Query 011802
Match_columns 477
No_of_seqs 308 out of 1327
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 05:23:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011802.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011802hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00600 rad2 DNA excision re 100.0 1.1E-42 2.3E-47 392.5 20.2 225 5-247 763-989 (1034)
2 KOG2520 5'-3' exonuclease [Rep 100.0 3.4E-41 7.3E-46 370.5 16.2 232 4-251 456-687 (815)
3 PTZ00217 flap endonuclease-1; 100.0 4.4E-40 9.5E-45 342.9 19.2 198 7-245 131-332 (393)
4 PRK03980 flap endonuclease-1; 100.0 2.8E-39 6.1E-44 325.2 17.8 191 9-248 78-281 (292)
5 cd00128 XPG Xeroderma pigmento 100.0 4.5E-37 9.8E-42 310.9 18.9 192 7-239 121-313 (316)
6 TIGR03674 fen_arch flap struct 100.0 9.2E-36 2E-40 305.2 17.8 190 9-246 125-326 (338)
7 KOG2519 5'-3' exonuclease [Rep 100.0 1.1E-33 2.5E-38 293.7 12.6 282 11-336 129-420 (449)
8 smart00475 53EXOc 5'-3' exonuc 99.9 1.1E-26 2.3E-31 230.7 16.4 136 6-141 76-219 (259)
9 cd00008 53EXOc 5'-3' exonuclea 99.9 6.9E-25 1.5E-29 215.2 16.9 132 6-142 77-217 (240)
10 PRK14976 5'-3' exonuclease; Pr 99.9 1.3E-24 2.7E-29 218.2 17.3 136 5-141 81-224 (281)
11 PF00867 XPG_I: XPG I-region; 99.9 9.7E-25 2.1E-29 185.4 7.4 86 24-109 1-94 (94)
12 PRK09482 flap endonuclease-lik 99.9 1.5E-23 3.2E-28 207.9 16.3 141 5-150 75-224 (256)
13 KOG2518 5'-3' exonuclease [Rep 99.9 4.3E-24 9.4E-29 224.9 10.3 126 6-133 120-249 (556)
14 TIGR00593 pola DNA polymerase 99.9 2E-22 4.3E-27 228.4 15.6 134 7-141 77-218 (887)
15 PRK05755 DNA polymerase I; Pro 99.9 4.5E-22 9.7E-27 226.1 17.9 135 6-141 78-220 (880)
16 COG0258 Exo 5'-3' exonuclease 99.9 2.1E-21 4.5E-26 196.7 12.3 131 8-139 90-229 (310)
17 smart00484 XPGI Xeroderma pigm 99.7 3.3E-18 7.1E-23 140.0 8.1 70 25-94 2-73 (73)
18 PHA00439 exonuclease 99.6 1.7E-14 3.6E-19 145.2 11.1 107 8-128 92-206 (286)
19 cd00080 HhH2_motif Helix-hairp 99.4 1.9E-13 4.1E-18 112.2 5.5 50 91-140 2-54 (75)
20 PHA02567 rnh RnaseH; Provision 99.1 2.1E-10 4.5E-15 116.5 11.1 99 8-116 93-207 (304)
21 PF01367 5_3_exonuc: 5'-3' exo 99.1 3E-12 6.4E-17 111.1 -5.3 49 94-142 1-52 (101)
22 smart00279 HhH2 Helix-hairpin- 99.0 6E-10 1.3E-14 79.6 3.9 33 96-129 1-36 (36)
23 PF02739 5_3_exonuc_N: 5'-3' e 98.6 3.8E-08 8.3E-13 92.5 4.7 83 8-92 80-169 (169)
24 PF12813 XPG_I_2: XPG domain c 98.4 1.6E-06 3.4E-11 86.3 10.1 87 15-104 5-107 (246)
25 PF00385 Chromo: Chromo (CHRro 97.0 0.0011 2.3E-08 50.6 4.6 50 277-326 3-55 (55)
26 smart00298 CHROMO Chromatin or 95.9 0.012 2.6E-07 44.1 4.2 50 277-327 4-54 (55)
27 cd00024 CHROMO Chromatin organ 95.4 0.015 3.3E-07 43.6 3.2 47 278-325 6-54 (55)
28 COG5366 Protein involved in pr 94.1 0.023 4.9E-07 61.1 1.5 112 19-131 134-247 (531)
29 PF12826 HHH_2: Helix-hairpin- 92.2 0.11 2.5E-06 41.3 2.5 21 113-133 7-27 (64)
30 KOG1911 Heterochromatin-associ 91.8 0.12 2.7E-06 52.0 2.9 55 276-331 50-104 (270)
31 PRK00116 ruvA Holliday junctio 90.0 0.36 7.9E-06 46.4 4.1 30 113-142 77-106 (192)
32 PRK14602 ruvA Holliday junctio 89.7 0.55 1.2E-05 45.7 5.1 67 78-150 44-115 (203)
33 KOG2748 Uncharacterized conser 89.5 0.18 3.9E-06 52.6 1.7 61 277-339 13-76 (369)
34 PRK14605 ruvA Holliday junctio 88.4 0.52 1.1E-05 45.6 3.9 64 78-147 43-111 (194)
35 PRK14606 ruvA Holliday junctio 88.2 0.72 1.6E-05 44.5 4.7 67 78-150 43-114 (188)
36 TIGR00084 ruvA Holliday juncti 86.5 0.68 1.5E-05 44.7 3.5 64 78-147 42-110 (191)
37 PRK14603 ruvA Holliday junctio 86.2 0.63 1.4E-05 45.2 3.1 67 78-150 42-113 (197)
38 PRK14601 ruvA Holliday junctio 84.9 0.82 1.8E-05 44.0 3.2 67 78-150 43-114 (183)
39 PF00633 HHH: Helix-hairpin-he 84.8 0.72 1.6E-05 31.8 2.0 15 113-127 15-29 (30)
40 PRK13901 ruvA Holliday junctio 84.5 0.9 1.9E-05 44.3 3.3 55 90-150 58-113 (196)
41 PRK14604 ruvA Holliday junctio 83.9 0.92 2E-05 44.0 3.1 56 89-150 58-114 (195)
42 PF04599 Pox_G5: Poxvirus G5 p 83.8 1.5 3.3E-05 47.1 4.9 113 19-138 148-272 (425)
43 PRK14600 ruvA Holliday junctio 82.3 0.82 1.8E-05 44.1 2.1 55 86-146 55-110 (186)
44 PHA03065 Hypothetical protein; 81.4 2.7 5.8E-05 45.3 5.6 107 20-138 151-274 (438)
45 COG0632 RuvA Holliday junction 81.0 4 8.6E-05 40.0 6.2 62 83-150 52-114 (201)
46 PF10391 DNA_pol_lambd_f: Fing 76.7 3.2 6.8E-05 32.1 3.3 22 112-133 5-27 (52)
47 smart00278 HhH1 Helix-hairpin- 74.9 2.3 5E-05 27.9 1.8 18 111-128 3-20 (26)
48 PRK14601 ruvA Holliday junctio 72.4 2.6 5.7E-05 40.6 2.3 36 93-129 92-128 (183)
49 PRK14671 uvrC excinuclease ABC 70.7 3.5 7.7E-05 46.6 3.2 25 112-136 572-596 (621)
50 PRK13901 ruvA Holliday junctio 69.0 3.3 7.2E-05 40.4 2.2 35 94-129 92-127 (196)
51 PRK14604 ruvA Holliday junctio 68.4 3.5 7.6E-05 40.0 2.3 35 94-129 93-128 (195)
52 PRK14606 ruvA Holliday junctio 67.7 3.7 8.1E-05 39.6 2.3 36 93-129 92-128 (188)
53 PRK14669 uvrC excinuclease ABC 67.5 4.4 9.6E-05 45.9 3.1 22 112-133 555-576 (624)
54 PRK14603 ruvA Holliday junctio 67.2 3.7 8.1E-05 39.9 2.2 36 94-130 92-128 (197)
55 PRK14667 uvrC excinuclease ABC 67.0 5.1 0.00011 44.9 3.5 23 111-133 516-538 (567)
56 PRK14600 ruvA Holliday junctio 66.8 4.7 0.0001 38.9 2.8 34 94-129 93-127 (186)
57 TIGR00194 uvrC excinuclease AB 65.9 5 0.00011 45.1 3.1 22 112-133 544-565 (574)
58 PRK14670 uvrC excinuclease ABC 64.2 6.3 0.00014 44.3 3.5 24 110-133 515-538 (574)
59 COG5049 XRN1 5'-3' exonuclease 64.1 17 0.00037 41.8 6.8 86 33-118 186-327 (953)
60 PF14520 HHH_5: Helix-hairpin- 64.0 5.2 0.00011 31.1 2.0 21 113-133 9-30 (60)
61 COG0632 RuvA Holliday junction 63.5 7 0.00015 38.3 3.3 36 94-129 93-128 (201)
62 PRK14602 ruvA Holliday junctio 62.9 5.1 0.00011 39.1 2.2 35 94-129 94-129 (203)
63 PF02371 Transposase_20: Trans 61.8 6.2 0.00013 32.9 2.3 24 110-133 3-26 (87)
64 PRK14672 uvrC excinuclease ABC 56.5 10 0.00022 43.5 3.5 23 111-133 610-632 (691)
65 PF11798 IMS_HHH: IMS family H 54.0 9.1 0.0002 26.6 1.7 14 113-126 15-28 (32)
66 PRK00558 uvrC excinuclease ABC 50.6 14 0.0003 41.8 3.3 22 112-133 546-567 (598)
67 cd00034 ChSh Chromo Shadow Dom 50.5 48 0.001 25.7 5.4 37 288-327 14-50 (54)
68 PRK12766 50S ribosomal protein 50.4 15 0.00032 36.9 3.1 23 111-133 5-28 (232)
69 TIGR01448 recD_rel helicase, p 47.7 22 0.00047 41.0 4.4 35 92-132 73-107 (720)
70 PRK14605 ruvA Holliday junctio 47.2 12 0.00025 36.3 1.9 36 94-130 93-129 (194)
71 COG0353 RecR Recombinational D 46.8 18 0.00038 35.5 3.0 17 112-128 15-31 (198)
72 TIGR00084 ruvA Holliday juncti 46.1 16 0.00036 35.2 2.7 17 111-127 109-125 (191)
73 PRK14668 uvrC excinuclease ABC 45.8 16 0.00035 41.1 3.0 23 111-133 527-549 (577)
74 TIGR00575 dnlj DNA ligase, NAD 42.3 22 0.00048 40.6 3.4 21 113-133 502-522 (652)
75 PRK14351 ligA NAD-dependent DN 42.3 23 0.00049 40.8 3.4 21 113-133 532-552 (689)
76 PRK00076 recR recombination pr 42.2 38 0.00081 33.2 4.4 17 112-128 14-30 (196)
77 PRK14666 uvrC excinuclease ABC 41.5 23 0.00051 40.7 3.3 22 112-133 640-661 (694)
78 TIGR00615 recR recombination p 41.2 40 0.00088 33.0 4.5 17 112-128 14-30 (195)
79 TIGR01259 comE comEA protein. 40.8 33 0.00072 30.6 3.6 17 113-129 72-88 (120)
80 smart00300 ChSh Chromo Shadow 40.5 47 0.001 26.3 4.0 39 286-327 18-56 (61)
81 COG0322 UvrC Nuclease subunit 39.9 25 0.00054 39.7 3.2 22 112-133 533-554 (581)
82 TIGR00305 probable toxin-antit 39.7 24 0.00053 30.4 2.5 28 35-62 86-113 (114)
83 PF14520 HHH_5: Helix-hairpin- 38.7 27 0.00059 27.0 2.4 19 111-129 40-58 (60)
84 PF01393 Chromo_shadow: Chromo 38.0 91 0.002 24.6 5.2 46 279-326 7-52 (58)
85 COG1555 ComEA DNA uptake prote 37.3 45 0.00098 31.1 4.0 15 113-127 101-115 (149)
86 PRK13844 recombination protein 35.9 57 0.0012 32.1 4.6 17 112-128 18-34 (200)
87 TIGR00114 lumazine-synth 6,7-d 34.2 1.1E+02 0.0024 28.2 6.0 46 10-55 13-65 (138)
88 KOG2044 5'-3' exonuclease HKE1 32.9 47 0.001 38.9 3.9 92 27-118 190-351 (931)
89 COG1948 MUS81 ERCC4-type nucle 32.6 39 0.00084 34.4 3.0 21 113-133 186-206 (254)
90 TIGR00596 rad1 DNA repair prot 31.5 24 0.00051 41.5 1.4 24 110-133 758-781 (814)
91 PRK07956 ligA NAD-dependent DN 30.2 41 0.00089 38.6 3.0 13 19-31 241-253 (665)
92 PRK02515 psbU photosystem II c 29.6 58 0.0013 30.1 3.3 27 113-139 65-93 (132)
93 COG1453 Predicted oxidoreducta 28.8 1.9E+02 0.0042 31.2 7.4 108 9-142 29-143 (391)
94 smart00483 POLXc DNA polymeras 28.6 37 0.0008 35.5 2.1 17 113-130 93-109 (334)
95 PRK13766 Hef nuclease; Provisi 28.2 49 0.0011 38.0 3.2 23 111-133 717-739 (773)
96 PF00885 DMRL_synthase: 6,7-di 28.0 1.5E+02 0.0032 27.5 5.8 46 10-55 16-68 (144)
97 PF14716 HHH_8: Helix-hairpin- 26.6 45 0.00097 26.6 1.8 16 111-126 49-64 (68)
98 PF01399 PCI: PCI domain; Int 26.0 1.3E+02 0.0028 24.6 4.6 40 21-64 65-104 (105)
99 PF03159 XRN_N: XRN 5'-3' exon 25.9 32 0.00069 34.5 1.0 38 27-64 172-222 (237)
100 cd00141 NT_POLXc Nucleotidyltr 25.8 46 0.001 34.3 2.2 17 113-130 89-105 (307)
101 COG0258 Exo 5'-3' exonuclease 25.7 31 0.00068 35.4 1.0 35 8-43 98-132 (310)
102 PRK12419 riboflavin synthase s 25.7 1.5E+02 0.0033 28.1 5.5 46 10-55 23-75 (158)
103 TIGR00426 competence protein C 25.3 58 0.0013 25.8 2.2 15 114-128 22-36 (69)
104 COG4277 Predicted DNA-binding 24.3 95 0.002 32.8 4.1 48 81-128 276-349 (404)
105 COG0272 Lig NAD-dependent DNA 23.1 60 0.0013 37.3 2.6 21 113-133 515-535 (667)
106 TIGR00290 MJ0570_dom MJ0570-re 22.4 1.7E+02 0.0038 29.0 5.5 42 16-58 47-94 (223)
107 TIGR00289 conserved hypothetic 22.4 1.9E+02 0.004 28.8 5.6 43 16-59 47-95 (222)
108 COG1936 Predicted nucleotide k 21.7 68 0.0015 31.1 2.3 21 112-132 6-26 (180)
109 PLN02404 6,7-dimethyl-8-ribity 21.6 2.1E+02 0.0046 26.6 5.5 46 10-55 20-72 (141)
110 PF11731 Cdd1: Pathogenicity l 21.1 68 0.0015 27.9 2.0 20 112-131 15-35 (93)
111 PRK01229 N-glycosylase/DNA lya 20.9 68 0.0015 31.6 2.2 16 113-128 123-138 (208)
112 PRK00116 ruvA Holliday junctio 20.7 69 0.0015 30.8 2.2 20 112-131 111-130 (192)
113 PRK00061 ribH 6,7-dimethyl-8-r 20.2 2.2E+02 0.0047 26.8 5.3 46 10-55 25-77 (154)
No 1
>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=392.49 Aligned_cols=225 Identities=32% Similarity=0.520 Sum_probs=184.5
Q ss_pred ccCCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEEe
Q 011802 5 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYE 84 (477)
Q Consensus 5 ~Rn~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y~ 84 (477)
+|..-.++..|+..|++||++||||||+||||||||||+|++.|+||+|+|+|+|+|+||+++||||++. .+.+|++|.
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 5777889999999999999999999999999999999999999999999999999999999999999875 457899999
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCC--HHHHHHHHhcChhHHHHhhhhcccCcccccC
Q 011802 85 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD--NVVLQRIASEGLSFVKRAKNSKKEGWSFKCN 162 (477)
Q Consensus 85 ~~~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs--~~iL~~i~~~~~~~~~k~~~~~k~~~~~~c~ 162 (477)
.++|.+.+||++++||+||+|+||||++||+|||+++|++||++||+ ++-|..|.. |+....... ....
T Consensus 842 ~~~i~~~lglt~~qli~laiL~G~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~----w~~~~~~~~-~~~~---- 912 (1034)
T TIGR00600 842 YVDIHNQLGLDRNKLINLAYLLGSDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKE----WWHEAQKDK-KKRE---- 912 (1034)
T ss_pred HHHHHHHhCCCHHHHHHHHHeeCCCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHH----HHHHhhhcc-cccc----
Confidence 99999999999999999999999999999999999999999999996 555555554 333221100 0000
Q ss_pred CccccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccceeeh
Q 011802 163 NKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILP 242 (477)
Q Consensus 163 ~~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP 242 (477)
+...... ....+...+|.+||+..|+++|++|.|+.+...+.|+. .+..+|+.||.++|+|+..++++.|.|
T Consensus 913 ~~~~~~~---~~~~~~~~lp~~FP~~~V~~~yl~P~V~~~~~~f~W~~-----PD~e~L~~Fl~~~~gws~eRv~~~l~p 984 (1034)
T TIGR00600 913 NPNDTKV---KKKLRLLQLTPGFPNPAVADAYLRPVVDDSKGSFLWGK-----PDLDKIREFCQRYFGWNREKTDEVLLP 984 (1034)
T ss_pred ccchhhh---hhcccccccCCCCCcHHHHHHhcCCCCCCCcCCCCCCC-----CCHHHHHHHHHHccCCCHHHHHHHHHH
Confidence 0000000 00112345899999999999999999997655554432 267899999999999999999999999
Q ss_pred hhhHH
Q 011802 243 KIAER 247 (477)
Q Consensus 243 ll~e~ 247 (477)
++..+
T Consensus 985 likk~ 989 (1034)
T TIGR00600 985 VLKKL 989 (1034)
T ss_pred HHHHH
Confidence 99733
No 2
>KOG2520 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=3.4e-41 Score=370.53 Aligned_cols=232 Identities=33% Similarity=0.557 Sum_probs=192.1
Q ss_pred cccCCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEE
Q 011802 4 LRRNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCY 83 (477)
Q Consensus 4 ~~Rn~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y 83 (477)
-.|...+++..|+.+||++|+.||||||+||+|||||||.|.+.++||||||+|||+|+||+.+||||+|. ++++|+.|
T Consensus 456 ~~r~~~evt~~m~~e~QElL~~fGIPyI~APmEAEAQCa~Le~~~LvdGiITDDSDV~LFGg~~VYrn~F~-knk~ve~y 534 (815)
T KOG2520|consen 456 QSRGADEVTSDMFKELQELLRLFGIPYIIAPMEAEAQCAFLEQLNLVDGIITDDSDVFLFGGTRVYRNFFN-KNKYVEKY 534 (815)
T ss_pred HhccCchhHHHHHHHHHHHHHHcCCceecccccHHHHHHHHHHcCCcceeecccccceeeccchhhHHHhh-cCccceee
Confidence 35888899999999999999999999999999999999999999999999999999999999999999997 45889999
Q ss_pred eHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhhhhcccCcccccCC
Q 011802 84 EMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAKNSKKEGWSFKCNN 163 (477)
Q Consensus 84 ~~~~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~~~~k~~~~~~c~~ 163 (477)
.+.+|+..||++|..||-+|.|+||||+.||+||||++|+++|.+|++.+-|..|.+ |..... ....... +
T Consensus 535 ~~~di~kel~l~R~~lI~lA~LlGsDYt~Gl~giGpV~AlEil~Efp~~~~l~~f~~----w~~~~~-~~~~~~~----s 605 (815)
T KOG2520|consen 535 QLDDIEKELGLDRPNLISLAQLLGSDYTEGLKGIGPVSALEILAEFPGDENLLKFKK----WVQQTG-PADKEVG----S 605 (815)
T ss_pred ehHHHHHHHccCchhhHHHHHhcccccccCCCcccchHHHHHHHHcCCcchhHHHHH----HHHHhC-ccccccc----c
Confidence 999999999999999999999999999999999999999999999998755777766 333111 0000000 0
Q ss_pred ccccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccceeehh
Q 011802 164 KEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPK 243 (477)
Q Consensus 164 ~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPl 243 (477)
.......+ .+.+.+..+|.+||.+.|+++||+|.|+.....+.|+. .+.+.||+||++.|+|+..++++.++|+
T Consensus 606 ~~~~~lrk-kl~n~~~~l~~~fP~~~v~~AYLrP~VD~sk~~f~WG~-----pdl~~lRef~~~~fgW~~~kT~~~l~p~ 679 (815)
T KOG2520|consen 606 TQQKMLRK-KLKNPKIILPSDFPNPNVIEAYLRPEVDDSKEKFRWGK-----PDLDILREFMKRLFGWPDEKTDEELIPV 679 (815)
T ss_pred HHHHHHHH-HhcCcccccCcCCCchhHHHHhhCCccCCCcccccCCC-----CCHHHHHHHHHHHcCCCccccchhhhhh
Confidence 00000000 11222356888999999999999999998766666653 2567899999999999999999999999
Q ss_pred hhHHHHhh
Q 011802 244 IAERDLRR 251 (477)
Q Consensus 244 l~e~~lr~ 251 (477)
+++...+.
T Consensus 680 ~~~~~~~~ 687 (815)
T KOG2520|consen 680 IKRLEKKK 687 (815)
T ss_pred HHHHHHHh
Confidence 98887765
No 3
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=4.4e-40 Score=342.88 Aligned_cols=198 Identities=21% Similarity=0.342 Sum_probs=171.3
Q ss_pred CCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCC--CceEEEEe
Q 011802 7 NMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGE--RGYVVCYE 84 (477)
Q Consensus 7 n~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~--~~~v~~y~ 84 (477)
+.-..+.+|+..++++|++|||||++||||||||||+|++.|+||+|+|+|+|+|+||+++++++++..+ ...+++|+
T Consensus 131 r~~~vt~~~~~~~~~lL~~~Gip~i~AP~EAdaq~A~L~~~g~v~~ViS~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~ 210 (393)
T PTZ00217 131 RTVRVTKEQNEDAKKLLRLMGIPVIEAPCEAEAQCAELVKKGKVYAVATEDMDALTFGTPVLLRNLNFSEAKKRPIQEIN 210 (393)
T ss_pred hcccCCHHHHHHHHHHHHHcCCceEECCcCHHHHHHHHHHCCCeEEEeCCCcCeeecCCcEEEEcccccccCCCCeEEEE
Confidence 3445678999999999999999999999999999999999999999999999999999999999987532 24588999
Q ss_pred HHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcChhHHHHhhhhcccCcccccCC
Q 011802 85 MDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEGWSFKCNN 163 (477)
Q Consensus 85 ~~~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~~~~~~~k~~~~~k~~~~~~c~~ 163 (477)
.+.+.+.+|++++||+|+|+|+||||+|||||||+|+|++||++||++ +++++++..
T Consensus 211 ~~~v~~~~gl~~~q~id~~iL~G~Dy~pgi~GIG~ktA~~Li~~~gsle~il~~~~~~---------------------- 268 (393)
T PTZ00217 211 LSTVLEELGLSMDQFIDLCILCGCDYCDTIKGIGPKTAYKLIKKYKSIEEILEHLDKT---------------------- 268 (393)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHHHHhc----------------------
Confidence 999999999999999999999999999999999999999999999997 477776531
Q ss_pred ccccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCC-hHHHHHHhhhcccChHHHHHHHHHhcCCCcccccceeeh
Q 011802 164 KEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSAD-SEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILP 242 (477)
Q Consensus 164 ~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d-~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llP 242 (477)
+..+|++||+.++.+.|++|.|..+. .++.| .+.+..+|++||.+.++|+..++++.|-+
T Consensus 269 --------------k~~~p~~~~~~~~~~~f~~p~V~~~~~~~l~w-----~~pD~~~l~~fl~~e~~f~~~rv~~~i~r 329 (393)
T PTZ00217 269 --------------KYPVPENFDYKEARELFLNPEVTPAEEIDLKW-----NEPDEEGLKKFLVKEKNFNEERVEKYIER 329 (393)
T ss_pred --------------CCCCCCCCChHHHHHHhcCCCcCCCCCCCCCC-----CCCCHHHHHHHHHhccCCCHHHHHHHHHH
Confidence 13478899999999999999998643 12222 13467899999999999999999998766
Q ss_pred hhh
Q 011802 243 KIA 245 (477)
Q Consensus 243 ll~ 245 (477)
+.+
T Consensus 330 l~~ 332 (393)
T PTZ00217 330 LKK 332 (393)
T ss_pred HHH
Confidence 544
No 4
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2.8e-39 Score=325.22 Aligned_cols=191 Identities=23% Similarity=0.361 Sum_probs=164.1
Q ss_pred cchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCC-----------
Q 011802 9 GSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER----------- 77 (477)
Q Consensus 9 ~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~----------- 77 (477)
-..+.+|++.++++|++|||||++||||||||||+|++.|+||+|+|+|+|+|+||+++|+++++..+.
T Consensus 78 ~~vt~~~~~~~k~lL~~~GIp~i~AP~EAEAq~A~L~~~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~~~~~ 157 (292)
T PRK03980 78 SRLTDEIVEDSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNVYVE 157 (292)
T ss_pred ccCCHHHHHHHHHHHHHCCCCEEecCchHHHHHHHHHHCCCeEEEecCCcCeeeecCCEEEEeecccccccCcccccccc
Confidence 346788999999999999999999999999999999999999999999999999999999999876431
Q ss_pred ceEEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHH-HHHHHHhcChhHHHHhhhhcccC
Q 011802 78 GYVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEG 156 (477)
Q Consensus 78 ~~v~~y~~~~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~-iL~~i~~~~~~~~~k~~~~~k~~ 156 (477)
..+++|+.+.+.+++|++++||+|+|+|+||||+|||||||+|+|++||++||+++ +++++.
T Consensus 158 ~~~e~~~~~~vl~~lgl~~~q~id~~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~----------------- 220 (292)
T PRK03980 158 VKPELIELEEVLKELGITREQLIDIAILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERG----------------- 220 (292)
T ss_pred ccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhcc-----------------
Confidence 14568999999999999999999999999999999999999999999999999974 665211
Q ss_pred cccccCCccccccccccccCCcCCCCCCCCc-HHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCccc
Q 011802 157 WSFKCNNKEESLNQEINVNGTDHSLQRETPF-SQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEK 235 (477)
Q Consensus 157 ~~~~c~~~~~~~~~e~~~~~~~~~ip~~FP~-~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~ 235 (477)
.+||. .+|++.|++|.|.. +.++.|+ ..+..+|++|+.+..+|+.++
T Consensus 221 --------------------------~~~~~~~~~r~~f~~p~v~~-~~~~~~~-----~pd~~~l~~fl~~e~~f~~~r 268 (292)
T PRK03980 221 --------------------------FEIENYDEIREFFLNPPVTD-DYELKWK-----EPDKEGIIEFLVEEHDFSEER 268 (292)
T ss_pred --------------------------CCCCCHHHHHHHhcCCCCCC-CCCccCC-----CCCHHHHHHHHhccCCCCHHH
Confidence 13444 89999999999985 3333332 236789999999999999999
Q ss_pred ccceeehhhhHHH
Q 011802 236 TDEYILPKIAERD 248 (477)
Q Consensus 236 ~~e~llPll~e~~ 248 (477)
+++.+-++.+.+.
T Consensus 269 v~~~~~~l~~~~~ 281 (292)
T PRK03980 269 VKKALERLEKAVK 281 (292)
T ss_pred HHHHHHHHHHHhc
Confidence 9999888876543
No 5
>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=4.5e-37 Score=310.88 Aligned_cols=192 Identities=29% Similarity=0.442 Sum_probs=162.2
Q ss_pred CCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEEeHH
Q 011802 7 NMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMD 86 (477)
Q Consensus 7 n~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y~~~ 86 (477)
+..+.+..|+..++++|+.|||||++||+|||||||+|++.|.||+|+|+|+|+|+||+++|+++++..+...+++|+.+
T Consensus 121 ~~~~~~~~~~~~~~~lL~~~gi~~i~ap~EAdaq~a~l~~~g~v~~i~S~DsD~l~fg~~~vi~~~~~~~~~~~~~~~~~ 200 (316)
T cd00128 121 RAVRVTPQMIEEAKELLRLMGIPYIVAPYEAEAQCAYLAKKGLVDAIITEDSDLLLFGAPRVYRNLFDSGAKPVEEIDLE 200 (316)
T ss_pred ccCcCCHHHHHHHHHHHHHcCCCEEECCcCHHHHHHHHHhCCCeeEEEecCCCeeeecCceEEEecccCCCCceEEEEHH
Confidence 33456789999999999999999999999999999999999999999999999999999999999875321478899999
Q ss_pred HHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcChhHHHHhhhhcccCcccccCCcc
Q 011802 87 DIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEGWSFKCNNKE 165 (477)
Q Consensus 87 ~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~~~~~~~k~~~~~k~~~~~~c~~~~ 165 (477)
.+.+.+|++++||+|+|+|+||||+|||||||+|||++||++||++ .+++++...
T Consensus 201 ~~~~~lgl~~~q~id~~~L~G~Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l~~~------------------------ 256 (316)
T cd00128 201 KILKELGLTREKLIDLAILLGCDYTEGIPGIGPVTALKLIKKYGDIEKDIERLKKK------------------------ 256 (316)
T ss_pred HHHHHcCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCChHHHHHHHHHh------------------------
Confidence 9999999999999999999999999999999999999999999996 366665430
Q ss_pred ccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccccce
Q 011802 166 ESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEY 239 (477)
Q Consensus 166 ~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~ 239 (477)
...+|.+||...+.++|.+|.++.......|. ..+..+|+.|+...++|+.+++...
T Consensus 257 ------------~~~~~~~~~~~~~~~~f~~p~~~~~~~~~~~~-----~p~~~~l~~~~~~~~~~~~~rv~~~ 313 (316)
T cd00128 257 ------------LYRSPEDFPLKEAREFFLNPEVTDDFIDLRWR-----DPDEEGIIEFLCKEHGFNEDRVLKP 313 (316)
T ss_pred ------------CccCCCcCChHHHHHHHcCCCCCCCCCceeec-----CCCHHHHHHHccCCCCCCHHHHHhh
Confidence 12345689999999999999987542222221 2256789999999999997665443
No 6
>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=9.2e-36 Score=305.17 Aligned_cols=190 Identities=24% Similarity=0.390 Sum_probs=161.1
Q ss_pred cchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCc----------
Q 011802 9 GSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERG---------- 78 (477)
Q Consensus 9 ~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~---------- 78 (477)
...+.+|++.++++|++|||||++||||||||||+|++.|.||+|+|+|+|+|+||+++|+++++..+..
T Consensus 125 ~~~~~~~~~~~k~lL~~~Gip~i~AP~EAeaq~a~L~~~g~vd~v~S~D~D~l~fg~~~vi~~~~~~~~~~~~~~~~~~~ 204 (338)
T TIGR03674 125 SRLTSEIVESSKKLLDLMGIPYVQAPSEGEAQAAYMAKKGDVDYVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKNIYVE 204 (338)
T ss_pred CCCCHHHHHHHHHHHHHcCCeEEECCccHHHHHHHHHHCCCeeEEecCCcCeeeecCCEEEEecccccccCCCccccccc
Confidence 4456789999999999999999999999999999999999999999999999999999999998764311
Q ss_pred -eEEEEeHHHHHHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcChhHHHHhhhhcccC
Q 011802 79 -YVVCYEMDDIERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAKNSKKEG 156 (477)
Q Consensus 79 -~v~~y~~~~I~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~~~~~~~k~~~~~k~~ 156 (477)
++++|+.+.+.+++|++++||+|+|+|+||||+|||||||+|||++||++||++ +++++++.
T Consensus 205 ~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~dyn~Gv~GIG~ktA~kli~~~gsie~il~~~~~---------------- 268 (338)
T TIGR03674 205 VKPELIELEEVLSELGITREQLIDIAILVGTDYNEGVKGIGPKTALKLIKEHGDLEKVLKARGE---------------- 268 (338)
T ss_pred ccceeeeHHHHHHHhCCCHHHHHHHHHhcCCCCCCCCCCccHHHHHHHHHHcCCHHHHHHhhcC----------------
Confidence 456799999999999999999999999999999999999999999999999997 47766421
Q ss_pred cccccCCccccccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCChHHHHHHhhhcccChHHHHHHHHHhcCCCcccc
Q 011802 157 WSFKCNNKEESLNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADSEAVHRVLAQHLFQHARLHQVCAQFFQWPPEKT 236 (477)
Q Consensus 157 ~~~~c~~~~~~~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~ 236 (477)
.+. +..++++.|++|.|..+ .+..| .+.+.++|++|+.+.++|+.+++
T Consensus 269 -----------------------~~~---~~~~~~~~f~~~~v~~~-~~~~~-----~~pd~e~l~~fl~~e~~~~~~rv 316 (338)
T TIGR03674 269 -----------------------DIE---NYDEIREFFLNPPVTDD-YELKW-----RKPDKEGIIEFLCDEHDFSEDRV 316 (338)
T ss_pred -----------------------CCC---CHHHHHHHhCCCCCCCC-CCccC-----CCCCHHHHHHHHhhcCCCCHHHH
Confidence 011 23789999999988753 22222 23467899999999999999999
Q ss_pred cceeehhhhH
Q 011802 237 DEYILPKIAE 246 (477)
Q Consensus 237 ~e~llPll~e 246 (477)
+..+-++.+.
T Consensus 317 ~~~~~~l~~~ 326 (338)
T TIGR03674 317 ERALERLEAA 326 (338)
T ss_pred HHHHHHHHHh
Confidence 8888887544
No 7
>KOG2519 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=100.00 E-value=1.1e-33 Score=293.66 Aligned_cols=282 Identities=24% Similarity=0.283 Sum_probs=218.0
Q ss_pred hhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCC--CCceEEEEeHHHH
Q 011802 11 EFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLG--ERGYVVCYEMDDI 88 (477)
Q Consensus 11 ~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~--~~~~v~~y~~~~I 88 (477)
.+++...+|++||..|||||++||+|||||||+|+++|.|++++|+|+|+|.||++.++|++..+ .+..|.+|+++.|
T Consensus 129 vtk~~~dEak~LL~lmGIp~i~ap~EAEAqCA~Lnk~g~V~~~at~DsD~l~fg~~~~lr~l~~s~~~~~pv~e~~~~~i 208 (449)
T KOG2519|consen 129 VTKQHNDEAKRLLSLMGIPVLDAPGEAEAQCAALNKAGKVYAVATEDSDALTFGAPVKLRHLIHSLASGLPVSEYDMSRI 208 (449)
T ss_pred hcchhhHHHHHHHHHcCCeeecCCchHHHHHHHHhhcCceeeeeccccchhhccCHHHHHHhccchhcCCCeEEeeHHHH
Confidence 45566679999999999999999999999999999999999999999999999999999988743 4578999999999
Q ss_pred HHHhCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHH-HHHHHHhcChhHHHHhhhhcccCcccccCCcccc
Q 011802 89 ERKLGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNV-VLQRIASEGLSFVKRAKNSKKEGWSFKCNNKEES 167 (477)
Q Consensus 89 ~~~lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~-iL~~i~~~~~~~~~k~~~~~k~~~~~~c~~~~~~ 167 (477)
.+.|++++++|||+|+|+|||||++|.|||+++|++||++|++.+ +++- ..
T Consensus 209 l~~l~l~~~~fidL~lLlGCDYc~~I~Gig~~~al~lir~~~~i~~ile~-~~--------------------------- 260 (449)
T KOG2519|consen 209 LEGLGLSRESFIDLCLLLGCDYCPTIRGIGPKKALKLIRQHGDIENILEI-NS--------------------------- 260 (449)
T ss_pred HHHhcccHHHHHHHHHHhcCcccccccccChHHHHHHHHHhcCHHHHhhh-cc---------------------------
Confidence 999999999999999999999999999999999999999999863 4442 11
Q ss_pred ccccccccCCcCCCCCCCCcHHHHHHhcCCccCCCCh--HHHHHHhhhcccChHHHHHHHHHhcCCCcccccceeehhhh
Q 011802 168 LNQEINVNGTDHSLQRETPFSQVIDAYSNPKCYSADS--EAVHRVLAQHLFQHARLHQVCAQFFQWPPEKTDEYILPKIA 245 (477)
Q Consensus 168 ~~~e~~~~~~~~~ip~~FP~~~Vi~~Yl~P~vs~~d~--e~~~~~~~~~~~~~~~L~~f~~~~f~W~~~~~~e~llPll~ 245 (477)
..++..+|++||...+...|+.|.+....+ +.-|. ..+...|.+|+....+|+..++..-+.++++
T Consensus 261 -------~~~~~~ip~~w~~~~~r~~f~~p~~~~~~~~~~i~w~-----~pd~~~li~fl~~~~~f~~~rv~~~~~kl~~ 328 (449)
T KOG2519|consen 261 -------DLKEYPIPEDWSYKLARKLFLEPEFPNPESILDLKWK-----TPDTEGLIQFLVGEKQFNEERVRKGIRKLKS 328 (449)
T ss_pred -------chhhcCCCCCccHHHHHHHhcCcccCCccceeecccC-----CCChHHHHHHHHhhhccCHHHHhhhhHHHhh
Confidence 012356889999999999999999986544 22222 2256789999999999999999999999999
Q ss_pred HHHHhhhhhhcccccccCCCCCCCCcCCCCCcceeeecc-----ccCCceeeEEEecccCcceeeeeehhhhhhhcchhH
Q 011802 246 ERDLRRFANLRANTLALGVDLPLQKVPVKCPITGIIKSR-----KLQGKECFEVSWEESYGLKSSVVPADLIESACPEKI 320 (477)
Q Consensus 246 e~~lr~~~~l~~~ss~~~~~~~l~~~~v~~~~~~I~K~R-----~~~gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v 320 (477)
.+++...+.+...-....-..|+. +......+..+ ..++..|+-+-.+....+.++-.|-..+.+|+|..+
T Consensus 329 ~~~~~~qgrl~~f~~~~~~~~~~~----~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~~~r~~~t~~~l~~l~~~~p~~~ 404 (449)
T KOG2519|consen 329 SLKLGTQGRLDSFFKRIPKGSPVR----KLKLIDAKGKAEEVIKALNKKEKPKGQTGKIKRFKTTDKPLTMLPSATPLFT 404 (449)
T ss_pred hhccccccchhhhhcccCCCCCcc----hhHHHHHHhhhhhccCcchhhhhhccCCCccccceeecchHhhcccCCccHH
Confidence 998876443322110000000000 00001111111 123444555667777888899999999999999999
Q ss_pred HHHHHHHhccCCCCcC
Q 011802 321 VEFEERRALRQPKKSK 336 (477)
Q Consensus 321 ~~f~~~~~~~~~kk~~ 336 (477)
..|+..+-.+..+++.
T Consensus 405 ~~~l~~k~~~~~~~~~ 420 (449)
T KOG2519|consen 405 FIFLIPKEYPHLKTKR 420 (449)
T ss_pred HHHhhhhhcccccccc
Confidence 9999888877544443
No 8
>smart00475 53EXOc 5'-3' exonuclease.
Probab=99.94 E-value=1.1e-26 Score=230.68 Aligned_cols=136 Identities=24% Similarity=0.261 Sum_probs=118.5
Q ss_pred cCCcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHHC----CCeeEEecCCCcEEeecccEEEEeccCCCCceE
Q 011802 6 RNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNLE----SLCDGCFSSDSDIFLFGARTVYRDIWLGERGYV 80 (477)
Q Consensus 6 Rn~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~~----G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v 80 (477)
..+++.+..|++.++++|++||||++.+|+ ||||+||+|++. |..+.|+|+|+|++||+++.|.......+....
T Consensus 76 ~~~pe~L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~ 155 (259)
T smart00475 76 PKTPDELLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEAEGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEF 155 (259)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHhCCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCcc
Confidence 346889999999999999999999999997 999999999873 788899999999999988765432222222234
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhc
Q 011802 81 VCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 141 (477)
Q Consensus 81 ~~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~ 141 (477)
.+|+.+.+.+++|++|+||+|+++|+| |||+|||||||+|||.+||++||++ ++++++++.
T Consensus 156 ~~~~~~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~ 219 (259)
T smart00475 156 ELYTPENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKL 219 (259)
T ss_pred EEEcHHHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 689999999999999999999999999 8999999999999999999999997 599998874
No 9
>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=99.93 E-value=6.9e-25 Score=215.16 Aligned_cols=132 Identities=25% Similarity=0.293 Sum_probs=116.3
Q ss_pred cCCcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecccEEEE-eccCCCCce
Q 011802 6 RNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTVYR-DIWLGERGY 79 (477)
Q Consensus 6 Rn~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~~Vir-n~~~~~~~~ 79 (477)
..+++.+..|++.++++|++||||++.+|+ ||||+||+|++ .|...+|+|.|+|+++|++.+|.. +.. .
T Consensus 77 ~~~p~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~~g~~~~I~S~DkD~~ql~~~~v~~~~~~-----~ 151 (240)
T cd00008 77 KKMPEELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEAEGYKVVIVSGDKDLLQLVSDNVKVVSPM-----K 151 (240)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHcCCeEEEEeCCCChhhhCCCCEEEEeCC-----C
Confidence 356889999999999999999999999996 99999999985 578889999999999997665433 221 2
Q ss_pred EEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcC
Q 011802 80 VVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEG 142 (477)
Q Consensus 80 v~~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~~ 142 (477)
...++.+.+.+++|++|+||+|+++|+| |||+|||||||||+|.+||++||++ +++++++..+
T Consensus 152 ~~~i~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~ 217 (240)
T cd00008 152 KKLVTEENVIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIK 217 (240)
T ss_pred ceEEeHHHHHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHh
Confidence 3578999999999999999999999999 8999999999999999999999997 5999987743
No 10
>PRK14976 5'-3' exonuclease; Provisional
Probab=99.92 E-value=1.3e-24 Score=218.16 Aligned_cols=136 Identities=19% Similarity=0.230 Sum_probs=117.1
Q ss_pred ccCCcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecccEEEEeccCCCCce
Q 011802 5 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGY 79 (477)
Q Consensus 5 ~Rn~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~ 79 (477)
|.-+++.+..|++.++++|+++|||++.+|| ||||+||+|++ .|....|+|.|+|++||.+++|........ ..
T Consensus 81 R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~-~~ 159 (281)
T PRK14976 81 RKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSKQNITVLIYSSDKDLLQLVNENTDVLLKKKG-TS 159 (281)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHHCCCeEEEEeCCCCcCccCCCCeEEEEecCC-CC
Confidence 3345788999999999999999999999997 99999999876 466678999999999998865433222222 22
Q ss_pred EEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhc
Q 011802 80 VVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 141 (477)
Q Consensus 80 v~~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~ 141 (477)
..+|+.+.+.+++|++|+||+|+++|+| |||+|||||||+|||.+||++||++ ++|+++++.
T Consensus 160 ~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~ 224 (281)
T PRK14976 160 HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKI 224 (281)
T ss_pred cEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHH
Confidence 4679999999999999999999999999 8999999999999999999999997 599998874
No 11
>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=9.7e-25 Score=185.38 Aligned_cols=86 Identities=40% Similarity=0.618 Sum_probs=75.3
Q ss_pred HHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEecc-CC-C------CceEEEEeHHHHHHHhCCC
Q 011802 24 LSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIW-LG-E------RGYVVCYEMDDIERKLGFG 95 (477)
Q Consensus 24 ~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~-~~-~------~~~v~~y~~~~I~~~lgL~ 95 (477)
++|||||++||||||||||+|+++|+||+|+|+|+|+|+||+++||++++ .. + ...+++|+...+.+.+|++
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 32 1 2468999999999999999
Q ss_pred HHHHHHHHHHhCCC
Q 011802 96 RNSLITLALLLGSD 109 (477)
Q Consensus 96 r~q~IdlaiL~GsD 109 (477)
+++|+++|+|+|||
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 12
>PRK09482 flap endonuclease-like protein; Provisional
Probab=99.91 E-value=1.5e-23 Score=207.87 Aligned_cols=141 Identities=21% Similarity=0.241 Sum_probs=119.4
Q ss_pred ccCCcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecccEEE-EeccCCCCc
Q 011802 5 RRNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTVY-RDIWLGERG 78 (477)
Q Consensus 5 ~Rn~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~~Vi-rn~~~~~~~ 78 (477)
|+-+|+++..|++.++++|++||||++..|| ||||.||.|+. .|.-..|+|.|+|++|+..+.|. .+.. .
T Consensus 75 R~~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~I~S~DKDl~Qlv~~~v~~~~~~--~-- 150 (256)
T PRK09482 75 RKPMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQAGHQATIVSTDKGYCQLLSPTIQIRDYF--Q-- 150 (256)
T ss_pred CCCCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHHCCCeEEEEECCCCccccCCCCeEEEecc--c--
Confidence 4567899999999999999999999999997 99999999875 46666799999999998765543 3322 1
Q ss_pred eEEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhcChhHHHHhh
Q 011802 79 YVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 79 ~v~~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~~~~~~~k~~ 150 (477)
..+++.+.+.+++|++|+|++||++|+| +||+|||||||+|||.+||++||++ ++|++++.....+.+++.
T Consensus 151 -~~~~~~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~ 224 (256)
T PRK09482 151 -KRWLDAPFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLE 224 (256)
T ss_pred -cccCCHHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHHHHHHH
Confidence 2368999999999999999999999999 8999999999999999999999997 599998775434555443
No 13
>KOG2518 consensus 5'-3' exonuclease [Replication, recombination and repair]
Probab=99.90 E-value=4.3e-24 Score=224.91 Aligned_cols=126 Identities=21% Similarity=0.237 Sum_probs=111.8
Q ss_pred cCCcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEEeH
Q 011802 6 RNMGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEM 85 (477)
Q Consensus 6 Rn~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y~~ 85 (477)
|.+-+++.+|...+.++|+..||+||+||||||||+|||++.|+||+|||+|||+++|||..||..+... +....++.
T Consensus 120 qr~VdIT~~ma~~lI~~~r~~nVe~IVAPyEADAQlayL~~~~~i~~IITEDSDLl~fGc~~vifK~d~~--G~~le~~~ 197 (556)
T KOG2518|consen 120 QRCVDITPEMAHKLIQYLRSQNVEYIVAPYEADAQLAYLEREGIVDAIITEDSDLLVFGCKKVIFKMDSF--GNGLEINR 197 (556)
T ss_pred HHhccCcHHHHHHHHHHHHHcCCceEecCccccchhHHHHhcCcceEEEeccccccccCchhheeeccCC--CCcccccH
Confidence 3456789999999999999999999999999999999999999999999999999999999999987642 34445677
Q ss_pred HHHHHHhC----CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHH
Q 011802 86 DDIERKLG----FGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 86 ~~I~~~lg----L~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
..+...++ ++.++|..+|+|+||||++||||||.+||+++|+.|.+.+
T Consensus 198 ~~l~~~~~l~~~~~~ekfr~mciLSGCDYl~slpGvGl~tA~k~l~k~~~~d 249 (556)
T KOG2518|consen 198 SKLPECKPLGDKFTEEKFRRMCILSGCDYLSSLPGVGLATAHKLLSKYNTPD 249 (556)
T ss_pred hhhhhccccccccCHHHHHHHHHhcCCcccccCccccHHHHHHHHHhcCcHH
Confidence 66665443 5689999999999999999999999999999999999965
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=99.88 E-value=2e-22 Score=228.44 Aligned_cols=134 Identities=25% Similarity=0.275 Sum_probs=117.3
Q ss_pred CCcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecccEEEEeccCCCCceEE
Q 011802 7 NMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVV 81 (477)
Q Consensus 7 n~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~ 81 (477)
-+|+++..|++.++++|++||||++.+|| ||||+||+|++ .|+.+.|+|.|+|++|+++++|...... .+....
T Consensus 77 ~~Pe~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~~g~~v~IvS~DkDllQLv~~~v~~~~~~-~~~~~~ 155 (887)
T TIGR00593 77 PTPEELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEKEGYEVRIISGDKDLLQLVSDNVKVLIPK-GKTSFT 155 (887)
T ss_pred CChHHHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHhCCCcEEEEECCCChhhcCCCCEEEEecc-CCCCce
Confidence 46889999999999999999999999997 99999999986 4888899999999999988755322111 111345
Q ss_pred EEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhc
Q 011802 82 CYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 141 (477)
Q Consensus 82 ~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~ 141 (477)
.|+.+.+.+++|++|+||+||++|+| |||+|||||||+|||.+||++||++ ++|+++++.
T Consensus 156 ~~~~~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i 218 (887)
T TIGR00593 156 EITPEYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQI 218 (887)
T ss_pred EEcHHHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHh
Confidence 79999999999999999999999999 7999999999999999999999997 599998875
No 15
>PRK05755 DNA polymerase I; Provisional
Probab=99.88 E-value=4.5e-22 Score=226.10 Aligned_cols=135 Identities=21% Similarity=0.242 Sum_probs=117.0
Q ss_pred cCCcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecccEEEEeccCCCCceE
Q 011802 6 RNMGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYV 80 (477)
Q Consensus 6 Rn~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v 80 (477)
..+|+.+..|++.++++|+++|||++.+|| ||||+||+|+. .|..+.|+|.|+|+++++++.|....... +...
T Consensus 78 ~~~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~~i~S~DkD~~ql~~~~v~~~~~~~-~~~~ 156 (880)
T PRK05755 78 PPMPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEAAGYEVLIVTGDKDLLQLVDDNVTLLDTMG-VSKN 156 (880)
T ss_pred CCCcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHhCCCcEEEEcCCCChhhhCCCCEEEeeccC-CCCC
Confidence 356889999999999999999999999997 99999999984 58899999999999999886542211111 1234
Q ss_pred EEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHhc
Q 011802 81 VCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIASE 141 (477)
Q Consensus 81 ~~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~~ 141 (477)
..++.+.+.+++|++|+||+|+++|+| |||+|||||||+|||.+||++||++ +++++++..
T Consensus 157 ~~~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~ 220 (880)
T PRK05755 157 EELDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEI 220 (880)
T ss_pred eEEcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHh
Confidence 579999999999999999999999999 8999999999999999999999997 599998764
No 16
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=99.86 E-value=2.1e-21 Score=196.72 Aligned_cols=131 Identities=25% Similarity=0.346 Sum_probs=112.1
Q ss_pred CcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecccEEEEeccCCCCceEEE
Q 011802 8 MGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVC 82 (477)
Q Consensus 8 ~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~ 82 (477)
+++.+..++..+.+++.++|++++..+| ||||.++.+++ .|.+++|+|+|+|++||+++++.......+ .....
T Consensus 90 ~p~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~~g~~~~I~S~DkD~lql~~~~~~~~~~~~~-~~~~~ 168 (310)
T COG0258 90 MPDELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYKKGDVVLIISGDKDLLQLVSPNVLVINGKKG-EPEKF 168 (310)
T ss_pred CHHHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHhcCCeEEEEeCCcchhhhcCCCcEEEeccCC-CCccc
Confidence 5678999999999999999999999887 88887777654 799999999999999999998654333222 11115
Q ss_pred EeHHHHHHHh-CCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHH-HHHHHH
Q 011802 83 YEMDDIERKL-GFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDNV-VLQRIA 139 (477)
Q Consensus 83 y~~~~I~~~l-gL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~~-iL~~i~ 139 (477)
++...+.+++ |+++.||+|+++|+| |||+|||+|||+|||++||++||+.+ ++++++
T Consensus 169 ~~~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~ 229 (310)
T COG0258 169 LDLEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLD 229 (310)
T ss_pred CCHHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhh
Confidence 8999999999 999999999999999 99999999999999999999999975 777765
No 17
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=99.75 E-value=3.3e-18 Score=139.95 Aligned_cols=70 Identities=33% Similarity=0.635 Sum_probs=64.5
Q ss_pred HcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCC--ceEEEEeHHHHHHHhCC
Q 011802 25 SLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGER--GYVVCYEMDDIERKLGF 94 (477)
Q Consensus 25 ~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~--~~v~~y~~~~I~~~lgL 94 (477)
.+||||++||+|||||||+|+++|+||+|+|+|+|+|+||+++++++++..++ ..++.++...+.+++|+
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 68999999999999999999999999999999999999999999999987543 26889999999999885
No 18
>PHA00439 exonuclease
Probab=99.56 E-value=1.7e-14 Score=145.17 Aligned_cols=107 Identities=12% Similarity=0.057 Sum_probs=85.6
Q ss_pred CcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCC-eeEEecCCCcEEeecccEEEEeccCCCCceEE
Q 011802 8 MGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESL-CDGCFSSDSDIFLFGARTVYRDIWLGERGYVV 81 (477)
Q Consensus 8 ~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~-VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~ 81 (477)
++.. ..+++.++++++++||+++..|| ||||.+|.|++ .|. -..|+|.|+|++|+....++.+ .. +.+.
T Consensus 92 ~p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~~g~~~vvIvS~DKDl~QLv~~~~~~~-~~---~~~~ 166 (286)
T PHA00439 92 KRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSLFGFKKAVLVSCDKDFKTIPNCDFLWC-TT---GNIL 166 (286)
T ss_pred CCCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHHCCCCeEEEEeCCCCHhhcCcceEEEc-cC---CceE
Confidence 3455 67889999999999999999997 99999999875 465 5689999999999975544432 11 1111
Q ss_pred EEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHH
Q 011802 82 CYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKS 128 (477)
Q Consensus 82 ~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~ 128 (477)
.++.+ .+++++++.+|+| +|++||||||| |||.+||++
T Consensus 167 ~~~~~--------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 167 TQTPE--------TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred EcCcc--------cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhC
Confidence 13322 3899999999999 89999999999 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=99.42 E-value=1.9e-13 Score=112.17 Aligned_cols=50 Identities=38% Similarity=0.687 Sum_probs=46.4
Q ss_pred HhCCCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCH-HHHHHHHh
Q 011802 91 KLGFGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDN-VVLQRIAS 140 (477)
Q Consensus 91 ~lgL~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~-~iL~~i~~ 140 (477)
++|++|+||+++|+|+| |||+|||||||+|+|.+||++|++. +++++++.
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 58999999999999999 9999999999999999999999997 47777765
No 20
>PHA02567 rnh RnaseH; Provisional
Probab=99.15 E-value=2.1e-10 Score=116.49 Aligned_cols=99 Identities=16% Similarity=0.045 Sum_probs=78.3
Q ss_pred CcchhHHHH--------HHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeecc-cEEEEecc
Q 011802 8 MGSEFSCMI--------KEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGA-RTVYRDIW 73 (477)
Q Consensus 8 ~~~~~~~~i--------~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~-~~Virn~~ 73 (477)
+++++..++ +.+++++.+|||+++..|| |||+.+|.|++ .|.-..|+|.|+|++|+-. +.|....
T Consensus 93 ~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~~g~~VvIvS~DKDl~QLv~~~~v~~~~- 171 (304)
T PHA02567 93 DREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSAEGRPVLIVSSDGDFTQLHKYPGVKQWS- 171 (304)
T ss_pred CChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHhCCCcEEEEeCCCChhhccCCCCeEEee-
Confidence 456655544 6678899999999999997 99999999875 5677789999999999853 3332211
Q ss_pred CCCCceEEEEeHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCC
Q 011802 74 LGERGYVVCYEMDDIERKLGFGRNSLITLALLLG--SDYSQGVRG 116 (477)
Q Consensus 74 ~~~~~~v~~y~~~~I~~~lgL~r~q~IdlaiL~G--sDY~pGVpG 116 (477)
.++...+..++| .|.|++|+.+|+| +|++||||-
T Consensus 172 --------~~~~~~V~~k~G-~P~q~iD~kaL~GDsSDNIPGVp~ 207 (304)
T PHA02567 172 --------PMQKKWVKPKYG-SPEKDLMTKIIKGDKKDGVASIKV 207 (304)
T ss_pred --------cCCHHHHHHHhC-CHHHHHHHHHhCCcccCCcCCCCC
Confidence 123477888999 5999999999999 899999994
No 21
>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=99.07 E-value=3e-12 Score=111.07 Aligned_cols=49 Identities=24% Similarity=0.466 Sum_probs=38.2
Q ss_pred CCHHHHHHHHHHhC--CCCCCCCCCCcHHHHHHHHHHhCCHH-HHHHHHhcC
Q 011802 94 FGRNSLITLALLLG--SDYSQGVRGLGPESACQIVKSVGDNV-VLQRIASEG 142 (477)
Q Consensus 94 L~r~q~IdlaiL~G--sDY~pGVpGIG~ktA~kLIk~~gs~~-iL~~i~~~~ 142 (477)
+.|+|++||.+|+| +|++|||||||+|||.+||++||+++ +|++++...
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~ 52 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIK 52 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhcc
Confidence 57999999999999 89999999999999999999999964 888887643
No 22
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=98.96 E-value=6e-10 Score=79.60 Aligned_cols=33 Identities=42% Similarity=0.901 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhCCCCC---CCCCCCcHHHHHHHHHHh
Q 011802 96 RNSLITLALLLGSDYS---QGVRGLGPESACQIVKSV 129 (477)
Q Consensus 96 r~q~IdlaiL~GsDY~---pGVpGIG~ktA~kLIk~~ 129 (477)
|+||+++|+|+| ||. |||||||+|+|.+||++|
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 555 599999999999999986
No 23
>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=98.60 E-value=3.8e-08 Score=92.48 Aligned_cols=83 Identities=27% Similarity=0.243 Sum_probs=64.8
Q ss_pred CcchhHHHHHHHHHHHHHcCCCEEeccc-hHHHHHHHHHH----CCCeeEEecCCCcEEeeccc--EEEEeccCCCCceE
Q 011802 8 MGSEFSCMIKEAKALGLSLGVPCLEGVE-EAEAQCALLNL----ESLCDGCFSSDSDIFLFGAR--TVYRDIWLGERGYV 80 (477)
Q Consensus 8 ~~~~~~~~i~~ik~LL~~~GIp~i~APg-EAEAqcA~L~~----~G~VD~ViS~DsD~llFG~~--~Virn~~~~~~~~v 80 (477)
+++.+..|++.++++++.+||+++..|| ||||.+|.|++ .|.-..|+|.|+|++|+... .|+..-. +....
T Consensus 80 ~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~~~~~v~IvS~DkD~~QLv~~~~~V~~~~~--~~~~~ 157 (169)
T PF02739_consen 80 MPEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASEEGFEVIIVSGDKDLLQLVDENVNVYLLDP--GKKKF 157 (169)
T ss_dssp HHHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHHTTCEEEEE-SSGGGGGGTCS-TSEEEEET--TTTCS
T ss_pred CCHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhccCCCEEEEEcCCCCHHHhcCCCceEEEeec--CCCCC
Confidence 5678999999999999999999999997 99999999876 57777899999999999877 4544211 12445
Q ss_pred EEEeHHHHHHHh
Q 011802 81 VCYEMDDIERKL 92 (477)
Q Consensus 81 ~~y~~~~I~~~l 92 (477)
.+|+.+.|.++|
T Consensus 158 ~~~~~~~v~eky 169 (169)
T PF02739_consen 158 KVYDPEEVEEKY 169 (169)
T ss_dssp -EB-HHHHHHHT
T ss_pred EEEcHHHHhhcC
Confidence 789999998875
No 24
>PF12813 XPG_I_2: XPG domain containing
Probab=98.39 E-value=1.6e-06 Score=86.26 Aligned_cols=87 Identities=23% Similarity=0.318 Sum_probs=65.8
Q ss_pred HHHHHHHHHHHc---CCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecc----cEE-EEeccCCC------Cc--
Q 011802 15 MIKEAKALGLSL---GVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGA----RTV-YRDIWLGE------RG-- 78 (477)
Q Consensus 15 ~i~~ik~LL~~~---GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~----~~V-irn~~~~~------~~-- 78 (477)
+.+.+.+.|+.+ |++++..|||||+.||.++++.-+ .|+|+|||+|+|+. ..+ +..+.... +.
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 356677888888 999999999999999999975444 89999999999976 222 22222211 12
Q ss_pred eEEEEeHHHHHHHhCCCHHHHHHHHH
Q 011802 79 YVVCYEMDDIERKLGFGRNSLITLAL 104 (477)
Q Consensus 79 ~v~~y~~~~I~~~lgL~r~q~Idlai 104 (477)
...+|+.+.|.+.+|+. .|..||.
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 7776666
No 25
>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=97.01 E-value=0.0011 Score=50.59 Aligned_cols=50 Identities=26% Similarity=0.470 Sum_probs=45.2
Q ss_pred cceeeeccccCCce---eeEEEecccCcceeeeeehhhhhhhcchhHHHHHHH
Q 011802 277 ITGIIKSRKLQGKE---CFEVSWEESYGLKSSVVPADLIESACPEKIVEFEER 326 (477)
Q Consensus 277 ~~~I~K~R~~~gv~---cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~ 326 (477)
|.+|+..|...+.. -|-|.|.+.+.-..||+|++-+...+|++|.+|+++
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 45889999877777 899999999999999999999999999999999875
No 26
>smart00298 CHROMO Chromatin organization modifier domain.
Probab=95.92 E-value=0.012 Score=44.06 Aligned_cols=50 Identities=18% Similarity=0.424 Sum_probs=44.1
Q ss_pred cceeeecc-ccCCceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHHHH
Q 011802 277 ITGIIKSR-KLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 327 (477)
Q Consensus 277 ~~~I~K~R-~~~gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~~ 327 (477)
+.+|+..| ...|..-|.|.|.+.+.-..+|+|.+-+.. +|++|.+|.++.
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 778888999999999888889999999998 999999998864
No 27
>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=95.43 E-value=0.015 Score=43.64 Aligned_cols=47 Identities=26% Similarity=0.386 Sum_probs=42.7
Q ss_pred ceeeeccccC--CceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHH
Q 011802 278 TGIIKSRKLQ--GKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEE 325 (477)
Q Consensus 278 ~~I~K~R~~~--gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~ 325 (477)
.+|+..|... |..-|.|.|.+.+.-..+|+|++-+..+ +.+|.+|++
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 8999999999999888999999999988 999999975
No 28
>COG5366 Protein involved in propagation of M2 dsRNA satellite of L-A virus [General function prediction only]
Probab=94.11 E-value=0.023 Score=61.13 Aligned_cols=112 Identities=21% Similarity=0.337 Sum_probs=86.9
Q ss_pred HHHHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeecc-cEEEEeccCCCC-ceEEEEeHHHHHHHhCCCH
Q 011802 19 AKALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFGA-RTVYRDIWLGER-GYVVCYEMDDIERKLGFGR 96 (477)
Q Consensus 19 ik~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG~-~~Virn~~~~~~-~~v~~y~~~~I~~~lgL~r 96 (477)
+-..+..-|+.++.+|+-|..|||||.....++++.. -+|+++|.+ ++++-.+.++.+ ..+.+|+.....+-.-.+-
T Consensus 134 ~sk~~~~~~~a~~i~~ys~~fq~AYl~~~~~~~~~~g-p~d~l~ld~vdr~il~m~fg~d~Ppl~~~~vp~~lem~l~s~ 212 (531)
T COG5366 134 ASKILEEKGVAVIIAPYSATFQCAYLMSAETCSYAFG-PSDILLLDGVDRIILDMSFGSDKPPLDVFHVPRFLEMFLLSS 212 (531)
T ss_pred ccccccccceEEEehhhHHHHHHHHHHHHHHHHhcCC-chHhHHHhhhhhheeecccCCCCCCCcccccchHHHhccccc
Confidence 3456778899999999999999999999889988877 899999965 566655544322 5677888877766666777
Q ss_pred HHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCC
Q 011802 97 NSLITLALLLGSDYSQGVRGLGPESACQIVKSVGD 131 (477)
Q Consensus 97 ~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs 131 (477)
.-|..+-.|.|||+++.++.|-.-.+..+-+-+|+
T Consensus 213 ~lFya~~ll~~c~~~s~~~~C~~da~f~l~qvigd 247 (531)
T COG5366 213 RLFYALGLLLGCDFCSTIPRCATDADFSLNQVIGD 247 (531)
T ss_pred chhhhhcccccccccccccccccchhHHHHHHHhc
Confidence 88999999999999999998766445555554444
No 29
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=92.19 E-value=0.11 Score=41.26 Aligned_cols=21 Identities=29% Similarity=0.512 Sum_probs=18.0
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 011802 113 GVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~gs~~ 133 (477)
||||||+++|..|++.||+.+
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 999999999999999999975
No 30
>KOG1911 consensus Heterochromatin-associated protein HP1 and related CHROMO domain proteins [Chromatin structure and dynamics]
Probab=91.83 E-value=0.12 Score=52.01 Aligned_cols=55 Identities=29% Similarity=0.428 Sum_probs=47.1
Q ss_pred CcceeeeccccCCceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHHHHhccC
Q 011802 276 PITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALRQ 331 (477)
Q Consensus 276 ~~~~I~K~R~~~gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~~~~~~ 331 (477)
.+..|.++|..+|..+|=|.|.|.+.--.+|+|..-. .-||++|.+|.+..+..+
T Consensus 50 vvEki~~~r~~~g~~eYlvkW~Gy~~~~ntWEPee~~-~~C~~li~~~~~~~~~~k 104 (270)
T KOG1911|consen 50 VVEKILKRRKKNGKIEYLVKWKGYPDPDNTWEPEEHN-LDCPELIDEFEKSQKKLK 104 (270)
T ss_pred hhhhhhhccccCCCceeeeecCCCCCccccCCchhhc-cccHHHHHHHHHHhcccC
Confidence 4578999999999999999999999999999999622 235999999999877764
No 31
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=89.96 E-value=0.36 Score=46.40 Aligned_cols=30 Identities=30% Similarity=0.502 Sum_probs=24.8
Q ss_pred CCCCCcHHHHHHHHHHhCCHHHHHHHHhcC
Q 011802 113 GVRGLGPESACQIVKSVGDNVVLQRIASEG 142 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~gs~~iL~~i~~~~ 142 (477)
.|||||||+|.+++..||..++.+.+....
T Consensus 77 ~i~GIGpk~A~~il~~fg~~~l~~~i~~~d 106 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSPEELVQAIANGD 106 (192)
T ss_pred cCCCCCHHHHHHHHHhCCHHHHHHHHHhCC
Confidence 599999999999999999876666665543
No 32
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=89.66 E-value=0.55 Score=45.75 Aligned_cols=67 Identities=19% Similarity=0.325 Sum_probs=46.1
Q ss_pred ceEEEEeHH----HHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 78 GYVVCYEMD----DIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 78 ~~v~~y~~~----~I~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
..+.+|... +-..-||| +.+.--.|-.|. +|.|||||+|+.++..++..++.+.+.+.+.+...+..
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 345555443 33346887 455555555553 79999999999999999888888888876665554443
No 33
>KOG2748 consensus Uncharacterized conserved protein, contains chromo domain [Chromatin structure and dynamics]
Probab=89.49 E-value=0.18 Score=52.65 Aligned_cols=61 Identities=28% Similarity=0.395 Sum_probs=49.9
Q ss_pred cceeeeccccCCceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHHHHhcc---CCCCcCCCc
Q 011802 277 ITGIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERRALR---QPKKSKPKS 339 (477)
Q Consensus 277 ~~~I~K~R~~~gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~~~~~---~~kk~~~~~ 339 (477)
+-.|+|+|.+.|+-=|-|.|.|-..=+.+|+|.+=+ -=|-+++.|+.+..++ ++||++++-
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 2388999999888777 456655543
No 34
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.43 E-value=0.52 Score=45.62 Aligned_cols=64 Identities=17% Similarity=0.322 Sum_probs=42.7
Q ss_pred ceEEEEeHHHH----HHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHH
Q 011802 78 GYVVCYEMDDI----ERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVK 147 (477)
Q Consensus 78 ~~v~~y~~~~I----~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~ 147 (477)
..+.+|....+ ..-||+ +++.--.|..|. +|+|||||+|+.++..|+..++...+...+.+...
T Consensus 43 ~~~~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~ 111 (194)
T PRK14605 43 QRVRVFTHLHVREDALSLFGFATTEELSLFETLI------DVSGIGPKLGLAMLSAMNAEALASAIISGNAELLS 111 (194)
T ss_pred CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------CCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHH
Confidence 34555544333 345787 444444455553 89999999999999999988888888665544433
No 35
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=88.18 E-value=0.72 Score=44.52 Aligned_cols=67 Identities=21% Similarity=0.256 Sum_probs=45.9
Q ss_pred ceEEEEeH----HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 78 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 78 ~~v~~y~~----~~I~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
..+.+|.. ++...-||| +.+.--.|..|. +|.|||||+|+.++..+.-.++.+.+...+.....+..
T Consensus 43 ~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li------~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vp 114 (188)
T PRK14606 43 GECFLHTFLSVSQDGITLYGFSNERKKELFLSLT------KVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLP 114 (188)
T ss_pred CeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHh------ccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 44555543 333446887 444555555553 79999999999999998888888888877665555443
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=86.52 E-value=0.68 Score=44.71 Aligned_cols=64 Identities=19% Similarity=0.247 Sum_probs=41.8
Q ss_pred ceEEEEeHHHH----HHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHH
Q 011802 78 GYVVCYEMDDI----ERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVK 147 (477)
Q Consensus 78 ~~v~~y~~~~I----~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~ 147 (477)
..+.+|....+ ..-||+ +++.--.|..|. +|+|||||+|+.++..++..++.+.+.+.+.....
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 44555544333 346787 444444454443 89999999999999988777788888765444333
No 37
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=86.21 E-value=0.63 Score=45.20 Aligned_cols=67 Identities=19% Similarity=0.240 Sum_probs=44.3
Q ss_pred ceEEEEeHHH----HHHHhCCC-HHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 78 GYVVCYEMDD----IERKLGFG-RNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 78 ~~v~~y~~~~----I~~~lgL~-r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
..+.+|.... -..-|||. .+.--.|-.| -+|.|||||+|+.++..+...++.+.+.+.+.+...+..
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 QEAELHTRLVVREDALSLYGFPDEDSLELFELL------LGVSGVGPKLALALLSALPPALLARALLEGDARLLTSAS 113 (197)
T ss_pred CeEEEEEEEEEccCCceeeCcCCHHHHHHHHHH------hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 4445444333 33457874 3333334444 289999999999999998888888888877666555544
No 38
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.91 E-value=0.82 Score=44.02 Aligned_cols=67 Identities=19% Similarity=0.332 Sum_probs=45.5
Q ss_pred ceEEEEeH----HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 78 GYVVCYEM----DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 78 ~~v~~y~~----~~I~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
..+.+|.. ++-..-||| +.+.--.|-.|. +|.|||||+|+.++..+...++...+.+.+.+...+..
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 34444443 333345787 444444555553 79999999999999999888888888887665555443
No 39
>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=84.79 E-value=0.72 Score=31.79 Aligned_cols=15 Identities=33% Similarity=0.720 Sum_probs=12.1
Q ss_pred CCCCCcHHHHHHHHH
Q 011802 113 GVRGLGPESACQIVK 127 (477)
Q Consensus 113 GVpGIG~ktA~kLIk 127 (477)
.+||||+++|..++.
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 789999999988764
No 40
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=84.49 E-value=0.9 Score=44.27 Aligned_cols=55 Identities=24% Similarity=0.497 Sum_probs=40.1
Q ss_pred HHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 90 RKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 90 ~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
.-||+ +.+..-.|-.|. +|.|||||+|+.++..+...++.+.+.+.+.+...+..
T Consensus 58 ~LYGF~t~~Er~lF~~Li------sVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vp 113 (196)
T PRK13901 58 KLFGFLNSSEREVFEELI------GVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVK 113 (196)
T ss_pred eeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 45787 444555555553 79999999999999998888888888776665554443
No 41
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=83.91 E-value=0.92 Score=44.02 Aligned_cols=56 Identities=25% Similarity=0.368 Sum_probs=40.0
Q ss_pred HHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 89 ERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 89 ~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
..-||| +.+.--.|..|. +|.|||||+|+.++..+...++...+.+.+.+...+..
T Consensus 58 ~~LyGF~~~~Er~lF~~Li------~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvp 114 (195)
T PRK14604 58 LTLYGFSTPAQRQLFELLI------GVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVP 114 (195)
T ss_pred ceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCC
Confidence 345787 444444444443 79999999999999988777888888877666555544
No 42
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=83.80 E-value=1.5 Score=47.15 Aligned_cols=113 Identities=19% Similarity=0.150 Sum_probs=61.0
Q ss_pred HHHHHHHc--CCCEEeccc-hHHHH-HHH----HHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEEeHHHHHH
Q 011802 19 AKALGLSL--GVPCLEGVE-EAEAQ-CAL----LNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIER 90 (477)
Q Consensus 19 ik~LL~~~--GIp~i~APg-EAEAq-cA~----L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y~~~~I~~ 90 (477)
+.++|..+ +|..+.-.| .||=+ |+. ..+.|.=-.++|.|.|.++|.+......+.... ...-.|-+.
T Consensus 148 l~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~~~KiI~t~-~~~Y~~~P~---- 222 (425)
T PF04599_consen 148 LESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDTPPKIIKTM-NQLYKFIPC---- 222 (425)
T ss_pred HHHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCchHHHHHhH-HhHeeecCC----
Confidence 33444444 788887776 78764 554 234687778999999999997632211111000 000011111
Q ss_pred HhCCCHHHHHHHHHHhCCCCCCCCCCCc--HHHH--HHHHHHhCCHHHHHHH
Q 011802 91 KLGFGRNSLITLALLLGSDYSQGVRGLG--PESA--CQIVKSVGDNVVLQRI 138 (477)
Q Consensus 91 ~lgL~r~q~IdlaiL~GsDY~pGVpGIG--~ktA--~kLIk~~gs~~iL~~i 138 (477)
..+.---...++.-||||.||+-|+- +++- .+|...|--.++++.+
T Consensus 223 --~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dFti~Ni~~SL 272 (425)
T PF04599_consen 223 --SKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDFTIDNILQSL 272 (425)
T ss_pred --chHHHHHHHHHHHhcccccCCcceeEechhhccceeccccccHHHHHHHH
Confidence 11222233456777999999999964 3332 3343334334555544
No 43
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=82.35 E-value=0.82 Score=44.06 Aligned_cols=55 Identities=22% Similarity=0.385 Sum_probs=39.4
Q ss_pred HHHHHHhCC-CHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHH
Q 011802 86 DDIERKLGF-GRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFV 146 (477)
Q Consensus 86 ~~I~~~lgL-~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~ 146 (477)
++...-||+ +++.--.|-.|. +|.|||||+|+.++..+.-.++...+.+.+....
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Li------sV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L 110 (186)
T PRK14600 55 DNVTQLYGFLNREEQDCLRMLV------KVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL 110 (186)
T ss_pred cCCceeeCCCCHHHHHHHHHHh------CcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe
Confidence 333456887 444444444442 8999999999999999888888888887665544
No 44
>PHA03065 Hypothetical protein; Provisional
Probab=81.42 E-value=2.7 Score=45.32 Aligned_cols=107 Identities=21% Similarity=0.228 Sum_probs=61.8
Q ss_pred HHHHHHc--CCCEEeccc-hHHH-HHHHH----HHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEEeHHHHHHH
Q 011802 20 KALGLSL--GVPCLEGVE-EAEA-QCALL----NLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCYEMDDIERK 91 (477)
Q Consensus 20 k~LL~~~--GIp~i~APg-EAEA-qcA~L----~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y~~~~I~~~ 91 (477)
.+.|..+ ++.++.-.| .||= +|+.- .+.|.=-.++|.|.|.++|.+..-...+ +++.. +-
T Consensus 151 ~~~L~~~~~~v~I~yCdgvDAEfvMC~~ak~~a~~~g~WPl~iStDQDtllf~s~D~~~Ki---------I~t~~---~~ 218 (438)
T PHA03065 151 ESALARLGENVEIVYCDGVDAEFVMCARAKELAATTGEWPLLISTDQDTLLFSSCDRLPKI---------IKTAN---QL 218 (438)
T ss_pred HHHHHhccCCceEEEECCcchhHHHHHHHHHHHhhcCCCceEEeccCCeeEEEecCcHHHH---------HHhHH---HH
Confidence 3456667 788887776 7775 46542 2468777899999999999653211100 11111 12
Q ss_pred hCCCH-----HHHHHHHHHhCCCCCCCCCCCc--HHHH--HHHHHHhCCHHHHHHH
Q 011802 92 LGFGR-----NSLITLALLLGSDYSQGVRGLG--PESA--CQIVKSVGDNVVLQRI 138 (477)
Q Consensus 92 lgL~r-----~q~IdlaiL~GsDY~pGVpGIG--~ktA--~kLIk~~gs~~iL~~i 138 (477)
|.+-| ---...++.-||||.||+-|+- +++- .+|...|--.++++.+
T Consensus 219 Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it~~~l~r~~LF~dFt~~Nv~~SL 274 (438)
T PHA03065 219 YKFIPCAKTRYLSKLVALVNGCDFFPGLYGISITPKSLNRIQLFDDFTIDNVVRSL 274 (438)
T ss_pred heeCCChhHHHHHHHHHHHhcccccCccceEEechhhccceechhhhhHHHHHHHH
Confidence 22222 2223345667899999999964 4432 4455555544555543
No 45
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=81.00 E-value=4 Score=40.02 Aligned_cols=62 Identities=24% Similarity=0.326 Sum_probs=41.0
Q ss_pred EeHHHHHHHhCCCH-HHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCHHHHHHHHhcChhHHHHhh
Q 011802 83 YEMDDIERKLGFGR-NSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDNVVLQRIASEGLSFVKRAK 150 (477)
Q Consensus 83 y~~~~I~~~lgL~r-~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~~iL~~i~~~~~~~~~k~~ 150 (477)
+-.++...-||+.. +.=-.|..| -.|.|||||+|+.++..+.-.++.+.+...+.+...+..
T Consensus 52 ~vREd~~~LyGF~~~~ER~lF~~L------isVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~P 114 (201)
T COG0632 52 VVREDAHLLYGFLTEEERELFRLL------ISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIP 114 (201)
T ss_pred eehhhHHHHcCCCCHHHHHHHHHH------HccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCC
Confidence 34466677899843 333333333 278999999999999887777777777766555444443
No 46
>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=76.65 E-value=3.2 Score=32.14 Aligned_cols=22 Identities=23% Similarity=0.442 Sum_probs=15.1
Q ss_pred CCCCCCcHHHHHHHHHH-hCCHH
Q 011802 112 QGVRGLGPESACQIVKS-VGDNV 133 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~-~gs~~ 133 (477)
-+|.|||++||.++... +.+++
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~ 27 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLE 27 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHH
T ss_pred hhcccccHHHHHHHHHhCCCCHH
Confidence 37999999999999986 66654
No 47
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=74.87 E-value=2.3 Score=27.91 Aligned_cols=18 Identities=33% Similarity=0.612 Sum_probs=15.2
Q ss_pred CCCCCCCcHHHHHHHHHH
Q 011802 111 SQGVRGLGPESACQIVKS 128 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~ 128 (477)
+..|||||+++|..++..
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 357999999999999863
No 48
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.37 E-value=2.6 Score=40.59 Aligned_cols=36 Identities=36% Similarity=0.556 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHh
Q 011802 93 GFGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 93 gL~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~ 129 (477)
++++++|+. |+..| ...+..+||||+|||-+|+-+.
T Consensus 92 ~~~~~el~~-aI~~~D~~~L~~vpGIGkKtAeRIilEL 128 (183)
T PRK14601 92 SLDVNSFYK-ALSLGDESVLKKVPGIGPKSAKRIIAEL 128 (183)
T ss_pred CCCHHHHHH-HHHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 356666654 33334 2344699999999999999653
No 49
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=70.71 E-value=3.5 Score=46.63 Aligned_cols=25 Identities=16% Similarity=0.405 Sum_probs=21.8
Q ss_pred CCCCCCcHHHHHHHHHHhCCHHHHH
Q 011802 112 QGVRGLGPESACQIVKSVGDNVVLQ 136 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~~iL~ 136 (477)
.||||||+++|..|++.||+.+-+.
T Consensus 572 ~~I~GIG~k~a~~Ll~~Fgs~~~i~ 596 (621)
T PRK14671 572 TDIAGIGEKTAEKLLEHFGSVEKVA 596 (621)
T ss_pred hcCCCcCHHHHHHHHHHcCCHHHHH
Confidence 5999999999999999999975443
No 50
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=69.04 E-value=3.3 Score=40.40 Aligned_cols=35 Identities=17% Similarity=0.205 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHh
Q 011802 94 FGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 94 L~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~ 129 (477)
+++++|+.. +..| -..+..|||||+|||-+|+-+.
T Consensus 92 ~~~~el~~a-I~~~D~~~L~~vpGIGkKtAeRIIlEL 127 (196)
T PRK13901 92 IKYNEFRDA-IDREDIELISKVKGIGNKMAGKIFLKL 127 (196)
T ss_pred CCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 466665543 3333 2344699999999999999653
No 51
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.36 E-value=3.5 Score=40.03 Aligned_cols=35 Identities=23% Similarity=0.202 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHh
Q 011802 94 FGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 94 L~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~ 129 (477)
+++++|+.. +..| ...+..+||||+|||-+|+-+.
T Consensus 93 ~~~~el~~a-I~~~D~~~L~kvpGIGkKtAerIilEL 128 (195)
T PRK14604 93 GTPDELQLA-IAGGDVARLARVPGIGKKTAERIVLEL 128 (195)
T ss_pred CCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 566666543 2223 2344699999999999999653
No 52
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.71 E-value=3.7 Score=39.64 Aligned_cols=36 Identities=17% Similarity=0.240 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHh
Q 011802 93 GFGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 93 gL~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~ 129 (477)
++++++|+.. +..| ...+-.+||||+|||-+|+-+.
T Consensus 92 ~~~~~el~~a-I~~~D~~~L~~vpGIGkKtAerIilEL 128 (188)
T PRK14606 92 NEDAETLVTM-IASQDVEGLSKLPGISKKTAERIVMEL 128 (188)
T ss_pred CCCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHH
Confidence 3566666543 3333 2444699999999999999653
No 53
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=67.47 E-value=4.4 Score=45.92 Aligned_cols=22 Identities=18% Similarity=0.409 Sum_probs=20.5
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 011802 112 QGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
.+|||||++++.+|++.||+.+
T Consensus 555 ~~IpGIG~kr~~~LL~~FgSi~ 576 (624)
T PRK14669 555 LEIPGVGAKTVQRLLKHFGSLE 576 (624)
T ss_pred hcCCCCCHHHHHHHHHHcCCHH
Confidence 5999999999999999999974
No 54
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=67.18 E-value=3.7 Score=39.87 Aligned_cols=36 Identities=22% Similarity=0.252 Sum_probs=24.0
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHhC
Q 011802 94 FGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSVG 130 (477)
Q Consensus 94 L~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~g 130 (477)
+++++|+.. +..| -..+..|||||+|||-+|+-+..
T Consensus 92 ~~~~~l~~a-I~~~D~~~L~kvpGIGkKtAerIilELk 128 (197)
T PRK14603 92 LPPALLARA-LLEGDARLLTSASGVGKKLAERIALELK 128 (197)
T ss_pred CCHHHHHHH-HHhCCHHHHhhCCCCCHHHHHHHHHHHH
Confidence 566666543 2222 12336999999999999996643
No 55
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=67.04 E-value=5.1 Score=44.93 Aligned_cols=23 Identities=13% Similarity=0.195 Sum_probs=20.9
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHH
Q 011802 111 SQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
+.+|||||+++..+|++.||+.+
T Consensus 516 Ld~I~GiG~kr~~~Ll~~Fgs~~ 538 (567)
T PRK14667 516 LDKIKGIGEVKKEIIYRNFKTLY 538 (567)
T ss_pred cccCCCCCHHHHHHHHHHhCCHH
Confidence 35999999999999999999974
No 56
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=66.81 E-value=4.7 Score=38.88 Aligned_cols=34 Identities=15% Similarity=0.276 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHh
Q 011802 94 FGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 94 L~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~ 129 (477)
+++++|+.. +-.| ..-+ .|||||+|||-+|+-+.
T Consensus 93 ~~~~~l~~a-I~~~D~~~L-~vpGIGkKtAerIilEL 127 (186)
T PRK14600 93 LTPEQLFSA-IVNEDKAAL-KVNGIGEKLINRIITEL 127 (186)
T ss_pred CCHHHHHHH-HHcCCHhhe-ECCCCcHHHHHHHHHHH
Confidence 577776653 3344 3446 99999999999999653
No 57
>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=65.93 E-value=5 Score=45.09 Aligned_cols=22 Identities=18% Similarity=0.344 Sum_probs=20.6
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 011802 112 QGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
.+|||||+++..+|++.||+.+
T Consensus 544 d~I~GIG~kr~~~LL~~Fgs~~ 565 (574)
T TIGR00194 544 LKIPGVGEKRVQKLLKYFGSLK 565 (574)
T ss_pred hcCCCCCHHHHHHHHHHcCCHH
Confidence 5999999999999999999975
No 58
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=64.18 E-value=6.3 Score=44.31 Aligned_cols=24 Identities=29% Similarity=0.498 Sum_probs=21.5
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHH
Q 011802 110 YSQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 110 Y~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
-+.+|||||+++..+|++.||+.+
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~ 538 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYK 538 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHH
Confidence 446999999999999999999974
No 59
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=64.10 E-value=17 Score=41.82 Aligned_cols=86 Identities=17% Similarity=0.303 Sum_probs=58.9
Q ss_pred ccchHHHHHHHHHHC---------CCeeEEecCCCcEEeecc----c--EEEE-eccCCC--------------------
Q 011802 33 GVEEAEAQCALLNLE---------SLCDGCFSSDSDIFLFGA----R--TVYR-DIWLGE-------------------- 76 (477)
Q Consensus 33 APgEAEAqcA~L~~~---------G~VD~ViS~DsD~llFG~----~--~Vir-n~~~~~-------------------- 76 (477)
.|||.|.-+-.+.+. .-..+|.+-|.|++++|- + .++| +++.+.
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 489999876655442 357799999999999984 2 4677 444321
Q ss_pred -----CceEEEEeHHHHHHHh-------C------CCH--HHHHHHHHHhCCCCCCCCCCCc
Q 011802 77 -----RGYVVCYEMDDIERKL-------G------FGR--NSLITLALLLGSDYSQGVRGLG 118 (477)
Q Consensus 77 -----~~~v~~y~~~~I~~~l-------g------L~r--~q~IdlaiL~GsDY~pGVpGIG 118 (477)
..++.+++.+-+.+.+ + +.| +.||.+|-++|.|++|.+|++-
T Consensus 266 ~k~~~~q~F~~LhiSlLREYLe~Ef~~~~~~ftfdlERilDDwIf~~FfvGNDFLPhLP~Ld 327 (953)
T COG5049 266 CKVLTHQPFYLLHISLLREYLEREFREPTLPFTFDLERILDDWIFLCFFVGNDFLPHLPCLD 327 (953)
T ss_pred hcccccCceEEEEHHHHHHHHHHHhhccCCCccccHHHhhhhheeeeeeeccccCCCCCccc
Confidence 0235677776554422 1 222 6778899999999999999874
No 60
>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=63.98 E-value=5.2 Score=31.08 Aligned_cols=21 Identities=19% Similarity=0.464 Sum_probs=18.7
Q ss_pred CCCCCcHHHHHHHHHH-hCCHH
Q 011802 113 GVRGLGPESACQIVKS-VGDNV 133 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~-~gs~~ 133 (477)
.|||||+++|..|... |++.+
T Consensus 9 ~I~Gig~~~a~~L~~~G~~t~~ 30 (60)
T PF14520_consen 9 SIPGIGPKRAEKLYEAGIKTLE 30 (60)
T ss_dssp TSTTCHHHHHHHHHHTTCSSHH
T ss_pred cCCCCCHHHHHHHHhcCCCcHH
Confidence 7999999999999999 88753
No 61
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=63.49 E-value=7 Score=38.30 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHh
Q 011802 94 FGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 94 L~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~ 129 (477)
++++.|+..-..---.++-.+||||+|+|.+|+-+-
T Consensus 93 ~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleL 128 (201)
T COG0632 93 LDPEELAQAIANEDVKALSKIPGIGKKTAERIVLEL 128 (201)
T ss_pred CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHH
Confidence 356666554333223455799999999999998653
No 62
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.90 E-value=5.1 Score=39.10 Aligned_cols=35 Identities=20% Similarity=0.239 Sum_probs=23.7
Q ss_pred CCHHHHHHHHHHhC-CCCCCCCCCCcHHHHHHHHHHh
Q 011802 94 FGRNSLITLALLLG-SDYSQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 94 L~r~q~IdlaiL~G-sDY~pGVpGIG~ktA~kLIk~~ 129 (477)
+++++|+. ++..| ..-+..|||||+|||-+|+-+.
T Consensus 94 ~~~~~l~~-aI~~~D~~~L~~ipGIGkKtAerIilEL 129 (203)
T PRK14602 94 FRPDDLRR-LVAEEDVAALTRVSGIGKKTAQHIFLEL 129 (203)
T ss_pred CCHHHHHH-HHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 46665553 33333 2344699999999999999653
No 63
>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=61.76 E-value=6.2 Score=32.94 Aligned_cols=24 Identities=25% Similarity=0.567 Sum_probs=20.5
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHH
Q 011802 110 YSQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 110 Y~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
-+..|||||+.+|..|+.+.|+..
T Consensus 3 ~l~sipGig~~~a~~llaeigd~~ 26 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLAEIGDIS 26 (87)
T ss_pred hhcCCCCccHHHHHHHHHHHcCch
Confidence 356899999999999999998753
No 64
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=56.54 E-value=10 Score=43.47 Aligned_cols=23 Identities=13% Similarity=0.173 Sum_probs=20.9
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHH
Q 011802 111 SQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
+..|||||++++.+|++.||+.+
T Consensus 610 L~~IpGiG~kr~~~LL~~FgS~~ 632 (691)
T PRK14672 610 FERLPHVGKVRAHRLLAHFGSFR 632 (691)
T ss_pred cccCCCCCHHHHHHHHHHhcCHH
Confidence 35999999999999999999974
No 65
>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=54.01 E-value=9.1 Score=26.55 Aligned_cols=14 Identities=21% Similarity=0.411 Sum_probs=11.2
Q ss_pred CCCCCcHHHHHHHH
Q 011802 113 GVRGLGPESACQIV 126 (477)
Q Consensus 113 GVpGIG~ktA~kLI 126 (477)
-++|||++|+.+|-
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 66
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=50.64 E-value=14 Score=41.82 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=20.3
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 011802 112 QGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
.+|||||++++.+|++.||+.+
T Consensus 546 ~~IpGIG~k~~k~Ll~~FgS~~ 567 (598)
T PRK00558 546 DDIPGIGPKRRKALLKHFGSLK 567 (598)
T ss_pred hhCCCcCHHHHHHHHHHcCCHH
Confidence 4999999999999999999964
No 67
>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=50.47 E-value=48 Score=25.68 Aligned_cols=37 Identities=27% Similarity=0.629 Sum_probs=32.1
Q ss_pred CceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHHHH
Q 011802 288 GKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 327 (477)
Q Consensus 288 gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~~ 327 (477)
|-=-|-+.|.+ + ..++||+.++..-||.+|-+|=++.
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 77788999999 5 4568999999999999999997654
No 68
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=50.44 E-value=15 Score=36.92 Aligned_cols=23 Identities=17% Similarity=0.342 Sum_probs=20.6
Q ss_pred CCCCCCCcHHHHHHHHHH-hCCHH
Q 011802 111 SQGVRGLGPESACQIVKS-VGDNV 133 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~-~gs~~ 133 (477)
+..|||||+++|.+|++. |++.+
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve 28 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVE 28 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHH
Confidence 458999999999999999 99964
No 69
>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=47.72 E-value=22 Score=41.03 Aligned_cols=35 Identities=20% Similarity=0.424 Sum_probs=26.7
Q ss_pred hCCCHHHHHHHHHHhCCCCCCCCCCCcHHHHHHHHHHhCCH
Q 011802 92 LGFGRNSLITLALLLGSDYSQGVRGLGPESACQIVKSVGDN 132 (477)
Q Consensus 92 lgL~r~q~IdlaiL~GsDY~pGVpGIG~ktA~kLIk~~gs~ 132 (477)
+--+.+.++.|.. . ..|||||+++|.+|+..||..
T Consensus 73 ~p~~~~~i~~yL~-s-----~~~~GIG~~~A~~iv~~fg~~ 107 (720)
T TIGR01448 73 APTSKEGIVAYLS-S-----RSIKGVGKKLAQRIVKTFGEA 107 (720)
T ss_pred CCCCHHHHHHHHh-c-----CCCCCcCHHHHHHHHHHhCHh
Confidence 3346677887644 2 249999999999999999974
No 70
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=47.24 E-value=12 Score=36.32 Aligned_cols=36 Identities=19% Similarity=0.413 Sum_probs=22.8
Q ss_pred CCHHHHHHHHHHhCC-CCCCCCCCCcHHHHHHHHHHhC
Q 011802 94 FGRNSLITLALLLGS-DYSQGVRGLGPESACQIVKSVG 130 (477)
Q Consensus 94 L~r~q~IdlaiL~Gs-DY~pGVpGIG~ktA~kLIk~~g 130 (477)
+++++|+..- ..+. ..+-.|||||+|||-+|+-+..
T Consensus 93 ~~~~~l~~aI-~~~D~~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 93 MNAEALASAI-ISGNAELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred CCHHHHHHHH-HhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4566654432 2231 2235899999999999986533
No 71
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=46.84 E-value=18 Score=35.52 Aligned_cols=17 Identities=29% Similarity=0.554 Sum_probs=14.3
Q ss_pred CCCCCCcHHHHHHHHHH
Q 011802 112 QGVRGLGPESACQIVKS 128 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~ 128 (477)
.-+||||+|+|.++.-.
T Consensus 15 ~kLPGvG~KsA~R~Afh 31 (198)
T COG0353 15 KKLPGVGPKSAQRLAFH 31 (198)
T ss_pred hhCCCCChhHHHHHHHH
Confidence 46899999999988754
No 72
>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=46.13 E-value=16 Score=35.23 Aligned_cols=17 Identities=18% Similarity=0.354 Sum_probs=14.9
Q ss_pred CCCCCCCcHHHHHHHHH
Q 011802 111 SQGVRGLGPESACQIVK 127 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk 127 (477)
+-.|||||+|||.+++-
T Consensus 109 L~~ipGiGkKtAerIil 125 (191)
T TIGR00084 109 LVKIPGVGKKTAERLLL 125 (191)
T ss_pred HHhCCCCCHHHHHHHHH
Confidence 35999999999999983
No 73
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=45.85 E-value=16 Score=41.08 Aligned_cols=23 Identities=26% Similarity=0.543 Sum_probs=20.9
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHH
Q 011802 111 SQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
+..|||||++++.+|++.||+.+
T Consensus 527 L~~IpGIG~kr~~~LL~~FGS~~ 549 (577)
T PRK14668 527 LDDVPGVGPETRKRLLRRFGSVE 549 (577)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHH
Confidence 46999999999999999999974
No 74
>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=42.33 E-value=22 Score=40.57 Aligned_cols=21 Identities=29% Similarity=0.438 Sum_probs=16.5
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 011802 113 GVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~gs~~ 133 (477)
||||||+++|..|++.|++.+
T Consensus 502 gIpgVG~~~ak~L~~~f~sl~ 522 (652)
T TIGR00575 502 GIRHVGEVTAKNLAKHFGTLD 522 (652)
T ss_pred cCCCcCHHHHHHHHHHhCCHH
Confidence 788888888888888888754
No 75
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=42.27 E-value=23 Score=40.81 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=17.7
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 011802 113 GVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~gs~~ 133 (477)
||||||+++|..|++.|++.+
T Consensus 532 gIpgIG~~~ak~L~~~F~si~ 552 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFE 552 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHH
Confidence 788888888888888888864
No 76
>PRK00076 recR recombination protein RecR; Reviewed
Probab=42.16 E-value=38 Score=33.21 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=14.4
Q ss_pred CCCCCCcHHHHHHHHHH
Q 011802 112 QGVRGLGPESACQIVKS 128 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~ 128 (477)
.-+||||+|+|.+++-.
T Consensus 14 ~~LPGIG~KsA~Rla~~ 30 (196)
T PRK00076 14 RKLPGIGPKSAQRLAFH 30 (196)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999998865
No 77
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=41.49 E-value=23 Score=40.73 Aligned_cols=22 Identities=32% Similarity=0.502 Sum_probs=20.3
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 011802 112 QGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
..|||||++++.+|++.||+.+
T Consensus 640 ~~IPGIGpkr~k~LL~~FGSle 661 (694)
T PRK14666 640 QRVEGIGPATARLLWERFGSLQ 661 (694)
T ss_pred hhCCCCCHHHHHHHHHHhCCHH
Confidence 4899999999999999999974
No 78
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=41.18 E-value=40 Score=32.99 Aligned_cols=17 Identities=29% Similarity=0.573 Sum_probs=14.3
Q ss_pred CCCCCCcHHHHHHHHHH
Q 011802 112 QGVRGLGPESACQIVKS 128 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~ 128 (477)
.-+||||+|+|.+|+-.
T Consensus 14 ~~LPGIG~KsA~RlA~~ 30 (195)
T TIGR00615 14 KKLPGIGPKSAQRLAFH 30 (195)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 36899999999998754
No 79
>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=40.76 E-value=33 Score=30.65 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=15.5
Q ss_pred CCCCCcHHHHHHHHHHh
Q 011802 113 GVRGLGPESACQIVKSV 129 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~ 129 (477)
.+||||+++|.++|..+
T Consensus 72 ~lpGIG~~~A~~Ii~~R 88 (120)
T TIGR01259 72 ALPGIGPAKAKAIIEYR 88 (120)
T ss_pred cCCCCCHHHHHHHHHHH
Confidence 78999999999999875
No 80
>smart00300 ChSh Chromo Shadow Domain.
Probab=40.51 E-value=47 Score=26.30 Aligned_cols=39 Identities=28% Similarity=0.640 Sum_probs=33.2
Q ss_pred cCCceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHHHH
Q 011802 286 LQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEERR 327 (477)
Q Consensus 286 ~~gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~~ 327 (477)
..|-=-|-+.|.+ . ..++||+.++..-||.+|-+|=++.
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 5677778999999 5 4568999999999999999997654
No 81
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=39.91 E-value=25 Score=39.72 Aligned_cols=22 Identities=23% Similarity=0.521 Sum_probs=20.4
Q ss_pred CCCCCCcHHHHHHHHHHhCCHH
Q 011802 112 QGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
.+|||||++...+|++.||+..
T Consensus 533 d~I~GiG~~r~~~LL~~Fgs~~ 554 (581)
T COG0322 533 DDIPGIGPKRRKALLKHFGSLK 554 (581)
T ss_pred ccCCCcCHHHHHHHHHHhhCHH
Confidence 5999999999999999999974
No 82
>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=39.69 E-value=24 Score=30.38 Aligned_cols=28 Identities=11% Similarity=0.275 Sum_probs=21.7
Q ss_pred chHHHHHHHHHHCCCeeEEecCCCcEEe
Q 011802 35 EEAEAQCALLNLESLCDGCFSSDSDIFL 62 (477)
Q Consensus 35 gEAEAqcA~L~~~G~VD~ViS~DsD~ll 62 (477)
-..|+.+..++..+-+|+++|+|+|+|.
T Consensus 86 D~~D~~~l~~A~~~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 86 DKKDNKFLNTAYASKANALITGDTDLLV 113 (114)
T ss_pred CchhHHHHHHHHhcCCCEEEECCHHHhh
Confidence 3556666667777889999999999763
No 83
>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=38.69 E-value=27 Score=26.97 Aligned_cols=19 Identities=21% Similarity=0.487 Sum_probs=15.9
Q ss_pred CCCCCCCcHHHHHHHHHHh
Q 011802 111 SQGVRGLGPESACQIVKSV 129 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~~ 129 (477)
+-.|||||+++|-+|+...
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 4478999999999998753
No 84
>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=38.04 E-value=91 Score=24.57 Aligned_cols=46 Identities=26% Similarity=0.610 Sum_probs=35.8
Q ss_pred eeeeccccCCceeeEEEecccCcceeeeeehhhhhhhcchhHHHHHHH
Q 011802 279 GIIKSRKLQGKECFEVSWEESYGLKSSVVPADLIESACPEKIVEFEER 326 (477)
Q Consensus 279 ~I~K~R~~~gv~cyev~w~~~~~l~~s~vP~~lv~~a~Pe~v~~f~~~ 326 (477)
.|+..=...|-=-|=|.|.+.+ ..++||+.++...||.+|-.|-++
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 3444333447677889999877 477999999999999999999765
No 85
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=37.30 E-value=45 Score=31.05 Aligned_cols=15 Identities=33% Similarity=0.749 Sum_probs=13.7
Q ss_pred CCCCCcHHHHHHHHH
Q 011802 113 GVRGLGPESACQIVK 127 (477)
Q Consensus 113 GVpGIG~ktA~kLIk 127 (477)
.+||||+++|..++.
T Consensus 101 ~lpgIG~~kA~aIi~ 115 (149)
T COG1555 101 ALPGIGPKKAQAIID 115 (149)
T ss_pred HCCCCCHHHHHHHHH
Confidence 679999999999996
No 86
>PRK13844 recombination protein RecR; Provisional
Probab=35.89 E-value=57 Score=32.09 Aligned_cols=17 Identities=12% Similarity=0.227 Sum_probs=14.4
Q ss_pred CCCCCCcHHHHHHHHHH
Q 011802 112 QGVRGLGPESACQIVKS 128 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~ 128 (477)
.-+||||+|+|.+|+-.
T Consensus 18 ~~LPGIG~KsA~Rla~~ 34 (200)
T PRK13844 18 RKLPTIGKKSSQRLALY 34 (200)
T ss_pred HHCCCCCHHHHHHHHHH
Confidence 46899999999998865
No 87
>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=34.19 E-value=1.1e+02 Score=28.21 Aligned_cols=46 Identities=15% Similarity=0.017 Sum_probs=36.9
Q ss_pred chhHHHHHHHHHHHHHcCCC-----EEeccc--hHHHHHHHHHHCCCeeEEec
Q 011802 10 SEFSCMIKEAKALGLSLGVP-----CLEGVE--EAEAQCALLNLESLCDGCFS 55 (477)
Q Consensus 10 ~~~~~~i~~ik~LL~~~GIp-----~i~APg--EAEAqcA~L~~~G~VD~ViS 55 (477)
..+..+++-+.+.|+..|+. .+..|| |.=-.+..|.+.|-.|+|++
T Consensus 13 ~i~~~L~~ga~~~l~~~g~~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavI~ 65 (138)
T TIGR00114 13 DITDMLLKGAIDALKRLGAEVDNIDVIWVPGAFELPLAVKKLAETGKYDAVIA 65 (138)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 56788899999999999976 666897 65556667888888888876
No 88
>KOG2044 consensus 5'-3' exonuclease HKE1/RAT1 [Replication, recombination and repair; RNA processing and modification]
Probab=32.95 E-value=47 Score=38.87 Aligned_cols=92 Identities=13% Similarity=0.282 Sum_probs=59.9
Q ss_pred CCCEEe----ccchHHHHHHHHHH---C------CCeeEEecCCCcEEeeccc------EEEEeccCCC-----------
Q 011802 27 GVPCLE----GVEEAEAQCALLNL---E------SLCDGCFSSDSDIFLFGAR------TVYRDIWLGE----------- 76 (477)
Q Consensus 27 GIp~i~----APgEAEAqcA~L~~---~------G~VD~ViS~DsD~llFG~~------~Virn~~~~~----------- 76 (477)
+|.+|- .|||.|--+-...+ . .-+.++++-|.|++++|-- .|+|..+..+
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 455665 48999986554332 2 3478999999999999832 4677543300
Q ss_pred ----------------C---------ceEEEEeHHHHHH----HhCC---------CH--HHHHHHHHHhCCCCCCCCCC
Q 011802 77 ----------------R---------GYVVCYEMDDIER----KLGF---------GR--NSLITLALLLGSDYSQGVRG 116 (477)
Q Consensus 77 ----------------~---------~~v~~y~~~~I~~----~lgL---------~r--~q~IdlaiL~GsDY~pGVpG 116 (477)
+ +.+.+++..-+.+ ++-+ .| +.||.+|-++|.||+|.+|-
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 2355666654443 3322 22 66778999999999999997
Q ss_pred Cc
Q 011802 117 LG 118 (477)
Q Consensus 117 IG 118 (477)
+-
T Consensus 350 Le 351 (931)
T KOG2044|consen 350 LE 351 (931)
T ss_pred hh
Confidence 64
No 89
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=32.61 E-value=39 Score=34.41 Aligned_cols=21 Identities=29% Similarity=0.591 Sum_probs=19.6
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 011802 113 GVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~gs~~ 133 (477)
++||||++.|..|++.||+.+
T Consensus 186 s~pgig~~~a~~ll~~fgS~~ 206 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVE 206 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHH
Confidence 899999999999999999964
No 90
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=31.50 E-value=24 Score=41.46 Aligned_cols=24 Identities=13% Similarity=0.119 Sum_probs=21.1
Q ss_pred CCCCCCCCcHHHHHHHHHHhCCHH
Q 011802 110 YSQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 110 Y~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
|+-++||||++.|..|+..||++.
T Consensus 758 ~L~~lPgI~~~~a~~ll~~f~si~ 781 (814)
T TIGR00596 758 FLLKLPGVTKKNYRNLRKKVKSIR 781 (814)
T ss_pred HHHHCCCCCHHHHHHHHHHcCCHH
Confidence 444899999999999999999974
No 91
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=30.24 E-value=41 Score=38.61 Aligned_cols=13 Identities=23% Similarity=0.194 Sum_probs=8.3
Q ss_pred HHHHHHHcCCCEE
Q 011802 19 AKALGLSLGVPCL 31 (477)
Q Consensus 19 ik~LL~~~GIp~i 31 (477)
..+.|+.+|+|+.
T Consensus 241 ~l~~L~~~GF~v~ 253 (665)
T PRK07956 241 ALEFLKAWGFPVN 253 (665)
T ss_pred HHHHHHHCCCCcC
Confidence 4456777777764
No 92
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=29.64 E-value=58 Score=30.11 Aligned_cols=27 Identities=22% Similarity=0.230 Sum_probs=18.6
Q ss_pred CCCCCcHHHHHHHHHH--hCCHHHHHHHH
Q 011802 113 GVRGLGPESACQIVKS--VGDNVVLQRIA 139 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~--~gs~~iL~~i~ 139 (477)
.+|||||+.|.++++. |.+.+=+.++.
T Consensus 65 ~lpGigP~~A~~IV~nGpf~sveDL~~V~ 93 (132)
T PRK02515 65 QFPGMYPTLAGKIVKNAPYDSVEDVLNLP 93 (132)
T ss_pred HCCCCCHHHHHHHHHCCCCCCHHHHHcCC
Confidence 4799999999999963 55544333343
No 93
>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]
Probab=28.80 E-value=1.9e+02 Score=31.23 Aligned_cols=108 Identities=19% Similarity=0.228 Sum_probs=63.8
Q ss_pred cchhHHHHHHHHHHHHHcCCCEEec--c---chHHHHHHHHHHCCCeeEEecCCCcEEeecccEEEEeccCCCCceEEEE
Q 011802 9 GSEFSCMIKEAKALGLSLGVPCLEG--V---EEAEAQCALLNLESLCDGCFSSDSDIFLFGARTVYRDIWLGERGYVVCY 83 (477)
Q Consensus 9 ~~~~~~~i~~ik~LL~~~GIp~i~A--P---gEAEAqcA~L~~~G~VD~ViS~DsD~llFG~~~Virn~~~~~~~~v~~y 83 (477)
++...+.+....+..-..||.||.. | |++|-+++..-..|+-. -+.+.. .+-.+. +=
T Consensus 29 ~~id~~~~~~~i~~aie~GiNyidTA~~Yh~g~sE~~lgkaL~~~~Re--------kv~LaT--Klp~~~--------~~ 90 (391)
T COG1453 29 GSIDEENANETIDYAIEHGINYIDTAWPYHGGESEEFLGKALKDGYRE--------KVKLAT--KLPSWP--------VK 90 (391)
T ss_pred CCccHHHHHHHHHHHHHcCCceEeecccccCCCchHHHHHHhhhcccc--------eEEEEe--ecCCcc--------cc
Confidence 3444555556666666789999995 3 59999999877666521 111111 111011 11
Q ss_pred eHHHHHHHhCCCHHHHHHHHHHhCCCCCC--CCCCCcHHHHHHHHHHhCCHHHHHHHHhcC
Q 011802 84 EMDDIERKLGFGRNSLITLALLLGSDYSQ--GVRGLGPESACQIVKSVGDNVVLQRIASEG 142 (477)
Q Consensus 84 ~~~~I~~~lgL~r~q~IdlaiL~GsDY~p--GVpGIG~ktA~kLIk~~gs~~iL~~i~~~~ 142 (477)
+.+++.+.|. +|| -=+|.||++ +|.|++. .-.+-++++|..+.+++++.+|
T Consensus 91 ~~edm~r~fn---eqL----ekl~~Dy~D~yliH~l~~-e~~~k~~~~g~~df~~kak~eG 143 (391)
T COG1453 91 DREDMERIFN---EQL----EKLGTDYIDYYLIHGLNT-ETWEKIERLGVFDFLEKAKAEG 143 (391)
T ss_pred CHHHHHHHHH---HHH----HHhCCchhhhhhhccccH-HHHHHHHccChHHHHHHHHhcC
Confidence 3334433321 121 236889997 9999999 6677777888777777766543
No 94
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=28.56 E-value=37 Score=35.47 Aligned_cols=17 Identities=35% Similarity=0.686 Sum_probs=15.4
Q ss_pred CCCCCcHHHHHHHHHHhC
Q 011802 113 GVRGLGPESACQIVKSVG 130 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~g 130 (477)
.||||||++|..|.+ .|
T Consensus 93 ~i~GiGpk~a~~l~~-lG 109 (334)
T smart00483 93 NVFGVGPKTAAKWYR-KG 109 (334)
T ss_pred ccCCcCHHHHHHHHH-hC
Confidence 899999999999998 54
No 95
>PRK13766 Hef nuclease; Provisional
Probab=28.16 E-value=49 Score=37.97 Aligned_cols=23 Identities=17% Similarity=0.345 Sum_probs=20.5
Q ss_pred CCCCCCCcHHHHHHHHHHhCCHH
Q 011802 111 SQGVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLIk~~gs~~ 133 (477)
+.++||||+++|.+|++.||+..
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~ 739 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVE 739 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHH
Confidence 35899999999999999999963
No 96
>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=27.98 E-value=1.5e+02 Score=27.47 Aligned_cols=46 Identities=13% Similarity=0.001 Sum_probs=37.7
Q ss_pred chhHHHHHHHHHHHHHcCC-----CEEeccc--hHHHHHHHHHHCCCeeEEec
Q 011802 10 SEFSCMIKEAKALGLSLGV-----PCLEGVE--EAEAQCALLNLESLCDGCFS 55 (477)
Q Consensus 10 ~~~~~~i~~ik~LL~~~GI-----p~i~APg--EAEAqcA~L~~~G~VD~ViS 55 (477)
.....+++.+.+.|...|+ ..+..|| |-=-.+..|.+.|-.|+|+.
T Consensus 16 ~i~~~ll~~a~~~l~~~g~~~~~i~~~~VPGa~ElP~a~~~l~~~~~~Davi~ 68 (144)
T PF00885_consen 16 EITDRLLEGALEELKRHGVAEENIEVIRVPGAFELPLAAKRLAESGRYDAVIA 68 (144)
T ss_dssp HHHHHHHHHHHHHHHHTTTTGGCEEEEEESSGGGHHHHHHHHHHCSTESEEEE
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEEcCCHHHHHHHHHHHhcccCccEEEE
Confidence 4677888999999999987 6677787 66667778889998998876
No 97
>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=26.62 E-value=45 Score=26.58 Aligned_cols=16 Identities=25% Similarity=0.318 Sum_probs=13.6
Q ss_pred CCCCCCCcHHHHHHHH
Q 011802 111 SQGVRGLGPESACQIV 126 (477)
Q Consensus 111 ~pGVpGIG~ktA~kLI 126 (477)
..++||||.++|.++-
T Consensus 49 ~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKID 64 (68)
T ss_dssp HCTSTTTTHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHH
Confidence 3699999999998874
No 98
>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=25.99 E-value=1.3e+02 Score=24.61 Aligned_cols=40 Identities=18% Similarity=0.185 Sum_probs=31.5
Q ss_pred HHHHHcCCCEEeccchHHHHHHHHHHCCCeeEEecCCCcEEeec
Q 011802 21 ALGLSLGVPCLEGVEEAEAQCALLNLESLCDGCFSSDSDIFLFG 64 (477)
Q Consensus 21 ~LL~~~GIp~i~APgEAEAqcA~L~~~G~VD~ViS~DsD~llFG 64 (477)
.+.+.++++. .|+|..++.+...|.+.|-+..-..++.|+
T Consensus 65 ~ia~~l~~~~----~~vE~~l~~~I~~~~i~~~ID~~~~~v~~~ 104 (105)
T PF01399_consen 65 EIAKALQLSE----EEVESILIDLISNGLIKAKIDQVNGVVVFS 104 (105)
T ss_dssp HHHHHHTCCH----HHHHHHHHHHHHTTSSEEEEETTTTEEEE-
T ss_pred HHHHHhccch----HHHHHHHHHHHHCCCEEEEEECCCCEEEec
Confidence 4455566655 688899999999999999999888777765
No 99
>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=25.92 E-value=32 Score=34.50 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=24.4
Q ss_pred CCCEEec----cchHHHHHHHHHH---------CCCeeEEecCCCcEEeec
Q 011802 27 GVPCLEG----VEEAEAQCALLNL---------ESLCDGCFSSDSDIFLFG 64 (477)
Q Consensus 27 GIp~i~A----PgEAEAqcA~L~~---------~G~VD~ViS~DsD~llFG 64 (477)
++.++.+ |||+|--+....+ .....+|+|.|+|+++++
T Consensus 172 ~~~vi~S~~~vpGEGE~KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~ 222 (237)
T PF03159_consen 172 NLKVIFSGSDVPGEGEHKIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLS 222 (237)
T ss_dssp CSEEEEE-TTSSS-HHHHHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHH
T ss_pred ceEEEEeCCCCCCccHHHHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHH
Confidence 4566664 7999986554322 256889999999999986
No 100
>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=25.75 E-value=46 Score=34.33 Aligned_cols=17 Identities=35% Similarity=0.761 Sum_probs=14.8
Q ss_pred CCCCCcHHHHHHHHHHhC
Q 011802 113 GVRGLGPESACQIVKSVG 130 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~g 130 (477)
+|+||||++|.+|. ..|
T Consensus 89 ~i~GiGpk~a~~l~-~lG 105 (307)
T cd00141 89 RVPGVGPKTARKLY-ELG 105 (307)
T ss_pred cCCCCCHHHHHHHH-HcC
Confidence 89999999999999 533
No 101
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=25.71 E-value=31 Score=35.37 Aligned_cols=35 Identities=17% Similarity=0.041 Sum_probs=27.2
Q ss_pred CcchhHHHHHHHHHHHHHcCCCEEeccchHHHHHHH
Q 011802 8 MGSEFSCMIKEAKALGLSLGVPCLEGVEEAEAQCAL 43 (477)
Q Consensus 8 ~~~~~~~~i~~ik~LL~~~GIp~i~APgEAEAqcA~ 43 (477)
.+..+..+......+|+.+|++ .++|.|++|+||+
T Consensus 98 ~~~i~~~~~~~~~~~l~~~G~e-add~i~t~A~~a~ 132 (310)
T COG0258 98 IPILTELLVALGIPLLELMGIE-ADDPIETLAQKAY 132 (310)
T ss_pred HHHHHHHHHHhCcHhhhcCCCC-cchhHHHHHHHHH
Confidence 3445556667778888899998 8888888888886
No 102
>PRK12419 riboflavin synthase subunit beta; Provisional
Probab=25.65 E-value=1.5e+02 Score=28.09 Aligned_cols=46 Identities=13% Similarity=-0.056 Sum_probs=36.6
Q ss_pred chhHHHHHHHHHHHHHcC-----CCEEeccc--hHHHHHHHHHHCCCeeEEec
Q 011802 10 SEFSCMIKEAKALGLSLG-----VPCLEGVE--EAEAQCALLNLESLCDGCFS 55 (477)
Q Consensus 10 ~~~~~~i~~ik~LL~~~G-----Ip~i~APg--EAEAqcA~L~~~G~VD~ViS 55 (477)
..+..+++-+.+.|...| |.++..|| |.=..+..|.+.|..|+|+.
T Consensus 23 ~It~~Ll~gA~~~l~~~G~~~~~i~v~~VPGA~EiP~~a~~l~~~~~yDaiIa 75 (158)
T PRK12419 23 DIVDQARKGFVAEIAARGGAASQVDIFDVPGAFEIPLHAQTLAKTGRYAAIVA 75 (158)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 467788999999999999 56677897 66666777888888888776
No 103
>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=25.25 E-value=58 Score=25.77 Aligned_cols=15 Identities=33% Similarity=0.461 Sum_probs=13.4
Q ss_pred CCCCcHHHHHHHHHH
Q 011802 114 VRGLGPESACQIVKS 128 (477)
Q Consensus 114 VpGIG~ktA~kLIk~ 128 (477)
+||||+++|.+|+..
T Consensus 22 ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 22 MNGVGLKKAEAIVSY 36 (69)
T ss_pred CCCCCHHHHHHHHHH
Confidence 789999999999976
No 104
>COG4277 Predicted DNA-binding protein with the Helix-hairpin-helix motif [General function prediction only]
Probab=24.27 E-value=95 Score=32.82 Aligned_cols=48 Identities=29% Similarity=0.339 Sum_probs=35.2
Q ss_pred EEEeHHHHHHHhCCCHHHHHHH--------------HHHhCCCCCC------------CCCCCcHHHHHHHHHH
Q 011802 81 VCYEMDDIERKLGFGRNSLITL--------------ALLLGSDYSQ------------GVRGLGPESACQIVKS 128 (477)
Q Consensus 81 ~~y~~~~I~~~lgL~r~q~Idl--------------aiL~GsDY~p------------GVpGIG~ktA~kLIk~ 128 (477)
..|..+++...||+..+.+.+- ++|--.|..| -|||||+|+|..++..
T Consensus 276 RLYQADwLlrfYgF~~~Ei~~~g~~~ld~~lDPK~~wAl~~~d~FPVdvn~A~~~~llRVPGiG~ksa~rIv~~ 349 (404)
T COG4277 276 RLYQADWLLRFYGFSADEILASGGDFLDPDLDPKTAWALKHMDRFPVDVNKAPYKELLRVPGIGVKSARRIVMT 349 (404)
T ss_pred HHHHHHHHHHHhCCCHHHHHhcCCCccCCCCChhhHHHHhccccccccccccCHHHhcccCCCChHHHHHHHHH
Confidence 3678899999999988777642 3444344333 6899999999999865
No 105
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=23.10 E-value=60 Score=37.29 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=19.9
Q ss_pred CCCCCcHHHHHHHHHHhCCHH
Q 011802 113 GVRGLGPESACQIVKSVGDNV 133 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~~gs~~ 133 (477)
||+.||.++|..|.+.|++.+
T Consensus 515 GIr~VG~~~Ak~La~~f~sl~ 535 (667)
T COG0272 515 GIRHVGETTAKSLARHFGTLE 535 (667)
T ss_pred CCchhhHHHHHHHHHHhhhHH
Confidence 999999999999999999975
No 106
>TIGR00290 MJ0570_dom MJ0570-related uncharacterized domain. Proteins with this uncharacterized domain include two apparent ortholog families in the Archaea, one of which is universal among the first four completed archaeal genomes, and YLR143W, a much longer protein from Saccharomyces cerevisiae. The domain comprises the full length of the archaeal proteins and the first third of the yeast protein.
Probab=22.44 E-value=1.7e+02 Score=29.04 Aligned_cols=42 Identities=12% Similarity=0.136 Sum_probs=26.7
Q ss_pred HHHHHHHHHHcCCCEEe--ccchHH----HHHHHHHHCCCeeEEecCCC
Q 011802 16 IKEAKALGLSLGVPCLE--GVEEAE----AQCALLNLESLCDGCFSSDS 58 (477)
Q Consensus 16 i~~ik~LL~~~GIp~i~--APgEAE----AqcA~L~~~G~VD~ViS~Ds 58 (477)
++.++...++||||.+. .+++-+ +.-..|...| +++|+++|-
T Consensus 47 ~~~~~~qA~algipl~~~~~~~~~e~~~e~l~~~l~~~g-v~~vv~GdI 94 (223)
T TIGR00290 47 AHLTDLQAESIGIPLIKLYTEGTEEDEVEELKGILHTLD-VEAVVFGAI 94 (223)
T ss_pred HHHHHHHHHHcCCCeEEeecCCCccHHHHHHHHHHHHcC-CCEEEECCc
Confidence 36677888999999886 333223 3334445555 777777665
No 107
>TIGR00289 conserved hypothetical protein TIGR00289. Homologous proteins related to MJ0570 of Methanococcus jannaschii include both the apparent orthologs found by this model above the trusted cutoff, the much longer protein YLR143W from Saccharomyces cerevisiae, and second homologous proteins from Archaeoglobus fulgidus and Pyrococcus horikoshii that appear to represent a second orthologous group.
Probab=22.43 E-value=1.9e+02 Score=28.81 Aligned_cols=43 Identities=12% Similarity=0.162 Sum_probs=27.8
Q ss_pred HHHHHHHHHHcCCCEEec--cchHH----HHHHHHHHCCCeeEEecCCCc
Q 011802 16 IKEAKALGLSLGVPCLEG--VEEAE----AQCALLNLESLCDGCFSSDSD 59 (477)
Q Consensus 16 i~~ik~LL~~~GIp~i~A--PgEAE----AqcA~L~~~G~VD~ViS~DsD 59 (477)
++.++...+++|||.+.. +++.| +....|...| +++|+++|-+
T Consensus 47 ~~~~~~qA~algiPl~~~~~~~~~e~~~~~l~~~l~~~g-v~~vv~GdI~ 95 (222)
T TIGR00289 47 LHLTDLVAEAVGIPLIKLYTSGEEEKEVEDLAGQLGELD-VEALCIGAIE 95 (222)
T ss_pred HHHHHHHHHHcCCCeEEEEcCCchhHHHHHHHHHHHHcC-CCEEEECccc
Confidence 366788899999997753 45333 3344454455 7777776653
No 108
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=21.73 E-value=68 Score=31.11 Aligned_cols=21 Identities=24% Similarity=0.770 Sum_probs=18.4
Q ss_pred CCCCCCcHHHHHHHHHHhCCH
Q 011802 112 QGVRGLGPESACQIVKSVGDN 132 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs~ 132 (477)
.|-||+|..|++++|+.+|-.
T Consensus 6 TGTPGvGKTT~~~~L~~lg~~ 26 (180)
T COG1936 6 TGTPGVGKTTVCKLLRELGYK 26 (180)
T ss_pred eCCCCCchHHHHHHHHHhCCc
Confidence 599999999999999977653
No 109
>PLN02404 6,7-dimethyl-8-ribityllumazine synthase
Probab=21.64 E-value=2.1e+02 Score=26.60 Aligned_cols=46 Identities=11% Similarity=-0.080 Sum_probs=35.9
Q ss_pred chhHHHHHHHHHHHHHcCC-----CEEeccc--hHHHHHHHHHHCCCeeEEec
Q 011802 10 SEFSCMIKEAKALGLSLGV-----PCLEGVE--EAEAQCALLNLESLCDGCFS 55 (477)
Q Consensus 10 ~~~~~~i~~ik~LL~~~GI-----p~i~APg--EAEAqcA~L~~~G~VD~ViS 55 (477)
..+..+++-+.+.|...|+ .++..|| |.=-.+..|.+.|-.|+|++
T Consensus 20 ~I~~~Ll~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~s~~~DavIa 72 (141)
T PLN02404 20 IITKNLLEGALETFKRYSVKEENIDVVWVPGSFEIPVVAQRLAKSGKYDAILC 72 (141)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEEcCcHHHHHHHHHHHHhcCCCCEEEE
Confidence 5678889999999999997 4566787 65556667888887888776
No 110
>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=21.14 E-value=68 Score=27.91 Aligned_cols=20 Identities=10% Similarity=0.210 Sum_probs=16.1
Q ss_pred CCCCCCcHHHHHHHHHH-hCC
Q 011802 112 QGVRGLGPESACQIVKS-VGD 131 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~-~gs 131 (477)
..|||||+.+|..|..- +.+
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s 35 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRS 35 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCC
Confidence 47999999999999864 444
No 111
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=20.93 E-value=68 Score=31.64 Aligned_cols=16 Identities=19% Similarity=0.638 Sum_probs=14.2
Q ss_pred CCCCCcHHHHHHHHHH
Q 011802 113 GVRGLGPESACQIVKS 128 (477)
Q Consensus 113 GVpGIG~ktA~kLIk~ 128 (477)
.+||||+|||--++..
T Consensus 123 ~lpGIG~KTAd~vL~~ 138 (208)
T PRK01229 123 NIKGIGYKEASHFLRN 138 (208)
T ss_pred cCCCCcHHHHHHHHHH
Confidence 8999999999888854
No 112
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=20.71 E-value=69 Score=30.78 Aligned_cols=20 Identities=35% Similarity=0.523 Sum_probs=17.0
Q ss_pred CCCCCCcHHHHHHHHHHhCC
Q 011802 112 QGVRGLGPESACQIVKSVGD 131 (477)
Q Consensus 112 pGVpGIG~ktA~kLIk~~gs 131 (477)
-.|||||+|+|.+++..+.+
T Consensus 111 ~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 111 TKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HhCCCCCHHHHHHHHHHHHH
Confidence 48999999999999987543
No 113
>PRK00061 ribH 6,7-dimethyl-8-ribityllumazine synthase; Provisional
Probab=20.22 E-value=2.2e+02 Score=26.79 Aligned_cols=46 Identities=13% Similarity=0.004 Sum_probs=35.2
Q ss_pred chhHHHHHHHHHHHHHcCC-----CEEeccc--hHHHHHHHHHHCCCeeEEec
Q 011802 10 SEFSCMIKEAKALGLSLGV-----PCLEGVE--EAEAQCALLNLESLCDGCFS 55 (477)
Q Consensus 10 ~~~~~~i~~ik~LL~~~GI-----p~i~APg--EAEAqcA~L~~~G~VD~ViS 55 (477)
..+..++.-+.+.|...|+ ..+..|| |-=-.+..|.+.+-.|+|++
T Consensus 25 ~i~~~l~~ga~~~l~~~gv~~~~i~v~~VPGa~EiP~a~~~l~~~~~~DavIa 77 (154)
T PRK00061 25 FITDALLEGALDALKRHGVSEENIDVVRVPGAFEIPLAAKKLAESGKYDAVIA 77 (154)
T ss_pred HHHHHHHHHHHHHHHHcCCCccceEEEECCCHHHHHHHHHHHHHcCCCCEEEE
Confidence 4567889999999999994 4555797 55556667888887888876
Done!