~p~te~em 78 (959)
|||+++..||... .. ..+...-.|. -+=||.+..||.|......+ ........
T Consensus 1 MGI~gL~~~l~~~----~~----~~~i~~l~g~-----------------~vaIDa~~wl~~~~~~~~~~~~~~~~~~~~ 55 (99)
T smart00485 1 MGIKGLWPLLKPV----VR----EVPLEALRGK-----------------TLAIDASIWLYQFLTACREKLGTPLPNSKH 55 (99)
T ss_pred CCHhHHHHHHHHh----cc----cCCHHHhCCc-----------------eEeccHHHHHHHHHHHHhhhhcCCCCchHH
Confidence 9999999999875 11 1010001122 45578888888765432110 11222335
Q ss_pred HHHHHHHHHHHHh-hcccceEEEEEecCCCchhhhHHHHHhhhhH
Q 002147 79 FKSIFDYIDHIFL-LVRPRKLLYLAIDGVAPRAKMNQQRTRRFRA 122 (959)
Q Consensus 79 ~~~If~yID~L~~-~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrs 122 (959)
+..+|..|.+|++ -|.| ++.+||.+|-+|...+..||-+.
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 5666666666553 2343 58899999999999998887654
No 12
>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=94.33 E-value=0.053 Score=50.60 Aligned_cols=95 Identities=18% Similarity=0.354 Sum_probs=56.1
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccccccCCCCCCCC--CHHHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHPCFHPDGKPAPT--SYDDV 78 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~C~H~~~~p~p~--te~em 78 (959)
|||+++..+|.... .+..+--+ +. +| --|=||.+..||.+.+....+... ..+..
T Consensus 1 MGI~gL~~~l~~~~--~v~~~~~~-------------~l-----~g---~~vaID~s~wl~~~~~~~~~~~~~~~~~~~~ 57 (101)
T PF00752_consen 1 MGIKGLWQLLKPAA--AVRKVSLS-------------EL-----RG---KRVAIDASCWLHQFLFSCREELGQGVGTDSH 57 (101)
T ss_dssp ---TTHHHHCHHHE--GEEEEEGG-------------GG-----TT---CEEEEEHHHHHHHHHHHSBCTTSCB-BS-HH
T ss_pred CCcccHHHHHHhhc--cCCccCHH-------------Hh-----CC---CEEEEEcHHHHHHHHHHhHHHhccccchHHH
Confidence 99999999999976 22211000 00 11 357899999999876544322111 11456
Q ss_pred HHHHHHHHHHHH-hhcccceEEEEEecCCCchhhhHHHHHhhhhH
Q 002147 79 FKSIFDYIDHIF-LLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRA 122 (959)
Q Consensus 79 ~~~If~yID~L~-~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrs 122 (959)
+..++..+..|. .-|+| ++.+||.+|-+|......||-+.
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 667777776654 34555 68999999999998888776544
No 13
>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=91.95 E-value=0.71 Score=43.00 Aligned_cols=89 Identities=20% Similarity=0.352 Sum_probs=55.0
Q ss_pred cEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCchhHHhhhccccceEEEeeccc-cCCCCCcccccccc
Q 002147 192 TKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLSLATHEIHFSILREVI-TLPGQQEKCFVCGQ 270 (959)
Q Consensus 192 lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~LatHe~~f~ILRE~v-~~~~~~~~c~~c~q 270 (959)
+.+|+ -|||+|.=+--.-|. +..+.|++-|+|+++.|-- .|+|... ... .+|
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------KVIRKLSDKSS---GKC----- 57 (94)
T ss_dssp -EEEE-----SS-HHHHHHHHHHT---------TSSSEEE-SSSHHHHTT-S------EEEESST-CSC---CST-----
T ss_pred CeEEE----cCchHHHHHHHHHHh---------cceeEEEecCCCEEeeCCC------EEEEecccccc---CCc-----
Confidence 45555 479999988866552 5679999999999999754 4566532 010 011
Q ss_pred cCcccccccCCCCCCCCCCCCCCCCccccCceEEEehHHHHHHHHhhcCCCCCCCCCchhhhHhHHHHHhhhhcCC
Q 002147 271 VGHLAAECHGKPGDNPADWNGVDDTPIHKKKYQFLNIWVLREYLQYELDIPNPPFPINFERIVDDFVFLCFFVGND 346 (959)
Q Consensus 271 ~gh~~~~c~g~~~~~~~d~~~~~~~~~~~~~f~~l~I~vLREYL~~E~~~~~~pf~~dlERiIDDFVFLcffvGND 346 (959)
. ......+.+++..-+.+.|... -+.|+.+|+|+|.|
T Consensus 58 --------~----------------~~~~~~~~~~~~~~i~~~l~l~---------------~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 58 --------S----------------SKSEKEVEVIDLDDILKELGLT---------------REQFIDLCILCGCD 94 (94)
T ss_dssp --------S-----------------CCESEEEEEEHHHHHHHHTTS---------------HHHHHHHHHHHHET
T ss_pred --------c----------------cccccceEEEEHHHHHHHcCCC---------------HHHHHHHheecCCC
Confidence 0 0012457788887776664311 25799999999998
No 14
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=89.83 E-value=2.8 Score=50.18 Aligned_cols=92 Identities=22% Similarity=0.345 Sum_probs=53.8
Q ss_pred CccchHHHHHHhhCCCcccccccCCCccCCCCccccCCCCCCCCCCcccCeEEEeccccccc----cccCCCCCCCCCHH
Q 002147 1 MGVPAFYRWLADRYPLSIVDVVEEDPQVDGEGVARPVDVSKPNPNGMEFDNLYLDMNGIIHP----CFHPDGKPAPTSYD 76 (959)
Q Consensus 1 MGVP~FfRWL~~rYP~ii~~~~e~~~~~~~~g~~~p~d~s~pnpng~efDnLYLDMNgIIH~----C~H~~~~p~p~te~ 76 (959)
|||.+|+-.|... ..++ .+++ ++.+-|=+|.-+-+|. |.+.-....|+ +
T Consensus 1 MGI~GLlp~~k~~----~~~~----------------hi~~-----~~g~tvavD~y~WLhrg~~~Ca~el~~~~pT--~ 53 (556)
T KOG2518|consen 1 MGIQGLLPLLKPA----LKPI----------------HISE-----YKGKTVAVDGYCWLHRGALACAEKLAKGKPT--D 53 (556)
T ss_pred CCcchhHHHHHHH----hhhh----------------hHHH-----hcCceEEEehhhHHhhhHHhHHHHHhcCCCh--H
Confidence 9999999888762 2211 1111 2456778888888885 44432222232 4
Q ss_pred HHHHHHHHHHHHHH-hhcccceEEEEEecCCCchhhhHHHHHhhhhHH
Q 002147 77 DVFKSIFDYIDHIF-LLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRAA 123 (959)
Q Consensus 77 em~~~If~yID~L~-~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrsa 123 (959)
..+.-+..++..|. .-|+| +|.+||=.=-+|--+-|.||-+..
T Consensus 54 ryi~y~ik~v~lL~~~gikP----ilVFDG~~LP~K~~te~~Rr~~R~ 97 (556)
T KOG2518|consen 54 RYIQFFIKRVKLLLSYGIKP----ILVFDGDPLPSKKETERKRRERRK 97 (556)
T ss_pred HHHHHHHHHHHHHHhcCCeE----EEEecCCCcccccccchHHHHHHH
Confidence 44344444444443 23455 799999887777777666665544
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=89.76 E-value=0.19 Score=33.91 Aligned_cols=16 Identities=56% Similarity=1.410 Sum_probs=14.8
Q ss_pred ccccccccCccccccc
Q 002147 264 KCFVCGQVGHLAAECH 279 (959)
Q Consensus 264 ~c~~c~q~gh~~~~c~ 279 (959)
.|+.||+.||++.+|.
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 6999999999999995
No 16
>PRK14976 5'-3' exonuclease; Provisional
Probab=89.50 E-value=7.3 Score=43.53 Aligned_cols=57 Identities=19% Similarity=0.278 Sum_probs=38.7
Q ss_pred eEEEeccccccccccCCCC--CC----CCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCCc
Q 002147 51 NLYLDMNGIIHPCFHPDGK--PA----PTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (959)
Q Consensus 51 nLYLDMNgIIH~C~H~~~~--p~----p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVAP 108 (959)
=|.||.|++|+-|+|.... +. .-.......-+++.|-+++...+|..+ .+|+||-.|
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 4689999999998887421 11 011224445667777788888899886 699998543
No 17
>PRK05755 DNA polymerase I; Provisional
Probab=86.74 E-value=14 Score=47.50 Aligned_cols=56 Identities=11% Similarity=0.134 Sum_probs=36.4
Q ss_pred eEEEeccccccccccCCCCC---CCCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCC
Q 002147 51 NLYLDMNGIIHPCFHPDGKP---APTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVA 107 (959)
Q Consensus 51 nLYLDMNgIIH~C~H~~~~p---~p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVA 107 (959)
-|.||.|.+++-+.|.-... ..-........++..|-+++...+|..+ .+|+||-.
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 0111223444555666677777889775 69999843
No 18
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=83.19 E-value=29 Score=39.13 Aligned_cols=62 Identities=18% Similarity=0.354 Sum_probs=44.7
Q ss_pred eEEEeccccccccccCCCC------CCCCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCCc--hhhhHHHH
Q 002147 51 NLYLDMNGIIHPCFHPDGK------PAPTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP--RAKMNQQR 116 (959)
Q Consensus 51 nLYLDMNgIIH~C~H~~~~------p~p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVAP--rAKMNQQR 116 (959)
-|-||-+++++.+.|.... ..++. ....+...|.++++..+|.+ ..+++||-.| |.++...|
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 6889999999998886521 12222 55666777889999999966 4699999777 55555544
No 19
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=81.18 E-value=70 Score=38.27 Aligned_cols=35 Identities=23% Similarity=0.444 Sum_probs=23.4
Q ss_pred HhHHHHHhhhhcCCCCCCCCccccCcChHHHHHHHHH
Q 002147 333 VDDFVFLCFFVGNDFLPHMPTLEIREGAINLLMHVYR 369 (959)
Q Consensus 333 IDDFVFLcffvGNDFLPhLPsl~I~eGaid~Li~~Yk 369 (959)
+.-||-||+|+|+||.|.+-+ |..+..-.|++.|+
T Consensus 216 ~~~fidL~lLlGCDYc~~I~G--ig~~~al~lir~~~ 250 (449)
T KOG2519|consen 216 RESFIDLCLLLGCDYCPTIRG--IGPKKALKLIRQHG 250 (449)
T ss_pred HHHHHHHHHHhcCcccccccc--cChHHHHHHHHHhc
Confidence 356888999999999999643 34333333555554
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=76.43 E-value=78 Score=41.11 Aligned_cols=56 Identities=13% Similarity=0.204 Sum_probs=34.4
Q ss_pred EEEeccccccccccCCCC-CC---CCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCCc
Q 002147 52 LYLDMNGIIHPCFHPDGK-PA---PTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (959)
Q Consensus 52 LYLDMNgIIH~C~H~~~~-p~---p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVAP 108 (959)
|.||.|++|+-++|.-.. +- .-.......-++.-+-+|+...+|..+ .+|+||-.|
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 579999999998885411 00 001112333444555566666789875 699998654
No 21
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=66.77 E-value=55 Score=41.51 Aligned_cols=153 Identities=14% Similarity=0.065 Sum_probs=101.7
Q ss_pred CCCCCCCcEEEEEeeCCCCC-CCCCCCCCCCCCCCCcCCCCCCCCCCcccccCCccc-cCCCCCCCCCCCCCCCCCChhH
Q 002147 683 LPDIERNQAINVTYLNPQKH-RHIPEPPKGATIPAKTLKPIDIKPFPTLWHEDNSRR-QQGRERPQVPGAIAGPVLGEAA 760 (959)
Q Consensus 683 l~di~~n~~~~~~y~~P~~~-~~~~~ll~g~~~p~~~l~~~d~~~~~~lw~~~~~~r-~~~~~r~~~~~~~~~~~~~~~~ 760 (959)
|+..-.-.+.++.+..|+.+ .||+..+.|.+.+.++++..++...+-+||++...+ ..-+.+.++.+.++ |.+|+++
T Consensus 699 ~~~~~~p~~~~~~~~~~~~~~~~i~~~p~~~~~~~~~~~~v~~~~~~~~~~ed~~~~a~~l~G~~~p~~~lk-P~dwn~s 777 (931)
T KOG2044|consen 699 LAHGVDPGLNGAISKDPEGLESGISKSPPGGLSDYNTNTGVCLKYVDPEYPEDYIFPAIRLDGAKEPEKVLK-PDDWNDR 777 (931)
T ss_pred cccccCcccceeeccCccccccccccCChhhcccCCccceeeecccCccccccccchhhhcCCCCCCccccC-cchhhhh
Confidence 33333446678889999765 799999999999999999999999999999998743 23445566667788 9999999
Q ss_pred HHHHHhhhcccCCC--CCCCCCCCCcCCCCCCccCcccccCCCCCCCCCCCcCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 002147 761 HRLIKNTLNYKPNG--SPGFFEQPSYHNFQGNYANAVTRLRPAAPSGHERGYGDESRYNYGNYNYPQGMRGNSRFPVPSN 838 (959)
Q Consensus 761 ~r~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 838 (959)
|++.+..++..+- ..+...+..++..++++.+ .+|++|-+.+|..-+.++.+. ..++.+.++||+|.+.+
T Consensus 778 -R~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~------~~~~ggr~~~~~~~~~G~~~~-~y~~~~~~~~~~p~~~~ 849 (931)
T KOG2044|consen 778 -RDGRYQPQAGFNRNAPRGSLPQSGHRQVHHYVRG------GGGGGGRGYSYDPRRGGKGGG-GYNDRQDGGPRNPGGRD 849 (931)
T ss_pred -hhhhcCcccccccCCCCCcCCcccccccCcCCCC------CCCCCCCCCCCCCccccccCC-cccccccCCCCCCCccC
Confidence 9999999987764 2233344444433322221 111222223333322233333 55666788999998888
Q ss_pred CCCCCc
Q 002147 839 GMQGNK 844 (959)
Q Consensus 839 ~~~~~~ 844 (959)
++++-+
T Consensus 850 ~~~~~~ 855 (931)
T KOG2044|consen 850 GSGPYN 855 (931)
T ss_pred CCCCcc
Confidence 877433
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=61.97 E-value=12 Score=48.72 Aligned_cols=39 Identities=15% Similarity=0.072 Sum_probs=30.3
Q ss_pred ccEEEEeCCCCCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCchhHHhhh
Q 002147 191 FTKVILSDANVPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLSL 242 (959)
Q Consensus 191 ~lkVIlSds~VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~L 242 (959)
++-+|.+ |||+|.=+-...+ -.....|++-|+|+++.|=
T Consensus 785 GIP~i~A----P~EAEAqcA~L~~---------~G~vd~V~TeDsD~llFGa 823 (1034)
T TIGR00600 785 GIPYIVA----PMEAEAQCAILDL---------LDQTSGTITDDSDIWLFGA 823 (1034)
T ss_pred CCCeeeC----CccHHHHHHHHHh---------CCCeEEEEccccceeccCC
Confidence 4667754 8999998877754 2567999999999997764
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=61.14 E-value=29 Score=45.35 Aligned_cols=66 Identities=21% Similarity=0.335 Sum_probs=35.6
Q ss_pred eEEEecccccccc---ccCCCCCCCCCHHHHHHHHHHHHHHHH-hhcccceEEEEEecCCCchhhhHHHHHhhhhH
Q 002147 51 NLYLDMNGIIHPC---FHPDGKPAPTSYDDVFKSIFDYIDHIF-LLVRPRKLLYLAIDGVAPRAKMNQQRTRRFRA 122 (959)
Q Consensus 51 nLYLDMNgIIH~C---~H~~~~p~p~te~em~~~If~yID~L~-~~VrPrKlLyiAIDGVAPrAKMNQQRsRRFrs 122 (959)
-|=||.-.-||.+ ++...... .+...+ ..+|..|.+|+ .-|+| ++.+||.+|-.|...-..||-|.
T Consensus 26 ~vAIDasiWL~q~l~~vr~~~g~~-l~n~hl-~g~f~Ri~~Ll~~gI~P----VfVFDG~~p~lK~~t~~~R~~rR 95 (1034)
T TIGR00600 26 RLAVDISIWLNQALKGVRDREGNA-IKNSHL-LTLFHRLCKLLFFRIRP----IFVFDGGAPLLKRQTLAKRRQRR 95 (1034)
T ss_pred EEEechHHHHHHHHHHHHhccCCc-cCCHHH-HHHHHHHHHHHHCCCeE----EEEECCCCchHhHHHHHHHHHHH
Confidence 4455666667743 22222111 122333 34455555554 34454 68899999998887655554433
No 24
>PF13696 zf-CCHC_2: Zinc knuckle
Probab=59.66 E-value=3.8 Score=31.87 Aligned_cols=19 Identities=37% Similarity=0.807 Sum_probs=16.5
Q ss_pred CcccccccccCcccccccC
Q 002147 262 QEKCFVCGQVGHLAAECHG 280 (959)
Q Consensus 262 ~~~c~~c~q~gh~~~~c~g 280 (959)
.-.|.+|++.||+..+|-.
T Consensus 8 ~Y~C~~C~~~GH~i~dCP~ 26 (32)
T PF13696_consen 8 GYVCHRCGQKGHWIQDCPT 26 (32)
T ss_pred CCEeecCCCCCccHhHCCC
Confidence 4579999999999999964
No 25
>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=52.84 E-value=13 Score=33.60 Aligned_cols=21 Identities=33% Similarity=0.779 Sum_probs=18.6
Q ss_pred hHHHHHhhhhc--CCCCCCCCcc
Q 002147 334 DDFVFLCFFVG--NDFLPHMPTL 354 (959)
Q Consensus 334 DDFVFLcffvG--NDFLPhLPsl 354 (959)
+.|+-+|.|+| -|++|++|.+
T Consensus 8 ~q~~d~~~L~GD~~D~i~gv~gi 30 (75)
T cd00080 8 EQFIDLAILVGDKSDNIPGVPGI 30 (75)
T ss_pred HHHHHHHHHcCCccccCCCCCcc
Confidence 46778999999 9999999984
No 26
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=35.18 E-value=30 Score=27.33 Aligned_cols=20 Identities=20% Similarity=0.612 Sum_probs=16.0
Q ss_pred hHHHHHhhhhcCCCCCCCCcc
Q 002147 334 DDFVFLCFFVGNDFLPHMPTL 354 (959)
Q Consensus 334 DDFVFLcffvGNDFLPhLPsl 354 (959)
+-|+-+|.|+| |+.+.+|++
T Consensus 2 ~q~~~~~~L~G-D~~dni~Gv 21 (36)
T smart00279 2 EQLIDYAILVG-DYSDNIPGV 21 (36)
T ss_pred HHHHHHHHHhC-cCCCCCCCC
Confidence 35788999999 999966654
No 27
>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=35.12 E-value=1.3e+02 Score=31.18 Aligned_cols=56 Identities=16% Similarity=0.284 Sum_probs=39.6
Q ss_pred EEEeccccccccccCCCC-CC---CCCHHHHHHHHHHHHHHHHhhcccceEEEEEecCCCc
Q 002147 52 LYLDMNGIIHPCFHPDGK-PA---PTSYDDVFKSIFDYIDHIFLLVRPRKLLYLAIDGVAP 108 (959)
Q Consensus 52 LYLDMNgIIH~C~H~~~~-p~---p~te~em~~~If~yID~L~~~VrPrKlLyiAIDGVAP 108 (959)
|.||.|+++|-+.|.-.. +. .-..-..+...++.|.+|+...+|.. +.+|+|+-.+
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 789999999999986542 10 00112355566777778888889987 5699999887
No 28
>KOG0921 consensus Dosage compensation complex, subunit MLE [Transcription]
Probab=34.26 E-value=1e+02 Score=39.95 Aligned_cols=27 Identities=11% Similarity=0.293 Sum_probs=16.2
Q ss_pred ccccCCCCChHhHhhhccCCCCCCCCc
Q 002147 521 TFFLGEPFRPFDQLMGTLPAASSSALP 547 (959)
Q Consensus 521 ~F~~g~Pf~PfeQLM~VLP~~S~~~LP 547 (959)
.++...+.+|+--+++-||-.-.-.+|
T Consensus 835 ~ld~n~elt~lg~~la~l~iep~~~k~ 861 (1282)
T KOG0921|consen 835 ALDANDELTPLGRMLARLPIEPRIGKM 861 (1282)
T ss_pred hhhccCcccchhhhhhhccCcccccce
Confidence 345566777777777776655444333
No 29
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=33.50 E-value=32 Score=31.22 Aligned_cols=34 Identities=18% Similarity=0.281 Sum_probs=27.7
Q ss_pred CCCchhHHHHHHHHHhhcCCCCCCCCcEEEEecCchhHHhhhc
Q 002147 201 VPGEGEHKIMSYIRLQRNLPGFDPNTRHCLYGLDADLIMLSLA 243 (959)
Q Consensus 201 VPGEGEHKImdfIR~qr~~p~ydpNt~HcIYGlDADLImL~La 243 (959)
-|||+|.-+--.-+ ...-+.|+|.|+|+++.|--
T Consensus 10 AP~eAeAq~A~L~~---------~g~vdav~s~D~D~llfG~~ 43 (73)
T smart00484 10 APYEAEAQCAYLAK---------SGLVDAIITEDSDLLLFGAP 43 (73)
T ss_pred cCCcHHHHHHHHHh---------CCCeeEEEcCccceEecCCc
Confidence 48999998877766 24679999999999998764
No 30
>smart00343 ZnF_C2HC zinc finger.
Probab=31.22 E-value=23 Score=25.55 Aligned_cols=16 Identities=50% Similarity=1.364 Sum_probs=14.2
Q ss_pred ccccccccCccccccc
Q 002147 264 KCFVCGQVGHLAAECH 279 (959)
Q Consensus 264 ~c~~c~q~gh~~~~c~ 279 (959)
+|+.|++.||.+.+|.
T Consensus 1 ~C~~CG~~GH~~~~C~ 16 (26)
T smart00343 1 KCYNCGKEGHIARDCP 16 (26)
T ss_pred CCccCCCCCcchhhCC
Confidence 4889999999999986
No 31
>PHA02567 rnh RnaseH; Provisional
Probab=25.16 E-value=80 Score=36.15 Aligned_cols=58 Identities=16% Similarity=0.133 Sum_probs=43.2
Q ss_pred cCeEEEeccccccccccCCCCCCCCCHHHHH-HHHHHHHHHHHhhcccce-EEEEEecCC
Q 002147 49 FDNLYLDMNGIIHPCFHPDGKPAPTSYDDVF-KSIFDYIDHIFLLVRPRK-LLYLAIDGV 106 (959)
Q Consensus 49 fDnLYLDMNgIIH~C~H~~~~p~p~te~em~-~~If~yID~L~~~VrPrK-lLyiAIDGV 106 (959)
-+-+.||++.|+--|++.+-.+.......|+ ..|++-|..++..++|.- -+.+|+|+-
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 3679999999999999987555434444555 558888888888877762 167999974
No 32
>PF14392 zf-CCHC_4: Zinc knuckle
Probab=24.64 E-value=34 Score=28.51 Aligned_cols=21 Identities=38% Similarity=0.901 Sum_probs=17.6
Q ss_pred CCCCcccccccccCccccccc
Q 002147 259 PGQQEKCFVCGQVGHLAAECH 279 (959)
Q Consensus 259 ~~~~~~c~~c~q~gh~~~~c~ 279 (959)
...+..|+.||..||...+|.
T Consensus 28 E~lp~~C~~C~~~gH~~~~C~ 48 (49)
T PF14392_consen 28 ERLPRFCFHCGRIGHSDKECP 48 (49)
T ss_pred CCcChhhcCCCCcCcCHhHcC
Confidence 344678999999999999985
No 33
>PF13917 zf-CCHC_3: Zinc knuckle
Probab=23.37 E-value=43 Score=27.64 Aligned_cols=19 Identities=42% Similarity=0.935 Sum_probs=16.6
Q ss_pred CcccccccccCcccccccC
Q 002147 262 QEKCFVCGQVGHLAAECHG 280 (959)
Q Consensus 262 ~~~c~~c~q~gh~~~~c~g 280 (959)
...|..|++.||...+|..
T Consensus 4 ~~~CqkC~~~GH~tyeC~~ 22 (42)
T PF13917_consen 4 RVRCQKCGQKGHWTYECPN 22 (42)
T ss_pred CCcCcccCCCCcchhhCCC
Confidence 3579999999999999984
No 34
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=22.82 E-value=36 Score=36.40 Aligned_cols=45 Identities=22% Similarity=0.527 Sum_probs=28.7
Q ss_pred CCcEEEEecCchhHHhhhcc--ccceEEEeeccccCCCCCcccccccccCccccccc
Q 002147 225 NTRHCLYGLDADLIMLSLAT--HEIHFSILREVITLPGQQEKCFVCGQVGHLAAECH 279 (959)
Q Consensus 225 Nt~HcIYGlDADLImL~Lat--He~~f~ILRE~v~~~~~~~~c~~c~q~gh~~~~c~ 279 (959)
..-|..+--.++|=... +. |-.+=. .+..+|++||+.||++.+|.
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 45577777776555554 21 321111 12368999999999999994
No 35
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=21.39 E-value=40 Score=36.08 Aligned_cols=18 Identities=50% Similarity=1.145 Sum_probs=16.3
Q ss_pred CcccccccccCccccccc
Q 002147 262 QEKCFVCGQVGHLAAECH 279 (959)
Q Consensus 262 ~~~c~~c~q~gh~~~~c~ 279 (959)
...|++|||.||...+|-
T Consensus 60 ~~~C~nCg~~GH~~~DCP 77 (190)
T COG5082 60 NPVCFNCGQNGHLRRDCP 77 (190)
T ss_pred ccccchhcccCcccccCC
Confidence 458999999999999996
No 36
>COG5350 Predicted protein tyrosine phosphatase [General function prediction only]
Probab=20.59 E-value=1.1e+02 Score=32.20 Aligned_cols=42 Identities=24% Similarity=0.559 Sum_probs=35.2
Q ss_pred CccEEEEeCCCCCCch--------hHHHHHHHHHhhcCCCCCCCCcEEEEecC
Q 002147 190 QFTKVILSDANVPGEG--------EHKIMSYIRLQRNLPGFDPNTRHCLYGLD 234 (959)
Q Consensus 190 ~~lkVIlSds~VPGEG--------EHKImdfIR~qr~~p~ydpNt~HcIYGlD 234 (959)
+++.+.+.|-.+||+| =++|+||++ ..|.+.|=--||.-|.-
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 3689999999999999 368999998 56788888889988754
Done!