Query psy14488
Match_columns 368
No_of_seqs 115 out of 298
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 21:05:04 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14488.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14488hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG2925 SbcB Exonuclease I [DN 100.0 2E-135 5E-140 994.8 32.6 355 1-365 115-475 (475)
2 PRK11779 sbcB exonuclease I; P 100.0 4E-106 1E-110 824.7 33.3 358 1-367 112-475 (476)
3 PF08411 Exonuc_X-T_C: Exonucl 100.0 1.7E-83 3.7E-88 617.4 22.6 263 98-364 1-269 (269)
4 cd06138 ExoI_N N-terminal DEDD 99.3 4.5E-13 9.7E-18 121.7 3.6 80 2-81 104-183 (183)
5 PRK06310 DNA polymerase III su 97.7 3.4E-05 7.4E-10 74.0 3.5 41 47-87 134-174 (250)
6 TIGR00573 dnaq exonuclease, DN 97.5 0.00013 2.8E-09 68.2 5.1 44 48-91 136-181 (217)
7 smart00479 EXOIII exonuclease 97.2 0.00054 1.2E-08 59.7 5.4 39 48-86 127-166 (169)
8 PRK07942 DNA polymerase III su 97.2 0.00022 4.8E-09 67.6 2.9 43 48-90 141-183 (232)
9 PRK09145 DNA polymerase III su 97.2 0.00016 3.5E-09 66.6 2.0 42 46-87 160-201 (202)
10 PRK07740 hypothetical protein; 97.1 0.00027 5.9E-09 67.5 2.7 52 22-83 171-222 (244)
11 TIGR01407 dinG_rel DnaQ family 96.7 0.0011 2.3E-08 73.8 3.8 41 48-88 126-166 (850)
12 PRK09182 DNA polymerase III su 96.7 0.0013 2.9E-08 64.7 3.9 58 37-98 154-213 (294)
13 PRK06309 DNA polymerase III su 96.7 0.0011 2.3E-08 62.8 2.7 40 47-86 126-165 (232)
14 PRK07883 hypothetical protein; 96.4 0.0024 5.3E-08 68.0 3.8 44 46-89 141-184 (557)
15 cd06127 DEDDh DEDDh 3'-5' exon 96.4 0.0019 4.1E-08 54.7 2.2 33 48-80 125-158 (159)
16 PRK08074 bifunctional ATP-depe 96.4 0.0022 4.7E-08 72.1 3.2 39 48-86 130-168 (928)
17 PRK09146 DNA polymerase III su 96.3 0.0022 4.7E-08 61.3 2.4 65 22-86 159-226 (239)
18 PRK06063 DNA polymerase III su 96.2 0.0053 1.1E-07 60.9 4.6 40 46-85 138-177 (313)
19 cd06133 ERI-1_3'hExo_like DEDD 96.2 0.003 6.6E-08 55.7 2.5 36 48-83 139-175 (176)
20 PRK07247 DNA polymerase III su 95.7 0.011 2.4E-07 54.9 3.8 66 46-122 129-194 (195)
21 PRK08517 DNA polymerase III su 95.6 0.011 2.3E-07 57.2 3.7 58 18-89 176-233 (257)
22 cd06130 DNA_pol_III_epsilon_li 94.7 0.031 6.7E-07 48.3 3.4 32 47-79 122-153 (156)
23 cd06136 TREX1_2 DEDDh 3'-5' ex 94.6 0.014 3E-07 52.9 1.1 31 51-81 144-175 (177)
24 PRK07246 bifunctional ATP-depe 94.4 0.03 6.4E-07 62.5 3.4 39 48-86 131-169 (820)
25 PRK06807 DNA polymerase III su 94.4 0.032 6.9E-07 55.5 3.2 40 47-87 133-172 (313)
26 TIGR01405 polC_Gram_pos DNA po 94.0 0.041 8.9E-07 63.7 3.4 39 47-85 315-353 (1213)
27 cd06134 RNaseT DEDDh 3'-5' exo 93.7 0.048 1E-06 50.0 2.6 37 49-85 149-187 (189)
28 cd06137 DEDDh_RNase DEDDh 3'-5 93.3 0.032 6.9E-07 49.7 0.9 33 47-79 123-159 (161)
29 PF00929 RNase_T: Exonuclease; 93.2 0.047 1E-06 46.1 1.7 33 47-79 130-163 (164)
30 PRK07748 sporulation inhibitor 93.1 0.089 1.9E-06 48.8 3.6 38 48-85 140-178 (207)
31 PRK06195 DNA polymerase III su 93.1 0.059 1.3E-06 53.2 2.4 39 46-85 124-162 (309)
32 cd06149 ISG20 DEDDh 3'-5' exon 93.0 0.041 8.9E-07 49.0 1.2 34 47-80 119-156 (157)
33 cd06131 DNA_pol_III_epsilon_Ec 92.2 0.11 2.4E-06 45.7 2.8 34 49-82 130-165 (167)
34 cd06144 REX4_like DEDDh 3'-5' 92.0 0.069 1.5E-06 47.1 1.2 34 47-80 116-151 (152)
35 cd06135 Orn DEDDh 3'-5' exonuc 91.9 0.24 5.2E-06 44.7 4.6 27 59-85 144-170 (173)
36 PRK07983 exodeoxyribonuclease 91.7 0.18 3.9E-06 47.7 3.7 66 50-128 112-182 (219)
37 PRK05168 ribonuclease T; Provi 91.7 0.1 2.2E-06 48.8 2.0 38 50-87 162-201 (211)
38 PRK00448 polC DNA polymerase I 91.3 0.16 3.5E-06 59.8 3.5 39 47-85 544-582 (1437)
39 PRK05711 DNA polymerase III su 91.0 0.21 4.5E-06 48.0 3.4 38 50-87 137-176 (240)
40 cd06145 REX1_like DEDDh 3'-5' 91.0 0.12 2.6E-06 45.6 1.6 32 49-80 114-149 (150)
41 TIGR01298 RNaseT ribonuclease 90.8 0.13 2.9E-06 47.5 1.9 38 49-86 152-191 (200)
42 TIGR01406 dnaQ_proteo DNA poly 89.8 0.26 5.6E-06 46.6 2.9 39 49-87 132-172 (225)
43 PRK06722 exonuclease; Provisio 89.8 0.35 7.6E-06 47.6 3.9 34 51-84 144-178 (281)
44 PRK05359 oligoribonuclease; Pr 89.2 0.55 1.2E-05 42.9 4.5 48 19-86 127-174 (181)
45 COG0847 DnaQ DNA polymerase II 82.0 1.6 3.5E-05 40.9 3.8 57 17-86 123-181 (243)
46 PRK05601 DNA polymerase III su 77.5 5.2 0.00011 41.1 6.0 39 47-85 197-247 (377)
47 cd07357 HN_L-whirlin_R2_like S 68.1 16 0.00035 29.7 5.6 51 305-361 15-65 (81)
48 PTZ00315 2'-phosphotransferase 66.0 4.8 0.00011 43.6 2.9 40 47-86 214-254 (582)
49 PF00901 Orbi_VP5: Orbivirus o 39.6 74 0.0016 34.0 6.3 112 111-236 353-486 (508)
50 PF02084 Bindin: Bindin; Inte 34.0 50 0.0011 31.9 3.7 32 211-242 129-163 (238)
51 PF03682 UPF0158: Uncharacteri 29.1 53 0.0011 29.8 3.0 57 257-323 64-127 (163)
52 PF11588 DUF3243: Protein of u 28.8 52 0.0011 26.9 2.5 51 311-361 7-63 (81)
53 PF05367 Phage_endo_I: Phage e 26.1 28 0.00061 31.3 0.7 32 257-290 68-99 (149)
54 cd06125 DnaQ_like_exo DnaQ-lik 25.4 83 0.0018 25.5 3.3 45 18-80 51-95 (96)
55 cd07347 harmonin_N_like N-term 25.4 1.6E+02 0.0036 23.7 4.9 49 304-359 14-62 (78)
56 PF10163 EnY2: Transcription f 22.6 2.4E+02 0.0052 22.7 5.4 52 311-362 33-86 (86)
57 cd07354 HN_L-delphilin-R1_like 22.1 1.3E+02 0.0029 24.5 3.7 32 332-363 5-36 (80)
58 PF08800 VirE_N: VirE N-termin 21.6 76 0.0016 27.7 2.5 45 113-170 9-54 (136)
59 KOG0772|consensus 21.0 60 0.0013 35.1 1.9 34 116-150 256-289 (641)
No 1
>COG2925 SbcB Exonuclease I [DNA replication, recombination, and repair]
Probab=100.00 E-value=2.3e-135 Score=994.76 Aligned_cols=355 Identities=35% Similarity=0.663 Sum_probs=346.1
Q ss_pred CccccCcccccccccCCCcccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHH
Q psy14488 1 MFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLA 80 (368)
Q Consensus 1 ~fYRNf~dPY~~ew~nGnSRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lA 80 (368)
+|||||+|||+||||||||||||+||||+|||||||||+||+++||.||||||+||+||||+|++||||||||||||+||
T Consensus 115 ~fyRNF~DPYa~sWqngNSRWDLLD~~RacyALRPeGI~Wp~n~dG~pSFkLEhLt~ANgieH~nAHdAmsDVyATIamA 194 (475)
T COG2925 115 IFYRNFYDPYAWSWQNGNSRWDLLDVVRACYALRPEGINWPENDDGLPSFKLEHLTKANGIEHSNAHDAMSDVYATIAMA 194 (475)
T ss_pred HHHHhcCchhhhhhcCCCchhHHHHHHHHHHhcCcccCCCCcCCCCCcchhhHHHhhccccccchhhHHHHHHHHHHHHH
Confidence 59999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCcchHHHHHhccCHHHHHhhhCCCCCCceEEEecccCCCCCCceEEEeecccCCCCCeEEEEeCCCCchHhhcC
Q psy14488 81 RLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLN 160 (368)
Q Consensus 81 kLIk~kqPkL~~~~~~~r~K~~v~~~l~~~~~~P~lhvs~~f~a~~~~~~~v~pl~~hp~n~N~vi~~DL~~Dp~~L~~l 160 (368)
||||++||+||||+|.+|+|+.|.++||+.+++|+||||||||+.+||+++|+||+|||+|+|+||||||..||++|++|
T Consensus 195 klvk~~QPrLfdy~f~~R~K~~~~~lid~~~~~PlvHVSgm~ga~r~~~s~V~PLaWHP~N~NalIv~DL~~Di~~Ll~l 274 (475)
T COG2925 195 KLVKTAQPRLFDYLFQLRKKHKLLALIDIPNMQPLVHVSGMFGAERGNTSWVLPLAWHPTNRNAVIVCDLAGDISPLLEL 274 (475)
T ss_pred HHHHhhCcHHHHHHHHhccHHHHHHHhcccccCceEEeecccchhhCCceEEEeecccCCCCceEEEEEccCChHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHhccccccCCCC---CCceEEeecCCcccccccccCChhhhhhhcCCHHHHHHHHHhHHHHhhChhHHHHHHH
Q psy14488 161 DINKIRDYLCFKKNSFKED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFL 237 (368)
Q Consensus 161 ~~~~i~~~l~t~~~~l~e~---~plk~i~iNk~P~v~~p~~~l~~~~a~rl~id~~~~~~~~~~~~~l~~~~~l~~kl~~ 237 (368)
++++|++||||++.+|+|| +|||.||||||||| +|+++|+++++.|||||.+.|++|++. |+.+|++++|+..
T Consensus 275 ~a~~lr~rLyT~~~dL~eg~~~vP~KlvHiNkcPil-ap~ktL~~eda~RlGidr~~c~~~~~~---l~~~p~~rekv~~ 350 (475)
T COG2925 275 DADTLRERLYTRKADLGEGELAVPVKLVHINKCPIL-APAKTLRPEDADRLGIDRQHCLDNLEL---LRENPDVREKVVA 350 (475)
T ss_pred CHHHHHHHhccccccccCCcccCceEEEEecCCCee-cchhhcChhhhhhcCCcHHHHHHHHHH---HhhCchHHHHHHH
Confidence 9999999999999999999 99999999999999 999999999999999999999999999 9999999999999
Q ss_pred HhhhcC-CCCCCCccHHhhccCCChHHHHHHHHHHcCChhhhhccCCCCCCccHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q psy14488 238 DYKINN-SDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELKRWKK 316 (368)
Q Consensus 238 ~~~~~~-~~~~~d~d~~LY~GF~s~~Dk~~m~~i~~~~p~~l~~~~~~F~D~Rl~eLlfRyraRN~P~~L~~~E~~~W~~ 316 (368)
+|++.. |.+..|||++||+||||++||+.|+++|.++|++|+++...|.|+||.+|+|||||||||+|||.+||++|.+
T Consensus 351 if~~e~~f~~~~dvd~~LY~GFf~~~Dr~~~~ilR~~~pe~La~~~~~f~D~Rl~~LlFrYRARnfp~tLt~~Eq~rW~~ 430 (475)
T COG2925 351 IFAEEEPFNPSDDVDAQLYNGFFSDADRAAMKILRETEPENLAALDITFVDKRLEELLFRYRARNFPETLTDAEQQRWLE 430 (475)
T ss_pred HHhccccCCCccchhHHHHccccCHHHHHHHHHHHhCChhhhhhccCCccchhHHHHHHHHHhhcCccccCHHHHHHHHH
Confidence 999765 8888999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcccCCCccccHHHHHHHHHHHHhhcccc--HHHHHHHHHHHHHHhh
Q psy14488 317 YRISRFYNKKNNLYNINMFYLEIESLLKKANEH--DTKILNALLMYGKSIT 365 (368)
Q Consensus 317 ~~~~rl~~~~~~~~~~~~~~~~l~~L~~~~~~~--~~~iL~~L~~y~~~l~ 365 (368)
||++||+. ..+.|...|+.+..+++.+ |+.+|++|++|+++|.
T Consensus 431 ~rr~~l~~------~~~~~~~tl~~~~~~~~~d~~k~~lL~~l~~y~~~l~ 475 (475)
T COG2925 431 HRRQRLTP------ELQGYELTLQALVQEHSDDKEKLALLKALYEYAAELV 475 (475)
T ss_pred HHHHhcCh------hhhhhHHHHHHHHHHhhcchHHHHHHHHHHHHHHhhC
Confidence 99999974 2577888888889888887 9999999999998863
No 2
>PRK11779 sbcB exonuclease I; Provisional
Probab=100.00 E-value=4.4e-106 Score=824.69 Aligned_cols=358 Identities=35% Similarity=0.666 Sum_probs=347.0
Q ss_pred CccccCcccccccccCCCcccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHH
Q psy14488 1 MFWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLA 80 (368)
Q Consensus 1 ~fYRNf~dPY~~ew~nGnSRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lA 80 (368)
+|||||+|||.++|+|||+|||++|++|++|++||+||.||.+++|.+||||++|+.+|||.|++|||||+||+||++||
T Consensus 112 ~~~r~~~d~y~~~~~~~n~r~D~LDl~rl~~~lrp~~i~~P~~~~g~~s~rLe~L~~~~gI~~~~AHdALsDa~aT~~la 191 (476)
T PRK11779 112 IFYRNFYDPYAREWQNGNSRWDLLDVVRACYALRPEGINWPENEDGLPSFKLEHLTKANGIEHENAHDAMSDVYATIAMA 191 (476)
T ss_pred HHHhccchHHHHHhcCCCCccCHHHHHHHHHHhccccccCcccccCCCCCcHHHHHHHcCCCCCCCCCcHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCcchHHHHHhccCHHHHHhhhCCCCCCceEEEecccCCCCCCceEEEeecccCCCCCeEEEEeCCCCchHhhcC
Q psy14488 81 RLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLN 160 (368)
Q Consensus 81 kLIk~kqPkL~~~~~~~r~K~~v~~~l~~~~~~P~lhvs~~f~a~~~~~~~v~pl~~hp~n~N~vi~~DL~~Dp~~L~~l 160 (368)
++|+++||+||+|+|++|+|+.|++++++.+++|++|||++||+.+||+++|+|||+||+|+|++|||||+.||++|++|
T Consensus 192 ~~l~~~qP~l~~~~~~~~~k~~v~~l~~~~~~~p~~~~s~~fg~~~g~~~~v~pl~~hp~n~n~~i~~DL~~d~~~l~~l 271 (476)
T PRK11779 192 KLIKQKQPKLFDYLFQLRNKRKVAALIDVPAMKPLVHVSGMFGAERGCTSWVAPLAWHPTNKNAVIVCDLAGDPSPLLEL 271 (476)
T ss_pred HHHHHhChHHHHHHHHhcchHHHHHHhhhhccCCceEEeeecccccCceeEEeccccCCCCCCcEEEEECcCChHHHhcC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHhccccccCCCC---CCceEEeecCCcccccccccCChhhhhhhcCCHHHHHHHHHhHHHHhhChhHHHHHHH
Q psy14488 161 DINKIRDYLCFKKNSFKED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFL 237 (368)
Q Consensus 161 ~~~~i~~~l~t~~~~l~e~---~plk~i~iNk~P~v~~p~~~l~~~~a~rl~id~~~~~~~~~~~~~l~~~~~l~~kl~~ 237 (368)
|+++|++||||++++|||| +|||+||||||||| +|+++|++++++|||||+++|++|+++ |+++|+|++|+++
T Consensus 272 ~~~~l~~~l~~~~~~l~~~~~~~plk~i~~Nk~P~l-~p~~~l~~~~~~rl~~d~~~~~~~~~~---l~~~~~~~~~~~~ 347 (476)
T PRK11779 272 DADTLRERLYTRRADLAEGELPVPLKLVHLNKCPVL-APAKTLRPEDAERLGIDRQQCLDNLAL---LRQNPDLREKVVA 347 (476)
T ss_pred CHHHHHHHhccChhhccccCCCCCceEEEeCCCCEe-cchhhCCHHHHHHhCCcHHHHHHHHHH---HHhCHHHHHHHHH
Confidence 9999999999999999998 89999999999999 999999999999999999999999999 9999999999999
Q ss_pred HhhhcC-CCCCCCccHHhhccCCChHHHHHHHHHHcCChhhhhccCCCCCCccHHHHHHHHHHhcCCCCCCHHHHHHHHH
Q psy14488 238 DYKINN-SDLELNIDEELYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELKRWKK 316 (368)
Q Consensus 238 ~~~~~~-~~~~~d~d~~LY~GF~s~~Dk~~m~~i~~~~p~~l~~~~~~F~D~Rl~eLlfRyraRN~P~~L~~~E~~~W~~ 316 (368)
+|++.. +.++.|||+|||+||||++||++|++||.++|++|+++...|+|+||++|+|||||||||+||+++|+++|++
T Consensus 348 ~~~~~~~~~~~~d~d~~lY~gF~~~~D~~~~~~~~~~~~~~l~~~~~~f~D~Rl~~l~~ry~arn~p~~L~~~e~~~w~~ 427 (476)
T PRK11779 348 VFAEAEPFAPSDDVDAQLYDGFFSDADRRLMEIIRETEPENLAALDLTFDDPRLEELLFRYRARNFPETLDDEEQQRWLE 427 (476)
T ss_pred HHhccccCCCCCCHHHHHhCCCCCHHHHHHHHHHHcCCHHHHHhccccCCChhHHHHHHHHHHccChhhCCHHHHHHHHH
Confidence 997543 6777899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcccCCCccccHHHHHHHHHHHHhhcccc--HHHHHHHHHHHHHHhhhc
Q psy14488 317 YRISRFYNKKNNLYNINMFYLEIESLLKKANEH--DTKILNALLMYGKSITQK 367 (368)
Q Consensus 317 ~~~~rl~~~~~~~~~~~~~~~~l~~L~~~~~~~--~~~iL~~L~~y~~~l~~~ 367 (368)
||++||+.+ .+++|.++|++|+++++.+ |..||++|++|++++.+.
T Consensus 428 ~~~~rl~~~-----~~~~~~~~~~~l~~~~~~~~~~~~~L~~l~~y~~~~~~~ 475 (476)
T PRK11779 428 HRRQRLTPE-----RLQQYAAELEQLAQEYEDDEEKQALLKALYDYAEELVPT 475 (476)
T ss_pred HHHHHhccc-----hHHHHHHHHHHHHhhccCCHHHHHHHHHHHHHHHHHhcc
Confidence 999999752 2899999999999998777 889999999999998754
No 3
>PF08411 Exonuc_X-T_C: Exonuclease C-terminal; InterPro: IPR013620 This bacterial domain is found at the C terminus of exodeoxyribonuclease I/Exonuclease I (IPR013520 from INTERPRO), which is a single-strand specific DNA nuclease affecting recombination and expression pathways. The exonuclease I protein in Escherichia coli is associated with DNA deoxyribophosphodiesterase (dRPase) []. ; GO: 0008852 exodeoxyribonuclease I activity, 0006281 DNA repair; PDB: 2QXF_A 3C94_A 3HL8_A 3C95_A 1FXX_A 3HP9_A.
Probab=100.00 E-value=1.7e-83 Score=617.36 Aligned_cols=263 Identities=31% Similarity=0.511 Sum_probs=206.2
Q ss_pred cCHHHHHhhhCCCCCCceEEEecccCCCCCCceEEEeecccCCCCCeEEEEeCCCCchHhhcCCHHHHHHHhccccccCC
Q psy14488 98 RKKKYVLAEIGWPIARPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDINKIRDYLCFKKNSFK 177 (368)
Q Consensus 98 r~K~~v~~~l~~~~~~P~lhvs~~f~a~~~~~~~v~pl~~hp~n~N~vi~~DL~~Dp~~L~~l~~~~i~~~l~t~~~~l~ 177 (368)
|+|++|+++|++.+++||||||||||+.+||+++|+|||+||+|+|+||||||+.||++|+++|+++|++||||+.++||
T Consensus 1 R~K~~v~~lid~~~~~P~lhvS~~~~a~~~~~~~v~Pla~hp~nkN~vI~~DL~~Dp~~l~~l~~eei~~~lft~~~~l~ 80 (269)
T PF08411_consen 1 RDKKAVAKLIDLNSMKPLLHVSGMFGAERGCTSLVLPLAQHPTNKNAVICFDLSSDPEPLLDLSAEEIRERLFTKREDLP 80 (269)
T ss_dssp TSHHHHHHT--TTTT--EEEE-GGG-GGGTTEEEEEEEEE-SS-TTEEEEEETTS--HHHHHS-HHHHHHHHHHTTS---
T ss_pred CCHHHHHHHhCccCCCcEEEecccchhhcCCceEEEeeeeCCCCCCeEEEEECCCCHHHHHcCCHHHHHHHhccChhhhc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CC---CCceEEeecCCcccccccccCChhhhhhhcCCHHHHHHHHHhHHHHhhChhHHHHHHHHhhh-cCCCCCCCccHH
Q psy14488 178 ED---IPISMIHLNRSPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIFLDYKI-NNSDLELNIDEE 253 (368)
Q Consensus 178 e~---~plk~i~iNk~P~v~~p~~~l~~~~a~rl~id~~~~~~~~~~~~~l~~~~~l~~kl~~~~~~-~~~~~~~d~d~~ 253 (368)
|| +|||+||||||||| +|+++|+++.++|||||+++|++|+++ |+++++|++||.++|+. ..+.++.|||++
T Consensus 81 eg~~r~plk~i~iNk~Pvl-~p~~~l~~~~a~rL~iD~~~~~~~~~~---l~~~~~l~~kl~~v~~~~~~~~~~~D~D~~ 156 (269)
T PF08411_consen 81 EGVERLPLKTIHINKCPVL-APAKVLRPEDAERLGIDRDLCRKNAEL---LRANPDLQEKLQEVFAEERPFPPPTDPDQQ 156 (269)
T ss_dssp -------EEEEETTS--EE-EEGGGS-HHHHHHHT--HHHHHHHHHH---HHH-THHHHHHHHHHC--------S-GGG-
T ss_pred ccccCCCceEEeeCCCCcc-CccccCCHhHHHHcCCcHHHHHHHHHH---HHhCHHHHHHHHHHHhccccCCCCCChhHH
Confidence 99 99999999999999 999999999999999999999999999 99999999999999994 446788999999
Q ss_pred hhccCCChHHHHHHHHHHcCChhhhhccCCCCCCccHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHcccCCCccccHH
Q psy14488 254 LYNNFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYRARNFIETLSYKELKRWKKYRISRFYNKKNNLYNIN 333 (368)
Q Consensus 254 LY~GF~s~~Dk~~m~~i~~~~p~~l~~~~~~F~D~Rl~eLlfRyraRN~P~~L~~~E~~~W~~~~~~rl~~~~~~~~~~~ 333 (368)
||+||||++||++|++||.++|++++++.+.|+|+||++|+|||||||||+|||++|+++|++||++||.++.++++|++
T Consensus 157 LY~GF~s~~Dk~~m~~ir~~~p~~l~~~~~~F~D~RL~eLlfRyraRN~P~tL~~~E~~~W~~~~~~rL~~~~~~~~tl~ 236 (269)
T PF08411_consen 157 LYSGFFSDADKRLMDQIRQASPEQLAELAFNFEDPRLPELLFRYRARNFPETLSEEEQQRWQEYCQQRLTDPDGGWLTLE 236 (269)
T ss_dssp GGG----HHHHHHHHHHHHS-GGGSTT-----SSTHHHHHHHHHHHHH-GGG--HHHHHHHHHHHHHHS-HHH-----HH
T ss_pred HHccCCCHHHHHHHHHHHcCCHHHHHhccCCCCChhHHHHHHHHHHhcChhhCCHHHHHHHHHHHHHHccCCccchHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999987777889999
Q ss_pred HHHHHHHHHHhhcccc--HHHHHHHHHHHHHHh
Q psy14488 334 MFYLEIESLLKKANEH--DTKILNALLMYGKSI 364 (368)
Q Consensus 334 ~~~~~l~~L~~~~~~~--~~~iL~~L~~y~~~l 364 (368)
+|.++|++|+++++.+ |++||++|++|+++|
T Consensus 237 ~~~~~i~~L~~~~~~~~~~~~lL~~L~~Y~~~l 269 (269)
T PF08411_consen 237 EYFQEIEELRAEYDDDEEKQALLEALEDYAESL 269 (269)
T ss_dssp HHHHHHHHHHHHTTT-HHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHhhccCCHHHHHHHHHHHHHHhcC
Confidence 9999999999999887 999999999999875
No 4
>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=99.35 E-value=4.5e-13 Score=121.68 Aligned_cols=80 Identities=59% Similarity=1.114 Sum_probs=75.9
Q ss_pred ccccCcccccccccCCCcccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHHH
Q psy14488 2 FWRNLINPYEREWKNNCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLAR 81 (368)
Q Consensus 2 fYRNf~dPY~~ew~nGnSRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAk 81 (368)
|+|+.++|+...|.++|.++|.++++|.++.++|+++.||..+.|.+|+||+.|+...||.+.+||+|++|+.||.+|++
T Consensus 104 ~~r~~~~~~~~~~~~~~~~~dtl~l~r~~~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gi~~~~~H~Al~Da~~ta~l~~ 183 (183)
T cd06138 104 FYRNLYDPYTWEWKNGNSRWDLLDVVRAYYALRPDGIVWPKNDDGKPSFKLEDLAQANGIEHSNAHDALSDVEATIALAK 183 (183)
T ss_pred HHHCCCcccceeccCCccccccHHHHHHHHhhChhhccCccccCCCcchhHHHHHHHCCCCccccccHHHHHHHHHHHhC
Confidence 67899999999999999999999999999999999999999888889999999999999999999999999999988764
No 5
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.65 E-value=3.4e-05 Score=73.97 Aligned_cols=41 Identities=22% Similarity=0.288 Sum_probs=37.3
Q ss_pred CcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhC
Q psy14488 47 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 87 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kq 87 (368)
.|+.+|+.|+..-|+.+.+||+|++||+||.++.+.+.++.
T Consensus 134 ~~~~~L~~l~~~~g~~~~~aH~Al~Da~at~~vl~~l~~~~ 174 (250)
T PRK06310 134 SPNNSLEALAVHFNVPYDGNHRAMKDVEINIKVFKHLCKRF 174 (250)
T ss_pred CCCCCHHHHHHHCCCCCCCCcChHHHHHHHHHHHHHHHHhc
Confidence 47899999999999999999999999999999998887654
No 6
>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=97.50 E-value=0.00013 Score=68.19 Aligned_cols=44 Identities=16% Similarity=0.141 Sum_probs=40.5
Q ss_pred cceecccchhhhCcccc--cchhhhhhHHHHHHHHHHHHhhCcchH
Q psy14488 48 PSFKLEHLSFVNNLSHK--KAHDALSDVRATLGLARLIRNNNPRLF 91 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~--~AHDAlsDV~ATI~lAkLIk~kqPkL~ 91 (368)
.+++|+.|+...||.+. .||||++|+.||..|.+.+.+++|++.
T Consensus 136 ~~~~L~~l~~~~gl~~~~~~~H~Al~DA~~ta~l~~~l~~~~~~~~ 181 (217)
T TIGR00573 136 KRNTLDALCKRYEITNSHRALHGALADAFILAKLYLVMTGKQTKYG 181 (217)
T ss_pred CCCCHHHHHHHcCCCCCCcccCCHHHHHHHHHHHHHHHHhcchhhc
Confidence 35899999999999865 999999999999999999999999877
No 7
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=97.23 E-value=0.00054 Score=59.73 Aligned_cols=39 Identities=28% Similarity=0.294 Sum_probs=35.0
Q ss_pred cceecccchhhhCcccccc-hhhhhhHHHHHHHHHHHHhh
Q psy14488 48 PSFKLEHLSFVNNLSHKKA-HDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~~A-HDAlsDV~ATI~lAkLIk~k 86 (368)
++.+|+.|++..|+.+.++ |+|++||.+|+.|.+.+.++
T Consensus 127 ~~~~L~~l~~~~~~~~~~~~H~A~~Da~~t~~l~~~~~~~ 166 (169)
T smart00479 127 RKYSLKKLAERLGLEVIGRAHRALDDARATAKLFKKLVER 166 (169)
T ss_pred CCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHH
Confidence 4899999999999998775 99999999999999888653
No 8
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=97.20 E-value=0.00022 Score=67.56 Aligned_cols=43 Identities=23% Similarity=0.207 Sum_probs=39.7
Q ss_pred cceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhCcch
Q psy14488 48 PSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRL 90 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kqPkL 90 (368)
.+.+|+.|+...||.+.+||+|++||.||..|...+.++.|+|
T Consensus 141 ~~~~L~~l~~~~gi~~~~aH~Al~Da~ata~l~~~l~~~~~~l 183 (232)
T PRK07942 141 GKRTLTALCEHYGVRLDNAHEATADALAAARVAWALARRFPEL 183 (232)
T ss_pred CCCCHHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHHHHHHHh
Confidence 3679999999999999999999999999999999999988855
No 9
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=97.20 E-value=0.00016 Score=66.59 Aligned_cols=42 Identities=17% Similarity=0.159 Sum_probs=36.9
Q ss_pred CCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhC
Q psy14488 46 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 87 (368)
Q Consensus 46 G~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kq 87 (368)
|.++++|++|+...||.+.++|+|++|++||..|-..+++-|
T Consensus 160 ~~~~~~L~~l~~~~gi~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (202)
T PRK09145 160 AYIDLRFDAILKHLDLPVLGRHDALNDAIMAALIFLRLRKGD 201 (202)
T ss_pred cccCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHhcC
Confidence 677899999999999999999999999999988777666543
No 10
>PRK07740 hypothetical protein; Provisional
Probab=97.13 E-value=0.00027 Score=67.54 Aligned_cols=52 Identities=19% Similarity=0.161 Sum_probs=39.3
Q ss_pred HHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHHHHH
Q psy14488 22 DLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLI 83 (368)
Q Consensus 22 Dli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLI 83 (368)
..+|+++++..+.|+ ..+.+|+.|+...||...++|+|++||+||..|-+.+
T Consensus 171 ~~iDt~~l~r~l~~~----------~~~~sL~~l~~~~gi~~~~~H~Al~Da~ata~l~~~l 222 (244)
T PRK07740 171 RLIDTMFLTKLLAHE----------RDFPTLDDALAYYGIPIPRRHHALGDALMTAKLWAIL 222 (244)
T ss_pred CeechHHHHHHHcCC----------CCCCCHHHHHHHCCcCCCCCCCcHHHHHHHHHHHHHH
Confidence 345555555555442 2467899999999999999999999999998764443
No 11
>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=96.75 E-value=0.0011 Score=73.76 Aligned_cols=41 Identities=34% Similarity=0.369 Sum_probs=37.2
Q ss_pred cceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhCc
Q psy14488 48 PSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNP 88 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kqP 88 (368)
+|++|++|+..-||.|.+||+|++|+.||.+|...+.++-+
T Consensus 126 ~~~~L~~l~~~~gi~~~~~H~Al~DA~ata~l~~~l~~~~~ 166 (850)
T TIGR01407 126 ESYQLSELSEALGLTHENPHRADSDAQATAELLLLLFEKME 166 (850)
T ss_pred CCCCHHHHHHHCCCCCCCCCChHHHHHHHHHHHHHHHHHHH
Confidence 57999999999999999999999999999998888877644
No 12
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=96.74 E-value=0.0013 Score=64.73 Aligned_cols=58 Identities=26% Similarity=0.335 Sum_probs=42.1
Q ss_pred CcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHHHH-HHh-hCcchHHHHHhcc
Q psy14488 37 GITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARL-IRN-NNPRLFNFILSLR 98 (368)
Q Consensus 37 gi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkL-Ik~-kqPkL~~~~~~~r 98 (368)
.|.|+. .|..+.||+.|+...|+. .+||+|++||.||.+|... +.. .+|.| +.++...
T Consensus 154 ~i~~~~--~~~~~~kL~~La~~~g~~-~~aHrAl~Da~Ata~ll~~~l~~~~~~~l-~~Ll~~~ 213 (294)
T PRK09182 154 EIDWSA--RGFEGTKLGYLAGQAGFF-HEGHRAVDDCQALLELLARPLPETGQPPL-AELLEAS 213 (294)
T ss_pred HHhhcc--ccCCCCCHHHHHHHcCCC-CCCcChHHHHHHHHHHHHHHHhhcCCcCH-HHHHHHh
Confidence 467874 466899999999999965 5799999999999888773 222 22443 5554443
No 13
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=96.69 E-value=0.0011 Score=62.84 Aligned_cols=40 Identities=25% Similarity=0.309 Sum_probs=34.9
Q ss_pred CcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhh
Q psy14488 47 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
.++.+|+.|+..-|+.+.+||+|++||+||..+.+-+.++
T Consensus 126 ~~~~~L~~l~~~~~~~~~~aH~Al~Da~~t~~vl~~l~~~ 165 (232)
T PRK06309 126 LPKHNLQYLRQVYGFEENQAHRALDDVITLHRVFSALVGD 165 (232)
T ss_pred CCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999999999999998887776543
No 14
>PRK07883 hypothetical protein; Validated
Probab=96.44 E-value=0.0024 Score=68.01 Aligned_cols=44 Identities=23% Similarity=0.290 Sum_probs=39.1
Q ss_pred CCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhCcc
Q psy14488 46 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPR 89 (368)
Q Consensus 46 G~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kqPk 89 (368)
+.++.+|+.|+...||.+.++|+||+||.||.++...+-++.+.
T Consensus 141 ~~~~~~L~~L~~~~gi~~~~~H~Al~DA~ata~l~~~l~~~~~~ 184 (557)
T PRK07883 141 EAPNVRLSTLARLFGATTTPTHRALDDARATVDVLHGLIERLGN 184 (557)
T ss_pred CCCCCCHHHHHHHCCcccCCCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 66789999999999999999999999999999998887666543
No 15
>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=96.39 E-value=0.0019 Score=54.71 Aligned_cols=33 Identities=33% Similarity=0.291 Sum_probs=28.2
Q ss_pred cceecccc-hhhhCcccccchhhhhhHHHHHHHH
Q psy14488 48 PSFKLEHL-SFVNNLSHKKAHDALSDVRATLGLA 80 (368)
Q Consensus 48 pSFKLe~L-t~ANgi~h~~AHDAlsDV~ATI~lA 80 (368)
.+-+|..+ ....|+.+.++||||+||.||.++-
T Consensus 125 ~~~~l~~~~~~~~~~~~~~~H~Al~Da~~t~~l~ 158 (159)
T cd06127 125 RSHRLGLLLAERYGIPLEGAHRALADALATAELL 158 (159)
T ss_pred CcCchHHHHHHHcCCCCCCCCCcHHHHHHHHHHh
Confidence 34577777 8899999999999999999998763
No 16
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=96.38 E-value=0.0022 Score=72.10 Aligned_cols=39 Identities=36% Similarity=0.346 Sum_probs=35.1
Q ss_pred cceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhh
Q psy14488 48 PSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
+|+||++|+..-||.|+++|+|++|++||..|...+.++
T Consensus 130 ~~~~L~~l~~~l~i~~~~~H~Al~DA~ata~l~~~l~~~ 168 (928)
T PRK08074 130 ESYKLRDLSEELGLEHDQPHRADSDAEVTAELFLQLLNK 168 (928)
T ss_pred CCCCHHHHHHhCCCCCCCCCChHHHHHHHHHHHHHHHHH
Confidence 589999999999999999999999999998887776554
No 17
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.33 E-value=0.0022 Score=61.31 Aligned_cols=65 Identities=20% Similarity=0.204 Sum_probs=50.0
Q ss_pred HHHHHHHHHHhhcCC--CcccCCC-CCCCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhh
Q psy14488 22 DLINVIKAFYVLSPY--GITWPYK-NNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 22 Dli~vvra~yalrPe--gi~WP~~-~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
-.+|.++++..+.|. +-.||.. ..+.+|++|++++..=||...++|+|++|+.||.+|-.-+.++
T Consensus 159 ~~iDTl~Lar~l~~~~~~~~~~~~~~~~~~~~~L~~l~~~~gl~~~~~H~Al~DA~ata~l~~~~~~~ 226 (239)
T PRK09146 159 PVIDTMEIEARIQRKQAGGLWNRLKGKKPESIRLADSRLRYGLPAYSPHHALTDAIATAELLQAQIAH 226 (239)
T ss_pred ceechHHHHHHHcccccccccchhccCCCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHHH
Confidence 357777777777776 3456653 3345899999999999999999999999999997776655443
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.22 E-value=0.0053 Score=60.93 Aligned_cols=40 Identities=33% Similarity=0.523 Sum_probs=35.0
Q ss_pred CCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHh
Q psy14488 46 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 46 G~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
+.++.||+.|+..-||...++|||++|++||-.+...+.+
T Consensus 138 ~~~~~kL~~l~~~~gi~~~~~H~Al~DA~ata~l~~~ll~ 177 (313)
T PRK06063 138 GLPNLRLETLAAHWGVPQQRPHDALDDARVLAGILRPSLE 177 (313)
T ss_pred CCCCCCHHHHHHHcCCCCCCCCCcHHHHHHHHHHHHHHHH
Confidence 3468999999999999999999999999999888765544
No 19
>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=96.21 E-value=0.003 Score=55.67 Aligned_cols=36 Identities=17% Similarity=0.178 Sum_probs=31.9
Q ss_pred cceecccchhhhCcccc-cchhhhhhHHHHHHHHHHH
Q psy14488 48 PSFKLEHLSFVNNLSHK-KAHDALSDVRATLGLARLI 83 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~-~AHDAlsDV~ATI~lAkLI 83 (368)
++.+|+.|+..=||.+. ++|+||+|+++|-.+.+.|
T Consensus 139 ~~~~L~~l~~~~gi~~~~~~H~Al~DA~~~a~l~~~~ 175 (176)
T cd06133 139 KRTGLSKALEYLGLEFEGRHHRGLDDARNIARILKRL 175 (176)
T ss_pred CCCCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHh
Confidence 57889999999999997 8999999999998777654
No 20
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=95.67 E-value=0.011 Score=54.93 Aligned_cols=66 Identities=21% Similarity=0.318 Sum_probs=51.7
Q ss_pred CCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhCcchHHHHHhccCHHHHHhhhCCCCCCceEEEeccc
Q psy14488 46 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMF 122 (368)
Q Consensus 46 G~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kqPkL~~~~~~~r~K~~v~~~l~~~~~~P~lhvs~~f 122 (368)
|.++.||+.|+..=||.. .+|+|++|+++|..+.+.+.+ ..+.|+...+.=.+.+.+||..+.|.|
T Consensus 129 ~~~~~~L~~La~~~gi~~-~~HrAl~DA~~ta~v~~~ll~----------~~~~~~~~~~~~~~~~~~~~~~~~~~~ 194 (195)
T PRK07247 129 GIANLKLQTVADFLGIKG-RGHNSLEDARMTARVYESFLE----------SDQNKEYLEQQEEVTSDNPFAALGGLF 194 (195)
T ss_pred CCCCCCHHHHHHhcCCCC-CCcCCHHHHHHHHHHHHHHHh----------hccchhhhhcchhhccCCchhhhhccc
Confidence 567899999999999984 689999999999877766644 345676666665666788988777665
No 21
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=95.62 E-value=0.011 Score=57.24 Aligned_cols=58 Identities=19% Similarity=0.222 Sum_probs=45.9
Q ss_pred CcccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhCcc
Q psy14488 18 CSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNNPR 89 (368)
Q Consensus 18 nSRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kqPk 89 (368)
|-+.|.+++.|.++ | .++++|+.|+..=||..+.+|+|++||.||..+.+.+..+.|+
T Consensus 176 ~~~ldtl~la~~~~---------~-----~~~~~L~~L~~~lgi~~~~~HrAl~DA~ata~ll~~ll~~~~~ 233 (257)
T PRK08517 176 NRKLCTIDLAKRTI---------E-----SPRYGLSFLKELLGIEIEVHHRAYADALAAYEIFKICLLNLPS 233 (257)
T ss_pred CCcEehHHHHHHHc---------c-----CCCCCHHHHHHHcCcCCCCCCChHHHHHHHHHHHHHHHHHhHH
Confidence 33457777766543 1 1357899999999999999999999999999998888877764
No 22
>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=94.67 E-value=0.031 Score=48.33 Aligned_cols=32 Identities=31% Similarity=0.408 Sum_probs=28.9
Q ss_pred CcceecccchhhhCcccccchhhhhhHHHHHHH
Q psy14488 47 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGL 79 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~l 79 (368)
.++.+|+.|+..=|+... +|+|++|++||-.|
T Consensus 122 ~~~~~L~~l~~~~g~~~~-~H~Al~Da~~ta~l 153 (156)
T cd06130 122 LPNHKLNTVAEHLGIELN-HHDALEDARACAEI 153 (156)
T ss_pred CCCCCHHHHHHHcCCCcc-CcCchHHHHHHHHH
Confidence 567999999999999988 99999999999655
No 23
>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=94.60 E-value=0.014 Score=52.88 Aligned_cols=31 Identities=32% Similarity=0.157 Sum_probs=26.7
Q ss_pred ecccchhh-hCcccccchhhhhhHHHHHHHHH
Q psy14488 51 KLEHLSFV-NNLSHKKAHDALSDVRATLGLAR 81 (368)
Q Consensus 51 KLe~Lt~A-Ngi~h~~AHDAlsDV~ATI~lAk 81 (368)
+|+.|+.. =|+.+.++|+|++||.||..+.+
T Consensus 144 ~L~~l~~~~~~~~~~~~H~A~~Da~at~~v~~ 175 (177)
T cd06136 144 SLGSLYKRLFGQEPKNSHTAEGDVLALLKCAL 175 (177)
T ss_pred hHHHHHHHHhCCCcccccchHHHHHHHHHHHh
Confidence 89999875 59999999999999999966654
No 24
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=94.43 E-value=0.03 Score=62.46 Aligned_cols=39 Identities=33% Similarity=0.386 Sum_probs=35.4
Q ss_pred cceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhh
Q psy14488 48 PSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
++++|++|+..=||.|.++|+|++|++||..|...+.++
T Consensus 131 ~~~~L~~L~~~lgl~~~~~H~Al~DA~ata~L~~~l~~~ 169 (820)
T PRK07246 131 EKYSLSHLSRELNIDLADAHTAIADARATAELFLKLLQK 169 (820)
T ss_pred CCCCHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHH
Confidence 579999999999999999999999999999888777655
No 25
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=94.41 E-value=0.032 Score=55.54 Aligned_cols=40 Identities=20% Similarity=0.263 Sum_probs=34.9
Q ss_pred CcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhhC
Q psy14488 47 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNNN 87 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~kq 87 (368)
.|++||+.|+..=||.. ++|+|+.|+.||.++.+.+..+.
T Consensus 133 ~~~~kL~~L~~~lgi~~-~~H~Al~DA~~ta~l~~~l~~~~ 172 (313)
T PRK06807 133 APNHKLETLKRMLGIRL-SSHNAFDDCITCAAVYQKCASIE 172 (313)
T ss_pred CCCCCHHHHHHHcCCCC-CCcChHHHHHHHHHHHHHHHHhh
Confidence 46789999999999998 99999999999999877666554
No 26
>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=93.97 E-value=0.041 Score=63.69 Aligned_cols=39 Identities=18% Similarity=0.154 Sum_probs=35.1
Q ss_pred CcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHh
Q psy14488 47 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
..+++|+.|+...|+...++|+|+.|+.||..+.+.+.+
T Consensus 315 ~k~~kL~~Lak~lgi~~~~~HrAl~DA~aTa~I~~~ll~ 353 (1213)
T TIGR01405 315 YKSHRLGNICKKLGVDLDDHHRADYDAEATAKVFKVMVE 353 (1213)
T ss_pred CCCCCHHHHHHHcCCCCCCCcCHHHHHHHHHHHHHHHHH
Confidence 357999999999999999999999999999988877754
No 27
>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=93.66 E-value=0.048 Score=49.97 Aligned_cols=37 Identities=30% Similarity=0.262 Sum_probs=30.8
Q ss_pred ceecccchhhhCcc--cccchhhhhhHHHHHHHHHHHHh
Q psy14488 49 SFKLEHLSFVNNLS--HKKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 49 SFKLe~Lt~ANgi~--h~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
+++|+.++..=||. +.++|+||+|++||-+|-..+.+
T Consensus 149 ~~~L~~l~~~~gi~~~~~~~H~Al~DA~ata~lf~~l~~ 187 (189)
T cd06134 149 QTVLAKACQAAGIEFDNKEAHSALYDTQKTAELFCKIVN 187 (189)
T ss_pred CCcHHHHHHHCCCCCCCCCCcChHHHHHHHHHHHHHHHH
Confidence 45899999999997 46899999999999777666554
No 28
>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=93.35 E-value=0.032 Score=49.71 Aligned_cols=33 Identities=27% Similarity=0.290 Sum_probs=27.8
Q ss_pred Ccceecccchhh-hCccc---ccchhhhhhHHHHHHH
Q psy14488 47 KPSFKLEHLSFV-NNLSH---KKAHDALSDVRATLGL 79 (368)
Q Consensus 47 ~pSFKLe~Lt~A-Ngi~h---~~AHDAlsDV~ATI~l 79 (368)
.++++|+.|+.. -|+.. ..+|||++|+.||..|
T Consensus 123 ~~~~~L~~L~~~~~~~~~~~~~~~H~A~~DA~at~~l 159 (161)
T cd06137 123 KRQWSLRTLCRDFLGLKIQGGGEGHDSLEDALAAREV 159 (161)
T ss_pred CCCccHHHHHHHHCCchhcCCCCCCCcHHHHHHHHHH
Confidence 478999999987 67654 5799999999999665
No 29
>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=93.22 E-value=0.047 Score=46.10 Aligned_cols=33 Identities=36% Similarity=0.514 Sum_probs=28.3
Q ss_pred CcceecccchhhhCccccc-chhhhhhHHHHHHH
Q psy14488 47 KPSFKLEHLSFVNNLSHKK-AHDALSDVRATLGL 79 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~-AHDAlsDV~ATI~l 79 (368)
.+..+|+.|+..=|+.... ||+|++||++|+.|
T Consensus 130 ~~~~~l~~l~~~~~~~~~~~~H~Al~Da~~t~~l 163 (164)
T PF00929_consen 130 RKKYSLDDLAEYFGIPFDGTAHDALDDARATAEL 163 (164)
T ss_dssp HHHHSHHHHHHHTTSSSTSTTTSHHHHHHHHHHH
T ss_pred cccCCHHHHHHHcCCCCCCCCcChHHHHHHHhCc
Confidence 3348999999999998776 89999999999875
No 30
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=93.14 E-value=0.089 Score=48.77 Aligned_cols=38 Identities=21% Similarity=0.110 Sum_probs=32.5
Q ss_pred cceecccchhhhCccc-ccchhhhhhHHHHHHHHHHHHh
Q psy14488 48 PSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 48 pSFKLe~Lt~ANgi~h-~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
.+.+|+++...-||.. +++|+||+|+++|-.|.+.+.+
T Consensus 140 ~~~~L~~~~~~~gi~~~~~~H~Al~DA~~ta~l~~~l~~ 178 (207)
T PRK07748 140 NQTGLWKAIEEYGKEGTGKHHCALDDAMTTYNIFKLVEK 178 (207)
T ss_pred CCCCHHHHHHHcCCCCCCCCcChHHHHHHHHHHHHHHHh
Confidence 3568999999999996 6799999999999888877664
No 31
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=93.06 E-value=0.059 Score=53.22 Aligned_cols=39 Identities=23% Similarity=0.221 Sum_probs=32.5
Q ss_pred CCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHh
Q psy14488 46 GKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 46 G~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
|.++++|+.|+.+=|+.+ .+|+|++|++||-.|...+.+
T Consensus 124 ~~~~~~L~~L~~~~gi~~-~~H~Al~DA~ata~l~~~l~~ 162 (309)
T PRK06195 124 NIDNARLNTVNNFLGYEF-KHHDALADAMACSNILLNISK 162 (309)
T ss_pred CCCcCCHHHHHHHcCCCC-cccCCHHHHHHHHHHHHHHHH
Confidence 347899999999999986 699999999999777655544
No 32
>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=93.05 E-value=0.041 Score=48.99 Aligned_cols=34 Identities=24% Similarity=0.329 Sum_probs=28.8
Q ss_pred Ccceecccchhhh---Cccc-ccchhhhhhHHHHHHHH
Q psy14488 47 KPSFKLEHLSFVN---NLSH-KKAHDALSDVRATLGLA 80 (368)
Q Consensus 47 ~pSFKLe~Lt~AN---gi~h-~~AHDAlsDV~ATI~lA 80 (368)
.++.+|+.|+..= ||.+ +++|||++|+.||.+|-
T Consensus 119 ~~~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~at~~l~ 156 (157)
T cd06149 119 NCRVSLKVLAKRLLHRDIQVGRQGHSSVEDARATMELY 156 (157)
T ss_pred cCChhHHHHHHHHcChhhcCCCCCcCcHHHHHHHHHHh
Confidence 4679999999986 7877 67999999999997664
No 33
>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=92.22 E-value=0.11 Score=45.71 Aligned_cols=34 Identities=18% Similarity=0.112 Sum_probs=28.6
Q ss_pred ceecccchhhhCccc--ccchhhhhhHHHHHHHHHH
Q psy14488 49 SFKLEHLSFVNNLSH--KKAHDALSDVRATLGLARL 82 (368)
Q Consensus 49 SFKLe~Lt~ANgi~h--~~AHDAlsDV~ATI~lAkL 82 (368)
+.+|+.++..=||.. .++|+|++|+.+|-+|...
T Consensus 130 ~~~L~~l~~~~~i~~~~~~~H~Al~Da~~~a~l~~~ 165 (167)
T cd06131 130 PNSLDALCKRFGIDNSHRTLHGALLDAELLAEVYLE 165 (167)
T ss_pred CCCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHH
Confidence 469999999999976 3799999999999776654
No 34
>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=92.03 E-value=0.069 Score=47.07 Aligned_cols=34 Identities=26% Similarity=0.280 Sum_probs=28.4
Q ss_pred Ccceecccchhh-hCccc-ccchhhhhhHHHHHHHH
Q psy14488 47 KPSFKLEHLSFV-NNLSH-KKAHDALSDVRATLGLA 80 (368)
Q Consensus 47 ~pSFKLe~Lt~A-Ngi~h-~~AHDAlsDV~ATI~lA 80 (368)
.+|.+|+.|++. =||.. .++|+|++|++||..|-
T Consensus 116 ~~~~sL~~l~~~~lgi~~~~~~H~Al~DA~at~~l~ 151 (152)
T cd06144 116 GKSPSLKKLAKQLLGLDIQEGEHSSVEDARAAMRLY 151 (152)
T ss_pred CCChhHHHHHHHHcCcccCCCCcCcHHHHHHHHHHh
Confidence 478999999997 48874 57999999999997653
No 35
>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=91.90 E-value=0.24 Score=44.65 Aligned_cols=27 Identities=26% Similarity=0.434 Sum_probs=23.4
Q ss_pred hCcccccchhhhhhHHHHHHHHHHHHh
Q psy14488 59 NNLSHKKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 59 Ngi~h~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
.|+.++.+|.||+|+.||+++.|-.++
T Consensus 144 ~~~~~~~~HrAl~Da~~~~~~~~~~~~ 170 (173)
T cd06135 144 KAPKKKGTHRALDDIRESIAELKYYRE 170 (173)
T ss_pred cCCCCCCCcchHHHHHHHHHHHHHHHH
Confidence 478899999999999999998886654
No 36
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=91.70 E-value=0.18 Score=47.66 Aligned_cols=66 Identities=21% Similarity=0.115 Sum_probs=41.4
Q ss_pred eecccchhhhCccc-----ccchhhhhhHHHHHHHHHHHHhhCcchHHHHHhccCHHHHHhhhCCCCCCceEEEecccCC
Q psy14488 50 FKLEHLSFVNNLSH-----KKAHDALSDVRATLGLARLIRNNNPRLFNFILSLRKKKYVLAEIGWPIARPFFYITHMFSS 124 (368)
Q Consensus 50 FKLe~Lt~ANgi~h-----~~AHDAlsDV~ATI~lAkLIk~kqPkL~~~~~~~r~K~~v~~~l~~~~~~P~lhvs~~f~a 124 (368)
.+|+.|+..=||.. .+||+|++||+||-.|...+.+... . .+.++++. +.+|-+.-.-.||.
T Consensus 112 ~~l~~L~~~~~l~~~~~~~~~aHrAl~Da~ata~ll~~l~~~~~--------~----~~~~l~~~-~~~~~~~~~~~fGk 178 (219)
T PRK07983 112 YSNMALYKSRKLNVQTPPGLHHHRALYDCYITAALLIDIMNTSG--------W----TAEEMADI-TGRPSLLTTFTFGK 178 (219)
T ss_pred CCHHHHHHHcCCCCCCCCCCCCCcHHHHHHHHHHHHHHHHHHcC--------C----CHHHHHHH-hcCCccCCCccccC
Confidence 67888888878753 5799999999999776665543211 0 12444443 23565544445666
Q ss_pred CCCC
Q psy14488 125 KHSY 128 (368)
Q Consensus 125 ~~~~ 128 (368)
.+|-
T Consensus 179 ~kg~ 182 (219)
T PRK07983 179 YRGK 182 (219)
T ss_pred ccCc
Confidence 6554
No 37
>PRK05168 ribonuclease T; Provisional
Probab=91.70 E-value=0.1 Score=48.75 Aligned_cols=38 Identities=29% Similarity=0.209 Sum_probs=30.9
Q ss_pred eecccchhhhCcc--cccchhhhhhHHHHHHHHHHHHhhC
Q psy14488 50 FKLEHLSFVNNLS--HKKAHDALSDVRATLGLARLIRNNN 87 (368)
Q Consensus 50 FKLe~Lt~ANgi~--h~~AHDAlsDV~ATI~lAkLIk~kq 87 (368)
.+|+.++..=||. +..+|+|++|+.||-+|-..+.++.
T Consensus 162 ~~L~~l~~~~gl~~~~~~~H~Al~DA~ata~l~~~l~~~~ 201 (211)
T PRK05168 162 TVLAKACQAAGIEFDNKEAHSALYDTEKTAELFCEIVNRW 201 (211)
T ss_pred CCHHHHHHHCCCCCCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 4799888888887 4579999999999988777666653
No 38
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.32 E-value=0.16 Score=59.81 Aligned_cols=39 Identities=23% Similarity=0.089 Sum_probs=35.1
Q ss_pred CcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHh
Q psy14488 47 KPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRN 85 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~ 85 (368)
..+++|+.|+..-||...++|+|+.|++||..+...+.+
T Consensus 544 ~k~~kL~~LAk~lGL~~~~~HrAl~DA~aTa~lf~~ll~ 582 (1437)
T PRK00448 544 LKSHRLNTLAKKFGVELEHHHRADYDAEATAYLLIKFLK 582 (1437)
T ss_pred cccccHHHHHHHcCCCCCCCcChHHHHHHHHHHHHHHHH
Confidence 468999999999999999999999999999888777654
No 39
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=90.98 E-value=0.21 Score=47.98 Aligned_cols=38 Identities=16% Similarity=0.163 Sum_probs=30.2
Q ss_pred eecccchhhhCccc--ccchhhhhhHHHHHHHHHHHHhhC
Q psy14488 50 FKLEHLSFVNNLSH--KKAHDALSDVRATLGLARLIRNNN 87 (368)
Q Consensus 50 FKLe~Lt~ANgi~h--~~AHDAlsDV~ATI~lAkLIk~kq 87 (368)
.+|+.|+..=||.. ..+|+|++|+++|-.+-..+...|
T Consensus 137 ~~L~aL~~~~gi~~~~r~~H~AL~DA~~~A~v~~~l~~~~ 176 (240)
T PRK05711 137 NSLDALCKRYGIDNSHRTLHGALLDAEILAEVYLAMTGGQ 176 (240)
T ss_pred CCHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCcc
Confidence 58999999999964 478999999999976665554433
No 40
>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=90.95 E-value=0.12 Score=45.60 Aligned_cols=32 Identities=28% Similarity=0.404 Sum_probs=26.4
Q ss_pred ceecccchhh-hC--ccc-ccchhhhhhHHHHHHHH
Q psy14488 49 SFKLEHLSFV-NN--LSH-KKAHDALSDVRATLGLA 80 (368)
Q Consensus 49 SFKLe~Lt~A-Ng--i~h-~~AHDAlsDV~ATI~lA 80 (368)
+.+|+.|+.. +| |.+ ..+|+|++|++||..|.
T Consensus 114 ~~~L~~L~~~~~~~~i~~~~~~H~Al~DA~~t~~l~ 149 (150)
T cd06145 114 KPSLKNLAKKYLGRDIQQGEGGHDSVEDARAALELV 149 (150)
T ss_pred ChhHHHHHHHHCCcceeCCCCCCCcHHHHHHHHHHh
Confidence 6899999987 46 455 58999999999997664
No 41
>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=90.81 E-value=0.13 Score=47.53 Aligned_cols=38 Identities=26% Similarity=0.181 Sum_probs=30.6
Q ss_pred ceecccchhhhCccc--ccchhhhhhHHHHHHHHHHHHhh
Q psy14488 49 SFKLEHLSFVNNLSH--KKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 49 SFKLe~Lt~ANgi~h--~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
+.+|+.|+..=||.. .++|+|++|+.||-.|-..+.++
T Consensus 152 ~~~L~~l~~~~gi~~~~~~~H~Al~Da~ata~lf~~l~~~ 191 (200)
T TIGR01298 152 QTVLAKACQAAGXDFDSTQAHSALYDTEKTAELFCEIVNR 191 (200)
T ss_pred cccHHHHHHHcCCCccccchhhhHHhHHHHHHHHHHHHHH
Confidence 357999999889974 58999999999997766665544
No 42
>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=89.78 E-value=0.26 Score=46.61 Aligned_cols=39 Identities=15% Similarity=0.138 Sum_probs=31.2
Q ss_pred ceecccchhhhCccc--ccchhhhhhHHHHHHHHHHHHhhC
Q psy14488 49 SFKLEHLSFVNNLSH--KKAHDALSDVRATLGLARLIRNNN 87 (368)
Q Consensus 49 SFKLe~Lt~ANgi~h--~~AHDAlsDV~ATI~lAkLIk~kq 87 (368)
+.+|+.|+..=||.. ..+|+||.|+++|-.+-..+...|
T Consensus 132 ~~~L~~L~~~~gi~~~~r~~H~Al~DA~~~a~v~~~l~~~~ 172 (225)
T TIGR01406 132 RNSLDALCKRFKVDNSHRTLHGALLDAHLLAEVYLALTGGQ 172 (225)
T ss_pred CCCHHHHHHhcCCCCCCCCCcCHHHHHHHHHHHHHHHHcCC
Confidence 479999999999963 469999999999977766555444
No 43
>PRK06722 exonuclease; Provisional
Probab=89.76 E-value=0.35 Score=47.63 Aligned_cols=34 Identities=24% Similarity=0.132 Sum_probs=28.8
Q ss_pred ecccchhhhCccc-ccchhhhhhHHHHHHHHHHHH
Q psy14488 51 KLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIR 84 (368)
Q Consensus 51 KLe~Lt~ANgi~h-~~AHDAlsDV~ATI~lAkLIk 84 (368)
+|+.|+..=||.. +++|+||+|+++|-.|...+.
T Consensus 144 sL~~l~~~lgL~~~g~~HrAL~DA~~TA~L~l~l~ 178 (281)
T PRK06722 144 SLQSAVEQLGLIWEGKQHRALADAENTANILLKAY 178 (281)
T ss_pred CHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHh
Confidence 5999999999996 689999999999977765543
No 44
>PRK05359 oligoribonuclease; Provisional
Probab=89.25 E-value=0.55 Score=42.95 Aligned_cols=48 Identities=19% Similarity=0.300 Sum_probs=36.3
Q ss_pred cccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHHHHHHhh
Q psy14488 19 SRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 19 SRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
...|+..+-.++.-+.|+. ..|+.+.++|-||+|+.+||+..+-.|+.
T Consensus 127 ~~~Dv~tl~~l~r~~~P~~--------------------~~~~~~~~~HRal~D~~~s~~~~~~~~~~ 174 (181)
T PRK05359 127 RNLDVSTLKELARRWKPEI--------------------LNGFKKQGTHRALADIRESIAELKYYREH 174 (181)
T ss_pred cccchhHHHHHHHHhChhh--------------------hhCCCCcCCcccHHHHHHHHHHHHHHHHH
Confidence 3446544446777776653 13889999999999999999999988773
No 45
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=81.95 E-value=1.6 Score=40.87 Aligned_cols=57 Identities=21% Similarity=0.225 Sum_probs=42.9
Q ss_pred CCcccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcc--cccchhhhhhHHHHHHHHHHHHhh
Q psy14488 17 NCSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLS--HKKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 17 GnSRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~--h~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
++..-|-+.+.|..+ | |..+-+|+.|+...||. +.+.|+|+.|+.||-++...+-..
T Consensus 123 ~~~~~~t~~~~r~~~---------~----~~~~~~L~~l~~~~gi~~~~~~~H~Al~Da~~~a~~~~~~~~~ 181 (243)
T COG0847 123 GDPVLDTLALARRHF---------P----GFDRSSLDALAERLGIDRNPFHPHRALFDALALAELFLLLQTG 181 (243)
T ss_pred cCceehHHHHHHHHc---------C----CCccchHHHHHHHcCCCcCCcCCcchHHHHHHHHHHHHHHHhc
Confidence 445556666666532 2 25678999999999999 778999999999998866655443
No 46
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=77.49 E-value=5.2 Score=41.13 Aligned_cols=39 Identities=13% Similarity=0.160 Sum_probs=32.9
Q ss_pred CcceecccchhhhCccc----------ccchhhhh--hHHHHHHHHHHHHh
Q psy14488 47 KPSFKLEHLSFVNNLSH----------KKAHDALS--DVRATLGLARLIRN 85 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h----------~~AHDAls--DV~ATI~lAkLIk~ 85 (368)
.++.||+.|+..=||.+ ...|+||+ |+..+.+|....++
T Consensus 197 l~~~rL~~La~~lGi~~p~~~A~~~Ra~~p~~~l~~~Da~ll~~l~~~~~~ 247 (377)
T PRK05601 197 LDDIRIRGVAHTLGLDAPAAEASVERAQVPHRQLCREETLLVARLYFALRA 247 (377)
T ss_pred CCCCCHHHHHHHhCCCCCchhhhhhhhcCChhhhhhHHHHHHHHHHHHhhc
Confidence 45799999999999998 78899997 99999888766543
No 47
>cd07357 HN_L-whirlin_R2_like Second harmonin_N_like domain (repeat 2) of the long isoform of whirlin, and related domains. This subgroup contains the second of two harmonin_N_like domains found in the long isoform of whirlin, and related domains. Whirlin is a postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold protein which binds various components of the Usher protein network of the inner ear and the retina: erythrocyte protein p55, usherin, VlGR1, and myosin XVa. The long isoform of whirlin contains two harmonin_N_like domains, and three PDZ protein-binding domains, PDZ1-3. The short whirlin isoform, derived from an alternative start ATG, lacks the first harmonin_N_like domain but has in common with the long isoform, this second harmonin_N_like domain (designated repeat 2, included in this subgroup) and PDZ3. This second harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=68.13 E-value=16 Score=29.71 Aligned_cols=51 Identities=14% Similarity=0.077 Sum_probs=42.9
Q ss_pred CCCHHHHHHHHHHHHHHcccCCCccccHHHHHHHHHHHHhhccccHHHHHHHHHHHH
Q psy14488 305 TLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTKILNALLMYG 361 (368)
Q Consensus 305 ~L~~~E~~~W~~~~~~rl~~~~~~~~~~~~~~~~l~~L~~~~~~~~~~iL~~L~~y~ 361 (368)
.||++|+.--..|+++.-. +.++++.+...+-+|+..++ |..+|.++..+.
T Consensus 15 lL~e~E~~tm~yyl~eY~~----~~~tVealV~aL~elLnt~~--K~sLLsEiR~lI 65 (81)
T cd07357 15 LLSENERATLSYYLDEYRS----GHISVDALVMALFELLNTHE--KFSLLSEIRELI 65 (81)
T ss_pred HcCHHHHHHHHHHHHHHHc----CCCCHHHHHHHHHHHhccHH--HHHHHHHHHHhc
Confidence 5799999999889986654 57899999999999998766 999998887654
No 48
>PTZ00315 2'-phosphotransferase; Provisional
Probab=66.00 E-value=4.8 Score=43.56 Aligned_cols=40 Identities=10% Similarity=0.106 Sum_probs=33.6
Q ss_pred CcceecccchhhhCccc-ccchhhhhhHHHHHHHHHHHHhh
Q psy14488 47 KPSFKLEHLSFVNNLSH-KKAHDALSDVRATLGLARLIRNN 86 (368)
Q Consensus 47 ~pSFKLe~Lt~ANgi~h-~~AHDAlsDV~ATI~lAkLIk~k 86 (368)
..+.+|+++...=||++ +++|.|+.|+++|..|.+.+.++
T Consensus 214 ~~~~~L~~al~~lgL~~eGr~HrAlDDA~ntA~L~~~Ll~~ 254 (582)
T PTZ00315 214 LGPSDMPDMLQMLGLPLQGRHHSGIDDCRNIAAVLCELLRR 254 (582)
T ss_pred cCCcCHHHHHHHCCCCCCCCCcCcHHHHHHHHHHHHHHHHc
Confidence 45688999999999995 57999999999997777766554
No 49
>PF00901 Orbi_VP5: Orbivirus outer capsid protein VP5; InterPro: IPR000145 The orbivirus VP5 protein is one of the two proteins (with VP2) which make up the virus particle outer capsid. Cryoelectron microscopy indicates that VP5 is a trimer suggesting that there are 360 copies of VP5 per virion [].; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=39.56 E-value=74 Score=34.02 Aligned_cols=112 Identities=16% Similarity=0.188 Sum_probs=65.8
Q ss_pred CCCceEEEec-ccCCCCCCceEEEeecccCCCCCeEEEEeCCCCchHhhcCCHH-----------------HHHHHhccc
Q psy14488 111 IARPFFYITH-MFSSKHSYISLMWPICIHPMNKNILITWNLLHDPKKFLLNDIN-----------------KIRDYLCFK 172 (368)
Q Consensus 111 ~~~P~lhvs~-~f~a~~~~~~~v~pl~~hp~n~N~vi~~DL~~Dp~~L~~l~~~-----------------~i~~~l~t~ 172 (368)
..+|.+||=. =+.+. +..++-||+.|-.|..=++||||..|---+-+++.. +-....|.-
T Consensus 353 ~q~P~IHiYtaPwDSD--~Vfifh~isPhH~~~sF~lgfDL~id~V~feDl~~~~H~l~g~a~~~~grtf~~Ay~eFf~~ 430 (508)
T PF00901_consen 353 TQQPQIHIYTAPWDSD--YVFIFHCISPHHQNESFFLGFDLEIDYVHFEDLTVHWHALHGGAQEAVGRTFREAYSEFFNL 430 (508)
T ss_pred ccCCceEEecCCCCCC--cEEEEEeecCcCCCceeEEEEecccceEEEEeccccccccccccccccCccHHHHHHHHHHH
Confidence 5689998742 44444 677788899999999999999999986555554421 111111111
Q ss_pred cccCCCCCCceEEeecC----CcccccccccCChhhhhhhcCCHHHHHHHHHhHHHHhhChhHHHHHH
Q psy14488 173 KNSFKEDIPISMIHLNR----SPIVISNLKVLSSNLMFRYKFDLNCAFKNIKCASSILNNTYIWKKIF 236 (368)
Q Consensus 173 ~~~l~e~~plk~i~iNk----~P~v~~p~~~l~~~~a~rl~id~~~~~~~~~~~~~l~~~~~l~~kl~ 236 (368)
....|....+-.=++-+ .||- +- ..-+.+.+++.+.|+.. |-.+++|+..+.
T Consensus 431 a~~~~~ss~iH~~Rl~RS~~~hPIY-lG--------S~~Y~~sY~ql~~NA~~---lv~d~eLQ~HvL 486 (508)
T PF00901_consen 431 AASHPGSSEIHKRRLQRSRGVHPIY-LG--------SMHYDISYEQLKSNAMR---LVYDPELQMHVL 486 (508)
T ss_pred HhcCCCCcHHHHHHHHhccCCCCee-ec--------CcCccccHHHHHHHHHH---HhCCHHHHHHHH
Confidence 11111100010001111 3333 21 11246789999999999 999999887764
No 50
>PF02084 Bindin: Bindin; InterPro: IPR000775 Bindin, the major protein component of the acrosome granule of sea urchin sperm, mediates species-specific adhesion of sperm to the egg surface during fertilisation [, ]. The protein coats the acrosomal process after externalisation by the acrosome reaction; it binds to sulphated, fucose-containing polysaccharides on the vitelline-layer receptor proteoglycans that cover the egg plasma membrane. Bindins from different genera show high levels of sequence similarity in both the mature bindin domain and in the probindin precursor region. The most highly conserved region is a 42-residue segment in the central portion of the mature bindin protein. This domain may be responsible for conserved functions of bindin, while the more highly divergent flanking regions may be responsible for its species-specific properties [].; GO: 0007342 fusion of sperm to egg plasma membrane
Probab=33.97 E-value=50 Score=31.88 Aligned_cols=32 Identities=16% Similarity=0.344 Sum_probs=25.9
Q ss_pred CHHHHHHHHHhHHHHhhC---hhHHHHHHHHhhhc
Q psy14488 211 DLNCAFKNIKCASSILNN---TYIWKKIFLDYKIN 242 (368)
Q Consensus 211 d~~~~~~~~~~~~~l~~~---~~l~~kl~~~~~~~ 242 (368)
|+-+++||++--|.|..| |++++.|..++++.
T Consensus 129 DlGLLLRhLRHHSNLLAnIgdP~VreqVLsAMqEe 163 (238)
T PF02084_consen 129 DLGLLLRHLRHHSNLLANIGDPEVREQVLSAMQEE 163 (238)
T ss_pred hHHHHHHHHHHHHHHHhhcCCHHHHHHHHHHHhhh
Confidence 567778888777777776 99999999999865
No 51
>PF03682 UPF0158: Uncharacterised protein family (UPF0158); InterPro: IPR005361 This is a small family of hypothetical bacterial proteins of unknown function.
Probab=29.10 E-value=53 Score=29.82 Aligned_cols=57 Identities=21% Similarity=0.226 Sum_probs=40.6
Q ss_pred cCCChHHHHHHHHHHcCChhhhhccCCCCCCccHHHHHHHHH-----HhcCCCCCC--HHHHHHHHHHHHHHcc
Q psy14488 257 NFISKKDNLKLAILRSMSPKKLSNVNFCFENKKLEELIFLYR-----ARNFIETLS--YKELKRWKKYRISRFY 323 (368)
Q Consensus 257 GF~s~~Dk~~m~~i~~~~p~~l~~~~~~F~D~Rl~eLlfRyr-----aRN~P~~L~--~~E~~~W~~~~~~rl~ 323 (368)
...+....++|+.|-.+ ...|+.+++.|.+-+ .|+|-+.|. ++++++|.+|+..++.
T Consensus 64 ~~~~~~~~~iMe~Fv~~----------~v~d~~l~~~L~~ai~grgafrrFKd~L~~~~~~~e~Wy~F~~~~~r 127 (163)
T PF03682_consen 64 PLDSIEEYRIMEDFVEE----------KVEDPDLRERLLRAIQGRGAFRRFKDILSEYPELRERWYAFREERLR 127 (163)
T ss_pred CCchHHHHHHHHHHHHH----------hCCCHHHHHHHHHHHhCCcHHHHHHHHHHHCHHHHHHHHHHHHHHHH
Confidence 34556677899887632 146777777776655 357888885 4789999999998874
No 52
>PF11588 DUF3243: Protein of unknown function (DUF3243); InterPro: IPR021637 This family of proteins with unknown function includes uncharacterised proteins ymfJ and yflH. The family appears to be restricted to Firmicutes.; PDB: 3D0W_B.
Probab=28.79 E-value=52 Score=26.86 Aligned_cols=51 Identities=18% Similarity=0.304 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHcccCCC---ccccHHHHHHHHHHHHhhcccc---HHHHHHHHHHHH
Q psy14488 311 LKRWKKYRISRFYNKKN---NLYNINMFYLEIESLLKKANEH---DTKILNALLMYG 361 (368)
Q Consensus 311 ~~~W~~~~~~rl~~~~~---~~~~~~~~~~~l~~L~~~~~~~---~~~iL~~L~~y~ 361 (368)
=..|+.|+-+|+..... +.-++.+...+|-..++++..+ +.++|++|-+=+
T Consensus 7 f~~wK~~Lg~~v~~ae~~Gms~e~i~~~A~~iGdyLA~~vdP~N~EerlLkELW~va 63 (81)
T PF11588_consen 7 FDQWKDFLGDRVEQAEKLGMSEETIANLAYQIGDYLAKNVDPKNPEERLLKELWDVA 63 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTT----HHHHHHHHHHT-----SHHHHHHHHHHHC-
T ss_pred HHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhC
Confidence 36899999999954333 2236777777887777766555 888999997655
No 53
>PF05367 Phage_endo_I: Phage endonuclease I; InterPro: IPR008029 Endonuclease I (3.1.21.2 from EC) is a junction-resolving enzyme encoded by bacteriophage T7, that selectively binds and cleaves four-way Holliday DNA junctions []. The structure of the enzyme shows that it forms a symmetric homodimer arranged in two well-separated domains. Each domain, however, is composed of elements from both subunits, and amino acid side chains from both protomers contribute to the active site []. ; GO: 0008833 deoxyribonuclease IV (phage-T4-induced) activity, 0015074 DNA integration, 0016032 viral reproduction; PDB: 3CAE_A 1M0D_A 1M0I_C 1FZR_B 2PFJ_B.
Probab=26.14 E-value=28 Score=31.31 Aligned_cols=32 Identities=16% Similarity=0.401 Sum_probs=24.7
Q ss_pred cCCChHHHHHHHHHHcCChhhhhccCCCCCCccH
Q psy14488 257 NFISKKDNLKLAILRSMSPKKLSNVNFCFENKKL 290 (368)
Q Consensus 257 GF~s~~Dk~~m~~i~~~~p~~l~~~~~~F~D~Rl 290 (368)
|+|..+||+.|-.|++.-|+ ..+.+.|++++-
T Consensus 68 G~f~~~DR~K~l~Ik~q~P~--LDIR~VFq~~~~ 99 (149)
T PF05367_consen 68 GRFDAEDRRKHLLIKEQYPE--LDIRFVFQSSRT 99 (149)
T ss_dssp SS--HHHHHHHHHHHHH-TT--SEEEEEES-TTS
T ss_pred eccCcchhHHHHHHHHhCCC--ccEEEEEecCCC
Confidence 89999999999999999888 588888888764
No 54
>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=25.42 E-value=83 Score=25.46 Aligned_cols=45 Identities=22% Similarity=0.316 Sum_probs=25.7
Q ss_pred CcccHHHHHHHHHHhhcCCCcccCCCCCCCcceecccchhhhCcccccchhhhhhHHHHHHHH
Q psy14488 18 CSRWDLINVIKAFYVLSPYGITWPYKNNGKPSFKLEHLSFVNNLSHKKAHDALSDVRATLGLA 80 (368)
Q Consensus 18 nSRwDli~vvra~yalrPegi~WP~~~dG~pSFKLe~Lt~ANgi~h~~AHDAlsDV~ATI~lA 80 (368)
|++||+ .+++..+.. .|+.+|... .+.+-.-.+ |+.||+-|..+.
T Consensus 51 n~~fD~-~fL~~~~~~--~~~~~p~~~--~~~lDT~~l-------------~~~~~~~~~~~~ 95 (96)
T cd06125 51 NGSFDL-PFLNNRCAE--LGLKYPLLA--GSWIDTIKL-------------AADDVENTLQIT 95 (96)
T ss_pred CcHHhH-HHHHHHHHH--cCCCCCCcC--CcEEEehHH-------------hhhhHHHHHHhh
Confidence 348997 555554433 377777432 233322222 999999987653
No 55
>cd07347 harmonin_N_like N-terminal protein-binding module of harmonin and similar domains. This domain is found in harmonin, and similar proteins such as delphilin, and whirlin. These are postsynaptic density-95/discs-large/ZO-1 (PDZ) domain-containing scaffold proteins. Harmonin and whirlin are organizers of the Usher protein network of the inner ear and the retina, delphilin is found at the cerebellar parallel fiber-Purkinje cell synapses. This harmonin_N_like domain is found in either one or two copies. Harmonin contains a single copy, which is found at its N-terminus and binds specifically to a short internal peptide fragment of the cadherin 23 cytoplasmic domain; cadherin 23 is a component of the Usher protein network. Whirlin contains two copies of the harmonin_N_like domain; the first of these has been assayed for interaction with the cytoplasmic domain of cadherin 23 and no interaction could be detected.
Probab=25.39 E-value=1.6e+02 Score=23.70 Aligned_cols=49 Identities=12% Similarity=0.048 Sum_probs=37.4
Q ss_pred CCCCHHHHHHHHHHHHHHcccCCCccccHHHHHHHHHHHHhhccccHHHHHHHHHH
Q psy14488 304 ETLSYKELKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKANEHDTKILNALLM 359 (368)
Q Consensus 304 ~~L~~~E~~~W~~~~~~rl~~~~~~~~~~~~~~~~l~~L~~~~~~~~~~iL~~L~~ 359 (368)
..||+.|++.--.++.+--. ..+++.+...|-.++..+. |..||..+..
T Consensus 14 ~LL~~~Er~~~~~~L~~Y~~-----~~~Vd~LV~~L~~vLdtPa--K~~Ll~~iR~ 62 (78)
T cd07347 14 HLLTDAEREQVTRALERYHQ-----ERNVDDLVRDLYLVLDTPA--KLPLLQFLRQ 62 (78)
T ss_pred HHCCHHHHHHHHHHHHHHHh-----cCCHHHHHHHHHHHcCcHh--HHHHHHHHHH
Confidence 36899999888777775543 2489999999999887655 8888887754
No 56
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=22.61 E-value=2.4e+02 Score=22.69 Aligned_cols=52 Identities=6% Similarity=0.056 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHcccCCCccccHHHHHHHHHHHHhhc-ccc-HHHHHHHHHHHHH
Q psy14488 311 LKRWKKYRISRFYNKKNNLYNINMFYLEIESLLKKA-NEH-DTKILNALLMYGK 362 (368)
Q Consensus 311 ~~~W~~~~~~rl~~~~~~~~~~~~~~~~l~~L~~~~-~~~-~~~iL~~L~~y~~ 362 (368)
++..+++|++.+...+....|+++-.++|.--+..- +.. |..++..+..|.+
T Consensus 33 ~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~Ar~~VP~~vk~ell~~Ir~~L~ 86 (86)
T PF10163_consen 33 RDEVRQLCREIIRERGIDNLTFEDLLEEITPKARAMVPDEVKKELLQRIRAFLD 86 (86)
T ss_dssp HHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHHHHHCS-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHhC
Confidence 455677788777653335578888888877765553 233 8888888887763
No 57
>cd07354 HN_L-delphilin-R1_like First harmonin_N_like domain (repeat 1) of L-delphilin, and related domains. This subgroup contains the first of two harmonin_N_like domains of an alternatively spliced longer variant of mouse delphilin (L-delphilin, isoform 1), and related domains. Delphilin is a scaffold protein which binds the glutamate receptor delta-2 (GRID2) subunit and the monocarboxylate transporter 2 at the cerebellar parallel fiber-Purkinje cell synapses. The N-terminus of L-delphilin contains this harmonin_N_like domain preceded by a postsynaptic density-95/discs-large/ZO-1 (PDZ) protein-binding domain, PDZ1. L-delphilin, in common with the shorter C-terminal isoforms (S-delphilin/delphilin alpha and delphilin beta) has a second harmonin_N_like domain (not belonging to this subgroup) and a second PDZ domain, PDZ2. This first harmonin_N_like domain is a putative protein-binding module based on its sequence similarity to the harmonin N-domain.
Probab=22.09 E-value=1.3e+02 Score=24.50 Aligned_cols=32 Identities=16% Similarity=0.324 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHhhccccHHHHHHHHHHHHHH
Q psy14488 332 INMFYLEIESLLKKANEHDTKILNALLMYGKS 363 (368)
Q Consensus 332 ~~~~~~~l~~L~~~~~~~~~~iL~~L~~y~~~ 363 (368)
-.+|..+.+.++...+..|.++.++|.+|+..
T Consensus 5 A~eF~~Kvd~iL~~dp~~Ke~l~~aLk~Ya~~ 36 (80)
T cd07354 5 AQEFSRKVDAILGDDPVKKEQVFAALKQYAAD 36 (80)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHH
Confidence 36899999998854332389999999999965
No 58
>PF08800 VirE_N: VirE N-terminal domain; InterPro: IPR014907 This domain is associated with the N terminus of Virulence E proteins. The function of the domain is unknown.
Probab=21.58 E-value=76 Score=27.69 Aligned_cols=45 Identities=20% Similarity=0.304 Sum_probs=33.1
Q ss_pred CceEEEecccCCCCCCceEEEeecccCCCCCeEEEEeCCCC-chHhhcCCHHHHHHHhc
Q psy14488 113 RPFFYITHMFSSKHSYISLMWPICIHPMNKNILITWNLLHD-PKKFLLNDINKIRDYLC 170 (368)
Q Consensus 113 ~P~lhvs~~f~a~~~~~~~v~pl~~hp~n~N~vi~~DL~~D-p~~L~~l~~~~i~~~l~ 170 (368)
=|.+.+||.|...++...+. ..|+++|+|+.+- ++ .+++++++++
T Consensus 9 LP~vt~~g~F~~~r~~~~l~--------~~sglv~lDiD~l~~e-----e~~~~r~~l~ 54 (136)
T PF08800_consen 9 LPYVTPSGTFSGGRNADNLK--------AYSGLVVLDIDHLDPE-----EAEELRQLLF 54 (136)
T ss_pred CCEEEEEEEECCCcchhhhh--------hCCCcEEEEeCCCCHH-----HHHHHHHHHh
Confidence 38999999999866655544 4477999998754 33 3468888886
No 59
>KOG0772|consensus
Probab=20.97 E-value=60 Score=35.06 Aligned_cols=34 Identities=29% Similarity=0.459 Sum_probs=27.5
Q ss_pred EEEecccCCCCCCceEEEeecccCCCCCeEEEEeC
Q psy14488 116 FYITHMFSSKHSYISLMWPICIHPMNKNILITWNL 150 (368)
Q Consensus 116 lhvs~~f~a~~~~~~~v~pl~~hp~n~N~vi~~DL 150 (368)
-||..|+.. .|+++-+.+-+|||.|+++++.+-.
T Consensus 256 QYI~Dm~nT-KGHia~lt~g~whP~~k~~FlT~s~ 289 (641)
T KOG0772|consen 256 QYIRDMYNT-KGHIAELTCGCWHPDNKEEFLTCSY 289 (641)
T ss_pred hhhhhhhcc-CCceeeeeccccccCcccceEEecC
Confidence 366767764 4899999999999999999998543
Done!