Query psy6931
Match_columns 81
No_of_seqs 101 out of 359
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 22:11:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6931.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6931hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04857 CAF1: CAF1 family rib 99.9 1E-24 2.2E-29 157.2 4.5 69 5-73 2-70 (262)
2 KOG0304|consensus 99.7 1.5E-17 3.2E-22 119.5 5.8 70 7-76 6-75 (239)
3 COG5228 POP2 mRNA deadenylase 99.4 4E-13 8.8E-18 97.7 5.3 65 8-73 25-90 (299)
4 KOG1990|consensus 99.1 1.8E-11 3.9E-16 97.1 -0.4 69 8-77 1-71 (564)
5 PRK09145 DNA polymerase III su 95.3 0.037 8E-07 38.2 4.4 23 17-39 21-43 (202)
6 PRK05168 ribonuclease T; Provi 94.3 0.095 2.1E-06 36.7 4.6 41 15-76 7-47 (211)
7 PRK07247 DNA polymerase III su 94.3 0.051 1.1E-06 38.0 3.2 27 26-74 6-32 (195)
8 smart00479 EXOIII exonuclease 94.0 0.086 1.9E-06 34.2 3.6 14 26-39 1-14 (169)
9 PRK07748 sporulation inhibitor 93.4 0.14 3.1E-06 35.5 4.1 17 24-40 3-19 (207)
10 PRK09146 DNA polymerase III su 93.4 0.12 2.6E-06 37.2 3.8 20 21-40 43-62 (239)
11 TIGR00573 dnaq exonuclease, DN 93.3 0.12 2.6E-06 36.2 3.6 19 21-39 3-21 (217)
12 cd06133 ERI-1_3'hExo_like DEDD 93.3 0.13 2.8E-06 33.8 3.6 34 27-76 1-34 (176)
13 PRK06310 DNA polymerase III su 92.9 0.14 3E-06 36.9 3.5 19 21-39 3-21 (250)
14 PF00929 RNase_T: Exonuclease; 92.9 0.12 2.6E-06 32.5 2.8 12 28-39 1-12 (164)
15 PRK07883 hypothetical protein; 92.6 0.12 2.5E-06 41.5 3.0 23 17-39 7-29 (557)
16 COG0349 Rnd Ribonuclease D [Tr 92.6 0.12 2.7E-06 39.8 3.0 28 13-40 5-32 (361)
17 PF01612 DNA_pol_A_exo1: 3'-5' 92.0 0.17 3.8E-06 32.8 2.8 28 12-39 7-34 (176)
18 PRK07942 DNA polymerase III su 91.5 0.32 7E-06 34.6 4.0 17 23-39 4-20 (232)
19 PRK09182 DNA polymerase III su 91.5 0.31 6.8E-06 36.2 4.0 30 26-76 38-67 (294)
20 TIGR01298 RNaseT ribonuclease 91.4 0.39 8.5E-06 33.4 4.2 19 22-40 5-23 (200)
21 PRK06807 DNA polymerase III su 91.2 0.26 5.5E-06 36.9 3.3 28 25-73 8-35 (313)
22 PRK06063 DNA polymerase III su 91.1 0.29 6.3E-06 36.5 3.5 31 24-75 14-44 (313)
23 cd06127 DEDDh DEDDh 3'-5' exon 91.0 0.25 5.4E-06 31.0 2.7 28 28-76 1-28 (159)
24 PRK05359 oligoribonuclease; Pr 90.9 0.15 3.2E-06 35.1 1.7 18 24-41 2-19 (181)
25 cd06130 DNA_pol_III_epsilon_li 90.8 0.31 6.8E-06 31.4 3.1 11 27-37 1-11 (156)
26 cd06134 RNaseT DEDDh 3'-5' exo 90.6 0.52 1.1E-05 32.3 4.2 19 23-41 3-21 (189)
27 cd06149 ISG20 DEDDh 3'-5' exon 89.7 0.14 3.1E-06 34.2 0.8 13 28-40 1-13 (157)
28 PRK07740 hypothetical protein; 89.7 0.24 5.2E-06 35.6 1.9 23 18-40 52-74 (244)
29 cd06131 DNA_pol_III_epsilon_Ec 88.9 0.62 1.4E-05 30.6 3.4 13 27-39 1-13 (167)
30 TIGR01388 rnd ribonuclease D. 88.8 0.57 1.2E-05 35.6 3.6 26 13-38 6-31 (367)
31 cd06135 Orn DEDDh 3'-5' exonuc 88.2 0.64 1.4E-05 31.4 3.1 14 27-40 1-14 (173)
32 PRK08517 DNA polymerase III su 87.7 0.83 1.8E-05 33.2 3.7 33 21-74 64-96 (257)
33 PRK05601 DNA polymerase III su 86.8 0.46 1E-05 36.9 2.0 21 21-41 42-62 (377)
34 cd06137 DEDDh_RNase DEDDh 3'-5 86.5 0.25 5.3E-06 33.0 0.3 13 28-40 1-13 (161)
35 cd06141 WRN_exo DEDDy 3'-5' ex 86.3 1.2 2.6E-05 29.4 3.6 27 13-39 5-32 (170)
36 cd06144 REX4_like DEDDh 3'-5' 85.5 0.33 7.1E-06 32.1 0.5 13 28-40 1-13 (152)
37 KOG2249|consensus 85.4 0.46 9.9E-06 35.6 1.3 16 26-41 106-121 (280)
38 PRK10829 ribonuclease D; Provi 85.2 1.2 2.6E-05 34.3 3.5 27 12-38 9-35 (373)
39 TIGR01407 dinG_rel DnaQ family 83.5 1.4 3.1E-05 36.7 3.5 28 26-74 1-28 (850)
40 cd06146 mut-7_like_exo DEDDy 3 81.8 2.2 4.9E-05 29.3 3.5 27 13-39 8-36 (193)
41 PRK05755 DNA polymerase I; Pro 81.2 1.9 4E-05 36.3 3.4 27 13-39 303-329 (880)
42 PRK07246 bifunctional ATP-depe 80.9 2.1 4.5E-05 36.0 3.6 15 24-38 6-20 (820)
43 PRK08074 bifunctional ATP-depe 80.6 2.1 4.6E-05 36.2 3.6 30 25-74 3-32 (928)
44 TIGR01405 polC_Gram_pos DNA po 78.9 2.4 5.2E-05 37.3 3.5 18 23-40 188-205 (1213)
45 COG0847 DnaQ DNA polymerase II 78.4 3.1 6.6E-05 29.0 3.4 15 25-39 13-27 (243)
46 cd06145 REX1_like DEDDh 3'-5' 77.3 0.9 1.9E-05 30.1 0.4 13 28-40 1-13 (150)
47 cd06129 RNaseD_like DEDDy 3'-5 77.1 2.8 6E-05 27.7 2.7 25 15-39 2-27 (161)
48 PRK06195 DNA polymerase III su 76.5 3.5 7.6E-05 30.5 3.3 12 26-37 2-13 (309)
49 cd06136 TREX1_2 DEDDh 3'-5' ex 74.3 1.8 4E-05 29.3 1.3 12 27-38 1-12 (177)
50 cd06148 Egl_like_exo DEDDy 3'- 74.2 3.1 6.6E-05 28.6 2.4 23 19-41 4-26 (197)
51 COG1949 Orn Oligoribonuclease 73.2 2.3 5E-05 30.0 1.6 17 25-41 6-22 (184)
52 COG3325 ChiA Chitinase [Carboh 72.5 6.1 0.00013 31.4 3.9 60 1-61 145-204 (441)
53 PRK05711 DNA polymerase III su 71.7 2.6 5.6E-05 30.4 1.6 17 24-40 3-19 (240)
54 TIGR01406 dnaQ_proteo DNA poly 71.4 2.8 6.1E-05 29.7 1.7 15 26-40 1-15 (225)
55 PTZ00315 2'-phosphotransferase 70.1 6.5 0.00014 32.3 3.7 32 25-74 56-87 (582)
56 cd06143 PAN2_exo DEDDh 3'-5' e 68.3 0.54 1.2E-05 32.8 -2.4 14 28-41 1-14 (174)
57 KOG3242|consensus 66.5 3.6 7.9E-05 29.5 1.4 15 26-40 27-41 (208)
58 cd06125 DnaQ_like_exo DnaQ-lik 66.3 3 6.4E-05 25.6 0.9 14 28-41 1-14 (96)
59 PRK06309 DNA polymerase III su 64.4 5.2 0.00011 28.3 1.9 15 26-40 3-17 (232)
60 PF14943 MRP-S26: Mitochondria 63.1 6.2 0.00013 27.4 2.0 31 2-33 136-166 (170)
61 PF08947 BPS: BPS (Between PH 61.9 5 0.00011 22.7 1.2 25 21-51 2-26 (49)
62 PRK11779 sbcB exonuclease I; P 61.5 5.7 0.00012 31.6 1.9 18 23-40 4-21 (476)
63 PF12617 LdpA_C: Iron-Sulfur b 51.7 24 0.00052 25.0 3.5 52 9-68 21-72 (183)
64 TIGR02841 spore_YyaC putative 49.0 24 0.00052 24.0 3.0 27 9-35 47-73 (140)
65 PRK07983 exodeoxyribonuclease 48.8 12 0.00025 26.6 1.6 12 27-38 2-13 (219)
66 PF05470 eIF-3c_N: Eukaryotic 47.0 1.9 4.1E-05 35.2 -3.0 12 64-75 502-513 (595)
67 COG3172 NadR Predicted ATPase/ 39.4 42 0.00092 23.9 3.2 45 4-63 137-181 (187)
68 cd06395 PB1_Map2k5 PB1 domain 38.8 34 0.00073 21.6 2.3 27 8-34 22-48 (91)
69 KOG1990|consensus 37.3 25 0.00053 28.6 1.9 60 10-71 113-172 (564)
70 PRK13772 formimidoylglutamase; 37.2 1.7E+02 0.0037 21.6 8.0 65 9-75 222-294 (314)
71 PF09587 PGA_cap: Bacterial ca 36.5 1.2E+02 0.0026 21.3 5.2 48 10-57 22-72 (250)
72 KOG1076|consensus 34.0 4.4 9.6E-05 34.3 -2.8 13 64-76 532-544 (843)
73 cd07381 MPP_CapA CapA and rela 33.7 53 0.0011 22.8 3.0 31 7-37 20-50 (239)
74 PRK00448 polC DNA polymerase I 32.2 30 0.00065 31.4 1.8 20 21-40 415-434 (1437)
75 PF06866 DUF1256: Protein of u 30.5 65 0.0014 22.3 2.9 28 9-36 71-98 (163)
76 KOG0967|consensus 30.4 41 0.00088 28.4 2.2 61 11-76 402-465 (714)
77 COG2176 PolC DNA polymerase II 30.2 33 0.0007 31.1 1.7 22 20-41 416-437 (1444)
78 COG4152 ABC-type uncharacteriz 30.2 73 0.0016 24.2 3.3 28 13-40 137-164 (300)
79 smart00854 PGA_cap Bacterial c 29.7 65 0.0014 22.5 2.9 30 8-37 16-45 (239)
80 PRK06722 exonuclease; Provisio 29.0 32 0.0007 25.6 1.3 13 24-36 4-16 (281)
81 PRK14975 bifunctional 3'-5' ex 26.7 42 0.00091 26.9 1.6 25 14-38 11-35 (553)
82 PF00491 Arginase: Arginase fa 26.6 2.2E+02 0.0047 20.2 5.2 65 10-76 183-256 (277)
83 cd06138 ExoI_N N-terminal DEDD 25.0 41 0.00089 22.6 1.2 12 29-40 2-13 (183)
84 cd06139 DNA_polA_I_Ecoli_like_ 24.6 53 0.0012 21.4 1.6 17 22-38 2-18 (193)
85 PF13486 Dehalogenase: Reducti 23.5 70 0.0015 23.8 2.2 36 43-80 134-169 (308)
86 COG1618 Predicted nucleotide k 23.0 99 0.0021 21.9 2.7 23 9-31 84-107 (179)
87 cd03114 ArgK-like The function 22.4 1.4E+02 0.003 19.5 3.3 16 23-40 90-105 (148)
88 PF06938 DUF1285: Protein of u 22.1 44 0.00095 22.7 0.8 17 21-37 49-65 (148)
89 PF14305 ATPgrasp_TupA: TupA-l 22.0 1.1E+02 0.0025 21.8 3.0 24 9-32 179-202 (239)
90 COG1099 Predicted metal-depend 22.0 1.1E+02 0.0023 22.9 2.8 28 4-31 71-101 (254)
91 PF00113 Enolase_C: Enolase, C 21.8 1.2E+02 0.0026 22.7 3.2 32 7-38 75-111 (295)
92 TIGR01229 rocF_arginase argina 20.1 3.6E+02 0.0078 19.7 7.4 63 11-75 202-273 (300)
No 1
>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=99.90 E-value=1e-24 Score=157.16 Aligned_cols=69 Identities=38% Similarity=0.561 Sum_probs=62.2
Q ss_pred cCccccHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeee
Q psy6931 5 QHPMILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAF 73 (81)
Q Consensus 5 ~~~~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F 73 (81)
+|+++||+++||.|+++|++|+|||||+||||+..++.....+|+++||+++|++|+.|.++|+|||+|
T Consensus 2 ~Vt~~Nf~~~l~~i~~~i~~~~fvaiD~EftGl~~~~~~~~~~t~~~rY~~~r~~v~~~~iiQ~Glt~f 70 (262)
T PF04857_consen 2 EVTRSNFEEELPEILQAISKADFVAIDTEFTGLVSKPPRSRFDTPEERYEKLRANVETFQIIQFGLTLF 70 (262)
T ss_dssp EE-CCCHHHHHHHHHHHHHHSSEEEEEEEES-S-SSS-SHCSSHHHHHHHHHHHHHTTBEEEEEEEEEE
T ss_pred cccHHHHHHHHHHHHHHHhhCCEEEEEeeccccccCCCccccccHHHHHHHHHHhhcccccceeeEEEe
Confidence 689999999999999999999999999999999988753389999999999999999999999999999
No 2
>KOG0304|consensus
Probab=99.71 E-value=1.5e-17 Score=119.48 Aligned_cols=70 Identities=19% Similarity=0.200 Sum_probs=62.3
Q ss_pred ccccHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 7 PMILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 7 ~~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
=+.|+++++..|+++|++|+||||||||||+..++......+.+.+|+.+|.||+..++||+|||.+-..
T Consensus 6 W~~Nl~~Em~~Ir~~v~~y~~IamDTEFPGvv~rp~~~f~s~~d~~Y~~lk~NVd~lklIQlGlTlsd~~ 75 (239)
T KOG0304|consen 6 WRSNLEEEMALIRECVKDYPYIAMDTEFPGVVARPIGTFRSSDDYHYQTLKCNVDNLKLIQLGLTLSDEK 75 (239)
T ss_pred HHHhHHHHHHHHHHHHHhCCeeEecCcCCceeeecCccccCChHHHHHHHHhchhhhhhhheeeeeeccC
Confidence 3689999999999999999999999999999988853333688889999999999999999999998654
No 3
>COG5228 POP2 mRNA deadenylase subunit [RNA processing and modification]
Probab=99.40 E-value=4e-13 Score=97.68 Aligned_cols=65 Identities=20% Similarity=0.225 Sum_probs=57.4
Q ss_pred cccHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCH-HHHHHHHHhccccccceeeeeeee
Q psy6931 8 MILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTP-AQYYDKIRQGSMDFLLIQFGLCAF 73 (81)
Q Consensus 8 ~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~-eerY~~~k~~v~~f~iiQ~Gl~~F 73 (81)
+.|+..++..|+++|.++.+|+|||||+|+..+|. ..+.+. +=.|+.+|.||+..+|||+||+.-
T Consensus 25 k~NL~~Em~~I~qLi~rYn~vSmdTEFpGvvArPi-G~FkSs~dyhYQtlraNVD~LkiIQlGlsLS 90 (299)
T COG5228 25 KSNLYSEMAVIRQLISRYNHVSMDTEFPGVVARPI-GTFKSSVDYHYQTLRANVDFLKIIQLGLSLS 90 (299)
T ss_pred HhhHHHHHHHHHHHHHhCCceeeccccCceeeccc-ccccccchHHHHHHhcccchhhhhheeeeec
Confidence 48999999999999999999999999999999885 444444 445999999999999999999873
No 4
>KOG1990|consensus
Probab=99.07 E-value=1.8e-11 Score=97.13 Aligned_cols=69 Identities=22% Similarity=0.279 Sum_probs=64.3
Q ss_pred cccHHHHHHHHHHHhccCCeEEEeccCCCCccCCC--CCCCCCHHHHHHHHHhccccccceeeeeeeeeecC
Q psy6931 8 MILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPN--TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYDN 77 (81)
Q Consensus 8 ~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~--~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~~ 77 (81)
|.||+. +..+...|.+++|+++|.|++|+...+. .+.+|+++.+|++.|.++..|.++|+|+|.|.++.
T Consensus 1 ~~~~~~-~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~y~k~k~~~~~~~~~q~~~~~~~~~~ 71 (564)
T KOG1990|consen 1 RSNFES-LSLAELTVDEADLRRLRLVATGMTSAPWKAGSTFDTVEAIYLKWKDNEEVYLKFQFGLCLFMKRS 71 (564)
T ss_pred CCcccc-hhHHHhhcCHHHHHHHhhhhccceecccccccchhhhHHHHHHHHhhhhhheeeccccchhHHHh
Confidence 579999 9999999999999999999999987664 68899999999999999999999999999999874
No 5
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=95.26 E-value=0.037 Score=38.23 Aligned_cols=23 Identities=26% Similarity=0.277 Sum_probs=17.5
Q ss_pred HHHHHhccCCeEEEeccCCCCcc
Q psy6931 17 RYAKAIKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 17 ~i~~~I~~a~FVAiD~EFtGl~~ 39 (81)
.+.+......||+||+|.||+.+
T Consensus 21 ~~~~~~~~~~~vviD~ETTGl~~ 43 (202)
T PRK09145 21 FLFEPPPPDEWVALDCETTGLDP 43 (202)
T ss_pred HHhcCCCCCCEEEEEeECCCCCC
Confidence 34444566799999999999854
No 6
>PRK05168 ribonuclease T; Provisional
Probab=94.33 E-value=0.095 Score=36.74 Aligned_cols=41 Identities=24% Similarity=0.341 Sum_probs=31.6
Q ss_pred HHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 15 TTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 15 l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
+.-|...++...||++|+|-||+..... .|||+|...++.+
T Consensus 7 ~~~~~~~~~~~~~vv~D~ETTGl~~~~d---------------------~IieIgaV~v~~d 47 (211)
T PRK05168 7 LNPLKDRFRGFLPVVIDVETAGFNAKTD---------------------ALLEIAAVTLKMD 47 (211)
T ss_pred cchHHHHhcCCceEEEEeeCCCCCCCCC---------------------EEEEEeEEEEEec
Confidence 4457888999999999999999976431 2888887776643
No 7
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=94.31 E-value=0.051 Score=38.02 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=20.8
Q ss_pred CeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeee
Q psy6931 26 LFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFK 74 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~ 74 (81)
.||++|+|.||+.. . -.|||+|...+.
T Consensus 6 ~~vvlD~EtTGl~~--~--------------------~eIIeIgaV~v~ 32 (195)
T PRK07247 6 TYIAFDLEFNTVNG--V--------------------SHIIQVSAVKYD 32 (195)
T ss_pred eEEEEEeeCCCCCC--C--------------------CeEEEEEEEEEE
Confidence 79999999999842 1 158999987664
No 8
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=93.96 E-value=0.086 Score=34.20 Aligned_cols=14 Identities=50% Similarity=0.634 Sum_probs=12.2
Q ss_pred CeEEEeccCCCCcc
Q psy6931 26 LFVTIDGEFTGLNN 39 (81)
Q Consensus 26 ~FVAiD~EFtGl~~ 39 (81)
.||++|+|+||+.+
T Consensus 1 ~~v~~D~Ettg~~~ 14 (169)
T smart00479 1 TLVVIDCETTGLDP 14 (169)
T ss_pred CEEEEEeeCCCCCC
Confidence 48999999999865
No 9
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=93.43 E-value=0.14 Score=35.51 Aligned_cols=17 Identities=29% Similarity=0.303 Sum_probs=14.2
Q ss_pred cCCeEEEeccCCCCccC
Q psy6931 24 SALFVTIDGEFTGLNNG 40 (81)
Q Consensus 24 ~a~FVAiD~EFtGl~~~ 40 (81)
+..||++|+|.||+...
T Consensus 3 ~~~~vvlD~EtTg~~~~ 19 (207)
T PRK07748 3 EQQFLFLDFEFTMPQHK 19 (207)
T ss_pred cceEEEEEeecCCcCCC
Confidence 46799999999998654
No 10
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=93.38 E-value=0.12 Score=37.17 Aligned_cols=20 Identities=35% Similarity=0.502 Sum_probs=17.4
Q ss_pred HhccCCeEEEeccCCCCccC
Q psy6931 21 AIKSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~~ 40 (81)
-+.+.+||++|+|-||+.+.
T Consensus 43 ~~~~~~~vviD~ETTGl~p~ 62 (239)
T PRK09146 43 PLSEVPFVALDFETTGLDAE 62 (239)
T ss_pred CcccCCEEEEEeECCCCCCC
Confidence 57789999999999999753
No 11
>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=93.34 E-value=0.12 Score=36.22 Aligned_cols=19 Identities=32% Similarity=0.163 Sum_probs=16.4
Q ss_pred HhccCCeEEEeccCCCCcc
Q psy6931 21 AIKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~ 39 (81)
.++...||++|+|-||+.+
T Consensus 3 ~l~~~~fvv~D~ETTGl~~ 21 (217)
T TIGR00573 3 QLVLDTETTGDNETTGLYA 21 (217)
T ss_pred eEEecCEEEEEecCCCCCC
Confidence 4678899999999999864
No 12
>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=93.29 E-value=0.13 Score=33.79 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=23.3
Q ss_pred eEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 27 FVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 27 FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
||.+|+|.||+..... .-..-.|+|+|...+..+
T Consensus 1 ~vv~D~Ettg~~~~~~----------------~~~~~~IieIgav~v~~~ 34 (176)
T cd06133 1 YLVIDFEATCWEGNSK----------------PDYPNEIIEIGAVLVDVK 34 (176)
T ss_pred CEEEEeeccccCCCCC----------------CCCCcceEEEEEEEEEcC
Confidence 7999999999976431 111235899998766543
No 13
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=92.91 E-value=0.14 Score=36.91 Aligned_cols=19 Identities=42% Similarity=0.580 Sum_probs=16.6
Q ss_pred HhccCCeEEEeccCCCCcc
Q psy6931 21 AIKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~ 39 (81)
+|++..||.+|+|-||+..
T Consensus 3 ~l~~~~~v~~D~ETTGl~~ 21 (250)
T PRK06310 3 LLKDTEFVCLDCETTGLDV 21 (250)
T ss_pred cccCCcEEEEEEeCCCCCC
Confidence 5677899999999999865
No 14
>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=92.91 E-value=0.12 Score=32.51 Aligned_cols=12 Identities=50% Similarity=0.661 Sum_probs=10.7
Q ss_pred EEEeccCCCCcc
Q psy6931 28 VTIDGEFTGLNN 39 (81)
Q Consensus 28 VAiD~EFtGl~~ 39 (81)
|.||+|+||+..
T Consensus 1 v~~D~Ettg~~~ 12 (164)
T PF00929_consen 1 VVFDTETTGLDP 12 (164)
T ss_dssp EEEEEEESSSTT
T ss_pred cEEEeEcCCCCC
Confidence 689999999976
No 15
>PRK07883 hypothetical protein; Validated
Probab=92.64 E-value=0.12 Score=41.50 Aligned_cols=23 Identities=26% Similarity=0.368 Sum_probs=19.3
Q ss_pred HHHHHhccCCeEEEeccCCCCcc
Q psy6931 17 RYAKAIKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 17 ~i~~~I~~a~FVAiD~EFtGl~~ 39 (81)
.+..-|++..||+||+|.||+.+
T Consensus 7 ~~~~~~~~~~~Vv~D~ETTGl~p 29 (557)
T PRK07883 7 DLGTPLRDVTFVVVDLETTGGSP 29 (557)
T ss_pred hhCCCCcCCCEEEEEEecCCCCC
Confidence 44567889999999999999954
No 16
>COG0349 Rnd Ribonuclease D [Translation, ribosomal structure and biogenesis]
Probab=92.62 E-value=0.12 Score=39.80 Aligned_cols=28 Identities=18% Similarity=0.288 Sum_probs=23.5
Q ss_pred HHHHHHHHHhccCCeEEEeccCCCCccC
Q psy6931 13 NITTRYAKAIKSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 13 ~~l~~i~~~I~~a~FVAiD~EFtGl~~~ 40 (81)
+.+..+...+..|.+|||||||.|+...
T Consensus 5 ~~l~~~~~~~~~~~~iAiDTEf~r~~t~ 32 (361)
T COG0349 5 DLLAAACALLRGSKAIAIDTEFMRLRTY 32 (361)
T ss_pred hHHHHHHHHhcCCCceEEeccccccccc
Confidence 4567778889999999999999998653
No 17
>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=91.98 E-value=0.17 Score=32.77 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=24.5
Q ss_pred HHHHHHHHHHhccCCeEEEeccCCCCcc
Q psy6931 12 HNITTRYAKAIKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 12 ~~~l~~i~~~I~~a~FVAiD~EFtGl~~ 39 (81)
.+.+..+.+.+.++..||+|+|.+|+..
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 4667788889999999999999999876
No 18
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=91.54 E-value=0.32 Score=34.55 Aligned_cols=17 Identities=24% Similarity=0.331 Sum_probs=14.8
Q ss_pred ccCCeEEEeccCCCCcc
Q psy6931 23 KSALFVTIDGEFTGLNN 39 (81)
Q Consensus 23 ~~a~FVAiD~EFtGl~~ 39 (81)
.+..||++|+|-||+.+
T Consensus 4 ~~~~~vv~D~ETTGl~p 20 (232)
T PRK07942 4 HPGPLAAFDLETTGVDP 20 (232)
T ss_pred ccCcEEEEEeccCCCCC
Confidence 46789999999999964
No 19
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=91.49 E-value=0.31 Score=36.18 Aligned_cols=30 Identities=43% Similarity=0.633 Sum_probs=23.2
Q ss_pred CeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 26 LFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
.+|++|+|-||+.... =.|||+|+..|..+
T Consensus 38 ~~vvlD~ETTGLd~~~---------------------d~IIEIg~V~v~~~ 67 (294)
T PRK09182 38 LGVILDTETTGLDPRK---------------------DEIIEIGMVAFEYD 67 (294)
T ss_pred eEEEEEeeCCCCCCCC---------------------CeEEEEEEEEEEec
Confidence 5899999999997543 24888888887754
No 20
>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=91.37 E-value=0.39 Score=33.35 Aligned_cols=19 Identities=32% Similarity=0.375 Sum_probs=16.0
Q ss_pred hccCCeEEEeccCCCCccC
Q psy6931 22 IKSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 22 I~~a~FVAiD~EFtGl~~~ 40 (81)
-..+.||++|+|-||+.+.
T Consensus 5 ~~~~~~vv~D~ETTGl~~~ 23 (200)
T TIGR01298 5 FRGYLPVVVDVETGGFNAK 23 (200)
T ss_pred hcCCeeEEEEeeCCCCCCC
Confidence 3568899999999999764
No 21
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=91.22 E-value=0.26 Score=36.92 Aligned_cols=28 Identities=32% Similarity=0.328 Sum_probs=21.5
Q ss_pred CCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeee
Q psy6931 25 ALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAF 73 (81)
Q Consensus 25 a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F 73 (81)
.+||++|+|.||+.+. .-.|||+|...+
T Consensus 8 ~~~Vv~DlETTGl~p~---------------------~~eIIEIgaV~v 35 (313)
T PRK06807 8 LDYVVIDFETTGFNPY---------------------NDKIIQVAAVKY 35 (313)
T ss_pred CCEEEEEEECCCCCCC---------------------CCeEEEEEEEEE
Confidence 3799999999998642 136899997665
No 22
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=91.12 E-value=0.29 Score=36.50 Aligned_cols=31 Identities=16% Similarity=0.292 Sum_probs=22.7
Q ss_pred cCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeee
Q psy6931 24 SALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75 (81)
Q Consensus 24 ~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~ 75 (81)
.-+||++|+|-||+.... -.|||+|+..+..
T Consensus 14 ~~~fvvlD~ETTGl~p~~---------------------d~IIeIgav~v~~ 44 (313)
T PRK06063 14 PRGWAVVDVETSGFRPGQ---------------------ARIISLAVLGLDA 44 (313)
T ss_pred CCCEEEEEEECCCCCCCC---------------------CEEEEEEEEEEEC
Confidence 357999999999986431 2578888776653
No 23
>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=91.01 E-value=0.25 Score=31.02 Aligned_cols=28 Identities=29% Similarity=0.331 Sum_probs=19.7
Q ss_pred EEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 28 VTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 28 VAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
|.+|+|.||+.+. .-.|+|+|.+.+..+
T Consensus 1 v~~D~Ettg~~~~---------------------~~~iiei~~v~~~~~ 28 (159)
T cd06127 1 VVFDTETTGLDPK---------------------KDRIIEIGAVKVDGG 28 (159)
T ss_pred CeEEeeCCCcCCC---------------------CCeEEEEEEEEEECC
Confidence 5799999998642 234777777776543
No 24
>PRK05359 oligoribonuclease; Provisional
Probab=90.92 E-value=0.15 Score=35.10 Aligned_cols=18 Identities=33% Similarity=0.385 Sum_probs=14.7
Q ss_pred cCCeEEEeccCCCCccCC
Q psy6931 24 SALFVTIDGEFTGLNNGP 41 (81)
Q Consensus 24 ~a~FVAiD~EFtGl~~~~ 41 (81)
.-.||++|+|.|||.+..
T Consensus 2 ~~~~vvlD~ETTGLdp~~ 19 (181)
T PRK05359 2 EDNLIWIDLEMTGLDPER 19 (181)
T ss_pred CCcEEEEEeecCCCCCCC
Confidence 347999999999998643
No 25
>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=90.83 E-value=0.31 Score=31.40 Aligned_cols=11 Identities=45% Similarity=0.477 Sum_probs=10.0
Q ss_pred eEEEeccCCCC
Q psy6931 27 FVTIDGEFTGL 37 (81)
Q Consensus 27 FVAiD~EFtGl 37 (81)
||++|+|.||.
T Consensus 1 ~v~~D~Ettg~ 11 (156)
T cd06130 1 FVAIDFETANA 11 (156)
T ss_pred CEEEEEeCCCC
Confidence 79999999984
No 26
>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=90.62 E-value=0.52 Score=32.34 Aligned_cols=19 Identities=32% Similarity=0.349 Sum_probs=15.3
Q ss_pred ccCCeEEEeccCCCCccCC
Q psy6931 23 KSALFVTIDGEFTGLNNGP 41 (81)
Q Consensus 23 ~~a~FVAiD~EFtGl~~~~ 41 (81)
+...+|++|+|-||+.+..
T Consensus 3 ~~~~~vv~D~ETTGl~~~~ 21 (189)
T cd06134 3 RGFLPVVVDVETGGFNPQT 21 (189)
T ss_pred ccceeEEEEecCCCCCCCC
Confidence 4567899999999997643
No 27
>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=89.70 E-value=0.14 Score=34.21 Aligned_cols=13 Identities=46% Similarity=0.700 Sum_probs=11.4
Q ss_pred EEEeccCCCCccC
Q psy6931 28 VTIDGEFTGLNNG 40 (81)
Q Consensus 28 VAiD~EFtGl~~~ 40 (81)
||||+|+||+.+.
T Consensus 1 v~~D~EttGl~~~ 13 (157)
T cd06149 1 VAIDCEMVGTGPG 13 (157)
T ss_pred CEEEeEeccccCC
Confidence 6899999999864
No 28
>PRK07740 hypothetical protein; Provisional
Probab=89.66 E-value=0.24 Score=35.59 Aligned_cols=23 Identities=26% Similarity=0.306 Sum_probs=18.0
Q ss_pred HHHHhccCCeEEEeccCCCCccC
Q psy6931 18 YAKAIKSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 18 i~~~I~~a~FVAiD~EFtGl~~~ 40 (81)
+..-+++.+||.+|+|.||+.+.
T Consensus 52 ~~~~~~~~~~vv~D~ETTGl~p~ 74 (244)
T PRK07740 52 LDIPLTDLPFVVFDLETTGFSPQ 74 (244)
T ss_pred cCCCccCCCEEEEEEeCCCCCCC
Confidence 33446778999999999998753
No 29
>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=88.87 E-value=0.62 Score=30.58 Aligned_cols=13 Identities=38% Similarity=0.583 Sum_probs=11.5
Q ss_pred eEEEeccCCCCcc
Q psy6931 27 FVTIDGEFTGLNN 39 (81)
Q Consensus 27 FVAiD~EFtGl~~ 39 (81)
||++|+|-||+.+
T Consensus 1 ~v~~D~ETTGl~~ 13 (167)
T cd06131 1 QIVLDTETTGLDP 13 (167)
T ss_pred CEEEEeeCCCCCC
Confidence 6899999999864
No 30
>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=88.84 E-value=0.57 Score=35.63 Aligned_cols=26 Identities=23% Similarity=0.370 Sum_probs=21.7
Q ss_pred HHHHHHHHHhccCCeEEEeccCCCCc
Q psy6931 13 NITTRYAKAIKSALFVTIDGEFTGLN 38 (81)
Q Consensus 13 ~~l~~i~~~I~~a~FVAiD~EFtGl~ 38 (81)
+.|..+.+.+..++.|||||||.+..
T Consensus 6 ~~l~~~~~~l~~~~~ia~DtE~~~~~ 31 (367)
T TIGR01388 6 DELATVCEAVRTFPFVALDTEFVRER 31 (367)
T ss_pred HHHHHHHHHHhcCCEEEEeccccCCC
Confidence 56777778888999999999998763
No 31
>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=88.17 E-value=0.64 Score=31.42 Aligned_cols=14 Identities=50% Similarity=0.596 Sum_probs=12.0
Q ss_pred eEEEeccCCCCccC
Q psy6931 27 FVTIDGEFTGLNNG 40 (81)
Q Consensus 27 FVAiD~EFtGl~~~ 40 (81)
||.+|+|-||+.+.
T Consensus 1 lv~iD~ETTGl~p~ 14 (173)
T cd06135 1 LVWIDLEMTGLDPE 14 (173)
T ss_pred CEEEEEecCCCCCC
Confidence 68899999999763
No 32
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=87.69 E-value=0.83 Score=33.24 Aligned_cols=33 Identities=27% Similarity=0.389 Sum_probs=25.3
Q ss_pred HhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeee
Q psy6931 21 AIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFK 74 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~ 74 (81)
-+.+..||++|+|-||+.... -.|||+|...+.
T Consensus 64 ~~~~~~~vv~DiETTG~~~~~---------------------~~IIEIGAv~v~ 96 (257)
T PRK08517 64 PIKDQVFCFVDIETNGSKPKK---------------------HQIIEIGAVKVK 96 (257)
T ss_pred CCCCCCEEEEEEeCCCCCCCC---------------------CeEEEEEEEEEE
Confidence 357889999999999975432 258888887764
No 33
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=86.82 E-value=0.46 Score=36.89 Aligned_cols=21 Identities=29% Similarity=0.479 Sum_probs=18.1
Q ss_pred HhccCCeEEEeccCCCCccCC
Q psy6931 21 AIKSALFVTIDGEFTGLNNGP 41 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~~~ 41 (81)
.++++.||+||+|-|||.+..
T Consensus 42 ~~~~~~fVvlDiETTGLdp~~ 62 (377)
T PRK05601 42 AIEAAPFVAVSIQTSGIHPST 62 (377)
T ss_pred CCCCCCEEEEEEECCCCCCCC
Confidence 578899999999999997643
No 34
>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=86.50 E-value=0.25 Score=33.04 Aligned_cols=13 Identities=46% Similarity=0.866 Sum_probs=11.3
Q ss_pred EEEeccCCCCccC
Q psy6931 28 VTIDGEFTGLNNG 40 (81)
Q Consensus 28 VAiD~EFtGl~~~ 40 (81)
|++|+|+||+.+.
T Consensus 1 v~lD~EttGl~~~ 13 (161)
T cd06137 1 VALDCEMVGLADG 13 (161)
T ss_pred CEEEeeeeeEcCC
Confidence 6899999999764
No 35
>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=86.26 E-value=1.2 Score=29.37 Aligned_cols=27 Identities=15% Similarity=0.065 Sum_probs=20.2
Q ss_pred HHHHHHHHHhc-cCCeEEEeccCCCCcc
Q psy6931 13 NITTRYAKAIK-SALFVTIDGEFTGLNN 39 (81)
Q Consensus 13 ~~l~~i~~~I~-~a~FVAiD~EFtGl~~ 39 (81)
+.+..+.+.+. ++..|++|+|+++...
T Consensus 5 ~~~~~~~~~~~~~~~~ig~D~E~~~~~~ 32 (170)
T cd06141 5 QDAEEAVKELLGKEKVVGFDTEWRPSFR 32 (170)
T ss_pred HHHHHHHHHHhcCCCEEEEeCccCCccC
Confidence 34455555555 9999999999999754
No 36
>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=85.49 E-value=0.33 Score=32.09 Aligned_cols=13 Identities=31% Similarity=0.583 Sum_probs=11.1
Q ss_pred EEEeccCCCCccC
Q psy6931 28 VTIDGEFTGLNNG 40 (81)
Q Consensus 28 VAiD~EFtGl~~~ 40 (81)
|+||+|.||+..+
T Consensus 1 v~lD~EttGl~~~ 13 (152)
T cd06144 1 VALDCEMVGVGPD 13 (152)
T ss_pred CEEEEEeecccCC
Confidence 6899999999754
No 37
>KOG2249|consensus
Probab=85.38 E-value=0.46 Score=35.60 Aligned_cols=16 Identities=25% Similarity=0.391 Sum_probs=14.2
Q ss_pred CeEEEeccCCCCccCC
Q psy6931 26 LFVTIDGEFTGLNNGP 41 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~~ 41 (81)
.+|||||||-|++++.
T Consensus 106 r~vAmDCEMVG~Gp~G 121 (280)
T KOG2249|consen 106 RVVAMDCEMVGVGPDG 121 (280)
T ss_pred eEEEEeeeEeccCCCc
Confidence 4999999999998864
No 38
>PRK10829 ribonuclease D; Provisional
Probab=85.16 E-value=1.2 Score=34.28 Aligned_cols=27 Identities=15% Similarity=0.233 Sum_probs=21.4
Q ss_pred HHHHHHHHHHhccCCeEEEeccCCCCc
Q psy6931 12 HNITTRYAKAIKSALFVTIDGEFTGLN 38 (81)
Q Consensus 12 ~~~l~~i~~~I~~a~FVAiD~EFtGl~ 38 (81)
.+.|..+.+.+..++.||+||||.+..
T Consensus 9 ~~~L~~~~~~l~~~~~lalDtEf~~~~ 35 (373)
T PRK10829 9 DDALASVCEAARAFPAIALDTEFVRTR 35 (373)
T ss_pred HHHHHHHHHHHhcCCeEEEecccccCc
Confidence 355666666789999999999998754
No 39
>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=83.45 E-value=1.4 Score=36.75 Aligned_cols=28 Identities=25% Similarity=0.294 Sum_probs=20.9
Q ss_pred CeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeee
Q psy6931 26 LFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFK 74 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~ 74 (81)
.||++|+|-||+.+.. =.|||+|...+.
T Consensus 1 ~~vvvD~ETTG~~~~~---------------------~~IIeig~v~v~ 28 (850)
T TIGR01407 1 RYAVVDLETTGTQLSF---------------------DKIIQIGIVVVE 28 (850)
T ss_pred CEEEEEEECCCCCCCC---------------------CeEEEEEEEEEE
Confidence 4999999999986422 238888887763
No 40
>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=81.79 E-value=2.2 Score=29.33 Aligned_cols=27 Identities=19% Similarity=0.097 Sum_probs=20.3
Q ss_pred HHHHHHHHH--hccCCeEEEeccCCCCcc
Q psy6931 13 NITTRYAKA--IKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 13 ~~l~~i~~~--I~~a~FVAiD~EFtGl~~ 39 (81)
+++..+... +.++.-||+|+|+.+...
T Consensus 8 ~el~~~~~~~~l~~~~vig~D~Ew~~~~~ 36 (193)
T cd06146 8 EELEALLLALSLEAGRVVGIDSEWKPSFL 36 (193)
T ss_pred HHHHHHHHHHhhccCCEEEEECccCCCcc
Confidence 445555555 999999999999986543
No 41
>PRK05755 DNA polymerase I; Provisional
Probab=81.18 E-value=1.9 Score=36.30 Aligned_cols=27 Identities=22% Similarity=0.252 Sum_probs=21.2
Q ss_pred HHHHHHHHHhccCCeEEEeccCCCCcc
Q psy6931 13 NITTRYAKAIKSALFVTIDGEFTGLNN 39 (81)
Q Consensus 13 ~~l~~i~~~I~~a~FVAiD~EFtGl~~ 39 (81)
+.+..+...+.++.++|+|+|++|+..
T Consensus 303 ~~L~~~l~~l~~~~~~a~DtEt~~l~~ 329 (880)
T PRK05755 303 EELEAWLAKLKAAGLFAFDTETTSLDP 329 (880)
T ss_pred HHHHHHHHHhhccCeEEEEeccCCCCc
Confidence 445555666788999999999999853
No 42
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=80.88 E-value=2.1 Score=35.96 Aligned_cols=15 Identities=27% Similarity=0.299 Sum_probs=13.1
Q ss_pred cCCeEEEeccCCCCc
Q psy6931 24 SALFVTIDGEFTGLN 38 (81)
Q Consensus 24 ~a~FVAiD~EFtGl~ 38 (81)
...||++|+|-||+.
T Consensus 6 ~~~~vvvD~ETTGl~ 20 (820)
T PRK07246 6 LRKYAVVDLEATGAG 20 (820)
T ss_pred CCCEEEEEEecCCcC
Confidence 467999999999984
No 43
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=80.55 E-value=2.1 Score=36.21 Aligned_cols=30 Identities=27% Similarity=0.246 Sum_probs=22.7
Q ss_pred CCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeee
Q psy6931 25 ALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFK 74 (81)
Q Consensus 25 a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~ 74 (81)
-.||++|+|.||+.+... -.|||+|.+.+.
T Consensus 3 ~~~vvvD~ETTG~~p~~~--------------------d~IIeigav~v~ 32 (928)
T PRK08074 3 KRFVVVDLETTGNSPKKG--------------------DKIIQIAAVVVE 32 (928)
T ss_pred CCEEEEEEeCCCCCCCCC--------------------CcEEEEEEEEEE
Confidence 369999999999754320 269999998874
No 44
>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=78.87 E-value=2.4 Score=37.30 Aligned_cols=18 Identities=39% Similarity=0.469 Sum_probs=15.9
Q ss_pred ccCCeEEEeccCCCCccC
Q psy6931 23 KSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 23 ~~a~FVAiD~EFtGl~~~ 40 (81)
+++.||++|+|-||+.+.
T Consensus 188 ~~~~~VVfDiETTGL~~~ 205 (1213)
T TIGR01405 188 DDATYVVFDIETTGLSPQ 205 (1213)
T ss_pred cCCcEEEEEeEecCCCCC
Confidence 788999999999998653
No 45
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=78.43 E-value=3.1 Score=29.02 Aligned_cols=15 Identities=60% Similarity=0.678 Sum_probs=13.8
Q ss_pred CCeEEEeccCCCCcc
Q psy6931 25 ALFVTIDGEFTGLNN 39 (81)
Q Consensus 25 a~FVAiD~EFtGl~~ 39 (81)
..||++|+|-||+..
T Consensus 13 ~~~vv~D~ETtg~~~ 27 (243)
T COG0847 13 TRFVVIDLETTGLNP 27 (243)
T ss_pred CcEEEEecccCCCCC
Confidence 789999999999876
No 46
>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=77.25 E-value=0.9 Score=30.06 Aligned_cols=13 Identities=23% Similarity=0.383 Sum_probs=10.5
Q ss_pred EEEeccCCCCccC
Q psy6931 28 VTIDGEFTGLNNG 40 (81)
Q Consensus 28 VAiD~EFtGl~~~ 40 (81)
||||||++|+...
T Consensus 1 ~~iD~E~~g~~~g 13 (150)
T cd06145 1 FALDCEMCYTTDG 13 (150)
T ss_pred CEEeeeeeeecCC
Confidence 6899999998653
No 47
>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=77.12 E-value=2.8 Score=27.75 Aligned_cols=25 Identities=8% Similarity=0.125 Sum_probs=19.8
Q ss_pred HHHHHHHhc-cCCeEEEeccCCCCcc
Q psy6931 15 TTRYAKAIK-SALFVTIDGEFTGLNN 39 (81)
Q Consensus 15 l~~i~~~I~-~a~FVAiD~EFtGl~~ 39 (81)
|..+.+.++ ++.-|++|+|+.....
T Consensus 2 l~~~~~~l~~~~~~ig~D~E~~~~~~ 27 (161)
T cd06129 2 LSSLCEDLSMDGDVIAFDMEWPPGRR 27 (161)
T ss_pred HHHHHHHHhcCCCEEEEECCccCCCC
Confidence 445666777 9999999999998653
No 48
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=76.51 E-value=3.5 Score=30.49 Aligned_cols=12 Identities=42% Similarity=0.310 Sum_probs=10.8
Q ss_pred CeEEEeccCCCC
Q psy6931 26 LFVTIDGEFTGL 37 (81)
Q Consensus 26 ~FVAiD~EFtGl 37 (81)
+||+||+|-||.
T Consensus 2 ~~vviD~ETTg~ 13 (309)
T PRK06195 2 NFVAIDFETANE 13 (309)
T ss_pred cEEEEEEeCCCC
Confidence 799999999974
No 49
>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=74.32 E-value=1.8 Score=29.26 Aligned_cols=12 Identities=58% Similarity=0.692 Sum_probs=11.3
Q ss_pred eEEEeccCCCCc
Q psy6931 27 FVTIDGEFTGLN 38 (81)
Q Consensus 27 FVAiD~EFtGl~ 38 (81)
||++|+|=||+.
T Consensus 1 ~vv~D~ETTGl~ 12 (177)
T cd06136 1 FVFLDLETTGLP 12 (177)
T ss_pred CeEEeeecCCCC
Confidence 799999999997
No 50
>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=74.19 E-value=3.1 Score=28.64 Aligned_cols=23 Identities=17% Similarity=0.125 Sum_probs=18.5
Q ss_pred HHHhccCCeEEEeccCCCCccCC
Q psy6931 19 AKAIKSALFVTIDGEFTGLNNGP 41 (81)
Q Consensus 19 ~~~I~~a~FVAiD~EFtGl~~~~ 41 (81)
.+.|+++.-||+|+|+.+++..+
T Consensus 4 ~~~l~~~~~i~~D~E~~~~~~~~ 26 (197)
T cd06148 4 IIHLKKQKVIGLDCEGVNLGRKG 26 (197)
T ss_pred hhhhhhCCEEEEEcccccCCCCC
Confidence 35678899999999998876643
No 51
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=73.25 E-value=2.3 Score=30.05 Aligned_cols=17 Identities=35% Similarity=0.403 Sum_probs=13.9
Q ss_pred CCeEEEeccCCCCccCC
Q psy6931 25 ALFVTIDGEFTGLNNGP 41 (81)
Q Consensus 25 a~FVAiD~EFtGl~~~~ 41 (81)
=..|=||+|||||.+..
T Consensus 6 ~nLiWIDlEMTGLd~~~ 22 (184)
T COG1949 6 NNLIWIDLEMTGLDPER 22 (184)
T ss_pred CceEEEeeeeccCCcCc
Confidence 35688999999998764
No 52
>COG3325 ChiA Chitinase [Carbohydrate transport and metabolism]
Probab=72.50 E-value=6.1 Score=31.44 Aligned_cols=60 Identities=15% Similarity=0.052 Sum_probs=40.0
Q ss_pred CCCCcCccccHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccc
Q psy6931 1 MAPTQHPMILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSM 61 (81)
Q Consensus 1 ~~~~~~~~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~ 61 (81)
||-.+-.|+||...--++.+-.. .|.|=||-|+||-..........-.-+.|..+.+.++
T Consensus 145 ~aad~a~re~Fa~saVe~~r~~~-FDGVDIDWEYP~~~~~~~~~~~~~d~~ny~~Ll~eLR 204 (441)
T COG3325 145 MAADDASRENFAKSAVEFMRTYG-FDGVDIDWEYPGSGGDAGNCGRPKDKANYVLLLQELR 204 (441)
T ss_pred hhcCHHHHHHHHHHHHHHHHhcC-CCceeeccccCCCCCCCCCCCCcccHHHHHHHHHHHH
Confidence 45566778999987777766666 7889999999996554422222233345766655554
No 53
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=71.70 E-value=2.6 Score=30.42 Aligned_cols=17 Identities=35% Similarity=0.397 Sum_probs=14.0
Q ss_pred cCCeEEEeccCCCCccC
Q psy6931 24 SALFVTIDGEFTGLNNG 40 (81)
Q Consensus 24 ~a~FVAiD~EFtGl~~~ 40 (81)
.-.||++|+|-||+.+.
T Consensus 3 ~~r~vvlDtETTGldp~ 19 (240)
T PRK05711 3 IMRQIVLDTETTGLNQR 19 (240)
T ss_pred CCeEEEEEeeCCCcCCC
Confidence 34799999999999753
No 54
>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=71.43 E-value=2.8 Score=29.68 Aligned_cols=15 Identities=33% Similarity=0.419 Sum_probs=12.7
Q ss_pred CeEEEeccCCCCccC
Q psy6931 26 LFVTIDGEFTGLNNG 40 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~ 40 (81)
.||.+|+|-||+.+.
T Consensus 1 r~vvlD~ETTGl~p~ 15 (225)
T TIGR01406 1 RQIILDTETTGLDPK 15 (225)
T ss_pred CEEEEEeeCCCcCCC
Confidence 489999999999754
No 55
>PTZ00315 2'-phosphotransferase; Provisional
Probab=70.14 E-value=6.5 Score=32.25 Aligned_cols=32 Identities=22% Similarity=0.191 Sum_probs=22.9
Q ss_pred CCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeee
Q psy6931 25 ALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFK 74 (81)
Q Consensus 25 a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~ 74 (81)
-.||++|+|.||+..... +.-.||+||...+.
T Consensus 56 d~~IV~DlETTgl~~~~~------------------~~dEIIEIGaV~Vd 87 (582)
T PTZ00315 56 DAYVVLDFEATCEADRRI------------------EDAEVIEFPMVLVD 87 (582)
T ss_pred CeEEEEEEecCCCCCCCC------------------CCCceEEEEEEEEE
Confidence 358999999999743221 12359999998875
No 56
>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=68.31 E-value=0.54 Score=32.84 Aligned_cols=14 Identities=43% Similarity=0.603 Sum_probs=9.5
Q ss_pred EEEeccCCCCccCC
Q psy6931 28 VTIDGEFTGLNNGP 41 (81)
Q Consensus 28 VAiD~EFtGl~~~~ 41 (81)
||+|+||-|+....
T Consensus 1 ~a~d~e~v~~~~~~ 14 (174)
T cd06143 1 VAIDAEFVKLKPEE 14 (174)
T ss_pred CceeeeEEEecchh
Confidence 57777777776653
No 57
>KOG3242|consensus
Probab=66.54 E-value=3.6 Score=29.45 Aligned_cols=15 Identities=47% Similarity=0.530 Sum_probs=12.8
Q ss_pred CeEEEeccCCCCccC
Q psy6931 26 LFVTIDGEFTGLNNG 40 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~ 40 (81)
+.|=||+|||||...
T Consensus 27 ~lVWiD~EMTGLdve 41 (208)
T KOG3242|consen 27 PLVWIDCEMTGLDVE 41 (208)
T ss_pred ceEEEeeeccccccc
Confidence 578999999999764
No 58
>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=66.25 E-value=3 Score=25.60 Aligned_cols=14 Identities=43% Similarity=0.643 Sum_probs=11.1
Q ss_pred EEEeccCCCCccCC
Q psy6931 28 VTIDGEFTGLNNGP 41 (81)
Q Consensus 28 VAiD~EFtGl~~~~ 41 (81)
+++|+|++|+....
T Consensus 1 ~~~DiEt~~~~~~~ 14 (96)
T cd06125 1 IAIDTEATGLDGAV 14 (96)
T ss_pred CEEEEECCCCCCCC
Confidence 58999999986543
No 59
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=64.37 E-value=5.2 Score=28.29 Aligned_cols=15 Identities=27% Similarity=0.264 Sum_probs=12.8
Q ss_pred CeEEEeccCCCCccC
Q psy6931 26 LFVTIDGEFTGLNNG 40 (81)
Q Consensus 26 ~FVAiD~EFtGl~~~ 40 (81)
.||.+|+|-||+...
T Consensus 3 ~~vv~D~ETTGl~~~ 17 (232)
T PRK06309 3 ALIFYDTETTGTQID 17 (232)
T ss_pred cEEEEEeeCCCCCCC
Confidence 589999999999753
No 60
>PF14943 MRP-S26: Mitochondrial ribosome subunit S26
Probab=63.08 E-value=6.2 Score=27.41 Aligned_cols=31 Identities=13% Similarity=-0.109 Sum_probs=26.2
Q ss_pred CCCcCccccHHHHHHHHHHHhccCCeEEEecc
Q psy6931 2 APTQHPMILQHNITTRYAKAIKSALFVTIDGE 33 (81)
Q Consensus 2 ~~~~~~~~NF~~~l~~i~~~I~~a~FVAiD~E 33 (81)
+.+-.|+.|+++.+........++.| |||.+
T Consensus 136 sk~FIT~ENLd~~IeeALdnp~~YNf-aID~~ 166 (170)
T PF14943_consen 136 SKNFITRENLDAAIEEALDNPVDYNF-AIDLE 166 (170)
T ss_pred hcCcCCHHhHHHHHHHHHcCCcccce-eeCCC
Confidence 45778999999999999999889998 68754
No 61
>PF08947 BPS: BPS (Between PH and SH2) ; InterPro: IPR015042 The BPS (Between PH and SH2) domain, comprised of 2 beta strands and a C-terminal helix, is an approximately 45 residue region found in the adaptor proteins Grb7/10/14 that mediates inhibition of the tyrosine kinase domain of the insulin receptor by binding of the N-terminal portion of the BPS domain to the substrate peptide groove of the kinase, acting as a pseudosubstrate inhibitor []. ; PDB: 2AUH_B.
Probab=61.88 E-value=5 Score=22.72 Aligned_cols=25 Identities=20% Similarity=0.511 Sum_probs=8.5
Q ss_pred HhccCCeEEEeccCCCCccCCCCCCCCCHHH
Q psy6931 21 AIKSALFVTIDGEFTGLNNGPNTTPYDTPAQ 51 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~~~~~~~~dt~ee 51 (81)
.+++..+|||| |||-..+ ..++|.|
T Consensus 2 SvSe~slVaMD--FsG~~GR----vIenP~E 26 (49)
T PF08947_consen 2 SVSENSLVAMD--FSGQTGR----VIENPKE 26 (49)
T ss_dssp -------EEEE---SSSS------B---HHH
T ss_pred cccccceEEee--ecCCccc----ccCCHHH
Confidence 46778899999 8885432 3445544
No 62
>PRK11779 sbcB exonuclease I; Provisional
Probab=61.53 E-value=5.7 Score=31.61 Aligned_cols=18 Identities=28% Similarity=0.180 Sum_probs=15.2
Q ss_pred ccCCeEEEeccCCCCccC
Q psy6931 23 KSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 23 ~~a~FVAiD~EFtGl~~~ 40 (81)
....||.+|+|-||+.+.
T Consensus 4 ~~~~fvv~D~ETTGLdP~ 21 (476)
T PRK11779 4 MQPTFLWHDYETFGANPA 21 (476)
T ss_pred CCCcEEEEEEECCCCCCC
Confidence 356799999999999864
No 63
>PF12617 LdpA_C: Iron-Sulfur binding protein C terminal; InterPro: IPR021039 This entry represents the C-terminal region of the iron-sulphur protein LdpA (Light dependent period), which is found in phototropic organisms. LdpA was originally identified in cyanobacteria where it is involved in light-dependent modulation of the circadian clock. The presence of iron-sulphur clusters on LdpA suggests that it may modulate the circadian clock as an indirect function of light intensity by sensing changes in cellular physiology [].
Probab=51.74 E-value=24 Score=25.01 Aligned_cols=52 Identities=17% Similarity=0.098 Sum_probs=40.6
Q ss_pred ccHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceee
Q psy6931 9 ILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQF 68 (81)
Q Consensus 9 ~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~ 68 (81)
+-|++.|..|...+..=..|||.|-- | ..+.+-..++|+.++. -....|.|.
T Consensus 21 ~~F~~lw~~l~~~~~~Lk~lAiSc~~-~------~~li~~L~~~~~~l~~-l~~~~iWQ~ 72 (183)
T PF12617_consen 21 AAFERLWQALAPSVPQLKLLAISCPD-G------EGLIDYLWQLYEILRP-LPCPLIWQL 72 (183)
T ss_pred HHHHHHHHHHHhhhhhccEEEEECCC-C------HHHHHHHHHHHHHHhc-cCCCeeEee
Confidence 78999999999999999999999755 3 2355566778888886 444667775
No 64
>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=48.98 E-value=24 Score=24.03 Aligned_cols=27 Identities=11% Similarity=0.037 Sum_probs=24.4
Q ss_pred ccHHHHHHHHHHHhccCCeEEEeccCC
Q psy6931 9 ILQHNITTRYAKAIKSALFVTIDGEFT 35 (81)
Q Consensus 9 ~NF~~~l~~i~~~I~~a~FVAiD~EFt 35 (81)
.|+++.+..|.+.-.++-.||||.=..
T Consensus 47 ~NL~e~l~~I~~~~~~~~iIAIDAcLG 73 (140)
T TIGR02841 47 KNLEEKLKIIKKKHPNPFIIAIDACLG 73 (140)
T ss_pred ccHHHHHHHHHHhCCCCeEEEEECccC
Confidence 799999999999999999999997543
No 65
>PRK07983 exodeoxyribonuclease X; Provisional
Probab=48.80 E-value=12 Score=26.58 Aligned_cols=12 Identities=42% Similarity=0.551 Sum_probs=10.8
Q ss_pred eEEEeccCCCCc
Q psy6931 27 FVTIDGEFTGLN 38 (81)
Q Consensus 27 FVAiD~EFtGl~ 38 (81)
|+.+|+|-||+.
T Consensus 2 ~~vlD~ETTGl~ 13 (219)
T PRK07983 2 LRVIDTETCGLQ 13 (219)
T ss_pred eEEEEEECCCCC
Confidence 789999999984
No 66
>PF05470 eIF-3c_N: Eukaryotic translation initiation factor 3 subunit 8 N-terminus; InterPro: IPR008905 The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA [].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation, 0005852 eukaryotic translation initiation factor 3 complex
Probab=46.96 E-value=1.9 Score=35.22 Aligned_cols=12 Identities=50% Similarity=1.148 Sum_probs=8.8
Q ss_pred cceeeeeeeeee
Q psy6931 64 LLIQFGLCAFKY 75 (81)
Q Consensus 64 ~iiQ~Gl~~F~~ 75 (81)
.+.|+|||+|+.
T Consensus 502 ~~vQLGLcAFR~ 513 (595)
T PF05470_consen 502 AMVQLGLCAFRA 513 (595)
T ss_pred HHHHHHHHHHHc
Confidence 567888888765
No 67
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=39.42 E-value=42 Score=23.85 Aligned_cols=45 Identities=16% Similarity=0.169 Sum_probs=34.3
Q ss_pred CcCccccHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccc
Q psy6931 4 TQHPMILQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDF 63 (81)
Q Consensus 4 ~~~~~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f 63 (81)
....|.-|..++....+.- +-+||.|+-| +-.+||....++|+.+
T Consensus 137 ~~~~R~~F~~~l~~~L~~~-~~~~v~i~~~--------------~y~eR~~~~~~aV~el 181 (187)
T COG3172 137 SSVQRQEFQNLLEQMLEEN-NIPFVVIEGE--------------DYLERYLQAVEAVEEL 181 (187)
T ss_pred cHhHHHHHHHHHHHHHHHh-CCcEEEEcCC--------------CHHHHHHHHHHHHHHH
Confidence 3445677888887766665 7789999866 5678999999988765
No 68
>cd06395 PB1_Map2k5 PB1 domain is essential part of the mitogen-activated protein kinase kinase 5 (Map2k5, alias MEK5) one of the key member of the signaling kinases cascade which involved in angiogenesis and early cardiovascular development. The PB1 domain of Map2k5 interacts with the PB1 domain of another members of kinase cascade MEKK2 (or MEKK3). A canonical PB1-PB1 interaction, involving heterodimerization of two PB1 domain, is required for the formation of macromolecular signaling complexes ensuring specificity and fidelity during cellular signaling. The interaction between two PB1 domain depends on the type of PB1. There are three types of PB1 domains: type I which contains an OPCA motif, acidic aminoacid cluster, type II which contains a basic cluster, and type I/II which contains both an OPCA motif and a basic cluster. The Map2k5 protein contains a type I PB1 domain.
Probab=38.84 E-value=34 Score=21.58 Aligned_cols=27 Identities=11% Similarity=0.100 Sum_probs=24.0
Q ss_pred cccHHHHHHHHHHHhccCCeEEEeccC
Q psy6931 8 MILQHNITTRYAKAIKSALFVTIDGEF 34 (81)
Q Consensus 8 ~~NF~~~l~~i~~~I~~a~FVAiD~EF 34 (81)
--||.+.|..|.+.+.++.=-|++-|=
T Consensus 22 ~L~F~DvL~~I~~vlp~aT~tAFeYED 48 (91)
T cd06395 22 QLLFRDVLDVIGQVLPEATTTAFEYED 48 (91)
T ss_pred cccHHHHHHHHHHhcccccccceeecc
Confidence 379999999999999999999988663
No 69
>KOG1990|consensus
Probab=37.26 E-value=25 Score=28.60 Aligned_cols=60 Identities=13% Similarity=0.019 Sum_probs=45.1
Q ss_pred cHHHHHHHHHHHhccCCeEEEeccCCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeee
Q psy6931 10 LQHNITTRYAKAIKSALFVTIDGEFTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLC 71 (81)
Q Consensus 10 NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~ 71 (81)
|+...++.....+.+..+.+++.|++|+..... .....+..++++......+..+-+|+.
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~dl~~~~i~~~~~p~r~l~~~~~ 172 (564)
T KOG1990|consen 113 NQAGKWPSELEKEKNELLDSLGPELSDWGGSDR--LSVDADLLPEKIPDYMRPFRTLPVGSP 172 (564)
T ss_pred hhhhhhHHHHHHHHHHHhhccCcccccCCCCCC--ccchhhhchhhhhcccChhccCCCCCh
Confidence 788999999999999999999999999976543 333444566777666666666665553
No 70
>PRK13772 formimidoylglutamase; Provisional
Probab=37.17 E-value=1.7e+02 Score=21.64 Aligned_cols=65 Identities=11% Similarity=0.002 Sum_probs=42.3
Q ss_pred ccHHHHHHHHHHHhccCC--eEEEecc------CCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeee
Q psy6931 9 ILQHNITTRYAKAIKSAL--FVTIDGE------FTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75 (81)
Q Consensus 9 ~NF~~~l~~i~~~I~~a~--FVAiD~E------FtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~ 75 (81)
.++...+..+...++.++ ||+||.. .+|.+... +..+ |..|...-++..++.-+++=+.|+-+..
T Consensus 222 ~g~~~~~~~i~~~l~~~~~vylS~DiD~lDps~aPGvgtP~-pgGl-t~~e~~~il~~l~~~~~v~g~DvvEv~P 294 (314)
T PRK13772 222 RHLDARLAELDALLDAADHVYLTIDLDVLPAAVAPGVSAPA-AYGV-PLPVVEEIVLHVRASGKLRVADLAEYNP 294 (314)
T ss_pred cCHHHHHHHHHHHHhcCCeEEEEEEecCcCcccCCCCCCCC-CCCC-CHHHHHHHHHHHHhcCCeeEEEEEEECC
Confidence 346677788888887555 8899965 56654443 3444 6777777777766665677666655443
No 71
>PF09587 PGA_cap: Bacterial capsule synthesis protein PGA_cap; InterPro: IPR019079 CapA is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein [].
Probab=36.45 E-value=1.2e+02 Score=21.33 Aligned_cols=48 Identities=17% Similarity=0.187 Sum_probs=34.4
Q ss_pred cHHHHHHHHHHHhccCCeEEEeccCCCCccCCC---CCCCCCHHHHHHHHH
Q psy6931 10 LQHNITTRYAKAIKSALFVTIDGEFTGLNNGPN---TTPYDTPAQYYDKIR 57 (81)
Q Consensus 10 NF~~~l~~i~~~I~~a~FVAiD~EFtGl~~~~~---~~~~dt~eerY~~~k 57 (81)
++...+..|...++++|++-..+|.+=...... ...+.++.+.-..++
T Consensus 22 ~~~~~~~~v~~~l~~aD~~~~NlE~~v~~~~~~~~~~~~f~~~~~~~~~L~ 72 (250)
T PF09587_consen 22 GFDYIFEDVKPLLQSADLVVANLETPVTDSGQPASGYPHFNAPPEILDALK 72 (250)
T ss_pred ChHHHHHHHHHHHhhCCEEEEEeeecCcCCCCcCCCcceecCCHHHHHHHH
Confidence 899999999999999999999999886544331 124444444444443
No 72
>KOG1076|consensus
Probab=33.98 E-value=4.4 Score=34.30 Aligned_cols=13 Identities=46% Similarity=1.073 Sum_probs=10.0
Q ss_pred cceeeeeeeeeec
Q psy6931 64 LLIQFGLCAFKYD 76 (81)
Q Consensus 64 ~iiQ~Gl~~F~~~ 76 (81)
.+.|+|||+|+..
T Consensus 532 tmvQLGLCAFR~G 544 (843)
T KOG1076|consen 532 TMVQLGLCAFRQG 544 (843)
T ss_pred HHHHHHHHHHHcc
Confidence 5678888888753
No 73
>cd07381 MPP_CapA CapA and related proteins, metallophosphatase domain. CapA is one of three membrane-associated enzymes in Bacillus anthracis that is required for synthesis of gamma-polyglutamic acid (PGA), a major component of the bacterial capsule. The YwtB and PgsA proteins of Bacillus subtilis are closely related to CapA and are also included in this alignment model. CapA belongs to the metallophosphatase (MPP) superfamily. MPPs are functionally diverse, but all share a conserved domain with an active site consisting of two metal ions (usually manganese, iron, or zinc) coordinated with octahedral geometry by a cage of histidine, aspartate, and asparagine residues. The MPP superfamily includes: Mre11/SbcD-like exonucleases, Dbr1-like RNA lariat debranching enzymes, YfcE-like phosphodiesterases, purple acid phosphatases (PAPs), YbbF-like UDP-2,3-diacylglucosamine hydrolases, and acid sphingomyelinases (ASMases). The conserved domain is a double beta-sheet sandwich with a di-metal
Probab=33.72 E-value=53 Score=22.81 Aligned_cols=31 Identities=6% Similarity=-0.186 Sum_probs=27.5
Q ss_pred ccccHHHHHHHHHHHhccCCeEEEeccCCCC
Q psy6931 7 PMILQHNITTRYAKAIKSALFVTIDGEFTGL 37 (81)
Q Consensus 7 ~~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl 37 (81)
...++...+..+...++++|++...+|.+=.
T Consensus 20 ~~~~~~~~~~~v~~~~~~~D~~~~NlE~~~~ 50 (239)
T cd07381 20 RKYDFDPLFEDVKPLLRAADLAIGNLETPLT 50 (239)
T ss_pred CCCCchhHHHHHHHHHhcCCEEEEEeecCcc
Confidence 3478999999999999999999999998744
No 74
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=32.23 E-value=30 Score=31.36 Aligned_cols=20 Identities=40% Similarity=0.501 Sum_probs=16.6
Q ss_pred HhccCCeEEEeccCCCCccC
Q psy6931 21 AIKSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl~~~ 40 (81)
.++++.||++|+|.||+...
T Consensus 415 ~L~~~~~VVfDLETTGL~~~ 434 (1437)
T PRK00448 415 DLKDATYVVFDVETTGLSAV 434 (1437)
T ss_pred hhccCcEEEEEhhhcCCCCc
Confidence 45678999999999998653
No 75
>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=30.49 E-value=65 Score=22.34 Aligned_cols=28 Identities=11% Similarity=0.138 Sum_probs=24.6
Q ss_pred ccHHHHHHHHHHHhccCCeEEEeccCCC
Q psy6931 9 ILQHNITTRYAKAIKSALFVTIDGEFTG 36 (81)
Q Consensus 9 ~NF~~~l~~i~~~I~~a~FVAiD~EFtG 36 (81)
.|+++.+..|.+.-.+.-.||||.=+.-
T Consensus 71 ~NL~e~l~~I~~~~~~~~IIAIDAcLG~ 98 (163)
T PF06866_consen 71 LNLEETLNEIKKKHPNPFIIAIDACLGR 98 (163)
T ss_pred hhHHHHHHHHHHHCCCCeEEEEECCCCC
Confidence 7999999999999999999999976543
No 76
>KOG0967|consensus
Probab=30.41 E-value=41 Score=28.40 Aligned_cols=61 Identities=20% Similarity=0.331 Sum_probs=38.3
Q ss_pred HHHHHHHHHHHhcc--CCeEEEeccCCCCccCCC-CCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 11 QHNITTRYAKAIKS--ALFVTIDGEFTGLNNGPN-TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 11 F~~~l~~i~~~I~~--a~FVAiD~EFtGl~~~~~-~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
|.+....+....+. .+|| +|+|--+...... ...|. ..=.+-|.+|+ -.=|++++|.|-+|
T Consensus 402 YPDi~~~~~~~~kp~v~sFI-lD~EvVA~Dr~~~~IlpFQ---vLSTRkRk~v~-v~dikV~Vcvf~FD 465 (714)
T KOG0967|consen 402 YPDIIEVISKLKKPSVKSFI-LDCEVVAWDREKGKILPFQ---VLSTRKRKNVD-VNDIKVKVCVFVFD 465 (714)
T ss_pred CccHHHHHHHhhCCccceeE-EeeeEEEEeccCCccCchh---hhhhhhccccc-hhhceEEEEEEEEe
Confidence 44555555555555 5676 8888888766542 23333 22334556665 56789999999887
No 77
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=30.22 E-value=33 Score=31.07 Aligned_cols=22 Identities=32% Similarity=0.362 Sum_probs=18.9
Q ss_pred HHhccCCeEEEeccCCCCccCC
Q psy6931 20 KAIKSALFVTIDGEFTGLNNGP 41 (81)
Q Consensus 20 ~~I~~a~FVAiD~EFtGl~~~~ 41 (81)
..|.++.||.+|.|=|||.+.-
T Consensus 416 ~~l~datyVVfDiETTGLs~~~ 437 (1444)
T COG2176 416 QKLDDATYVVFDIETTGLSPVY 437 (1444)
T ss_pred cccccccEEEEEeecCCcCccc
Confidence 3588999999999999997753
No 78
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=30.16 E-value=73 Score=24.23 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=24.6
Q ss_pred HHHHHHHHHhccCCeEEEeccCCCCccC
Q psy6931 13 NITTRYAKAIKSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 13 ~~l~~i~~~I~~a~FVAiD~EFtGl~~~ 40 (81)
+....|...|-+-++|-+|--||||.+-
T Consensus 137 QKIQfisaviHePeLlILDEPFSGLDPV 164 (300)
T COG4152 137 QKIQFISAVIHEPELLILDEPFSGLDPV 164 (300)
T ss_pred HHHHHHHHHhcCCCEEEecCCccCCChh
Confidence 4567888899999999999999999764
No 79
>smart00854 PGA_cap Bacterial capsule synthesis protein PGA_cap. This protein is a putative poly-gamma-glutamate capsule biosynthesis protein found in bacteria. Poly-gamma-glutamate is a natural polymer that may be involved in virulence and may help bacteria survive in high salt concentrations. It is a surface-associated protein.
Probab=29.71 E-value=65 Score=22.49 Aligned_cols=30 Identities=7% Similarity=-0.251 Sum_probs=26.7
Q ss_pred cccHHHHHHHHHHHhccCCeEEEeccCCCC
Q psy6931 8 MILQHNITTRYAKAIKSALFVTIDGEFTGL 37 (81)
Q Consensus 8 ~~NF~~~l~~i~~~I~~a~FVAiD~EFtGl 37 (81)
+.+|...+..++..+++||++-+.+|.+=.
T Consensus 16 ~~~~~~~~~~v~~~~~~aD~~~~NlE~~~~ 45 (239)
T smart00854 16 KADFSPPFAGVKPLLRAADLAIGNLETPIT 45 (239)
T ss_pred ccCcchHHHHHHHHHhcCCEeEEEeecccc
Confidence 368999999999999999999999998743
No 80
>PRK06722 exonuclease; Provisional
Probab=28.98 E-value=32 Score=25.56 Aligned_cols=13 Identities=23% Similarity=0.176 Sum_probs=11.2
Q ss_pred cCCeEEEeccCCC
Q psy6931 24 SALFVTIDGEFTG 36 (81)
Q Consensus 24 ~a~FVAiD~EFtG 36 (81)
...||++|+|.||
T Consensus 4 ~~~~vViD~ETT~ 16 (281)
T PRK06722 4 ATHFIVFDIERNF 16 (281)
T ss_pred CCEEEEEEeeCCC
Confidence 3679999999996
No 81
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=26.68 E-value=42 Score=26.89 Aligned_cols=25 Identities=24% Similarity=0.065 Sum_probs=20.4
Q ss_pred HHHHHHHHhccCCeEEEeccCCCCc
Q psy6931 14 ITTRYAKAIKSALFVTIDGEFTGLN 38 (81)
Q Consensus 14 ~l~~i~~~I~~a~FVAiD~EFtGl~ 38 (81)
.+......+..+.++|+||||....
T Consensus 11 ~l~~~~~~l~~~~~~a~DtEf~r~~ 35 (553)
T PRK14975 11 ELGAALERLSPAGVVAGDTETTGDD 35 (553)
T ss_pred hhHHHHHHhccCCceeCCccccCCc
Confidence 3446677789999999999998765
No 82
>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=26.57 E-value=2.2e+02 Score=20.21 Aligned_cols=65 Identities=11% Similarity=0.189 Sum_probs=43.0
Q ss_pred cHHHHHHHHHHHhc---cCCeEEEecc------CCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeeec
Q psy6931 10 LQHNITTRYAKAIK---SALFVTIDGE------FTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYD 76 (81)
Q Consensus 10 NF~~~l~~i~~~I~---~a~FVAiD~E------FtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~ 76 (81)
++.+.+..+.+.+. +.-||+||.. ++|..... +.. -+++|..+-++...+...++=+.||-+...
T Consensus 183 g~~~~~~~~~~~~~~~~~~vylsiDiDvlDp~~~pg~~~p~-pgG-l~~~e~~~~l~~l~~~~~vvg~di~E~~P~ 256 (277)
T PF00491_consen 183 GIDAVLEEILEALGSGTDPVYLSIDIDVLDPAFAPGVGTPE-PGG-LSPRELLQLLRALARSGKVVGLDIVEYNPD 256 (277)
T ss_dssp HHHHHHHHHHHHHTTSTSEEEEEEEGGGBBTTTSTSBSS-B-SS--B-HHHHHHHHHHHHHHSEEEEEEEE-B-GG
T ss_pred hhhhHHHHHHHHHhcCCCeEEEEEehhhcChhhCCCcCCCc-CCC-CCHHHHHHHHHHHcccCCeEEEEEEEECCC
Confidence 44556788888884 6778999975 45543322 223 377888888888777789998888877654
No 83
>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=25.02 E-value=41 Score=22.61 Aligned_cols=12 Identities=42% Similarity=0.304 Sum_probs=9.7
Q ss_pred EEeccCCCCccC
Q psy6931 29 TIDGEFTGLNNG 40 (81)
Q Consensus 29 AiD~EFtGl~~~ 40 (81)
-+|+|-||+...
T Consensus 2 ~~D~ETTGl~~~ 13 (183)
T cd06138 2 FYDYETFGLNPS 13 (183)
T ss_pred EEEeecCCCCCC
Confidence 489999999753
No 84
>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=24.59 E-value=53 Score=21.39 Aligned_cols=17 Identities=29% Similarity=0.399 Sum_probs=14.1
Q ss_pred hccCCeEEEeccCCCCc
Q psy6931 22 IKSALFVTIDGEFTGLN 38 (81)
Q Consensus 22 I~~a~FVAiD~EFtGl~ 38 (81)
..+..++|+|+|-+|+.
T Consensus 2 ~~~~~~~a~d~e~~~~~ 18 (193)
T cd06139 2 LEKAKVFAFDTETTSLD 18 (193)
T ss_pred CccCCeEEEEeecCCCC
Confidence 35678999999999976
No 85
>PF13486 Dehalogenase: Reductive dehalogenase subunit
Probab=23.45 E-value=70 Score=23.79 Aligned_cols=36 Identities=25% Similarity=0.267 Sum_probs=29.3
Q ss_pred CCCCCCHHHHHHHHHhccccccceeeeeeeeeecCCCC
Q psy6931 43 TTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKYDNTTK 80 (81)
Q Consensus 43 ~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~~~~~~ 80 (81)
+.-.-||||--+-+|.+++-|-.-++|++-. |++.+
T Consensus 134 PkWqGTPEEN~~miRaA~r~fGa~~VG~~el--d~~~k 169 (308)
T PF13486_consen 134 PKWQGTPEENLRMIRAAARFFGAPDVGVAEL--DENTK 169 (308)
T ss_pred CcccCCHHHHHHHHHHHHHHcCCCceeEEEe--cCCce
Confidence 3455789999999999999999999999865 44433
No 86
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=22.97 E-value=99 Score=21.90 Aligned_cols=23 Identities=17% Similarity=0.081 Sum_probs=19.9
Q ss_pred ccHH-HHHHHHHHHhccCCeEEEe
Q psy6931 9 ILQH-NITTRYAKAIKSALFVTID 31 (81)
Q Consensus 9 ~NF~-~~l~~i~~~I~~a~FVAiD 31 (81)
++|+ -..|.|+.+.+.||-|.||
T Consensus 84 ~~le~i~~~al~rA~~~aDvIIID 107 (179)
T COG1618 84 EGLEEIAIPALRRALEEADVIIID 107 (179)
T ss_pred HHHHHHhHHHHHHHhhcCCEEEEe
Confidence 5677 4569999999999999999
No 87
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=22.40 E-value=1.4e+02 Score=19.51 Aligned_cols=16 Identities=6% Similarity=0.229 Sum_probs=13.3
Q ss_pred ccCCeEEEeccCCCCccC
Q psy6931 23 KSALFVTIDGEFTGLNNG 40 (81)
Q Consensus 23 ~~a~FVAiD~EFtGl~~~ 40 (81)
..+|||=||+ +|+...
T Consensus 90 ~~~D~iiIDt--aG~~~~ 105 (148)
T cd03114 90 AGFDVIIVET--VGVGQS 105 (148)
T ss_pred cCCCEEEEEC--CccChh
Confidence 5799999999 997643
No 88
>PF06938 DUF1285: Protein of unknown function (DUF1285); InterPro: IPR010707 This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown.; PDB: 2RA9_A 2RE3_B.
Probab=22.13 E-value=44 Score=22.66 Aligned_cols=17 Identities=24% Similarity=0.470 Sum_probs=13.1
Q ss_pred HhccCCeEEEeccCCCC
Q psy6931 21 AIKSALFVTIDGEFTGL 37 (81)
Q Consensus 21 ~I~~a~FVAiD~EFtGl 37 (81)
.+++++|+++|.++.|-
T Consensus 49 ~VEDaPf~iv~~~~~~~ 65 (148)
T PF06938_consen 49 QVEDAPFLIVDVDVEGE 65 (148)
T ss_dssp EESS-SEEEEEEEECS-
T ss_pred EEecCcEEEEEEEEecc
Confidence 36789999999999964
No 89
>PF14305 ATPgrasp_TupA: TupA-like ATPgrasp
Probab=22.04 E-value=1.1e+02 Score=21.79 Aligned_cols=24 Identities=21% Similarity=0.066 Sum_probs=22.6
Q ss_pred ccHHHHHHHHHHHhccCCeEEEec
Q psy6931 9 ILQHNITTRYAKAIKSALFVTIDG 32 (81)
Q Consensus 9 ~NF~~~l~~i~~~I~~a~FVAiD~ 32 (81)
.||++.+..-+.+-+..+||=+|+
T Consensus 179 ~~l~emi~iA~~Ls~~f~fvRVDl 202 (239)
T PF14305_consen 179 KNLEEMIEIAEKLSKGFPFVRVDL 202 (239)
T ss_pred hhHHHHHHHHHHHccCCCEEEEEE
Confidence 899999999999999999999996
No 90
>COG1099 Predicted metal-dependent hydrolases with the TIM-barrel fold [General function prediction only]
Probab=22.04 E-value=1.1e+02 Score=22.86 Aligned_cols=28 Identities=14% Similarity=0.165 Sum_probs=24.4
Q ss_pred CcCcc---ccHHHHHHHHHHHhccCCeEEEe
Q psy6931 4 TQHPM---ILQHNITTRYAKAIKSALFVTID 31 (81)
Q Consensus 4 ~~~~~---~NF~~~l~~i~~~I~~a~FVAiD 31 (81)
..||| .|+++.+..+...+.+.+-|||-
T Consensus 71 GvHPr~iP~e~~~~l~~L~~~l~~e~VvAiG 101 (254)
T COG1099 71 GVHPRAIPPELEEVLEELEELLSNEDVVAIG 101 (254)
T ss_pred ccCCCCCCchHHHHHHHHHhhcccCCeeEee
Confidence 35777 67999999999999999999985
No 91
>PF00113 Enolase_C: Enolase, C-terminal TIM barrel domain; InterPro: IPR020810 Enolase (2-phospho-D-glycerate hydrolase) is an essential glycolytic enzyme that catalyses the interconversion of 2-phosphoglycerate and phosphoenolpyruvate [, ]. In vertebrates, there are 3 different, tissue-specific isoenzymes, designated alpha, beta and gamma. Alpha is present in most tissues, beta is localised in muscle tissue, and gamma is found only in nervous tissue. The functional enzyme exists as a dimer of any 2 isoforms. In immature organs and in adult liver, it is usually an alpha homodimer, in adult skeletal muscle, a beta homodimer, and in adult neurons, a gamma homodimer. In developing muscle, it is usually an alpha/beta heterodimer, and in the developing nervous system, an alpha/gamma heterodimer []. The tissue specific forms display minor kinetic differences. Tau-crystallin, one of the major lens proteins in some fish, reptiles and birds, has been shown [] to be evolutionary related to enolase. Neuron-specific enolase is released in a variety of neurological diseases, such as multiple sclerosis and after seizures or acute stroke. Several tumour cells have also been found positive for neuron-specific enolase. Beta-enolase deficiency is associated with glycogenosis type XIII defect.; GO: 0000287 magnesium ion binding, 0004634 phosphopyruvate hydratase activity, 0006096 glycolysis, 0000015 phosphopyruvate hydratase complex; PDB: 2FYM_D 3H8A_C 1E9I_D 3TQP_B 2PU1_A 1OEP_A 2PA6_A 1PDY_A 1PDZ_A 3UJ2_E ....
Probab=21.81 E-value=1.2e+02 Score=22.71 Aligned_cols=32 Identities=16% Similarity=0.125 Sum_probs=24.5
Q ss_pred ccccHHHHHHHHHHHhccCCe-----EEEeccCCCCc
Q psy6931 7 PMILQHNITTRYAKAIKSALF-----VTIDGEFTGLN 38 (81)
Q Consensus 7 ~~~NF~~~l~~i~~~I~~a~F-----VAiD~EFtGl~ 38 (81)
+..+.++.|..|.++|++|-| ||||+-=+-+.
T Consensus 75 ~~~~~eeaL~ll~~Ai~~aGy~~~v~ialD~AAsefy 111 (295)
T PF00113_consen 75 NIDDNEEALDLLMEAIKEAGYEPDVAIALDVAASEFY 111 (295)
T ss_dssp SBSSHHHHHHHHHHHHHHTT-TTTBEEEEE--GGGGE
T ss_pred CCcchhHHHHHHHHHHHHccccceeeeeccccHHHhh
Confidence 446679999999999999986 99998776665
No 92
>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=20.06 E-value=3.6e+02 Score=19.69 Aligned_cols=63 Identities=8% Similarity=-0.078 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHhccCC---eEEEecc------CCCCccCCCCCCCCCHHHHHHHHHhccccccceeeeeeeeee
Q psy6931 11 QHNITTRYAKAIKSAL---FVTIDGE------FTGLNNGPNTTPYDTPAQYYDKIRQGSMDFLLIQFGLCAFKY 75 (81)
Q Consensus 11 F~~~l~~i~~~I~~a~---FVAiD~E------FtGl~~~~~~~~~dt~eerY~~~k~~v~~f~iiQ~Gl~~F~~ 75 (81)
.++.+..+.+.++..+ ||++|.. ++|..... +.. -++.|....++..++...++=+.|+-+..
T Consensus 202 ~~~v~~~~~~~l~~~~~~vyvS~DiDvlDps~aPgv~tp~-pgG-l~~~e~~~~l~~i~~~~~v~g~DivE~~P 273 (300)
T TIGR01229 202 IGKVVEETLEYLKAEDGPIHLSLDVDGLDPSLAPATGTPV-VGG-LTFREGLLIMEMLYETGLLTALDVVEVNP 273 (300)
T ss_pred HHHHHHHHHHHHhcCCCeEEEEEeccccCcccCCCCCCCC-CCC-CCHHHHHHHHHHHHhcCCEEEEEEEEECc
Confidence 4455667777776655 9999964 56654433 233 35566667777777777777666665544
Done!