Query 027882
Match_columns 217
No_of_seqs 83 out of 85
Neff 3.1
Searched_HMMs 46136
Date Fri Mar 29 02:53:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027882.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027882hhsearch_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 5.3E-26 1.1E-30 216.1 8.7 179 6-200 13-308 (557)
2 PRK07740 hypothetical protein; 99.5 2.1E-14 4.5E-19 123.9 6.2 83 7-91 58-237 (244)
3 cd06133 ERI-1_3'hExo_like DEDD 99.5 6.6E-14 1.4E-18 109.7 6.4 74 10-83 1-176 (176)
4 PRK08517 DNA polymerase III su 99.5 6E-14 1.3E-18 122.8 6.2 82 6-91 66-241 (257)
5 PRK07246 bifunctional ATP-depe 99.4 2.5E-13 5.4E-18 134.8 7.2 129 4-141 3-236 (820)
6 PRK09145 DNA polymerase III su 99.4 3.5E-13 7.5E-18 111.5 6.7 76 6-83 27-198 (202)
7 PRK07247 DNA polymerase III su 99.4 3.4E-13 7.4E-18 113.7 6.5 71 8-83 5-166 (195)
8 PRK07748 sporulation inhibitor 99.4 5.6E-13 1.2E-17 111.1 7.4 75 7-83 3-177 (207)
9 smart00479 EXOIII exonuclease 99.4 4.5E-13 9.8E-18 103.4 6.4 72 9-84 1-165 (169)
10 PF00929 RNase_T: Exonuclease; 99.4 3E-13 6.4E-18 100.8 5.0 39 11-51 1-39 (164)
11 PRK09146 DNA polymerase III su 99.4 7.3E-13 1.6E-17 114.6 6.6 44 6-51 45-88 (239)
12 cd06131 DNA_pol_III_epsilon_Ec 99.4 1E-12 2.2E-17 103.6 6.1 72 10-83 1-167 (167)
13 PRK06807 DNA polymerase III su 99.4 1.1E-12 2.3E-17 117.9 7.0 76 7-86 7-172 (313)
14 PRK07942 DNA polymerase III su 99.4 1.1E-12 2.5E-17 112.0 6.6 77 4-84 2-178 (232)
15 PRK06063 DNA polymerase III su 99.4 1.3E-12 2.7E-17 117.0 6.9 73 7-83 14-176 (313)
16 cd06136 TREX1_2 DEDDh 3'-5' ex 99.4 8.8E-13 1.9E-17 107.8 5.4 32 10-42 1-32 (177)
17 TIGR00573 dnaq exonuclease, DN 99.3 1.2E-12 2.6E-17 110.0 5.8 74 6-83 5-174 (217)
18 PRK06310 DNA polymerase III su 99.3 1.7E-12 3.8E-17 112.4 6.4 81 7-91 6-180 (250)
19 cd06130 DNA_pol_III_epsilon_li 99.3 1.9E-12 4.2E-17 99.9 5.1 28 52-79 127-154 (156)
20 PRK09182 DNA polymerase III su 99.3 3E-12 6.5E-17 114.3 6.5 83 7-91 36-209 (294)
21 PRK06722 exonuclease; Provisio 99.3 7.9E-12 1.7E-16 111.8 7.0 77 6-83 3-178 (281)
22 TIGR01298 RNaseT ribonuclease 99.3 7.8E-12 1.7E-16 104.6 6.3 34 52-85 155-191 (200)
23 COG2176 PolC DNA polymerase II 99.3 3.6E-12 7.8E-17 131.7 4.9 85 3-91 416-597 (1444)
24 PRK05168 ribonuclease T; Provi 99.3 1.1E-11 2.3E-16 104.6 6.7 34 52-85 164-200 (211)
25 TIGR01406 dnaQ_proteo DNA poly 99.2 9.4E-12 2E-16 106.3 6.2 73 10-84 2-170 (225)
26 PRK06195 DNA polymerase III su 99.2 8.7E-12 1.9E-16 110.6 5.7 69 9-83 2-161 (309)
27 cd06127 DEDDh DEDDh 3'-5' exon 99.2 1.3E-11 2.8E-16 92.1 5.5 38 11-51 1-38 (159)
28 cd06134 RNaseT DEDDh 3'-5' exo 99.2 1.6E-11 3.6E-16 101.5 6.3 32 52-83 152-186 (189)
29 TIGR01405 polC_Gram_pos DNA po 99.2 1E-11 2.2E-16 128.6 5.8 82 6-91 188-366 (1213)
30 PRK05711 DNA polymerase III su 99.2 2.8E-11 6.1E-16 105.3 6.7 76 7-84 3-174 (240)
31 PRK08074 bifunctional ATP-depe 99.2 1.9E-11 4E-16 122.5 6.3 73 8-83 3-166 (928)
32 cd06135 Orn DEDDh 3'-5' exonuc 99.2 3.3E-11 7.2E-16 98.2 6.1 37 10-48 1-37 (173)
33 TIGR01407 dinG_rel DnaQ family 99.2 3.3E-11 7.2E-16 119.2 6.2 71 9-83 1-162 (850)
34 PRK06309 DNA polymerase III su 99.2 1.1E-10 2.5E-15 99.4 8.3 38 52-89 131-169 (232)
35 cd06138 ExoI_N N-terminal DEDD 99.1 4.8E-11 1E-15 97.7 4.3 37 11-51 1-38 (183)
36 PRK07983 exodeoxyribonuclease 99.1 7.4E-11 1.6E-15 101.2 5.3 67 10-83 2-151 (219)
37 PRK05359 oligoribonuclease; Pr 99.0 6.6E-10 1.4E-14 92.3 6.6 32 7-40 2-33 (181)
38 PRK11779 sbcB exonuclease I; P 99.0 1.2E-09 2.5E-14 104.0 7.1 35 5-41 3-37 (476)
39 COG0847 DnaQ DNA polymerase II 99.0 1.1E-09 2.4E-14 91.5 5.9 74 8-84 13-180 (243)
40 PRK00448 polC DNA polymerase I 98.9 7.9E-10 1.7E-14 116.3 3.3 81 7-91 418-595 (1437)
41 cd06149 ISG20 DEDDh 3'-5' exon 98.9 1.8E-09 3.9E-14 87.2 4.3 30 11-40 1-30 (157)
42 PTZ00315 2'-phosphotransferase 98.8 4.1E-09 8.9E-14 103.0 6.0 42 8-51 56-100 (582)
43 cd06137 DEDDh_RNase DEDDh 3'-5 98.8 6.6E-09 1.4E-13 83.7 4.6 30 11-42 1-30 (161)
44 PRK05601 DNA polymerase III su 98.7 1.9E-08 4E-13 94.2 6.1 42 6-51 44-86 (377)
45 cd06144 REX4_like DEDDh 3'-5' 98.7 2.1E-08 4.6E-13 79.9 4.4 29 52-80 121-152 (152)
46 PRK14667 uvrC excinuclease ABC 98.3 2.9E-07 6.3E-12 89.6 3.2 68 105-173 8-87 (567)
47 PRK12306 uvrC excinuclease ABC 98.3 1E-07 2.3E-12 91.8 -1.2 66 107-172 4-81 (519)
48 PRK14671 uvrC excinuclease ABC 98.3 1.1E-07 2.3E-12 93.2 -1.4 68 105-172 14-94 (621)
49 PRK14666 uvrC excinuclease ABC 98.2 1.3E-07 2.8E-12 94.2 -1.3 66 107-172 6-84 (694)
50 PRK14669 uvrC excinuclease ABC 98.2 1.4E-07 2.9E-12 92.8 -1.5 56 107-162 7-66 (624)
51 cd06145 REX1_like DEDDh 3'-5' 98.2 1E-06 2.2E-11 70.6 3.8 29 52-80 117-150 (150)
52 PRK00558 uvrC excinuclease ABC 98.2 1.8E-07 3.9E-12 91.0 -0.8 68 107-174 8-87 (598)
53 COG0322 UvrC Nuclease subunit 98.1 2.1E-07 4.5E-12 91.0 -2.6 57 107-164 9-68 (581)
54 COG5018 KapD Inhibitor of the 98.1 2E-06 4.3E-11 75.1 3.7 85 7-91 3-191 (210)
55 TIGR00194 uvrC excinuclease AB 98.1 4.3E-07 9.3E-12 88.4 -1.2 66 107-173 5-82 (574)
56 PRK10545 nucleotide excision r 98.0 4.4E-07 9.6E-12 82.0 -2.0 64 106-173 27-103 (286)
57 PRK14672 uvrC excinuclease ABC 98.0 7.2E-07 1.6E-11 89.0 -1.4 86 106-200 14-111 (691)
58 PRK14668 uvrC excinuclease ABC 98.0 7.7E-07 1.7E-11 86.7 -1.7 64 107-173 10-85 (577)
59 COG1949 Orn Oligoribonuclease 97.1 0.0017 3.7E-08 56.4 6.6 34 3-38 1-34 (184)
60 KOG0542 Predicted exonuclease 95.2 0.067 1.5E-06 49.3 7.0 32 52-83 206-239 (280)
61 PRK14670 uvrC excinuclease ABC 94.5 0.0048 1E-07 60.8 -2.2 53 119-172 1-65 (574)
62 smart00465 GIYc GIY-YIG type n 94.3 0.0074 1.6E-07 41.7 -1.1 32 113-144 1-35 (84)
63 cd05160 DEDDy_DNA_polB_exo DED 94.0 0.064 1.4E-06 43.8 3.7 31 10-42 1-35 (199)
64 PHA02598 denA endonuclease II; 93.4 0.024 5.1E-07 47.6 0.2 43 101-143 21-65 (138)
65 COG3359 Predicted exonuclease 92.0 0.24 5.2E-06 45.7 4.6 33 6-40 96-128 (278)
66 PHA02570 dexA exonuclease; Pro 89.0 0.87 1.9E-05 40.8 5.4 47 11-62 4-50 (220)
67 PF13482 RNase_H_2: RNase_H su 85.6 0.65 1.4E-05 36.5 2.4 30 11-42 1-30 (164)
68 cd06125 DnaQ_like_exo DnaQ-lik 84.6 1.3 2.9E-05 33.2 3.5 29 11-41 1-29 (96)
69 PF01541 GIY-YIG: GIY-YIG cata 80.3 0.25 5.4E-06 34.1 -1.7 34 114-147 2-38 (80)
70 KOG3242 Oligoribonuclease (3'- 77.0 2.9 6.3E-05 37.3 3.5 31 8-40 26-56 (208)
71 cd05780 DNA_polB_Kod1_like_exo 59.8 17 0.00036 30.3 4.5 27 8-36 3-33 (195)
72 COG2925 SbcB Exonuclease I [DN 56.5 8.7 0.00019 37.9 2.5 31 52-82 166-197 (475)
73 TIGR01453 grpIintron_endo grou 49.0 4.7 0.0001 34.7 -0.5 34 114-147 2-39 (214)
74 cd05781 DNA_polB_B3_exo DEDDy 45.6 29 0.00064 29.1 3.7 29 8-38 3-35 (188)
75 cd06139 DNA_polA_I_Ecoli_like_ 45.2 33 0.00071 27.1 3.8 27 5-33 2-28 (193)
76 cd06143 PAN2_exo DEDDh 3'-5' e 41.3 20 0.00043 30.9 2.1 29 52-80 143-174 (174)
77 KOG4793 Three prime repair exo 33.0 31 0.00067 32.7 2.1 33 51-83 254-288 (318)
78 PF01612 DNA_pol_A_exo1: 3'-5' 32.1 93 0.002 23.9 4.4 30 8-40 20-49 (176)
79 TIGR02894 DNA_bind_RsfA transc 31.4 15 0.00032 31.8 -0.2 30 163-192 30-60 (161)
80 PRK05755 DNA polymerase I; Pro 25.5 1.5E+02 0.0033 30.7 5.8 31 7-40 314-344 (880)
81 cd06129 RNaseD_like DEDDy 3'-5 23.8 1.2E+02 0.0025 24.3 3.7 27 7-33 12-38 (161)
82 KOG3242 Oligoribonuclease (3'- 21.5 46 0.001 29.9 1.1 19 63-81 176-194 (208)
83 PF08523 MBF1: Multiprotein br 20.3 34 0.00074 25.6 0.0 16 181-196 1-17 (71)
No 1
>PRK07883 hypothetical protein; Validated
Probab=99.93 E-value=5.3e-26 Score=216.07 Aligned_cols=179 Identities=27% Similarity=0.304 Sum_probs=141.6
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH----------------------------------
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL---------------------------------- 51 (217)
.+..||+||+||||.++.. ++|||||||+|..+.+ ++.|++|
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 027882 52 ----------------------------------------------------------LASLATYFGLG-QQTHRSLDDV 72 (217)
Q Consensus 52 ----------------------------------------------------------LatLA~~Fg~~-~~~HRALdDa 72 (217)
|++|+.+||+. .+.||||+||
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 hccHHHHHHhh------hhhhhhcCcCccccccccCCc------cccccCCCCCCeeeeccCCc--ce-ecccceeeecc
Q 027882 73 RMNLEVLKYCA------TVLFLESGLPDIFTVNRWEMC------SAASVSEGSSGYARFMEPDE--LY-CSRLKIRYGIS 137 (217)
Q Consensus 73 r~tvdVl~~~~------gV~~lE~~~p~~~~~~~~v~p------~la~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVr 137 (217)
++|++||.+++ |+.+++++ ..+.+.++| +....+|..||||.|.+.++ || |.+.|||.||+
T Consensus 169 ~ata~l~~~l~~~~~~~~~~~~~~l----~~~~~~~~~~~~~~~~~~~~lP~~PGVY~~~d~~g~viYVGKAknLr~Rv~ 244 (557)
T PRK07883 169 RATVDVLHGLIERLGNLGVHTLEEL----LTYLPRVTPAQRRKRHLADGLPHAPGVYLFRGPSGEVLYVGTAVNLRRRVR 244 (557)
T ss_pred HHHHHHHHHHHHHHHhcCCCCHHHH----HHhhhhcChhhhcchHHHhhCCCCceEEEEECCCCcEEEeehhhhHHHHHH
Confidence 99999999998 67777777 445545555 45689999999999999988 99 99999999999
Q ss_pred ccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHHhhccCCCCCCCccceeeccCCCccEEEe
Q 027882 138 TRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKKLFEDSRSNSEWNPVVTRQSGNDPAARLR 200 (217)
Q Consensus 138 syFt~se~RpRm~emVdla~~---------v~~Vl~~Cd~~a~~~~~~~gs~s~W~p~v~~~~gn~ptvrl~ 200 (217)
+||..+..++|...||.-..+ +++.|-.|.-|-|-... +|-.. |..-.+|.++|.
T Consensus 245 sYF~~~~~~~k~~~lv~~i~~ie~i~t~sE~eAllLE~~lIk~~~P~-------yN~~l-kd~k~ypyi~i~ 308 (557)
T PRK07883 245 SYFTAAETRGRMREMVALAERVDHVECAHALEAEVRELRLIAAHKPP-------YNRRS-KFPERRWWVRLT 308 (557)
T ss_pred HHcCCCCCCchHHHHHhhhceEEEEEeCCHHHHHHHHHHHHHHhCCc-------chhhc-cCCCCceEEEEe
Confidence 999988778898888876655 45566666555443222 34333 333356666664
No 2
>PRK07740 hypothetical protein; Provisional
Probab=99.51 E-value=2.1e-14 Score=123.89 Aligned_cols=83 Identities=23% Similarity=0.336 Sum_probs=72.9
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-----------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL----------------------------------- 51 (217)
+..|||||+||||.+|..+ .+|||||||++..+.+ |.++|+++
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 4579999999999988763 7999999999998876 66788777
Q ss_pred -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 027882 52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN 75 (217)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t 75 (217)
|.+|+.+||+. ...|+||+||++|
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 HHHHHHhh------hhhhhhcC
Q 027882 76 LEVLKYCA------TVLFLESG 91 (217)
Q Consensus 76 vdVl~~~~------gV~~lE~~ 91 (217)
++||++++ |+.++.++
T Consensus 216 a~l~~~ll~~~~~~~~~~~~dl 237 (244)
T PRK07740 216 AKLWAILLVEAQQRGITTLHDL 237 (244)
T ss_pred HHHHHHHHHHHHHcCCcCHHHH
Confidence 99999996 77777665
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=99.48 E-value=6.6e-14 Score=109.68 Aligned_cols=74 Identities=32% Similarity=0.424 Sum_probs=63.0
Q ss_pred EEEEEeecCCCCCCC---CceeEEEEeeEEEecCceeecccHHHH-----------------------------------
Q 027882 10 IAFFDVETAFPNPPG---QRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (217)
Q Consensus 10 ~vffDvETT~~~~~~---~~~~ilEfgAI~V~p~~l~e~~sf~TL----------------------------------- 51 (217)
+|+||+||||+.+.. ...+|||||||+|.++...++++|+++
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 689999999998752 348999999999999875445666555
Q ss_pred --------------------------------------------------------------HHHHHHhhCCC-C-Cccc
Q 027882 52 --------------------------------------------------------------LASLATYFGLG-Q-QTHR 67 (217)
Q Consensus 52 --------------------------------------------------------------LatLA~~Fg~~-~-~~HR 67 (217)
|++||.+||++ . +.|+
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 cchhhhccHHHHHHhh
Q 027882 68 SLDDVRMNLEVLKYCA 83 (217)
Q Consensus 68 ALdDar~tvdVl~~~~ 83 (217)
||+||++|++||++++
T Consensus 161 Al~DA~~~a~l~~~~~ 176 (176)
T cd06133 161 GLDDARNIARILKRLL 176 (176)
T ss_pred cHHHHHHHHHHHHHhC
Confidence 9999999999999874
No 4
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=99.47 E-value=6e-14 Score=122.78 Aligned_cols=82 Identities=24% Similarity=0.399 Sum_probs=69.6
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH----------------------------------
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL---------------------------------- 51 (217)
.+..||+||+||||+++.. .+|||||||+|..|.+ +++|+++
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 027882 52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL 76 (217)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~tv 76 (217)
|++|+++||+. .+.||||+||.+|+
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-----hhhhhhcC
Q 027882 77 EVLKYCA-----TVLFLESG 91 (217)
Q Consensus 77 dVl~~~~-----gV~~lE~~ 91 (217)
+||..|+ .+.+++++
T Consensus 222 ~ll~~ll~~~~~~~~t~~~L 241 (257)
T PRK08517 222 EIFKICLLNLPSYIKTTEDL 241 (257)
T ss_pred HHHHHHHHHhHHhhcCHHHH
Confidence 9999998 45566666
No 5
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.42 E-value=2.5e-13 Score=134.79 Aligned_cols=129 Identities=17% Similarity=0.161 Sum_probs=99.2
Q ss_pred CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH--------------------------------
Q 027882 4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------- 51 (217)
Q Consensus 4 ~~~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL-------------------------------- 51 (217)
......||+||+||||.++ . ++|||||||+|..|++ +++|++|
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 027882 52 ---------------------------------------------------------LASLATYFGLG-QQTHRSLDDVR 73 (217)
Q Consensus 52 ---------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar 73 (217)
|.+|+++||+. .+.||||+||+
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 ccHHHHHHhh------hhhhhhcCcCccccccccCC-c-------cccccCCCCCCeeeeccCCcce-ecccceeeeccc
Q 027882 74 MNLEVLKYCA------TVLFLESGLPDIFTVNRWEM-C-------SAASVSEGSSGYARFMEPDELY-CSRLKIRYGIST 138 (217)
Q Consensus 74 ~tvdVl~~~~------gV~~lE~~~p~~~~~~~~v~-p-------~la~~lp~~pGvy~F~~p~dLy-gts~~vR~rVrs 138 (217)
+|.+||..|. ++.+++++ ........ + ......+..|+.|.|.+.-.|+ +.....+.++++
T Consensus 158 ata~L~~~l~~~l~~l~~~~l~~l----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~l~~ 233 (820)
T PRK07246 158 ATAELFLKLLQKIESLPKECLERL----LEYADSLLFESYLVIEEALANAKPYSSPDYIKVQGIVLKKTAASLKPRKLSQ 233 (820)
T ss_pred HHHHHHHHHHHHHhhcCchhHHHH----HHHHhhccccHHHHHHHHHHhcCCCCCCceEEecCeeeecccccccccchhh
Confidence 9999999988 55567765 33222111 1 2344666788889988766677 766666666777
Q ss_pred ccc
Q 027882 139 RFV 141 (217)
Q Consensus 139 yFt 141 (217)
+|.
T Consensus 234 ~F~ 236 (820)
T PRK07246 234 DFS 236 (820)
T ss_pred cCc
Confidence 664
No 6
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=99.41 E-value=3.5e-13 Score=111.50 Aligned_cols=76 Identities=17% Similarity=0.166 Sum_probs=64.0
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH----------------------------------
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL---------------------------------- 51 (217)
.+..+|+||+||||.++.. .+|||||||++.++.++..++|+++
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 7999999999998876543455443
Q ss_pred -------------------------------------------------------------HHHHHHhhCCC-CCccccc
Q 027882 52 -------------------------------------------------------------LASLATYFGLG-QQTHRSL 69 (217)
Q Consensus 52 -------------------------------------------------------------LatLA~~Fg~~-~~~HRAL 69 (217)
|++|+++||+. .+.||||
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 hhhhccHHHHHHhh
Q 027882 70 DDVRMNLEVLKYCA 83 (217)
Q Consensus 70 dDar~tvdVl~~~~ 83 (217)
+||++|++||.++.
T Consensus 185 ~DA~ata~l~~~l~ 198 (202)
T PRK09145 185 NDAIMAALIFLRLR 198 (202)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999875
No 7
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=99.41 E-value=3.4e-13 Score=113.69 Aligned_cols=71 Identities=23% Similarity=0.328 Sum_probs=63.1
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH------------------------------------
Q 027882 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------ 51 (217)
Q Consensus 8 ~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------------ 51 (217)
..||+||+||||.++ ..+|||||||+|..|.+ +++|++|
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 36799999999999876 5677777
Q ss_pred -------------------------------------------------------HHHHHHhhCCCCCccccchhhhccH
Q 027882 52 -------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNL 76 (217)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~tv 76 (217)
|.+||++||++...||||+||++|.
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 HHHHHhh
Q 027882 77 EVLKYCA 83 (217)
Q Consensus 77 dVl~~~~ 83 (217)
+||.+++
T Consensus 160 ~v~~~ll 166 (195)
T PRK07247 160 RVYESFL 166 (195)
T ss_pred HHHHHHH
Confidence 9999997
No 8
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=99.40 E-value=5.6e-13 Score=111.11 Aligned_cols=75 Identities=21% Similarity=0.308 Sum_probs=64.2
Q ss_pred CceEEEEEeecCCCCCCC----CceeEEEEeeEEEecCceeecccHHHH-------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPG----QRIAILEFGAILVCPKTLEELQPYSTL------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~----~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------- 51 (217)
+-.||+||+||||+++.. ...+|||||||+|..+.+ +++|++|
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 457999999999975432 236899999999999976 5788888
Q ss_pred ---------------------------------------------------------------HHHHHHhhCCC--CCcc
Q 027882 52 ---------------------------------------------------------------LASLATYFGLG--QQTH 66 (217)
Q Consensus 52 ---------------------------------------------------------------LatLA~~Fg~~--~~~H 66 (217)
|++++++||+. ..+|
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 ccchhhhccHHHHHHhh
Q 027882 67 RSLDDVRMNLEVLKYCA 83 (217)
Q Consensus 67 RALdDar~tvdVl~~~~ 83 (217)
|||+||++|.+||..+.
T Consensus 161 ~Al~DA~~ta~l~~~l~ 177 (207)
T PRK07748 161 CALDDAMTTYNIFKLVE 177 (207)
T ss_pred ChHHHHHHHHHHHHHHH
Confidence 99999999999999987
No 9
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=99.40 E-value=4.5e-13 Score=103.44 Aligned_cols=72 Identities=29% Similarity=0.382 Sum_probs=62.0
Q ss_pred eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-------------------------------------
Q 027882 9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------- 51 (217)
Q Consensus 9 e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------------- 51 (217)
.+|+||+||||.++.. .+|||||||++.++.+ .++|+++
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 4899999999998764 8999999999999873 4556555
Q ss_pred ------------------------------------------------------HHHHHHhhCCC-CCc-cccchhhhcc
Q 027882 52 ------------------------------------------------------LASLATYFGLG-QQT-HRSLDDVRMN 75 (217)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~-HRALdDar~t 75 (217)
|.+|+.+||+. .++ |||++||++|
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 HHHHHHhhh
Q 027882 76 LEVLKYCAT 84 (217)
Q Consensus 76 vdVl~~~~g 84 (217)
++|++.+..
T Consensus 157 ~~l~~~~~~ 165 (169)
T smart00479 157 AKLFKKLVE 165 (169)
T ss_pred HHHHHHHHH
Confidence 999998864
No 10
>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=99.40 E-value=3e-13 Score=100.76 Aligned_cols=39 Identities=33% Similarity=0.480 Sum_probs=32.6
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL 51 (217)
||||+||||+++.. ..|+|||||++.++...++++|+++
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 79999999998844 8999999999999985445666665
No 11
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=99.38 E-value=7.3e-13 Score=114.58 Aligned_cols=44 Identities=16% Similarity=0.108 Sum_probs=36.3
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL 51 (217)
.+..||+||+||||.++.. .+|||+|||++.++.++..++|++|
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 12
>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=99.36 E-value=1e-12 Score=103.57 Aligned_cols=72 Identities=24% Similarity=0.323 Sum_probs=58.9
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH--------------------------------------
Q 027882 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------- 51 (217)
Q Consensus 10 ~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL-------------------------------------- 51 (217)
.|+||+||||+++.+ +++|||||||+|..+.+ ..++|+++
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 489999999999844 38999999999988765 22355444
Q ss_pred ------------------------------------------------------HHHHHHhhCCC---CCccccchhhhc
Q 027882 52 ------------------------------------------------------LASLATYFGLG---QQTHRSLDDVRM 74 (217)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~---~~~HRALdDar~ 74 (217)
|++|++++|+. .+.||||+||++
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 cHHHHHHhh
Q 027882 75 NLEVLKYCA 83 (217)
Q Consensus 75 tvdVl~~~~ 83 (217)
|.+|+..++
T Consensus 159 ~a~l~~~l~ 167 (167)
T cd06131 159 LAEVYLELT 167 (167)
T ss_pred HHHHHHHhC
Confidence 999998763
No 13
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=99.36 E-value=1.1e-12 Score=117.94 Aligned_cols=76 Identities=22% Similarity=0.364 Sum_probs=66.6
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-----------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL----------------------------------- 51 (217)
-..+|+||+||||.++.. ++|||||||+|+.|.+ +++|++|
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 027882 52 -------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNL 76 (217)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~tv 76 (217)
|.+|+.+||+..+.||||+||++|.
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 027882 77 EVLKYCATVL 86 (217)
Q Consensus 77 dVl~~~~gV~ 86 (217)
+|+.+|..-.
T Consensus 163 ~l~~~l~~~~ 172 (313)
T PRK06807 163 AVYQKCASIE 172 (313)
T ss_pred HHHHHHHHhh
Confidence 9999999654
No 14
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=99.36 E-value=1.1e-12 Score=111.98 Aligned_cols=77 Identities=21% Similarity=0.226 Sum_probs=66.1
Q ss_pred CCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeecccHHHH-------------------------------
Q 027882 4 RQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL------------------------------- 51 (217)
Q Consensus 4 ~~~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p-~~l~e~~sf~TL------------------------------- 51 (217)
.=.+..||+||+||||.++.. .+|||+|+|+|.. |.+ +++|++|
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 027882 52 -------------------------------------------------------------------LASLATYFGLG-Q 63 (217)
Q Consensus 52 -------------------------------------------------------------------LatLA~~Fg~~-~ 63 (217)
|++|+.+||+. .
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 88999999999 8
Q ss_pred CccccchhhhccHHHHHHhhh
Q 027882 64 QTHRSLDDVRMNLEVLKYCAT 84 (217)
Q Consensus 64 ~~HRALdDar~tvdVl~~~~g 84 (217)
+.||||+||+||++||..++.
T Consensus 158 ~aH~Al~Da~ata~l~~~l~~ 178 (232)
T PRK07942 158 NAHEATADALAAARVAWALAR 178 (232)
T ss_pred CCCChHHHHHHHHHHHHHHHH
Confidence 899999999999999999873
No 15
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=99.35 E-value=1.3e-12 Score=116.98 Aligned_cols=73 Identities=29% Similarity=0.326 Sum_probs=64.3
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeecccHHHH----------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL---------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p-~~l~e~~sf~TL---------------------------------- 51 (217)
..+||+||+||||+++.. .+|||||||+|.. |.+ +++|++|
T Consensus 14 ~~~fvvlD~ETTGl~p~~--d~IIeIgav~v~~~g~i--~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~l~ 89 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQ--ARIISLAVLGLDADGNV--EQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGEVA 89 (313)
T ss_pred CCCEEEEEEECCCCCCCC--CEEEEEEEEEEECCcee--eeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHHHH
Confidence 467999999999998865 8999999999975 555 4667666
Q ss_pred ------------------------------------------------------HHHHHHhhCCC-CCccccchhhhccH
Q 027882 52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL 76 (217)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~tv 76 (217)
|.+|+.+||+. .+.||||+||++|.
T Consensus 90 ~~l~~~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~lar~~~~~~~~~kL~~l~~~~gi~~~~~H~Al~DA~ata 169 (313)
T PRK06063 90 ELLRGRTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVELARRLGLGLPNLRLETLAAHWGVPQQRPHDALDDARVLA 169 (313)
T ss_pred HHcCCCEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHHHHHHhccCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHH
Confidence 99999999999 88999999999999
Q ss_pred HHHHHhh
Q 027882 77 EVLKYCA 83 (217)
Q Consensus 77 dVl~~~~ 83 (217)
+||.+++
T Consensus 170 ~l~~~ll 176 (313)
T PRK06063 170 GILRPSL 176 (313)
T ss_pred HHHHHHH
Confidence 9998886
No 16
>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=99.35 E-value=8.8e-13 Score=107.77 Aligned_cols=32 Identities=25% Similarity=0.261 Sum_probs=27.6
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 027882 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTL 42 (217)
Q Consensus 10 ~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l 42 (217)
||+||+||||+++.++ .+|||+|||+|.++.+
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 6899999999985443 8999999999998764
No 17
>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=99.34 E-value=1.2e-12 Score=110.01 Aligned_cols=74 Identities=18% Similarity=0.120 Sum_probs=62.4
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH----------------------------------
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL---------------------------------- 51 (217)
.+.+||+||+||||+++.. . |||||||+|..+..+ .++|++|
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 027882 52 -----------------------------------------------------------LASLATYFGLG-Q--QTHRSL 69 (217)
Q Consensus 52 -----------------------------------------------------------LatLA~~Fg~~-~--~~HRAL 69 (217)
|.+|+.++|+. . ..||||
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 hhhhccHHHHHHhh
Q 027882 70 DDVRMNLEVLKYCA 83 (217)
Q Consensus 70 dDar~tvdVl~~~~ 83 (217)
+||++|.+||.+++
T Consensus 161 ~DA~~ta~l~~~l~ 174 (217)
T TIGR00573 161 ADAFILAKLYLVMT 174 (217)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999999997
No 18
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=99.33 E-value=1.7e-12 Score=112.35 Aligned_cols=81 Identities=28% Similarity=0.340 Sum_probs=67.9
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-----------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL----------------------------------- 51 (217)
+..+|+||+||||.++.. .+|||||||+|.++.+ +++|++|
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 027882 52 ---------------------------------------------------------LASLATYFGLG-QQTHRSLDDVR 73 (217)
Q Consensus 52 ---------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar 73 (217)
|++|+.+||+. ...|||++||.
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 88899999999 88999999999
Q ss_pred ccHHHHHHhh-hhhhhhcC
Q 027882 74 MNLEVLKYCA-TVLFLESG 91 (217)
Q Consensus 74 ~tvdVl~~~~-gV~~lE~~ 91 (217)
+|.+||++++ ....+|++
T Consensus 162 at~~vl~~l~~~~~~~~~l 180 (250)
T PRK06310 162 INIKVFKHLCKRFRTLEQL 180 (250)
T ss_pred HHHHHHHHHHHhcccHHHH
Confidence 9999999987 44444544
No 19
>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=99.32 E-value=1.9e-12 Score=99.89 Aligned_cols=28 Identities=32% Similarity=0.554 Sum_probs=25.9
Q ss_pred HHHHHHhhCCCCCccccchhhhccHHHH
Q 027882 52 LASLATYFGLGQQTHRSLDDVRMNLEVL 79 (217)
Q Consensus 52 LatLA~~Fg~~~~~HRALdDar~tvdVl 79 (217)
|++|+++||+..+.||||+||++|.++|
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 20
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=99.31 E-value=3e-12 Score=114.31 Aligned_cols=83 Identities=25% Similarity=0.210 Sum_probs=69.5
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEec---Ccee-ecccHHHH-------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCP---KTLE-ELQPYSTL------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p---~~l~-e~~sf~TL------------------------------- 51 (217)
...+|+||+||||.++.. ++|||||||+|.. |.+. .+++|++|
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 027882 52 -----------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNLEV 78 (217)
Q Consensus 52 -----------------------------------------------------LatLA~~Fg~~~~~HRALdDar~tvdV 78 (217)
|.+|+.+||.....||||+||.+|++|
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 HHHhh---hhhhhhcC
Q 027882 79 LKYCA---TVLFLESG 91 (217)
Q Consensus 79 l~~~~---gV~~lE~~ 91 (217)
|..++ |...|+++
T Consensus 194 l~~~l~~~~~~~l~~L 209 (294)
T PRK09182 194 LARPLPETGQPPLAEL 209 (294)
T ss_pred HHHHHhhcCCcCHHHH
Confidence 99887 66677777
No 21
>PRK06722 exonuclease; Provisional
Probab=99.27 E-value=7.9e-12 Score=111.78 Aligned_cols=77 Identities=26% Similarity=0.416 Sum_probs=63.8
Q ss_pred CCceEEEEEeecCCCCCC--CCceeEEEEeeEEEecCceeecccHHHH--------------------------------
Q 027882 6 DRFEIAFFDVETAFPNPP--GQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------- 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~--~~~~~ilEfgAI~V~p~~l~e~~sf~TL-------------------------------- 51 (217)
....||+||+|||+ +|. ..+++|||||||+|..|.+..++.|++|
T Consensus 3 ~~~~~vViD~ETT~-~p~~~~~~deIIEIGAVkV~~g~i~Ivd~F~sLV~P~~~I~~~i~~LTGIT~emV~~AP~f~eVl 81 (281)
T PRK06722 3 NATHFIVFDIERNF-RPYKSEDPSEIVDIGAVKIEASTMKVIGEFSELVKPGARLTRHTTKLTGITKKDLIGVEKFPQII 81 (281)
T ss_pred CCCEEEEEEeeCCC-CCCCCCCCCeEEEEEEEEEECCceeEEeeEEEEECCCCcCCHhHhhhcCCCHHHHcCCCCHHHHH
Confidence 35789999999995 442 2358999999999999843336789888
Q ss_pred ---------------------------------------------------------------HHHHHHhhCCC--CCcc
Q 027882 52 ---------------------------------------------------------------LASLATYFGLG--QQTH 66 (217)
Q Consensus 52 ---------------------------------------------------------------LatLA~~Fg~~--~~~H 66 (217)
|++|+++||++ .+.|
T Consensus 82 ~ef~~fig~~~lvahna~FD~~FL~~~l~~~gi~~p~~~~~~~idl~~la~~~~~~l~~~~~sL~~l~~~lgL~~~g~~H 161 (281)
T PRK06722 82 EKFIQFIGEDSIFVTWGKEDYRFLSHDCTLHSVECPCMEKERRIDLQKFVFQAYEELFEHTPSLQSAVEQLGLIWEGKQH 161 (281)
T ss_pred HHHHHHHCCCcEEEEEeHHHHHHHHHHHHHcCCCCCcccccchhHHHHHHHHHhhhhccCCCCHHHHHHHCCCCCCCCCc
Confidence 67888999999 4689
Q ss_pred ccchhhhccHHHHHHhh
Q 027882 67 RSLDDVRMNLEVLKYCA 83 (217)
Q Consensus 67 RALdDar~tvdVl~~~~ 83 (217)
|||+||++|..+|..++
T Consensus 162 rAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 162 RALADAENTANILLKAY 178 (281)
T ss_pred CcHHHHHHHHHHHHHHh
Confidence 99999999999999886
No 22
>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=99.26 E-value=7.8e-12 Score=104.59 Aligned_cols=34 Identities=24% Similarity=0.212 Sum_probs=29.7
Q ss_pred HHHHHHhhCCC---CCccccchhhhccHHHHHHhhhh
Q 027882 52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKYCATV 85 (217)
Q Consensus 52 LatLA~~Fg~~---~~~HRALdDar~tvdVl~~~~gV 85 (217)
|+.|++++|+. .+.||||+||.+|.+||..++.-
T Consensus 155 L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~ 191 (200)
T TIGR01298 155 LAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNR 191 (200)
T ss_pred HHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHH
Confidence 77888899987 48999999999999999998743
No 23
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=99.26 E-value=3.6e-12 Score=131.74 Aligned_cols=85 Identities=20% Similarity=0.266 Sum_probs=79.7
Q ss_pred CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-------------------------------
Q 027882 3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------- 51 (217)
Q Consensus 3 ~~~~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------- 51 (217)
+.-+++++|+||+||||+++.- ..||||||+++..|++ ++.|+.+
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 8899998
Q ss_pred -----------------------------------------------------------HHHHHHhhCCC-CCccccchh
Q 027882 52 -----------------------------------------------------------LASLATYFGLG-QQTHRSLDD 71 (217)
Q Consensus 52 -----------------------------------------------------------LatLA~~Fg~~-~~~HRALdD 71 (217)
|++|+.-||+. .++|||.+|
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 hhccHHHHHHhh------hhhhhhcC
Q 027882 72 VRMNLEVLKYCA------TVLFLESG 91 (217)
Q Consensus 72 ar~tvdVl~~~~------gV~~lE~~ 91 (217)
|.+|..||..+. |+..|+++
T Consensus 572 aeat~~vf~~f~~~~ke~Gi~~l~el 597 (1444)
T COG2176 572 AEATAKVFFVFLKDLKEKGITNLSEL 597 (1444)
T ss_pred HHHHHHHHHHHHHHHHHhchhhHHHH
Confidence 999999999888 99999887
No 24
>PRK05168 ribonuclease T; Provisional
Probab=99.25 E-value=1.1e-11 Score=104.57 Aligned_cols=34 Identities=21% Similarity=0.239 Sum_probs=29.2
Q ss_pred HHHHHHhhCCC---CCccccchhhhccHHHHHHhhhh
Q 027882 52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKYCATV 85 (217)
Q Consensus 52 LatLA~~Fg~~---~~~HRALdDar~tvdVl~~~~gV 85 (217)
|.+++.++|++ ...||||+||.+|.+||.+++.-
T Consensus 164 L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~ 200 (211)
T PRK05168 164 LAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNR 200 (211)
T ss_pred HHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHH
Confidence 66778888987 36899999999999999998854
No 25
>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=99.25 E-value=9.4e-12 Score=106.35 Aligned_cols=73 Identities=25% Similarity=0.316 Sum_probs=62.5
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH--------------------------------------
Q 027882 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------- 51 (217)
Q Consensus 10 ~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL-------------------------------------- 51 (217)
+|+||+||||+++..+ .+|||||||++..+.+ ..++|+++
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-HRIVEIGAVELVNRML-TGDNFHVYVNPERDMPAEAAKVHGITDEFLADKPKFKEIADEFLDF 79 (225)
T ss_pred EEEEEeeCCCcCCCCC-CeEEEEEEEEEECCcE-ecceEEEEECcCCCCCHHHHhccCCCHHHHhCCCCHHHHHHHHHHH
Confidence 7999999999998763 8999999999987765 23567666
Q ss_pred -------------------------------------------------------HHHHHHhhCCCC---Cccccchhhh
Q 027882 52 -------------------------------------------------------LASLATYFGLGQ---QTHRSLDDVR 73 (217)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~~---~~HRALdDar 73 (217)
|.+|+++||+.. +.||||+||+
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 ccHHHHHHhhh
Q 027882 74 MNLEVLKYCAT 84 (217)
Q Consensus 74 ~tvdVl~~~~g 84 (217)
++.+|+..+.|
T Consensus 160 ~~a~v~~~l~~ 170 (225)
T TIGR01406 160 LLAEVYLALTG 170 (225)
T ss_pred HHHHHHHHHHc
Confidence 99999999884
No 26
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=99.24 E-value=8.7e-12 Score=110.57 Aligned_cols=69 Identities=20% Similarity=0.289 Sum_probs=60.6
Q ss_pred eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-------------------------------------
Q 027882 9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------- 51 (217)
Q Consensus 9 e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------------- 51 (217)
+||+||+|||++. +.+|+|+|||+|..+.+ +++|++|
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 6999999999752 37899999999999887 4556666
Q ss_pred ------------------------------------------------------HHHHHHhhCCCCCccccchhhhccHH
Q 027882 52 ------------------------------------------------------LASLATYFGLGQQTHRSLDDVRMNLE 77 (217)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~~~~HRALdDar~tvd 77 (217)
|.+|+.+||+...+||||+||++|.+
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 HHHHhh
Q 027882 78 VLKYCA 83 (217)
Q Consensus 78 Vl~~~~ 83 (217)
||..++
T Consensus 156 l~~~l~ 161 (309)
T PRK06195 156 ILLNIS 161 (309)
T ss_pred HHHHHH
Confidence 999987
No 27
>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=99.23 E-value=1.3e-11 Score=92.12 Aligned_cols=38 Identities=34% Similarity=0.455 Sum_probs=31.0
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL 51 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL 51 (217)
||||+||||.++.. .+|+|+|||++..+ +.++++|+.+
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 68999999998754 89999999999988 3345666655
No 28
>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=99.23 E-value=1.6e-11 Score=101.46 Aligned_cols=32 Identities=22% Similarity=0.287 Sum_probs=28.3
Q ss_pred HHHHHHhhCCC---CCccccchhhhccHHHHHHhh
Q 027882 52 LASLATYFGLG---QQTHRSLDDVRMNLEVLKYCA 83 (217)
Q Consensus 52 LatLA~~Fg~~---~~~HRALdDar~tvdVl~~~~ 83 (217)
|++|+++||++ ...||||+||.+|.++|.+++
T Consensus 152 L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~ 186 (189)
T cd06134 152 LAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIV 186 (189)
T ss_pred HHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHH
Confidence 78888999997 368999999999999998875
No 29
>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=99.22 E-value=1e-11 Score=128.60 Aligned_cols=82 Identities=26% Similarity=0.342 Sum_probs=70.2
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH----------------------------------
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL---------------------------------- 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL---------------------------------- 51 (217)
++.+||+||+||||+++.. .+|||||||+|..|.++ ++|++|
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 027882 52 --------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRM 74 (217)
Q Consensus 52 --------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~ 74 (217)
|++||.+||+. .+.|||++||++
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 cHHHHHHhh------hhhhhhcC
Q 027882 75 NLEVLKYCA------TVLFLESG 91 (217)
Q Consensus 75 tvdVl~~~~------gV~~lE~~ 91 (217)
|++||..++ |+..++++
T Consensus 344 Ta~I~~~ll~~l~~~~i~~~~~l 366 (1213)
T TIGR01405 344 TAKVFKVMVEQLKEKGITNLEEL 366 (1213)
T ss_pred HHHHHHHHHHHHHHcCCccHHHH
Confidence 999999998 66666665
No 30
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=99.20 E-value=2.8e-11 Score=105.26 Aligned_cols=76 Identities=22% Similarity=0.271 Sum_probs=63.8
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-----------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL----------------------------------- 51 (217)
+-.+|+||+||||+++.. +.+|||||||++..+++. .++|+++
T Consensus 3 ~~r~vvlDtETTGldp~~-~drIIEIGaV~v~~~~~~-~~~f~~~i~P~~~i~~~a~~VHGIT~e~l~~~p~f~ev~~~f 80 (240)
T PRK05711 3 IMRQIVLDTETTGLNQRE-GHRIIEIGAVELINRRLT-GRNFHVYIKPDRLVDPEALAVHGITDEFLADKPTFAEVADEF 80 (240)
T ss_pred CCeEEEEEeeCCCcCCCC-CCeEEEEEEEEEECCEEe-ccEEEEEECcCCcCCHHHhhhcCCCHHHHcCCCCHHHHHHHH
Confidence 346899999999999873 389999999999988763 2466655
Q ss_pred ----------------------------------------------------------HHHHHHhhCCCC---Cccccch
Q 027882 52 ----------------------------------------------------------LASLATYFGLGQ---QTHRSLD 70 (217)
Q Consensus 52 ----------------------------------------------------------LatLA~~Fg~~~---~~HRALd 70 (217)
|.+|+.+||++. ..|+||.
T Consensus 81 ~~fi~~~~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~p~~~~~L~aL~~~~gi~~~~r~~H~AL~ 160 (240)
T PRK05711 81 LDFIRGAELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMFPGKRNSLDALCKRYGIDNSHRTLHGALL 160 (240)
T ss_pred HHHhCCCEEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHcCCCCCCHHHHHHHCCCCCCCCCCCCHHH
Confidence 889999999983 3599999
Q ss_pred hhhccHHHHHHhhh
Q 027882 71 DVRMNLEVLKYCAT 84 (217)
Q Consensus 71 Dar~tvdVl~~~~g 84 (217)
||+++.+|+..+.|
T Consensus 161 DA~~~A~v~~~l~~ 174 (240)
T PRK05711 161 DAEILAEVYLAMTG 174 (240)
T ss_pred HHHHHHHHHHHHHC
Confidence 99999999998873
No 31
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=99.20 E-value=1.9e-11 Score=122.53 Aligned_cols=73 Identities=25% Similarity=0.359 Sum_probs=66.8
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH------------------------------------
Q 027882 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------ 51 (217)
Q Consensus 8 ~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------------ 51 (217)
..||+||+||||.++..+ .+|||||||+|..|++ +++|+++
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 469999999999987764 8999999999999988 5688888
Q ss_pred ------------------------------------------------------HHHHHHhhCCC-CCccccchhhhccH
Q 027882 52 ------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNL 76 (217)
Q Consensus 52 ------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~tv 76 (217)
|++||++||++ ...||||+||++|+
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 HHHHHhh
Q 027882 77 EVLKYCA 83 (217)
Q Consensus 77 dVl~~~~ 83 (217)
++|.+++
T Consensus 160 ~l~~~l~ 166 (928)
T PRK08074 160 ELFLQLL 166 (928)
T ss_pred HHHHHHH
Confidence 9999997
No 32
>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=99.19 E-value=3.3e-11 Score=98.21 Aligned_cols=37 Identities=19% Similarity=0.147 Sum_probs=29.5
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccH
Q 027882 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPY 48 (217)
Q Consensus 10 ~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf 48 (217)
+++||+||||.+|.+ .+|||+|||++.++.....++|
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 8999999999998644323333
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=99.17 E-value=3.3e-11 Score=119.18 Aligned_cols=71 Identities=24% Similarity=0.313 Sum_probs=64.5
Q ss_pred eEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-------------------------------------
Q 027882 9 EIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------- 51 (217)
Q Consensus 9 e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------------- 51 (217)
+||+||+||||+++.. ++|||||||+|..|++ ++.|+++
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 027882 52 -----------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMNLE 77 (217)
Q Consensus 52 -----------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~tvd 77 (217)
|++|++++|+. .+.||||+||++|++
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 888999999999999
Q ss_pred HHHHhh
Q 027882 78 VLKYCA 83 (217)
Q Consensus 78 Vl~~~~ 83 (217)
+|.+++
T Consensus 157 l~~~l~ 162 (850)
T TIGR01407 157 LLLLLF 162 (850)
T ss_pred HHHHHH
Confidence 999997
No 34
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=99.16 E-value=1.1e-10 Score=99.39 Aligned_cols=38 Identities=32% Similarity=0.358 Sum_probs=33.0
Q ss_pred HHHHHHhhCCC-CCccccchhhhccHHHHHHhhhhhhhh
Q 027882 52 LASLATYFGLG-QQTHRSLDDVRMNLEVLKYCATVLFLE 89 (217)
Q Consensus 52 LatLA~~Fg~~-~~~HRALdDar~tvdVl~~~~gV~~lE 89 (217)
|.+|+.+||+. ...|||++||.+|.+||.+++.-+..+
T Consensus 131 L~~l~~~~~~~~~~aH~Al~Da~~t~~vl~~l~~~~~~~ 169 (232)
T PRK06309 131 LQYLRQVYGFEENQAHRALDDVITLHRVFSALVGDLSPQ 169 (232)
T ss_pred HHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 88899999999 889999999999999999998443333
No 35
>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=99.12 E-value=4.8e-11 Score=97.67 Aligned_cols=37 Identities=32% Similarity=0.443 Sum_probs=29.1
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecC-ceeecccHHHH
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPK-TLEELQPYSTL 51 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~-~l~e~~sf~TL 51 (217)
++||+||||.++.. .+|||+|||+|.++ .+ +++|+++
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 2455554
No 36
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=99.11 E-value=7.4e-11 Score=101.16 Aligned_cols=67 Identities=24% Similarity=0.253 Sum_probs=58.3
Q ss_pred EEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH--------------------------------------
Q 027882 10 IAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL-------------------------------------- 51 (217)
Q Consensus 10 ~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL-------------------------------------- 51 (217)
+++||+||||.++ .|||+||++|..+++ +++|++|
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 7899999999963 299999999998887 4567666
Q ss_pred ---------------------------------------HHHHHHhhCCC------CCccccchhhhccHHHHHHhh
Q 027882 52 ---------------------------------------LASLATYFGLG------QQTHRSLDDVRMNLEVLKYCA 83 (217)
Q Consensus 52 ---------------------------------------LatLA~~Fg~~------~~~HRALdDar~tvdVl~~~~ 83 (217)
+.+|+.+||++ ...||||+||.+|.+||.+++
T Consensus 75 ~~lVaHNa~FD~~~L~~~~~~~idTl~lar~l~p~~~~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~ 151 (219)
T PRK07983 75 EWYVAHNASFDRRVLPEMPGEWICTMKLARRLWPGIKYSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIM 151 (219)
T ss_pred CEEEEeCcHhhHHHHhCcCCCcEeHHHHHHHHccCCCCCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 88899999986 359999999999999999998
No 37
>PRK05359 oligoribonuclease; Provisional
Probab=99.01 E-value=6.6e-10 Score=92.29 Aligned_cols=32 Identities=19% Similarity=0.270 Sum_probs=28.4
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~ 40 (217)
+..||+||+||||++|.. .+|||+|||++..+
T Consensus 2 ~~~~vvlD~ETTGLdp~~--d~IieIgaV~~~~~ 33 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER--DRIIEIATIVTDAD 33 (181)
T ss_pred CCcEEEEEeecCCCCCCC--CeEEEEEEEEEcCC
Confidence 457999999999999976 79999999998765
No 38
>PRK11779 sbcB exonuclease I; Provisional
Probab=98.96 E-value=1.2e-09 Score=104.04 Aligned_cols=35 Identities=20% Similarity=0.086 Sum_probs=30.5
Q ss_pred CCCceEEEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 027882 5 QDRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKT 41 (217)
Q Consensus 5 ~~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~ 41 (217)
..+.+||+||+||||.+|.. .+|||||||+|..+.
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=98.95 E-value=1.1e-09 Score=91.54 Aligned_cols=74 Identities=30% Similarity=0.374 Sum_probs=65.3
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH------------------------------------
Q 027882 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL------------------------------------ 51 (217)
Q Consensus 8 ~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL------------------------------------ 51 (217)
..+|+||+||||.++.+ .+|||+|||.+..+.+++ .+|+++
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 47899999999999854 899999999999999854 336666
Q ss_pred -------------------------------------------------------HHHHHHhhCCC---CCccccchhhh
Q 027882 52 -------------------------------------------------------LASLATYFGLG---QQTHRSLDDVR 73 (217)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~---~~~HRALdDar 73 (217)
|..|+.++|+. ...||||.||.
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 ccHHHHHHhhh
Q 027882 74 MNLEVLKYCAT 84 (217)
Q Consensus 74 ~tvdVl~~~~g 84 (217)
++.+|+..+.+
T Consensus 170 ~~a~~~~~~~~ 180 (243)
T COG0847 170 ALAELFLLLQT 180 (243)
T ss_pred HHHHHHHHHHh
Confidence 99999988885
No 40
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=98.89 E-value=7.9e-10 Score=116.34 Aligned_cols=81 Identities=23% Similarity=0.250 Sum_probs=68.6
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHH-----------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTL----------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TL----------------------------------- 51 (217)
+.++|+||+||||.++.. ..|||+||+++..|.++ +.|+++
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 222221
Q ss_pred -------------------------------------------------------HHHHHHhhCCC-CCccccchhhhcc
Q 027882 52 -------------------------------------------------------LASLATYFGLG-QQTHRSLDDVRMN 75 (217)
Q Consensus 52 -------------------------------------------------------LatLA~~Fg~~-~~~HRALdDar~t 75 (217)
|.+||.+||+. .++||||+||++|
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 HHHHHHhh------hhhhhhcC
Q 027882 76 LEVLKYCA------TVLFLESG 91 (217)
Q Consensus 76 vdVl~~~~------gV~~lE~~ 91 (217)
.+||..++ |+.+++++
T Consensus 574 a~lf~~ll~~l~~~gi~~~~~L 595 (1437)
T PRK00448 574 AYLLIKFLKDLKEKGITNLDEL 595 (1437)
T ss_pred HHHHHHHHHHHHHcCCCCHHHH
Confidence 99999998 78888776
No 41
>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=98.88 E-value=1.8e-09 Score=87.23 Aligned_cols=30 Identities=13% Similarity=0.135 Sum_probs=25.2
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~ 40 (217)
|+||+||||.++.++...|+++++|.+..+
T Consensus 1 v~~D~EttGl~~~~~~~~i~~i~~v~~~g~ 30 (157)
T cd06149 1 VAIDCEMVGTGPGGRESELARCSIVNYHGD 30 (157)
T ss_pred CEEEeEeccccCCCCeEEEEEEEEEeCCCC
Confidence 689999999998765689999999986544
No 42
>PTZ00315 2'-phosphotransferase; Provisional
Probab=98.83 E-value=4.1e-09 Score=102.96 Aligned_cols=42 Identities=17% Similarity=0.244 Sum_probs=32.4
Q ss_pred ceEEEEEeecCCCCCCC-CceeEEEEeeEEEe--cCceeecccHHHH
Q 027882 8 FEIAFFDVETAFPNPPG-QRIAILEFGAILVC--PKTLEELQPYSTL 51 (217)
Q Consensus 8 ~e~vffDvETT~~~~~~-~~~~ilEfgAI~V~--p~~l~e~~sf~TL 51 (217)
..|++||+|||++++.. ...+|||||||+|. .+++ ++.|++|
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 56999999999987642 24799999999996 4444 4566666
No 43
>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=98.78 E-value=6.6e-09 Score=83.74 Aligned_cols=30 Identities=13% Similarity=0.076 Sum_probs=26.2
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTL 42 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l 42 (217)
|+||+||||.++.+ .+|+|+|||++..|++
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 8999999999976664
No 44
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=98.72 E-value=1.9e-08 Score=94.24 Aligned_cols=42 Identities=7% Similarity=0.185 Sum_probs=34.8
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEec-CceeecccHHHH
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCP-KTLEELQPYSTL 51 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p-~~l~e~~sf~TL 51 (217)
.+..||+||+||||+++.. .+|||||||++.+ |.+ +++|++|
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 4777777
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=98.67 E-value=2.1e-08 Score=79.94 Aligned_cols=29 Identities=31% Similarity=0.581 Sum_probs=25.0
Q ss_pred HHHHHHh-hCCC--CCccccchhhhccHHHHH
Q 027882 52 LASLATY-FGLG--QQTHRSLDDVRMNLEVLK 80 (217)
Q Consensus 52 LatLA~~-Fg~~--~~~HRALdDar~tvdVl~ 80 (217)
|++||++ +|++ ...||||+||++|.+||+
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
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=98.33 E-value=2.9e-07 Score=89.56 Aligned_cols=68 Identities=9% Similarity=0.164 Sum_probs=55.8
Q ss_pred cccccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeeccc---------cchHHHHHHHHHHHHH
Q 027882 105 SAASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDAS---------QSLCTVLDACEVVAKK 172 (217)
Q Consensus 105 ~la~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla---------~~v~~Vl~~Cd~~a~~ 172 (217)
+.++.+|..||||.|. .++ || |.+.|||.||++||+++..++|+..||.-. ..+++.|-.|.-|-+-
T Consensus 8 ~~l~~lP~~PGVYl~~-~~g~viYVGKAknLr~RV~sYF~~~~~~~K~~~lv~~i~~ie~i~t~sE~EALlLE~~LIK~~ 86 (567)
T PRK14667 8 ELIEKAPEEPGVYLFK-KKKRYIYIGKAKNIKNRLLQHYKQSETDPKERAIFSESSSLEWIITRNEYEALVLEIDLIQQY 86 (567)
T ss_pred HHHHhCCCCCeEEEEe-cCCeEEEeeCcHhHHHHHHHHcCCCCCChHHHHHHHhhCeEEEEEeCCHHHHHHHHHHHHHHh
Confidence 3467899999999999 777 99 999999999999999877789999898554 4556777777777654
Q ss_pred h
Q 027882 173 L 173 (217)
Q Consensus 173 ~ 173 (217)
.
T Consensus 87 ~ 87 (567)
T PRK14667 87 K 87 (567)
T ss_pred C
Confidence 3
No 47
>PRK12306 uvrC excinuclease ABC subunit C; Reviewed
Probab=98.27 E-value=1e-07 Score=91.76 Aligned_cols=66 Identities=15% Similarity=0.256 Sum_probs=54.4
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHH
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKK 172 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla~~---------v~~Vl~~Cd~~a~~ 172 (217)
.+.+|..||||.|.+.++ || |.+.|||.||++||+++..++|...||.-..+ +++.|-.|.-|-+-
T Consensus 4 l~~lP~~PGVYl~~d~~g~vIYVGKAknLr~RV~sYF~~~~~~~K~~~lv~~i~~ie~ivt~sE~eALlLE~~LIK~~ 81 (519)
T PRK12306 4 LSTIPTNPGCYLYKDEEGTIIYVGKAKNLKKRVSSYFQKKDHDPKTQSLVKAIRDIEFIVTDNEVEALLLENTLIKKH 81 (519)
T ss_pred hhHCCCCCeEEEEECCCCCEEEeccchhHHHHHHHhCCCCCCChHHHHHHHHhcEEEEEEeCCHHHHHHHHHHHHHHh
Confidence 357999999999999988 99 99999999999999987778898888765544 55666667666554
No 48
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=98.26 E-value=1.1e-07 Score=93.15 Aligned_cols=68 Identities=10% Similarity=0.141 Sum_probs=55.0
Q ss_pred cccccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCC-CCccceeeeccccc---------hHHHHHHHHHHHH
Q 027882 105 SAASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA-GRPRLSFVVDASQS---------LCTVLDACEVVAK 171 (217)
Q Consensus 105 ~la~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se-~RpRm~emVdla~~---------v~~Vl~~Cd~~a~ 171 (217)
...+.+|..||||.|.+.++ || |.+.|||.||++||+++. .++|+..||.-..+ +++.|-.|.-|-+
T Consensus 14 ~~l~~lP~~PGVYl~~d~~g~viYVGKAknLr~RV~sYF~~~~~~~~K~~~lv~~i~~ie~i~t~sE~EALlLE~~LIk~ 93 (621)
T PRK14671 14 EKLASLPTSPGVYQFKNAAGRVIYVGKAKNLRNRVRSYFRNSRQLSGKTLVLVGHIADLEVIITSSEVEALILENNLIKE 93 (621)
T ss_pred HHHHhCCCCCeEEEEECCCCCEEEeecchhHHHHHHHHcCCCCCCChHHHHHHHhhceEEEEEeCCHHHHHHHHHHHHHH
Confidence 34568999999999999988 99 999999999999999765 48898888876555 4566666666655
Q ss_pred H
Q 027882 172 K 172 (217)
Q Consensus 172 ~ 172 (217)
-
T Consensus 94 ~ 94 (621)
T PRK14671 94 L 94 (621)
T ss_pred h
Confidence 3
No 49
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=98.25 E-value=1.3e-07 Score=94.23 Aligned_cols=66 Identities=14% Similarity=0.190 Sum_probs=55.1
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCC-CCccceeeeccccc---------hHHHHHHHHHHHHH
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA-GRPRLSFVVDASQS---------LCTVLDACEVVAKK 172 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se-~RpRm~emVdla~~---------v~~Vl~~Cd~~a~~ 172 (217)
.+.+|..||||+|.+.++ || |.+.|||.||++||+++. .++|+..||.-..+ +++.|-.|.-|-|-
T Consensus 6 l~~LP~~PGVYlfkD~~G~VIYVGKAKNLR~RV~SYF~~~~~~~~K~~~Lv~~i~~Ie~ivT~sE~EALLLE~~LIK~~ 84 (694)
T PRK14666 6 LSTIPLTPGVYLYKDEAGRIIYVGKARHLRRRVASYFRDVSALTPKTVAMLRHAVTIDTLSTTTEKEALLLEASLIKKH 84 (694)
T ss_pred HhhCCCCCeEEEEECCCCCEEEeeCcHhHHHHHHHHcCCCCCCChHHHHHHHhcCeeEEEEeCCHHHHHHHHHHHHHHh
Confidence 568999999999999988 99 999999999999999866 68899888876655 45666667766654
No 50
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=98.23 E-value=1.4e-07 Score=92.78 Aligned_cols=56 Identities=11% Similarity=0.207 Sum_probs=48.5
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCC-CCCccceeeeccccchHHH
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQ-AGRPRLSFVVDASQSLCTV 162 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~s-e~RpRm~emVdla~~v~~V 162 (217)
...+|..||||+|.+.++ || |.+.|||.||++||+++ ..++|+..||.-..+++-|
T Consensus 7 l~~lP~~PGVYl~~d~~g~viYVGKAknLr~RV~sYF~~~~~~~~K~~~lv~~i~~ie~i 66 (624)
T PRK14669 7 IRTLPTSPGVYLYKNAGGEVIYVGKAKNLRSRVRSYFSEDKLGNIKTGSLIREAVDIDYI 66 (624)
T ss_pred HHhCCCCCeEEEEECCCCCEEEeeCchhHHHHHHHHhccCccCChHHHHHHHhhceEEEE
Confidence 457899999999999988 99 99999999999999965 5689999998877666544
No 51
>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=98.23 E-value=1e-06 Score=70.60 Aligned_cols=29 Identities=38% Similarity=0.614 Sum_probs=23.9
Q ss_pred HHHHHHhh-CCC----CCccccchhhhccHHHHH
Q 027882 52 LASLATYF-GLG----QQTHRSLDDVRMNLEVLK 80 (217)
Q Consensus 52 LatLA~~F-g~~----~~~HRALdDar~tvdVl~ 80 (217)
|.+|+.+| |.. ...||||+||++|.+|++
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 368999999999999875
No 52
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=98.22 E-value=1.8e-07 Score=91.00 Aligned_cols=68 Identities=13% Similarity=0.178 Sum_probs=55.6
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeecccc---------chHHHHHHHHHHHHHhh
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQ---------SLCTVLDACEVVAKKLF 174 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla~---------~v~~Vl~~Cd~~a~~~~ 174 (217)
.+.+|..||||.|.+.++ || |.+.|||.||++||+.+..++|...||.-.. .+++.|-.|.-|-+-..
T Consensus 8 l~~lP~~PGVY~~~d~~g~viYVGKAknLr~Rv~sYF~~~~~~~k~~~lv~~i~~ie~i~t~sE~eALlLE~~LIK~~~P 87 (598)
T PRK00558 8 LKTLPDSPGVYRMKDANGTVIYVGKAKNLKNRVRSYFRKSHDSPKTRAMVSEIADIEYIVTRSETEALLLENNLIKKYKP 87 (598)
T ss_pred HhhCCCCCeEEEEECCCCCEEEecCchhHHHHHHhhCCCCCcChHHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHhCC
Confidence 467999999999999988 99 9999999999999998777788877775544 45667777777766543
No 53
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=98.13 E-value=2.1e-07 Score=91.04 Aligned_cols=57 Identities=16% Similarity=0.234 Sum_probs=51.7
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeeccccchHHHHH
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQSLCTVLD 164 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla~~v~~Vl~ 164 (217)
...+|+.||||.|.+.++ || |.+.|||.||++||.++.. +|+..||.-+..++.|+-
T Consensus 9 l~~lP~~PGvY~~~d~~g~VlYVGKAknLr~Rv~sYF~~~~~-~kt~~lv~~i~~iE~ivt 68 (581)
T COG0322 9 LKNLPHSPGVYLMKDENGTVLYVGKAKNLRKRVSSYFRGRLD-PKTAALVENIADIEYIVT 68 (581)
T ss_pred HHhCCCCCeeEEEECCCCCEEEEeehhhHHHHHHHhhcCCCc-HHHHHHHHhhcceeEEEe
Confidence 457899999999999998 99 9999999999999998888 999999999888876653
No 54
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=98.13 E-value=2e-06 Score=75.09 Aligned_cols=85 Identities=25% Similarity=0.328 Sum_probs=68.8
Q ss_pred CceEEEEEeecCCCCCCCC--ceeEEEEeeEEEecCceeecccHHHH---------------------------------
Q 027882 7 RFEIAFFDVETAFPNPPGQ--RIAILEFGAILVCPKTLEELQPYSTL--------------------------------- 51 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~--~~~ilEfgAI~V~p~~l~e~~sf~TL--------------------------------- 51 (217)
.+...++|+|.|.+...+. ...|||++|.+|..---.+++.||..
T Consensus 3 ~~~lLIID~EaT~~eG~~~~~e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~Ckslt~I~Q~~VD~apifs~v 82 (210)
T COG5018 3 TNSLLIIDFEATMPEGKYSPQEFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRCKSLTKITQKQVDEAPIFSMV 82 (210)
T ss_pred CceEEEEEeeeeccCCCCCchhceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHHHHhhhhhhhhccccchHHHH
Confidence 3567899999999987764 78999999999976555567888877
Q ss_pred ------------------------------------------------------------------HHHHHHhhCCC--C
Q 027882 52 ------------------------------------------------------------------LASLATYFGLG--Q 63 (217)
Q Consensus 52 ------------------------------------------------------------------LatLA~~Fg~~--~ 63 (217)
|..-+.+.|.. .
T Consensus 83 ~E~f~r~L~~h~Pr~~~~wa~wG~~Dm~~l~q~~~~~~~~p~~~kgp~vdl~~~yk~v~~~pr~tgln~ale~~G~sf~G 162 (210)
T COG5018 83 FEDFIRKLNEHDPRKNSTWATWGNMDMKVLKQNCMFNHIPPFPFKGPMVDLSLEYKNVFGDPRLTGLNKALEEYGDSFTG 162 (210)
T ss_pred HHHHHHHHHhcCcccCCccccccchhHHHHHHHHHhcCCCCccccCccchHHHHHHHHhcCCccccHHHHHHHhccccCC
Confidence 77778888988 8
Q ss_pred CccccchhhhccHHHHHHhhhh-hhhhcC
Q 027882 64 QTHRSLDDVRMNLEVLKYCATV-LFLESG 91 (217)
Q Consensus 64 ~~HRALdDar~tvdVl~~~~gV-~~lE~~ 91 (217)
++||||||||-+..+||...-+ +.+|..
T Consensus 163 ~~HraldDArn~~rl~klv~~~~~~~e~~ 191 (210)
T COG5018 163 THHRALDDARNAYRLFKLVEQDKQYLEKP 191 (210)
T ss_pred chhhhHHHHHHHHHHHHHHcchhhhccCC
Confidence 9999999999999999987633 344444
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=98.09 E-value=4.3e-07 Score=88.39 Aligned_cols=66 Identities=9% Similarity=0.164 Sum_probs=52.8
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeeccccch---------HHHHHHHHHHHHHh
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQSL---------CTVLDACEVVAKKL 173 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla~~v---------~~Vl~~Cd~~a~~~ 173 (217)
...+|..||||.|.+..+ || |.+.|||.||++||+.+ .++|+..||.-..++ ++.|-.|.-|-+-.
T Consensus 5 l~~lP~~PGVYl~~d~~g~viYVGKAknLr~Rv~sYF~~~-~~~K~~~mv~~i~~ie~ivt~sE~eALlLE~~lIK~~~ 82 (574)
T TIGR00194 5 LKNLPDKPGCYLMKDRNGQVLYVGKAKNLKKRVSSYFREN-NSAKTQALVKQIADIEYILTKNENEALILEANLIKQYQ 82 (574)
T ss_pred HhhCCCCCeEEEEECCCCCEEEEecHHHHHHHHHHhcCCC-CCchHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 357899999999999988 99 99999999999999976 478888887766554 45555666665543
No 56
>PRK10545 nucleotide excision repair endonuclease; Provisional
Probab=98.04 E-value=4.4e-07 Score=81.96 Aligned_cols=64 Identities=13% Similarity=0.186 Sum_probs=50.3
Q ss_pred ccccCCCCCCeeeeccCCc---ce-ecccceeeeccccccCCCCCccceeeec---------cccchHHHHHHHHHHHHH
Q 027882 106 AASVSEGSSGYARFMEPDE---LY-CSRLKIRYGISTRFVDQAGRPRLSFVVD---------ASQSLCTVLDACEVVAKK 172 (217)
Q Consensus 106 la~~lp~~pGvy~F~~p~d---Ly-gts~~vR~rVrsyFt~se~RpRm~emVd---------la~~v~~Vl~~Cd~~a~~ 172 (217)
..+++|+.||||.|.+.++ || |++.|||.||++||++ +|...|+. -+..+.+.|-.++-|.+-
T Consensus 27 ~l~~LP~~PGVYlf~d~~g~~~LYVGKAknLR~RV~syF~~----~k~~~m~~~i~~Ie~i~T~sEleALLLE~~LIK~~ 102 (286)
T PRK10545 27 FLEDLPKLPGVYLFHGESDTMPLYIGKSVNIRSRVLSHLRT----PDEAAMLRQSRRISWICTAGEIGALLLEARLIKEQ 102 (286)
T ss_pred HHHhCCCCCeEEEEEcCCCCEEEEEechHhHHHHHHHHcCc----HHHHHHHHhcceEEEEEeCCHHHHHHHHHHHHHHh
Confidence 4689999999999998776 89 9999999999999975 22233333 345677888888888776
Q ss_pred h
Q 027882 173 L 173 (217)
Q Consensus 173 ~ 173 (217)
.
T Consensus 103 ~ 103 (286)
T PRK10545 103 Q 103 (286)
T ss_pred C
Confidence 4
No 57
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=98.01 E-value=7.2e-07 Score=88.97 Aligned_cols=86 Identities=14% Similarity=0.229 Sum_probs=60.3
Q ss_pred ccccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHHh
Q 027882 106 AASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKKL 173 (217)
Q Consensus 106 la~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla~~---------v~~Vl~~Cd~~a~~~ 173 (217)
-+..+|..||||+|.+.++ || |.+.|||.||++||+.. .++|...||.-..+ +++.|-.|.-|-+-.
T Consensus 14 ~~~~LP~~PGVYlfkd~~G~VLYVGKAKNLR~RV~SYF~~~-~~~K~~~Lv~~i~~Ie~ivT~sE~EALLLE~~LIK~~k 92 (691)
T PRK14672 14 QALSAPSTSGVYLWKDVHGVVIYVGKAKSLRTRLTSYFRCR-HDPKTRVLMSRAAALEYLQTQHEYEALLLENTLIKKHT 92 (691)
T ss_pred HHHhCCCCCeEEEEECCCCCEEEeeCcHHHHHHHHHHcCCC-CCchHHHHHHhhCcEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 3458999999999999988 99 99999999999999864 46666667665544 556666666665543
Q ss_pred hccCCCCCCCccceeeccCCCccEEEe
Q 027882 174 FEDSRSNSEWNPVVTRQSGNDPAARLR 200 (217)
Q Consensus 174 ~~~~gs~s~W~p~v~~~~gn~ptvrl~ 200 (217)
. ..|-.. |...++|.++|.
T Consensus 93 P-------~YNi~L-KddK~YpyI~It 111 (691)
T PRK14672 93 P-------RYNICL-KDGKTYPLLKLT 111 (691)
T ss_pred c-------hhhhhc-cCCCCceEEEEe
Confidence 2 222222 333356766665
No 58
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=97.99 E-value=7.7e-07 Score=86.68 Aligned_cols=64 Identities=14% Similarity=0.212 Sum_probs=50.6
Q ss_pred cccCCCCCCeeeeccCCc--ce-ecccceeeeccccccCCCCCccceeeeccc---------cchHHHHHHHHHHHHHh
Q 027882 107 ASVSEGSSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDAS---------QSLCTVLDACEVVAKKL 173 (217)
Q Consensus 107 a~~lp~~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla---------~~v~~Vl~~Cd~~a~~~ 173 (217)
++.+|..||||.|.+ ++ || |.+.|||.||++||+. ..+|...||.-. ..+++.|-.|.-|-+-.
T Consensus 10 ~~~LP~~PGVYl~~d-~g~viYVGKAknLr~RV~sYF~~--~~~k~~~lv~~i~~ie~i~t~sE~eALlLE~~LIK~~~ 85 (577)
T PRK14668 10 AAELPREPGVYQFVA-GGTVLYVGKAVDLRDRVRSYADP--RSERIRRMVERADDIDFAVTDTETQALLLEANLIKRHQ 85 (577)
T ss_pred HHhCCCCCEEEEEcC-CCeEEEeeCcHhHHHHHHHHcCC--CChHHHHHHHhhCeEEEEEeCCHHHHHHHHHHHHHHhC
Confidence 568999999999998 66 99 9999999999999975 356787777644 44567777777776543
No 59
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=97.06 E-value=0.0017 Score=56.43 Aligned_cols=34 Identities=18% Similarity=0.277 Sum_probs=29.2
Q ss_pred CCCCCceEEEEEeecCCCCCCCCceeEEEEeeEEEe
Q 027882 3 PRQDRFEIAFFDVETAFPNPPGQRIAILEFGAILVC 38 (217)
Q Consensus 3 ~~~~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~ 38 (217)
|...+...|-+|+|-||+++.. .+|||+++|+--
T Consensus 1 m~~~~~nLiWIDlEMTGLd~~~--drIIEiA~iVTD 34 (184)
T COG1949 1 MSANKNNLIWIDLEMTGLDPER--DRIIEIATIVTD 34 (184)
T ss_pred CCCcCCceEEEeeeeccCCcCc--ceEEEEEEEEec
Confidence 3566788999999999999988 899999998644
No 60
>KOG0542 consensus Predicted exonuclease [Replication, recombination and repair]
Probab=95.17 E-value=0.067 Score=49.27 Aligned_cols=32 Identities=19% Similarity=0.375 Sum_probs=28.8
Q ss_pred HHHHHHhhCCC--CCccccchhhhccHHHHHHhh
Q 027882 52 LASLATYFGLG--QQTHRSLDDVRMNLEVLKYCA 83 (217)
Q Consensus 52 LatLA~~Fg~~--~~~HRALdDar~tvdVl~~~~ 83 (217)
+..+-++.|+. +..|++||||+-...+...++
T Consensus 206 it~mLe~~gL~f~Gr~HsGiDDa~Nia~I~~kM~ 239 (280)
T KOG0542|consen 206 ITGMLEHYGLQFEGRAHSGIDDARNIARIAQKMI 239 (280)
T ss_pred HHHHHHHhCCcccCCcccCchhHHHHHHHHHHHH
Confidence 67777888999 889999999999999999888
No 61
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=94.55 E-value=0.0048 Score=60.81 Aligned_cols=53 Identities=11% Similarity=0.318 Sum_probs=39.9
Q ss_pred eccCCc--ce-ecccceeeeccccccCCCCCccceeeeccccc---------hHHHHHHHHHHHHH
Q 027882 119 FMEPDE--LY-CSRLKIRYGISTRFVDQAGRPRLSFVVDASQS---------LCTVLDACEVVAKK 172 (217)
Q Consensus 119 F~~p~d--Ly-gts~~vR~rVrsyFt~se~RpRm~emVdla~~---------v~~Vl~~Cd~~a~~ 172 (217)
|.+.++ || |.+.|||.||++||+.+ .++|...||.-..+ +++.|-.|.-|-|-
T Consensus 1 ~~d~~g~vIYVGKAknLr~RV~sYF~~~-~~~K~~~lv~~i~~ie~ivt~sE~EALlLE~~LIK~~ 65 (574)
T PRK14670 1 MYSENNKILYIGKAKNLRSRVKNYFLEK-ISHKTKILMKNVKNIEVITTNSEYEALLLECNLIKTH 65 (574)
T ss_pred CCCCCCCEEEeeCcHhHHHHHHHHcCCC-CCchHHHHHHhcCeEEEEEeCCHHHHHHHHHHHHHHh
Confidence 455666 99 99999999999999975 57888888876555 45666666666553
No 62
>smart00465 GIYc GIY-YIG type nucleases (URI domain).
Probab=94.27 E-value=0.0074 Score=41.74 Aligned_cols=32 Identities=16% Similarity=0.275 Sum_probs=28.5
Q ss_pred CCCeeeeccCCc--ce-ecccceeeeccccccCCC
Q 027882 113 SSGYARFMEPDE--LY-CSRLKIRYGISTRFVDQA 144 (217)
Q Consensus 113 ~pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se 144 (217)
.||+|.|...++ +| |++.+++.|++++|.+..
T Consensus 1 ~~gvY~i~~~~~~~~YVG~t~nl~~R~~~h~~~~~ 35 (84)
T smart00465 1 KPGVYYITNKKNGKLYVGKAKNLRNRLKRHFSGSR 35 (84)
T ss_pred CCEEEEEEECCCCEEEEEEccCHHHHHHHHHhCCC
Confidence 389999999666 99 999999999999998776
No 63
>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=94.04 E-value=0.064 Score=43.77 Aligned_cols=31 Identities=23% Similarity=0.203 Sum_probs=24.6
Q ss_pred EEEEEeecCCC----CCCCCceeEEEEeeEEEecCce
Q 027882 10 IAFFDVETAFP----NPPGQRIAILEFGAILVCPKTL 42 (217)
Q Consensus 10 ~vffDvETT~~----~~~~~~~~ilEfgAI~V~p~~l 42 (217)
+++||+|||++ ++.. ..|+++|++....|..
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 8999999998855543
No 64
>PHA02598 denA endonuclease II; Provisional
Probab=93.44 E-value=0.024 Score=47.64 Aligned_cols=43 Identities=14% Similarity=-0.012 Sum_probs=33.5
Q ss_pred cCCccccccCCCCCCeeeeccCCc-ce-ecccceeeeccccccCC
Q 027882 101 WEMCSAASVSEGSSGYARFMEPDE-LY-CSRLKIRYGISTRFVDQ 143 (217)
Q Consensus 101 ~v~p~la~~lp~~pGvy~F~~p~d-Ly-gts~~vR~rVrsyFt~s 143 (217)
.+.++.+....-.-|||.|...++ || |.+.+||.||++||++.
T Consensus 21 ~i~~~f~~~~~~~n~VY~~~~~~~viYVGKAknLkkRv~sYf~~~ 65 (138)
T PHA02598 21 RIDRSFIKCPNKKNVIYAIAVDDELVYIGKTKNLRKRIDYYRNSK 65 (138)
T ss_pred cCcccccCCcccceEEEEEEeCCeEEEEeehhhHHHHHHHHhCcc
Confidence 344556666666778999994444 99 99999999999999863
No 65
>COG3359 Predicted exonuclease [DNA replication, recombination, and repair]
Probab=91.99 E-value=0.24 Score=45.68 Aligned_cols=33 Identities=27% Similarity=0.345 Sum_probs=24.2
Q ss_pred CCceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 027882 6 DRFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (217)
Q Consensus 6 ~~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~ 40 (217)
++.+++|||+||||+++.+ ..|+=.|--.+..+
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 67766665444433
No 66
>PHA02570 dexA exonuclease; Provisional
Probab=89.01 E-value=0.87 Score=40.76 Aligned_cols=47 Identities=17% Similarity=0.188 Sum_probs=34.8
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCceeecccHHHHHHHHHHhhCCC
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTLEELQPYSTLLASLATYFGLG 62 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l~e~~sf~TLLatLA~~Fg~~ 62 (217)
+.+|+||-|..|. ..||++|||.+-|..- ....|..|. +++.++.+.
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 5799999999754 5899999999997543 478898885 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=85.64 E-value=0.65 Score=36.46 Aligned_cols=30 Identities=27% Similarity=0.368 Sum_probs=17.6
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCce
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKTL 42 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~~l 42 (217)
+|||+||||.++..+ .|.=||...+-.+..
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 589999999988763 466678877666554
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=84.63 E-value=1.3 Score=33.15 Aligned_cols=29 Identities=21% Similarity=0.135 Sum_probs=22.6
Q ss_pred EEEEeecCCCCCCCCceeEEEEeeEEEecCc
Q 027882 11 AFFDVETAFPNPPGQRIAILEFGAILVCPKT 41 (217)
Q Consensus 11 vffDvETT~~~~~~~~~~ilEfgAI~V~p~~ 41 (217)
++||+|||+.++.. ..|++++.....+++
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
>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=80.31 E-value=0.25 Score=34.08 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=28.5
Q ss_pred CCeeeeccCCc--ce-ecccceeeeccccccCCCCCc
Q 027882 114 SGYARFMEPDE--LY-CSRLKIRYGISTRFVDQAGRP 147 (217)
Q Consensus 114 pGvy~F~~p~d--Ly-gts~~vR~rVrsyFt~se~Rp 147 (217)
+|||.+...++ +| |.+.+++.|+++++.+.....
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 68999997776 79 999999999999998655443
No 70
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=76.99 E-value=2.9 Score=37.28 Aligned_cols=31 Identities=16% Similarity=0.158 Sum_probs=26.6
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 027882 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (217)
Q Consensus 8 ~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~ 40 (217)
.-+|-+|+|-||++..+ .+|+|+++|.--+.
T Consensus 26 q~lVWiD~EMTGLdvek--d~i~EiacIITD~d 56 (208)
T KOG3242|consen 26 QPLVWIDCEMTGLDVEK--DRIIEIACIITDGD 56 (208)
T ss_pred CceEEEeeecccccccc--ceeEEEEEEEecCC
Confidence 45999999999999999 79999999865443
No 71
>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=59.83 E-value=17 Score=30.27 Aligned_cols=27 Identities=26% Similarity=0.315 Sum_probs=20.2
Q ss_pred ceEEEEEeecCCC----CCCCCceeEEEEeeEE
Q 027882 8 FEIAFFDVETAFP----NPPGQRIAILEFGAIL 36 (217)
Q Consensus 8 ~e~vffDvETT~~----~~~~~~~~ilEfgAI~ 36 (217)
--+++||+|||.+ ++. ...|+=+|...
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 48999999765
No 72
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=56.52 E-value=8.7 Score=37.88 Aligned_cols=31 Identities=23% Similarity=0.387 Sum_probs=27.6
Q ss_pred HHHHHHhhCCC-CCccccchhhhccHHHHHHh
Q 027882 52 LASLATYFGLG-QQTHRSLDDVRMNLEVLKYC 82 (217)
Q Consensus 52 LatLA~~Fg~~-~~~HRALdDar~tvdVl~~~ 82 (217)
|+-|+.-=|+. ...|-|+.|++||+.+-|.+
T Consensus 166 LEhLt~ANgieH~nAHdAmsDVyATIamAklv 197 (475)
T COG2925 166 LEHLTKANGIEHSNAHDAMSDVYATIAMAKLV 197 (475)
T ss_pred hHHHhhccccccchhhHHHHHHHHHHHHHHHH
Confidence 99999999999 99999999999999865543
No 73
>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=48.96 E-value=4.7 Score=34.69 Aligned_cols=34 Identities=15% Similarity=0.284 Sum_probs=28.1
Q ss_pred CCeeeecc-CCc-ce-ecccceeeeccccccC-CCCCc
Q 027882 114 SGYARFME-PDE-LY-CSRLKIRYGISTRFVD-QAGRP 147 (217)
Q Consensus 114 pGvy~F~~-p~d-Ly-gts~~vR~rVrsyFt~-se~Rp 147 (217)
+|+|.+.. +++ .| |++.+|..|+++||.. ..+..
T Consensus 2 ~GIY~i~n~~ngk~YIGss~nl~~R~~~h~~~~~~~~~ 39 (214)
T TIGR01453 2 SGIYKITNNINGKIYVGSSVNLEKRLKEHLKLLKKGNR 39 (214)
T ss_pred CEEEEEEECCCCcEEEEeccCHHHHHHHHHHHHhcCCh
Confidence 79999988 554 99 9999999999999976 44444
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=45.62 E-value=29 Score=29.10 Aligned_cols=29 Identities=24% Similarity=0.304 Sum_probs=21.2
Q ss_pred ceEEEEEeecCC----CCCCCCceeEEEEeeEEEe
Q 027882 8 FEIAFFDVETAF----PNPPGQRIAILEFGAILVC 38 (217)
Q Consensus 8 ~e~vffDvETT~----~~~~~~~~~ilEfgAI~V~ 38 (217)
--+++||+||+. |++.. ..|+=||+....
T Consensus 3 l~~l~fDIEt~~~~gfp~~~~--d~Ii~Is~~~~~ 35 (188)
T cd05781 3 LKTLAFDIEVYSKYGTPNPRR--DPIIVISLATSN 35 (188)
T ss_pred ceEEEEEEEecCCCCCCCCCC--CCEEEEEEEeCC
Confidence 347899999994 34444 789999976643
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=45.24 E-value=33 Score=27.06 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=19.9
Q ss_pred CCCceEEEEEeecCCCCCCCCceeEEEEe
Q 027882 5 QDRFEIAFFDVETAFPNPPGQRIAILEFG 33 (217)
Q Consensus 5 ~~~~e~vffDvETT~~~~~~~~~~ilEfg 33 (217)
..+..+++||+|||+..+.. ..|+.++
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
>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=41.31 E-value=20 Score=30.92 Aligned_cols=29 Identities=38% Similarity=0.599 Sum_probs=23.3
Q ss_pred HHHHHHh-hCCC--CCccccchhhhccHHHHH
Q 027882 52 LASLATY-FGLG--QQTHRSLDDVRMNLEVLK 80 (217)
Q Consensus 52 LatLA~~-Fg~~--~~~HRALdDar~tvdVl~ 80 (217)
|..||.. +|.. +..|-+++|||+++++.+
T Consensus 143 Lk~La~~~L~~~IQ~~~HdSvEDArAam~Ly~ 174 (174)
T cd06143 143 LRFLAWYLLGEKIQSETHDSIEDARTALKLYR 174 (174)
T ss_pred HHHHHHHHcCCcccCCCcCcHHHHHHHHHHhC
Confidence 7888764 4666 568999999999999763
No 77
>KOG4793 consensus Three prime repair exonuclease [Replication, recombination and repair]
Probab=32.97 E-value=31 Score=32.71 Aligned_cols=33 Identities=36% Similarity=0.536 Sum_probs=29.0
Q ss_pred HHHHHHHhhCCC--CCccccchhhhccHHHHHHhh
Q 027882 51 LLASLATYFGLG--QQTHRSLDDVRMNLEVLKYCA 83 (217)
Q Consensus 51 LLatLA~~Fg~~--~~~HRALdDar~tvdVl~~~~ 83 (217)
.+++||.|.... -..|||+.|+-++-+|+.+.-
T Consensus 254 ~le~Lat~~~~~p~l~ahra~~Dv~~~~k~~q~~~ 288 (318)
T KOG4793|consen 254 SLEALATYYSLTPELDAHRALSDVLLLSKVFQKLT 288 (318)
T ss_pred hHHHHHHHhhcCcccchhhhccccchhhhHHHHhh
Confidence 389999988877 889999999999999998764
No 78
>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=32.14 E-value=93 Score=23.86 Aligned_cols=30 Identities=20% Similarity=0.198 Sum_probs=19.6
Q ss_pred ceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 027882 8 FEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (217)
Q Consensus 8 ~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~ 40 (217)
...++||+||++..+..... .+..|.+|.+
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 44899999999988844322 2344445555
No 79
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=31.37 E-value=15 Score=31.81 Aligned_cols=30 Identities=30% Similarity=0.412 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhccCC-CCCCCccceeeccC
Q 027882 163 LDACEVVAKKLFEDSR-SNSEWNPVVTRQSG 192 (217)
Q Consensus 163 l~~Cd~~a~~~~~~~g-s~s~W~p~v~~~~g 192 (217)
|.+||+++++++.-+. +.-.||.+|-++|-
T Consensus 30 L~AFeEvg~~L~RTsAACGFRWNs~VRkqY~ 60 (161)
T TIGR02894 30 LSAFEEVGRALNRTAAACGFRWNAYVRKQYE 60 (161)
T ss_pred HHHHHHHHHHHcccHHHhcchHHHHHHHHHH
Confidence 7899999999999887 88999999965664
No 80
>PRK05755 DNA polymerase I; Provisional
Probab=25.53 E-value=1.5e+02 Score=30.67 Aligned_cols=31 Identities=23% Similarity=0.249 Sum_probs=22.5
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEeeEEEecC
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFGAILVCPK 40 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfgAI~V~p~ 40 (217)
..++++||+||++.++.. ..|+.++. ...++
T Consensus 314 ~~~~~a~DtEt~~l~~~~--~~i~~i~l-s~~~g 344 (880)
T PRK05755 314 AAGLFAFDTETTSLDPMQ--AELVGLSF-AVEPG 344 (880)
T ss_pred ccCeEEEEeccCCCCccc--ccEEEEEE-EeCCC
Confidence 357899999999998765 56777762 34444
No 81
>cd06129 RNaseD_like DEDDy 3'-5' exonuclease domain of RNase D, WRN, and similar proteins. The RNase D-like group is composed of RNase D, WRN, and similar proteins. They contain a DEDDy-type, DnaQ-like, 3'-5' exonuclease domain that 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. RNase D is involved in the 3'-end processing of tRNA precursors. RNase D-like proteins in eukaryotes include yeast Rrp6p, human PM/Scl-100 and Drosophila melanogaster egalitarian (Egl) protein. WRN is a unique DNA helicase possessing exonuclease activity. Mutation in the WRN gene is implicated in Werner syndrome, a disease associated with premature aging and increased predisposition to cancer. Yeast Rrp6p and the human Polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100) are exosome-
Probab=23.80 E-value=1.2e+02 Score=24.31 Aligned_cols=27 Identities=15% Similarity=0.126 Sum_probs=21.1
Q ss_pred CceEEEEEeecCCCCCCCCceeEEEEe
Q 027882 7 RFEIAFFDVETAFPNPPGQRIAILEFG 33 (217)
Q Consensus 7 ~~e~vffDvETT~~~~~~~~~~ilEfg 33 (217)
...++.||+|+.......++-.||-++
T Consensus 12 ~~~~ig~D~E~~~~~~~~~~~~liQl~ 38 (161)
T cd06129 12 DGDVIAFDMEWPPGRRYYGEVALIQLC 38 (161)
T ss_pred CCCEEEEECCccCCCCCCCceEEEEEE
Confidence 677999999999877655567777775
No 82
>KOG3242 consensus Oligoribonuclease (3'->5' exoribonuclease) [RNA processing and modification]
Probab=21.54 E-value=46 Score=29.89 Aligned_cols=19 Identities=47% Similarity=0.896 Sum_probs=15.9
Q ss_pred CCccccchhhhccHHHHHH
Q 027882 63 QQTHRSLDDVRMNLEVLKY 81 (217)
Q Consensus 63 ~~~HRALdDar~tvdVl~~ 81 (217)
+-+||||||.|-++.=|+.
T Consensus 176 ~~~HrAldDI~ESI~ELq~ 194 (208)
T KOG3242|consen 176 KATHRALDDIRESIKELQY 194 (208)
T ss_pred ccccchHHHHHHHHHHHHH
Confidence 6789999999988776654
No 83
>PF08523 MBF1: Multiprotein bridging factor 1; InterPro: IPR013729 This domain is found in the multiprotein bridging factor 1 (MBF1) which forms a heterodimer with MBF2. It has been shown to make direct contact with the TATA-box binding protein (TBP) and interacts with Ftz-F1, stabilising the Ftz-F1-DNA complex []. It is also found in the endothelial differentiation-related factor (EDF-1). Human EDF-1 is involved in the repression of endothelial differentiation, interacts with CaM and is phosphorylated by PKC []. The domain is found in a wide range of eukaryotic proteins including metazoans, fungi and plants. A helix-turn-helix motif (IPR001387 from INTERPRO) is found to its C terminus. ; PDB: 1X57_A.
Probab=20.30 E-value=34 Score=25.65 Aligned_cols=16 Identities=31% Similarity=0.812 Sum_probs=0.0
Q ss_pred CCCccc-eeeccCCCcc
Q 027882 181 SEWNPV-VTRQSGNDPA 196 (217)
Q Consensus 181 s~W~p~-v~~~~gn~pt 196 (217)
+||.|| ||.+.+.+++
T Consensus 1 qDWd~vtvi~kk~p~~~ 17 (71)
T PF08523_consen 1 QDWDPVTVIGKKGPRAK 17 (71)
T ss_dssp -----------------
T ss_pred CCCcccceecccCCCcc
Confidence 689999 8888775443
Done!