Query psy5654
Match_columns 224
No_of_seqs 137 out of 1104
Neff 5.9
Searched_HMMs 46136
Date Fri Aug 16 23:15:13 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5654.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5654hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10829 ribonuclease D; Provi 99.6 1E-15 2.2E-20 142.3 11.3 104 116-223 3-107 (373)
2 cd06129 RNaseD_like DEDDy 3'-5 99.6 5.9E-15 1.3E-19 121.2 9.8 97 125-223 2-100 (161)
3 TIGR01388 rnd ribonuclease D. 99.6 7.3E-15 1.6E-19 136.1 10.7 102 118-223 1-103 (367)
4 cd06148 Egl_like_exo DEDDy 3'- 99.6 5.9E-15 1.3E-19 125.4 8.8 94 128-223 3-98 (197)
5 PF01612 DNA_pol_A_exo1: 3'-5' 99.6 2.1E-14 4.6E-19 116.4 11.6 105 116-223 1-110 (176)
6 cd06146 mut-7_like_exo DEDDy 3 99.6 2.3E-14 4.9E-19 121.6 10.0 106 116-223 1-121 (193)
7 cd06141 WRN_exo DEDDy 3'-5' ex 99.5 9.8E-14 2.1E-18 113.9 9.9 101 120-223 2-106 (170)
8 COG0349 Rnd Ribonuclease D [Tr 99.4 2.2E-13 4.8E-18 125.5 8.0 101 120-224 2-104 (361)
9 smart00474 35EXOc 3'-5' exonuc 99.2 8.9E-11 1.9E-15 94.2 10.7 104 117-223 2-107 (172)
10 cd06147 Rrp6p_like_exo DEDDy 3 99.2 3E-10 6.5E-15 95.4 11.5 105 116-223 5-110 (192)
11 cd06142 RNaseD_exo DEDDy 3'-5' 99.2 2.3E-10 5.1E-15 93.4 9.9 95 125-223 2-97 (178)
12 PRK05755 DNA polymerase I; Pro 99.0 1.2E-09 2.7E-14 111.2 11.0 137 68-223 264-403 (880)
13 KOG2206|consensus 99.0 2.2E-10 4.7E-15 110.7 2.3 104 116-222 193-297 (687)
14 cd09018 DEDDy_polA_RNaseD_like 98.9 8.6E-09 1.9E-13 81.6 8.3 83 138-223 2-86 (150)
15 cd00007 35EXOc 3'-5' exonuclea 98.8 3.7E-08 8.1E-13 77.4 8.1 83 137-223 2-87 (155)
16 cd06140 DNA_polA_I_Bacillus_li 98.7 3.8E-08 8.3E-13 80.9 7.6 85 135-223 3-89 (178)
17 cd06139 DNA_polA_I_Ecoli_like_ 98.5 3.6E-07 7.9E-12 75.3 7.9 87 134-223 4-100 (193)
18 COG0749 PolA DNA polymerase I 98.4 5.7E-07 1.2E-11 88.1 6.0 101 119-223 6-110 (593)
19 cd06128 DNA_polA_exo DEDDy 3'- 98.2 4.9E-06 1.1E-10 66.8 8.1 69 150-223 17-86 (151)
20 TIGR00593 pola DNA polymerase 98.1 1E-05 2.3E-10 83.0 10.0 100 116-223 304-411 (887)
21 cd06125 DnaQ_like_exo DnaQ-lik 97.3 0.00092 2E-08 50.6 6.8 73 138-222 1-83 (96)
22 KOG2405|consensus 97.2 5.9E-06 1.3E-10 77.1 -7.5 90 132-223 56-145 (458)
23 KOG2207|consensus 97.0 0.00038 8.2E-09 68.2 2.7 91 116-207 392-489 (617)
24 PRK14975 bifunctional 3'-5' ex 96.5 0.0025 5.5E-08 62.3 3.9 76 116-223 3-79 (553)
25 KOG2405|consensus 88.5 0.069 1.5E-06 50.5 -1.9 72 148-223 208-279 (458)
26 PRK06063 DNA polymerase III su 65.8 24 0.00053 32.2 7.1 39 181-221 87-130 (313)
27 cd06127 DEDDh DEDDh 3'-5' exon 62.1 15 0.00033 28.1 4.4 40 180-221 71-115 (159)
28 PRK07942 DNA polymerase III su 61.8 41 0.0009 29.2 7.5 33 190-222 93-131 (232)
29 PRK08517 DNA polymerase III su 57.0 56 0.0012 29.0 7.6 87 132-220 65-182 (257)
30 PRK06310 DNA polymerase III su 56.4 74 0.0016 28.0 8.3 40 181-221 80-126 (250)
31 PRK09146 DNA polymerase III su 56.2 51 0.0011 28.9 7.2 32 191-222 130-166 (239)
32 KOG4373|consensus 55.6 8.7 0.00019 35.6 2.3 68 151-220 147-215 (319)
33 PRK06807 DNA polymerase III su 55.1 59 0.0013 29.8 7.7 38 182-221 82-124 (313)
34 cd06131 DNA_pol_III_epsilon_Ec 52.0 51 0.0011 26.3 6.1 39 181-221 74-120 (167)
35 PRK09145 DNA polymerase III su 50.8 90 0.0019 26.1 7.6 38 181-220 104-146 (202)
36 KOG2249|consensus 49.4 48 0.001 30.2 5.9 119 67-207 56-201 (280)
37 PRK07883 hypothetical protein; 47.9 64 0.0014 31.9 7.1 88 132-221 12-131 (557)
38 cd06149 ISG20 DEDDh 3'-5' exon 45.5 56 0.0012 26.4 5.4 36 181-220 70-105 (157)
39 cd06144 REX4_like DEDDh 3'-5' 42.9 79 0.0017 25.3 5.8 37 181-221 70-106 (152)
40 PRK05601 DNA polymerase III su 42.0 91 0.002 29.7 6.8 74 132-207 43-142 (377)
41 TIGR00573 dnaq exonuclease, DN 40.5 86 0.0019 26.7 6.0 26 181-208 80-105 (217)
42 PRK05711 DNA polymerase III su 37.3 1.4E+02 0.003 26.2 7.0 38 182-221 80-126 (240)
43 TIGR01405 polC_Gram_pos DNA po 36.6 1.3E+02 0.0027 33.0 7.6 88 133-222 188-307 (1213)
44 cd06137 DEDDh_RNase DEDDh 3'-5 30.8 1.7E+02 0.0037 23.6 6.1 36 182-222 77-112 (161)
45 PF11577 NEMO: NF-kappa-B esse 29.7 40 0.00087 24.3 1.9 16 67-82 25-40 (68)
46 TIGR01407 dinG_rel DnaQ family 28.0 2.4E+02 0.0051 29.3 7.8 39 181-221 73-116 (850)
47 PRK07246 bifunctional ATP-depe 26.2 2.4E+02 0.0052 29.3 7.5 39 181-221 79-121 (820)
48 PRK07740 hypothetical protein; 25.7 3.3E+02 0.0072 23.7 7.4 38 182-221 135-177 (244)
49 TIGR01406 dnaQ_proteo DNA poly 24.4 3.1E+02 0.0068 23.6 6.9 40 181-222 75-123 (225)
50 cd06130 DNA_pol_III_epsilon_li 24.2 98 0.0021 24.1 3.4 39 181-221 70-113 (156)
51 PF13482 RNase_H_2: RNase_H su 20.9 1.2E+02 0.0025 24.0 3.3 69 138-209 1-77 (164)
No 1
>PRK10829 ribonuclease D; Provisional
Probab=99.64 E-value=1e-15 Score=142.28 Aligned_cols=104 Identities=23% Similarity=0.236 Sum_probs=95.6
Q ss_pred cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654 116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV 194 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV 194 (224)
|.+|+++++++.+++.+...+++++|+|+... .+++++|++||++. +.+|+||+.+..+. +.|+++|+++.+.||
T Consensus 3 ~~~I~t~~~L~~~~~~l~~~~~lalDtEf~~~~ty~~~l~LiQl~~~-~~~~LiD~l~~~d~---~~L~~ll~~~~ivKV 78 (373)
T PRK10829 3 YQMITTDDALASVCEAARAFPAIALDTEFVRTRTYYPQLGLIQLYDG-EQLSLIDPLGITDW---SPFKALLRDPQVTKF 78 (373)
T ss_pred cEEeCCHHHHHHHHHHHhcCCeEEEecccccCccCCCceeEEEEecC-CceEEEecCCccch---HHHHHHHcCCCeEEE
Confidence 78999999999999999999999999999877 78899999999975 57999999877554 689999999999999
Q ss_pred EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 195 IHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
+|++++|+..|++.+|+.+.++||||+|+
T Consensus 79 ~H~~~~Dl~~l~~~~g~~p~~~fDTqiaa 107 (373)
T PRK10829 79 LHAGSEDLEVFLNAFGELPQPLIDTQILA 107 (373)
T ss_pred EeChHhHHHHHHHHcCCCcCCeeeHHHHH
Confidence 99999999999888999999999999986
No 2
>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=99.59 E-value=5.9e-15 Score=121.21 Aligned_cols=97 Identities=29% Similarity=0.459 Sum_probs=84.9
Q ss_pred HHHHHHHHc-cCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHH
Q psy5654 125 CSSVVEELM-RNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDS 202 (224)
Q Consensus 125 La~lie~L~-~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl 202 (224)
++++++.+. ...++|||+|+.+. .+.++++++||++..+.+|+||+....... ..|+++|+++.+.||+|++|.|+
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~~~~~~~liQl~~~~~~~~l~d~~~~~~~~--~~L~~lL~d~~i~Kvg~~~k~D~ 79 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRRYYGEVALIQLCVSEEKCYLFDPLSLSVDW--QGLKMLLENPSIVKALHGIEGDL 79 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCCCCCceEEEEEEECCCCEEEEecccCccCH--HHHHHHhCCCCEEEEEeccHHHH
Confidence 567788888 89999999999877 566899999999964789999998765333 57899999999999999999999
Q ss_pred HHHHHhcCCccCCccchhhcc
Q psy5654 203 ILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 203 ~lL~~~~GI~L~nvFDTqLAa 223 (224)
..|.+.+|+.+.++|||++|+
T Consensus 80 ~~L~~~~gi~~~~~~D~~~aa 100 (161)
T cd06129 80 WKLLRDFGEKLQRLFDTTIAA 100 (161)
T ss_pred HHHHHHcCCCcccHhHHHHHH
Confidence 999777999999999999975
No 3
>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=99.58 E-value=7.3e-15 Score=136.14 Aligned_cols=102 Identities=26% Similarity=0.315 Sum_probs=90.7
Q ss_pred EecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEE
Q psy5654 118 VITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIH 196 (224)
Q Consensus 118 vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~H 196 (224)
+|++.++++.+++.+..+++++||+|+... .+++++|++|+++. +.+|+||+....+. ..|+++|+++.+.||+|
T Consensus 1 ~I~t~~~l~~~~~~l~~~~~ia~DtE~~~~~~y~~~l~LiQia~~-~~~~liD~~~~~~~---~~L~~lL~d~~i~KV~h 76 (367)
T TIGR01388 1 WITTDDELATVCEAVRTFPFVALDTEFVRERTFWPQLGLIQVADG-EQLALIDPLVIIDW---SPLKELLRDESVVKVLH 76 (367)
T ss_pred CcCCHHHHHHHHHHHhcCCEEEEeccccCCCCCCCcceEEEEeeC-CeEEEEeCCCcccH---HHHHHHHCCCCceEEEe
Confidence 367899999999999999999999999877 78899999999985 57899999876443 68999999999999999
Q ss_pred ecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 197 DCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 197 d~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
++|+|+..|++.+|+.+.++||||+|+
T Consensus 77 ~~k~Dl~~L~~~~~~~~~~~fDtqlAa 103 (367)
T TIGR01388 77 AASEDLEVFLNLFGELPQPLFDTQIAA 103 (367)
T ss_pred ecHHHHHHHHHHhCCCCCCcccHHHHH
Confidence 999999999876777778899999986
No 4
>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=99.58 E-value=5.9e-15 Score=125.39 Aligned_cols=94 Identities=44% Similarity=0.833 Sum_probs=82.3
Q ss_pred HHHHHccCCeEEEEEeeeCCCccceEEEEEEEeeCCeEEEEeCCCCcc--ccccchhHhhhcCCCceEEEEecHHHHHHH
Q psy5654 128 VVEELMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPE--VVGTGGLSKLLESENVIKVIHDCRNDSILL 205 (224)
Q Consensus 128 lie~L~~~~~Ia~D~E~~~l~~~g~L~lIQIat~~g~a~lIDi~al~~--l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL 205 (224)
.++.+..+..+|||+|+...+.+|+++++|+++..+.+|+||+.+++. .. ..|+++|+++.+.||+||+|.|+..|
T Consensus 3 ~~~~l~~~~~i~~D~E~~~~~~~~~~~LiQia~~~~~v~l~D~~~~~~~~~~--~~L~~iLe~~~i~Kv~h~~k~D~~~L 80 (197)
T cd06148 3 AIIHLKKQKVIGLDCEGVNLGRKGKLCLVQIATRTGQIYLFDILKLGSIVFI--NGLKDILESKKILKVIHDCRRDSDAL 80 (197)
T ss_pred hhhhhhhCCEEEEEcccccCCCCCCEEEEEEeeCCCcEEEEEhhhccchhHH--HHHHHHhcCCCccEEEEechhHHHHH
Confidence 456677789999999998776689999999998647999999998752 22 57899999999999999999999999
Q ss_pred HHhcCCccCCccchhhcc
Q psy5654 206 YEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 206 ~~~~GI~L~nvFDTqLAa 223 (224)
++.+|+.+.++|||++|+
T Consensus 81 ~~~~gi~~~~~fDt~iA~ 98 (197)
T cd06148 81 YHQYGIKLNNVFDTQVAD 98 (197)
T ss_pred HHhcCccccceeeHHHHH
Confidence 778999999999999985
No 5
>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=99.58 E-value=2.1e-14 Score=116.37 Aligned_cols=105 Identities=31% Similarity=0.480 Sum_probs=89.8
Q ss_pred cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-C--ccceEEEEEEEeeCCeEEEEeCCCCccc--cccchhHhhhcCCC
Q psy5654 116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-G--IKGQITLFSLGLLSGQVYIFDLVTCPEV--VGTGGLSKLLESEN 190 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~--~~g~L~lIQIat~~g~a~lIDi~al~~l--~~~~~Lr~lLed~~ 190 (224)
|++|++.+++.++++.+.....++||+|+.+. . ..+.++++|+++. ..+|+++....... . ..|+++|+++.
T Consensus 1 y~~v~~~~~l~~~~~~l~~~~~~a~D~E~~~~~~~~~~~~~~~iq~~~~-~~~~i~~~~~~~~~~~~--~~l~~ll~~~~ 77 (176)
T PF01612_consen 1 YQIVDTEEELEEAIKKLKNAKVLAFDTETTGLDPYSYNPKIALIQLATG-EGCYIIDPIDLGDNWIL--DALKELLEDPN 77 (176)
T ss_dssp SEEEHSHHHHHHHHHHHTTTSEEEEEEEEETSTSTTSSEEEEEEEEEES-CEEEEECGTTSTTTTHH--HHHHHHHTTTT
T ss_pred CEecCCHHHHHHHHHHHcCCCeEEEEEEECCCCccccCCeEEEEEEecC-CCceeeeeccccccchH--HHHHHHHhCCC
Confidence 57899999999999999999999999999877 4 4677999999986 57788887765542 3 57999999999
Q ss_pred ceEEEEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 191 VIKVIHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 191 I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
+.||+||+|+|..+|++.+|+.+.+++|||+|+
T Consensus 78 i~kv~~n~~~D~~~L~~~~~i~~~~~~D~~l~~ 110 (176)
T PF01612_consen 78 IIKVGHNAKFDLKWLYRSFGIDLKNVFDTMLAA 110 (176)
T ss_dssp SEEEESSHHHHHHHHHHHHTS--SSEEEHHHHH
T ss_pred ccEEEEEEechHHHHHHHhccccCCccchhhhh
Confidence 999999999999999877999999999999875
No 6
>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=99.55 E-value=2.3e-14 Score=121.63 Aligned_cols=106 Identities=20% Similarity=0.282 Sum_probs=89.4
Q ss_pred cEEecCHHHHHHHHHH--HccCCeEEEEEeeeCC---CccceEEEEEEEeeCCeEEEEeCCCCcc----ccccchhHhhh
Q psy5654 116 TKVITNIKECSSVVEE--LMRNELVTFDCEGINP---GIKGQITLFSLGLLSGQVYIFDLVTCPE----VVGTGGLSKLL 186 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~--L~~~~~Ia~D~E~~~l---~~~g~L~lIQIat~~g~a~lIDi~al~~----l~~~~~Lr~lL 186 (224)
+.+|++++++.+++++ +....++|||+|+... +..++++++||++. +.+|+||+..++. .+. ..|+++|
T Consensus 1 ~~~i~~~~el~~~~~~~~l~~~~vig~D~Ew~~~~~~~~~~~v~LiQiat~-~~~~lid~~~~~~~~~~~~~-~~L~~ll 78 (193)
T cd06146 1 IHIVDSEEELEALLLALSLEAGRVVGIDSEWKPSFLGDSDPRVAILQLATE-DEVFLLDLLALENLESEDWD-RLLKRLF 78 (193)
T ss_pred CeEecCHHHHHHHHHHHhhccCCEEEEECccCCCccCCCCCCceEEEEecC-CCEEEEEchhccccchHHHH-HHHHHHh
Confidence 4688999999999999 8889999999999755 23688999999985 6899999987641 111 4689999
Q ss_pred cCCCceEEEEecHHHHHHHHHhcCCc------cCCccchhhcc
Q psy5654 187 ESENVIKVIHDCRNDSILLYEQFGIT------LRNVFDTQLLF 223 (224)
Q Consensus 187 ed~~I~KV~Hd~K~Dl~lL~~~~GI~------L~nvFDTqLAa 223 (224)
+++.+.||||+++.|+..|++.+|+. +.++|||+.++
T Consensus 79 ~d~~i~KVg~~~~~D~~~L~~~~~~~~~~~~~~~~v~Dl~~~a 121 (193)
T cd06146 79 EDPDVLKLGFGFKQDLKALSASYPALKCMFERVQNVLDLQNLA 121 (193)
T ss_pred CCCCeeEEEechHHHHHHHHHhcCccccccccCCceEEHHHHH
Confidence 99999999999999999999889974 57899998653
No 7
>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=99.51 E-value=9.8e-14 Score=113.91 Aligned_cols=101 Identities=26% Similarity=0.416 Sum_probs=88.4
Q ss_pred cCHHHHHHHHHHHc-cCCeEEEEEeeeCC-C--ccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEE
Q psy5654 120 TNIKECSSVVEELM-RNELVTFDCEGINP-G--IKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVI 195 (224)
Q Consensus 120 dt~eeLa~lie~L~-~~~~Ia~D~E~~~l-~--~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~ 195 (224)
+++.++..+++.+. ....+|||+|+.+. . ..+.++++|+|+. +.+|+||+....... ..|+++|+++.+.||+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~ig~D~E~~~~~~~~~~~~~~liQl~~~-~~~~l~~~~~~~~~~--~~l~~ll~~~~i~kv~ 78 (170)
T cd06141 2 DSAQDAEEAVKELLGKEKVVGFDTEWRPSFRKGKRNKVALLQLATE-SRCLLFQLAHMDKLP--PSLKQLLEDPSILKVG 78 (170)
T ss_pred CCHHHHHHHHHHHhcCCCEEEEeCccCCccCCCCCCCceEEEEecC-CcEEEEEhhhhhccc--HHHHHHhcCCCeeEEE
Confidence 46778999999998 89999999999876 3 6788999999974 689999998764443 5799999999999999
Q ss_pred EecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 196 HDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 196 Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
|++|.|+..|.+.+|+.+.++|||++|+
T Consensus 79 ~~~k~D~~~L~~~~g~~~~~~~Dl~~aa 106 (170)
T cd06141 79 VGIKGDARKLARDFGIEVRGVVDLSHLA 106 (170)
T ss_pred eeeHHHHHHHHhHcCCCCCCeeeHHHHH
Confidence 9999999999878999999999999985
No 8
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=99.44 E-value=2.2e-13 Score=125.55 Aligned_cols=101 Identities=23% Similarity=0.270 Sum_probs=90.2
Q ss_pred cCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCc-cccccchhHhhhcCCCceEEEEe
Q psy5654 120 TNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCP-EVVGTGGLSKLLESENVIKVIHD 197 (224)
Q Consensus 120 dt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~-~l~~~~~Lr~lLed~~I~KV~Hd 197 (224)
++.+.++.++..+..++.+++|+|+... ++++++|+||++..++ +++||+.... +. ..|..+|.|++|.||+|.
T Consensus 2 ~~~~~l~~~~~~~~~~~~iAiDTEf~r~~t~~p~LcLIQi~~~e~-~~lIdpl~~~~d~---~~l~~Ll~d~~v~KIfHa 77 (361)
T COG0349 2 TTGDLLAAACALLRGSKAIAIDTEFMRLRTYYPRLCLIQISDGEG-ASLIDPLAGILDL---PPLVALLADPNVVKIFHA 77 (361)
T ss_pred CchhHHHHHHHHhcCCCceEEecccccccccCCceEEEEEecCCC-ceEeccccccccc---chHHHHhcCCceeeeecc
Confidence 4566788899998889999999999988 9999999999998766 9999998743 33 578999999999999999
Q ss_pred cHHHHHHHHHhcCCccCCccchhhccC
Q psy5654 198 CRNDSILLYEQFGITLRNVFDTQLLFL 224 (224)
Q Consensus 198 ~K~Dl~lL~~~~GI~L~nvFDTqLAa~ 224 (224)
+++|+.+|++.||+.+.++|||++|++
T Consensus 78 a~~DL~~l~~~~g~~p~plfdTqiAa~ 104 (361)
T COG0349 78 ARFDLEVLLNLFGLLPTPLFDTQIAAK 104 (361)
T ss_pred ccccHHHHHHhcCCCCCchhHHHHHHH
Confidence 999999999999999999999999973
No 9
>smart00474 35EXOc 3'-5' exonuclease. 3\' -5' exonuclease proofreading domain present in DNA polymerase I, Werner syndrome helicase, RNase D and other enzymes
Probab=99.23 E-value=8.9e-11 Score=94.17 Aligned_cols=104 Identities=29% Similarity=0.438 Sum_probs=78.5
Q ss_pred EEecCHHHHHHHHHHHc-cCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654 117 KVITNIKECSSVVEELM-RNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV 194 (224)
Q Consensus 117 ~vIdt~eeLa~lie~L~-~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV 194 (224)
.+|++.+++..+++.+. ....+++|+|+... .+.+++++++++...+.+|+++........ ..|+++|+++.+.||
T Consensus 2 ~~i~~~~~~~~~~~~~~~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~~~~i~~~~~~~~~~--~~l~~~l~~~~~~kv 79 (172)
T smart00474 2 RVVTDSETLEELLEKLRAAGGEVALDTETTGLNSYSGKLVLIQISVTGEGAFIIDPLALGDDL--EILKDLLEDETITKV 79 (172)
T ss_pred EEecCHHHHHHHHHHHHhcCCeEEEeccccCCccCCCCEEEEEEeEcCCceEEEEeccchhhH--HHHHHHhcCCCceEE
Confidence 46777787888776665 45689999987655 456889999999642244544332222212 358899999999999
Q ss_pred EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 195 IHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
+||+|.|.+.|.+ +|+.+.++||||+|+
T Consensus 80 ~~d~k~~~~~L~~-~gi~~~~~~D~~laa 107 (172)
T smart00474 80 GHNAKFDLHVLAR-FGIELENIFDTMLAA 107 (172)
T ss_pred EechHHHHHHHHH-CCCcccchhHHHHHH
Confidence 9999999999974 999998889999986
No 10
>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=99.17 E-value=3e-10 Score=95.41 Aligned_cols=105 Identities=23% Similarity=0.320 Sum_probs=80.7
Q ss_pred cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654 116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV 194 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV 194 (224)
|.++++++++..+++.+...+.+++++|+... ++.+++++++++..++ +|+||+....... ..|+++|+++.+.|+
T Consensus 5 ~~~i~~~~~l~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~l~l~~~~~-~~~i~~l~~~~~~--~~L~~~L~~~~i~kv 81 (192)
T cd06147 5 LTFVDTEEKLEELVEKLKNCKEIAVDLEHHSYRSYLGFTCLMQISTREE-DYIVDTLKLRDDM--HILNEVFTDPNILKV 81 (192)
T ss_pred cEEECCHHHHHHHHHHHhcCCeEEEEeEecCCccCCCceEEEEEecCCC-cEEEEecccccch--HHHHHHhcCCCceEE
Confidence 66786667778877666555689999976554 5578899999997554 7888742221111 358899999999999
Q ss_pred EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 195 IHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
+||+|.+++.|.+.+|+.+.++||||+|+
T Consensus 82 ~~d~K~~~~~L~~~~gi~~~~~fD~~laa 110 (192)
T cd06147 82 FHGADSDIIWLQRDFGLYVVNLFDTGQAA 110 (192)
T ss_pred EechHHHHHHHHHHhCCCcCchHHHHHHH
Confidence 99999999999647999997779999986
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=99.16 E-value=2.3e-10 Score=93.43 Aligned_cols=95 Identities=29% Similarity=0.449 Sum_probs=73.5
Q ss_pred HHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHH
Q psy5654 125 CSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSI 203 (224)
Q Consensus 125 La~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~ 203 (224)
+.++++.+...+.+++|+|+... +..++++++++++. +.+|+||+... ... ..|+++|+++.+.||+||+|.|.+
T Consensus 2 ~~~~~~~l~~~~~l~~~~e~~~~~~~~~~~~~i~l~~~-~~~~~i~~~~~-~~~--~~l~~ll~~~~i~kv~~d~K~~~~ 77 (178)
T cd06142 2 LEDLCERLASAGVIAVDTEFMRLNTYYPRLCLIQISTG-GEVYLIDPLAI-GDL--SPLKELLADPNIVKVFHAAREDLE 77 (178)
T ss_pred HHHHHHHHhcCCeEEEECCccCCCcCCCceEEEEEeeC-CCEEEEeCCCc-ccH--HHHHHHHcCCCceEEEeccHHHHH
Confidence 34455555445689999987554 44688999999986 56899986533 222 468899999999999999999999
Q ss_pred HHHHhcCCccCCccchhhcc
Q psy5654 204 LLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 204 lL~~~~GI~L~nvFDTqLAa 223 (224)
.|.+.+|+..+++|||++|+
T Consensus 78 ~L~~~~gi~~~~~~D~~laa 97 (178)
T cd06142 78 LLKRDFGILPQNLFDTQIAA 97 (178)
T ss_pred HHHHHcCCCCCCcccHHHHH
Confidence 99766699955679999985
No 12
>PRK05755 DNA polymerase I; Provisional
Probab=99.03 E-value=1.2e-09 Score=111.21 Aligned_cols=137 Identities=22% Similarity=0.290 Sum_probs=105.3
Q ss_pred cchHHHHHHHHHHHHHHhhcccCCCCCCCCCCccccCCCCccccCCCCcEEecCHHHHHHHHHHHccCCeEEEEEeeeCC
Q psy5654 68 NQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGINP 147 (224)
Q Consensus 68 ~~~~~q~~~~~~~~~l~~n~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l 147 (224)
...|..=+..+.++.|....+-.. .+ ..+.+ .|.+|++++++..+++.+.....+++|+|+...
T Consensus 264 ~~~l~~~~~~~~~~~~~~~~~~~~--------~~-------~~~~~-~~~~I~~~~~L~~~l~~l~~~~~~a~DtEt~~l 327 (880)
T PRK05755 264 REKLIALFKELEFKSLLRRAAAAE--------AA-------PLDEE-DYETILDEEELEAWLAKLKAAGLFAFDTETTSL 327 (880)
T ss_pred HHHHHHHHHHhCcHHHHHHhhccc--------cc-------cCCCC-ceEEeCCHHHHHHHHHHhhccCeEEEEeccCCC
Confidence 356777777788888776421000 00 01112 267888999999999998888899999999877
Q ss_pred -CccceEEEEEEEeeCCeEEEEeCCCCc-cccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc-CCccchhhcc
Q psy5654 148 -GIKGQITLFSLGLLSGQVYIFDLVTCP-EVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL-RNVFDTQLLF 223 (224)
Q Consensus 148 -~~~g~L~lIQIat~~g~a~lIDi~al~-~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L-~nvFDTqLAa 223 (224)
++.+++++++++..++.++++|+...+ ... ..|+++|+++.+.||+||+|+|+.+|. .+|+.+ ..+||||+|+
T Consensus 328 ~~~~~~i~~i~ls~~~g~~~~ip~~~i~~~~l--~~l~~~L~d~~v~kV~HNakfDl~~L~-~~gi~~~~~~~DT~iAa 403 (880)
T PRK05755 328 DPMQAELVGLSFAVEPGEAAYIPLDQLDREVL--AALKPLLEDPAIKKVGQNLKYDLHVLA-RYGIELRGIAFDTMLAS 403 (880)
T ss_pred CcccccEEEEEEEeCCCcEEEEecccccHHHH--HHHHHHHhCCCCcEEEeccHhHHHHHH-hCCCCcCCCcccHHHHH
Confidence 788999999999877778999885433 222 578899999999999999999999997 489987 5689999985
No 13
>KOG2206|consensus
Probab=98.96 E-value=2.2e-10 Score=110.71 Aligned_cols=104 Identities=24% Similarity=0.317 Sum_probs=94.9
Q ss_pred cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654 116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV 194 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV 194 (224)
+.+|++..++.++.+.+....++++|.|.... .+.|-.|++||+|.+ +.|+||...+.+.+ +.|++.|.+|.+.||
T Consensus 193 ~~~I~t~~el~~l~~~l~~~~Efavdlehhsyrsf~gltclmqISTr~-ed~iIDt~~l~~~i--~~l~e~fsdp~ivkv 269 (687)
T KOG2206|consen 193 KVWICTLGELEALPEILDSVIEFAVDLEHHSYRSFLGLTCLMQISTRT-EDFIIDTFKLRDHI--GILNEVFSDPGIVKV 269 (687)
T ss_pred ceeeechHHHHHHHHHHhhhhhhhhhccccchhhhcCceeEEEeeccc-hhheehhHHHHHHH--HHhhhhccCCCeEEE
Confidence 57789999999999999889999999999888 888999999999964 77999998887666 789999999999999
Q ss_pred EEecHHHHHHHHHhcCCccCCccchhhc
Q psy5654 195 IHDCRNDSILLYEQFGITLRNVFDTQLL 222 (224)
Q Consensus 195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLA 222 (224)
+|++..|+.||++.|||.+.++|||.-|
T Consensus 270 fhgaD~diiwlqrdfgiyvvnLfdt~~a 297 (687)
T KOG2206|consen 270 FHGADTDIIWLQRDFGIYVVNLFDTIQA 297 (687)
T ss_pred EecCccchhhhhccceEEEEechhhHHH
Confidence 9999999999999999999999999766
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=98.88 E-value=8.6e-09 Score=81.61 Aligned_cols=83 Identities=28% Similarity=0.325 Sum_probs=64.2
Q ss_pred EEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccC-C
Q psy5654 138 VTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLR-N 215 (224)
Q Consensus 138 Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~-n 215 (224)
+++|+|+.+. ++.++++++|++..++.+|++++....... ..|+++|+++.+.|++||+|.|++.|. ..|+.+. +
T Consensus 2 ~~~~~e~~~~~~~~~~~~~l~l~~~~~~~~~i~~~~~~~~~--~~l~~~l~~~~~~kv~~d~K~~~~~L~-~~~~~~~~~ 78 (150)
T cd09018 2 FAFDTETDSLDNISANLVLIQLAIEPGVAALIPVAHDYLAL--ELLKPLLEDEKALKVGQNLKYDRGILL-NYFIELRGI 78 (150)
T ss_pred EEEEeecCCCCCCCceEEEEEEEcCCCcEEEEEcCCcccCH--HHHHHHhcCCCCceeeecHHHHHHHHH-HcCCccCCc
Confidence 6788876554 457889999999754558888865321012 468899999999999999999999996 5787774 5
Q ss_pred ccchhhcc
Q psy5654 216 VFDTQLLF 223 (224)
Q Consensus 216 vFDTqLAa 223 (224)
+||||+|+
T Consensus 79 ~~D~~laa 86 (150)
T cd09018 79 AFDTMLEA 86 (150)
T ss_pred chhHHHHH
Confidence 69999986
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=98.75 E-value=3.7e-08 Score=77.41 Aligned_cols=83 Identities=31% Similarity=0.373 Sum_probs=61.5
Q ss_pred eEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCC-ccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc-
Q psy5654 137 LVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTC-PEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL- 213 (224)
Q Consensus 137 ~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al-~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L- 213 (224)
.+++|+|+.+. ++.++++++++++. +.+++++.... .... ..++++|+++.+.||+||+|+|...|.+ .|+..
T Consensus 2 ~l~~d~e~~~~~~~~~~i~~~~l~~~-~~~~~i~~~~~~~~~~--~~l~~~l~~~~~~~v~~~~k~d~~~L~~-~~~~~~ 77 (155)
T cd00007 2 EVAFDTETTGLNYHRGKLVGIQIATA-GEAAYIPDELELEEDL--EALKELLEDEDITKVGHDAKFDLVVLAR-DGIELP 77 (155)
T ss_pred ceEEEEecCCCCcCCCeEEEEEEEEC-CcEEEEEcCCCHHHHH--HHHHHHHcCCCCcEEeccHHHHHHHHHH-CCCCCC
Confidence 47889987654 45788999999975 44666654322 1122 3588899999999999999999999965 55544
Q ss_pred CCccchhhcc
Q psy5654 214 RNVFDTQLLF 223 (224)
Q Consensus 214 ~nvFDTqLAa 223 (224)
..+|||++|+
T Consensus 78 ~~~~D~~~~a 87 (155)
T cd00007 78 GNIFDTMLAA 87 (155)
T ss_pred CCcccHHHHH
Confidence 5679999985
No 16
>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=98.72 E-value=3.8e-08 Score=80.87 Aligned_cols=85 Identities=26% Similarity=0.265 Sum_probs=66.7
Q ss_pred CCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCcc
Q psy5654 135 NELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITL 213 (224)
Q Consensus 135 ~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L 213 (224)
.+.+++++|.... ++.+++++++++..+ ++|++++....... ..++++|+++.+.|++||+|++++.|. .+|+.+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~l~~i~l~~~~-~~~~i~~~~~~~~~--~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~~ 78 (178)
T cd06140 3 ADEVALYVELLGENYHTADIIGLALANGG-GAYYIPLELALLDL--AALKEWLEDEKIPKVGHDAKRAYVALK-RHGIEL 78 (178)
T ss_pred CCceEEEEEEcCCCcceeeEEEEEEEeCC-cEEEEeccchHHHH--HHHHHHHhCCCCceeccchhHHHHHHH-HCCCcC
Confidence 3567889888766 678899999999754 68888753210111 458889999999999999999999996 599998
Q ss_pred CC-ccchhhcc
Q psy5654 214 RN-VFDTQLLF 223 (224)
Q Consensus 214 ~n-vFDTqLAa 223 (224)
.+ +||||+|+
T Consensus 79 ~~~~fDt~laa 89 (178)
T cd06140 79 AGVAFDTMLAA 89 (178)
T ss_pred CCcchhHHHHH
Confidence 54 69999986
No 17
>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=98.52 E-value=3.6e-07 Score=75.31 Aligned_cols=87 Identities=30% Similarity=0.434 Sum_probs=66.6
Q ss_pred cCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCC------c--cccccchhHhhhcCCCceEEEEecHHHHHH
Q psy5654 134 RNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTC------P--EVVGTGGLSKLLESENVIKVIHDCRNDSIL 204 (224)
Q Consensus 134 ~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al------~--~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~l 204 (224)
+.+.+++|+|..+. ++.+++++++++..++..+++++... . ... ..|+++|++..+.+|+||+|+|+.+
T Consensus 4 ~~~~~a~d~e~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~~~~~~v~hn~k~d~~~ 81 (193)
T cd06139 4 KAKVFAFDTETTSLDPMQAELVGISFAVEPGEAYYIPLGHDYGGEQLPREEVL--AALKPLLEDPSIKKVGQNLKFDLHV 81 (193)
T ss_pred cCCeEEEEeecCCCCcCCCeEEEEEEEcCCCCEEEEecCCCccccCCCHHHHH--HHHHHHHhCCCCcEEeeccHHHHHH
Confidence 45679999987665 56788999999976555788875431 1 111 3488899998889999999999999
Q ss_pred HHHhcCCccC-Cccchhhcc
Q psy5654 205 LYEQFGITLR-NVFDTQLLF 223 (224)
Q Consensus 205 L~~~~GI~L~-nvFDTqLAa 223 (224)
|. .+|+.+. .+|||++++
T Consensus 82 l~-~~gi~~~~~~~Dt~l~a 100 (193)
T cd06139 82 LA-NHGIELRGPAFDTMLAS 100 (193)
T ss_pred HH-HCCCCCCCCcccHHHHH
Confidence 96 5898874 469999985
No 18
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=98.36 E-value=5.7e-07 Score=88.06 Aligned_cols=101 Identities=25% Similarity=0.282 Sum_probs=79.7
Q ss_pred ecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCc---cccccchhHhhhcCCCceEE
Q psy5654 119 ITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCP---EVVGTGGLSKLLESENVIKV 194 (224)
Q Consensus 119 Idt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~---~l~~~~~Lr~lLed~~I~KV 194 (224)
+.+...+..|.........+++|+|...+ +..++++++.++..+ +++|++....+ ... +.|++||+++...|+
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~a~~~et~~l~~~~~~lvg~s~~~~~-~~~yi~~~~~~~~~~~~--~~l~~~l~~~~~~kv 82 (593)
T COG0749 6 ITDLAVLNAWLTKLNAAANIAFDTETDGLDPHGADLVGLSVASEE-EAAYIPLLHGPEQLNVL--AALKPLLEDEGIKKV 82 (593)
T ss_pred hhHHHHHHHHHHHHhhcccceeeccccccCcccCCeeEEEeeccc-cceeEeeccchhhhhhH--HHHHHHhhCcccchh
Confidence 44555677777776666669999998877 777889999999866 77888776522 222 689999999999999
Q ss_pred EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 195 IHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
+||.|+|.++|. .+|+..+..||||+|+
T Consensus 83 ~~~~K~d~~~l~-~~Gi~~~~~~Dtmlas 110 (593)
T COG0749 83 GQNLKYDYKVLA-NLGIEPGVAFDTMLAS 110 (593)
T ss_pred ccccchhHHHHH-HcCCcccchHHHHHHH
Confidence 999999999996 5996645569999985
No 19
>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=98.25 E-value=4.9e-06 Score=66.75 Aligned_cols=69 Identities=25% Similarity=0.350 Sum_probs=53.4
Q ss_pred cceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccCC-ccchhhcc
Q psy5654 150 KGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRN-VFDTQLLF 223 (224)
Q Consensus 150 ~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~n-vFDTqLAa 223 (224)
.+++.++.++..+ ++|++++... ... +.|+++|+++.+.|++||.|.++++|. .+|+.+.+ +||||||+
T Consensus 17 ~~~~~glal~~~~-~~~yi~~~~~-~~~--~~l~~~l~~~~~~ki~~d~K~~~~~l~-~~gi~l~~~~fD~~LAa 86 (151)
T cd06128 17 SANLVGLAFAIEG-VAAYIPVAHD-YAL--ELLKPLLEDEKALKVGQNLKYDRVILA-NYGIELRGIAFDTMLEA 86 (151)
T ss_pred cCcEEEEEEEcCC-CeEEEeCCCC-cCH--HHHHHHHcCCCCCEEeeehHHHHHHHH-HCCCCCCCcchhHHHHH
Confidence 5678888888754 4777763211 012 468899999999999999999999995 69999866 59999986
No 20
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.15 E-value=1e-05 Score=82.98 Aligned_cols=100 Identities=17% Similarity=0.085 Sum_probs=72.0
Q ss_pred cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeC-CeEEEEeCCC-----CccccccchhHhhhcC
Q psy5654 116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLS-GQVYIFDLVT-----CPEVVGTGGLSKLLES 188 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~-g~a~lIDi~a-----l~~l~~~~~Lr~lLed 188 (224)
+..+.+.+++..+++. ...+.+++ ... ++.+++.++++++.+ +.+||++... ..... ..|+++|++
T Consensus 304 ~~~~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~l~~~l~~ 376 (887)
T TIGR00593 304 AKESEEAAPLANPAEK-AEVGGFVL----ERLLDQLKKALALAFATENQSYVAYASEADGIPLLTILTD--DKFARWLLN 376 (887)
T ss_pred ceEeCCHHHHHHHHHh-CcCCeEEE----cCcccccCceeEEEEEecCCCceEEEecccchhhhhHHHH--HHHHHHHhC
Confidence 4456566777777755 33445666 222 456778899999865 5578887531 00111 458899999
Q ss_pred CCceEEEEecHHHHHHHHHhcCCccCC-ccchhhcc
Q psy5654 189 ENVIKVIHDCRNDSILLYEQFGITLRN-VFDTQLLF 223 (224)
Q Consensus 189 ~~I~KV~Hd~K~Dl~lL~~~~GI~L~n-vFDTqLAa 223 (224)
+.+.||+||+|+|+++|. .+|+.+.+ +||||+|+
T Consensus 377 ~~~~~v~~n~K~d~~~l~-~~gi~~~~~~~Dt~la~ 411 (887)
T TIGR00593 377 EQIKKIGHDAKFLMHLLK-REGIELGGVIFDTMLAA 411 (887)
T ss_pred CCCcEEEeeHHHHHHHHH-hCCCCCCCcchhHHHHH
Confidence 999999999999999996 69999854 69999986
No 21
>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=97.30 E-value=0.00092 Score=50.57 Aligned_cols=73 Identities=23% Similarity=0.309 Sum_probs=53.0
Q ss_pred EEEEEeeeCC-CccceEEEEEEEee-CCeEEEEeCCCCccccccchhHhhhcCCC-ceEEEEecHHHHHHHHHh---cCC
Q psy5654 138 VTFDCEGINP-GIKGQITLFSLGLL-SGQVYIFDLVTCPEVVGTGGLSKLLESEN-VIKVIHDCRNDSILLYEQ---FGI 211 (224)
Q Consensus 138 Ia~D~E~~~l-~~~g~L~lIQIat~-~g~a~lIDi~al~~l~~~~~Lr~lLed~~-I~KV~Hd~K~Dl~lL~~~---~GI 211 (224)
+++|+|..+. +...++++++++.. ++..|++| +.+++++.. ...|+|++++|...|.+. +|+
T Consensus 1 ~~~DiEt~~~~~~~~~i~~i~~~~~~~~~~~~~~------------f~~~l~~~~~~v~V~hn~~fD~~fL~~~~~~~~~ 68 (96)
T cd06125 1 IAIDTEATGLDGAVHEIIEIALADVNPEDTAVID------------LKDILRDKPLAILVGHNGSFDLPFLNNRCAELGL 68 (96)
T ss_pred CEEEEECCCCCCCCCcEEEEEEEEccCCCEEEeh------------HHHHHhhCCCCEEEEeCcHHhHHHHHHHHHHcCC
Confidence 4789998877 77788999999875 35667654 445777766 678999999998777643 343
Q ss_pred cc----CCccchhhc
Q psy5654 212 TL----RNVFDTQLL 222 (224)
Q Consensus 212 ~L----~nvFDTqLA 222 (224)
.. ...+||+.+
T Consensus 69 ~~p~~~~~~lDT~~l 83 (96)
T cd06125 69 KYPLLAGSWIDTIKL 83 (96)
T ss_pred CCCCcCCcEEEehHH
Confidence 32 446899865
No 22
>KOG2405|consensus
Probab=97.20 E-value=5.9e-06 Score=77.06 Aligned_cols=90 Identities=34% Similarity=0.529 Sum_probs=70.3
Q ss_pred HccCCeEEEEEeeeCCCccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCC
Q psy5654 132 LMRNELVTFDCEGINPGIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGI 211 (224)
Q Consensus 132 L~~~~~Ia~D~E~~~l~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI 211 (224)
++.+... ...|+.....+|++|++|.++. -..|++|+..+........++-++++.+|.|+.|+|+.-++.+.++|||
T Consensus 56 ik~qn~~-~~~e~a~~~~~~~l~~~q~~~~-~~~yl~~i~~~~~~~~~n~~q~~~~~k~i~~~~~d~~~~~~~~~~~~~i 133 (458)
T KOG2405|consen 56 IKKQNVL-VAAEGANVCRHGKLCWLQVATN-CRVYLFDIFLLGSRAFHNGLQMILEDKRILKVIHDCRWLSDCLSHQYGI 133 (458)
T ss_pred hHhhcCc-ccccCccccccCcchhHHHHHH-HHHHHHHHHHhhhHHHHHHHHHHhhhhhHhhhHHHHHHHHHHhccccee
Confidence 4444443 4566766667889999999974 3678888876542111156788999999999999999999999999999
Q ss_pred ccCCccchhhcc
Q psy5654 212 TLRNVFDTQLLF 223 (224)
Q Consensus 212 ~L~nvFDTqLAa 223 (224)
.+.++|||++|.
T Consensus 134 ~~n~v~~~q~~d 145 (458)
T KOG2405|consen 134 LLNNVFDTQVAD 145 (458)
T ss_pred eecchhhhhhhh
Confidence 999999999874
No 23
>KOG2207|consensus
Probab=97.03 E-value=0.00038 Score=68.21 Aligned_cols=91 Identities=23% Similarity=0.283 Sum_probs=71.5
Q ss_pred cEEecCHHHHHHHH-HHHccC-CeEEEEEeeeCC--CccceEEEEEEEeeCCeEEEEeCCCCcccccc---chhHhhhcC
Q psy5654 116 TKVITNIKECSSVV-EELMRN-ELVTFDCEGINP--GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGT---GGLSKLLES 188 (224)
Q Consensus 116 ~~vIdt~eeLa~li-e~L~~~-~~Ia~D~E~~~l--~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~---~~Lr~lLed 188 (224)
+.++.++.++..++ +.+... .++|+|+||.+. ....+++.+|++.. ..+|++|+.++.....+ -.+..+|++
T Consensus 392 i~~V~~e~El~~l~l~~l~~e~~yVGiDsEwkps~~v~dsk~~IlQif~~-~~v~Lidc~~l~~~~se~w~~~~s~if~s 470 (617)
T KOG2207|consen 392 IGMVGNEKELRDLLLESLSEELRYVGIDSEWKPSKKVSDSKLAILQIFFK-DCVYLIDCVKLENLASEIWHLLLSQIFES 470 (617)
T ss_pred eeeeCCHHHHHHHHHHHhhhcCEEEEEccccCcccCCChhHHHHHHHHhc-CeEEEeehHHhhhchHHHHHHHHHHHccC
Confidence 67789999998887 455555 779999999765 33577999999985 58999999876422110 245569999
Q ss_pred CCceEEEEecHHHHHHHHH
Q psy5654 189 ENVIKVIHDCRNDSILLYE 207 (224)
Q Consensus 189 ~~I~KV~Hd~K~Dl~lL~~ 207 (224)
+.+.|||++.+.|+..+.+
T Consensus 471 ~~i~kvGf~~~eDL~~l~~ 489 (617)
T KOG2207|consen 471 KSILKVGFSMREDLEVLEA 489 (617)
T ss_pred CceeeeecchhhhHHHHHh
Confidence 9999999999999999974
No 24
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=96.49 E-value=0.0025 Score=62.35 Aligned_cols=76 Identities=20% Similarity=0.178 Sum_probs=60.0
Q ss_pred cEEecCHHHHHHHHHHHccCCeEEEEEeeeCC-CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEE
Q psy5654 116 TKVITNIKECSSVVEELMRNELVTFDCEGINP-GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKV 194 (224)
Q Consensus 116 ~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV 194 (224)
+.+|++.+++..+++.+...+.+++|+|+... . .++++|++.. +.+|++|.... +.++
T Consensus 3 ~~~I~~~~~l~~~~~~l~~~~~~a~DtEf~r~~t---~l~liQ~~~~-~~~~liDpl~~--------l~~~--------- 61 (553)
T PRK14975 3 MKVILAPEELGAALERLSPAGVVAGDTETTGDDA---AAAAAQEGEE-EPRWVWASTAA--------LYPR--------- 61 (553)
T ss_pred ceEEeccchhHHHHHHhccCCceeCCccccCCcc---hhheeeecCC-CceEEECchHH--------hHHH---------
Confidence 56888999999999999999999999999865 3 7889999864 57898876321 1111
Q ss_pred EEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 195 IHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 195 ~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
|. .+|+.+.++||||+|+
T Consensus 62 ----------L~-~~Gv~~~~~fDT~LAa 79 (553)
T PRK14975 62 ----------LL-AAGVRVERCHDLMLAS 79 (553)
T ss_pred ----------HH-HCCCccCCCchHHHHH
Confidence 43 4799988899999986
No 25
>KOG2405|consensus
Probab=88.50 E-value=0.069 Score=50.46 Aligned_cols=72 Identities=24% Similarity=0.211 Sum_probs=52.2
Q ss_pred CccceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHHhcCCccCCccchhhcc
Q psy5654 148 GIKGQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLLF 223 (224)
Q Consensus 148 ~~~g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqLAa 223 (224)
...++.+..++|+. .++|++|...-+.....+..+..|+...+ +. |++.+...+...|++.+.+++|||+|+
T Consensus 208 ~~~~e~~~m~ia~~-n~i~llD~~~sdi~il~~gyK~~LEs~~~--vi-Dr~r~~e~l~~~y~~~L~nVkDtQia~ 279 (458)
T KOG2405|consen 208 ILALEATYMNIADG-NEIFLLDSLPSDIRILFGGYKRELESLEK--VI-DRIRLIEQLDTTYHSALKNVKDTQIAS 279 (458)
T ss_pred hhhhhhhhhhhccc-chhhhhhhccCCcEEecccchhhhhhcce--eh-hhhhhhHHHHhHHHHHHHhhHHHHHHH
Confidence 34455666777764 47888888654311111446667877655 55 999999999999999999999999985
No 26
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=65.84 E-value=24 Score=32.19 Aligned_cols=39 Identities=26% Similarity=0.246 Sum_probs=26.3
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc--CCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYE---QFGITL--RNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L--~nvFDTqL 221 (224)
.|..++.+ -.-|+||+.+|...|.+ ++|+.+ ...+||+.
T Consensus 87 ~l~~~l~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~ldTl~ 130 (313)
T PRK06063 87 EVAELLRG--RTLVAHNVAFDYSFLAAEAERAGAELPVDQVMCTVE 130 (313)
T ss_pred HHHHHcCC--CEEEEeCHHHHHHHHHHHHHHcCCCCCCCCEEehHH
Confidence 45556654 35699999999988864 356554 33578874
No 27
>cd06127 DEDDh DEDDh 3'-5' exonuclease domain family. DEDDh exonucleases, part of the DnaQ-like (or DEDD) exonuclease superfamily, catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. These proteins contain four invariant acidic residues in three conserved sequence motifs termed ExoI, ExoII and ExoIII. DEDDh exonucleases are classified as such because of the presence of specific Hx(4)D conserved pattern at the ExoIII motif. The four conserved acidic residues are clustered around the active site and serve as ligands for the two metal ions required for catalysis. Most DEDDh exonucleases are the proofreading subunits (epsilon) or domains of bacterial DNA polymerase III, the main replicating enzyme in bacteria, which functions as the chromosomal replicase. Other members include other DNA and RNA exonucleases such as RNase T, Oligoribonuclease, and RNA exonuclease (REX), among others.
Probab=62.12 E-value=15 Score=28.05 Aligned_cols=40 Identities=18% Similarity=0.120 Sum_probs=26.5
Q ss_pred chhHhhhcCCCceEEEEecHHHHHHHHHhcC-----CccCCccchhh
Q psy5654 180 GGLSKLLESENVIKVIHDCRNDSILLYEQFG-----ITLRNVFDTQL 221 (224)
Q Consensus 180 ~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~G-----I~L~nvFDTqL 221 (224)
..+..+++. ...|+|+..+|..+|.+.+. ......+||+.
T Consensus 71 ~~~~~~l~~--~~~v~~n~~fD~~~l~~~~~~~~~~~~~~~~iDt~~ 115 (159)
T cd06127 71 PEFLEFLGG--RVLVAHNASFDLRFLNRELRRLGGPPLPNPWIDTLR 115 (159)
T ss_pred HHHHHHHCC--CEEEEeCcHhhHHHHHHHHHHhCCCCCCCCeeEHHH
Confidence 345556765 56799999999998865332 12244578874
No 28
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=61.79 E-value=41 Score=29.15 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=21.9
Q ss_pred CceEEEEecHHHHHHHHH---hcCCcc---CCccchhhc
Q psy5654 190 NVIKVIHDCRNDSILLYE---QFGITL---RNVFDTQLL 222 (224)
Q Consensus 190 ~I~KV~Hd~K~Dl~lL~~---~~GI~L---~nvFDTqLA 222 (224)
...-|+||+.+|...|.+ ++|+.. ..++||+..
T Consensus 93 ~~~lVahNa~FD~~fL~~~~~r~~~~~~~~~~~iDt~~l 131 (232)
T PRK07942 93 GVPVVVFNAPYDLTVLDRELRRHGLPSLVPGPVIDPYVI 131 (232)
T ss_pred CCEEEEeCcHhhHHHHHHHHHHcCCCCccCCcEeeHHHH
Confidence 345699999999988754 355432 346787653
No 29
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=56.98 E-value=56 Score=29.05 Aligned_cols=87 Identities=16% Similarity=0.151 Sum_probs=46.3
Q ss_pred HccCCeEEEEEeeeCC-CccceEEEEEEEe-eCCeE-----EEEeCCCCc-----------cccc-c-------chhHhh
Q psy5654 132 LMRNELVTFDCEGINP-GIKGQITLFSLGL-LSGQV-----YIFDLVTCP-----------EVVG-T-------GGLSKL 185 (224)
Q Consensus 132 L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat-~~g~a-----~lIDi~al~-----------~l~~-~-------~~Lr~l 185 (224)
+.....+.+|+|+.+. +..+++.-++... ..++. .++.+...+ +.+. + ..+..+
T Consensus 65 ~~~~~~vv~DiETTG~~~~~~~IIEIGAv~v~~g~i~~~f~~~v~p~~ip~~~~~itGIt~e~l~~ap~~~evl~~f~~f 144 (257)
T PRK08517 65 IKDQVFCFVDIETNGSKPKKHQIIEIGAVKVKNGEIIDRFESFVKAKEVPEYITELTGITYEDLENAPSLKEVLEEFRLF 144 (257)
T ss_pred CCCCCEEEEEEeCCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCChhhhhhcCcCHHHHcCCCCHHHHHHHHHHH
Confidence 4456789999998876 4444544333222 23321 233332111 0000 0 345556
Q ss_pred hcCCCceEEEEecHHHHHHHHH---hcCCcc--CCccchh
Q psy5654 186 LESENVIKVIHDCRNDSILLYE---QFGITL--RNVFDTQ 220 (224)
Q Consensus 186 Led~~I~KV~Hd~K~Dl~lL~~---~~GI~L--~nvFDTq 220 (224)
+.+. .-|+||+.+|..+|.+ ++|... ...+||+
T Consensus 145 l~~~--v~VaHNa~FD~~fL~~~l~r~g~~~~~~~~ldtl 182 (257)
T PRK08517 145 LGDS--VFVAHNVNFDYNFISRSLEEIGLGPLLNRKLCTI 182 (257)
T ss_pred HCCC--eEEEECHHHHHHHHHHHHHHcCCCCCCCCcEehH
Confidence 6643 4689999999988853 455443 2245654
No 30
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=56.41 E-value=74 Score=27.96 Aligned_cols=40 Identities=20% Similarity=0.189 Sum_probs=25.5
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc----CCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYE---QFGITL----RNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L----~nvFDTqL 221 (224)
.+..++.+. ..-|+|++.+|...|.+ +.|+.. ...+||+-
T Consensus 80 ~~~~fl~~~-~~lvghn~~FD~~~L~~~~~r~g~~~~~~~~~~iDtl~ 126 (250)
T PRK06310 80 QIKGFFKEG-DYIVGHSVGFDLQVLSQESERIGETFLSKHYYIIDTLR 126 (250)
T ss_pred HHHHHhCCC-CEEEEECHHHHHHHHHHHHHHcCCCccccCCcEEehHH
Confidence 344455442 35799999999988853 345543 23578764
No 31
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=56.20 E-value=51 Score=28.90 Aligned_cols=32 Identities=25% Similarity=0.268 Sum_probs=21.4
Q ss_pred ceEEEEecHHHHHHHHHh----cCCcc-CCccchhhc
Q psy5654 191 VIKVIHDCRNDSILLYEQ----FGITL-RNVFDTQLL 222 (224)
Q Consensus 191 I~KV~Hd~K~Dl~lL~~~----~GI~L-~nvFDTqLA 222 (224)
-.-|+|++.+|...|.+. +|..+ ..++||+..
T Consensus 130 ~~lVaHna~FD~~fL~~~l~~~~~~~~~~~~iDTl~L 166 (239)
T PRK09146 130 KVVVVHYRRIERDFLDQALRNRIGEGIEFPVIDTMEI 166 (239)
T ss_pred CEEEEECHHHHHHHHHHHHHHhcCCCCCCceechHHH
Confidence 356899999999988643 23333 345788753
No 32
>KOG4373|consensus
Probab=55.62 E-value=8.7 Score=35.59 Aligned_cols=68 Identities=16% Similarity=0.153 Sum_probs=52.1
Q ss_pred ceEEEEEEEeeCCeEEEEeCCCCccccccchhHhhhcCCCceEEEEecHHHHHHHHH-hcCCccCCccchh
Q psy5654 151 GQITLFSLGLLSGQVYIFDLVTCPEVVGTGGLSKLLESENVIKVIHDCRNDSILLYE-QFGITLRNVFDTQ 220 (224)
Q Consensus 151 g~L~lIQIat~~g~a~lIDi~al~~l~~~~~Lr~lLed~~I~KV~Hd~K~Dl~lL~~-~~GI~L~nvFDTq 220 (224)
+....+||++.+..++++-+..+.... ..|+.+|+|+....|+-..+.|..-|.| .+++.+....|+.
T Consensus 147 P~~~~lqlcV~en~C~I~ql~~~~~IP--~~LR~fl~D~~~~~vgv~~d~D~~KL~r~~hql~I~~~~dlr 215 (319)
T KOG4373|consen 147 PPPDTLQLCVGENRCLIIQLIHCKRIP--HELRSFLEDPDHTFVGVWNDQDAGKLERKEHQLEIGELEDLR 215 (319)
T ss_pred CCcchhhhhhcccceeeEEeeccccch--HHHHHhhcCCCceEEeccccccHHHHhhhhhcccHHhhhhHH
Confidence 346678999977788888666655443 5788899999999999999999988766 7887776555543
No 33
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=55.10 E-value=59 Score=29.78 Aligned_cols=38 Identities=24% Similarity=0.380 Sum_probs=24.5
Q ss_pred hHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc--CCccchhh
Q psy5654 182 LSKLLESENVIKVIHDCRNDSILLYE---QFGITL--RNVFDTQL 221 (224)
Q Consensus 182 Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L--~nvFDTqL 221 (224)
|..++.+. .-|+|++.+|...|.+ ++|+.. ...+||+.
T Consensus 82 f~~fl~~~--~lVaHNa~FD~~fL~~~~~~~gl~~~~~~~iDtl~ 124 (313)
T PRK06807 82 FLAFLHTN--VIVAHNASFDMRFLKSNVNMLGLPEPKNKVIDTVF 124 (313)
T ss_pred HHHHHcCC--eEEEEcHHHHHHHHHHHHHHcCCCCCCCCEeeHHH
Confidence 44455443 3499999999998865 355532 33578765
No 34
>cd06131 DNA_pol_III_epsilon_Ecoli_like DEDDh 3'-5' exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III and similar proteins. This subfamily is composed of the epsilon subunit of Escherichia coli DNA polymerase III (Pol III) and similar proteins. Pol III is the main DNA replicating enzyme in bacteria, functioning as the chromosomal replicase. It is a holoenzyme complex of ten different subunits, three of which (alpha, epsilon, and theta) compose the catalytic core. The Pol III epsilon subunit, encoded by the dnaQ gene, is a DEDDh-type 3'-5' exonuclease which is responsible for the proofreading activity of the polymerase, increasing the fidelity of DNA synthesis. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The epsilon
Probab=51.97 E-value=51 Score=26.29 Aligned_cols=39 Identities=23% Similarity=0.262 Sum_probs=24.6
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc-----CCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYE---QFGITL-----RNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L-----~nvFDTqL 221 (224)
.|..++.+. .-|+||+.+|..+|.+ ++|+.. ...+||+.
T Consensus 74 ~l~~~l~~~--~lv~hn~~fD~~~l~~~~~~~~~~~~~~~~~~~idt~~ 120 (167)
T cd06131 74 EFLDFIRGA--ELVIHNASFDVGFLNAELSLLGLGKKIIDFCRVIDTLA 120 (167)
T ss_pred HHHHHHCCC--eEEEeChHHhHHHHHHHHHHhCCCcccccCCCceEhHH
Confidence 455566553 3589999999988854 234321 23578864
No 35
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=50.83 E-value=90 Score=26.13 Aligned_cols=38 Identities=18% Similarity=0.153 Sum_probs=23.9
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHHh----cCCcc-CCccchh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYEQ----FGITL-RNVFDTQ 220 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~----~GI~L-~nvFDTq 220 (224)
.+..++.+ ...|+|+..+|...|.+. +|..+ ...+|++
T Consensus 104 ~~~~~i~~--~~lv~hn~~fD~~fL~~~~~~~~~~~~~~~~id~~ 146 (202)
T PRK09145 104 QLLAFIGN--RPLVGYYLEFDVAMLNRYVRPLLGIPLPNPLIEVS 146 (202)
T ss_pred HHHHHHcC--CeEEEeCHHHHHHHHHHHHHHhcCCCCCCCeeeHH
Confidence 45556654 346999999999888542 34444 2346764
No 36
>KOG2249|consensus
Probab=49.38 E-value=48 Score=30.20 Aligned_cols=119 Identities=23% Similarity=0.230 Sum_probs=64.6
Q ss_pred ccchHHHHHHHHHHHHHHhhcccCCCCCCCCCCccccCCCCccccCCCCcEEecCHHHHHHHHHHHccCCeEEEEEeeeC
Q psy5654 67 QNQTFKQRFNSLVLKTIAQNTEKDQRYPSSNGGYVANNSDNFKTKVLQNTKVITNIKECSSVVEELMRNELVTFDCEGIN 146 (224)
Q Consensus 67 ~~~~~~q~~~~~~~~~l~~n~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~vIdt~eeLa~lie~L~~~~~Ia~D~E~~~ 146 (224)
-.+.+.||.|..-.+..+++-.+..+-....++ ....+.- . .....+....++++|||-.+
T Consensus 56 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~----~-------k~s~~~~~~r~vAmDCEMVG 116 (280)
T KOG2249|consen 56 GKNIFSQRGNRFKATIKASPGKRRIHQGSCQAS--------CRMAALG----S-------KDSRMGSLTRVVAMDCEMVG 116 (280)
T ss_pred cCccccchhhHHHhhHhhcCCcchhhhcccCCC--------ccccccc----h-------hhccccccceEEEEeeeEec
Confidence 356688999999988888877766642221111 0000000 0 00011112368999999766
Q ss_pred CCccce---EEEEEEEeeCCeEEEEeCCCCc-----c------------cccc-------chhHhhhcCCCceEEEEecH
Q psy5654 147 PGIKGQ---ITLFSLGLLSGQVYIFDLVTCP-----E------------VVGT-------GGLSKLLESENVIKVIHDCR 199 (224)
Q Consensus 147 l~~~g~---L~lIQIat~~g~a~lIDi~al~-----~------------l~~~-------~~Lr~lLed~~I~KV~Hd~K 199 (224)
.+..|. ++-++|-...|.+. +|-.-.+ + +..+ ..+.++|.+ -+.|||+++
T Consensus 117 ~Gp~G~~s~lARvSIVN~~G~Vv-yDkyVkP~~~VtDyRT~vSGIrpehm~~A~pf~~aQ~ev~klL~g--RIlVGHaLh 193 (280)
T KOG2249|consen 117 VGPDGRESLLARVSIVNYHGHVV-YDKYVKPTEPVTDYRTRVSGIRPEHMRDAMPFKVAQKEVLKLLKG--RILVGHALH 193 (280)
T ss_pred cCCCccceeeeEEEEeeccCcEe-eeeecCCCcccccceeeecccCHHHhccCccHHHHHHHHHHHHhC--CEEeccccc
Confidence 644554 44455554445433 3443111 0 0000 235557765 456999999
Q ss_pred HHHHHHHH
Q psy5654 200 NDSILLYE 207 (224)
Q Consensus 200 ~Dl~lL~~ 207 (224)
+|+.+|.-
T Consensus 194 nDl~~L~l 201 (280)
T KOG2249|consen 194 NDLQALKL 201 (280)
T ss_pred cHHHHHhh
Confidence 99999864
No 37
>PRK07883 hypothetical protein; Validated
Probab=47.86 E-value=64 Score=31.94 Aligned_cols=88 Identities=18% Similarity=0.148 Sum_probs=48.5
Q ss_pred HccCCeEEEEEeeeCC-CccceEEEEEEEe-eCCe-----EEEEeCCC-Cc-----------cccc-c-------chhHh
Q psy5654 132 LMRNELVTFDCEGINP-GIKGQITLFSLGL-LSGQ-----VYIFDLVT-CP-----------EVVG-T-------GGLSK 184 (224)
Q Consensus 132 L~~~~~Ia~D~E~~~l-~~~g~L~lIQIat-~~g~-----a~lIDi~a-l~-----------~l~~-~-------~~Lr~ 184 (224)
+.....+.||+|+.++ +....++-|+.-. ..+. ..++.+.. .+ +.+. + ..|..
T Consensus 12 ~~~~~~Vv~D~ETTGl~p~~~~IIEIgaV~v~~g~iv~~f~~lV~P~~~i~~~~~~itGIt~e~l~~ap~~~evl~~f~~ 91 (557)
T PRK07883 12 LRDVTFVVVDLETTGGSPAGDAITEIGAVKVRGGEVLGEFATLVNPGRPIPPFITVLTGITTAMVAGAPPIEEVLPAFLE 91 (557)
T ss_pred CcCCCEEEEEEecCCCCCCCCeEEEEEEEEEECCEEEEEEEEEECCCCCCChhHHhhcCCCHHHHhCCCCHHHHHHHHHH
Confidence 4456789999998876 4444544433332 2232 12333321 10 0000 0 24455
Q ss_pred hhcCCCceEEEEecHHHHHHHHH---hcCCccC--Cccchhh
Q psy5654 185 LLESENVIKVIHDCRNDSILLYE---QFGITLR--NVFDTQL 221 (224)
Q Consensus 185 lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L~--nvFDTqL 221 (224)
++.+ ..-|+||+.+|...|.+ ++|+... ..+||+.
T Consensus 92 fl~~--~~lVaHNa~FD~~fL~~~~~r~g~~~~~~~~iDTl~ 131 (557)
T PRK07883 92 FARG--AVLVAHNAPFDIGFLRAAAARCGYPWPGPPVLCTVR 131 (557)
T ss_pred HhcC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCcEecHH
Confidence 6664 45689999999988854 4566652 3578864
No 38
>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=45.55 E-value=56 Score=26.45 Aligned_cols=36 Identities=25% Similarity=0.120 Sum_probs=22.5
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHHhcCCccCCccchh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQ 220 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTq 220 (224)
.+..++.+ -.-|+|++++|+..|... .....+.||.
T Consensus 70 ~l~~~l~~--~vlV~Hn~~~D~~~l~~~--~~~~~~~Dt~ 105 (157)
T cd06149 70 EILKILKG--KVVVGHAIHNDFKALKYF--HPKHMTRDTS 105 (157)
T ss_pred HHHHHcCC--CEEEEeCcHHHHHHhccc--CCCcCEEECc
Confidence 44556643 457999999999988532 1112355764
No 39
>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=42.89 E-value=79 Score=25.25 Aligned_cols=37 Identities=27% Similarity=0.284 Sum_probs=24.2
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHHhcCCccCCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqL 221 (224)
.|..++.+ . .-|+|++.+|+..|. .+.....++||..
T Consensus 70 ~l~~~l~~-~-vlVgHn~~fD~~~L~--~~~~~~~~~dt~~ 106 (152)
T cd06144 70 KVAELLKG-R-ILVGHALKNDLKVLK--LDHPKKLIRDTSK 106 (152)
T ss_pred HHHHHhCC-C-EEEEcCcHHHHHHhc--CcCCCccEEEeEE
Confidence 46667765 4 359999999999984 3322234567653
No 40
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=42.01 E-value=91 Score=29.67 Aligned_cols=74 Identities=9% Similarity=0.109 Sum_probs=41.1
Q ss_pred HccCCeEEEEEeeeCC-CccceEEEEEEE-ee-CCe---E--EEEeCCC------Cc----ccc-cc-------chhHhh
Q psy5654 132 LMRNELVTFDCEGINP-GIKGQITLFSLG-LL-SGQ---V--YIFDLVT------CP----EVV-GT-------GGLSKL 185 (224)
Q Consensus 132 L~~~~~Ia~D~E~~~l-~~~g~L~lIQIa-t~-~g~---a--~lIDi~a------l~----~l~-~~-------~~Lr~l 185 (224)
+.....++||+|..++ +...++.-|..- .. ++. . .+|.+.. +. +.+ .+ ..|.++
T Consensus 43 ~~~~~fVvlDiETTGLdp~~drIIeIgAV~i~~~g~ive~f~tLVnP~~~~~p~~LHGIT~e~La~AP~f~eVl~el~~f 122 (377)
T PRK05601 43 IEAAPFVAVSIQTSGIHPSTSRLITIDAVTLTADGEEVEHFHAVLNPGEDPGPFHLHGLSAEEFAQGKRFSQILKPLDRL 122 (377)
T ss_pred CCCCCEEEEEEECCCCCCCCCeEEEEEEEEEEcCCEEEEEEEEEECcCCCCCCccccCCCHHHHhcCCCHHHHHHHHHHH
Confidence 4556899999999887 655664433222 22 221 1 2333321 00 000 00 345556
Q ss_pred hcCCCceEEEEecHHHHHHHHH
Q psy5654 186 LESENVIKVIHDCRNDSILLYE 207 (224)
Q Consensus 186 Led~~I~KV~Hd~K~Dl~lL~~ 207 (224)
+.+ ...|+||+.+|+..|.+
T Consensus 123 L~g--~vLVaHNA~FD~~FL~~ 142 (377)
T PRK05601 123 IDG--RTLILHNAPRTWGFIVS 142 (377)
T ss_pred hCC--CEEEEECcHHHHHHHHH
Confidence 664 35699999999998754
No 41
>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=40.49 E-value=86 Score=26.71 Aligned_cols=26 Identities=19% Similarity=0.235 Sum_probs=18.7
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHHh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYEQ 208 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~ 208 (224)
.|..++.+ -.-|+||+.+|..+|.+.
T Consensus 80 ~~~~~~~~--~~lVaHNa~FD~~fL~~~ 105 (217)
T TIGR00573 80 DFADYIRG--AELVIHNASFDVGFLNYE 105 (217)
T ss_pred HHHHHhCC--CEEEEeccHHHHHHHHHH
Confidence 34455554 356899999999998754
No 42
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=37.29 E-value=1.4e+02 Score=26.24 Aligned_cols=38 Identities=18% Similarity=0.197 Sum_probs=23.8
Q ss_pred hHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc------CCccchhh
Q psy5654 182 LSKLLESENVIKVIHDCRNDSILLYE---QFGITL------RNVFDTQL 221 (224)
Q Consensus 182 Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L------~nvFDTqL 221 (224)
|..++.+. ..|+||+.+|+..|.+ ++|..+ ..++||+.
T Consensus 80 f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~ 126 (240)
T PRK05711 80 FLDFIRGA--ELIIHNAPFDIGFMDYEFALLGRDIPKTNTFCKVTDTLA 126 (240)
T ss_pred HHHHhCCC--EEEEEccHHhHHHHHHHHHHhCCCCCcccccCceeeHHH
Confidence 44455543 3589999999988753 344322 23678764
No 43
>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=36.57 E-value=1.3e+02 Score=33.02 Aligned_cols=88 Identities=19% Similarity=0.242 Sum_probs=49.2
Q ss_pred ccCCeEEEEEeeeCC-CccceEEEEEEEe-eCCeE-----EEEeCCC-Cc-----------cccc-----c---chhHhh
Q psy5654 133 MRNELVTFDCEGINP-GIKGQITLFSLGL-LSGQV-----YIFDLVT-CP-----------EVVG-----T---GGLSKL 185 (224)
Q Consensus 133 ~~~~~Ia~D~E~~~l-~~~g~L~lIQIat-~~g~a-----~lIDi~a-l~-----------~l~~-----~---~~Lr~l 185 (224)
.....+.||+|+.++ +...+++-++... .++.. .++.+.. .+ +.+. . ..+..+
T Consensus 188 ~~~~~VVfDiETTGL~~~~d~IIEIGAVkv~~g~iid~f~~~V~P~~~I~~~~~~ltGIT~e~L~~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQYDEIIEFGAVKVKNGRIIDKFQFFIKPHEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEF 267 (1213)
T ss_pred cCCcEEEEEeEecCCCCCCCeEEEEEEEEEECCeEEEEEEEEECCCCCCCHHHHHHhCCCHHHHhCCCCHHHHHHHHHHH
Confidence 456789999999877 5555655444432 23322 2222210 00 0000 0 345556
Q ss_pred hcCCCceEEEEecHHHHHHHHH---hcCCcc--CCccchhhc
Q psy5654 186 LESENVIKVIHDCRNDSILLYE---QFGITL--RNVFDTQLL 222 (224)
Q Consensus 186 Led~~I~KV~Hd~K~Dl~lL~~---~~GI~L--~nvFDTqLA 222 (224)
+.+ -.-|+||+.+|...|.+ ++|+.. ...+||+..
T Consensus 268 l~~--~iLVaHNa~FD~~fL~~~~~r~g~~~~~~~~IDTl~l 307 (1213)
T TIGR01405 268 FKD--SILVAHNASFDIGFLNTNFEKVGLEPLENPVIDTLEL 307 (1213)
T ss_pred hCC--CeEEEEChHHHHHHHHHHHHHcCCCccCCCEeEHHHH
Confidence 654 35699999999988864 356542 345788643
No 44
>cd06137 DEDDh_RNase DEDDh 3'-5' exonuclease domain of the eukaryotic exoribonucleases PAN2, RNA exonuclease (REX)-1,-3, and -4, ISG20, and similar proteins. This group is composed of eukaryotic exoribonucleases that include PAN2, RNA exonuclease 1 (REX1 or Rex1p), REX3 (Rex3p), REX4 (or Rex4p), ISG20, and similar proteins. They are DEDDh-type DnaQ-like 3'-5' exonucleases containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. PAN2 is the catalytic subunit of poly(A) nuclease (PAN), a Pab1p-dependent 3'-5' exoribonuclease which plays an important role in the posttranscriptional maturation of pre-mRNAs. REX proteins are required for the processing and maturation of many RNA species, and ISG20 is an interferon-induced antiviral exonuclease with a strong prefere
Probab=30.83 E-value=1.7e+02 Score=23.56 Aligned_cols=36 Identities=33% Similarity=0.371 Sum_probs=22.9
Q ss_pred hHhhhcCCCceEEEEecHHHHHHHHHhcCCccCCccchhhc
Q psy5654 182 LSKLLESENVIKVIHDCRNDSILLYEQFGITLRNVFDTQLL 222 (224)
Q Consensus 182 Lr~lLed~~I~KV~Hd~K~Dl~lL~~~~GI~L~nvFDTqLA 222 (224)
|..++.+. ..-|+|++.+|+..|.. . ...+.||...
T Consensus 77 ~~~~i~~~-~vlVgHn~~fD~~fL~~-~---~~~~iDT~~l 112 (161)
T cd06137 77 LWKFIDPD-TILVGHSLQNDLDALRM-I---HTRVVDTAIL 112 (161)
T ss_pred HHHhcCCC-cEEEeccHHHHHHHHhC-c---CCCeeEehhh
Confidence 34455432 45699999999999853 2 2345677643
No 45
>PF11577 NEMO: NF-kappa-B essential modulator NEMO; InterPro: IPR021063 This entry represents a conserved domain found at the N-terminal of NF-kappa-B essential modulator (NEMO) and optineurin proteins. NEMO is a regulatory protein which is part of the IKK complex along with the catalytic IKKalpha and beta kinases. The IKK complex phosphorylates IkappaB targeting it for degradation which results in the release of NF-kappaB which initiates the inflammatory response, cell proliferation or cell differentiation []. NEMO activates the IKK complex's activity by associating with the unphosphorylated IKK kinase C termini. The core domain of NEMO is a dimer which binds to two fragments of IKK []. ; PDB: 3BRT_B 3BRV_D.
Probab=29.72 E-value=40 Score=24.31 Aligned_cols=16 Identities=38% Similarity=0.588 Sum_probs=13.9
Q ss_pred ccchHHHHHHHHHHHH
Q psy5654 67 QNQTFKQRFNSLVLKT 82 (224)
Q Consensus 67 ~~~~~~q~~~~~~~~~ 82 (224)
-|+++|+|++.|..|.
T Consensus 25 ~N~~Mker~e~l~~wq 40 (68)
T PF11577_consen 25 NNQAMKERFEELLAWQ 40 (68)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3889999999999875
No 46
>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=28.01 E-value=2.4e+02 Score=29.34 Aligned_cols=39 Identities=28% Similarity=0.262 Sum_probs=25.8
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc--CCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYE---QFGITL--RNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L--~nvFDTqL 221 (224)
.|..++.+ -.-|+||+.+|...|.+ +.|+.. ...+||+.
T Consensus 73 ~l~~~l~~--~~~VahN~~fD~~fL~~~~~~~g~~~~~~~~iDt~~ 116 (850)
T TIGR01407 73 EIYDLLED--GIFVAHNVHFDLNFLAKALKDCGYEPLPKPRIDTVE 116 (850)
T ss_pred HHHHHhCC--CEEEEeCcHHHHHHHHHHHHHcCCCCCCCCeEeHHH
Confidence 34456654 34699999999988864 356553 34578864
No 47
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=26.18 E-value=2.4e+02 Score=29.34 Aligned_cols=39 Identities=33% Similarity=0.343 Sum_probs=26.2
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHHh---cCCcc-CCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYEQ---FGITL-RNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~~---~GI~L-~nvFDTqL 221 (224)
.+.+++.+ ..-|+||+.+|+..|.+. .|..+ ...+||+.
T Consensus 79 ~~~~~l~~--~~lVaHN~~FD~~fL~~~~~~~g~~~~~~~iDT~~ 121 (820)
T PRK07246 79 HIYDLIED--CIFVAHNVKFDANLLAEALFLEGYELRTPRVDTVE 121 (820)
T ss_pred HHHHHhCC--CEEEEECcHHHHHHHHHHHHHcCCCCCCCceeHHH
Confidence 34556654 446999999999988643 45555 33578764
No 48
>PRK07740 hypothetical protein; Provisional
Probab=25.71 E-value=3.3e+02 Score=23.72 Aligned_cols=38 Identities=16% Similarity=0.324 Sum_probs=23.3
Q ss_pred hHhhhcCCCceEEEEecHHHHHHHHHh----cCCcc-CCccchhh
Q psy5654 182 LSKLLESENVIKVIHDCRNDSILLYEQ----FGITL-RNVFDTQL 221 (224)
Q Consensus 182 Lr~lLed~~I~KV~Hd~K~Dl~lL~~~----~GI~L-~nvFDTqL 221 (224)
|..++.+ -.-|+|++.+|...|.+. ++..+ ...+||+.
T Consensus 135 f~~fi~~--~~lVahna~fD~~fL~~~~~~~~~~~~~~~~iDt~~ 177 (244)
T PRK07740 135 FYAFIGA--GVLVAHHAGHDKAFLRHALWRTYRQPFTHRLIDTMF 177 (244)
T ss_pred HHHHhCC--CEEEEeCHHHHHHHHHHHHHHhcCCCcCCCeechHH
Confidence 3334443 356899999999877532 33333 34578764
No 49
>TIGR01406 dnaQ_proteo DNA polymerase III, epsilon subunit, Proteobacterial. This model represents DnaQ, the DNA polymerase III epsilon subunit, as found in most Proteobacteria. It consists largely of an exonuclease domain as described in pfam model pfam00929. In Gram-positive bacteria, closely related regions are found both in the Gram-positive type DNA polymerase III alpha subunit and as an additional N-terminal domain of a DinG-family helicase. Both are excluded from this model, as are smaller proteins, also outside the Proteobacteria, that are similar in size to the epsilon subunit but as different in sequence as are the epsilon-like regions found in Gram-positive bacteria.
Probab=24.38 E-value=3.1e+02 Score=23.57 Aligned_cols=40 Identities=23% Similarity=0.277 Sum_probs=25.3
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHH---hcCC--c-c---CCccchhhc
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYE---QFGI--T-L---RNVFDTQLL 222 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI--~-L---~nvFDTqLA 222 (224)
.|..++.+. .-|+||+.+|+.+|.+ ++|. . + ..++||+..
T Consensus 75 ~f~~fi~~~--~lVaHNa~FD~~fL~~el~r~g~~~~~~~~~~~~iDTl~l 123 (225)
T TIGR01406 75 EFLDFIGGS--ELVIHNAAFDVGFLNYELERLGPTIKKIGEFCRVIDTLAM 123 (225)
T ss_pred HHHHHhCCC--EEEEEecHHHHHHHHHHHHHhCCCCcccccCCCEEEHHHH
Confidence 344566543 3589999999988853 3552 2 1 346788653
No 50
>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=24.22 E-value=98 Score=24.06 Aligned_cols=39 Identities=18% Similarity=0.253 Sum_probs=26.8
Q ss_pred hhHhhhcCCCceEEEEecHHHHHHHHH---hcCCcc--CCccchhh
Q psy5654 181 GLSKLLESENVIKVIHDCRNDSILLYE---QFGITL--RNVFDTQL 221 (224)
Q Consensus 181 ~Lr~lLed~~I~KV~Hd~K~Dl~lL~~---~~GI~L--~nvFDTqL 221 (224)
.|..++++ ..-|+||+.+|...|.+ ++|+.. ...+||+.
T Consensus 70 ~l~~~l~~--~~lv~hn~~fD~~~l~~~~~~~g~~~~~~~~idt~~ 113 (156)
T cd06130 70 EIKPFLGG--SLVVAHNASFDRSVLRAALEAYGLPPPPYQYLCTVR 113 (156)
T ss_pred HHHHHhCC--CEEEEeChHHhHHHHHHHHHHcCCCCCCCCEEEHHH
Confidence 46667765 45699999999998853 356654 33578764
No 51
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=20.86 E-value=1.2e+02 Score=24.03 Aligned_cols=69 Identities=16% Similarity=0.107 Sum_probs=31.3
Q ss_pred EEEEEeeeCC-CccceEEEEEEEe-eCCe-EEEEeCCCCc-cccccchhH---hhhcCCCceEEEEe-cHHHHHHHHHhc
Q psy5654 138 VTFDCEGINP-GIKGQITLFSLGL-LSGQ-VYIFDLVTCP-EVVGTGGLS---KLLESENVIKVIHD-CRNDSILLYEQF 209 (224)
Q Consensus 138 Ia~D~E~~~l-~~~g~L~lIQIat-~~g~-a~lIDi~al~-~l~~~~~Lr---~lLed~~I~KV~Hd-~K~Dl~lL~~~~ 209 (224)
+.||+|+.++ +..+.+.++.++. .+++ .++....... ... ..+. ..+...... |+|+ ..+|...|.+.+
T Consensus 1 l~~DIET~Gl~~~~~~i~liG~~~~~~~~~~~~~~~~~~~~~ee--~~~~~~~~~l~~~~~i-v~yng~~FD~p~L~~~~ 77 (164)
T PF13482_consen 1 LFFDIETTGLSPDNDTIYLIGVADFDDDEIITFIQWFAEDPDEE--EIILEFFELLDEADNI-VTYNGKNFDIPFLKRRA 77 (164)
T ss_dssp --EEEEESS-GG-G---EEEEEEE-ETTTTE-EEEE-GGGHHHH--HHHHH--HHHHTT--E-EESSTTTTHHHHHHHHH
T ss_pred CcEEecCCCCCCCCCCEEEEEEEEeCCCceEEeeHhhccCcHHH--HHHHHHHHHHhcCCeE-EEEeCcccCHHHHHHHH
Confidence 4689999877 5566777777775 2222 2233222111 110 1222 345555443 5555 577998887544
Done!