Query 048636
Match_columns 150
No_of_seqs 115 out of 445
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 11:26:39 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048636.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048636hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0304 mRNA deadenylase subun 100.0 1.9E-40 4.1E-45 265.4 7.6 116 23-150 1-116 (239)
2 PF04857 CAF1: CAF1 family rib 100.0 6.5E-35 1.4E-39 239.2 8.2 113 25-150 1-114 (262)
3 COG5228 POP2 mRNA deadenylase 100.0 2.4E-35 5.3E-40 237.5 5.5 116 21-150 17-132 (299)
4 KOG1990 Poly(A)-specific exori 98.6 8E-09 1.7E-13 93.5 0.3 104 29-145 1-110 (564)
5 cd06133 ERI-1_3'hExo_like DEDD 93.6 0.2 4.4E-06 37.4 5.6 59 48-139 1-59 (176)
6 PRK05168 ribonuclease T; Provi 85.6 2.1 4.6E-05 34.0 5.4 24 36-59 7-30 (211)
7 PRK09145 DNA polymerase III su 82.7 1.7 3.7E-05 34.0 3.6 22 38-59 21-42 (202)
8 PF00929 RNase_T: Exonuclease; 82.1 3.3 7.2E-05 29.4 4.7 44 49-130 1-44 (164)
9 cd06134 RNaseT DEDDh 3'-5' exo 81.1 4.1 8.8E-05 31.7 5.2 33 44-104 3-35 (189)
10 COG0349 Rnd Ribonuclease D [Tr 80.7 1.2 2.5E-05 38.9 2.2 26 34-59 5-30 (361)
11 PF01612 DNA_pol_A_exo1: 3'-5' 80.0 1.6 3.4E-05 32.2 2.4 28 33-60 7-34 (176)
12 PRK07247 DNA polymerase III su 79.2 2.6 5.7E-05 33.3 3.6 13 47-59 6-18 (195)
13 cd06130 DNA_pol_III_epsilon_li 78.4 4.6 0.0001 29.4 4.6 11 48-58 1-11 (156)
14 smart00479 EXOIII exonuclease 77.7 2.4 5.2E-05 31.1 2.8 13 47-59 1-13 (169)
15 TIGR01298 RNaseT ribonuclease 77.4 5.8 0.00013 31.2 5.1 16 44-59 6-21 (200)
16 cd06127 DEDDh DEDDh 3'-5' exon 76.6 2.1 4.5E-05 30.5 2.2 14 92-105 16-29 (159)
17 PRK07942 DNA polymerase III su 75.3 3.2 6.9E-05 33.5 3.1 35 44-106 4-38 (232)
18 PRK06063 DNA polymerase III su 71.2 3.7 8E-05 34.8 2.7 33 46-106 15-47 (313)
19 PRK05601 DNA polymerase III su 70.3 6.3 0.00014 34.7 4.0 37 42-106 42-78 (377)
20 TIGR00573 dnaq exonuclease, DN 69.8 6.3 0.00014 31.2 3.6 17 43-59 4-20 (217)
21 PRK06807 DNA polymerase III su 69.2 6.6 0.00014 33.4 3.8 13 47-59 9-21 (313)
22 PRK09146 DNA polymerase III su 68.4 5.1 0.00011 32.6 2.9 17 43-59 44-60 (239)
23 PRK05359 oligoribonuclease; Pr 67.6 5.6 0.00012 30.9 2.9 14 46-59 3-16 (181)
24 TIGR01388 rnd ribonuclease D. 67.2 4.7 0.0001 34.9 2.6 26 33-58 5-30 (367)
25 PRK06310 DNA polymerase III su 66.9 4.6 0.0001 33.0 2.4 18 42-59 3-20 (250)
26 PRK07883 hypothetical protein; 64.3 7.2 0.00016 35.7 3.3 20 40-59 9-28 (557)
27 PRK10829 ribonuclease D; Provi 64.0 5.4 0.00012 34.8 2.4 25 34-58 10-34 (373)
28 PRK07748 sporulation inhibitor 61.5 9.5 0.00021 29.9 3.2 16 45-60 3-18 (207)
29 cd06141 WRN_exo DEDDy 3'-5' ex 60.2 8.4 0.00018 28.7 2.6 28 33-60 4-32 (170)
30 cd06146 mut-7_like_exo DEDDy 3 59.9 7.6 0.00017 30.3 2.3 27 33-59 7-35 (193)
31 PRK09182 DNA polymerase III su 59.4 13 0.00028 31.4 3.7 30 47-104 38-67 (294)
32 PRK11779 sbcB exonuclease I; P 59.1 28 0.00061 31.5 6.0 33 45-105 5-37 (476)
33 PTZ00315 2'-phosphotransferase 58.4 28 0.0006 32.4 6.0 48 47-129 57-104 (582)
34 TIGR02841 spore_YyaC putative 58.3 8.2 0.00018 29.5 2.2 30 26-55 43-72 (140)
35 PF11959 DUF3473: Domain of un 52.7 27 0.00057 26.1 4.1 46 8-53 83-128 (133)
36 cd06131 DNA_pol_III_epsilon_Ec 51.3 16 0.00036 27.0 2.9 12 48-59 1-12 (167)
37 PF13606 Ank_3: Ankyrin repeat 50.9 16 0.00035 19.9 2.1 16 135-150 14-29 (30)
38 cd06136 TREX1_2 DEDDh 3'-5' ex 50.7 16 0.00036 27.9 2.8 31 48-105 1-31 (177)
39 TIGR01229 rocF_arginase argina 50.3 46 0.00099 27.8 5.6 69 26-103 196-273 (300)
40 PRK08517 DNA polymerase III su 49.3 26 0.00056 28.9 3.9 23 37-59 59-81 (257)
41 cd06149 ISG20 DEDDh 3'-5' exon 45.3 8.7 0.00019 29.0 0.5 13 49-61 1-13 (157)
42 cd06138 ExoI_N N-terminal DEDD 43.5 59 0.0013 24.8 5.0 14 93-106 17-30 (183)
43 KOG2249 3'-5' exonuclease [Rep 43.3 11 0.00023 32.0 0.7 17 47-63 106-122 (280)
44 PF06866 DUF1256: Protein of u 43.2 18 0.00039 28.3 2.0 32 25-56 66-97 (163)
45 PRK07740 hypothetical protein; 43.1 10 0.00022 30.8 0.7 17 43-59 56-72 (244)
46 PRK13772 formimidoylglutamase; 42.9 87 0.0019 26.4 6.2 69 26-103 218-294 (314)
47 cd06135 Orn DEDDh 3'-5' exonuc 42.5 27 0.00058 26.6 2.8 29 48-104 1-29 (173)
48 PF04405 ScdA_N: Domain of Unk 41.3 20 0.00043 22.9 1.7 15 135-149 12-26 (56)
49 PRK06195 DNA polymerase III su 40.8 50 0.0011 27.7 4.5 11 47-57 2-12 (309)
50 cd06129 RNaseD_like DEDDy 3'-5 38.0 25 0.00055 26.2 2.1 24 36-59 2-26 (161)
51 cd06137 DEDDh_RNase DEDDh 3'-5 37.7 12 0.00026 28.1 0.3 12 49-60 1-12 (161)
52 PRK05755 DNA polymerase I; Pro 35.6 29 0.00062 33.4 2.5 26 34-59 303-328 (880)
53 TIGR01407 dinG_rel DnaQ family 35.0 31 0.00067 33.0 2.6 13 47-59 1-13 (850)
54 cd06144 REX4_like DEDDh 3'-5' 34.8 15 0.00033 27.2 0.4 12 49-60 1-12 (152)
55 cd06148 Egl_like_exo DEDDy 3'- 32.5 28 0.00061 27.1 1.6 20 41-60 5-24 (197)
56 cd06145 REX1_like DEDDh 3'-5' 32.0 18 0.00038 27.0 0.3 12 49-60 1-12 (150)
57 PRK06309 DNA polymerase III su 30.4 37 0.00079 27.2 2.0 13 47-59 3-15 (232)
58 PRK01722 formimidoylglutamase; 30.0 1.3E+02 0.0029 25.1 5.4 69 26-103 217-293 (320)
59 TIGR03358 VI_chp_5 type VI sec 30.0 44 0.00096 26.0 2.3 38 3-42 35-72 (159)
60 PRK02190 agmatinase; Provision 29.5 1.4E+02 0.0031 24.8 5.4 66 28-103 200-272 (301)
61 TIGR01405 polC_Gram_pos DNA po 28.5 75 0.0016 32.2 4.1 16 44-59 188-203 (1213)
62 PRK07246 bifunctional ATP-depe 28.1 48 0.001 31.9 2.6 15 45-59 6-20 (820)
63 PRK13775 formimidoylglutamase; 27.4 2E+02 0.0044 24.3 6.1 69 26-103 225-301 (328)
64 TIGR01227 hutG formimidoylglut 26.8 2.2E+02 0.0048 23.7 6.2 64 31-103 215-286 (307)
65 KOG1990 Poly(A)-specific exori 26.3 13 0.00027 34.3 -1.6 72 21-101 101-174 (564)
66 PF00491 Arginase: Arginase fa 26.0 67 0.0014 26.1 2.8 72 23-103 175-255 (277)
67 PRK13776 formimidoylglutamase; 23.1 2.5E+02 0.0055 23.6 5.8 69 26-103 219-295 (318)
68 cd06125 DnaQ_like_exo DnaQ-lik 22.9 34 0.00073 23.5 0.4 11 49-59 1-11 (96)
69 PF05591 DUF770: Protein of un 21.5 61 0.0013 25.0 1.6 38 4-43 35-72 (157)
70 PRK08074 bifunctional ATP-depe 21.4 77 0.0017 30.8 2.6 13 46-58 3-15 (928)
71 cd06143 PAN2_exo DEDDh 3'-5' e 21.1 32 0.00069 27.1 -0.0 13 49-61 1-13 (174)
72 PF04386 SspB: Stringent starv 21.0 43 0.00094 25.5 0.7 17 45-61 31-47 (155)
73 COG0358 DnaG DNA primase (bact 20.9 90 0.002 28.5 2.9 30 77-106 3-44 (568)
No 1
>KOG0304 consensus mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=1.9e-40 Score=265.36 Aligned_cols=116 Identities=59% Similarity=0.977 Sum_probs=109.1
Q ss_pred eEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeec
Q 048636 23 IIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD 102 (150)
Q Consensus 23 ~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~ 102 (150)
.|||||+.|+++||..|+++|++|+||||||||||++.+|. +.|.+ +.+++|+.||+|||.+++||+|||+++
T Consensus 1 ~ireVW~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~-----~~f~s--~~d~~Y~~lk~NVd~lklIQlGlTlsd 73 (239)
T KOG0304|consen 1 FIREVWRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPI-----GTFRS--SDDYHYQTLKCNVDNLKLIQLGLTLSD 73 (239)
T ss_pred ChhHHHHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecC-----ccccC--ChHHHHHHHHhchhhhhhhheeeeeec
Confidence 47999999999999999999999999999999999999998 67766 569999999999999999999999999
Q ss_pred CCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636 103 SSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE 150 (150)
Q Consensus 103 ~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn 150 (150)
.+|++|..| ..+|||||..|+..+|+++++||+||+++|+||.
T Consensus 74 ~~Gn~p~~g-----~~tWqfNF~dF~~~~D~~a~~SIElLr~~Gidf~ 116 (239)
T KOG0304|consen 74 EKGNLPDCG-----TDTWQFNFSDFNLEKDMYAQDSIELLRRSGIDFE 116 (239)
T ss_pred cCCCCCCCC-----CceeEEecccCCchhhccchhhHHHHHHcCcCHH
Confidence 999999664 4699999999999999999999999999999984
No 2
>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=100.00 E-value=6.5e-35 Score=239.15 Aligned_cols=113 Identities=40% Similarity=0.697 Sum_probs=97.5
Q ss_pred EEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeee-cC
Q 048636 25 REVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLS-DS 103 (150)
Q Consensus 25 ~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f-~~ 103 (150)
+|||++||+++|+.|+++|++|+|||||+||||+..++.. ..++ ++++||+++|+||+.+.|||+|||+| +.
T Consensus 1 m~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~----~~~~---t~~~rY~~~r~~v~~~~iiQ~Glt~f~~~ 73 (262)
T PF04857_consen 1 MEVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPR----SRFD---TPEERYEKLRANVETFQIIQFGLTLFHDE 73 (262)
T ss_dssp EEE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-S----HCSS---HHHHHHHHHHHHHTTBEEEEEEEEEETTT
T ss_pred CcccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCc----cccc---cHHHHHHHHHHhhcccccceeeEEEeecc
Confidence 6999999999999999999999999999999999988872 2333 78999999999999999999999999 66
Q ss_pred CCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636 104 SGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE 150 (150)
Q Consensus 104 ~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn 150 (150)
+++.|. .|.+|+|||++||..++.++++||+||++||||||
T Consensus 74 ~~~~~~------~~~~~~~nf~~f~~~~~~~~~~sl~FL~~~gfDFn 114 (262)
T PF04857_consen 74 DGNIPS------SYNVWPFNFYLFPLDRDFSQASSLQFLRKNGFDFN 114 (262)
T ss_dssp TSEEEC------CEEEEEEEBSTTSTTTCEEEHHHHHHHHHTT--HH
T ss_pred cccCCc------eeEEEEeeeeccccccceecchhHHHHHHcccCHH
Confidence 777653 58999999999999999889999999999999996
No 3
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=100.00 E-value=2.4e-35 Score=237.49 Aligned_cols=116 Identities=52% Similarity=0.882 Sum_probs=110.1
Q ss_pred CceEEEecccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeee
Q 048636 21 SIIIREVWASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTL 100 (150)
Q Consensus 21 ~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~ 100 (150)
-.+|||||+.|+..||..|+++|.+|++|+|||||||++++|. |.|+++ .+.+||.||+|||-++|||+||++
T Consensus 17 ~~~irdVWk~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPi-----G~FkSs--~dyhYQtlraNVD~LkiIQlGlsL 89 (299)
T COG5228 17 YLFIRDVWKSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPI-----GTFKSS--VDYHYQTLRANVDFLKIIQLGLSL 89 (299)
T ss_pred hHHHHHHHHhhHHHHHHHHHHHHHhCCceeeccccCceeeccc-----cccccc--chHHHHHHhcccchhhhhheeeee
Confidence 3579999999999999999999999999999999999999998 899984 599999999999999999999999
Q ss_pred ecCCCCCCCCCCCCCCeeEEEEeccccCCCCCCcchhHHHHHHHcCCCCC
Q 048636 101 SDSSGNLPDLGSGGNNKFIWEFNFRDFDVATDAHAPDSIELLRLQGIDFE 150 (150)
Q Consensus 101 f~~~g~~p~~g~~~~~~~~~~FNF~~F~~~~d~~~~sSi~FL~~~GfDFn 150 (150)
.+++|+.|. ..++|||||- |+..+|++.++||++|+++|+||.
T Consensus 90 SDe~GN~P~------~~sTWQFNF~-F~l~~dmya~ESieLL~ksgIdFk 132 (299)
T COG5228 90 SDENGNKPN------GPSTWQFNFE-FDLKKDMYATESIELLRKSGIDFK 132 (299)
T ss_pred ccccCCCCC------CCceeEEEEE-ecchhhhcchHHHHHHHHcCCChh
Confidence 999999984 3799999999 999999999999999999999994
No 4
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=98.61 E-value=8e-09 Score=93.52 Aligned_cols=104 Identities=17% Similarity=0.126 Sum_probs=83.3
Q ss_pred ccCHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCC
Q 048636 29 ASNLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLP 108 (150)
Q Consensus 29 ~~Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p 108 (150)
+.||+. +..++..|+.+.|+|+|.|++|+...+..+ ...++ +++.+|+++|.++..+.++|+|+|+|.+++...
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~--~~~~~---~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~~~~ 74 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKA--GSTFD---TVEAIYLKWKDNEEVYLKFQFGLCLFMKRSHEA 74 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceeccccc--ccchh---hhHHHHHHHHhhhhhheeeccccchhHHHhhhH
Confidence 468889 999999999999999999999998887521 12244 899999999999999999999999999987643
Q ss_pred CCCCCCCCeeEEEEeccccCCC------CCCcchhHHHHHHHc
Q 048636 109 DLGSGGNNKFIWEFNFRDFDVA------TDAHAPDSIELLRLQ 145 (150)
Q Consensus 109 ~~g~~~~~~~~~~FNF~~F~~~------~d~~~~sSi~FL~~~ 145 (150)
.+..-.+||++|+.. +.+|+.+++.|+.++
T Consensus 75 -------~~~~~~~n~~~~~~g~~~s~~~~~~~~~~~~~~~~~ 110 (564)
T KOG1990|consen 75 -------LEMSTGGNFVVWSRGDSISSPEFLCQRSPVDFVARQ 110 (564)
T ss_pred -------hhccCCCceeeeecCccccCCccceeecchhhhhhh
Confidence 233345666666642 337899999998876
No 5
>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=93.64 E-value=0.2 Score=37.44 Aligned_cols=59 Identities=15% Similarity=0.069 Sum_probs=36.6
Q ss_pred ceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEecccc
Q 048636 48 FISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDF 127 (150)
Q Consensus 48 fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF~~F 127 (150)
||.+|+|++|+...... ... -.|||+|....+.++. ...-.|+.++-
T Consensus 1 ~vv~D~Ettg~~~~~~~----~~~-------------------~~IieIgav~v~~~~~----------~~~~~f~~~i~ 47 (176)
T cd06133 1 YLVIDFEATCWEGNSKP----DYP-------------------NEIIEIGAVLVDVKTK----------EIIDTFSSYVK 47 (176)
T ss_pred CEEEEeeccccCCCCCC----CCC-------------------cceEEEEEEEEEcCCC----------eEEeeeeeeEC
Confidence 79999999998643210 000 1499999999887653 24556777766
Q ss_pred CCCCCCcchhHH
Q 048636 128 DVATDAHAPDSI 139 (150)
Q Consensus 128 ~~~~d~~~~sSi 139 (150)
|......++.+.
T Consensus 48 P~~~~~i~~~~~ 59 (176)
T cd06133 48 PVINPKLSDFCT 59 (176)
T ss_pred CCcCCchhHHHH
Confidence 654233344333
No 6
>PRK05168 ribonuclease T; Provisional
Probab=85.59 E-value=2.1 Score=33.96 Aligned_cols=24 Identities=13% Similarity=0.259 Sum_probs=20.4
Q ss_pred HHHHHHHhhhCCceeccccccccc
Q 048636 36 FELISQVIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 36 l~~I~~~i~~~~fIAiDtEF~Gl~ 59 (150)
+.-|..-++...||++|+|-||+.
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~ 30 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFN 30 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCC
Confidence 455777788999999999999985
No 7
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=82.68 E-value=1.7 Score=33.96 Aligned_cols=22 Identities=18% Similarity=0.280 Sum_probs=16.3
Q ss_pred HHHHHhhhCCceeccccccccc
Q 048636 38 LISQVIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 38 ~I~~~i~~~~fIAiDtEF~Gl~ 59 (150)
.+.+.....+||+||+|.||+.
T Consensus 21 ~~~~~~~~~~~vviD~ETTGl~ 42 (202)
T PRK09145 21 FLFEPPPPDEWVALDCETTGLD 42 (202)
T ss_pred HHhcCCCCCCEEEEEeECCCCC
Confidence 3444445569999999999974
No 8
>PF00929 RNase_T: Exonuclease; InterPro: IPR013520 This entry includes a variety of exonuclease proteins, such as ribonuclease T [] and the epsilon subunit of DNA polymerase III. Ribonuclease T is responsible for the end-turnover of tRNA,and removes the terminal AMP residue from uncharged tRNA. DNA polymerase III is a complex, multichain enzyme responsible for most of the replicative synthesis in bacteria, and also exhibits 3' to 5' exonuclease activity.; PDB: 3CM6_A 3CM5_A 3CG7_A 1ZBU_B 1ZBH_A 1W0H_A 3NGY_C 2IS3_B 3NH1_C 3NH2_F ....
Probab=82.12 E-value=3.3 Score=29.43 Aligned_cols=44 Identities=27% Similarity=0.256 Sum_probs=29.8
Q ss_pred eecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEeccccC
Q 048636 49 ISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRDFD 128 (150)
Q Consensus 49 IAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF~~F~ 128 (150)
|.+|+|++|+..+. -.|||+|.-..+.+.. ...-.|+.++.|
T Consensus 1 v~~D~Ettg~~~~~----------------------------~~iieig~v~~~~~~~----------~~~~~~~~~i~p 42 (164)
T PF00929_consen 1 VVFDTETTGLDPRQ----------------------------DEIIEIGAVKVDDDEN----------EEVESFNSLIRP 42 (164)
T ss_dssp EEEEEEESSSTTTT----------------------------CTEEEEEEEEEETTTT----------EEEEEEEEEBEH
T ss_pred cEEEeEcCCCCCCC----------------------------CeEEEEEEEEeeCCcc----------ccceeeeecccc
Confidence 67999999985321 1389999988777542 244567777555
Q ss_pred CC
Q 048636 129 VA 130 (150)
Q Consensus 129 ~~ 130 (150)
..
T Consensus 43 ~~ 44 (164)
T PF00929_consen 43 EE 44 (164)
T ss_dssp SS
T ss_pred cc
Confidence 43
No 9
>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=81.07 E-value=4.1 Score=31.68 Aligned_cols=33 Identities=15% Similarity=0.249 Sum_probs=24.5
Q ss_pred hhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCC
Q 048636 44 DRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSS 104 (150)
Q Consensus 44 ~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~ 104 (150)
+.+.+|++|+|-||+..... .|||+|...+..+
T Consensus 3 ~~~~~vv~D~ETTGl~~~~d----------------------------~Iieigav~v~~~ 35 (189)
T cd06134 3 RGFLPVVVDVETGGFNPQTD----------------------------ALLEIAAVTLEMD 35 (189)
T ss_pred ccceeEEEEecCCCCCCCCC----------------------------eEEEEEEEEEEEC
Confidence 34678999999999853211 2899999988753
No 10
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=80.68 E-value=1.2 Score=38.95 Aligned_cols=26 Identities=23% Similarity=0.259 Sum_probs=21.3
Q ss_pred HHHHHHHHHhhhCCceeccccccccc
Q 048636 34 SEFELISQVIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 34 ~el~~I~~~i~~~~fIAiDtEF~Gl~ 59 (150)
+++..+...+..+++|||||||-|+.
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~~ 30 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRLR 30 (361)
T ss_pred hHHHHHHHHhcCCCceEEeccccccc
Confidence 45666777788899999999999974
No 11
>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=79.96 E-value=1.6 Score=32.18 Aligned_cols=28 Identities=29% Similarity=0.324 Sum_probs=23.5
Q ss_pred HHHHHHHHHHhhhCCceecccccccccc
Q 048636 33 ESEFELISQVIDRYPFISMDTEFPGLVY 60 (150)
Q Consensus 33 ~~el~~I~~~i~~~~fIAiDtEF~Gl~~ 60 (150)
++++..+.+.+.+++.||+|+|.+|+..
T Consensus 7 ~~~l~~~~~~l~~~~~~a~D~E~~~~~~ 34 (176)
T PF01612_consen 7 EEELEEAIKKLKNAKVLAFDTETTGLDP 34 (176)
T ss_dssp HHHHHHHHHHHTTTSEEEEEEEEETSTS
T ss_pred HHHHHHHHHHHcCCCeEEEEEEECCCCc
Confidence 4677778888899999999999998754
No 12
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=79.20 E-value=2.6 Score=33.31 Aligned_cols=13 Identities=31% Similarity=0.603 Sum_probs=11.6
Q ss_pred Cceeccccccccc
Q 048636 47 PFISMDTEFPGLV 59 (150)
Q Consensus 47 ~fIAiDtEF~Gl~ 59 (150)
.||++|+|.+|+.
T Consensus 6 ~~vvlD~EtTGl~ 18 (195)
T PRK07247 6 TYIAFDLEFNTVN 18 (195)
T ss_pred eEEEEEeeCCCCC
Confidence 7999999999973
No 13
>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=78.42 E-value=4.6 Score=29.40 Aligned_cols=11 Identities=27% Similarity=0.519 Sum_probs=9.6
Q ss_pred ceecccccccc
Q 048636 48 FISMDTEFPGL 58 (150)
Q Consensus 48 fIAiDtEF~Gl 58 (150)
||++|+|.+|.
T Consensus 1 ~v~~D~Ettg~ 11 (156)
T cd06130 1 FVAIDFETANA 11 (156)
T ss_pred CEEEEEeCCCC
Confidence 79999999983
No 14
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=77.67 E-value=2.4 Score=31.11 Aligned_cols=13 Identities=31% Similarity=0.516 Sum_probs=11.2
Q ss_pred Cceeccccccccc
Q 048636 47 PFISMDTEFPGLV 59 (150)
Q Consensus 47 ~fIAiDtEF~Gl~ 59 (150)
.||++|+|++|+.
T Consensus 1 ~~v~~D~Ettg~~ 13 (169)
T smart00479 1 TLVVIDCETTGLD 13 (169)
T ss_pred CEEEEEeeCCCCC
Confidence 4899999999974
No 15
>TIGR01298 RNaseT ribonuclease T. in gamma-subdivision Proteobacteria such as Escherichia coli and Xylella fastidiosa. Ribonuclease T is homologous to the DNA polymerase III alpha chain. It can liberate AMP from the common C-C-A terminus of uncharged tRNA. It appears also to be involved in RNA maturation. It also acts as a 3' to 5' single-strand DNA-specific exonuclease; it is distinctive for its ability to remove residues near a double-stranded stem. Ribonuclease T is a high copy suppressor in E. coli of a uv-repair defect caused by deletion of three other single-stranded DNA exonucleases.
Probab=77.38 E-value=5.8 Score=31.16 Aligned_cols=16 Identities=25% Similarity=0.314 Sum_probs=13.8
Q ss_pred hhCCceeccccccccc
Q 048636 44 DRYPFISMDTEFPGLV 59 (150)
Q Consensus 44 ~~~~fIAiDtEF~Gl~ 59 (150)
..+.||++|+|-||+.
T Consensus 6 ~~~~~vv~D~ETTGl~ 21 (200)
T TIGR01298 6 RGYLPVVVDVETGGFN 21 (200)
T ss_pred cCCeeEEEEeeCCCCC
Confidence 4578999999999975
No 16
>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=76.60 E-value=2.1 Score=30.48 Aligned_cols=14 Identities=21% Similarity=0.363 Sum_probs=11.6
Q ss_pred ceeeeeeeeecCCC
Q 048636 92 NLIQVGLTLSDSSG 105 (150)
Q Consensus 92 ~iiQlGlt~f~~~g 105 (150)
.|||+|...++.++
T Consensus 16 ~iiei~~v~~~~~~ 29 (159)
T cd06127 16 RIIEIGAVKVDGGI 29 (159)
T ss_pred eEEEEEEEEEECCc
Confidence 38999999998763
No 17
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=75.27 E-value=3.2 Score=33.48 Aligned_cols=35 Identities=20% Similarity=0.362 Sum_probs=26.1
Q ss_pred hhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCC
Q 048636 44 DRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGN 106 (150)
Q Consensus 44 ~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~ 106 (150)
.+.+||++|+|-||+.... + .|||+|+..++.+|.
T Consensus 4 ~~~~~vv~D~ETTGl~p~~---------d-------------------~Iieig~v~v~~~g~ 38 (232)
T PRK07942 4 HPGPLAAFDLETTGVDPET---------A-------------------RIVTAALVVVDADGE 38 (232)
T ss_pred ccCcEEEEEeccCCCCCCC---------C-------------------eeEEEEEEEEeCCCc
Confidence 4578999999999984211 1 389999998886665
No 18
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=71.24 E-value=3.7 Score=34.78 Aligned_cols=33 Identities=21% Similarity=0.283 Sum_probs=25.4
Q ss_pred CCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCC
Q 048636 46 YPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGN 106 (150)
Q Consensus 46 ~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~ 106 (150)
-+||++|+|-+|+.... -.|||+|+..++.+|+
T Consensus 15 ~~fvvlD~ETTGl~p~~----------------------------d~IIeIgav~v~~~g~ 47 (313)
T PRK06063 15 RGWAVVDVETSGFRPGQ----------------------------ARIISLAVLGLDADGN 47 (313)
T ss_pred CCEEEEEEECCCCCCCC----------------------------CEEEEEEEEEEECCce
Confidence 57999999999984211 1389999998887765
No 19
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=70.32 E-value=6.3 Score=34.68 Aligned_cols=37 Identities=19% Similarity=0.406 Sum_probs=28.3
Q ss_pred HhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCC
Q 048636 42 VIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGN 106 (150)
Q Consensus 42 ~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~ 106 (150)
.+.+.+||+||+|-||+..... .||++|.-.+..+|.
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~d----------------------------rIIeIgAV~i~~~g~ 78 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPSTS----------------------------RLITIDAVTLTADGE 78 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCCC----------------------------eEEEEEEEEEEcCCE
Confidence 5677899999999999842211 388999888877764
No 20
>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=69.82 E-value=6.3 Score=31.24 Aligned_cols=17 Identities=24% Similarity=0.094 Sum_probs=14.4
Q ss_pred hhhCCceeccccccccc
Q 048636 43 IDRYPFISMDTEFPGLV 59 (150)
Q Consensus 43 i~~~~fIAiDtEF~Gl~ 59 (150)
+....||++|+|-||+.
T Consensus 4 l~~~~fvv~D~ETTGl~ 20 (217)
T TIGR00573 4 LVLDTETTGDNETTGLY 20 (217)
T ss_pred EEecCEEEEEecCCCCC
Confidence 45678999999999973
No 21
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=69.25 E-value=6.6 Score=33.36 Aligned_cols=13 Identities=23% Similarity=0.498 Sum_probs=11.8
Q ss_pred Cceeccccccccc
Q 048636 47 PFISMDTEFPGLV 59 (150)
Q Consensus 47 ~fIAiDtEF~Gl~ 59 (150)
+||++|+|.+|+.
T Consensus 9 ~~Vv~DlETTGl~ 21 (313)
T PRK06807 9 DYVVIDFETTGFN 21 (313)
T ss_pred CEEEEEEECCCCC
Confidence 7999999999974
No 22
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=68.44 E-value=5.1 Score=32.61 Aligned_cols=17 Identities=35% Similarity=0.704 Sum_probs=14.8
Q ss_pred hhhCCceeccccccccc
Q 048636 43 IDRYPFISMDTEFPGLV 59 (150)
Q Consensus 43 i~~~~fIAiDtEF~Gl~ 59 (150)
+.+.+|+++|+|-||+.
T Consensus 44 ~~~~~~vviD~ETTGl~ 60 (239)
T PRK09146 44 LSEVPFVALDFETTGLD 60 (239)
T ss_pred cccCCEEEEEeECCCCC
Confidence 45779999999999975
No 23
>PRK05359 oligoribonuclease; Provisional
Probab=67.59 E-value=5.6 Score=30.89 Aligned_cols=14 Identities=36% Similarity=0.427 Sum_probs=12.4
Q ss_pred CCceeccccccccc
Q 048636 46 YPFISMDTEFPGLV 59 (150)
Q Consensus 46 ~~fIAiDtEF~Gl~ 59 (150)
-.||++|+|.||+.
T Consensus 3 ~~~vvlD~ETTGLd 16 (181)
T PRK05359 3 DNLIWIDLEMTGLD 16 (181)
T ss_pred CcEEEEEeecCCCC
Confidence 47999999999985
No 24
>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=67.25 E-value=4.7 Score=34.87 Aligned_cols=26 Identities=27% Similarity=0.692 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhhhCCceecccccccc
Q 048636 33 ESEFELISQVIDRYPFISMDTEFPGL 58 (150)
Q Consensus 33 ~~el~~I~~~i~~~~fIAiDtEF~Gl 58 (150)
.++|..+.+.+..++.|||||||...
T Consensus 5 ~~~l~~~~~~l~~~~~ia~DtE~~~~ 30 (367)
T TIGR01388 5 DDELATVCEAVRTFPFVALDTEFVRE 30 (367)
T ss_pred HHHHHHHHHHHhcCCEEEEeccccCC
Confidence 35677777778889999999999765
No 25
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=66.92 E-value=4.6 Score=32.99 Aligned_cols=18 Identities=28% Similarity=0.534 Sum_probs=15.5
Q ss_pred HhhhCCceeccccccccc
Q 048636 42 VIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 42 ~i~~~~fIAiDtEF~Gl~ 59 (150)
+|++..||.+|+|-||+.
T Consensus 3 ~l~~~~~v~~D~ETTGl~ 20 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLD 20 (250)
T ss_pred cccCCcEEEEEEeCCCCC
Confidence 467789999999999974
No 26
>PRK07883 hypothetical protein; Validated
Probab=64.28 E-value=7.2 Score=35.71 Aligned_cols=20 Identities=20% Similarity=0.278 Sum_probs=16.7
Q ss_pred HHHhhhCCceeccccccccc
Q 048636 40 SQVIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 40 ~~~i~~~~fIAiDtEF~Gl~ 59 (150)
..-+.+..||+||+|.||+.
T Consensus 9 ~~~~~~~~~Vv~D~ETTGl~ 28 (557)
T PRK07883 9 GTPLRDVTFVVVDLETTGGS 28 (557)
T ss_pred CCCCcCCCEEEEEEecCCCC
Confidence 34577889999999999983
No 27
>PRK10829 ribonuclease D; Provisional
Probab=64.04 E-value=5.4 Score=34.80 Aligned_cols=25 Identities=24% Similarity=0.477 Sum_probs=20.3
Q ss_pred HHHHHHHHHhhhCCceecccccccc
Q 048636 34 SEFELISQVIDRYPFISMDTEFPGL 58 (150)
Q Consensus 34 ~el~~I~~~i~~~~fIAiDtEF~Gl 58 (150)
+++..+.+.+..++.||+||||-+.
T Consensus 10 ~~L~~~~~~l~~~~~lalDtEf~~~ 34 (373)
T PRK10829 10 DALASVCEAARAFPAIALDTEFVRT 34 (373)
T ss_pred HHHHHHHHHHhcCCeEEEecccccC
Confidence 5666666668999999999999764
No 28
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=61.51 E-value=9.5 Score=29.92 Aligned_cols=16 Identities=25% Similarity=0.251 Sum_probs=13.3
Q ss_pred hCCceecccccccccc
Q 048636 45 RYPFISMDTEFPGLVY 60 (150)
Q Consensus 45 ~~~fIAiDtEF~Gl~~ 60 (150)
+..||++|+|.||+..
T Consensus 3 ~~~~vvlD~EtTg~~~ 18 (207)
T PRK07748 3 EQQFLFLDFEFTMPQH 18 (207)
T ss_pred cceEEEEEeecCCcCC
Confidence 4579999999999754
No 29
>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=60.17 E-value=8.4 Score=28.73 Aligned_cols=28 Identities=14% Similarity=0.129 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhh-hCCceecccccccccc
Q 048636 33 ESEFELISQVID-RYPFISMDTEFPGLVY 60 (150)
Q Consensus 33 ~~el~~I~~~i~-~~~fIAiDtEF~Gl~~ 60 (150)
++++..+.+.+. ....|++|+|+.+...
T Consensus 4 ~~~~~~~~~~~~~~~~~ig~D~E~~~~~~ 32 (170)
T cd06141 4 AQDAEEAVKELLGKEKVVGFDTEWRPSFR 32 (170)
T ss_pred HHHHHHHHHHHhcCCCEEEEeCccCCccC
Confidence 345556666666 9999999999987643
No 30
>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=59.88 E-value=7.6 Score=30.27 Aligned_cols=27 Identities=19% Similarity=0.326 Sum_probs=21.1
Q ss_pred HHHHHHHHHH--hhhCCceeccccccccc
Q 048636 33 ESEFELISQV--IDRYPFISMDTEFPGLV 59 (150)
Q Consensus 33 ~~el~~I~~~--i~~~~fIAiDtEF~Gl~ 59 (150)
.+++..+... +.+.+.|++|+|+.+..
T Consensus 7 ~~el~~~~~~~~l~~~~vig~D~Ew~~~~ 35 (193)
T cd06146 7 EEELEALLLALSLEAGRVVGIDSEWKPSF 35 (193)
T ss_pred HHHHHHHHHHHhhccCCEEEEECccCCCc
Confidence 3566666666 89999999999997653
No 31
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=59.41 E-value=13 Score=31.36 Aligned_cols=30 Identities=30% Similarity=0.422 Sum_probs=23.3
Q ss_pred CceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCC
Q 048636 47 PFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSS 104 (150)
Q Consensus 47 ~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~ 104 (150)
.+|++|+|-||+..... .|||+|+..++.+
T Consensus 38 ~~vvlD~ETTGLd~~~d----------------------------~IIEIg~V~v~~~ 67 (294)
T PRK09182 38 LGVILDTETTGLDPRKD----------------------------EIIEIGMVAFEYD 67 (294)
T ss_pred eEEEEEeeCCCCCCCCC----------------------------eEEEEEEEEEEec
Confidence 57999999999853211 3999999999864
No 32
>PRK11779 sbcB exonuclease I; Provisional
Probab=59.07 E-value=28 Score=31.46 Aligned_cols=33 Identities=18% Similarity=-0.040 Sum_probs=24.8
Q ss_pred hCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCC
Q 048636 45 RYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSG 105 (150)
Q Consensus 45 ~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g 105 (150)
...||.+|+|-||+... .+ .|||+|.-..+.++
T Consensus 5 ~~~fvv~D~ETTGLdP~---------~D-------------------rIIeiAaVrvd~~~ 37 (476)
T PRK11779 5 QPTFLWHDYETFGANPA---------LD-------------------RPAQFAGIRTDADL 37 (476)
T ss_pred CCcEEEEEEECCCCCCC---------CC-------------------eeEEEEEEEEeCCC
Confidence 46799999999998532 11 28999998777654
No 33
>PTZ00315 2'-phosphotransferase; Provisional
Probab=58.40 E-value=28 Score=32.44 Aligned_cols=48 Identities=19% Similarity=0.141 Sum_probs=31.4
Q ss_pred CceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCCCCCCCCCCCCCeeEEEEeccc
Q 048636 47 PFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSGNLPDLGSGGNNKFIWEFNFRD 126 (150)
Q Consensus 47 ~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g~~p~~g~~~~~~~~~~FNF~~ 126 (150)
.||+||.|.||..... .. .-.||++|...++..+. -....|..|+
T Consensus 57 ~~IV~DlETTgl~~~~--------~~-----------------~dEIIEIGaV~Vd~~ng----------~Ii~~F~~yV 101 (582)
T PTZ00315 57 AYVVLDFEATCEADRR--------IE-----------------DAEVIEFPMVLVDARTA----------TPVAEFQRYV 101 (582)
T ss_pred eEEEEEEecCCCCCCC--------CC-----------------CCceEEEEEEEEEccCC----------EEEEEEEEEE
Confidence 6899999999963211 11 11499999999975321 2446677776
Q ss_pred cCC
Q 048636 127 FDV 129 (150)
Q Consensus 127 F~~ 129 (150)
-|.
T Consensus 102 kP~ 104 (582)
T PTZ00315 102 RPV 104 (582)
T ss_pred CCC
Confidence 664
No 34
>TIGR02841 spore_YyaC putative sporulation protein YyaC. A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, also called YyaC, is a member of that panel and is otherwise uncharacterized. The second round of PSI-BLAST shows many similarities to the germination protease GPR, which is found in exactly the same set of organisms and has a known role in the sporulation/germination process.
Probab=58.29 E-value=8.2 Score=29.49 Aligned_cols=30 Identities=27% Similarity=0.342 Sum_probs=27.0
Q ss_pred EecccCHHHHHHHHHHHhhhCCceeccccc
Q 048636 26 EVWASNLESEFELISQVIDRYPFISMDTEF 55 (150)
Q Consensus 26 dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF 55 (150)
-|.+-|+++.+..|.+.-++.-.||||.-.
T Consensus 43 PVHA~NL~e~l~~I~~~~~~~~iIAIDAcL 72 (140)
T TIGR02841 43 PVHAKNLEEKLKIIKKKHPNPFIIAIDACL 72 (140)
T ss_pred CcccccHHHHHHHHHHhCCCCeEEEEECcc
Confidence 478999999999999998998899999865
No 35
>PF11959 DUF3473: Domain of unknown function (DUF3473); InterPro: IPR022560 This domain, found in bacteria and archaea, is functionally uncharacterised. It is about 130 amino acids in length and is found C-terminal to PF01522 from PFAM. It contains two completely conserved residues (P and H) that may be functionally important.
Probab=52.73 E-value=27 Score=26.10 Aligned_cols=46 Identities=13% Similarity=0.194 Sum_probs=35.3
Q ss_pred cccccCCCCCCCCCceEEEecccCHHHHHHHHHHHhhhCCceeccc
Q 048636 8 TDLDSSSNSSSSNSIIIREVWASNLESEFELISQVIDRYPFISMDT 53 (150)
Q Consensus 8 ~~~~~~~~~~~~~~~~v~dV~~~Nf~~el~~I~~~i~~~~fIAiDt 53 (150)
.|+|..+......+..-+=.+..|++.....|+.+|+++.|..|+.
T Consensus 83 wE~dp~qpr~~~~~~~~rf~~y~~l~~~~~rl~~Ll~~f~f~t~~~ 128 (133)
T PF11959_consen 83 WEFDPDQPRVPGAPLKSRFRHYNNLDRMEKRLDRLLSDFRFGTMRE 128 (133)
T ss_pred eecCCCCcccCCCCcceeEEEEcCHHHHHHHHHHHHhhCceEEHHH
Confidence 3677777643333444566788999999999999999999998874
No 36
>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=51.27 E-value=16 Score=26.98 Aligned_cols=12 Identities=50% Similarity=0.545 Sum_probs=10.7
Q ss_pred ceeccccccccc
Q 048636 48 FISMDTEFPGLV 59 (150)
Q Consensus 48 fIAiDtEF~Gl~ 59 (150)
||++|+|-||+.
T Consensus 1 ~v~~D~ETTGl~ 12 (167)
T cd06131 1 QIVLDTETTGLD 12 (167)
T ss_pred CEEEEeeCCCCC
Confidence 799999999984
No 37
>PF13606 Ank_3: Ankyrin repeat
Probab=50.88 E-value=16 Score=19.93 Aligned_cols=16 Identities=19% Similarity=0.293 Sum_probs=14.2
Q ss_pred chhHHHHHHHcCCCCC
Q 048636 135 APDSIELLRLQGIDFE 150 (150)
Q Consensus 135 ~~sSi~FL~~~GfDFn 150 (150)
+.+-+++|.++|.|.|
T Consensus 14 ~~e~v~~Ll~~gadvn 29 (30)
T PF13606_consen 14 NIEIVKYLLEHGADVN 29 (30)
T ss_pred CHHHHHHHHHcCCCCC
Confidence 6788999999999986
No 38
>cd06136 TREX1_2 DEDDh 3'-5' exonuclease domain of three prime repair exonuclease (TREX)1, TREX2, and similar proteins. Three prime repair exonuclease (TREX)1 and TREX2 are closely related DEDDh-type DnaQ-like 3'-5' exonucleases. They contain three conserved sequence motifs known as ExoI, II, and III, with a specific Hx(4)D conserved pattern at ExoIII. These motifs contain four conserved acidic residues that participate in coordination of divalent metal ions required for catalysis. Both proteins play a role in the metabolism and clearance of DNA. TREX1 is the major 3'-5' exonuclease activity detected in mammalian cells. Mutations in the human TREX1 gene can cause Aicardi-Goutieres syndrome (AGS), which is characterized by perturbed innate immunity and presents itself as a severe neurological disease. TREX1 degrades ssDNA generated by aberrant replication intermediates to prevent checkpoint activation and autoimmune disease. There are distinct structural differences between TREX1 and TRE
Probab=50.71 E-value=16 Score=27.90 Aligned_cols=31 Identities=19% Similarity=0.248 Sum_probs=22.4
Q ss_pred ceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCCC
Q 048636 48 FISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSSG 105 (150)
Q Consensus 48 fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~g 105 (150)
||++|+|-||+.. +. .+ .|||+|......++
T Consensus 1 ~vv~D~ETTGl~~-~~-------~d-------------------~Iiei~av~v~~~~ 31 (177)
T cd06136 1 FVFLDLETTGLPK-HN-------RP-------------------EITELCLVAVHRDH 31 (177)
T ss_pred CeEEeeecCCCCC-CC-------CC-------------------ceEEEEEEEEeccc
Confidence 7999999999842 11 01 28999999877654
No 39
>TIGR01229 rocF_arginase arginase. This model helps resolve arginases from known and putative agmatinases, formiminoglutamases, and other related proteins of unknown specifity. The pathway from arginine to the polyamine putrescine may procede by hydrolysis to remove urea (arginase) followed by decarboxylation (ornithine decarboxylase), or by decarboxylation first (arginine decarboxylase) followed by removal of urea (agmatinase).
Probab=50.32 E-value=46 Score=27.76 Aligned_cols=69 Identities=9% Similarity=-0.010 Sum_probs=45.3
Q ss_pred EecccCHHHHHHHHHHHhhhCC---ceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeee
Q 048636 26 EVWASNLESEFELISQVIDRYP---FISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQV 96 (150)
Q Consensus 26 dV~~~Nf~~el~~I~~~i~~~~---fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQl 96 (150)
+|++...++.+..+.+.++... ||++|. .+||+..... +-+ ++.|-.+.++.-....+++=+
T Consensus 196 ~i~~~g~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~p-----gGl----~~~e~~~~l~~i~~~~~v~g~ 266 (300)
T TIGR01229 196 EIDELGIGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPVV-----GGL----TFREGLLIMEMLYETGLLTAL 266 (300)
T ss_pred HHhhhhHHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCCC-----CCC----CHHHHHHHHHHHHhcCCEEEE
Confidence 3344445566777777776544 999997 5677644322 223 568888888888877788767
Q ss_pred eeeeecC
Q 048636 97 GLTLSDS 103 (150)
Q Consensus 97 Glt~f~~ 103 (150)
.|+=++.
T Consensus 267 DivE~~P 273 (300)
T TIGR01229 267 DVVEVNP 273 (300)
T ss_pred EEEEECc
Confidence 7766655
No 40
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=49.34 E-value=26 Score=28.89 Aligned_cols=23 Identities=22% Similarity=0.085 Sum_probs=17.2
Q ss_pred HHHHHHhhhCCceeccccccccc
Q 048636 37 ELISQVIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 37 ~~I~~~i~~~~fIAiDtEF~Gl~ 59 (150)
.....-+.+..||.+|+|-+|..
T Consensus 59 ~~~~~~~~~~~~vv~DiETTG~~ 81 (257)
T PRK08517 59 KTRFTPIKDQVFCFVDIETNGSK 81 (257)
T ss_pred ccCCCCCCCCCEEEEEEeCCCCC
Confidence 33334467889999999999963
No 41
>cd06149 ISG20 DEDDh 3'-5' exonuclease domain of Interferon Stimulated Gene product of 20 kDa, and similar proteins. Interferon (IFN) Stimulated Gene product of 20 kDa (ISG20) is an IFN-induced antiviral exonuclease with a strong preference for single-stranded RNA and minor activity towards single-stranded DNA. It was also independently identified by its response to estrogen and was called HEM45 (human estrogen regulated transcript). ISG20 is a DEDDh-type DnaQ-like 3'-5' exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. ISG20 may be a major effector of innate immunity against pathogens including viruses, bacteria, and parasites. It is located in promyelocytic leukemia (PML) nuclear bodies, sites for oncogenic DNA viral transcription and repli
Probab=45.29 E-value=8.7 Score=28.96 Aligned_cols=13 Identities=23% Similarity=0.314 Sum_probs=10.9
Q ss_pred eeccccccccccc
Q 048636 49 ISMDTEFPGLVYR 61 (150)
Q Consensus 49 IAiDtEF~Gl~~~ 61 (150)
||||+|++|+..+
T Consensus 1 v~~D~EttGl~~~ 13 (157)
T cd06149 1 VAIDCEMVGTGPG 13 (157)
T ss_pred CEEEeEeccccCC
Confidence 6899999999643
No 42
>cd06138 ExoI_N N-terminal DEDDh 3'-5' exonuclease domain of Escherichia coli exonuclease I and similar proteins. This subfamily is composed of the N-terminal domain of Escherichia coli exonuclease I (ExoI) and similar proteins. ExoI is a monomeric enzyme that hydrolyzes single stranded DNA in the 3' to 5' direction. It plays a role in DNA recombination and repair. It primarily functions in repairing frameshift mutations. The N-terminal domain of ExoI is a DEDDh-type DnaQ-like 3'-5 exonuclease containing three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The ExoI structure is unique among DnaQ family enzymes in that there is a large distance between the two metal ions required for catalysis and the catalytic histidine is oriented away from the active site.
Probab=43.52 E-value=59 Score=24.81 Aligned_cols=14 Identities=21% Similarity=0.259 Sum_probs=10.7
Q ss_pred eeeeeeeeecCCCC
Q 048636 93 LIQVGLTLSDSSGN 106 (150)
Q Consensus 93 iiQlGlt~f~~~g~ 106 (150)
|||+|.-.++.++.
T Consensus 17 Iieig~v~v~~~~~ 30 (183)
T cd06138 17 ILQFAAIRTDENFN 30 (183)
T ss_pred eEEEEEEEECCCCC
Confidence 89999987766543
No 43
>KOG2249 consensus 3'-5' exonuclease [Replication, recombination and repair]
Probab=43.31 E-value=11 Score=31.97 Aligned_cols=17 Identities=24% Similarity=0.298 Sum_probs=13.8
Q ss_pred CceecccccccccccCC
Q 048636 47 PFISMDTEFPGLVYRPD 63 (150)
Q Consensus 47 ~fIAiDtEF~Gl~~~~~ 63 (150)
.+||||+||-|+..+..
T Consensus 106 r~vAmDCEMVG~Gp~G~ 122 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDGR 122 (280)
T ss_pred eEEEEeeeEeccCCCcc
Confidence 59999999999866543
No 44
>PF06866 DUF1256: Protein of unknown function (DUF1256); InterPro: IPR009665 This family consists of several uncharacterised bacterial proteins, which seem to be specific to the orders Clostridia and Bacillales. Family members are typically around 180 residues in length. The function of this family is unknown.
Probab=43.15 E-value=18 Score=28.27 Aligned_cols=32 Identities=25% Similarity=0.211 Sum_probs=27.8
Q ss_pred EEecccCHHHHHHHHHHHhhhCCceecccccc
Q 048636 25 REVWASNLESEFELISQVIDRYPFISMDTEFP 56 (150)
Q Consensus 25 ~dV~~~Nf~~el~~I~~~i~~~~fIAiDtEF~ 56 (150)
.-|.+-|+++.+..|.+.-++.-.||||.-+.
T Consensus 66 ~PVHA~NL~e~l~~I~~~~~~~~IIAIDAcLG 97 (163)
T PF06866_consen 66 EPVHALNLEETLNEIKKKHPNPFIIAIDACLG 97 (163)
T ss_pred CCcchhhHHHHHHHHHHHCCCCeEEEEECCCC
Confidence 34889999999999999888888899998763
No 45
>PRK07740 hypothetical protein; Provisional
Probab=43.14 E-value=10 Score=30.81 Aligned_cols=17 Identities=29% Similarity=0.653 Sum_probs=14.2
Q ss_pred hhhCCceeccccccccc
Q 048636 43 IDRYPFISMDTEFPGLV 59 (150)
Q Consensus 43 i~~~~fIAiDtEF~Gl~ 59 (150)
+.+.+||.+|+|.||+.
T Consensus 56 ~~~~~~vv~D~ETTGl~ 72 (244)
T PRK07740 56 LTDLPFVVFDLETTGFS 72 (244)
T ss_pred ccCCCEEEEEEeCCCCC
Confidence 45568999999999974
No 46
>PRK13772 formimidoylglutamase; Provisional
Probab=42.88 E-value=87 Score=26.37 Aligned_cols=69 Identities=10% Similarity=0.127 Sum_probs=45.9
Q ss_pred EecccCHHHHHHHHHHHhhhC--Cceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeee
Q 048636 26 EVWASNLESEFELISQVIDRY--PFISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVG 97 (150)
Q Consensus 26 dV~~~Nf~~el~~I~~~i~~~--~fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlG 97 (150)
|++..+++..+..|...++.. -||+||. ..||+..... +-+ ++.|-.+.++.-+..-+++=+.
T Consensus 218 e~~~~g~~~~~~~i~~~l~~~~~vylS~DiD~lDps~aPGvgtP~p-----gGl----t~~e~~~il~~l~~~~~v~g~D 288 (314)
T PRK13772 218 DMQERHLDARLAELDALLDAADHVYLTIDLDVLPAAVAPGVSAPAA-----YGV----PLPVVEEIVLHVRASGKLRVAD 288 (314)
T ss_pred hhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcCcccCCCCCCCCC-----CCC----CHHHHHHHHHHHHhcCCeeEEE
Confidence 455556777788888888644 4888886 3566543332 223 5688888888877766777666
Q ss_pred eeeecC
Q 048636 98 LTLSDS 103 (150)
Q Consensus 98 lt~f~~ 103 (150)
|+-++.
T Consensus 289 vvEv~P 294 (314)
T PRK13772 289 LAEYNP 294 (314)
T ss_pred EEEECC
Confidence 665554
No 47
>cd06135 Orn DEDDh 3'-5' exonuclease domain of oligoribonuclease and similar proteins. Oligoribonuclease (Orn) is a DEDDh-type DnaQ-like 3'-5' exoribonuclease that is responsible for degrading small oligoribonucleotides to mononucleotides. It contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, with a specific Hx(4)D conserved pattern at ExoIII. These motifs are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. Orn is essential for Escherichia coli survival. The human homolog, also called Sfn (small fragment nuclease), is able to hydrolyze short single-stranded RNA and DNA oligomers. It plays a role in cellular nucleotide recycling.
Probab=42.52 E-value=27 Score=26.61 Aligned_cols=29 Identities=17% Similarity=0.368 Sum_probs=21.3
Q ss_pred ceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeecCC
Q 048636 48 FISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSDSS 104 (150)
Q Consensus 48 fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~~~ 104 (150)
+|.+|+|-||+.... + .|||+|...++..
T Consensus 1 lv~iD~ETTGl~p~~---------d-------------------~IieIgaV~~~~~ 29 (173)
T cd06135 1 LVWIDLEMTGLDPEK---------D-------------------RILEIACIITDGD 29 (173)
T ss_pred CEEEEEecCCCCCCC---------C-------------------eeEEEEEEEEeCC
Confidence 578999999985211 1 2899999987654
No 48
>PF04405 ScdA_N: Domain of Unknown function (DUF542) ; InterPro: IPR007500 This is a domain of unknown function found at the N terminus of genes involved in cell wall development and nitrous oxide protection. ScdA is required for normal cell growth and development; mutants have an increased level of peptidoglycan cross-linking and aberrant cellular morphology suggesting a role for ScdA in cell wall metabolism []. NorA1, NorA2, and YtfE are involved in the nitrous oxide response. NorA1 and NorA2, which are similar to YtfE, are co-transcribed with the membrane-bound nitrous oxide (NO) reductases. The genes appear to be involved in NO protection but their function is unknown [, ].
Probab=41.28 E-value=20 Score=22.92 Aligned_cols=15 Identities=40% Similarity=0.771 Sum_probs=13.0
Q ss_pred chhHHHHHHHcCCCC
Q 048636 135 APDSIELLRLQGIDF 149 (150)
Q Consensus 135 ~~sSi~FL~~~GfDF 149 (150)
.+.+.+.|.++||||
T Consensus 12 ~p~~a~vf~~~gIDf 26 (56)
T PF04405_consen 12 DPRAARVFRKYGIDF 26 (56)
T ss_pred ChHHHHHHHHcCCcc
Confidence 467888999999998
No 49
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=40.85 E-value=50 Score=27.69 Aligned_cols=11 Identities=27% Similarity=0.528 Sum_probs=9.9
Q ss_pred Cceeccccccc
Q 048636 47 PFISMDTEFPG 57 (150)
Q Consensus 47 ~fIAiDtEF~G 57 (150)
.||+||+|-+|
T Consensus 2 ~~vviD~ETTg 12 (309)
T PRK06195 2 NFVAIDFETAN 12 (309)
T ss_pred cEEEEEEeCCC
Confidence 69999999986
No 50
>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=38.05 E-value=25 Score=26.20 Aligned_cols=24 Identities=17% Similarity=0.249 Sum_probs=18.3
Q ss_pred HHHHHHHhh-hCCceeccccccccc
Q 048636 36 FELISQVID-RYPFISMDTEFPGLV 59 (150)
Q Consensus 36 l~~I~~~i~-~~~fIAiDtEF~Gl~ 59 (150)
+..+.+.+. +++.|++|||+....
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~ 26 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGR 26 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCC
Confidence 345566667 999999999997653
No 51
>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=37.74 E-value=12 Score=28.12 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=10.2
Q ss_pred eecccccccccc
Q 048636 49 ISMDTEFPGLVY 60 (150)
Q Consensus 49 IAiDtEF~Gl~~ 60 (150)
|++|+|.+|+..
T Consensus 1 v~lD~EttGl~~ 12 (161)
T cd06137 1 VALDCEMVGLAD 12 (161)
T ss_pred CEEEeeeeeEcC
Confidence 689999999853
No 52
>PRK05755 DNA polymerase I; Provisional
Probab=35.59 E-value=29 Score=33.44 Aligned_cols=26 Identities=23% Similarity=0.222 Sum_probs=19.5
Q ss_pred HHHHHHHHHhhhCCceeccccccccc
Q 048636 34 SEFELISQVIDRYPFISMDTEFPGLV 59 (150)
Q Consensus 34 ~el~~I~~~i~~~~fIAiDtEF~Gl~ 59 (150)
+++..+.+.+..+.++|+|||++|+.
T Consensus 303 ~~L~~~l~~l~~~~~~a~DtEt~~l~ 328 (880)
T PRK05755 303 EELEAWLAKLKAAGLFAFDTETTSLD 328 (880)
T ss_pred HHHHHHHHHhhccCeEEEEeccCCCC
Confidence 34555455567899999999999974
No 53
>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=34.97 E-value=31 Score=33.01 Aligned_cols=13 Identities=23% Similarity=0.327 Sum_probs=11.4
Q ss_pred Cceeccccccccc
Q 048636 47 PFISMDTEFPGLV 59 (150)
Q Consensus 47 ~fIAiDtEF~Gl~ 59 (150)
.||++|+|-||+.
T Consensus 1 ~~vvvD~ETTG~~ 13 (850)
T TIGR01407 1 RYAVVDLETTGTQ 13 (850)
T ss_pred CEEEEEEECCCCC
Confidence 4899999999974
No 54
>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=34.82 E-value=15 Score=27.24 Aligned_cols=12 Identities=25% Similarity=0.462 Sum_probs=10.0
Q ss_pred eecccccccccc
Q 048636 49 ISMDTEFPGLVY 60 (150)
Q Consensus 49 IAiDtEF~Gl~~ 60 (150)
|+||+|.+|+..
T Consensus 1 v~lD~EttGl~~ 12 (152)
T cd06144 1 VALDCEMVGVGP 12 (152)
T ss_pred CEEEEEeecccC
Confidence 689999999853
No 55
>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=32.46 E-value=28 Score=27.07 Aligned_cols=20 Identities=20% Similarity=0.122 Sum_probs=15.8
Q ss_pred HHhhhCCceecccccccccc
Q 048636 41 QVIDRYPFISMDTEFPGLVY 60 (150)
Q Consensus 41 ~~i~~~~fIAiDtEF~Gl~~ 60 (150)
+.|++.+.||+|||+.+...
T Consensus 5 ~~l~~~~~i~~D~E~~~~~~ 24 (197)
T cd06148 5 IHLKKQKVIGLDCEGVNLGR 24 (197)
T ss_pred hhhhhCCEEEEEcccccCCC
Confidence 45678999999999976543
No 56
>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=32.03 E-value=18 Score=27.01 Aligned_cols=12 Identities=17% Similarity=0.088 Sum_probs=9.7
Q ss_pred eecccccccccc
Q 048636 49 ISMDTEFPGLVY 60 (150)
Q Consensus 49 IAiDtEF~Gl~~ 60 (150)
||||+|++|+..
T Consensus 1 ~~iD~E~~g~~~ 12 (150)
T cd06145 1 FALDCEMCYTTD 12 (150)
T ss_pred CEEeeeeeeecC
Confidence 689999999753
No 57
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=30.36 E-value=37 Score=27.19 Aligned_cols=13 Identities=38% Similarity=0.406 Sum_probs=11.5
Q ss_pred Cceeccccccccc
Q 048636 47 PFISMDTEFPGLV 59 (150)
Q Consensus 47 ~fIAiDtEF~Gl~ 59 (150)
.||.+|+|-||+.
T Consensus 3 ~~vv~D~ETTGl~ 15 (232)
T PRK06309 3 ALIFYDTETTGTQ 15 (232)
T ss_pred cEEEEEeeCCCCC
Confidence 5899999999985
No 58
>PRK01722 formimidoylglutamase; Provisional
Probab=30.04 E-value=1.3e+02 Score=25.14 Aligned_cols=69 Identities=16% Similarity=0.257 Sum_probs=47.1
Q ss_pred EecccCHHHHHHHHHHHhhh--CCceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeee
Q 048636 26 EVWASNLESEFELISQVIDR--YPFISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVG 97 (150)
Q Consensus 26 dV~~~Nf~~el~~I~~~i~~--~~fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlG 97 (150)
+|++.++++.+..+.+.++. .-||++|. ..||+..... +-+ ++.|-.+.++.-....+++=+.
T Consensus 217 ~i~~~g~~~~~~~~~~~i~~~~~vyvS~DiDvlDps~aPgtgtp~p-----gGl----s~~e~~~il~~l~~~~~vvg~D 287 (320)
T PRK01722 217 DVRERGLKDILTELQEFIDQVDYIYLTIDLDVLPAAEAPGVSAPAA-----GGV----PLETLLRAIEPICRSGKLQAAD 287 (320)
T ss_pred HhhhcCHHHHHHHHHHHHhcCCeEEEEEEecCcChhhCCCCCCCcC-----CCC----CHHHHHHHHHHHHhcCCEEEEE
Confidence 55555677777888877763 36899886 4677654322 223 5688888888877777888777
Q ss_pred eeeecC
Q 048636 98 LTLSDS 103 (150)
Q Consensus 98 lt~f~~ 103 (150)
|+=++.
T Consensus 288 ivE~~P 293 (320)
T PRK01722 288 LVEYNP 293 (320)
T ss_pred EEEECC
Confidence 776655
No 59
>TIGR03358 VI_chp_5 type VI secretion protein, VC_A0107 family. Work by Mougous, et al. (2006), describes IAHP-related loci as a type VI secretion system (PubMed:16763151). This protein family is associated with type VI secretion loci, although not treated explicitly by Mougous, et al.
Probab=30.02 E-value=44 Score=25.98 Aligned_cols=38 Identities=18% Similarity=0.169 Sum_probs=24.9
Q ss_pred CCCCccccccCCCCCCCCCceEEEecccCHHHHHHHHHHH
Q 048636 3 AGDFSTDLDSSSNSSSSNSIIIREVWASNLESEFELISQV 42 (150)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~~~v~dV~~~Nf~~el~~I~~~ 42 (150)
.||||-.- .....+-..-..++|.++||.+.|..+.=-
T Consensus 35 lgD~sg~~--~~~~~~l~eRk~v~IDkdNFd~Vm~~~~p~ 72 (159)
T TIGR03358 35 LGDLSGGP--TEPLTPLEERKFVEVDKDNFDEVMEAMNPR 72 (159)
T ss_pred EecCCCCC--CCCCCChhhcCceecccccHHHHHHhCCCc
Confidence 37887651 111222334578999999999999887543
No 60
>PRK02190 agmatinase; Provisional
Probab=29.48 E-value=1.4e+02 Score=24.79 Aligned_cols=66 Identities=14% Similarity=0.241 Sum_probs=41.0
Q ss_pred cccCHHHHHHHHHHHhhhC-Cceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeee
Q 048636 28 WASNLESEFELISQVIDRY-PFISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTL 100 (150)
Q Consensus 28 ~~~Nf~~el~~I~~~i~~~-~fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~ 100 (150)
++..+++.+..+.+.+... -||+||. ..||+..... +-+ +..+-...++. +...+++=+.|+-
T Consensus 200 ~~~g~~~~~~~~~~~l~~~~vyiSiDiDvlDps~aPg~~~p~p-----gGl----~~~e~~~il~~-i~~~~vvg~DivE 269 (301)
T PRK02190 200 NDRGVDAIIAQIKQIVGDMPVYLTFDIDCLDPAFAPGTGTPVI-----GGL----TSAQALKILRG-LKGLNIVGMDVVE 269 (301)
T ss_pred hccCHHHHHHHHHHHhCCCEEEEEEeecccCcccCCCCCCCCC-----CCc----CHHHHHHHHHH-HhcCCeEEEEeee
Confidence 3444566667777777544 4899987 4566543322 223 45778888886 4446777777776
Q ss_pred ecC
Q 048636 101 SDS 103 (150)
Q Consensus 101 f~~ 103 (150)
++.
T Consensus 270 ~~P 272 (301)
T PRK02190 270 VAP 272 (301)
T ss_pred ecC
Confidence 654
No 61
>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=28.46 E-value=75 Score=32.16 Aligned_cols=16 Identities=31% Similarity=0.549 Sum_probs=14.2
Q ss_pred hhCCceeccccccccc
Q 048636 44 DRYPFISMDTEFPGLV 59 (150)
Q Consensus 44 ~~~~fIAiDtEF~Gl~ 59 (150)
+...||++|+|-||+.
T Consensus 188 ~~~~~VVfDiETTGL~ 203 (1213)
T TIGR01405 188 DDATYVVFDIETTGLS 203 (1213)
T ss_pred cCCcEEEEEeEecCCC
Confidence 6779999999999974
No 62
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=28.14 E-value=48 Score=31.88 Aligned_cols=15 Identities=20% Similarity=0.162 Sum_probs=12.8
Q ss_pred hCCceeccccccccc
Q 048636 45 RYPFISMDTEFPGLV 59 (150)
Q Consensus 45 ~~~fIAiDtEF~Gl~ 59 (150)
...||++|+|-||+.
T Consensus 6 ~~~~vvvD~ETTGl~ 20 (820)
T PRK07246 6 LRKYAVVDLEATGAG 20 (820)
T ss_pred CCCEEEEEEecCCcC
Confidence 468999999999973
No 63
>PRK13775 formimidoylglutamase; Provisional
Probab=27.43 E-value=2e+02 Score=24.30 Aligned_cols=69 Identities=12% Similarity=0.200 Sum_probs=41.9
Q ss_pred EecccCHHHHHHHHHHHhhhC--Cceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeee
Q 048636 26 EVWASNLESEFELISQVIDRY--PFISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVG 97 (150)
Q Consensus 26 dV~~~Nf~~el~~I~~~i~~~--~fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlG 97 (150)
+|++...+..+..+...++.. -||++|. ..||+..... +-+ ++.|-...+|.-+..-+++=+.
T Consensus 225 ~i~~~g~~~v~~~~~~~~~~~~~vyvS~DiD~lDps~aPGtgtP~p-----gGL----t~~e~~~il~~l~~~~~vvg~D 295 (328)
T PRK13775 225 DIYQMGHQKVCRAIDRFLEGQERVYLTIDMDCFSVGAAPGVSAIQS-----LGV----DPNLAVLVLQHIAASGKLVGFD 295 (328)
T ss_pred HhhhcCHHHHHHHHHHHHhcCCeEEEEEEcCccCcccCCCCCCCCC-----CCC----CHHHHHHHHHHHHhCCCEEEEE
Confidence 334444444566666666544 4999986 4566543322 222 5678888888877776777666
Q ss_pred eeeecC
Q 048636 98 LTLSDS 103 (150)
Q Consensus 98 lt~f~~ 103 (150)
|+=++.
T Consensus 296 ivEv~P 301 (328)
T PRK13775 296 VVEVSP 301 (328)
T ss_pred EEEECC
Confidence 665554
No 64
>TIGR01227 hutG formimidoylglutamase. Formiminoglutamase, the fourth enzyme of histidine degradation, is similar to arginases and agmatinases. It is often encoded near other enzymes of the histidine degredation pathway: histidine ammonia-lyase, urocanate hydratase, and imidazolonepropionase.
Probab=26.78 E-value=2.2e+02 Score=23.69 Aligned_cols=64 Identities=11% Similarity=0.227 Sum_probs=39.3
Q ss_pred CHHHHHHHHHHHhhhCC--ceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeeeeeec
Q 048636 31 NLESEFELISQVIDRYP--FISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGLTLSD 102 (150)
Q Consensus 31 Nf~~el~~I~~~i~~~~--fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGlt~f~ 102 (150)
+.......++.+++... ||++|. ..||+..... +-+ ++.|-.+.+|.-....+++=+.|+=++
T Consensus 215 ~~~~i~~~~~~~~~~~~~vyvs~DiDvlDps~aPgtg~p~p-----gGL----t~~e~~~il~~l~~~~~vvg~DvvE~~ 285 (307)
T TIGR01227 215 LLPTIKDILPVFLDKVDHIYLTVDMDVLDAAHAPGVSAPAP-----GGL----YPDELLELVKRIAASDKVRGAEIAEVN 285 (307)
T ss_pred CHHHHHHHHHHHHhCCCeEEEEEEecccChhhCCCCCCCCC-----CCC----CHHHHHHHHHHHhcCCCEEEEEEEEEC
Confidence 33334445555554444 899987 4667654332 223 568888888887777777766666555
Q ss_pred C
Q 048636 103 S 103 (150)
Q Consensus 103 ~ 103 (150)
.
T Consensus 286 P 286 (307)
T TIGR01227 286 P 286 (307)
T ss_pred C
Confidence 4
No 65
>KOG1990 consensus Poly(A)-specific exoribonuclease PARN [Replication, recombination and repair]
Probab=26.34 E-value=13 Score=34.33 Aligned_cols=72 Identities=8% Similarity=-0.043 Sum_probs=50.0
Q ss_pred CceEEEeccc--CHHHHHHHHHHHhhhCCceecccccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeeee
Q 048636 21 SIIIREVWAS--NLESEFELISQVIDRYPFISMDTEFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVGL 98 (150)
Q Consensus 21 ~~~v~dV~~~--Nf~~el~~I~~~i~~~~fIAiDtEF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlGl 98 (150)
.+++..+-++ |+...++.....+.+..+.++++|+.++...... +. ..+..+++++.-.....++-+|+
T Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~----~~dl~~~~i~~~~~p~r~l~~~~ 171 (564)
T KOG1990|consen 101 RSPVDFVARQQENQAGKWPSELEKEKNELLDSLGPELSDWGGSDRL-----SV----DADLLPEKIPDYMRPFRTLPVGS 171 (564)
T ss_pred ecchhhhhhhchhhhhhhHHHHHHHHHHHhhccCcccccCCCCCCc-----cc----hhhhchhhhhcccChhccCCCCC
Confidence 4555666666 7888877777777888999999999998655431 12 23667777777777666666666
Q ss_pred eee
Q 048636 99 TLS 101 (150)
Q Consensus 99 t~f 101 (150)
...
T Consensus 172 ~~~ 174 (564)
T KOG1990|consen 172 PPL 174 (564)
T ss_pred hhh
Confidence 543
No 66
>PF00491 Arginase: Arginase family; InterPro: IPR006035 The ureohydrolase superfamily includes arginase (3.5.3.1 from EC), agmatinase (3.5.3.11 from EC), formiminoglutamase (3.5.3.8 from EC) and proclavaminate amidinohydrolase (3.5.3.22 from EC) []. These enzymes share a 3-layer alpha-beta-alpha structure [, , ], and play important roles in arginine/agmatine metabolism, the urea cycle, histidine degradation, and other pathways. Arginase, which catalyses the conversion of arginine to urea and ornithine, is one of the five members of the urea cycle enzymes that convert ammonia to urea as the principal product of nitrogen excretion []. There are several arginase isozymes that differ in catalytic, molecular and immunological properties. Deficiency in the liver isozyme leads to argininemia, which is usually associated with hyperammonemia. Agmatinase hydrolyses agmatine to putrescine, the precursor for the biosynthesis of higher polyamines, spermidine and spermine. In addition, agmatine may play an important regulatory role in mammals. Formiminoglutamase catalyses the fourth step in histidine degradation, acting to hydrolyse N-formimidoyl-L-glutamate to L-glutamate and formamide. Proclavaminate amidinohydrolase is involved in clavulanic acid biosynthesis. Clavulanic acid acts as an inhibitor of a wide range of beta-lactamase enzymes that are used by various microorganisms to resist beta-lactam antibiotics. As a result, this enzyme improves the effectiveness of beta-lactamase antibiotics [].; GO: 0016813 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amidines, 0046872 metal ion binding; PDB: 4DZ4_A 3SL0_A 3MMR_A 3SL1_A 2EF5_D 2EIV_K 2EF4_A 3NIO_F 3THH_A 1WVA_A ....
Probab=26.00 E-value=67 Score=26.05 Aligned_cols=72 Identities=13% Similarity=0.258 Sum_probs=46.9
Q ss_pred eEEEecccCHHHHHHHHHHHhh---hCCceecccc------cccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccce
Q 048636 23 IIREVWASNLESEFELISQVID---RYPFISMDTE------FPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNL 93 (150)
Q Consensus 23 ~v~dV~~~Nf~~el~~I~~~i~---~~~fIAiDtE------F~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~i 93 (150)
...+|.+.+..+.+..+.+.+. +.-||+||.. +||+..... +-+ ++++-.+.++.-....++
T Consensus 175 ~~~~i~~~g~~~~~~~~~~~~~~~~~~vylsiDiDvlDp~~~pg~~~p~p-----gGl----~~~e~~~~l~~l~~~~~v 245 (277)
T PF00491_consen 175 SADEIREDGIDAVLEEILEALGSGTDPVYLSIDIDVLDPAFAPGVGTPEP-----GGL----SPRELLQLLRALARSGKV 245 (277)
T ss_dssp EHHHHHHHHHHHHHHHHHHHHTTSTSEEEEEEEGGGBBTTTSTSBSS-BS-----S-B-----HHHHHHHHHHHHHHSEE
T ss_pred ehhHhhhhhhhhHHHHHHHHHhcCCCeEEEEEehhhcChhhCCCcCCCcC-----CCC----CHHHHHHHHHHHcccCCe
Confidence 3345555566667888888884 5678888863 566533222 222 568999999996667899
Q ss_pred eeeeeeeecC
Q 048636 94 IQVGLTLSDS 103 (150)
Q Consensus 94 iQlGlt~f~~ 103 (150)
+=+.|+-++.
T Consensus 246 vg~di~E~~P 255 (277)
T PF00491_consen 246 VGLDIVEYNP 255 (277)
T ss_dssp EEEEEE-B-G
T ss_pred EEEEEEEECC
Confidence 8888887665
No 67
>PRK13776 formimidoylglutamase; Provisional
Probab=23.07 E-value=2.5e+02 Score=23.63 Aligned_cols=69 Identities=10% Similarity=0.119 Sum_probs=46.0
Q ss_pred EecccCHHHHHHHHHHHhhhC--Cceeccc------ccccccccCCCCCCCCCCCCCCCchHHHHHHHHhhhccceeeee
Q 048636 26 EVWASNLESEFELISQVIDRY--PFISMDT------EFPGLVYRPDVDPSTRPYFRQRKPSDHYKVLKSNVDALNLIQVG 97 (150)
Q Consensus 26 dV~~~Nf~~el~~I~~~i~~~--~fIAiDt------EF~Gl~~~~~~~~~~~~~~~~~t~eerY~~lr~nv~~~~iiQlG 97 (150)
+|++..++..+..++..+... -||++|. ..||+..... +-+ +..|-...+|.-...-+++=+.
T Consensus 219 ei~~~g~~~v~~~~~~~~~~~~~vyvS~DiD~lDps~aPGtgtP~p-----gGL----t~~e~~~il~~l~~~~~vvg~D 289 (318)
T PRK13776 219 DMYEWSLARILAFLDDFIANVDHIYLTICLDVLPAAVAPGVSAPAA-----RGV----SLWVIEPLVKRIIASGKLRLAD 289 (318)
T ss_pred HhhhcCHHHHHHHHHHHHhcCCeEEEEEEeCCcCcccCCCCCCCCC-----CCC----CHHHHHHHHHHHHccCCEEEEE
Confidence 555556677777777777544 6799887 4677544433 223 5688888888877777777666
Q ss_pred eeeecC
Q 048636 98 LTLSDS 103 (150)
Q Consensus 98 lt~f~~ 103 (150)
|+-++.
T Consensus 290 vvEv~P 295 (318)
T PRK13776 290 IAELNP 295 (318)
T ss_pred EEEECC
Confidence 665554
No 68
>cd06125 DnaQ_like_exo DnaQ-like (or DEDD) 3'-5' exonuclease domain superfamily. The DnaQ-like exonuclease superfamily is a structurally conserved group of 3'-5' exonucleases, which catalyze the excision of nucleoside monophosphates at the DNA or RNA termini in the 3'-5' direction. It is also called the DEDD superfamily, after the four invariant acidic residues present in the catalytic site of its members. The superfamily consists of DNA- and RNA-processing enzymes such as the proofreading domains of DNA polymerases, other DNA exonucleases, RNase D, RNase T, Oligoribonuclease and RNA exonucleases (REX). The DnaQ-like exonuclease domain contains three conserved sequence motifs termed ExoI, ExoII and ExoIII, which are clustered around the active site and contain four conserved acidic residues that serve as ligands for the two metal ions required for catalysis. The conservation patterns of the three motifs may vary among different subfamilies. DnaQ-like exonucleases are classified as DEDDy
Probab=22.95 E-value=34 Score=23.54 Aligned_cols=11 Identities=55% Similarity=0.724 Sum_probs=9.4
Q ss_pred eeccccccccc
Q 048636 49 ISMDTEFPGLV 59 (150)
Q Consensus 49 IAiDtEF~Gl~ 59 (150)
|++|+|++|+.
T Consensus 1 ~~~DiEt~~~~ 11 (96)
T cd06125 1 IAIDTEATGLD 11 (96)
T ss_pred CEEEEECCCCC
Confidence 68999999964
No 69
>PF05591 DUF770: Protein of unknown function (DUF770); InterPro: IPR008312 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, these proteins are encoded in type VI secretion loci (including the SCI genomic island in Salmonella enterica and the imp locus in Rhizobium leguminosarum) implicated in pathogenicity and protein secretion [, , [].
Probab=21.49 E-value=61 Score=25.03 Aligned_cols=38 Identities=16% Similarity=0.228 Sum_probs=25.2
Q ss_pred CCCccccccCCCCCCCCCceEEEecccCHHHHHHHHHHHh
Q 048636 4 GDFSTDLDSSSNSSSSNSIIIREVWASNLESEFELISQVI 43 (150)
Q Consensus 4 ~~~~~~~~~~~~~~~~~~~~v~dV~~~Nf~~el~~I~~~i 43 (150)
||||-+- .....+-..-.+++|.++||.+.|..+.--+
T Consensus 35 gDfsg~~--~~~~~~l~eR~~v~ID~dNFd~Vm~~~~p~l 72 (157)
T PF05591_consen 35 GDFSGRP--REDKPPLEERKFVEIDKDNFDDVMASMAPRL 72 (157)
T ss_pred ecCCCCC--CCCCcChhhhhccccccccHHHHHHhCCCce
Confidence 7777632 2222333345689999999999998876443
No 70
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=21.45 E-value=77 Score=30.84 Aligned_cols=13 Identities=31% Similarity=0.416 Sum_probs=11.5
Q ss_pred CCceecccccccc
Q 048636 46 YPFISMDTEFPGL 58 (150)
Q Consensus 46 ~~fIAiDtEF~Gl 58 (150)
-.||++|+|.||+
T Consensus 3 ~~~vvvD~ETTG~ 15 (928)
T PRK08074 3 KRFVVVDLETTGN 15 (928)
T ss_pred CCEEEEEEeCCCC
Confidence 4699999999996
No 71
>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=21.11 E-value=32 Score=27.09 Aligned_cols=13 Identities=31% Similarity=0.496 Sum_probs=9.8
Q ss_pred eeccccccccccc
Q 048636 49 ISMDTEFPGLVYR 61 (150)
Q Consensus 49 IAiDtEF~Gl~~~ 61 (150)
||+|+||-|+...
T Consensus 1 ~a~d~e~v~~~~~ 13 (174)
T cd06143 1 VAIDAEFVKLKPE 13 (174)
T ss_pred CceeeeEEEecch
Confidence 6888888887654
No 72
>PF04386 SspB: Stringent starvation protein B; InterPro: IPR007481 Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB is a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA []. However, more recent work has cast doubt on the importance of SspB in wild-type cells []. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of all ClpXP substrates [].; PDB: 2NYS_A 2QAZ_D 2QAS_A 1OX9_A 1OX8_A 1YFN_C 1TWB_B 1OU9_C 1OU8_B 1ZSZ_B ....
Probab=21.05 E-value=43 Score=25.54 Aligned_cols=17 Identities=35% Similarity=0.901 Sum_probs=12.1
Q ss_pred hCCceeccccccccccc
Q 048636 45 RYPFISMDTEFPGLVYR 61 (150)
Q Consensus 45 ~~~fIAiDtEF~Gl~~~ 61 (150)
..+||.+||..+|+...
T Consensus 31 ~tpyI~v~t~~pgV~vP 47 (155)
T PF04386_consen 31 HTPYITVDTDYPGVQVP 47 (155)
T ss_dssp --EEEEEETTSTT-BSS
T ss_pred CeEEEEEEeCCCCCCCC
Confidence 35999999999997533
No 73
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=20.93 E-value=90 Score=28.51 Aligned_cols=30 Identities=20% Similarity=0.412 Sum_probs=24.2
Q ss_pred chHHHHHHHHhhhccceee------------eeeeeecCCCC
Q 048636 77 PSDHYKVLKSNVDALNLIQ------------VGLTLSDSSGN 106 (150)
Q Consensus 77 ~eerY~~lr~nv~~~~iiQ------------lGlt~f~~~g~ 106 (150)
+.+-...||..++-..+|. .|+|.|+.+.+
T Consensus 3 ~~~~i~~l~~~~dIvdvI~~~v~Lkk~G~~y~~lCPFH~Ekt 44 (568)
T COG0358 3 PREFIDELRERIDIVDVIGEYVKLKKQGANYTGLCPFHAEKT 44 (568)
T ss_pred CHHHHHHHHHcCCHHHHHhhheEeeecCCCceeECcCCCCCC
Confidence 3567888999999888887 78898888765
Done!