Query psy12566
Match_columns 220
No_of_seqs 205 out of 1063
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 22:38:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12566.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12566hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd06146 mut-7_like_exo DEDDy 3 99.9 3.2E-25 6.9E-30 183.4 14.6 126 83-211 1-126 (193)
2 KOG2207|consensus 99.9 4E-26 8.6E-31 210.3 8.8 190 14-209 319-516 (617)
3 cd06129 RNaseD_like DEDDy 3'-5 99.8 1.6E-20 3.5E-25 150.8 11.0 102 92-211 2-105 (161)
4 cd06141 WRN_exo DEDDy 3'-5' ex 99.8 2.3E-20 5.1E-25 150.5 12.0 110 86-211 1-111 (170)
5 PRK10829 ribonuclease D; Provi 99.8 1.4E-18 2.9E-23 156.7 12.2 110 82-210 2-111 (373)
6 cd06148 Egl_like_exo DEDDy 3'- 99.7 1.6E-17 3.4E-22 137.8 10.9 100 95-211 3-103 (197)
7 PF01612 DNA_pol_A_exo1: 3'-5' 99.7 4.2E-17 9.1E-22 130.7 12.1 115 83-211 1-115 (176)
8 TIGR01388 rnd ribonuclease D. 99.7 2E-17 4.3E-22 149.2 11.4 108 85-211 1-108 (367)
9 COG0349 Rnd Ribonuclease D [Tr 99.5 1.2E-13 2.7E-18 122.7 9.5 106 86-210 1-107 (361)
10 smart00474 35EXOc 3'-5' exonuc 99.2 3E-10 6.5E-15 90.1 12.0 110 83-211 1-112 (172)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.1 7E-10 1.5E-14 89.2 11.3 101 92-211 2-102 (178)
12 KOG2206|consensus 99.1 5.1E-11 1.1E-15 110.6 4.6 117 77-211 187-303 (687)
13 cd06147 Rrp6p_like_exo DEDDy 3 99.0 1.3E-08 2.8E-13 83.7 12.4 114 80-211 2-115 (192)
14 cd09018 DEDDy_polA_RNaseD_like 98.8 3.3E-08 7.2E-13 77.0 9.1 90 107-211 1-91 (150)
15 cd00007 35EXOc 3'-5' exonuclea 98.8 7.3E-08 1.6E-12 74.8 10.1 93 106-212 1-93 (155)
16 PRK05755 DNA polymerase I; Pro 98.6 4.9E-07 1.1E-11 90.2 12.9 114 81-211 294-408 (880)
17 KOG4373|consensus 98.0 6E-06 1.3E-10 72.5 4.6 96 103-211 125-223 (319)
18 cd06139 DNA_polA_I_Ecoli_like_ 97.5 0.0017 3.8E-08 52.4 10.9 100 102-211 2-105 (193)
19 cd06140 DNA_polA_I_Bacillus_li 97.5 0.00096 2.1E-08 53.6 9.0 91 106-211 4-94 (178)
20 cd06125 DnaQ_like_exo DnaQ-lik 96.9 0.0053 1.1E-07 44.9 7.3 79 108-205 1-83 (96)
21 PRK14975 bifunctional 3'-5' ex 96.9 0.0016 3.5E-08 62.1 5.5 54 83-144 3-56 (553)
22 KOG2405|consensus 96.4 0.00012 2.6E-09 65.7 -5.5 96 91-204 48-143 (458)
23 KOG2405|consensus 91.8 0.019 4.1E-07 52.0 -2.6 98 104-218 194-292 (458)
24 KOG2248|consensus 90.0 0.84 1.8E-05 41.7 6.3 80 102-188 213-315 (380)
25 TIGR00593 pola DNA polymerase 89.5 4.9 0.00011 40.8 11.7 109 84-211 305-416 (887)
26 PRK06310 DNA polymerase III su 88.9 4 8.6E-05 35.0 9.4 102 102-209 4-131 (250)
27 cd06128 DNA_polA_exo DEDDy 3'- 88.4 0.68 1.5E-05 35.9 3.9 68 129-211 23-91 (151)
28 KOG2249|consensus 88.1 2.9 6.3E-05 36.3 7.8 82 105-188 105-205 (280)
29 TIGR00573 dnaq exonuclease, DN 85.8 7.8 0.00017 32.3 9.2 100 102-211 4-131 (217)
30 PRK07942 DNA polymerase III su 85.0 10 0.00022 32.1 9.6 102 102-210 3-136 (232)
31 COG0749 PolA DNA polymerase I 83.9 2.4 5.2E-05 40.9 5.8 104 87-209 7-113 (593)
32 cd06137 DEDDh_RNase DEDDh 3'-5 83.2 9.6 0.00021 30.1 8.2 42 159-211 77-118 (161)
33 cd06143 PAN2_exo DEDDh 3'-5' e 79.9 2.2 4.7E-05 34.8 3.4 40 159-207 95-134 (174)
34 PRK06807 DNA polymerase III su 79.6 14 0.00031 32.8 8.8 100 104-211 7-131 (313)
35 PRK09146 DNA polymerase III su 78.6 18 0.00038 30.9 8.8 103 102-212 44-173 (239)
36 PRK09145 DNA polymerase III su 74.0 47 0.001 27.1 10.3 106 91-207 18-150 (202)
37 cd06130 DNA_pol_III_epsilon_li 73.4 38 0.00083 25.8 9.7 50 159-211 71-120 (156)
38 PRK07740 hypothetical protein; 73.3 57 0.0012 27.7 11.0 41 169-211 143-184 (244)
39 PRK07883 hypothetical protein; 68.4 32 0.00069 33.1 8.7 102 102-211 12-138 (557)
40 cd05780 DNA_polB_Kod1_like_exo 68.2 23 0.0005 28.9 6.8 81 105-186 3-92 (195)
41 cd05160 DEDDy_DNA_polB_exo DED 67.9 39 0.00085 27.2 8.2 33 154-187 66-100 (199)
42 smart00479 EXOIII exonuclease 64.8 61 0.0013 24.8 10.1 97 106-211 1-125 (169)
43 cd05785 DNA_polB_like2_exo Unc 62.4 37 0.00081 28.1 7.1 80 103-187 7-95 (207)
44 PRK06063 DNA polymerase III su 62.2 99 0.0021 27.4 10.1 99 104-210 14-136 (313)
45 PRK05711 DNA polymerase III su 59.9 1.1E+02 0.0024 26.1 9.9 99 104-210 3-132 (240)
46 cd06127 DEDDh DEDDh 3'-5' exon 56.5 20 0.00043 26.9 4.2 50 159-211 73-122 (159)
47 PRK07748 sporulation inhibitor 56.1 1.1E+02 0.0024 25.0 9.9 54 154-210 82-136 (207)
48 cd06133 ERI-1_3'hExo_like DEDD 56.0 94 0.002 24.1 8.4 52 159-211 82-136 (176)
49 PRK08517 DNA polymerase III su 54.4 1.1E+02 0.0025 26.2 8.9 100 102-209 65-188 (257)
50 PRK06309 DNA polymerase III su 53.6 1.2E+02 0.0026 25.4 8.9 97 106-211 3-124 (232)
51 cd06144 REX4_like DEDDh 3'-5' 52.6 69 0.0015 24.8 6.8 24 159-184 71-94 (152)
52 PF04857 CAF1: CAF1 family rib 52.2 24 0.00052 30.3 4.4 118 89-209 9-200 (262)
53 cd05783 DNA_polB_B1_exo DEDDy 48.5 1.5E+02 0.0033 24.4 9.0 82 104-187 4-108 (204)
54 smart00667 LisH Lissencephaly 47.4 47 0.001 18.1 4.0 31 9-39 3-33 (34)
55 PF12244 DUF3606: Protein of u 47.1 10 0.00022 25.0 1.0 23 21-43 15-37 (57)
56 PF03909 BSD: BSD domain ; I 44.7 12 0.00027 24.8 1.1 35 2-38 17-51 (62)
57 PRK08074 bifunctional ATP-depe 43.5 3.2E+02 0.007 28.0 11.5 98 105-211 3-127 (928)
58 cd06149 ISG20 DEDDh 3'-5' exon 41.0 1.6E+02 0.0034 23.0 7.2 30 154-186 67-96 (157)
59 TIGR01407 dinG_rel DnaQ family 40.9 1.9E+02 0.0042 29.2 9.4 96 106-211 1-123 (850)
60 cd06145 REX1_like DEDDh 3'-5' 39.1 32 0.00069 26.8 2.9 40 159-209 69-108 (150)
61 PRK06195 DNA polymerase III su 37.6 2.8E+02 0.0061 24.3 9.6 96 106-211 2-123 (309)
62 PRK05601 DNA polymerase III su 36.8 3.4E+02 0.0074 25.0 10.0 102 102-211 43-195 (377)
63 TIGR01405 polC_Gram_pos DNA po 36.8 2E+02 0.0044 30.6 8.9 98 103-210 188-312 (1213)
64 cd05777 DNA_polB_delta_exo DED 36.4 1.4E+02 0.003 24.9 6.6 84 102-186 4-107 (230)
65 smart00751 BSD domain in trans 33.0 40 0.00086 21.4 2.1 35 2-38 12-46 (51)
66 COG1419 FlhF Flagellar GTP-bin 32.6 63 0.0014 29.9 4.1 37 79-118 259-295 (407)
67 COG4328 Predicted nuclease (RN 31.8 61 0.0013 27.8 3.5 35 106-146 2-36 (266)
68 PHA02528 43 DNA polymerase; Pr 31.7 2.3E+02 0.0051 29.0 8.2 82 103-186 104-214 (881)
69 PF08279 HTH_11: HTH domain; 29.9 62 0.0013 20.2 2.7 38 13-54 2-39 (55)
70 PF13289 SIR2_2: SIR2-like dom 28.2 54 0.0012 24.5 2.5 33 153-185 74-107 (143)
71 PF07721 TPR_4: Tetratricopept 27.3 1.1E+02 0.0023 16.2 3.2 24 11-34 2-25 (26)
72 cd06134 RNaseT DEDDh 3'-5' exo 25.6 1.5E+02 0.0033 23.9 4.9 44 168-211 103-148 (189)
73 COG1949 Orn Oligoribonuclease 25.4 26 0.00057 28.5 0.3 59 158-219 92-150 (184)
74 KOG0304|consensus 23.6 63 0.0014 27.5 2.2 118 89-209 11-194 (239)
75 PF01724 DUF29: Domain of unkn 23.3 51 0.0011 25.7 1.6 49 2-52 81-134 (139)
76 smart00550 Zalpha Z-DNA-bindin 23.2 2E+02 0.0042 19.2 4.3 42 9-54 4-46 (68)
77 PF02641 DUF190: Uncharacteriz 22.7 1.5E+02 0.0032 21.6 3.9 31 70-100 54-85 (101)
78 PRK07246 bifunctional ATP-depe 20.4 9.1E+02 0.02 24.5 11.5 97 103-211 5-128 (820)
No 1
>cd06146 mut-7_like_exo DEDDy 3'-5' exonuclease domain of Caenorhabditis elegans mut-7 and similar proteins. The mut-7 subfamily is composed of Caenorhabditis elegans mut-7 and similar proteins found in plants and metazoans. Mut-7 is implicated in posttranscriptional gene silencing. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing 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.
Probab=99.93 E-value=3.2e-25 Score=183.41 Aligned_cols=126 Identities=33% Similarity=0.590 Sum_probs=108.0
Q ss_pred EEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhc
Q psy12566 83 IILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIV 162 (220)
Q Consensus 83 I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~l 162 (220)
|++|+|++++++++..+ .+...++||||+||.|.+..+..+++|||||||.+.|||||+..++..+ .+.+.++|+++
T Consensus 1 ~~~i~~~~el~~~~~~~-~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~~~~~lid~~~~~~~~--~~~~~~~L~~l 77 (193)
T cd06146 1 IHIVDSEEELEALLLAL-SLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATEDEVFLLDLLALENLE--SEDWDRLLKRL 77 (193)
T ss_pred CeEecCHHHHHHHHHHH-hhccCCEEEEECccCCCccCCCCCCceEEEEecCCCEEEEEchhccccc--hHHHHHHHHHH
Confidence 68999999999999885 2688999999999999986556899999999999999999999875322 24456689999
Q ss_pred ccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 163 FANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 163 l~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
|+||+|+|||||+++|++.|++.|+...+....++|++||+.+++.+..
T Consensus 78 l~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a~~l~~ 126 (193)
T cd06146 78 FEDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLAKELQK 126 (193)
T ss_pred hCCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHHHHHhh
Confidence 9999999999999999999999999843322358999999999998875
No 2
>KOG2207|consensus
Probab=99.93 E-value=4e-26 Score=210.29 Aligned_cols=190 Identities=21% Similarity=0.314 Sum_probs=146.4
Q ss_pred HHHHHHHHhcCCHHHHHHHHHHcCCCCCCCchhhHHHHhhhhhhhh-----hcCCCCccCccccccccccCCCcEEEEeC
Q psy12566 14 KELIDLCVQYYDCKEAYYWCQKFKLNPNCVGFDLRDKIAEEESEQD-----VDNGWDVCKPAEEYYSLTLPPNSIILVDT 88 (220)
Q Consensus 14 ~~lv~~l~~~~d~~~A~~wa~~~~l~~~~lP~~v~~~~~~~~~~~~-----~~~~~~~~~~~~~y~~l~l~~~~I~~Vdt 88 (220)
+.++.||+++|...+|++|+.+.+|++.++|..+....++.+.-.+ ..... |..+++.|...|.++.+|++|++
T Consensus 319 ~~~lkyLw~~~~~iEai~~~~~~~i~~~d~~~el~~~~s~~~~~k~~~~~~~~~~~-pl~~~~~~~~~~~~~~~i~~V~~ 397 (617)
T KOG2207|consen 319 ENLLKYLWSFGEHIEAIYLATYDNIDPKDDAKELEKRTSRRGAGKTLFNQRMTTNV-PLVCEDLFLFEPPWVESIGMVGN 397 (617)
T ss_pred hhHHHHHHHHHHhhhhhhhhhhhcCCCchhHHHHhchhhhcccChhhhhccccccc-CccchhhhccCCCcccceeeeCC
Confidence 7999999999889999999999999844455554433333211111 11122 54466677777889999999999
Q ss_pred HHHHHHHHHHHhccCCC-CeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCC
Q psy12566 89 ADKFASALQDFARLDHN-SHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDD 167 (220)
Q Consensus 89 ~~~l~~~~~~l~~l~~~-~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~ 167 (220)
+.++..++ ++.++++ .+||+|+||+|+ .++..+++|++||++.++|||+|+.++...+ .+.|..+++.||++++
T Consensus 398 e~El~~l~--l~~l~~e~~yVGiDsEwkps-~~v~dsk~~IlQif~~~~v~Lidc~~l~~~~--se~w~~~~s~if~s~~ 472 (617)
T KOG2207|consen 398 EKELRDLL--LESLSEELRYVGIDSEWKPS-KKVSDSKLAILQIFFKDCVYLIDCVKLENLA--SEIWHLLLSQIFESKS 472 (617)
T ss_pred HHHHHHHH--HHHhhhcCEEEEEccccCcc-cCCChhHHHHHHHHhcCeEEEeehHHhhhch--HHHHHHHHHHHccCCc
Confidence 99999988 3336655 999999999998 4567999999999999999999999997676 5779999999999999
Q ss_pred eEEEEEcchhhHHHHHhhCCCCcc-c-cCCcCceeeHHHHHHHh
Q psy12566 168 LLKIGFNLMPDVSIIKTSLPFSEC-S-SYNKTSYLDLQLLWSKL 209 (220)
Q Consensus 168 IlKvG~~~~~Dl~~L~~~~~~~~~-~-~~~~~~~~DL~~l~~~l 209 (220)
|+||||++.+|+..|+++.|.++. + .+.+++++++..++.++
T Consensus 473 i~kvGf~~~eDL~~l~~s~pa~~~q~ki~~~~l~~~~~kl~e~~ 516 (617)
T KOG2207|consen 473 ILKVGFSMREDLEVLEASSPALRFQMKIEGLQLVSCVLKLAENV 516 (617)
T ss_pred eeeeecchhhhHHHHHhhhhhhhhcccccchHHHHHHHHHHHHH
Confidence 999999999999999988885322 1 23455555555554443
No 3
>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=99.84 E-value=1.6e-20 Score=150.82 Aligned_cols=102 Identities=19% Similarity=0.241 Sum_probs=89.6
Q ss_pred HHHHHHHHhccC-CCCeEEEeeeeccCCCCCCCCCceEEEeEeC-CeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeE
Q psy12566 92 FASALQDFARLD-HNSHLGLDTEWKPNLSGGSPPTLALLQIATR-DRVYILDIITLSKLPCYAQLCHDLELIVFANDDLL 169 (220)
Q Consensus 92 l~~~~~~l~~l~-~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~-~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~Il 169 (220)
++++++. +. ..++||||+||+|.+. ..+++|||||||+ ++|||||+..++..+ . .++.+|+|++|+
T Consensus 2 l~~~~~~---l~~~~~~ig~D~E~~~~~~--~~~~~~liQl~~~~~~~~l~d~~~~~~~~---~----~L~~lL~d~~i~ 69 (161)
T cd06129 2 LSSLCED---LSMDGDVIAFDMEWPPGRR--YYGEVALIQLCVSEEKCYLFDPLSLSVDW---Q----GLKMLLENPSIV 69 (161)
T ss_pred HHHHHHH---HhcCCCEEEEECCccCCCC--CCCceEEEEEEECCCCEEEEecccCccCH---H----HHHHHhCCCCEE
Confidence 5778888 88 9999999999999874 5689999999999 999999999875333 2 378999999999
Q ss_pred EEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 170 KIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 170 KvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
||||++++|+..|.+.+++ .+.|++|++.+++.+..
T Consensus 70 Kvg~~~k~D~~~L~~~~gi------~~~~~~D~~~aa~ll~~ 105 (161)
T cd06129 70 KALHGIEGDLWKLLRDFGE------KLQRLFDTTIAANLKGL 105 (161)
T ss_pred EEEeccHHHHHHHHHHcCC------CcccHhHHHHHHHHhCC
Confidence 9999999999999988888 78899999999887754
No 4
>cd06141 WRN_exo DEDDy 3'-5' exonuclease domain of WRN and similar proteins. WRN is a unique RecQ DNA helicase exhibiting an exonuclease activity. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing 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. Mutations in the WRN gene cause Werner syndrome, an autosomal recessive disorder associated with premature aging and increased susceptibility to cancer and type II diabetes. WRN interacts with key proteins involved in DNA replication, recombination, and repair. It is believed to maintain genomic stability and life span by participating in DNA processes. WRN is stimulated by Ku70/80, an important regulator of genomic stability.
Probab=99.84 E-value=2.3e-20 Score=150.45 Aligned_cols=110 Identities=25% Similarity=0.469 Sum_probs=98.7
Q ss_pred EeCHHHHHHHHHHHhccC-CCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhccc
Q psy12566 86 VDTADKFASALQDFARLD-HNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFA 164 (220)
Q Consensus 86 Vdt~~~l~~~~~~l~~l~-~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~ 164 (220)
++++++++++++. +. ...+||||+||.|.+..+..+++|||||||+++|||||+..+..+| . .++.+|+
T Consensus 1 ~~~~~~~~~~~~~---~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~~~~~l~~~~~~~~~~---~----~l~~ll~ 70 (170)
T cd06141 1 TDSAQDAEEAVKE---LLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATESRCLLFQLAHMDKLP---P----SLKQLLE 70 (170)
T ss_pred CCCHHHHHHHHHH---HhcCCCEEEEeCccCCccCCCCCCCceEEEEecCCcEEEEEhhhhhccc---H----HHHHHhc
Confidence 3678899999999 87 9999999999999875567899999999999999999999875555 2 4789999
Q ss_pred CCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 165 NDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 165 ~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+++|.||||++++|+..|.+.++. .+++++|++.++..+..
T Consensus 71 ~~~i~kv~~~~k~D~~~L~~~~g~------~~~~~~Dl~~aa~ll~~ 111 (170)
T cd06141 71 DPSILKVGVGIKGDARKLARDFGI------EVRGVVDLSHLAKRVGP 111 (170)
T ss_pred CCCeeEEEeeeHHHHHHHHhHcCC------CCCCeeeHHHHHHHhCC
Confidence 999999999999999999999998 78899999999988876
No 5
>PRK10829 ribonuclease D; Provisional
Probab=99.78 E-value=1.4e-18 Score=156.71 Aligned_cols=110 Identities=16% Similarity=0.184 Sum_probs=98.7
Q ss_pred cEEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHh
Q psy12566 82 SIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELI 161 (220)
Q Consensus 82 ~I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ 161 (220)
++.+|+|+++++++++. +...++||+||||...+ ++.+++|||||++++.+||||+.++..+ . .|+.
T Consensus 2 ~~~~I~t~~~L~~~~~~---l~~~~~lalDtEf~~~~--ty~~~l~LiQl~~~~~~~LiD~l~~~d~-------~-~L~~ 68 (373)
T PRK10829 2 NYQMITTDDALASVCEA---ARAFPAIALDTEFVRTR--TYYPQLGLIQLYDGEQLSLIDPLGITDW-------S-PFKA 68 (373)
T ss_pred CcEEeCCHHHHHHHHHH---HhcCCeEEEecccccCc--cCCCceeEEEEecCCceEEEecCCccch-------H-HHHH
Confidence 36799999999999999 99999999999999864 5889999999999999999999987432 2 3789
Q ss_pred cccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhh
Q psy12566 162 VFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 162 ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~ 210 (220)
+|+|++|+||||+.++|+..|.+.++. .+.++||++..++.+.
T Consensus 69 ll~~~~ivKV~H~~~~Dl~~l~~~~g~------~p~~~fDTqiaa~~lg 111 (373)
T PRK10829 69 LLRDPQVTKFLHAGSEDLEVFLNAFGE------LPQPLIDTQILAAFCG 111 (373)
T ss_pred HHcCCCeEEEEeChHhHHHHHHHHcCC------CcCCeeeHHHHHHHcC
Confidence 999999999999999999999999998 7899999999887654
No 6
>cd06148 Egl_like_exo DEDDy 3'-5' exonuclease domain of Drosophila Egalitarian (Egl) and similar proteins. The Egalitarian (Egl) protein subfamily is composed of Drosophila Egl and similar proteins. Egl is a component of an mRNA-binding complex which is required for oocyte specification. Egl contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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 conservation of this subfamily throughout eukaryotes suggests that its members may be part of ancient RNA processing complexes that are likely to participate in the regulated processing of specific mRNAs. Some members of this subfamily do not have a completely conserved YX(3)D pattern at the ExoIII motif.
Probab=99.74 E-value=1.6e-17 Score=137.76 Aligned_cols=100 Identities=23% Similarity=0.267 Sum_probs=85.6
Q ss_pred HHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeC-CeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEE
Q psy12566 95 ALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATR-DRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGF 173 (220)
Q Consensus 95 ~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~-~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~ 173 (220)
++++ ++++++||||+||...+ ..+++|||||||. +.|||||+..++. ..+...++.+|+|++|+||||
T Consensus 3 ~~~~---l~~~~~i~~D~E~~~~~---~~~~~~LiQia~~~~~v~l~D~~~~~~-----~~~~~~L~~iLe~~~i~Kv~h 71 (197)
T cd06148 3 AIIH---LKKQKVIGLDCEGVNLG---RKGKLCLVQIATRTGQIYLFDILKLGS-----IVFINGLKDILESKKILKVIH 71 (197)
T ss_pred hhhh---hhhCCEEEEEcccccCC---CCCCEEEEEEeeCCCcEEEEEhhhccc-----hhHHHHHHHHhcCCCccEEEE
Confidence 5566 89999999999998653 4789999999999 9999999998742 123345889999999999999
Q ss_pred cchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 174 NLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 174 ~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+++.|+..|++.+++ .+.|++|++.++..+..
T Consensus 72 ~~k~D~~~L~~~~gi------~~~~~fDt~iA~~lL~~ 103 (197)
T cd06148 72 DCRRDSDALYHQYGI------KLNNVFDTQVADALLQE 103 (197)
T ss_pred echhHHHHHHHhcCc------cccceeeHHHHHHHHHH
Confidence 999999999888988 78899999998877665
No 7
>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=99.73 E-value=4.2e-17 Score=130.66 Aligned_cols=115 Identities=25% Similarity=0.308 Sum_probs=97.2
Q ss_pred EEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhc
Q psy12566 83 IILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIV 162 (220)
Q Consensus 83 I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~l 162 (220)
+++|+|.++++++++. +...+++|||+||.+.......++++++|+++.+.+|++|....... .+...|+.+
T Consensus 1 y~~v~~~~~l~~~~~~---l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~~~~~i~~~~~~~~~-----~~~~~l~~l 72 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKK---LKNAKVLAFDTETTGLDPYSYNPKIALIQLATGEGCYIIDPIDLGDN-----WILDALKEL 72 (176)
T ss_dssp SEEEHSHHHHHHHHHH---HTTTSEEEEEEEEETSTSTTSSEEEEEEEEEESCEEEEECGTTSTTT-----THHHHHHHH
T ss_pred CEecCCHHHHHHHHHH---HcCCCeEEEEEEECCCCccccCCeEEEEEEecCCCceeeeecccccc-----chHHHHHHH
Confidence 4789999999999999 99999999999999976555789999999999999999999876421 123468999
Q ss_pred ccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 163 FANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 163 l~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
|+||+|+||||+++.|+..|.+.+++ .++|++|++..+..+..
T Consensus 73 l~~~~i~kv~~n~~~D~~~L~~~~~i------~~~~~~D~~l~~~~l~~ 115 (176)
T PF01612_consen 73 LEDPNIIKVGHNAKFDLKWLYRSFGI------DLKNVFDTMLAAYLLDP 115 (176)
T ss_dssp HTTTTSEEEESSHHHHHHHHHHHHTS--------SSEEEHHHHHHHTTT
T ss_pred HhCCCccEEEEEEechHHHHHHHhcc------ccCCccchhhhhhcccc
Confidence 99999999999999999999999888 89999999655555443
No 8
>TIGR01388 rnd ribonuclease D. This model describes ribonuclease D, a 3'-exonuclease shown to act on tRNA both in vitro and when overexpressed in vivo. Trusted members of this family are restricted to the Proteobacteria; Aquifex, Mycobacterial, and eukaryotic homologs are not full-length homologs. Ribonuclease D is not essential in E. coli and is deleterious when overexpressed. Its precise biological role is still unknown.
Probab=99.73 E-value=2e-17 Score=149.20 Aligned_cols=108 Identities=16% Similarity=0.194 Sum_probs=94.6
Q ss_pred EEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhccc
Q psy12566 85 LVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFA 164 (220)
Q Consensus 85 ~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~ 164 (220)
+|+|+++++++++. +...++|||||||.... ++.+++|||||||++.+||||+.++..++ .|..+|+
T Consensus 1 ~I~t~~~l~~~~~~---l~~~~~ia~DtE~~~~~--~y~~~l~LiQia~~~~~~liD~~~~~~~~--------~L~~lL~ 67 (367)
T TIGR01388 1 WITTDDELATVCEA---VRTFPFVALDTEFVRER--TFWPQLGLIQVADGEQLALIDPLVIIDWS--------PLKELLR 67 (367)
T ss_pred CcCCHHHHHHHHHH---HhcCCEEEEeccccCCC--CCCCcceEEEEeeCCeEEEEeCCCcccHH--------HHHHHHC
Confidence 58999999999999 89999999999998763 57899999999999999999998763221 3788999
Q ss_pred CCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 165 NDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 165 ~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
|++|+||||+++.|+..|.+.++. .+.+++|++..+..+..
T Consensus 68 d~~i~KV~h~~k~Dl~~L~~~~~~------~~~~~fDtqlAa~lL~~ 108 (367)
T TIGR01388 68 DESVVKVLHAASEDLEVFLNLFGE------LPQPLFDTQIAAAFCGF 108 (367)
T ss_pred CCCceEEEeecHHHHHHHHHHhCC------CCCCcccHHHHHHHhCC
Confidence 999999999999999999887776 67899999998776654
No 9
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.49 E-value=1.2e-13 Score=122.73 Aligned_cols=106 Identities=22% Similarity=0.243 Sum_probs=93.3
Q ss_pred EeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCC-CCCCchhhhhHHHHHhccc
Q psy12566 86 VDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITL-SKLPCYAQLCHDLELIVFA 164 (220)
Q Consensus 86 Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l-~~~~~~~~~~~~~l~~ll~ 164 (220)
|++.+.++.++.. +...+.|++|||+...+ ++.+++|||||+.++.+.|||+... ...+ .|..+|.
T Consensus 1 i~~~~~l~~~~~~---~~~~~~iAiDTEf~r~~--t~~p~LcLIQi~~~e~~~lIdpl~~~~d~~--------~l~~Ll~ 67 (361)
T COG0349 1 ITTGDLLAAACAL---LRGSKAIAIDTEFMRLR--TYYPRLCLIQISDGEGASLIDPLAGILDLP--------PLVALLA 67 (361)
T ss_pred CCchhHHHHHHHH---hcCCCceEEeccccccc--ccCCceEEEEEecCCCceEecccccccccc--------hHHHHhc
Confidence 4667888899999 89999999999999864 6899999999999999999999984 3333 2689999
Q ss_pred CCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhh
Q psy12566 165 NDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 165 ~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~ 210 (220)
|++|+||+|+.+.|+..|.+.|+. .+.++||++...+-..
T Consensus 68 d~~v~KIfHaa~~DL~~l~~~~g~------~p~plfdTqiAa~l~g 107 (361)
T COG0349 68 DPNVVKIFHAARFDLEVLLNLFGL------LPTPLFDTQIAAKLAG 107 (361)
T ss_pred CCceeeeeccccccHHHHHHhcCC------CCCchhHHHHHHHHhC
Confidence 999999999999999999999998 8999999999876543
No 10
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.19 E-value=3e-10 Score=90.05 Aligned_cols=110 Identities=20% Similarity=0.292 Sum_probs=85.8
Q ss_pred EEEEeCHHHHHHHHHHHhccC-CCCeEEEeeeeccCCCCCCCCCceEEEeEeCC-eEEEEEccCCCCCCchhhhhHHHHH
Q psy12566 83 IILVDTADKFASALQDFARLD-HNSHLGLDTEWKPNLSGGSPPTLALLQIATRD-RVYILDIITLSKLPCYAQLCHDLEL 160 (220)
Q Consensus 83 I~~Vdt~~~l~~~~~~l~~l~-~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~-~v~LiD~~~l~~~~~~~~~~~~~l~ 160 (220)
+.+|+|++++.+++.. +. ....+|+|+||.+... ..++++.+|+|+.+ .+|+++..... .. ...++
T Consensus 1 ~~~i~~~~~~~~~~~~---~~~~~~~l~~~~e~~~~~~--~~~~~~~l~l~~~~~~~~i~~~~~~~------~~-~~~l~ 68 (172)
T smart00474 1 VRVVTDSETLEELLEK---LRAAGGEVALDTETTGLNS--YSGKLVLIQISVTGEGAFIIDPLALG------DD-LEILK 68 (172)
T ss_pred CEEecCHHHHHHHHHH---HHhcCCeEEEeccccCCcc--CCCCEEEEEEeEcCCceEEEEeccch------hh-HHHHH
Confidence 4689999888887766 55 5679999999987642 36789999999644 78887654322 11 12468
Q ss_pred hcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 161 IVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 161 ~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
.+|+++++.|+||+.+.|+..|++ ++. .+.+++|++..+..+.+
T Consensus 69 ~~l~~~~~~kv~~d~k~~~~~L~~-~gi------~~~~~~D~~laayll~p 112 (172)
T smart00474 69 DLLEDETITKVGHNAKFDLHVLAR-FGI------ELENIFDTMLAAYLLLG 112 (172)
T ss_pred HHhcCCCceEEEechHHHHHHHHH-CCC------cccchhHHHHHHHHHcC
Confidence 899999999999999999999986 776 67788999999887765
No 11
>cd06142 RNaseD_exo DEDDy 3'-5' exonuclease domain of Ribonuclease D and similar proteins. Ribonuclease (RNase) D is a bacterial enzyme involved in the maturation of small stable RNAs and the 3' maturation of tRNA. It contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing 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. In vivo, RNase D only becomes essential upon removal of other ribonucleases. Eukaryotic RNase D homologs include yeast Rrp6p, human PM/Scl-100, and the Drosophila melanogaster egalitarian protein.
Probab=99.13 E-value=7e-10 Score=89.21 Aligned_cols=101 Identities=20% Similarity=0.247 Sum_probs=79.2
Q ss_pred HHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEE
Q psy12566 92 FASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKI 171 (220)
Q Consensus 92 l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKv 171 (220)
+++++.. +.+...+|+|+||.+.. ...++++.+|+|+.+.+|+||+..+ ..+ ..++.+|+|++|.|+
T Consensus 2 ~~~~~~~---l~~~~~l~~~~e~~~~~--~~~~~~~~i~l~~~~~~~~i~~~~~-~~~-------~~l~~ll~~~~i~kv 68 (178)
T cd06142 2 LEDLCER---LASAGVIAVDTEFMRLN--TYYPRLCLIQISTGGEVYLIDPLAI-GDL-------SPLKELLADPNIVKV 68 (178)
T ss_pred HHHHHHH---HhcCCeEEEECCccCCC--cCCCceEEEEEeeCCCEEEEeCCCc-ccH-------HHHHHHHcCCCceEE
Confidence 3455555 55667999999997653 2367899999999976999996533 221 236889999999999
Q ss_pred EEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 172 GFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 172 G~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
||+.+.|+..|.+.+++ ...+++|++..+..+.+
T Consensus 69 ~~d~K~~~~~L~~~~gi------~~~~~~D~~laayLl~p 102 (178)
T cd06142 69 FHAAREDLELLKRDFGI------LPQNLFDTQIAARLLGL 102 (178)
T ss_pred EeccHHHHHHHHHHcCC------CCCCcccHHHHHHHhCC
Confidence 99999999999888887 36678999988877776
No 12
>KOG2206|consensus
Probab=99.11 E-value=5.1e-11 Score=110.59 Aligned_cols=117 Identities=17% Similarity=0.163 Sum_probs=103.1
Q ss_pred ccCCCcEEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhH
Q psy12566 77 TLPPNSIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCH 156 (220)
Q Consensus 77 ~l~~~~I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~ 156 (220)
|+...+.+||++..++.++.+. +......++|+|.... +++.+-.|||||+|+..-||||...+. +...
T Consensus 187 ~le~T~~~~I~t~~el~~l~~~---l~~~~Efavdlehhsy--rsf~gltclmqISTr~ed~iIDt~~l~------~~i~ 255 (687)
T KOG2206|consen 187 PLEITPKVWICTLGELEALPEI---LDSVIEFAVDLEHHSY--RSFLGLTCLMQISTRTEDFIIDTFKLR------DHIG 255 (687)
T ss_pred cccccCceeeechHHHHHHHHH---Hhhhhhhhhhccccch--hhhcCceeEEEeeccchhheehhHHHH------HHHH
Confidence 3444568999999999999999 8889999999999875 468899999999999999999999884 2333
Q ss_pred HHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 157 DLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 157 ~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
++...|+||+|+||.||...|+..|++.|++ -+.|++|+-...|.|.-
T Consensus 256 -~l~e~fsdp~ivkvfhgaD~diiwlqrdfgi------yvvnLfdt~~a~r~L~~ 303 (687)
T KOG2206|consen 256 -ILNEVFSDPGIVKVFHGADTDIIWLQRDFGI------YVVNLFDTIQASRLLGL 303 (687)
T ss_pred -HhhhhccCCCeEEEEecCccchhhhhccceE------EEEechhhHHHHHHhCC
Confidence 7899999999999999999999999999999 89999999998877654
No 13
>cd06147 Rrp6p_like_exo DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins. Yeast Rrp6p and its human homolog, the polymyositis/scleroderma autoantigen 100kDa (PM/Scl-100), are exosome-associated proteins involved in the degradation and processing of precursors to stable RNAs. Both proteins contain a DEDDy-type DnaQ-like 3'-5' exonuclease domain possessing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. The 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. PM/Scl-100, an autoantigen present in the nucleolar compartment of the cell, reacts with autoantibodies produced by about 50% of patients with polymyositis-scleroderma overlap syndrome.
Probab=98.96 E-value=1.3e-08 Score=83.73 Aligned_cols=114 Identities=20% Similarity=0.273 Sum_probs=87.3
Q ss_pred CCcEEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHH
Q psy12566 80 PNSIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLE 159 (220)
Q Consensus 80 ~~~I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l 159 (220)
.+++.+|++++++..+++. +.....+++|+|..+.. ....+++.+|+++.+.+|+||+..... ....+
T Consensus 2 ~~~~~~i~~~~~l~~~~~~---l~~~~~l~~~~e~~~~~--~~~~~~~~l~l~~~~~~~~i~~l~~~~-------~~~~L 69 (192)
T cd06147 2 ETPLTFVDTEEKLEELVEK---LKNCKEIAVDLEHHSYR--SYLGFTCLMQISTREEDYIVDTLKLRD-------DMHIL 69 (192)
T ss_pred CCCcEEECCHHHHHHHHHH---HhcCCeEEEEeEecCCc--cCCCceEEEEEecCCCcEEEEeccccc-------chHHH
Confidence 5789999877888886666 55566999999886532 235789999999987788888522211 11236
Q ss_pred HhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 160 LIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 160 ~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+.+|++++|.|+||+.+.|+..|.+.+++ .+.+++|++..+..+.+
T Consensus 70 ~~~L~~~~i~kv~~d~K~~~~~L~~~~gi------~~~~~fD~~laaYLL~p 115 (192)
T cd06147 70 NEVFTDPNILKVFHGADSDIIWLQRDFGL------YVVNLFDTGQAARVLNL 115 (192)
T ss_pred HHHhcCCCceEEEechHHHHHHHHHHhCC------CcCchHHHHHHHHHhCC
Confidence 78999999999999999999999757776 55666999998887766
No 14
>cd09018 DEDDy_polA_RNaseD_like_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases, RNase D, WRN, and similar proteins. DEDDy 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. They contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDy exonucleases are classified as such because of the presence of a specific YX(3)D pattern at ExoIII. The four conserved acidic residues serve as ligands for the two metal ions required for catalysis. This family of DEDDy exonucleases includes the proofreading domains of family A DNA polymerases, as well as RNases such as RNase D and yeast Rrp6p. The Egalitarian (Egl) and Bacillus-like DNA Polymerase I subfamilies do not possess a completely conserved YX(3)D pattern at the ExoIII motif. In addition, the Bacillus-like DNA polymerase I subfamily has inactive 3'-5' exonucle
Probab=98.80 E-value=3.3e-08 Score=77.03 Aligned_cols=90 Identities=21% Similarity=0.161 Sum_probs=68.9
Q ss_pred eEEEeeeeccCCCCCCCCCceEEEeEeCC-eEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEEcchhhHHHHHhh
Q psy12566 107 HLGLDTEWKPNLSGGSPPTLALLQIATRD-RVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTS 185 (220)
Q Consensus 107 ~VG~D~Ew~p~~~~~~~~~vaLlQiat~~-~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~ 185 (220)
++|+|+||.+.. ....+++.+|+|+++ ++|++|+... .. ....++.+|+|+++.|+||+.+.|+..|.+.
T Consensus 1 ~~~~~~e~~~~~--~~~~~~~~l~l~~~~~~~~~i~~~~~-~~------~~~~l~~~l~~~~~~kv~~d~K~~~~~L~~~ 71 (150)
T cd09018 1 VFAFDTETDSLD--NISANLVLIQLAIEPGVAALIPVAHD-YL------ALELLKPLLEDEKALKVGQNLKYDRGILLNY 71 (150)
T ss_pred CEEEEeecCCCC--CCCceEEEEEEEcCCCcEEEEEcCCc-cc------CHHHHHHHhcCCCCceeeecHHHHHHHHHHc
Confidence 589999998754 236789999999974 4889985431 11 1223789999999999999999999999765
Q ss_pred CCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 186 LPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 186 ~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
... ...+++|++.++..+.+
T Consensus 72 ~~~------~~~~~~D~~laayLl~p 91 (150)
T cd09018 72 FIE------LRGIAFDTMLEAYILNS 91 (150)
T ss_pred CCc------cCCcchhHHHHHHHhCC
Confidence 443 45678999999887776
No 15
>cd00007 35EXOc 3'-5' exonuclease. The 35EXOc domain is responsible for the 3'-5' exonuclease proofreading activity of prokaryotic DNA polymerase I (pol I) 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 pol I. 35EXOc is also found in the Werner syndrome helicase (WRN), focus forming activity 1 protein (FFA-1) and ribonuclease D (RNase D).
Probab=98.77 E-value=7.3e-08 Score=74.84 Aligned_cols=93 Identities=17% Similarity=0.048 Sum_probs=68.6
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEEcchhhHHHHHhh
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTS 185 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~ 185 (220)
..+|+|+||.+.. ...++++.+|+|+.+.++.+....- . ....+.++.+|+|+++.||||+.+.|+..|.+.
T Consensus 1 ~~l~~d~e~~~~~--~~~~~i~~~~l~~~~~~~~i~~~~~--~----~~~~~~l~~~l~~~~~~~v~~~~k~d~~~L~~~ 72 (155)
T cd00007 1 KEVAFDTETTGLN--YHRGKLVGIQIATAGEAAYIPDELE--L----EEDLEALKELLEDEDITKVGHDAKFDLVVLARD 72 (155)
T ss_pred CceEEEEecCCCC--cCCCeEEEEEEEECCcEEEEEcCCC--H----HHHHHHHHHHHcCCCCcEEeccHHHHHHHHHHC
Confidence 3689999998753 2468899999999653444432211 0 122224788999999999999999999999876
Q ss_pred CCCCccccCCcCceeeHHHHHHHhhhc
Q psy12566 186 LPFSECSSYNKTSYLDLQLLWSKLVAE 212 (220)
Q Consensus 186 ~~~~~~~~~~~~~~~DL~~l~~~l~~~ 212 (220)
+.. .+.+++|++.++..+.+.
T Consensus 73 ~~~------~~~~~~D~~~~ayll~~~ 93 (155)
T cd00007 73 GIE------LPGNIFDTMLAAYLLNPG 93 (155)
T ss_pred CCC------CCCCcccHHHHHHHhCCC
Confidence 544 567899999999888773
No 16
>PRK05755 DNA polymerase I; Provisional
Probab=98.61 E-value=4.9e-07 Score=90.19 Aligned_cols=114 Identities=15% Similarity=0.105 Sum_probs=91.5
Q ss_pred CcEEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCe-EEEEEccCCCCCCchhhhhHHHH
Q psy12566 81 NSIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDR-VYILDIITLSKLPCYAQLCHDLE 159 (220)
Q Consensus 81 ~~I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~-v~LiD~~~l~~~~~~~~~~~~~l 159 (220)
.++.+|++++++.++++. +....++++|+|..+. ....++++.+|+++.+. +|++++..+ + ...+ ..+
T Consensus 294 ~~~~~I~~~~~L~~~l~~---l~~~~~~a~DtEt~~l--~~~~~~i~~i~ls~~~g~~~~ip~~~i---~--~~~l-~~l 362 (880)
T PRK05755 294 EDYETILDEEELEAWLAK---LKAAGLFAFDTETTSL--DPMQAELVGLSFAVEPGEAAYIPLDQL---D--REVL-AAL 362 (880)
T ss_pred CceEEeCCHHHHHHHHHH---hhccCeEEEEeccCCC--CcccccEEEEEEEeCCCcEEEEecccc---c--HHHH-HHH
Confidence 357789999999999988 8889999999999874 24688999999999876 899987443 2 1222 247
Q ss_pred HhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 160 LIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 160 ~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
..+|+|+.+.||||+.+.|+..|.+ ++. ....+++|++.++..+.+
T Consensus 363 ~~~L~d~~v~kV~HNakfDl~~L~~-~gi-----~~~~~~~DT~iAa~Ll~~ 408 (880)
T PRK05755 363 KPLLEDPAIKKVGQNLKYDLHVLAR-YGI-----ELRGIAFDTMLASYLLDP 408 (880)
T ss_pred HHHHhCCCCcEEEeccHhHHHHHHh-CCC-----CcCCCcccHHHHHHHcCC
Confidence 8899999999999999999999985 454 234679999998887766
No 17
>KOG4373|consensus
Probab=98.02 E-value=6e-06 Score=72.52 Aligned_cols=96 Identities=20% Similarity=0.261 Sum_probs=80.0
Q ss_pred CCCCeEEEeeeeccCCCCC-CCCCceEEEeEeC-CeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEEcchhhHH
Q psy12566 103 DHNSHLGLDTEWKPNLSGG-SPPTLALLQIATR-DRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVS 180 (220)
Q Consensus 103 ~~~~~VG~D~Ew~p~~~~~-~~~~vaLlQiat~-~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~ 180 (220)
.....++.+.||.|.+..+ ..|+++.+|||+. ++|+|+.+..-+.+| .. |+.+|+|+++++||.+..+|..
T Consensus 125 s~~~~~~~~~e~~~~~d~~~~~P~~~~lqlcV~en~C~I~ql~~~~~IP---~~----LR~fl~D~~~~~vgv~~d~D~~ 197 (319)
T KOG4373|consen 125 SDPPFVCYRREAQPYLDMGRSDPPPDTLQLCVGENRCLIIQLIHCKRIP---HE----LRSFLEDPDHTFVGVWNDQDAG 197 (319)
T ss_pred cCCcceeecccccccccccccCCCcchhhhhhcccceeeEEeeccccch---HH----HHHhhcCCCceEEeccccccHH
Confidence 5678899999999987543 4677999999998 899999988877777 33 5677999999999999999999
Q ss_pred HHHh-hCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 181 IIKT-SLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 181 ~L~~-~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+|.+ .++. .+.-+.||..+.....+
T Consensus 198 KL~r~~hql------~I~~~~dlr~~~~d~~g 223 (319)
T KOG4373|consen 198 KLERKEHQL------EIGELEDLRLLVNDSLG 223 (319)
T ss_pred HHhhhhhcc------cHHhhhhHHhhcchhhc
Confidence 9998 6776 78889999887665544
No 18
>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=97.48 E-value=0.0017 Score=52.41 Aligned_cols=100 Identities=17% Similarity=0.167 Sum_probs=68.4
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCe-EEEEEccCC--C-CCCchhhhhHHHHHhcccCCCeEEEEEcchh
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDR-VYILDIITL--S-KLPCYAQLCHDLELIVFANDDLLKIGFNLMP 177 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~-v~LiD~~~l--~-~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~ 177 (220)
+.+...+++|+|.... .....++.-++++..+. +|.+++..- + ... .+..+ ..+..+|++.++.||||+.+.
T Consensus 2 ~~~~~~~a~d~e~~~~--~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~-~~l~~~l~~~~~~~v~hn~k~ 77 (193)
T cd06139 2 LEKAKVFAFDTETTSL--DPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLP-REEVL-AALKPLLEDPSIKKVGQNLKF 77 (193)
T ss_pred CccCCeEEEEeecCCC--CcCCCeEEEEEEEcCCCCEEEEecCCCccccCCC-HHHHH-HHHHHHHhCCCCcEEeeccHH
Confidence 3567889999987542 12356788899998754 777765431 0 111 11222 236788999999999999999
Q ss_pred hHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 178 DVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 178 Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
|+..|++ ++. .....++|+..+++.+.+
T Consensus 78 d~~~l~~-~gi-----~~~~~~~Dt~l~a~ll~p 105 (193)
T cd06139 78 DLHVLAN-HGI-----ELRGPAFDTMLASYLLNP 105 (193)
T ss_pred HHHHHHH-CCC-----CCCCCcccHHHHHHHhCC
Confidence 9999975 344 134567999999887766
No 19
>cd06140 DNA_polA_I_Bacillus_like_exo inactive DEDDy 3'-5' exonuclease domain of Bacillus stearothermophilus DNA polymerase I and similar family-A DNA polymerases. Bacillus stearothermophilus-like Polymerase I (Pol I), a subgroup of the family-A DNA polymerases, contains an inactive DnaQ-like 3'-5' exonuclease domain in the same polypeptide chain as the polymerase region. The exonuclease-like domain of these proteins possess the same fold as the Klenow fragment (KF) of Escherichia coli Pol I, but does not contain the four critical metal-binding residues necessary for activity. The function of this domain is unknown. It might act as a spacer between the polymerase and the 5'-3' exonuclease domains. Some members of this subgroup, such as those from Bacillus sphaericus and Thermus aquaticus, are thermostable DNA polymerases.
Probab=97.45 E-value=0.00096 Score=53.58 Aligned_cols=91 Identities=14% Similarity=0.055 Sum_probs=65.9
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEEcchhhHHHHHhh
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTS 185 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~ 185 (220)
..+++|+|.... .....++..+++++.+++|.+++... . .....++.+|+|+++.|+||+.+.|+..|.+
T Consensus 4 ~~~~~~~~~~~~--~~~~~~l~~i~l~~~~~~~~i~~~~~--~-----~~~~~l~~~l~~~~~~ki~~d~K~~~~~l~~- 73 (178)
T cd06140 4 DEVALYVELLGE--NYHTADIIGLALANGGGAYYIPLELA--L-----LDLAALKEWLEDEKIPKVGHDAKRAYVALKR- 73 (178)
T ss_pred CceEEEEEEcCC--CcceeeEEEEEEEeCCcEEEEeccch--H-----HHHHHHHHHHhCCCCceeccchhHHHHHHHH-
Confidence 456777777643 12457889999999888888884320 0 0123478899999999999999999999964
Q ss_pred CCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 186 LPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 186 ~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
++. .....++|++..+.-+.+
T Consensus 74 ~gi-----~~~~~~fDt~laaYLL~p 94 (178)
T cd06140 74 HGI-----ELAGVAFDTMLAAYLLDP 94 (178)
T ss_pred CCC-----cCCCcchhHHHHHHHcCC
Confidence 565 123456999999888876
No 20
>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=96.90 E-value=0.0053 Score=44.94 Aligned_cols=79 Identities=16% Similarity=0.196 Sum_probs=56.3
Q ss_pred EEEeeeeccCCCCCCCCCceEEEeEeC--CeEEEEEccCCCCCCchhhhhHHHHHhcccCCC-eEEEEEcchhhHHHHHh
Q psy12566 108 LGLDTEWKPNLSGGSPPTLALLQIATR--DRVYILDIITLSKLPCYAQLCHDLELIVFANDD-LLKIGFNLMPDVSIIKT 184 (220)
Q Consensus 108 VG~D~Ew~p~~~~~~~~~vaLlQiat~--~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~-IlKvG~~~~~Dl~~L~~ 184 (220)
+++|+|.... .+..+++.++|++.. ++.|++| + ..++.+.. .++|||+..-|+..|.+
T Consensus 1 ~~~DiEt~~~--~~~~~~i~~i~~~~~~~~~~~~~~---f--------------~~~l~~~~~~v~V~hn~~fD~~fL~~ 61 (96)
T cd06125 1 IAIDTEATGL--DGAVHEIIEIALADVNPEDTAVID---L--------------KDILRDKPLAILVGHNGSFDLPFLNN 61 (96)
T ss_pred CEEEEECCCC--CCCCCcEEEEEEEEccCCCEEEeh---H--------------HHHHhhCCCCEEEEeCcHHhHHHHHH
Confidence 5799999653 457899999999876 7788877 1 23444444 67899999999998887
Q ss_pred hCCCCcc-ccCCcCceeeHHHH
Q psy12566 185 SLPFSEC-SSYNKTSYLDLQLL 205 (220)
Q Consensus 185 ~~~~~~~-~~~~~~~~~DL~~l 205 (220)
.+...+. .+....+++|+..+
T Consensus 62 ~~~~~~~~~p~~~~~~lDT~~l 83 (96)
T cd06125 62 RCAELGLKYPLLAGSWIDTIKL 83 (96)
T ss_pred HHHHcCCCCCCcCCcEEEehHH
Confidence 7654221 11135679999876
No 21
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=96.87 E-value=0.0016 Score=62.07 Aligned_cols=54 Identities=15% Similarity=0.160 Sum_probs=48.7
Q ss_pred EEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccC
Q psy12566 83 IILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIIT 144 (220)
Q Consensus 83 I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~ 144 (220)
+.+|++.+++..++.. +....++++|+|+.+.. ..++|+|+++.+.+||||..+
T Consensus 3 ~~~I~~~~~l~~~~~~---l~~~~~~a~DtEf~r~~-----t~l~liQ~~~~~~~~liDpl~ 56 (553)
T PRK14975 3 MKVILAPEELGAALER---LSPAGVVAGDTETTGDD-----AAAAAAQEGEEEPRWVWASTA 56 (553)
T ss_pred ceEEeccchhHHHHHH---hccCCceeCCccccCCc-----chhheeeecCCCceEEECchH
Confidence 5789999999999999 99999999999998753 199999999999999999654
No 22
>KOG2405|consensus
Probab=96.36 E-value=0.00012 Score=65.71 Aligned_cols=96 Identities=22% Similarity=0.279 Sum_probs=74.5
Q ss_pred HHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEE
Q psy12566 91 KFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLK 170 (220)
Q Consensus 91 ~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlK 170 (220)
+|-.+..+ ++...+. .-.|-.-. -..+++|-+|.||.-++||+|+..++ +..+.+++..+++|.+|+|
T Consensus 48 kf~~~~~~---ik~qn~~-~~~e~a~~---~~~~~l~~~q~~~~~~~yl~~i~~~~-----~~~~~n~~q~~~~~k~i~~ 115 (458)
T KOG2405|consen 48 KFGAAILH---IKKQNVL-VAAEGANV---CRHGKLCWLQVATNCRVYLFDIFLLG-----SRAFHNGLQMILEDKRILK 115 (458)
T ss_pred HHhHHHHh---hHhhcCc-ccccCccc---cccCcchhHHHHHHHHHHHHHHHHhh-----hHHHHHHHHHHhhhhhHhh
Confidence 35555555 4443333 33333322 24569999999999999999999885 4778999999999999999
Q ss_pred EEEcchhhHHHHHhhCCCCccccCCcCceeeHHH
Q psy12566 171 IGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQL 204 (220)
Q Consensus 171 vG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~ 204 (220)
+-|.++.=++.++..|++ ..++++|++.
T Consensus 116 ~~~d~~~~~~~~~~~~~i------~~n~v~~~q~ 143 (458)
T KOG2405|consen 116 VIHDCRWLSDCLSHQYGI------LLNNVFDTQV 143 (458)
T ss_pred hHHHHHHHHHHhccccee------eecchhhhhh
Confidence 999988878888888888 7899999988
No 23
>KOG2405|consensus
Probab=91.79 E-value=0.019 Score=51.97 Aligned_cols=98 Identities=12% Similarity=-0.001 Sum_probs=71.6
Q ss_pred CCCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEEcchhhHHHHH
Q psy12566 104 HNSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIK 183 (220)
Q Consensus 104 ~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~ 183 (220)
+..+||.|+-. ..++-...+.++|||+...+||+|...-+..- .+. -.+..+++..+ +- +...+...+.
T Consensus 194 e~~~i~~~~~s---~~~~~~~e~~~m~ia~~n~i~llD~~~sdi~i----l~~-gyK~~LEs~~~--vi-Dr~r~~e~l~ 262 (458)
T KOG2405|consen 194 EVWFIRPVSPS---LLKILALEATYMNIADGNEIFLLDSLPSDIRI----LFG-GYKRELESLEK--VI-DRIRLIEQLD 262 (458)
T ss_pred ceeEeecCchh---HHHhhhhhhhhhhhcccchhhhhhhccCCcEE----ecc-cchhhhhhcce--eh-hhhhhhHHHH
Confidence 45567766533 33445667778999999999999987543110 111 12456666655 22 8889999999
Q ss_pred hhCCCCccccCCcCceeeHHHHHHHhhh-ccCccCC
Q psy12566 184 TSLPFSECSSYNKTSYLDLQLLWSKLVA-ETTLQLP 218 (220)
Q Consensus 184 ~~~~~~~~~~~~~~~~~DL~~l~~~l~~-~~~~~~p 218 (220)
..|+. ..+++.|.|..++.+.+ .+|.+.|
T Consensus 263 ~~y~~------~L~nVkDtQia~sLve~~e~grr~p 292 (458)
T KOG2405|consen 263 TTYHS------ALKNVKDTQIASSLVEPSEYGRRHP 292 (458)
T ss_pred hHHHH------HHHhhHHHHHHHHHhhhHHhcccCC
Confidence 99998 99999999999999988 6798887
No 24
>KOG2248|consensus
Probab=90.05 E-value=0.84 Score=41.72 Aligned_cols=80 Identities=21% Similarity=0.290 Sum_probs=50.5
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe---CCeEEEEEccCCCCCC---------c-----------hhhhhHHH
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT---RDRVYILDIITLSKLP---------C-----------YAQLCHDL 158 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat---~~~v~LiD~~~l~~~~---------~-----------~~~~~~~~ 158 (220)
.....++++|||=.-+ ..+ ..|.-+.. ..+| |+|.......| + +-...+..
T Consensus 213 ~~~~~i~AlDCEm~~t----e~g-~el~RVt~VD~~~~v-i~D~fVkP~~~VvDy~T~~SGIT~~~~e~~t~tl~dvq~~ 286 (380)
T KOG2248|consen 213 SKSPNIFALDCEMVVT----ENG-LELTRVTAVDRDGKV-ILDTFVKPNKPVVDYNTRYSGITEEDLENSTITLEDVQKE 286 (380)
T ss_pred CCCCCeEEEEeeeeee----ccc-eeeEEeeeeeccCcE-EeEEeecCCCcccccccccccccHHHHhcCccCHHHHHHH
Confidence 4568899999998643 333 44444432 4455 77776553222 1 11233445
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCC
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPF 188 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~ 188 (220)
+..+++...|+ |||+..+||+.|+..++.
T Consensus 287 l~~~~~~~TIL-VGHSLenDL~aLKl~H~~ 315 (380)
T KOG2248|consen 287 LLELISKNTIL-VGHSLENDLKALKLDHPS 315 (380)
T ss_pred HHhhcCcCcEE-EeechhhHHHHHhhhCCc
Confidence 66755555555 999999999999987775
No 25
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.54 E-value=4.9 Score=40.84 Aligned_cols=109 Identities=17% Similarity=0.025 Sum_probs=67.5
Q ss_pred EEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEeCC--eEEEEEccCCC-CCCchhhhhHHHHH
Q psy12566 84 ILVDTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIATRD--RVYILDIITLS-KLPCYAQLCHDLEL 160 (220)
Q Consensus 84 ~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~--~v~LiD~~~l~-~~~~~~~~~~~~l~ 160 (220)
..|.+.+++..++.. .....+++ ..+.|. ...+.-+-+|+.+ ..|-+.+. .+ .++ .......++
T Consensus 305 ~~~~~~~~~~~~~~~----~~~~~~~~-~~~~~~-----~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~--~~~~~~~l~ 371 (887)
T TIGR00593 305 KESEEAAPLANPAEK----AEVGGFVL-ERLLDQ-----LKKALALAFATENQSYVAYASEA-DGIPLL--TILTDDKFA 371 (887)
T ss_pred eEeCCHHHHHHHHHh----CcCCeEEE-cCcccc-----cCceeEEEEEecCCCceEEEecc-cchhhh--hHHHHHHHH
Confidence 356677777776543 34446777 333331 2345556667754 35545432 21 111 122223578
Q ss_pred hcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 161 IVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 161 ~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
.+|+|+++.|+||+.+.|+..|. .+++ .....++|+...+..+.+
T Consensus 372 ~~l~~~~~~~v~~n~K~d~~~l~-~~gi-----~~~~~~~Dt~la~yll~~ 416 (887)
T TIGR00593 372 RWLLNEQIKKIGHDAKFLMHLLK-REGI-----ELGGVIFDTMLAAYLLDP 416 (887)
T ss_pred HHHhCCCCcEEEeeHHHHHHHHH-hCCC-----CCCCcchhHHHHHHHcCC
Confidence 99999999999999999999996 4565 122357899988877765
No 26
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=88.94 E-value=4 Score=35.01 Aligned_cols=102 Identities=14% Similarity=0.100 Sum_probs=58.4
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CC-----eEEEEEccC-CC-------CCC--------chhhhhH
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RD-----RVYILDIIT-LS-------KLP--------CYAQLCH 156 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~-----~v~LiD~~~-l~-------~~~--------~~~~~~~ 156 (220)
+++.++|.||+|.... ...+-.+||||. .+ ...++++.. +. .+. ...+.+.
T Consensus 4 l~~~~~v~~D~ETTGl----~~~~d~IIEIa~v~v~~~~~~~~~~~li~P~~~I~~~a~~ihgIt~e~v~~~p~~~ev~~ 79 (250)
T PRK06310 4 LKDTEFVCLDCETTGL----DVKKDRIIEFAAIRFTFDEVIDSVEFLINPERVVSAESQRIHHISDAMLRDKPKIAEVFP 79 (250)
T ss_pred ccCCcEEEEEEeCCCC----CCCCCeEEEEEEEEEECCeEEEEEEEEECcCCCCCHhhhhccCcCHHHHhCCCCHHHHHH
Confidence 6778999999999752 233457888874 12 223444321 10 110 0111222
Q ss_pred HHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCcc-ccCCcCceeeHHHHHHHh
Q psy12566 157 DLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSEC-SSYNKTSYLDLQLLWSKL 209 (220)
Q Consensus 157 ~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~-~~~~~~~~~DL~~l~~~l 209 (220)
. +..++.+.. +-|||++.-|...|.+.+.-.+. +......++|+..+++.+
T Consensus 80 ~-~~~fl~~~~-~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~lar~~ 131 (250)
T PRK06310 80 Q-IKGFFKEGD-YIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLRLAKEY 131 (250)
T ss_pred H-HHHHhCCCC-EEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHHHHHhc
Confidence 2 334455544 45999999999999877643111 101225799999988865
No 27
>cd06128 DNA_polA_exo DEDDy 3'-5' exonuclease domain of family-A DNA polymerases. The 3'-5' exonuclease domain of family-A DNA polymerases has a fundamental role in reducing polymerase errors and is involved in proofreading activity. Family-A DNA polymerases contain a DnaQ-like exonuclease domain in the same polypeptide chain as the polymerase domain, similar to family-B DNA polymerases. The exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four invariant acidic residues that serve as ligands for the two metal ions required for catalysis. The Klenow fragment (KF) of Escherichia coli Pol I, the Thermus aquaticus (Taq) Pol I, and Bacillus stearothermophilus (BF) Pol I are examples of family-A DNA polymerases. They are involved in nucleotide excision repair and in the processing of Okazaki fragments that are generated during lagging strand synthesis. The N-terminal domains of BF Pol I and Taq Po
Probab=88.38 E-value=0.68 Score=35.92 Aligned_cols=68 Identities=19% Similarity=0.161 Sum_probs=46.1
Q ss_pred EEeEeCCeEEEEEccCCCCCCchhhhhHHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcC-ceeeHHHHHH
Q psy12566 129 LQIATRDRVYILDIITLSKLPCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKT-SYLDLQLLWS 207 (220)
Q Consensus 129 lQiat~~~v~LiD~~~l~~~~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~-~~~DL~~l~~ 207 (220)
+=+++.+.+|.|++.. . .. ...++.+|+|+++.|+||+.+.++..|. .+++ ... .++|+...+-
T Consensus 23 lal~~~~~~~yi~~~~-~-~~------~~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi------~l~~~~fD~~LAaY 87 (151)
T cd06128 23 LAFAIEGVAAYIPVAH-D-YA------LELLKPLLEDEKALKVGQNLKYDRVILA-NYGI------ELRGIAFDTMLEAY 87 (151)
T ss_pred EEEEcCCCeEEEeCCC-C-cC------HHHHHHHHcCCCCCEEeeehHHHHHHHH-HCCC------CCCCcchhHHHHHH
Confidence 4555665576666221 0 01 1136789999999999999999999985 4565 333 3588888877
Q ss_pred Hhhh
Q psy12566 208 KLVA 211 (220)
Q Consensus 208 ~l~~ 211 (220)
.+.+
T Consensus 88 LL~p 91 (151)
T cd06128 88 LLDP 91 (151)
T ss_pred HcCC
Confidence 7776
No 28
>KOG2249|consensus
Probab=88.06 E-value=2.9 Score=36.33 Aligned_cols=82 Identities=17% Similarity=0.194 Sum_probs=48.5
Q ss_pred CCeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCCCCC---------c-hhh---------hhHHHHHhcccC
Q psy12566 105 NSHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLSKLP---------C-YAQ---------LCHDLELIVFAN 165 (220)
Q Consensus 105 ~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~~~~---------~-~~~---------~~~~~l~~ll~~ 165 (220)
.++|++|||....-.+|..+-+|=+-|-...--.|+|-..-...+ + .++ ....=+..||.+
T Consensus 105 ~r~vAmDCEMVG~Gp~G~~s~lARvSIVN~~G~VvyDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g 184 (280)
T KOG2249|consen 105 TRVVAMDCEMVGVGPDGRESLLARVSIVNYHGHVVYDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG 184 (280)
T ss_pred ceEEEEeeeEeccCCCccceeeeEEEEeeccCcEeeeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC
Confidence 369999999987533333444444455444445566765432111 0 011 111224566766
Q ss_pred CCeEEEEEcchhhHHHHHhhCCC
Q psy12566 166 DDLLKIGFNLMPDVSIIKTSLPF 188 (220)
Q Consensus 166 ~~IlKvG~~~~~Dl~~L~~~~~~ 188 (220)
.| -|||++.+|++.|.-.+|-
T Consensus 185 -RI-lVGHaLhnDl~~L~l~hp~ 205 (280)
T KOG2249|consen 185 -RI-LVGHALHNDLQALKLEHPR 205 (280)
T ss_pred -CE-EeccccccHHHHHhhhCch
Confidence 34 4999999999999977775
No 29
>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=85.78 E-value=7.8 Score=32.29 Aligned_cols=100 Identities=10% Similarity=-0.013 Sum_probs=56.7
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE------EEEEccCCCCCC------------------chhh
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV------YILDIITLSKLP------------------CYAQ 153 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v------~LiD~~~l~~~~------------------~~~~ 153 (220)
|....+|.||+|...- .+.-.+||||. .+.. .++++.. .++ ..++
T Consensus 4 l~~~~fvv~D~ETTGl-----~~~~~IIeIgav~v~~~~~~~~~f~~li~P~~--~i~~~a~~ihGIt~e~l~~~p~~~e 76 (217)
T TIGR00573 4 LVLDTETTGDNETTGL-----YAGHDIIEIGAVEIINRRITGNKFHTYIKPDR--PIDPDAIKIHGITDDMLKDKPDFKE 76 (217)
T ss_pred EEecCEEEEEecCCCC-----CCCCCEEEEEEEEEECCCEeeeEEEEEECcCC--CCCHHHHhhcCCCHHHHcCCCCHHH
Confidence 6678899999999752 22223899963 1211 2222221 111 0122
Q ss_pred hhHHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 154 LCHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 154 ~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
.+.. +..++.+ . +-|||+..-|...|.+.+.-..........++|+..+.+.+.+
T Consensus 77 v~~~-~~~~~~~-~-~lVaHNa~FD~~fL~~~~~r~~~~~~~~~~~~dtl~l~~~~~~ 131 (217)
T TIGR00573 77 IAED-FADYIRG-A-ELVIHNASFDVGFLNYEFSKLYKVEPKTNDVIDTTDTLQYARP 131 (217)
T ss_pred HHHH-HHHHhCC-C-EEEEeccHHHHHHHHHHHHHhcCCCCCccceecHHHHHHHHHH
Confidence 2333 3344444 3 3489999999999998875322111234578898887766554
No 30
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=85.02 E-value=10 Score=32.08 Aligned_cols=102 Identities=16% Similarity=0.137 Sum_probs=57.0
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe---C--C-----eEEEEEccCCCCCC-------c---------h---h
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT---R--D-----RVYILDIITLSKLP-------C---------Y---A 152 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat---~--~-----~v~LiD~~~l~~~~-------~---------~---~ 152 (220)
..+.+++.||+|..... ..+-.+||||. . + ..++++... .+| + + .
T Consensus 3 ~~~~~~vv~D~ETTGl~----p~~d~Iieig~v~v~~~g~~~~~~~~lv~P~~--~i~~~a~~IhGIt~e~l~~~g~~~~ 76 (232)
T PRK07942 3 WHPGPLAAFDLETTGVD----PETARIVTAALVVVDADGEVVESREWLADPGV--EIPEEASAVHGITTEYARAHGRPAA 76 (232)
T ss_pred cccCcEEEEEeccCCCC----CCCCeeEEEEEEEEeCCCccccceEEEECCCC--CCCHHHHHHhCCCHHHHHhhCCCHH
Confidence 45678999999997531 22335677763 1 2 234666532 121 0 0 1
Q ss_pred hhhHHHH---HhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhh
Q psy12566 153 QLCHDLE---LIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 153 ~~~~~~l---~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~ 210 (220)
+.+..++ ...+.+..++ |||+..-|+..|.+.+.-.+........++|...+.+.+.
T Consensus 77 ~vl~e~~~~l~~~~~~~~~l-VahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l~~~~~ 136 (232)
T PRK07942 77 EVLAEIADALREAWARGVPV-VVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVIDKAVD 136 (232)
T ss_pred HHHHHHHHHHHHHhhcCCEE-EEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHHHhhhh
Confidence 1222222 2224344444 9999999999998776432111012356889888776553
No 31
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=83.94 E-value=2.4 Score=40.90 Aligned_cols=104 Identities=17% Similarity=0.177 Sum_probs=62.1
Q ss_pred eCHHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeE--eCC-eEEEEEccCCCCCCchhhhhHHHHHhcc
Q psy12566 87 DTADKFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIA--TRD-RVYILDIITLSKLPCYAQLCHDLELIVF 163 (220)
Q Consensus 87 dt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQia--t~~-~v~LiD~~~l~~~~~~~~~~~~~l~~ll 163 (220)
.+.+.+..+... +.....+++|+|..... ....+++=++ ..+ ..|+.....-..+ . ....++.+|
T Consensus 7 ~~~~~~~~~~~~---~~~~~~~a~~~et~~l~----~~~~~lvg~s~~~~~~~~yi~~~~~~~~~----~-~~~~l~~~l 74 (593)
T COG0749 7 TDLAVLNAWLTK---LNAAANIAFDTETDGLD----PHGADLVGLSVASEEEAAYIPLLHGPEQL----N-VLAALKPLL 74 (593)
T ss_pred hHHHHHHHHHHH---HhhcccceeeccccccC----cccCCeeEEEeeccccceeEeeccchhhh----h-hHHHHHHHh
Confidence 344455555555 44444499999997542 2333444433 233 3454444310011 1 234589999
Q ss_pred cCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHh
Q psy12566 164 ANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKL 209 (220)
Q Consensus 164 ~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l 209 (220)
+|+++.|+|++.+-|...|++.. + .....+|+....-.+
T Consensus 75 ~~~~~~kv~~~~K~d~~~l~~~G-i------~~~~~~DtmlasYll 113 (593)
T COG0749 75 EDEGIKKVGQNLKYDYKVLANLG-I------EPGVAFDTMLASYLL 113 (593)
T ss_pred hCcccchhccccchhHHHHHHcC-C------cccchHHHHHHHhcc
Confidence 99999999999999999998654 4 245566666554333
No 32
>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=83.17 E-value=9.6 Score=30.12 Aligned_cols=42 Identities=19% Similarity=0.275 Sum_probs=29.5
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+..++.+..+ -|||+...|+..|... ...++|+..+++.+.+
T Consensus 77 ~~~~i~~~~v-lVgHn~~fD~~fL~~~----------~~~~iDT~~l~~~~~~ 118 (161)
T cd06137 77 LWKFIDPDTI-LVGHSLQNDLDALRMI----------HTRVVDTAILTREAVK 118 (161)
T ss_pred HHHhcCCCcE-EEeccHHHHHHHHhCc----------CCCeeEehhhhhhccC
Confidence 4455655444 4999999999999642 2347888888876654
No 33
>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=79.86 E-value=2.2 Score=34.84 Aligned_cols=40 Identities=18% Similarity=0.295 Sum_probs=27.4
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHH
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWS 207 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~ 207 (220)
+..++ +++.+-|||+..+|++.|+-.+|. ..++|+..++.
T Consensus 95 l~~li-~~~tILVGHsL~nDL~aL~l~hp~--------~~viDTa~l~~ 134 (174)
T cd06143 95 LRLLV-DLGCIFVGHGLAKDFRVINIQVPK--------EQVIDTVELFH 134 (174)
T ss_pred HHHHc-CCCCEEEeccchhHHHHhcCcCCC--------cceEEcHHhcc
Confidence 44555 445566999999999999765543 35677766643
No 34
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=79.60 E-value=14 Score=32.80 Aligned_cols=100 Identities=12% Similarity=0.144 Sum_probs=57.1
Q ss_pred CCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccC-C-------CCCC--------chhhhhHHH
Q psy12566 104 HNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIIT-L-------SKLP--------CYAQLCHDL 158 (220)
Q Consensus 104 ~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~-l-------~~~~--------~~~~~~~~~ 158 (220)
...+|.||+|.... ...+-.+||||. .+.+ .++.+.. + ..+. ...+.+..|
T Consensus 7 ~~~~Vv~DlETTGl----~p~~~eIIEIgaV~v~~g~i~~~f~~lVkP~~~I~~~a~~ihGIT~e~l~~~~~~~evl~~f 82 (313)
T PRK06807 7 PLDYVVIDFETTGF----NPYNDKIIQVAAVKYRNHELVDQFVSYVNPERPIPDRITSLTGITNYRVSDAPTIEEVLPLF 82 (313)
T ss_pred CCCEEEEEEECCCC----CCCCCeEEEEEEEEEECCEEEEEEEEEECcCCCCCHhhhccCCCCHHHHhCCCCHHHHHHHH
Confidence 46799999998532 223457899974 2222 2233221 0 0010 012233444
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+ .++.+. ++ |||+..-|+..|.+.+...+. +.....++|+..+++.+.+
T Consensus 83 ~-~fl~~~-~l-VaHNa~FD~~fL~~~~~~~gl-~~~~~~~iDtl~la~~~~~ 131 (313)
T PRK06807 83 L-AFLHTN-VI-VAHNASFDMRFLKSNVNMLGL-PEPKNKVIDTVFLAKKYMK 131 (313)
T ss_pred H-HHHcCC-eE-EEEcHHHHHHHHHHHHHHcCC-CCCCCCEeeHHHHHHHHhC
Confidence 3 344544 44 899999999999987643221 1134569999998887654
No 35
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=78.58 E-value=18 Score=30.86 Aligned_cols=103 Identities=12% Similarity=0.097 Sum_probs=59.0
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-------EEEEccC-CC-------CCC-----c---hhhh
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-------YILDIIT-LS-------KLP-----C---YAQL 154 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-------~LiD~~~-l~-------~~~-----~---~~~~ 154 (220)
+...+++.||+|...- ...+-.+||||. .+.+ .+++... +. .+. . .++.
T Consensus 44 ~~~~~~vviD~ETTGl----~p~~d~IieIg~v~v~~~~i~~~~~~~~li~P~~~i~~~~~~IhGIt~e~l~~ap~~~ev 119 (239)
T PRK09146 44 LSEVPFVALDFETTGL----DAEQDAIVSIGLVPFTLQRIRCRQARHWVVKPRRPLEEESVVIHGITHSELQDAPDLERI 119 (239)
T ss_pred cccCCEEEEEeECCCC----CCCCCcEEEEEEEEEECCeEeecceEEEEECCCCCCChhhhhhcCCCHHHHhCCCCHHHH
Confidence 6778899999999753 123457788874 2333 3444321 11 111 0 1122
Q ss_pred hHHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhhc
Q psy12566 155 CHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVAE 212 (220)
Q Consensus 155 ~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~~ 212 (220)
+..++ ..+.+ + +-|||+..-|...|.+.+...... .....++|+..+++.+.++
T Consensus 120 l~~l~-~~~~~-~-~lVaHna~FD~~fL~~~l~~~~~~-~~~~~~iDTl~Lar~l~~~ 173 (239)
T PRK09146 120 LDELL-EALAG-K-VVVVHYRRIERDFLDQALRNRIGE-GIEFPVIDTMEIEARIQRK 173 (239)
T ss_pred HHHHH-HHhCC-C-EEEEECHHHHHHHHHHHHHHhcCC-CCCCceechHHHHHHHccc
Confidence 33332 23333 3 458999999999998765321111 1245699999999887543
No 36
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=74.03 E-value=47 Score=27.10 Aligned_cols=106 Identities=18% Similarity=0.237 Sum_probs=57.6
Q ss_pred HHHHHHHHHhccCCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-------EEEEccC-CC-------CC---
Q psy12566 91 KFASALQDFARLDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-------YILDIIT-LS-------KL--- 148 (220)
Q Consensus 91 ~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-------~LiD~~~-l~-------~~--- 148 (220)
.+..+.+. ..+..+|.+|+|.... ...+-.+|||+. .+.+ .+++... +. .+
T Consensus 18 ~~~~~~~~---~~~~~~vviD~ETTGl----~~~~d~IieIgaV~~~~~~~~~~~~f~~~i~p~~~i~~~~~~ihGIt~~ 90 (202)
T PRK09145 18 RYAFLFEP---PPPDEWVALDCETTGL----DPRRAEIVSIAAVKIRGNRILTSERLELLVRPPQSLSAESIKIHRLRHQ 90 (202)
T ss_pred HHHHHhcC---CCCCCEEEEEeECCCC----CCCCCceEEEEEEEEECCEEeecCceEEEECCCCCCCHhHhhhcCcCHH
Confidence 33444444 5667999999999753 122347888873 2322 2333321 00 00
Q ss_pred -----CchhhhhHHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHH
Q psy12566 149 -----PCYAQLCHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWS 207 (220)
Q Consensus 149 -----~~~~~~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~ 207 (220)
|..++.+..+ ...+.+ . +-|||+..-|...|.+.+.-.... ..+...+|+..++.
T Consensus 91 ~l~~~~~~~~vl~~~-~~~i~~-~-~lv~hn~~fD~~fL~~~~~~~~~~-~~~~~~id~~~l~~ 150 (202)
T PRK09145 91 DLEDGLSEEEALRQL-LAFIGN-R-PLVGYYLEFDVAMLNRYVRPLLGI-PLPNPLIEVSALYY 150 (202)
T ss_pred HHhcCCCHHHHHHHH-HHHHcC-C-eEEEeCHHHHHHHHHHHHHHhcCC-CCCCCeeeHHHHHH
Confidence 0012233333 334444 3 358999999999998664321111 13456899988764
No 37
>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=73.42 E-value=38 Score=25.82 Aligned_cols=50 Identities=16% Similarity=0.080 Sum_probs=33.8
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+...+++ . +-|||+...|...|.+.+...+. .......+|+..+.+.+.+
T Consensus 71 l~~~l~~-~-~lv~hn~~fD~~~l~~~~~~~g~-~~~~~~~idt~~~~~~~~~ 120 (156)
T cd06130 71 IKPFLGG-S-LVVAHNASFDRSVLRAALEAYGL-PPPPYQYLCTVRLARRVWP 120 (156)
T ss_pred HHHHhCC-C-EEEEeChHHhHHHHHHHHHHcCC-CCCCCCEEEHHHHHHHHhc
Confidence 3445555 3 45899999999999876643211 1134679999998887654
No 38
>PRK07740 hypothetical protein; Provisional
Probab=73.27 E-value=57 Score=27.73 Aligned_cols=41 Identities=12% Similarity=0.066 Sum_probs=28.3
Q ss_pred EEEEEcchhhHHHHHhhCC-CCccccCCcCceeeHHHHHHHhhh
Q psy12566 169 LKIGFNLMPDVSIIKTSLP-FSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 169 lKvG~~~~~Dl~~L~~~~~-~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+-|||+..-|...|.+.+- ... . .-...++|+..+++.+.+
T Consensus 143 ~lVahna~fD~~fL~~~~~~~~~-~-~~~~~~iDt~~l~r~l~~ 184 (244)
T PRK07740 143 VLVAHHAGHDKAFLRHALWRTYR-Q-PFTHRLIDTMFLTKLLAH 184 (244)
T ss_pred EEEEeCHHHHHHHHHHHHHHhcC-C-CcCCCeechHHHHHHHcC
Confidence 4589999999998876431 111 1 134689999999887654
No 39
>PRK07883 hypothetical protein; Validated
Probab=68.39 E-value=32 Score=33.13 Aligned_cols=102 Identities=13% Similarity=0.116 Sum_probs=59.1
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccC-C-------CCCC--------chhhhhH
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIIT-L-------SKLP--------CYAQLCH 156 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~-l-------~~~~--------~~~~~~~ 156 (220)
+.+..+|.||+|+... ....-.++||+. .+.+ .++++.. + ..+. ...+.+.
T Consensus 12 ~~~~~~Vv~D~ETTGl----~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~ 87 (557)
T PRK07883 12 LRDVTFVVVDLETTGG----SPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLP 87 (557)
T ss_pred CcCCCEEEEEEecCCC----CCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHH
Confidence 6778999999999742 234468889874 2322 2343321 1 0111 0112233
Q ss_pred HHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 157 DLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 157 ~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
. +..++.+ . +-|||+..-|...|.+.+.-.+.- .....++|+..+++.+.+
T Consensus 88 ~-f~~fl~~-~-~lVaHNa~FD~~fL~~~~~r~g~~-~~~~~~iDTl~lar~l~~ 138 (557)
T PRK07883 88 A-FLEFARG-A-VLVAHNAPFDIGFLRAAAARCGYP-WPGPPVLCTVRLARRVLP 138 (557)
T ss_pred H-HHHHhcC-C-EEEEeCcHHHHHHHHHHHHHcCCC-CCCCCcEecHHHHHHhcc
Confidence 3 3344554 3 458999999999998765432110 123468999998877544
No 40
>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=68.16 E-value=23 Score=28.88 Aligned_cols=81 Identities=15% Similarity=0.158 Sum_probs=42.9
Q ss_pred CCeEEEeeeeccCCCCCCCCCceEEEeEeC----CeEEEEEccC---CCCCCchhhhhHHHHHhccc-CCCeEEEEEcch
Q psy12566 105 NSHLGLDTEWKPNLSGGSPPTLALLQIATR----DRVYILDIIT---LSKLPCYAQLCHDLELIVFA-NDDLLKIGFNLM 176 (220)
Q Consensus 105 ~~~VG~D~Ew~p~~~~~~~~~vaLlQiat~----~~v~LiD~~~---l~~~~~~~~~~~~~l~~ll~-~~~IlKvG~~~~ 176 (220)
-+++.||.|......-....+=.++|||.. +.++.+.-.. +.....-.+++..|+..+-+ ||+++ +||+..
T Consensus 3 l~i~~fDIEt~~~~g~p~~~~d~Ii~Is~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~i~~~dpdii-vgyN~~ 81 (195)
T cd05780 3 LKILSFDIEVLNHEGEPNPEKDPIIMISFADEGGNKVITWKKFDLPFVEVVKTEKEMIKRFIEIVKEKDPDVI-YTYNGD 81 (195)
T ss_pred ceEEEEEEEecCCCCCCCCCCCcEEEEEEecCCCceEEEecCCCCCeEEEeCCHHHHHHHHHHHHHHcCCCEE-EecCCC
Confidence 468999999974221012334466777752 1233222110 00011012445555544433 48875 999986
Q ss_pred h-hHHHHHhhC
Q psy12566 177 P-DVSIIKTSL 186 (220)
Q Consensus 177 ~-Dl~~L~~~~ 186 (220)
+ |+..|...+
T Consensus 82 ~FD~pyL~~R~ 92 (195)
T cd05780 82 NFDFPYLKKRA 92 (195)
T ss_pred CCcHHHHHHHH
Confidence 5 999988654
No 41
>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=67.94 E-value=39 Score=27.22 Aligned_cols=33 Identities=21% Similarity=0.302 Sum_probs=21.3
Q ss_pred hhHHHHHhccc-CCCeEEEEEcc-hhhHHHHHhhCC
Q psy12566 154 LCHDLELIVFA-NDDLLKIGFNL-MPDVSIIKTSLP 187 (220)
Q Consensus 154 ~~~~~l~~ll~-~~~IlKvG~~~-~~Dl~~L~~~~~ 187 (220)
++..|+..+=. ||+|+ +||+. .-|+..|.+.+.
T Consensus 66 lL~~f~~~i~~~dpdii-vg~N~~~FD~~~L~~R~~ 100 (199)
T cd05160 66 LLKRFFDIIREYDPDIL-TGYNIDDFDLPYLLKRAE 100 (199)
T ss_pred HHHHHHHHHHhcCCCEE-EEeccCCCcHHHHHHHHH
Confidence 34444433322 47775 99999 679999986544
No 42
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=64.85 E-value=61 Score=24.82 Aligned_cols=97 Identities=16% Similarity=0.167 Sum_probs=53.6
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEe----CCe-EE----EEEccCCCCCC------------------chhhhhHHH
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIAT----RDR-VY----ILDIITLSKLP------------------CYAQLCHDL 158 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~-v~----LiD~~~l~~~~------------------~~~~~~~~~ 158 (220)
.+|.||+|.... ...+-.++||+. .+. +- ++.+. ..++ ...+.+.+
T Consensus 1 ~~v~~D~Ettg~----~~~~~~Iieig~v~~~~~~~~~~f~~~v~p~--~~i~~~~~~~~Git~~~l~~~~~~~~~~~~- 73 (169)
T smart00479 1 TLVVIDCETTGL----DPGKDEIIEIAAVDVDGGRIIVVFDTYVKPD--RPITDYATEIHGITPEMLDDAPTFEEVLEE- 73 (169)
T ss_pred CEEEEEeeCCCC----CCCCCeEEEEEEEEEECCEeEEEEEEEECCC--CCCCHHHHHHhCCCHHHHhCCCCHHHHHHH-
Confidence 378999999753 233568999974 222 11 22221 1111 01223333
Q ss_pred HHhcccCCCeEEEEEcc-hhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFANDDLLKIGFNL-MPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~-~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+..++.+. ++ |||+. ..|+..|.+.+...+.-......++|+..+.+...+
T Consensus 74 ~~~~l~~~-~~-v~~n~~~fD~~~L~~~~~~~~~~~~~~~~~iD~~~~~~~~~~ 125 (169)
T smart00479 74 LLEFLKGK-IL-VAGNALNFDLRFLKLEHPRLGIKDPPKNPVIDTLKLARALNP 125 (169)
T ss_pred HHHHhcCC-EE-EEeCCHHHhHHHHHHHHHHhCCCCCcCCCeeEHHHHHHHHCC
Confidence 34555553 43 55555 999999998766422110123458999998876654
No 43
>cd05785 DNA_polB_like2_exo Uncharacterized bacterial subgroup of the DEDDy 3'-5' exonuclease domain of family-B DNA polymerases. A subfamily of the 3'-5' exonuclease domain of family-B DNA polymerases. This subfamily is composed of uncharacterized bacterial family-B DNA polymerases. 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 exonuclease domain contains three sequence motifs termed ExoI, ExoII and ExoIII, with a specific YX(3)D pattern at ExoIII. These motifs are involved in metal binding and catalysis. The exonuclease domain of family-B DNA polymerases has a fundamental role in proofreading activity. It contains a beta hairpin structure that plays an important role in active site switching in the event of a nucleotide misincorporation. Family-B DNA polymerases are predominantly involved in DNA replication and DNA repair.
Probab=62.44 E-value=37 Score=28.13 Aligned_cols=80 Identities=20% Similarity=0.173 Sum_probs=45.9
Q ss_pred CCCCeEEEeeeeccCCCC----CCCCCceEEEeEeCC---eEEEEEccCCCCCCchhhhhHHHHHhccc-CCCeEEEEEc
Q psy12566 103 DHNSHLGLDTEWKPNLSG----GSPPTLALLQIATRD---RVYILDIITLSKLPCYAQLCHDLELIVFA-NDDLLKIGFN 174 (220)
Q Consensus 103 ~~~~~VG~D~Ew~p~~~~----~~~~~vaLlQiat~~---~v~LiD~~~l~~~~~~~~~~~~~l~~ll~-~~~IlKvG~~ 174 (220)
.+-+++.||.|-...... ....+-.++|||..+ ...++ ... .+.-.+++..|+..+-. ||+|+ +||+
T Consensus 7 ~~lkilsfDIE~~~~~~~~~p~p~~~~d~Ii~Is~~~~~~~~~~~---~~~-~~~E~~lL~~f~~~i~~~dPdii-~g~N 81 (207)
T cd05785 7 DDLRRLQLDIETYSLPGFFFSNPDRGDDRIIIVALRDNRGWEEVL---HAE-DAAEKELLEELVAIIRERDPDVI-EGHN 81 (207)
T ss_pred CCceEEEEEEEecCCCCccCCCCCCCCCeEEEEecccCCCceeee---ccC-CCCHHHHHHHHHHHHHHhCCCEE-eccC
Confidence 456799999999653211 123445799998742 12222 111 11113445555554444 57865 8999
Q ss_pred c-hhhHHHHHhhCC
Q psy12566 175 L-MPDVSIIKTSLP 187 (220)
Q Consensus 175 ~-~~Dl~~L~~~~~ 187 (220)
. .-|+..|.+.+.
T Consensus 82 ~~~FD~pyl~~R~~ 95 (207)
T cd05785 82 IFRFDLPYLRRRCR 95 (207)
T ss_pred CcccCHHHHHHHHH
Confidence 8 559998875533
No 44
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=62.15 E-value=99 Score=27.39 Aligned_cols=99 Identities=13% Similarity=0.100 Sum_probs=56.8
Q ss_pred CCCeEEEeeeeccCCCCCCCCCceEEEeEe-----CCe-----EEEEEccC------CCCCC--------chhhhhHHHH
Q psy12566 104 HNSHLGLDTEWKPNLSGGSPPTLALLQIAT-----RDR-----VYILDIIT------LSKLP--------CYAQLCHDLE 159 (220)
Q Consensus 104 ~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat-----~~~-----v~LiD~~~------l~~~~--------~~~~~~~~~l 159 (220)
...+|.||+|...- ...+-.+|||+. .++ ..+++... +..+. ...+.+.. +
T Consensus 14 ~~~fvvlD~ETTGl----~p~~d~IIeIgav~v~~~g~i~~~~~~lv~P~~~~~~~~IhGIt~e~l~~ap~f~ev~~~-l 88 (313)
T PRK06063 14 PRGWAVVDVETSGF----RPGQARIISLAVLGLDADGNVEQSVVTLLNPGVDPGPTHVHGLTAEMLEGQPQFADIAGE-V 88 (313)
T ss_pred CCCEEEEEEECCCC----CCCCCEEEEEEEEEEECCceeeeEEEEEECcCCCCCCeecCCCCHHHHhCCCCHHHHHHH-H
Confidence 45799999999742 233457888863 122 23444321 11111 01222333 4
Q ss_pred HhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhh
Q psy12566 160 LIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 160 ~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~ 210 (220)
..++.+ . +-|||+..-|+..|.+.+..... ......++|+..+++.+.
T Consensus 89 ~~~l~~-~-~lVaHNa~FD~~fL~~~~~r~g~-~~~~~~~ldTl~lar~~~ 136 (313)
T PRK06063 89 AELLRG-R-TLVAHNVAFDYSFLAAEAERAGA-ELPVDQVMCTVELARRLG 136 (313)
T ss_pred HHHcCC-C-EEEEeCHHHHHHHHHHHHHHcCC-CCCCCCEEehHHHHHHhc
Confidence 455555 3 45899999999999877643211 013356899999887653
No 45
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=59.92 E-value=1.1e+02 Score=26.07 Aligned_cols=99 Identities=11% Similarity=0.034 Sum_probs=55.6
Q ss_pred CCCeEEEeeeeccCCCCCCCCCceEEEeEe----CC------eEEEEEccCCCCCC------------------chhhhh
Q psy12566 104 HNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RD------RVYILDIITLSKLP------------------CYAQLC 155 (220)
Q Consensus 104 ~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~------~v~LiD~~~l~~~~------------------~~~~~~ 155 (220)
..++|.||+|...-. ...+-.+|+|+. .+ --.++++.. .++ ..++.+
T Consensus 3 ~~r~vvlDtETTGld---p~~~drIIEIGaV~v~~~~~~~~~f~~~i~P~~--~i~~~a~~VHGIT~e~l~~~p~f~ev~ 77 (240)
T PRK05711 3 IMRQIVLDTETTGLN---QREGHRIIEIGAVELINRRLTGRNFHVYIKPDR--LVDPEALAVHGITDEFLADKPTFAEVA 77 (240)
T ss_pred CCeEEEEEeeCCCcC---CCCCCeEEEEEEEEEECCEEeccEEEEEECcCC--cCCHHHhhhcCCCHHHHcCCCCHHHHH
Confidence 356899999997521 112457888863 11 123444421 111 012233
Q ss_pred HHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCc-ccc--CCcCceeeHHHHHHHhh
Q psy12566 156 HDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSE-CSS--YNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 156 ~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~-~~~--~~~~~~~DL~~l~~~l~ 210 (220)
..| ..++.+. . -|||+..-|+..|.+.+.-.+ .++ .....++|+..+++.+.
T Consensus 78 ~~f-~~fi~~~-~-lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~lar~~~ 132 (240)
T PRK05711 78 DEF-LDFIRGA-E-LIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLAMARRMF 132 (240)
T ss_pred HHH-HHHhCCC-E-EEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHHHHHHHc
Confidence 333 3444553 3 389999999999987654321 110 12356999998887653
No 46
>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=56.51 E-value=20 Score=26.91 Aligned_cols=50 Identities=14% Similarity=0.117 Sum_probs=36.3
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+..++.+ -+.|||+...|...|.+.+.... .......++|+..+++.+.+
T Consensus 73 ~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~-~~~~~~~~iDt~~~~~~~~~ 122 (159)
T cd06127 73 FLEFLGG--RVLVAHNASFDLRFLNRELRRLG-GPPLPNPWIDTLRLARRLLP 122 (159)
T ss_pred HHHHHCC--CEEEEeCcHhhHHHHHHHHHHhC-CCCCCCCeeEHHHHHHHHcC
Confidence 4455655 45699999999999988766422 11256789999999887765
No 47
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=56.14 E-value=1.1e+02 Score=25.01 Aligned_cols=54 Identities=15% Similarity=-0.004 Sum_probs=32.6
Q ss_pred hhHHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCc-cccCCcCceeeHHHHHHHhh
Q psy12566 154 LCHDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSE-CSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 154 ~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~-~~~~~~~~~~DL~~l~~~l~ 210 (220)
.+.. +..++.+...+-++| ..-|+..|.+.+...+ .+ .....++|++.+++.+.
T Consensus 82 vl~~-f~~~~~~~~~~iv~~-~~fD~~fL~~~~~~~~~~~-~~~~~~~dl~~~~~~~~ 136 (207)
T PRK07748 82 LVEK-LAEYDKRCKPTIVTW-GNMDMKVLKHNCEKAGVPF-PFKGQCRDLSLEYKKFF 136 (207)
T ss_pred HHHH-HHHHhCcCCeEEEEE-CHHHHHHHHHHHHHcCCCC-cccccceeHHHHHHHHh
Confidence 3444 455666644555666 4789999987764211 11 12367899988776543
No 48
>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=56.02 E-value=94 Score=24.09 Aligned_cols=52 Identities=10% Similarity=-0.003 Sum_probs=31.2
Q ss_pred HHhcccCC-CeEEEEEcchhhHHHHHhhCCCCcc--ccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFAND-DLLKIGFNLMPDVSIIKTSLPFSEC--SSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~-~IlKvG~~~~~Dl~~L~~~~~~~~~--~~~~~~~~~DL~~l~~~l~~ 211 (220)
+..++.+. ...-++|+ ..|...+.+.+...+. ......+++|++.+++...+
T Consensus 82 ~~~~l~~~~~~~~v~~~-~~d~~~l~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~ 136 (176)
T cd06133 82 FLEWLGKNGKYAFVTWG-DWDLKDLLQNQCKYKIINLPPFFRQWIDLKKEFAKFYG 136 (176)
T ss_pred HHHHHHhCCCeEEEeec-HhhHHHHHHHHHHhcCCCCcccccceEEHHHHHHHHhC
Confidence 34555554 25557776 7887766654222111 11256789999999887654
No 49
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=54.40 E-value=1.1e+02 Score=26.22 Aligned_cols=100 Identities=11% Similarity=0.105 Sum_probs=56.2
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccCCC-------CCC--------chhhhhHH
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIITLS-------KLP--------CYAQLCHD 157 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~l~-------~~~--------~~~~~~~~ 157 (220)
+.+..+|.+|+|+.... ..+-.+|+|+. .+.+ .++....+. .+. ...+.+..
T Consensus 65 ~~~~~~vv~DiETTG~~----~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~ 140 (257)
T PRK08517 65 IKDQVFCFVDIETNGSK----PKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEE 140 (257)
T ss_pred CCCCCEEEEEEeCCCCC----CCCCeEEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHH
Confidence 57789999999997532 22337888873 2322 233332111 010 01223344
Q ss_pred HHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHh
Q psy12566 158 LELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKL 209 (220)
Q Consensus 158 ~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l 209 (220)
| ...+.+ + +.|||+..-|...|.+.+...+ +.......+|+..+++..
T Consensus 141 f-~~fl~~-~-v~VaHNa~FD~~fL~~~l~r~g-~~~~~~~~ldtl~la~~~ 188 (257)
T PRK08517 141 F-RLFLGD-S-VFVAHNVNFDYNFISRSLEEIG-LGPLLNRKLCTIDLAKRT 188 (257)
T ss_pred H-HHHHCC-C-eEEEECHHHHHHHHHHHHHHcC-CCCCCCCcEehHHHHHHH
Confidence 3 344454 3 4689999999999986553211 111345578888777654
No 50
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=53.62 E-value=1.2e+02 Score=25.37 Aligned_cols=97 Identities=11% Similarity=0.087 Sum_probs=55.0
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEeCC----e--EEEEEccCCCCCC-------c-----------hhhhhHHHHHh
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIATRD----R--VYILDIITLSKLP-------C-----------YAQLCHDLELI 161 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~----~--v~LiD~~~l~~~~-------~-----------~~~~~~~~l~~ 161 (220)
++|.||+|...- ...+=.+||||.-+ . ..++++.. .+| + ..+.+.. +..
T Consensus 3 ~~vv~D~ETTGl----~~~~d~IIeig~v~~~~~~~f~~lv~P~~--~I~~~a~~IhGIt~e~v~~~p~f~ev~~~-~~~ 75 (232)
T PRK06309 3 ALIFYDTETTGT----QIDKDRIIEIAAYNGVTSESFQTLVNPEI--PIPAEASKIHGITTDEVADAPKFPEAYQK-FIE 75 (232)
T ss_pred cEEEEEeeCCCC----CCCCCEEEEEEEEcCccccEEEEEeCCCC--CCChhHHhhcCCCHHHHhCCCCHHHHHHH-HHH
Confidence 589999999752 22334789997521 1 22444321 111 0 0112222 234
Q ss_pred cccCCCeEEEEEcc-hhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 162 VFANDDLLKIGFNL-MPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 162 ll~~~~IlKvG~~~-~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
++.+.. +-|||+. .-|...|.+.+.....- .....++|+..+++.+.+
T Consensus 76 fi~~~~-~lVaHN~~~FD~~~L~~e~~r~g~~-~~~~~~iDt~~l~~~~~~ 124 (232)
T PRK06309 76 FCGTDN-ILVAHNNDAFDFPLLRKECRRHGLE-PPTLRTIDSLKWAQKYRP 124 (232)
T ss_pred HHcCCC-EEEEeCCHHHHHHHHHHHHHHcCCC-CCCCcEEeHHHHHHHHcC
Confidence 444433 4599995 79999998776432111 123579999999887654
No 51
>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=52.57 E-value=69 Score=24.82 Aligned_cols=24 Identities=21% Similarity=0.416 Sum_probs=18.5
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKT 184 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~ 184 (220)
+..++.+ +++ |||+...|+..|..
T Consensus 71 l~~~l~~-~vl-VgHn~~fD~~~L~~ 94 (152)
T cd06144 71 VAELLKG-RIL-VGHALKNDLKVLKL 94 (152)
T ss_pred HHHHhCC-CEE-EEcCcHHHHHHhcC
Confidence 4455665 565 99999999999974
No 52
>PF04857 CAF1: CAF1 family ribonuclease; InterPro: IPR006941 CAF1 is an RNase of the DEDD superfamily, and a subunit of the Ccr4-Not complex that mediates 3' to 5' mRNA deadenylation. The major pathways of mRNA turnover in eukaryotes initiate with shortening of the poly(A) tail. CAF1 P39008 from SWISSPROT encodes a critical component of the major cytoplasmic deadenylase in yeast. Caf1p is required for normal mRNA deadenylation in vivo and localises to the cytoplasm. Caf1p copurifies with a Ccr4p-dependent poly(A)-specific exonuclease activity. Some members of this family contain a single-stranded nucleic acid binding domain, R3H.; GO: 0005634 nucleus; PDB: 3D45_B 1UG8_A 2D5R_A 2A1S_C 2A1R_A 2FC6_A 1UOC_A 3G10_A 2P51_A 3G0Z_A.
Probab=52.22 E-value=24 Score=30.27 Aligned_cols=118 Identities=14% Similarity=0.107 Sum_probs=65.4
Q ss_pred HHHHHHHHHHHhccCCCCeEEEeeeeccCCCCCC-----------------CCCceEEEeEe--C----C------eEEE
Q psy12566 89 ADKFASALQDFARLDHNSHLGLDTEWKPNLSGGS-----------------PPTLALLQIAT--R----D------RVYI 139 (220)
Q Consensus 89 ~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~~~~-----------------~~~vaLlQiat--~----~------~v~L 139 (220)
++.+..+.+. +.++..|+||+|+.....+.. -.+..+||++. - + .++-
T Consensus 9 ~~~l~~i~~~---i~~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~~~~~~~~~~~~~ 85 (262)
T PF04857_consen 9 EEELPEILQA---ISKADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLFHDEDGNIPSSYNVWP 85 (262)
T ss_dssp HHHHHHHHHH---HHHSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEETTTTSEEECCEEEEE
T ss_pred HHHHHHHHHH---HhhCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEeecccccCCceeEEEE
Confidence 4566777777 889999999999976543211 25789999963 1 1 1334
Q ss_pred EEccCCC--C-CC---------------------c--hhhhh-------HHHHHhccc---CCCeEEEEEcchhhHHHHH
Q psy12566 140 LDIITLS--K-LP---------------------C--YAQLC-------HDLELIVFA---NDDLLKIGFNLMPDVSIIK 183 (220)
Q Consensus 140 iD~~~l~--~-~~---------------------~--~~~~~-------~~~l~~ll~---~~~IlKvG~~~~~Dl~~L~ 183 (220)
+.....+ . .. + +-..- ...++.++. +.++.-|||++--|+-.|.
T Consensus 86 ~nf~~f~~~~~~~~~~sl~FL~~~gfDFn~~~~~GI~y~~~~ee~~~~~~~g~~~v~~~~~~~~~p~Vghn~~~Dl~~l~ 165 (262)
T PF04857_consen 86 FNFYLFPLDRDFSQASSLQFLRKNGFDFNKWFRDGIPYLSFAEEEKARELLGFSGVIDALKSSKKPIVGHNGLYDLMYLY 165 (262)
T ss_dssp EEBSTTSTTTCEEEHHHHHHHHHTT--HHHHHHH-B-HHHHHHHHHHHHHHHTCCCSSHCHCC-SEEEESSTHHHHHHHH
T ss_pred eeeeccccccceecchhHHHHHHcccCHHHHHHhCCCcccccccchhhhhHHHHHHHHHhhccCCcEEEeChHhHHHHHH
Confidence 3333221 0 00 0 00000 012244454 3347889999999999988
Q ss_pred hhCCC-Cc----ccc----CCcCceeeHHHHHHHh
Q psy12566 184 TSLPF-SE----CSS----YNKTSYLDLQLLWSKL 209 (220)
Q Consensus 184 ~~~~~-~~----~~~----~~~~~~~DL~~l~~~l 209 (220)
+.+-. +. .|. .....++|+..+++..
T Consensus 166 ~~f~~~LP~t~~eF~~~~~~~FP~i~DtK~la~~~ 200 (262)
T PF04857_consen 166 KKFIGPLPETLEEFKELLRELFPRIYDTKYLAEEC 200 (262)
T ss_dssp HHHTTS--SSHHHHHHHHHHHSSSEEEHHHHHTST
T ss_pred HHhcCCCCCCHHHHHHHHHHHCcccccHHHHHHhc
Confidence 77544 21 111 1124588988887754
No 53
>cd05783 DNA_polB_B1_exo DEDDy 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal family-B DNA polymerases. The 3'-5' exonuclease domain of Sulfolobus solfataricus DNA polymerase B1 and similar archaeal proteins. B1 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. B1displays thermostable 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. Family-B DNA polymerases from thermophilic archaea are uniq
Probab=48.55 E-value=1.5e+02 Score=24.38 Aligned_cols=82 Identities=13% Similarity=0.141 Sum_probs=45.6
Q ss_pred CCCeEEEeeeeccC----CCCCCCCCceEEEeEeCC-----eEEEEEccCCC-------------CCCchhhhhHHHHHh
Q psy12566 104 HNSHLGLDTEWKPN----LSGGSPPTLALLQIATRD-----RVYILDIITLS-------------KLPCYAQLCHDLELI 161 (220)
Q Consensus 104 ~~~~VG~D~Ew~p~----~~~~~~~~vaLlQiat~~-----~v~LiD~~~l~-------------~~~~~~~~~~~~l~~ 161 (220)
+-++++||.|-... |.......--++|||..+ +++++...... ....-.+++..|+..
T Consensus 4 ~lrilsfDIE~~~~~~~~fP~~~~~~d~IisI~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~v~~~~~E~~lL~~F~~~ 83 (204)
T cd05783 4 KLKRIAIDIEVYTPIKGRIPDPKTAEYPVISVALAGSDGLKRVLVLKREGVEGLEGLLPEGAEVEFFDSEKELIREAFKI 83 (204)
T ss_pred CceEEEEEEEECCCCCCCCcCCCCCCCeEEEEEEcCCCCCcEEEEEecCCcccccccCCCCCeEEecCCHHHHHHHHHHH
Confidence 34689999999642 211122224689999743 47777531100 001112445555544
Q ss_pred cccCCCeEEEEEcch-hhHHHHHhhCC
Q psy12566 162 VFANDDLLKIGFNLM-PDVSIIKTSLP 187 (220)
Q Consensus 162 ll~~~~IlKvG~~~~-~Dl~~L~~~~~ 187 (220)
+.+..+ -+||+.. -|+..|.....
T Consensus 84 -i~~~~~-iig~N~~~FDlpyl~~R~~ 108 (204)
T cd05783 84 -ISEYPI-VLTFNGDNFDLPYLYNRAL 108 (204)
T ss_pred -HhcCCE-EEEeCCCCcCHHHHHHHHH
Confidence 444454 4799876 59998875543
No 54
>smart00667 LisH Lissencephaly type-1-like homology motif. Alpha-helical motif present in Lis1, treacle, Nopp140, some katanin p60 subunits, muskelin, tonneau, LEUNIG and numerous WD40 repeat-containing proteins. It is suggested that LisH motifs contribute to the regulation of microtubule dynamics, either by mediating dimerisation, or else by binding cytoplasmic dynein heavy chain or microtubules directly.
Probab=47.38 E-value=47 Score=18.11 Aligned_cols=31 Identities=13% Similarity=0.081 Sum_probs=25.5
Q ss_pred ChHHHHHHHHHHHhcCCHHHHHHHHHHcCCC
Q psy12566 9 NPELQKELIDLCVQYYDCKEAYYWCQKFKLN 39 (220)
Q Consensus 9 d~~Lq~~lv~~l~~~~d~~~A~~wa~~~~l~ 39 (220)
...|.+-++++|.+.|-...|.......+++
T Consensus 3 ~~~l~~lI~~yL~~~g~~~ta~~l~~e~~~~ 33 (34)
T smart00667 3 RSELNRLILEYLLRNGYEETAETLQKESGLS 33 (34)
T ss_pred HHHHHHHHHHHHHHcCHHHHHHHHHHHhCCC
Confidence 4568888999999998888888888877765
No 55
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=47.13 E-value=10 Score=25.02 Aligned_cols=23 Identities=17% Similarity=0.525 Sum_probs=18.6
Q ss_pred HhcCCHHHHHHHHHHcCCCCCCC
Q psy12566 21 VQYYDCKEAYYWCQKFKLNPNCV 43 (220)
Q Consensus 21 ~~~~d~~~A~~wa~~~~l~~~~l 43 (220)
++.++.-+-.+||++||+++++|
T Consensus 15 I~~~e~~ev~ywa~~~gvt~~~L 37 (57)
T PF12244_consen 15 IDLSEPYEVRYWAKRFGVTEEQL 37 (57)
T ss_pred cCCCCHHHHHHHHHHHCcCHHHH
Confidence 34578889999999999995554
No 56
>PF03909 BSD: BSD domain ; InterPro: IPR005607 The BSD domain is an about 60-residue long domain named after the BTF2-like transcription factors, Synapse-associated proteins and DOS2-like proteins in which it is found. Additionally, it is also found in several hypothetical proteins. The BSD domain occurs in one or two copies in a variety of species ranging from primal protozoan to human. It can be found associated with other domains such as the BTB domain (see PDOC50097 from PROSITEDOC) or the U-box in multidomain proteins. The function of the BSD domain is yet unknown []. Secondary structure prediction indicates the presence of three predicted alpha helices, which probably form a three-helical bundle in small domains. The third predicted helix contains neighbouring phenylalanine and tryptophan residues - less common amino acids that are invariant in all the BSD domains identified and that are the most striking sequence features of the domain []. Some proteins known to contain one or two BSD domains are listed below: Mammalian TFIIH basal transcription factor complex p62 subunit (GTF2H1). Yeast RNA polymerase II transcription factor B 73 kDa subunit (TFB1), the homologue of BTF2. Yeast DOS2 protein. It is involved in single-copy DNA replication and ubiquitination. Drosophila synapse-associated protein SAP47. Mammalian SYAP1. Various Arabidopsis thaliana (Mouse-ear cress) hypothetical proteins.; PDB: 1X3A_A 1PFJ_A 2RNR_B 2DII_A.
Probab=44.66 E-value=12 Score=24.77 Aligned_cols=35 Identities=20% Similarity=0.390 Sum_probs=24.4
Q ss_pred hhhhhcCChHHHHHHHHHHHhcCCHHHHHHHHHHcCC
Q psy12566 2 ALDIVKDNPELQKELIDLCVQYYDCKEAYYWCQKFKL 38 (220)
Q Consensus 2 v~~~v~~d~~Lq~~lv~~l~~~~d~~~A~~wa~~~~l 38 (220)
+..++..||.|+.-.-+++ -+...+..+|+++|..
T Consensus 17 i~~lL~~~p~l~~~~~~lV--P~~~~e~~FW~rYf~~ 51 (62)
T PF03909_consen 17 IKKLLEEDPNLRKLYNELV--PSKMSEEEFWKRYFYR 51 (62)
T ss_dssp HHHHHHH-HHHHHHHHHCC--TTTS-HHHHHHHHHCH
T ss_pred HHHHHHhCHHHHHHHHHhC--CCCCCHHHHHHHHHHH
Confidence 3556778888887666655 3678899999998863
No 57
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=43.45 E-value=3.2e+02 Score=28.04 Aligned_cols=98 Identities=14% Similarity=0.154 Sum_probs=56.2
Q ss_pred CCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccCCCCCC-------c-----------hhhhhHH
Q psy12566 105 NSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIITLSKLP-------C-----------YAQLCHD 157 (220)
Q Consensus 105 ~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~l~~~~-------~-----------~~~~~~~ 157 (220)
..+|.||+|..... ....-.+|||+. .+++ .++++. ..+| + ..+.+..
T Consensus 3 ~~~vvvD~ETTG~~---p~~~d~IIeigav~v~~~~i~~~f~~~v~P~--~~i~~~~~~ltGIt~~~l~~ap~f~ev~~~ 77 (928)
T PRK08074 3 KRFVVVDLETTGNS---PKKGDKIIQIAAVVVEDGEILERFSSFVNPE--RPIPPFITELTGISEEMVKQAPLFEDVAPE 77 (928)
T ss_pred CCEEEEEEeCCCCC---CCCCCcEEEEEEEEEECCEEEEEEEEEECcC--CCCCHHHhhcCCCCHHHHhcCCCHHHHHHH
Confidence 46899999986421 112257999985 3333 233332 1222 0 1122222
Q ss_pred HHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 158 LELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 158 ~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+..++.+ .+-|||++.-|...|.+.+...+ .......++|+..+++.+-+
T Consensus 78 -l~~~l~~--~~~VaHN~~FD~~fL~~~~~~~g-~~~~~~~~iDt~~la~~~~p 127 (928)
T PRK08074 78 -IVELLEG--AYFVAHNVHFDLNFLNEELERAG-YTEIHCPKLDTVELARILLP 127 (928)
T ss_pred -HHHHhCC--CeEEEEChHHHHHHHHHHHHHcC-CCCCCCCeeeHHHHHHHhcC
Confidence 4455554 34599999999999987643211 11134578999998876543
No 58
>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=40.95 E-value=1.6e+02 Score=23.03 Aligned_cols=30 Identities=13% Similarity=0.202 Sum_probs=20.3
Q ss_pred hhHHHHHhcccCCCeEEEEEcchhhHHHHHhhC
Q psy12566 154 LCHDLELIVFANDDLLKIGFNLMPDVSIIKTSL 186 (220)
Q Consensus 154 ~~~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~ 186 (220)
.+.. +..++.+ . +-|||+...|+..|...+
T Consensus 67 v~~~-l~~~l~~-~-vlV~Hn~~~D~~~l~~~~ 96 (157)
T cd06149 67 AQKE-ILKILKG-K-VVVGHAIHNDFKALKYFH 96 (157)
T ss_pred HHHH-HHHHcCC-C-EEEEeCcHHHHHHhcccC
Confidence 3344 3455543 3 459999999999998653
No 59
>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=40.86 E-value=1.9e+02 Score=29.24 Aligned_cols=96 Identities=11% Similarity=0.095 Sum_probs=55.7
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccCCCCCC-------c-----------hhhhhHHH
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIITLSKLP-------C-----------YAQLCHDL 158 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~l~~~~-------~-----------~~~~~~~~ 158 (220)
.+|.+|+|.... ...+-.+||||. .+++ .++++.. .+| + ..+.+..
T Consensus 1 ~~vvvD~ETTG~----~~~~~~IIeig~v~v~~~~i~~~f~~~v~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~~~- 73 (850)
T TIGR01407 1 RYAVVDLETTGT----QLSFDKIIQIGIVVVEDGEIVDTFHTDVNPNE--PIPPFIQELTGISDNMLQQAPYFSQVAQE- 73 (850)
T ss_pred CEEEEEEECCCC----CCCCCeEEEEEEEEEECCEEEEEEEEEeCCCC--CCChhhhhhcCcCHHHHhCCCCHHHHHHH-
Confidence 378999999753 234577899874 2332 3444321 121 0 1112222
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
+..++.+ .+ -|||++.-|...|.+.+...+ .......++|+..+++.+-+
T Consensus 74 l~~~l~~-~~-~VahN~~fD~~fL~~~~~~~g-~~~~~~~~iDt~~l~~~~~p 123 (850)
T TIGR01407 74 IYDLLED-GI-FVAHNVHFDLNFLAKALKDCG-YEPLPKPRIDTVELAQIFFP 123 (850)
T ss_pred HHHHhCC-CE-EEEeCcHHHHHHHHHHHHHcC-CCCCCCCeEeHHHHHHHhcC
Confidence 3455554 34 599999999999987653211 11135678999888876643
No 60
>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=39.11 E-value=32 Score=26.81 Aligned_cols=40 Identities=20% Similarity=0.356 Sum_probs=26.7
Q ss_pred HHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHh
Q psy12566 159 ELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKL 209 (220)
Q Consensus 159 l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l 209 (220)
+..++.... +-|||+...|+..|... ...++|+..+++.+
T Consensus 69 ~~~fl~~~~-vlVgHn~~fD~~fL~~~----------~~~~iDT~~l~r~~ 108 (150)
T cd06145 69 LLSLISPDT-ILVGHSLENDLKALKLI----------HPRVIDTAILFPHP 108 (150)
T ss_pred HHHHhCCCC-EEEEcChHHHHHHhhcc----------CCCEEEcHHhcccc
Confidence 345554333 45999999999999642 13478888776653
No 61
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=37.62 E-value=2.8e+02 Score=24.29 Aligned_cols=96 Identities=15% Similarity=0.212 Sum_probs=54.3
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEe----CCe-----EEEEEccC--CC-------CCC--------chhhhhHHHH
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIAT----RDR-----VYILDIIT--LS-------KLP--------CYAQLCHDLE 159 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~-----v~LiD~~~--l~-------~~~--------~~~~~~~~~l 159 (220)
.+|.||+|... ..+=.++||+. .+. -.++++.. +. .+. ...+.+..+
T Consensus 2 ~~vviD~ETTg------~~~d~IieIgav~v~~g~i~~~f~~lv~P~~~~~~~~~~~IhGIT~e~v~~ap~f~ev~~~~- 74 (309)
T PRK06195 2 NFVAIDFETAN------EKRNSPCSIGIVVVKDGEIVEKVHYLIKPKEMRFMPINIGIHGIRPHMVEDELEFDKIWEKI- 74 (309)
T ss_pred cEEEEEEeCCC------CCCCceEEEEEEEEECCEEEEEEEEEECCCCCCCChhheeccCcCHHHHhCCCCHHHHHHHH-
Confidence 47999999862 12345788863 233 24666532 11 111 012234433
Q ss_pred HhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 160 LIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 160 ~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
...+.+ . +-|||+..-|+..|.+.+...+. ......++|+..+++.+.+
T Consensus 75 ~~fl~~-~-~lVaHNa~FD~~fL~~~~~r~~~-~~~~~~~idT~~lar~l~~ 123 (309)
T PRK06195 75 KHYFNN-N-LVIAHNASFDISVLRKTLELYNI-PMPSFEYICTMKLAKNFYS 123 (309)
T ss_pred HHHhCC-C-EEEEECcHHHHHHHHHHHHHhCC-CCCCCCEEEHHHHHHHHcC
Confidence 344443 3 45899999999999876532111 0123468999988887654
No 62
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=36.83 E-value=3.4e+02 Score=24.97 Aligned_cols=102 Identities=12% Similarity=0.019 Sum_probs=59.2
Q ss_pred cCCCCeEEEeeeeccCCCCCCCCCceEEEeEe-----CC-----eEEEEEccC------CCCCC--------chhhhhHH
Q psy12566 102 LDHNSHLGLDTEWKPNLSGGSPPTLALLQIAT-----RD-----RVYILDIIT------LSKLP--------CYAQLCHD 157 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat-----~~-----~v~LiD~~~------l~~~~--------~~~~~~~~ 157 (220)
+....+|.||+|...- ....-.+|+|+. .+ ...||+... +..+. ...+.+..
T Consensus 43 ~~~~~fVvlDiETTGL----dp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~e 118 (377)
T PRK05601 43 IEAAPFVAVSIQTSGI----HPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKP 118 (377)
T ss_pred CCCCCEEEEEEECCCC----CCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHH
Confidence 6778999999999753 234457888752 12 233444322 11111 11233443
Q ss_pred HHHhcccCCCeEEEEEcchhhHHHHHhhCCCC---------------------------ccccCCcCceeeHHHHHHHhh
Q psy12566 158 LELIVFANDDLLKIGFNLMPDVSIIKTSLPFS---------------------------ECSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 158 ~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~---------------------------~~~~~~~~~~~DL~~l~~~l~ 210 (220)
|..++.+. +-|||+..-|+..|.+.+.-. ... ..+..++|+-.++|.+.
T Consensus 119 -l~~fL~g~--vLVaHNA~FD~~FL~~e~~r~~~~a~~~n~~~~r~~~~~~~~~rr~~~g~~-p~p~~~iDTL~LARrl~ 194 (377)
T PRK05601 119 -LDRLIDGR--TLILHNAPRTWGFIVSEAKRAMNAAARANRNRNRGNRRGGRGRRRQRVGHI-PKPVVIVDTLATARRQG 194 (377)
T ss_pred -HHHHhCCC--EEEEECcHHHHHHHHHHHHHhhhhhhhcccccccccccccccccccccCCC-CCCCCEEEhHHHHHHHc
Confidence 44566544 358999999999988754210 011 23456899999888765
Q ss_pred h
Q psy12566 211 A 211 (220)
Q Consensus 211 ~ 211 (220)
.
T Consensus 195 p 195 (377)
T PRK05601 195 V 195 (377)
T ss_pred C
Confidence 4
No 63
>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=36.76 E-value=2e+02 Score=30.57 Aligned_cols=98 Identities=14% Similarity=0.176 Sum_probs=58.9
Q ss_pred CCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccCCCCCC------------------chhhhh
Q psy12566 103 DHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIITLSKLP------------------CYAQLC 155 (220)
Q Consensus 103 ~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~l~~~~------------------~~~~~~ 155 (220)
....+|.||+|...- ....-.+||||. .+.+ .++.+. ..+| ...+.+
T Consensus 188 ~~~~~VVfDiETTGL----~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~--~~I~~~~~~ltGIT~e~L~~ap~~~evl 261 (1213)
T TIGR01405 188 DDATYVVFDIETTGL----SPQYDEIIEFGAVKVKNGRIIDKFQFFIKPH--EPLSAFVTELTGITQDMLENAPEIEEVL 261 (1213)
T ss_pred cCCcEEEEEeEecCC----CCCCCeEEEEEEEEEECCeEEEEEEEEECCC--CCCCHHHHHHhCCCHHHHhCCCCHHHHH
Confidence 778999999999752 234568888874 2322 122221 0111 012334
Q ss_pred HHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhh
Q psy12566 156 HDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLV 210 (220)
Q Consensus 156 ~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~ 210 (220)
..| ..++.+ . +-|||+..-|+..|++.+.-.+. ......++|+..+++.+.
T Consensus 262 ~~f-~~fl~~-~-iLVaHNa~FD~~fL~~~~~r~g~-~~~~~~~IDTl~lar~l~ 312 (1213)
T TIGR01405 262 EKF-KEFFKD-S-ILVAHNASFDIGFLNTNFEKVGL-EPLENPVIDTLELARALN 312 (1213)
T ss_pred HHH-HHHhCC-C-eEEEEChHHHHHHHHHHHHHcCC-CccCCCEeEHHHHHHHHh
Confidence 443 344544 3 44899999999999876543211 113467999999988765
No 64
>cd05777 DNA_polB_delta_exo DEDDy 3'-5' exonuclease domain of eukaryotic DNA polymerase delta, a family-B DNA polymerase. The 3'-5' exonuclease domain of eukaryotic DNA polymerase delta. DNA polymerase delta is a family-B DNA polymerase with a catalytic subunit that contains a DEDDy-type DnaQ-like 3'-5' exonuclease domain. It is one of the three DNA-dependent type B DNA polymerases (alpha and epsilon are the other two) that have been identified as essential for nuclear DNA replication in eukaryotes. DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand. It is also implicated in mismatch repair (MMR) and base excision repair (BER). The catalytic subunit displays both polymerase and 3'-5' exonuclease activities. The 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 contain four conserved acidic
Probab=36.44 E-value=1.4e+02 Score=24.91 Aligned_cols=84 Identities=17% Similarity=0.236 Sum_probs=45.5
Q ss_pred cCCCCeEEEeeeeccCCCC-CCCCCceEEEeEeC----C-------eEEEEE-ccCCCC-----CCchhhhhHHHHHhcc
Q psy12566 102 LDHNSHLGLDTEWKPNLSG-GSPPTLALLQIATR----D-------RVYILD-IITLSK-----LPCYAQLCHDLELIVF 163 (220)
Q Consensus 102 l~~~~~VG~D~Ew~p~~~~-~~~~~vaLlQiat~----~-------~v~LiD-~~~l~~-----~~~~~~~~~~~l~~ll 163 (220)
..+-++++||.|-.+...+ ....+=.++|||.. + .++.+. .....+ .+.-.+++..|+..+-
T Consensus 4 ~p~l~~ls~DIE~~s~~g~fP~p~~D~Ii~Is~~~~~~~~~~~~~~~~~~l~~~~~~~~~~v~~~~~E~eLL~~f~~~i~ 83 (230)
T cd05777 4 IAPLRILSFDIECAGRKGVFPEPEKDPVIQIANVVTRQGEGEPFIRNIFTLKTCAPIVGAQVFSFETEEELLLAWRDFVQ 83 (230)
T ss_pred CCCceEEEEEEEECCCCCCCCCCCCCeEEEEEEEEEeCCCCCCceeEEEEeCCCCCCCCCEEEEECCHHHHHHHHHHHHH
Confidence 3456789999999754211 12233478888732 1 233321 101110 0111234555555444
Q ss_pred c-CCCeEEEEEcchh-hHHHHHhhC
Q psy12566 164 A-NDDLLKIGFNLMP-DVSIIKTSL 186 (220)
Q Consensus 164 ~-~~~IlKvG~~~~~-Dl~~L~~~~ 186 (220)
. ||+|+ +||++.+ |+..|.+..
T Consensus 84 ~~DPDii-~GyN~~~FDl~yL~~R~ 107 (230)
T cd05777 84 EVDPDII-TGYNICNFDLPYLLERA 107 (230)
T ss_pred hcCCCEE-EEecCCCCCHHHHHHHH
Confidence 4 58886 9999876 998887554
No 65
>smart00751 BSD domain in transcription factors and synapse-associated proteins.
Probab=33.01 E-value=40 Score=21.35 Aligned_cols=35 Identities=29% Similarity=0.440 Sum_probs=25.2
Q ss_pred hhhhhcCChHHHHHHHHHHHhcCCHHHHHHHHHHcCC
Q psy12566 2 ALDIVKDNPELQKELIDLCVQYYDCKEAYYWCQKFKL 38 (220)
Q Consensus 2 v~~~v~~d~~Lq~~lv~~l~~~~d~~~A~~wa~~~~l 38 (220)
+...+.++|.|+.-.-+ |+- +...+..+|+++|..
T Consensus 12 i~~il~~~p~l~~~~~~-lVP-~~~se~~FW~ryF~~ 46 (51)
T smart00751 12 IESLLKENPLLKKLYNE-LVP-KVLSEEEFWARYFYL 46 (51)
T ss_pred HHHHHHHCHHHHHHHHH-HCC-CCCCHHHHHHHHHHH
Confidence 34667788888876666 443 568889999998753
No 66
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=32.61 E-value=63 Score=29.94 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=32.3
Q ss_pred CCCcEEEEeCHHHHHHHHHHHhccCCCCeEEEeeeeccCC
Q psy12566 79 PPNSIILVDTADKFASALQDFARLDHNSHLGLDTEWKPNL 118 (220)
Q Consensus 79 ~~~~I~~Vdt~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~ 118 (220)
-.-++++|+++++|+.++.. +....+|-+||..++..
T Consensus 259 m~vp~~vv~~~~el~~ai~~---l~~~d~ILVDTaGrs~~ 295 (407)
T COG1419 259 MGVPLEVVYSPKELAEAIEA---LRDCDVILVDTAGRSQY 295 (407)
T ss_pred hCCceEEecCHHHHHHHHHH---hhcCCEEEEeCCCCCcc
Confidence 35679999999999999999 99999999999998753
No 67
>COG4328 Predicted nuclease (RNAse H fold) [General function prediction only]
Probab=31.83 E-value=61 Score=27.75 Aligned_cols=35 Identities=31% Similarity=0.589 Sum_probs=25.1
Q ss_pred CeEEEeeeeccCCCCCCCCCceEEEeEeCCeEEEEEccCCC
Q psy12566 106 SHLGLDTEWKPNLSGGSPPTLALLQIATRDRVYILDIITLS 146 (220)
Q Consensus 106 ~~VG~D~Ew~p~~~~~~~~~vaLlQiat~~~v~LiD~~~l~ 146 (220)
++||||.-|+. ..+..+-+|++.. .+-|.|.....
T Consensus 2 ~fvGiDlaW~~-----~ppg~~cl~~~dg-~~~i~~~~rr~ 36 (266)
T COG4328 2 KFVGIDLAWAS-----RPPGLCCLQLADG-GLLIGDLARRD 36 (266)
T ss_pred ceEEeeeeccc-----CCCceEEEEEcCC-CceEeechhhh
Confidence 58999999975 4577777787766 56666665543
No 68
>PHA02528 43 DNA polymerase; Provisional
Probab=31.71 E-value=2.3e+02 Score=29.03 Aligned_cols=82 Identities=21% Similarity=0.232 Sum_probs=47.0
Q ss_pred CCCCeEEEeeeeccCCCCCCCCCc---eEEEeEeC----CeEEEEEcc--------------C-CCC-----CCchhhhh
Q psy12566 103 DHNSHLGLDTEWKPNLSGGSPPTL---ALLQIATR----DRVYILDII--------------T-LSK-----LPCYAQLC 155 (220)
Q Consensus 103 ~~~~~VG~D~Ew~p~~~~~~~~~v---aLlQiat~----~~v~LiD~~--------------~-l~~-----~~~~~~~~ 155 (220)
.+-+++.||+|-.+.. +...+.. -|++|+.. ++++++.+. . ... .+.-.+++
T Consensus 104 p~lrv~s~DIE~~~~~-gfP~p~~~~d~IisIsl~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~sE~eLL 182 (881)
T PHA02528 104 SKIRIANLDIEVTAED-GFPDPEEAKYEIDAITHYDSIDDRFYVFDLGSVEEWDAKGDEVPQEILDKVVYMPFDTEREML 182 (881)
T ss_pred CCccEEEEEEEECCCC-CCCCcccCCCcEEEEEEecCCCCEEEEEEecCcccccccCCcccccccCCeeEEEcCCHHHHH
Confidence 4678999999996422 1122222 48888863 354455430 0 000 11112455
Q ss_pred HHHHHhc-ccCCCeEEEEEcchh-hHHHHHhhC
Q psy12566 156 HDLELIV-FANDDLLKIGFNLMP-DVSIIKTSL 186 (220)
Q Consensus 156 ~~~l~~l-l~~~~IlKvG~~~~~-Dl~~L~~~~ 186 (220)
..|+..+ -.||+|+ +||++.+ |+..|.+..
T Consensus 183 ~~F~~~i~~~DPDII-~GyNi~~FDlpYL~~Ra 214 (881)
T PHA02528 183 LEYINFWEENTPVIF-TGWNVELFDVPYIINRI 214 (881)
T ss_pred HHHHHHHHHhCCcEE-EecCCccCCHHHHHHHH
Confidence 6666555 3578887 9999865 998877443
No 69
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=29.88 E-value=62 Score=20.25 Aligned_cols=38 Identities=18% Similarity=0.220 Sum_probs=29.6
Q ss_pred HHHHHHHHHhcCCHHHHHHHHHHcCCCCCCCchhhHHHHhhh
Q psy12566 13 QKELIDLCVQYYDCKEAYYWCQKFKLNPNCVGFDLRDKIAEE 54 (220)
Q Consensus 13 q~~lv~~l~~~~d~~~A~~wa~~~~l~~~~lP~~v~~~~~~~ 54 (220)
|..++.+|...++...+.+.|..+++. ...|...+...
T Consensus 2 ~~~il~~L~~~~~~it~~eLa~~l~vS----~rTi~~~i~~L 39 (55)
T PF08279_consen 2 QKQILKLLLESKEPITAKELAEELGVS----RRTIRRDIKEL 39 (55)
T ss_dssp HHHHHHHHHHTTTSBEHHHHHHHCTS-----HHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHhCCC----HHHHHHHHHHH
Confidence 567899998777778999999999999 66777666654
No 70
>PF13289 SIR2_2: SIR2-like domain
Probab=28.15 E-value=54 Score=24.47 Aligned_cols=33 Identities=18% Similarity=0.284 Sum_probs=24.7
Q ss_pred hhhHHHHHhcccCCCeEEEEEcchh-hHHHHHhh
Q psy12566 153 QLCHDLELIVFANDDLLKIGFNLMP-DVSIIKTS 185 (220)
Q Consensus 153 ~~~~~~l~~ll~~~~IlKvG~~~~~-Dl~~L~~~ 185 (220)
..+...++.++.+..++.|||++.. |++.+.+.
T Consensus 74 ~~~~~~l~~~l~~~~~lfiGys~~D~~i~~~l~~ 107 (143)
T PF13289_consen 74 PWFPNFLRSLLRSKTLLFIGYSFNDPDIRQLLRS 107 (143)
T ss_pred HHHHHHHHHHHcCCCEEEEEECCCCHHHHHHHHH
Confidence 3456678899999999999999864 55555533
No 71
>PF07721 TPR_4: Tetratricopeptide repeat; InterPro: IPR011717 This entry includes tetratricopeptide-like repeats not detected by the IPR001440 from INTERPRO, IPR013105 from INTERPRO and IPR011716 from INTERPRO models. The tetratricopeptide repeat (TPR) motif is a protein-protein interaction module found in multiple copies in a number of functionally different proteins that facilitates specific interactions with a partner protein(s) [].; GO: 0042802 identical protein binding
Probab=27.28 E-value=1.1e+02 Score=16.20 Aligned_cols=24 Identities=17% Similarity=-0.031 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHhcCCHHHHHHHHH
Q psy12566 11 ELQKELIDLCVQYYDCKEAYYWCQ 34 (220)
Q Consensus 11 ~Lq~~lv~~l~~~~d~~~A~~wa~ 34 (220)
+.+..+-..+...||..+|..+.+
T Consensus 2 ~a~~~la~~~~~~G~~~eA~~~l~ 25 (26)
T PF07721_consen 2 RARLALARALLAQGDPDEAERLLR 25 (26)
T ss_pred HHHHHHHHHHHHcCCHHHHHHHHh
Confidence 345556677788899999998764
No 72
>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=25.58 E-value=1.5e+02 Score=23.87 Aligned_cols=44 Identities=14% Similarity=0.190 Sum_probs=29.5
Q ss_pred eEEEEEcchhhHHHHHhhCCCCcc--ccCCcCceeeHHHHHHHhhh
Q psy12566 168 LLKIGFNLMPDVSIIKTSLPFSEC--SSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 168 IlKvG~~~~~Dl~~L~~~~~~~~~--~~~~~~~~~DL~~l~~~l~~ 211 (220)
-+-|||+..-|+..|.+.+.-.+. .......++|+..+++.+.+
T Consensus 103 ~~lVaHna~FD~~fL~~~~~~~~~~~~~~~~~~~lDt~~la~~~~~ 148 (189)
T cd06134 103 AILVGHNAHFDLGFLNAAVARCKIKRNPFHPFSTFDTATLAGLAYG 148 (189)
T ss_pred CeEEEecchhhHHHHHHHHHHhCCCCCCCCCCcEEEHHHHHHHHhC
Confidence 356999999999999876532211 00134468999999876543
No 73
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=25.40 E-value=26 Score=28.49 Aligned_cols=59 Identities=15% Similarity=0.082 Sum_probs=41.3
Q ss_pred HHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhhccCccCCC
Q psy12566 158 LELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVAETTLQLPY 219 (220)
Q Consensus 158 ~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~~~~~~~p~ 219 (220)
|++.-.-...-.-.|-++.+|-+.|.+..|-+... ---..+|++.+ |++..||.=++++
T Consensus 92 flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le~y--fHYR~lDVSTl-KELa~RW~P~i~~ 150 (184)
T COG1949 92 FLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLEAY--FHYRYLDVSTL-KELARRWNPEILA 150 (184)
T ss_pred HHHHhCCCCCCCCccchhhHHHHHHHHHhhhHHHH--hhhHhhhHHHH-HHHHHhhCcHhhh
Confidence 44444333333346999999999999999986543 34568999998 7888888765543
No 74
>KOG0304|consensus
Probab=23.56 E-value=63 Score=27.50 Aligned_cols=118 Identities=11% Similarity=0.059 Sum_probs=66.9
Q ss_pred HHHHHHHHHHHhccCCCCeEEEeeeeccCCC-----------------CCCCCCceEEEeEe---C---------CeEEE
Q psy12566 89 ADKFASALQDFARLDHNSHLGLDTEWKPNLS-----------------GGSPPTLALLQIAT---R---------DRVYI 139 (220)
Q Consensus 89 ~~~l~~~~~~l~~l~~~~~VG~D~Ew~p~~~-----------------~~~~~~vaLlQiat---~---------~~v~L 139 (220)
.++++.+.+. ++..++|++|||+..... +..-..+.|||+.. . ..++=
T Consensus 11 ~~Em~~Ir~~---v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~Gn~p~~g~~tWq 87 (239)
T KOG0304|consen 11 EEEMALIREC---VKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEKGNLPDCGTDTWQ 87 (239)
T ss_pred HHHHHHHHHH---HHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccCCCCCCCCCceeE
Confidence 3566666677 899999999999954321 11235678899863 1 12555
Q ss_pred EEccCCC---CCC--------------------ch--hhhhHHHH--HhcccCCCeEEEEEcchhhHHHHHhhCCC--Cc
Q psy12566 140 LDIITLS---KLP--------------------CY--AQLCHDLE--LIVFANDDLLKIGFNLMPDVSIIKTSLPF--SE 190 (220)
Q Consensus 140 iD~~~l~---~~~--------------------~~--~~~~~~~l--~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~--~~ 190 (220)
|.....+ +.- .| ...|.+.+ .-+..+++|..|-|-..-|.-.|.+-+.. +.
T Consensus 88 fNF~dF~~~~D~~a~~SIElLr~~Gidf~K~~e~GI~~~~F~ellm~sg~v~~~~V~WvTFhs~YDfgYLlK~Lt~~~LP 167 (239)
T KOG0304|consen 88 FNFSDFNLEKDMYAQDSIELLRRSGIDFEKHREEGIDIEEFAELLMTSGLVLDENVTWVTFHSGYDFGYLLKILTGKPLP 167 (239)
T ss_pred EecccCCchhhccchhhHHHHHHcCcCHHHHHHcCCCHHHHHHHHHHhhhhccCceEEEEeeccchHHHHHHHHcCCCCc
Confidence 5544221 000 00 01111111 12334679999999999999888765443 11
Q ss_pred ----cc----cCCcCceeeHHHHHHHh
Q psy12566 191 ----CS----SYNKTSYLDLQLLWSKL 209 (220)
Q Consensus 191 ----~~----~~~~~~~~DL~~l~~~l 209 (220)
.| ..-...+.|+..+++-.
T Consensus 168 ~~~~eF~~~v~~~fp~vYDiK~l~~~c 194 (239)
T KOG0304|consen 168 ETEEEFFEIVRQLFPFVYDVKYLMKFC 194 (239)
T ss_pred chHHHHHHHHHHHcchhhhHHHHHHhh
Confidence 01 01235677888777654
No 75
>PF01724 DUF29: Domain of unknown function DUF29; InterPro: IPR002636 This entry is represented by Ralstonia phage RSS1, Orf11. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of various hypothetical proteins from cyanobacteria, none of which are functionally described. The aligned region is approximately 120-140 amino acids long corresponding to almost the entire length of the proteins in the family.; PDB: 3FCN_A.
Probab=23.32 E-value=51 Score=25.69 Aligned_cols=49 Identities=16% Similarity=0.264 Sum_probs=24.4
Q ss_pred hhhhhcCChHHHHHHHHHHHhcCCHHHHHHHH-HHcCCCC----CCCchhhHHHHh
Q psy12566 2 ALDIVKDNPELQKELIDLCVQYYDCKEAYYWC-QKFKLNP----NCVGFDLRDKIA 52 (220)
Q Consensus 2 v~~~v~~d~~Lq~~lv~~l~~~~d~~~A~~wa-~~~~l~~----~~lP~~v~~~~~ 52 (220)
++..+.++|+|+..+-+.+.. ....|...| +..+++. ..+|+++.+.+.
T Consensus 81 i~~~l~~sPSLk~~l~~~l~~--~Y~~A~~~a~~et~l~~~~fP~~CPysleqiLd 134 (139)
T PF01724_consen 81 IEDLLEDSPSLKNYLEEILEE--AYQDARKLAARETGLPLETFPEECPYSLEQILD 134 (139)
T ss_dssp HHHH----GGGGGG--HHHHH--HHHHH-HHHHHHTT---TT--SS-SS-HHHHHS
T ss_pred HHHHhcccccHHHHHHHHHHH--HHHHHHHHHHHHhCCCcccCcccCCCCHHHHhh
Confidence 456788899999988888775 244454444 5678874 567888765553
No 76
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=23.16 E-value=2e+02 Score=19.22 Aligned_cols=42 Identities=10% Similarity=0.140 Sum_probs=33.7
Q ss_pred ChHHHHHHHHHHHhcCC-HHHHHHHHHHcCCCCCCCchhhHHHHhhh
Q psy12566 9 NPELQKELIDLCVQYYD-CKEAYYWCQKFKLNPNCVGFDLRDKIAEE 54 (220)
Q Consensus 9 d~~Lq~~lv~~l~~~~d-~~~A~~wa~~~~l~~~~lP~~v~~~~~~~ 54 (220)
.....+.++++|...|. ...|...|+.+|++ +..+...+...
T Consensus 4 ~~~~~~~IL~~L~~~g~~~~ta~eLa~~lgl~----~~~v~r~L~~L 46 (68)
T smart00550 4 QDSLEEKILEFLENSGDETSTALQLAKNLGLP----KKEVNRVLYSL 46 (68)
T ss_pred chHHHHHHHHHHHHCCCCCcCHHHHHHHHCCC----HHHHHHHHHHH
Confidence 45678899999999877 48899999999999 44677666655
No 77
>PF02641 DUF190: Uncharacterized ACR, COG1993; InterPro: IPR003793 This is an uncharacterised domain found in proteins of unknown function.; PDB: 2DCL_C 1O51_A.
Probab=22.75 E-value=1.5e+02 Score=21.57 Aligned_cols=31 Identities=23% Similarity=0.353 Sum_probs=18.5
Q ss_pred ccccccccc-CCCcEEEEeCHHHHHHHHHHHh
Q psy12566 70 AEEYYSLTL-PPNSIILVDTADKFASALQDFA 100 (220)
Q Consensus 70 ~~~y~~l~l-~~~~I~~Vdt~~~l~~~~~~l~ 100 (220)
+..++.+.. .+--|.+||+++.+++++..+.
T Consensus 54 ~~~~~~l~~~lPvvIe~id~~eki~~~l~~l~ 85 (101)
T PF02641_consen 54 SARLLELSDDLPVVIEFIDTEEKIEAFLPELK 85 (101)
T ss_dssp -------TTS-EEEEEEEEEHHHHHHHHHHHC
T ss_pred ccchhhhcCCCCEEEEEEcCHHHHHHHHHHHH
Confidence 345555432 1336889999999999999965
No 78
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=20.44 E-value=9.1e+02 Score=24.51 Aligned_cols=97 Identities=12% Similarity=0.111 Sum_probs=55.8
Q ss_pred CCCCeEEEeeeeccCCCCCCCCCceEEEeEe----CCeE-----EEEEccCCCCCC-------c-----------hhhhh
Q psy12566 103 DHNSHLGLDTEWKPNLSGGSPPTLALLQIAT----RDRV-----YILDIITLSKLP-------C-----------YAQLC 155 (220)
Q Consensus 103 ~~~~~VG~D~Ew~p~~~~~~~~~vaLlQiat----~~~v-----~LiD~~~l~~~~-------~-----------~~~~~ 155 (220)
....+|.||+|.... .++-.+|||+. .+++ .++++.. .+| + ..+.+
T Consensus 5 ~~~~~vvvD~ETTGl-----~~~d~IIeIgaV~v~~g~i~~~f~~lv~P~~--~i~~~~~~ltGIt~e~l~~ap~~~ev~ 77 (820)
T PRK07246 5 KLRKYAVVDLEATGA-----GPNASIIQVGIVIIEGGEIIDSYTTDVNPHE--PLDEHIKHLTGITDQQLAQAPDFSQVA 77 (820)
T ss_pred cCCCEEEEEEecCCc-----CCCCeEEEEEEEEEECCEEEEEEEEEeCcCC--CCCHhHhhcCCCCHHHHhcCCCHHHHH
Confidence 456799999999753 22458999974 2332 2233211 122 0 11222
Q ss_pred HHHHHhcccCCCeEEEEEcchhhHHHHHhhCCCCccccCCcCceeeHHHHHHHhhh
Q psy12566 156 HDLELIVFANDDLLKIGFNLMPDVSIIKTSLPFSECSSYNKTSYLDLQLLWSKLVA 211 (220)
Q Consensus 156 ~~~l~~ll~~~~IlKvG~~~~~Dl~~L~~~~~~~~~~~~~~~~~~DL~~l~~~l~~ 211 (220)
.. +..++.+ . +-|||++.-|+..|.+.+... .. ......+|+..+++.+-+
T Consensus 78 ~~-~~~~l~~-~-~lVaHN~~FD~~fL~~~~~~~-g~-~~~~~~iDT~~la~~~~p 128 (820)
T PRK07246 78 RH-IYDLIED-C-IFVAHNVKFDANLLAEALFLE-GY-ELRTPRVDTVELAQVFFP 128 (820)
T ss_pred HH-HHHHhCC-C-EEEEECcHHHHHHHHHHHHHc-CC-CCCCCceeHHHHHHHHhC
Confidence 33 3345554 3 459999999999998754211 11 123567999988876554
Done!