Query 009898
Match_columns 523
No_of_seqs 314 out of 1608
Neff 5.5
Searched_HMMs 46136
Date Thu Mar 28 18:39:00 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009898.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009898hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00217 flap endonuclease-1; 100.0 5.7E-50 1.2E-54 422.4 22.5 249 2-291 74-332 (393)
2 PRK03980 flap endonuclease-1; 100.0 1.4E-49 3.1E-54 404.8 21.6 244 2-294 19-281 (292)
3 cd00128 XPG Xeroderma pigmento 100.0 3.9E-46 8.6E-51 382.8 21.8 242 2-284 64-312 (316)
4 TIGR03674 fen_arch flap struct 100.0 3E-45 6.5E-50 380.2 21.1 243 2-292 66-326 (338)
5 TIGR00600 rad2 DNA excision re 100.0 1.1E-42 2.5E-47 396.8 20.1 225 51-293 763-989 (1034)
6 KOG2519 5'-3' exonuclease [Rep 100.0 1.3E-42 2.7E-47 363.7 16.7 335 3-381 69-419 (449)
7 KOG2520 5'-3' exonuclease [Rep 100.0 1.1E-40 2.4E-45 370.4 16.1 231 51-297 457-687 (815)
8 KOG2518 5'-3' exonuclease [Rep 100.0 9.2E-35 2E-39 307.7 12.9 176 2-179 64-249 (556)
9 smart00475 53EXOc 5'-3' exonuc 100.0 1.6E-29 3.4E-34 254.1 17.6 163 8-187 49-219 (259)
10 cd00008 53EXOc 5'-3' exonuclea 100.0 2.3E-28 4.9E-33 243.1 17.7 159 8-187 50-216 (240)
11 PRK14976 5'-3' exonuclease; Pr 100.0 1.2E-27 2.5E-32 243.1 17.6 162 8-187 55-224 (281)
12 COG0258 Exo 5'-3' exonuclease 99.9 3.2E-26 7E-31 235.2 14.6 165 8-185 60-229 (310)
13 PRK09482 flap endonuclease-lik 99.9 6.1E-25 1.3E-29 220.2 18.0 167 8-196 47-224 (256)
14 TIGR00593 pola DNA polymerase 99.9 7.8E-25 1.7E-29 251.2 17.4 162 8-187 49-218 (887)
15 PRK05755 DNA polymerase I; Pro 99.9 1.7E-24 3.7E-29 249.5 18.7 161 8-187 51-220 (880)
16 PF00867 XPG_I: XPG I-region; 99.9 7.6E-25 1.6E-29 188.3 6.6 86 70-155 1-94 (94)
17 smart00484 XPGI Xeroderma pigm 99.7 3.7E-18 8E-23 140.9 7.3 70 71-140 2-73 (73)
18 PHA00439 exonuclease 99.7 3.1E-16 6.7E-21 159.3 12.8 135 8-174 64-206 (286)
19 cd00080 HhH2_motif Helix-hairp 99.4 4.8E-13 1E-17 111.0 5.4 50 137-186 2-54 (75)
20 PHA02567 rnh RnaseH; Provision 99.4 3.3E-12 7.3E-17 130.7 12.4 137 7-162 62-207 (304)
21 PF02739 5_3_exonuc_N: 5'-3' e 99.0 1.6E-10 3.5E-15 109.8 3.9 111 9-138 52-169 (169)
22 smart00279 HhH2 Helix-hairpin- 98.9 9.2E-10 2E-14 79.1 4.0 33 142-175 1-36 (36)
23 PF01367 5_3_exonuc: 5'-3' exo 98.9 3.5E-11 7.6E-16 105.4 -4.9 48 140-187 1-51 (101)
24 PF12813 XPG_I_2: XPG domain c 98.6 2.4E-07 5.1E-12 93.2 9.5 87 61-150 5-107 (246)
25 PF00752 XPG_N: XPG N-terminal 98.3 2.1E-07 4.6E-12 80.5 1.5 35 2-36 66-100 (101)
26 smart00485 XPGN Xeroderma pigm 98.3 4.8E-07 1E-11 78.2 2.7 35 2-36 64-98 (99)
27 TIGR00600 rad2 DNA excision re 97.4 0.00011 2.5E-09 86.4 4.1 38 1-38 62-99 (1034)
28 PF00385 Chromo: Chromo (CHRro 96.6 0.0024 5.1E-08 49.2 3.8 50 323-372 3-55 (55)
29 smart00298 CHROMO Chromatin or 95.5 0.018 4E-07 43.6 3.8 50 323-373 4-54 (55)
30 COG5366 Protein involved in pr 95.3 0.008 1.7E-07 64.9 1.7 113 64-177 133-247 (531)
31 cd00024 CHROMO Chromatin organ 94.8 0.025 5.5E-07 42.9 2.9 47 324-371 6-54 (55)
32 PRK14605 ruvA Holliday junctio 91.4 0.32 6.9E-06 47.6 5.1 65 124-194 43-112 (194)
33 PHA03065 Hypothetical protein; 91.3 0.68 1.5E-05 50.1 7.9 108 65-184 150-274 (438)
34 PF04599 Pox_G5: Poxvirus G5 p 91.3 0.74 1.6E-05 50.0 8.2 113 65-184 148-272 (425)
35 PRK14602 ruvA Holliday junctio 91.3 0.3 6.5E-06 48.1 4.9 67 124-196 44-115 (203)
36 TIGR00084 ruvA Holliday juncti 90.2 0.41 8.8E-06 46.8 4.7 64 124-193 42-110 (191)
37 PF12826 HHH_2: Helix-hairpin- 90.2 0.23 5.1E-06 39.9 2.5 21 159-179 7-27 (64)
38 PF03159 XRN_N: XRN 5'-3' exon 89.4 0.32 6.9E-06 49.1 3.4 39 73-111 172-223 (237)
39 PRK14601 ruvA Holliday junctio 89.4 0.46 9.9E-06 46.2 4.3 67 124-196 43-114 (183)
40 PRK14606 ruvA Holliday junctio 89.3 0.49 1.1E-05 46.2 4.4 68 123-196 42-114 (188)
41 PRK00116 ruvA Holliday junctio 89.0 0.44 9.6E-06 46.4 3.9 51 132-188 55-106 (192)
42 PRK13901 ruvA Holliday junctio 88.9 0.56 1.2E-05 46.2 4.5 59 132-196 54-113 (196)
43 PRK14604 ruvA Holliday junctio 88.2 0.59 1.3E-05 45.8 4.3 67 124-196 43-114 (195)
44 KOG1911 Heterochromatin-associ 88.1 0.39 8.5E-06 49.1 3.0 57 322-379 50-106 (270)
45 KOG2748 Uncharacterized conser 86.5 0.36 7.9E-06 50.8 1.7 61 323-385 13-76 (369)
46 PRK14603 ruvA Holliday junctio 85.9 0.62 1.3E-05 45.7 3.0 67 124-196 42-113 (197)
47 COG5049 XRN1 5'-3' exonuclease 85.7 5.8 0.00013 45.8 10.6 86 79-164 186-327 (953)
48 PF00633 HHH: Helix-hairpin-he 84.4 0.76 1.7E-05 31.8 2.0 15 159-173 15-29 (30)
49 COG0632 RuvA Holliday junction 84.2 2.5 5.4E-05 41.8 6.3 61 129-195 52-113 (201)
50 PRK14600 ruvA Holliday junctio 82.1 0.81 1.8E-05 44.6 1.9 56 131-192 54-110 (186)
51 KOG2045 5'-3' exonuclease XRN1 79.0 5.3 0.00011 47.3 7.3 97 77-173 170-308 (1493)
52 smart00278 HhH1 Helix-hairpin- 72.9 2.7 5.9E-05 27.7 1.8 18 157-174 3-20 (26)
53 PF10391 DNA_pol_lambd_f: Fing 66.9 8.3 0.00018 30.1 3.6 20 159-178 6-26 (52)
54 PRK14601 ruvA Holliday junctio 65.3 4.3 9.2E-05 39.6 2.2 37 139-176 92-129 (183)
55 PRK14671 uvrC excinuclease ABC 65.0 5.4 0.00012 45.8 3.2 25 158-182 572-596 (621)
56 PF14520 HHH_5: Helix-hairpin- 64.0 6.2 0.00014 30.9 2.5 20 159-178 9-29 (60)
57 PRK13901 ruvA Holliday junctio 62.6 5.1 0.00011 39.5 2.2 37 139-176 91-128 (196)
58 PRK14604 ruvA Holliday junctio 62.3 5.2 0.00011 39.3 2.2 36 140-176 93-129 (195)
59 PF02371 Transposase_20: Trans 61.6 7.4 0.00016 32.8 2.7 23 156-178 3-25 (87)
60 PRK14606 ruvA Holliday junctio 61.0 5.7 0.00012 38.8 2.2 41 135-176 87-129 (188)
61 KOG2044 5'-3' exonuclease HKE1 60.9 32 0.00069 40.5 8.2 93 73-165 190-352 (931)
62 PRK14603 ruvA Holliday junctio 60.0 6 0.00013 38.9 2.1 42 134-177 85-129 (197)
63 PRK14600 ruvA Holliday junctio 59.1 7.7 0.00017 37.8 2.7 40 135-176 87-128 (186)
64 PRK14667 uvrC excinuclease ABC 58.8 8.8 0.00019 43.6 3.5 23 157-179 516-538 (567)
65 PRK14669 uvrC excinuclease ABC 58.7 7.9 0.00017 44.5 3.1 22 158-179 555-576 (624)
66 TIGR00194 uvrC excinuclease AB 56.9 8.9 0.00019 43.6 3.1 22 158-179 544-565 (574)
67 PRK14602 ruvA Holliday junctio 56.2 7.6 0.00016 38.3 2.2 36 140-176 94-130 (203)
68 COG0632 RuvA Holliday junction 55.8 11 0.00024 37.3 3.2 37 140-176 93-129 (201)
69 PRK14670 uvrC excinuclease ABC 55.0 11 0.00024 42.9 3.5 24 156-179 515-538 (574)
70 PF11798 IMS_HHH: IMS family H 49.2 12 0.00026 26.1 1.7 14 159-172 15-28 (32)
71 PRK14672 uvrC excinuclease ABC 48.0 17 0.00037 42.2 3.5 23 157-179 610-632 (691)
72 PRK00558 uvrC excinuclease ABC 47.2 15 0.00032 42.1 2.9 22 158-179 546-567 (598)
73 cd00034 ChSh Chromo Shadow Dom 44.8 48 0.001 25.9 4.6 37 334-373 14-50 (54)
74 PRK14668 uvrC excinuclease ABC 44.3 16 0.00035 41.7 2.6 22 157-178 527-548 (577)
75 COG0258 Exo 5'-3' exonuclease 42.6 20 0.00044 37.2 2.9 39 57-95 93-132 (310)
76 PRK12766 50S ribosomal protein 42.0 24 0.00051 35.8 3.1 23 157-179 5-28 (232)
77 COG0353 RecR Recombinational D 41.8 24 0.00052 34.9 3.0 17 158-174 15-31 (198)
78 TIGR01448 recD_rel helicase, p 41.7 32 0.0007 40.2 4.6 35 138-178 73-107 (720)
79 TIGR00084 ruvA Holliday juncti 41.0 21 0.00046 34.9 2.6 33 141-174 93-126 (191)
80 PRK00076 recR recombination pr 40.3 59 0.0013 32.2 5.6 17 158-174 14-30 (196)
81 PRK02515 psbU photosystem II c 38.5 27 0.00058 32.5 2.6 19 159-177 65-85 (132)
82 PRK14666 uvrC excinuclease ABC 38.4 26 0.00057 40.7 3.2 25 158-182 640-665 (694)
83 COG1948 MUS81 ERCC4-type nucle 34.4 33 0.00072 35.2 2.8 20 159-178 186-205 (254)
84 TIGR03090 SASP_tlp small, acid 33.9 7.5 0.00016 32.2 -1.5 53 469-521 1-66 (70)
85 TIGR00575 dnlj DNA ligase, NAD 33.4 37 0.00081 39.3 3.4 19 159-177 502-520 (652)
86 PF01399 PCI: PCI domain; Int 33.4 1E+02 0.0022 25.6 5.3 41 66-110 64-104 (105)
87 PF14520 HHH_5: Helix-hairpin- 33.3 37 0.00081 26.5 2.4 19 157-175 40-58 (60)
88 PRK14351 ligA NAD-dependent DN 32.9 39 0.00084 39.4 3.4 20 159-178 532-551 (689)
89 TIGR02765 crypto_DASH cryptoch 32.7 91 0.002 33.7 6.1 41 61-101 62-102 (429)
90 TIGR01259 comE comEA protein. 32.3 57 0.0012 29.4 3.8 17 159-175 72-88 (120)
91 PF05991 NYN_YacP: YacP-like N 31.9 57 0.0012 31.0 3.9 34 73-106 67-106 (166)
92 smart00300 ChSh Chromo Shadow 31.8 69 0.0015 25.6 3.8 39 332-373 18-56 (61)
93 TIGR00615 recR recombination p 31.2 30 0.00065 34.2 1.9 17 158-174 14-30 (195)
94 COG0322 UvrC Nuclease subunit 31.0 42 0.00091 38.4 3.2 22 158-179 533-554 (581)
95 PRK14605 ruvA Holliday junctio 29.4 33 0.00072 33.6 1.9 36 140-177 93-130 (194)
96 COG1555 ComEA DNA uptake prote 28.3 78 0.0017 29.8 4.1 16 159-174 101-116 (149)
97 PRK13844 recombination protein 27.8 37 0.00081 33.7 1.9 17 158-174 18-34 (200)
98 TIGR00591 phr2 photolyase PhrI 27.3 1.3E+02 0.0027 33.0 6.1 40 62-101 80-119 (454)
99 smart00753 PAM PCI/PINT associ 27.1 1.6E+02 0.0035 24.1 5.4 44 65-112 27-70 (88)
100 smart00088 PINT motif in prote 27.1 1.6E+02 0.0035 24.1 5.4 44 65-112 27-70 (88)
101 PF01393 Chromo_shadow: Chromo 26.4 1.3E+02 0.0028 23.9 4.4 46 325-372 7-52 (58)
102 PF02677 DUF208: Uncharacteriz 25.1 1.9E+02 0.0041 28.2 6.1 83 62-176 44-127 (176)
103 smart00483 POLXc DNA polymeras 24.9 47 0.001 35.1 2.2 18 159-177 93-110 (334)
104 TIGR00114 lumazine-synth 6,7-d 24.7 1.4E+02 0.003 27.9 5.0 45 57-101 14-65 (138)
105 TIGR00426 competence protein C 24.5 1.1E+02 0.0023 24.5 3.7 15 160-174 22-36 (69)
106 COG2974 RdgC DNA recombination 24.1 39 0.00084 35.2 1.3 32 351-382 72-103 (303)
107 PRK13766 Hef nuclease; Provisi 23.9 64 0.0014 37.6 3.2 22 157-178 717-738 (773)
108 TIGR00305 probable toxin-antit 23.8 50 0.0011 28.8 1.8 29 80-108 85-113 (114)
109 TIGR00596 rad1 DNA repair prot 23.7 41 0.00089 40.0 1.6 25 155-179 757-781 (814)
110 PF01927 Mut7-C: Mut7-C RNAse 23.3 67 0.0015 29.8 2.6 48 60-108 7-54 (147)
111 PF14716 HHH_8: Helix-hairpin- 23.2 57 0.0012 26.3 1.9 15 158-172 50-64 (68)
112 PRK07956 ligA NAD-dependent DN 22.8 67 0.0014 37.4 3.0 28 64-91 240-273 (665)
113 cd08556 GDPD Glycerophosphodie 22.8 99 0.0021 28.5 3.7 39 63-102 150-188 (189)
114 PRK10674 deoxyribodipyrimidine 22.7 1.7E+02 0.0038 32.3 6.1 41 61-101 58-102 (472)
115 cd00141 NT_POLXc Nucleotidyltr 22.2 59 0.0013 34.0 2.2 17 159-176 89-105 (307)
116 PF11731 Cdd1: Pathogenicity l 22.0 63 0.0014 28.3 2.0 20 158-177 15-35 (93)
117 COG1936 Predicted nucleotide k 21.0 72 0.0016 31.2 2.4 20 158-177 6-25 (180)
118 TIGR02766 crypt_chrom_pln cryp 20.9 1.6E+02 0.0036 32.3 5.5 11 8-18 24-34 (475)
119 PF00885 DMRL_synthase: 6,7-di 20.3 1.8E+02 0.0038 27.3 4.8 45 57-101 17-68 (144)
No 1
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=5.7e-50 Score=422.35 Aligned_cols=249 Identities=18% Similarity=0.324 Sum_probs=217.5
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCccccc------cccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCC
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVP 75 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~------~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp 75 (523)
.+|+++||+|||||||.+|++|.+++.+|+++|.++.. +.|+.+++.++.++...++..|+..++++|+.||||
T Consensus 74 ~~Ll~~gikPv~VFDG~~p~~K~~~~~~Rk~~R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip 153 (393)
T PTZ00217 74 IRLLEAGIKPVYVFDGKPPELKSGELEKRRERREEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIP 153 (393)
T ss_pred HHHHHCCCCEEEEEcCCCchhhHHHHHHHHHHHHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCc
Confidence 36789999999999999999999999999999987542 467778888888888889999999999999999999
Q ss_pred cccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCC--CCceEEEEeHHHHHHHhCCChhHHHHHHHHhC
Q 009898 76 CLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLG--ERGYVVCYEMDDIERKLGFGRNSLITLALLLG 153 (523)
Q Consensus 76 ~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~--~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G 153 (523)
|++||||||||||+|++.|+||+|+|+|+|+|+||+++++++++.. ....+++|+.+.+.+.+|++++||+|+|+|+|
T Consensus 154 ~i~AP~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G 233 (393)
T PTZ00217 154 VIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCG 233 (393)
T ss_pred eEECCcCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhC
Confidence 9999999999999999999999999999999999999999998752 22457899999999999999999999999999
Q ss_pred CCCCCCCCCCcHHHHHHHHHHhCC-HHHHHHHHhcCchHHHHhhhhcccCcccccCCccccccccccccCCcCcCCCCCC
Q 009898 154 SDYSQGVRGLGPESACQIVKSVGD-NVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETP 232 (523)
Q Consensus 154 ~DY~pGVpGIG~ktA~kLl~~~g~-~~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~~~~~~~~~e~~~~~~~~~ip~~FP 232 (523)
|||+|||||||+|||++||++||+ ++++++++.. +..+|++||
T Consensus 234 ~Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~~~------------------------------------k~~~p~~~~ 277 (393)
T PTZ00217 234 CDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKT------------------------------------KYPVPENFD 277 (393)
T ss_pred CCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhc------------------------------------CCCCCCCCC
Confidence 999999999999999999999999 4577776530 134788999
Q ss_pred cHHHHHHhcCCccCCCCh-HHHHHHhhhcccCHHHHHHHHHHhcCCCcccccchhhhhhh
Q 009898 233 FSQVIDAYSNPKCYSADS-EAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIA 291 (523)
Q Consensus 233 ~~~Vi~~Yl~P~vs~~~~-e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll~ 291 (523)
+.++.+.|++|.|..+.. ++.| . +.+..+|++||.+.++|+..++++.|-++.+
T Consensus 278 ~~~~~~~f~~p~V~~~~~~~l~w----~-~pD~~~l~~fl~~e~~f~~~rv~~~i~rl~~ 332 (393)
T PTZ00217 278 YKEARELFLNPEVTPAEEIDLKW----N-EPDEEGLKKFLVKEKNFNEERVEKYIERLKK 332 (393)
T ss_pred hHHHHHHhcCCCcCCCCCCCCCC----C-CCCHHHHHHHHHhccCCCHHHHHHHHHHHHH
Confidence 999999999999986431 2211 1 3378899999999999999999998766544
No 2
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=1.4e-49 Score=404.85 Aligned_cols=244 Identities=21% Similarity=0.335 Sum_probs=210.6
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCccccc------cccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCC
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVP 75 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~------~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp 75 (523)
-+|+++||+|||||||.+|++|.+++.+|+++|.++.. +.|+.+++.++.++..++++.|++.++++|++||||
T Consensus 19 ~~ll~~gi~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~vt~~~~~~~k~lL~~~GIp 98 (292)
T PRK03980 19 INLLENGIKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSRLTDEIVEDSKKLLDLMGIP 98 (292)
T ss_pred HHHHHCCCEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhccccCCHHHHHHHHHHHHHCCCC
Confidence 36889999999999999999999999999999987542 356777888888888889999999999999999999
Q ss_pred cccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCC-----------ceEEEEeHHHHHHHhCCChhH
Q 009898 76 CLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER-----------GYVVCYEMDDIERKLGFGRNS 144 (523)
Q Consensus 76 ~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~-----------~~v~~y~~~~i~~~lgl~r~q 144 (523)
|++||||||||||+|++.|+||+|+|+|+|+|+||+++|+++++..+. ..+++|+.+.+.+.+|++++|
T Consensus 99 ~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~~~~e~~~~~~vl~~lgl~~~q 178 (292)
T PRK03980 99 YVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVEVKPELIELEEVLKELGITREQ 178 (292)
T ss_pred EEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCccccccccccceeeeHHHHHHHhCCCHHH
Confidence 999999999999999999999999999999999999999999875421 145689999999999999999
Q ss_pred HHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcCchHHHHhhhhcccCcccccCCccccccccccccCC
Q 009898 145 LITLALLLGSDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGT 223 (523)
Q Consensus 145 lidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~-~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~~~~~~~~~e~~~~~~ 223 (523)
|+|+|+|+||||+|||||||+|||++||++||+. ++++.+.
T Consensus 179 ~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~-------------------------------------- 220 (292)
T PRK03980 179 LIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG-------------------------------------- 220 (292)
T ss_pred HHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhcc--------------------------------------
Confidence 9999999999999999999999999999999994 5665211
Q ss_pred cCcCCCCCCc-HHHHHHhcCCccCCCChHHHHHHhhhcccCHHHHHHHHHHhcCCCcccccchhhhhhhHHH
Q 009898 224 DHSLQRETPF-SQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERD 294 (523)
Q Consensus 224 ~~~ip~~FP~-~~Vi~~Yl~P~vs~~~~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll~e~~ 294 (523)
.+||. .+|++.|++|.|.. +.++.|+ ..+.++|++|+.+..+|+.++++..+-++.+.+.
T Consensus 221 -----~~~~~~~~~r~~f~~p~v~~-~~~~~~~-----~pd~~~l~~fl~~e~~f~~~rv~~~~~~l~~~~~ 281 (292)
T PRK03980 221 -----FEIENYDEIREFFLNPPVTD-DYELKWK-----EPDKEGIIEFLVEEHDFSEERVKKALERLEKAVK 281 (292)
T ss_pred -----CCCCCHHHHHHHhcCCCCCC-CCCccCC-----CCCHHHHHHHHhccCCCCHHHHHHHHHHHHHHhc
Confidence 12444 89999999999985 3233222 2378899999999999999999999988876543
No 3
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=100.00 E-value=3.9e-46 Score=382.77 Aligned_cols=242 Identities=26% Similarity=0.398 Sum_probs=204.3
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCcccc------ccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCC
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVT------QDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVP 75 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~------~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp 75 (523)
..|+++||+|||||||.+|+.|.++..+|+..|.+.. .+.++.+++.++.+....++..++..++++|+.||||
T Consensus 64 ~~L~~~~i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~ 143 (316)
T cd00128 64 CRLLELGIKPVFVFDGKPPPLKAETLAKRRERREEAEEEAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIP 143 (316)
T ss_pred HHHHHCCCEEEEEEcCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCC
Confidence 5688999999999999999999999999998886632 1245566677777777778899999999999999999
Q ss_pred cccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhCCC
Q 009898 76 CLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLGSD 155 (523)
Q Consensus 76 ~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G~D 155 (523)
|++||+|||||||+|++.|.||+|+|+|+|+|+||+++|+++++..+...+++|+.+.+.+.+|++++||+++|+|+|||
T Consensus 144 ~i~ap~EAdaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G~D 223 (316)
T cd00128 144 YIVAPYEAEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLGCD 223 (316)
T ss_pred EEECCcCHHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999887532146889999999999999999999999999999
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcCchHHHHhhhhcccCcccccCCccccccccccccCCcCcCCCCCCcH
Q 009898 156 YSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPFS 234 (523)
Q Consensus 156 Y~pGVpGIG~ktA~kLl~~~g~~-~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~~~~~~~~~e~~~~~~~~~ip~~FP~~ 234 (523)
|+|||||||+|||++||++||+. .+++++... ...+|.+||..
T Consensus 224 y~~gv~giG~k~A~~li~~~~~~~~~~~~l~~~------------------------------------~~~~~~~~~~~ 267 (316)
T cd00128 224 YTEGIPGIGPVTALKLIKKYGDIEKDIERLKKK------------------------------------LYRSPEDFPLK 267 (316)
T ss_pred CCCCCCCccHHHHHHHHHHcCChHHHHHHHHHh------------------------------------CccCCCcCChH
Confidence 99999999999999999999994 466665431 02345689999
Q ss_pred HHHHHhcCCccCCCChHHHHHHhhhcccCHHHHHHHHHHhcCCCcccccc
Q 009898 235 QVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDE 284 (523)
Q Consensus 235 ~Vi~~Yl~P~vs~~~~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e 284 (523)
.+.++|.+|.++.......| . ..+..+|+.|+...++|+.+++..
T Consensus 268 ~~~~~f~~p~~~~~~~~~~~----~-~p~~~~l~~~~~~~~~~~~~rv~~ 312 (316)
T cd00128 268 EAREFFLNPEVTDDFIDLRW----R-DPDEEGIIEFLCKEHGFNEDRVLK 312 (316)
T ss_pred HHHHHHcCCCCCCCCCceee----c-CCCHHHHHHHccCCCCCCHHHHHh
Confidence 99999999998764222222 1 225688999999999999765543
No 4
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=100.00 E-value=3e-45 Score=380.22 Aligned_cols=243 Identities=22% Similarity=0.358 Sum_probs=206.8
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCccccc------cccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCC
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVP 75 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~------~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp 75 (523)
.+|+++||+|||||||.+|++|.+++.+|++.|.++.+ +.++.+++.++.++..+++..|++.++++|++||||
T Consensus 66 ~~ll~~~i~Pv~VFDG~~p~~K~~~~~~R~~~r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip 145 (338)
T TIGR03674 66 INLLENGIKPVYVFDGKPPELKAETLEERREIREEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIP 145 (338)
T ss_pred HHHHHCCCeEEEEECCCChhhhHhhHHHHHHHHHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCe
Confidence 46789999999999999999999999999999877432 356677788887777788899999999999999999
Q ss_pred cccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCc-----------eEEEEeHHHHHHHhCCChhH
Q 009898 76 CLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERG-----------YVVCYEMDDIERKLGFGRNS 144 (523)
Q Consensus 76 ~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~-----------~v~~y~~~~i~~~lgl~r~q 144 (523)
|++||||||||||+|++.|.||+|+|+|+|+|+||+++|+++++..+.. .+++|+.+.+.+.+|++++|
T Consensus 146 ~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q 225 (338)
T TIGR03674 146 YVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQ 225 (338)
T ss_pred EEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHH
Confidence 9999999999999999999999999999999999999999998753211 35679999999999999999
Q ss_pred HHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcCchHHHHhhhhcccCcccccCCccccccccccccCC
Q 009898 145 LITLALLLGSDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGT 223 (523)
Q Consensus 145 lidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~-~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~~~~~~~~~e~~~~~~ 223 (523)
|+|+|+|+||||+|||||||+|||++||++||+. +++++++.
T Consensus 226 ~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~~------------------------------------- 268 (338)
T TIGR03674 226 LIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGE------------------------------------- 268 (338)
T ss_pred HHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcC-------------------------------------
Confidence 9999999999999999999999999999999994 57766321
Q ss_pred cCcCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccCHHHHHHHHHHhcCCCcccccchhhhhhhH
Q 009898 224 DHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAE 292 (523)
Q Consensus 224 ~~~ip~~FP~~~Vi~~Yl~P~vs~~~~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll~e 292 (523)
.++ +..++.+.|++|.|..+ .+..| .+.+.++|+.|+.+.++|+.++++..+-++.+.
T Consensus 269 --~~~---~~~~~~~~f~~~~v~~~-~~~~~-----~~pd~e~l~~fl~~e~~~~~~rv~~~~~~l~~~ 326 (338)
T TIGR03674 269 --DIE---NYDEIREFFLNPPVTDD-YELKW-----RKPDKEGIIEFLCDEHDFSEDRVERALERLEAA 326 (338)
T ss_pred --CCC---CHHHHHHHhCCCCCCCC-CCccC-----CCCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHh
Confidence 011 23689999999988753 22222 234788999999999999999999888887554
No 5
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=1.1e-42 Score=396.85 Aligned_cols=225 Identities=32% Similarity=0.523 Sum_probs=184.0
Q ss_pred HhhcccccHHHHHHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEe
Q 009898 51 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 130 (523)
Q Consensus 51 ~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~ 130 (523)
.|.+..++..|+.+|++||++||||||+||||||||||+|++.|+||+|+|+|+|+|+||+++||||++. .+.+|++|.
T Consensus 763 ~r~~~~vt~~m~~~~~~LL~~~GIP~i~AP~EAEAqcA~L~~~G~vd~V~TeDsD~llFGa~~v~rn~~~-~~~~ve~~~ 841 (1034)
T TIGR00600 763 KRIAAEVTGQMILESQELLRLFGIPYIVAPMEAEAQCAILDLLDQTSGTITDDSDIWLFGARHVYKNFFN-QNKFVEYYQ 841 (1034)
T ss_pred ccccccCCHHHHHHHHHHHHHCCCCeeeCCccHHHHHHHHHhCCCeEEEEccccceeccCCceeeecccC-CCCceEEee
Confidence 5666789999999999999999999999999999999999999999999999999999999999999875 447899999
Q ss_pred HHHHHHHhCCChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCC--HHHHHHHHhcCchHHHHhhhhcccCcccccC
Q 009898 131 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD--NVVLQRIASEGLSFVKRAKNSKKEGWSFKCN 208 (523)
Q Consensus 131 ~~~i~~~lgl~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~--~~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~ 208 (523)
+++|.+.+||++++||+||+|+||||++||+||||+||++||++||+ .+-|..|.. |+....... .....
T Consensus 842 ~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~----w~~~~~~~~-~~~~~--- 913 (1034)
T TIGR00600 842 YVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKE----WWHEAQKDK-KKREN--- 913 (1034)
T ss_pred HHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHH----HHHHhhhcc-ccccc---
Confidence 99999999999999999999999999999999999999999999996 444555554 444332110 00000
Q ss_pred CccccccccccccCCcCcCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccCHHHHHHHHHHhcCCCcccccchhhh
Q 009898 209 NKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILP 288 (523)
Q Consensus 209 ~~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~~~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP 288 (523)
..... .....+...+|.+||+..|+++|++|.|+.+...+.|+ .| +..+|+.||.++|+|+..+++++|.|
T Consensus 914 -~~~~~---~~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~~~f~W~----~P-D~e~L~~Fl~~~~gws~eRv~~~l~p 984 (1034)
T TIGR00600 914 -PNDTK---VKKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWG----KP-DLDKIREFCQRYFGWNREKTDEVLLP 984 (1034)
T ss_pred -cchhh---hhhcccccccCCCCCcHHHHHHhcCCCCCCCcCCCCCC----CC-CHHHHHHHHHHccCCCHHHHHHHHHH
Confidence 00000 00011224589999999999999999999765444443 23 78899999999999999999999999
Q ss_pred hhhHH
Q 009898 289 KIAER 293 (523)
Q Consensus 289 ll~e~ 293 (523)
++..+
T Consensus 985 likk~ 989 (1034)
T TIGR00600 985 VLKKL 989 (1034)
T ss_pred HHHHH
Confidence 99733
No 6
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.3e-42 Score=363.69 Aligned_cols=335 Identities=23% Similarity=0.267 Sum_probs=262.6
Q ss_pred hhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCccccc------cccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCc
Q 009898 3 SYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQ------DDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPC 76 (523)
Q Consensus 3 ~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~------~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~ 76 (523)
+|.++||+|||||||.+|.+|..++.+|..+|.++.. +.+....+.++.++...+|.+...+|+.||..|||||
T Consensus 69 ~l~~~gi~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~ 148 (449)
T KOG2519|consen 69 RLIENGIKPVYVFDGKPPDLKSQELAKRSERRSEADKELKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPV 148 (449)
T ss_pred HHHHcCCcEEEEECCCCCCcchHHHHHHHHHhhhhhhhhhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCee
Confidence 5779999999999999999999999999998865432 2334455667777777788889999999999999999
Q ss_pred ccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccC--CCCceEEEEeHHHHHHHhCCChhHHHHHHHHhCC
Q 009898 77 LEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWL--GERGYVVCYEMDDIERKLGFGRNSLITLALLLGS 154 (523)
Q Consensus 77 i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~--~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G~ 154 (523)
++||+|||||||+|++.|.|++++|+|+|+|.||++.+++++.. +.+..|.+|+++.|.+.|++++++|||+|+|+||
T Consensus 149 i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlGC 228 (449)
T KOG2519|consen 149 LDAPGEAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLGC 228 (449)
T ss_pred ecCCchHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhcC
Confidence 99999999999999999999999999999999999999998764 3457899999999999999999999999999999
Q ss_pred CCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcCchHHHHhhhhcccCcccccCCccccccccccccCCcCcCCCCCCc
Q 009898 155 DYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEESLNQEINVNGTDHSLQRETPF 233 (523)
Q Consensus 155 DY~pGVpGIG~ktA~kLl~~~g~~-~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~~~~~~~~~e~~~~~~~~~ip~~FP~ 233 (523)
||+++|.|||+++|++||++|++. ++++- .+ ..++..+|++||.
T Consensus 229 DYc~~I~Gig~~~al~lir~~~~i~~ile~-~~----------------------------------~~~~~~ip~~w~~ 273 (449)
T KOG2519|consen 229 DYCPTIRGIGPKKALKLIRQHGDIENILEI-NS----------------------------------DLKEYPIPEDWSY 273 (449)
T ss_pred cccccccccChHHHHHHHHHhcCHHHHhhh-cc----------------------------------chhhcCCCCCccH
Confidence 999999999999999999999984 45542 11 0122468899999
Q ss_pred HHHHHHhcCCccCCCCh--HHHHHHhhhcccCHHHHHHHHHHhcCCCcccccchhhhhhhHHHHHhhhhhcccccccCCC
Q 009898 234 SQVIDAYSNPKCYSADS--EAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIAERDLRRFANLRANTLALGVD 311 (523)
Q Consensus 234 ~~Vi~~Yl~P~vs~~~~--e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll~e~~lr~~~~l~~~~s~~~~~ 311 (523)
..+...|+.|.+....+ +.-|. .| +...|.+|+....+|+..++..-+.+++..+++...+.+.. +-..
T Consensus 274 ~~~r~~f~~p~~~~~~~~~~i~w~----~p-d~~~li~fl~~~~~f~~~rv~~~~~kl~~~~~~~~qgrl~~----f~~~ 344 (449)
T KOG2519|consen 274 KLARKLFLEPEFPNPESILDLKWK----TP-DTEGLIQFLVGEKQFNEERVRKGIRKLKSSLKLGTQGRLDS----FFKR 344 (449)
T ss_pred HHHHHHhcCcccCCccceeecccC----CC-ChHHHHHHHHhhhccCHHHHhhhhHHHhhhhccccccchhh----hhcc
Confidence 99999999999987544 22221 12 67789999999999999999999999999998875433211 1111
Q ss_pred CCCCCcCCCCCccceeecc-----cccCccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHHHhccCCCCC
Q 009898 312 LPLQKVPVKCPITGIIKSR-----KLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPKKS 381 (523)
Q Consensus 312 ~~l~~~~v~~~~~~I~k~R-----~~~gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~~~~~kk~ 381 (523)
.|-.-.+.+......+..+ ..++-.|+.+-.+....+.++-.|-.++.+|+|..+..|...|-.+..+++
T Consensus 345 ~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~r~~~t~~~l~~l~~~~p~~~~~~l~~k~~~~~~~~ 419 (449)
T KOG2519|consen 345 IPKGSPVRKLKLIDAKGKAEEVIKALNKKEKPKGQTGKIKRFKTTDKPLTMLPSATPLFTFIFLIPKEYPHLKTK 419 (449)
T ss_pred cCCCCCcchhHHHHHHhhhhhccCcchhhhhhccCCCccccceeecchHhhcccCCccHHHHHhhhhhccccccc
Confidence 1100000000000111111 233445666777888899999999999999999999999988877654443
No 7
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-40 Score=370.40 Aligned_cols=231 Identities=34% Similarity=0.570 Sum_probs=189.9
Q ss_pred HhhcccccHHHHHHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEe
Q 009898 51 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 130 (523)
Q Consensus 51 ~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~ 130 (523)
.|.+..++..|+.+||++|+.||||||+||+|||||||.|.+.++||||||+|||+|+||+++||||||.. +++|+.|.
T Consensus 457 ~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~k-nk~ve~y~ 535 (815)
T KOG2520|consen 457 SRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFNK-NKYVEKYQ 535 (815)
T ss_pred hccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhhc-Cccceeee
Confidence 45666789999999999999999999999999999999999999999999999999999999999999874 48899999
Q ss_pred HHHHHHHhCCChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhhhhcccCcccccCCc
Q 009898 131 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNNK 210 (523)
Q Consensus 131 ~~~i~~~lgl~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~~~~k~~~~~~c~~~ 210 (523)
+.+|+..||++|..||-+|.|+||||+.||+||||++|+++|.+|++.+-|..|.+ |+....-..++ .+ + .
T Consensus 536 ~~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~----w~~~~~~~~~~-~~---s-~ 606 (815)
T KOG2520|consen 536 LDDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKK----WVQQTGPADKE-VG---S-T 606 (815)
T ss_pred hHHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHH----HHHHhCccccc-cc---c-H
Confidence 99999999999999999999999999999999999999999999998655777775 44421100000 00 0 0
Q ss_pred cccccccccccCCcCcCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccCHHHHHHHHHHhcCCCcccccchhhhhh
Q 009898 211 EESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKI 290 (523)
Q Consensus 211 ~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~~~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll 290 (523)
......+ .+.+.+..++.+||++.|+++||+|.|+.....+.|+. | +.+.||+||++.|+|+..++++.|+|++
T Consensus 607 ~~~~lrk-kl~n~~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~----p-dl~~lRef~~~~fgW~~~kT~~~l~p~~ 680 (815)
T KOG2520|consen 607 QQKMLRK-KLKNPKIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGK----P-DLDILREFMKRLFGWPDEKTDEELIPVI 680 (815)
T ss_pred HHHHHHH-HhcCcccccCcCCCchhHHHHhhCCccCCCcccccCCC----C-CHHHHHHHHHHHcCCCccccchhhhhhH
Confidence 0000000 11122345788999999999999999998765555543 2 6788999999999999999999999999
Q ss_pred hHHHHHh
Q 009898 291 AERDLRR 297 (523)
Q Consensus 291 ~e~~lr~ 297 (523)
.+...+.
T Consensus 681 ~~~~~~~ 687 (815)
T KOG2520|consen 681 KRLEKKK 687 (815)
T ss_pred HHHHHHh
Confidence 8887664
No 8
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=9.2e-35 Score=307.69 Aligned_cols=176 Identities=19% Similarity=0.200 Sum_probs=157.4
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCcccc------ccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCC
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVT------QDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVP 75 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~------~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp 75 (523)
+.|+.+||+||+||||.+.|.|..|..+|+.+|++.. ...|+..+|..++|++.++|+.|...+.+.|+..||+
T Consensus 64 ~lL~~~gikPilVFDG~~LP~K~~te~~Rr~~R~~n~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe 143 (556)
T KOG2518|consen 64 KLLLSYGIKPILVFDGDPLPSKKETERKRRERRKKNLDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVE 143 (556)
T ss_pred HHHHhcCCeEEEEecCCCcccccccchHHHHHHHHhHHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCc
Confidence 5688999999999999999999999999999987743 2367778889999999999999999999999999999
Q ss_pred cccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHh----CCChhHHHHHHHH
Q 009898 76 CLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKL----GFGRNSLITLALL 151 (523)
Q Consensus 76 ~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~l----gl~r~qlidlaiL 151 (523)
||+||||||||+|||++.|+||||||+|||+++|||+.||..+... +....++...+.... +++.++|..+|+|
T Consensus 144 ~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~--G~~le~~~~~l~~~~~l~~~~~~ekfr~mciL 221 (556)
T KOG2518|consen 144 YIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSF--GNGLEINRSKLPECKPLGDKFTEEKFRRMCIL 221 (556)
T ss_pred eEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCC--CCcccccHhhhhhccccccccCHHHHHHHHHh
Confidence 9999999999999999999999999999999999999999987642 344556777776543 3678999999999
Q ss_pred hCCCCCCCCCCCcHHHHHHHHHHhCCHH
Q 009898 152 LGSDYSQGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 152 ~G~DY~pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
+||||++||||||.+||+++++.|.+.+
T Consensus 222 SGCDYl~slpGvGl~tA~k~l~k~~~~d 249 (556)
T KOG2518|consen 222 SGCDYLSSLPGVGLATAHKLLSKYNTPD 249 (556)
T ss_pred cCCcccccCccccHHHHHHHHHhcCcHH
Confidence 9999999999999999999999999954
No 9
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.96 E-value=1.6e-29 Score=254.12 Aligned_cols=163 Identities=21% Similarity=0.238 Sum_probs=139.9
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAq 86 (523)
.-++++||||..+.+|++.+..|+++|.++++ .+..+++.++++|+.||||++.+|+ |||++
T Consensus 49 p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~pe-----------------~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~ 111 (259)
T smart00475 49 PTYVAVVFDAKGKTFRHELYPEYKANRPKTPD-----------------ELLEQIPLIKELLDALGIPVLEVEGYEADDV 111 (259)
T ss_pred CCeEEEEEeCCCCccccchhHHHHhCCCCCCH-----------------HHHHHHHHHHHHHHHCCCCEEeeCCcCHHHH
Confidence 35679999999999999999999999987543 2456789999999999999999996 99999
Q ss_pred HHHHHHc----CCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCCCCC
Q 009898 87 CALLNLE----SLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGV 160 (523)
Q Consensus 87 cA~L~~~----G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~pGV 160 (523)
||+|++. |....|+|.|+|+++|+++.|......++.....+|+.+.+.+++|++|+||+|+++|+| |||+|||
T Consensus 112 iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV 191 (259)
T smart00475 112 IATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGV 191 (259)
T ss_pred HHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCC
Confidence 9999874 778899999999999998765432222211234679999999999999999999999999 8999999
Q ss_pred CCCcHHHHHHHHHHhCC-HHHHHHHHhc
Q 009898 161 RGLGPESACQIVKSVGD-NVVLQRIASE 187 (523)
Q Consensus 161 pGIG~ktA~kLl~~~g~-~~iL~~~~~~ 187 (523)
||||||||.+||++||+ +++++++++.
T Consensus 192 ~GIG~KtA~~Ll~~ygsle~i~~~~~~~ 219 (259)
T smart00475 192 PGIGEKTAAKLLKEFGSLENILENLDKL 219 (259)
T ss_pred CCCCHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 99999999999999999 5699998763
No 10
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=99.96 E-value=2.3e-28 Score=243.08 Aligned_cols=159 Identities=21% Similarity=0.246 Sum_probs=138.4
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAq 86 (523)
..++++||||..+.+|++.+..|+++|.+.+. .+..+++.++++|+.||||++.+|+ ||||+
T Consensus 50 p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p~-----------------~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ 112 (240)
T cd00008 50 PTYVAVVFDAGGKTFRHELYPEYKANRKKMPE-----------------ELREQIPLIKELLEALGIPVLEIEGYEADDV 112 (240)
T ss_pred CCeEEEEEeCCCCcccccccHHHHcCCCCCCH-----------------HHHHHHHHHHHHHHHCCCCEEecCCcCHHHH
Confidence 47899999999999999999999999976432 3467889999999999999999996 99999
Q ss_pred HHHHHH----cCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCCCCC
Q 009898 87 CALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGV 160 (523)
Q Consensus 87 cA~L~~----~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~pGV 160 (523)
||+|+. .|....|+|.|+|++++++.+|...... ....++.+.+.+++|++++|++++++|+| |||+|||
T Consensus 113 ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~~~----~~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv 188 (240)
T cd00008 113 IGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPM----KKKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGV 188 (240)
T ss_pred HHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEeCC----CceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCC
Confidence 999985 5778899999999999977655332111 12468999999999999999999999999 8999999
Q ss_pred CCCcHHHHHHHHHHhCC-HHHHHHHHhc
Q 009898 161 RGLGPESACQIVKSVGD-NVVLQRIASE 187 (523)
Q Consensus 161 pGIG~ktA~kLl~~~g~-~~iL~~~~~~ 187 (523)
||||||||.+||++||+ ++|+++++..
T Consensus 189 ~GiG~ktA~~Ll~~~gsle~i~~~~~~~ 216 (240)
T cd00008 189 PGIGEKTAAKLLKEYGSLEGILENLDKI 216 (240)
T ss_pred CccCHHHHHHHHHHhCCHHHHHHhHHHH
Confidence 99999999999999999 5699988764
No 11
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.95 E-value=1.2e-27 Score=243.15 Aligned_cols=162 Identities=17% Similarity=0.222 Sum_probs=138.8
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAq 86 (523)
.-++++||||..|.+|++.+..|+++|.+.+. .+..+++.++++|+.+|||++.+|+ |||+.
T Consensus 55 p~~~~v~fD~~~~~~R~~l~p~YKanR~~~p~-----------------~l~~q~~~i~~~l~~~gi~~~~~~g~EADDv 117 (281)
T PRK14976 55 PSYILIAFDAGRKTFRHQLYDEYKQGRKKTPE-----------------SLISQIPLLKKILKLAGIKWEEQPGYEADDL 117 (281)
T ss_pred CCEEEEEEECCCCcccccccHHHhcCCCCCCH-----------------HHHHHHHHHHHHHHHCCCCEEecCCcCHHHH
Confidence 46899999999999999999999999986542 3456789999999999999999996 99999
Q ss_pred HHHHHH----cCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCCCCC
Q 009898 87 CALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGV 160 (523)
Q Consensus 87 cA~L~~----~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~pGV 160 (523)
||+|+. .|.-..|+|.|+|+++|.+++|........ .....|+.+.+.+++|++|+||+|+++|+| |||+|||
T Consensus 118 iatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~-~~~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGV 196 (281)
T PRK14976 118 IGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKG-TSHFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGV 196 (281)
T ss_pred HHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEecCC-CCcEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCC
Confidence 999976 366667999999999999875533222222 224579999999999999999999999999 8999999
Q ss_pred CCCcHHHHHHHHHHhCC-HHHHHHHHhc
Q 009898 161 RGLGPESACQIVKSVGD-NVVLQRIASE 187 (523)
Q Consensus 161 pGIG~ktA~kLl~~~g~-~~iL~~~~~~ 187 (523)
||||+|||.+||++||+ ++|++++.+.
T Consensus 197 pGIG~KtA~~LL~~~gsle~i~~~~~~~ 224 (281)
T PRK14976 197 KGIGPKTAIKLLNKYGNIENIYENIDKI 224 (281)
T ss_pred CcccHHHHHHHHHHcCCHHHHHHhHHHH
Confidence 99999999999999999 5699988764
No 12
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.94 E-value=3.2e-26 Score=235.19 Aligned_cols=165 Identities=18% Similarity=0.234 Sum_probs=128.5
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCcc-ccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcchHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSE-VTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~-~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~EAEAq 86 (523)
.++|++||||.+|.+|++++.+|+++|.+ .+. .+......++..+......++..+|+| ..+|.|++||
T Consensus 60 ~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p~---------~l~~q~~~i~~~~~~~~~~~l~~~G~e-add~i~t~A~ 129 (310)
T COG0258 60 PTHPVVVFDGKPPTFRHELLEEYKANREKEMPD---------ELAPQIPILTELLVALGIPLLELMGIE-ADDPIETLAQ 129 (310)
T ss_pred CCcEEEEEcCCCCcchHHHHHHHHhCCCccCHH---------HHHHHHHHHHHHHHHhCcHhhhcCCCC-cchhHHHHHH
Confidence 39999999999999999999999999987 542 222222223344444555566666666 5666666667
Q ss_pred HHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHh-CCChhHHHHHHHHhC--CCCCCCCCCC
Q 009898 87 CALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKL-GFGRNSLITLALLLG--SDYSQGVRGL 163 (523)
Q Consensus 87 cA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~l-gl~r~qlidlaiL~G--~DY~pGVpGI 163 (523)
||+ +.|.+++|+|+|+|+++|+++++.......+ .....++...+.+.+ |++++||+|+++|+| |||+|||+||
T Consensus 130 ~a~--~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~-~~~~~~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GI 206 (310)
T COG0258 130 KAY--KKGDVVLIISGDKDLLQLVSPNVLVINGKKG-EPEKFLDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGI 206 (310)
T ss_pred HHH--hcCCeEEEEeCCcchhhhcCCCcEEEeccCC-CCcccCCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCc
Confidence 776 7899999999999999999998654333221 111157999999999 999999999999999 9999999999
Q ss_pred cHHHHHHHHHHhCCH-HHHHHHH
Q 009898 164 GPESACQIVKSVGDN-VVLQRIA 185 (523)
Q Consensus 164 G~ktA~kLl~~~g~~-~iL~~~~ 185 (523)
|+|||++||++||+. .++++++
T Consensus 207 G~ktA~~Ll~~~gs~e~i~~~~~ 229 (310)
T COG0258 207 GPKTALKLLQEYGSLEGLYENLD 229 (310)
T ss_pred CHHHHHHHHHHhCCHHHHHHhhh
Confidence 999999999999995 4777765
No 13
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.93 E-value=6.1e-25 Score=220.19 Aligned_cols=167 Identities=17% Similarity=0.204 Sum_probs=138.9
Q ss_pred CcEEEEEEcCCCCc--hhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHH
Q 009898 8 SSALLRSLNGSIPA--IKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAE 84 (523)
Q Consensus 8 gI~PVFVFDG~~P~--~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAE 84 (523)
.-+.++||||..+. +|++.+..||++|.+.+. .+..|+..+++++.++|||++..|+ |||
T Consensus 47 p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~~~Pe-----------------~l~~Q~~~i~~~l~~~gi~~~~~~g~EAD 109 (256)
T PRK09482 47 PTHAVAVFDGDARSSGWRHQLLPDYKAGRKPMPE-----------------ALQQGLPAIRAAFEELGIDSWHADGNEAD 109 (256)
T ss_pred CCEEEEEEeCCCCCcccHHHHhHHHhcCCCCCcH-----------------HHHHHHHHHHHHHHhCCCCEeccCCcCHH
Confidence 34688999998887 999999999999987542 3567889999999999999999997 999
Q ss_pred HHHHHHHH----cCCeeEEecCCCceEeecccEEE-EEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCC
Q 009898 85 AQCALLNL----ESLCDGCFSSDSDIFLFGARTVY-RDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYS 157 (523)
Q Consensus 85 AqcA~L~~----~G~vdaViS~DsD~llfG~~~Vi-r~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~ 157 (523)
+.||.|+. .|.-..|+|.|+|++++-.+.|. ++.. . ..+++.+.+.+++|++|+|++|+++|+| +|++
T Consensus 110 DvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~--~---~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnI 184 (256)
T PRK09482 110 DLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYF--Q---KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKI 184 (256)
T ss_pred HHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEecc--c---cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCC
Confidence 99999975 35555789999999998776543 3322 1 1368999999999999999999999999 8999
Q ss_pred CCCCCCcHHHHHHHHHHhCC-HHHHHHHHhcCchHHHHhh
Q 009898 158 QGVRGLGPESACQIVKSVGD-NVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~-~~iL~~~~~~~~~~~~k~~ 196 (523)
|||||||||||.+||++||+ ++|+++++.....+.+++.
T Consensus 185 pGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~ 224 (256)
T PRK09482 185 PGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLE 224 (256)
T ss_pred CCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHHHHHHH
Confidence 99999999999999999999 5699998764334444443
No 14
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.92 E-value=7.8e-25 Score=251.20 Aligned_cols=162 Identities=22% Similarity=0.284 Sum_probs=139.4
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAq 86 (523)
.-+.+|||||..|.+|++.+..|+++|.+++. .+..++..++++|++||||++.+|+ ||||+
T Consensus 49 p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~Pe-----------------~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDi 111 (887)
T TIGR00593 49 PTYVAVAFDSGTPTFRHEAYAEYKANRAPTPE-----------------ELIEQIPLIKELLDALGIPILEVEGYEADDV 111 (887)
T ss_pred CCEEEEEEcCCCCcchHHHHHHHHhCCCCChH-----------------HHHHHHHHHHHHHHHCCCcEEeeCCccHHHH
Confidence 34669999999999999999999999987643 3456889999999999999999997 99999
Q ss_pred HHHHHH----cCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCCCCC
Q 009898 87 CALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGV 160 (523)
Q Consensus 87 cA~L~~----~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~pGV 160 (523)
||+|++ .|....|+|.|+|+++++++.|...... .+.....|+.+.+.+++|++|+||+|+++|+| |||+|||
T Consensus 112 Iatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~-~~~~~~~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGV 190 (887)
T TIGR00593 112 IATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPK-GKTSFTEITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGV 190 (887)
T ss_pred HHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEecc-CCCCceEEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCC
Confidence 999986 4788899999999999998765322111 11134579999999999999999999999999 6999999
Q ss_pred CCCcHHHHHHHHHHhCC-HHHHHHHHhc
Q 009898 161 RGLGPESACQIVKSVGD-NVVLQRIASE 187 (523)
Q Consensus 161 pGIG~ktA~kLl~~~g~-~~iL~~~~~~ 187 (523)
||||+|||.+||++||+ ++|+++++.-
T Consensus 191 pGIG~KtA~kLL~~ygsle~i~~~~~~i 218 (887)
T TIGR00593 191 KGIGEKTAAKLLQEFGSLENIYENLDQI 218 (887)
T ss_pred CCcCHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 99999999999999999 5799998764
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=99.92 E-value=1.7e-24 Score=249.48 Aligned_cols=161 Identities=18% Similarity=0.250 Sum_probs=138.3
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAq 86 (523)
.-+.+|||||..+.+|++.+..|+++|.+.+. .+..++..++++|+.+|||++.+|+ ||||+
T Consensus 51 p~~~~v~fD~~~~~~R~~~~~~YK~~R~~~p~-----------------~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ 113 (880)
T PRK05755 51 PTHVAVAFDAKGKTFRHELYPEYKANRPPMPE-----------------DLREQIPLIRELLRALGIPLLELEGYEADDV 113 (880)
T ss_pred CCEEEEEEECCCCccccccCHHHhCCCCCCcH-----------------HHHHHHHHHHHHHHHCCCCEEeeCCccHHHH
Confidence 34569999999999999999999999986542 3456789999999999999999996 99999
Q ss_pred HHHHHH----cCCeeEEecCCCceEeecccEEE-EEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCCCC
Q 009898 87 CALLNL----ESLCDGCFSSDSDIFLFGARTVY-RDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQG 159 (523)
Q Consensus 87 cA~L~~----~G~vdaViS~DsD~llfG~~~Vi-r~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~pG 159 (523)
||+|+. .|..+.|+|.|+|+++++++.|. .+.. . +.....++.+.+.+++|++|+||+|+++|+| |||+||
T Consensus 114 ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~~~-~-~~~~~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipG 191 (880)
T PRK05755 114 IGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTM-G-VSKNEELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPG 191 (880)
T ss_pred HHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEeecc-C-CCCCeEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCC
Confidence 999984 57889999999999999987542 2211 1 1234579999999999999999999999999 799999
Q ss_pred CCCCcHHHHHHHHHHhCC-HHHHHHHHhc
Q 009898 160 VRGLGPESACQIVKSVGD-NVVLQRIASE 187 (523)
Q Consensus 160 VpGIG~ktA~kLl~~~g~-~~iL~~~~~~ 187 (523)
|||||+|||.+||++||+ ++|+++++.-
T Consensus 192 v~GiG~ktA~~Ll~~~gsle~i~~~~~~~ 220 (880)
T PRK05755 192 VPGIGEKTAAKLLQEYGSLEGLYENLDEI 220 (880)
T ss_pred CCCccHHHHHHHHHHcCCHHHHHHhHHHh
Confidence 999999999999999999 5799988753
No 16
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.91 E-value=7.6e-25 Score=188.29 Aligned_cols=86 Identities=40% Similarity=0.618 Sum_probs=75.1
Q ss_pred HHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEcc-CC-C------CceEEEEeHHHHHHHhCCC
Q 009898 70 LSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIW-LG-E------RGYVVCYEMDDIERKLGFG 141 (523)
Q Consensus 70 ~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~-~~-~------~~~v~~y~~~~i~~~lgl~ 141 (523)
++|||||++||||||||||||+++|+||+|+|+|||+|+||+++||++++ .. + ...+++|+...+.+.++++
T Consensus 1 ~~~gv~~i~AP~EAeAq~A~L~~~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~l~l~ 80 (94)
T PF00867_consen 1 RLMGVPYIVAPYEAEAQCAYLERNGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILKELGLT 80 (94)
T ss_dssp HHHT-EEEE-SS-HHHHHHHHHHTTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHHHHTTS
T ss_pred CCCCCeEEEcCchHHHHHHHHHHhcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHHHcCCC
Confidence 57999999999999999999999999999999999999999999999997 22 1 2468999999999999999
Q ss_pred hhHHHHHHHHhCCC
Q 009898 142 RNSLITLALLLGSD 155 (523)
Q Consensus 142 r~qlidlaiL~G~D 155 (523)
+++|+++|+|+|||
T Consensus 81 ~~~fi~~~iL~G~D 94 (94)
T PF00867_consen 81 REQFIDLCILCGCD 94 (94)
T ss_dssp HHHHHHHHHHHHET
T ss_pred HHHHHHHheecCCC
Confidence 99999999999998
No 17
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.74 E-value=3.7e-18 Score=140.89 Aligned_cols=70 Identities=33% Similarity=0.635 Sum_probs=64.0
Q ss_pred HhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCC--ceEEEEeHHHHHHHhCC
Q 009898 71 SLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER--GYVVCYEMDDIERKLGF 140 (523)
Q Consensus 71 ~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~--~~v~~y~~~~i~~~lgl 140 (523)
.+||||++||+|||||||+|++.|+||+|+|+|+|+|+||+++++++++..++ ..++.++...+.+++|+
T Consensus 2 ~~gi~~i~AP~eAeAq~A~L~~~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l 73 (73)
T smart00484 2 LMGIPYIVAPYEAEAQCAYLAKSGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred cCCCeEEEcCCcHHHHHHHHHhCCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 58999999999999999999999999999999999999999999999876542 25888999999999885
No 18
>PHA00439 exonuclease
Probab=99.67 E-value=3.1e-16 Score=159.25 Aligned_cols=135 Identities=10% Similarity=0.043 Sum_probs=106.7
Q ss_pred CcEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHH
Q 009898 8 SSALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQ 86 (523)
Q Consensus 8 gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAq 86 (523)
.-+.+++|| ..+.+|++.+..|+++|.+.+.. ..++..+++++..+||+++..|+ |||+.
T Consensus 64 p~~i~vaFD-~~~tfR~elyp~YKanR~~~p~~------------------~~~~~~i~el~~~~gi~~i~~~G~EADDv 124 (286)
T PHA00439 64 DAPIVLAFT-DSVNWRKEVVPTYKANRKAKRKP------------------VGYRKFLEELMAREEWKSILEPGLEGDDV 124 (286)
T ss_pred CCeEEEEEC-CCCChHhhhhhHhcCCCCCCCCc------------------hhhHHHHHHHHHhCCCCEEeeCCccHHHH
Confidence 456678899 57899999999999999875431 23466788999999999999997 99999
Q ss_pred HHHHHH----cCC-eeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCCCC
Q 009898 87 CALLNL----ESL-CDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQG 159 (523)
Q Consensus 87 cA~L~~----~G~-vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~pG 159 (523)
+|.|++ .|. -..|+|.|+|++++....++.. .. +.+..++.+ .+++++++.+|+| +|++||
T Consensus 125 Igtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~~~-~~---~~~~~~~~~--------~p~~~~d~~AL~GDsSDNIPG 192 (286)
T PHA00439 125 MGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWC-TT---GNILTQTPE--------TADRWHLFQTIKGDSTDGYSG 192 (286)
T ss_pred HHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEEEc-cC---CceEEcCcc--------cHHHHHhhhhcccccccCCCC
Confidence 999975 455 4579999999999975544432 11 121113322 3899999999999 899999
Q ss_pred CCCCcHHHHHHHHHH
Q 009898 160 VRGLGPESACQIVKS 174 (523)
Q Consensus 160 VpGIG~ktA~kLl~~ 174 (523)
||||| |||.+||++
T Consensus 193 VpGIG-KTA~kLL~~ 206 (286)
T PHA00439 193 IPGWG-DTAEAFLEN 206 (286)
T ss_pred CCCcC-HHHHHHHhC
Confidence 99999 999999998
No 19
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=99.38 E-value=4.8e-13 Score=110.96 Aligned_cols=50 Identities=38% Similarity=0.687 Sum_probs=46.2
Q ss_pred HhCCChhHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHh
Q 009898 137 KLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIAS 186 (523)
Q Consensus 137 ~lgl~r~qlidlaiL~G--~DY~pGVpGIG~ktA~kLl~~~g~~-~iL~~~~~ 186 (523)
++|++++||+++|+|+| |||+|||||||+|||.+|+++||+. .++++++.
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~ 54 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDK 54 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 57999999999999999 9999999999999999999999994 58887765
No 20
>PHA02567 rnh RnaseH; Provisional
Probab=99.37 E-value=3.3e-12 Score=130.72 Aligned_cols=137 Identities=12% Similarity=0.035 Sum_probs=101.7
Q ss_pred cCcEEEEEEcCCC-CchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHH
Q 009898 7 YSSALLRSLNGSI-PAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAE 84 (523)
Q Consensus 7 ~gI~PVFVFDG~~-P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAE 84 (523)
..-+.+++||+.. +.+|++.+..||++|.+.+..... +... .+..+-..+++++..|||+++..|+ |||
T Consensus 62 ~~~~i~vaFD~~~~~tfR~elyp~YKAnR~~~Peel~~--q~~~-------l~~~l~~ii~el~~~~gi~~l~~~g~EAD 132 (304)
T PHA02567 62 EYPEIVLAFDNSKSGYWRRDIAWYYKKNRKKDREESPW--DWEG-------LFEAINKIVDEIKENMPYKVMKIDKAEAD 132 (304)
T ss_pred CCCeEEEEEeCCCCCCchhhhhhHhhcCCCCCChHHHH--HHHH-------hhhhHHHHHHHHHHHCCCCEEEeCCccHH
Confidence 3445899999975 789999999999999876532110 0000 1122235578889999999999997 999
Q ss_pred HHHHHHHH----cCCeeEEecCCCceEeecc-cEEEEEccCCCCceEEEEeHHHHHHHhCCChhHHHHHHHHhC--CCCC
Q 009898 85 AQCALLNL----ESLCDGCFSSDSDIFLFGA-RTVYRDIWLGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYS 157 (523)
Q Consensus 85 AqcA~L~~----~G~vdaViS~DsD~llfG~-~~Vir~~~~~~~~~v~~y~~~~i~~~lgl~r~qlidlaiL~G--~DY~ 157 (523)
+.+|.|++ .|.-..|+|.|+|++++-. +.|... . .++...+.+++| .|.|++++.+|+| +|++
T Consensus 133 DvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~~-~--------~~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNI 202 (304)
T PHA02567 133 DIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQW-S--------PMQKKWVKPKYG-SPEKDLMTKIIKGDKKDGV 202 (304)
T ss_pred HHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeEEe-e--------cCCHHHHHHHhC-CHHHHHHHHHhCCcccCCc
Confidence 99999875 4666689999999999863 333211 0 123467888999 5999999999999 8999
Q ss_pred CCCCC
Q 009898 158 QGVRG 162 (523)
Q Consensus 158 pGVpG 162 (523)
||||-
T Consensus 203 PGVp~ 207 (304)
T PHA02567 203 ASIKV 207 (304)
T ss_pred CCCCC
Confidence 99983
No 21
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=99.02 E-value=1.6e-10 Score=109.79 Aligned_cols=111 Identities=21% Similarity=0.226 Sum_probs=85.7
Q ss_pred cEEEEEEcCCCCchhhhHHHHHhhcCccccccccchHHHHHHHhhcccccHHHHHHHHHHHHHhCCCcccCcc-hHHHHH
Q 009898 9 SALLRSLNGSIPAIKLSTYRRRLNSGSEVTQDDKNLDKMSSLRRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQC 87 (523)
Q Consensus 9 I~PVFVFDG~~P~~K~~t~~kRk~~R~~~~~~~~~~e~a~~~~R~~~~~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAqc 87 (523)
-++++|||+..+.+|++.+..|+++|.+.+. .+..+++.++++++.+||+++..|| |||+.+
T Consensus 52 ~~~vv~fD~~~~~fR~~l~p~YKanR~~~p~-----------------~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvI 114 (169)
T PF02739_consen 52 DYVVVAFDSKGPTFRKELYPEYKANRKPMPE-----------------ELIPQLPYIKELLEALGIPVLEVPGYEADDVI 114 (169)
T ss_dssp EEEEEEEEBSSCHHHHHCCTTTTHHHHHHHH-----------------HHHHHHHHHHHHHHHTTSEEEEETTB-HHHHH
T ss_pred ceEEEEecCCCcchHHHHHHHHHhCCCCCCH-----------------HHHHHHHHHHHHHHHCCCCEecCCCCcHHHHH
Confidence 5789999999999999999999999865432 3456788999999999999999997 999999
Q ss_pred HHHHH----cCCeeEEecCCCceEeeccc--EEEEEccCCCCceEEEEeHHHHHHHh
Q 009898 88 ALLNL----ESLCDGCFSSDSDIFLFGAR--TVYRDIWLGERGYVVCYEMDDIERKL 138 (523)
Q Consensus 88 A~L~~----~G~vdaViS~DsD~llfG~~--~Vir~~~~~~~~~v~~y~~~~i~~~l 138 (523)
|.|++ .|.-..|+|.|+|++++... .|+.- .. +.....+|+.+.+.+++
T Consensus 115 atla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~~~-~~-~~~~~~~~~~~~v~eky 169 (169)
T PF02739_consen 115 ATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVYLL-DP-GKKKFKVYDPEEVEEKY 169 (169)
T ss_dssp HHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEEEE-ET-TTTCS-EB-HHHHHHHT
T ss_pred HHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEEEe-ec-CCCCCEEEcHHHHhhcC
Confidence 99975 46666899999999999888 55442 11 12334689999988764
No 22
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.93 E-value=9.2e-10 Score=79.12 Aligned_cols=33 Identities=42% Similarity=0.913 Sum_probs=30.3
Q ss_pred hhHHHHHHHHhCCCCCC---CCCCCcHHHHHHHHHHh
Q 009898 142 RNSLITLALLLGSDYSQ---GVRGLGPESACQIVKSV 175 (523)
Q Consensus 142 r~qlidlaiL~G~DY~p---GVpGIG~ktA~kLl~~~ 175 (523)
++||+++|+|+| ||.+ ||||||+|+|++|+++|
T Consensus 1 p~q~~~~~~L~G-D~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVG-DYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhC-cCCCCCCCCCcccHHHHHHHHHhC
Confidence 589999999999 7766 99999999999999986
No 23
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=98.91 E-value=3.5e-11 Score=105.37 Aligned_cols=48 Identities=25% Similarity=0.508 Sum_probs=38.0
Q ss_pred CChhHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCC-HHHHHHHHhc
Q 009898 140 FGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGD-NVVLQRIASE 187 (523)
Q Consensus 140 l~r~qlidlaiL~G--~DY~pGVpGIG~ktA~kLl~~~g~-~~iL~~~~~~ 187 (523)
+.|+|++|+.+|+| +|++|||||||+|||.+||++||+ ++||++++..
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~ 51 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEI 51 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhc
Confidence 47899999999999 899999999999999999999999 5688887764
No 24
>PF12813 XPG_I_2: XPG domain containing
Probab=98.56 E-value=2.4e-07 Score=93.24 Aligned_cols=87 Identities=23% Similarity=0.299 Sum_probs=67.8
Q ss_pred HHHHHHHHHHHh---CCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecc----cEEEE-EccCCC------Cc--
Q 009898 61 MIKEAKALGLSL---GVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGA----RTVYR-DIWLGE------RG-- 124 (523)
Q Consensus 61 ~i~~ik~lL~~~---GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~----~~Vir-~~~~~~------~~-- 124 (523)
+...+.+.|+.+ |++++..|+|||+.||.++++.-+ +|+|+|||+++|+. ..+.. .+.... +.
T Consensus 5 ~~~~~~e~L~~~~~~~~~~~~~~~EAD~~~A~~A~~~~~-~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~~~~i 83 (246)
T PF12813_consen 5 LVPAFIEALRESWRYGVPVVQCPGEADRECAALARKWGC-PVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGSGSYI 83 (246)
T ss_pred hHHHHHHHHHHHhhcCCcEEEcCccchHHHHHHHHHcCC-eEEccCCCEEEeccCCCceEEEeeeeEeecccccCCCCee
Confidence 456678888888 999999999999999999987666 99999999999987 33322 221111 12
Q ss_pred eEEEEeHHHHHHHhCCChhHHHHHHH
Q 009898 125 YVVCYEMDDIERKLGFGRNSLITLAL 150 (523)
Q Consensus 125 ~v~~y~~~~i~~~lgl~r~qlidlai 150 (523)
...+|+.+.|++.+|+. .|+.||.
T Consensus 84 ~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 84 SAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred EEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 24579999999999999 7777777
No 25
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=98.31 E-value=2.1e-07 Score=80.54 Aligned_cols=35 Identities=20% Similarity=0.247 Sum_probs=30.0
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCcc
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSE 36 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~ 36 (523)
..|+.+||+|||||||.+|+.|.+|..+|+.+|++
T Consensus 66 ~~L~~~gI~PifVFDG~~~~~K~~~~~~R~~~r~~ 100 (101)
T PF00752_consen 66 CRLLEHGIKPIFVFDGKPPPLKRETIQKRRKRREE 100 (101)
T ss_dssp HHHHHTTEEEEEEE--STTGGCHHHHHHHHHHHHH
T ss_pred HHHHHCCCEEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 46899999999999999999999999999988754
No 26
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=98.26 E-value=4.8e-07 Score=78.19 Aligned_cols=35 Identities=20% Similarity=0.305 Sum_probs=32.2
Q ss_pred hhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCcc
Q 009898 2 KSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSE 36 (523)
Q Consensus 2 k~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~ 36 (523)
..|+++||+|||||||.+|+.|.+|..+|+.+|++
T Consensus 64 ~~L~~~~I~PifVFDG~~~~~K~~t~~~R~~~r~~ 98 (99)
T smart00485 64 CRLLEFGIKPIFVFDGKPPPLKSETLAKRRERREE 98 (99)
T ss_pred HHHHHCCCeEEEEECCCCchhhHHHHHHHHHHHhc
Confidence 56899999999999999999999999999988764
No 27
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.40 E-value=0.00011 Score=86.38 Aligned_cols=38 Identities=16% Similarity=0.278 Sum_probs=34.6
Q ss_pred ChhhhhcCcEEEEEEcCCCCchhhhHHHHHhhcCcccc
Q 009898 1 MKSYLHYSSALLRSLNGSIPAIKLSTYRRRLNSGSEVT 38 (523)
Q Consensus 1 Lk~Ll~~gI~PVFVFDG~~P~~K~~t~~kRk~~R~~~~ 38 (523)
+.+|+.+||+|||||||.+|++|.+|..+|+.+|.++.
T Consensus 62 i~~Ll~~gI~PVfVFDG~~p~lK~~t~~~R~~rR~~a~ 99 (1034)
T TIGR00600 62 LCKLLFFRIRPIFVFDGGAPLLKRQTLAKRRQRRDGAS 99 (1034)
T ss_pred HHHHHHCCCeEEEEECCCCchHhHHHHHHHHHHHHHHH
Confidence 35799999999999999999999999999999997753
No 28
>PF00385 Chromo: Chromo (CHRromatin Organisation MOdifier) domain; InterPro: IPR023780 The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain, with weak but significant sequence similarity to the N-terminal chromo domain,[], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1). The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigen and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1. Functional dissections of chromo domain proteins suggests a mechanistic role for chromo domains in targeting chromo domain proteins to specific regions of the nucleus. The mechanism of targeting may involve protein-protein and/or protein/nucleic acid interactions. Hence, several line of evidence show that the HP1 chromo domain is a methyl-specific histone binding module, whereas the chromo domain of two protein components of the drosophila dosage compensation complex, MSL3 and MOF, contain chromo domains that bind to RNA in vitro []. The high resolution structures of HP1-family protein chromo and chromo shadow domain reveal a conserved chromo domain fold motif consisting of three beta strands packed against an alpha helix. The chromo domain fold belongs to the OB (oligonucleotide/oligosaccharide binding)-fold class found in a variety of prokaryotic and eukaryotic nucleic acid binding protein [].; PDB: 2H1E_B 3MWY_W 2DY8_A 1KNE_A 1KNA_A 1Q3L_A 2EE1_A 1AP0_A 1GUW_A 1X3P_A ....
Probab=96.62 E-value=0.0024 Score=49.23 Aligned_cols=50 Identities=26% Similarity=0.470 Sum_probs=45.0
Q ss_pred ccceeecccccCcc---ceEEeecCCCCceeeceehhhhhhhcchhHHHHHHH
Q 009898 323 ITGIIKSRKLQGKE---CFEVSWEESYGLKSSVVPADLIESACPEKIVEFEER 372 (523)
Q Consensus 323 ~~~I~k~R~~~gv~---c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~ 372 (523)
|.+|+..|...+.. =|-|.|.|.+.-..+|+|++-+...+|++|.+|+++
T Consensus 3 Ve~Il~~r~~~~~~~~~~ylVkW~g~~~~~~tWe~~~~l~~~~~~li~~f~~r 55 (55)
T PF00385_consen 3 VERILDHRVVKGGNKVYEYLVKWKGYPYSENTWEPEENLKNCFPELIEEFEKR 55 (55)
T ss_dssp EEEEEEEEEETTEESEEEEEEEETTSSGGGEEEEEGGGCSSHCHHHHHHHHHH
T ss_pred EEEEEEEEEeCCCcccEEEEEEECCCCCCCCeEeeHHHHhHhhHHHHHHHhCC
Confidence 45888888877777 799999999999999999999999999999999975
No 29
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=95.47 E-value=0.018 Score=43.57 Aligned_cols=50 Identities=18% Similarity=0.424 Sum_probs=44.1
Q ss_pred ccceeecc-cccCccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHHH
Q 009898 323 ITGIIKSR-KLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 373 (523)
Q Consensus 323 ~~~I~k~R-~~~gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~ 373 (523)
+.+|+..| ...|...|.|.|.+.+.-..+|+|.+-+.. +|++|.+|.++.
T Consensus 4 v~~Il~~r~~~~~~~~ylVkW~g~~~~~~tW~~~~~l~~-~~~~v~~~~~~~ 54 (55)
T smart00298 4 VEKILDHRWKKKGELEYLVKWKGYSYSEDTWEPEENLLN-CSKKLDNYKKKE 54 (55)
T ss_pred hheeeeeeecCCCcEEEEEEECCCCCccCceeeHHHHHH-HHHHHHHHHHhh
Confidence 35788888 788888999999999888889999999998 999999998864
No 30
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=95.30 E-value=0.008 Score=64.95 Aligned_cols=113 Identities=21% Similarity=0.328 Sum_probs=86.8
Q ss_pred HHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecc-cEEEEEccCCCC-ceEEEEeHHHHHHHhCCC
Q 009898 64 EAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGA-RTVYRDIWLGER-GYVVCYEMDDIERKLGFG 141 (523)
Q Consensus 64 ~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~-~~Vir~~~~~~~-~~v~~y~~~~i~~~lgl~ 141 (523)
.+-..+..-|+.|+++|+-|.+|||||.....++++.. -+|+++|.+ ++++-.+.++.+ ..+.+|......+-.-.+
T Consensus 133 ~~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~~lem~l~s 211 (531)
T COG5366 133 VASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAFG-PSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLEMFLLS 211 (531)
T ss_pred cccccccccceEEEehhhHHHHHHHHHHHHHHHHhcCC-chHhHHHhhhhhheeecccCCCCCCCcccccchHHHhcccc
Confidence 34567788899999999999999999999999998886 889998866 456655544333 457778877766666667
Q ss_pred hhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCC
Q 009898 142 RNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD 177 (523)
Q Consensus 142 r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~ 177 (523)
-.-|...-.|.|||+++.++.|-.--+.-+-+-+|+
T Consensus 212 ~~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd 247 (531)
T COG5366 212 SRLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGD 247 (531)
T ss_pred cchhhhhcccccccccccccccccchhHHHHHHHhc
Confidence 788999999999999999998655335555554444
No 31
>cd00024 CHROMO Chromatin organization modifier (chromo) domain is a conserved region of around 50 amino acids found in a variety of chromosomal proteins, which appear to play a role in the functional organization of the eukaryotic nucleus. Experimental evidence implicates the chromo domain in the binding activity of these proteins to methylated histone tails and maybe RNA. May occur as single instance, in a tandem arrangement or followd by a related "chromo shadow" domain.
Probab=94.85 E-value=0.025 Score=42.95 Aligned_cols=47 Identities=26% Similarity=0.386 Sum_probs=42.6
Q ss_pred cceeeccccc--CccceEEeecCCCCceeeceehhhhhhhcchhHHHHHH
Q 009898 324 TGIIKSRKLQ--GKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEE 371 (523)
Q Consensus 324 ~~I~k~R~~~--gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~ 371 (523)
.+|+..|... |..-|.|.|.+.+.-.-+|+|++-+..+ +.+|.+|++
T Consensus 6 e~Il~~r~~~~~~~~~y~VkW~g~~~~~~tWe~~~~l~~~-~~~i~~~~~ 54 (55)
T cd00024 6 EKILDHRKKKDGGEYEYLVKWKGYSYSEDTWEPEENLEDC-KELIDEFKK 54 (55)
T ss_pred eeeeeeeecCCCCcEEEEEEECCCCCccCccccHHHhCch-HHHHHHHHh
Confidence 5788888877 8999999999999888899999999988 999999986
No 32
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.35 E-value=0.32 Score=47.61 Aligned_cols=65 Identities=18% Similarity=0.353 Sum_probs=44.3
Q ss_pred ceEEEEeH----HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHH
Q 009898 124 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKR 194 (523)
Q Consensus 124 ~~v~~y~~----~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k 194 (523)
..+.+|.. ++....||| +++.--.|-.|. +|+|||||+|+.++..|+...+...+...+.+...+
T Consensus 43 ~~~~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~ 112 (194)
T PRK14605 43 QRVRVFTHLHVREDALSLFGFATTEELSLFETLI------DVSGIGPKLGLAMLSAMNAEALASAIISGNAELLST 112 (194)
T ss_pred CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHh
Confidence 44555443 344456887 455555555553 899999999999999999888888876655444433
No 33
>PHA03065 Hypothetical protein; Provisional
Probab=91.31 E-value=0.68 Score=50.10 Aligned_cols=108 Identities=22% Similarity=0.228 Sum_probs=62.7
Q ss_pred HHHHHHHh--CCCcccCcc-hHHHH-HHH---H-HHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHH
Q 009898 65 AKALGLSL--GVPCLEGVE-EAEAQ-CAL---L-NLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIER 136 (523)
Q Consensus 65 ik~lL~~~--GIp~i~AP~-EAEAq-cA~---L-~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~ 136 (523)
+...|..+ +|.++...| .||-. |++ + .+.|.=-.++|.|-|+++|.+..-..++. +++ .+
T Consensus 150 l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~KiI---------~t~---~~ 217 (438)
T PHA03065 150 LESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKII---------KTA---NQ 217 (438)
T ss_pred HHHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHHH---------HhH---HH
Confidence 34456667 788888776 77764 543 2 34687789999999999998742211110 111 11
Q ss_pred HhCC-----ChhHHHHHHHHhCCCCCCCCCCCcH--HH--HHHHHHHhCCHHHHHHH
Q 009898 137 KLGF-----GRNSLITLALLLGSDYSQGVRGLGP--ES--ACQIVKSVGDNVVLQRI 184 (523)
Q Consensus 137 ~lgl-----~r~qlidlaiL~G~DY~pGVpGIG~--kt--A~kLl~~~g~~~iL~~~ 184 (523)
.+.+ +.---.+.++.-||||.||+-|+-. ++ -.+|...|--+++++.+
T Consensus 218 ~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dFt~~Nv~~SL 274 (438)
T PHA03065 218 LYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDFTIDNVVRSL 274 (438)
T ss_pred HheeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhhhHHHHHHHH
Confidence 1211 2222234566679999999999753 32 23444455445555543
No 34
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=91.30 E-value=0.74 Score=49.97 Aligned_cols=113 Identities=20% Similarity=0.169 Sum_probs=62.8
Q ss_pred HHHHHHHh--CCCcccCcc-hHHHH-HHH----HHHcCCeeEEecCCCceEeecccEEEEEccCCCCceEEEEeHHHHHH
Q 009898 65 AKALGLSL--GVPCLEGVE-EAEAQ-CAL----LNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIER 136 (523)
Q Consensus 65 ik~lL~~~--GIp~i~AP~-EAEAq-cA~----L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~v~~y~~~~i~~ 136 (523)
+..+|..+ +|.++...| .||-. |+. ..+.|.=-.++|.|-|+++|.+.....++-... .. +|..-
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~-~~--~Y~~~---- 220 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTM-NQ--LYKFI---- 220 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhH-Hh--Heeec----
Confidence 44555555 788888776 78864 443 234787789999999999998753322211000 00 11100
Q ss_pred HhCCChhHHHHHHHHhCCCCCCCCCCCcH--HHH--HHHHHHhCCHHHHHHH
Q 009898 137 KLGFGRNSLITLALLLGSDYSQGVRGLGP--ESA--CQIVKSVGDNVVLQRI 184 (523)
Q Consensus 137 ~lgl~r~qlidlaiL~G~DY~pGVpGIG~--ktA--~kLl~~~g~~~iL~~~ 184 (523)
-...+.---.+.++.-||||.||+-|+-. ++- .+|...|--+++++.+
T Consensus 221 P~~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dFti~Ni~~SL 272 (425)
T PF04599_consen 221 PCSKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDFTIDNILQSL 272 (425)
T ss_pred CCchHHHHHHHHHHHhcccccCCcceeEechhhccceeccccccHHHHHHHH
Confidence 00112222334567789999999999753 322 3343334334555544
No 35
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.25 E-value=0.3 Score=48.13 Aligned_cols=67 Identities=19% Similarity=0.339 Sum_probs=47.1
Q ss_pred ceEEEEeH----HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhh
Q 009898 124 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 124 ~~v~~y~~----~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~ 196 (523)
..+.+|.. ++....||| +.+..-.|-.|. +|.|||||+|+.++..++.+++.+.+...+.+...+..
T Consensus 44 ~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ip 115 (203)
T PRK14602 44 GQVSFFVHTVVREDALELFGFATWDERQTFIVLI------SISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVS 115 (203)
T ss_pred CeEEEEEEEEEecCcceeeCCCCHHHHHHHHHHh------CCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCC
Confidence 44554443 344456887 456666666663 79999999999999999888888888876655554443
No 36
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=90.23 E-value=0.41 Score=46.75 Aligned_cols=64 Identities=20% Similarity=0.301 Sum_probs=43.2
Q ss_pred ceEEEEeH----HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHH
Q 009898 124 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVK 193 (523)
Q Consensus 124 ~~v~~y~~----~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~ 193 (523)
..+.+|.. ++....||| +++.--.|..|. +|+|||||+|+.++..++.+++.+.+.+.+.....
T Consensus 42 ~~v~l~t~~~vred~~~LyGF~~~~Er~lF~~L~------~V~GIGpK~Al~iL~~~~~~el~~aI~~~d~~~L~ 110 (191)
T TIGR00084 42 QKAQVFTHLVVREDAELLFGFNTLEERELFKELI------KVNGVGPKLALAILSNMSPEEFVYAIETEEVKALV 110 (191)
T ss_pred CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHhcCCHHHHHHHHHhCCHHHHH
Confidence 44555443 333456787 455555555553 89999999999999988777788887765444333
No 37
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=90.21 E-value=0.23 Score=39.88 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=17.7
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 009898 159 GVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~g~~~ 179 (523)
||||||+++|..|++.||+.+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~ 27 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLE 27 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHH
T ss_pred CCCCccHHHHHHHHHHcCCHH
Confidence 999999999999999999954
No 38
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=89.42 E-value=0.32 Score=49.13 Aligned_cols=39 Identities=15% Similarity=0.187 Sum_probs=24.5
Q ss_pred CCCcccC----cchHHHHHHHHHH---------cCCeeEEecCCCceEeecc
Q 009898 73 GVPCLEG----VEEAEAQCALLNL---------ESLCDGCFSSDSDIFLFGA 111 (523)
Q Consensus 73 GIp~i~A----P~EAEAqcA~L~~---------~G~vdaViS~DsD~llfG~ 111 (523)
++.++.+ |||+|--+....+ .+....|+|.|+|+++++-
T Consensus 172 ~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L 223 (237)
T PF03159_consen 172 NLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSL 223 (237)
T ss_dssp CSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHH
T ss_pred ceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHH
Confidence 3445543 7999986654332 2568899999999999874
No 39
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.40 E-value=0.46 Score=46.22 Aligned_cols=67 Identities=19% Similarity=0.332 Sum_probs=46.8
Q ss_pred ceEEEEeH----HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhh
Q 009898 124 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 124 ~~v~~y~~----~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~ 196 (523)
..+.+|.. ++....||| +.+.--.|-.|. +|.|||||+|+.++..+...++...+.+.+.+...+..
T Consensus 43 ~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vp 114 (183)
T PRK14601 43 EKHELFITQIIKEDSNKLYGFLDKDEQKMFEMLL------KVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVP 114 (183)
T ss_pred CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 44444443 444456887 455555555553 79999999999999999888888888877665555443
No 40
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.30 E-value=0.49 Score=46.19 Aligned_cols=68 Identities=21% Similarity=0.248 Sum_probs=47.4
Q ss_pred CceEEEEeH----HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhh
Q 009898 123 RGYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 123 ~~~v~~y~~----~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~ 196 (523)
+..+.+|.. ++....||| +.+.--.|-.|. +|.|||||+|+.++..+.-.++.+.+...+.+...+..
T Consensus 42 g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vp 114 (188)
T PRK14606 42 GGECFLHTFLSVSQDGITLYGFSNERKKELFLSLT------KVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLP 114 (188)
T ss_pred CCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 344555443 444457887 455555566653 79999999999999998888888888876665555443
No 41
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=89.01 E-value=0.44 Score=46.40 Aligned_cols=51 Identities=27% Similarity=0.399 Sum_probs=33.6
Q ss_pred HHHHHHhCCCh-hHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcC
Q 009898 132 DDIERKLGFGR-NSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEG 188 (523)
Q Consensus 132 ~~i~~~lgl~r-~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~ 188 (523)
++....+|+.. ..--.+..|. .|||||||+|.+++..||.+.+.+.+....
T Consensus 55 d~~~~l~gF~~~~ek~~f~~L~------~i~GIGpk~A~~il~~fg~~~l~~~i~~~d 106 (192)
T PRK00116 55 EDAILLYGFLTKEERELFRLLI------SVSGVGPKLALAILSGLSPEELVQAIANGD 106 (192)
T ss_pred chhHHHcCcCCHHHHHHHHHHh------cCCCCCHHHHHHHHHhCCHHHHHHHHHhCC
Confidence 44445577742 1111144443 599999999999999999876666665543
No 42
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.88 E-value=0.56 Score=46.15 Aligned_cols=59 Identities=24% Similarity=0.474 Sum_probs=42.6
Q ss_pred HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhh
Q 009898 132 DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 132 ~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~ 196 (523)
++-...||| +.+..-.|-.|. +|.|||||+|+.++..+...++.+.+...+.+...+..
T Consensus 54 ED~~~LYGF~t~~Er~lF~~Li------sVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vp 113 (196)
T PRK13901 54 EDELKLFGFLNSSEREVFEELI------GVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVK 113 (196)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 344456887 455555555553 79999999999999999888888888776665554443
No 43
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.24 E-value=0.59 Score=45.84 Aligned_cols=67 Identities=25% Similarity=0.369 Sum_probs=45.8
Q ss_pred ceEEEEeH----HHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhh
Q 009898 124 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 124 ~~v~~y~~----~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~ 196 (523)
..+.+|.. ++....||| +.+.--.|..|. +|.|||||+|+.++..+.-.++...+.+.+.+...+..
T Consensus 43 ~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvp 114 (195)
T PRK14604 43 DEVFLYTHLIVREDALTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVP 114 (195)
T ss_pred CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 44544443 444456787 445555555553 79999999999999988777888888877666555544
No 44
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=88.09 E-value=0.39 Score=49.06 Aligned_cols=57 Identities=30% Similarity=0.429 Sum_probs=47.7
Q ss_pred CccceeecccccCccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHHHhccCCC
Q 009898 322 PITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQPK 379 (523)
Q Consensus 322 ~~~~I~k~R~~~gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~~~~~k 379 (523)
.+..|++.|..+|..+|=|.|.|.+.---+|.|..-. .-||++|.+|.+..+..+.+
T Consensus 50 vvEki~~~r~~~g~~eYlvkW~Gy~~~~ntWEPee~~-~~C~~li~~~~~~~~~~k~~ 106 (270)
T KOG1911|consen 50 VVEKILKRRKKNGKIEYLVKWKGYPDPDNTWEPEEHN-LDCPELIDEFEKSQKKLKKK 106 (270)
T ss_pred hhhhhhhccccCCCceeeeecCCCCCccccCCchhhc-cccHHHHHHHHHHhcccCcc
Confidence 4578999999999999999999999999999999622 33599999999987776433
No 45
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics]
Probab=86.45 E-value=0.36 Score=50.83 Aligned_cols=61 Identities=28% Similarity=0.395 Sum_probs=50.4
Q ss_pred ccceeecccccCccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHHHhcc---CCCCCCCCc
Q 009898 323 ITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALR---QPKKSKPKS 385 (523)
Q Consensus 323 ~~~I~k~R~~~gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~~~~---~~kk~~~~~ 385 (523)
+-.|++.|.+.|+.=|=|.|.|-..=..+|+|.+=| --|-|+++|+++..++ ++||++++-
T Consensus 13 aEsIlkkRirKGrvEYlVKWkGWs~kyNTWEPEENI--LDpRLi~AFe~rErek~~~~~kKrgpkP 76 (369)
T KOG2748|consen 13 AESILKKRIRKGRVEYLVKWKGWSQKYNTWEPEENI--LDPRLIAAFEQREREKELYGKKKRGPKP 76 (369)
T ss_pred HHHHHHHHhhccceEEEEEecccccccCccCccccc--cCHHHHHHHHhhhHHHhhhhhhccCCCC
Confidence 358999999999999999999999999999998633 3488999999998877 456655543
No 46
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=85.91 E-value=0.62 Score=45.75 Aligned_cols=67 Identities=22% Similarity=0.338 Sum_probs=45.5
Q ss_pred ceEEEEeH----HHHHHHhCCC-hhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHhh
Q 009898 124 GYVVCYEM----DDIERKLGFG-RNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 196 (523)
Q Consensus 124 ~~v~~y~~----~~i~~~lgl~-r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~~ 196 (523)
..+.+|.. ++....|||. .+.--.|-.|. +|.|||||+|+.++..++.+++.+.+.+.+.+...+..
T Consensus 42 ~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~L~------~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvp 113 (197)
T PRK14603 42 QEAELHTRLVVREDALSLYGFPDEDSLELFELLL------GVSGVGPKLALALLSALPPALLARALLEGDARLLTSAS 113 (197)
T ss_pred CeEEEEEEEEEccCCceeeCcCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 44554443 3344567873 44444444443 79999999999999998888888888877666555444
No 47
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=85.67 E-value=5.8 Score=45.75 Aligned_cols=86 Identities=16% Similarity=0.310 Sum_probs=57.7
Q ss_pred CcchHHHHHHHHHHc---------CCeeEEecCCCceEeeccc------EEEE-EccCCCC-------------------
Q 009898 79 GVEEAEAQCALLNLE---------SLCDGCFSSDSDIFLFGAR------TVYR-DIWLGER------------------- 123 (523)
Q Consensus 79 AP~EAEAqcA~L~~~---------G~vdaViS~DsD~llfG~~------~Vir-~~~~~~~------------------- 123 (523)
.|||.|.-+-...+. +-..+|.+-|.|++++|-. .++| ..+++.+
T Consensus 186 vPGEGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLREdVff~~~~~~k~k~~~~g~t~~~~e~ 265 (953)
T COG5049 186 VPGEGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILREDVFFGSKSRRKRKCTKCGRTGHSDEE 265 (953)
T ss_pred CCCccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEeechhccCcccccccccccccccccchhh
Confidence 589999876655442 3577999999999999953 4666 3332110
Q ss_pred ------ceEEEEeHHHHHHH-------------hCCCh--hHHHHHHHHhCCCCCCCCCCCc
Q 009898 124 ------GYVVCYEMDDIERK-------------LGFGR--NSLITLALLLGSDYSQGVRGLG 164 (523)
Q Consensus 124 ------~~v~~y~~~~i~~~-------------lgl~r--~qlidlaiL~G~DY~pGVpGIG 164 (523)
.++.+.+.+-+.+. +.+.| +.+|.+|-++|+||+|.+|++-
T Consensus 266 ~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ld 327 (953)
T COG5049 266 CKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLD 327 (953)
T ss_pred hcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccc
Confidence 12445555544331 12222 6788899999999999999874
No 48
>PF00633 HHH: Helix-hairpin-helix motif; InterPro: IPR000445 The HhH motif is an around 20 amino acids domain present in prokaryotic and eukaryotic non-sequence-specific DNA binding proteins [, , ]. The HhH motif is similar to, but distinct from, the HtH motif. Both of these motifs have two helices connected by a short turn. In the HtH motif the second helix binds to DNA with the helix in the major groove. This allows the contact between specific base and residues throughout the protein. In the HhH motif the second helix does not protrude from the surface of the protein and therefore cannot lie in the major groove of the DNA. Crystallographic studies suggest that the interaction of the HhH domain with DNA is mediated by amino acids located in the strongly conserved loop (L-P-G-V) and at the N-terminal end of the second helix []. This interaction could involve the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups []. The structural difference between the HtH and HhH domains is reflected at the functional level: whereas the HtH domain, found primarily in gene regulatory proteins, binds DNA in a sequence specific manner, the HhH domain is rather found in proteins involved in enzymatic activities and binds DNA with no sequence specificity []. The HhH domain of DisA, a bacterial checkpoint control protein, is a DNA-binding domain [].; GO: 0003677 DNA binding; PDB: 3C1Z_A 3C23_A 3C1Y_A 3C21_A 1Z00_A 2A1J_B 1KEA_A 1VRL_A 1RRQ_A 3G0Q_A ....
Probab=84.42 E-value=0.76 Score=31.84 Aligned_cols=15 Identities=33% Similarity=0.720 Sum_probs=12.2
Q ss_pred CCCCCcHHHHHHHHH
Q 009898 159 GVRGLGPESACQIVK 173 (523)
Q Consensus 159 GVpGIG~ktA~kLl~ 173 (523)
.+||||++||-.++.
T Consensus 15 ~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 15 KLPGIGPKTANAILS 29 (30)
T ss_dssp TSTT-SHHHHHHHHH
T ss_pred hCCCcCHHHHHHHHh
Confidence 789999999988864
No 49
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=84.17 E-value=2.5 Score=41.79 Aligned_cols=61 Identities=25% Similarity=0.364 Sum_probs=42.5
Q ss_pred EeHHHHHHHhCCC-hhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHHHHh
Q 009898 129 YEMDDIERKLGFG-RNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRA 195 (523)
Q Consensus 129 y~~~~i~~~lgl~-r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~~k~ 195 (523)
+-.++....|||. .+.--.|..|. .|.|||||+|+.++....-.++.+.+...+.+...+.
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~Li------sVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~ 113 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLLI------SVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKI 113 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHHH------ccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcC
Confidence 4457777789984 33344444442 7899999999999998777777777776655544443
No 50
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.08 E-value=0.81 Score=44.61 Aligned_cols=56 Identities=21% Similarity=0.369 Sum_probs=40.8
Q ss_pred HHHHHHHhCC-ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcCchHH
Q 009898 131 MDDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFV 192 (523)
Q Consensus 131 ~~~i~~~lgl-~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~~iL~~~~~~~~~~~ 192 (523)
.++....||| +++.--.|-.|. +|.|||||+|+.++..+.-.++...+...+.+..
T Consensus 54 rEd~~~LyGF~~~~Er~lF~~Li------sV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L 110 (186)
T PRK14600 54 RDNVTQLYGFLNREEQDCLRMLV------KVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL 110 (186)
T ss_pred ecCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe
Confidence 3444456887 445555555553 8999999999999999988888888887665544
No 51
>KOG2045 consensus 5'-3' exonuclease XRN1/KEM1/SEP1 involved in DNA strand exchange and mRNA turnover [Replication, recombination and repair; Cell cycle control, cell division, chromosome partitioning]
Probab=79.03 E-value=5.3 Score=47.32 Aligned_cols=97 Identities=19% Similarity=0.282 Sum_probs=56.4
Q ss_pred ccCcchHHHHHHHHHH---------cCCeeEEecCCCceEeeccc------EEEEE-ccCC---CCce-----EEEEeHH
Q 009898 77 LEGVEEAEAQCALLNL---------ESLCDGCFSSDSDIFLFGAR------TVYRD-IWLG---ERGY-----VVCYEMD 132 (523)
Q Consensus 77 i~AP~EAEAqcA~L~~---------~G~vdaViS~DsD~llfG~~------~Vir~-~~~~---~~~~-----v~~y~~~ 132 (523)
+.+|||.|--+--..+ -+--.++..=|.|++++|-- .++|- ..++ ..+. +-..+++
T Consensus 170 hevPGEGEHKIMdyIRt~kaq~dydpNTRHClYGLDADLImLGL~tHepHF~lLREEVtFgrrn~~k~lehqkFyLLHLs 249 (1493)
T KOG2045|consen 170 HEVPGEGEHKIMDYIRTMKAQPDYDPNTRHCLYGLDADLIMLGLCTHEPHFVLLREEVTFGRRNKRKSLEHQKFYLLHLS 249 (1493)
T ss_pred CcCCCcchHHHHHHHHHhhcCCCCCCCcceeecccchhhheeeeccCCcceeeeeeeeecccccccchhhhhhhhhhHHH
Confidence 3579999976543322 13355788889999999852 34542 1111 1111 1122222
Q ss_pred -----------HHHH----HhCCCh--hHHHHHHHHhCCCCCCCCCCCcH-HHHHHHHH
Q 009898 133 -----------DIER----KLGFGR--NSLITLALLLGSDYSQGVRGLGP-ESACQIVK 173 (523)
Q Consensus 133 -----------~i~~----~lgl~r--~qlidlaiL~G~DY~pGVpGIG~-ktA~kLl~ 173 (523)
++.. +|.+.+ +.||+++.|+|+||+|.+|++-+ +.|+-|+-
T Consensus 250 LLREYlelEF~e~rdt~~fkyd~erIlDD~ILl~flVGNDFLPhLP~LHIn~gAlplly 308 (1493)
T KOG2045|consen 250 LLREYLELEFDELRDTDEFKYDIERILDDWILLGFLVGNDFLPHLPCLHINSGALPLLY 308 (1493)
T ss_pred HHHHHHHHHHHHhhhccchhhhHHHHHHHHHHHHHhhccccccCCCccccCCChHHHHH
Confidence 2221 223333 66788888899999999999875 35666553
No 52
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=72.93 E-value=2.7 Score=27.73 Aligned_cols=18 Identities=33% Similarity=0.612 Sum_probs=15.2
Q ss_pred CCCCCCCcHHHHHHHHHH
Q 009898 157 SQGVRGLGPESACQIVKS 174 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~ 174 (523)
+..|||||+++|..++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 357999999999999863
No 53
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=66.92 E-value=8.3 Score=30.06 Aligned_cols=20 Identities=25% Similarity=0.518 Sum_probs=14.1
Q ss_pred CCCCCcHHHHHHHHHH-hCCH
Q 009898 159 GVRGLGPESACQIVKS-VGDN 178 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~-~g~~ 178 (523)
+|.|||++||.++... +.+.
T Consensus 6 ~I~GVG~~tA~~w~~~G~rtl 26 (52)
T PF10391_consen 6 GIWGVGPKTARKWYAKGIRTL 26 (52)
T ss_dssp TSTT--HHHHHHHHHTT--SH
T ss_pred hcccccHHHHHHHHHhCCCCH
Confidence 7999999999999986 6664
No 54
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.29 E-value=4.3 Score=39.57 Aligned_cols=37 Identities=35% Similarity=0.548 Sum_probs=25.4
Q ss_pred CCChhHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHHhC
Q 009898 139 GFGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 139 gl~r~qlidlaiL~G~-DY~pGVpGIG~ktA~kLl~~~g 176 (523)
++++++|.. |+..|. ..+..+||||+|||-+|+-+..
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 456666654 344442 3446999999999999996544
No 55
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=65.02 E-value=5.4 Score=45.76 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=21.5
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHH
Q 009898 158 QGVRGLGPESACQIVKSVGDNVVLQ 182 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~~~iL~ 182 (523)
.||||||+++|..|++.||+.+-+.
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~ 596 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVA 596 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHH
Confidence 5999999999999999999965333
No 56
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=63.99 E-value=6.2 Score=30.93 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=18.1
Q ss_pred CCCCCcHHHHHHHHHH-hCCH
Q 009898 159 GVRGLGPESACQIVKS-VGDN 178 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~-~g~~ 178 (523)
.|||||+++|..|... |++.
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~ 29 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTL 29 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSH
T ss_pred cCCCCCHHHHHHHHhcCCCcH
Confidence 7999999999999998 7774
No 57
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.62 E-value=5.1 Score=39.52 Aligned_cols=37 Identities=22% Similarity=0.297 Sum_probs=25.0
Q ss_pred CCChhHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHHhC
Q 009898 139 GFGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 139 gl~r~qlidlaiL~G~-DY~pGVpGIG~ktA~kLl~~~g 176 (523)
.+++++|+. |+..|. ..+..|||||+|||-+|+-+..
T Consensus 91 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIIlELk 128 (196)
T PRK13901 91 GIKYNEFRD-AIDREDIELISKVKGIGNKMAGKIFLKLR 128 (196)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 356666654 333442 3346999999999999996544
No 58
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.30 E-value=5.2 Score=39.27 Aligned_cols=36 Identities=22% Similarity=0.186 Sum_probs=24.5
Q ss_pred CChhHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 009898 140 FGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 140 l~r~qlidlaiL~G-~DY~pGVpGIG~ktA~kLl~~~g 176 (523)
+++++|+.. +..| -..+..+||||+|||-+|+-+..
T Consensus 93 ~~~~el~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 129 (195)
T PRK14604 93 GTPDELQLA-IAGGDVARLARVPGIGKKTAERIVLELK 129 (195)
T ss_pred CCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 567766543 3333 23346999999999999996544
No 59
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=61.57 E-value=7.4 Score=32.85 Aligned_cols=23 Identities=26% Similarity=0.606 Sum_probs=20.1
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCH
Q 009898 156 YSQGVRGLGPESACQIVKSVGDN 178 (523)
Q Consensus 156 Y~pGVpGIG~ktA~kLl~~~g~~ 178 (523)
-+..|||||+.+|..|+.+.|+.
T Consensus 3 ~l~sipGig~~~a~~llaeigd~ 25 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDI 25 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCc
Confidence 35689999999999999999874
No 60
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=61.00 E-value=5.7 Score=38.78 Aligned_cols=41 Identities=15% Similarity=0.219 Sum_probs=27.0
Q ss_pred HHHh-CCChhHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHHhC
Q 009898 135 ERKL-GFGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 135 ~~~l-gl~r~qlidlaiL~G~-DY~pGVpGIG~ktA~kLl~~~g 176 (523)
..-+ ++++++|+.. +..|. ..+-.+||||+|||-+|+-+..
T Consensus 87 L~iLs~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerIilELk 129 (188)
T PRK14606 87 LKIISNEDAETLVTM-IASQDVEGLSKLPGISKKTAERIVMELK 129 (188)
T ss_pred HHHHcCCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 3344 4566766543 33342 3446999999999999996544
No 61
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=60.86 E-value=32 Score=40.47 Aligned_cols=93 Identities=14% Similarity=0.278 Sum_probs=58.0
Q ss_pred CCCccc----CcchHHHHHHHHHH---c------CCeeEEecCCCceEeeccc------EEEEEccCC-----------C
Q 009898 73 GVPCLE----GVEEAEAQCALLNL---E------SLCDGCFSSDSDIFLFGAR------TVYRDIWLG-----------E 122 (523)
Q Consensus 73 GIp~i~----AP~EAEAqcA~L~~---~------G~vdaViS~DsD~llfG~~------~Vir~~~~~-----------~ 122 (523)
+|.+|- .|||.|--+-...+ . +-+.++.+-|.|++++|-- .|+|..+.. .
T Consensus 190 NikvIlSDAnVPGEGEHKIM~yIR~QR~~P~~dPNT~HclyGlDADLImLgLATHE~hF~IlRE~~~P~~~~~C~~cgq~ 269 (931)
T KOG2044|consen 190 NIKVILSDANVPGEGEHKIMSYIRSQRAQPGYDPNTHHCLYGLDADLIMLGLATHEPHFSILREEFFPNKPRRCFLCGQT 269 (931)
T ss_pred ceEEEEecCCCCCcchhHHHHHHHHccCCCCCCCCceeeeecCCccceeeeccccCCceEEeeeeecCCCcccchhhccc
Confidence 455554 48999986554433 2 3477999999999999853 366643220 0
Q ss_pred --------C-----------------ceEEEEeHHHHH----HHhC---------CCh--hHHHHHHHHhCCCCCCCCCC
Q 009898 123 --------R-----------------GYVVCYEMDDIE----RKLG---------FGR--NSLITLALLLGSDYSQGVRG 162 (523)
Q Consensus 123 --------~-----------------~~v~~y~~~~i~----~~lg---------l~r--~qlidlaiL~G~DY~pGVpG 162 (523)
| +.+..++..-+. .+|- +.| +.+|.+|-++|+||+|.+|-
T Consensus 270 gh~~~dc~g~~~~~~~~~~~~~~~~ek~fifl~I~vLREYLe~El~~p~lPf~fd~ER~iDDwVF~CFFvGNDFLPHlPs 349 (931)
T KOG2044|consen 270 GHEAKDCEGKPRLGETNELADVPGVEKPFIFLNISVLREYLERELRMPNLPFTFDLERAIDDWVFLCFFVGNDFLPHLPS 349 (931)
T ss_pred CCcHhhcCCcCCcccccccccCcccccceEEEEHHHHHHHHHHHhcCCCCCccccHHhhhcceEEEEeeecCccCCCCCc
Confidence 0 123344443332 2332 222 66778999999999999997
Q ss_pred CcH
Q 009898 163 LGP 165 (523)
Q Consensus 163 IG~ 165 (523)
+-+
T Consensus 350 LeI 352 (931)
T KOG2044|consen 350 LEI 352 (931)
T ss_pred hhh
Confidence 643
No 62
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.95 E-value=6 Score=38.92 Aligned_cols=42 Identities=21% Similarity=0.166 Sum_probs=27.3
Q ss_pred HHHHhC-CChhHHHHHHHHhCCCC--CCCCCCCcHHHHHHHHHHhCC
Q 009898 134 IERKLG-FGRNSLITLALLLGSDY--SQGVRGLGPESACQIVKSVGD 177 (523)
Q Consensus 134 i~~~lg-l~r~qlidlaiL~G~DY--~pGVpGIG~ktA~kLl~~~g~ 177 (523)
-..-++ +++++|+.. +.. .|. +..+||||+|||-+|+-+..+
T Consensus 85 AL~iLs~~~~~~l~~a-I~~-~D~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 85 ALALLSALPPALLARA-LLE-GDARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred HHHHHcCCCHHHHHHH-HHh-CCHHHHhhCCCCCHHHHHHHHHHHHH
Confidence 334444 677766543 333 333 359999999999999976543
No 63
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=59.11 E-value=7.7 Score=37.84 Aligned_cols=40 Identities=15% Similarity=0.231 Sum_probs=26.9
Q ss_pred HHHhC-CChhHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHHhC
Q 009898 135 ERKLG-FGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 135 ~~~lg-l~r~qlidlaiL~G~-DY~pGVpGIG~ktA~kLl~~~g 176 (523)
..-++ +++++|+.. +-.|. .-+ .|||||+|||-+|+-+..
T Consensus 87 l~iLs~~~~~~l~~a-I~~~D~~~L-~vpGIGkKtAerIilELk 128 (186)
T PRK14600 87 MSILSKLTPEQLFSA-IVNEDKAAL-KVNGIGEKLINRIITELQ 128 (186)
T ss_pred HHHHccCCHHHHHHH-HHcCCHhhe-ECCCCcHHHHHHHHHHHH
Confidence 34443 677776653 34443 445 899999999999996543
No 64
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=58.79 E-value=8.8 Score=43.60 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=20.6
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHH
Q 009898 157 SQGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
+.+|||||+++..+|++.||+.+
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fgs~~ 538 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFKTLY 538 (567)
T ss_pred cccCCCCCHHHHHHHHHHhCCHH
Confidence 35999999999999999999953
No 65
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=58.73 E-value=7.9 Score=44.45 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=20.2
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 009898 158 QGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
.+|||||++++.+|++.||+.+
T Consensus 555 ~~IpGIG~kr~~~LL~~FgSi~ 576 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFGSLE 576 (624)
T ss_pred hcCCCCCHHHHHHHHHHcCCHH
Confidence 5999999999999999999953
No 66
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=56.85 E-value=8.9 Score=43.62 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=20.3
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 009898 158 QGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
.+|||||+++..+|++.||+.+
T Consensus 544 d~I~GIG~kr~~~LL~~Fgs~~ 565 (574)
T TIGR00194 544 LKIPGVGEKRVQKLLKYFGSLK 565 (574)
T ss_pred hcCCCCCHHHHHHHHHHcCCHH
Confidence 4999999999999999999954
No 67
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.16 E-value=7.6 Score=38.34 Aligned_cols=36 Identities=19% Similarity=0.236 Sum_probs=24.6
Q ss_pred CChhHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHHhC
Q 009898 140 FGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 140 l~r~qlidlaiL~G~-DY~pGVpGIG~ktA~kLl~~~g 176 (523)
+++++|+. |+..|. .-+..+||||+|||-+|+-+..
T Consensus 94 ~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilELk 130 (203)
T PRK14602 94 FRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLELK 130 (203)
T ss_pred CCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHHH
Confidence 56666553 344442 3346999999999999996543
No 68
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=55.83 E-value=11 Score=37.31 Aligned_cols=37 Identities=16% Similarity=0.167 Sum_probs=24.6
Q ss_pred CChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhC
Q 009898 140 FGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 140 l~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g 176 (523)
++++.|+..-..-=-.++-.+||||.|||-+|+-+..
T Consensus 93 ~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk 129 (201)
T COG0632 93 LDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELK 129 (201)
T ss_pred CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHh
Confidence 3556655443322234456999999999999996544
No 69
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=55.04 E-value=11 Score=42.87 Aligned_cols=24 Identities=29% Similarity=0.498 Sum_probs=21.2
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHH
Q 009898 156 YSQGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 156 Y~pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
-+.+|||||+++..+|++.||+.+
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~ 538 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYK 538 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHH
Confidence 346999999999999999999953
No 70
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=49.19 E-value=12 Score=26.12 Aligned_cols=14 Identities=21% Similarity=0.411 Sum_probs=11.1
Q ss_pred CCCCCcHHHHHHHH
Q 009898 159 GVRGLGPESACQIV 172 (523)
Q Consensus 159 GVpGIG~ktA~kLl 172 (523)
-++|||.+|+.+|-
T Consensus 15 ~~~GIG~kt~~kL~ 28 (32)
T PF11798_consen 15 KFWGIGKKTAKKLN 28 (32)
T ss_dssp GSTTS-HHHHHHHH
T ss_pred hhCCccHHHHHHHH
Confidence 68999999998863
No 71
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=48.02 E-value=17 Score=42.23 Aligned_cols=23 Identities=13% Similarity=0.173 Sum_probs=20.6
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHH
Q 009898 157 SQGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
+..|||||++++..|++.||+..
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~~ 632 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSFR 632 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCHH
Confidence 35999999999999999999953
No 72
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=47.24 E-value=15 Score=42.10 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=20.1
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 009898 158 QGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
.+|||||++++.+|++.||+..
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~ 567 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLK 567 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHH
Confidence 4999999999999999999953
No 73
>cd00034 ChSh Chromo Shadow Domain, found in association with N-terminal chromo (CHRromatin Organization MOdifier) domain; Chromo domains mediate the interaction of the heterochromatin with other heterochromatin proteins, thereby affecting chromatin structure (e.g. Drosophila and human heterochromatin protein (HP1) and mammalian modifier 1 and modifier 2)
Probab=44.77 E-value=48 Score=25.89 Aligned_cols=37 Identities=27% Similarity=0.629 Sum_probs=31.8
Q ss_pred CccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHHH
Q 009898 334 GKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 373 (523)
Q Consensus 334 gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~ 373 (523)
|-=-|-+.|.+ + ..++||+.++..-||.+|-+|=++.
T Consensus 14 g~l~fl~kwk~-~--~~~lVp~~~~~~k~P~~vI~FYE~~ 50 (54)
T cd00034 14 GELTFLAKWKD-G--QASLVPNKELNVKCPLLVISFYEEH 50 (54)
T ss_pred CeEEEEEEEeC-C--eEEEEEHHHHHhhCcHHHHHHHHHh
Confidence 77778899999 5 4568999999999999999997664
No 74
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=44.28 E-value=16 Score=41.66 Aligned_cols=22 Identities=27% Similarity=0.596 Sum_probs=20.2
Q ss_pred CCCCCCCcHHHHHHHHHHhCCH
Q 009898 157 SQGVRGLGPESACQIVKSVGDN 178 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~~g~~ 178 (523)
+..|||||++++.+|++.||+.
T Consensus 527 L~~IpGIG~kr~~~LL~~FGS~ 548 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFGSV 548 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcCCH
Confidence 3599999999999999999995
No 75
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=42.61 E-value=20 Score=37.22 Aligned_cols=39 Identities=28% Similarity=0.332 Sum_probs=34.8
Q ss_pred ccHHHHHHHHHHHHHhCCCcccCcc-hHHHHHHHHHHcCC
Q 009898 57 EFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNLESL 95 (523)
Q Consensus 57 ~~~~~i~~ik~lL~~~GIp~i~AP~-EAEAqcA~L~~~G~ 95 (523)
.+..++..+.+++..+|++++..+| ||||.++.+++.-.
T Consensus 93 ~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~ 132 (310)
T COG0258 93 ELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAY 132 (310)
T ss_pred HHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHH
Confidence 4567788999999999999999997 99999999998744
No 76
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=41.98 E-value=24 Score=35.80 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=20.3
Q ss_pred CCCCCCCcHHHHHHHHHH-hCCHH
Q 009898 157 SQGVRGLGPESACQIVKS-VGDNV 179 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~-~g~~~ 179 (523)
+..|||||+++|.+|++. |++..
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve 28 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVE 28 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHH
Confidence 358999999999999999 99953
No 77
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=41.79 E-value=24 Score=34.90 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=14.6
Q ss_pred CCCCCCcHHHHHHHHHH
Q 009898 158 QGVRGLGPESACQIVKS 174 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~ 174 (523)
.-+||||+|+|.+++-.
T Consensus 15 ~kLPGvG~KsA~R~Afh 31 (198)
T COG0353 15 KKLPGVGPKSAQRLAFH 31 (198)
T ss_pred hhCCCCChhHHHHHHHH
Confidence 46899999999999864
No 78
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=41.71 E-value=32 Score=40.16 Aligned_cols=35 Identities=20% Similarity=0.400 Sum_probs=26.2
Q ss_pred hCCChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH
Q 009898 138 LGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDN 178 (523)
Q Consensus 138 lgl~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g~~ 178 (523)
+--+.+.++.+.. +| .++|||+++|-+|+..||..
T Consensus 73 ~p~~~~~i~~yL~-s~-----~~~GIG~~~A~~iv~~fg~~ 107 (720)
T TIGR01448 73 APTSKEGIVAYLS-SR-----SIKGVGKKLAQRIVKTFGEA 107 (720)
T ss_pred CCCCHHHHHHHHh-cC-----CCCCcCHHHHHHHHHHhCHh
Confidence 3345677776643 22 48999999999999999974
No 79
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=41.04 E-value=21 Score=34.85 Aligned_cols=33 Identities=9% Similarity=0.140 Sum_probs=21.1
Q ss_pred ChhHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHH
Q 009898 141 GRNSLITLALLLGS-DYSQGVRGLGPESACQIVKS 174 (523)
Q Consensus 141 ~r~qlidlaiL~G~-DY~pGVpGIG~ktA~kLl~~ 174 (523)
++++|+..+. .|. ..+-.|||||+|||-+|+-+
T Consensus 93 ~~~el~~aI~-~~d~~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 93 SPEEFVYAIE-TEEVKALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred CHHHHHHHHH-hCCHHHHHhCCCCCHHHHHHHHHH
Confidence 5555554332 221 22358999999999999843
No 80
>PRK00076 recR recombination protein RecR; Reviewed
Probab=40.34 E-value=59 Score=32.16 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=14.7
Q ss_pred CCCCCCcHHHHHHHHHH
Q 009898 158 QGVRGLGPESACQIVKS 174 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~ 174 (523)
.-+||||+|+|.+|+-.
T Consensus 14 ~~LPGIG~KsA~Rla~~ 30 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFH 30 (196)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999999865
No 81
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=38.52 E-value=27 Score=32.49 Aligned_cols=19 Identities=32% Similarity=0.385 Sum_probs=15.4
Q ss_pred CCCCCcHHHHHHHHHH--hCC
Q 009898 159 GVRGLGPESACQIVKS--VGD 177 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~--~g~ 177 (523)
.+|||||++|.+|++. |.+
T Consensus 65 ~lpGigP~~A~~IV~nGpf~s 85 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDS 85 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCC
Confidence 4799999999999963 444
No 82
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=38.41 E-value=26 Score=40.74 Aligned_cols=25 Identities=28% Similarity=0.466 Sum_probs=21.2
Q ss_pred CCCCCCcHHHHHHHHHHhCCH-HHHH
Q 009898 158 QGVRGLGPESACQIVKSVGDN-VVLQ 182 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~~-~iL~ 182 (523)
..|||||++++.+|++.||+. +|++
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSle~I~~ 665 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSLQAMAA 665 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCHHHHHh
Confidence 489999999999999999995 3443
No 83
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=34.36 E-value=33 Score=35.24 Aligned_cols=20 Identities=30% Similarity=0.652 Sum_probs=19.0
Q ss_pred CCCCCcHHHHHHHHHHhCCH
Q 009898 159 GVRGLGPESACQIVKSVGDN 178 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~g~~ 178 (523)
++||||++.|..|++.||+.
T Consensus 186 s~pgig~~~a~~ll~~fgS~ 205 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSV 205 (254)
T ss_pred cCCCccHHHHHHHHHHhcCH
Confidence 78999999999999999995
No 84
>TIGR03090 SASP_tlp small, acid-soluble spore protein tlp. This protein family is restricted to a subset of endospore-forming bacteria such as Bacillus subtilis, all of which are in the Firmicutes (low-GC Gram-positive) lineage. Although previously designated tlp (thioredoxin-like protein), the B. subtilis protein was shown to be a minor small acid-soluble spore protein SASP, unique to spores. The motif E[VIL]XDE near the C-terminus probably represents at a germination protease cleavage site.
Probab=33.86 E-value=7.5 Score=32.25 Aligned_cols=53 Identities=25% Similarity=0.471 Sum_probs=35.4
Q ss_pred CCcc-cccccccccccCCCCeeeeeCCCC----CCCCChHHHH--------HHHHHHHHHHHhhhh
Q 009898 469 PSPV-QCRNVSRIREMSDQPINTIELSDS----ETEKSPELER--------KARALRMFIASIRDD 521 (523)
Q Consensus 469 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~~--------~~~~~~~~~~~~~~~ 521 (523)
|.|- ++++|-|.|++-++.|+=|+..+- -+|+|++.++ +-..|..|=+-|+||
T Consensus 1 ~kPDdRsDNVEkLQ~mi~nTieN~~eAee~l~~~~el~~~~~~~i~eKN~RR~eSi~~~r~EIkDE 66 (70)
T TIGR03090 1 AKPDDRSDNVEKLQQMIDNTIENMEEANEYIEAHAELSEEEKQRIEEKNERREQSIDGFRSEIKDE 66 (70)
T ss_pred CCCCcccchHHHHHHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHHhHHHHHHHHHHHHHhH
Confidence 5788 999999999998887765554332 1156776554 334466666666665
No 85
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=33.45 E-value=37 Score=39.31 Aligned_cols=19 Identities=32% Similarity=0.587 Sum_probs=11.2
Q ss_pred CCCCCcHHHHHHHHHHhCC
Q 009898 159 GVRGLGPESACQIVKSVGD 177 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~g~ 177 (523)
||||||+++|..|++.|++
T Consensus 502 gIpgVG~~~ak~L~~~f~s 520 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGT 520 (652)
T ss_pred cCCCcCHHHHHHHHHHhCC
Confidence 5555666666655555555
No 86
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=33.37 E-value=1e+02 Score=25.61 Aligned_cols=41 Identities=17% Similarity=0.182 Sum_probs=33.3
Q ss_pred HHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeec
Q 009898 66 KALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFG 110 (523)
Q Consensus 66 k~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG 110 (523)
..+.+.++++. .|+|..++.|...|.+.|-|..-..++.|+
T Consensus 64 ~~ia~~l~~~~----~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 64 SEIAKALQLSE----EEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHHTCCH----HHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHHhccch----HHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 45556667766 789999999999999999999888888775
No 87
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=33.29 E-value=37 Score=26.48 Aligned_cols=19 Identities=21% Similarity=0.487 Sum_probs=15.8
Q ss_pred CCCCCCCcHHHHHHHHHHh
Q 009898 157 SQGVRGLGPESACQIVKSV 175 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~~ 175 (523)
+-.|||||+++|-+|+...
T Consensus 40 L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 40 LAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHTSTTSSHHHHHHHHHHH
T ss_pred HhcCCCCCHHHHHHHHHHH
Confidence 3478999999999998753
No 88
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=32.93 E-value=39 Score=39.43 Aligned_cols=20 Identities=25% Similarity=0.596 Sum_probs=14.5
Q ss_pred CCCCCcHHHHHHHHHHhCCH
Q 009898 159 GVRGLGPESACQIVKSVGDN 178 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~g~~ 178 (523)
||||||+++|..|++.|++.
T Consensus 532 gIpgIG~~~ak~L~~~F~si 551 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTF 551 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCH
Confidence 67777777777777777764
No 89
>TIGR02765 crypto_DASH cryptochrome, DASH family. Photolyases and cryptochromes are related flavoproteins. Photolyases harness the energy of blue light to repair DNA damage by removing pyrimidine dimers. Cryptochromes do not repair DNA and are presumed to act instead in some other (possibly unknown) process such as entraining circadian rhythms. This model describes the cryptochrome DASH subfamily, one of at least five major subfamilies, which is found in plants, animals, marine bacteria, etc. Members of this family bind both folate and FAD. They may show weak photolyase activity in vitro but have not been shown to affect DNA repair in vivo. Rather, DASH family cryptochromes have been shown to bind RNA (Vibrio cholerae VC1814), or DNA, and seem likely to act in light-responsive regulatory processes.
Probab=32.72 E-value=91 Score=33.75 Aligned_cols=41 Identities=20% Similarity=0.055 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEec
Q 009898 61 MIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFS 101 (523)
Q Consensus 61 ~i~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS 101 (523)
-+.++++-|+.+|++.+..-|++...+..|.+.--+..|++
T Consensus 62 sL~~L~~~L~~~g~~L~v~~G~~~~vl~~L~~~~~~~~V~~ 102 (429)
T TIGR02765 62 SLKDLRTSLRKLGSDLLVRSGKPEDVLPELIKELGVRTVFL 102 (429)
T ss_pred HHHHHHHHHHHcCCCeEEEeCCHHHHHHHHHHHhCCCEEEE
Confidence 35666666777777777777777777777665544555555
No 90
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=32.30 E-value=57 Score=29.44 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=15.5
Q ss_pred CCCCCcHHHHHHHHHHh
Q 009898 159 GVRGLGPESACQIVKSV 175 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~ 175 (523)
.+||||+++|.+|+..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 78999999999999875
No 91
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=31.88 E-value=57 Score=30.98 Aligned_cols=34 Identities=24% Similarity=0.175 Sum_probs=22.6
Q ss_pred CCCcccCc--chHHHHHHHHHHc----CCeeEEecCCCce
Q 009898 73 GVPCLEGV--EEAEAQCALLNLE----SLCDGCFSSDSDI 106 (523)
Q Consensus 73 GIp~i~AP--~EAEAqcA~L~~~----G~vdaViS~DsD~ 106 (523)
||.++-++ ..||..+-.|... +.-..|+|.|...
T Consensus 67 gi~Vvft~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~i 106 (166)
T PF05991_consen 67 GIEVVFTKEGETADDYIERLVRELKNRPRQVTVVTSDREI 106 (166)
T ss_pred ceEEEECCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHH
Confidence 56666666 4799887776542 4455788877654
No 92
>smart00300 ChSh Chromo Shadow Domain.
Probab=31.84 E-value=69 Score=25.56 Aligned_cols=39 Identities=28% Similarity=0.640 Sum_probs=32.9
Q ss_pred ccCccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHHH
Q 009898 332 LQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 373 (523)
Q Consensus 332 ~~gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~~ 373 (523)
.+|-=-|-+.|.+ . ..++||+.++..-||.+|-+|=++.
T Consensus 18 ~~G~l~flikwk~-~--~~~lVp~~~~~~k~P~~vI~FYE~~ 56 (61)
T smart00300 18 DDGELTFLIKWKD-D--AASLVPNKEANVKCPQKVIRFYESH 56 (61)
T ss_pred CCCeEEEEEEEeC-C--cEEEEEHHHHHHHChHHHHHHHHHh
Confidence 5666778899999 5 4568999999999999999997654
No 93
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.16 E-value=30 Score=34.18 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=14.5
Q ss_pred CCCCCCcHHHHHHHHHH
Q 009898 158 QGVRGLGPESACQIVKS 174 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~ 174 (523)
.-+||||+|+|.+|+-.
T Consensus 14 ~~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFH 30 (195)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999999765
No 94
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=31.00 E-value=42 Score=38.39 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=20.2
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 009898 158 QGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
.+|||||++....|++.||+..
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~ 554 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLK 554 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCHH
Confidence 4999999999999999999954
No 95
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.42 E-value=33 Score=33.58 Aligned_cols=36 Identities=22% Similarity=0.457 Sum_probs=23.3
Q ss_pred CChhHHHHHHHHhCCCC--CCCCCCCcHHHHHHHHHHhCC
Q 009898 140 FGRNSLITLALLLGSDY--SQGVRGLGPESACQIVKSVGD 177 (523)
Q Consensus 140 l~r~qlidlaiL~G~DY--~pGVpGIG~ktA~kLl~~~g~ 177 (523)
+++++|+.. +..+ |. +-.|||||+|||-+|+-+..+
T Consensus 93 ~~~~~l~~a-I~~~-D~~~L~~vpGIGkKtAerIilELk~ 130 (194)
T PRK14605 93 MNAEALASA-IISG-NAELLSTIPGIGKKTASRIVLELKD 130 (194)
T ss_pred CCHHHHHHH-HHhC-CHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 456655432 2233 33 348999999999999865443
No 96
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=28.28 E-value=78 Score=29.77 Aligned_cols=16 Identities=31% Similarity=0.663 Sum_probs=14.2
Q ss_pred CCCCCcHHHHHHHHHH
Q 009898 159 GVRGLGPESACQIVKS 174 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~ 174 (523)
.+||||+++|.+|+..
T Consensus 101 ~lpgIG~~kA~aIi~y 116 (149)
T COG1555 101 ALPGIGPKKAQAIIDY 116 (149)
T ss_pred HCCCCCHHHHHHHHHH
Confidence 6899999999999963
No 97
>PRK13844 recombination protein RecR; Provisional
Probab=27.84 E-value=37 Score=33.69 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=14.7
Q ss_pred CCCCCCcHHHHHHHHHH
Q 009898 158 QGVRGLGPESACQIVKS 174 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~ 174 (523)
.-+||||+|+|.+|+-.
T Consensus 18 ~~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 18 RKLPTIGKKSSQRLALY 34 (200)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999999865
No 98
>TIGR00591 phr2 photolyase PhrII. All proteins in this family for which functions are known are DNA-photolyases used for the direct repair of UV irradiation induced DNA damage. Some repair 6-4 photoproducts while others repair cyclobutane pyrimidine dimers. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.33 E-value=1.3e+02 Score=33.01 Aligned_cols=40 Identities=8% Similarity=-0.104 Sum_probs=21.8
Q ss_pred HHHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEec
Q 009898 62 IKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFS 101 (523)
Q Consensus 62 i~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS 101 (523)
+.++++-|+.+|++.++--|+....+..|.+.--++.|++
T Consensus 80 L~~L~~~L~~~g~~L~v~~g~~~~~l~~l~~~~~i~~V~~ 119 (454)
T TIGR00591 80 LDEVANECERLIIPFHLLDGPPKELLPYFVDLHAAAAVVT 119 (454)
T ss_pred HHHHHHHHHHcCCceEEeecChHHHHHHHHHHcCCCEEEE
Confidence 4455555556666666665555555555554433444444
No 99
>smart00753 PAM PCI/PINT associated module.
Probab=27.07 E-value=1.6e+02 Score=24.14 Aligned_cols=44 Identities=16% Similarity=0.080 Sum_probs=35.5
Q ss_pred HHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeeccc
Q 009898 65 AKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGAR 112 (523)
Q Consensus 65 ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~ 112 (523)
+..+.+.++++.- |+|..+..+...|.++|-+-....++.|...
T Consensus 27 ~~~i~~~~~l~~~----~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~ 70 (88)
T smart00753 27 LSDLAKLLGLSVP----EVEKLVSKAIRDGEISAKIDQVNGIVEFEEV 70 (88)
T ss_pred HHHHHHHhCcCHH----HHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence 4556677888742 7999999999999999999988888887653
No 100
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=27.07 E-value=1.6e+02 Score=24.14 Aligned_cols=44 Identities=16% Similarity=0.080 Sum_probs=35.5
Q ss_pred HHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeeccc
Q 009898 65 AKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGAR 112 (523)
Q Consensus 65 ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~ 112 (523)
+..+.+.++++.- |+|..+..+...|.++|-+-....++.|...
T Consensus 27 ~~~i~~~~~l~~~----~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~~ 70 (88)
T smart00088 27 LSDLAKLLGLSVP----EVEKLVSKAIRDGEISAKIDQVNGIVEFEEV 70 (88)
T ss_pred HHHHHHHhCcCHH----HHHHHHHHHHHCCCeEEEEcCcCCEEEECCC
Confidence 4556677888742 7999999999999999999988888887653
No 101
>PF01393 Chromo_shadow: Chromo shadow domain Web page maintained by Rein Aasland; InterPro: IPR008251 Chromo shadow domain is distantly related to chromo domain. It is always found in association with a chromo domain. The CHROMO (CHRromatin Organization MOdifier) domain [, , , ] is a conserved region of around 60 amino acids, originally identified in Drosophila modifiers of variegation. These are proteins that alter the structure of chromatin to the condensed morphology of heterochromatin, a cytologically visible condition where gene expression is repressed. In one of these proteins, Polycomb, the chromo domain has been shown to be important for chromatin targeting. Proteins that contain a chromo domain appear to fall into 3 classes. The first class includes proteins having an N-terminal chromo domain followed by a region termed the chromo shadow domain [], eg. Drosophila and human heterochromatin protein Su(var)205 (HP1); and mammalian modifier 1 and modifier 2. The second class includes proteins with a single chromo domain, eg. Drosophila protein Polycomb (Pc); mammalian modifier 3; human Mi-2 autoantigenand and several yeast and Caenorhabditis elegans hypothetical proteins. In the third class paired tandem chromo domains are found, eg. in mammalian DNA-binding/helicase proteins CHD-1 to CHD-4 and yeast protein CHD1.; GO: 0005634 nucleus; PDB: 3Q6S_C 2FMM_B 3P7J_B 1E0B_B 3I3C_A 1DZ1_B 1S4Z_A 3KUP_D.
Probab=26.40 E-value=1.3e+02 Score=23.91 Aligned_cols=46 Identities=26% Similarity=0.610 Sum_probs=34.7
Q ss_pred ceeecccccCccceEEeecCCCCceeeceehhhhhhhcchhHHHHHHH
Q 009898 325 GIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEER 372 (523)
Q Consensus 325 ~I~k~R~~~gv~c~ei~w~~~~~l~~~~vP~~lv~~a~Pe~v~~f~~~ 372 (523)
.|+..=...|---|=|.|.+.+ ..++||+.++...||.+|-.|=+.
T Consensus 7 ~Ivg~~d~~G~l~~likwk~~~--~~~~v~~~~~~~k~Pq~vI~FYE~ 52 (58)
T PF01393_consen 7 KIVGATDTNGELMFLIKWKNSG--EKDLVPSKEANEKCPQKVIKFYES 52 (58)
T ss_dssp EEEEEEECTSSEEEEEEETTSS--SEEEEEHHHHHHHSHHHHHHHHHH
T ss_pred HHheeecCCCcEEEEEEECCCC--ceEEeeHHHHHHHCcHHHHHHHHH
Confidence 3444333346556668999877 477899999999999999999765
No 102
>PF02677 DUF208: Uncharacterized BCR, COG1636; InterPro: IPR003828 This entry describes proteins of unknown function.
Probab=25.07 E-value=1.9e+02 Score=28.24 Aligned_cols=83 Identities=24% Similarity=0.333 Sum_probs=47.6
Q ss_pred HHHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEeecccEEEEEccCCCCce-EEEEeHHHHHHHhCC
Q 009898 62 IKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGY-VVCYEMDDIERKLGF 140 (523)
Q Consensus 62 i~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~llfG~~~Vir~~~~~~~~~-v~~y~~~~i~~~lgl 140 (523)
.++++++.+.+||+++..+|.-++-+....- +-+ ...+|.. ..||++
T Consensus 44 ~~~~~~~~~~~~i~~i~~~Y~~~~w~~~v~~--~e~---------------------epE~g~RC~~Cy~~--------- 91 (176)
T PF02677_consen 44 LEELKRFAEKLGIPLIEGDYDPEEWLRAVKG--LED---------------------EPEGGKRCRVCYDL--------- 91 (176)
T ss_pred HHHHHHHHHHcCCCEEecCCCHHHHHHHHhh--Ccc---------------------CCccCchhHHHHHH---------
Confidence 3567888888999999999977665543321 110 0001111 113332
Q ss_pred ChhHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhC
Q 009898 141 GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVG 176 (523)
Q Consensus 141 ~r~qlidlaiL~G~DY~pGVpGIG~ktA~kLl~~~g 176 (523)
--+.-..+|.-.|.|+.-..--+.|..-.++|..-|
T Consensus 92 RL~~tA~~A~e~gfd~FtTTL~~Sp~k~~~~I~~iG 127 (176)
T PF02677_consen 92 RLEKTAQYAKELGFDYFTTTLLISPYKNHELINEIG 127 (176)
T ss_pred HHHHHHHHHHHcCCCEEEccccCcCccCHHHHHHHH
Confidence 113334566667778777666677776666666554
No 103
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=24.89 E-value=47 Score=35.15 Aligned_cols=18 Identities=33% Similarity=0.578 Sum_probs=15.9
Q ss_pred CCCCCcHHHHHHHHHHhCC
Q 009898 159 GVRGLGPESACQIVKSVGD 177 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~g~ 177 (523)
.||||||++|..|.+ .|=
T Consensus 93 ~i~GiGpk~a~~l~~-lGi 110 (334)
T smart00483 93 NVFGVGPKTAAKWYR-KGI 110 (334)
T ss_pred ccCCcCHHHHHHHHH-hCC
Confidence 899999999999998 553
No 104
>TIGR00114 lumazine-synth 6,7-dimethyl-8-ribityllumazine synthase. Archaeal members of this family are considered putative, although included in the seed and scoring above the trusted cutoff.
Probab=24.67 E-value=1.4e+02 Score=27.87 Aligned_cols=45 Identities=16% Similarity=0.014 Sum_probs=35.9
Q ss_pred ccHHHHHHHHHHHHHhCCC-----cccCcc--hHHHHHHHHHHcCCeeEEec
Q 009898 57 EFSCMIKEAKALGLSLGVP-----CLEGVE--EAEAQCALLNLESLCDGCFS 101 (523)
Q Consensus 57 ~~~~~i~~ik~lL~~~GIp-----~i~AP~--EAEAqcA~L~~~G~vdaViS 101 (523)
++..++.-+.+.|+..|+. .+..|| |.=-.+..|.+.|-.|+|++
T Consensus 14 i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~ 65 (138)
T TIGR00114 14 ITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIA 65 (138)
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 5567888899999999975 667887 66566677888888899987
No 105
>TIGR00426 competence protein ComEA helix-hairpin-helix repeat region. Members of the subfamily recognized by this model include competence protein ComEA and closely related proteins from a number of species that exhibit competence for transformation by exongenous DNA, including Streptococcus pneumoniae, Bacillus subtilis, Neisseria meningitidis, and Haemophilus influenzae. This model represents a region of two tandem copies of a helix-hairpin-helix domain (pfam00633), each about 30 residues in length. Limited sequence similarity can be found among some members of this family N-terminal to the region covered by this model.
Probab=24.45 E-value=1.1e+02 Score=24.49 Aligned_cols=15 Identities=33% Similarity=0.461 Sum_probs=13.5
Q ss_pred CCCCcHHHHHHHHHH
Q 009898 160 VRGLGPESACQIVKS 174 (523)
Q Consensus 160 VpGIG~ktA~kLl~~ 174 (523)
+||+|+++|.+|+..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 789999999999987
No 106
>COG2974 RdgC DNA recombination-dependent growth factor C [DNA replication, recombination, and repair]
Probab=24.08 E-value=39 Score=35.16 Aligned_cols=32 Identities=31% Similarity=0.509 Sum_probs=26.4
Q ss_pred eceehhhhhhhcchhHHHHHHHHhccCCCCCC
Q 009898 351 SVVPADLIESACPEKIVEFEERRALRQPKKSK 382 (523)
Q Consensus 351 ~~vP~~lv~~a~Pe~v~~f~~~~~~~~~kk~~ 382 (523)
.+.|+.+|..++-++|.|-+.+++.+=+||-|
T Consensus 72 KiLPasVVkd~L~~ki~eiE~~q~rkl~kkEk 103 (303)
T COG2974 72 KILPASVVKDALEAKIEEIEAKQGRKLKKKEK 103 (303)
T ss_pred ccCCHHHHHHHHHHHHHHHHHHhCCCcchhhH
Confidence 38999999999999999999998875444433
No 107
>PRK13766 Hef nuclease; Provisional
Probab=23.94 E-value=64 Score=37.59 Aligned_cols=22 Identities=18% Similarity=0.389 Sum_probs=19.9
Q ss_pred CCCCCCCcHHHHHHHHHHhCCH
Q 009898 157 SQGVRGLGPESACQIVKSVGDN 178 (523)
Q Consensus 157 ~pGVpGIG~ktA~kLl~~~g~~ 178 (523)
+.++||||+++|.+|++.||+.
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~ 738 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSV 738 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCH
Confidence 3589999999999999999994
No 108
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=23.75 E-value=50 Score=28.81 Aligned_cols=29 Identities=10% Similarity=0.243 Sum_probs=23.1
Q ss_pred cchHHHHHHHHHHcCCeeEEecCCCceEe
Q 009898 80 VEEAEAQCALLNLESLCDGCFSSDSDIFL 108 (523)
Q Consensus 80 P~EAEAqcA~L~~~G~vdaViS~DsD~ll 108 (523)
+-..|+-+..++..+-+|+++|.|.|+|.
T Consensus 85 ~D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 85 RDKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CCchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 34567777778888889999999999763
No 109
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=23.74 E-value=41 Score=40.02 Aligned_cols=25 Identities=16% Similarity=0.177 Sum_probs=21.6
Q ss_pred CCCCCCCCCcHHHHHHHHHHhCCHH
Q 009898 155 DYSQGVRGLGPESACQIVKSVGDNV 179 (523)
Q Consensus 155 DY~pGVpGIG~ktA~kLl~~~g~~~ 179 (523)
+|+-++||||++.|..|+..||+..
T Consensus 757 ~~L~~lPgI~~~~a~~ll~~f~si~ 781 (814)
T TIGR00596 757 DFLLKLPGVTKKNYRNLRKKVKSIR 781 (814)
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCHH
Confidence 4455899999999999999999953
No 110
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=23.35 E-value=67 Score=29.82 Aligned_cols=48 Identities=17% Similarity=0.071 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecCCCceEe
Q 009898 60 CMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFL 108 (523)
Q Consensus 60 ~~i~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~DsD~ll 108 (523)
.|+..+-..|+.+|+..+..+...|+++..++...-- .++|-|.+++-
T Consensus 7 ~~L~~Lar~LR~lG~Dt~~~~~~~D~~il~~A~~e~R-illTrd~~l~~ 54 (147)
T PF01927_consen 7 AMLGRLARWLRLLGYDTLYSRDIDDDEILELAREEGR-ILLTRDRDLLK 54 (147)
T ss_pred CCHHHHHHHHHHCCCcEEEeCCCChHHHHHHhhhCCe-EEEECCHHHHH
Confidence 3556788899999999999997788888888764322 58999998653
No 111
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=23.15 E-value=57 Score=26.26 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=13.1
Q ss_pred CCCCCCcHHHHHHHH
Q 009898 158 QGVRGLGPESACQIV 172 (523)
Q Consensus 158 pGVpGIG~ktA~kLl 172 (523)
.++||||.++|.++-
T Consensus 50 ~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 50 KKLPGIGKSIAKKID 64 (68)
T ss_dssp CTSTTTTHHHHHHHH
T ss_pred hhCCCCCHHHHHHHH
Confidence 699999999998874
No 112
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=22.83 E-value=67 Score=37.38 Aligned_cols=28 Identities=25% Similarity=0.173 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCcccC------cchHHHHHHHHH
Q 009898 64 EAKALGLSLGVPCLEG------VEEAEAQCALLN 91 (523)
Q Consensus 64 ~ik~lL~~~GIp~i~A------P~EAEAqcA~L~ 91 (523)
+..+.|+.+|||+... ..|+.+.+.++.
T Consensus 240 e~l~~L~~~GF~v~~~~~~~~~~~ei~~~~~~~~ 273 (665)
T PRK07956 240 EALEFLKAWGFPVNPYRKLCTSIEEVLAFYEEIE 273 (665)
T ss_pred HHHHHHHHCCCCcCCceEeeCCHHHHHHHHHHHH
Confidence 4566788999987532 235566666665
No 113
>cd08556 GDPD Glycerophosphodiester phosphodiesterase domain as found in prokaryota and eukaryota, and similar proteins. The typical glycerophosphodiester phosphodiesterase domain (GDPD) consists of a TIM barrel and a small insertion domain named the GDPD-insertion (GDPD-I) domain, which is specific for GDPD proteins. This family corresponds to both typical GDPD domain and GDPD-like domain which lacks the GDPD-I region. Members in this family mainly consist of a large family of prokaryotic and eukaryotic glycerophosphodiester phosphodiesterases (GP-GDEs, EC 3.1.4.46), and a number of uncharacterized homologs. Sphingomyelinases D (SMases D) (sphingomyelin phosphodiesterase D, EC 3.1.4.41) from spider venom, SMases D-like proteins, and phospholipase D (PLD) from several pathogenic bacteria are also included in this family. GDPD plays an essential role in glycerol metabolism and catalyzes the hydrolysis of glycerophosphodiesters to sn-glycerol-3-phosphate (G3P) and the corresponding alcoho
Probab=22.81 E-value=99 Score=28.53 Aligned_cols=39 Identities=13% Similarity=0.055 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCcccCcchHHHHHHHHHHcCCeeEEecC
Q 009898 63 KEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSS 102 (523)
Q Consensus 63 ~~ik~lL~~~GIp~i~AP~EAEAqcA~L~~~G~vdaViS~ 102 (523)
..+.+.++..|++++.-.-.-.++..++.+.| ||+|+|+
T Consensus 150 ~~~i~~~~~~g~~v~~wtvn~~~~~~~~~~~G-VdgI~TD 188 (189)
T cd08556 150 PELVRAAHAAGLKVYVWTVNDPEDARRLLALG-VDGIITD 188 (189)
T ss_pred HHHHHHHHHcCCEEEEEcCCCHHHHHHHHHCC-CCEEecC
Confidence 44555666678888776554455566666666 7888885
No 114
>PRK10674 deoxyribodipyrimidine photolyase; Provisional
Probab=22.71 E-value=1.7e+02 Score=32.29 Aligned_cols=41 Identities=10% Similarity=-0.015 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhCCCcccCcc----hHHHHHHHHHHcCCeeEEec
Q 009898 61 MIKEAKALGLSLGVPCLEGVE----EAEAQCALLNLESLCDGCFS 101 (523)
Q Consensus 61 ~i~~ik~lL~~~GIp~i~AP~----EAEAqcA~L~~~G~vdaViS 101 (523)
-+.++++-|+.+|++.++.-| +....+..|.+.--|+.|+.
T Consensus 58 sL~~L~~~L~~~g~~L~v~~g~~~g~~~~vl~~l~~~~~i~~v~~ 102 (472)
T PRK10674 58 QLNALQIALAEKGIPLLFHEVDDFAASVEWLKQFCQQHQVTHLFY 102 (472)
T ss_pred HHHHHHHHHHHcCCceEEEecCCcCCHHHHHHHHHHHcCCCEEEE
Confidence 345566666666776666543 46666666655434444444
No 115
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=22.15 E-value=59 Score=33.97 Aligned_cols=17 Identities=35% Similarity=0.761 Sum_probs=15.0
Q ss_pred CCCCCcHHHHHHHHHHhC
Q 009898 159 GVRGLGPESACQIVKSVG 176 (523)
Q Consensus 159 GVpGIG~ktA~kLl~~~g 176 (523)
+|+||||++|.+|. ..|
T Consensus 89 ~i~GiGpk~a~~l~-~lG 105 (307)
T cd00141 89 RVPGVGPKTARKLY-ELG 105 (307)
T ss_pred cCCCCCHHHHHHHH-HcC
Confidence 89999999999999 544
No 116
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=22.05 E-value=63 Score=28.32 Aligned_cols=20 Identities=10% Similarity=0.210 Sum_probs=16.2
Q ss_pred CCCCCCcHHHHHHHHHH-hCC
Q 009898 158 QGVRGLGPESACQIVKS-VGD 177 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~-~g~ 177 (523)
..|||||+.+|..|..- +.+
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCC
Confidence 47999999999999964 444
No 117
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=21.03 E-value=72 Score=31.22 Aligned_cols=20 Identities=25% Similarity=0.795 Sum_probs=18.0
Q ss_pred CCCCCCcHHHHHHHHHHhCC
Q 009898 158 QGVRGLGPESACQIVKSVGD 177 (523)
Q Consensus 158 pGVpGIG~ktA~kLl~~~g~ 177 (523)
.|-||+|..|++++|+.+|-
T Consensus 6 TGTPGvGKTT~~~~L~~lg~ 25 (180)
T COG1936 6 TGTPGVGKTTVCKLLRELGY 25 (180)
T ss_pred eCCCCCchHHHHHHHHHhCC
Confidence 48999999999999997775
No 118
>TIGR02766 crypt_chrom_pln cryptochrome, plant family. At least five major families of cryptochomes and photolyases share FAD cofactor binding, sequence homology, and the ability to react to short wavelengths of visible light. Photolysases are responsible for light-dependent DNA repair by removal of two types of uv-induced DNA dimerizations. Cryptochromes have other functions, often regulatory and often largely unknown, which may include circadian clock entrainment and control of development. Members of this subfamily are known so far only in plants; they may show some photolyase activity in vitro but appear mostly to be regulatory proteins that respond to blue light.
Probab=20.93 E-value=1.6e+02 Score=32.34 Aligned_cols=11 Identities=0% Similarity=-0.254 Sum_probs=9.2
Q ss_pred CcEEEEEEcCC
Q 009898 8 SSALLRSLNGS 18 (523)
Q Consensus 8 gI~PVFVFDG~ 18 (523)
.|.||||||..
T Consensus 24 ~vlpvyi~dp~ 34 (475)
T TIGR02766 24 PVIPVFVWAPE 34 (475)
T ss_pred CEEEEEEechH
Confidence 58899999964
No 119
>PF00885 DMRL_synthase: 6,7-dimethyl-8-ribityllumazine synthase; InterPro: IPR002180 6,7-dimethyl-8-ribityllumazine synthase (riboflavin synthase) catalyses the biosynthesis of riboflavin according to the reaction: 2 6,7-dimethyl-8-(1-D-ribityl)lumazine = riboflavin + 4-(1-D-ribitylamino)-5-amino-2,6-dihydroxypyrimidine. The biosynthesis of one riboflavin molecule requires one molecule of GTP and two molecules of ribulose 5-phosphate as substrates. The final step in the biosynthesis of the vitamin involves the dismutation of 6,7-dimethyl-8-ribityllumazine catalyzed by riboflavin synthase. The second product, 5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione, is recycled in the biosynthetic pathway by 6,7-dimethyl-8-ribityllumazine synthase []. N-[2,4-dioxo-6-d-ribitylamino-1,2,3,4-tetrahydropyrimidin-5-yl]oxalamic acid derivatives inhibit riboflavin synthase []. This family includes the beta chain of 6,7-dimethyl-8-ribityllumazine synthase 2.5.1.9 from EC. The family also includes a subfamily of distant archaebacterial proteins that may also have the same function for example O28856 from SWISSPROT.; GO: 0009231 riboflavin biosynthetic process, 0009349 riboflavin synthase complex; PDB: 2O6H_D 1C41_C 2OBX_H 1VSX_H 1VSW_3 3JV8_C 3MK3_r 3NQ4_G 2A58_A 2A57_D ....
Probab=20.26 E-value=1.8e+02 Score=27.25 Aligned_cols=45 Identities=13% Similarity=-0.000 Sum_probs=36.8
Q ss_pred ccHHHHHHHHHHHHHhCC-----CcccCcc--hHHHHHHHHHHcCCeeEEec
Q 009898 57 EFSCMIKEAKALGLSLGV-----PCLEGVE--EAEAQCALLNLESLCDGCFS 101 (523)
Q Consensus 57 ~~~~~i~~ik~lL~~~GI-----p~i~AP~--EAEAqcA~L~~~G~vdaViS 101 (523)
++..+++.+.+.|...|+ ..+..|| |-=..+..|.+.|-.|+|+.
T Consensus 17 i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~ 68 (144)
T PF00885_consen 17 ITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIA 68 (144)
T ss_dssp HHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEE
T ss_pred HHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEE
Confidence 456778889999999987 6667786 77777888999999999987
Done!