Query 030072
Match_columns 183
No_of_seqs 153 out of 1091
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 08:05:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02739 5_3_exonuc_N: 5'-3' e 99.7 1.2E-17 2.7E-22 135.4 5.4 62 108-175 1-63 (169)
2 smart00475 53EXOc 5'-3' exonuc 99.6 1E-15 2.2E-20 131.8 7.3 59 109-175 2-61 (259)
3 PHA00439 exonuclease 99.6 3.4E-15 7.4E-20 131.7 7.7 65 107-174 5-74 (286)
4 PRK09482 flap endonuclease-lik 99.6 4.3E-15 9.3E-20 128.8 7.4 58 108-177 3-61 (256)
5 PRK14976 5'-3' exonuclease; Pr 99.6 6.3E-15 1.4E-19 128.2 7.2 65 108-176 3-68 (281)
6 TIGR00593 pola DNA polymerase 99.5 1.2E-14 2.5E-19 143.2 6.9 61 110-176 1-62 (887)
7 cd00008 53EXOc 5'-3' exonuclea 99.5 6.1E-14 1.3E-18 118.7 7.2 59 109-175 2-62 (240)
8 PRK05755 DNA polymerase I; Pro 99.4 1.8E-13 3.9E-18 133.5 7.4 61 108-175 2-63 (880)
9 COG0258 Exo 5'-3' exonuclease 99.3 2.2E-12 4.8E-17 112.2 6.7 64 106-176 9-73 (310)
10 PHA02567 rnh RnaseH; Provision 98.9 1.2E-09 2.5E-14 97.6 6.1 58 107-174 13-74 (304)
11 TIGR03674 fen_arch flap struct 98.7 1.4E-08 3E-13 90.5 4.2 64 107-176 20-85 (338)
12 PTZ00217 flap endonuclease-1; 98.7 3.1E-08 6.8E-13 90.3 5.4 64 107-175 27-92 (393)
13 cd00128 XPG Xeroderma pigmento 98.3 1E-06 2.2E-11 76.7 5.6 60 107-175 23-82 (316)
14 PF00752 XPG_N: XPG N-terminal 96.1 0.011 2.3E-07 43.4 4.4 57 109-175 27-84 (101)
15 smart00485 XPGN Xeroderma pigm 95.5 0.022 4.8E-07 41.7 4.1 58 108-175 24-82 (99)
16 PF05991 NYN_YacP: YacP-like N 92.0 0.17 3.7E-06 41.1 3.4 53 111-173 1-53 (166)
17 COG3688 Predicted RNA-binding 76.1 3.3 7.2E-05 35.2 3.5 53 107-173 2-58 (173)
18 TIGR00600 rad2 DNA excision re 69.5 6.1 0.00013 41.3 4.3 59 107-175 23-81 (1034)
19 PF03159 XRN_N: XRN 5'-3' exon 57.6 14 0.00031 32.1 3.8 58 110-177 32-91 (237)
20 KOG2519 5'-3' exonuclease [Rep 55.1 24 0.00053 34.0 5.2 57 110-175 30-86 (449)
21 COG1515 Nfi Deoxyinosine 3'end 23.8 36 0.00077 29.8 0.8 21 107-127 95-115 (212)
22 PF14421 LmjF365940-deam: A di 22.2 1.1E+02 0.0025 26.5 3.5 38 143-183 155-192 (193)
23 COG0462 PrsA Phosphoribosylpyr 22.0 1.3E+02 0.0028 27.8 4.0 50 122-183 91-143 (314)
24 COG2812 DnaX DNA polymerase II 21.9 1.2E+02 0.0025 29.7 3.9 43 104-174 116-158 (515)
25 KOG3348 BolA (bacterial stress 21.7 1E+02 0.0023 23.6 2.9 31 153-183 6-38 (85)
26 KOG2518 5'-3' exonuclease [Rep 20.9 1.6E+02 0.0035 29.3 4.7 56 108-173 24-80 (556)
No 1
>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=99.70 E-value=1.2e-17 Score=135.44 Aligned_cols=62 Identities=31% Similarity=0.646 Sum_probs=55.4
Q ss_pred CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC 175 (183)
Q Consensus 108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk 175 (183)
++|+||||++|+||+|||.+.. ++ .+++|+|||||+||++||+++++ ++|+|++||||.+++
T Consensus 1 k~llLIDg~~l~~Ra~~a~~~~----~l--~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~ 63 (169)
T PF02739_consen 1 KKLLLIDGNSLLFRAYYALPKD----PL--RNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGP 63 (169)
T ss_dssp -EEEEEEHHHHHHHCCCCCTTS----T---BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSC
T ss_pred CeEEEEechHHHHHHHHhhccC----CC--cCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCc
Confidence 4799999999999999999843 56 89999999999999999999999 999999999998876
No 2
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.61 E-value=1e-15 Score=131.79 Aligned_cols=59 Identities=25% Similarity=0.590 Sum_probs=54.7
Q ss_pred cEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072 109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC 175 (183)
Q Consensus 109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk 175 (183)
+++||||++++||+|||.+ .+ .+++|.||||++||+++++++++ ++|+|++||||.+++
T Consensus 2 ~lllIDg~~~i~R~~~a~~------~l--~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~ 61 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALP------PL--KNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGK 61 (259)
T ss_pred cEEEEeCcHHHHHHHHCCC------cc--cCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCC
Confidence 5999999999999999986 45 88999999999999999999999 999999999997654
No 3
>PHA00439 exonuclease
Probab=99.58 E-value=3.4e-15 Score=131.66 Aligned_cols=65 Identities=12% Similarity=0.137 Sum_probs=54.6
Q ss_pred CCcEEEEecchHHHhhccccccccc-cCCCcccCCCCceeehhHHHHHHHHHHHh----hCCCEEEEEEeCCC
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLH-HGHLSHADGNGDWVLTIFSALSLIIDVLE----FIPSHVAVCFSCPS 174 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~-~~~L~~~ns~G~PTnAVyGFl~mLlkLLk----~~PthIaVaFDs~g 174 (183)
.++|+||||++|+||||||.....+ ..++ .+++|.||||+|||++||+++++ ++|+|++|||| ++
T Consensus 5 ~~~llLIDG~~l~fRA~~A~~~~~~~~~~l--~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~ 74 (286)
T PHA00439 5 DKGVLVMDGDYLVFQAMAAAEVETDWGEDI--WTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DS 74 (286)
T ss_pred CCcEEEEeCcHHHHHHHHccCcccccCCCC--CCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CC
Confidence 6689999999999999999842110 0035 79999999999999999999996 48999999999 44
No 4
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.57 E-value=4.3e-15 Score=128.78 Aligned_cols=58 Identities=16% Similarity=0.167 Sum_probs=51.9
Q ss_pred CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCccc
Q 030072 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCMS 177 (183)
Q Consensus 108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~s 177 (183)
++|+||||++|+||+|||.+ +++|. |||||||+++|+++++ ++|+|++||||.+++++
T Consensus 3 ~~llLiDg~~l~~R~~~a~~-----------~~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~ 61 (256)
T PRK09482 3 NHLLIIDALNLIRRIHAVQP-----------SPNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSS 61 (256)
T ss_pred CeEEEEeCcHHHHHHHhCCC-----------CCCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCc
Confidence 46999999999999999974 24577 9999999999999999 99999999999987653
No 5
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.56 E-value=6.3e-15 Score=128.19 Aligned_cols=65 Identities=29% Similarity=0.519 Sum_probs=56.2
Q ss_pred CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCcc
Q 030072 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCM 176 (183)
Q Consensus 108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~ 176 (183)
++++||||++++||+|||..... ..+ .+++|.||||++||+++|+++++ ++|+|++||||.++++
T Consensus 3 ~~~lliDg~~~~~ra~~a~~~~~--~~l--~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~ 68 (281)
T PRK14976 3 KKALLIDGNSLIFRSYYATLKQG--PKL--KNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKT 68 (281)
T ss_pred CcEEEEeCcHHHHHHHHccCccC--CCc--cCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCc
Confidence 46999999999999999974221 135 89999999999999999999999 9999999999986543
No 6
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.52 E-value=1.2e-14 Score=143.19 Aligned_cols=61 Identities=28% Similarity=0.549 Sum_probs=55.2
Q ss_pred EEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCcc
Q 030072 110 VMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCM 176 (183)
Q Consensus 110 LLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~ 176 (183)
|+||||++++||+|||.+.. ++ .+++|.||||||||++||+++++ ++|+|++||||.++++
T Consensus 1 l~lIDg~~l~~Ra~~a~~~~----~l--~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~t 62 (887)
T TIGR00593 1 LLLIDGHSLAFRAYFALKNK----PL--TNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPT 62 (887)
T ss_pred CEEEeCcHHHHHHHHCCCcc----cC--cCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCc
Confidence 58999999999999999632 35 89999999999999999999999 9999999999987643
No 7
>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=99.48 E-value=6.1e-14 Score=118.69 Aligned_cols=59 Identities=31% Similarity=0.635 Sum_probs=53.4
Q ss_pred cEEEEecchHHHhhccccccccccCCCcccCC-CCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072 109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADG-NGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC 175 (183)
Q Consensus 109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns-~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk 175 (183)
+++||||++++||+|||.+ .+ .+. +|.||||++||+++++++++ ++|+|++||||.+++
T Consensus 2 ~~llIDg~~l~yr~~~a~~------~~--~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~ 62 (240)
T cd00008 2 RLLLIDGSSLAYRAYFALP------PL--KNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGK 62 (240)
T ss_pred cEEEEEChHHHHHHHHCCC------Cc--CCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCC
Confidence 6999999999999999986 23 566 89999999999999999999 999999999998743
No 8
>PRK05755 DNA polymerase I; Provisional
Probab=99.43 E-value=1.8e-13 Score=133.51 Aligned_cols=61 Identities=31% Similarity=0.636 Sum_probs=55.2
Q ss_pred CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCc
Q 030072 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSC 175 (183)
Q Consensus 108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk 175 (183)
++++||||++++||+|||.+. .+ .+++|.|||||+||+++++++++ ++|+|++||||.+++
T Consensus 2 ~~~~liDg~~~~~r~~~a~~~-----~~--~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~ 63 (880)
T PRK05755 2 KTLLLIDGSSLLFRAFYALLP-----TL--RNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGK 63 (880)
T ss_pred CeEEEEeCcHHHHHHHHCCCC-----cc--cCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCC
Confidence 469999999999999999831 45 89999999999999999999999 999999999998654
No 9
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.33 E-value=2.2e-12 Score=112.17 Aligned_cols=64 Identities=27% Similarity=0.471 Sum_probs=57.1
Q ss_pred CCCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCCCcc
Q 030072 106 SNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCPSCM 176 (183)
Q Consensus 106 ~~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~gk~ 176 (183)
..+++++|||++++||+|||++.. + .+.+|.||||++||.+||.++++ .+|+|.+||||.+.++
T Consensus 9 ~~~~l~~IDg~~~lyr~~~a~~~~-----~--~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~t 73 (310)
T COG0258 9 KSGKLLLIDGSSLLYRALHALPQP-----L--GNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPT 73 (310)
T ss_pred ccCcEEEEechHHHHHHHHhcchh-----c--CCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCc
Confidence 355799999999999999999732 4 78999999999999999999999 9999999999995543
No 10
>PHA02567 rnh RnaseH; Provisional
Probab=98.95 E-value=1.2e-09 Score=97.63 Aligned_cols=58 Identities=17% Similarity=0.132 Sum_probs=50.4
Q ss_pred CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehh-HHHHHHHHHHHh-hCC--CEEEEEEeCCC
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTI-FSALSLIIDVLE-FIP--SHVAVCFSCPS 174 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAV-yGFl~mLlkLLk-~~P--thIaVaFDs~g 174 (183)
+..++||||++|+||+|||. + .+++|.++||| ++|+++|.++++ ++| +|++||||.++
T Consensus 13 ~~~~~LiDgs~i~~~~~~a~--------l--~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~ 74 (304)
T PHA02567 13 KEGVNLIDFSQIIIATIMAN--------F--KPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSK 74 (304)
T ss_pred CCCEEEEehHHHHHHHHHhh--------C--CCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCC
Confidence 45699999999999999994 3 78889999999 559999999999 655 55999999875
No 11
>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=98.69 E-value=1.4e-08 Score=90.51 Aligned_cols=64 Identities=20% Similarity=0.286 Sum_probs=53.1
Q ss_pred CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCcc
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSCM 176 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk~ 176 (183)
.+++++|||++++||+||+.... .+.++ .+++|.||++++||+.+++++++ .+| ++|||.+.+.
T Consensus 20 ~gk~vaIDas~~L~r~~~a~~~~-~g~~l--~~~~G~~t~~l~g~~~~~~~ll~~~i~P---v~VFDG~~p~ 85 (338)
T TIGR03674 20 SGKVVAVDAFNALYQFLSSIRQP-DGTPL--MDSRGRITSHLSGLFYRTINLLENGIKP---VYVFDGKPPE 85 (338)
T ss_pred CCCEEEEeHHHHHHHHHHHHhcc-ccchh--hhccCCCcHHHHHHHHHHHHHHHCCCeE---EEEECCCChh
Confidence 45699999999999999997521 12245 89999999999999999999998 556 9999987653
No 12
>PTZ00217 flap endonuclease-1; Provisional
Probab=98.65 E-value=3.1e-08 Score=90.34 Aligned_cols=64 Identities=25% Similarity=0.360 Sum_probs=52.7
Q ss_pred CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh--hCCCEEEEEEeCCCc
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE--FIPSHVAVCFSCPSC 175 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk--~~PthIaVaFDs~gk 175 (183)
.++.++|||++++||+|||.+...++.++ .+++|.+|++|+||+..+++|++ .+| ++|||.+.+
T Consensus 27 ~gk~vaIDa~~~lyr~~~a~~~~~~~~~l--~~~~G~~t~~l~g~~~r~~~Ll~~gikP---v~VFDG~~p 92 (393)
T PTZ00217 27 FGRVIAIDASMALYQFLIAIRDDSQGGNL--TNEAGEVTSHISGLFNRTIRLLEAGIKP---VYVFDGKPP 92 (393)
T ss_pred CCcEEEEeHHHHHHHHHHHcccccccccc--hhccCCccHHHHHHHHHHHHHHHCCCCE---EEEEcCCCc
Confidence 44799999999999999998631122245 89999999999999999999998 577 689997653
No 13
>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=98.30 E-value=1e-06 Score=76.66 Aligned_cols=60 Identities=13% Similarity=0.135 Sum_probs=49.8
Q ss_pred CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC 175 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk 175 (183)
.++.++|||++++||+||+.... ...+|.|+++++||++.+.++++++ -+.++|||...+
T Consensus 23 ~gk~laID~~~~l~r~~~a~~~~--------~~~~g~~~~~l~~~~~rl~~L~~~~-i~pvfVFDG~~~ 82 (316)
T cd00128 23 RGKKVAIDASIWLYQFLKACRQE--------LGSGGETTSHLQGFFYRTCRLLELG-IKPVFVFDGKPP 82 (316)
T ss_pred CCcEEEecHHHHHHHHHHHhhhh--------ccCCCCCcHHHHHHHHHHHHHHHCC-CEEEEEEcCCCc
Confidence 44689999999999999997522 3478999999999999999999855 478889997644
No 14
>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=96.06 E-value=0.011 Score=43.40 Aligned_cols=57 Identities=16% Similarity=0.139 Sum_probs=38.4
Q ss_pred cEEEEecchHHHhhccccccccccCCCcccCCCCce-eehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072 109 RVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDW-VLTIFSALSLIIDVLEFIPSHVAVCFSCPSC 175 (183)
Q Consensus 109 kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~P-TnAVyGFl~mLlkLLk~~PthIaVaFDs~gk 175 (183)
+.+-|||+.++||.+++.... + ..+.+ +..+.+++..+..|++++= ..++|||...+
T Consensus 27 ~~vaID~s~wl~~~~~~~~~~-----~----~~~~~~~~~~~~~~~r~~~L~~~gI-~PifVFDG~~~ 84 (101)
T PF00752_consen 27 KRVAIDASCWLHQFLFSCREE-----L----GQGVGTDSHLRGLFSRLCRLLEHGI-KPIFVFDGKPP 84 (101)
T ss_dssp CEEEEEHHHHHHHHHHHSBCT-----T----SCB-BS-HHHHHHHHHHHHHHHTTE-EEEEEE--STT
T ss_pred CEEEEEcHHHHHHHHHHhHHH-----h----ccccchHHHHHHHHHHHHHHHHCCC-EEEEEECCCCc
Confidence 679999999999999987522 1 12222 4778888888888887332 34799998654
No 15
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=95.46 E-value=0.022 Score=41.72 Aligned_cols=58 Identities=19% Similarity=0.174 Sum_probs=41.4
Q ss_pred CcEEEEecchHHHhhccccccccccCCCcccCCCCceee-hhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVL-TIFSALSLIIDVLEFIPSHVAVCFSCPSC 175 (183)
Q Consensus 108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTn-AVyGFl~mLlkLLk~~PthIaVaFDs~gk 175 (183)
++.+-||++..+||.+++.... . ..+.+.. .+.+++..+..|++++-+ .+++||...+
T Consensus 24 g~~vaIDa~~wl~~~~~~~~~~-----~----~~~~~~~~~l~~~~~rl~~L~~~~I~-PifVFDG~~~ 82 (99)
T smart00485 24 GKTLAIDASIWLYQFLTACREK-----L----GTPLPNSKHLMGLFYRTCRLLEFGIK-PIFVFDGKPP 82 (99)
T ss_pred CceEeccHHHHHHHHHHHHhhh-----h----cCCCCchHHHHHHHHHHHHHHHCCCe-EEEEECCCCc
Confidence 4688999999999999986422 1 1123334 888999999988884333 4789997654
No 16
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=92.03 E-value=0.17 Score=41.10 Aligned_cols=53 Identities=23% Similarity=0.284 Sum_probs=31.2
Q ss_pred EEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCC
Q 030072 111 MLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCP 173 (183)
Q Consensus 111 LLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~ 173 (183)
|||||++++|. ++. +.....++.--.|=--++.+|..+..+....++||||..
T Consensus 1 LlIDGYNli~~----~~~------l~~~~~~~~l~~aR~~Li~~L~~y~~~~~~~v~VVFDa~ 53 (166)
T PF05991_consen 1 LLIDGYNLIHA----WPE------LRSLAERGDLEAARERLIEMLSEYAQFSGYEVIVVFDAY 53 (166)
T ss_pred CeEcchhhhCC----CHH------HHhhcCcCCHHHHHHHHHHHHHHHhcccCCEEEEEEeCC
Confidence 69999999975 331 100111222234444555555554445668999999974
No 17
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=76.06 E-value=3.3 Score=35.17 Aligned_cols=53 Identities=26% Similarity=0.418 Sum_probs=30.3
Q ss_pred CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh----hCCCEEEEEEeCC
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE----FIPSHVAVCFSCP 173 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk----~~PthIaVaFDs~ 173 (183)
++.+|||||+++| +.+..+ +.+ +.. |.+-..=..|+..|. +.-..++||||..
T Consensus 2 ~~~iLLVDGYNmI-----gaWp~L--k~l--kd~-----~~LE~AR~~LIe~l~~Y~s~~g~~iivVFDA~ 58 (173)
T COG3688 2 KMRILLVDGYNMI-----GAWPEL--KQL--KDR-----NGLEAARDKLIEALAEYQSFTGYKIIVVFDAH 58 (173)
T ss_pred CceEEEeccchhc-----cccHHH--HHH--Hhh-----ccHHHHHHHHHHHHHHhhcccCceEEEEEEcc
Confidence 4579999999998 322210 012 222 223333344555444 4558899999964
No 18
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=69.50 E-value=6.1 Score=41.32 Aligned_cols=59 Identities=14% Similarity=0.170 Sum_probs=42.2
Q ss_pred CCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072 107 NGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC 175 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk 175 (183)
.++.+=||++.-|||+-++.... ..++....-+.||++-+.+|+.++ =.-++|||.+.+
T Consensus 23 ~Gk~vAIDasiWL~q~l~~vr~~---------~g~~l~n~hl~g~f~Ri~~Ll~~g-I~PVfVFDG~~p 81 (1034)
T TIGR00600 23 EGKRLAVDISIWLNQALKGVRDR---------EGNAIKNSHLLTLFHRLCKLLFFR-IRPIFVFDGGAP 81 (1034)
T ss_pred CCeEEEechHHHHHHHHHHHHhc---------cCCccCCHHHHHHHHHHHHHHHCC-CeEEEEECCCCc
Confidence 34689999999999998886421 112234467889999999999832 224888998653
No 19
>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=57.56 E-value=14 Score=32.09 Aligned_cols=58 Identities=10% Similarity=0.015 Sum_probs=31.1
Q ss_pred EEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCC-CEEEEEEeCCCccc
Q 030072 110 VMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIP-SHVAVCFSCPSCMS 177 (183)
Q Consensus 110 LLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~P-thIaVaFDs~gk~s 177 (183)
=|.||-++++|.+.+..... . ... --..+..++..|-.++. .+| .-+.+|+|..++.+
T Consensus 32 ~LYiDmN~IIH~~~~~~~~~-----~--~~~---~~~~~~~i~~~id~l~~~v~P~k~l~iavDGvaP~A 91 (237)
T PF03159_consen 32 NLYIDMNGIIHNCIHPNDSS-----I--PKT---EEEIFQRIFNYIDRLVRIVRPRKLLYIAVDGVAPRA 91 (237)
T ss_dssp EEEEETHHHHHHHHS-SSS-----------S---HHHHHHHHHHHHHHHHHHH-ESSEEEEE---S--HH
T ss_pred EEEEEcchhhhHhcCCcccC-----C--Ccc---HHHHHHHHHHHHHHhheeecCceEEEEEcCCCCCch
Confidence 68899999999998875421 0 001 11234455556666666 778 45569999877644
No 20
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=55.14 E-value=24 Score=33.95 Aligned_cols=57 Identities=12% Similarity=0.138 Sum_probs=44.9
Q ss_pred EEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCc
Q 030072 110 VMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSC 175 (183)
Q Consensus 110 LLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk 175 (183)
=+-|||+-.+|+-+=+... - ++..|.++.-+.|++.-.+.+++. --..++|||...+
T Consensus 30 kVAID~s~~lyqfl~~v~~------~--~~~~~~~~~HL~g~f~Rt~~l~~~-gi~Pv~VfDG~pP 86 (449)
T KOG2519|consen 30 KVAIDASMWLYQFLIVVRS------C--RNEAGEPTSHLMGMFYRTIRLIEN-GIKPVYVFDGKPP 86 (449)
T ss_pred eEEEecceeHhhHhhhhcc------c--cccCCCchHHHHHHHHHHHHHHHc-CCcEEEEECCCCC
Confidence 4899999999998766541 1 567899999999999998888873 3456788997654
No 21
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=23.75 E-value=36 Score=29.79 Aligned_cols=21 Identities=19% Similarity=0.322 Sum_probs=18.2
Q ss_pred CCcEEEEecchHHHhhccccc
Q 030072 107 NGRVMLIDGTSIIYRAYYKIL 127 (183)
Q Consensus 107 ~~kLLLIDGssLlFRAYYA~p 127 (183)
+..++||||+++++.-.++++
T Consensus 95 ~~d~ilVDG~GiaHPR~~GlA 115 (212)
T COG1515 95 KPDLLLVDGHGIAHPRRLGLA 115 (212)
T ss_pred CCCEEEEcCcceecCcccChh
Confidence 446999999999999888875
No 22
>PF14421 LmjF365940-deam: A distinct subfamily of CDD/CDA-like deaminases
Probab=22.20 E-value=1.1e+02 Score=26.51 Aligned_cols=38 Identities=16% Similarity=0.188 Sum_probs=28.9
Q ss_pred ceeehhHHHHHHHHHHHhhCCCEEEEEEeCCCccccccccC
Q 030072 143 DWVLTIFSALSLIIDVLEFIPSHVAVCFSCPSCMSMFHVPI 183 (183)
Q Consensus 143 ~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~gk~s~~~~~~ 183 (183)
.|-+|. -.||.|+-+.+|+..++.||...+--.+-.||
T Consensus 155 ~PCGaC---~ewL~KIAe~np~f~v~mFd~t~c~~vy~~~i 192 (193)
T PF14421_consen 155 FPCGAC---KEWLRKIAEANPDFRVYMFDDTRCRNVYILPI 192 (193)
T ss_pred CcchHH---HHHHHHHHHhCCCeEEEEecCCCcceEEEeec
Confidence 466664 46777777799999999999987776665554
No 23
>COG0462 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]
Probab=22.05 E-value=1.3e+02 Score=27.78 Aligned_cols=50 Identities=16% Similarity=0.250 Sum_probs=37.3
Q ss_pred hccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCC--CccccccccC
Q 030072 122 AYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCP--SCMSMFHVPI 183 (183)
Q Consensus 122 AYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~--gk~s~~~~~~ 183 (183)
-||+...| .- ....|+|+.| +++.++|. ..-++++ .+|-. .-++.|++|+
T Consensus 91 PY~gYARQ----Dk--~~~~repIsa-----klvA~lL~~aG~drv~-TvDlH~~qiqgfFdipv 143 (314)
T COG0462 91 PYFGYARQ----DK--AFKPREPISA-----KLVANLLETAGADRVL-TVDLHAPQIQGFFDIPV 143 (314)
T ss_pred ecchhhcc----Cc--ccCCCCCEeH-----HHHHHHHHHcCCCeEE-EEcCCchhhcccCCCcc
Confidence 48887654 22 3478999997 99999999 7788875 58855 5678888874
No 24
>COG2812 DnaX DNA polymerase III, gamma/tau subunits [DNA replication, recombination, and repair]
Probab=21.86 E-value=1.2e+02 Score=29.70 Aligned_cols=43 Identities=23% Similarity=0.350 Sum_probs=31.6
Q ss_pred CCCCCcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHhhCCCEEEEEEeCCC
Q 030072 104 KPSNGRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLEFIPSHVAVCFSCPS 174 (183)
Q Consensus 104 ~~~~~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk~~PthIaVaFDs~g 174 (183)
...+.++++||--.|+- .+.++.|+|.|++.|.|+.+.|=...
T Consensus 116 ~~~ryKVyiIDEvHMLS----------------------------~~afNALLKTLEEPP~hV~FIlATTe 158 (515)
T COG2812 116 SEGRYKVYIIDEVHMLS----------------------------KQAFNALLKTLEEPPSHVKFILATTE 158 (515)
T ss_pred ccccceEEEEecHHhhh----------------------------HHHHHHHhcccccCccCeEEEEecCC
Confidence 44566899999755431 12368889999999999999996543
No 25
>KOG3348 consensus BolA (bacterial stress-induced morphogen)-related protein [Signal transduction mechanisms]
Probab=21.74 E-value=1e+02 Score=23.59 Aligned_cols=31 Identities=35% Similarity=0.484 Sum_probs=23.9
Q ss_pred HHHHHHHh--hCCCEEEEEEeCCCccccccccC
Q 030072 153 SLIIDVLE--FIPSHVAVCFSCPSCMSMFHVPI 183 (183)
Q Consensus 153 ~mLlkLLk--~~PthIaVaFDs~gk~s~~~~~~ 183 (183)
..|-.+|. ..|.|+-|.=-++|+-+||-|-|
T Consensus 6 ~~l~~~L~~~l~p~~v~V~D~SgGCG~~F~v~I 38 (85)
T KOG3348|consen 6 ERLEELLTEALEPEHVEVQDVSGGCGSMFDVVI 38 (85)
T ss_pred HHHHHHHHhhcCceEEEEEEcCCCccceEEEEE
Confidence 34566666 89999988766889999998743
No 26
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=20.88 E-value=1.6e+02 Score=29.27 Aligned_cols=56 Identities=14% Similarity=0.138 Sum_probs=43.4
Q ss_pred CcEEEEecchHHHhhccccccccccCCCcccCCCCceeehhHHHHHHHHHHHh-hCCCEEEEEEeCC
Q 030072 108 GRVMLIDGTSIIYRAYYKILAKLHHGHLSHADGNGDWVLTIFSALSLIIDVLE-FIPSHVAVCFSCP 173 (183)
Q Consensus 108 ~kLLLIDGssLlFRAYYA~p~~~~~~~L~~~ns~G~PTnAVyGFl~mLlkLLk-~~PthIaVaFDs~ 173 (183)
...+-|||+..+||+=.+-... -..|.||.--..|+.--.++|. ++- .-++|||.+
T Consensus 24 g~tvavD~y~WLhrg~~~Ca~e---------l~~~~pT~ryi~y~ik~v~lL~~~gi-kPilVFDG~ 80 (556)
T KOG2518|consen 24 GKTVAVDGYCWLHRGALACAEK---------LAKGKPTDRYIQFFIKRVKLLLSYGI-KPILVFDGD 80 (556)
T ss_pred CceEEEehhhHHhhhHHhHHHH---------HhcCCChHHHHHHHHHHHHHHHhcCC-eEEEEecCC
Confidence 3589999999999998886532 3469999888888888888888 543 356779965
Done!