Query psy13232
Match_columns 111
No_of_seqs 130 out of 663
Neff 4.4
Searched_HMMs 46136
Date Fri Aug 16 23:29:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13232.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13232hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG1949 Orn Oligoribonuclease 100.0 1.1E-43 2.3E-48 270.9 7.3 103 2-108 14-124 (184)
2 KOG3242|consensus 100.0 3.5E-42 7.7E-47 265.5 6.0 102 3-108 35-144 (208)
3 PRK05359 oligoribonuclease; Pr 99.9 4E-22 8.6E-27 149.8 7.6 103 2-108 11-121 (181)
4 cd06135 Orn DEDDh 3'-5' exonuc 99.5 6.5E-14 1.4E-18 103.7 7.4 102 2-107 7-116 (173)
5 PRK09145 DNA polymerase III su 98.5 3.4E-07 7.5E-12 68.9 6.0 86 2-104 37-130 (202)
6 smart00479 EXOIII exonuclease 98.3 1.1E-06 2.4E-11 62.0 5.3 90 2-107 8-103 (169)
7 cd06131 DNA_pol_III_epsilon_Ec 98.3 1.1E-06 2.4E-11 63.2 4.1 88 2-106 7-102 (167)
8 cd06127 DEDDh DEDDh 3'-5' exon 98.1 2.1E-06 4.6E-11 58.7 2.8 89 2-107 6-101 (159)
9 cd06138 ExoI_N N-terminal DEDD 98.0 1.2E-05 2.7E-10 59.7 4.9 91 2-104 6-104 (183)
10 TIGR01406 dnaQ_proteo DNA poly 97.6 7.5E-05 1.6E-09 58.0 4.0 87 2-105 8-102 (225)
11 PRK06309 DNA polymerase III su 97.5 0.00018 3.8E-09 55.8 4.7 90 2-106 10-102 (232)
12 PRK06310 DNA polymerase III su 97.5 0.00032 7E-09 55.2 6.0 89 2-106 15-109 (250)
13 PRK05711 DNA polymerase III su 97.4 0.00023 5E-09 56.2 4.8 88 2-106 12-107 (240)
14 cd06133 ERI-1_3'hExo_like DEDD 97.3 0.00048 1E-08 49.2 5.1 90 2-103 7-108 (176)
15 PRK07740 hypothetical protein; 97.1 0.0011 2.5E-08 51.9 5.2 86 2-104 67-160 (244)
16 cd06144 REX4_like DEDDh 3'-5' 96.8 0.0019 4.1E-08 46.7 4.0 56 42-106 42-98 (152)
17 TIGR01298 RNaseT ribonuclease 96.7 0.002 4.3E-08 48.9 3.9 94 2-104 16-124 (200)
18 PRK09146 DNA polymerase III su 96.7 0.0024 5.2E-08 50.2 4.5 87 2-104 55-148 (239)
19 PRK07942 DNA polymerase III su 96.7 0.0035 7.5E-08 48.7 5.3 93 2-106 14-114 (232)
20 PRK11779 sbcB exonuclease I; P 96.7 0.0024 5.2E-08 55.3 4.7 93 2-106 14-115 (476)
21 TIGR00573 dnaq exonuclease, DN 96.7 0.0041 8.8E-08 47.5 5.3 88 2-107 15-109 (217)
22 PRK06807 DNA polymerase III su 96.6 0.0046 1E-07 50.6 5.6 87 3-106 17-109 (313)
23 PRK05168 ribonuclease T; Provi 96.6 0.0021 4.6E-08 49.2 3.3 94 2-104 25-133 (211)
24 cd06134 RNaseT DEDDh 3'-5' exo 96.6 0.0025 5.4E-08 47.9 3.5 94 2-104 13-121 (189)
25 cd06130 DNA_pol_III_epsilon_li 96.3 0.0071 1.5E-07 42.4 4.5 56 42-106 42-98 (156)
26 PRK08517 DNA polymerase III su 96.2 0.015 3.2E-07 46.3 6.0 86 3-106 77-168 (257)
27 PRK06063 DNA polymerase III su 96.1 0.0043 9.3E-08 50.6 2.7 86 2-106 23-115 (313)
28 cd06145 REX1_like DEDDh 3'-5' 96.0 0.011 2.3E-07 42.9 4.3 64 31-106 32-97 (150)
29 PRK07883 hypothetical protein; 96.0 0.016 3.4E-07 50.8 5.7 85 3-104 24-114 (557)
30 cd06137 DEDDh_RNase DEDDh 3'-5 95.3 0.02 4.3E-07 41.8 3.4 87 3-105 7-104 (161)
31 TIGR01405 polC_Gram_pos DNA po 95.3 0.033 7.1E-07 53.2 5.6 87 3-106 199-291 (1213)
32 PF00929 RNase_T: Exonuclease; 94.8 0.02 4.2E-07 38.9 2.0 94 3-105 7-111 (164)
33 cd06149 ISG20 DEDDh 3'-5' exon 94.5 0.091 2E-06 38.4 5.0 88 3-106 7-98 (157)
34 PRK09182 DNA polymerase III su 94.0 0.032 6.9E-07 45.4 1.9 88 2-107 45-143 (294)
35 TIGR01407 dinG_rel DnaQ family 93.9 0.13 2.8E-06 46.8 5.6 86 2-104 8-99 (850)
36 cd06136 TREX1_2 DEDDh 3'-5' ex 93.7 0.16 3.4E-06 37.6 4.9 90 2-104 7-118 (177)
37 PRK06722 exonuclease; Provisio 93.5 0.21 4.6E-06 40.7 5.9 54 42-103 55-108 (281)
38 PRK08074 bifunctional ATP-depe 93.1 0.2 4.4E-06 46.2 5.6 86 2-104 11-103 (928)
39 PRK05601 DNA polymerase III su 92.0 0.15 3.3E-06 43.5 3.2 84 2-104 54-144 (377)
40 PRK07748 sporulation inhibitor 88.9 0.46 1E-05 35.9 3.1 56 42-104 57-112 (207)
41 PRK00448 polC DNA polymerase I 88.7 0.74 1.6E-05 45.1 5.0 88 3-107 428-521 (1437)
42 PRK07246 bifunctional ATP-depe 83.5 2.2 4.8E-05 39.2 5.1 84 2-103 15-104 (820)
43 PRK07247 DNA polymerase III su 82.8 1.6 3.5E-05 33.3 3.4 85 3-104 14-104 (195)
44 COG0847 DnaQ DNA polymerase II 82.7 2.3 4.9E-05 32.3 4.2 91 2-108 21-118 (243)
45 PF08914 Myb_DNA-bind_2: Rap1 79.6 2.6 5.5E-05 27.5 3.0 25 71-96 10-35 (65)
46 PRK06195 DNA polymerase III su 78.8 3.2 6.8E-05 33.6 4.0 81 8-104 13-99 (309)
47 KOG2248|consensus 74.8 3 6.5E-05 35.6 3.0 65 32-108 251-317 (380)
48 smart00653 eIF2B_5 domain pres 71.3 2.5 5.4E-05 30.2 1.4 31 60-93 59-89 (110)
49 PTZ00315 2'-phosphotransferase 71.1 6.8 0.00015 35.4 4.4 59 42-103 108-172 (582)
50 TIGR00311 aIF-2beta translatio 70.5 2.6 5.6E-05 31.1 1.4 60 31-93 30-106 (133)
51 PRK03988 translation initiatio 70.1 2.6 5.7E-05 31.2 1.4 61 30-93 34-111 (138)
52 PF01873 eIF-5_eIF-2B: Domain 66.3 3.3 7.2E-05 30.1 1.2 31 60-93 72-102 (125)
53 PRK12336 translation initiatio 62.9 4.3 9.3E-05 31.4 1.4 30 61-93 78-107 (201)
54 PF04423 Rad50_zn_hook: Rad50 54.9 19 0.00041 21.9 3.1 30 68-97 3-34 (54)
55 PF05822 UMPH-1: Pyrimidine 5' 50.2 7.7 0.00017 31.4 0.9 48 36-83 52-108 (246)
56 PHA02570 dexA exonuclease; Pro 46.7 27 0.00058 28.0 3.5 38 64-101 85-124 (220)
57 cd06143 PAN2_exo DEDDh 3'-5' e 46.5 23 0.0005 27.2 3.0 78 16-105 31-122 (174)
58 PF07377 DUF1493: Protein of u 45.9 27 0.00059 24.2 3.1 29 68-96 2-36 (111)
59 COG1601 GCD7 Translation initi 44.0 13 0.00029 28.0 1.3 47 44-93 64-114 (151)
60 KOG1316|consensus 43.4 13 0.00027 32.6 1.2 23 82-104 197-220 (464)
61 PF01726 LexA_DNA_bind: LexA D 41.9 13 0.00027 23.9 0.8 17 67-83 4-20 (65)
62 KOG2034|consensus 39.5 9.9 0.00022 36.1 0.0 55 47-102 845-903 (911)
63 cd06296 PBP1_CatR_like Ligand- 39.2 50 0.0011 24.2 3.7 54 38-93 134-187 (270)
64 COG2176 PolC DNA polymerase II 36.8 38 0.00082 33.8 3.4 84 3-104 430-520 (1444)
65 PF11186 DUF2972: Protein of u 35.7 6.6 0.00014 30.3 -1.5 40 70-111 145-185 (199)
66 KOG4236|consensus 34.6 17 0.00036 33.9 0.6 53 49-106 52-108 (888)
67 KOG1946|consensus 32.6 46 0.001 26.9 2.8 20 62-81 116-135 (240)
68 KOG2249|consensus 32.1 61 0.0013 27.0 3.5 49 53-107 157-206 (280)
69 PF01418 HTH_6: Helix-turn-hel 32.0 24 0.00053 22.7 1.0 28 55-82 2-29 (77)
70 PF13482 RNase_H_2: RNase_H su 31.6 31 0.00067 24.2 1.5 38 68-106 41-79 (164)
71 PF12674 Zn_ribbon_2: Putative 28.8 1.4E+02 0.0031 20.0 4.4 36 64-107 41-77 (81)
72 PHA03299 envelope glycoprotein 27.8 46 0.001 26.2 2.0 40 41-81 91-130 (195)
73 PRK10246 exonuclease subunit S 26.9 58 0.0013 30.9 2.8 17 78-94 496-514 (1047)
74 PF05402 PqqD: Coenzyme PQQ sy 23.3 71 0.0015 19.4 1.9 34 49-82 28-62 (68)
75 KOG0262|consensus 22.9 1E+02 0.0022 31.1 3.7 60 47-109 161-225 (1640)
76 PF12123 Amidase02_C: N-acetyl 22.7 40 0.00087 20.7 0.7 15 35-49 24-38 (45)
77 PF02563 Poly_export: Polysacc 22.1 37 0.00081 22.0 0.5 28 56-83 45-72 (82)
78 smart00463 SMR Small MutS-rela 22.0 1.2E+02 0.0026 19.2 2.9 40 64-103 8-58 (80)
79 COG1729 Uncharacterized protei 21.7 1.3E+02 0.0027 24.7 3.6 24 67-93 157-180 (262)
80 smart00391 MBD Methyl-CpG bind 21.5 50 0.0011 21.9 1.0 24 6-29 33-56 (77)
81 PF04025 DUF370: Domain of unk 21.3 67 0.0015 21.6 1.6 18 17-34 46-63 (73)
82 COG2008 GLY1 Threonine aldolas 20.9 2.2E+02 0.0047 24.3 4.9 62 6-67 104-184 (342)
83 PLN02965 Probable pheophorbida 20.9 1.1E+02 0.0024 22.7 2.9 53 51-107 41-96 (255)
84 PRK06489 hypothetical protein; 20.9 1.5E+02 0.0032 23.7 3.8 44 64-108 132-179 (360)
85 PF08269 Cache_2: Cache domain 20.7 46 0.001 21.7 0.7 25 57-81 27-51 (95)
86 PF12677 DUF3797: Domain of un 20.3 61 0.0013 20.5 1.1 18 73-93 5-22 (49)
87 PRK00199 ihfB integration host 20.1 1.3E+02 0.0028 19.9 2.8 28 52-79 2-31 (94)
No 1
>COG1949 Orn Oligoribonuclease (3'-5' exoribonuclease) [RNA processing and modification]
Probab=100.00 E-value=1.1e-43 Score=270.88 Aligned_cols=103 Identities=28% Similarity=0.409 Sum_probs=99.6
Q ss_pred CCCCCCCCccccccHhhhhhheeeCC-------ceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQG-------TCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-------G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
.-||++|-++++-+ +|+||||. ||++|||||+++|+.|||||+++|++|||++||++|.+|+++||.++
T Consensus 14 EMTGLd~~~drIIE----iA~iVTD~~Lnilaegp~~~Ihq~~e~L~~Mdew~~~~H~~sGL~~rV~~S~~t~~~aE~~~ 89 (184)
T COG1949 14 EMTGLDPERDRIIE----IATIVTDANLNILAEGPVIAIHQSDEQLAKMDEWNTETHGRSGLTERVKASTVTEAEAEAQT 89 (184)
T ss_pred eeccCCcCcceEEE----EEEEEecCcccccccCceEEEeCCHHHHHHHHHHHHHccccccHHHHHHHhhccHHHHHHHH
Confidence 35899999999999 99999974 89999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV 108 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv 108 (111)
|+||++|||++.+|||||| +||||||.||||+|.
T Consensus 90 l~flkkwvp~~~spicGNSI~qDRrFl~r~MP~Le 124 (184)
T COG1949 90 LDFLKKWVPKGVSPICGNSIAQDRRFLFRYMPKLE 124 (184)
T ss_pred HHHHHHhCCCCCCCCccchhhHHHHHHHHHhhhHH
Confidence 9999999999999999999 999999999999984
No 2
>KOG3242|consensus
Probab=100.00 E-value=3.5e-42 Score=265.49 Aligned_cols=102 Identities=28% Similarity=0.480 Sum_probs=98.9
Q ss_pred CCCCCCCccccccHhhhhhheeeCC-------ceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQG-------TCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~-------G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
-||++--++++-+ +||||||+ ||++|||||+++|++|+|||++||++|||+++|++|++|++|||+++|
T Consensus 35 MTGLdvekd~i~E----iacIITD~dL~~~~egpd~vI~~~~evld~MneWc~ehhg~SGLt~kv~~S~~tl~~aEnevl 110 (208)
T KOG3242|consen 35 MTGLDVEKDRIIE----IACIITDGDLNPVAEGPDLVIHQPKEVLDKMNEWCIEHHGNSGLTEKVLASKITLADAENEVL 110 (208)
T ss_pred ccccccccceeEE----EEEEEecCCccccccCccchhcCCHHHHHHHHHHHHHhccchhHHHHHHHhhccHHHHHHHHH
Confidence 4899999999999 99999975 999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV 108 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv 108 (111)
+||++|+|+|.||||||| |+||+||.||||+++
T Consensus 111 ~yikk~ip~~~~~laGNSV~~DrlFl~k~mPk~~ 144 (208)
T KOG3242|consen 111 EYIKKHIPKGKCPLAGNSVYMDRLFLKKYMPKLI 144 (208)
T ss_pred HHHHHhCCCCCCCccCcchhhHHHHHHHHhHHHH
Confidence 999999999999999999 999999999999975
No 3
>PRK05359 oligoribonuclease; Provisional
Probab=99.87 E-value=4e-22 Score=149.83 Aligned_cols=103 Identities=28% Similarity=0.412 Sum_probs=96.1
Q ss_pred CCCCCCCCccccccHhhhhhheeeCC-------ceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQG-------TCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-------G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|.++.+.| .++|++|+ ++.++|+++.+++..|++||+++|+.|||++++.+++.++++|..++
T Consensus 11 ETTGLdp~~d~Iie----IgaV~~~~~~~~~~~~~~~~i~~~~~~l~~~~~~~~~ih~~tGIt~~~l~~~~~~~e~~~~~ 86 (181)
T PRK05359 11 EMTGLDPERDRIIE----IATIVTDADLNILAEGPVIAIHQSDEALAAMDEWNTRTHTRSGLIDRVRASTVSEAEAEAQT 86 (181)
T ss_pred ecCCCCCCCCeEEE----EEEEEEcCCceEcccceEEEECCCHHHhhccChHHHHhcccccCcHHHHhcCCCHHHHHHHH
Confidence 36999999999999 88888864 57889999999999999999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV 108 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv 108 (111)
++|++.+++.+.+|||||+ ++|+.||.++||++-
T Consensus 87 l~fl~~~~~~~~~~l~g~~v~FD~~FL~~~~~~~~ 121 (181)
T PRK05359 87 LEFLKQWVPAGKSPLCGNSIGQDRRFLARYMPELE 121 (181)
T ss_pred HHHHHHhcCCCCCceeecchhhCHHHHHHHHHHhc
Confidence 9999999998899999999 999999999998754
No 4
>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=99.50 E-value=6.5e-14 Score=103.67 Aligned_cols=102 Identities=34% Similarity=0.583 Sum_probs=92.2
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|.++++.| .+++.++++ +...|+++..+...+.+|+.++|..+|++++..++..++++|-.++
T Consensus 7 ETTGl~p~~d~Iie----IgaV~~~~~~~~i~~~f~~~i~p~~~~~~~~~~~~~~ih~~tgIt~~~l~~~~~~~~vl~~~ 82 (173)
T cd06135 7 EMTGLDPEKDRILE----IACIITDGDLNIIAEGPELVIHQPDEVLDGMDEWCTEMHTKSGLTERVRASTVTLAQAEAEL 82 (173)
T ss_pred ecCCCCCCCCeeEE----EEEEEEeCCCceecCceeEEECCCHHHhhhccHHHHHcccccccHHHHHhCCCCHHHHHHHH
Confidence 36999999999999 788888663 5678888888888899999999999999999999999999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
++|+..++..+.++++||+ .+|+.||.++++++
T Consensus 83 ~~f~~~~~~~~~~~lvgh~~~FD~~fL~~~~~~~ 116 (173)
T cd06135 83 LEFIKKYVPKGKSPLAGNSVHQDRRFLDKYMPEL 116 (173)
T ss_pred HHHHHHhcCCCCCceeecchhhCHHHHHHHHHHH
Confidence 9999999888889999999 99999999988754
No 5
>PRK09145 DNA polymerase III subunit epsilon; Validated
Probab=98.47 E-value=3.4e-07 Score=68.88 Aligned_cols=86 Identities=22% Similarity=0.303 Sum_probs=70.4
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc-------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT-------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|.++..-| .+++.+|++ +...|+++ ..++++|++.| |++++-.+...+.++|-.++
T Consensus 37 ETTGl~~~~d~Iie----IgaV~~~~~~~~~~~~f~~~i~p~----~~i~~~~~~ih---GIt~~~l~~~~~~~~vl~~~ 105 (202)
T PRK09145 37 ETTGLDPRRAEIVS----IAAVKIRGNRILTSERLELLVRPP----QSLSAESIKIH---RLRHQDLEDGLSEEEALRQL 105 (202)
T ss_pred ECCCCCCCCCceEE----EEEEEEECCEEeecCceEEEECCC----CCCCHhHhhhc---CcCHHHHhcCCCHHHHHHHH
Confidence 36899999999888 788887654 34456665 35889999998 68877777889999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
++|++. .+++|.. .+|+.||.+++
T Consensus 106 ~~~i~~------~~lv~hn~~fD~~fL~~~~ 130 (202)
T PRK09145 106 LAFIGN------RPLVGYYLEFDVAMLNRYV 130 (202)
T ss_pred HHHHcC------CeEEEeCHHHHHHHHHHHH
Confidence 999953 5799999 99999999875
No 6
>smart00479 EXOIII exonuclease domain in DNA-polymerase alpha and epsilon chain, ribonuclease T and other exonucleases.
Probab=98.33 E-value=1.1e-06 Score=61.98 Aligned_cols=90 Identities=18% Similarity=0.261 Sum_probs=72.0
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ 76 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~ 76 (111)
..+|++|.+..+-+ .+++.++++ ++..|.+ . ..+.++|++.| |++++-.+...+.++|-+++.+
T Consensus 8 Ettg~~~~~~~Iie----ig~v~~~~~~~~~~f~~~v~p-~---~~i~~~~~~~~---Git~~~l~~~~~~~~~~~~~~~ 76 (169)
T smart00479 8 ETTGLDPGKDEIIE----IAAVDVDGGRIIVVFDTYVKP-D---RPITDYATEIH---GITPEMLDDAPTFEEVLEELLE 76 (169)
T ss_pred eCCCCCCCCCeEEE----EEEEEEECCEeEEEEEEEECC-C---CCCCHHHHHHh---CCCHHHHhCCCCHHHHHHHHHH
Confidence 35899998888888 677777775 3334444 2 46788999988 7998888889999999999999
Q ss_pred HHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 77 FVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 77 fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
|+... ..++||+ .+|..||.+++++.
T Consensus 77 ~l~~~-----~~v~~n~~~fD~~~L~~~~~~~ 103 (169)
T smart00479 77 FLKGK-----ILVAGNALNFDLRFLKLEHPRL 103 (169)
T ss_pred HhcCC-----EEEEeCCHHHhHHHHHHHHHHh
Confidence 99653 4689999 99999999988764
No 7
>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=98.26 E-value=1.1e-06 Score=63.16 Aligned_cols=88 Identities=16% Similarity=0.204 Sum_probs=67.0
Q ss_pred CCCCCCC-CccccccHhhhhhheee------CCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRP-SNTALSSMEQVKAYLQT------QGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p-~~~~l~s~~q~~~~lvT------d~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++| .++.+-| .+++.. ++.+...|+++. .+++.+++.| |++++..+...+.++|..++
T Consensus 7 ETTGl~~~~~~~iie----ig~v~v~~~~~~~~~~~~~v~P~~----~i~~~~~~ih---GIt~e~l~~~~~~~~v~~~l 75 (167)
T cd06131 7 ETTGLDPREGHRIIE----IGCVELINRRLTGNTFHVYINPER----DIPEEAFKVH---GITDEFLADKPKFAEIADEF 75 (167)
T ss_pred eCCCCCCCCCCeEEE----EEEEEEECCcEeccEEEEEECCCC----CCCHHHHHHh---CCCHHHHhcCCCHHHHHHHH
Confidence 4689999 4566666 555543 233455666553 4899999999 79999988889999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
++|+.+ ++++|.. .+|+.||.+++++
T Consensus 76 ~~~l~~------~~lv~hn~~fD~~~l~~~~~~ 102 (167)
T cd06131 76 LDFIRG------AELVIHNASFDVGFLNAELSL 102 (167)
T ss_pred HHHHCC------CeEEEeChHHhHHHHHHHHHH
Confidence 999855 4577777 9999999988765
No 8
>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=98.11 E-value=2.1e-06 Score=58.67 Aligned_cols=89 Identities=15% Similarity=0.174 Sum_probs=68.3
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
..||++|....+-+ .+++..+++ .+..|+++.. +.+.++.. +|++.+..++..+.++|..+++
T Consensus 6 Ettg~~~~~~~iie----i~~v~~~~~~~~~~~~~~~i~p~~~----~~~~~~~~---~gi~~~~~~~~~~~~~~~~~~~ 74 (159)
T cd06127 6 ETTGLDPKKDRIIE----IGAVKVDGGIEIVERFETLVNPGRP----IPPEATAI---HGITDEMLADAPPFEEVLPEFL 74 (159)
T ss_pred eCCCcCCCCCeEEE----EEEEEEECCcChhhhhheeeCcCCc----CCHhheec---cCCCHHHHhcCCCHHHHHHHHH
Confidence 35899998887777 677777654 3455655543 44445443 7889888889999999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
+|+++ .+++|.. .+|+.||.+++++.
T Consensus 75 ~~l~~------~~~v~~n~~fD~~~l~~~~~~~ 101 (159)
T cd06127 75 EFLGG------RVLVAHNASFDLRFLNRELRRL 101 (159)
T ss_pred HHHCC------CEEEEeCcHhhHHHHHHHHHHh
Confidence 99876 5799999 99999999998753
No 9
>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=97.98 E-value=1.2e-05 Score=59.73 Aligned_cols=91 Identities=18% Similarity=0.146 Sum_probs=62.8
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE~~l 74 (111)
..||++|.++..-| .+++..+++ ++..|+.++.+. ..+..... +|++++ +..++.+..+|-.++
T Consensus 6 ETTGl~~~~d~Iie----ig~v~v~~~~~~~~~~~~~v~p~~~~~--~~~~a~~i---hGIt~e~l~~~~~~~~~~l~~~ 76 (183)
T cd06138 6 ETFGLNPSFDQILQ----FAAIRTDENFNEIEPFNIFCRLPPDVL--PSPEALIV---TGITPQQLLKEGLSEYEFIAKI 76 (183)
T ss_pred ecCCCCCCCCceEE----EEEEEECCCCCCccceeEEEeCCCCCC--CCHHHHHH---hCCCHHHHHhcCCCHHHHHHHH
Confidence 36899999998888 788877765 444565554321 22223333 577655 555478999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
++|+.+ ++..++|.|. .+|+.||.+.+
T Consensus 77 ~~~~~~---~~~~lVahn~~~FD~~fL~~~~ 104 (183)
T cd06138 77 HRLFNT---PGTCIVGYNNIRFDDEFLRFAF 104 (183)
T ss_pred HHHHcc---CCCcEEeeCchhhHHHHHHHHH
Confidence 999875 3334666798 99999998765
No 10
>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=97.59 E-value=7.5e-05 Score=57.95 Aligned_cols=87 Identities=15% Similarity=0.172 Sum_probs=66.4
Q ss_pred CCCCCCCCc-cccccHhhhhhhe------eeCCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSN-TALSSMEQVKAYL------QTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~-~~l~s~~q~~~~l------vTd~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|.. ++.-+ .+++ +|.+.+...|++.. .+++.+.+.| |++++-.+...+.++|-.++
T Consensus 8 ETTGl~p~~~d~IIE----Igav~~~~~~~~~~~f~~~i~P~~----~i~~~a~~vh---GIt~e~l~~~p~f~ev~~~f 76 (225)
T TIGR01406 8 ETTGLDPKGGHRIVE----IGAVELVNRMLTGDNFHVYVNPER----DMPAEAAKVH---GITDEFLADKPKFKEIADEF 76 (225)
T ss_pred eCCCcCCCCCCeEEE----EEEEEEECCcEecceEEEEECcCC----CCCHHHHhcc---CCCHHHHhCCCCHHHHHHHH
Confidence 368999974 77777 5554 23345677777653 4788999998 99988888889999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDH 105 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP 105 (111)
++|++. ++|.|-- .+|+.||.+++.
T Consensus 77 ~~fi~~------~~lVaHNa~FD~~fL~~el~ 102 (225)
T TIGR01406 77 LDFIGG------SELVIHNAAFDVGFLNYELE 102 (225)
T ss_pred HHHhCC------CEEEEEecHHHHHHHHHHHH
Confidence 999854 4566655 999999987753
No 11
>PRK06309 DNA polymerase III subunit epsilon; Validated
Probab=97.48 E-value=0.00018 Score=55.75 Aligned_cols=90 Identities=13% Similarity=0.103 Sum_probs=65.1
Q ss_pred CCCCCCCCccccccHhhhhhhe--eeCCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYL--QTQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVA 79 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~l--vTd~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fik 79 (111)
..||++|.+++.-| .+++ .+.+-....|.+... ..+-+...| |++++-.+...+..+|-.++++|+.
T Consensus 10 ETTGl~~~~d~IIe----ig~v~~~~~~~f~~lv~P~~~----I~~~a~~Ih---GIt~e~v~~~p~f~ev~~~~~~fi~ 78 (232)
T PRK06309 10 ETTGTQIDKDRIIE----IAAYNGVTSESFQTLVNPEIP----IPAEASKIH---GITTDEVADAPKFPEAYQKFIEFCG 78 (232)
T ss_pred eCCCCCCCCCEEEE----EEEEcCccccEEEEEeCCCCC----CChhHHhhc---CCCHHHHhCCCCHHHHHHHHHHHHc
Confidence 46899999998888 4444 223334445554332 344566666 9998888888899999999999984
Q ss_pred hhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 80 KYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 80 k~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
. ....+|-|+ .+|+.||.+.+.+
T Consensus 79 ~----~~~lVaHN~~~FD~~~L~~e~~r 102 (232)
T PRK06309 79 T----DNILVAHNNDAFDFPLLRKECRR 102 (232)
T ss_pred C----CCEEEEeCCHHHHHHHHHHHHHH
Confidence 2 234678898 9999999988754
No 12
>PRK06310 DNA polymerase III subunit epsilon; Validated
Probab=97.45 E-value=0.00032 Score=55.20 Aligned_cols=89 Identities=11% Similarity=0.079 Sum_probs=66.9
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ 76 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~ 76 (111)
..||++|..++.-+ .++|.++.+ .+..|++.. ...+-+...| |++++..+...+.+++-.++++
T Consensus 15 ETTGl~~~~d~IIE----Ia~v~v~~~~~~~~~~~li~P~~----~I~~~a~~ih---gIt~e~v~~~p~~~ev~~~~~~ 83 (250)
T PRK06310 15 ETTGLDVKKDRIIE----FAAIRFTFDEVIDSVEFLINPER----VVSAESQRIH---HISDAMLRDKPKIAEVFPQIKG 83 (250)
T ss_pred eCCCCCCCCCeEEE----EEEEEEECCeEEEEEEEEECcCC----CCCHhhhhcc---CcCHHHHhCCCCHHHHHHHHHH
Confidence 46899999999888 777777543 333455442 2444555555 5888888888899999999999
Q ss_pred HHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 77 FVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 77 fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
|+.. ..+|+|.+ .+|+.||.+.+++
T Consensus 84 fl~~-----~~~lvghn~~FD~~~L~~~~~r 109 (250)
T PRK06310 84 FFKE-----GDYIVGHSVGFDLQVLSQESER 109 (250)
T ss_pred HhCC-----CCEEEEECHHHHHHHHHHHHHH
Confidence 9853 25799999 9999999988754
No 13
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=97.42 E-value=0.00023 Score=56.18 Aligned_cols=88 Identities=11% Similarity=0.131 Sum_probs=67.5
Q ss_pred CCCCCCCC-ccccccHhhhhhhee------eCCceeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPS-NTALSSMEQVKAYLQ------TQGTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~-~~~l~s~~q~~~~lv------Td~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|. +++.-| .++|. |.+.+...|++.. .+++.+.+.| |++++....+.+.+++-.++
T Consensus 12 ETTGldp~~~drIIE----IGaV~v~~~~~~~~~f~~~i~P~~----~i~~~a~~VH---GIT~e~l~~~p~f~ev~~~f 80 (240)
T PRK05711 12 ETTGLNQREGHRIIE----IGAVELINRRLTGRNFHVYIKPDR----LVDPEALAVH---GITDEFLADKPTFAEVADEF 80 (240)
T ss_pred eCCCcCCCCCCeEEE----EEEEEEECCEEeccEEEEEECcCC----cCCHHHhhhc---CCCHHHHcCCCCHHHHHHHH
Confidence 36899998 788888 55543 3344566676643 5889999998 99999888889999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
++|++. ++|+|-- .+|+.||.+++.+
T Consensus 81 ~~fi~~------~~lVaHNa~FD~~fL~~el~r 107 (240)
T PRK05711 81 LDFIRG------AELIIHNAPFDIGFMDYEFAL 107 (240)
T ss_pred HHHhCC------CEEEEEccHHhHHHHHHHHHH
Confidence 999854 4566766 9999999987533
No 14
>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=97.32 E-value=0.00048 Score=49.18 Aligned_cols=90 Identities=12% Similarity=0.072 Sum_probs=64.3
Q ss_pred CCCCCCCCc-----cccccHhhhhhheeeCC-c------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHH
Q psy13232 2 DNIGNRPSN-----TALSSMEQVKAYLQTQG-T------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEE 69 (111)
Q Consensus 2 ~~~~~~p~~-----~~l~s~~q~~~~lvTd~-G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~ 69 (111)
..+|+.|.. +.+-| .+++..|+ + ++..|+++.. ..+++++.+. +|++.+-.++..+.++
T Consensus 7 Ettg~~~~~~~~~~~~Iie----Igav~v~~~~~~~~~~f~~~i~P~~~--~~i~~~~~~i---~gIt~e~l~~~~~~~~ 77 (176)
T cd06133 7 EATCWEGNSKPDYPNEIIE----IGAVLVDVKTKEIIDTFSSYVKPVIN--PKLSDFCTEL---TGITQEDVDNAPSFPE 77 (176)
T ss_pred eccccCCCCCCCCCcceEE----EEEEEEEcCCCeEEeeeeeeECCCcC--CchhHHHHHh---cCcCHHHHhcCCCHHH
Confidence 357888864 56666 55555443 3 3456665542 4678889888 6799888888899999
Q ss_pred HHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhc
Q psy13232 70 ADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDS 103 (111)
Q Consensus 70 AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~ky 103 (111)
|-.++++|++... ...+++|..+|.+||.++
T Consensus 78 vl~~~~~~l~~~~---~~~~v~~~~~d~~~l~~~ 108 (176)
T cd06133 78 VLKEFLEWLGKNG---KYAFVTWGDWDLKDLLQN 108 (176)
T ss_pred HHHHHHHHHHhCC---CeEEEeecHhhHHHHHHH
Confidence 9999999998863 357889996666666554
No 15
>PRK07740 hypothetical protein; Provisional
Probab=97.06 E-value=0.0011 Score=51.95 Aligned_cols=86 Identities=19% Similarity=0.228 Sum_probs=64.7
Q ss_pred CCCCCCCCc-cccccHhhhhhheeeCCcee------eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSN-TALSSMEQVKAYLQTQGTCK------CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~-~~l~s~~q~~~~lvTd~G~~------~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|+. +.+.| .+++.+++|.. ..|+++. .+.+.+++. +|++++..+...+.++|-.++
T Consensus 67 ETTGl~p~~~deIIe----IgaV~~~~~~i~~~~f~~lv~P~~----~i~~~~~~l---tGIt~e~l~~ap~~~evl~~f 135 (244)
T PRK07740 67 ETTGFSPQQGDEILS----IGAVKTKGGEVETDTFYSLVKPKR----PIPEHILEL---TGITAEDVAFAPPLAEVLHRF 135 (244)
T ss_pred eCCCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEEeCcCC----CCChhheec---cCCCHHHHhCCCCHHHHHHHH
Confidence 368999985 77777 78888887643 2444432 567777765 578877777788999999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
++|+.. .+++|-. .+|+.||.+.+
T Consensus 136 ~~fi~~------~~lVahna~fD~~fL~~~~ 160 (244)
T PRK07740 136 YAFIGA------GVLVAHHAGHDKAFLRHAL 160 (244)
T ss_pred HHHhCC------CEEEEeCHHHHHHHHHHHH
Confidence 998753 4788988 99999998754
No 16
>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=96.78 E-value=0.0019 Score=46.65 Aligned_cols=56 Identities=14% Similarity=0.230 Sum_probs=45.8
Q ss_pred hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
.+.+++++.| |++++-.+...+.++|-.++++|+.. ++|.|-. .+|+.||....|+
T Consensus 42 ~i~~~~~~ih---GIt~~~v~~a~~~~~~~~~l~~~l~~------~vlVgHn~~fD~~~L~~~~~~ 98 (152)
T cd06144 42 PVTDYRTAVS---GIRPEHLKDAPDFEEVQKKVAELLKG------RILVGHALKNDLKVLKLDHPK 98 (152)
T ss_pred CCCcccccCC---CCCHHHHcCCCCHHHHHHHHHHHhCC------CEEEEcCcHHHHHHhcCcCCC
Confidence 4778999887 88876666788999999999999842 5788877 9999999876664
No 17
>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=96.72 E-value=0.002 Score=48.95 Aligned_cols=94 Identities=21% Similarity=0.150 Sum_probs=64.7
Q ss_pred CCCCCCCCccccccHhhhhhheee--C--------CceeeeeecCHHHHhhccchhhhccccccchH-HHHhCCCCHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQT--Q--------GTCKCGLYYNEEVLQNMNEWCVEHHNASGLTD-RVRASSVSIEEA 70 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvT--d--------~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~-~vr~S~~s~~~A 70 (111)
..||++|.++.+-| .+++.. | +.+...|+++.. ..+.....+. .|+++ +......+.++|
T Consensus 16 ETTGl~~~~d~Iie----Igav~v~~~~~g~i~~~~~f~~~v~p~p~--~~i~~~a~~i---hGIt~~~~~~~~~~~~~~ 86 (200)
T TIGR01298 16 ETGGFNAKTDALLE----IAAITLKMDEQGWLFPDTTLHFHVEPFEG--ANIQPEALEF---TGIDLDHPLRGAVSEYEA 86 (200)
T ss_pred eCCCCCCCCCeEEE----EEEEEEEEcCCCcEeecceeEEEEcCCCC--CCCCHHHHHc---cCCChhhhhhcCcchHHH
Confidence 36899999998888 555543 2 223445554221 2344555555 47774 445567899999
Q ss_pred HHHHHHHHHhhCC---CCCCcccCCc-HHhHHHHhhcc
Q psy13232 71 DKRLHQFVAKYVK---PKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 71 E~~ll~fikk~vp---~~~~pLaGNS-~~DR~FL~kym 104 (111)
-.++++|+.+++. .+.++|+|-- -+|.+||.+++
T Consensus 87 ~~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~ 124 (200)
T TIGR01298 87 LHEIFKVVRKAMKASGCQRAILVGHNANFDLGFLNAAV 124 (200)
T ss_pred HHHHHHHHHHHHHhcccCCCEEEEECchhhHHHHHHHH
Confidence 9999999988864 2567888877 99999998865
No 18
>PRK09146 DNA polymerase III subunit epsilon; Validated
Probab=96.72 E-value=0.0024 Score=50.21 Aligned_cols=87 Identities=15% Similarity=0.113 Sum_probs=62.2
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCce-------eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGTC-------KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G~-------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~l 74 (111)
..||++|.++..-| .+++..++|- ...|++.. ...+.+.+.| |++++-.+...+.+++-.++
T Consensus 55 ETTGl~p~~d~Iie----Ig~v~v~~~~i~~~~~~~~li~P~~----~i~~~~~~Ih---GIt~e~l~~ap~~~evl~~l 123 (239)
T PRK09146 55 ETTGLDAEQDAIVS----IGLVPFTLQRIRCRQARHWVVKPRR----PLEEESVVIH---GITHSELQDAPDLERILDEL 123 (239)
T ss_pred ECCCCCCCCCcEEE----EEEEEEECCeEeecceEEEEECCCC----CCChhhhhhc---CCCHHHHhCCCCHHHHHHHH
Confidence 36899999999888 7777776652 23344432 3566777776 56666666678999999999
Q ss_pred HHHHHhhCCCCCCcccCCcHHhHHHHhhcc
Q psy13232 75 HQFVAKYVKPKTAPMVGEYHTSKELLKDSD 104 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS~~DR~FL~kym 104 (111)
++|++. ..++|.|-.+|+.||.+.+
T Consensus 124 ~~~~~~-----~~lVaHna~FD~~fL~~~l 148 (239)
T PRK09146 124 LEALAG-----KVVVVHYRRIERDFLDQAL 148 (239)
T ss_pred HHHhCC-----CEEEEECHHHHHHHHHHHH
Confidence 998743 3355666699999998864
No 19
>PRK07942 DNA polymerase III subunit epsilon; Provisional
Probab=96.71 E-value=0.0035 Score=48.72 Aligned_cols=93 Identities=14% Similarity=0.084 Sum_probs=65.1
Q ss_pred CCCCCCCCccccccHhhhhhheeeCC-c-----eeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQG-T-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEADKRL 74 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE~~l 74 (111)
..||++|..+..-| .+++..|. | ....|.+.. .+.+-+.+.| |++++ ++..+...+++=.++
T Consensus 14 ETTGl~p~~d~Iie----ig~v~v~~~g~~~~~~~~lv~P~~----~i~~~a~~Ih---GIt~e~l~~~g~~~~~vl~e~ 82 (232)
T PRK07942 14 ETTGVDPETARIVT----AALVVVDADGEVVESREWLADPGV----EIPEEASAVH---GITTEYARAHGRPAAEVLAEI 82 (232)
T ss_pred ccCCCCCCCCeeEE----EEEEEEeCCCccccceEEEECCCC----CCCHHHHHHh---CCCHHHHHhhCCCHHHHHHHH
Confidence 36899999988887 66666663 3 223344332 3677778776 56654 454477888999999
Q ss_pred HHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 75 HQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 75 l~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
+++|++++..+. +|+|-- .+|+.||.+.+.+
T Consensus 83 ~~~l~~~~~~~~-~lVahNa~FD~~fL~~~~~r 114 (232)
T PRK07942 83 ADALREAWARGV-PVVVFNAPYDLTVLDRELRR 114 (232)
T ss_pred HHHHHHHhhcCC-EEEEeCcHhhHHHHHHHHHH
Confidence 999998874454 566655 9999999887643
No 20
>PRK11779 sbcB exonuclease I; Provisional
Probab=96.69 E-value=0.0024 Score=55.28 Aligned_cols=93 Identities=15% Similarity=0.108 Sum_probs=64.0
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCce-------eeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGTC-------KCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEADKR 73 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G~-------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~AE~~ 73 (111)
..||++|..++..+ .++|.+|++. +..+.++...+-.-. ... -+|++++ ++..++++.++-.+
T Consensus 14 ETTGLdP~~DrIIe----iAaVrvd~~~~~i~e~~~~~~~P~~~~lp~p~--a~~---IhGIT~e~l~~~g~~e~e~~~~ 84 (476)
T PRK11779 14 ETFGANPALDRPAQ----FAGIRTDADLNIIGEPLVFYCKPADDYLPSPE--AVL---ITGITPQEALEKGLPEAEFAAR 84 (476)
T ss_pred ECCCCCCCCCeeEE----EEEEEEeCCCceecceeEEEEcCCcCcCCCHH--HHH---HhCCCHHHHHhcCCCHHHHHHH
Confidence 36999999999999 8999888763 233444332332111 122 2578865 45678899999999
Q ss_pred HHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 74 LHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 74 ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
+.+|+.. ++.+.++-|+ .+|..||.+.+.+
T Consensus 85 i~~~l~~---~~~~lVGhNni~FD~eflr~~~~r 115 (476)
T PRK11779 85 IHAEFSQ---PGTCILGYNNIRFDDEVTRYIFYR 115 (476)
T ss_pred HHHHHhc---CCCEEEEeCchhhcHHHHHHHHHh
Confidence 9999862 4556565688 9999999886643
No 21
>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=96.67 E-value=0.0041 Score=47.54 Aligned_cols=88 Identities=11% Similarity=0.140 Sum_probs=63.3
Q ss_pred CCCCCCCCccccccHhhhhhhee-eCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQ-TQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lv-Td~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
..||++|.++ .-| .+++. .+++. ...|.+. ..+++-+...| |++++-.+...+.+++-.++.
T Consensus 15 ETTGl~~~~~-IIe----Igav~v~~~~~~~~~f~~li~P~----~~i~~~a~~ih---GIt~e~l~~~p~~~ev~~~~~ 82 (217)
T TIGR00573 15 ETTGLYAGHD-IIE----IGAVEIINRRITGNKFHTYIKPD----RPIDPDAIKIH---GITDDMLKDKPDFKEIAEDFA 82 (217)
T ss_pred cCCCCCCCCC-EEE----EEEEEEECCCEeeeEEEEEECcC----CCCCHHHHhhc---CCCHHHHcCCCCHHHHHHHHH
Confidence 4689999888 666 56655 44432 2344433 35677777776 688777777889999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
+|++. .++.|-. .+|+.||.+.+.++
T Consensus 83 ~~~~~------~~lVaHNa~FD~~fL~~~~~r~ 109 (217)
T TIGR00573 83 DYIRG------AELVIHNASFDVGFLNYEFSKL 109 (217)
T ss_pred HHhCC------CEEEEeccHHHHHHHHHHHHHh
Confidence 98853 4677777 99999999987653
No 22
>PRK06807 DNA polymerase III subunit epsilon; Validated
Probab=96.61 E-value=0.0046 Score=50.58 Aligned_cols=87 Identities=15% Similarity=0.153 Sum_probs=64.2
Q ss_pred CCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF 77 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f 77 (111)
.||++|..+.+-+ .+++..+.| ++..|.+.. .+.+.+++.| |++++..+...+.++|-.++++|
T Consensus 17 TTGl~p~~~eIIE----IgaV~v~~g~i~~~f~~lVkP~~----~I~~~a~~ih---GIT~e~l~~~~~~~evl~~f~~f 85 (313)
T PRK06807 17 TTGFNPYNDKIIQ----VAAVKYRNHELVDQFVSYVNPER----PIPDRITSLT---GITNYRVSDAPTIEEVLPLFLAF 85 (313)
T ss_pred CCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECcCC----CCCHhhhccC---CCCHHHHhCCCCHHHHHHHHHHH
Confidence 5899998888777 666666665 233455432 4677777664 68888888888999999999999
Q ss_pred HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
+... +|.|.- .+|++||.+.+.+
T Consensus 86 l~~~------~lVaHNa~FD~~fL~~~~~~ 109 (313)
T PRK06807 86 LHTN------VIVAHNASFDMRFLKSNVNM 109 (313)
T ss_pred HcCC------eEEEEcHHHHHHHHHHHHHH
Confidence 8643 355555 9999999987644
No 23
>PRK05168 ribonuclease T; Provisional
Probab=96.59 E-value=0.0021 Score=49.19 Aligned_cols=94 Identities=20% Similarity=0.185 Sum_probs=66.1
Q ss_pred CCCCCCCCccccccHhhhhhheee--C--------CceeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQT--Q--------GTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEA 70 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvT--d--------~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~A 70 (111)
..||++|.+++.-| .+++.. | +-+...|.+++. ....+-+++.| |++++ ..+..++.++|
T Consensus 25 ETTGl~~~~d~Iie----IgaV~v~~d~~g~i~~~~~f~~lv~P~~~--~~i~~~~~~ih---GIt~e~~~~~~~~~~~~ 95 (211)
T PRK05168 25 ETAGFNAKTDALLE----IAAVTLKMDEQGWLYPDETLHFHVEPFEG--ANLEPEALAFN---GIDPDNPLRGAVSEKEA 95 (211)
T ss_pred eCCCCCCCCCEEEE----EeEEEEEecCCCcEeccceEEEEECCCCC--CCCCHHHHhhc---CCCchhhhhcCCChHHH
Confidence 36899999988888 444432 2 223344555322 13566677665 66754 45667899999
Q ss_pred HHHHHHHHHhhCCC---CCCcccCCc-HHhHHHHhhcc
Q psy13232 71 DKRLHQFVAKYVKP---KTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 71 E~~ll~fikk~vp~---~~~pLaGNS-~~DR~FL~kym 104 (111)
-.++++|+.+++.. +.++++|=- .+|..||.+++
T Consensus 96 l~~~~~~l~~~~~~~~~~~~~lVaHNa~FD~~fL~~~~ 133 (211)
T PRK05168 96 LHEIFKMVRKGIKASGCNRAILVAHNAHFDLSFLMAAA 133 (211)
T ss_pred HHHHHHHHHHHHHhcccCCceEEEeccHHhHHHHHHHH
Confidence 99999999988642 346888888 99999998865
No 24
>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=96.56 E-value=0.0025 Score=47.86 Aligned_cols=94 Identities=22% Similarity=0.210 Sum_probs=65.0
Q ss_pred CCCCCCCCccccccHhhhhhheeeC----------CceeeeeecCHHHHhhccchhhhccccccchHH-HHhCCCCHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQ----------GTCKCGLYYNEEVLQNMNEWCVEHHNASGLTDR-VRASSVSIEEA 70 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd----------~G~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~-vr~S~~s~~~A 70 (111)
..||++|.+++.-| .+++..+ +.+...|.++++ ....+...+.| |++++ ..+..+..+++
T Consensus 13 ETTGl~~~~d~Iie----igav~v~~~~~~~i~~~~~f~~lv~P~~~--~~i~~~~~~ih---GIt~~~~~~~~~~~~~~ 83 (189)
T cd06134 13 ETGGFNPQTDALLE----IAAVTLEMDEQGNLYPDETFHFHILPFEG--ANLDPAALEFN---GIDPFHPFRFAVDEKEA 83 (189)
T ss_pred cCCCCCCCCCeEEE----EEEEEEEECCCCceeccceEEEEEcCCCC--CCCCHHHHhhc---CCCchhhhccccchHHH
Confidence 46999999999888 5555332 223344554322 24556666665 56654 35567888889
Q ss_pred HHHHHHHHHhhCCC---CCCcccCCc-HHhHHHHhhcc
Q psy13232 71 DKRLHQFVAKYVKP---KTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 71 E~~ll~fikk~vp~---~~~pLaGNS-~~DR~FL~kym 104 (111)
-.++++||.+++.. +.++|+|=- .+|+.||.+++
T Consensus 84 ~~~~~~~l~~~~~~~~~~~~~lVaHna~FD~~fL~~~~ 121 (189)
T cd06134 84 LKEIFKPIRKALKAQGCTRAILVGHNAHFDLGFLNAAV 121 (189)
T ss_pred HHHHHHHHHHHHhhcccCCCeEEEecchhhHHHHHHHH
Confidence 99999999988742 346888877 99999999875
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=96.35 E-value=0.0071 Score=42.42 Aligned_cols=56 Identities=13% Similarity=0.207 Sum_probs=44.5
Q ss_pred hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
.+.+-+++. +|++.+-.+...+.++|-+++++|+.+ .++.|.. .+|+.||.+++.+
T Consensus 42 ~~~~~~~~i---~GIt~e~l~~~~~~~~v~~~l~~~l~~------~~lv~hn~~fD~~~l~~~~~~ 98 (156)
T cd06130 42 RFDPFNIAI---HGITPEDVADAPTFPEVWPEIKPFLGG------SLVVAHNASFDRSVLRAALEA 98 (156)
T ss_pred CCChhhccc---cCcCHHHHhcCCCHHHHHHHHHHHhCC------CEEEEeChHHhHHHHHHHHHH
Confidence 556666655 578877766777899999999999865 5789999 9999999987755
No 26
>PRK08517 DNA polymerase III subunit epsilon; Provisional
Probab=96.17 E-value=0.015 Score=46.34 Aligned_cols=86 Identities=13% Similarity=0.174 Sum_probs=64.0
Q ss_pred CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF 77 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f 77 (111)
.+|++|.++..-| .+++..++|- ...|.++ .+.+.+++. .|++++-.....+.++|-.++++|
T Consensus 77 TTG~~~~~~~IIE----IGAv~v~~g~i~~~f~~~v~p~-----~ip~~~~~i---tGIt~e~l~~ap~~~evl~~f~~f 144 (257)
T PRK08517 77 TNGSKPKKHQIIE----IGAVKVKNGEIIDRFESFVKAK-----EVPEYITEL---TGITYEDLENAPSLKEVLEEFRLF 144 (257)
T ss_pred CCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECCC-----CCChhhhhh---cCcCHHHHcCCCCHHHHHHHHHHH
Confidence 5899999888777 6777666552 2345543 456677766 578877766788999999999999
Q ss_pred HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
+.. ++++|.. .+|..||.+++.+
T Consensus 145 l~~------~v~VaHNa~FD~~fL~~~l~r 168 (257)
T PRK08517 145 LGD------SVFVAHNVNFDYNFISRSLEE 168 (257)
T ss_pred HCC------CeEEEECHHHHHHHHHHHHHH
Confidence 854 4678888 9999999876543
No 27
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=96.11 E-value=0.0043 Score=50.56 Aligned_cols=86 Identities=15% Similarity=0.150 Sum_probs=61.2
Q ss_pred CCCCCCCCccccccHhhhhhheeeCC-c-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQG-T-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~-G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
..||++|..+..-| .+++..+. | +...|.+. .+...+..| |++++-.+...+.+++-.++.
T Consensus 23 ETTGl~p~~d~IIe----Igav~v~~~g~i~~~~~~lv~P~------~~~~~~~Ih---GIt~e~l~~ap~f~ev~~~l~ 89 (313)
T PRK06063 23 ETSGFRPGQARIIS----LAVLGLDADGNVEQSVVTLLNPG------VDPGPTHVH---GLTAEMLEGQPQFADIAGEVA 89 (313)
T ss_pred ECCCCCCCCCEEEE----EEEEEEECCceeeeEEEEEECcC------CCCCCeecC---CCCHHHHhCCCCHHHHHHHHH
Confidence 36899999888888 77777653 3 11233332 345666666 899888778788999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
+|++. .+|+|-- .+|+.||.+.+.+
T Consensus 90 ~~l~~------~~lVaHNa~FD~~fL~~~~~r 115 (313)
T PRK06063 90 ELLRG------RTLVAHNVAFDYSFLAAEAER 115 (313)
T ss_pred HHcCC------CEEEEeCHHHHHHHHHHHHHH
Confidence 99842 3455555 9999999987643
No 28
>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=96.04 E-value=0.011 Score=42.89 Aligned_cols=64 Identities=16% Similarity=0.237 Sum_probs=46.9
Q ss_pred eeeecCHHHHhhccchhhhccccccchHHHHhCC-CCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 31 CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASS-VSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 31 ~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~-~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
-.|+++. ...++.++. +|++++-.+.. .+.++|..++++|+++ .++|+|.. .+|.+||....|+
T Consensus 32 ~lv~P~~----~i~~~~t~i---tGIt~~~l~~a~~~~~~v~~~~~~fl~~-----~~vlVgHn~~fD~~fL~~~~~~ 97 (150)
T cd06145 32 ELVKPDG----EIVDYNTRF---SGITEEMLENVTTTLEDVQKKLLSLISP-----DTILVGHSLENDLKALKLIHPR 97 (150)
T ss_pred EeECCCC----ccchhccCc---CCCCHHHhccCCCCHHHHHHHHHHHhCC-----CCEEEEcChHHHHHHhhccCCC
Confidence 3455543 355555555 78996554444 6999999999999962 36899999 9999999876654
No 29
>PRK07883 hypothetical protein; Validated
Probab=95.96 E-value=0.016 Score=50.80 Aligned_cols=85 Identities=16% Similarity=0.218 Sum_probs=64.8
Q ss_pred CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF 77 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f 77 (111)
.||++|.++.+-+ .+++..++|- ...|.+. ..+.+-++..| |++++..+...+.++|-.++++|
T Consensus 24 TTGl~p~~~~IIE----IgaV~v~~g~iv~~f~~lV~P~----~~i~~~~~~it---GIt~e~l~~ap~~~evl~~f~~f 92 (557)
T PRK07883 24 TTGGSPAGDAITE----IGAVKVRGGEVLGEFATLVNPG----RPIPPFITVLT---GITTAMVAGAPPIEEVLPAFLEF 92 (557)
T ss_pred cCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEECCC----CCCChhHHhhc---CCCHHHHhCCCCHHHHHHHHHHH
Confidence 6899999888888 7777776652 2344443 24566677664 68888888889999999999999
Q ss_pred HHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 78 VAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 78 ikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
+.. ++++|.. .+|+.||.+.+
T Consensus 93 l~~------~~lVaHNa~FD~~fL~~~~ 114 (557)
T PRK07883 93 ARG------AVLVAHNAPFDIGFLRAAA 114 (557)
T ss_pred hcC------CEEEEeCcHHHHHHHHHHH
Confidence 863 5788977 99999998764
No 30
>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=95.33 E-value=0.02 Score=41.77 Aligned_cols=87 Identities=13% Similarity=0.178 Sum_probs=55.5
Q ss_pred CCCCCCCccccccHhhhhhheeeCCce---eeeeecCHHHHhhccchhhhccccccchHHHHhCCCC-------HHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTC---KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVS-------IEEADK 72 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~---~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s-------~~~AE~ 72 (111)
.||++|.++.+-+ .+++.-.+|- +..|.++ ..+.++.++.| |++++-.+...+ .++|..
T Consensus 7 ttGl~~~~d~ii~----Ig~V~v~~g~i~~~~~v~P~----~~i~~~~~~i~---GIt~~~l~~a~~~~~~~~~~~~~~~ 75 (161)
T cd06137 7 MVGLADGDSEVVR----ISAVDVLTGEVLIDSLVRPS----VRVTDWRTRFS---GVTPADLEEAAKAGKTIFGWEAARA 75 (161)
T ss_pred eeeEcCCCCEEEE----EEEEEcCCCeEEEeccccCC----CCCCccceecc---CCCHHHHhhhhhcCCccccHHHHHH
Confidence 5899998888777 5555553332 2223332 34567777664 666554333222 358888
Q ss_pred HHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccc
Q psy13232 73 RLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDH 105 (111)
Q Consensus 73 ~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP 105 (111)
++++|++. .++|.|-. .+|.+||....|
T Consensus 76 ~~~~~i~~-----~~vlVgHn~~fD~~fL~~~~~ 104 (161)
T cd06137 76 ALWKFIDP-----DTILVGHSLQNDLDALRMIHT 104 (161)
T ss_pred HHHHhcCC-----CcEEEeccHHHHHHHHhCcCC
Confidence 88888742 36899999 999999986544
No 31
>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=95.31 E-value=0.033 Score=53.24 Aligned_cols=87 Identities=13% Similarity=0.180 Sum_probs=65.7
Q ss_pred CCCCCCCccccccHhhhhhheeeCCcee-----eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTCK-----CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF 77 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~-----~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f 77 (111)
.||++|.++.+-+ .+++..+.|-. ..|. |. ....+.+++ -+|++++..++..+.++|-.++++|
T Consensus 199 TTGL~~~~d~IIE----IGAVkv~~g~iid~f~~~V~-P~---~~I~~~~~~---ltGIT~e~L~~ap~~~evl~~f~~f 267 (1213)
T TIGR01405 199 TTGLSPQYDEIIE----FGAVKVKNGRIIDKFQFFIK-PH---EPLSAFVTE---LTGITQDMLENAPEIEEVLEKFKEF 267 (1213)
T ss_pred ecCCCCCCCeEEE----EEEEEEECCeEEEEEEEEEC-CC---CCCCHHHHH---HhCCCHHHHhCCCCHHHHHHHHHHH
Confidence 5899999999888 77777776622 2343 32 234555555 4688988888899999999999999
Q ss_pred HHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
++. ++|+|-. .+|..||.+.+.+
T Consensus 268 l~~------~iLVaHNa~FD~~fL~~~~~r 291 (1213)
T TIGR01405 268 FKD------SILVAHNASFDIGFLNTNFEK 291 (1213)
T ss_pred hCC------CeEEEEChHHHHHHHHHHHHH
Confidence 853 5677777 9999999987654
No 32
>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=94.81 E-value=0.02 Score=38.86 Aligned_cols=94 Identities=17% Similarity=0.236 Sum_probs=64.8
Q ss_pred CCCCCCCccccccHhhhhhheeeCC-c------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQG-T------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~-G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
.+|++|.+...-| .+++..+. . ++..|.+.. -..+++|+++.|+ ++.+-.+...+..+|-.++.
T Consensus 7 ttg~~~~~~~iie----ig~v~~~~~~~~~~~~~~~~i~p~~--~~~i~~~~~~~~g---It~~~l~~~~~~~~~~~~~~ 77 (164)
T PF00929_consen 7 TTGLDPRQDEIIE----IGAVKVDDDENEEVESFNSLIRPEE--PPKISPWATKVHG---ITQEDLEDAPSFEEALDEFE 77 (164)
T ss_dssp ESSSTTTTCTEEE----EEEEEEETTTTEEEEEEEEEBEHSS--HCSSEHHHHHHHH---HCHHHHHCHCEHHHHHHHHH
T ss_pred cCCCCCCCCeEEE----EEEEEeeCCccccceeeeecccccc--cccCCHHHeeecC---CcccccccCCcHHHHHHhhh
Confidence 4788887777776 44444433 2 233343333 2579999999885 66666667778999999999
Q ss_pred HHHHhh---CCCCCCcccCCc-HHhHHHHhhccc
Q psy13232 76 QFVAKY---VKPKTAPMVGEY-HTSKELLKDSDH 105 (111)
Q Consensus 76 ~fikk~---vp~~~~pLaGNS-~~DR~FL~kymP 105 (111)
+|+++. +..+....+|.. ..+++++.+.+|
T Consensus 78 ~~~~~~~~~v~~n~~fd~~~l~~~~~~~~~~~~~ 111 (164)
T PF00929_consen 78 EFLKKNDILVGHNASFDIGFLRREDKRFLGKPIP 111 (164)
T ss_dssp HHHHHHTEEEETTCCHEEESSHHHHHHHHHHHHH
T ss_pred hhhhcccccccccccchhhHHHHhhhhccccccc
Confidence 999853 224456677778 888888777665
No 33
>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=94.49 E-value=0.091 Score=38.38 Aligned_cols=88 Identities=15% Similarity=0.151 Sum_probs=58.9
Q ss_pred CCCCCCCccccccHhhhhhheeeCCcee---eeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTCK---CGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVA 79 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~---~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fik 79 (111)
-||++|.+.. . +..++.+|...|-. ..|.++ ..+.+|.++. +|++++-.+...+.++|..++++|++
T Consensus 7 ttGl~~~~~~-~--~i~~i~~v~~~g~~~~~~lv~P~----~~i~~~~~~i---~GIt~~~l~~a~~~~~v~~~l~~~l~ 76 (157)
T cd06149 7 MVGTGPGGRE-S--ELARCSIVNYHGDVLYDKYIRPE----GPVTDYRTRW---SGIRRQHLVNATPFAVAQKEILKILK 76 (157)
T ss_pred eccccCCCCe-E--EEEEEEEEeCCCCEEEEEeECCC----CccCccceEC---CCCCHHHHhcCCCHHHHHHHHHHHcC
Confidence 5899997511 1 22234444423322 223333 2356777766 58887776778999999999999984
Q ss_pred hhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 80 KYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 80 k~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
. ++|.|=+ .+|-.||....|.
T Consensus 77 ~------~vlV~Hn~~~D~~~l~~~~~~ 98 (157)
T cd06149 77 G------KVVVGHAIHNDFKALKYFHPK 98 (157)
T ss_pred C------CEEEEeCcHHHHHHhcccCCC
Confidence 3 5799999 9999999987443
No 34
>PRK09182 DNA polymerase III subunit epsilon; Validated
Probab=94.03 E-value=0.032 Score=45.38 Aligned_cols=88 Identities=9% Similarity=0.071 Sum_probs=51.3
Q ss_pred CCCCCCCCccccccHhhhhhheeeC---Cce--------eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQ---GTC--------KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEA 70 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd---~G~--------~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~A 70 (111)
..||++|..+...+ .++|..+ .|- ...+. |. ..+.+.++.. +|++++-....-...
T Consensus 45 ETTGLd~~~d~IIE----Ig~V~v~~~~~g~i~~v~~~~~~lv~-P~---~~I~~~~t~I---hGIt~e~v~~~~~~~-- 111 (294)
T PRK09182 45 ETTGLDPRKDEIIE----IGMVAFEYDDDGRIGDVLDTFGGLQQ-PS---RPIPPEITRL---TGITDEMVAGQTIDP-- 111 (294)
T ss_pred eCCCCCCCCCeEEE----EEEEEEEecCCCceeeeeeEEEEEeC-CC---CCCCHHHHHh---cCCCHHHHhcCCCcH--
Confidence 36899999998888 6666654 231 11222 22 1244555555 467766544432221
Q ss_pred HHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhccccc
Q psy13232 71 DKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFL 107 (111)
Q Consensus 71 E~~ll~fikk~vp~~~~pLaGNS~~DR~FL~kymP~l 107 (111)
..+.+|++. ....+|=|..+||.||.+++|.+
T Consensus 112 -~~l~~fl~~----~~vlVAHNA~FD~~fL~~~~~~~ 143 (294)
T PRK09182 112 -AAVDALIAP----ADLIIAHNAGFDRPFLERFSPVF 143 (294)
T ss_pred -HHHHHHhcC----CCEEEEeCHHHHHHHHHHHHHhc
Confidence 246666653 22234556699999999987653
No 35
>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=93.85 E-value=0.13 Score=46.84 Aligned_cols=86 Identities=12% Similarity=0.185 Sum_probs=61.8
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ 76 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~ 76 (111)
..||++|.++.+-+ .+++..++| +...|.+.. .+.+-+++. +|++++-.+...+.+++-.++.+
T Consensus 8 ETTG~~~~~~~IIe----ig~v~v~~~~i~~~f~~~v~P~~----~i~~~~~~l---tGIt~e~l~~ap~~~ev~~~l~~ 76 (850)
T TIGR01407 8 ETTGTQLSFDKIIQ----IGIVVVEDGEIVDTFHTDVNPNE----PIPPFIQEL---TGISDNMLQQAPYFSQVAQEIYD 76 (850)
T ss_pred ECCCCCCCCCeEEE----EEEEEEECCEEEEEEEEEeCCCC----CCChhhhhh---cCcCHHHHhCCCCHHHHHHHHHH
Confidence 36899999888777 666666554 233444432 456666655 57776666667889999999999
Q ss_pred HHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 77 FVAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 77 fikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
|+. .++++|-. .+|+.||.+++
T Consensus 77 ~l~------~~~~VahN~~fD~~fL~~~~ 99 (850)
T TIGR01407 77 LLE------DGIFVAHNVHFDLNFLAKAL 99 (850)
T ss_pred HhC------CCEEEEeCcHHHHHHHHHHH
Confidence 984 24688877 99999999864
No 36
>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=93.67 E-value=0.16 Score=37.64 Aligned_cols=90 Identities=10% Similarity=0.159 Sum_probs=55.3
Q ss_pred CCCCCC-CCccccccHhhhhhheeeCCc------------------eeeeeecCHHHHhhccchhhhccccccchHHHHh
Q psy13232 2 DNIGNR-PSNTALSSMEQVKAYLQTQGT------------------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRA 62 (111)
Q Consensus 2 ~~~~~~-p~~~~l~s~~q~~~~lvTd~G------------------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~ 62 (111)
..||++ |.++..-| .+++..++| +...|.+.. .+.+-.++.| |++++-..
T Consensus 7 ETTGl~~~~~d~Iie----i~av~v~~~~~~~~~~~~~~~~~~~~~~~~lv~P~~----~I~~~a~~Ih---GIt~e~l~ 75 (177)
T cd06136 7 ETTGLPKHNRPEITE----LCLVAVHRDHLLNTSRDKPALPRVLDKLSLCFNPGR----AISPGASEIT---GLSNDLLE 75 (177)
T ss_pred ecCCCCCCCCCceEE----EEEEEEecccccccccccccccceeeeeeEEeCCCC----cCChhHHHHh---CcCHHHHh
Confidence 369999 68888888 666665543 233444431 3444445554 66644443
Q ss_pred CCCCH-HHHHHHHHHHHHhhCCCCCCcccC-Cc-HHhHHHHhhcc
Q psy13232 63 SSVSI-EEADKRLHQFVAKYVKPKTAPMVG-EY-HTSKELLKDSD 104 (111)
Q Consensus 63 S~~s~-~~AE~~ll~fikk~vp~~~~pLaG-NS-~~DR~FL~kym 104 (111)
..-+. +++.+.+.+|+... .+.++|+| |. .+|.+||.+.+
T Consensus 76 ~~~~~~~~~~~~l~~f~~~~--~~~~~lVaHNa~~FD~~fL~~~~ 118 (177)
T cd06136 76 HKAPFDSDTANLIKLFLRRQ--PKPICLVAHNGNRFDFPILRSEL 118 (177)
T ss_pred cCCCccHHHHHHHHHHHHhc--CCCCEEEEcCCcccCHHHHHHHH
Confidence 33343 35667777887754 33456666 87 89999998765
No 37
>PRK06722 exonuclease; Provisional
Probab=93.55 E-value=0.21 Score=40.69 Aligned_cols=54 Identities=11% Similarity=0.155 Sum_probs=44.1
Q ss_pred hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhc
Q psy13232 42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDS 103 (111)
Q Consensus 42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~ky 103 (111)
...++|++.| |++++-.....+.++|=.++++|+.. ..++|.|..+|++||.+.
T Consensus 55 ~I~~~i~~LT---GIT~emV~~AP~f~eVl~ef~~fig~-----~~lvahna~FD~~FL~~~ 108 (281)
T PRK06722 55 RLTRHTTKLT---GITKKDLIGVEKFPQIIEKFIQFIGE-----DSIFVTWGKEDYRFLSHD 108 (281)
T ss_pred cCCHhHhhhc---CCCHHHHcCCCCHHHHHHHHHHHHCC-----CcEEEEEeHHHHHHHHHH
Confidence 5678898876 77877777788999999999999853 347888997799999984
No 38
>PRK08074 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=93.08 E-value=0.2 Score=46.23 Aligned_cols=86 Identities=13% Similarity=0.213 Sum_probs=61.8
Q ss_pred CCCCCCCCc-cccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 2 DNIGNRPSN-TALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 2 ~~~~~~p~~-~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
..||++|.. +.+-+ .+++..++| +...|++. ..+.+.+++.| |++++-.+...+.++|-.++.
T Consensus 11 ETTG~~p~~~d~IIe----igav~v~~~~i~~~f~~~v~P~----~~i~~~~~~lt---GIt~~~l~~ap~f~ev~~~l~ 79 (928)
T PRK08074 11 ETTGNSPKKGDKIIQ----IAAVVVEDGEILERFSSFVNPE----RPIPPFITELT---GISEEMVKQAPLFEDVAPEIV 79 (928)
T ss_pred eCCCCCCCCCCcEEE----EEEEEEECCEEEEEEEEEECcC----CCCCHHHhhcC---CCCHHHHhcCCCHHHHHHHHH
Confidence 368999875 55666 556555554 33345543 24667777664 688777777889999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
+|++ .++++|-. .+|+.||.+.+
T Consensus 80 ~~l~------~~~~VaHN~~FD~~fL~~~~ 103 (928)
T PRK08074 80 ELLE------GAYFVAHNVHFDLNFLNEEL 103 (928)
T ss_pred HHhC------CCeEEEEChHHHHHHHHHHH
Confidence 9984 35788866 99999998854
No 39
>PRK05601 DNA polymerase III subunit epsilon; Validated
Probab=91.97 E-value=0.15 Score=43.47 Aligned_cols=84 Identities=14% Similarity=0.160 Sum_probs=59.8
Q ss_pred CCCCCCCCccccccHhhhhhheeeC-Cc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQ-GT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd-~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
..||++|+.+.+-| .++|..+ +| +...|.++... ..+ | =.||+++-.+...+.+++-.+++
T Consensus 54 ETTGLdp~~drIIe----IgAV~i~~~g~ive~f~tLVnP~~~~----~p~----~-LHGIT~e~La~AP~f~eVl~el~ 120 (377)
T PRK05601 54 QTSGIHPSTSRLIT----IDAVTLTADGEEVEHFHAVLNPGEDP----GPF----H-LHGLSAEEFAQGKRFSQILKPLD 120 (377)
T ss_pred ECCCCCCCCCeEEE----EEEEEEEcCCEEEEEEEEEECcCCCC----CCc----c-ccCCCHHHHhcCCCHHHHHHHHH
Confidence 36899999998888 6566433 33 33445544311 111 2 57999999999999999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
+||+.. +|.|-- .+|..||.+.+
T Consensus 121 ~fL~g~------vLVaHNA~FD~~FL~~e~ 144 (377)
T PRK05601 121 RLIDGR------TLILHNAPRTWGFIVSEA 144 (377)
T ss_pred HHhCCC------EEEEECcHHHHHHHHHHH
Confidence 999753 455555 99999998854
No 40
>PRK07748 sporulation inhibitor KapD; Provisional
Probab=88.93 E-value=0.46 Score=35.92 Aligned_cols=56 Identities=20% Similarity=0.299 Sum_probs=43.3
Q ss_pred hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhcc
Q psy13232 42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSD 104 (111)
Q Consensus 42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~kym 104 (111)
...+.|++.| |++++-.+...+.++|-.++++|+... ...+++|+.+|.+||.+..
T Consensus 57 ~i~~~~~~lt---GIt~~~l~~ap~~~evl~~f~~~~~~~----~~~iv~~~~fD~~fL~~~~ 112 (207)
T PRK07748 57 SLTERCKSFL---GITQEDVDKGISFEELVEKLAEYDKRC----KPTIVTWGNMDMKVLKHNC 112 (207)
T ss_pred ccChhhhhhc---CcCHHHHccCCCHHHHHHHHHHHhCcC----CeEEEEECHHHHHHHHHHH
Confidence 4677888776 778776677899999999999988542 3467788888999997654
No 41
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=88.71 E-value=0.74 Score=45.06 Aligned_cols=88 Identities=14% Similarity=0.171 Sum_probs=57.5
Q ss_pred CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF 77 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f 77 (111)
.||++|..+..-+ .+++..+.|. +..|.+. ....+.+++.| |++++......++++|-.++++|
T Consensus 428 TTGL~~~~deIIE----IgAV~V~~G~iie~F~~~V~P~----~~I~~~~~~LT---GIT~e~L~~aps~~EaL~~f~~f 496 (1437)
T PRK00448 428 TTGLSAVYDEIIE----IGAVKIKNGEIIDKFEFFIKPG----HPLSAFTTELT---GITDDMVKDAPSIEEVLPKFKEF 496 (1437)
T ss_pred hcCCCCchhhhhe----eeeEEEeCCeEeeeEEEEECCC----CCCCHHHHHHh---CCCHHHHcCCCCHHHHHHHHHHH
Confidence 4788888776666 3444445442 2233322 12345555554 88888887889999999999988
Q ss_pred HHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 78 VAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 78 ikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
+. + +++.|-. .+|..||.+.+.++
T Consensus 497 ig-----g-~vLVAHNa~FD~~fL~~~l~rl 521 (1437)
T PRK00448 497 CG-----D-SILVAHNASFDVGFINTNYEKL 521 (1437)
T ss_pred hC-----C-CEEEEeCccccHHHHHHHHHHc
Confidence 74 3 3455555 99999998765554
No 42
>PRK07246 bifunctional ATP-dependent DNA helicase/DNA polymerase III subunit epsilon; Validated
Probab=83.48 E-value=2.2 Score=39.22 Aligned_cols=84 Identities=13% Similarity=0.266 Sum_probs=57.6
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQ 76 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~ 76 (111)
..||++|. +.+-+ .+++..++|- ...|.+. ..+.+-++.. +|++++-.+...+.++|-.++++
T Consensus 15 ETTGl~~~-d~IIe----IgaV~v~~g~i~~~f~~lv~P~----~~i~~~~~~l---tGIt~e~l~~ap~~~ev~~~~~~ 82 (820)
T PRK07246 15 EATGAGPN-ASIIQ----VGIVIIEGGEIIDSYTTDVNPH----EPLDEHIKHL---TGITDQQLAQAPDFSQVARHIYD 82 (820)
T ss_pred ecCCcCCC-CeEEE----EEEEEEECCEEEEEEEEEeCcC----CCCCHhHhhc---CCCCHHHHhcCCCHHHHHHHHHH
Confidence 35899884 55555 4555444442 2224332 2455666655 57887777778899999999999
Q ss_pred HHHhhCCCCCCcccCCc-HHhHHHHhhc
Q psy13232 77 FVAKYVKPKTAPMVGEY-HTSKELLKDS 103 (111)
Q Consensus 77 fikk~vp~~~~pLaGNS-~~DR~FL~ky 103 (111)
|+. .++++|-. .+|+.||.+.
T Consensus 83 ~l~------~~~lVaHN~~FD~~fL~~~ 104 (820)
T PRK07246 83 LIE------DCIFVAHNVKFDANLLAEA 104 (820)
T ss_pred HhC------CCEEEEECcHHHHHHHHHH
Confidence 975 35788888 9999999875
No 43
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=82.85 E-value=1.6 Score=33.35 Aligned_cols=85 Identities=11% Similarity=0.118 Sum_probs=53.6
Q ss_pred CCCCCCCccccccHhhhhhheeeCCce-----eeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTC-----KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQF 77 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~-----~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~f 77 (111)
.||++|.+. +-+ ..++..++|- +.-|. |+. .....+++. +|++++-.+...++.+|-.++++|
T Consensus 14 tTGl~~~~e-IIe----IgaV~v~~g~~~~~f~~lv~-P~~---~i~~~~~~l---hGIt~~~v~~ap~~~evl~~f~~f 81 (195)
T PRK07247 14 FNTVNGVSH-IIQ----VSAVKYDDHKEVDSFDSYVY-TDV---PLQSFINGL---TGITADKIADAPKVEEVLAAFKEF 81 (195)
T ss_pred CCCCCCCCe-EEE----EEEEEEECCEEEEEEEEEEC-CCC---CCCccceec---CCCCHHHHhCCCCHHHHHHHHHHH
Confidence 478876433 334 4444444442 22232 332 335556654 689988777888999999999999
Q ss_pred HHhhCCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 78 VAKYVKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 78 ikk~vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
++.. ..++=|. .+|..||.++.
T Consensus 82 ~~~~-----~lVaHNa~~fD~~fL~~~g 104 (195)
T PRK07247 82 VGEL-----PLIGYNAQKSDLPILAENG 104 (195)
T ss_pred HCCC-----eEEEEeCcHhHHHHHHHcC
Confidence 8544 2444566 68999998863
No 44
>COG0847 DnaQ DNA polymerase III, epsilon subunit and related 3'-5' exonucleases [DNA replication, recombination, and repair]
Probab=82.72 E-value=2.3 Score=32.25 Aligned_cols=91 Identities=14% Similarity=0.149 Sum_probs=60.7
Q ss_pred CCCCCCCCccccccHhhhhhheeeCCc------eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHH
Q psy13232 2 DNIGNRPSNTALSSMEQVKAYLQTQGT------CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 2 ~~~~~~p~~~~l~s~~q~~~~lvTd~G------~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
..+|.+|..+++-+ .+++.-..+ +...|++ +.. +.+-..+.| |++.+-........++-.+++
T Consensus 21 ETtg~~~~~~~iie----Igav~~~~~~i~~~~~~~~v~P-~~~---i~~~~~~i~---git~e~l~~~p~~~~v~~~~~ 89 (243)
T COG0847 21 ETTGLNPKKDRIIE----IGAVTLEDGRIVERSFHTLVNP-ERP---IPPEIFKIH---GITDEMLADAPKFAEVLPEFL 89 (243)
T ss_pred ccCCCCCCCCceEE----EEeEEEECCeeecceeEEEECC-CCC---CChhhhhhc---CCCHHHHhcCCCHHHHHHHHH
Confidence 35888987777777 444443333 2344554 322 444444444 566677677788999999999
Q ss_pred HHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232 76 QFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV 108 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv 108 (111)
+|+... +.++|=. .+|..||.+.+.+.-
T Consensus 90 ~~i~~~-----~~~Vahna~fD~~fl~~~~~~~~ 118 (243)
T COG0847 90 DFIGGL-----RLLVAHNAAFDVGFLRVESERLG 118 (243)
T ss_pred HHHCCC-----CeEEEEchhhcHHHHHHHHHHcC
Confidence 998874 4677777 999999988776543
No 45
>PF08914 Myb_DNA-bind_2: Rap1 Myb domain; InterPro: IPR015010 Rap1 Myb adopts a canonical three-helix bundle tertiary structure, with the second and third helices forming a helix-turn-helix variant motif. The function is unclear but it may either interact with DNA via an adaptor protein or it may be only involved in protein-protein interactions []. ; PDB: 1FEX_A.
Probab=79.55 E-value=2.6 Score=27.48 Aligned_cols=25 Identities=16% Similarity=0.275 Sum_probs=19.1
Q ss_pred HHHHHHHHHhhCCCCCCcccCCc-HHh
Q psy13232 71 DKRLHQFVAKYVKPKTAPMVGEY-HTS 96 (111)
Q Consensus 71 E~~ll~fikk~vp~~~~pLaGNS-~~D 96 (111)
++.|++||+++-+.+ +++.||. +++
T Consensus 10 D~~l~~~v~~~~~~~-~~~~Gn~iwk~ 35 (65)
T PF08914_consen 10 DAALLDYVKENERQG-GSVSGNKIWKE 35 (65)
T ss_dssp HHHHHHHHHHT--ST-TTTTSSHHHHH
T ss_pred HHHHHHHHHHhccCC-CCCchHHHHHH
Confidence 567899999987555 6789999 986
No 46
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=78.83 E-value=3.2 Score=33.57 Aligned_cols=81 Identities=5% Similarity=0.089 Sum_probs=52.5
Q ss_pred CCccccccHhhhhhheeeCCc-----eeeeeecCHHHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhC
Q psy13232 8 PSNTALSSMEQVKAYLQTQGT-----CKCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYV 82 (111)
Q Consensus 8 p~~~~l~s~~q~~~~lvTd~G-----~~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~v 82 (111)
|.++..-| .+++..++| ....|.++. ....+.|+.. .|++++-.+...+..+|-.++++|+..
T Consensus 13 ~~~d~Iie----Igav~v~~g~i~~~f~~lv~P~~---~~~~~~~~~I---hGIT~e~v~~ap~f~ev~~~~~~fl~~-- 80 (309)
T PRK06195 13 EKRNSPCS----IGIVVVKDGEIVEKVHYLIKPKE---MRFMPINIGI---HGIRPHMVEDELEFDKIWEKIKHYFNN-- 80 (309)
T ss_pred CCCCceEE----EEEEEEECCEEEEEEEEEECCCC---CCCChhheec---cCcCHHHHhCCCCHHHHHHHHHHHhCC--
Confidence 44555555 455554443 223454432 1345567655 578877666677899999999999843
Q ss_pred CCCCCcccCCc-HHhHHHHhhcc
Q psy13232 83 KPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 83 p~~~~pLaGNS-~~DR~FL~kym 104 (111)
++|+|-- .+|+.||.+.+
T Consensus 81 ----~~lVaHNa~FD~~fL~~~~ 99 (309)
T PRK06195 81 ----NLVIAHNASFDISVLRKTL 99 (309)
T ss_pred ----CEEEEECcHHHHHHHHHHH
Confidence 5677777 99999997753
No 47
>KOG2248|consensus
Probab=74.82 E-value=3 Score=35.62 Aligned_cols=65 Identities=22% Similarity=0.290 Sum_probs=48.2
Q ss_pred eeecCHHHHhhccchhhhccccccchHHHH-hCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccccc
Q psy13232 32 GLYYNEEVLQNMNEWCVEHHNASGLTDRVR-ASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLV 108 (111)
Q Consensus 32 vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr-~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv 108 (111)
.|.+..+|++.-. .-||++++.. ++++|+++.+.++++|+.+- ..|+|-| .-|-+=|+-.-|..|
T Consensus 251 fVkP~~~VvDy~T-------~~SGIT~~~~e~~t~tl~dvq~~l~~~~~~~-----TILVGHSLenDL~aLKl~H~~Vi 317 (380)
T KOG2248|consen 251 FVKPNKPVVDYNT-------RYSGITEEDLENSTITLEDVQKELLELISKN-----TILVGHSLENDLKALKLDHPSVI 317 (380)
T ss_pred eecCCCccccccc-------ccccccHHHHhcCccCHHHHHHHHHhhcCcC-----cEEEeechhhHHHHHhhhCCcee
Confidence 4455555555433 5699998887 58999999999988866443 4799999 999988887666543
No 48
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=71.30 E-value=2.5 Score=30.16 Aligned_cols=31 Identities=16% Similarity=0.380 Sum_probs=27.1
Q ss_pred HHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 60 VRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 60 vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
+.+...+.++.|..+-+||++|| .|+-|||.
T Consensus 59 ii~G~~~~~~i~~~l~~yI~~yV---lC~~C~sp 89 (110)
T smart00653 59 IVNGRFTPKKLQDLLRRYIKEYV---LCPECGSP 89 (110)
T ss_pred EEEEeeCHHHHHHHHHHHHHhcE---ECCCCCCC
Confidence 34567899999999999999999 78899986
No 49
>PTZ00315 2'-phosphotransferase; Provisional
Probab=71.07 E-value=6.8 Score=35.37 Aligned_cols=59 Identities=15% Similarity=0.146 Sum_probs=46.0
Q ss_pred hccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCC-----CCCCcccCCcHHhH-HHHhhc
Q psy13232 42 NMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVK-----PKTAPMVGEYHTSK-ELLKDS 103 (111)
Q Consensus 42 ~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp-----~~~~pLaGNS~~DR-~FL~ky 103 (111)
.+.++|++. +|++++-.++..+..+|-.++++||+++.. .+...+|=|+.+|. .||.++
T Consensus 108 ~Ls~fct~L---TGITqe~V~~Ap~F~eVl~ef~~fL~~~~~~e~~~~~~~~vah~g~fDl~~fL~~e 172 (582)
T PTZ00315 108 VLSRFCTEL---TGITQSMVSRADPFPVVYCEALQFLAEAGLGDAPPLRSYCVVTCGDWDLKTMLPSQ 172 (582)
T ss_pred CCChhHhhh---cCcCHHHHhcCCCHHHHHHHHHHHHhccccccccccCceEEEeccHHHHHHHHHHH
Confidence 477899987 588888888899999999999999998841 22345666779997 588643
No 50
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=70.46 E-value=2.6 Score=31.06 Aligned_cols=60 Identities=17% Similarity=0.196 Sum_probs=41.2
Q ss_pred eeeecCHHHHhhccchhhhcccc--------------ccchH---HHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 31 CGLYYNEEVLQNMNEWCVEHHNA--------------SGLTD---RVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 31 ~vIhqp~~vL~~MdeWc~~~H~~--------------SGL~~---~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
+.+.-.+.++.|+.+-|+.+|.. .|-++ -+.+...+.++.+..+-+||++|| .||-|||.
T Consensus 30 v~~eG~kTvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~~~rlii~G~~~~~~i~~~L~~yI~~yV---lC~~C~sP 106 (133)
T TIGR00311 30 IVIEGNRTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLEGGRLILQGKFTHFLLNERIEDYVRKYV---ICRECNRP 106 (133)
T ss_pred EEEEcCcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceecCCEEEEEeecCHHHHHHHHHHHHhheE---ECCCCCCC
Confidence 33444455666666677666542 22222 223467889999999999999999 78999987
No 51
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=70.07 E-value=2.6 Score=31.18 Aligned_cols=61 Identities=16% Similarity=0.315 Sum_probs=42.2
Q ss_pred eeeeecCHHHHhhccchhhhcccc--------------ccchHH---HHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCC
Q psy13232 30 KCGLYYNEEVLQNMNEWCVEHHNA--------------SGLTDR---VRASSVSIEEADKRLHQFVAKYVKPKTAPMVGE 92 (111)
Q Consensus 30 ~~vIhqp~~vL~~MdeWc~~~H~~--------------SGL~~~---vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGN 92 (111)
.+.+.-.+.+..|+.+-|+.+|.. +|-++. +.+...+.++.|..+-+||++|| .|+-|||
T Consensus 34 ~v~~eG~kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i~~~~lii~G~~~~~~i~~~L~~yI~~yV---lC~~C~s 110 (138)
T PRK03988 34 DVRIEGNRTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIEGGRLILQGKFSPRVINEKIDRYVKEYV---ICPECGS 110 (138)
T ss_pred eEEEEcCcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceeecCCEEEEEEeeCHHHHHHHHHHHHHhcE---ECCCCCC
Confidence 344444455666777777776643 232211 22356789999999999999999 7999998
Q ss_pred c
Q psy13232 93 Y 93 (111)
Q Consensus 93 S 93 (111)
.
T Consensus 111 p 111 (138)
T PRK03988 111 P 111 (138)
T ss_pred C
Confidence 7
No 52
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=66.26 E-value=3.3 Score=30.09 Aligned_cols=31 Identities=23% Similarity=0.419 Sum_probs=27.2
Q ss_pred HHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 60 VRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 60 vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
+.+..++.++.+..|-+||++|| .||-|||.
T Consensus 72 ii~G~~~~~~i~~~L~~fI~~yV---lC~~C~sp 102 (125)
T PF01873_consen 72 IINGRFSSKQIQDLLDKFIKEYV---LCPECGSP 102 (125)
T ss_dssp EEESSSSCCHHHHHHHHHHCHHS---SCTSTSSS
T ss_pred EEEEecCHHHHHHHHHHHHHHEE---EcCCCCCC
Confidence 34578899999999999999999 79999986
No 53
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=62.93 E-value=4.3 Score=31.42 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=26.1
Q ss_pred HhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 61 RASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 61 r~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
.+..++.++.|+.+-+||++|| .|+-|||.
T Consensus 78 i~G~~~~~~i~~~l~~yi~~yV---~C~~C~~p 107 (201)
T PRK12336 78 FNGKFTEEDIQAAIDAYVDEYV---ICSECGLP 107 (201)
T ss_pred EEeeeCHHHHHHHHHHHHHheE---ECCCCCCC
Confidence 4467889999999999999998 78888886
No 54
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=54.86 E-value=19 Score=21.87 Aligned_cols=30 Identities=10% Similarity=0.312 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHHhhCC-CCCCcccCCc-HHhH
Q psy13232 68 EEADKRLHQFVAKYVK-PKTAPMVGEY-HTSK 97 (111)
Q Consensus 68 ~~AE~~ll~fikk~vp-~~~~pLaGNS-~~DR 97 (111)
+....++-++|.+--. .+.|||||-. .-|+
T Consensus 3 ~~~~~~~~k~i~~l~~~~~~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 3 KSEIEELKKYIEELKEAKGCCPLCGRPLDEEH 34 (54)
T ss_dssp HHHHHHHHHHHHHHTT-SEE-TTT--EE-HHH
T ss_pred hHHHHHHHHHHHHHhcCCCcCCCCCCCCCHHH
Confidence 3444555666666544 4499999998 4443
No 55
>PF05822 UMPH-1: Pyrimidine 5'-nucleotidase (UMPH-1); InterPro: IPR006434 This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue []. The structure of mouse sequence has been reported []. This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs [] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.; GO: 0000287 magnesium ion binding, 0008253 5'-nucleotidase activity, 0005737 cytoplasm; PDB: 2BDU_B 2G07_A 2G06_A 2G0A_A 2Q4T_A 2G09_A 2G08_A 2VKQ_A 2CN1_A 2JGA_A.
Probab=50.17 E-value=7.7 Score=31.37 Aligned_cols=48 Identities=19% Similarity=0.415 Sum_probs=36.7
Q ss_pred CHHHHhhccchhhhcc--------ccccchHHHHhCCCCHHHHHHHHHHHHHhh-CC
Q psy13232 36 NEEVLQNMNEWCVEHH--------NASGLTDRVRASSVSIEEADKRLHQFVAKY-VK 83 (111)
Q Consensus 36 p~~vL~~MdeWc~~~H--------~~SGL~~~vr~S~~s~~~AE~~ll~fikk~-vp 83 (111)
.+|.+..|-||.++.| +++-+-+.|++|.+.+.+--.++++.+.++ ||
T Consensus 52 ~eEK~p~M~EWw~kah~llv~~~l~k~~i~~~V~~s~i~LRdg~~~~f~~L~~~~IP 108 (246)
T PF05822_consen 52 IEEKIPHMEEWWTKAHELLVEQGLTKSEIEEAVKESDIMLRDGVEEFFDKLEEHNIP 108 (246)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHT-BGGGHHHHHHCS---B-BTHHHHHHHHHCTT--
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCcCHHHHHHHHHhcchhhhcCHHHHHHHHHhcCCC
Confidence 4788999999999998 467777889999999999999999999876 65
No 56
>PHA02570 dexA exonuclease; Provisional
Probab=46.70 E-value=27 Score=28.05 Aligned_cols=38 Identities=16% Similarity=0.107 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHHhhC-CCCCCcccCCc-HHhHHHHh
Q psy13232 64 SVSIEEADKRLHQFVAKYV-KPKTAPMVGEY-HTSKELLK 101 (111)
Q Consensus 64 ~~s~~~AE~~ll~fikk~v-p~~~~pLaGNS-~~DR~FL~ 101 (111)
.+++.+|=.++.+||+++. ..+...+.||+ .+|..-|.
T Consensus 85 ~~~l~~al~~F~~fi~~~~~~~~~~~vWgnG~sFD~~IL~ 124 (220)
T PHA02570 85 DVSTYEGHKKFFEYLEANGVDPWKSQGWCRGNSFDFPILV 124 (220)
T ss_pred cccHHHHHHHHHHHHHHcCCCccceeEecCCCccCHHHHH
Confidence 3889999999999999996 46778999999 99999885
No 57
>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=46.47 E-value=23 Score=27.23 Aligned_cols=78 Identities=12% Similarity=0.069 Sum_probs=53.0
Q ss_pred HhhhhhheeeC----Cce---eeeeecCHHHHhhccchhhhccccccchHHHHhCC------CCHHHHHHHHHHHHHhhC
Q psy13232 16 MEQVKAYLQTQ----GTC---KCGLYYNEEVLQNMNEWCVEHHNASGLTDRVRASS------VSIEEADKRLHQFVAKYV 82 (111)
Q Consensus 16 ~~q~~~~lvTd----~G~---~~vIhqp~~vL~~MdeWc~~~H~~SGL~~~vr~S~------~s~~~AE~~ll~fikk~v 82 (111)
++=+|+.+|.- .|- +.-|.++. .+-+|.++ -||++.+-.++. .|+++|.+++.++|.
T Consensus 31 ~~LaRVsiVd~~~~~~g~vllD~~VkP~~----~V~DYrT~---~SGIt~~~L~~a~~~~~~~t~~~v~~~l~~li~--- 100 (174)
T cd06143 31 MSLARVSVVRGEGELEGVPFIDDYISTTE----PVVDYLTR---FSGIKPGDLDPKTSSKNLTTLKSAYLKLRLLVD--- 100 (174)
T ss_pred ceeEEEEEEcCCCCcCCCEEEeeeECCCC----CccCcCcc---ccccCHHHcCccccccccCCHHHHHHHHHHHcC---
Confidence 34568888883 332 22344444 44556663 499998887654 468999999888763
Q ss_pred CCCCCcccCCc-HHhHHHHhhccc
Q psy13232 83 KPKTAPMVGEY-HTSKELLKDSDH 105 (111)
Q Consensus 83 p~~~~pLaGNS-~~DR~FL~kymP 105 (111)
++ ..|.|-| .-|-+-|.=.-|
T Consensus 101 -~~-tILVGHsL~nDL~aL~l~hp 122 (174)
T cd06143 101 -LG-CIFVGHGLAKDFRVINIQVP 122 (174)
T ss_pred -CC-CEEEeccchhHHHHhcCcCC
Confidence 33 4799999 999988876544
No 58
>PF07377 DUF1493: Protein of unknown function (DUF1493); InterPro: IPR010862 This family consists of several bacterial proteins of around 115 residues in length. Members of this family are largely found in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.
Probab=45.95 E-value=27 Score=24.20 Aligned_cols=29 Identities=14% Similarity=0.433 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHHhhCCC----CCCcccCCc--HHh
Q psy13232 68 EEADKRLHQFVAKYVKP----KTAPMVGEY--HTS 96 (111)
Q Consensus 68 ~~AE~~ll~fikk~vp~----~~~pLaGNS--~~D 96 (111)
.+.++++++||+++.+. +.-++--|| ..|
T Consensus 2 ~~i~~~I~~fi~~~~~~~~~~~~~~it~dt~L~~D 36 (111)
T PF07377_consen 2 DDIEQEIIEFIREENGPYLFFKKKPITPDTDLQED 36 (111)
T ss_pred chHHHHHHHHHHHHcCcccccCcccCCCCCcHHHh
Confidence 46789999999999875 566787888 455
No 59
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=43.98 E-value=13 Score=28.03 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=37.0
Q ss_pred cchhhhccccccchHH----HHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 44 NEWCVEHHNASGLTDR----VRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 44 deWc~~~H~~SGL~~~----vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
-++.++.=+.+|.++. |++..+|.++.++.+..|+..|| +|+-||.-
T Consensus 64 ~k~l~kel~t~g~~d~~~rlvl~g~f~~~~i~~~i~~yi~~yv---~C~~c~s~ 114 (151)
T COG1601 64 VKFLKKELGTAGSIDGKGRLVLQGKFSDSEIVNEIERYIAEYV---KCKECGSP 114 (151)
T ss_pred HHHHHHHhccccccCCcceEEEEecccHHHHHHHHHHHHHhee---EeccCCCC
Confidence 3455555667777766 56778999999999999999998 68888864
No 60
>KOG1316|consensus
Probab=43.38 E-value=13 Score=32.59 Aligned_cols=23 Identities=13% Similarity=0.231 Sum_probs=20.1
Q ss_pred CCCCCCcccCCc-HHhHHHHhhcc
Q psy13232 82 VKPKTAPMVGEY-HTSKELLKDSD 104 (111)
Q Consensus 82 vp~~~~pLaGNS-~~DR~FL~kym 104 (111)
.|-|.+-||||- ..||.||.+..
T Consensus 197 ~PLGagALAGnpl~iDR~~la~~L 220 (464)
T KOG1316|consen 197 LPLGAGALAGNPLGIDREFLAEEL 220 (464)
T ss_pred CCcccchhcCCCCCccHHHHHHhc
Confidence 467888999999 99999999864
No 61
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=41.92 E-value=13 Score=23.93 Aligned_cols=17 Identities=24% Similarity=0.679 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHhhCC
Q psy13232 67 IEEADKRLHQFVAKYVK 83 (111)
Q Consensus 67 ~~~AE~~ll~fikk~vp 83 (111)
+.+-+.++|+||++|+.
T Consensus 4 LT~rQ~~vL~~I~~~~~ 20 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIE 20 (65)
T ss_dssp --HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHH
Confidence 45678899999999864
No 62
>KOG2034|consensus
Probab=39.55 E-value=9.9 Score=36.08 Aligned_cols=55 Identities=18% Similarity=0.424 Sum_probs=40.6
Q ss_pred hhhccccccchHHHHhCC-CCHHHHHHHHHHHHHhhCCCCCCcccCCc---HHhHHHHhh
Q psy13232 47 CVEHHNASGLTDRVRASS-VSIEEADKRLHQFVAKYVKPKTAPMVGEY---HTSKELLKD 102 (111)
Q Consensus 47 c~~~H~~SGL~~~vr~S~-~s~~~AE~~ll~fikk~vp~~~~pLaGNS---~~DR~FL~k 102 (111)
|...|..+++.++..+-. .+++.--.++.++|.+-| ...||+||+= --|+-|+..
T Consensus 845 Cl~~~v~~~~~~~~~~~~a~~l~~k~~~l~~~l~~ii-aaeC~lCg~l~I~~Id~Pf~~d 903 (911)
T KOG2034|consen 845 CLIRHVLSLLSEELSQKTAIELQAKRKKLKNELEDII-AAECPLCGELAINKIDQPFSDD 903 (911)
T ss_pred HHHHHHHccccHhhhhhhhhhhhhHHHHHHHHHHHHH-HhhCccchHHHHHhccCCCCCc
Confidence 777788888888854433 556666678888888877 7789999974 567777654
No 63
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=39.23 E-value=50 Score=24.16 Aligned_cols=54 Identities=19% Similarity=0.084 Sum_probs=34.5
Q ss_pred HHHhhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 38 EVLQNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 38 ~vL~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
+..++..++|+++ +-..-...+.....+.+++.+.+.+|++++ |.-.+.+|+|.
T Consensus 134 ~r~~gf~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~-~~~~ai~~~~d 187 (270)
T cd06296 134 ARLDGYRAALAEA-GIPVDPALVREGDFSTESGFRAAAELLALP-ERPTAIFAGND 187 (270)
T ss_pred HHHHHHHHHHHHc-CCCCChHHheeCCCCHHHHHHHHHHHHhCC-CCCcEEEEcCc
Confidence 3456667777653 222222233344567788888889998876 55677888887
No 64
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=36.83 E-value=38 Score=33.77 Aligned_cols=84 Identities=14% Similarity=0.211 Sum_probs=58.0
Q ss_pred CCCCCCCccccccHhhhhhheeeCCceeeeeecCHHHHhhccchhhhccc-------cccchHHHHhCCCCHHHHHHHHH
Q psy13232 3 NIGNRPSNTALSSMEQVKAYLQTQGTCKCGLYYNEEVLQNMNEWCVEHHN-------ASGLTDRVRASSVSIEEADKRLH 75 (111)
Q Consensus 3 ~~~~~p~~~~l~s~~q~~~~lvTd~G~~~vIhqp~~vL~~MdeWc~~~H~-------~SGL~~~vr~S~~s~~~AE~~ll 75 (111)
.||+||..+-+-+ .+ .|.-+.-++.+.++.+..-.|. -+|.|++-.+....+++|=.++.
T Consensus 430 TTGLs~~~d~iIE----~a---------AvKikng~iId~f~~Fi~P~~pl~~~~telTgITdeml~~a~~i~~vL~kf~ 496 (1444)
T COG2176 430 TTGLSPVYDEIIE----IA---------AVKIKNGRIIDKFQFFIKPGRPLSATITELTGITDEMLENAPEIEEVLEKFR 496 (1444)
T ss_pred cCCcCcccchhhh----he---------eeeeeCCcchHHHHHhcCCCCcCchhhhhccccCHHHHcCCccHHHHHHHHH
Confidence 5788877666555 12 2222333455777766665543 46888998888899999988888
Q ss_pred HHHHhhCCCCCCcccCCcHHhHHHHhhcc
Q psy13232 76 QFVAKYVKPKTAPMVGEYHTSKELLKDSD 104 (111)
Q Consensus 76 ~fikk~vp~~~~pLaGNS~~DR~FL~kym 104 (111)
+|++..| ..|=|-.+|-.||....
T Consensus 497 ~~~~d~I-----lVAHNasFD~gFl~~~~ 520 (1444)
T COG2176 497 EFIGDSI-----LVAHNASFDMGFLNTNY 520 (1444)
T ss_pred HHhcCcE-----EEeccCccchhHHHHHH
Confidence 8887765 56677799999997643
No 65
>PF11186 DUF2972: Protein of unknown function (DUF2972); InterPro: IPR021353 Some members in this family of proteins with unknown function are annotated as sugar transferase proteins, however this cannot be confirmed.
Probab=35.75 E-value=6.6 Score=30.33 Aligned_cols=40 Identities=13% Similarity=0.229 Sum_probs=29.2
Q ss_pred HHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccccccC
Q psy13232 70 ADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFLVFSW 111 (111)
Q Consensus 70 AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~lv~~~ 111 (111)
-|..+|+|++++- ..+.-.=|- --+-.||..+=|..|-||
T Consensus 145 ~E~diL~ylk~nk--~l~~k~K~ilD~EL~~IKq~rPDIVaSW 185 (199)
T PF11186_consen 145 KEKDILEYLKNNK--DLRRKFKKILDKELQHIKQHRPDIVASW 185 (199)
T ss_pred CHHHHHHHHHhCH--HHHHHHHHHHHHHHHHHHHhCHHHHHHH
Confidence 3678999999882 223333444 566789999999999999
No 66
>KOG4236|consensus
Probab=34.57 E-value=17 Score=33.86 Aligned_cols=53 Identities=26% Similarity=0.269 Sum_probs=43.4
Q ss_pred hccccccchHHH---HhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 49 EHHNASGLTDRV---RASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 49 ~~H~~SGL~~~v---r~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
..|-..||+.+- ..-.++++++.+.+++++++-+ |=||++ -.|+..|.|+-|.
T Consensus 52 sf~lq~Gltre~V~l~~~e~~l~~v~~~a~s~v~q~~-----pe~G~~~~~dkilLfrHd~~ 108 (888)
T KOG4236|consen 52 SFHLQIGLTRESVLLEAHEISLAHVRDMACSIVDQKF-----PECGFYGLYDKILLFRHDPN 108 (888)
T ss_pred EEEEEecccccceeecchhhHHHHHHHHHHHHHHHhc-----cCcCcccccceeEEEecCCC
Confidence 447788888663 3347889999999999998876 678999 9999999999875
No 67
>KOG1946|consensus
Probab=32.63 E-value=46 Score=26.87 Aligned_cols=20 Identities=15% Similarity=0.316 Sum_probs=18.6
Q ss_pred hCCCCHHHHHHHHHHHHHhh
Q psy13232 62 ASSVSIEEADKRLHQFVAKY 81 (111)
Q Consensus 62 ~S~~s~~~AE~~ll~fikk~ 81 (111)
.|.+|..+|...|++||++|
T Consensus 116 ~~~lsR~~vvk~iw~YIke~ 135 (240)
T KOG1946|consen 116 TSELSRTDVVKKIWAYIKEH 135 (240)
T ss_pred cccccHHHHHHHHHHHHHHh
Confidence 57889999999999999998
No 68
>KOG2249|consensus
Probab=32.07 E-value=61 Score=27.05 Aligned_cols=49 Identities=18% Similarity=0.250 Sum_probs=40.5
Q ss_pred cccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 53 ASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 53 ~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
-||...+-..-.++.+.|+.++++||+--| |.|-- |-|-.=|.-..|+-
T Consensus 157 vSGIrpehm~~A~pf~~aQ~ev~klL~gRI------lVGHaLhnDl~~L~l~hp~s 206 (280)
T KOG2249|consen 157 VSGIRPEHMRDAMPFKVAQKEVLKLLKGRI------LVGHALHNDLQALKLEHPRS 206 (280)
T ss_pred ecccCHHHhccCccHHHHHHHHHHHHhCCE------EeccccccHHHHHhhhCchh
Confidence 489887776678999999999999998754 88999 99988887766653
No 69
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=32.02 E-value=24 Score=22.72 Aligned_cols=28 Identities=14% Similarity=0.421 Sum_probs=19.8
Q ss_pred cchHHHHhCCCCHHHHHHHHHHHHHhhC
Q psy13232 55 GLTDRVRASSVSIEEADKRLHQFVAKYV 82 (111)
Q Consensus 55 GL~~~vr~S~~s~~~AE~~ll~fikk~v 82 (111)
+|+++++...-++...|+.+.+||.++.
T Consensus 2 ~l~~~i~~~~~~ls~~e~~Ia~yil~~~ 29 (77)
T PF01418_consen 2 NLLEKIRSQYNSLSPTEKKIADYILENP 29 (77)
T ss_dssp -HHHHHHHHGGGS-HHHHHHHHHHHH-H
T ss_pred cHHHHHHHHHhhCCHHHHHHHHHHHhCH
Confidence 4667777665667788999999998874
No 70
>PF13482 RNase_H_2: RNase_H superfamily; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=31.59 E-value=31 Score=24.22 Aligned_cols=38 Identities=8% Similarity=0.093 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhcccc
Q psy13232 68 EEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHF 106 (111)
Q Consensus 68 ~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~ 106 (111)
.+.|..+++++ +.+.......+=|. .+|..||.+.+++
T Consensus 41 ~~ee~~~~~~~-~~l~~~~~iv~yng~~FD~p~L~~~~~~ 79 (164)
T PF13482_consen 41 PDEEEIILEFF-ELLDEADNIVTYNGKNFDIPFLKRRAKR 79 (164)
T ss_dssp HHHHHHHHH---HHHHTT--EEESSTTTTHHHHHHHHH-H
T ss_pred cHHHHHHHHHH-HHHhcCCeEEEEeCcccCHHHHHHHHHH
Confidence 45677777766 33334455666688 9999999998854
No 71
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=28.83 E-value=1.4e+02 Score=19.97 Aligned_cols=36 Identities=11% Similarity=0.158 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCcccCCc-HHhHHHHhhccccc
Q psy13232 64 SVSIEEADKRLHQFVAKYVKPKTAPMVGEY-HTSKELLKDSDHFL 107 (111)
Q Consensus 64 ~~s~~~AE~~ll~fikk~vp~~~~pLaGNS-~~DR~FL~kymP~l 107 (111)
.+|++|.-+..+.|+.++-+ -+ ..=|.++.+++|.|
T Consensus 41 ~~t~eemie~~~~~~~~~~~--------~~~~~a~~~~~~~lp~L 77 (81)
T PF12674_consen 41 DITMEEMIEFCVPFMDEFNG--------MTPEEARKMMPRYLPTL 77 (81)
T ss_pred cCCHHHHHHHHHHHHHHhCC--------CCHHHHHHHHHHHccCC
Confidence 46777777777777777642 45 56677777777776
No 72
>PHA03299 envelope glycoprotein L; Provisional
Probab=27.81 E-value=46 Score=26.24 Aligned_cols=40 Identities=15% Similarity=0.253 Sum_probs=33.1
Q ss_pred hhccchhhhccccccchHHHHhCCCCHHHHHHHHHHHHHhh
Q psy13232 41 QNMNEWCVEHHNASGLTDRVRASSVSIEEADKRLHQFVAKY 81 (111)
Q Consensus 41 ~~MdeWc~~~H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~ 81 (111)
..|--|+.-.-+-+|+.+.|.+|+. ...+...+..|+|+-
T Consensus 91 k~~A~WvNP~ia~~~~~edvl~sgl-ddsvk~gl~~flk~i 130 (195)
T PHA03299 91 KGVAAWVNPIIGTSLMMEDVLKSGL-DDSVKAGLGTFLKRI 130 (195)
T ss_pred CceeEEeChHHHHHHHHHHHHHhcc-chhhHHhHHHHHHHH
Confidence 7899999999999999999999976 355667777887764
No 73
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=26.94 E-value=58 Score=30.86 Aligned_cols=17 Identities=18% Similarity=0.309 Sum_probs=13.1
Q ss_pred HHhh-CCCCCCcccCCc-H
Q psy13232 78 VAKY-VKPKTAPMVGEY-H 94 (111)
Q Consensus 78 ikk~-vp~~~~pLaGNS-~ 94 (111)
++.. .|...||+||+. |
T Consensus 496 Lr~~L~~GePCPVCGS~~H 514 (1047)
T PRK10246 496 QRAQLQAGQPCPLCGSTSH 514 (1047)
T ss_pred HHHhCCCCCCcCCCCcccC
Confidence 4444 567789999999 8
No 74
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=23.25 E-value=71 Score=19.43 Aligned_cols=34 Identities=18% Similarity=0.337 Sum_probs=24.1
Q ss_pred hccccccchHHHHhC-CCCHHHHHHHHHHHHHhhC
Q psy13232 49 EHHNASGLTDRVRAS-SVSIEEADKRLHQFVAKYV 82 (111)
Q Consensus 49 ~~H~~SGL~~~vr~S-~~s~~~AE~~ll~fikk~v 82 (111)
..++-.-+++++.+. .++.+++++.+.+||.+-.
T Consensus 28 g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~ 62 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLR 62 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 456777788777543 7888999999999998764
No 75
>KOG0262|consensus
Probab=22.88 E-value=1e+02 Score=31.13 Aligned_cols=60 Identities=18% Similarity=0.249 Sum_probs=39.3
Q ss_pred hhhccccccchHHHHhCCC-----CHHHHHHHHHHHHHhhCCCCCCcccCCcHHhHHHHhhccccccc
Q psy13232 47 CVEHHNASGLTDRVRASSV-----SIEEADKRLHQFVAKYVKPKTAPMVGEYHTSKELLKDSDHFLVF 109 (111)
Q Consensus 47 c~~~H~~SGL~~~vr~S~~-----s~~~AE~~ll~fikk~vp~~~~pLaGNS~~DR~FL~kymP~lv~ 109 (111)
|+..|..--+-+.+.++.. +.+.-.+.+-+|++.+...++||.||++ +.+++|.+-+.||
T Consensus 161 ~~~~~v~~~i~~~~~~~~~~~t~~~~~~~~~lv~~f~k~~l~~kkC~~C~~~---~p~~rk~~~~kv~ 225 (1640)
T KOG0262|consen 161 CRAQYVTEAISEALLDKSEPNTKNSTELKKKLVTAFLKNALSRKKCPRCKHS---NPKLRKDGFRKVF 225 (1640)
T ss_pred hhhhhccHHHHHHhhcCCCccchhhHHHHHHHHHHHHHHhhccccCCcccCC---Cchhhccccceee
Confidence 4445555555555555433 3566677888999999999999999998 2234454444443
No 76
>PF12123 Amidase02_C: N-acetylmuramoyl-l-alanine amidase; InterPro: IPR021976 This domain is found in bacteria and viruses. This domain is about 50 amino acids in length. This domain is classified with the enzyme classification code 3.5.1.28 from EC. This domain is the C-terminal of the enzyme which hydrolyses the link between N-acetylmuramoyl residues and L-amino acid residues in certain cell-wall glycopeptides. ; PDB: 2L48_B.
Probab=22.74 E-value=40 Score=20.69 Aligned_cols=15 Identities=20% Similarity=0.510 Sum_probs=11.2
Q ss_pred cCHHHHhhccchhhh
Q psy13232 35 YNEEVLQNMNEWCVE 49 (111)
Q Consensus 35 qp~~vL~~MdeWc~~ 49 (111)
.|+..|++|.+|..+
T Consensus 24 ~s~~~L~k~~~wld~ 38 (45)
T PF12123_consen 24 LSDAELDKFTAWLDE 38 (45)
T ss_dssp --HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHh
Confidence 467899999999864
No 77
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=22.05 E-value=37 Score=22.04 Aligned_cols=28 Identities=29% Similarity=0.565 Sum_probs=20.9
Q ss_pred chHHHHhCCCCHHHHHHHHHHHHHhhCC
Q psy13232 56 LTDRVRASSVSIEEADKRLHQFVAKYVK 83 (111)
Q Consensus 56 L~~~vr~S~~s~~~AE~~ll~fikk~vp 83 (111)
++-+++.++.|++||++.+-+-+++|+.
T Consensus 45 ~iG~v~v~G~T~~e~~~~I~~~l~~~~~ 72 (82)
T PF02563_consen 45 LIGPVKVAGLTLEEAEEEIKQRLQKYYR 72 (82)
T ss_dssp TTEEEE-TT--HHHHHHHHHHHHTTTSS
T ss_pred ccceEEECCCCHHHHHHHHHHHHHHHhc
Confidence 3467778899999999999999988863
No 78
>smart00463 SMR Small MutS-related domain.
Probab=22.03 E-value=1.2e+02 Score=19.20 Aligned_cols=40 Identities=25% Similarity=0.320 Sum_probs=26.9
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCC----CcccCCc-HHh------HHHHhhc
Q psy13232 64 SVSIEEADKRLHQFVAKYVKPKT----APMVGEY-HTS------KELLKDS 103 (111)
Q Consensus 64 ~~s~~~AE~~ll~fikk~vp~~~----~pLaGNS-~~D------R~FL~ky 103 (111)
..+.++|...+.+||.+....+. -.+.|-. |.. |.++.++
T Consensus 8 G~~~~eA~~~l~~~l~~~~~~~~~~~~~II~G~G~~s~~g~~~i~~~l~~~ 58 (80)
T smart00463 8 GLTVEEALTALDKFLNNARLKGLEQKLVIITGKGKHSLGGKSGVKPALKEH 58 (80)
T ss_pred CCCHHHHHHHHHHHHHHHHHcCCCceEEEEEcccCCCccchhhHHHHHHhc
Confidence 46789999999999988754332 2556655 555 4555554
No 79
>COG1729 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.69 E-value=1.3e+02 Score=24.71 Aligned_cols=24 Identities=25% Similarity=0.544 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHhhCCCCCCcccCCc
Q psy13232 67 IEEADKRLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 67 ~~~AE~~ll~fikk~vp~~~~pLaGNS 93 (111)
..+|++...+||++| ++ ++.+.|.
T Consensus 157 y~~A~~~F~~fi~~Y--P~-s~~~~nA 180 (262)
T COG1729 157 YAEAEQAFQAFIKKY--PN-STYTPNA 180 (262)
T ss_pred HHHHHHHHHHHHHcC--CC-Ccccchh
Confidence 899999999999999 22 2355555
No 80
>smart00391 MBD Methyl-CpG binding domain. Methyl-CpG binding domain, also known as the TAM (TTF-IIP5, ARBP, MeCP1) domain
Probab=21.51 E-value=50 Score=21.90 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=20.3
Q ss_pred CCCCccccccHhhhhhheeeCCce
Q psy13232 6 NRPSNTALSSMEQVKAYLQTQGTC 29 (111)
Q Consensus 6 ~~p~~~~l~s~~q~~~~lvTd~G~ 29 (111)
.+|++..|.|+.|+..||-..+..
T Consensus 33 ~sP~GkklRs~~ev~~YL~~~~~~ 56 (77)
T smart00391 33 ISPCGKKLRSKSELARYLHKNGDL 56 (77)
T ss_pred ECCCCCeeeCHHHHHHHHHhCCCc
Confidence 489999999999999999765543
No 81
>PF04025 DUF370: Domain of unknown function (DUF370); InterPro: IPR007169 This is a bacterial family of unknown function.
Probab=21.34 E-value=67 Score=21.59 Aligned_cols=18 Identities=6% Similarity=-0.082 Sum_probs=13.4
Q ss_pred hhhhhheeeCCceeeeee
Q psy13232 17 EQVKAYLQTQGTCKCGLY 34 (111)
Q Consensus 17 ~q~~~~lvTd~G~~~vIh 34 (111)
.++|+.|+||.|..+.-.
T Consensus 46 rktrsviitdsghviLSa 63 (73)
T PF04025_consen 46 RKTRSVIITDSGHVILSA 63 (73)
T ss_pred CceeEEEEEcCCcEEEee
Confidence 357999999998755443
No 82
>COG2008 GLY1 Threonine aldolase [Amino acid transport and metabolism]
Probab=20.93 E-value=2.2e+02 Score=24.34 Aligned_cols=62 Identities=21% Similarity=0.281 Sum_probs=40.4
Q ss_pred CCCCccccccHhhhhhheeeCCcee------eeee--------cCHHHHhhccchhhhc----ccccc-chHHHHhCCCC
Q psy13232 6 NRPSNTALSSMEQVKAYLQTQGTCK------CGLY--------YNEEVLQNMNEWCVEH----HNASG-LTDRVRASSVS 66 (111)
Q Consensus 6 ~~p~~~~l~s~~q~~~~lvTd~G~~------~vIh--------qp~~vL~~MdeWc~~~----H~~SG-L~~~vr~S~~s 66 (111)
..|+++...++||+++.|.+++... +.+. +|.+.|+.+.++|+++ |-.-- |...+-+.+++
T Consensus 104 ~~~g~~Gklt~e~v~~~i~~~d~~~~~~~~~~~e~~~te~GtVy~l~el~~i~~~~k~~~l~LHmDGAR~~nA~valg~~ 183 (342)
T COG2008 104 IVPGADGKLTPEDVEAAIRPDDIHHAPTPLAVLENTATEGGTVYPLDELEAISAVCKEHGLPLHMDGARLANALVALGVA 183 (342)
T ss_pred cCCCCCCCcCHHHHHHhhcCCCcccCCCceEEEeeccCCCceecCHHHHHHHHHHHHHhCCceeechHHHHHHHHHcCCC
Confidence 3577788889999999888865211 1122 4678899999999976 43221 44555555544
Q ss_pred H
Q psy13232 67 I 67 (111)
Q Consensus 67 ~ 67 (111)
+
T Consensus 184 ~ 184 (342)
T COG2008 184 L 184 (342)
T ss_pred H
Confidence 3
No 83
>PLN02965 Probable pheophorbidase
Probab=20.91 E-value=1.1e+02 Score=22.69 Aligned_cols=53 Identities=13% Similarity=0.065 Sum_probs=34.9
Q ss_pred cccccchHHHHhCCCCHHHHHHHHHHHHHhhCCCCCCcccCCc--H-HhHHHHhhccccc
Q psy13232 51 HNASGLTDRVRASSVSIEEADKRLHQFVAKYVKPKTAPMVGEY--H-TSKELLKDSDHFL 107 (111)
Q Consensus 51 H~~SGL~~~vr~S~~s~~~AE~~ll~fikk~vp~~~~pLaGNS--~-~DR~FL~kymP~l 107 (111)
||.|.-. ..+.+|+++--+.+.+++++.-..+...|.|.| + .=..+..+| |..
T Consensus 41 ~G~S~~~---~~~~~~~~~~a~dl~~~l~~l~~~~~~~lvGhSmGG~ia~~~a~~~-p~~ 96 (255)
T PLN02965 41 AGISLTD---SNTVSSSDQYNRPLFALLSDLPPDHKVILVGHSIGGGSVTEALCKF-TDK 96 (255)
T ss_pred CCCCCCC---ccccCCHHHHHHHHHHHHHhcCCCCCEEEEecCcchHHHHHHHHhC-chh
Confidence 7777422 123567877777899999885323578999999 3 356666666 443
No 84
>PRK06489 hypothetical protein; Provisional
Probab=20.86 E-value=1.5e+02 Score=23.66 Aligned_cols=44 Identities=7% Similarity=-0.019 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHHhhCCCCCCc-ccCCc---HHhHHHHhhcccccc
Q psy13232 64 SVSIEEADKRLHQFVAKYVKPKTAP-MVGEY---HTSKELLKDSDHFLV 108 (111)
Q Consensus 64 ~~s~~~AE~~ll~fikk~vp~~~~p-LaGNS---~~DR~FL~kymP~lv 108 (111)
.+++++..+.+++++.++...++.. ++|.| ..=-.|..+| |+.|
T Consensus 132 ~~~~~~~a~~~~~~l~~~lgi~~~~~lvG~SmGG~vAl~~A~~~-P~~V 179 (360)
T PRK06489 132 RYDYDDMVEAQYRLVTEGLGVKHLRLILGTSMGGMHAWMWGEKY-PDFM 179 (360)
T ss_pred cccHHHHHHHHHHHHHHhcCCCceeEEEEECHHHHHHHHHHHhC-chhh
Confidence 4688887778888886666545554 89999 3444555554 5443
No 85
>PF08269 Cache_2: Cache domain; InterPro: IPR013163 Cache is an extracellular domain that is predicted to have a role in small-molecule recognition in a wide range of proteins, including the animal dihydropyridine-sensitive voltage-gated Ca2+ channel; alpha-2delta subunit, and various bacterial chemotaxis receptors. The name Cache comes from CAlcium channels and CHEmotaxis receptors. This domain consists of an N-terminal part with three predicted strands and an alpha-helix, and a C-terminal part with a strand dyad followed by a relatively unstructured region. The N-terminal portion of the (unpermuted) Cache domain contains three predicted strands that could form a sheet analogous to that present in the core of the PAS domain structure. Cache domains are particularly widespread in bacteria, with Vibrio cholerae. The animal calcium channel alpha-2delta subunits might have acquired a part of their extracellular domains from a bacterial source []. The Cache domain appears to have arisen from the GAF-PAS fold despite their divergent functions []. This entry is composed of the type 2 Cache domain.; PDB: 2QHK_A 4EXO_A.
Probab=20.69 E-value=46 Score=21.68 Aligned_cols=25 Identities=20% Similarity=0.244 Sum_probs=14.3
Q ss_pred hHHHHhCCCCHHHHHHHHHHHHHhh
Q psy13232 57 TDRVRASSVSIEEADKRLHQFVAKY 81 (111)
Q Consensus 57 ~~~vr~S~~s~~~AE~~ll~fikk~ 81 (111)
-++..+..+|.++|++++++.|++.
T Consensus 27 ~~~~~~g~ls~eea~~~a~~~l~~~ 51 (95)
T PF08269_consen 27 YAQAQAGKLSEEEAQQQAREALRAL 51 (95)
T ss_dssp HHC-STT-----TTHHHHHHHHHH-
T ss_pred HHHHhcCCccHHHHHHHHHHHHhcc
Confidence 3445556799999999999999775
No 86
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=20.26 E-value=61 Score=20.47 Aligned_cols=18 Identities=22% Similarity=0.449 Sum_probs=12.6
Q ss_pred HHHHHHHhhCCCCCCcccCCc
Q psy13232 73 RLHQFVAKYVKPKTAPMVGEY 93 (111)
Q Consensus 73 ~ll~fikk~vp~~~~pLaGNS 93 (111)
+++....+|. .||-|||-
T Consensus 5 ~~~~L~~kY~---~Cp~CGN~ 22 (49)
T PF12677_consen 5 KTLKLSNKYC---KCPKCGND 22 (49)
T ss_pred hhcchhhhhc---cCcccCCc
Confidence 4556666765 78989884
No 87
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=20.07 E-value=1.3e+02 Score=19.89 Aligned_cols=28 Identities=18% Similarity=0.395 Sum_probs=20.8
Q ss_pred ccccchHHHHh--CCCCHHHHHHHHHHHHH
Q psy13232 52 NASGLTDRVRA--SSVSIEEADKRLHQFVA 79 (111)
Q Consensus 52 ~~SGL~~~vr~--S~~s~~~AE~~ll~fik 79 (111)
+++.|++++.+ +.+|.++|+..+=.|+.
T Consensus 2 tk~eli~~ia~~~~~~s~~~~~~vv~~~~~ 31 (94)
T PRK00199 2 TKSELIERLAARNPHLSAKDVENAVKEILE 31 (94)
T ss_pred CHHHHHHHHHHHcCCCCHHHHHHHHHHHHH
Confidence 46778888864 57899888887766654
Done!