Query psy6081
Match_columns 226
No_of_seqs 147 out of 418
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 17:10:07 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6081.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6081hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2044|consensus 100.0 5.6E-82 1.2E-86 622.4 16.8 190 17-226 11-201 (931)
2 COG5049 XRN1 5'-3' exonuclease 100.0 7.9E-62 1.7E-66 476.5 11.6 173 17-226 11-187 (953)
3 PF03159 XRN_N: XRN 5'-3' exon 100.0 4.1E-58 8.8E-63 404.6 9.8 155 52-226 29-183 (237)
4 KOG2045|consensus 100.0 2.6E-56 5.6E-61 445.7 13.3 152 33-226 20-173 (1493)
5 PF00752 XPG_N: XPG N-terminal 86.0 0.46 1E-05 35.9 1.7 61 55-119 28-91 (101)
6 smart00485 XPGN Xeroderma pigm 79.7 2.1 4.5E-05 32.4 3.1 58 56-119 27-89 (99)
7 PF02739 5_3_exonuc_N: 5'-3' e 75.2 13 0.00029 31.4 7.0 56 56-112 4-63 (169)
8 PHA02567 rnh RnaseH; Provision 69.0 7.7 0.00017 36.5 4.5 58 53-110 14-73 (304)
9 cd00008 53EXOc 5'-3' exonuclea 68.6 8.7 0.00019 34.0 4.6 56 56-112 4-62 (240)
10 COG0258 Exo 5'-3' exonuclease 65.3 18 0.00039 33.0 6.1 55 55-113 13-73 (310)
11 cd00128 XPG Xeroderma pigmento 58.7 9.2 0.0002 34.8 3.0 62 55-119 26-89 (316)
12 PRK03980 flap endonuclease-1; 54.8 32 0.0007 31.7 5.9 33 83-119 11-44 (292)
13 TIGR03674 fen_arch flap struct 54.0 29 0.00063 32.4 5.5 61 55-119 23-91 (338)
14 smart00475 53EXOc 5'-3' exonuc 53.7 22 0.00048 32.1 4.5 56 56-112 4-61 (259)
15 PRK14976 5'-3' exonuclease; Pr 53.2 23 0.0005 32.4 4.6 57 55-112 5-67 (281)
16 PRK09482 flap endonuclease-lik 52.3 31 0.00067 31.5 5.2 55 55-112 5-59 (256)
17 PHA03065 Hypothetical protein; 39.8 4E+02 0.0087 26.7 11.2 50 36-94 14-63 (438)
18 PTZ00217 flap endonuclease-1; 36.6 98 0.0021 29.8 6.2 60 55-119 30-99 (393)
19 PF00301 Rubredoxin: Rubredoxi 32.4 17 0.00037 25.2 0.3 12 182-193 19-30 (47)
20 PTZ00225 60S ribosomal protein 32.1 91 0.002 27.6 4.9 46 55-105 153-198 (214)
21 PF13186 SPASM: Iron-sulfur cl 31.7 33 0.00071 22.8 1.6 19 52-70 4-22 (64)
22 PF06575 DUF1132: Protein of u 28.6 55 0.0012 26.2 2.6 28 194-225 36-63 (95)
23 PF05413 Peptidase_C34: Putati 23.5 25 0.00053 27.7 -0.2 32 52-94 8-39 (92)
24 PF01359 Transposase_1: Transp 23.4 1.3E+02 0.0029 22.6 3.8 46 53-101 32-77 (81)
25 COG1515 Nfi Deoxyinosine 3'end 23.4 45 0.00098 30.0 1.4 20 52-71 95-119 (212)
26 PRK15348 type III secretion sy 23.0 3.2E+02 0.0068 25.1 6.8 64 157-220 65-129 (249)
27 PHA00439 exonuclease 22.6 1.1E+02 0.0024 28.6 3.8 53 56-109 9-73 (286)
28 cd00730 rubredoxin Rubredoxin; 21.4 48 0.001 23.2 1.0 12 182-193 19-30 (50)
No 1
>KOG2044|consensus
Probab=100.00 E-value=5.6e-82 Score=622.43 Aligned_cols=190 Identities=72% Similarity=1.190 Sum_probs=186.1
Q ss_pred CCCCCccccccccc-ccccCCccccCCCCCCCCCCCccCeEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHh
Q psy6081 17 QDSKPYSFASLVSL-PQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFR 95 (226)
Q Consensus 17 ~~~~p~~~~~~~~~-p~~~~g~~~p~d~~~pn~n~~~~DnLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv~ 95 (226)
+.+||.+|++++|+ |.+++|+.||+|.|+|||||.||||||||||||||||+||+++|+|+||||||+.||+||||||.
T Consensus 11 s~kyp~~I~~viEe~p~~~~g~~ip~D~s~pNPNg~E~DNLYLDMNGIIHPC~HPEdkPaP~tedEm~~avFeyiDrlf~ 90 (931)
T KOG2044|consen 11 SRKYPKTISPVIEEEPVDVDGVKIPVDYSKPNPNGVEFDNLYLDMNGIIHPCTHPEDKPAPETEDEMFVAVFEYIDRLFS 90 (931)
T ss_pred HHhcchhhhhhhhcCcccCCCcccccccCCCCCCcccccceeeecCcccccCCCCCCCCCCccHHHHHHHHHHHHHHHHH
Confidence 57899999999995 89999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhcccceEEEEEeCCCCccccccccccccccccCCCchhhhhhhhhhhhhcHHHHHHHHHHHHHHHHHHhcCCCCCCCcc
Q psy6081 96 IVRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKE 175 (226)
Q Consensus 96 iVrPrKllylAiDGVAPrAKmnQQ~~~~~~~~~~~~~~~~~~~RsRRfrsake~~e~~~~~~~~~~~l~~~g~~lp~~~~ 175 (226)
+||||||||||||||||||||||| |+||||||||++|+.+|++++++++.++|..||++ .
T Consensus 91 mvRPRkLLymAIDGVAPRAKMNQQ-------------------RsRRFRaaKeaae~~~e~e~~ree~~~~G~~lpp~-~ 150 (931)
T KOG2044|consen 91 MVRPRKLLYMAIDGVAPRAKMNQQ-------------------RSRRFRAAKEAAEKEAEIERLREEFEAEGKFLPPK-V 150 (931)
T ss_pred hccchheeEEeecccCchhhhhHH-------------------HHHHHhhhhHHHHHHHHHHHHHHHHHhcCCcCCch-h
Confidence 999999999999999999999999 99999999999999999999999999999999986 6
Q ss_pred cCCCCCCCccCCCChhHHHHHHHHHHHHHHHhcCCCCCCCcEEEEcCCCCC
Q psy6081 176 KGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226 (226)
Q Consensus 176 ~~~~fDsN~ITPGT~FM~~L~~~L~~yI~~kl~~dp~W~~i~VI~Sds~VP 226 (226)
+.++||||||||||+||++|+.+|+|||+.|||+||+|+||+||+|||+||
T Consensus 151 ~~e~fDSNcITPGTpFM~~La~aLrYyI~~rLn~DPgWkNikvIlSDAnVP 201 (931)
T KOG2044|consen 151 KKETFDSNCITPGTPFMDRLAKALRYYIHDRLNSDPGWKNIKVILSDANVP 201 (931)
T ss_pred hccccccCccCCCChHHHHHHHHHHHHHHHhhcCCccccceEEEEecCCCC
Confidence 678999999999999999999999999999999999999999999999999
No 2
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=100.00 E-value=7.9e-62 Score=476.48 Aligned_cols=173 Identities=49% Similarity=0.865 Sum_probs=145.6
Q ss_pred CCCCCcccccccccccccCCccccCCCCCCCCCCCccCeEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHhh
Q psy6081 17 QDSKPYSFASLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRI 96 (226)
Q Consensus 17 ~~~~p~~~~~~~~~p~~~~g~~~p~d~~~pn~n~~~~DnLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv~i 96 (226)
+.|||.++..+.|.+ +| +|||||||||||+|+|+||++.+.|.+|+|||..||+|||+|+.+
T Consensus 11 S~r~p~ii~~I~e~~-------~P-----------~~DNLYLDMNgIlH~CtHp~d~~~petEeEm~~aVf~Yidhil~~ 72 (953)
T COG5049 11 SERYPKIIQLIEEKQ-------IP-----------EFDNLYLDMNGILHNCTHPNDGSPPETEEEMYKAVFEYIDHILLK 72 (953)
T ss_pred HhhhhHhhhhhhccC-------CC-----------CcceeEEecccccccCCCCCCCCCCCCHHHHHHHHHHHHHHHHHh
Confidence 467888877775552 33 669999999999999999999999999999999999999999999
Q ss_pred hcccceEEEEEeCCCCccccccccccccccccCCCchhhhhhhhhhhhhcHHHHHHHHHHHHHHHHHH----hcCCCCCC
Q psy6081 97 VRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLL----ADGCILPP 172 (226)
Q Consensus 97 VrPrKllylAiDGVAPrAKmnQQ~~~~~~~~~~~~~~~~~~~RsRRfrsake~~e~~~~~~~~~~~l~----~~g~~lp~ 172 (226)
+|||||||||||||||||||||| |+||||+|+++..++.+.+...+++. ..|..+..
T Consensus 73 irPrKllymAVDGvAPRAKMNQQ-------------------RaRRFRsAkda~~A~~Kae~~~e~~~e~~~e~g~~id~ 133 (953)
T COG5049 73 IRPRKLLYMAVDGVAPRAKMNQQ-------------------RARRFRSAKDASAAALKAEPNGEEIPEEKDEIGNEIDT 133 (953)
T ss_pred cCcceEEEEEecccCchhhhhHH-------------------HHHhhhhhhhhHHHHhhccccccccchhccccCCccch
Confidence 99999999999999999999999 99999999985433222221222222 22333333
Q ss_pred CcccCCCCCCCccCCCChhHHHHHHHHHHHHHHHhcCCCCCCCcEEEEcCCCCC
Q psy6081 173 EKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226 (226)
Q Consensus 173 ~~~~~~~fDsN~ITPGT~FM~~L~~~L~~yI~~kl~~dp~W~~i~VI~Sds~VP 226 (226)
...+.+.||||||||||+||++|+..|+|||+.||++||.|+|++|||||+.||
T Consensus 134 ~~~~kk~fDSNcITPGTpFMerLak~L~Y~i~~KlssDp~Wrnl~iI~S~~~vP 187 (953)
T COG5049 134 IDVEKKKFDSNCITPGTPFMERLAKVLRYYIHCKLSSDPEWRNLRIIFSGHLVP 187 (953)
T ss_pred hhhhhccccccCCCCCChHHHHHHHHHHHHHHhhhcCCccceeEEEEEecCcCC
Confidence 334567899999999999999999999999999999999999999999999998
No 3
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=100.00 E-value=4.1e-58 Score=404.60 Aligned_cols=155 Identities=61% Similarity=1.063 Sum_probs=124.7
Q ss_pred ccCeEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCCccccccccccccccccCCC
Q psy6081 52 EFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDRGN 131 (226)
Q Consensus 52 ~~DnLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAPrAKmnQQ~~~~~~~~~~~~ 131 (226)
+|||||||||||||+|+|++..+.+.+++++|++||+|||+||++|||||+||||||||||+||||||
T Consensus 29 ~~D~LYiDmN~IIH~~~~~~~~~~~~~~~~~~~~i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQ------------ 96 (237)
T PF03159_consen 29 EFDNLYIDMNGIIHNCIHPNDSSIPKTEEEIFQRIFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQ------------ 96 (237)
T ss_dssp -ESEEEEETHHHHHHHHS-SSS----SHHHHHHHHHHHHHHHHHHH-ESSEEEEE---S--HHHHHHH------------
T ss_pred cCCEEEEEcchhhhHhcCCcccCCCccHHHHHHHHHHHHHHhheeecCceEEEEEcCCCCCchHHHHH------------
Confidence 79999999999999999999888889999999999999999999999999999999999999999999
Q ss_pred chhhhhhhhhhhhhcHHHHHHHHHHHHHHHHHHhcCCCCCCCcccCCCCCCCccCCCChhHHHHHHHHHHHHHHHhcCCC
Q psy6081 132 YSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDP 211 (226)
Q Consensus 132 ~~~~~~~RsRRfrsake~~e~~~~~~~~~~~l~~~g~~lp~~~~~~~~fDsN~ITPGT~FM~~L~~~L~~yI~~kl~~dp 211 (226)
|+|||+++++..+...+.....++...+|...+.. .....||+|+|||||+||.+|+.+|++||++|+++||
T Consensus 97 -------R~RRf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~fdsn~ITPGT~FM~~l~~~L~~~~~~k~~~~~ 168 (237)
T PF03159_consen 97 -------RSRRFKSAKESEENNKEESEIKEEIDEEGEQLPPE-DQEEKFDSNCITPGTEFMEKLSDALRYYIKKKLNSDP 168 (237)
T ss_dssp -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHT--B-HH-HHS----GGGSSTTSHHHHHHHHHHHHHHHHHHHH-G
T ss_pred -------HHHHHHHhhcchhHHHHHHHHhhhhhhcccccccc-ccccccccceeccCCHHHHHHHHHHHHHHHHHhcCCC
Confidence 99999999999887777667777777777655432 3458899999999999999999999999999999999
Q ss_pred CCCCcEEEEcCCCCC
Q psy6081 212 GWKGIKVILSDANVP 226 (226)
Q Consensus 212 ~W~~i~VI~Sds~VP 226 (226)
.|++++||+||++||
T Consensus 169 ~~~~~~vi~S~~~vp 183 (237)
T PF03159_consen 169 KWQNLKVIFSGSDVP 183 (237)
T ss_dssp GGCCSEEEEE-TTSS
T ss_pred CcCceEEEEeCCCCC
Confidence 999999999999998
No 4
>KOG2045|consensus
Probab=100.00 E-value=2.6e-56 Score=445.75 Aligned_cols=152 Identities=51% Similarity=0.939 Sum_probs=136.9
Q ss_pred ccCCccccCCCCCCCCCCCccCeEEEecccccccccCCCCC--CCCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCC
Q psy6081 33 EVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDK--PAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGV 110 (226)
Q Consensus 33 ~~~g~~~p~d~~~pn~n~~~~DnLYLDmNgIIH~c~h~~~~--~~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGV 110 (226)
.+.+..|| ||||||||||||||+|+|+++. ..+.+|+|||.+||.|||+||.+++|+|++|||||||
T Consensus 20 liee~qIP-----------EFDNLYLDMNgIlHNCsH~nDddvt~rLtEeEif~~IfnYIdhLf~~IkPqKlffMAVDGv 88 (1493)
T KOG2045|consen 20 LIEEHQIP-----------EFDNLYLDMNGILHNCSHPNDDDVTFRLTEEEIFQEIFNYIDHLFYLIKPQKLFFMAVDGV 88 (1493)
T ss_pred HhhhccCC-----------cccceeeecccccccCCCCCCCccCcCCCHHHHHHHHHHHHHHHHHhhCcceEEEEeeccc
Confidence 34566677 9999999999999999999874 4578999999999999999999999999999999999
Q ss_pred CCccccccccccccccccCCCchhhhhhhhhhhhhcHHHHHHHHHHHHHHHHHHhcCCCCCCCcccCCCCCCCccCCCCh
Q psy6081 111 APRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTP 190 (226)
Q Consensus 111 APrAKmnQQ~~~~~~~~~~~~~~~~~~~RsRRfrsake~~e~~~~~~~~~~~l~~~g~~lp~~~~~~~~fDsN~ITPGT~ 190 (226)
||||||||| |+||||+|+++....+ +....|+..|. +.||||||||||+
T Consensus 89 APRAKMNQQ-------------------RsRRFrTArdAe~qla-------KA~enGe~~p~-----erFDSNcITPGTe 137 (1493)
T KOG2045|consen 89 APRAKMNQQ-------------------RSRRFRTARDAEQQLA-------KAAENGELRPH-----ERFDSNCITPGTE 137 (1493)
T ss_pred CchhhhhHH-------------------HHHhhhhhhhHHHHHH-------HHHhccccCcc-----cccccCCCCCcHH
Confidence 999999999 9999999998754322 23445777654 6799999999999
Q ss_pred hHHHHHHHHHHHHHHHhcCCCCCCCcEEEEcCCCCC
Q psy6081 191 FMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226 (226)
Q Consensus 191 FM~~L~~~L~~yI~~kl~~dp~W~~i~VI~Sds~VP 226 (226)
||.+|++.|+|||++|+.+|+.|++++|||||++||
T Consensus 138 FM~rl~~~L~yfIktKistDs~Wq~~~vIlSGhevP 173 (1493)
T KOG2045|consen 138 FMVRLQEGLRYFIKTKISTDSLWQRCTVILSGHEVP 173 (1493)
T ss_pred HHHHHHHHHHHHHHhccccchhhcccEEEEeCCcCC
Confidence 999999999999999999999999999999999998
No 5
>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=86.00 E-value=0.46 Score=35.95 Aligned_cols=61 Identities=18% Similarity=0.292 Sum_probs=38.3
Q ss_pred eEEEecccccccccCCCCCCCC--CCHHHHHHHHHHHHHHHH-hhhcccceEEEEEeCCCCccccccc
Q psy6081 55 NLYLDMNGIIHPCTHPEDKPAP--KDEDEMMVAIFECIDRLF-RIVRPRKLLYMAIDGVAPRAKMNQP 119 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~~~~~~~--~~e~e~~~~If~yID~Lv-~iVrPrKllylAiDGVAPrAKmnQQ 119 (226)
-|=||.+..||.+.+....... ...+..+..++..+..|. .-|.| ++.+||.+|-.|....
T Consensus 28 ~vaID~s~wl~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~L~~~gI~P----ifVFDG~~~~~K~~~~ 91 (101)
T PF00752_consen 28 RVAIDASCWLHQFLFSCREELGQGVGTDSHLRGLFSRLCRLLEHGIKP----IFVFDGKPPPLKRETI 91 (101)
T ss_dssp EEEEEHHHHHHHHHHHSBCTTSCB-BS-HHHHHHHHHHHHHHHTTEEE----EEEE--STTGGCHHHH
T ss_pred EEEEEcHHHHHHHHHHhHHHhccccchHHHHHHHHHHHHHHHHCCCEE----EEEECCCCchhhHHHH
Confidence 4678999999986543321111 111456677777777764 34544 6889999999998887
No 6
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=79.74 E-value=2.1 Score=32.40 Aligned_cols=58 Identities=19% Similarity=0.282 Sum_probs=36.9
Q ss_pred EEEecccccccccCC----CCCCCCCCHHHHHHHHHHHHHHHHh-hhcccceEEEEEeCCCCccccccc
Q psy6081 56 LYLDMNGIIHPCTHP----EDKPAPKDEDEMMVAIFECIDRLFR-IVRPRKLLYMAIDGVAPRAKMNQP 119 (226)
Q Consensus 56 LYLDmNgIIH~c~h~----~~~~~~~~e~e~~~~If~yID~Lv~-iVrPrKllylAiDGVAPrAKmnQQ 119 (226)
+=||.+..||.+... .... .........+|..|.+|++ -|.| ++-+||.+|-+|...+
T Consensus 27 vaIDa~~wl~~~~~~~~~~~~~~--~~~~~~l~~~~~rl~~L~~~~I~P----ifVFDG~~~~~K~~t~ 89 (99)
T smart00485 27 LAIDASIWLYQFLTACREKLGTP--LPNSKHLMGLFYRTCRLLEFGIKP----IFVFDGKPPPLKSETL 89 (99)
T ss_pred EeccHHHHHHHHHHHHhhhhcCC--CCchHHHHHHHHHHHHHHHCCCeE----EEEECCCCchhhHHHH
Confidence 457888889876432 1111 2222255566666666653 2333 5789999999999888
No 7
>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=75.25 E-value=13 Score=31.35 Aligned_cols=56 Identities=18% Similarity=0.335 Sum_probs=39.4
Q ss_pred EEEecccccccccCCCCC-CCC---CCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCC
Q psy6081 56 LYLDMNGIIHPCTHPEDK-PAP---KDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 112 (226)
Q Consensus 56 LYLDmNgIIH~c~h~~~~-~~~---~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAP 112 (226)
|.||.|+++|-+.|.-.. +.. ...-.....++..|.+|+...+|.. +.+|+||-.+
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 678999999999886531 110 1111245567788888888888986 5699999887
No 8
>PHA02567 rnh RnaseH; Provisional
Probab=68.99 E-value=7.7 Score=36.48 Aligned_cols=58 Identities=16% Similarity=0.139 Sum_probs=44.1
Q ss_pred cCeEEEecccccccccCCCCCCC-CCCHHHHHHHHHHHHHHHHhhhcccc-eEEEEEeCC
Q psy6081 53 FDNLYLDMNGIIHPCTHPEDKPA-PKDEDEMMVAIFECIDRLFRIVRPRK-LLYMAIDGV 110 (226)
Q Consensus 53 ~DnLYLDmNgIIH~c~h~~~~~~-~~~e~e~~~~If~yID~Lv~iVrPrK-llylAiDGV 110 (226)
-+-+.||++.|+--|.+.+..+. ..++..+...+++.|.+++..++|.- -+.+|+|+-
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 46688999999999999876554 34444444668999999998877762 168999985
No 9
>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=68.62 E-value=8.7 Score=33.99 Aligned_cols=56 Identities=9% Similarity=0.096 Sum_probs=39.4
Q ss_pred EEEecccccccccCCCCCCC---CCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCC
Q psy6081 56 LYLDMNGIIHPCTHPEDKPA---PKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 112 (226)
Q Consensus 56 LYLDmNgIIH~c~h~~~~~~---~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAP 112 (226)
|.||.|.+||-+.|...... .-........++..|.+++...+|.+. .+++||-.|
T Consensus 4 llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~-~~~fD~~~~ 62 (240)
T cd00008 4 LLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYV-AVVFDAGGK 62 (240)
T ss_pred EEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeE-EEEEeCCCC
Confidence 67999999998877642111 112223456677888888888899887 789999744
No 10
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=65.31 E-value=18 Score=33.02 Aligned_cols=55 Identities=20% Similarity=0.388 Sum_probs=40.1
Q ss_pred eEEEecccccccccCCCCC------CCCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCCc
Q psy6081 55 NLYLDMNGIIHPCTHPEDK------PAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPR 113 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~~~~------~~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAPr 113 (226)
-|-||-+++++.+.|.-.. ..+.+ ....+...|.++++..+|.+ ..+++||-.|.
T Consensus 13 l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~---~~~~~~~~l~~~~~~~~~~~-~~~vFD~~~~t 73 (310)
T COG0258 13 LLLIDGSSLLYRALHALPQPLGNPLGDPTG---AVSGFLGMLYRLIRLLEPTH-PVVVFDGKPPT 73 (310)
T ss_pred EEEEechHHHHHHHHhcchhcCCCCCCCcc---HHHHHHHHHHHHHHhcCCCc-EEEEEcCCCCc
Confidence 4689999999998876421 11222 55677888999999999955 56899995554
No 11
>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=58.68 E-value=9.2 Score=34.76 Aligned_cols=62 Identities=15% Similarity=0.153 Sum_probs=36.8
Q ss_pred eEEEecccccccccCCCCC--CCCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCCccccccc
Q psy6081 55 NLYLDMNGIIHPCTHPEDK--PAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQP 119 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~~~~--~~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAPrAKmnQQ 119 (226)
-|=||.++.+|.+...-.. ............++..+.+|+.. . -+ ..+++||.+|..|....
T Consensus 26 ~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~~-~-i~-pvfVFDG~~~~~K~~~~ 89 (316)
T cd00128 26 KVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLEL-G-IK-PVFVFDGKPPPLKAETL 89 (316)
T ss_pred EEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHHC-C-CE-EEEEEcCCCchhhHHHH
Confidence 4789999999986543110 01112223445566666666542 2 23 34679999998887665
No 12
>PRK03980 flap endonuclease-1; Provisional
Probab=54.78 E-value=32 Score=31.68 Aligned_cols=33 Identities=24% Similarity=0.408 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHhh-hcccceEEEEEeCCCCccccccc
Q psy6081 83 MVAIFECIDRLFRI-VRPRKLLYMAIDGVAPRAKMNQP 119 (226)
Q Consensus 83 ~~~If~yID~Lv~i-VrPrKllylAiDGVAPrAKmnQQ 119 (226)
+..+|..+-+|+.. ++| .+++||.+|-.|...-
T Consensus 11 l~g~~~r~~~ll~~gi~P----vfVFDG~~p~~K~~~~ 44 (292)
T PRK03980 11 LSGIFYRTINLLENGIKP----VYVFDGKPPELKAEEI 44 (292)
T ss_pred HHHHHHHHHHHHHCCCEE----EEEECCCCchHHHHHH
Confidence 44566666667766 778 7999999997665543
No 13
>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=54.03 E-value=29 Score=32.43 Aligned_cols=61 Identities=15% Similarity=0.207 Sum_probs=37.1
Q ss_pred eEEEecccccccccCC----CCCCCC---CCHHHHHHHHHHHHHHHHhh-hcccceEEEEEeCCCCccccccc
Q psy6081 55 NLYLDMNGIIHPCTHP----EDKPAP---KDEDEMMVAIFECIDRLFRI-VRPRKLLYMAIDGVAPRAKMNQP 119 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~----~~~~~~---~~e~e~~~~If~yID~Lv~i-VrPrKllylAiDGVAPrAKmnQQ 119 (226)
-+-||....||.+... ...+.. -....-+..+|..+-+|+.. ++| .+++||-+|-.|...-
T Consensus 23 ~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~~i~P----v~VFDG~~p~~K~~~~ 91 (338)
T TIGR03674 23 VVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLENGIKP----VYVFDGKPPELKAETL 91 (338)
T ss_pred EEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHCCCeE----EEEECCCChhhhHhhH
Confidence 4678999999975432 111100 00112344555666666666 777 7899999998776665
No 14
>smart00475 53EXOc 5'-3' exonuclease.
Probab=53.65 E-value=22 Score=32.09 Aligned_cols=56 Identities=9% Similarity=0.161 Sum_probs=37.8
Q ss_pred EEEecccccccccCCCCC--CCCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCC
Q psy6081 56 LYLDMNGIIHPCTHPEDK--PAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 112 (226)
Q Consensus 56 LYLDmNgIIH~c~h~~~~--~~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAP 112 (226)
|-||.|++||-+.|.-.. ...-........++..+.+|+...+|..+ .+|+||-.|
T Consensus 4 llIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~-~~~fD~~~~ 61 (259)
T smart00475 4 LLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYV-AVVFDAKGK 61 (259)
T ss_pred EEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeE-EEEEeCCCC
Confidence 679999999988775311 00111223455677888888888899775 599998544
No 15
>PRK14976 5'-3' exonuclease; Provisional
Probab=53.23 E-value=23 Score=32.38 Aligned_cols=57 Identities=16% Similarity=0.222 Sum_probs=39.1
Q ss_pred eEEEecccccccccCCCC--CC----CCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCC
Q psy6081 55 NLYLDMNGIIHPCTHPED--KP----APKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 112 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~~~--~~----~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAP 112 (226)
=|-||.|++||-+.|... .+ ..-.......-+++.|-++++..+|..+ -+|+||-.|
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 357999999999887631 11 1112223456677888888888899876 689998654
No 16
>PRK09482 flap endonuclease-like protein; Provisional
Probab=52.30 E-value=31 Score=31.48 Aligned_cols=55 Identities=22% Similarity=0.314 Sum_probs=40.0
Q ss_pred eEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHhhhcccceEEEEEeCCCC
Q psy6081 55 NLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDGVAP 112 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv~iVrPrKllylAiDGVAP 112 (226)
=|.||-+++||-.+|.... +.........++..|.+|+...+|+.+ .+|+||-.+
T Consensus 5 llLiDg~~l~~R~~~a~~~--~~g~t~av~gf~~~l~~ll~~~~p~~i-~v~fD~~~~ 59 (256)
T PRK09482 5 LLIIDALNLIRRIHAVQPS--PNDINACVETCQHALDKLIRHSQPTHA-VAVFDGDAR 59 (256)
T ss_pred EEEEeCcHHHHHHHhCCCC--CCCcchHHHHHHHHHHHHHHHcCCCEE-EEEEeCCCC
Confidence 3678999999987776421 122244556677888888988999886 689999765
No 17
>PHA03065 Hypothetical protein; Provisional
Probab=39.82 E-value=4e+02 Score=26.66 Aligned_cols=50 Identities=14% Similarity=0.313 Sum_probs=37.1
Q ss_pred CccccCCCCCCCCCCCccCeEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHH
Q psy6081 36 GQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLF 94 (226)
Q Consensus 36 g~~~p~d~~~pn~n~~~~DnLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv 94 (226)
|.-.++|...++ .+--+|+|..|+.-.-.|.- .+++|+...+.+||....
T Consensus 14 gsL~~~~~~~~~----~~~~iFVD~ms~fmsiAysv-----~~~~eL~~~~~~~iq~w~ 63 (438)
T PHA03065 14 GSLTKLDNNLKD----RFNGIFVDTMSVFMSIAYSV-----NNLDELRSTFEEYVQQWV 63 (438)
T ss_pred CCcccccccccc----cCceEEEechhhhhhhhhhh-----CCHHHHHHHHHHHHHHHH
Confidence 444555544443 57789999999988877753 478899999999998876
No 18
>PTZ00217 flap endonuclease-1; Provisional
Probab=36.64 E-value=98 Score=29.81 Aligned_cols=60 Identities=15% Similarity=0.225 Sum_probs=36.6
Q ss_pred eEEEecccccccccCC-----CCCCC----CCCHHHHHHHHHHHHHHHHhh-hcccceEEEEEeCCCCccccccc
Q psy6081 55 NLYLDMNGIIHPCTHP-----EDKPA----PKDEDEMMVAIFECIDRLFRI-VRPRKLLYMAIDGVAPRAKMNQP 119 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~-----~~~~~----~~~e~e~~~~If~yID~Lv~i-VrPrKllylAiDGVAPrAKmnQQ 119 (226)
-+-||....||..... ...+. -... .-+.-+|..+-+|+.. ++| .+++||.+|..|...-
T Consensus 30 ~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t-~~l~g~~~r~~~Ll~~gikP----v~VFDG~~p~~K~~~~ 99 (393)
T PTZ00217 30 VIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVT-SHISGLFNRTIRLLEAGIKP----VYVFDGKPPELKSGEL 99 (393)
T ss_pred EEEEeHHHHHHHHHHHcccccccccchhccCCcc-HHHHHHHHHHHHHHHCCCCE----EEEEcCCCchhhHHHH
Confidence 4678999999984321 11110 0111 2344566677777764 788 4799999998776543
No 19
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=32.36 E-value=17 Score=25.20 Aligned_cols=12 Identities=58% Similarity=0.974 Sum_probs=7.1
Q ss_pred CCccCCCChhHH
Q psy6081 182 SNCITPGTPFMA 193 (226)
Q Consensus 182 sN~ITPGT~FM~ 193 (226)
.+.|.|||+|.+
T Consensus 19 ~~~i~pGt~F~~ 30 (47)
T PF00301_consen 19 ENGIPPGTPFED 30 (47)
T ss_dssp GGTB-TT--GGG
T ss_pred ccCcCCCCCHHH
Confidence 378999999975
No 20
>PTZ00225 60S ribosomal protein L10a; Provisional
Probab=32.14 E-value=91 Score=27.63 Aligned_cols=46 Identities=11% Similarity=0.211 Sum_probs=36.1
Q ss_pred eEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHhhhcccceEEE
Q psy6081 55 NLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRKLLYM 105 (226)
Q Consensus 55 nLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv~iVrPrKllyl 105 (226)
.+-+|=+|++|.|.-..+ .+.+++.+++...|+.|.+.. |++.-||
T Consensus 153 ~~r~~k~~~~~~~VGk~~----m~~e~i~eNi~a~l~~l~~~~-p~k~~nI 198 (214)
T PTZ00225 153 KFQLKKVLCLGTCVGHVE----MTEEQLRQNVVMAINFLVSLL-KKNWQNL 198 (214)
T ss_pred EEEecCccEEEeEEccCC----CCHHHHHHHHHHHHHHHHHhC-CcCCceE
Confidence 356789999999976543 688999999999999998874 5655443
No 21
>PF13186 SPASM: Iron-sulfur cluster-binding domain
Probab=31.68 E-value=33 Score=22.81 Aligned_cols=19 Identities=37% Similarity=0.922 Sum_probs=16.4
Q ss_pred ccCeEEEecccccccccCC
Q psy6081 52 EFDNLYLDMNGIIHPCTHP 70 (226)
Q Consensus 52 ~~DnLYLDmNgIIH~c~h~ 70 (226)
.+..|+||.||-|.+|.+.
T Consensus 4 ~~~~~~I~~dG~v~pC~~~ 22 (64)
T PF13186_consen 4 GWNSLYIDPDGDVYPCCHD 22 (64)
T ss_pred cCeEEEEeeCccEEeCCCC
Confidence 4678999999999999655
No 22
>PF06575 DUF1132: Protein of unknown function (DUF1132); InterPro: IPR009509 This family consists of several hypothetical proteins from Neisseria meningitidis. The function of this family is unknown.
Probab=28.59 E-value=55 Score=26.17 Aligned_cols=28 Identities=29% Similarity=0.655 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHhcCCCCCCCcEEEEcCCCC
Q psy6081 194 CLSACLHYYIHDRLNNDPGWKGIKVILSDANV 225 (226)
Q Consensus 194 ~L~~~L~~yI~~kl~~dp~W~~i~VI~Sds~V 225 (226)
.+-+++.+|.-+|+.+| .|+ +.|||-+|
T Consensus 36 ~vie~fs~F~Nrri~~n-IWk---I~FsD~S~ 63 (95)
T PF06575_consen 36 DVIECFSHFWNRRISNN-IWK---IYFSDESV 63 (95)
T ss_pred eHHHHHHHHHHHHhhcC-eEE---EEeCCCce
Confidence 46778899999999987 575 88999765
No 23
>PF05413 Peptidase_C34: Putative closterovirus papain-like endopeptidase; InterPro: IPR008744 RNA-directed RNA polymerase (RdRp) (2.7.7.48 from EC) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage [, ]. It catalyses synthesis of the RNA strand complementary to a given RNA template, but the precise molecular mechanism remains unclear. The postulated RNA replication process is a two-step mechanism. First, the initiation step of RNA synthesis begins at or near the 3' end of the RNA template by means of a primer-independent (de novo) mechanism. The de novo initiation consists in the addition of a nucleotide tri-phosphate (NTP) to the 3'-OH of the first initiating NTP. During the following so-called elongation phase, this nucleotidyl transfer reaction is repeated with subsequent NTPs to generate the complementary RNA product []. All the RNA-directed RNA polymerases, and many DNA-directed polymerases, employ a fold whose organisation has been likened to the shape of a right hand with three subdomains termed fingers, palm and thumb []. Only the catalytic palm subdomain, composed of a four-stranded antiparallel beta-sheet with two alpha-helices, is well conserved among all of these enzymes. In RdRp, the palm subdomain comprises three well conserved motifs (A, B and C). Motif A (D-x(4,5)-D) and motif C (GDD) are spatially juxtaposed; the Asp residues of these motifs are implied in the binding of Mg2+ and/or Mn2+. The Asn residue of motif B is involved in selection of ribonucleoside triphosphates over dNTPs and thus determines whether RNA is synthesised rather than DNA []. The domain organisation [] and the 3D structure of the catalytic centre of a wide range of RdPp's, even those with a low overall sequence homology, are conserved. The catalytic centre is formed by several motifs containing a number of conserved amino acid residues. There are 4 superfamilies of viruses that cover all RNA containing viruses with no DNA stage: Viruses containing positive-strand RNA or double-strand RNA, except retroviruses and Birnaviridae: viral RNA-directed RNA polymerases including all positive-strand RNA viruses with no DNA stage, double-strand RNA viruses, and the Cystoviridae, Reoviridae, Hypoviridae, Partitiviridae, Totiviridae families. Mononegavirales (negative-strand RNA viruses with non-segmented genomes). Negative-strand RNA viruses with segmented genomes, i.e. Orthomyxoviruses (including influenza A, B, and C viruses, Thogotoviruses, and the infectious salmon anemia virus), Arenaviruses, Bunyaviruses, Hantaviruses, Nairoviruses, Phleboviruses, Tenuiviruses and Tospoviruses. Birnaviridae family of dsRNA viruses. The RNA-directed RNA polymerases in the first of the above superfamilies can be divided into the following three subgroups: All positive-strand RNA eukaryotic viruses with no DNA stage. All RNA-containing bacteriophages -there are two families of RNA-containing bacteriophages: Leviviridae (positive ssRNA phages) and Cystoviridae (dsRNA phages). Reoviridae family of dsRNA viruses. This signature is found in the RNA-direct RNA polymerase of apple chlorotic leaf spot virus and cherry mottle virus.; GO: 0003723 RNA binding, 0003968 RNA-directed RNA polymerase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=23.48 E-value=25 Score=27.75 Aligned_cols=32 Identities=31% Similarity=0.635 Sum_probs=26.1
Q ss_pred ccCeEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHH
Q psy6081 52 EFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLF 94 (226)
Q Consensus 52 ~~DnLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv 94 (226)
.||+|+.-+-.||| +..+|++..+-+-+||-+
T Consensus 8 k~DClf~s~a~~I~-----------Kkpeevm~~~phvldRCi 39 (92)
T PF05413_consen 8 KYDCLFVSVAEIIH-----------KKPEEVMMFLPHVLDRCI 39 (92)
T ss_pred ccccHHHHHHHHHh-----------cCHHHHHHhChHHHHHHH
Confidence 79999999999999 455778777778788765
No 24
>PF01359 Transposase_1: Transposase (partial DDE domain); InterPro: IPR001888 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. This family includes the mariner transposase []. More information about these proteins can be found at Protein of the Month: Transposase [].; PDB: 3HOT_B 3HOS_A 3K9K_B 3F2K_B 3K9J_B 2F7T_A.
Probab=23.44 E-value=1.3e+02 Score=22.63 Aligned_cols=46 Identities=22% Similarity=0.331 Sum_probs=30.6
Q ss_pred cCeEEEecccccccccCCCCCCCCCCHHHHHHHHHHHHHHHHhhhcccc
Q psy6081 53 FDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLFRIVRPRK 101 (226)
Q Consensus 53 ~DnLYLDmNgIIH~c~h~~~~~~~~~e~e~~~~If~yID~Lv~iVrPrK 101 (226)
-=+++-|..||||-..=+.+. .-..+.|...++.+-.-+..-||+.
T Consensus 32 Ml~vwWd~~Gvi~~e~L~~~~---TIts~~Y~~ql~~l~~~l~~krp~~ 77 (81)
T PF01359_consen 32 MLSVWWDAKGVIHYELLPPGK---TITSEYYCQQLDKLKQALREKRPEL 77 (81)
T ss_dssp EEEEEEETTEEEEEEEESTT------SHHHHHHHHHHHHHHHHHHTCCC
T ss_pred EEEEEeeccCcEeeeeCCCCc---cccHHHHHHHHHHHHHHHHHhChHh
Confidence 347889999999988766543 1235577766666666666667753
No 25
>COG1515 Nfi Deoxyinosine 3'endonuclease (endonuclease V) [DNA replication, recombination, and repair]
Probab=23.37 E-value=45 Score=30.03 Aligned_cols=20 Identities=40% Similarity=0.589 Sum_probs=17.2
Q ss_pred ccCeEEEeccccccc-----ccCCC
Q psy6081 52 EFDNLYLDMNGIIHP-----CTHPE 71 (226)
Q Consensus 52 ~~DnLYLDmNgIIH~-----c~h~~ 71 (226)
++|-|.+|-|||.|| ++|-.
T Consensus 95 ~~d~ilVDG~GiaHPR~~GlAsH~G 119 (212)
T COG1515 95 KPDLLLVDGHGIAHPRRLGLASHIG 119 (212)
T ss_pred CCCEEEEcCcceecCcccChhheee
Confidence 689999999999999 56743
No 26
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=22.98 E-value=3.2e+02 Score=25.07 Aligned_cols=64 Identities=16% Similarity=0.044 Sum_probs=40.6
Q ss_pred HHHHHHHHhcCCCCCCCcccCCCCCCCcc-CCCChhHHHHHHHHHHHHHHHhcCCCCCCCcEEEE
Q psy6081 157 ARIREKLLADGCILPPEKEKGSHFDSNCI-TPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVIL 220 (226)
Q Consensus 157 ~~~~~~l~~~g~~lp~~~~~~~~fDsN~I-TPGT~FM~~L~~~L~~yI~~kl~~dp~W~~i~VI~ 220 (226)
.+.+..|.++|..-......+..||.+.. +-=|+|+.++.-+++--+.+-|.+-++=..-+|-+
T Consensus 65 ~~Ar~~La~~GLP~~g~~~~~~lFd~~~l~~t~te~~qki~y~regELarTI~~idgV~~ArVhL 129 (249)
T PRK15348 65 INAVELLRLNGYPHRQFTTADKMFPANQLVVSPQEEQQKINFLKEQRIEGMLSQMEGVINAKVTI 129 (249)
T ss_pred HHHHHHHHHcCCCCCCCccHHHhCCccccccChhHHHHHHHHHHHHHHHHHHHhCCCeeEeEEEE
Confidence 34566677777532221122347887764 44599999999988888888887655555545543
No 27
>PHA00439 exonuclease
Probab=22.60 E-value=1.1e+02 Score=28.57 Aligned_cols=53 Identities=9% Similarity=0.105 Sum_probs=33.6
Q ss_pred EEEecccccccccCCCC------CC---CCCCHHHHHHHHHHHHHHHHhh---hcccceEEEEEeC
Q psy6081 56 LYLDMNGIIHPCTHPED------KP---APKDEDEMMVAIFECIDRLFRI---VRPRKLLYMAIDG 109 (226)
Q Consensus 56 LYLDmNgIIH~c~h~~~------~~---~~~~e~e~~~~If~yID~Lv~i---VrPrKllylAiDG 109 (226)
|.||.+++|+-++|.-. .+ ..-.......-+++.|.+++.. .+|..+ .+|+|+
T Consensus 9 lLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i-~vaFD~ 73 (286)
T PHA00439 9 LVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPI-VLAFTD 73 (286)
T ss_pred EEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeE-EEEECC
Confidence 56899999998888641 10 0111222344555666677766 789765 689995
No 28
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=21.42 E-value=48 Score=23.21 Aligned_cols=12 Identities=50% Similarity=0.902 Sum_probs=9.9
Q ss_pred CCccCCCChhHH
Q psy6081 182 SNCITPGTPFMA 193 (226)
Q Consensus 182 sN~ITPGT~FM~ 193 (226)
...|.|||+|.+
T Consensus 19 ~~~i~pGt~f~~ 30 (50)
T cd00730 19 DEGIPPGTPFED 30 (50)
T ss_pred ccCcCCCCCHhH
Confidence 367999999975
Done!