Query 023627
Match_columns 279
No_of_seqs 85 out of 87
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 05:27:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023627.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023627hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK07883 hypothetical protein; 99.9 1.2E-23 2.6E-28 206.7 4.4 176 6-199 13-307 (557)
2 PRK07740 hypothetical protein; 99.4 5.3E-13 1.2E-17 119.1 7.0 78 7-91 58-226 (244)
3 cd06133 ERI-1_3'hExo_like DEDD 99.4 6.6E-13 1.4E-17 107.6 6.5 73 10-82 1-175 (176)
4 PRK08517 DNA polymerase III su 99.4 1.2E-12 2.5E-17 118.6 6.8 74 6-83 66-228 (257)
5 PRK07247 DNA polymerase III su 99.3 1.5E-12 3.3E-17 113.5 6.6 76 8-93 5-171 (195)
6 PF00929 RNase_T: Exonuclease; 99.3 1.3E-12 2.8E-17 100.7 5.1 39 11-51 1-39 (164)
7 smart00479 EXOIII exonuclease 99.3 2.5E-12 5.4E-17 102.7 6.9 71 9-83 1-164 (169)
8 PRK09145 DNA polymerase III su 99.3 2.8E-12 6E-17 109.8 6.8 74 6-81 27-196 (202)
9 PRK07748 sporulation inhibitor 99.3 4.1E-12 9E-17 109.5 7.6 73 7-81 3-175 (207)
10 PRK09146 DNA polymerase III su 99.3 3.4E-12 7.4E-17 114.1 7.0 44 6-51 45-88 (239)
11 PRK06807 DNA polymerase III su 99.3 3.7E-12 8E-17 118.3 7.3 76 7-86 7-172 (313)
12 PRK07942 DNA polymerase III su 99.3 3E-12 6.5E-17 113.1 6.2 92 4-99 2-194 (232)
13 PRK06063 DNA polymerase III su 99.3 4.9E-12 1.1E-16 117.0 7.3 77 6-91 13-179 (313)
14 cd06131 DNA_pol_III_epsilon_Ec 99.3 5E-12 1.1E-16 103.1 6.1 71 10-82 1-166 (167)
15 cd06136 TREX1_2 DEDDh 3'-5' ex 99.3 4.1E-12 8.8E-17 107.4 5.5 32 10-42 1-32 (177)
16 TIGR00573 dnaq exonuclease, DN 99.3 6.2E-12 1.4E-16 109.3 6.1 76 6-90 5-176 (217)
17 cd06130 DNA_pol_III_epsilon_li 99.3 5.9E-12 1.3E-16 100.6 5.2 28 52-79 127-154 (156)
18 PRK06310 DNA polymerase III su 99.3 8.6E-12 1.9E-16 111.7 6.9 78 7-93 6-176 (250)
19 TIGR01298 RNaseT ribonuclease 99.2 3.5E-11 7.5E-16 104.1 6.6 30 52-81 155-187 (200)
20 PRK05168 ribonuclease T; Provi 99.2 3.8E-11 8.3E-16 104.6 6.8 31 6-38 15-45 (211)
21 PRK06722 exonuclease; Provisio 99.2 4.5E-11 9.9E-16 110.5 7.1 45 6-51 3-49 (281)
22 cd06134 RNaseT DEDDh 3'-5' exo 99.2 4.8E-11 1E-15 102.1 6.7 34 52-90 152-188 (189)
23 PRK07246 bifunctional ATP-depe 99.2 3.6E-11 7.8E-16 123.6 6.6 127 4-141 3-236 (820)
24 cd06127 DEDDh DEDDh 3'-5' exon 99.2 5.4E-11 1.2E-15 91.9 5.5 38 11-51 1-38 (159)
25 PRK06195 DNA polymerase III su 99.1 5.7E-11 1.2E-15 109.0 6.1 74 9-93 2-166 (309)
26 TIGR01406 dnaQ_proteo DNA poly 99.1 6.9E-11 1.5E-15 104.5 6.1 70 10-81 2-167 (225)
27 PRK09182 DNA polymerase III su 99.1 9.8E-11 2.1E-15 108.2 7.3 74 7-82 36-197 (294)
28 PRK08074 bifunctional ATP-depe 99.1 6.1E-11 1.3E-15 122.9 6.5 76 8-91 3-169 (928)
29 cd06135 Orn DEDDh 3'-5' exonuc 99.1 9.7E-11 2.1E-15 98.7 6.4 37 10-48 1-37 (173)
30 PRK06309 DNA polymerase III su 99.1 2.2E-10 4.7E-15 101.0 7.9 40 52-96 131-171 (232)
31 TIGR01405 polC_Gram_pos DNA po 99.1 1.1E-10 2.3E-15 125.1 6.5 73 6-82 188-351 (1213)
32 COG2176 PolC DNA polymerase II 99.1 7E-11 1.5E-15 126.1 5.1 81 3-92 416-587 (1444)
33 TIGR01407 dinG_rel DnaQ family 99.1 1.2E-10 2.6E-15 119.2 6.4 70 9-82 1-161 (850)
34 PRK05711 DNA polymerase III su 99.1 2.5E-10 5.5E-15 102.7 6.9 43 7-51 3-45 (240)
35 PRK07983 exodeoxyribonuclease 99.0 2.7E-10 5.9E-15 101.0 5.8 70 10-91 2-154 (219)
36 cd06138 ExoI_N N-terminal DEDD 99.0 1.9E-10 4.1E-15 97.4 4.4 37 11-51 1-38 (183)
37 PRK05359 oligoribonuclease; Pr 98.9 2E-09 4.3E-14 92.5 7.1 32 7-40 2-33 (181)
38 PRK11779 sbcB exonuclease I; P 98.9 4.6E-09 1E-13 103.3 7.4 35 5-41 3-37 (476)
39 COG0847 DnaQ DNA polymerase II 98.8 5.2E-09 1.1E-13 90.6 6.0 71 8-81 13-177 (243)
40 cd06149 ISG20 DEDDh 3'-5' exon 98.8 6.4E-09 1.4E-13 86.9 4.4 30 11-40 1-30 (157)
41 PRK00448 polC DNA polymerase I 98.7 1.1E-08 2.3E-13 111.5 4.1 71 7-81 418-579 (1437)
42 PRK05601 DNA polymerase III su 98.7 2.5E-08 5.4E-13 96.4 6.0 42 6-51 44-86 (377)
43 PTZ00315 2'-phosphotransferase 98.7 3E-08 6.5E-13 100.1 6.8 42 8-51 56-100 (582)
44 cd06137 DEDDh_RNase DEDDh 3'-5 98.7 2.3E-08 5E-13 83.3 4.6 30 11-42 1-30 (161)
45 cd06144 REX4_like DEDDh 3'-5' 98.6 6.7E-08 1.4E-12 79.7 4.4 29 52-80 121-152 (152)
46 cd06145 REX1_like DEDDh 3'-5' 98.1 3.2E-06 7E-11 70.1 3.8 29 52-80 117-150 (150)
47 PRK14667 uvrC excinuclease ABC 98.0 3.5E-06 7.7E-11 84.9 2.5 66 106-173 10-87 (567)
48 COG5018 KapD Inhibitor of the 98.0 6.2E-06 1.3E-10 74.3 3.7 45 7-51 3-49 (210)
49 PRK14671 uvrC excinuclease ABC 97.9 1.5E-06 3.2E-11 88.2 -1.6 66 106-172 16-94 (621)
50 PRK12306 uvrC excinuclease ABC 97.9 1.6E-06 3.5E-11 86.5 -1.4 65 107-172 5-81 (519)
51 PRK14666 uvrC excinuclease ABC 97.9 1.9E-06 4.1E-11 88.8 -1.5 65 107-172 7-84 (694)
52 PRK14669 uvrC excinuclease ABC 97.9 1.8E-06 3.9E-11 87.9 -1.7 55 107-162 8-66 (624)
53 PRK00558 uvrC excinuclease ABC 97.9 2.5E-06 5.5E-11 86.0 -0.8 67 107-174 9-87 (598)
54 COG0322 UvrC Nuclease subunit 97.7 2.2E-06 4.8E-11 86.7 -3.1 55 107-163 10-67 (581)
55 TIGR00194 uvrC excinuclease AB 97.7 5.1E-06 1.1E-10 83.7 -1.5 64 107-172 6-81 (574)
56 PRK14668 uvrC excinuclease ABC 97.7 2E-05 4.3E-10 79.6 2.0 64 106-173 10-85 (577)
57 PRK14672 uvrC excinuclease ABC 97.6 1.1E-05 2.4E-10 83.3 -1.3 65 106-172 15-91 (691)
58 PRK10545 nucleotide excision r 97.5 8.2E-06 1.8E-10 76.3 -2.2 82 106-200 28-122 (286)
59 COG1949 Orn Oligoribonuclease 96.8 0.004 8.6E-08 55.9 6.6 34 3-38 1-34 (184)
60 KOG0542 Predicted exonuclease 93.0 0.24 5.2E-06 47.2 6.1 30 52-81 206-237 (280)
61 cd05160 DEDDy_DNA_polB_exo DED 92.9 0.12 2.6E-06 43.7 3.6 31 10-42 1-35 (199)
62 PRK14670 uvrC excinuclease ABC 92.5 0.016 3.5E-07 59.1 -2.4 52 119-171 1-64 (574)
63 smart00465 GIYc GIY-YIG type n 92.2 0.021 4.5E-07 40.9 -1.5 31 114-144 2-35 (84)
64 COG3359 Predicted exonuclease 90.7 0.37 7.9E-06 46.0 4.6 33 6-40 96-128 (278)
65 PHA02598 denA endonuclease II; 88.9 0.11 2.3E-06 45.3 -0.4 37 107-143 27-65 (138)
66 PHA02570 dexA exonuclease; Pro 86.3 1.5 3.2E-05 40.7 5.4 47 11-62 4-50 (220)
67 PF13482 RNase_H_2: RNase_H su 82.3 1.1 2.3E-05 36.6 2.4 30 11-42 1-30 (164)
68 cd06125 DnaQ_like_exo DnaQ-lik 81.2 2.1 4.5E-05 33.3 3.5 29 11-41 1-29 (96)
69 KOG3242 Oligoribonuclease (3'- 71.0 4.8 0.0001 37.1 3.5 30 8-39 26-55 (208)
70 PF01541 GIY-YIG: GIY-YIG cata 69.4 0.51 1.1E-05 33.7 -2.4 34 114-147 2-38 (80)
71 KOG4027 Uncharacterized conser 66.3 4.1 8.8E-05 37.0 2.0 98 177-277 76-184 (187)
72 cd05780 DNA_polB_Kod1_like_exo 51.8 24 0.00052 30.4 4.3 27 8-36 3-33 (195)
73 COG2925 SbcB Exonuclease I [DN 48.8 15 0.00032 37.5 2.8 30 52-81 166-196 (475)
74 cd05781 DNA_polB_B3_exo DEDDy 38.5 42 0.00091 29.2 3.7 28 8-37 3-34 (188)
75 cd06139 DNA_polA_I_Ecoli_like_ 37.8 48 0.001 27.1 3.8 27 5-33 2-28 (193)
76 cd04489 ExoVII_LU_OBF ExoVII_L 37.2 16 0.00034 26.4 0.8 52 219-275 24-75 (78)
77 TIGR01453 grpIintron_endo grou 34.1 9.8 0.00021 34.0 -0.9 34 114-147 2-39 (214)
78 cd06143 PAN2_exo DEDDh 3'-5' e 32.3 33 0.00072 30.6 2.2 29 52-80 143-174 (174)
79 PF01612 DNA_pol_A_exo1: 3'-5' 26.5 1.3E+02 0.0027 24.0 4.4 30 8-40 20-49 (176)
80 KOG4793 Three prime repair exo 24.2 53 0.0011 32.3 2.1 31 51-81 254-286 (318)
81 PRK05755 DNA polymerase I; Pro 20.5 2.1E+02 0.0046 30.8 5.8 25 7-33 314-338 (880)
No 1
>PRK07883 hypothetical protein; Validated
Probab=99.88 E-value=1.2e-23 Score=206.65 Aligned_cols=176 Identities=26% Similarity=0.325 Sum_probs=136.3
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL---------------------------------- 51 (279)
.+..||+||+||||.++.. ++|+|||||+|..+.+ ++.|++|
T Consensus 13 ~~~~~Vv~D~ETTGl~p~~--~~IIEIgaV~v~~g~i--v~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~ 88 (557)
T PRK07883 13 RDVTFVVVDLETTGGSPAG--DAITEIGAVKVRGGEV--LGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPA 88 (557)
T ss_pred cCCCEEEEEEecCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHH
Confidence 4578999999999998865 8999999999998877 4456555
Q ss_pred ----------------------------------------------------------HHHHHHhhCCC-CCccccchhh
Q 023627 52 ----------------------------------------------------------LASLATYFGLG-QQTHRSLDDV 72 (279)
Q Consensus 52 ----------------------------------------------------------LatLA~~Fg~~-~~~HRALdDa 72 (279)
|++|+.+||++ .+.||||+||
T Consensus 89 f~~fl~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~lar~l~~~~~~~~~~L~~L~~~~gi~~~~~H~Al~DA 168 (557)
T PRK07883 89 FLEFARGAVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVRLARRVLPRDEAPNVRLSTLARLFGATTTPTHRALDDA 168 (557)
T ss_pred HHHHhcCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHHHHHHhcccCCCCCCCHHHHHHHCCcccCCCCCHHHHH
Confidence 89999999999 8999999999
Q ss_pred hccHHHHHhhhHHHHhhhccC------cccccC-cccCcc-------ccCCCCCCCCeeeecCCCc--cc-ccCcceeee
Q 023627 73 RMNLEVLKYCATVLFLESGLP------DIFTVN-RWEMCS-------AASVSEGSSGYARFMEPDE--LY-CSRLKIRYG 135 (279)
Q Consensus 73 r~t~dVl~~catvlllE~~~~------~~l~~~-~~~~p~-------a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~r 135 (279)
++|++||.. ++++... ++|..+ +..+|. ...+| ..||||.|.+.++ || |.+.|||.|
T Consensus 169 ~ata~l~~~-----l~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~lP-~~PGVY~~~d~~g~viYVGKAknLr~R 242 (557)
T PRK07883 169 RATVDVLHG-----LIERLGNLGVHTLEELLTYLPRVTPAQRRKRHLADGLP-HAPGVYLFRGPSGEVLYVGTAVNLRRR 242 (557)
T ss_pred HHHHHHHHH-----HHHHHHhcCCCCHHHHHHhhhhcChhhhcchHHHhhCC-CCceEEEEECCCCcEEEeehhhhHHHH
Confidence 999999999 7776643 344444 444442 46799 9999999999988 99 999999999
Q ss_pred ccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHhhhccCCCCCCcccceeeccCCCcceEE
Q 023627 136 ISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARL 199 (279)
Q Consensus 136 VrsyFt~se~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~~~~~sgs~S~W~p~v~~~~gn~ptvRl 199 (279)
|++||..+..++|...||.-..+ +++.|-.|.-|-|-... +|-.+ |..-.+|.|+|
T Consensus 243 v~sYF~~~~~~~k~~~lv~~i~~ie~i~t~sE~eAllLE~~lIk~~~P~-------yN~~l-kd~k~ypyi~i 307 (557)
T PRK07883 243 VRSYFTAAETRGRMREMVALAERVDHVECAHALEAEVRELRLIAAHKPP-------YNRRS-KFPERRWWVRL 307 (557)
T ss_pred HHHHcCCCCCCchHHHHHhhhceEEEEEeCCHHHHHHHHHHHHHHhCCc-------chhhc-cCCCCceEEEE
Confidence 99999987788898888776555 55666666655443221 33332 33335666666
No 2
>PRK07740 hypothetical protein; Provisional
Probab=99.39 E-value=5.3e-13 Score=119.05 Aligned_cols=78 Identities=24% Similarity=0.393 Sum_probs=68.3
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------- 51 (279)
+..|||||+||||.+|..+ .+|||||||++..+.+ |.++|+++
T Consensus 58 ~~~~vv~D~ETTGl~p~~~-deIIeIgaV~~~~~~i-~~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~evl~~f 135 (244)
T PRK07740 58 DLPFVVFDLETTGFSPQQG-DEILSIGAVKTKGGEV-ETDTFYSLVKPKRPIPEHILELTGITAEDVAFAPPLAEVLHRF 135 (244)
T ss_pred CCCEEEEEEeCCCCCCCCC-CeEEEEEEEEEECCEE-EEEEEEEEeCcCCCCChhheeccCCCHHHHhCCCCHHHHHHHH
Confidence 4479999999999988753 7999999999998876 66788777
Q ss_pred -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627 52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN 75 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t 75 (279)
|.+|+.+||++ ...|+||+||++|
T Consensus 136 ~~fi~~~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~l~r~l~~~~~~~sL~~l~~~~gi~~~~~H~Al~Da~at 215 (244)
T PRK07740 136 YAFIGAGVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMFLTKLLAHERDFPTLDDALAYYGIPIPRRHHALGDALMT 215 (244)
T ss_pred HHHhCCCEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHHHHHHHcCCCCCCCHHHHHHHCCcCCCCCCCcHHHHHHH
Confidence 89999999999 7889999999999
Q ss_pred HHHHHhhhHHHHhhhc
Q 023627 76 LEVLKYCATVLFLESG 91 (279)
Q Consensus 76 ~dVl~~catvlllE~~ 91 (279)
++||++ ++++.
T Consensus 216 a~l~~~-----ll~~~ 226 (244)
T PRK07740 216 AKLWAI-----LLVEA 226 (244)
T ss_pred HHHHHH-----HHHHH
Confidence 999999 66553
No 3
>cd06133 ERI-1_3'hExo_like DEDDh 3'-5' exonuclease domain of Caenorhabditis elegans ERI-1, human 3' exonuclease, and similar proteins. This subfamily is composed of Caenorhabditis elegans ERI-1, human 3' exonuclease (3'hExo), Drosophila exonuclease snipper (snp), and similar proteins from eukaryotes and bacteria. These are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ERI-1 has been implicated in the degradation of small interfering RNAs (RNAi). 3'hExo participates in the degradation of histone mRNAs. Snp is a non-essential exonuclease that efficiently degrades structured RNA and DNA substrates as long as there is a minimum of 2 nucleotides in the 3' overhang to initiate degradation. Snp is not a functional ho
Probab=99.39 E-value=6.6e-13 Score=107.60 Aligned_cols=73 Identities=33% Similarity=0.435 Sum_probs=62.1
Q ss_pred EEEEEeecCCCCCCC---CceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627 10 IAFFDVETAFPNPPG---QRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (279)
Q Consensus 10 ~vffDvETT~p~~~~---~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------- 51 (279)
+|+||+||||+.+.. ...+|||||||+|.++...++++|+++
T Consensus 1 ~vv~D~Ettg~~~~~~~~~~~~IieIgav~v~~~~~~~~~~f~~~i~P~~~~~i~~~~~~i~gIt~e~l~~~~~~~~vl~ 80 (176)
T cd06133 1 YLVIDFEATCWEGNSKPDYPNEIIEIGAVLVDVKTKEIIDTFSSYVKPVINPKLSDFCTELTGITQEDVDNAPSFPEVLK 80 (176)
T ss_pred CEEEEeeccccCCCCCCCCCcceEEEEEEEEEcCCCeEEeeeeeeECCCcCCchhHHHHHhcCcCHHHHhcCCCHHHHHH
Confidence 689999999998852 248999999999999875445666555
Q ss_pred --------------------------------------------------------------HHHHHHhhCCC-C-Cccc
Q 023627 52 --------------------------------------------------------------LASLATYFGLG-Q-QTHR 67 (279)
Q Consensus 52 --------------------------------------------------------------LatLA~~Fg~~-~-~~HR 67 (279)
|.+|+.+||++ . +.||
T Consensus 81 ~~~~~l~~~~~~~~v~~~~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~~H~ 160 (176)
T cd06133 81 EFLEWLGKNGKYAFVTWGDWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYGLKKRTGLSKALEYLGLEFEGRHHR 160 (176)
T ss_pred HHHHHHHhCCCeEEEeecHhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhCCCCCCCHHHHHHHCCCCCCCCCcC
Confidence 89999999999 4 7999
Q ss_pred cchhhhccHHHHHhh
Q 023627 68 SLDDVRMNLEVLKYC 82 (279)
Q Consensus 68 ALdDar~t~dVl~~c 82 (279)
||+||++|++||+++
T Consensus 161 Al~DA~~~a~l~~~~ 175 (176)
T cd06133 161 GLDDARNIARILKRL 175 (176)
T ss_pred cHHHHHHHHHHHHHh
Confidence 999999999999983
No 4
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.35 E-value=1.2e-12 Score=118.56 Aligned_cols=74 Identities=26% Similarity=0.463 Sum_probs=64.0
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL---------------------------------- 51 (279)
.+..||+||+||||+++.. .+|||||||+|..|.+ +++|+++
T Consensus 66 ~~~~~vv~DiETTG~~~~~--~~IIEIGAv~v~~g~i--~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f 141 (257)
T PRK08517 66 KDQVFCFVDIETNGSKPKK--HQIIEIGAVKVKNGEI--IDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEF 141 (257)
T ss_pred CCCCEEEEEEeCCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHH
Confidence 4568999999999998876 6999999999998877 3455433
Q ss_pred ------------------------------------------------------HHHHHHhhCCC-CCccccchhhhccH
Q 023627 52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL 76 (279)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t~ 76 (279)
|++|+++||+. .+.||||+||.+|+
T Consensus 142 ~~fl~~~v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl~la~~~~~~~~~~L~~L~~~lgi~~~~~HrAl~DA~ata 221 (257)
T PRK08517 142 RLFLGDSVFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTIDLAKRTIESPRYGLSFLKELLGIEIEVHHRAYADALAAY 221 (257)
T ss_pred HHHHCCCeEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehHHHHHHHccCCCCCHHHHHHHcCcCCCCCCChHHHHHHHH
Confidence 88999999999 79999999999999
Q ss_pred HHHHhhh
Q 023627 77 EVLKYCA 83 (279)
Q Consensus 77 dVl~~ca 83 (279)
+||..|.
T Consensus 222 ~ll~~ll 228 (257)
T PRK08517 222 EIFKICL 228 (257)
T ss_pred HHHHHHH
Confidence 9999943
No 5
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.34 E-value=1.5e-12 Score=113.46 Aligned_cols=76 Identities=26% Similarity=0.378 Sum_probs=66.0
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH------------------------------------
Q 023627 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------ 51 (279)
Q Consensus 8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------ 51 (279)
..||+||+||||.++ +.+|||||||+|..+.+ +++|++|
T Consensus 5 ~~~vvlD~EtTGl~~---~~eIIeIgaV~v~~g~~--~~~f~~lv~P~~~i~~~~~~lhGIt~~~v~~ap~~~evl~~f~ 79 (195)
T PRK07247 5 ETYIAFDLEFNTVNG---VSHIIQVSAVKYDDHKE--VDSFDSYVYTDVPLQSFINGLTGITADKIADAPKVEEVLAAFK 79 (195)
T ss_pred CeEEEEEeeCCCCCC---CCeEEEEEEEEEECCEE--EEEEEEEECCCCCCCccceecCCCCHHHHhCCCCHHHHHHHHH
Confidence 479999999999874 36899999999999876 5677777
Q ss_pred -------------------------------------------------------HHHHHHhhCCCCCccccchhhhccH
Q 023627 52 -------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNL 76 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~ 76 (279)
|.+||++||++...||||+||++|.
T Consensus 80 ~f~~~~~lVaHNa~~fD~~fL~~~g~~~~~~~~idt~~~~~~~~~~~~~~~~~~~L~~La~~~gi~~~~HrAl~DA~~ta 159 (195)
T PRK07247 80 EFVGELPLIGYNAQKSDLPILAENGLDLSDQYQVDLYDEAFERRSSDLNGIANLKLQTVADFLGIKGRGHNSLEDARMTA 159 (195)
T ss_pred HHHCCCeEEEEeCcHhHHHHHHHcCCCcCCCceeehHHHHHHhhccccCCCCCCCHHHHHHhcCCCCCCcCCHHHHHHHH
Confidence 7899999999977899999999999
Q ss_pred HHHHhhhHHHHhhhccC
Q 023627 77 EVLKYCATVLFLESGLP 93 (279)
Q Consensus 77 dVl~~catvlllE~~~~ 93 (279)
.||.+ +++.--+
T Consensus 160 ~v~~~-----ll~~~~~ 171 (195)
T PRK07247 160 RVYES-----FLESDQN 171 (195)
T ss_pred HHHHH-----HHhhccc
Confidence 99999 7776554
No 6
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=99.34 E-value=1.3e-12 Score=100.73 Aligned_cols=39 Identities=33% Similarity=0.480 Sum_probs=32.6
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL 51 (279)
||||+||||+++.. ..|+|||||++.++...+.++|+++
T Consensus 1 v~~D~Ettg~~~~~--~~iieig~v~~~~~~~~~~~~~~~~ 39 (164)
T PF00929_consen 1 VVFDTETTGLDPRQ--DEIIEIGAVKVDDDENEEVESFNSL 39 (164)
T ss_dssp EEEEEEESSSTTTT--CTEEEEEEEEEETTTTEEEEEEEEE
T ss_pred cEEEeEcCCCCCCC--CeEEEEEEEEeeCCccccceeeeec
Confidence 79999999999844 8999999999999985445566665
No 7
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.34 E-value=2.5e-12 Score=102.73 Aligned_cols=71 Identities=30% Similarity=0.388 Sum_probs=60.9
Q ss_pred eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------------
Q 023627 9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------- 51 (279)
Q Consensus 9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------- 51 (279)
.+|+||+||||+++.. .+|+|||||++.++.+ .++|+++
T Consensus 1 ~~v~~D~Ettg~~~~~--~~Iieig~v~~~~~~~--~~~f~~~v~p~~~i~~~~~~~~Git~~~l~~~~~~~~~~~~~~~ 76 (169)
T smart00479 1 TLVVIDCETTGLDPGK--DEIIEIAAVDVDGGRI--IVVFDTYVKPDRPITDYATEIHGITPEMLDDAPTFEEVLEELLE 76 (169)
T ss_pred CEEEEEeeCCCCCCCC--CeEEEEEEEEEECCEe--EEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHH
Confidence 4899999999998864 8999999999999873 4556555
Q ss_pred ------------------------------------------------------HHHHHHhhCCC-CCc-cccchhhhcc
Q 023627 52 ------------------------------------------------------LASLATYFGLG-QQT-HRSLDDVRMN 75 (279)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~-HRALdDar~t 75 (279)
|.+|+.+||+. .++ ||||+||++|
T Consensus 77 ~l~~~~~v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~~~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t 156 (169)
T smart00479 77 FLKGKILVAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNPGRKYSLKKLAERLGLEVIGRAHRALDDARAT 156 (169)
T ss_pred HhcCCEEEEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCcCcHHHHHHH
Confidence 89999999999 555 9999999999
Q ss_pred HHHHHhhh
Q 023627 76 LEVLKYCA 83 (279)
Q Consensus 76 ~dVl~~ca 83 (279)
++|++.+.
T Consensus 157 ~~l~~~~~ 164 (169)
T smart00479 157 AKLFKKLV 164 (169)
T ss_pred HHHHHHHH
Confidence 99999943
No 8
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.32 E-value=2.8e-12 Score=109.76 Aligned_cols=74 Identities=18% Similarity=0.179 Sum_probs=62.6
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL---------------------------------- 51 (279)
.+..+|+||+||||+++.. .+|||||||++.++.++..++|+++
T Consensus 27 ~~~~~vviD~ETTGl~~~~--d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~~l~~~~~~~~vl~~ 104 (202)
T PRK09145 27 PPDEWVALDCETTGLDPRR--AEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQDLEDGLSEEEALRQ 104 (202)
T ss_pred CCCCEEEEEeECCCCCCCC--CceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHHHHhcCCCHHHHHHH
Confidence 4468999999999998865 7999999999998876533455443
Q ss_pred -------------------------------------------------------------HHHHHHhhCCC-CCccccc
Q 023627 52 -------------------------------------------------------------LASLATYFGLG-QQTHRSL 69 (279)
Q Consensus 52 -------------------------------------------------------------LatLA~~Fg~~-~~~HRAL 69 (279)
|++|+++||++ ...||||
T Consensus 105 ~~~~i~~~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~~l~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~H~Al 184 (202)
T PRK09145 105 LLAFIGNRPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVSALYYDKKERHLPDAYIDLRFDAILKHLDLPVLGRHDAL 184 (202)
T ss_pred HHHHHcCCeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHHHHHHHHhhccCCCcccCCCHHHHHHHcCCCCCCCCCcH
Confidence 77889999999 7899999
Q ss_pred hhhhccHHHHHh
Q 023627 70 DDVRMNLEVLKY 81 (279)
Q Consensus 70 dDar~t~dVl~~ 81 (279)
+||++|++||.+
T Consensus 185 ~DA~ata~l~~~ 196 (202)
T PRK09145 185 NDAIMAALIFLR 196 (202)
T ss_pred HHHHHHHHHHHH
Confidence 999999999988
No 9
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.32 E-value=4.1e-12 Score=109.50 Aligned_cols=73 Identities=22% Similarity=0.316 Sum_probs=62.6
Q ss_pred CceEEEEEeecCCCCCCC----CceeEEEEeeEEEecCceeeccchHHH-------------------------------
Q 023627 7 RFEIAFFDVETAFPNPPG----QRIAILEFGAILVCPKTLEELQPYSTL------------------------------- 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~----~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------- 51 (279)
+-.||+||+||||+++.. ...+|||||||+|..+.+ +++|++|
T Consensus 3 ~~~~vvlD~EtTg~~~~~~~~~~~~eIIeIGaV~v~~~~i--~~~f~~lV~P~~~~~i~~~~~~ltGIt~~~l~~ap~~~ 80 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHKKKPKGFFPEIIEVGLVSVVGCEV--EDTFSSYVKPKTFPSLTERCKSFLGITQEDVDKGISFE 80 (207)
T ss_pred cceEEEEEeecCCcCCCCCCCCCCCceEEEeEEEEecCcC--hhhhcceECCCccCccChhhhhhcCcCHHHHccCCCHH
Confidence 457999999999976432 136899999999999976 5788888
Q ss_pred ---------------------------------------------------------------HHHHHHhhCCC--CCcc
Q 023627 52 ---------------------------------------------------------------LASLATYFGLG--QQTH 66 (279)
Q Consensus 52 ---------------------------------------------------------------LatLA~~Fg~~--~~~H 66 (279)
|++++++||++ ..+|
T Consensus 81 evl~~f~~~~~~~~~~iv~~~~fD~~fL~~~~~~~~~~~~~~~~~~dl~~~~~~~~~~~~~~~L~~~~~~~gi~~~~~~H 160 (207)
T PRK07748 81 ELVEKLAEYDKRCKPTIVTWGNMDMKVLKHNCEKAGVPFPFKGQCRDLSLEYKKFFGERNQTGLWKAIEEYGKEGTGKHH 160 (207)
T ss_pred HHHHHHHHHhCcCCeEEEEECHHHHHHHHHHHHHcCCCCcccccceeHHHHHHHHhCcCCCCCHHHHHHHcCCCCCCCCc
Confidence 88899999999 4589
Q ss_pred ccchhhhccHHHHHh
Q 023627 67 RSLDDVRMNLEVLKY 81 (279)
Q Consensus 67 RALdDar~t~dVl~~ 81 (279)
|||+||++|.++|..
T Consensus 161 ~Al~DA~~ta~l~~~ 175 (207)
T PRK07748 161 CALDDAMTTYNIFKL 175 (207)
T ss_pred ChHHHHHHHHHHHHH
Confidence 999999999999999
No 10
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.31 E-value=3.4e-12 Score=114.13 Aligned_cols=44 Identities=16% Similarity=0.108 Sum_probs=36.2
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL 51 (279)
.+..||+||+||||.++.. .+|||+|||++.++.++..++|++|
T Consensus 45 ~~~~~vviD~ETTGl~p~~--d~IieIg~v~v~~~~i~~~~~~~~l 88 (239)
T PRK09146 45 SEVPFVALDFETTGLDAEQ--DAIVSIGLVPFTLQRIRCRQARHWV 88 (239)
T ss_pred ccCCEEEEEeECCCCCCCC--CcEEEEEEEEEECCeEeecceEEEE
Confidence 3568999999999999865 8999999999999877544555555
No 11
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.31 E-value=3.7e-12 Score=118.29 Aligned_cols=76 Identities=22% Similarity=0.364 Sum_probs=65.6
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------- 51 (279)
...+|+||+||||.++.. ++|||||||+|+.|.+ +++|++|
T Consensus 7 ~~~~Vv~DlETTGl~p~~--~eIIEIgaV~v~~g~i--~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f 82 (313)
T PRK06807 7 PLDYVVIDFETTGFNPYN--DKIIQVAAVKYRNHEL--VDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82 (313)
T ss_pred CCCEEEEEEECCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHH
Confidence 357999999999998865 7999999999999877 4555444
Q ss_pred -------------------------------------------------------HHHHHHhhCCCCCccccchhhhccH
Q 023627 52 -------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNL 76 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~ 76 (279)
|.+|+.+||++.+.||||+||++|.
T Consensus 83 ~~fl~~~~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~la~~~~~~~~~~kL~~L~~~lgi~~~~H~Al~DA~~ta 162 (313)
T PRK06807 83 LAFLHTNVIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVFLAKKYMKHAPNHKLETLKRMLGIRLSSHNAFDDCITCA 162 (313)
T ss_pred HHHHcCCeEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcChHHHHHHHH
Confidence 8999999999988999999999999
Q ss_pred HHHHhhhHHH
Q 023627 77 EVLKYCATVL 86 (279)
Q Consensus 77 dVl~~catvl 86 (279)
+|+.+|..-.
T Consensus 163 ~l~~~l~~~~ 172 (313)
T PRK06807 163 AVYQKCASIE 172 (313)
T ss_pred HHHHHHHHhh
Confidence 9999965533
No 12
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.30 E-value=3e-12 Score=113.13 Aligned_cols=92 Identities=20% Similarity=0.176 Sum_probs=71.5
Q ss_pred CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeeccchHHH-------------------------------
Q 023627 4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL------------------------------- 51 (279)
Q Consensus 4 ~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp-~~l~e~~sf~TL------------------------------- 51 (279)
.=.+..||+||+||||.++.. .+|||+|+|+|.+ |.+ +++|++|
T Consensus 2 ~~~~~~~vv~D~ETTGl~p~~--d~Iieig~v~v~~~g~~--~~~~~~lv~P~~~i~~~a~~IhGIt~e~l~~~g~~~~~ 77 (232)
T PRK07942 2 SWHPGPLAAFDLETTGVDPET--ARIVTAALVVVDADGEV--VESREWLADPGVEIPEEASAVHGITTEYARAHGRPAAE 77 (232)
T ss_pred CcccCcEEEEEeccCCCCCCC--CeeEEEEEEEEeCCCcc--ccceEEEECCCCCCCHHHHHHhCCCHHHHHhhCCCHHH
Confidence 345678999999999999865 7999999999985 655 4556555
Q ss_pred -------------------------------------------------------------------HHHHHHhhCCC-C
Q 023627 52 -------------------------------------------------------------------LASLATYFGLG-Q 63 (279)
Q Consensus 52 -------------------------------------------------------------------LatLA~~Fg~~-~ 63 (279)
|++|+.+||+. .
T Consensus 78 vl~e~~~~l~~~~~~~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~~~~~~~~~L~~l~~~~gi~~~ 157 (232)
T PRK07942 78 VLAEIADALREAWARGVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVDRYRKGKRTLTALCEHYGVRLD 157 (232)
T ss_pred HHHHHHHHHHHHhhcCCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhhcccCCCCCHHHHHHHcCCCCC
Confidence 88899999999 8
Q ss_pred CccccchhhhccHHHHHhhhHHHH-hhhccCcccccC
Q 023627 64 QTHRSLDDVRMNLEVLKYCATVLF-LESGLPDIFTVN 99 (279)
Q Consensus 64 ~~HRALdDar~t~dVl~~catvll-lE~~~~~~l~~~ 99 (279)
+.||||+||+||++||..++.-.- |..+..++|...
T Consensus 158 ~aH~Al~Da~ata~l~~~l~~~~~~l~~~~~~~l~~~ 194 (232)
T PRK07942 158 NAHEATADALAAARVAWALARRFPELAALSPAELHEL 194 (232)
T ss_pred CCCChHHHHHHHHHHHHHHHHHHHHhhcCCHHHHHHH
Confidence 899999999999999999554432 333333444433
No 13
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.29 E-value=4.9e-12 Score=117.01 Aligned_cols=77 Identities=30% Similarity=0.324 Sum_probs=66.1
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeeccchHHH---------------------------------
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL--------------------------------- 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp-~~l~e~~sf~TL--------------------------------- 51 (279)
....||+||+||||+++.. .+|||||||+|.. |.+ +++|++|
T Consensus 13 ~~~~fvvlD~ETTGl~p~~--d~IIeIgav~v~~~g~i--~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l 88 (313)
T PRK06063 13 YPRGWAVVDVETSGFRPGQ--ARIISLAVLGLDADGNV--EQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEV 88 (313)
T ss_pred CCCCEEEEEEECCCCCCCC--CEEEEEEEEEEECCcee--eeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHH
Confidence 3467999999999998865 8999999999975 555 4667666
Q ss_pred -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627 52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN 75 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t 75 (279)
|.+|+.+||+. .+.||||+||++|
T Consensus 89 ~~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~~~H~Al~DA~at 168 (313)
T PRK06063 89 AELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVL 168 (313)
T ss_pred HHHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHH
Confidence 99999999999 8899999999999
Q ss_pred HHHHHhhhHHHHhhhc
Q 023627 76 LEVLKYCATVLFLESG 91 (279)
Q Consensus 76 ~dVl~~catvlllE~~ 91 (279)
.+||.+ ++++.
T Consensus 169 a~l~~~-----ll~~~ 179 (313)
T PRK06063 169 AGILRP-----SLERA 179 (313)
T ss_pred HHHHHH-----HHHHH
Confidence 999998 66664
No 14
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=99.29 E-value=5e-12 Score=103.08 Aligned_cols=71 Identities=24% Similarity=0.324 Sum_probs=58.3
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------------
Q 023627 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------- 51 (279)
Q Consensus 10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------------- 51 (279)
.|+||+||||+++.. +++|||||||+|..+.+ ..++|+++
T Consensus 1 ~v~~D~ETTGl~~~~-~~~iieig~v~v~~~~~-~~~~~~~~v~P~~~i~~~~~~ihGIt~e~l~~~~~~~~v~~~l~~~ 78 (167)
T cd06131 1 QIVLDTETTGLDPRE-GHRIIEIGCVELINRRL-TGNTFHVYINPERDIPEEAFKVHGITDEFLADKPKFAEIADEFLDF 78 (167)
T ss_pred CEEEEeeCCCCCCCC-CCeEEEEEEEEEECCcE-eccEEEEEECCCCCCCHHHHHHhCCCHHHHhcCCCHHHHHHHHHHH
Confidence 389999999999844 38999999999988765 22355444
Q ss_pred ------------------------------------------------------HHHHHHhhCCC---CCccccchhhhc
Q 023627 52 ------------------------------------------------------LASLATYFGLG---QQTHRSLDDVRM 74 (279)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~---~~~HRALdDar~ 74 (279)
|++|++++|++ .+.||||+||++
T Consensus 79 l~~~~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~~~~~~~~~~~~~L~~l~~~~~i~~~~~~~H~Al~Da~~ 158 (167)
T cd06131 79 IRGAELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLALARKKFPGKPNSLDALCKRFGIDNSHRTLHGALLDAEL 158 (167)
T ss_pred HCCCeEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCChHHHHHH
Confidence 89999999998 256999999999
Q ss_pred cHHHHHhh
Q 023627 75 NLEVLKYC 82 (279)
Q Consensus 75 t~dVl~~c 82 (279)
|.+||..+
T Consensus 159 ~a~l~~~l 166 (167)
T cd06131 159 LAEVYLEL 166 (167)
T ss_pred HHHHHHHh
Confidence 99999874
No 15
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=99.28 E-value=4.1e-12 Score=107.40 Aligned_cols=32 Identities=25% Similarity=0.261 Sum_probs=27.6
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTL 42 (279)
Q Consensus 10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l 42 (279)
||+||+||||+++..+ .+|||+|||+|.++.+
T Consensus 1 ~vv~D~ETTGl~~~~~-d~Iiei~av~v~~~~~ 32 (177)
T cd06136 1 FVFLDLETTGLPKHNR-PEITELCLVAVHRDHL 32 (177)
T ss_pred CeEEeeecCCCCCCCC-CceEEEEEEEEecccc
Confidence 6999999999995443 8999999999998764
No 16
>TIGR00573 dnaq exonuclease, DNA polymerase III, epsilon subunit family. All proteins in this family for which functions are known are components of the DNA polymerase III complex (epsilon subunit). There is, however, an outgroup that includes paralogs in some gamma-proteobacteria and the n-terminal region of DinG from some low GC gram positive bacteria. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.27 E-value=6.2e-12 Score=109.32 Aligned_cols=76 Identities=17% Similarity=0.117 Sum_probs=63.0
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL---------------------------------- 51 (279)
.+.+||+||+||||+++.. . |||||||+|.++... .++|++|
T Consensus 5 ~~~~fvv~D~ETTGl~~~~--~-IIeIgav~v~~~~~~-~~~f~~li~P~~~i~~~a~~ihGIt~e~l~~~p~~~ev~~~ 80 (217)
T TIGR00573 5 VLDTETTGDNETTGLYAGH--D-IIEIGAVEIINRRIT-GNKFHTYIKPDRPIDPDAIKIHGITDDMLKDKPDFKEIAED 80 (217)
T ss_pred EecCEEEEEecCCCCCCCC--C-EEEEEEEEEECCCEe-eeEEEEEECcCCCCCHHHHhhcCCCHHHHcCCCCHHHHHHH
Confidence 3568999999999998754 5 999999998877542 3566655
Q ss_pred -----------------------------------------------------------HHHHHHhhCCC-C--Cccccc
Q 023627 52 -----------------------------------------------------------LASLATYFGLG-Q--QTHRSL 69 (279)
Q Consensus 52 -----------------------------------------------------------LatLA~~Fg~~-~--~~HRAL 69 (279)
|.+|+.+||++ . ..||||
T Consensus 81 ~~~~~~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~~~~~~~~~L~~l~~~~gl~~~~~~~H~Al 160 (217)
T TIGR00573 81 FADYIRGAELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARPEFPGKRNTLDALCKRYEITNSHRALHGAL 160 (217)
T ss_pred HHHHhCCCEEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCcccCCHH
Confidence 88999999998 3 679999
Q ss_pred hhhhccHHHHHhhhHHHHhhh
Q 023627 70 DDVRMNLEVLKYCATVLFLES 90 (279)
Q Consensus 70 dDar~t~dVl~~catvlllE~ 90 (279)
+||++|.+||.+ ++++
T Consensus 161 ~DA~~ta~l~~~-----l~~~ 176 (217)
T TIGR00573 161 ADAFILAKLYLV-----MTGK 176 (217)
T ss_pred HHHHHHHHHHHH-----HHhc
Confidence 999999999999 6555
No 17
>cd06130 DNA_pol_III_epsilon_like an uncharacterized bacterial subgroup of the DEDDh 3'-5' exonuclease domain family with similarity to the epsilon subunit of DNA polymerase III. This subfamily is composed of uncharacterized bacterial proteins with similarity to the epsilon subunit of DNA polymerase III (Pol III), a multisubunit polymerase which is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. The Pol III holoenzyme is a complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that ser
Probab=99.26 E-value=5.9e-12 Score=100.56 Aligned_cols=28 Identities=32% Similarity=0.554 Sum_probs=25.8
Q ss_pred HHHHHHhhCCCCCccccchhhhccHHHH
Q 023627 52 LASLATYFGLGQQTHRSLDDVRMNLEVL 79 (279)
Q Consensus 52 LatLA~~Fg~~~~~HRALdDar~t~dVl 79 (279)
|.+|+++||+....||||+||++|.++|
T Consensus 127 L~~l~~~~g~~~~~H~Al~Da~~ta~l~ 154 (156)
T cd06130 127 LNTVAEHLGIELNHHDALEDARACAEIL 154 (156)
T ss_pred HHHHHHHcCCCccCcCchHHHHHHHHHH
Confidence 8999999999933999999999999987
No 18
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.26 E-value=8.6e-12 Score=111.70 Aligned_cols=78 Identities=27% Similarity=0.337 Sum_probs=66.3
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------- 51 (279)
+..+|+||+||||.++.. .+|||||||+|.++.+ +++|++|
T Consensus 6 ~~~~v~~D~ETTGl~~~~--d~IIEIa~v~v~~~~~--~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~~~ 81 (250)
T PRK06310 6 DTEFVCLDCETTGLDVKK--DRIIEFAAIRFTFDEV--IDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFPQI 81 (250)
T ss_pred CCcEEEEEEeCCCCCCCC--CeEEEEEEEEEECCeE--EEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHHHH
Confidence 367999999999998866 8999999999998866 3456555
Q ss_pred ---------------------------------------------------------HHHHHHhhCCC-CCccccchhhh
Q 023627 52 ---------------------------------------------------------LASLATYFGLG-QQTHRSLDDVR 73 (279)
Q Consensus 52 ---------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar 73 (279)
|++|+.+||+. ...|||++||.
T Consensus 82 ~~fl~~~~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~~~~~~~~L~~l~~~~g~~~~~aH~Al~Da~ 161 (250)
T PRK06310 82 KGFFKEGDYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEYGDSPNNSLEALAVHFNVPYDGNHRAMKDVE 161 (250)
T ss_pred HHHhCCCCEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhcccCCCCCHHHHHHHCCCCCCCCcChHHHHH
Confidence 78899999999 88999999999
Q ss_pred ccHHHHHhhhHHHHhhhccC
Q 023627 74 MNLEVLKYCATVLFLESGLP 93 (279)
Q Consensus 74 ~t~dVl~~catvlllE~~~~ 93 (279)
+|.+||.+ ++++..+
T Consensus 162 at~~vl~~-----l~~~~~~ 176 (250)
T PRK06310 162 INIKVFKH-----LCKRFRT 176 (250)
T ss_pred HHHHHHHH-----HHHhccc
Confidence 99999999 6666543
No 19
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=99.19 E-value=3.5e-11 Score=104.12 Aligned_cols=30 Identities=27% Similarity=0.267 Sum_probs=27.3
Q ss_pred HHHHHHhhCCC---CCccccchhhhccHHHHHh
Q 023627 52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKY 81 (279)
Q Consensus 52 LatLA~~Fg~~---~~~HRALdDar~t~dVl~~ 81 (279)
|..|++++|++ .+.||||+||.+|.+||..
T Consensus 155 L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~ 187 (200)
T TIGR01298 155 LAKACQAAGXDFDSTQAHSALYDTEKTAELFCE 187 (200)
T ss_pred HHHHHHHcCCCccccchhhhHHhHHHHHHHHHH
Confidence 77888899997 4899999999999999999
No 20
>PRK05168 ribonuclease T; Provisional
Probab=99.18 E-value=3.8e-11 Score=104.61 Aligned_cols=31 Identities=35% Similarity=0.273 Sum_probs=27.3
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEe
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVC 38 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vc 38 (279)
.+..+|+||+||||+++.+ .+|||||||+|.
T Consensus 15 ~~~~~vv~D~ETTGl~~~~--d~IieIgaV~v~ 45 (211)
T PRK05168 15 RGFLPVVIDVETAGFNAKT--DALLEIAAVTLK 45 (211)
T ss_pred cCCceEEEEeeCCCCCCCC--CEEEEEeEEEEE
Confidence 3567899999999999865 899999999987
No 21
>PRK06722 exonuclease; Provisional
Probab=99.17 E-value=4.5e-11 Score=110.49 Aligned_cols=45 Identities=24% Similarity=0.477 Sum_probs=35.0
Q ss_pred CCceEEEEEeecCCCCCC--CCceeEEEEeeEEEecCceeeccchHHH
Q 023627 6 DRFEIAFFDVETAFPNPP--GQRIAILEFGAILVCPKTLEELQPYSTL 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~--~~~~~ilEfgAI~Vcp~~l~e~~sf~TL 51 (279)
....||+||+|||+ +|. ..+.+|||||||+|..|.+..++.|++|
T Consensus 3 ~~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sL 49 (281)
T PRK06722 3 NATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSEL 49 (281)
T ss_pred CCCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEE
Confidence 34789999999995 442 2358999999999999843336789888
No 22
>cd06134 RNaseT DEDDh 3'-5' exonuclease domain of RNase T. RNase T is a DEDDh-type DnaQ-like 3'-5' exoribonuclease E implicated in the 3' maturation of small stable RNAs and 23srRNA, and in the end turnover of tRNA. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. RNase T is related to the proofreading domain of DNA polymerase III. Despite its important role, RNase T is mainly found only in gammaproteobacteria. It is speculated that it might have originated from DNA polymerase III at the time the gamma division of proteobacteria diverged from other bacteria. RNase T is a homodimer with the catalytic residues of one monomer contacting a large basic patch on the other monomer to form a functional active site.
Probab=99.17 E-value=4.8e-11 Score=102.08 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=29.6
Q ss_pred HHHHHHhhCCC---CCccccchhhhccHHHHHhhhHHHHhhh
Q 023627 52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKYCATVLFLES 90 (279)
Q Consensus 52 LatLA~~Fg~~---~~~HRALdDar~t~dVl~~catvlllE~ 90 (279)
|++|+++||++ ...||||+||.+|.++|.+ ++++
T Consensus 152 L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~-----l~~~ 188 (189)
T cd06134 152 LAKACQAAGIEFDNKEAHSALYDTQKTAELFCK-----IVNR 188 (189)
T ss_pred HHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHH-----HHHh
Confidence 78888999997 3689999999999999999 6654
No 23
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.16 E-value=3.6e-11 Score=123.64 Aligned_cols=127 Identities=18% Similarity=0.205 Sum_probs=91.2
Q ss_pred CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------
Q 023627 4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------- 51 (279)
Q Consensus 4 ~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------- 51 (279)
......||+||+||||.++ . ++|||||||+|..+++ +++|++|
T Consensus 3 ~~~~~~~vvvD~ETTGl~~-~--d~IIeIgaV~v~~g~i--~~~f~~lv~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~ 77 (820)
T PRK07246 3 QKKLRKYAVVDLEATGAGP-N--ASIIQVGIVIIEGGEI--IDSYTTDVNPHEPLDEHIKHLTGITDQQLAQAPDFSQVA 77 (820)
T ss_pred cccCCCEEEEEEecCCcCC-C--CeEEEEEEEEEECCEE--EEEEEEEeCcCCCCCHhHhhcCCCCHHHHhcCCCHHHHH
Confidence 3445789999999999985 2 7999999999999988 5788877
Q ss_pred ---------------------------------------------------------HHHHHHhhCCC-CCccccchhhh
Q 023627 52 ---------------------------------------------------------LASLATYFGLG-QQTHRSLDDVR 73 (279)
Q Consensus 52 ---------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar 73 (279)
|.+|+++||++ .+.||||+||+
T Consensus 78 ~~~~~~l~~~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~la~~~~p~~~~~~L~~L~~~lgl~~~~~H~Al~DA~ 157 (820)
T PRK07246 78 RHIYDLIEDCIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVELAQVFFPTLEKYSLSHLSRELNIDLADAHTAIADAR 157 (820)
T ss_pred HHHHHHhCCCEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHHHHHHHhCCCCCCCHHHHHHHcCCCCCCCCCHHHHHH
Confidence 99999999999 78899999999
Q ss_pred ccHHHHHhhhHHHHhhhc--cC----cccccCc-ccC-c------c--ccCCCCCCCCeeeecCCCccc-ccCcceeeec
Q 023627 74 MNLEVLKYCATVLFLESG--LP----DIFTVNR-WEM-C------S--AASVSEGSSGYARFMEPDELY-CSRLKIRYGI 136 (279)
Q Consensus 74 ~t~dVl~~catvlllE~~--~~----~~l~~~~-~~~-p------~--a~~lp~~~pGvy~F~~p~dLy-gt~~~vR~rV 136 (279)
+|.++|.. ++++. +| ++|.... ... + . ....+ ..|+.|.|.+.-.|+ +.....+.++
T Consensus 158 ata~L~~~-----l~~~l~~l~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~l 231 (820)
T PRK07246 158 ATAELFLK-----LLQKIESLPKECLERLLEYADSLLFESYLVIEEALANAKP-YSSPDYIKVQGIVLKKTAASLKPRKL 231 (820)
T ss_pred HHHHHHHH-----HHHHHhhcCchhHHHHHHHHhhccccHHHHHHHHHHhcCC-CCCCceEEecCeeeecccccccccch
Confidence 99999999 56554 23 3222221 110 1 0 11222 467778877755566 6555555566
Q ss_pred ccccc
Q 023627 137 STRFV 141 (279)
Q Consensus 137 rsyFt 141 (279)
+++|.
T Consensus 232 ~~~F~ 236 (820)
T PRK07246 232 SQDFS 236 (820)
T ss_pred hhcCc
Confidence 66553
No 24
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=99.15 E-value=5.4e-11 Score=91.87 Aligned_cols=38 Identities=34% Similarity=0.455 Sum_probs=30.8
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL 51 (279)
||||+||||+++.. .+|+|+|||++.++ +.++++|+.+
T Consensus 1 v~~D~Ettg~~~~~--~~iiei~~v~~~~~-~~~~~~~~~~ 38 (159)
T cd06127 1 VVFDTETTGLDPKK--DRIIEIGAVKVDGG-IEIVERFETL 38 (159)
T ss_pred CeEEeeCCCcCCCC--CeEEEEEEEEEECC-cChhhhhhee
Confidence 68999999998744 89999999999987 3345666655
No 25
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.14 E-value=5.7e-11 Score=108.98 Aligned_cols=74 Identities=19% Similarity=0.239 Sum_probs=62.9
Q ss_pred eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------------
Q 023627 9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------- 51 (279)
Q Consensus 9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------- 51 (279)
+||+||+|||++. +.+|+|+|||+|..+.+ +++|++|
T Consensus 2 ~~vviD~ETTg~~----~d~IieIgav~v~~g~i--~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~~ 75 (309)
T PRK06195 2 NFVAIDFETANEK----RNSPCSIGIVVVKDGEI--VEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKIK 75 (309)
T ss_pred cEEEEEEeCCCCC----CCceEEEEEEEEECCEE--EEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHHH
Confidence 6999999999763 37899999999999887 4556666
Q ss_pred ------------------------------------------------------HHHHHHhhCCCCCccccchhhhccHH
Q 023627 52 ------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNLE 77 (279)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~d 77 (279)
|.+|+.+||+...+||||+||++|.+
T Consensus 76 ~fl~~~~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~idT~~lar~l~~~~~~~~L~~L~~~~gi~~~~H~Al~DA~ata~ 155 (309)
T PRK06195 76 HYFNNNLVIAHNASFDISVLRKTLELYNIPMPSFEYICTMKLAKNFYSNIDNARLNTVNNFLGYEFKHHDALADAMACSN 155 (309)
T ss_pred HHhCCCEEEEECcHHHHHHHHHHHHHhCCCCCCCCEEEHHHHHHHHcCCCCcCCHHHHHHHcCCCCcccCCHHHHHHHHH
Confidence 89999999999679999999999999
Q ss_pred HHHhhhHHHHhhhccC
Q 023627 78 VLKYCATVLFLESGLP 93 (279)
Q Consensus 78 Vl~~catvlllE~~~~ 93 (279)
||.. ++++...
T Consensus 156 l~~~-----l~~~~~~ 166 (309)
T PRK06195 156 ILLN-----ISKELNS 166 (309)
T ss_pred HHHH-----HHHHhcc
Confidence 9998 6666544
No 26
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=99.13 E-value=6.9e-11 Score=104.45 Aligned_cols=70 Identities=26% Similarity=0.339 Sum_probs=60.1
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------------
Q 023627 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------- 51 (279)
Q Consensus 10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------------- 51 (279)
+|+||+||||+++..+ .+|||||||++..+.+. .++|+++
T Consensus 2 ~vvlD~ETTGl~p~~~-d~IIEIgav~~~~~~~~-~~~f~~~i~P~~~i~~~a~~vhGIt~e~l~~~p~f~ev~~~f~~f 79 (225)
T TIGR01406 2 QIILDTETTGLDPKGG-HRIVEIGAVELVNRMLT-GDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDF 79 (225)
T ss_pred EEEEEeeCCCcCCCCC-CeEEEEEEEEEECCcEe-cceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHH
Confidence 7999999999998753 89999999999877652 3567666
Q ss_pred -------------------------------------------------------HHHHHHhhCCCC---Cccccchhhh
Q 023627 52 -------------------------------------------------------LASLATYFGLGQ---QTHRSLDDVR 73 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~~---~~HRALdDar 73 (279)
|.+|+.+||++. +.||||+||+
T Consensus 80 i~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~~L~~~~gi~~~~r~~H~Al~DA~ 159 (225)
T TIGR01406 80 IGGSELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAMARERFPGQRNSLDALCKRFKVDNSHRTLHGALLDAH 159 (225)
T ss_pred hCCCEEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHHHHHHcCCCCCCHHHHHHhcCCCCCCCCCcCHHHHHH
Confidence 899999999982 4699999999
Q ss_pred ccHHHHHh
Q 023627 74 MNLEVLKY 81 (279)
Q Consensus 74 ~t~dVl~~ 81 (279)
++.+|+..
T Consensus 160 ~~a~v~~~ 167 (225)
T TIGR01406 160 LLAEVYLA 167 (225)
T ss_pred HHHHHHHH
Confidence 99999998
No 27
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.13 E-value=9.8e-11 Score=108.19 Aligned_cols=74 Identities=27% Similarity=0.280 Sum_probs=62.3
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEec---Ccee-eccchHHH-------------------------------
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCP---KTLE-ELQPYSTL------------------------------- 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp---~~l~-e~~sf~TL------------------------------- 51 (279)
...+|+||+||||.++.. ++|||||||+|.. |.+. .+++|++|
T Consensus 36 ~~~~vvlD~ETTGLd~~~--d~IIEIg~V~v~~~~~g~i~~v~~~~~~lv~P~~~I~~~~t~IhGIt~e~v~~~~~~~~~ 113 (294)
T PRK09182 36 VRLGVILDTETTGLDPRK--DEIIEIGMVAFEYDDDGRIGDVLDTFGGLQQPSRPIPPEITRLTGITDEMVAGQTIDPAA 113 (294)
T ss_pred CCeEEEEEeeCCCCCCCC--CeEEEEEEEEEEecCCCceeeeeeEEEEEeCCCCCCCHHHHHhcCCCHHHHhcCCCcHHH
Confidence 356899999999999876 8999999999983 4442 34567666
Q ss_pred -----------------------------------------------------HHHHHHhhCCCCCccccchhhhccHHH
Q 023627 52 -----------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNLEV 78 (279)
Q Consensus 52 -----------------------------------------------------LatLA~~Fg~~~~~HRALdDar~t~dV 78 (279)
|.+|+.+||.....||||+||++|++|
T Consensus 114 l~~fl~~~~vlVAHNA~FD~~fL~~~~~~~~~~~~~ct~~~i~~~~~~~~~~kL~~La~~~g~~~~aHrAl~Da~Ata~l 193 (294)
T PRK09182 114 VDALIAPADLIIAHNAGFDRPFLERFSPVFATKPWACSVSEIDWSARGFEGTKLGYLAGQAGFFHEGHRAVDDCQALLEL 193 (294)
T ss_pred HHHHhcCCCEEEEeCHHHHHHHHHHHHHhccCCcccccHHHHhhccccCCCCCHHHHHHHcCCCCCCcChHHHHHHHHHH
Confidence 899999999668899999999999999
Q ss_pred HHhh
Q 023627 79 LKYC 82 (279)
Q Consensus 79 l~~c 82 (279)
|..|
T Consensus 194 l~~~ 197 (294)
T PRK09182 194 LARP 197 (294)
T ss_pred HHHH
Confidence 9983
No 28
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.13 E-value=6.1e-11 Score=122.93 Aligned_cols=76 Identities=25% Similarity=0.368 Sum_probs=67.8
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH------------------------------------
Q 023627 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------ 51 (279)
Q Consensus 8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------ 51 (279)
..||+||+||||.++..+ .+|||||||+|..|++ +++|+++
T Consensus 3 ~~~vvvD~ETTG~~p~~~-d~IIeigav~v~~~~i--~~~f~~~v~P~~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~l~ 79 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKG-DKIIQIAAVVVEDGEI--LERFSSFVNPERPIPPFITELTGISEEMVKQAPLFEDVAPEIV 79 (928)
T ss_pred CCEEEEEEeCCCCCCCCC-CcEEEEEEEEEECCEE--EEEEEEEECcCCCCCHHHhhcCCCCHHHHhcCCCHHHHHHHHH
Confidence 469999999999987753 8999999999999988 5688888
Q ss_pred ------------------------------------------------------HHHHHHhhCCC-CCccccchhhhccH
Q 023627 52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL 76 (279)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t~ 76 (279)
|++||++||++ ...||||+||++|+
T Consensus 80 ~~l~~~~~VaHN~~FD~~fL~~~~~~~g~~~~~~~~iDt~~la~~~~p~~~~~~L~~l~~~l~i~~~~~H~Al~DA~ata 159 (928)
T PRK08074 80 ELLEGAYFVAHNVHFDLNFLNEELERAGYTEIHCPKLDTVELARILLPTAESYKLRDLSEELGLEHDQPHRADSDAEVTA 159 (928)
T ss_pred HHhCCCeEEEEChHHHHHHHHHHHHHcCCCCCCCCeeeHHHHHHHhcCCCCCCCHHHHHHhCCCCCCCCCChHHHHHHHH
Confidence 89999999999 88899999999999
Q ss_pred HHHHhhhHHHHhhhc
Q 023627 77 EVLKYCATVLFLESG 91 (279)
Q Consensus 77 dVl~~catvlllE~~ 91 (279)
++|.+ ++++.
T Consensus 160 ~l~~~-----l~~~~ 169 (928)
T PRK08074 160 ELFLQ-----LLNKL 169 (928)
T ss_pred HHHHH-----HHHHH
Confidence 99999 55554
No 29
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=99.13 E-value=9.7e-11 Score=98.75 Aligned_cols=37 Identities=19% Similarity=0.147 Sum_probs=29.5
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccch
Q 023627 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPY 48 (279)
Q Consensus 10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf 48 (279)
+++||+||||.+|.+ .+|||+|||++.++.....++|
T Consensus 1 lv~iD~ETTGl~p~~--d~IieIgaV~~~~~~~~i~~~f 37 (173)
T cd06135 1 LVWIDLEMTGLDPEK--DRILEIACIITDGDLNIIAEGP 37 (173)
T ss_pred CEEEEEecCCCCCCC--CeeEEEEEEEEeCCCceecCce
Confidence 589999999999865 8999999999998643323333
No 30
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.10 E-value=2.2e-10 Score=101.04 Aligned_cols=40 Identities=30% Similarity=0.411 Sum_probs=34.4
Q ss_pred HHHHHHhhCCC-CCccccchhhhccHHHHHhhhHHHHhhhccCccc
Q 023627 52 LASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLESGLPDIF 96 (279)
Q Consensus 52 LatLA~~Fg~~-~~~HRALdDar~t~dVl~~catvlllE~~~~~~l 96 (279)
|.+|+.+||+. ...|||++||.+|.+||.+ ++++...+++
T Consensus 131 L~~l~~~~~~~~~~aH~Al~Da~~t~~vl~~-----l~~~~~~~~l 171 (232)
T PRK06309 131 LQYLRQVYGFEENQAHRALDDVITLHRVFSA-----LVGDLSPQQV 171 (232)
T ss_pred HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHH-----HHHHHHHhhH
Confidence 88899999999 8899999999999999999 6776655433
No 31
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=99.09 E-value=1.1e-10 Score=125.13 Aligned_cols=73 Identities=26% Similarity=0.378 Sum_probs=63.5
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH----------------------------------
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL---------------------------------- 51 (279)
++.+||+||+||||+++.. .+|||||||++..+.++ ++|++|
T Consensus 188 ~~~~~VVfDiETTGL~~~~--d~IIEIGAVkv~~g~ii--d~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~ 263 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQY--DEIIEFGAVKVKNGRII--DKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEK 263 (1213)
T ss_pred cCCcEEEEEeEecCCCCCC--CeEEEEEEEEEECCeEE--EEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHH
Confidence 3568999999999998865 89999999999998773 444443
Q ss_pred --------------------------------------------------------HHHHHHhhCCC-CCccccchhhhc
Q 023627 52 --------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRM 74 (279)
Q Consensus 52 --------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~ 74 (279)
|++||.+||+. .+.|||++||++
T Consensus 264 f~~fl~~~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~lar~l~p~~k~~kL~~Lak~lgi~~~~~HrAl~DA~a 343 (1213)
T TIGR01405 264 FKEFFKDSILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLELARALNPEYKSHRLGNICKKLGVDLDDHHRADYDAEA 343 (1213)
T ss_pred HHHHhCCCeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHHHHHHhccCCCCCHHHHHHHcCCCCCCCcCHHHHHHH
Confidence 89999999999 889999999999
Q ss_pred cHHHHHhh
Q 023627 75 NLEVLKYC 82 (279)
Q Consensus 75 t~dVl~~c 82 (279)
|++||..+
T Consensus 344 Ta~I~~~l 351 (1213)
T TIGR01405 344 TAKVFKVM 351 (1213)
T ss_pred HHHHHHHH
Confidence 99999993
No 32
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.09 E-value=7e-11 Score=126.08 Aligned_cols=81 Identities=22% Similarity=0.322 Sum_probs=74.7
Q ss_pred CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------
Q 023627 3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------- 51 (279)
Q Consensus 3 ~~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------- 51 (279)
+.-+++++|+||+||||+++.- ..||||||+++..|++ ++.|+.+
T Consensus 416 ~~l~datyVVfDiETTGLs~~~--d~iIE~aAvKikng~i--Id~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~v 491 (1444)
T COG2176 416 QKLDDATYVVFDIETTGLSPVY--DEIIEIAAVKIKNGRI--IDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEV 491 (1444)
T ss_pred cccccccEEEEEeecCCcCccc--chhhhheeeeeeCCcc--hHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHH
Confidence 4456789999999999999988 8999999999999999 7899998
Q ss_pred -----------------------------------------------------------HHHHHHhhCCC-CCccccchh
Q 023627 52 -----------------------------------------------------------LASLATYFGLG-QQTHRSLDD 71 (279)
Q Consensus 52 -----------------------------------------------------------LatLA~~Fg~~-~~~HRALdD 71 (279)
|++|+.-||+. .++|||.+|
T Consensus 492 L~kf~~~~~d~IlVAHNasFD~gFl~~~~~k~~~~~~~~pvIDTL~lar~L~P~~ksh~Lg~l~kk~~v~le~hHRA~yD 571 (1444)
T COG2176 492 LEKFREFIGDSILVAHNASFDMGFLNTNYEKYGLEPLTNPVIDTLELARALNPEFKSHRLGTLCKKLGVELERHHRADYD 571 (1444)
T ss_pred HHHHHHHhcCcEEEeccCccchhHHHHHHHHhCCccccCchhhHHHHHHHhChhhhhcchHHHHHHhCccHHHhhhhhhh
Confidence 99999999999 999999999
Q ss_pred hhccHHHHHhhhHHHHhhhcc
Q 023627 72 VRMNLEVLKYCATVLFLESGL 92 (279)
Q Consensus 72 ar~t~dVl~~catvlllE~~~ 92 (279)
+.+|..||.. |++.+-
T Consensus 572 aeat~~vf~~-----f~~~~k 587 (1444)
T COG2176 572 AEATAKVFFV-----FLKDLK 587 (1444)
T ss_pred HHHHHHHHHH-----HHHHHH
Confidence 9999999999 777653
No 33
>TIGR01407 dinG_rel DnaQ family exonuclease/DinG family helicase, putative. This model represents a family of proteins in Gram-positive bacteria. The N-terminal region of about 200 amino acids resembles the epsilon subunit of E. coli DNA polymerase III and the homologous region of the Gram-positive type DNA polymerase III alpha subunit. The epsilon subunit contains an exonuclease domain. The remainder of this protein family resembles a predicted ATP-dependent helicase, the DNA damage-inducible protein DinG of E. coli.
Probab=99.09 E-value=1.2e-10 Score=119.21 Aligned_cols=70 Identities=24% Similarity=0.328 Sum_probs=63.3
Q ss_pred eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-------------------------------------
Q 023627 9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------- 51 (279)
Q Consensus 9 e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------- 51 (279)
+||+||+||||+++.. ++|||||||+|..|++ ++.|+++
T Consensus 1 ~~vvvD~ETTG~~~~~--~~IIeig~v~v~~~~i--~~~f~~~v~P~~~i~~~~~~ltGIt~e~l~~ap~~~ev~~~l~~ 76 (850)
T TIGR01407 1 RYAVVDLETTGTQLSF--DKIIQIGIVVVEDGEI--VDTFHTDVNPNEPIPPFIQELTGISDNMLQQAPYFSQVAQEIYD 76 (850)
T ss_pred CEEEEEEECCCCCCCC--CeEEEEEEEEEECCEE--EEEEEEEeCCCCCCChhhhhhcCcCHHHHhCCCCHHHHHHHHHH
Confidence 4899999999998765 8999999999999887 4677776
Q ss_pred -----------------------------------------------------HHHHHHhhCCC-CCccccchhhhccHH
Q 023627 52 -----------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNLE 77 (279)
Q Consensus 52 -----------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t~d 77 (279)
|.+|+++||+. ...||||+||++|++
T Consensus 77 ~l~~~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~l~~~~~p~~~~~~L~~l~~~~gi~~~~~H~Al~DA~ata~ 156 (850)
T TIGR01407 77 LLEDGIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVELAQIFFPTEESYQLSELSEALGLTHENPHRADSDAQATAE 156 (850)
T ss_pred HhCCCEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHHHHHHhcCCCCCCCHHHHHHHCCCCCCCCCChHHHHHHHHH
Confidence 99999999999 788999999999999
Q ss_pred HHHhh
Q 023627 78 VLKYC 82 (279)
Q Consensus 78 Vl~~c 82 (279)
+|.++
T Consensus 157 l~~~l 161 (850)
T TIGR01407 157 LLLLL 161 (850)
T ss_pred HHHHH
Confidence 99994
No 34
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.07 E-value=2.5e-10 Score=102.67 Aligned_cols=43 Identities=21% Similarity=0.227 Sum_probs=34.6
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL 51 (279)
+-.+|+||+||||+++.. +.+|||||||++..+++. .++|+++
T Consensus 3 ~~r~vvlDtETTGldp~~-~drIIEIGaV~v~~~~~~-~~~f~~~ 45 (240)
T PRK05711 3 IMRQIVLDTETTGLNQRE-GHRIIEIGAVELINRRLT-GRNFHVY 45 (240)
T ss_pred CCeEEEEEeeCCCcCCCC-CCeEEEEEEEEEECCEEe-ccEEEEE
Confidence 346899999999999873 389999999999988763 2466655
No 35
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.04 E-value=2.7e-10 Score=100.95 Aligned_cols=70 Identities=23% Similarity=0.282 Sum_probs=59.3
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH--------------------------------------
Q 023627 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------- 51 (279)
Q Consensus 10 ~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL-------------------------------------- 51 (279)
+++||+||||.++ .|||+||++|..+++ +++|++|
T Consensus 2 ~~vlD~ETTGl~~-----~IieIg~v~v~~~~i--~~~~~~lv~P~~~i~~~~~~ihgIt~e~v~~ap~~~ev~~~~~~~ 74 (219)
T PRK07983 2 LRVIDTETCGLQG-----GIVEIASVDVIDGKI--VNPMSHLVRPDRPISPQAMAIHRITEAMVADKPWIEDVIPHYYGS 74 (219)
T ss_pred eEEEEEECCCCCC-----CCEEEEEEEEECCEE--EEEEEEEECcCCCCCHHHhhcCCCCHHHHcCCCCHHHHHHHHcCC
Confidence 7899999999964 299999999998877 4567666
Q ss_pred ---------------------------------------HHHHHHhhCCC------CCccccchhhhccHHHHHhhhHHH
Q 023627 52 ---------------------------------------LASLATYFGLG------QQTHRSLDDVRMNLEVLKYCATVL 86 (279)
Q Consensus 52 ---------------------------------------LatLA~~Fg~~------~~~HRALdDar~t~dVl~~catvl 86 (279)
+.+|+.+||++ ...||||+||.+|.+||.+
T Consensus 75 ~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~----- 149 (219)
T PRK07983 75 EWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLID----- 149 (219)
T ss_pred CEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHH-----
Confidence 88899999986 3599999999999999999
Q ss_pred Hhhhc
Q 023627 87 FLESG 91 (279)
Q Consensus 87 llE~~ 91 (279)
+++..
T Consensus 150 l~~~~ 154 (219)
T PRK07983 150 IMNTS 154 (219)
T ss_pred HHHHc
Confidence 66544
No 36
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=99.03 E-value=1.9e-10 Score=97.37 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=29.0
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecC-ceeeccchHHH
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPK-TLEELQPYSTL 51 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~-~l~e~~sf~TL 51 (279)
+|||+||||+++.. .+|||+|||+|.++ .. +++|+++
T Consensus 1 ~~~D~ETTGl~~~~--d~Iieig~v~v~~~~~~--~~~~~~~ 38 (183)
T cd06138 1 LFYDYETFGLNPSF--DQILQFAAIRTDENFNE--IEPFNIF 38 (183)
T ss_pred CEEEeecCCCCCCC--CceEEEEEEEECCCCCC--ccceeEE
Confidence 58999999999865 79999999999876 33 2455544
No 37
>PRK05359 oligoribonuclease; Provisional
Probab=98.94 E-value=2e-09 Score=92.48 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=28.4
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~ 40 (279)
+..||+||+||||++|.. .+|||+|||++..+
T Consensus 2 ~~~~vvlD~ETTGLdp~~--d~IieIgaV~~~~~ 33 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER--DRIIEIATIVTDAD 33 (181)
T ss_pred CCcEEEEEeecCCCCCCC--CeEEEEEEEEEcCC
Confidence 457999999999999976 79999999998665
No 38
>PRK11779 sbcB exonuclease I; Provisional
Probab=98.86 E-value=4.6e-09 Score=103.32 Aligned_cols=35 Identities=20% Similarity=0.086 Sum_probs=30.5
Q ss_pred CCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 023627 5 QDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKT 41 (279)
Q Consensus 5 ~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~ 41 (279)
..+.+|||||+||||.+|.. .+|||||||+|..+.
T Consensus 3 ~~~~~fvv~D~ETTGLdP~~--DrIIeiAaVrvd~~~ 37 (476)
T PRK11779 3 KMQPTFLWHDYETFGANPAL--DRPAQFAGIRTDADL 37 (476)
T ss_pred CCCCcEEEEEEECCCCCCCC--CeeEEEEEEEEeCCC
Confidence 34678999999999999976 899999999998763
No 39
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=98.83 E-value=5.2e-09 Score=90.55 Aligned_cols=71 Identities=30% Similarity=0.386 Sum_probs=63.2
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH------------------------------------
Q 023627 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------ 51 (279)
Q Consensus 8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL------------------------------------ 51 (279)
..+|+||+||||.++.+ .+|||+|||.+..+.+++ .+|+++
T Consensus 13 ~~~vv~D~ETtg~~~~~--~~iieIgav~~~~~~i~~-~~~~~~v~P~~~i~~~~~~i~git~e~l~~~p~~~~v~~~~~ 89 (243)
T COG0847 13 TRFVVIDLETTGLNPKK--DRIIEIGAVTLEDGRIVE-RSFHTLVNPERPIPPEIFKIHGITDEMLADAPKFAEVLPEFL 89 (243)
T ss_pred CcEEEEecccCCCCCCC--CceEEEEeEEEECCeeec-ceeEEEECCCCCCChhhhhhcCCCHHHHhcCCCHHHHHHHHH
Confidence 47899999999999844 899999999999999854 346666
Q ss_pred -------------------------------------------------------HHHHHHhhCCC---CCccccchhhh
Q 023627 52 -------------------------------------------------------LASLATYFGLG---QQTHRSLDDVR 73 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~---~~~HRALdDar 73 (279)
|..|+.++|+. ...||||.||.
T Consensus 90 ~~i~~~~~~Vahna~fD~~fl~~~~~~~~~~~~~~~~~~t~~~~r~~~~~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~ 169 (243)
T COG0847 90 DFIGGLRLLVAHNAAFDVGFLRVESERLGIEIPGDPVLDTLALARRHFPGFDRSSLDALAERLGIDRNPFHPHRALFDAL 169 (243)
T ss_pred HHHCCCCeEEEEchhhcHHHHHHHHHHcCCCcccCceehHHHHHHHHcCCCccchHHHHHHHcCCCcCCcCCcchHHHHH
Confidence 99999999999 57799999999
Q ss_pred ccHHHHHh
Q 023627 74 MNLEVLKY 81 (279)
Q Consensus 74 ~t~dVl~~ 81 (279)
++.+++..
T Consensus 170 ~~a~~~~~ 177 (243)
T COG0847 170 ALAELFLL 177 (243)
T ss_pred HHHHHHHH
Confidence 99999988
No 40
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=98.77 E-value=6.4e-09 Score=86.89 Aligned_cols=30 Identities=13% Similarity=0.135 Sum_probs=25.1
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~ 40 (279)
|+||+||||.+|.++...|+++++|.+..+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~ 30 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGD 30 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCC
Confidence 689999999998765689999999986444
No 41
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=98.68 E-value=1.1e-08 Score=111.51 Aligned_cols=71 Identities=25% Similarity=0.294 Sum_probs=60.5
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHH-----------------------------------
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TL----------------------------------- 51 (279)
+.++|+||+||||+++.. ..||||||+++..|.++ +.|+++
T Consensus 418 ~~~~VVfDLETTGL~~~~--deIIEIgAV~V~~G~ii--e~F~~~V~P~~~I~~~~~~LTGIT~e~L~~aps~~EaL~~f 493 (1437)
T PRK00448 418 DATYVVFDVETTGLSAVY--DEIIEIGAVKIKNGEII--DKFEFFIKPGHPLSAFTTELTGITDDMVKDAPSIEEVLPKF 493 (1437)
T ss_pred cCcEEEEEhhhcCCCCch--hhhheeeeEEEeCCeEe--eeEEEEECCCCCCCHHHHHHhCCCHHHHcCCCCHHHHHHHH
Confidence 457999999999999876 79999999999877653 222211
Q ss_pred -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 023627 52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN 75 (279)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t 75 (279)
|.+||.+||+. .++||||+||++|
T Consensus 494 ~~figg~vLVAHNa~FD~~fL~~~l~rlgl~~l~~~~IDTLelar~l~p~~k~~kL~~LAk~lGL~~~~~HrAl~DA~aT 573 (1437)
T PRK00448 494 KEFCGDSILVAHNASFDVGFINTNYEKLGLEKIKNPVIDTLELSRFLYPELKSHRLNTLAKKFGVELEHHHRADYDAEAT 573 (1437)
T ss_pred HHHhCCCEEEEeCccccHHHHHHHHHHcCCccccccceeHHHHHHHHcCccccccHHHHHHHcCCCCCCCcChHHHHHHH
Confidence 88999999999 8899999999999
Q ss_pred HHHHHh
Q 023627 76 LEVLKY 81 (279)
Q Consensus 76 ~dVl~~ 81 (279)
.+||..
T Consensus 574 a~lf~~ 579 (1437)
T PRK00448 574 AYLLIK 579 (1437)
T ss_pred HHHHHH
Confidence 999999
No 42
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.68 E-value=2.5e-08 Score=96.41 Aligned_cols=42 Identities=7% Similarity=0.185 Sum_probs=34.7
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeeccchHHH
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL 51 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp-~~l~e~~sf~TL 51 (279)
.+..||+||+||||+++.. .+|||||||++.+ |.+ +++|++|
T Consensus 44 ~~~~fVvlDiETTGLdp~~--drIIeIgAV~i~~~g~i--ve~f~tL 86 (377)
T PRK05601 44 EAAPFVAVSIQTSGIHPST--SRLITIDAVTLTADGEE--VEHFHAV 86 (377)
T ss_pred CCCCEEEEEEECCCCCCCC--CeEEEEEEEEEEcCCEE--EEEEEEE
Confidence 3467999999999999866 8999999999985 544 4677777
No 43
>PTZ00315 2'-phosphotransferase; Provisional
Probab=98.68 E-value=3e-08 Score=100.14 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=32.3
Q ss_pred ceEEEEEeecCCCCCCC-CceeEEEEeeEEEe--cCceeeccchHHH
Q 023627 8 FEIAFFDVETAFPNPPG-QRIAILEFGAILVC--PKTLEELQPYSTL 51 (279)
Q Consensus 8 ~e~vffDvETT~p~~~~-~~~~ilEfgAI~Vc--p~~l~e~~sf~TL 51 (279)
..|++||+|||++++.. ...+|||||||+|. .+++ ++.|++|
T Consensus 56 d~~IV~DlETTgl~~~~~~~dEIIEIGaV~Vd~~ng~I--i~~F~~y 100 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRIEDAEVIEFPMVLVDARTATP--VAEFQRY 100 (582)
T ss_pred CeEEEEEEecCCCCCCCCCCCceEEEEEEEEEccCCEE--EEEEEEE
Confidence 56999999999987643 24799999999996 4444 4566666
No 44
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=98.67 E-value=2.3e-08 Score=83.33 Aligned_cols=30 Identities=13% Similarity=0.076 Sum_probs=26.1
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTL 42 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l 42 (279)
|+||+||||.++.+ .+|+|+|||++..|++
T Consensus 1 v~lD~EttGl~~~~--d~ii~Ig~V~v~~g~i 30 (161)
T cd06137 1 VALDCEMVGLADGD--SEVVRISAVDVLTGEV 30 (161)
T ss_pred CEEEeeeeeEcCCC--CEEEEEEEEEcCCCeE
Confidence 68999999999865 8999999999976654
No 45
>cd06144 REX4_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 4, XPMC2, Interferon Stimulated Gene product of 20 kDa, and similar proteins. This subfamily is composed of RNA exonuclease 4 (REX4 or Rex4p), XPMC2, Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20), and similar proteins. REX4 is involved in pre-rRNA processing. It controls the ratio between the two forms of 5.8S rRNA in yeast. XPMC2 is a Xenopus gene which was identified through its ability to correct a mitotic defect in fission yeast. The human homolog of XPMC2 (hPMC2) may be involved in angiotensin II-induced adrenal cell cycle progression and cell proliferation. ISG20 is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. These proteins are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clus
Probab=98.56 E-value=6.7e-08 Score=79.74 Aligned_cols=29 Identities=31% Similarity=0.581 Sum_probs=25.0
Q ss_pred HHHHHHh-hCCC--CCccccchhhhccHHHHH
Q 023627 52 LASLATY-FGLG--QQTHRSLDDVRMNLEVLK 80 (279)
Q Consensus 52 LatLA~~-Fg~~--~~~HRALdDar~t~dVl~ 80 (279)
|++||.+ +|++ ...||||+||++|.++|+
T Consensus 121 L~~l~~~~lgi~~~~~~H~Al~DA~at~~l~~ 152 (152)
T cd06144 121 LKKLAKQLLGLDIQEGEHSSVEDARAAMRLYR 152 (152)
T ss_pred HHHHHHHHcCcccCCCCcCcHHHHHHHHHHhC
Confidence 7889986 6998 368999999999999874
No 46
>cd06145 REX1_like DEDDh 3'-5' exonuclease domain of RNA exonuclease 1, -3 and similar eukaryotic proteins. This subfamily is composed of RNA exonuclease 1 (REX1 or Rex1p), REX3 (or Rex3p), and similar eukaryotic proteins. In yeast, REX1 and REX3 are required for 5S rRNA and MRP (mitochondrial RNA processing) RNA maturation, respectively. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. REX1 is the major exonuclease responsible for pre-tRNA trail trimming and may also be involved in nuclear CCA turnover. REX proteins function in the processing and maturation of many RNA species, similar to the function of Escherichia coli RNase T.
Probab=98.08 E-value=3.2e-06 Score=70.11 Aligned_cols=29 Identities=38% Similarity=0.614 Sum_probs=23.9
Q ss_pred HHHHHHhh-CCC----CCccccchhhhccHHHHH
Q 023627 52 LASLATYF-GLG----QQTHRSLDDVRMNLEVLK 80 (279)
Q Consensus 52 LatLA~~F-g~~----~~~HRALdDar~t~dVl~ 80 (279)
|.+|+.+| |.. ..+||||+||++|.+|++
T Consensus 117 L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~~ 150 (150)
T cd06145 117 LKNLAKKYLGRDIQQGEGGHDSVEDARAALELVK 150 (150)
T ss_pred HHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHhC
Confidence 88999776 543 378999999999999874
No 47
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=97.97 E-value=3.5e-06 Score=84.87 Aligned_cols=66 Identities=8% Similarity=0.169 Sum_probs=54.2
Q ss_pred ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecc---------ccchHHHHHHHHHHHHhh
Q 023627 106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDA---------SQSLCTVLDACEVVAKKL 173 (279)
Q Consensus 106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdl---------a~~v~~Vl~~Cd~~aq~~ 173 (279)
...+| ..||||.|. +++ || |.+.|||.||++||+++..++|+..||.- +..+++.|-.|.-|-+-.
T Consensus 10 l~~lP-~~PGVYl~~-~~g~viYVGKAknLr~RV~sYF~~~~~~~K~~~lv~~i~~ie~i~t~sE~EALlLE~~LIK~~~ 87 (567)
T PRK14667 10 IEKAP-EEPGVYLFK-KKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLIQQYK 87 (567)
T ss_pred HHhCC-CCCeEEEEe-cCCeEEEeeCcHhHHHHHHHHcCCCCCChHHHHHHHhhCeEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 35688 999999999 777 99 99999999999999987788999989854 455667777777776543
No 48
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=97.96 E-value=6.2e-06 Score=74.25 Aligned_cols=45 Identities=22% Similarity=0.270 Sum_probs=36.4
Q ss_pred CceEEEEEeecCCCCCCCC--ceeEEEEeeEEEecCceeeccchHHH
Q 023627 7 RFEIAFFDVETAFPNPPGQ--RIAILEFGAILVCPKTLEELQPYSTL 51 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~--~~~ilEfgAI~Vcp~~l~e~~sf~TL 51 (279)
.+...++|+|.|.+...+. .+.|||++|.+|..---.+++.||..
T Consensus 3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~sy 49 (210)
T COG5018 3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSY 49 (210)
T ss_pred CceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHh
Confidence 3567899999999988765 78999999999876554567888876
No 49
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=97.90 E-value=1.5e-06 Score=88.15 Aligned_cols=66 Identities=14% Similarity=0.193 Sum_probs=53.3
Q ss_pred ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCC-CCccceeeeccccc---------hHHHHHHHHHHHHh
Q 023627 106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA-GRPRLSFVVDASQS---------LCTVLDACEVVAKK 172 (279)
Q Consensus 106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se-~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~ 172 (279)
...+| ..||||.|.+.++ || |.+.|||.||++||+++. .++|+..||.-..+ +++.|-.|.-|-+-
T Consensus 16 l~~lP-~~PGVYl~~d~~g~viYVGKAknLr~RV~sYF~~~~~~~~K~~~lv~~i~~ie~i~t~sE~EALlLE~~LIk~~ 94 (621)
T PRK14671 16 LASLP-TSPGVYQFKNAAGRVIYVGKAKNLRNRVRSYFRNSRQLSGKTLVLVGHIADLEVIITSSEVEALILENNLIKEL 94 (621)
T ss_pred HHhCC-CCCeEEEEECCCCCEEEeecchhHHHHHHHHcCCCCCCChHHHHHHHhhceEEEEEeCCHHHHHHHHHHHHHHh
Confidence 45688 9999999999988 99 999999999999999765 48898888776554 55666666666553
No 50
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=97.89 E-value=1.6e-06 Score=86.49 Aligned_cols=65 Identities=14% Similarity=0.296 Sum_probs=53.3
Q ss_pred cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecccc---------chHHHHHHHHHHHHh
Q 023627 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQ---------SLCTVLDACEVVAKK 172 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~---------~v~~Vl~~Cd~~aq~ 172 (279)
..+| ..||||.|.+.++ || |.+.|||.||++||+++..++|...||.-.. .+++.|-.|.-|-+-
T Consensus 5 ~~lP-~~PGVYl~~d~~g~vIYVGKAknLr~RV~sYF~~~~~~~K~~~lv~~i~~ie~ivt~sE~eALlLE~~LIK~~ 81 (519)
T PRK12306 5 STIP-TNPGCYLYKDEEGTIIYVGKAKNLKKRVSSYFQKKDHDPKTQSLVKAIRDIEFIVTDNEVEALLLENTLIKKH 81 (519)
T ss_pred hHCC-CCCeEEEEECCCCCEEEeccchhHHHHHHHhCCCCCCChHHHHHHHHhcEEEEEEeCCHHHHHHHHHHHHHHh
Confidence 4578 8999999999988 99 9999999999999998777889888876554 456667677666554
No 51
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=97.86 E-value=1.9e-06 Score=88.84 Aligned_cols=65 Identities=12% Similarity=0.231 Sum_probs=53.9
Q ss_pred cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCC-CCccceeeeccccc---------hHHHHHHHHHHHHh
Q 023627 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA-GRPRLSFVVDASQS---------LCTVLDACEVVAKK 172 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se-~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~ 172 (279)
..+| ..||||.|.+.++ || |.+.|||.||++||+++. .++|+..||.-..+ +++.|-.|.-|-+-
T Consensus 7 ~~LP-~~PGVYlfkD~~G~VIYVGKAKNLR~RV~SYF~~~~~~~~K~~~Lv~~i~~Ie~ivT~sE~EALLLE~~LIK~~ 84 (694)
T PRK14666 7 STIP-LTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSALTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKH 84 (694)
T ss_pred hhCC-CCCeEEEEECCCCCEEEeeCcHhHHHHHHHHcCCCCCCChHHHHHHHhcCeeEEEEeCCHHHHHHHHHHHHHHh
Confidence 4688 8999999999988 99 999999999999999866 68999888876554 55667777766654
No 52
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=97.86 E-value=1.8e-06 Score=87.89 Aligned_cols=55 Identities=11% Similarity=0.251 Sum_probs=47.0
Q ss_pred cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCC-CCCccceeeeccccchHHH
Q 023627 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQ-AGRPRLSFVVDASQSLCTV 162 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~s-e~RpR~~~mVdla~~v~~V 162 (279)
..+| ..||||.|.+.++ || |.+.|||.||++||+++ ..++|+..||.-..+++-|
T Consensus 8 ~~lP-~~PGVYl~~d~~g~viYVGKAknLr~RV~sYF~~~~~~~~K~~~lv~~i~~ie~i 66 (624)
T PRK14669 8 RTLP-TSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFSEDKLGNIKTGSLIREAVDIDYI 66 (624)
T ss_pred HhCC-CCCeEEEEECCCCCEEEeeCchhHHHHHHHHhccCccCChHHHHHHHhhceEEEE
Confidence 4578 8999999999988 99 99999999999999964 5789999998876665443
No 53
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=97.85 E-value=2.5e-06 Score=85.98 Aligned_cols=67 Identities=13% Similarity=0.218 Sum_probs=54.4
Q ss_pred cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccc---------cchHHHHHHHHHHHHhhh
Q 023627 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDAS---------QSLCTVLDACEVVAKKLF 174 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla---------~~v~~Vl~~Cd~~aq~~~ 174 (279)
..+| ..||||.|.+.++ || |.+.|||.||++||+.+..++|...||.-. ..+++.|-.|.-|-+-..
T Consensus 9 ~~lP-~~PGVY~~~d~~g~viYVGKAknLr~Rv~sYF~~~~~~~k~~~lv~~i~~ie~i~t~sE~eALlLE~~LIK~~~P 87 (598)
T PRK00558 9 KTLP-DSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKKYKP 87 (598)
T ss_pred hhCC-CCCeEEEEECCCCCEEEecCchhHHHHHHhhCCCCCcChHHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHhCC
Confidence 4578 8999999999988 99 999999999999999877778887777544 455677777777766543
No 54
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=97.75 E-value=2.2e-06 Score=86.70 Aligned_cols=55 Identities=16% Similarity=0.295 Sum_probs=50.0
Q ss_pred cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccchHHHH
Q 023627 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVL 163 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~v~~Vl 163 (279)
..+| +.||||.|.+.++ || |.+.+||.||++||.++.. +|+..||.-+..++.|+
T Consensus 10 ~~lP-~~PGvY~~~d~~g~VlYVGKAknLr~Rv~sYF~~~~~-~kt~~lv~~i~~iE~iv 67 (581)
T COG0322 10 KNLP-HSPGVYLMKDENGTVLYVGKAKNLRKRVSSYFRGRLD-PKTAALVENIADIEYIV 67 (581)
T ss_pred HhCC-CCCeeEEEECCCCCEEEEeehhhHHHHHHHhhcCCCc-HHHHHHHHhhcceeEEE
Confidence 4578 9999999999998 99 9999999999999998888 99999999888877665
No 55
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=97.70 E-value=5.1e-06 Score=83.75 Aligned_cols=64 Identities=9% Similarity=0.192 Sum_probs=51.3
Q ss_pred cCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHh
Q 023627 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKK 172 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq~ 172 (279)
..+| ..||||.|.+..+ || |.+.|||.||++||+.+ .++|+..||.-..+ +++.|-.|.-|-+-
T Consensus 6 ~~lP-~~PGVYl~~d~~g~viYVGKAknLr~Rv~sYF~~~-~~~K~~~mv~~i~~ie~ivt~sE~eALlLE~~lIK~~ 81 (574)
T TIGR00194 6 KNLP-DKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQY 81 (574)
T ss_pred hhCC-CCCeEEEEECCCCCEEEEecHHHHHHHHHHhcCCC-CCchHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHh
Confidence 4578 8999999999988 99 99999999999999976 48888888776554 45556666666554
No 56
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=97.65 E-value=2e-05 Score=79.57 Aligned_cols=64 Identities=16% Similarity=0.255 Sum_probs=50.2
Q ss_pred ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccc---------cchHHHHHHHHHHHHhh
Q 023627 106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDAS---------QSLCTVLDACEVVAKKL 173 (279)
Q Consensus 106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla---------~~v~~Vl~~Cd~~aq~~ 173 (279)
...+| ..||||.|.+ ++ || |.+.|||.||++||+. ..+|...||.-. ..+++.|-.|.-|-+-.
T Consensus 10 ~~~LP-~~PGVYl~~d-~g~viYVGKAknLr~RV~sYF~~--~~~k~~~lv~~i~~ie~i~t~sE~eALlLE~~LIK~~~ 85 (577)
T PRK14668 10 AAELP-REPGVYQFVA-GGTVLYVGKAVDLRDRVRSYADP--RSERIRRMVERADDIDFAVTDTETQALLLEANLIKRHQ 85 (577)
T ss_pred HHhCC-CCCEEEEEcC-CCeEEEeeCcHhHHHHHHHHcCC--CChHHHHHHHhhCeEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 45688 9999999998 66 99 9999999999999975 356787777644 45667777777776543
No 57
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=97.56 E-value=1.1e-05 Score=83.33 Aligned_cols=65 Identities=15% Similarity=0.244 Sum_probs=51.0
Q ss_pred ccCCCCCCCCeeeecCCCc--cc-ccCcceeeeccccccCCCCCccceeeecccc---------chHHHHHHHHHHHHh
Q 023627 106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQ---------SLCTVLDACEVVAKK 172 (279)
Q Consensus 106 a~~lp~~~pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~---------~v~~Vl~~Cd~~aq~ 172 (279)
...+| ..||||.|.+.++ || |.+.|||.||++||+.. .++|...||.-.. .+++.|-.|.-|-+-
T Consensus 15 ~~~LP-~~PGVYlfkd~~G~VLYVGKAKNLR~RV~SYF~~~-~~~K~~~Lv~~i~~Ie~ivT~sE~EALLLE~~LIK~~ 91 (691)
T PRK14672 15 ALSAP-STSGVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCR-HDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKH 91 (691)
T ss_pred HHhCC-CCCeEEEEECCCCCEEEeeCcHHHHHHHHHHcCCC-CCchHHHHHHhhCcEEEEEeCCHHHHHHHHHHHHHHh
Confidence 45688 9999999999988 99 99999999999999864 5667666766544 456666667666553
No 58
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=97.55 E-value=8.2e-06 Score=76.31 Aligned_cols=82 Identities=13% Similarity=0.209 Sum_probs=57.7
Q ss_pred ccCCCCCCCCeeeecCCCc---cc-ccCcceeeeccccccCCCCCccceeeec---------cccchHHHHHHHHHHHHh
Q 023627 106 AASVSEGSSGYARFMEPDE---LY-CSRLKIRYGISTRFVDQAGRPRLSFVVD---------ASQSLCTVLDACEVVAKK 172 (279)
Q Consensus 106 a~~lp~~~pGvy~F~~p~d---Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVd---------la~~v~~Vl~~Cd~~aq~ 172 (279)
.+++| +.||||.|.+.++ || |++.|||.||++||++ +|...|+. -+..+.+.|-.++-|-+-
T Consensus 28 l~~LP-~~PGVYlf~d~~g~~~LYVGKAknLR~RV~syF~~----~k~~~m~~~i~~Ie~i~T~sEleALLLE~~LIK~~ 102 (286)
T PRK10545 28 LEDLP-KLPGVYLFHGESDTMPLYIGKSVNIRSRVLSHLRT----PDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQ 102 (286)
T ss_pred HHhCC-CCCeEEEEEcCCCCEEEEEechHhHHHHHHHHcCc----HHHHHHHHhcceEEEEEeCCHHHHHHHHHHHHHHh
Confidence 56799 9999999998776 89 9999999999999975 22233332 345677888888888776
Q ss_pred hhccCCCCCCcccceeeccCCCcceEEe
Q 023627 173 LFEDSRSNSEWNPVVTRQSGNDPAARLR 200 (279)
Q Consensus 173 ~~~~sgs~S~W~p~v~~~~gn~ptvRl~ 200 (279)
... .|-.. |+...+|.+|+.
T Consensus 103 ~P~-------yN~~l-k~~k~~~~i~l~ 122 (286)
T PRK10545 103 QPL-------FNKRL-RRNRQLCSLQLN 122 (286)
T ss_pred CCc-------chhhc-cCCCCCeEEEEE
Confidence 431 22221 333467777764
No 59
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=96.76 E-value=0.004 Score=55.92 Aligned_cols=34 Identities=18% Similarity=0.277 Sum_probs=29.1
Q ss_pred CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEe
Q 023627 3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVC 38 (279)
Q Consensus 3 ~~~~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vc 38 (279)
|...+...|-+|+|-||+++.. .+|||+++|+--
T Consensus 1 m~~~~~nLiWIDlEMTGLd~~~--drIIEiA~iVTD 34 (184)
T COG1949 1 MSANKNNLIWIDLEMTGLDPER--DRIIEIATIVTD 34 (184)
T ss_pred CCCcCCceEEEeeeeccCCcCc--ceEEEEEEEEec
Confidence 3566788999999999999988 899999998643
No 60
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=92.99 E-value=0.24 Score=47.22 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=26.3
Q ss_pred HHHHHHhhCCC--CCccccchhhhccHHHHHh
Q 023627 52 LASLATYFGLG--QQTHRSLDDVRMNLEVLKY 81 (279)
Q Consensus 52 LatLA~~Fg~~--~~~HRALdDar~t~dVl~~ 81 (279)
+..+-++.|+. +..|++||||+-...+...
T Consensus 206 it~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~k 237 (280)
T KOG0542|consen 206 ITGMLEHYGLQFEGRAHSGIDDARNIARIAQK 237 (280)
T ss_pred HHHHHHHhCCcccCCcccCchhHHHHHHHHHH
Confidence 67777888999 8899999999998888877
No 61
>cd05160 DEDDy_DNA_polB_exo DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. The 3'-5' exonuclease domain of family-B DNA polymerases. This domain has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. This domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The exonuclease domain of family B polymerase also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members include Escherichia coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative
Probab=92.89 E-value=0.12 Score=43.75 Aligned_cols=31 Identities=23% Similarity=0.203 Sum_probs=24.9
Q ss_pred EEEEEeecCCC----CCCCCceeEEEEeeEEEecCce
Q 023627 10 IAFFDVETAFP----NPPGQRIAILEFGAILVCPKTL 42 (279)
Q Consensus 10 ~vffDvETT~p----~~~~~~~~ilEfgAI~Vcp~~l 42 (279)
+++||+|||++ ++.. ..|+++|++....|..
T Consensus 1 v~~~DIEt~~~~~~p~~~~--d~Ii~I~~~~~~~g~~ 35 (199)
T cd05160 1 VLSFDIETTPPVGGPEPDR--DPIICITYADSFDGVK 35 (199)
T ss_pred CccEEEeecCCCCCcCCCC--CCEEEEEEEEeeCCce
Confidence 37899999998 5544 8999999998855654
No 62
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=92.54 E-value=0.016 Score=59.11 Aligned_cols=52 Identities=12% Similarity=0.321 Sum_probs=39.6
Q ss_pred ecCCCc--cc-ccCcceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHH
Q 023627 119 FMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAK 171 (279)
Q Consensus 119 F~~p~d--Ly-gt~~~vR~rVrsyFt~se~RpR~~~mVdla~~---------v~~Vl~~Cd~~aq 171 (279)
|.+.++ || |.+.|||.||++||+.+ .++|...||.-..+ +++.|-.|.-|-|
T Consensus 1 ~~d~~g~vIYVGKAknLr~RV~sYF~~~-~~~K~~~lv~~i~~ie~ivt~sE~EALlLE~~LIK~ 64 (574)
T PRK14670 1 MYSENNKILYIGKAKNLRSRVKNYFLEK-ISHKTKILMKNVKNIEVITTNSEYEALLLECNLIKT 64 (574)
T ss_pred CCCCCCCEEEeeCcHhHHHHHHHHcCCC-CCchHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHH
Confidence 445666 99 99999999999999975 57888888776554 5566666666655
No 63
>smart00465 GIYc GIY-YIG type nucleases (URI domain).
Probab=92.24 E-value=0.021 Score=40.93 Aligned_cols=31 Identities=16% Similarity=0.282 Sum_probs=28.0
Q ss_pred CCeeeecCCCc--cc-ccCcceeeeccccccCCC
Q 023627 114 SGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA 144 (279)
Q Consensus 114 pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se 144 (279)
||+|.|..+++ +| |++.+++.|++++|.+..
T Consensus 2 ~gvY~i~~~~~~~~YVG~t~nl~~R~~~h~~~~~ 35 (84)
T smart00465 2 PGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSR 35 (84)
T ss_pred CEEEEEEECCCCEEEEEEccCHHHHHHHHHhCCC
Confidence 79999999666 99 999999999999998766
No 64
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=90.73 E-value=0.37 Score=45.96 Aligned_cols=33 Identities=27% Similarity=0.345 Sum_probs=24.1
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (279)
Q Consensus 6 ~~~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~ 40 (279)
+..+++|||+||||+++.+ ..|+=.|--.+..+
T Consensus 96 ~~e~~~FFDiETTGL~~ag--~~I~~~g~a~~~~~ 128 (278)
T COG3359 96 EAEDVAFFDIETTGLDRAG--NTITLVGGARGVDD 128 (278)
T ss_pred cccceEEEeeeccccCCCC--CeEEEEEEEEccCc
Confidence 4678999999999999955 66666665444433
No 65
>PHA02598 denA endonuclease II; Provisional
Probab=88.93 E-value=0.11 Score=45.26 Aligned_cols=37 Identities=14% Similarity=0.072 Sum_probs=29.9
Q ss_pred cCCCCCCCCeeeecCCCc-cc-ccCcceeeeccccccCC
Q 023627 107 ASVSEGSSGYARFMEPDE-LY-CSRLKIRYGISTRFVDQ 143 (279)
Q Consensus 107 ~~lp~~~pGvy~F~~p~d-Ly-gt~~~vR~rVrsyFt~s 143 (279)
...|+-.-|||.|...++ || |.+.+||.||++||++.
T Consensus 27 ~~~~~~~n~VY~~~~~~~viYVGKAknLkkRv~sYf~~~ 65 (138)
T PHA02598 27 IKCPNKKNVIYAIAVDDELVYIGKTKNLRKRIDYYRNSK 65 (138)
T ss_pred cCCcccceEEEEEEeCCeEEEEeehhhHHHHHHHHhCcc
Confidence 345666779999994444 99 99999999999999853
No 66
>PHA02570 dexA exonuclease; Provisional
Probab=86.34 E-value=1.5 Score=40.67 Aligned_cols=47 Identities=17% Similarity=0.188 Sum_probs=34.7
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCceeeccchHHHHHHHHHhhCCC
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLG 62 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l~e~~sf~TLLatLA~~Fg~~ 62 (279)
+.+|+||-|..|. ..||++|||.+-|..- ....|..|. +++.++.+.
T Consensus 4 lMIDlETmG~~p~---AaIisIgAV~Fdp~~~-~g~tF~elV-~~~~~~k~d 50 (220)
T PHA02570 4 FIIDFETFGNTPD---GAVIDLAVIAFEHDPH-NPPTFEELV-SRGRRIKFD 50 (220)
T ss_pred EEEEeeccCCCCC---ceEEEEEEEEecCCCC-ccccHHHHh-hcccccccc
Confidence 5799999999764 5899999999997543 468898885 344444443
No 67
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=82.31 E-value=1.1 Score=36.57 Aligned_cols=30 Identities=27% Similarity=0.368 Sum_probs=17.4
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTL 42 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~l 42 (279)
+|||+||||.++..+ .|.=||...+-.+..
T Consensus 1 l~~DIET~Gl~~~~~--~i~liG~~~~~~~~~ 30 (164)
T PF13482_consen 1 LFFDIETTGLSPDND--TIYLIGVADFDDDEI 30 (164)
T ss_dssp --EEEEESS-GG-G-----EEEEEEE-ETTTT
T ss_pred CcEEecCCCCCCCCC--CEEEEEEEEeCCCce
Confidence 589999999988663 466678777666554
No 68
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=81.16 E-value=2.1 Score=33.27 Aligned_cols=29 Identities=21% Similarity=0.135 Sum_probs=22.6
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 023627 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKT 41 (279)
Q Consensus 11 vffDvETT~p~~~~~~~~ilEfgAI~Vcp~~ 41 (279)
++||+|||++++.. ..|++++.....+++
T Consensus 1 ~~~DiEt~~~~~~~--~~i~~i~~~~~~~~~ 29 (96)
T cd06125 1 IAIDTEATGLDGAV--HEIIEIALADVNPED 29 (96)
T ss_pred CEEEEECCCCCCCC--CcEEEEEEEEccCCC
Confidence 47999999988755 789999977653344
No 69
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=71.01 E-value=4.8 Score=37.12 Aligned_cols=30 Identities=17% Similarity=0.158 Sum_probs=26.2
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEec
Q 023627 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCP 39 (279)
Q Consensus 8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp 39 (279)
..+|-+|+|-||++..+ .+|+|+++|.--+
T Consensus 26 q~lVWiD~EMTGLdvek--d~i~EiacIITD~ 55 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEK--DRIIEIACIITDG 55 (208)
T ss_pred CceEEEeeecccccccc--ceeEEEEEEEecC
Confidence 45999999999999998 7999999986544
No 70
>PF01541 GIY-YIG: GIY-YIG catalytic domain; InterPro: IPR000305 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. The UvrC proteins contain 4 conserved regions: a central region which interacts with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases. It is found in the amino terminal region of excinuclease abc subunit c (uvrC), Bacteriophage T4 endonucleases segA, segB, segC, segD and segE; it is also found in putative endonucleases encoded by group I introns of fungi and phage.; GO: 0004518 nuclease activity, 0006281 DNA repair, 0005622 intracellular; PDB: 1YWL_A 1YD6_D 1YD5_A 1YD1_A 1YCZ_A 1YD0_A 1YD3_A 1YD4_A 1YD2_A 1LN0_A ....
Probab=69.43 E-value=0.51 Score=33.71 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=28.4
Q ss_pred CCeeeecCCCc--cc-ccCcceeeeccccccCCCCCc
Q 023627 114 SGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRP 147 (279)
Q Consensus 114 pGvy~F~~p~d--Ly-gt~~~vR~rVrsyFt~se~Rp 147 (279)
+|+|.+...++ +| |.+.+++.|+++++.+.....
T Consensus 2 ~gIY~i~~~~~~~~YIG~t~nl~~R~~~H~~~~~~~~ 38 (80)
T PF01541_consen 2 YGIYIIYNKDNKKIYIGSTKNLKKRLNEHFSGNKSKK 38 (80)
T ss_dssp EEEEEEEETTTEEEEEEEESSHHHHHHHHHHHCTHCS
T ss_pred cEEEEEEECCCCEEEEEEECCHHHHHHHHhcCCCCCc
Confidence 69999997776 79 999999999999998655443
No 71
>KOG4027 consensus Uncharacterized conserved protein [Function unknown]
Probab=66.26 E-value=4.1 Score=37.02 Aligned_cols=98 Identities=23% Similarity=0.237 Sum_probs=65.2
Q ss_pred CCCCCCcccceeeccC----CCcceE----EeccccccCCccceehhhhccCCCCCcceee--eccCChHhhhhhcCCCc
Q 023627 177 SRSNSEWNPVVTRQSG----NDPAAR----LRIPTVVFGDVAQYATEMYRKEPSGDIQKLE--FVRFDAAELDSLLKPGT 246 (279)
Q Consensus 177 sgs~S~W~p~v~~~~g----n~ptvR----l~Ipt~~~gd~a~y~T~iy~ke~sg~~qkl~--~s~~d~ael~s~~~~g~ 246 (279)
|-|--.|-++|.--|| ++.+++ ||||| +|.-..+...++--||+-++|++. |-+..++=-|-.+....
T Consensus 76 stsPygWPqivl~vfg~d~~G~d~v~GYg~~hiP~--~pgrh~~~vp~f~Pe~~s~~q~~tswl~rr~pE~~DPkv~a~~ 153 (187)
T KOG4027|consen 76 STSPYGWPQIVLNVFGKDHSGKDCVTGYGMLHIPT--EPGRHVCRVPCFLPEPSSTVQQLTSWLRRRNPEFVDPKVPANA 153 (187)
T ss_pred cCCCCCCceEEEEEecCCcCCcceeeeeeeEecCc--CCCceeEEEeeEecCCHHHHHHHHHHHHhcCccccCCcccccc
Confidence 3445579999877677 567776 99999 566689999999999999999875 34444444444444333
Q ss_pred eeeeeeecCccccc-cccccchhhhhhhhhcc
Q 023627 247 FVDAFLSLDPYDYV-YEQSAGIRLVAKKLIIH 277 (279)
Q Consensus 247 ~vDAf~sle~Ydy~-~qq~AGIrLvAkkL~ih 277 (279)
-=---.+.+.|.|| -|=|.=||- |.||-.|
T Consensus 154 ~gr~~~r~~s~G~v~l~~nvv~k~-arKlgy~ 184 (187)
T KOG4027|consen 154 DGRYACRTSSKGYVDLEINVVIKC-ARKLGYS 184 (187)
T ss_pred CCceEEEeeccceEEEEEeeeehh-hHhhccc
Confidence 22224567777776 234555555 7777655
No 72
>cd05780 DNA_polB_Kod1_like_exo DEDDy 3'-5' exonuclease domain of Pyrococcus kodakaraensis Kod1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal family-B DNA polymerases with similarity to Pyrococcus kodakaraensis Kod1, including polymerases from Desulfurococcus (D. Tok Pol) and Thermococcus gorgonarius (Tgo Pol). Kod1, D. Tok Pol, and Tgo Pol are thermostable enzymes that exhibit both polymerase and 3'-5' exonuclease activities. They are family-B DNA polymerases. Their amino termini harbor a DEDDy-type DnaQ-like 3'-5' exonuclease domain that contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Members of this subfamily show
Probab=51.82 E-value=24 Score=30.45 Aligned_cols=27 Identities=26% Similarity=0.315 Sum_probs=20.2
Q ss_pred ceEEEEEeecCCC----CCCCCceeEEEEeeEE
Q 023627 8 FEIAFFDVETAFP----NPPGQRIAILEFGAIL 36 (279)
Q Consensus 8 ~e~vffDvETT~p----~~~~~~~~ilEfgAI~ 36 (279)
--+++||+|||.+ ++. ...|+=+|...
T Consensus 3 l~i~~fDIEt~~~~g~p~~~--~d~Ii~Is~~~ 33 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPE--KDPIIMISFAD 33 (195)
T ss_pred ceEEEEEEEecCCCCCCCCC--CCcEEEEEEec
Confidence 3589999999843 333 48999999755
No 73
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=48.81 E-value=15 Score=37.54 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=27.3
Q ss_pred HHHHHHhhCCC-CCccccchhhhccHHHHHh
Q 023627 52 LASLATYFGLG-QQTHRSLDDVRMNLEVLKY 81 (279)
Q Consensus 52 LatLA~~Fg~~-~~~HRALdDar~t~dVl~~ 81 (279)
|.-|+.-=|+. ...|-||.|++||+.+-|.
T Consensus 166 LEhLt~ANgieH~nAHdAmsDVyATIamAkl 196 (475)
T COG2925 166 LEHLTKANGIEHSNAHDAMSDVYATIAMAKL 196 (475)
T ss_pred hHHHhhccccccchhhHHHHHHHHHHHHHHH
Confidence 99999999999 9999999999999986654
No 74
>cd05781 DNA_polB_B3_exo DEDDy 3'-5' exonuclease domain of Sulfurisphaera ohwakuensis DNA polymerase B3 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of archaeal proteins with similarity to Sulfurisphaera ohwakuensis DNA polymerase B3. B3 is a family-B DNA polymerase. Family-B DNA polymerases contain an N-terminal DEDDy DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-A DNA polymerases. B3 exhibits both polymerase and 3'-5' exonuclease activities. This exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and are involved in metal binding and catalysis. The exonuclease domain of family B polymerases also contains a beta hairpin structure that plays an important role in active site switching in the event of nucleotide misincorporation. Archaeal proteins that are involved in DNA replicatio
Probab=38.48 E-value=42 Score=29.21 Aligned_cols=28 Identities=25% Similarity=0.336 Sum_probs=20.5
Q ss_pred ceEEEEEeecCC----CCCCCCceeEEEEeeEEE
Q 023627 8 FEIAFFDVETAF----PNPPGQRIAILEFGAILV 37 (279)
Q Consensus 8 ~e~vffDvETT~----p~~~~~~~~ilEfgAI~V 37 (279)
--+++||+||+. |++.. ..|+=||+...
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~--d~Ii~Is~~~~ 34 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRR--DPIIVISLATS 34 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCC--CCEEEEEEEeC
Confidence 347899999994 34444 78999997553
No 75
>cd06139 DNA_polA_I_Ecoli_like_exo DEDDy 3'-5' exonuclease domain of Escherichia coli DNA polymerase I and similar bacterial family-A DNA polymerases. Escherichia coli-like Polymerase I (Pol I), a subgroup of family-A DNA polymerases, contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase domain. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The 3'-5' exonuclease domain of DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. E. coli DNA Pol I is involved in genome replication but is not the main replicating enzyme. It is also implicated in DNA repair.
Probab=37.83 E-value=48 Score=27.14 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=19.9
Q ss_pred CCCceEEEEEeecCCCCCCCCceeEEEEe
Q 023627 5 QDRFEIAFFDVETAFPNPPGQRIAILEFG 33 (279)
Q Consensus 5 ~~~~e~vffDvETT~p~~~~~~~~ilEfg 33 (279)
..+..+++||+|||+..+.. ..|+.++
T Consensus 2 ~~~~~~~a~d~e~~~~~~~~--~~i~~l~ 28 (193)
T cd06139 2 LEKAKVFAFDTETTSLDPMQ--AELVGIS 28 (193)
T ss_pred CccCCeEEEEeecCCCCcCC--CeEEEEE
Confidence 45678899999999987644 4566555
No 76
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=37.21 E-value=16 Score=26.38 Aligned_cols=52 Identities=19% Similarity=0.201 Sum_probs=41.3
Q ss_pred cCCCCCcceeeeccCChHhhhhhcCCCceeeeeeecCccccccccccchhhhhhhhh
Q 023627 219 KEPSGDIQKLEFVRFDAAELDSLLKPGTFVDAFLSLDPYDYVYEQSAGIRLVAKKLI 275 (279)
Q Consensus 219 ke~sg~~qkl~~s~~d~ael~s~~~~g~~vDAf~sle~Ydy~~qq~AGIrLvAkkL~ 275 (279)
.|.+|.+.-..|++. .+.+..++..|+.|=..=.++.|.| +.+++|.+.++.
T Consensus 24 ~D~~~~i~~~~f~~~-~~~~~~~l~~g~~v~v~g~v~~~~~----~~~~~l~v~~i~ 75 (78)
T cd04489 24 KDEDASIRCVMWRSN-ARRLGFPLEEGMEVLVRGKVSFYEP----RGGYQLIVEEIE 75 (78)
T ss_pred EeCCeEEEEEEEcch-hhhCCCCCCCCCEEEEEEEEEEECC----CCEEEEEEEEEE
Confidence 355678888888864 4668899999999999999888777 567899887763
No 77
>TIGR01453 grpIintron_endo group I intron endonuclease. This model represents one subfamily of endonucleases containing the endo/excinuclease amino terminal domain, Pfam:PF01541 at its amino end. A distinct subfamily includes excinuclease abc subunit c (uvrC). Members of pfam01541 are often termed GIY-YIG endonucleases after conserved motifs near the amino end. This subfamily in this model is found in open reading frames of group I introns in both phage and mitochondria. The closely related endonucleases of phage T4: segA, segB, segC, segD and segE, score below the trusted cutoff for the family.
Probab=34.13 E-value=9.8 Score=33.98 Aligned_cols=34 Identities=15% Similarity=0.284 Sum_probs=28.1
Q ss_pred CCeeeecC-CCc-cc-ccCcceeeeccccccC-CCCCc
Q 023627 114 SGYARFME-PDE-LY-CSRLKIRYGISTRFVD-QAGRP 147 (279)
Q Consensus 114 pGvy~F~~-p~d-Ly-gt~~~vR~rVrsyFt~-se~Rp 147 (279)
+|+|.+.. +++ .| |++.++..|+++||.. ..+..
T Consensus 2 ~GIY~i~n~~ngk~YIGss~nl~~R~~~h~~~~~~~~~ 39 (214)
T TIGR01453 2 SGIYKITNNINGKIYVGSSVNLEKRLKEHLKLLKKGNR 39 (214)
T ss_pred CEEEEEEECCCCcEEEEeccCHHHHHHHHHHHHhcCCh
Confidence 69999988 454 88 9999999999999976 44444
No 78
>cd06143 PAN2_exo DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonuclease PAN2. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. PAN catalyzes the deadenylation of poly(A) tails, which are initially synthesized to default lengths of 70 to 90, to mRNA-specific lengths of 55 to 71. Pab1p and PAN also play a role in the export and decay of mRNA. PAN2 contains a DEDDh-type DnaQ-like 3'-5' exonuclease domain with three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis.
Probab=32.30 E-value=33 Score=30.65 Aligned_cols=29 Identities=38% Similarity=0.599 Sum_probs=23.1
Q ss_pred HHHHHHh-hCCC--CCccccchhhhccHHHHH
Q 023627 52 LASLATY-FGLG--QQTHRSLDDVRMNLEVLK 80 (279)
Q Consensus 52 LatLA~~-Fg~~--~~~HRALdDar~t~dVl~ 80 (279)
|..||.. +|.. +..|-+++|||+++++.+
T Consensus 143 Lk~La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 143 LRFLAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 7788764 4666 568999999999999763
No 79
>PF01612 DNA_pol_A_exo1: 3'-5' exonuclease; InterPro: IPR002562 This domain is responsible for the 3'-5' exonuclease proofreading activity of Escherichia coli DNA polymerase I (polI) and other enzymes, it catalyses the hydrolysis of unpaired or mismatched nucleotides. This domain consists of the amino-terminal half of the Klenow fragment in E. coli polI it is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D) [].; GO: 0003676 nucleic acid binding, 0008408 3'-5' exonuclease activity, 0006139 nucleobase-containing compound metabolic process, 0005622 intracellular; PDB: 2HBK_A 2HBJ_A 2HBM_A 2HBL_A 2FC0_A 2FBY_A 2FBX_A 2FBT_A 2FBV_A 1YT3_A ....
Probab=26.45 E-value=1.3e+02 Score=24.03 Aligned_cols=30 Identities=20% Similarity=0.198 Sum_probs=19.6
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 023627 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (279)
Q Consensus 8 ~e~vffDvETT~p~~~~~~~~ilEfgAI~Vcp~ 40 (279)
...++||+||++..+..... .+..|.+|.+
T Consensus 20 ~~~~a~D~E~~~~~~~~~~~---~~~~iq~~~~ 49 (176)
T PF01612_consen 20 AKVLAFDTETTGLDPYSYNP---KIALIQLATG 49 (176)
T ss_dssp TSEEEEEEEEETSTSTTSSE---EEEEEEEEES
T ss_pred CCeEEEEEEECCCCccccCC---eEEEEEEecC
Confidence 34899999999988844322 2344445555
No 80
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=24.23 E-value=53 Score=32.27 Aligned_cols=31 Identities=39% Similarity=0.580 Sum_probs=28.1
Q ss_pred HHHHHHHhhCCC--CCccccchhhhccHHHHHh
Q 023627 51 LLASLATYFGLG--QQTHRSLDDVRMNLEVLKY 81 (279)
Q Consensus 51 LLatLA~~Fg~~--~~~HRALdDar~t~dVl~~ 81 (279)
.+++||.|.... -..|||+.|+-++-+|+.+
T Consensus 254 ~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~ 286 (318)
T KOG4793|consen 254 SLEALATYYSLTPELDAHRALSDVLLLSKVFQK 286 (318)
T ss_pred hHHHHHHHhhcCcccchhhhccccchhhhHHHH
Confidence 389999988877 8899999999999999988
No 81
>PRK05755 DNA polymerase I; Provisional
Probab=20.46 E-value=2.1e+02 Score=30.79 Aligned_cols=25 Identities=20% Similarity=0.263 Sum_probs=19.9
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEe
Q 023627 7 RFEIAFFDVETAFPNPPGQRIAILEFG 33 (279)
Q Consensus 7 ~~e~vffDvETT~p~~~~~~~~ilEfg 33 (279)
..++++||+|||+.++.. ..|+.++
T Consensus 314 ~~~~~a~DtEt~~l~~~~--~~i~~i~ 338 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQ--AELVGLS 338 (880)
T ss_pred ccCeEEEEeccCCCCccc--ccEEEEE
Confidence 357899999999998755 5677775
Done!