Query psy11328
Match_columns 410
No_of_seqs 187 out of 609
Neff 4.7
Searched_HMMs 46136
Date Fri Aug 16 15:33:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11328.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11328hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR00596 rad1 DNA repair prot 100.0 2.5E-82 5.5E-87 690.3 35.0 315 6-403 468-812 (814)
2 KOG0442|consensus 100.0 1.5E-79 3.2E-84 655.1 27.6 317 5-404 535-877 (892)
3 PRK13766 Hef nuclease; Provisi 100.0 2.5E-54 5.5E-59 466.9 31.3 294 10-404 437-772 (773)
4 COG1948 MUS81 ERCC4-type nucle 100.0 9E-47 2E-51 363.3 20.3 213 96-404 26-239 (254)
5 PF02732 ERCC4: ERCC4 domain; 99.9 1.4E-22 3.1E-27 174.7 13.7 127 102-260 1-143 (143)
6 KOG2379|consensus 99.7 5.2E-17 1.1E-21 168.6 16.2 127 97-263 230-373 (501)
7 KOG2841|consensus 99.7 1.2E-15 2.5E-20 146.1 15.4 198 95-404 53-252 (254)
8 COG1111 MPH1 ERCC4-like helica 99.5 7.8E-14 1.7E-18 145.5 7.9 69 10-78 439-507 (542)
9 TIGR00597 rad10 DNA repair pro 98.2 1E-05 2.2E-10 70.6 8.8 105 99-257 2-111 (112)
10 PF12826 HHH_2: Helix-hairpin- 98.1 2E-06 4.3E-11 67.3 3.1 51 353-403 8-59 (64)
11 PRK14669 uvrC excinuclease ABC 97.5 0.00014 2.9E-09 79.5 6.7 51 352-403 556-606 (624)
12 PRK14667 uvrC excinuclease ABC 97.4 0.00025 5.4E-09 76.7 6.0 60 341-401 507-567 (567)
13 PRK14670 uvrC excinuclease ABC 97.3 0.00026 5.7E-09 76.6 5.3 55 348-402 514-569 (574)
14 COG5241 RAD10 Nucleotide excis 97.2 0.00011 2.3E-09 69.4 1.1 185 97-404 33-224 (224)
15 PF14520 HHH_5: Helix-hairpin- 97.1 0.00088 1.9E-08 51.4 5.2 46 355-400 12-59 (60)
16 TIGR00575 dnlj DNA ligase, NAD 97.1 0.0012 2.5E-08 72.7 7.4 50 353-403 503-554 (652)
17 PRK12766 50S ribosomal protein 97.1 0.001 2.2E-08 64.7 6.1 52 350-401 5-58 (232)
18 PRK14351 ligA NAD-dependent DN 97.0 0.0015 3.4E-08 72.2 7.1 86 294-403 497-584 (689)
19 PRK07956 ligA NAD-dependent DN 96.9 0.0017 3.6E-08 71.6 7.1 50 353-403 516-567 (665)
20 PRK13482 DNA integrity scannin 96.8 0.0022 4.7E-08 65.9 5.9 53 349-401 288-341 (352)
21 PRK14671 uvrC excinuclease ABC 96.7 0.0028 6.1E-08 69.4 6.1 46 354-400 575-620 (621)
22 PRK00558 uvrC excinuclease ABC 96.6 0.003 6.5E-08 68.9 5.6 49 352-401 547-597 (598)
23 COG0322 UvrC Nuclease subunit 96.4 0.0032 7E-08 68.5 4.7 50 349-399 531-581 (581)
24 PRK14666 uvrC excinuclease ABC 96.2 0.0075 1.6E-07 66.8 5.8 54 350-403 639-693 (694)
25 PRK14672 uvrC excinuclease ABC 95.9 0.016 3.4E-07 64.2 6.8 65 337-401 597-662 (691)
26 PRK14668 uvrC excinuclease ABC 95.9 0.01 2.3E-07 64.5 5.4 47 352-399 529-577 (577)
27 COG0272 Lig NAD-dependent DNA 95.5 0.024 5.1E-07 62.5 6.0 137 240-403 418-567 (667)
28 KOG0354|consensus 95.2 0.044 9.6E-07 61.1 7.1 59 10-71 488-547 (746)
29 PRK14350 ligA NAD-dependent DN 95.1 0.05 1.1E-06 60.3 7.2 86 294-402 471-564 (669)
30 PRK00254 ski2-like helicase; P 94.8 0.045 9.8E-07 60.5 5.9 54 350-403 647-702 (720)
31 PF03834 Rad10: Binding domain 94.3 0.048 1E-06 44.1 3.4 62 99-169 2-68 (69)
32 PRK00116 ruvA Holliday junctio 94.2 0.092 2E-06 49.4 5.7 49 356-404 81-133 (192)
33 PRK08097 ligB NAD-dependent DN 93.8 0.12 2.7E-06 56.2 6.4 83 294-402 460-543 (562)
34 TIGR02236 recomb_radA DNA repa 93.2 0.16 3.6E-06 50.2 5.8 49 352-400 3-53 (310)
35 PRK04301 radA DNA repair and r 91.4 0.35 7.7E-06 48.3 5.6 52 350-401 8-61 (317)
36 TIGR00426 competence protein C 90.1 0.38 8.2E-06 37.7 3.6 39 356-399 25-67 (69)
37 COG1623 Predicted nucleic-acid 89.0 0.8 1.7E-05 46.5 5.8 52 349-400 294-346 (349)
38 TIGR00194 uvrC excinuclease AB 85.9 0.64 1.4E-05 50.9 3.3 32 350-381 543-574 (574)
39 TIGR01259 comE comEA protein. 85.9 0.54 1.2E-05 41.3 2.2 43 356-400 76-119 (120)
40 PLN03142 Probable chromatin-re 84.7 2.3 5E-05 49.7 7.2 52 14-65 558-612 (1033)
41 smart00611 SEC63 Domain of unk 84.0 2.1 4.6E-05 42.1 5.8 55 349-403 152-208 (312)
42 PRK00024 hypothetical protein; 84.0 1.4 3E-05 42.6 4.3 40 359-398 45-85 (224)
43 PF02889 Sec63: Sec63 Brl doma 82.5 2.3 5E-05 41.7 5.3 55 349-403 149-205 (314)
44 COG2003 RadC DNA repair protei 79.4 2.4 5.2E-05 41.5 4.1 29 359-387 45-73 (224)
45 cd00080 HhH2_motif Helix-hairp 78.6 1.6 3.5E-05 35.2 2.3 28 353-380 27-54 (75)
46 TIGR00608 radc DNA repair prot 77.5 3.1 6.8E-05 40.2 4.3 39 359-397 36-78 (218)
47 PRK01172 ski2-like helicase; P 76.4 4.5 9.7E-05 44.6 5.6 52 349-400 613-666 (674)
48 PRK02362 ski2-like helicase; P 73.4 5.7 0.00012 44.4 5.6 49 353-402 657-706 (737)
49 PF00633 HHH: Helix-hairpin-he 72.4 5.5 0.00012 27.1 3.2 29 370-398 1-30 (30)
50 PRK03352 DNA polymerase IV; Va 71.7 7.8 0.00017 39.0 5.7 49 352-401 181-230 (346)
51 TIGR01954 nusA_Cterm_rpt trans 71.7 8.9 0.00019 27.6 4.5 41 357-397 2-44 (50)
52 cd01702 PolY_Pol_eta DNA Polym 70.3 7.3 0.00016 40.1 5.2 50 352-402 186-239 (359)
53 PRK01216 DNA polymerase IV; Va 69.1 10 0.00022 39.0 5.9 51 350-401 180-231 (351)
54 cd00008 53EXOc 5'-3' exonuclea 68.6 3.8 8.3E-05 39.7 2.6 25 353-377 188-212 (240)
55 PRK03348 DNA polymerase IV; Pr 67.1 10 0.00022 40.3 5.5 50 352-402 184-234 (454)
56 PTZ00035 Rad51 protein; Provis 66.4 11 0.00023 38.6 5.4 49 353-401 28-78 (337)
57 KOG0387|consensus 66.1 16 0.00036 41.8 7.1 60 14-73 617-679 (923)
58 PRK09482 flap endonuclease-lik 65.7 4.7 0.0001 40.0 2.6 29 353-382 187-215 (256)
59 TIGR02238 recomb_DMC1 meiotic 65.2 12 0.00027 37.8 5.6 50 353-402 6-57 (313)
60 cd01703 PolY_Pol_iota DNA Poly 65.0 12 0.00025 38.9 5.5 49 353-402 177-241 (379)
61 PRK03858 DNA polymerase IV; Va 63.9 14 0.00031 37.8 5.8 48 353-401 178-226 (396)
62 smart00475 53EXOc 5'-3' exonuc 63.7 5.4 0.00012 39.4 2.6 25 353-377 191-215 (259)
63 PRK03980 flap endonuclease-1; 63.5 13 0.00028 37.5 5.2 24 353-376 194-217 (292)
64 COG0258 Exo 5'-3' exonuclease 62.8 13 0.00028 37.3 5.1 25 353-377 203-227 (310)
65 KOG0385|consensus 62.4 15 0.00033 42.0 6.0 51 14-64 558-611 (971)
66 cd01701 PolY_Rev1 DNA polymera 62.1 14 0.0003 38.4 5.4 50 352-402 226-278 (404)
67 PF01367 5_3_exonuc: 5'-3' exo 61.1 0.54 1.2E-05 40.4 -4.3 24 353-376 23-46 (101)
68 PLN03187 meiotic recombination 60.5 15 0.00033 37.8 5.3 47 354-400 37-85 (344)
69 PRK14976 5'-3' exonuclease; Pr 60.5 12 0.00025 37.5 4.3 24 353-376 196-219 (281)
70 KOG2093|consensus 60.5 22 0.00048 41.1 6.8 50 351-401 552-602 (1016)
71 TIGR00593 pola DNA polymerase 59.4 7.7 0.00017 44.8 3.2 25 353-377 190-214 (887)
72 TIGR02239 recomb_RAD51 DNA rep 59.2 18 0.00038 36.7 5.4 50 352-401 5-56 (316)
73 PRK02406 DNA polymerase IV; Va 59.0 17 0.00036 36.6 5.2 49 352-402 172-221 (343)
74 PF13543 KSR1-SAM: SAM like do 58.4 19 0.00041 32.5 4.8 33 355-387 77-109 (129)
75 PRK03103 DNA polymerase IV; Re 57.4 20 0.00043 37.0 5.6 48 353-402 186-234 (409)
76 TIGR03674 fen_arch flap struct 57.2 18 0.0004 37.0 5.2 25 353-377 241-265 (338)
77 TIGR00631 uvrb excinuclease AB 56.5 24 0.00052 39.5 6.3 62 7-68 503-571 (655)
78 PRK01810 DNA polymerase IV; Va 55.5 21 0.00046 36.8 5.3 47 353-401 184-231 (407)
79 PTZ00424 helicase 45; Provisio 55.2 13 0.00029 37.4 3.8 44 9-52 330-374 (401)
80 PRK07758 hypothetical protein; 54.9 36 0.00079 29.3 5.7 51 349-400 35-88 (95)
81 cd01700 PolY_Pol_V_umuC umuC s 54.4 22 0.00047 35.8 5.1 47 353-401 181-228 (344)
82 KOG0390|consensus 54.2 22 0.00048 40.7 5.5 52 14-65 666-720 (776)
83 cd08538 SAM_PNT-ESE-2-like Ste 53.9 15 0.00031 30.5 3.1 29 371-401 42-70 (78)
84 PRK14133 DNA polymerase IV; Pr 53.1 24 0.00053 35.6 5.3 48 352-401 177-225 (347)
85 cd08203 SAM_PNT Sterile alpha 53.0 16 0.00034 28.9 3.1 29 370-400 34-62 (66)
86 cd08757 SAM_PNT_ESE Sterile al 52.4 14 0.00031 29.4 2.8 30 370-401 36-65 (68)
87 PLN00206 DEAD-box ATP-dependen 51.1 30 0.00064 37.2 5.8 45 7-51 429-474 (518)
88 PRK11192 ATP-dependent RNA hel 51.0 31 0.00067 35.6 5.7 54 8-64 307-361 (434)
89 PRK02794 DNA polymerase IV; Pr 50.7 25 0.00054 36.6 5.0 49 352-402 213-262 (419)
90 PLN03186 DNA repair protein RA 50.7 28 0.00061 35.9 5.3 48 354-401 34-83 (342)
91 cd03586 PolY_Pol_IV_kappa DNA 49.9 29 0.00062 34.4 5.1 49 352-402 175-224 (334)
92 KOG0388|consensus 49.8 22 0.00047 40.8 4.5 51 15-65 1114-1167(1185)
93 PTZ00110 helicase; Provisional 49.6 35 0.00076 37.0 6.1 46 7-52 438-484 (545)
94 TIGR03817 DECH_helic helicase/ 49.6 30 0.00064 39.2 5.7 58 6-63 339-396 (742)
95 PF13871 Helicase_C_4: Helicas 48.7 38 0.00083 34.2 5.8 57 13-69 86-144 (278)
96 smart00478 ENDO3c endonuclease 48.4 29 0.00062 30.5 4.4 41 361-401 14-58 (149)
97 TIGR03252 uncharacterized HhH- 47.8 40 0.00087 32.0 5.4 46 356-401 31-90 (177)
98 cd00128 XPG Xeroderma pigmento 47.6 33 0.00072 34.3 5.2 23 353-375 228-250 (316)
99 cd03468 PolY_like DNA Polymera 47.4 30 0.00066 34.2 4.9 48 353-402 175-223 (335)
100 PF12836 HHH_3: Helix-hairpin- 46.8 21 0.00045 27.7 2.9 25 288-312 9-33 (65)
101 PRK04914 ATP-dependent helicas 46.7 24 0.00051 41.3 4.5 46 13-58 563-611 (956)
102 cd00424 PolY Y-family of DNA p 46.4 35 0.00076 34.4 5.2 49 352-402 177-227 (343)
103 PTZ00217 flap endonuclease-1; 46.4 32 0.00068 36.2 5.0 24 353-376 240-263 (393)
104 PRK01297 ATP-dependent RNA hel 45.9 37 0.0008 35.7 5.4 52 9-63 398-450 (475)
105 PRK03609 umuC DNA polymerase V 44.3 38 0.00083 35.3 5.2 49 352-402 183-232 (422)
106 PRK05755 DNA polymerase I; Pro 43.2 17 0.00037 41.7 2.6 25 353-377 192-216 (880)
107 PRK14605 ruvA Holliday junctio 42.7 55 0.0012 31.1 5.6 24 288-311 68-91 (194)
108 PRK11776 ATP-dependent RNA hel 42.3 43 0.00092 35.0 5.2 51 10-63 306-357 (460)
109 PRK02515 psbU photosystem II c 41.8 30 0.00064 31.5 3.4 21 356-376 69-91 (132)
110 PRK10590 ATP-dependent RNA hel 41.2 52 0.0011 34.5 5.7 54 7-63 306-360 (456)
111 PRK13910 DNA glycosylase MutY; 41.1 42 0.00091 34.0 4.7 45 356-400 10-57 (289)
112 PRK15363 pathogenicity island 40.8 47 0.001 30.9 4.6 41 360-400 12-62 (157)
113 PF02198 SAM_PNT: Sterile alph 40.7 19 0.00041 29.5 1.9 31 370-401 49-79 (84)
114 PRK07956 ligA NAD-dependent DN 40.2 43 0.00094 37.6 5.1 51 352-402 449-502 (665)
115 PTZ00205 DNA polymerase kappa; 39.1 1.4E+02 0.0031 33.2 8.7 48 353-401 314-370 (571)
116 PRK04837 ATP-dependent RNA hel 39.0 41 0.00089 34.7 4.5 54 7-63 316-370 (423)
117 PF00730 HhH-GPD: HhH-GPD supe 38.6 26 0.00055 29.0 2.4 45 356-400 9-63 (108)
118 cd00056 ENDO3c endonuclease II 38.6 41 0.00089 29.8 3.8 40 362-401 23-66 (158)
119 smart00279 HhH2 Helix-hairpin- 37.6 24 0.00053 24.8 1.8 16 353-368 21-36 (36)
120 TIGR00575 dnlj DNA ligase, NAD 37.3 49 0.0011 37.1 5.0 50 353-402 437-489 (652)
121 KOG0331|consensus 36.0 55 0.0012 35.9 5.0 54 8-61 403-457 (519)
122 PF00271 Helicase_C: Helicase 35.5 19 0.00041 27.6 1.0 31 10-40 47-77 (78)
123 PRK10880 adenine DNA glycosyla 35.3 36 0.00078 35.3 3.3 42 360-401 51-95 (350)
124 PRK14602 ruvA Holliday junctio 34.8 75 0.0016 30.4 5.2 23 288-310 69-91 (203)
125 TIGR00614 recQ_fam ATP-depende 34.0 57 0.0012 34.4 4.6 44 8-51 288-331 (470)
126 TIGR01083 nth endonuclease III 33.5 63 0.0014 30.1 4.4 41 361-401 48-92 (191)
127 PRK10702 endonuclease III; Pro 33.4 57 0.0012 31.4 4.1 41 361-401 51-95 (211)
128 cd08532 SAM_PNT-PDEF-like Ster 33.3 45 0.00098 27.4 3.0 28 371-400 42-69 (76)
129 cd00079 HELICc Helicase superf 32.9 41 0.0009 27.4 2.8 37 11-47 93-130 (131)
130 cd08531 SAM_PNT-ERG_FLI-1 Ster 32.9 43 0.00092 27.4 2.7 30 370-400 38-67 (75)
131 cd08533 SAM_PNT-ETS-1,2 Steril 32.2 44 0.00095 27.1 2.7 30 370-400 36-65 (71)
132 PRK05298 excinuclease ABC subu 32.0 94 0.002 34.7 6.1 49 6-54 506-559 (652)
133 KOG0392|consensus 32.0 36 0.00079 41.0 3.0 45 14-58 1413-1460(1549)
134 PF02373 JmjC: JmjC domain, hy 31.9 43 0.00094 27.4 2.7 26 111-136 69-94 (114)
135 PRK14351 ligA NAD-dependent DN 31.5 72 0.0016 36.1 5.1 49 353-402 467-519 (689)
136 TIGR01084 mutY A/G-specific ad 31.1 73 0.0016 31.9 4.6 41 360-400 47-90 (275)
137 cd08540 SAM_PNT-ERG Sterile al 30.5 49 0.0011 27.1 2.7 34 366-400 32-67 (75)
138 COG0556 UvrB Helicase subunit 30.3 62 0.0013 36.1 4.1 61 10-71 510-578 (663)
139 PF14229 DUF4332: Domain of un 30.1 69 0.0015 28.1 3.8 35 354-388 59-94 (122)
140 cd08537 SAM_PNT-ESE-1-like Ste 29.2 65 0.0014 26.9 3.2 30 370-401 44-73 (78)
141 cd08536 SAM_PNT-Mae Sterile al 29.1 46 0.001 26.5 2.3 31 370-402 34-64 (66)
142 COG0513 SrmB Superfamily II DN 29.1 61 0.0013 35.0 3.9 57 8-66 335-392 (513)
143 PRK08097 ligB NAD-dependent DN 28.9 83 0.0018 34.9 4.9 51 353-403 430-483 (562)
144 COG0177 Nth Predicted EndoIII- 28.9 83 0.0018 30.6 4.4 42 358-399 48-93 (211)
145 PF03118 RNA_pol_A_CTD: Bacter 28.7 69 0.0015 25.3 3.2 34 367-400 31-65 (66)
146 PRK11634 ATP-dependent RNA hel 28.7 1.1E+02 0.0023 34.1 5.8 51 10-63 309-360 (629)
147 PRK13913 3-methyladenine DNA g 28.7 60 0.0013 31.6 3.4 44 357-400 44-102 (218)
148 PF11731 Cdd1: Pathogenicity l 28.3 1.4E+02 0.003 25.6 5.1 31 356-386 20-51 (93)
149 cd00291 SirA_YedF_YeeD SirA, Y 28.3 75 0.0016 24.1 3.3 39 96-134 27-65 (69)
150 cd08535 SAM_PNT-Tel_Yan Steril 28.2 63 0.0014 26.0 2.9 29 370-400 35-63 (68)
151 PRK14552 C/D box methylation g 27.4 64 0.0014 34.3 3.7 44 356-403 270-313 (414)
152 smart00251 SAM_PNT SAM / Point 26.6 68 0.0015 26.5 2.9 29 370-400 49-77 (82)
153 cd08534 SAM_PNT-GABP-alpha Ste 26.3 64 0.0014 27.3 2.8 30 370-400 51-80 (89)
154 PRK15331 chaperone protein Sic 25.7 1.4E+02 0.0031 28.1 5.2 41 360-400 15-64 (165)
155 PF01798 Nop: Putative snoRNA 25.4 82 0.0018 29.0 3.5 42 356-401 38-79 (150)
156 smart00490 HELICc helicase sup 24.5 64 0.0014 23.9 2.3 31 10-40 51-81 (82)
157 PF02371 Transposase_20: Trans 24.5 54 0.0012 26.7 2.0 30 356-387 10-39 (87)
158 TIGR00084 ruvA Holliday juncti 24.2 1.7E+02 0.0036 27.8 5.5 22 288-309 67-88 (191)
159 TIGR00603 rad25 DNA repair hel 24.2 93 0.002 35.6 4.4 48 10-57 556-612 (732)
160 PRK12766 50S ribosomal protein 24.2 24 0.00052 34.8 -0.2 49 337-386 25-73 (232)
161 PRK10736 hypothetical protein; 24.1 89 0.0019 32.9 3.9 29 354-385 14-42 (374)
162 cd08539 SAM_PNT-ESE-3-like Ste 23.7 89 0.0019 25.8 3.1 29 370-400 39-67 (74)
163 PRK04537 ATP-dependent RNA hel 23.5 1.3E+02 0.0027 33.1 5.1 54 7-63 318-372 (572)
164 smart00483 POLXc DNA polymeras 23.3 1.9E+02 0.0041 29.6 6.1 26 353-378 94-120 (334)
165 PHA02558 uvsW UvsW helicase; P 22.9 72 0.0016 34.1 3.1 35 10-44 409-443 (501)
166 PRK14606 ruvA Holliday junctio 22.7 1.7E+02 0.0037 27.7 5.3 20 288-307 68-87 (188)
167 PRK14350 ligA NAD-dependent DN 22.7 1.2E+02 0.0027 34.2 4.9 50 353-402 441-493 (669)
168 COG0553 HepA Superfamily II DN 22.4 1.3E+02 0.0027 33.4 4.9 49 13-61 780-831 (866)
169 COG1194 MutY A/G-specific DNA 22.3 1.2E+02 0.0027 31.6 4.5 40 360-399 55-97 (342)
170 KOG0389|consensus 21.7 1.7E+02 0.0036 34.2 5.6 46 15-60 848-896 (941)
171 TIGR01448 recD_rel helicase, p 21.5 1.7E+02 0.0036 33.2 5.7 87 289-399 78-167 (720)
172 COG0353 RecR Recombinational D 21.4 1.4E+02 0.0031 28.9 4.4 24 356-385 20-43 (198)
173 cd08541 SAM_PNT-FLI-1 Sterile 21.2 1.1E+02 0.0024 26.1 3.3 35 366-401 44-80 (91)
174 cd08543 SAM_PNT-ETS-2 Sterile 21.1 91 0.002 26.5 2.7 29 371-400 52-80 (89)
175 PF04919 DUF655: Protein of un 21.0 78 0.0017 30.2 2.5 26 351-376 119-149 (181)
176 COG1498 SIK1 Protein implicate 20.9 1.1E+02 0.0023 32.7 3.7 44 356-403 248-291 (395)
177 PRK13901 ruvA Holliday junctio 20.9 2E+02 0.0044 27.7 5.3 23 288-310 67-89 (196)
178 KOG0384|consensus 20.8 1.5E+02 0.0032 36.1 5.1 48 15-62 771-821 (1373)
179 PRK00099 rplJ 50S ribosomal pr 20.3 3.3E+02 0.0071 24.9 6.5 52 241-300 77-129 (172)
180 cd08542 SAM_PNT-ETS-1 Sterile 20.1 1E+02 0.0022 26.1 2.8 29 371-400 52-80 (88)
No 1
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=100.00 E-value=2.5e-82 Score=690.35 Aligned_cols=315 Identities=50% Similarity=0.823 Sum_probs=285.8
Q ss_pred HHHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHhhccCCCC-C
Q psy11328 6 LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVP-T 84 (410)
Q Consensus 6 ~~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~rEk~af~~Li~~k~~m~ip-~ 84 (410)
+.++|++++|+||||||||++|||+||+|++++++.+++||||+|+||+|||+||+++||||+||++||++|++|++| .
T Consensus 468 ~~~~L~e~~P~~VImYEP~~sfIR~IEvyra~r~~r~~rVyfL~y~~S~EEq~yl~sirrEK~AFe~LIreka~m~~~~~ 547 (814)
T TIGR00596 468 LRCSLEELMPRYVIMYEPDISFIRQLEVYKASRPLRPLRVYFLYYGGSIEEQRYLTSLRREKDAFTKLIREKANMSIPFE 547 (814)
T ss_pred HHHHHhhhCCCEEEEECCChHHHHHHHHHHccCCCCCcEEEEEEECCcHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCcc
Confidence 668999999999999999999999999999999999999999999999999999999999999999999999999999 3
Q ss_pred CCCCCC-------------------------C-CCCCCCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCe
Q psy11328 85 EQDGVS-------------------------T-EPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDI 138 (410)
Q Consensus 85 ~~~~~~-------------------------~-~~~~~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i 138 (410)
.+++.. . .....+++||||+|||+|+||..||++|++|+|++|+||||||||+|
T Consensus 548 ~~~~~~~~~~~~~~~~~~~~~~~~tR~agg~~~~~~~~~~~IiVD~REfrS~lp~~L~~~G~~v~p~tL~VGDYilS~~i 627 (814)
T TIGR00596 548 TNEDLESKFLRLVNTRISKLRKSKTRNAGGQLGFANLTQPKVIVDMREFRSSLPSLLHRRGIRVIPCMLTVGDYILTPDI 627 (814)
T ss_pred cccccchhhhhcccccccccccccchhhccccccccCCCceEEEecCcccchhHHHHHHCCCEEEEEecCcccEEecCCe
Confidence 332110 0 01345789999999999999999999999999999999999999999
Q ss_pred EEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEEEEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccc
Q psy11328 139 CVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLS 218 (410)
Q Consensus 139 ~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~ 218 (410)
||||||++||++||+|||||+||++|++||++|+||||||.+++|++++..+.++.++
T Consensus 628 ~VERKSi~Dli~Sl~~gRL~~Q~~~m~~~Y~~PvLLIE~d~~~~f~l~~~~~~~~~~~---------------------- 685 (814)
T TIGR00596 628 CVERKSISDLIGSLNNGRLYNQCEKMLRYYAYPVLLIEFDQNKSFSLEPRNDLSQEIS---------------------- 685 (814)
T ss_pred EEEeCcHHHHHHHHhcchHHHHHHHHHHhcCCcEEEEEecCCcccccccccccccccC----------------------
Confidence 9999999999999999999999999999999999999999999999877555555444
Q ss_pred cccccCh--HHHHHHHHHHHhhCCCeEEEecCChhhHHHHHHHHhcCCCCCCcccccccCCCCCCCc-cccccHHHHHHH
Q psy11328 219 RDIAAKS--SDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDY-TDRYNAAIEDFI 295 (410)
Q Consensus 219 ~~~~~~~--~~I~~kL~~L~l~fp~l~IiwS~s~~eTA~ll~~Lk~~~eepd~~~a~~i~~~~~~~~-~~~~~~~~~~~l 295 (410)
+ ++|+++|++|+++||+++||||+|+++||.+|..||++++|||+.+++.+|.+..... ...++..++++|
T Consensus 686 ------~~~~~i~~~L~~L~l~fP~l~IiwS~s~~~TA~i~~~Lk~~e~epd~~~~v~i~~~~~~~~k~~~~~~~~q~~L 759 (814)
T TIGR00596 686 ------SVNNDIQQKLALLTLHFPKLRIIWSSSPYATAEIFEELKLGKEEPDPATAAALGSDENTTAEGLKFNDGPQDFL 759 (814)
T ss_pred ------ccHHHHHHHHHHHHHhcCCceEEecCCHHHHHHHHHHHHhcCCCCCcccceecCcccccccccccccHHHHHHH
Confidence 5 7999999999999999999999999999999999999988899999999985221110 235788999999
Q ss_pred HcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHH
Q psy11328 296 SKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALC 375 (410)
Q Consensus 296 ~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~ 375 (410)
.+||| ||++||++||.+|+|+++|+
T Consensus 760 ~~lPg-------------------------------------------------------I~~~~a~~ll~~f~si~~l~ 784 (814)
T TIGR00596 760 LKLPG-------------------------------------------------------VTKKNYRNLRKKVKSIRELA 784 (814)
T ss_pred HHCCC-------------------------------------------------------CCHHHHHHHHHHcCCHHHHH
Confidence 99999 99999999999999999999
Q ss_pred cCCHHHHHHhhCCchhHHHHHHHhccCC
Q psy11328 376 KLSEQELCSLVENTTLGNALYKALHTRP 403 (410)
Q Consensus 376 ~~s~eeL~~~~g~~~~a~~ly~fl~~~~ 403 (410)
++|++||++++|+++.|++||+|||++.
T Consensus 785 ~as~eeL~~~iG~~~~A~~i~~fl~~~~ 812 (814)
T TIGR00596 785 KLSQNELNELIGDEEAAKRLYDFLRTEK 812 (814)
T ss_pred hCCHHHHHHHhCCHHHHHHHHHHhcccc
Confidence 9999999999996689999999999874
No 2
>KOG0442|consensus
Probab=100.00 E-value=1.5e-79 Score=655.14 Aligned_cols=317 Identities=49% Similarity=0.773 Sum_probs=292.2
Q ss_pred HHHHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHhhccCCCCC
Q psy11328 5 DLSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPT 84 (410)
Q Consensus 5 ~~~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~rEk~af~~Li~~k~~m~ip~ 84 (410)
.|.++|++++|.+||||+|++.|||+||+|++++|..++|||||+|++|+|||+|++|+||||+||+.||+++++|.+|.
T Consensus 535 ~l~~~L~~~kP~yvi~y~~~~~~vRqiEvYka~~p~~~lkVYfl~y~~S~EeQ~yltSirREk~sFe~LIre~ssm~ip~ 614 (892)
T KOG0442|consen 535 ALERVLEELKPRYVIMYESDLTFVRQIEVYKATRPFRSLKVYFLYYGESTEEQRYLTSIRREKASFEKLIREKSSLRIPL 614 (892)
T ss_pred hHHHHHHhhCCceEEEEcCCCCceeeeeeeeccCCCCCceEEEEEecCchHHHHHHHHHHHhHHHHHHHHhhccceeeee
Confidence 57789999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred CCCCCCCC------------------------C-CCCCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeE
Q psy11328 85 EQDGVSTE------------------------P-EESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDIC 139 (410)
Q Consensus 85 ~~~~~~~~------------------------~-~~~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~ 139 (410)
+++|.... + .+....||||+|||+|+||..||++|++|+||+|+||||||||+||
T Consensus 615 e~dg~~~~~~~~~~~~~~~~~~~~tr~aggq~~~~t~e~pVIVDmREf~SsLP~~Lh~~G~~Vip~tL~vGDYIlSP~ic 694 (892)
T KOG0442|consen 615 EQDGDCDEANLLEITPASGDRNSNTRKAGGQQPEATKETPVIVDMREFRSSLPSLLHRKGLRVIPCTLEVGDYILSPDIC 694 (892)
T ss_pred ecccchhccccceeccccccccccccccCccccccccccceEeehHHHHhhchHHHHhCCceEEEEeecccCEEccccce
Confidence 87664210 0 1112239999999999999999999999999999999999999999
Q ss_pred EEEechhHHHhhhccChHHHHHHHHHhhcCCeEEEEEecCCCCcccccccccccchhhhhhhhhcCCCcccccccccccc
Q psy11328 140 VERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSR 219 (410)
Q Consensus 140 VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~ 219 (410)
|||||++||++||++||||.||+.|++||++||||||||++++|++++.+.++++++
T Consensus 695 VERKSIsDLi~SLnsgRly~Q~~~M~~~Y~~pvLLIEfd~~k~fs~~~~~~ls~e~s----------------------- 751 (892)
T KOG0442|consen 695 VERKSISDLIQSLNSGRLYNQCEMMQRYYERPVLLIEFDQEKSFSLQPRSDLSQELS----------------------- 751 (892)
T ss_pred eeeccHHHHHHhhhcchHHHHHHHHHHhccCcEEEEEecCCCCcCCCCccchhhhhh-----------------------
Confidence 999999999999999999999999999999999999999999999988776666555
Q ss_pred ccccChHHHHHHHHHHHhhCCCeEEEecCChhhHHHHHHHHhcCCCCCCcccccccCCCCCCC-ccccccHHHHHHHHcC
Q psy11328 220 DIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNED-YTDRYNAAIEDFISKL 298 (410)
Q Consensus 220 ~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eTA~ll~~Lk~~~eepd~~~a~~i~~~~~~~-~~~~~~~~~~~~l~~l 298 (410)
.++|+++|++|+++||++|||||+||.+||++|.+||.+++|||+..|..+|.+.... ..+.||+.+.++|.++
T Consensus 752 -----k~~i~skL~lLil~fP~LRilWS~Sp~~Ta~if~eLKl~~~epD~~~Ai~lg~~~~~~~~~~~~n~~~~~fll~l 826 (892)
T KOG0442|consen 752 -----KNDIVSKLTLLILAFPKLRILWSSSPLATAEIFEELKLSEPEPDPARAISLGTDEEGNSESESYNSSALDFLLSL 826 (892)
T ss_pred -----HHHHHHHHHHHHhcCCceEEEecCchhHHHHHHHHHhhcCCCCCcchheeecccccccccccccCchHHHHHhcC
Confidence 5789999999999999999999999999999999999999999999999999832221 1567899999999999
Q ss_pred CCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCC
Q psy11328 299 PGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLS 378 (410)
Q Consensus 299 Pgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s 378 (410)
|| |+..|+++++.+|+|+++|++.|
T Consensus 827 Pg-------------------------------------------------------Vs~~n~~~l~~k~ks~~~La~sS 851 (892)
T KOG0442|consen 827 PG-------------------------------------------------------VSYINYRNLRHKFKSLKELANSS 851 (892)
T ss_pred CC-------------------------------------------------------ccHHHHHHHHHHhhHHHHHHhCc
Confidence 99 88999999999999999999999
Q ss_pred HHHHHHhhCCchhHHHHHHHhccCCc
Q psy11328 379 EQELCSLVENTTLGNALYKALHTRPE 404 (410)
Q Consensus 379 ~eeL~~~~g~~~~a~~ly~fl~~~~~ 404 (410)
.++|..++|..++|+.||+|||+.+.
T Consensus 852 ~~el~el~~~~~~a~~LYdFi~~~~~ 877 (892)
T KOG0442|consen 852 QEELSELLGVHENAKLLYDFIHTEFA 877 (892)
T ss_pred HHHHHHHhcchHHHHHHHHHHHHhhh
Confidence 99999999988999999999999763
No 3
>PRK13766 Hef nuclease; Provisional
Probab=100.00 E-value=2.5e-54 Score=466.89 Aligned_cols=294 Identities=26% Similarity=0.361 Sum_probs=250.7
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHhhccCCCCC-----
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKTNMAVPT----- 84 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~rEk~af~~Li~~k~~m~ip~----- 84 (410)
++-..|++||+|||+++++|.|||.||++|..+++||+|+|++|.||++||+++++||+||+.|+++|++|..|.
T Consensus 437 ldi~~~~~VI~yd~~~s~~r~iQR~GR~gR~~~~~v~~l~~~~t~ee~~y~~~~~ke~~~~~~l~~~k~~l~~~~~~~~~ 516 (773)
T PRK13766 437 LDIPSVDLVIFYEPVPSEIRSIQRKGRTGRQEEGRVVVLIAKGTRDEAYYWSSRRKEKKMKEELKNLKGILNKKLQELDE 516 (773)
T ss_pred CCcccCCEEEEeCCCCCHHHHHHHhcccCcCCCCEEEEEEeCCChHHHHHHHhhHHHHHHHHHHHHHHHhhhhccccccc
Confidence 344689999999999999999999999999889999999999999999999999999999999999999998764
Q ss_pred -CCCCCC-------------------C-------------CCCCCCcEEEEeCCCCCCcchhHHHhCCcEEEEeeccccc
Q psy11328 85 -EQDGVS-------------------T-------------EPEESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGD 131 (410)
Q Consensus 85 -~~~~~~-------------------~-------------~~~~~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGD 131 (410)
.+.+.. + ..+...+.||||+||++|.+|..|+..|+++++++|+|||
T Consensus 517 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~vD~RE~~~~~~~~l~~~g~~~~~~~L~~gD 596 (773)
T PRK13766 517 EQKGEEEEKDEQLSLDDFVKSKGKEEEEEEEKEEKDKETEEDEPEGPKIIVDSRELRSNVARHLKRLGAEVELKTLEVGD 596 (773)
T ss_pred cccccccccccccchhhhccccccccccccccccccccccCCCCCCcEEEEeCCCccchhhHHHHhCCCEEEEEecCCCC
Confidence 111100 0 0134678999999999999999999999999999999999
Q ss_pred EEEeCCeEEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEEEEecCCCCcccccccccccchhhhhhhhhcCCCcccc
Q psy11328 132 YILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFEL 211 (410)
Q Consensus 132 Yils~~i~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~ 211 (410)
|++++++||||||++||++||+|||||+|+++|+++|.+|+|||||+. |. .+.++
T Consensus 597 y~~~~~~~vERK~~~Dl~~s~~~~r~~~q~~~l~~~~~~~~lliE~~~---~~-------~~~~~--------------- 651 (773)
T PRK13766 597 YVVSDRVAVERKTAEDFVDSIIDRRLFEQVKDLKRAYERPVLIIEGDL---YT-------IRNIH--------------- 651 (773)
T ss_pred EEccCCeEEEeCcHHHHHHHhhcCcHHHHHHHHHhcCCCcEEEEEcCc---hh-------hcccC---------------
Confidence 999999999999999999999999999999999999999999999972 21 11222
Q ss_pred ccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChhhHHHHHHHHhcCCC-CCCcccccccCCCCCCCccccccHH
Q psy11328 212 QGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQLFFELKQGRD-EPSAEVASSIGQTPNEDYTDRYNAA 290 (410)
Q Consensus 212 q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eTA~ll~~Lk~~~e-epd~~~a~~i~~~~~~~~~~~~~~~ 290 (410)
+++++++|++++++| +++|+||+|+++||.+|..|+++.. +|+...+...|. ... + ...
T Consensus 652 -------------~~~i~~~l~~l~~~~-~~~ii~~~~~~eta~~l~~l~~~~~~~~~~~~~~~~~~--~~~-~---~~~ 711 (773)
T PRK13766 652 -------------PNAIRGALASIAVDF-GIPILFTRDEEETADLLKVIAKREQEEEKREVSVHGEK--KAM-T---LKE 711 (773)
T ss_pred -------------HHHHHHHHHHHHHHc-CceEEEeCCHHHHHHHHHHHHhhccccCCCCcccccCC--CCC-C---HHH
Confidence 689999999999999 9999999999999999999998543 344333333332 111 1 223
Q ss_pred HHH-HHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCC
Q psy11328 291 IED-FISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGS 369 (410)
Q Consensus 291 ~~~-~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~ 369 (410)
.++ +|..+|| ||++++++|+++|+
T Consensus 712 ~~~~~L~~ipg-------------------------------------------------------ig~~~a~~Ll~~fg 736 (773)
T PRK13766 712 QQEYIVESLPD-------------------------------------------------------VGPVLARNLLEHFG 736 (773)
T ss_pred HHHHHHhcCCC-------------------------------------------------------CCHHHHHHHHHHcC
Confidence 333 7889999 89999999999999
Q ss_pred CHHHHHcCCHHHHHHh--hCCchhHHHHHHHhccCCc
Q psy11328 370 SLPALCKLSEQELCSL--VENTTLGNALYKALHTRPE 404 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl~~~~~ 404 (410)
|+++++++|.++|..+ +|. ..|+.|++||+.++.
T Consensus 737 s~~~i~~as~~~L~~i~Gig~-~~a~~i~~~~~~~~~ 772 (773)
T PRK13766 737 SVEAVMTASEEELMEVEGIGE-KTAKRIREVVTSEYK 772 (773)
T ss_pred CHHHHHhCCHHHHHhCCCCCH-HHHHHHHHHHhhhhc
Confidence 9999999999999999 664 789999999998764
No 4
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=100.00 E-value=9e-47 Score=363.30 Aligned_cols=213 Identities=31% Similarity=0.493 Sum_probs=184.2
Q ss_pred CCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEEE
Q psy11328 96 SCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLLI 175 (410)
Q Consensus 96 ~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLLI 175 (410)
..+.||||+||++|.+|..|+..|+++++++|+||||+|++++||||||++||++||.|||||+||.+|+++|.+|+|+|
T Consensus 26 ~~~~viVD~RE~rs~v~~~L~~~gv~v~~~~LevGDYvvs~~v~VERKs~~Dfv~Si~dgRlfeQ~~rL~~~y~rpvliV 105 (254)
T COG1948 26 FEVVVIVDSRELRSEVPRLLKRLGVKVEVRTLEVGDYVVSDDVIVERKSISDFVSSIIDGRLFEQAKRLKKSYERPVLIV 105 (254)
T ss_pred cceEEEEecchhcccchHHHHhCCCeEEEEecccccEEeecCeeEEeccHHHHHHHHhcchHHHHHHHHHhcCCccEEEE
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChhhHHH
Q psy11328 176 EFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTAQ 255 (410)
Q Consensus 176 E~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eTA~ 255 (410)
||+ ..|.. ...++ +++++++|++++++| +++||||+|+.+||.
T Consensus 106 egd--~~~~~------~~~i~----------------------------~~av~~al~s~~vdf-g~~vi~t~~~~~Ta~ 148 (254)
T COG1948 106 EGD--DSFSR------RPKIH----------------------------PNAVRGALASLAVDF-GLPVIWTRSPEETAE 148 (254)
T ss_pred Ecc--ccccc------ccccC----------------------------HHHHHHHHHHHHhhc-CceEEEeCCHHHHHH
Confidence 998 22211 01122 789999999999999 899999999999999
Q ss_pred HHHHHhcCCCCCCcccccccCCCCCCCccccccHHHHHHHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhh
Q psy11328 256 LFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSF 335 (410)
Q Consensus 256 ll~~Lk~~~eepd~~~a~~i~~~~~~~~~~~~~~~~~~~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 335 (410)
+|..|++...+ ........+..+ . ...++..+..+|.++||
T Consensus 149 ~i~~la~req~-e~~r~v~~~~~~--~-~~t~~e~q~~il~s~pg----------------------------------- 189 (254)
T COG1948 149 LIHELARREQE-ERKRSVNPHGKK--K-AKTLKELQLYILESIPG----------------------------------- 189 (254)
T ss_pred HHHHHHHHHHH-hccccccccccc--c-ccchHHHHHHHHHcCCC-----------------------------------
Confidence 99999984432 111111111111 1 34578888899999999
Q ss_pred hhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhCC-chhHHHHHHHhccCCc
Q psy11328 336 FLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVEN-TTLGNALYKALHTRPE 404 (410)
Q Consensus 336 ~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~-~~~a~~ly~fl~~~~~ 404 (410)
|++++|.+|+.+|+|+.+++++|.+||+.+.|. ++.|.+||+||.+++.
T Consensus 190 --------------------ig~~~a~~ll~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t~~~ 239 (254)
T COG1948 190 --------------------IGPKLAERLLKKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLRTEYK 239 (254)
T ss_pred --------------------ccHHHHHHHHHHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhchhh
Confidence 899999999999999999999999999999883 7899999999999986
No 5
>PF02732 ERCC4: ERCC4 domain; InterPro: IPR006166 This entry represents a structural motif found in several DNA repair nucleases, such as Rad1/Mus81/XPF endonucleases (3.1.22 from EC) [], and in ATP-dependent helicases. The XPF/Rad1/Mus81-dependent nuclease family specifically cleaves branched structures generated during DNA repair, replication, and recombination, and is essential for maintaining genome stability. The nuclease domain architecture exhibits remarkable similarity to those of restriction endonucleases.; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006259 DNA metabolic process; PDB: 2BHN_D 2BGW_B 1J22_A 1J25_A 1J24_A 1J23_A 2ZIU_A 2ZIW_A 2ZIV_A 2ZIX_A ....
Probab=99.89 E-value=1.4e-22 Score=174.68 Aligned_cols=127 Identities=32% Similarity=0.435 Sum_probs=106.3
Q ss_pred EeCCCCC-Cc---chhHHHhCCcEEEEeecccccEEEeC----------CeEEEEechhHHHhhhccChHHHHHHHHHh-
Q psy11328 102 VDMREFR-SE---LPVLLHKRGLYIEPVTISVGDYILSP----------DICVERKSISDLIGSLQSGRLYTQVQQMCR- 166 (410)
Q Consensus 102 VD~RE~r-S~---lp~~L~~~Gv~v~~~~L~VGDYils~----------~i~VERKSi~DLi~Sl~~GRL~~Q~~~L~~- 166 (410)
||+||++ ++ ++..|+..|+++++++|++|||+|.+ .++||||++.||++|+.+|||++|+.+|++
T Consensus 1 VD~re~~~~~~~~l~~~l~~~gv~~~~~~l~~gd~~~~~~~~~~~e~~~~~iverk~~~dl~~si~~~rl~~q~~rl~~~ 80 (143)
T PF02732_consen 1 VDSRELRSSGGEQLLEALRELGVKVEVRQLPVGDYIWWRINQISEETMVPVIVERKTLDDLVASIKDGRLEEQVQRLKRA 80 (143)
T ss_dssp EEGGGCTSSCHHHHHHHHHCTTSEEEEE--SSSSEEEEES----BESSECEEEEEEEHHHHHHHHHTTHHHHHHHHHHCC
T ss_pred CCchHhCcccHHHHHHHHHHCCCEEEEEECCCCCEEEECCCCCccccceEEEEEhhHHHHHHhhhcCCchHHHHHHHhhc
Confidence 8999998 66 99999999999999999999999998 999999999999999999999999999996
Q ss_pred -hcCCeEEEEEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEE
Q psy11328 167 -HYAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLI 245 (410)
Q Consensus 167 -~Y~~piLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~Ii 245 (410)
.+++++|||||.......... .. .+ ..+++|.++|+.|.+++ ++.|+
T Consensus 81 ~~~~~~~~lVEg~~~~~~~~~~-------~~--------------~~----------~~~~~i~~~L~~lq~~~-~~~v~ 128 (143)
T PF02732_consen 81 SPFKRVILLVEGLDSYLRKNKN-------YR--------------RQ----------QSPSAIEEALVELQLRY-GISVI 128 (143)
T ss_dssp HCSSEEEEEEESCSSTCCC--------------------------HS----------STHHHHHHHHHHHHHCS-S-EEE
T ss_pred CCCCeEEEEEEccCccccccch-------hc--------------cc----------CCHHHHHHHHHHHHHHc-CeEEE
Confidence 689999999998644322100 00 00 01679999999999999 99999
Q ss_pred ecCChhhHHHHHHHH
Q psy11328 246 WSSGPYNTAQLFFEL 260 (410)
Q Consensus 246 wS~s~~eTA~ll~~L 260 (410)
|+.|..+||+++..|
T Consensus 129 ~~~~~~et~~~l~~f 143 (143)
T PF02732_consen 129 FTESWEETADWLASF 143 (143)
T ss_dssp EESSHHHHHHHHHHH
T ss_pred EECCHHHHHHHhhhC
Confidence 999999999999765
No 6
>KOG2379|consensus
Probab=99.73 E-value=5.2e-17 Score=168.55 Aligned_cols=127 Identities=27% Similarity=0.382 Sum_probs=107.4
Q ss_pred CcEEEEeCCCCCCcchhHHHh-----CCcEEEEeecccccEEEeC-----------CeEEEEechhHHHhhhccChHHHH
Q psy11328 97 CGRVIVDMREFRSELPVLLHK-----RGLYIEPVTISVGDYILSP-----------DICVERKSISDLIGSLQSGRLYTQ 160 (410)
Q Consensus 97 ~~~IIVD~RE~rS~lp~~L~~-----~Gv~v~~~~L~VGDYils~-----------~i~VERKSi~DLi~Sl~~GRL~~Q 160 (410)
... |+|+||++|.++.+... .||+.+++.|++|||+|.- +.+||||.++||++||.|||+.+|
T Consensus 230 e~~-~~d~~~iks~~~~l~~~~~~~~~~v~~evR~L~vGD~lWVa~~k~~g~E~VLd~IVERKr~DDl~SSIrDgRf~EQ 308 (501)
T KOG2379|consen 230 EVF-IIDTREIKSLLRRLFFGEYFELEGVKHEVRSLEVGDFLWVARHKYDGTELVLDFIVERKRLDDLVSSIRDGRFKEQ 308 (501)
T ss_pred eee-eccCccccccchhhhhhhhhhhccceeeEEEecccceEEEecccCCCceEeeeeheeecchHHHHHHHhccchHHH
Confidence 344 89999999988777665 7999999999999999973 479999999999999999999999
Q ss_pred HHHHHhh-cCCeEEEEEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhC
Q psy11328 161 VQQMCRH-YAKPLLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHF 239 (410)
Q Consensus 161 ~~~L~~~-Y~~piLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~f 239 (410)
..||.+. .++.+||||++.+.. +++| ..+|..+++.+.+..
T Consensus 309 K~RLq~sGik~~iYlvE~~~~~n----------------------~~~~----------------~eslktA~~~t~v~~ 350 (501)
T KOG2379|consen 309 KNRLQRSGIKRIIYLVEEDGNPN----------------------QSKP----------------AESLKTAVTNTLVLE 350 (501)
T ss_pred HHHHHhcCcceEEEEEeccCCcc----------------------cccH----------------HHHHHHHHHHHhhhc
Confidence 9999997 699999999984211 1112 568888888877776
Q ss_pred CCeEEEecCChhhHHHHHHHHhcC
Q psy11328 240 PKLRLIWSSGPYNTAQLFFELKQG 263 (410)
Q Consensus 240 p~l~IiwS~s~~eTA~ll~~Lk~~ 263 (410)
|+.|+.|+|-.+|+..+..++++
T Consensus 351 -GF~V~RT~~l~et~s~l~y~tr~ 373 (501)
T KOG2379|consen 351 -GFDVIRTRDLGETVSKLAYLTRG 373 (501)
T ss_pred -ceEEEEecChhHHHHHHHHHhHH
Confidence 99999999999999999887764
No 7
>KOG2841|consensus
Probab=99.67 E-value=1.2e-15 Score=146.12 Aligned_cols=198 Identities=19% Similarity=0.242 Sum_probs=150.9
Q ss_pred CCCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccChHHHHHHHHHhhcCCeEEE
Q psy11328 95 ESCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRLYTQVQQMCRHYAKPLLL 174 (410)
Q Consensus 95 ~~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~GRL~~Q~~~L~~~Y~~piLL 174 (410)
...-.|+|..|+..+.|-..+. +++++...=-+-||++++..||-.-|+.+.. +.-+=+|..++.+.+.|+..|||
T Consensus 53 ~~~~~Ilvn~rQkGNplLk~vr--nv~w~f~ddi~PDf~lg~~~cvLyLSl~yH~--l~pdYi~~Ri~~l~k~yk~~VLl 128 (254)
T KOG2841|consen 53 VPGGHILVNPRQKGNPLLKHVR--NVKWEFGDDIIPDFVLGRGCCVLYLSLKYHK--LHPDYIYRRIRKLGKNYKLRVLL 128 (254)
T ss_pred CCCceEEeccccccChHHHHHh--cCCeEecCCCCcceEecCceEEEEeehHhhh--cCcHHHHHHHHHhcccccceEEE
Confidence 3456899999998655555544 8999999445899999999999444444332 22233588999998889999999
Q ss_pred EEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChhhHH
Q psy11328 175 IEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNTA 254 (410)
Q Consensus 175 IE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eTA 254 (410)
+--|.+.+ ...+. .|..++.-. .+.++-.++.+++|
T Consensus 129 ~~vd~~e~------------------------------------------~~~l~-el~k~~~l~-~~Tl~lA~s~Eeaa 164 (254)
T KOG2841|consen 129 VHVDMEEP------------------------------------------YKPLL-ELTKTCDLN-DVTLVLAWSMEEAA 164 (254)
T ss_pred EEecCcch------------------------------------------HHHHH-HHHHHHHhh-ceeeeeeccHHHHH
Confidence 99885432 23444 344444333 78999999999999
Q ss_pred HHHHHHhcCCCCC-CcccccccCCCCCCCccccccHHHHHHHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhh
Q psy11328 255 QLFFELKQGRDEP-SAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRAS 333 (410)
Q Consensus 255 ~ll~~Lk~~~eep-d~~~a~~i~~~~~~~~~~~~~~~~~~~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 (410)
.+|..++....+| |... .+. +..+....+.+|..+||
T Consensus 165 ryIE~~k~~ek~p~dli~---~~~------~~d~ls~~~~~Lt~i~~--------------------------------- 202 (254)
T KOG2841|consen 165 RYIETYKEYEKKPIDLIM---ERK------DRDLLSSLLGFLTTIPG--------------------------------- 202 (254)
T ss_pred HHHHHHHHhhcCCchhhh---hcc------cccHHHHHHHHHHhCCC---------------------------------
Confidence 9999998865443 2211 111 23456788899999999
Q ss_pred hhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCCc
Q psy11328 334 SFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRPE 404 (410)
Q Consensus 334 ~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~~ 404 (410)
||...|..||.+|+||+++++||.+||+.++| .+.+|++||+|||.++.
T Consensus 203 ----------------------VnKtda~~LL~~FgsLq~~~~AS~~ele~~~G~G~~kak~l~~~l~~pf~ 252 (254)
T KOG2841|consen 203 ----------------------VNKTDAQLLLQKFGSLQQISNASEGELEQCPGLGPAKAKRLHKFLHQPFL 252 (254)
T ss_pred ----------------------CCcccHHHHHHhcccHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHhcccc
Confidence 88999999999999999999999999999986 35899999999999986
No 8
>COG1111 MPH1 ERCC4-like helicases [DNA replication, recombination, and repair]
Probab=99.47 E-value=7.8e-14 Score=145.50 Aligned_cols=69 Identities=23% Similarity=0.246 Sum_probs=66.1
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYLIQEKT 78 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~rEk~af~~Li~~k~ 78 (410)
|+...+|+||||||+||.||.|||.|||+|+.+|+||+|+++||+||+|||+|+|+|++|-+.+...+.
T Consensus 439 LDIp~vDlVifYEpvpSeIR~IQR~GRTGR~r~Grv~vLvt~gtrdeayy~~s~rke~~m~e~i~~~~~ 507 (542)
T COG1111 439 LDIPEVDLVIFYEPVPSEIRSIQRKGRTGRKRKGRVVVLVTEGTRDEAYYYSSRRKEQKMIESIRGLSL 507 (542)
T ss_pred CCCCcccEEEEecCCcHHHHHHHhhCccccCCCCeEEEEEecCchHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678899999999999999999999999999999999999999999999999999999999999977764
No 9
>TIGR00597 rad10 DNA repair protein rad10. All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=98.17 E-value=1e-05 Score=70.60 Aligned_cols=105 Identities=23% Similarity=0.372 Sum_probs=85.7
Q ss_pred EEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccChH-----HHHHHHHHhhcCCeEE
Q psy11328 99 RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRL-----YTQVQQMCRHYAKPLL 173 (410)
Q Consensus 99 ~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~GRL-----~~Q~~~L~~~Y~~piL 173 (410)
.|+|..|.. +.|-+=+-+++.++...+ ++||++++..|| |+-|++.+|| +++++.|.+.|...+|
T Consensus 2 ~ilvs~~Qk--gNPlL~~i~nv~wey~di-~~Dy~~g~~~~v-------LFLSLkYH~L~peYi~~Ri~~L~~~~~lrvL 71 (112)
T TIGR00597 2 SILVNPRQK--GNPLLKHVRNVPWEYGDV-IPDYVLGQGTCA-------LFLSLRYHNLHPDYIHRRLQSLGKNFNLRIL 71 (112)
T ss_pred cEEeCcccc--CChHHHHHhcCCeEecCc-CCCEEEcCccEE-------EEEEhhhhccCHHHHHHHHHHhccccceeEE
Confidence 478888886 445333445788888775 899999999999 9999999995 8999999999999999
Q ss_pred EEEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChhhH
Q psy11328 174 LIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPYNT 253 (410)
Q Consensus 174 LIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~eT 253 (410)
|+--|.+.+ ...+. .|..++... ++.++-++|.+|+
T Consensus 72 L~~VDv~~~------------------------------------------~~~L~-eL~k~~~~~-~~TLilaws~eEa 107 (112)
T TIGR00597 72 LVQVDVKNP------------------------------------------QQALK-ELAKMCILN-DCTLILAWSFEEA 107 (112)
T ss_pred EEEEeCCch------------------------------------------HHHHH-HHHHHHHHc-CcEEEEECCHHHH
Confidence 999985321 23444 788888888 9999999999999
Q ss_pred HHHH
Q psy11328 254 AQLF 257 (410)
Q Consensus 254 A~ll 257 (410)
|.+|
T Consensus 108 a~Yl 111 (112)
T TIGR00597 108 ARYL 111 (112)
T ss_pred HHhh
Confidence 9987
No 10
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=98.11 E-value=2e-06 Score=67.35 Aligned_cols=51 Identities=22% Similarity=0.292 Sum_probs=40.8
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRP 403 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~ 403 (410)
.||||++.++.|+++|+|++.|.++|.|+|..+-| .+..|+.||+||+.+-
T Consensus 8 I~~VG~~~ak~L~~~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~ 59 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFGSLEALMNASVEELSAIPGIGPKIAQSIYEFFQDPE 59 (64)
T ss_dssp STT--HHHHHHHHHCCSCHHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HH
T ss_pred CCCccHHHHHHHHHHcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHH
Confidence 46799999999999999999999999999999944 3589999999999764
No 11
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=97.55 E-value=0.00014 Score=79.52 Aligned_cols=51 Identities=22% Similarity=0.257 Sum_probs=47.2
Q ss_pred CCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccCC
Q psy11328 352 PRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHTRP 403 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~~ 403 (410)
-.||||++.+++||.+|+|++++.+||.|||++++|. +.|+.||+|||.+.
T Consensus 556 ~IpGIG~kr~~~LL~~FgSi~~I~~As~eeL~~vi~~-k~A~~I~~~l~~~~ 606 (624)
T PRK14669 556 EIPGVGAKTVQRLLKHFGSLERVRAATETQLAAVVGR-AAAEAIIAHFTTEE 606 (624)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhCH-HHHHHHHHHhcCcC
Confidence 4466999999999999999999999999999999985 89999999999876
No 12
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=97.37 E-value=0.00025 Score=76.74 Aligned_cols=60 Identities=17% Similarity=0.112 Sum_probs=52.1
Q ss_pred hcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 341 RIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 341 ~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
+-|.+-..++.-.||||++..++||.+|||++++.+||.|||+++ | +.+.|+.||++||.
T Consensus 507 r~k~~~~S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 507 REKEGLKDILDKIKGIGEVKKEIIYRNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLSG 567 (567)
T ss_pred hhcccccCccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhcC
Confidence 344444557788899999999999999999999999999999999 5 46899999999973
No 13
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=97.31 E-value=0.00026 Score=76.65 Aligned_cols=55 Identities=13% Similarity=0.170 Sum_probs=50.2
Q ss_pred CCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 348 RESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 348 ~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
.++.-.||||++..+.||++|||++++.+||.|||+++-| ++..|+.||++|+..
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~~ 569 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEKQ 569 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHh
Confidence 4777889999999999999999999999999999999966 458999999999864
No 14
>COG5241 RAD10 Nucleotide excision repair endonuclease NEF1, RAD10 subunit [DNA replication, recombination, and repair]
Probab=97.24 E-value=0.00011 Score=69.39 Aligned_cols=185 Identities=15% Similarity=0.064 Sum_probs=131.6
Q ss_pred CcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccC-----hHHHHHHHHHhhcCCe
Q psy11328 97 CGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSG-----RLYTQVQQMCRHYAKP 171 (410)
Q Consensus 97 ~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~G-----RL~~Q~~~L~~~Y~~p 171 (410)
...|-|.-+. .+-|.+=+..+..++....-+.||.....+ .||+.|+.-+ -.+..+..+ +.|+..
T Consensus 33 s~~I~vsplQ--kgnp~l~~~~N~~w~y~~~i~Pd~~~~s~~-------~~lflslrfhs~~Peyi~~riSkl-KsYk~r 102 (224)
T COG5241 33 SLEIDVSPLQ--KGNPQLSRRINSNWVYNAFIKPDEWTDSKA-------TDLFLSLRFHSTRPEYIVLRISKL-KSYKER 102 (224)
T ss_pred eeEEecChhh--cCCCcccccccCcceeccccCcchhhcchH-------HHHHHHHhhhcCCCceEEEeeecc-cccccc
Confidence 3455555555 466766677888999888889999887554 5688887622 246666777 668888
Q ss_pred EEEEEecCCCCcccccccccccchhhhhhhhhcCCCccccccccccccccccChHHHHHHHHHHHhhCCCeEEEecCChh
Q psy11328 172 LLLIEFDHNKPFELQGNYYLSRDIAAKFLIEFDHNKPFELQGNYYLSRDIAAKSSDITAKLQLLTLHFPKLRLIWSSGPY 251 (410)
Q Consensus 172 iLLIE~d~~~~f~l~~~~~~~r~i~~~~~~~~~~~~pf~~q~~~~~~~~~~~~~~~I~~kL~~L~l~fp~l~IiwS~s~~ 251 (410)
+||+--|... + ...|+ .|+..+.-. .++...+.+
T Consensus 103 ~LL~hvd~~N---------------------------------~---------~asIq-Elv~Tt~in---ti~l~~sve 136 (224)
T COG5241 103 PLLNHVDSTN---------------------------------W---------RASIQ-ELVSTTGIN---TIYLDYSVE 136 (224)
T ss_pred ceeeeecccc---------------------------------H---------HHHHH-HHHHhcccc---eeehhhhhh
Confidence 8888776311 0 45677 566655332 889999999
Q ss_pred hHHHHHHHHhcCCC-CCCcccccccCCCCCCCccccccHHHHHHHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhh
Q psy11328 252 NTAQLFFELKQGRD-EPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELF 330 (410)
Q Consensus 252 eTA~ll~~Lk~~~e-epd~~~a~~i~~~~~~~~~~~~~~~~~~~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 330 (410)
+.+.+|..++.... .++.+. ...+ .+ + -+.++..||+
T Consensus 137 e~sry~~t~~~~~~~s~~iir----~~~s-~d----~---s~~fl~~i~~------------------------------ 174 (224)
T COG5241 137 ERSRYFLTLTYHKLYSDYIIR----RMQS-LD----R---SNEFLILIFI------------------------------ 174 (224)
T ss_pred HHHHHHHHhHHHhhcCHHHHH----hcCC-Cc----c---cccceEEEEe------------------------------
Confidence 99999999876321 122211 1110 01 1 1356667777
Q ss_pred hhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCCc
Q psy11328 331 RASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRPE 404 (410)
Q Consensus 331 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~~ 404 (410)
|+..|+..+|+.|++|....-+|..|++.+.| ..++|.+.-+++|.+|.
T Consensus 175 -------------------------Vnksds~~~L~d~g~L~rf~gaSrdE~e~l~g~g~~ka~~~ieyln~pFm 224 (224)
T COG5241 175 -------------------------VNKSDSEDTLNDIGKLCRFNGASRDEFELLLGFGFEKAAKYIEYLNLPFM 224 (224)
T ss_pred -------------------------eccccHHHHHHHHHHHHHHhccchhHHHHHHccCHHHHHHHHHHhcccCC
Confidence 88999999999999999999999999999988 56899999999998874
No 15
>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=97.15 E-value=0.00088 Score=51.38 Aligned_cols=46 Identities=13% Similarity=0.190 Sum_probs=41.4
Q ss_pred CcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhc
Q psy11328 355 RVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALH 400 (410)
Q Consensus 355 ~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~ 400 (410)
||+++.+.+|.+. |+|+++|.+++.++|.++-| ++..|+.|.+.++
T Consensus 12 Gig~~~a~~L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 12 GIGPKRAEKLYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp TCHHHHHHHHHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 3999999999999 99999999999999999955 4688999988775
No 16
>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=97.08 E-value=0.0012 Score=72.71 Aligned_cols=50 Identities=18% Similarity=0.158 Sum_probs=45.8
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHh--hCCchhHHHHHHHhccCC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKLSEQELCSL--VENTTLGNALYKALHTRP 403 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl~~~~ 403 (410)
.||||++.++.|+++|+|+.+|.++|.++|.++ +| +..|+.|++||+.+.
T Consensus 503 IpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG-~~~A~~I~~ff~~~~ 554 (652)
T TIGR00575 503 IRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVG-PKVAESIVNFFHDPN 554 (652)
T ss_pred CCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcC-HHHHHHHHHHHhhhh
Confidence 477999999999999999999999999999999 55 489999999998864
No 17
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=97.07 E-value=0.001 Score=64.69 Aligned_cols=52 Identities=12% Similarity=0.066 Sum_probs=46.3
Q ss_pred CCCCCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 350 SNPRPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 350 ~~~~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
+.-.||||++.+..|+++ |+|+.+|..+|.++|.++-| +...|+.|+++|+.
T Consensus 5 L~~IpGIG~krakkLl~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~ 58 (232)
T PRK12766 5 LEDISGVGPSKAEALREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGG 58 (232)
T ss_pred cccCCCcCHHHHHHHHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhcc
Confidence 345688999999999999 99999999999999999944 35899999999983
No 18
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.96 E-value=0.0015 Score=72.18 Aligned_cols=86 Identities=17% Similarity=0.189 Sum_probs=63.9
Q ss_pred HHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHH
Q psy11328 294 FISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPA 373 (410)
Q Consensus 294 ~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~ 373 (410)
-|..+||++++++.+.++.- |.-+.-.++..||-+ ..||||++.|+.|+++|+|+.+
T Consensus 497 ~L~~l~g~g~Ksa~~Ll~~I--------------e~sk~~~l~r~l~AL---------gIpgIG~~~ak~L~~~F~si~~ 553 (689)
T PRK14351 497 DLAELEGWGETSAENLLAEL--------------EASREPPLADFLVAL---------GIPEVGPTTARNLAREFGTFEA 553 (689)
T ss_pred HHhcCcCcchhHHHHHHHHH--------------HHHccCCHHHHHHHc---------CCCCcCHHHHHHHHHHhCCHHH
Confidence 37788888877666544421 111222334445544 3577999999999999999999
Q ss_pred HHcCCHHHHHHh--hCCchhHHHHHHHhccCC
Q psy11328 374 LCKLSEQELCSL--VENTTLGNALYKALHTRP 403 (410)
Q Consensus 374 l~~~s~eeL~~~--~g~~~~a~~ly~fl~~~~ 403 (410)
|.++|.++|.++ +|. ..|+.|++||+.+-
T Consensus 554 L~~As~eeL~~i~GIG~-k~A~sI~~ff~~~~ 584 (689)
T PRK14351 554 IMDADEEALRAVDDVGP-TVAEEIREFFDSER 584 (689)
T ss_pred HHhCCHHHHhccCCcCH-HHHHHHHHHHhhhH
Confidence 999999999999 554 89999999998753
No 19
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.94 E-value=0.0017 Score=71.64 Aligned_cols=50 Identities=24% Similarity=0.242 Sum_probs=45.7
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHh--hCCchhHHHHHHHhccCC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKLSEQELCSL--VENTTLGNALYKALHTRP 403 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl~~~~ 403 (410)
.||||++.++.|+++|+|+.+|.++|.++|.++ +| +..|+.|++||+.+.
T Consensus 516 i~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG-~~~A~sI~~ff~~~~ 567 (665)
T PRK07956 516 IRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVG-EVVAQSIVEFFAVEE 567 (665)
T ss_pred ccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcC-HHHHHHHHHHHhhhh
Confidence 477999999999999999999999999999999 55 489999999998754
No 20
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=96.78 E-value=0.0022 Score=65.89 Aligned_cols=53 Identities=19% Similarity=0.151 Sum_probs=45.5
Q ss_pred CCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 349 ESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
..+-.|||++.-|++|+++||||+++++||.+||+++-| .+..|+.+++.+..
T Consensus 288 iLs~IPrl~k~iAk~Ll~~FGSL~~Il~As~eeL~~VeGIGe~rA~~I~e~l~R 341 (352)
T PRK13482 288 LLSKIPRLPSAVIENLVEHFGSLQGLLAASIEDLDEVEGIGEVRARAIREGLSR 341 (352)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHcCCHHHHhhCCCcCHHHHHHHHHHHHH
Confidence 445557799999999999999999999999999999955 35889999888764
No 21
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=96.66 E-value=0.0028 Score=69.41 Aligned_cols=46 Identities=20% Similarity=0.311 Sum_probs=43.4
Q ss_pred CCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 354 PRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 354 ~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
||||++.+..|+++|+|+.+|.++|.++|.+++|. ..|+.|++||+
T Consensus 575 ~GIG~k~a~~Ll~~Fgs~~~i~~As~eeL~~vig~-k~A~~I~~~~~ 620 (621)
T PRK14671 575 AGIGEKTAEKLLEHFGSVEKVAKASLEELAAVAGP-KTAETIYRYYH 620 (621)
T ss_pred CCcCHHHHHHHHHHcCCHHHHHhCCHHHHHHHhCH-HHHHHHHHHhC
Confidence 45999999999999999999999999999999986 78999999996
No 22
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=96.57 E-value=0.003 Score=68.89 Aligned_cols=49 Identities=33% Similarity=0.496 Sum_probs=44.9
Q ss_pred CCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHh--hCCchhHHHHHHHhcc
Q psy11328 352 PRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSL--VENTTLGNALYKALHT 401 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl~~ 401 (410)
-.||||++.++.|+++|+|++++.++|.+||.++ +|. ..|+.|++|||.
T Consensus 547 ~IpGIG~k~~k~Ll~~FgS~~~i~~As~eeL~~v~Gig~-~~A~~I~~~l~~ 597 (598)
T PRK00558 547 DIPGIGPKRRKALLKHFGSLKAIKEASVEELAKVPGISK-KLAEAIYEALHK 597 (598)
T ss_pred hCCCcCHHHHHHHHHHcCCHHHHHhCCHHHHhhcCCcCH-HHHHHHHHHhcc
Confidence 4466999999999999999999999999999999 664 899999999985
No 23
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=96.43 E-value=0.0032 Score=68.47 Aligned_cols=50 Identities=26% Similarity=0.383 Sum_probs=45.3
Q ss_pred CCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHh
Q psy11328 349 ESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKAL 399 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl 399 (410)
.+.-.||||++-.+.||.||+|++.+.+||.+||.++ | +.+.|+++|++|
T Consensus 531 ~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~~~ 581 (581)
T COG0322 531 SLDDIPGIGPKRRKALLKHFGSLKGIKSASVEELAKV-GISKKLAEKIYEAL 581 (581)
T ss_pred ccccCCCcCHHHHHHHHHHhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHhhC
Confidence 4556789999999999999999999999999999999 7 568999999875
No 24
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=96.17 E-value=0.0075 Score=66.77 Aligned_cols=54 Identities=19% Similarity=0.132 Sum_probs=46.2
Q ss_pred CCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCC
Q psy11328 350 SNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRP 403 (410)
Q Consensus 350 ~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~ 403 (410)
+.-.|||+++-+++|+++|+|++++.++|.+||.++-| ....|+.|+++|+.-|
T Consensus 639 L~~IPGIGpkr~k~LL~~FGSle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~~~~ 693 (694)
T PRK14666 639 LQRVEGIGPATARLLWERFGSLQAMAAAGEEGLAAVPGIGPARAAALHEHLKTLF 693 (694)
T ss_pred HhhCCCCCHHHHHHHHHHhCCHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHHHhh
Confidence 33456699999999999999999999999999999933 3489999999998643
No 25
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=95.92 E-value=0.016 Score=64.21 Aligned_cols=65 Identities=15% Similarity=0.111 Sum_probs=53.3
Q ss_pred hhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 337 LLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 337 ~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
+---+-|.+-.-.+.-.||||++..+.||.+|+|+++|.+||.|||+++-| +.+.|+.||.+-..
T Consensus 597 hR~~R~k~~~~s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~ 662 (691)
T PRK14672 597 NRHLRTKKELVLSFERLPHVGKVRAHRLLAHFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATR 662 (691)
T ss_pred HHHHhhhhhcccccccCCCCCHHHHHHHHHHhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhc
Confidence 333344555556778889999999999999999999999999999999966 45889999887544
No 26
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=95.91 E-value=0.01 Score=64.55 Aligned_cols=47 Identities=19% Similarity=0.266 Sum_probs=42.1
Q ss_pred CCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHh--hCCchhHHHHHHHh
Q psy11328 352 PRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSL--VENTTLGNALYKAL 399 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl 399 (410)
-.||||++.++.||++|+|++++.++|.+||..+ +| ...|+.|+++|
T Consensus 529 ~IpGIG~kr~~~LL~~FGS~~~I~~As~eeL~~vpGi~-~~~A~~I~~~~ 577 (577)
T PRK14668 529 DVPGVGPETRKRLLRRFGSVEGVREASVEDLRDVPGVG-EKTAETIRERL 577 (577)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHhCCHHHHHhCCCCC-HHHHHHHHHhC
Confidence 3466999999999999999999999999999999 55 47899999875
No 27
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.47 E-value=0.024 Score=62.50 Aligned_cols=137 Identities=18% Similarity=0.110 Sum_probs=86.4
Q ss_pred CCeEEEecCC-hhhHHHHHHHHhcCCCCCCcccccccCCCCCCCc----cccccHH-------HHHHHHcCCCCchhhhh
Q psy11328 240 PKLRLIWSSG-PYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDY----TDRYNAA-------IEDFISKLPGMAEWSRA 307 (410)
Q Consensus 240 p~l~IiwS~s-~~eTA~ll~~Lk~~~eepd~~~a~~i~~~~~~~~----~~~~~~~-------~~~~l~~lPgi~~~~~~ 307 (410)
.+--.++|.+ +.--|++...|..-.. + .|..|..-..+-. ....-.. ..+=+..+||+.+.++.
T Consensus 418 ~~e~~~rC~n~~~C~aq~~e~l~hfvS-r---~AmdI~GLG~k~i~~L~e~~lI~~~~Dly~Lt~~~l~~l~~~~~ks~~ 493 (667)
T COG0272 418 EGEVVIRCTNGLNCPAQLKERLIHFVS-R---NALDIDGLGEKIIEQLFEKGLIKDIADLYTLTEEDLLSLEGFGEKSAE 493 (667)
T ss_pred cCceeEecCCCCCChHHHhhheeeEec-C---CccCCCCcCHHHHHHHHHcCccCCHHHHHhCCHHHHhhccchhhhHHH
Confidence 3566777877 5677788777766322 1 1222211000000 0000111 12346678887776666
Q ss_pred hhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC
Q psy11328 308 RTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE 387 (410)
Q Consensus 308 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g 387 (410)
+.++.- |.-+.-.+|..||-+ -.|.|++++|+.|..+|+|+.+|..+|.|+|..+-|
T Consensus 494 nLl~aI--------------e~sK~~~l~r~l~aL---------GIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~g 550 (667)
T COG0272 494 NLLNAI--------------EKSKKQPLARFLYAL---------GIRHVGETTAKSLARHFGTLEALLAASEEELASIPG 550 (667)
T ss_pred HHHHHH--------------HHhccCCHHHHHHHc---------CCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccc
Confidence 555531 223334445556655 235599999999999999999999999999999944
Q ss_pred -CchhHHHHHHHhccCC
Q psy11328 388 -NTTLGNALYKALHTRP 403 (410)
Q Consensus 388 -~~~~a~~ly~fl~~~~ 403 (410)
...-|+.|.+||+.+.
T Consensus 551 iG~~vA~si~~ff~~~~ 567 (667)
T COG0272 551 IGEVVARSIIEFFANEE 567 (667)
T ss_pred hhHHHHHHHHHHHcCHH
Confidence 2489999999999764
No 28
>KOG0354|consensus
Probab=95.20 E-value=0.044 Score=61.13 Aligned_cols=59 Identities=22% Similarity=0.182 Sum_probs=46.5
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHH-HHHHHHHHHHH
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYL-SDLRREKKAFE 71 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl-~si~rEk~af~ 71 (410)
||...+|.||.||.+-+.||.|||.|| +|...+++++|.. ++ ++..+- ...-+|+-|-.
T Consensus 488 LDI~ec~lVIcYd~~snpIrmIQrrGR-gRa~ns~~vll~t-~~-~~~~~E~~~~~~e~lm~~ 547 (746)
T KOG0354|consen 488 LDIGECNLVICYDYSSNPIRMVQRRGR-GRARNSKCVLLTT-GS-EVIEFERNNLAKEKLMNQ 547 (746)
T ss_pred CCcccccEEEEecCCccHHHHHHHhcc-ccccCCeEEEEEc-ch-hHHHHHHHHHhHHHHHHH
Confidence 778899999999999999999999999 9999999999988 44 333332 33355666633
No 29
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.09 E-value=0.05 Score=60.31 Aligned_cols=86 Identities=12% Similarity=0.140 Sum_probs=65.6
Q ss_pred HHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHH-hcCCCHH
Q psy11328 294 FISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVL-NRGSSLP 372 (410)
Q Consensus 294 ~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll-~~~~sl~ 372 (410)
-|.++||++++++.+.++.- |.-+.-.++..||-+ -.|+||.+.|+.|. ++|+|+.
T Consensus 471 ~l~~l~g~geksa~nl~~~I--------------e~sk~~~l~r~l~AL---------GI~~vG~~~ak~La~~~f~~~~ 527 (669)
T PRK14350 471 RLINLKGFKDKRINNLKRSI--------------EASKKRPFSKLLLSM---------GIKDLGENTILLLINNNLNSFD 527 (669)
T ss_pred HHhhccCccHHHHHHHHHHH--------------HHHhCCCHHHHHHHc---------CCCchhHHHHHHHHHHhhCCHH
Confidence 46678999988887766631 122333455556555 13669999999999 8999999
Q ss_pred HHHc------CCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 373 ALCK------LSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 373 ~l~~------~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
+|.+ ++.++|.++-| .+..|+.|++||+.+
T Consensus 528 ~l~~~~~~~~~~~e~l~~i~giG~~~a~si~~ff~~~ 564 (669)
T PRK14350 528 KISTLCQDREFALSKLLKIKGIGEKIALNIIEAFNDK 564 (669)
T ss_pred HHHhhhhccCCCHHHHhhCCCccHHHHHHHHHHHcCH
Confidence 9987 69999999955 358999999999875
No 30
>PRK00254 ski2-like helicase; Provisional
Probab=94.81 E-value=0.045 Score=60.55 Aligned_cols=54 Identities=17% Similarity=0.194 Sum_probs=47.4
Q ss_pred CCCCCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCC
Q psy11328 350 SNPRPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRP 403 (410)
Q Consensus 350 ~~~~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~ 403 (410)
+.-.||||.+-+++|+++ |+|+.+|++++.+||.++.| +++.|+.|+++||...
T Consensus 647 L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~~~~ 702 (720)
T PRK00254 647 LMRLPMIGRKRARALYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLGVEK 702 (720)
T ss_pred hhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhcccc
Confidence 344678999999999999 99999999999999999944 3589999999999653
No 31
>PF03834 Rad10: Binding domain of DNA repair protein Ercc1 (rad10/Swi10); InterPro: IPR004579 All proteins in this family for which functions are known are components in a multiprotein endonuclease complex (usually made up of Rad1 and Rad10 homologs). This complex is used primarily for nucleotide excision repair but also for some aspects of recombination repair. In yeast, Rad10 works as a heterodimer with Rad1, and is involved in nucleotide excision repair of DNA damaged with UV light, bulky adducts or cross-linking agents. The complex forms an endonuclease which specifically degrades single-stranded DNA. Ercc1 and XPF (xeroderma pigmentosum group F-complementing protein) are two structure-specific endonucleases of a class of seven containing an ERCC4 domain. Together they form an obligate complex that functions primarily in nucleotide excision repair (NER), a versatile pathway able to detect and remove a variety of DNA lesions induced by UV light and environmental carcinogens, and secondarily in DNA inter-strand cross-link repair and telomere maintenance. This domain in fact binds simultaneously to both XPF and single-stranded DNA; this ternary complex explains the important role of Ercc1 in targeting its catalytic XPF partner to the NER pre-incision complex [].; GO: 0003684 damaged DNA binding, 0004519 endonuclease activity, 0006281 DNA repair, 0005634 nucleus; PDB: 2JNW_A 2JPD_A 2A1I_A.
Probab=94.33 E-value=0.048 Score=44.07 Aligned_cols=62 Identities=29% Similarity=0.455 Sum_probs=43.9
Q ss_pred EEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEEeCCeEEEEechhHHHhhhccChH-----HHHHHHHHhhcC
Q psy11328 99 RVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYILSPDICVERKSISDLIGSLQSGRL-----YTQVQQMCRHYA 169 (410)
Q Consensus 99 ~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYils~~i~VERKSi~DLi~Sl~~GRL-----~~Q~~~L~~~Y~ 169 (410)
.|+|..|.. +.|-+=+-+++.++...--+.||++++..|| |+-||+..|| ++.++.|.+.|+
T Consensus 2 ~I~vn~~Qk--GNplL~~i~nv~we~~~~i~~Dy~vg~~~~v-------LFLSLkYH~L~P~YI~~Ri~~L~~~~~ 68 (69)
T PF03834_consen 2 SILVNPRQK--GNPLLKHIRNVPWEYDSDIVPDYVVGSTTCV-------LFLSLKYHRLHPEYIHERIKKLGKNYN 68 (69)
T ss_dssp SEEE-GGGT--T-CHHHH--SS-EEE----SSSEEEETTEEE-------EEEEHHHHHHSTCHHHHHHHHHTTSSS
T ss_pred cEEECchhc--CChHHHHHhcCCeEecCCCCCCEEECCeEEE-------EEEeeeeecCCHHHHHHHHHHhhhhcC
Confidence 377887776 4455445568999994445899999999999 9999999985 888988887765
No 32
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=94.21 E-value=0.092 Score=49.42 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=43.1
Q ss_pred cCHHHHHHHHhcCCC---HHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCCc
Q psy11328 356 VTSKNKAAVLNRGSS---LPALCKLSEQELCSLVE-NTTLGNALYKALHTRPE 404 (410)
Q Consensus 356 v~~~n~~~ll~~~~s---l~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~~ 404 (410)
||+|-|.+++++|++ .+.+.+.+.++|.++-| .++.|++|+..|+....
T Consensus 81 IGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 81 VGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred CCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 999999999999999 88899999999999944 35899999999987663
No 33
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=93.76 E-value=0.12 Score=56.22 Aligned_cols=83 Identities=19% Similarity=0.135 Sum_probs=60.8
Q ss_pred HHHcCCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHH
Q psy11328 294 FISKLPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPA 373 (410)
Q Consensus 294 ~l~~lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~ 373 (410)
=|.+++|++++++.+.++.- |.-+.-.++..||-+ -.|+||.+.++. +|+|+.+
T Consensus 460 ~l~~l~gfgeks~~nll~aI--------------e~sk~~~l~r~l~aL---------GI~~vG~~~ak~---~~~~i~~ 513 (562)
T PRK08097 460 QLANTPGIGKARAEQLWHQF--------------NLARQQPFSRWLKAL---------GIPLPQAALNAL---DDRSWQQ 513 (562)
T ss_pred HHhcCcCccHHHHHHHHHHH--------------HHHcCCCHHHHHHHc---------CCccHHHHHHHH---hcCCHHH
Confidence 46678998888777666631 122333445555554 236689887775 9999999
Q ss_pred HHcCCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 374 LCKLSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 374 l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
|.+++.|+|.++-| .+..|+.|++||+.+
T Consensus 514 l~~a~~e~l~~i~gIG~~~a~si~~~f~~~ 543 (562)
T PRK08097 514 LLSRSEQQWQQLPGIGEGRARQLIAFLQHP 543 (562)
T ss_pred HHcCCHHHHhcCCCchHHHHHHHHHHHcCH
Confidence 99999999999955 358999999999875
No 34
>TIGR02236 recomb_radA DNA repair and recombination protein RadA. This family consists exclusively of archaeal RadA protein, a homolog of bacterial RecA (TIGR02012), eukaryotic RAD51 (TIGR02239), and archaeal RadB (TIGR02237). This protein is involved in DNA repair and recombination. The member from Pyrococcus horikoshii contains an intein.
Probab=93.21 E-value=0.16 Score=50.16 Aligned_cols=49 Identities=14% Similarity=0.145 Sum_probs=44.0
Q ss_pred CCCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhCC-chhHHHHHHHhc
Q psy11328 352 PRPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVEN-TTLGNALYKALH 400 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g~-~~~a~~ly~fl~ 400 (410)
-.|||+++-+.+|.+. |.|+.+|.+++.++|.++.|. .+.|..|+....
T Consensus 3 ~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~ 53 (310)
T TIGR02236 3 DLPGVGPATAEKLREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAAR 53 (310)
T ss_pred ccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHH
Confidence 3577999999999998 999999999999999999994 568999988876
No 35
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=91.38 E-value=0.35 Score=48.25 Aligned_cols=52 Identities=13% Similarity=0.137 Sum_probs=45.9
Q ss_pred CCCCCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 350 SNPRPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 350 ~~~~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
..-.|||+++-+..|.+. |.|+++|++++.++|.++.| +.+.|..|++..+.
T Consensus 8 l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~ 61 (317)
T PRK04301 8 LEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAARE 61 (317)
T ss_pred HhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 455678999999999997 99999999999999999999 45789999987765
No 36
>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=90.14 E-value=0.38 Score=37.67 Aligned_cols=39 Identities=13% Similarity=0.140 Sum_probs=30.8
Q ss_pred cCHHHHHHHHhc---CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHh
Q psy11328 356 VTSKNKAAVLNR---GSSLPALCKLSEQELCSLVE-NTTLGNALYKAL 399 (410)
Q Consensus 356 v~~~n~~~ll~~---~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl 399 (410)
|+++-|.+|+++ ++.++ +.+||.++.| +++.|++|++|+
T Consensus 25 ig~~~a~~Il~~R~~~g~~~-----s~~dL~~v~gi~~~~~~~i~~~~ 67 (69)
T TIGR00426 25 VGLKKAEAIVSYREEYGPFK-----TVEDLKQVPGIGNSLVEKNLAVI 67 (69)
T ss_pred CCHHHHHHHHHHHHHcCCcC-----CHHHHHcCCCCCHHHHHHHHhhc
Confidence 888889999987 66654 7888888855 357899998886
No 37
>COG1623 Predicted nucleic-acid-binding protein (contains the HHH domain) [General function prediction only]
Probab=89.03 E-value=0.8 Score=46.54 Aligned_cols=52 Identities=15% Similarity=0.149 Sum_probs=44.2
Q ss_pred CCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhc
Q psy11328 349 ESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALH 400 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~ 400 (410)
..|-.|++...-+.+|.+.|++|.++.++|.|+|.++-| .+..|+.+.+=|+
T Consensus 294 ~l~kIpRlp~~iv~nlV~~F~~l~~il~As~edL~~VeGIGe~rAr~i~~Gl~ 346 (349)
T COG1623 294 LLNKIPRLPFAIVENLVRAFGTLDGILEASAEDLDAVEGIGEARARAIKEGLS 346 (349)
T ss_pred HHhcCcCccHHHHHHHHHHHhhHHHHHHhcHhHHhhhcchhHHHHHHHHHhHh
Confidence 455667799999999999999999999999999999977 4678888776543
No 38
>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=85.91 E-value=0.64 Score=50.93 Aligned_cols=32 Identities=28% Similarity=0.168 Sum_probs=28.1
Q ss_pred CCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHH
Q psy11328 350 SNPRPRVTSKNKAAVLNRGSSLPALCKLSEQE 381 (410)
Q Consensus 350 ~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~ee 381 (410)
+.-.||||++..++||.+|||++++.+||.||
T Consensus 543 Ld~I~GIG~kr~~~LL~~Fgs~~~i~~As~ee 574 (574)
T TIGR00194 543 LLKIPGVGEKRVQKLLKYFGSLKGIKKASVEE 574 (574)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhCCccC
Confidence 34456699999999999999999999999875
No 39
>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=85.87 E-value=0.54 Score=41.26 Aligned_cols=43 Identities=9% Similarity=0.001 Sum_probs=31.3
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhc
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSLVE-NTTLGNALYKALH 400 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~ 400 (410)
|+++.|.+|+..+.+ +---.|.+||.++-| ....+.+|.+||.
T Consensus 76 IG~~~A~~Ii~~R~~--~g~f~s~eeL~~V~GIg~k~~~~i~~~l~ 119 (120)
T TIGR01259 76 IGPAKAKAIIEYREE--NGAFKSVDDLTKVSGIGEKSLEKLKDYAT 119 (120)
T ss_pred CCHHHHHHHHHHHHh--cCCcCCHHHHHcCCCCCHHHHHHHHhceE
Confidence 889999999998754 122368889998844 2467888888763
No 40
>PLN03142 Probable chromatin-remodeling complex ATPase chain; Provisional
Probab=84.69 E-value=2.3 Score=49.73 Aligned_cols=52 Identities=19% Similarity=0.281 Sum_probs=42.0
Q ss_pred CCCEEEEEcCCchhhhhhhhhhcccC---CCceEEEEEEeCCcHHHHHHHHHHHH
Q psy11328 14 KPTSVIFYNADVAAIRQVEVYQCAQS---EVKVKVFFMQYGESVEEQAYLSDLRR 65 (410)
Q Consensus 14 ~p~~VI~Yep~~s~IR~IE~y~~~~~---~~~~~Vy~L~y~~S~EE~~yl~si~r 65 (410)
.-+.||+|||+-.--..+|+-+|.+| ..++.||-|++.+|+||.-+-...++
T Consensus 558 ~Ad~VIiyD~dWNP~~d~QAidRaHRIGQkk~V~VyRLIt~gTIEEkIlera~~K 612 (1033)
T PLN03142 558 TADIVILYDSDWNPQVDLQAQDRAHRIGQKKEVQVFRFCTEYTIEEKVIERAYKK 612 (1033)
T ss_pred hCCEEEEeCCCCChHHHHHHHHHhhhcCCCceEEEEEEEeCCcHHHHHHHHHHHH
Confidence 46899999999877778888777765 45899999999999999977554333
No 41
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=84.03 E-value=2.1 Score=42.06 Aligned_cols=55 Identities=22% Similarity=0.240 Sum_probs=47.3
Q ss_pred CCCCCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCc-hhHHHHHHHhccCC
Q psy11328 349 ESNPRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENT-TLGNALYKALHTRP 403 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~-~~a~~ly~fl~~~~ 403 (410)
...-.|+++.+.++++-+ ++.|+.+|.+++.+++..++|.. ..|+.++++++.=+
T Consensus 152 ~L~Qlp~i~~~~~~~l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P 208 (312)
T smart00611 152 PLLQLPHLPEEILKRLEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLP 208 (312)
T ss_pred ccccCCCCCHHHHHHHHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCC
Confidence 355578899999999988 47999999999999999999854 78999999998743
No 42
>PRK00024 hypothetical protein; Reviewed
Probab=83.96 E-value=1.4 Score=42.64 Aligned_cols=40 Identities=28% Similarity=0.160 Sum_probs=32.1
Q ss_pred HHHHHHHhcCCCHHHHHcCCHHHHHHhhCC-chhHHHHHHH
Q psy11328 359 KNKAAVLNRGSSLPALCKLSEQELCSLVEN-TTLGNALYKA 398 (410)
Q Consensus 359 ~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~-~~~a~~ly~f 398 (410)
.-|++|+++|+|+.+|+++|.+||+++-|. +.+|..|...
T Consensus 45 ~LA~~LL~~fgsL~~l~~as~~eL~~i~GIG~akA~~L~a~ 85 (224)
T PRK00024 45 DLARELLQRFGSLRGLLDASLEELQSIKGIGPAKAAQLKAA 85 (224)
T ss_pred HHHHHHHHHcCCHHHHHhCCHHHHhhccCccHHHHHHHHHH
Confidence 358899999999999999999999999552 4566665443
No 43
>PF02889 Sec63: Sec63 Brl domain; InterPro: IPR004179 This domain was named after the yeast Sec63 (or NPL1) (also known as the Brl domain) protein in which it was found. This protein is required for assembly of functional endoplasmic reticulum translocons [, ]. Other yeast proteins containing this domain include pre-mRNA splicing helicase BRR2, HFM1 protein and putative helicases. ; PDB: 3IM2_A 3IM1_A 3HIB_A 2Q0Z_X.
Probab=82.54 E-value=2.3 Score=41.73 Aligned_cols=55 Identities=24% Similarity=0.366 Sum_probs=42.0
Q ss_pred CCCCCCCcCHHHHHHHHhcC-CCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCC
Q psy11328 349 ESNPRPRVTSKNKAAVLNRG-SSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRP 403 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~~~-~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~ 403 (410)
.+.-+|+++++.++++-++- .|+.+|.+++.+|++.+++ ....|+.+.++++.=+
T Consensus 149 ~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~P 205 (314)
T PF02889_consen 149 PLLQLPHIGEESLKKLEKRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRIP 205 (314)
T ss_dssp GGGGSTT--HHHHHHHHHTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS-
T ss_pred hhhcCCCCCHHHHHHHhccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHCC
Confidence 44557889999999999864 8999999999999999997 6689999999998743
No 44
>COG2003 RadC DNA repair proteins [DNA replication, recombination, and repair]
Probab=79.42 E-value=2.4 Score=41.49 Aligned_cols=29 Identities=31% Similarity=0.243 Sum_probs=26.7
Q ss_pred HHHHHHHhcCCCHHHHHcCCHHHHHHhhC
Q psy11328 359 KNKAAVLNRGSSLPALCKLSEQELCSLVE 387 (410)
Q Consensus 359 ~n~~~ll~~~~sl~~l~~~s~eeL~~~~g 387 (410)
.-+++||++|+||.+|+++|.++|+.+-|
T Consensus 45 ~la~~lL~~fg~L~~l~~a~~~el~~v~G 73 (224)
T COG2003 45 DLAKELLQEFGSLAELLKASVEELSSVKG 73 (224)
T ss_pred HHHHHHHHHcccHHHHHhCCHHHHhhCCC
Confidence 35889999999999999999999999966
No 45
>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=78.55 E-value=1.6 Score=35.15 Aligned_cols=28 Identities=21% Similarity=0.243 Sum_probs=24.3
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcCCHH
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKLSEQ 380 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~s~e 380 (410)
.|||++|.|.+|+++++|++.+...-.+
T Consensus 27 v~giG~k~A~~ll~~~~~~~~~~~~~~~ 54 (75)
T cd00080 27 VPGIGPKTALKLLKEYGSLENLLENLDK 54 (75)
T ss_pred CCcccHHHHHHHHHHhCCHHHHHHHHHH
Confidence 4779999999999999999999976433
No 46
>TIGR00608 radc DNA repair protein radc. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.54 E-value=3.1 Score=40.24 Aligned_cols=39 Identities=21% Similarity=0.071 Sum_probs=31.3
Q ss_pred HHHHHHHhcC---CCHHHHHcCCHHHHHHhhCC-chhHHHHHH
Q psy11328 359 KNKAAVLNRG---SSLPALCKLSEQELCSLVEN-TTLGNALYK 397 (410)
Q Consensus 359 ~n~~~ll~~~---~sl~~l~~~s~eeL~~~~g~-~~~a~~ly~ 397 (410)
.-|+.|+++| +|+.+|.++|.+||+++-|. +.+|..|..
T Consensus 36 ~lA~~ll~~f~~~g~l~~l~~a~~~eL~~i~GiG~aka~~l~a 78 (218)
T TIGR00608 36 SLSKRLLDVFGRQDSLGHLLSAPPEELSSVPGIGEAKAIQLKA 78 (218)
T ss_pred HHHHHHHHHhcccCCHHHHHhCCHHHHHhCcCCcHHHHHHHHH
Confidence 3588999999 99999999999999999552 356655543
No 47
>PRK01172 ski2-like helicase; Provisional
Probab=76.38 E-value=4.5 Score=44.56 Aligned_cols=52 Identities=13% Similarity=0.165 Sum_probs=43.1
Q ss_pred CCCCCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhc
Q psy11328 349 ESNPRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVE-NTTLGNALYKALH 400 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~ 400 (410)
++.-.|||+..-|+.|.+ .+.|+.+|++++.++|.+++| ++..|+.++..++
T Consensus 613 ~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~ 666 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred hhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence 344467899999999998 699999999999999999966 4578888877643
No 48
>PRK02362 ski2-like helicase; Provisional
Probab=73.40 E-value=5.7 Score=44.38 Aligned_cols=49 Identities=10% Similarity=0.079 Sum_probs=44.0
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
.|||+.+-|+.|.+ .+.|+.+|++++.++|.+++|. ..|+.|.+.++..
T Consensus 657 ip~i~~~~a~~l~~~gi~s~~dl~~~~~~~l~~~~g~-~~~~~i~~~~~~~ 706 (737)
T PRK02362 657 LRGVGRVRARRLYNAGIESRADLRAADKSVVLAILGE-KIAENILEQAGRR 706 (737)
T ss_pred CCCCCHHHHHHHHHcCCCCHHHHHhCCHHHHHHHHCH-HHHHHHHHHhCcc
Confidence 46699999999987 5999999999999999999996 7999999998843
No 49
>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=72.39 E-value=5.5 Score=27.08 Aligned_cols=29 Identities=31% Similarity=0.267 Sum_probs=21.3
Q ss_pred CHHHHHcCCHHHHHHhhC-CchhHHHHHHH
Q psy11328 370 SLPALCKLSEQELCSLVE-NTTLGNALYKA 398 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g-~~~~a~~ly~f 398 (410)
|+..+..+|.|||+++-| .+..|..+..|
T Consensus 1 ~~~g~~pas~eeL~~lpGIG~~tA~~I~~~ 30 (30)
T PF00633_consen 1 SLDGLIPASIEELMKLPGIGPKTANAILSF 30 (30)
T ss_dssp SHHHHHTSSHHHHHTSTT-SHHHHHHHHHH
T ss_pred CCCCcCCCCHHHHHhCCCcCHHHHHHHHhC
Confidence 456778888888888855 34778877765
No 50
>PRK03352 DNA polymerase IV; Validated
Probab=71.75 E-value=7.8 Score=39.02 Aligned_cols=49 Identities=16% Similarity=0.057 Sum_probs=42.0
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
.+|||+++.+..|-+ .+.++.+|++++.++|.+.+|. ..|..||+..+.
T Consensus 181 ~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG~-~~~~~l~~~a~G 230 (346)
T PRK03352 181 ALWGVGPKTAKRLAALGITTVADLAAADPAELAATFGP-TTGPWLLLLARG 230 (346)
T ss_pred HcCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHhCh-HHHHHHHHHhCC
Confidence 356799999988766 6899999999999999999996 578999998544
No 51
>TIGR01954 nusA_Cterm_rpt transcription termination factor NusA, C-terminal duplication. NusA is a bacterial transcription termination factor. It is named for its interaction with phage lambda protein N, as part of the N utilization substance. Some members of the NusA family have a long C-terminal extension. This model represents an acidic 50-residue region found in two copies toward the C-terminus of most Proteobacterial NusA proteins, spaced about 26 residues apart. Analogous C-terminal extensions in some other bacterial lineages lack apparent homology but appear similarly acidic.
Probab=71.72 E-value=8.9 Score=27.57 Aligned_cols=41 Identities=12% Similarity=0.135 Sum_probs=31.0
Q ss_pred CHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhC-CchhHHHHHH
Q psy11328 357 TSKNKAAVLN-RGSSLPALCKLSEQELCSLVE-NTTLGNALYK 397 (410)
Q Consensus 357 ~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~ 397 (410)
++..+..|.+ .|.|+.+|..++.++|..+-| ++..|..+-.
T Consensus 2 ~~~~~~~L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~ 44 (50)
T TIGR01954 2 DEEIAQLLVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELIN 44 (50)
T ss_pred CHHHHHHHHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHH
Confidence 3445556665 599999999999999999977 4466666543
No 52
>cd01702 PolY_Pol_eta DNA Polymerase eta. Pol eta, also called Rad30A, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced lesions. Its activity is initiated by two simultaneous interactions: the PIP box in pol eta interacting with PCNA, and the UBZ (ubiquitin-binding zinc finger) in pol eta interacting with monoubiquitin attached to PCNA. Pol eta is more efficient in copying damaged DNA than undamaged DNA and seems to recognize when a lesion has been passed, facilitating a lesion-dependent dissociation from the DNA.
Probab=70.35 E-value=7.3 Score=40.07 Aligned_cols=50 Identities=18% Similarity=0.193 Sum_probs=42.8
Q ss_pred CCCCcCHHHHHHHHh--cCCCHHHHHcC--CHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN--RGSSLPALCKL--SEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~--~~~sl~~l~~~--s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
-.|||+.+.+..+++ .+.++.+|.++ +.++|.+.+|. ..|..||+.++..
T Consensus 186 ~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~fG~-~~g~~l~~~a~G~ 239 (359)
T cd01702 186 SIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGE-KLGEWLYNLLRGI 239 (359)
T ss_pred HhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHHHHH-HHHHHHHHHhCCC
Confidence 346799998888765 68899999999 99999999996 6899999988764
No 53
>PRK01216 DNA polymerase IV; Validated
Probab=69.09 E-value=10 Score=38.96 Aligned_cols=51 Identities=10% Similarity=0.115 Sum_probs=42.7
Q ss_pred CCCCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 350 SNPRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 350 ~~~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
....|||+++.+..|-+ .+.++.+|.+++.++|.+.+|. ..+..||+..+.
T Consensus 180 i~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L~~rfG~-~~~~~L~~~a~G 231 (351)
T PRK01216 180 IADIPGIGDITAEKLKKLGVNKLVDTLRIEFDELKGIIGE-AKAKYLFSLARN 231 (351)
T ss_pred cccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHCH-HHHHHHHHHhCC
Confidence 34556799998877766 6999999999999999999996 679999996654
No 54
>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=68.62 E-value=3.8 Score=39.73 Aligned_cols=25 Identities=24% Similarity=0.284 Sum_probs=23.1
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKL 377 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~ 377 (410)
.||||+|.|..||++++|++++.+.
T Consensus 188 v~GiG~ktA~~Ll~~~gsle~i~~~ 212 (240)
T cd00008 188 VPGIGEKTAAKLLKEYGSLEGILEN 212 (240)
T ss_pred CCccCHHHHHHHHHHhCCHHHHHHh
Confidence 5779999999999999999999875
No 55
>PRK03348 DNA polymerase IV; Provisional
Probab=67.06 E-value=10 Score=40.26 Aligned_cols=50 Identities=20% Similarity=0.182 Sum_probs=42.8
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
-+|||+++....|-+ .+.++.+|.+++.++|.+.+|. ..+..||+..+..
T Consensus 184 ~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~L~~~fG~-~~g~~L~~~a~G~ 234 (454)
T PRK03348 184 RLWGIGPVTEEKLHRLGIETIGDLAALSEAEVANLLGA-TVGPALHRLARGI 234 (454)
T ss_pred ccCCCCHHHHHHHHHcCCccHHHHhcCCHHHHHHHHCH-HHHHHHHHHHcCC
Confidence 457799998888766 6899999999999999999996 6899999986653
No 56
>PTZ00035 Rad51 protein; Provisional
Probab=66.42 E-value=11 Score=38.61 Aligned_cols=49 Identities=6% Similarity=0.167 Sum_probs=41.4
Q ss_pred CCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 353 RPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
.|||++..+.+|-++ +.|+.++..++..+|.++.| +...|.+|-.....
T Consensus 28 ~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~ 78 (337)
T PTZ00035 28 SAGINAADIKKLKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASK 78 (337)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 477999999999985 99999999999999999999 66777777765444
No 57
>KOG0387|consensus
Probab=66.06 E-value=16 Score=41.81 Aligned_cols=60 Identities=17% Similarity=0.196 Sum_probs=43.5
Q ss_pred CCCEEEEEcCC--chh-hhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHHHHHHHHHH
Q psy11328 14 KPTSVIFYNAD--VAA-IRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRREKKAFEYL 73 (410)
Q Consensus 14 ~p~~VI~Yep~--~s~-IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~rEk~af~~L 73 (410)
.-+-||+|||+ ||. .-.-||.=|.|....+-||=||+.||+||..|-.-+-++--.-..|
T Consensus 617 gAnRVIIfDPdWNPStD~QAreRawRiGQkkdV~VYRL~t~gTIEEkiY~rQI~Kq~Ltn~il 679 (923)
T KOG0387|consen 617 GANRVIIFDPDWNPSTDNQARERAWRIGQKKDVVVYRLMTAGTIEEKIYHRQIFKQFLTNRIL 679 (923)
T ss_pred cCceEEEECCCCCCccchHHHHHHHhhcCccceEEEEEecCCcHHHHHHHHHHHHHHHHHHHh
Confidence 45789999997 554 2233444445667789999999999999999988776655444444
No 58
>PRK09482 flap endonuclease-like protein; Provisional
Probab=65.71 E-value=4.7 Score=40.03 Aligned_cols=29 Identities=24% Similarity=0.236 Sum_probs=24.5
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcCCHHHH
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKLSEQEL 382 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL 382 (410)
.||||+|.|..||++|+|+..+.+. .+++
T Consensus 187 VpGIG~KtA~~LL~~~gsle~i~~~-~~~~ 215 (256)
T PRK09482 187 VAGIGPKSAAELLNQFRSLENIYES-LDAL 215 (256)
T ss_pred CCCcChHHHHHHHHHhCCHHHHHHh-HHHh
Confidence 4779999999999999999999865 3334
No 59
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1. This model describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (TIGR02236) and RadB (TIGR02237) and bacterial RecA (TIGR02012). It has been characterized for human as a recombinase active only in meiosis.
Probab=65.23 E-value=12 Score=37.81 Aligned_cols=50 Identities=6% Similarity=0.103 Sum_probs=42.2
Q ss_pred CCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
.+||++..+.+|-++ +.|+.++..++..||.++.| +...|.++-+....-
T Consensus 6 ~~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~~ 57 (313)
T TIGR02238 6 AHGINAADIKKLKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASKI 57 (313)
T ss_pred cCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHhh
Confidence 467999999999875 99999999999999999999 667788777655443
No 60
>cd01703 PolY_Pol_iota DNA Polymerase iota. Pol iota, also called Rad30B, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol iota is thought to be one of the least efficient polymerases, particularly when opposite pyrimidines; it can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine, and prefers to insert guanosine instead of adenosine opposite thymidine. Pol iota is believed to use Hoogsteen rather than Watson-Crick base pairing, which may explain the varying efficiency for different template nucleotides.
Probab=65.04 E-value=12 Score=38.95 Aligned_cols=49 Identities=22% Similarity=0.224 Sum_probs=42.6
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCC---------------HHHHHHhhCCchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLS---------------EQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s---------------~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
.|||+++.+..|-+ .+.++.+|.+++ .+.|.+.+|. ..|..||+..+..
T Consensus 177 l~GiG~~~~~kL~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~-~~g~~l~~~a~G~ 241 (379)
T cd01703 177 IPGIGYKTAAKLEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGE-GIGQRIWKLLFGR 241 (379)
T ss_pred cCCcCHHHHHHHHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCH-HHHHHHHHHHCCC
Confidence 45699999999887 588999999999 9999999995 5799999988764
No 61
>PRK03858 DNA polymerase IV; Validated
Probab=63.89 E-value=14 Score=37.78 Aligned_cols=48 Identities=21% Similarity=0.173 Sum_probs=42.1
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
+|||+++.+..|-+ .+.|+.+|.+++.++|.+.+|. ..++.||...+.
T Consensus 178 l~Gig~~~~~~L~~~Gi~t~~dl~~l~~~~L~~~fG~-~~~~~l~~~a~G 226 (396)
T PRK03858 178 LWGVGPVTAAKLRAHGITTVGDVAELPESALVSLLGP-AAGRHLHALAHN 226 (396)
T ss_pred cCCCCHHHHHHHHHhCCCcHHHHhcCCHHHHHHHhCc-HHHHHHHHHhCC
Confidence 56799999988876 6999999999999999999996 679999987754
No 62
>smart00475 53EXOc 5'-3' exonuclease.
Probab=63.70 E-value=5.4 Score=39.39 Aligned_cols=25 Identities=24% Similarity=0.258 Sum_probs=22.8
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKL 377 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~ 377 (410)
.||||+|.|..||++++|+.++.+.
T Consensus 191 V~GIG~KtA~~Ll~~ygsle~i~~~ 215 (259)
T smart00475 191 VPGIGEKTAAKLLKEFGSLENILEN 215 (259)
T ss_pred CCCCCHHHHHHHHHHhCCHHHHHHH
Confidence 5779999999999999999999865
No 63
>PRK03980 flap endonuclease-1; Provisional
Probab=63.50 E-value=13 Score=37.51 Aligned_cols=24 Identities=8% Similarity=0.173 Sum_probs=22.4
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHc
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCK 376 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~ 376 (410)
.||||+|.|..|+++++||+++..
T Consensus 194 I~GIG~ktA~kLi~~~~sle~i~~ 217 (292)
T PRK03980 194 IKGIGPKTALKLIKKHGDLEKVLE 217 (292)
T ss_pred CCCccHHHHHHHHHHCCCHHHHHH
Confidence 567999999999999999999987
No 64
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=62.79 E-value=13 Score=37.32 Aligned_cols=25 Identities=20% Similarity=0.158 Sum_probs=21.9
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKL 377 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~ 377 (410)
.||||+|+|..||+.++|++.|.+.
T Consensus 203 V~GIG~ktA~~Ll~~~gs~e~i~~~ 227 (310)
T COG0258 203 VKGIGPKTALKLLQEYGSLEGLYEN 227 (310)
T ss_pred CCCcCHHHHHHHHHHhCCHHHHHHh
Confidence 5669999999999999988888764
No 65
>KOG0385|consensus
Probab=62.42 E-value=15 Score=42.04 Aligned_cols=51 Identities=18% Similarity=0.241 Sum_probs=37.0
Q ss_pred CCCEEEEEcCCch---hhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHH
Q psy11328 14 KPTSVIFYNADVA---AIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLR 64 (410)
Q Consensus 14 ~p~~VI~Yep~~s---~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~ 64 (410)
--|.||+||.|-- -+-...|..|.|...+++||=|++++|+||..+-.+-.
T Consensus 558 aADtVIlyDSDWNPQ~DLQAmDRaHRIGQ~K~V~V~RLitentVEe~IveRA~~ 611 (971)
T KOG0385|consen 558 AADTVILYDSDWNPQVDLQAMDRAHRIGQKKPVVVYRLITENTVEEKIVERAAA 611 (971)
T ss_pred cccEEEEecCCCCchhhhHHHHHHHhhCCcCceEEEEEeccchHHHHHHHHHHH
Confidence 3589999998732 23334445555667799999999999999987655443
No 66
>cd01701 PolY_Rev1 DNA polymerase Rev1. Rev1 is a translesion synthesis (TLS) polymerase found in eukaryotes. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Rev1 has both structural and enzymatic roles. Structurally, it is believed to interact with other nonclassical polymerases and replication machinery to act as a scaffold. Enzymatically, it catalyzes the specific insertion of dCMP opposite abasic sites. Rev1 interacts with the Rev7 subunit of the B-family TLS polymerase Pol zeta (Rev3/Rev7). Rev1 is known to actively promote the introduction of mutations, potentially making it a significant target for cancer treatment.
Probab=62.07 E-value=14 Score=38.41 Aligned_cols=50 Identities=20% Similarity=0.201 Sum_probs=43.2
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCC--HHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLS--EQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s--~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
..|||+++-+..|.+ .+.++.+|.+++ .++|.+.+|. ..|..||+..+..
T Consensus 226 ~l~GIG~~~~~~L~~~Gi~t~~dl~~~~~~~~~L~~~fG~-~~g~~L~~~a~G~ 278 (404)
T cd01701 226 DLPGVGSSLAEKLVKLFGDTCGGLELRSKTKEKLQKVLGP-KTGEKLYDYCRGI 278 (404)
T ss_pred HhCCCCHHHHHHHHHcCCcchHHHHhCcccHHHHHHHHCH-HHHHHHHHHhCCc
Confidence 356799999988887 588999999999 9999999996 5799999988764
No 67
>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=61.08 E-value=0.54 Score=40.44 Aligned_cols=24 Identities=25% Similarity=0.306 Sum_probs=21.5
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHc
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCK 376 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~ 376 (410)
.||||+|.|..||++|+||+++..
T Consensus 23 V~GIG~KtA~~LL~~ygsle~i~~ 46 (101)
T PF01367_consen 23 VPGIGPKTAAKLLQEYGSLENILA 46 (101)
T ss_dssp -TTSTCHCCCCCHHHHTSCHCCCC
T ss_pred CCCCCHHHHHHHHHHcCCHHHHHH
Confidence 367999999999999999999876
No 68
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=60.53 E-value=15 Score=37.85 Aligned_cols=47 Identities=6% Similarity=0.067 Sum_probs=39.5
Q ss_pred CCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhc
Q psy11328 354 PRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALH 400 (410)
Q Consensus 354 ~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~ 400 (410)
+||++..+.+|.++ |.|+.+|..++..||.++.| +...|.+|.+...
T Consensus 37 ~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~ 85 (344)
T PLN03187 37 QGINAGDVKKLQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAE 85 (344)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 56999999999985 99999999999999999998 5667777665433
No 69
>PRK14976 5'-3' exonuclease; Provisional
Probab=60.53 E-value=12 Score=37.52 Aligned_cols=24 Identities=13% Similarity=0.224 Sum_probs=22.1
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHc
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCK 376 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~ 376 (410)
.||||+|.|..||++++|+.++.+
T Consensus 196 VpGIG~KtA~~LL~~~gsle~i~~ 219 (281)
T PRK14976 196 VKGIGPKTAIKLLNKYGNIENIYE 219 (281)
T ss_pred CCcccHHHHHHHHHHcCCHHHHHH
Confidence 567999999999999999999975
No 70
>KOG2093|consensus
Probab=60.48 E-value=22 Score=41.13 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=42.4
Q ss_pred CCCCCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 351 NPRPRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 351 ~~~~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
.-+||||..-..+|-+. ..+..+|=..++++|.+++|+ +.|..||.+.+.
T Consensus 552 ~~LPGVG~sm~~kL~s~~i~tCgdLq~~T~~kl~k~~G~-Klgq~i~~~CrG 602 (1016)
T KOG2093|consen 552 DDLPGVGSSMKSKLVSQFIQTCGDLQLITLIKLRKVFGP-KLGQKIYRGCRG 602 (1016)
T ss_pred ccCCCccHHHHHHHHHhccchhHHHHHHHHHHHHhhhcc-cHHHHHHHhcCC
Confidence 34566999988888874 578888999999999999997 799999999865
No 71
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.41 E-value=7.7 Score=44.78 Aligned_cols=25 Identities=20% Similarity=0.161 Sum_probs=22.6
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKL 377 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~ 377 (410)
.||||+|.|..||++++|++++.+.
T Consensus 190 VpGIG~KtA~kLL~~ygsle~i~~~ 214 (887)
T TIGR00593 190 VKGIGEKTAAKLLQEFGSLENIYEN 214 (887)
T ss_pred CCCcCHHHHHHHHHHcCCHHHHHHH
Confidence 4679999999999999999999864
No 72
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=59.20 E-value=18 Score=36.69 Aligned_cols=50 Identities=4% Similarity=0.072 Sum_probs=41.5
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
+.+|+++..+.+|-+ .+.|+.++..+|..||.++.| +...++.+...+..
T Consensus 5 ~~~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~~~ 56 (316)
T TIGR02239 5 EGNGITAADIKKLQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEAAK 56 (316)
T ss_pred hcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 346799999999987 699999999999999999988 56777777765543
No 73
>PRK02406 DNA polymerase IV; Validated
Probab=59.05 E-value=17 Score=36.64 Aligned_cols=49 Identities=18% Similarity=0.135 Sum_probs=42.0
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
..|||+++....|-. .+.++.||.+++.++|.+.+|. .+..+|+..+..
T Consensus 172 ~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~~~fG~--~~~~l~~~a~G~ 221 (343)
T PRK02406 172 KIPGVGKVTAEKLHALGIYTCADLQKYDLAELIRHFGK--FGRRLYERARGI 221 (343)
T ss_pred hhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHHhH--HHHHHHHHhCCC
Confidence 457799998888765 5999999999999999999995 688899988764
No 74
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=58.40 E-value=19 Score=32.54 Aligned_cols=33 Identities=24% Similarity=0.400 Sum_probs=30.6
Q ss_pred CcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC
Q psy11328 355 RVTSKNKAAVLNRGSSLPALCKLSEQELCSLVE 387 (410)
Q Consensus 355 ~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g 387 (410)
|+.+.-+..++.+..|+.+|.++|.+|+..++.
T Consensus 77 gl~~~~i~~i~~~~~tLe~Llemsd~el~~~l~ 109 (129)
T PF13543_consen 77 GLRPESIQAILSKVLTLEALLEMSDEELKEILN 109 (129)
T ss_pred CCCHHHHHHHHHhhcCHHHHHhCCHHHHHHHHH
Confidence 388999999999999999999999999999974
No 75
>PRK03103 DNA polymerase IV; Reviewed
Probab=57.38 E-value=20 Score=37.03 Aligned_cols=48 Identities=13% Similarity=0.029 Sum_probs=41.6
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
+|||+++....|-. .+.|+.+|.+++.++|.+.+|. .+..+|+.++..
T Consensus 186 l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~~~fG~--~~~~l~~~a~G~ 234 (409)
T PRK03103 186 LFGVGSRMEKHLRRMGIRTIGQLANTPLERLKKRWGI--NGEVLWRTANGI 234 (409)
T ss_pred cCCccHHHHHHHHHcCCCCHHHHhcCCHHHHHHHHCH--HHHHHHHHhcCC
Confidence 46799998888765 6899999999999999999995 699999998873
No 76
>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=57.22 E-value=18 Score=36.99 Aligned_cols=25 Identities=12% Similarity=0.151 Sum_probs=22.6
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKL 377 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~ 377 (410)
.||||+|.|..|++.++|++++.+.
T Consensus 241 v~GIG~ktA~kli~~~gsie~il~~ 265 (338)
T TIGR03674 241 VKGIGPKTALKLIKEHGDLEKVLKA 265 (338)
T ss_pred CCCccHHHHHHHHHHcCCHHHHHHh
Confidence 4569999999999999999999874
No 77
>TIGR00631 uvrb excinuclease ABC, B subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University)
Probab=56.54 E-value=24 Score=39.46 Aligned_cols=62 Identities=16% Similarity=0.128 Sum_probs=43.7
Q ss_pred HHhhhhhCCCEEEEEcCCc-----hhhhhhhhhhcccCCCceEEEEEEeCCc--HHHHHHHHHHHHHHH
Q psy11328 7 SSKLRSLKPTSVIFYNADV-----AAIRQVEVYQCAQSEVKVKVFFMQYGES--VEEQAYLSDLRREKK 68 (410)
Q Consensus 7 ~~~L~~~~p~~VI~Yep~~-----s~IR~IE~y~~~~~~~~~~Vy~L~y~~S--~EE~~yl~si~rEk~ 68 (410)
+.=++-...++||++|++. +.-.-||+-||++|...++|+++....+ ..++-..+..+|+++
T Consensus 503 ~rGfDiP~v~lVvi~DadifG~p~~~~~~iqriGRagR~~~G~vi~~~~~~~~~~~~ai~~~~~~~~iq 571 (655)
T TIGR00631 503 REGLDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIMYADKITDSMQKAIEETERRRKIQ 571 (655)
T ss_pred cCCeeeCCCcEEEEeCcccccCCCCHHHHHHHhcCCCCCCCCEEEEEEcCCCHHHHHHHHHHHhHHHHH
Confidence 3345667889999999754 3335689999999998999887777654 444555555666655
No 78
>PRK01810 DNA polymerase IV; Validated
Probab=55.46 E-value=21 Score=36.85 Aligned_cols=47 Identities=15% Similarity=0.091 Sum_probs=41.3
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
+|||+++.+..|-. .+.++.+|..++.++|.+.+|. .+..+|+.++.
T Consensus 184 l~giG~~~~~~L~~~Gi~tigdL~~~~~~~L~~rfG~--~g~~l~~~a~G 231 (407)
T PRK01810 184 MHGIGEKTAEKLKDIGIQTIGDLAKADEHILRAKLGI--NGVRLQRRANG 231 (407)
T ss_pred cCCcCHHHHHHHHHcCCCcHHHHHhCCHHHHHHHHhH--HHHHHHHHhcC
Confidence 56799998888765 5999999999999999999995 69999999885
No 79
>PTZ00424 helicase 45; Provisional
Probab=55.20 E-value=13 Score=37.44 Aligned_cols=44 Identities=9% Similarity=-0.037 Sum_probs=35.7
Q ss_pred hhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCC
Q psy11328 9 KLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGE 52 (410)
Q Consensus 9 ~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~ 52 (410)
=++-...++||+|++-.+...-+|+-||++|. ..+.++.++..+
T Consensus 330 GiDip~v~~VI~~~~p~s~~~y~qr~GRagR~g~~G~~i~l~~~~ 374 (401)
T PTZ00424 330 GIDVQQVSLVINYDLPASPENYIHRIGRSGRFGRKGVAINFVTPD 374 (401)
T ss_pred CcCcccCCEEEEECCCCCHHHEeecccccccCCCCceEEEEEcHH
Confidence 35667889999999999888899999999884 467888777543
No 80
>PRK07758 hypothetical protein; Provisional
Probab=54.89 E-value=36 Score=29.33 Aligned_cols=51 Identities=22% Similarity=0.184 Sum_probs=36.1
Q ss_pred CCCCCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHh--hCCchhHHHHHHHhc
Q psy11328 349 ESNPRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSL--VENTTLGNALYKALH 400 (410)
Q Consensus 349 ~~~~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl~ 400 (410)
+....|+++..-...|-+ .+.+|.+|+..|++||.++ +|. .--..|-+.|.
T Consensus 35 ~~~~~~~LSvRA~N~Lk~AGI~TL~dLv~~te~ELl~iknlGk-KSL~EIkekL~ 88 (95)
T PRK07758 35 KEGFLSLLSAPARRALEHHGIHTVEELSKYSEKEILKLHGMGP-ASLPKLRKALE 88 (95)
T ss_pred CCCCCccccHHHHHHHHHcCCCcHHHHHcCCHHHHHHccCCCH-HHHHHHHHHHH
Confidence 344566777665555644 6999999999999999999 554 44555555544
No 81
>cd01700 PolY_Pol_V_umuC umuC subunit of DNA Polymerase V. umuC subunit of Pol V. Pol V is a bacterial translesion synthesis (TLS) polymerase that consists of the heterotrimer of one umuC and two umuD subunits. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Pol V, RecA, single stranded DNA-binding protein, beta sliding clamp, and gamma clamp loading complex are responsible for inducing the SOS response in bacteria to repair UV-induced DNA damage.
Probab=54.41 E-value=22 Score=35.85 Aligned_cols=47 Identities=11% Similarity=0.039 Sum_probs=40.5
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
.|||+++....|-. .+.++.+|.+++.++|.+.+|. .+..+|+..+.
T Consensus 181 l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L~~rfG~--~~~~l~~~a~G 228 (344)
T cd01700 181 VWGIGRRTAKKLNAMGIHTAGDLAQADPDLLRKKFGV--VGERLVRELNG 228 (344)
T ss_pred cCccCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHHH--HHHHHHHHhCC
Confidence 46799998888765 6899999999999999999995 68888888765
No 82
>KOG0390|consensus
Probab=54.21 E-value=22 Score=40.68 Aligned_cols=52 Identities=15% Similarity=0.238 Sum_probs=38.1
Q ss_pred CCCEEEEEcCC--chhhhh-hhhhhcccCCCceEEEEEEeCCcHHHHHHHHHHHH
Q psy11328 14 KPTSVIFYNAD--VAAIRQ-VEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDLRR 65 (410)
Q Consensus 14 ~p~~VI~Yep~--~s~IR~-IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si~r 65 (410)
.-+.||||||+ ||.=+| |-|-=|-|...++-+|=|++.||.||..|-....+
T Consensus 666 GAsRlil~D~dWNPa~d~QAmaR~~RdGQKk~v~iYrLlatGtiEEk~~qrq~~K 720 (776)
T KOG0390|consen 666 GASRLILFDPDWNPAVDQQAMARAWRDGQKKPVYIYRLLATGTIEEKIYQRQTHK 720 (776)
T ss_pred ccceEEEeCCCCCchhHHHHHHHhccCCCcceEEEEEeecCCCchHHHHHHHHHh
Confidence 34679999997 665443 22333445567899999999999999999775544
No 83
>cd08538 SAM_PNT-ESE-2-like Sterile alpha motif (SAM)/Pointed domain of ESE-2 like ETS transcriptional regulators. SAM Pointed domain of ESE-2-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ESE-2 factors are involved in regulation of gene expression in a variety of epithelial (glandular and secretory) cells. ESE-2 mRNA was found in skin keratinocytes, salivary gland, mammary gland, stomach, prostate, and kidneys. The DNA binding consensus motif for ESE-2 consists of a GGA core and AT-rich flanks. The expression profiles of these factors are altered in epithelial cancers. Members of this subfamily are potential targets for cancer therapy.
Probab=53.88 E-value=15 Score=30.54 Aligned_cols=29 Identities=24% Similarity=0.387 Sum_probs=25.2
Q ss_pred HHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 371 LPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 371 l~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
=++||++|.||+....|+ .|.-||.-|..
T Consensus 42 Gk~LC~ms~eeF~~~~p~--~GdvLy~~lq~ 70 (78)
T cd08538 42 GLQLCSMTQEEFIEAAGI--CGEYLYFILQN 70 (78)
T ss_pred HHHHHcCCHHHHHHHccc--chHHHHHHHHH
Confidence 379999999999999985 89999988753
No 84
>PRK14133 DNA polymerase IV; Provisional
Probab=53.08 E-value=24 Score=35.57 Aligned_cols=48 Identities=19% Similarity=0.219 Sum_probs=41.2
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
.+|||+++-+..|-+ .++++.+|.+++.++|.+.+|. .+..+|+.++.
T Consensus 177 ~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L~~rfG~--~g~~l~~~a~G 225 (347)
T PRK14133 177 KVHGIGKKSVEKLNNIGIYTIEDLLKLSREFLIEYFGK--FGVEIYERIRG 225 (347)
T ss_pred ccCCCCHHHHHHHHHcCCccHHHHhhCCHHHHHHHHhH--HHHHHHHHhCC
Confidence 456799988888765 6999999999999999999994 68999998865
No 85
>cd08203 SAM_PNT Sterile alpha motif (SAM)/Pointed domain. Sterile alpha motif (SAM)/Pointed domain is found in about 40% of transcriptional regulators of ETS family (initially named for Erythroblastosis virus, E26-E Twenty Six). SAM Pointed domain containing proteins of this family additionally have C-terminal ETS DNA-binding domain. In a few cases, SAM Pointed domain appears as a single domain protein. Members of this group are mostly involved in regulation of embryonic development and growth control in eukaryotes. SAM Pointed domains mediate protein-protein interactions. Depending on the subgroup, they can interact with other SAM Pointed domains forming homo or hetero dimers/oligomers and/or they can recruit a protein kinase to its target which can be the SAM Pointed domain containing protein itself or another protein that has no kinase docking site. Thus, SAM Pointed domains participate in transcriptional regulation and signal transduction. Some genes coding ETS family transcripti
Probab=53.05 E-value=16 Score=28.89 Aligned_cols=29 Identities=24% Similarity=0.461 Sum_probs=25.4
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||.+|.|++....+. .|..||..|+
T Consensus 34 ~G~~Lc~ls~edF~~~~p~--~GdiL~~hL~ 62 (66)
T cd08203 34 NGKELCLLTKEDFLRRAPS--GGDILYEHLQ 62 (66)
T ss_pred CHHHHHhCCHHHHHHHcCC--cHHHHHHHHH
Confidence 3479999999999999975 8999999875
No 86
>cd08757 SAM_PNT_ESE Sterile alpha motif (SAM)/Pointed domain of ESE-like ETS transcriptional regulators. SAM Pointed domain of ESE-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. ETS factors are important for cell differentiation. They can be involved in regulation of gene expression in different types of epithelial cells. They are expressed in salivary gland, intestine, stomach, pancreas, lungs, kidneys, colon, mammary gland, and prostate. Members of this group are proto-oncogenes. Expression profiles of these factors are altered in epithelial cancers, which makes them potential targets for cancer therapy.
Probab=52.36 E-value=14 Score=29.39 Aligned_cols=30 Identities=27% Similarity=0.523 Sum_probs=26.0
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
+=++||.+|.|++....++ .|..||+-|+.
T Consensus 36 ~Gk~LC~ms~edF~~~~p~--~GdiL~~~l~~ 65 (68)
T cd08757 36 DGQTLCSMTEEEFREAAGS--YGSLLYAELQR 65 (68)
T ss_pred CHHHHHcCCHHHHHHHcCC--cHHHHHHHHHH
Confidence 3479999999999999975 79999998864
No 87
>PLN00206 DEAD-box ATP-dependent RNA helicase; Provisional
Probab=51.06 E-value=30 Score=37.16 Aligned_cols=45 Identities=11% Similarity=0.048 Sum_probs=36.3
Q ss_pred HHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCCC-ceEEEEEEeC
Q psy11328 7 SSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEV-KVKVFFMQYG 51 (410)
Q Consensus 7 ~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~-~~~Vy~L~y~ 51 (410)
++=++-...++||.||+-.+...-++|-||++|.. .+.++.++..
T Consensus 429 ~rGiDip~v~~VI~~d~P~s~~~yihRiGRaGR~g~~G~ai~f~~~ 474 (518)
T PLN00206 429 GRGVDLLRVRQVIIFDMPNTIKEYIHQIGRASRMGEKGTAIVFVNE 474 (518)
T ss_pred hccCCcccCCEEEEeCCCCCHHHHHHhccccccCCCCeEEEEEEch
Confidence 34456678999999999999989999999998854 6788777654
No 88
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=50.97 E-value=31 Score=35.60 Aligned_cols=54 Identities=9% Similarity=0.025 Sum_probs=40.7
Q ss_pred HhhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCCcHHHHHHHHHHH
Q psy11328 8 SKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGESVEEQAYLSDLR 64 (410)
Q Consensus 8 ~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~S~EE~~yl~si~ 64 (410)
.=++-...++||.||+-.+...-++|-||++|. ..+.++.++.. ++..++..+.
T Consensus 307 ~GiDip~v~~VI~~d~p~s~~~yiqr~GR~gR~g~~g~ai~l~~~---~d~~~~~~i~ 361 (434)
T PRK11192 307 RGIDIDDVSHVINFDMPRSADTYLHRIGRTGRAGRKGTAISLVEA---HDHLLLGKIE 361 (434)
T ss_pred cCccCCCCCEEEEECCCCCHHHHhhcccccccCCCCceEEEEecH---HHHHHHHHHH
Confidence 345667889999999999999999999999884 46777777643 5666665554
No 89
>PRK02794 DNA polymerase IV; Provisional
Probab=50.73 E-value=25 Score=36.63 Aligned_cols=49 Identities=14% Similarity=0.089 Sum_probs=42.3
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
-+|||+++....|-. .+.++.+|.+++..+|.+.+|. .|..+|+..+..
T Consensus 213 ~L~GiG~~~~~~L~~~GI~tigdL~~l~~~~L~~rfG~--~g~~l~~~a~G~ 262 (419)
T PRK02794 213 IIWGVGPATAARLARDGIRTIGDLQRADEADLMRRFGS--MGLRLWRLARGI 262 (419)
T ss_pred hhCCCCHHHHHHHHHhccchHHHHhhCCHHHHHHHHhH--HHHHHHHHhCCC
Confidence 356699998888865 5899999999999999999996 699999988764
No 90
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=50.65 E-value=28 Score=35.86 Aligned_cols=48 Identities=6% Similarity=0.096 Sum_probs=40.3
Q ss_pred CCcCHHHHHHHHhc-CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhcc
Q psy11328 354 PRVTSKNKAAVLNR-GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHT 401 (410)
Q Consensus 354 ~~v~~~n~~~ll~~-~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~ 401 (410)
+||++..+.+|-.+ +.|+.++..+|..+|.++.| +...+.++....+.
T Consensus 34 ~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~~~ 83 (342)
T PLN03186 34 SGIAALDIKKLKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAASK 83 (342)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHH
Confidence 56999999999875 99999999999999999998 56777767665543
No 91
>cd03586 PolY_Pol_IV_kappa DNA Polymerase IV/Kappa. Pol IV, also known as Pol kappa, DinB, and Dpo4, is a translesion synthesis (TLS) polymerase. Translesion synthesis is a process that allows the bypass of a variety of DNA lesions. TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. Known primarily as Pol IV in prokaryotes and Pol kappa in eukaryotes, this polymerase has a propensity for generating frameshift mutations. The eukaryotic Pol kappa differs from Pol IV and Dpo4 by an N-terminal extension of ~75 residues known as the "N-clasp" region. The structure of Pol kappa shows DNA that is almost totally encircled by Pol kappa, with the N-clasp region augmenting the interactions between DNA and the polymerase. Pol kappa is more resistant than Pol eta and Pol iota to bulky guanine adducts and is efficient at catalyzing the incorporation of dCTP. Bacterial pol IV has a
Probab=49.93 E-value=29 Score=34.44 Aligned_cols=49 Identities=20% Similarity=0.193 Sum_probs=41.3
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
.+|||+.+-+..|.. .+.++.||++++..+|.+..|. .+..+|+.++..
T Consensus 175 ~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~~~g~--~~~~l~~~~~G~ 224 (334)
T cd03586 175 KIPGVGKVTAEKLKELGIKTIGDLAKLDVELLKKLFGK--SGRRLYELARGI 224 (334)
T ss_pred hhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHHHHHHhH--HHHHHHHHhCCC
Confidence 456799888877765 5999999999999999999974 799999988764
No 92
>KOG0388|consensus
Probab=49.76 E-value=22 Score=40.77 Aligned_cols=51 Identities=22% Similarity=0.299 Sum_probs=34.9
Q ss_pred CCEEEEEcCCchhhhhhhhhhcc---cCCCceEEEEEEeCCcHHHHHHHHHHHH
Q psy11328 15 PTSVIFYNADVAAIRQVEVYQCA---QSEVKVKVFFMQYGESVEEQAYLSDLRR 65 (410)
Q Consensus 15 p~~VI~Yep~~s~IR~IE~y~~~---~~~~~~~Vy~L~y~~S~EE~~yl~si~r 65 (410)
.|-|||||.+---.=-.|.--++ |....+.||=|+++||+||.-.-.+-++
T Consensus 1114 ADTViFYdSDWNPT~D~QAMDRAHRLGQTrdvtvyrl~~rgTvEEk~l~rA~qK 1167 (1185)
T KOG0388|consen 1114 ADTVIFYDSDWNPTADQQAMDRAHRLGQTRDVTVYRLITRGTVEEKVLERANQK 1167 (1185)
T ss_pred cceEEEecCCCCcchhhHHHHHHHhccCccceeeeeecccccHHHHHHHHhhhH
Confidence 58899999874333333333333 3446899999999999999865554444
No 93
>PTZ00110 helicase; Provisional
Probab=49.63 E-value=35 Score=37.00 Aligned_cols=46 Identities=13% Similarity=-0.018 Sum_probs=36.9
Q ss_pred HHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCC
Q psy11328 7 SSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGE 52 (410)
Q Consensus 7 ~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~ 52 (410)
++=|+-...++||.||+-.+...-++|-||++|. ..+.++.++..+
T Consensus 438 ~rGIDi~~v~~VI~~d~P~s~~~yvqRiGRtGR~G~~G~ai~~~~~~ 484 (545)
T PTZ00110 438 SRGLDVKDVKYVINFDFPNQIEDYVHRIGRTGRAGAKGASYTFLTPD 484 (545)
T ss_pred hcCCCcccCCEEEEeCCCCCHHHHHHHhcccccCCCCceEEEEECcc
Confidence 3446677899999999998888899999999885 467777776664
No 94
>TIGR03817 DECH_helic helicase/secretion neighborhood putative DEAH-box helicase. A conserved gene neighborhood widely spread in the Actinobacteria contains this uncharacterized DEAH-box family helicase encoded convergently towards an operon of genes for protein homologous to type II secretion and pilus formation proteins. The context suggests that this helicase may play a role in conjugal transfer of DNA.
Probab=49.56 E-value=30 Score=39.17 Aligned_cols=58 Identities=5% Similarity=-0.110 Sum_probs=44.2
Q ss_pred HHHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeCCcHHHHHHHHHH
Q psy11328 6 LSSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 6 ~~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~EE~~yl~si 63 (410)
|+.=++.-..|+||.|+.-.+...-+||-||++|....-+.+++..++..+++|+...
T Consensus 339 lerGIDI~~vd~VI~~~~P~s~~~y~qRiGRaGR~G~~g~ai~v~~~~~~d~~~~~~~ 396 (742)
T TIGR03817 339 LELGVDISGLDAVVIAGFPGTRASLWQQAGRAGRRGQGALVVLVARDDPLDTYLVHHP 396 (742)
T ss_pred HhccCCcccccEEEEeCCCCCHHHHHHhccccCCCCCCcEEEEEeCCChHHHHHHhCH
Confidence 3444566778999999999999999999999998655445556666666677777765
No 95
>PF13871 Helicase_C_4: Helicase_C-like
Probab=48.71 E-value=38 Score=34.16 Aligned_cols=57 Identities=9% Similarity=0.088 Sum_probs=48.8
Q ss_pred hCCCEEEEEcCCchhhhhhhhhhcccCCC--ceEEEEEEeCCcHHHHHHHHHHHHHHHH
Q psy11328 13 LKPTSVIFYNADVAAIRQVEVYQCAQSEV--KVKVFFMQYGESVEEQAYLSDLRREKKA 69 (410)
Q Consensus 13 ~~p~~VI~Yep~~s~IR~IE~y~~~~~~~--~~~Vy~L~y~~S~EE~~yl~si~rEk~a 69 (410)
-++..=|..|+--+..+.||.+|++||.+ ....|.+++.+..-|.+|.+.+.+--+.
T Consensus 86 qr~Rv~i~le~pwsad~aiQ~~GR~hRsnQ~~~P~y~~l~t~~~gE~Rfas~va~rL~s 144 (278)
T PF13871_consen 86 QRRRVHITLELPWSADKAIQQFGRTHRSNQVSAPEYRFLVTDLPGERRFASTVARRLES 144 (278)
T ss_pred CCceEEEEeeCCCCHHHHHHHhccccccccccCCEEEEeecCCHHHHHHHHHHHHHHhh
Confidence 57888999999999999999999999965 4567999999888899999998874333
No 96
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=48.41 E-value=29 Score=30.49 Aligned_cols=41 Identities=15% Similarity=0.145 Sum_probs=31.9
Q ss_pred HHHHHhcCCCHHHHHcCCHHHHHHhh---C-CchhHHHHHHHhcc
Q psy11328 361 KAAVLNRGSSLPALCKLSEQELCSLV---E-NTTLGNALYKALHT 401 (410)
Q Consensus 361 ~~~ll~~~~sl~~l~~~s~eeL~~~~---g-~~~~a~~ly~fl~~ 401 (410)
+.+|.++|++.++|++++.++|.+++ | ...+|+.|.++.+.
T Consensus 14 ~~~l~~~~~~~~~l~~~~~~eL~~~l~~~g~~~~ka~~i~~~a~~ 58 (149)
T smart00478 14 TERLFEKFPTPEDLAAADEEELEELIRPLGFYRRKAKYLIELARI 58 (149)
T ss_pred HHHHHHHCCCHHHHHCCCHHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence 45567789999999999999997764 4 35688888876543
No 97
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=47.84 E-value=40 Score=31.98 Aligned_cols=46 Identities=11% Similarity=0.135 Sum_probs=36.1
Q ss_pred cCHHHHH----HHHhcC--CCHHHHHcCCHHHHHHhhCC--------chhHHHHHHHhcc
Q psy11328 356 VTSKNKA----AVLNRG--SSLPALCKLSEQELCSLVEN--------TTLGNALYKALHT 401 (410)
Q Consensus 356 v~~~n~~----~ll~~~--~sl~~l~~~s~eeL~~~~g~--------~~~a~~ly~fl~~ 401 (410)
.+.+|+. +|..+. .+.++|++++.+||++++.+ ..+|+.|+++.+.
T Consensus 31 Ttd~nv~kA~~~L~~~~g~~tp~~La~a~~eeL~~lI~~~pal~Gfy~~KAk~Lk~~a~~ 90 (177)
T TIGR03252 31 VPMERAFAGPHKIARRMGSLDAEDIAKYDPQAFVALFSERPAVHRFPGSMAKRVQALAQY 90 (177)
T ss_pred CcHHHHHHHHHHHHHHhCCCCHHHHHcCCHHHHHHHHhcCccccCchHHHHHHHHHHHHH
Confidence 7888887 565444 58999999999999999932 3789998887654
No 98
>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=47.57 E-value=33 Score=34.31 Aligned_cols=23 Identities=4% Similarity=0.078 Sum_probs=19.4
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHH
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALC 375 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~ 375 (410)
.||||+|+|..|+++++|+....
T Consensus 228 v~giG~k~A~~li~~~~~~~~~~ 250 (316)
T cd00128 228 IPGIGPVTALKLIKKYGDIEKDI 250 (316)
T ss_pred CCCccHHHHHHHHHHcCChHHHH
Confidence 56799999999999999975543
No 99
>cd03468 PolY_like DNA Polymerase Y-family. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in order to access the lesion. Because of their high error rates, TLS polymerases are potential targets for cancer treatment and prevention.
Probab=47.41 E-value=30 Score=34.21 Aligned_cols=48 Identities=15% Similarity=0.009 Sum_probs=40.9
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
.|||+++-...|-. .+.++.+|++++..+|...+|. .+..+|+.++..
T Consensus 175 ~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l~~rfG~--~~~~l~~~~~G~ 223 (335)
T cd03468 175 ALRLPPETVELLARLGLRTLGDLAALPRAELARRFGL--ALLLRLDQAYGR 223 (335)
T ss_pred HhCCCHHHHHHHHHhCcccHHHHHhCChHHHHhhcCH--HHHHHHHHHCCC
Confidence 56799998888776 6899999999999999999995 588888887753
No 100
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=46.84 E-value=21 Score=27.74 Aligned_cols=25 Identities=20% Similarity=0.325 Sum_probs=16.9
Q ss_pred cHHHHHHHHcCCCCchhhhhhhhhh
Q psy11328 288 NAAIEDFISKLPGMAEWSRARTLNL 312 (410)
Q Consensus 288 ~~~~~~~l~~lPgi~~~~~~~~~~~ 312 (410)
|.+..+-|.++|||+.+.+.+.++.
T Consensus 9 N~as~~eL~~lpgi~~~~A~~Iv~~ 33 (65)
T PF12836_consen 9 NTASAEELQALPGIGPKQAKAIVEY 33 (65)
T ss_dssp TTS-HHHHHTSTT--HHHHHHHHHH
T ss_pred ccCCHHHHHHcCCCCHHHHHHHHHH
Confidence 5556667889999998888777773
No 101
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=46.75 E-value=24 Score=41.33 Aligned_cols=46 Identities=2% Similarity=0.030 Sum_probs=39.1
Q ss_pred hCCCEEEEEcCCchhhhhhhhhhcccC---CCceEEEEEEeCCcHHHHH
Q psy11328 13 LKPTSVIFYNADVAAIRQVEVYQCAQS---EVKVKVFFMQYGESVEEQA 58 (410)
Q Consensus 13 ~~p~~VI~Yep~~s~IR~IE~y~~~~~---~~~~~Vy~L~y~~S~EE~~ 58 (410)
-..++||+||+.-..-.-+||-||++| ..++.||+++.++|.+|.-
T Consensus 563 q~a~~VInfDlP~nP~~~eQRIGR~~RiGQ~~~V~i~~~~~~~t~~e~i 611 (956)
T PRK04914 563 QFASHLVLFDLPFNPDLLEQRIGRLDRIGQKHDIQIHVPYLEGTAQERL 611 (956)
T ss_pred ccccEEEEecCCCCHHHHHHHhcccccCCCCceEEEEEccCCCCHHHHH
Confidence 456899999999999999999999877 4578999999999986653
No 102
>cd00424 PolY Y-family of DNA polymerases. Y-family DNA polymerases are a specialized subset of polymerases that facilitate translesion synthesis (TLS), a process that allows the bypass of a variety of DNA lesions. Unlike replicative polymerases, TLS polymerases lack proofreading activity and have low fidelity and low processivity. They use damaged DNA as templates and insert nucleotides opposite the lesions. The active sites of TLS polymerases are large and flexible to allow the accomodation of distorted bases. Most TLS polymerases are members of the Y-family, including Pol eta, Pol kappa/IV, Pol iota, Rev1, and Pol V, which is found exclusively in bacteria. In eukaryotes, the B-family polymerase Pol zeta also functions as a TLS polymerase. Expression of Y-family polymerases is often induced by DNA damage and is believed to be highly regulated. TLS is likely induced by the monoubiquitination of the replication clamp PCNA, which provides a scaffold for TLS polymerases to bind in ord
Probab=46.38 E-value=35 Score=34.39 Aligned_cols=49 Identities=16% Similarity=0.085 Sum_probs=40.7
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCC-HHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLS-EQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s-~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
.+|||+++-...|-. .+.++.||.+++ ...|....|. .|..+|+..+..
T Consensus 177 ~l~giG~~~~~~L~~~Gi~ti~dl~~~~~~~~l~~~fg~--~~~~l~~~a~G~ 227 (343)
T cd00424 177 DLPGIGAVTAKRLEAVGINPIGDLLAASPDALLALWGGV--SGERLWYALRGI 227 (343)
T ss_pred hcCCCCHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHhhH--HHHHHHHHhCCc
Confidence 356799998888876 689999999999 7778888874 799999988764
No 103
>PTZ00217 flap endonuclease-1; Provisional
Probab=46.37 E-value=32 Score=36.19 Aligned_cols=24 Identities=8% Similarity=0.145 Sum_probs=21.9
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHc
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCK 376 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~ 376 (410)
.||||+|+|..|+++++|++++.+
T Consensus 240 i~GIG~ktA~~Li~~~gsle~il~ 263 (393)
T PTZ00217 240 IKGIGPKTAYKLIKKYKSIEEILE 263 (393)
T ss_pred CCCccHHHHHHHHHHcCCHHHHHH
Confidence 567999999999999999999975
No 104
>PRK01297 ATP-dependent RNA helicase RhlB; Provisional
Probab=45.87 E-value=37 Score=35.72 Aligned_cols=52 Identities=8% Similarity=-0.072 Sum_probs=39.3
Q ss_pred hhhhhCCCEEEEEcCCchhhhhhhhhhcccCCC-ceEEEEEEeCCcHHHHHHHHHH
Q psy11328 9 KLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEV-KVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 9 ~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~-~~~Vy~L~y~~S~EE~~yl~si 63 (410)
=++-...++||.|++-.+..--+|+-||++|.. .+.++.+..+ ++++|+..+
T Consensus 398 GIDi~~v~~VI~~~~P~s~~~y~Qr~GRaGR~g~~g~~i~~~~~---~d~~~~~~~ 450 (475)
T PRK01297 398 GIHIDGISHVINFTLPEDPDDYVHRIGRTGRAGASGVSISFAGE---DDAFQLPEI 450 (475)
T ss_pred CCcccCCCEEEEeCCCCCHHHHHHhhCccCCCCCCceEEEEecH---HHHHHHHHH
Confidence 345667899999999988888999999998854 5666665543 367777665
No 105
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=44.31 E-value=38 Score=35.28 Aligned_cols=49 Identities=6% Similarity=-0.115 Sum_probs=41.5
Q ss_pred CCCCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
.+|||+++.+..|-+ .+.|+.+|.+++.+.|.+.+|. .+..+++.++..
T Consensus 183 ~l~GiG~~~~~~L~~lGi~TigdL~~~~~~~L~~~fG~--~~~~l~~~a~G~ 232 (422)
T PRK03609 183 EVWGVGRRISKKLNAMGIKTALDLADTNIRFIRKHFNV--VLERTVRELRGE 232 (422)
T ss_pred hcCCccHHHHHHHHHcCCCcHHHHhcCCHHHHHHHHCH--HHHHHHHHhCCC
Confidence 456799998888876 6999999999999999999985 688888777663
No 106
>PRK05755 DNA polymerase I; Provisional
Probab=43.22 E-value=17 Score=41.74 Aligned_cols=25 Identities=28% Similarity=0.312 Sum_probs=22.8
Q ss_pred CCCcCHHHHHHHHhcCCCHHHHHcC
Q psy11328 353 RPRVTSKNKAAVLNRGSSLPALCKL 377 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~~sl~~l~~~ 377 (410)
.||||+|.|..||++|+|++++.+.
T Consensus 192 v~GiG~ktA~~Ll~~~gsle~i~~~ 216 (880)
T PRK05755 192 VPGIGEKTAAKLLQEYGSLEGLYEN 216 (880)
T ss_pred CCCccHHHHHHHHHHcCCHHHHHHh
Confidence 5779999999999999999999854
No 107
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.72 E-value=55 Score=31.08 Aligned_cols=24 Identities=8% Similarity=0.126 Sum_probs=17.0
Q ss_pred cHHHHHHHHcCCCCchhhhhhhhh
Q psy11328 288 NAAIEDFISKLPGMAEWSRARTLN 311 (410)
Q Consensus 288 ~~~~~~~l~~lPgi~~~~~~~~~~ 311 (410)
....-+.|.+++||+...+-+.++
T Consensus 68 Er~lF~~Li~V~GIGpK~Al~ILs 91 (194)
T PRK14605 68 ELSLFETLIDVSGIGPKLGLAMLS 91 (194)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHH
Confidence 455667899999987766655554
No 108
>PRK11776 ATP-dependent RNA helicase DbpA; Provisional
Probab=42.25 E-value=43 Score=34.99 Aligned_cols=51 Identities=16% Similarity=0.012 Sum_probs=37.7
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCCcHHHHHHHHHH
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~S~EE~~yl~si 63 (410)
|+-...++||.||.-.+.-.-++|-||++|. ..+.+|.++..+ |.+++..+
T Consensus 306 iDi~~v~~VI~~d~p~~~~~yiqR~GRtGR~g~~G~ai~l~~~~---e~~~~~~i 357 (460)
T PRK11776 306 LDIKALEAVINYELARDPEVHVHRIGRTGRAGSKGLALSLVAPE---EMQRANAI 357 (460)
T ss_pred cchhcCCeEEEecCCCCHhHhhhhcccccCCCCcceEEEEEchh---HHHHHHHH
Confidence 5566789999999988888889999999884 467777776553 44444433
No 109
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=41.81 E-value=30 Score=31.50 Aligned_cols=21 Identities=5% Similarity=0.061 Sum_probs=15.3
Q ss_pred cCHHHHHHHHhc--CCCHHHHHc
Q psy11328 356 VTSKNKAAVLNR--GSSLPALCK 376 (410)
Q Consensus 356 v~~~n~~~ll~~--~~sl~~l~~ 376 (410)
|+++.|.+|+.| |+|++||.+
T Consensus 69 igP~~A~~IV~nGpf~sveDL~~ 91 (132)
T PRK02515 69 MYPTLAGKIVKNAPYDSVEDVLN 91 (132)
T ss_pred CCHHHHHHHHHCCCCCCHHHHHc
Confidence 788888888874 666666554
No 110
>PRK10590 ATP-dependent RNA helicase RhlE; Provisional
Probab=41.23 E-value=52 Score=34.51 Aligned_cols=54 Identities=13% Similarity=0.076 Sum_probs=39.5
Q ss_pred HHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCCcHHHHHHHHHH
Q psy11328 7 SSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 7 ~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~S~EE~~yl~si 63 (410)
+.=++-...++||.|++-.+...-+++-||++|. ..+.++.++.. +|..++..+
T Consensus 306 ~rGiDip~v~~VI~~~~P~~~~~yvqR~GRaGR~g~~G~ai~l~~~---~d~~~~~~i 360 (456)
T PRK10590 306 ARGLDIEELPHVVNYELPNVPEDYVHRIGRTGRAAATGEALSLVCV---DEHKLLRDI 360 (456)
T ss_pred hcCCCcccCCEEEEeCCCCCHHHhhhhccccccCCCCeeEEEEecH---HHHHHHHHH
Confidence 3345667788999999988888889999999884 46777777764 344444433
No 111
>PRK13910 DNA glycosylase MutY; Provisional
Probab=41.09 E-value=42 Score=33.96 Aligned_cols=45 Identities=18% Similarity=0.145 Sum_probs=35.9
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHh---hCCchhHHHHHHHhc
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSL---VENTTLGNALYKALH 400 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~---~g~~~~a~~ly~fl~ 400 (410)
|.+.-+.+++++|.++++|++++++||.++ +|=-.+|+.|+++..
T Consensus 10 v~~~yy~rf~~~fPt~e~La~a~~~el~~~~~glGyy~RAr~L~~~A~ 57 (289)
T PRK13910 10 VVERFYSPFLEAFPTLKDLANAPLEEVLLLWRGLGYYSRAKNLKKSAE 57 (289)
T ss_pred hHHHHHHHHHHHCCCHHHHHCCCHHHHHHHHHcCCcHHHHHHHHHHHH
Confidence 444556899999999999999999999997 552247888887654
No 112
>PRK15363 pathogenicity island 2 chaperone protein SscA; Provisional
Probab=40.79 E-value=47 Score=30.90 Aligned_cols=41 Identities=27% Similarity=0.336 Sum_probs=33.8
Q ss_pred HHHHHHhcCCCHHHHHcCC-HHHHHHh---------hCCchhHHHHHHHhc
Q psy11328 360 NKAAVLNRGSSLPALCKLS-EQELCSL---------VENTTLGNALYKALH 400 (410)
Q Consensus 360 n~~~ll~~~~sl~~l~~~s-~eeL~~~---------~g~~~~a~~ly~fl~ 400 (410)
-....++..+||+-|++.+ .++|+.+ .|.=..|+++|.|+-
T Consensus 12 ~~~~f~~~Ggsl~~l~~~~~~~~l~~lY~~A~~ly~~G~l~~A~~~f~~L~ 62 (157)
T PRK15363 12 DTMRFFRRGGSLRMLLDDDVTQPLNTLYRYAMQLMEVKEFAGAARLFQLLT 62 (157)
T ss_pred HHHHHHHcCCcHHHHHCCChHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4567888999999999999 9999877 455577889888874
No 113
>PF02198 SAM_PNT: Sterile alpha motif (SAM)/Pointed domain; InterPro: IPR003118 Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription []. The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain [, ]. This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain IPR000418 from INTERPRO has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others [, , ]. It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus. This entry describes the highly conserved PNT (or Pointed) domain which is found within a subset of the ETs domain (IPR000418 from INTERPRO ), including mammalian Ets-1, Ets-2, Erg, Fli-1, GABPalpha, and Tel, as well as Drosophila Pnt-P2 and Yan. The PNT domain (IPR001660 from INTERPRO ) through a common tertiary arrangement of four alpha-helices. A role in protein-protein association has been established for the PNT domain [, ].; GO: 0043565 sequence-specific DNA binding, 0005634 nucleus; PDB: 1SXE_A 1SXD_A 2KMD_A 2JV3_A 2E8P_A 1SV4_B 1SV0_B 1LKY_F 1JI7_B 2DKX_A ....
Probab=40.68 E-value=19 Score=29.45 Aligned_cols=31 Identities=23% Similarity=0.454 Sum_probs=26.3
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
+=++||.+|.+++....+. ..|..||..|+.
T Consensus 49 ~G~~Lc~lt~e~F~~~~~~-~~G~~Ly~~L~~ 79 (84)
T PF02198_consen 49 NGRELCSLTKEDFRRRFPS-GYGDILYSHLQL 79 (84)
T ss_dssp -HHHHHHSHHHHHHHHSTH-TTHHHHHHHHHH
T ss_pred CHHHHHHcCHHHHHHHcCC-CcHHHHHHHHHH
Confidence 3479999999999999985 689999998863
No 114
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=40.16 E-value=43 Score=37.61 Aligned_cols=51 Identities=16% Similarity=0.164 Sum_probs=42.2
Q ss_pred CCCCcCHHHHHHHHhc--CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 352 PRPRVTSKNKAAVLNR--GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 352 ~~~~v~~~n~~~ll~~--~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
-.||++++.+..|.++ ++|+.+|..+..++|..+-| .+..|+.|++.+...
T Consensus 449 ~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie~s 502 (665)
T PRK07956 449 DIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIEKS 502 (665)
T ss_pred CCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHHHh
Confidence 3578999999999985 78999999999999999844 346788888877653
No 115
>PTZ00205 DNA polymerase kappa; Provisional
Probab=39.10 E-value=1.4e+02 Score=33.24 Aligned_cols=48 Identities=15% Similarity=0.133 Sum_probs=37.2
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCCHH--------HHHHhhCCchhHHHHHHHhcc
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLSEQ--------ELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s~e--------eL~~~~g~~~~a~~ly~fl~~ 401 (410)
.||||++.+..|-. .+.++.||.+.+.+ .|..++|. ..|..+|...+.
T Consensus 314 i~GIG~~t~~~L~~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~-~~G~~l~~~a~G 370 (571)
T PTZ00205 314 VPGVGKVTEALLKGLGITTLSDIYNRRVELCYILHNNLFRFLLGA-SIGIMQWPDAAT 370 (571)
T ss_pred eCCcCHHHHHHHHHcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCc-hhhHHHHHHhcC
Confidence 45699999887765 68999999999976 46677885 578888877544
No 116
>PRK04837 ATP-dependent RNA helicase RhlB; Provisional
Probab=38.97 E-value=41 Score=34.68 Aligned_cols=54 Identities=13% Similarity=0.007 Sum_probs=39.1
Q ss_pred HHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCCcHHHHHHHHHH
Q psy11328 7 SSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 7 ~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~S~EE~~yl~si 63 (410)
++=++-...++||.||+-.+..--++|-||++|. ..+.++.++.. +|...+..+
T Consensus 316 ~rGiDip~v~~VI~~d~P~s~~~yiqR~GR~gR~G~~G~ai~~~~~---~~~~~~~~i 370 (423)
T PRK04837 316 ARGLHIPAVTHVFNYDLPDDCEDYVHRIGRTGRAGASGHSISLACE---EYALNLPAI 370 (423)
T ss_pred hcCCCccccCEEEEeCCCCchhheEeccccccCCCCCeeEEEEeCH---HHHHHHHHH
Confidence 3345667889999999988888889999999884 46777766654 344445444
No 117
>PF00730 HhH-GPD: HhH-GPD superfamily base excision DNA repair protein This entry corresponds to Endonuclease III This entry corresponds to Alkylbase DNA glycosidase; InterPro: IPR003265 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs (see IPR003651 from INTERPRO). The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The HhH-GPD domain gets its name from its hallmark helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate. This domain is found in a diverse range of structurally related DNA repair proteins that include: endonuclease III, 4.2.99.18 from EC and DNA glycosylase MutY, an A/G-specific adenine glycosylase. Both of these enzymes have a C-terminal iron-sulphur cluster loop (FCL). The methyl-CPG binding protein (MBD4) also contain a related domain that is a thymine DNA glycosylase. The family also includes DNA-3-methyladenine glycosylase II 3.2.2.21 from EC, 8-oxoguanine DNA glycosylases and other members of the AlkA family.; GO: 0006284 base-excision repair; PDB: 3F0Z_A 3I0X_A 3F10_A 3I0W_A 3S6I_D 3N5N_Y 1PU7_A 1PU8_B 1PU6_B 1NGN_A ....
Probab=38.64 E-value=26 Score=29.02 Aligned_cols=45 Identities=20% Similarity=0.220 Sum_probs=31.6
Q ss_pred cCHHHHH----HHHhcC--CCHHHHHcCCHHHHHHh---hC-CchhHHHHHHHhc
Q psy11328 356 VTSKNKA----AVLNRG--SSLPALCKLSEQELCSL---VE-NTTLGNALYKALH 400 (410)
Q Consensus 356 v~~~n~~----~ll~~~--~sl~~l~~~s~eeL~~~---~g-~~~~a~~ly~fl~ 400 (410)
++-+++. +|.+++ .|.++|.+++.+||.++ .| +..+|+.|.++.+
T Consensus 9 ~s~~~a~~~~~~l~~~~g~pt~~~l~~~~~~el~~~i~~~G~~~~ka~~i~~~a~ 63 (108)
T PF00730_consen 9 TSIKAARKIYRRLFERYGFPTPEALAEASEEELRELIRPLGFSRRKAKYIIELAR 63 (108)
T ss_dssp S-HHHHHHHHHHHHHHHSCSSHHHHHCSHHHHHHHHHTTSTSHHHHHHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHHhcCCCHHHHHhCCHHHHHHHhhccCCCHHHHHHHHHHHH
Confidence 4444444 444564 59999999999999998 45 2378888877653
No 118
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=38.63 E-value=41 Score=29.76 Aligned_cols=40 Identities=20% Similarity=0.231 Sum_probs=31.9
Q ss_pred HHHHhcC-CCHHHHHcCCHHHHHHhhCC---chhHHHHHHHhcc
Q psy11328 362 AAVLNRG-SSLPALCKLSEQELCSLVEN---TTLGNALYKALHT 401 (410)
Q Consensus 362 ~~ll~~~-~sl~~l~~~s~eeL~~~~g~---~~~a~~ly~fl~~ 401 (410)
.+|..++ .|.+.|.+++.++|.++..+ ..+|+.|.++.+.
T Consensus 23 ~~l~~~~gpt~~~l~~~~~~~l~~~~~~~G~~~kA~~i~~~a~~ 66 (158)
T cd00056 23 ERLFERYGPTPEALAAADEEELRELIRSLGYRRKAKYLKELARA 66 (158)
T ss_pred HHHHHHhCCCHHHHHCCCHHHHHHHHHhcChHHHHHHHHHHHHH
Confidence 3445566 79999999999999998654 5889999887654
No 119
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=37.60 E-value=24 Score=24.83 Aligned_cols=16 Identities=13% Similarity=0.040 Sum_probs=14.0
Q ss_pred CCCcCHHHHHHHHhcC
Q psy11328 353 RPRVTSKNKAAVLNRG 368 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~~ 368 (410)
.|||++|.|..|+++|
T Consensus 21 v~giG~ktA~~ll~~~ 36 (36)
T smart00279 21 VKGIGPKTALKLLREF 36 (36)
T ss_pred CCcccHHHHHHHHHhC
Confidence 5779999999999875
No 120
>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=37.26 E-value=49 Score=37.08 Aligned_cols=50 Identities=16% Similarity=0.203 Sum_probs=42.4
Q ss_pred CCCcCHHHHHHHHhc--CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLNR--GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~--~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
.||++++.+..|.++ +.|+.||..+..++|..+-| .+..|+.|.+.+...
T Consensus 437 I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie~s 489 (652)
T TIGR00575 437 IEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIEKS 489 (652)
T ss_pred CCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHHHh
Confidence 578999999999975 68999999999999999854 347888998888754
No 121
>KOG0331|consensus
Probab=36.00 E-value=55 Score=35.89 Aligned_cols=54 Identities=13% Similarity=-0.047 Sum_probs=39.4
Q ss_pred HhhhhhCCCEEEEEcCCchhhhhhhhhhcccC-CCceEEEEEEeCCcHHHHHHHH
Q psy11328 8 SKLRSLKPTSVIFYNADVAAIRQVEVYQCAQS-EVKVKVFFMQYGESVEEQAYLS 61 (410)
Q Consensus 8 ~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~-~~~~~Vy~L~y~~S~EE~~yl~ 61 (410)
+=|+-..+|+||.||+--..-=-|-|-|+|+| +..+..+.+++..-..-..++.
T Consensus 403 RGLDi~dV~lVInydfP~~vEdYVHRiGRTGRa~~~G~A~tfft~~~~~~a~~l~ 457 (519)
T KOG0331|consen 403 RGLDVPDVDLVINYDFPNNVEDYVHRIGRTGRAGKKGTAITFFTSDNAKLARELI 457 (519)
T ss_pred ccCCCccccEEEeCCCCCCHHHHHhhcCccccCCCCceEEEEEeHHHHHHHHHHH
Confidence 34677899999999998777777777788887 5578888888775444444333
No 122
>PF00271 Helicase_C: Helicase conserved C-terminal domain; InterPro: IPR001650 The domain, which defines this group of proteins is found in a wide variety of helicases and helicase related proteins. It may be that this is not an autonomously folding unit, but an integral part of the helicase. The eukaryotic translation initiation factor 4A (eIF4A) is a member of the DEA(D/H)-box RNA helicase family This is a diverse group of proteins that couples an ATPase activity to RNA binding and unwinding. The structure of the carboxyl-terminal domain of eIF4A has been determined to 1.75 A resolution; it has a parallel alpha-beta topology that superimposes, with minor variations, on the structures and conserved motifs of the equivalent domain in other, distantly related helicases [].; GO: 0003676 nucleic acid binding, 0004386 helicase activity, 0005524 ATP binding; PDB: 2Z83_A 2JGN_C 2I4I_A 2BMF_A 2BHR_B 1WP9_E 2WAX_C 2WAY_C 3JUX_A 3DIN_B ....
Probab=35.52 E-value=19 Score=27.65 Aligned_cols=31 Identities=16% Similarity=0.178 Sum_probs=26.0
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCC
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSE 40 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~ 40 (410)
++-...++||+|+|..+..--+|+.||.+|.
T Consensus 47 id~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~ 77 (78)
T PF00271_consen 47 IDLPDASHVIFYDPPWSPEEYIQRIGRAGRI 77 (78)
T ss_dssp STSTTESEEEESSSESSHHHHHHHHTTSSTT
T ss_pred ccccccccccccccCCCHHHHHHHhhcCCCC
Confidence 3445779999999999999999999998773
No 123
>PRK10880 adenine DNA glycosylase; Provisional
Probab=35.32 E-value=36 Score=35.34 Aligned_cols=42 Identities=17% Similarity=0.118 Sum_probs=33.9
Q ss_pred HHHHHHhcCCCHHHHHcCCHHHHHHh---hCCchhHHHHHHHhcc
Q psy11328 360 NKAAVLNRGSSLPALCKLSEQELCSL---VENTTLGNALYKALHT 401 (410)
Q Consensus 360 n~~~ll~~~~sl~~l~~~s~eeL~~~---~g~~~~a~~ly~fl~~ 401 (410)
-+.+++++|.|+++|++++++||.++ +|=-.+|+.|++....
T Consensus 51 ~~~rl~~~fPt~~~La~a~~eel~~~~~glGyy~RAr~L~~~A~~ 95 (350)
T PRK10880 51 YFERFMARFPTVTDLANAPLDEVLHLWTGLGYYARARNLHKAAQQ 95 (350)
T ss_pred HHHHHHHHCcCHHHHHCcCHHHHHHHHHcCChHHHHHHHHHHHHH
Confidence 35678999999999999999999986 5633578888877543
No 124
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.82 E-value=75 Score=30.41 Aligned_cols=23 Identities=4% Similarity=-0.052 Sum_probs=15.4
Q ss_pred cHHHHHHHHcCCCCchhhhhhhh
Q psy11328 288 NAAIEDFISKLPGMAEWSRARTL 310 (410)
Q Consensus 288 ~~~~~~~l~~lPgi~~~~~~~~~ 310 (410)
....-..|.++.||+.+.+-..+
T Consensus 69 Er~lF~~Li~V~GIGpK~Al~iL 91 (203)
T PRK14602 69 ERQTFIVLISISKVGAKTALAIL 91 (203)
T ss_pred HHHHHHHHhCCCCcCHHHHHHHH
Confidence 45566788899998776543333
No 125
>TIGR00614 recQ_fam ATP-dependent DNA helicase, RecQ family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.00 E-value=57 Score=34.42 Aligned_cols=44 Identities=11% Similarity=-0.010 Sum_probs=33.6
Q ss_pred HhhhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceEEEEEEeC
Q psy11328 8 SKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVKVFFMQYG 51 (410)
Q Consensus 8 ~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~Vy~L~y~ 51 (410)
.=++....++||.|++-.+...-+|+-||++|.......+++|.
T Consensus 288 ~GID~p~V~~VI~~~~P~s~~~y~Qr~GRaGR~G~~~~~~~~~~ 331 (470)
T TIGR00614 288 MGINKPDVRFVIHYSLPKSMESYYQESGRAGRDGLPSECHLFYA 331 (470)
T ss_pred ccCCcccceEEEEeCCCCCHHHHHhhhcCcCCCCCCceEEEEec
Confidence 34566778999999999999899999999998654444444554
No 126
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=33.47 E-value=63 Score=30.12 Aligned_cols=41 Identities=10% Similarity=0.066 Sum_probs=32.3
Q ss_pred HHHHHhcCCCHHHHHcCCHHHHHHh---hC-CchhHHHHHHHhcc
Q psy11328 361 KAAVLNRGSSLPALCKLSEQELCSL---VE-NTTLGNALYKALHT 401 (410)
Q Consensus 361 ~~~ll~~~~sl~~l~~~s~eeL~~~---~g-~~~~a~~ly~fl~~ 401 (410)
+.+|...|.+.++|++++.++|.++ +| ...+|+.|.+....
T Consensus 48 ~~~l~~~~pt~~~l~~~~~~~L~~~ir~~G~~~~Ka~~i~~~a~~ 92 (191)
T TIGR01083 48 TKKLFEVYPTPQALAQAGLEELEEYIKSIGLYRNKAKNIIALCRI 92 (191)
T ss_pred HHHHHHHCCCHHHHHcCCHHHHHHHHHhcCChHHHHHHHHHHHHH
Confidence 3557788999999999999999876 46 45688888876543
No 127
>PRK10702 endonuclease III; Provisional
Probab=33.43 E-value=57 Score=31.35 Aligned_cols=41 Identities=10% Similarity=0.132 Sum_probs=32.9
Q ss_pred HHHHHhcCCCHHHHHcCCHHHHHHh---hC-CchhHHHHHHHhcc
Q psy11328 361 KAAVLNRGSSLPALCKLSEQELCSL---VE-NTTLGNALYKALHT 401 (410)
Q Consensus 361 ~~~ll~~~~sl~~l~~~s~eeL~~~---~g-~~~~a~~ly~fl~~ 401 (410)
+.+|..+|.|.++|++++.++|+++ +| -..+|+.|.+..+.
T Consensus 51 ~~~L~~~~pt~e~l~~a~~~~l~~~i~~~G~y~~kA~~l~~~a~~ 95 (211)
T PRK10702 51 TAKLYPVANTPAAMLELGVEGVKTYIKTIGLYNSKAENVIKTCRI 95 (211)
T ss_pred HHHHHHHcCCHHHHHCCCHHHHHHHHHHcCCHHHHHHHHHHHHHH
Confidence 5577788999999999999999987 56 23688888776654
No 128
>cd08532 SAM_PNT-PDEF-like Sterile alpha motif (SAM)/Pointed domain of prostate-derived ETS factor. SAM Pointed domain of PDEF-like (Prostate-Derived ETS Factor) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. In human males this activator is highly expressed in the prostate gland and enhances androgen-mediated activation of the PSA promoter though interaction with the DNA binding domain of androgen receptor. PDEF may play a role in prostate cancer development as well as in goblet cell formation and mucus production in the epithelial lining of respiratory and intestinal tracts.
Probab=33.31 E-value=45 Score=27.36 Aligned_cols=28 Identities=29% Similarity=0.386 Sum_probs=24.1
Q ss_pred HHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 371 LPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 371 l~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
=++||.+|.|++....+. .|..||..|.
T Consensus 42 G~~LC~ls~edF~~r~p~--~GdiL~~hL~ 69 (76)
T cd08532 42 GKDLCALSEEDFRRRAPQ--GGDTLHAQLD 69 (76)
T ss_pred HHHHHcCCHHHHHHHcCC--chhHHHHHHH
Confidence 379999999999999864 8999998764
No 129
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=32.94 E-value=41 Score=27.42 Aligned_cols=37 Identities=14% Similarity=0.011 Sum_probs=29.6
Q ss_pred hhhCCCEEEEEcCCchhhhhhhhhhcccCCC-ceEEEE
Q psy11328 11 RSLKPTSVIFYNADVAAIRQVEVYQCAQSEV-KVKVFF 47 (410)
Q Consensus 11 ~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~-~~~Vy~ 47 (410)
+-...+.||+++|..+...-+|+-||.+|.. .++|++
T Consensus 93 d~~~~~~vi~~~~~~~~~~~~Q~~GR~~R~~~~~~~~~ 130 (131)
T cd00079 93 DLPNVSVVINYDLPWSPSSYLQRIGRAGRAGQKGTAIL 130 (131)
T ss_pred ChhhCCEEEEeCCCCCHHHheecccccccCCCCceEEe
Confidence 3345789999999999989999999988865 566655
No 130
>cd08531 SAM_PNT-ERG_FLI-1 Sterile alpha motif (SAM)/Pointed domain of ERG (Ets related gene) and FLI-1 (Friend leukemia integration 1) transcription factors. SAM Pointed domain of ERG/FLI-1 subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The ERG and FLI regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. They are proto-oncogenes implicated in cancer development such as myeloid leukemia, Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=32.87 E-value=43 Score=27.42 Aligned_cols=30 Identities=20% Similarity=0.371 Sum_probs=25.1
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||.+|.|+.....+. ..|.-||..|.
T Consensus 38 ~Gk~LC~lt~edF~~~~~~-~~GdiL~~hL~ 67 (75)
T cd08531 38 DGKELCKMTKEDFLRLTSA-YNADVLLSHLS 67 (75)
T ss_pred ChHHHHcCCHHHHHHHcCC-CcchHHHHHHH
Confidence 4479999999999999865 57899998775
No 131
>cd08533 SAM_PNT-ETS-1,2 Sterile alpha motif (SAM)/Pointed domain of ETS-1,2 family. SAM Pointed domain of ETS-1,2 family of transcriptional activators is a protein-protein interaction domain. It carries a kinase docking site and mediates interaction between ETS transcriptional activators and protein kinases. This group of transcriptional factors is involved in the Ras/MAP kinase signaling pathway. MAP kinases phosphorylate the transcription factors. Phosphorylated factors then recruit coactivators and enhance transactivation. Members of this group play a role in regulation of different embryonic developmental processes. ETS-1,2 transcriptional activators are proto-oncogenes involved in malignant transformation and tumor progression. They are potential molecular targets for selective cancer therapy.
Probab=32.16 E-value=44 Score=27.14 Aligned_cols=30 Identities=27% Similarity=0.516 Sum_probs=25.5
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||.+|.|+.....+. ..|.-||..|.
T Consensus 36 ~Gk~LC~ls~edF~~~~p~-~~GdIL~~hL~ 65 (71)
T cd08533 36 SGRDLCALGKERFLELAPD-FVGDILWEHLE 65 (71)
T ss_pred CHHHHHcCCHHHHHHHcCC-CcchHHHHHHH
Confidence 4479999999999999975 58999998764
No 132
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=32.04 E-value=94 Score=34.66 Aligned_cols=49 Identities=18% Similarity=0.106 Sum_probs=35.7
Q ss_pred HHHhhhhhCCCEEEEEcCCc-----hhhhhhhhhhcccCCCceEEEEEEeCCcH
Q psy11328 6 LSSKLRSLKPTSVIFYNADV-----AAIRQVEVYQCAQSEVKVKVFFMQYGESV 54 (410)
Q Consensus 6 ~~~~L~~~~p~~VI~Yep~~-----s~IR~IE~y~~~~~~~~~~Vy~L~y~~S~ 54 (410)
|++=++-...++||+||.+. +.-.-|++-||++|...+++++++...+.
T Consensus 506 L~rGfdlp~v~lVii~d~eifG~~~~~~~yiqr~GR~gR~~~G~~i~~~~~~~~ 559 (652)
T PRK05298 506 LREGLDIPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVILYADKITD 559 (652)
T ss_pred HhCCccccCCcEEEEeCCcccccCCCHHHHHHHhccccCCCCCEEEEEecCCCH
Confidence 34445667788999999752 23345899999999888998888875543
No 133
>KOG0392|consensus
Probab=31.96 E-value=36 Score=40.98 Aligned_cols=45 Identities=20% Similarity=0.336 Sum_probs=38.9
Q ss_pred CCCEEEEEcCCchhhhhhhhhhcccC---CCceEEEEEEeCCcHHHHH
Q psy11328 14 KPTSVIFYNADVAAIRQVEVYQCAQS---EVKVKVFFMQYGESVEEQA 58 (410)
Q Consensus 14 ~p~~VI~Yep~~s~IR~IE~y~~~~~---~~~~~Vy~L~y~~S~EE~~ 58 (410)
.-|-|||||=|---+|-+|.--|+|| .+.+.||=|+++||.||.-
T Consensus 1413 GADTVVFvEHDWNPMrDLQAMDRAHRIGQKrvVNVyRlItrGTLEEKV 1460 (1549)
T KOG0392|consen 1413 GADTVVFVEHDWNPMRDLQAMDRAHRIGQKRVVNVYRLITRGTLEEKV 1460 (1549)
T ss_pred CCceEEEEecCCCchhhHHHHHHHHhhcCceeeeeeeehhcccHHHHH
Confidence 46889999999999999998777665 5679999999999999973
No 134
>PF02373 JmjC: JmjC domain, hydroxylase; InterPro: IPR013129 Jumonji protein is required for neural tube formation in mice [].There is evidence of domain swapping within the jumonji family of transcription factors []. This domain is often associated with jmjN (see IPR003349 from INTERPRO) and belongs to the Cupin superfamily [].; PDB: 2YU2_A 2YU1_A 3AVR_A 3AVS_A 2OX0_B 2OQ6_B 2WWJ_A 2Q8D_A 3PDQ_A 2YBK_A ....
Probab=31.87 E-value=43 Score=27.43 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=19.9
Q ss_pred chhHHHhCCcEEEEeecccccEEEeC
Q psy11328 111 LPVLLHKRGLYIEPVTISVGDYILSP 136 (410)
Q Consensus 111 lp~~L~~~Gv~v~~~~L~VGDYils~ 136 (410)
.|..|.+.|+++....-..||+|+.+
T Consensus 69 ~p~~l~~~gi~~~~~~Q~~Ge~V~i~ 94 (114)
T PF02373_consen 69 SPEQLKKAGIPVYRFVQKPGEFVFIP 94 (114)
T ss_dssp GHHHHHHTTS--EEEEEETT-EEEE-
T ss_pred ceeeeeccCcccccceECCCCEEEEC
Confidence 57779999999999999999999975
No 135
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=31.50 E-value=72 Score=36.12 Aligned_cols=49 Identities=18% Similarity=0.212 Sum_probs=41.3
Q ss_pred CCCcCHHHHHHHHhc--CCCHHHHHcCCHHHHHHh--hCCchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLNR--GSSLPALCKLSEQELCSL--VENTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~--~~sl~~l~~~s~eeL~~~--~g~~~~a~~ly~fl~~~ 402 (410)
.+|++++.+..|.++ ++++.||..++.++|..+ +|. +.|+.|++.+...
T Consensus 467 I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~-Ksa~~Ll~~Ie~s 519 (689)
T PRK14351 467 IEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGE-TSAENLLAELEAS 519 (689)
T ss_pred CCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcch-hHHHHHHHHHHHH
Confidence 467999999999976 789999999999999988 554 6788888877654
No 136
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=31.07 E-value=73 Score=31.89 Aligned_cols=41 Identities=22% Similarity=0.199 Sum_probs=32.6
Q ss_pred HHHHHHhcCCCHHHHHcCCHHHHHHh---hCCchhHHHHHHHhc
Q psy11328 360 NKAAVLNRGSSLPALCKLSEQELCSL---VENTTLGNALYKALH 400 (410)
Q Consensus 360 n~~~ll~~~~sl~~l~~~s~eeL~~~---~g~~~~a~~ly~fl~ 400 (410)
-+.+++++|.|+++|++++++||.++ +|-..+|+.|+++..
T Consensus 47 ~~~rl~~~fpt~~~La~a~~eeL~~~~~~lG~y~RAr~L~~~A~ 90 (275)
T TIGR01084 47 YFERFLERFPTVQALANAPQDEVLKLWEGLGYYARARNLHKAAQ 90 (275)
T ss_pred HHHHHHHhCCCHHHHHCcCHHHHHHHHHHCCcHHHHHHHHHHHH
Confidence 46678889999999999999999876 553356888777654
No 137
>cd08540 SAM_PNT-ERG Sterile alpha motif (SAM)/Pointed domain of ERG transcription factor. SAM Pointed domain of ERG subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It may participate in formation of homodimers or heterodimers with ETS-2, Fli-1, ER81, and Pu-1. However, dimeric forms are inactive and SAM Pointed domain is not essential for dimerization, since ER81 and Pu-1 do not have it. In mouse, a regulator of this type binds the ESET histone H3-specific methyltransferase (human homolog is SETDB1), followed by modification of local chromatin structure through histone methylation. ERG regulators are involved in endothelial cell differentiation, bone morphogenesis and neural crest development. The Erg gene is a proto-oncogene. It is a target of chromosomal translocations resulting in fusions with new neighboring genes. Chimeric proteins were found in solid tumors such as myeloid leukemia or Ewing's sarcoma. Members of this subfamily are po
Probab=30.54 E-value=49 Score=27.14 Aligned_cols=34 Identities=21% Similarity=0.268 Sum_probs=28.2
Q ss_pred hcCC--CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 366 NRGS--SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 366 ~~~~--sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
.+|. +=++||.+|.|+.....++ -.|.-||..|.
T Consensus 32 ~~F~~m~Gk~LC~LskedF~~~ap~-~~GdiL~~HL~ 67 (75)
T cd08540 32 LLFQNIDGKELCKMTKDDFQRLTPS-YNADILLSHLH 67 (75)
T ss_pred ccccCCCHHHHHhCCHHHHHHHcCC-CCchHHHHHHH
Confidence 4563 7789999999999999975 68899988775
No 138
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=30.29 E-value=62 Score=36.06 Aligned_cols=61 Identities=21% Similarity=0.204 Sum_probs=46.8
Q ss_pred hhhhCCCEEEEEcCC-chhhhh----hhhhhcccCCCceEEEEEEeC---CcHHHHHHHHHHHHHHHHHH
Q psy11328 10 LRSLKPTSVIFYNAD-VAAIRQ----VEVYQCAQSEVKVKVFFMQYG---ESVEEQAYLSDLRREKKAFE 71 (410)
Q Consensus 10 L~~~~p~~VI~Yep~-~s~IR~----IE~y~~~~~~~~~~Vy~L~y~---~S~EE~~yl~si~rEk~af~ 71 (410)
|+-..+.+|.+.|+| ..|+|+ ||.-|++.|+..++|++ ++. +|..++-=-+..||++++--
T Consensus 510 LDiPEVsLVAIlDADKeGFLRse~SLIQtIGRAARN~~GkvIl-YAD~iT~sM~~Ai~ET~RRR~iQ~~y 578 (663)
T COG0556 510 LDLPEVSLVAILDADKEGFLRSERSLIQTIGRAARNVNGKVIL-YADKITDSMQKAIDETERRREIQMAY 578 (663)
T ss_pred CCCcceeEEEEeecCccccccccchHHHHHHHHhhccCCeEEE-EchhhhHHHHHHHHHHHHHHHHHHHH
Confidence 567889999999999 789987 89999999998999853 332 45566666667777776543
No 139
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=30.09 E-value=69 Score=28.11 Aligned_cols=35 Identities=11% Similarity=0.160 Sum_probs=30.6
Q ss_pred CCcCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhhCC
Q psy11328 354 PRVTSKNKAAVLN-RGSSLPALCKLSEQELCSLVEN 388 (410)
Q Consensus 354 ~~v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~g~ 388 (410)
|||++..+.-|.+ -+.|+++|.+.+.++|..-++.
T Consensus 59 ~gi~~~~a~LL~~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 59 PGIGPQYAELLEHAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred CCCCHHHHHHHHHhCcCcHHHHHhCCHHHHHHHHHH
Confidence 5699998888887 5899999999999999988863
No 140
>cd08537 SAM_PNT-ESE-1-like Sterile alpha motif (SAM)/Pointed domain of ESE-1 like ETS transcriptional regulators. SAM Pointed domain of ESE-1-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. SAM Pointed domain of ESE-1 provides a potential docking site for signaling kinase Pak1 in humans. ESE-1 factors are involved in regulation of gene expression in different types of epithelial cells. ESE-1 is expressed in many different organs including intestine, stomach, pancreas, lungs, kidneys, and prostate. The DNA binding consensus motif for ESE-1 consists of a purine-rich GGA[AT] core sequence. The expression profile of these factors is altered in epithelial cancers if compared to normal tissues. Members of this subfamily are potential targets for cancer therapy.
Probab=29.16 E-value=65 Score=26.89 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=26.1
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
+=++||+++.|++..+.|+ .|..||.-|..
T Consensus 44 nG~~LC~l~~e~F~~~a~p--~GdiLy~~L~~ 73 (78)
T cd08537 44 DGATLCNCALDQMRLVFGP--LGDQLYAQLRE 73 (78)
T ss_pred chHHHHccCHHHHHHHcCC--hHHHHHHHHHH
Confidence 4479999999999999986 89999998764
No 141
>cd08536 SAM_PNT-Mae Sterile alpha motif (SAM)/Pointed domain of Mae protein homolog. Mae (Modulator of the Activity of ETS) subfamily represents a group of SAM Pointed monodomain proteins. SAM Pointed domain is a protein-protein interaction domain. It can interact with other SAM pointed domains forming head-to-tail heterodimers and also provides a kinase docking site. For example, in Drosophila Mae is required for facilitating phosphorylation of the Yan factor and for blocking phosphorylation of the ETS-2 regulator. Mae interacts with the SAM Pointed domains of Yan and ETS-2. Binding enhances access of the kinase to the Yan phosphorylation site by providing a kinase docking site, or inhibits phosphorylation of ETS-2 by blocking its docking site. This type of factors participates in regulation of kinase signaling particularly during embryogenesis.
Probab=29.08 E-value=46 Score=26.53 Aligned_cols=31 Identities=26% Similarity=0.347 Sum_probs=25.6
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhccC
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALHTR 402 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~ 402 (410)
|=++||.+|.|+....... .|.-||+-|...
T Consensus 34 ~Gk~LC~ls~edF~~r~P~--~GdiL~~~lq~~ 64 (66)
T cd08536 34 NGKGLCLMSLEGFLYRVPV--GGKLLYEDFQRR 64 (66)
T ss_pred CHHHHHcCCHHHHHhhcCC--ccHHHHHHHHHH
Confidence 5589999999999988743 899999988653
No 142
>COG0513 SrmB Superfamily II DNA and RNA helicases [DNA replication, recombination, and repair / Transcription / Translation, ribosomal structure and biogenesis]
Probab=29.06 E-value=61 Score=34.99 Aligned_cols=57 Identities=16% Similarity=0.052 Sum_probs=43.0
Q ss_pred HhhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCCcHHHHHHHHHHHHH
Q psy11328 8 SKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGESVEEQAYLSDLRRE 66 (410)
Q Consensus 8 ~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~S~EE~~yl~si~rE 66 (410)
+=|+....++||-||.-...==-|.|.|||+|. ..|..+.+++. .+|..+|..+.+-
T Consensus 335 RGiDi~~v~~VinyD~p~~~e~yvHRiGRTgRaG~~G~ai~fv~~--~~e~~~l~~ie~~ 392 (513)
T COG0513 335 RGLDIPDVSHVINYDLPLDPEDYVHRIGRTGRAGRKGVAISFVTE--EEEVKKLKRIEKR 392 (513)
T ss_pred ccCCccccceeEEccCCCCHHHheeccCccccCCCCCeEEEEeCc--HHHHHHHHHHHHH
Confidence 557788899999999886555566788999885 46777777766 3478788777665
No 143
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=28.94 E-value=83 Score=34.87 Aligned_cols=51 Identities=10% Similarity=0.060 Sum_probs=42.4
Q ss_pred CCCcCHHHHHHHHhc--CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccCC
Q psy11328 353 RPRVTSKNKAAVLNR--GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTRP 403 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~--~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~~ 403 (410)
..|++++....|+++ ++++.||.+++.++|.++-| .++.|+.|++.+...-
T Consensus 430 I~GlGe~~i~~L~~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe~sk 483 (562)
T PRK08097 430 LDGIGEGTWRALHQTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFNLAR 483 (562)
T ss_pred CCCcCHHHHHHHHHcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHHHHc
Confidence 347999999999975 69999999999999999844 3478889988887643
No 144
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=28.90 E-value=83 Score=30.63 Aligned_cols=42 Identities=19% Similarity=0.216 Sum_probs=33.8
Q ss_pred HHHHHHHHhcCCCHHHHHcCCHHHHHHh---hC-CchhHHHHHHHh
Q psy11328 358 SKNKAAVLNRGSSLPALCKLSEQELCSL---VE-NTTLGNALYKAL 399 (410)
Q Consensus 358 ~~n~~~ll~~~~sl~~l~~~s~eeL~~~---~g-~~~~a~~ly~fl 399 (410)
.+-..+|..++++.++|+++++++|+++ .| -+.+|+.|...-
T Consensus 48 n~at~~Lf~~~~t~e~l~~a~~~~l~~~I~~iGlyr~KAk~I~~~~ 93 (211)
T COG0177 48 NKATPALFKRYPTPEDLLNADEEELEELIKSIGLYRNKAKNIKELA 93 (211)
T ss_pred HHHHHHHHHHcCCHHHHHcCCHHHHHHHHHhcCCcHHHHHHHHHHH
Confidence 4457789999999999999999999998 44 357888776543
No 145
>PF03118 RNA_pol_A_CTD: Bacterial RNA polymerase, alpha chain C terminal domain; InterPro: IPR011260 The core of the bacterial RNA polymerase (RNAP) consists of four subunits, two alpha, a beta and a beta', which are conserved from bacteria to mammals. The alpha subunit (RpoA) initiates RNAP assembly by dimerising to form a platform on which the beta subunits can interact. The alpha subunit consists of a N-terminal domain (NTD) and a C-terminal domain (CTD), connected by a short linker. The NTD is essential for RNAP assembly, while the CTD is necessary for transcription regulation, interacting with transcription factors and promoter upstream elements. In Escherichia coli, the catabolite activator protein (CAP or CRP) was shown to exert its effect through its interactions with the CTD, where CAP binding to CTD promotes RNAP binding to promoter DNA, thereby stimulating transcription initiation at class I CAP-dependent promoters. At class II CAP-dependent promoters, the interaction of CAP with CTD is one of multiple interactions involved in activation []. The CTD has a compact structure of four helices and two long arms enclosing its hydrophobic core, making its folding topology distinct from most other binding proteins. The upstream promoter element-binding site is formed from helices 1 and 4 [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3N97_B 1XS9_D 3K4G_A 3N4M_B 1COO_A 1LB2_E 3IYD_A 1Z3E_B 3GFK_B 3IHQ_B ....
Probab=28.72 E-value=69 Score=25.29 Aligned_cols=34 Identities=18% Similarity=0.186 Sum_probs=23.8
Q ss_pred cCCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhc
Q psy11328 367 RGSSLPALCKLSEQELCSLVE-NTTLGNALYKALH 400 (410)
Q Consensus 367 ~~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~ 400 (410)
++.|+.+|+..|.++|.++-| .+.-...|.+.|+
T Consensus 31 ~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~~L~ 65 (66)
T PF03118_consen 31 GIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKEKLK 65 (66)
T ss_dssp T--BHHHHHCS-HHHHHTSTTSHHHHHHHHHHHHH
T ss_pred CCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHHHHc
Confidence 689999999999999999944 2356666766654
No 146
>PRK11634 ATP-dependent RNA helicase DeaD; Provisional
Probab=28.69 E-value=1.1e+02 Score=34.12 Aligned_cols=51 Identities=12% Similarity=0.118 Sum_probs=36.9
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCCC-ceEEEEEEeCCcHHHHHHHHHH
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSEV-KVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~-~~~Vy~L~y~~S~EE~~yl~si 63 (410)
++-...++||.||+-.+.-.-+++-|+++|.. .+..++++.. .|.+++..+
T Consensus 309 IDip~V~~VI~~d~P~~~e~yvqRiGRtGRaGr~G~ai~~v~~---~e~~~l~~i 360 (629)
T PRK11634 309 LDVERISLVVNYDIPMDSESYVHRIGRTGRAGRAGRALLFVEN---RERRLLRNI 360 (629)
T ss_pred CCcccCCEEEEeCCCCCHHHHHHHhccccCCCCcceEEEEech---HHHHHHHHH
Confidence 56667899999998888888899999998854 4666666654 344444444
No 147
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=28.66 E-value=60 Score=31.59 Aligned_cols=44 Identities=11% Similarity=0.033 Sum_probs=32.6
Q ss_pred CHHHHHHHHhcC-----------CCHHHHHcCCHHHHHHhh---C-CchhHHHHHHHhc
Q psy11328 357 TSKNKAAVLNRG-----------SSLPALCKLSEQELCSLV---E-NTTLGNALYKALH 400 (410)
Q Consensus 357 ~~~n~~~ll~~~-----------~sl~~l~~~s~eeL~~~~---g-~~~~a~~ly~fl~ 400 (410)
+.+|+.+.+.++ .|.+.|++++.++|++++ | ...+|+.|.++..
T Consensus 44 ~~~~v~~a~~~L~~~~~~~~~~~~t~e~L~~a~~eeL~~~Irp~Gf~~~KA~~Lk~la~ 102 (218)
T PRK13913 44 KFEAVEKSLENLKNAFILENDDEINLKKIAYIEFSKLAECVRPSGFYNQKAKRLIDLSE 102 (218)
T ss_pred hHHHHHHHHHHHHHhcccccccCCCHHHHHcCCHHHHHHHHHhcCCHHHHHHHHHHHHH
Confidence 455555555443 389999999999999994 6 3578988887654
No 148
>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=28.34 E-value=1.4e+02 Score=25.63 Aligned_cols=31 Identities=13% Similarity=-0.010 Sum_probs=24.8
Q ss_pred cCHHHHHHHHh-cCCCHHHHHcCCHHHHHHhh
Q psy11328 356 VTSKNKAAVLN-RGSSLPALCKLSEQELCSLV 386 (410)
Q Consensus 356 v~~~n~~~ll~-~~~sl~~l~~~s~eeL~~~~ 386 (410)
||+.-|..|.. -+.|+.+|...+.++|-.-+
T Consensus 20 IG~a~a~DL~~LGi~s~~~L~g~dP~~Ly~~l 51 (93)
T PF11731_consen 20 IGKATAEDLRLLGIRSPADLKGRDPEELYERL 51 (93)
T ss_pred ccHHHHHHHHHcCCCCHHHHhCCCHHHHHHHH
Confidence 78887877776 68999999999998875443
No 149
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=28.32 E-value=75 Score=24.09 Aligned_cols=39 Identities=18% Similarity=0.209 Sum_probs=30.8
Q ss_pred CCcEEEEeCCCCCCcchhHHHhCCcEEEEeecccccEEE
Q psy11328 96 SCGRVIVDMREFRSELPVLLHKRGLYIEPVTISVGDYIL 134 (410)
Q Consensus 96 ~~~~IIVD~RE~rS~lp~~L~~~Gv~v~~~~L~VGDYil 134 (410)
....|++|..+....+|.++...|.++....-.-|.|.+
T Consensus 27 ~~l~v~~d~~~~~~~i~~~~~~~g~~~~~~~~~~~~~~i 65 (69)
T cd00291 27 EVLEVLLDDPGAVEDIPAWAKETGHEVLEVEEEGGVYRI 65 (69)
T ss_pred CEEEEEecCCcHHHHHHHHHHHcCCEEEEEEEeCCEEEE
Confidence 467999999988888999999999998765544455654
No 150
>cd08535 SAM_PNT-Tel_Yan Sterile alpha motif (SAM)/Pointed domain of Tel/Yan protein. SAM Pointed domain of Tel (Translocation, Ets, Leukemia)/Yan subfamily of ETS transcriptional repressors is a protein-protein interaction domain. SAM Pointed domains of this type of regulators can interact with each other, forming head-to-tail homodimers or homooligomers, and/or interact with SAM Pointed domains of another subfamily of ETS factors forming heterodimers. The oligomeric form is able to block transcription of target genesand is involved in MAPK signaling. They participate in regulation of different processes during embryo development including hematopoietic differentiation and eye development. Tel/Yan transcriptional factors are frequent targets of chromosomal translocations resulting in fusions of SAM domain with new neighboring genes. Such chimeric proteins were found in different tumors. Members of this subfamily are potential targets for cancer therapy.
Probab=28.20 E-value=63 Score=25.96 Aligned_cols=29 Identities=28% Similarity=0.466 Sum_probs=24.4
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||.+|.|+.....+ ..|.-||.-|+
T Consensus 35 nGk~LC~ls~edF~~r~p--~~GdiL~~hL~ 63 (68)
T cd08535 35 NGKALCLLTKEDFRYRSP--HSGDVLYELLQ 63 (68)
T ss_pred CHHHHhcCCHHHHhhhCC--CchHHHHHHHH
Confidence 447999999999998885 38999998775
No 151
>PRK14552 C/D box methylation guide ribonucleoprotein complex aNOP56 subunit; Provisional
Probab=27.38 E-value=64 Score=34.31 Aligned_cols=44 Identities=20% Similarity=0.327 Sum_probs=37.5
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccCC
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHTRP 403 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~~ 403 (410)
||+..+.+||.+.|+|..|+.++-..++ ++|. + |.|+..|.+..
T Consensus 270 VG~~lAArLIa~AGsL~~Lak~PastIq-iLGA-e--Kalf~~l~t~~ 313 (414)
T PRK14552 270 VGPSLGARLISLAGGLEELAKMPASTIQ-VLGA-E--KALFRHLRTGA 313 (414)
T ss_pred HhhHHHHHHHHHhCCHHHHhhCCchHHH-Hhch-h--hHHHHHhccCC
Confidence 8999999999999999999999999887 7886 3 34788887753
No 152
>smart00251 SAM_PNT SAM / Pointed domain. A subfamily of the SAM domain
Probab=26.62 E-value=68 Score=26.49 Aligned_cols=29 Identities=28% Similarity=0.419 Sum_probs=24.9
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||.+|.+++....+ ..|..||.-|.
T Consensus 49 ~G~~Lc~ls~edF~~~~p--~~GdiL~~hL~ 77 (82)
T smart00251 49 SGKELCSMSKEEFLERAP--FGGDILWSHLQ 77 (82)
T ss_pred CHHHHHcCCHHHHHHHcC--CchHHHHHHHH
Confidence 347999999999999996 58999998774
No 153
>cd08534 SAM_PNT-GABP-alpha Sterile alpha motif (SAM)/Pointed domain of GA-binding protein alpha chain. SAM Pointed domain of GABP-alpha subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. This type of transcriptional regulators forms heterotetramers containing two alpha and two beta subunits. It interacts with GA repeats (purine rich repeats). GABP transcriptional factors control gene expression in cell cycle control, apoptosis, and cellular respiration. GABP participates in regulation of transmembrane receptors and key hormones especially in myeloid cells and at the neuromuscular junction.
Probab=26.28 E-value=64 Score=27.33 Aligned_cols=30 Identities=23% Similarity=0.475 Sum_probs=25.6
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||.+|.|+.....+. ..|.-||..|.
T Consensus 51 ~Gk~LC~Ls~edF~~r~p~-~~GdiL~~hLe 80 (89)
T cd08534 51 TGRELCSLTQEEFFQRVPK-DPGDIFWTHLE 80 (89)
T ss_pred CHHHHhcCCHHHHHHHcCC-CccHHHHHHHH
Confidence 4579999999999999974 58999998775
No 154
>PRK15331 chaperone protein SicA; Provisional
Probab=25.74 E-value=1.4e+02 Score=28.05 Aligned_cols=41 Identities=10% Similarity=0.169 Sum_probs=32.6
Q ss_pred HHHHHHhcCCCHHHHHcCCHHHHHHh---------hCCchhHHHHHHHhc
Q psy11328 360 NKAAVLNRGSSLPALCKLSEQELCSL---------VENTTLGNALYKALH 400 (410)
Q Consensus 360 n~~~ll~~~~sl~~l~~~s~eeL~~~---------~g~~~~a~~ly~fl~ 400 (410)
.....++..+|+++|.+.|.++|+.+ -|.=..|+.+|.||-
T Consensus 15 ~i~~al~~G~tlk~l~gis~~~le~iY~~Ay~~y~~Gk~~eA~~~F~~L~ 64 (165)
T PRK15331 15 MIWDAVSEGATLKDVHGIPQDMMDGLYAHAYEFYNQGRLDEAETFFRFLC 64 (165)
T ss_pred HHHHHHHCCCCHHHHhCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 34556778899999999999999988 354467888888874
No 155
>PF01798 Nop: Putative snoRNA binding domain; InterPro: IPR002687 This domain is present in various pre-mRNA processing ribonucleoproteins. The function of the domain is unknown however it may be a common RNA or snoRNA or Nop1p binding domain. Proteins have been implicated in an expanding variety of functions during pre-mRNA splicing. Molecular cloning has identified genes encoding spliceosomal proteins that potentially act as novel RNA helicases, GTPases, or protein isomerases. Novel protein-protein and protein-RNA interactions that are required for functional spliceosome formation have also been described. Finally, growing evidence suggests that proteins may contribute directly to the spliceosome's active sites [].; PDB: 3GQX_B 3GQU_A 3NVM_A 3NMU_B 2NNW_C 3NVI_A 3NVK_A 2OZB_E 3SIU_B 3SIV_H ....
Probab=25.41 E-value=82 Score=28.95 Aligned_cols=42 Identities=24% Similarity=0.389 Sum_probs=33.6
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
||+.-+..|+.+.|+|.+|+.++-..++ ++|. ++ .++..|++
T Consensus 38 vG~~vaA~Li~~aGgL~~Lak~Pasniq-~lGa-eK--~~~~~l~~ 79 (150)
T PF01798_consen 38 VGSSVAARLISHAGGLENLAKMPASNIQ-VLGA-EK--ALFRGLKT 79 (150)
T ss_dssp HHHHHHHHHHHHHTSHHHHHTS-HHHHT-TSTC-HH--HHHHHHCC
T ss_pred HCcHHHHHHHHHcccHHHHHhCCHhhHH-HHHh-HH--HHhHHhcc
Confidence 8999999999999999999999999865 7886 33 45566654
No 156
>smart00490 HELICc helicase superfamily c-terminal domain.
Probab=24.49 E-value=64 Score=23.92 Aligned_cols=31 Identities=16% Similarity=0.078 Sum_probs=24.3
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCC
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSE 40 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~ 40 (410)
++-...+.||+++|..+...-+|+.|+++|.
T Consensus 51 i~~~~~~~vi~~~~~~~~~~~~Q~~gR~~R~ 81 (82)
T smart00490 51 LDLPGVDLVIIYDLPWSPASYIQRIGRAGRA 81 (82)
T ss_pred cChhcCCEEEEeCCCCCHHHHHHhhcccccC
Confidence 3344578999999988888888888887763
No 157
>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=24.46 E-value=54 Score=26.74 Aligned_cols=30 Identities=17% Similarity=0.220 Sum_probs=19.3
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhC
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSLVE 387 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g 387 (410)
|++..+..|+..++++... .+..+|..+.|
T Consensus 10 ig~~~a~~llaeigd~~rF--~~~~~l~~~~G 39 (87)
T PF02371_consen 10 IGPITAATLLAEIGDISRF--KSAKQLASYAG 39 (87)
T ss_pred ccHHHHHHHHHHHcCchhc--ccchhhhhccc
Confidence 7888888888766666442 34455666655
No 158
>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=24.24 E-value=1.7e+02 Score=27.77 Aligned_cols=22 Identities=9% Similarity=0.010 Sum_probs=15.8
Q ss_pred cHHHHHHHHcCCCCchhhhhhh
Q psy11328 288 NAAIEDFISKLPGMAEWSRART 309 (410)
Q Consensus 288 ~~~~~~~l~~lPgi~~~~~~~~ 309 (410)
+...-..|.++|||+.+.+-+.
T Consensus 67 Er~lF~~L~~V~GIGpK~Al~i 88 (191)
T TIGR00084 67 ERELFKELIKVNGVGPKLALAI 88 (191)
T ss_pred HHHHHHHHhCCCCCCHHHHHHH
Confidence 4455568899999987766444
No 159
>TIGR00603 rad25 DNA repair helicase rad25. All proteins in this family for which functions are known are DNA-DNA helicases used for the initiation of nucleotide excision repair and transacription as part of the TFIIH complex.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.19 E-value=93 Score=35.57 Aligned_cols=48 Identities=4% Similarity=-0.015 Sum_probs=37.5
Q ss_pred hhhhCCCEEEEEcCCc-hhhhhhhhhhcccCCC--------ceEEEEEEeCCcHHHH
Q psy11328 10 LRSLKPTSVIFYNADV-AAIRQVEVYQCAQSEV--------KVKVFFMQYGESVEEQ 57 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~-s~IR~IE~y~~~~~~~--------~~~Vy~L~y~~S~EE~ 57 (410)
++-...+.||++++.. +--..+||.||..|.. +..+|-|+..+|.|+.
T Consensus 556 IDlP~a~vvI~~s~~~gS~~q~iQRlGRilR~~~~~~~~~~~A~fY~lVs~dT~E~~ 612 (732)
T TIGR00603 556 IDLPEANVLIQISSHYGSRRQEAQRLGRILRAKKGSDAEEYNAFFYSLVSKDTQEMY 612 (732)
T ss_pred cCCCCCCEEEEeCCCCCCHHHHHHHhcccccCCCCCccccccceEEEEecCCchHHH
Confidence 5566789999999864 6667789999987743 2456999999998765
No 160
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=24.16 E-value=24 Score=34.84 Aligned_cols=49 Identities=12% Similarity=-0.005 Sum_probs=33.4
Q ss_pred hhhhhcCCCCCCCCCCCCCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHhh
Q psy11328 337 LLLFRIKPAPGRESNPRPRVTSKNKAAVLNRGSSLPALCKLSEQELCSLV 386 (410)
Q Consensus 337 ~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~ 386 (410)
.-+..|+.+.=.++...|||+.+.|..|.+.++.+.. ...+.+|+++--
T Consensus 25 ~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~-~~~~~~~~~~~~ 73 (232)
T PRK12766 25 ESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEV-SEETEAEVEDEG 73 (232)
T ss_pred CCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc-cccccchhcccc
Confidence 3455555555556677788999999999999986655 444455555443
No 161
>PRK10736 hypothetical protein; Provisional
Probab=24.08 E-value=89 Score=32.90 Aligned_cols=29 Identities=7% Similarity=0.047 Sum_probs=25.5
Q ss_pred CCcCHHHHHHHHhcCCCHHHHHcCCHHHHHHh
Q psy11328 354 PRVTSKNKAAVLNRGSSLPALCKLSEQELCSL 385 (410)
Q Consensus 354 ~~v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~ 385 (410)
|||+++..++|+++|+|.+ +++.++|...
T Consensus 14 ~giG~~~~~~L~~~~~~~~---~~~~~~l~~~ 42 (374)
T PRK10736 14 SSLYGDKMVRIAHRLLAQS---QIDAVVLQAT 42 (374)
T ss_pred CCCCHHHHHHHHHHhcChh---hCCHHHHHHc
Confidence 5699999999999999998 5688888775
No 162
>cd08539 SAM_PNT-ESE-3-like Sterile alpha motif (SAM)/Pointed domain of ESE-3 like ETS transcriptional regulators. SAM Pointed domain of ESE-3-like (Epithelium-Specific ETS) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. It can act as a major transactivator by providing a potential docking site for co-activators. The ESE-3 transcriptional activator is involved in regulation of glandular epithelium differentiation through the MAP kinase signaling cascade. It is found to be expressed in glandular epithelium of prostate, pancreas, salivary gland, and trachea. Additionally, ESE-3 is differentially expressed during monocyte-derived dendritic cells development. DNA binding consensus motif for ESE-3 consists of purine-rich GGAA/T core sequence. The expression profiles of these factors are altered in epithelial cancers. Members of this subfamily are potential targets for cancer therapy.
Probab=23.74 E-value=89 Score=25.79 Aligned_cols=29 Identities=31% Similarity=0.471 Sum_probs=24.4
Q ss_pred CHHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 370 SLPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 370 sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
+=++||++|.|++....|. .|.-||.-|.
T Consensus 39 nG~~LC~ms~e~F~~~~p~--~GdiLy~~l~ 67 (74)
T cd08539 39 NGEHLCSMSLQEFTRAAGT--AGQLLYSNLQ 67 (74)
T ss_pred ChHHHHccCHHHHhhcCCc--hHHHHHHHHH
Confidence 3479999999999988875 8999998764
No 163
>PRK04537 ATP-dependent RNA helicase RhlB; Provisional
Probab=23.47 E-value=1.3e+02 Score=33.08 Aligned_cols=54 Identities=13% Similarity=-0.021 Sum_probs=39.1
Q ss_pred HHhhhhhCCCEEEEEcCCchhhhhhhhhhcccCC-CceEEEEEEeCCcHHHHHHHHHH
Q psy11328 7 SSKLRSLKPTSVIFYNADVAAIRQVEVYQCAQSE-VKVKVFFMQYGESVEEQAYLSDL 63 (410)
Q Consensus 7 ~~~L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~-~~~~Vy~L~y~~S~EE~~yl~si 63 (410)
+.=|+-...++||.||.-.+...-++|-|+++|. ..+..+.++.. +|..++..+
T Consensus 318 arGIDip~V~~VInyd~P~s~~~yvqRiGRaGR~G~~G~ai~~~~~---~~~~~l~~i 372 (572)
T PRK04537 318 ARGLHIDGVKYVYNYDLPFDAEDYVHRIGRTARLGEEGDAISFACE---RYAMSLPDI 372 (572)
T ss_pred hcCCCccCCCEEEEcCCCCCHHHHhhhhcccccCCCCceEEEEecH---HHHHHHHHH
Confidence 3445667789999999988888899999999884 46777766644 344444444
No 164
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=23.31 E-value=1.9e+02 Score=29.62 Aligned_cols=26 Identities=23% Similarity=-0.001 Sum_probs=21.8
Q ss_pred CCCcCHHHHHHHHh-cCCCHHHHHcCC
Q psy11328 353 RPRVTSKNKAAVLN-RGSSLPALCKLS 378 (410)
Q Consensus 353 ~~~v~~~n~~~ll~-~~~sl~~l~~~s 378 (410)
.||||++.|+.+.+ .+.|+.+|-.+-
T Consensus 94 i~GiGpk~a~~l~~lGi~tl~eL~~a~ 120 (334)
T smart00483 94 VFGVGPKTAAKWYRKGIRTLEELKKNK 120 (334)
T ss_pred cCCcCHHHHHHHHHhCCCCHHHHHhcc
Confidence 36699999999988 688999997754
No 165
>PHA02558 uvsW UvsW helicase; Provisional
Probab=22.93 E-value=72 Score=34.11 Aligned_cols=35 Identities=14% Similarity=0.071 Sum_probs=30.4
Q ss_pred hhhhCCCEEEEEcCCchhhhhhhhhhcccCCCceE
Q psy11328 10 LRSLKPTSVIFYNADVAAIRQVEVYQCAQSEVKVK 44 (410)
Q Consensus 10 L~~~~p~~VI~Yep~~s~IR~IE~y~~~~~~~~~~ 44 (410)
++....|.||++.|.-|..+-+|+-||++|..+.+
T Consensus 409 ~Dip~ld~vIl~~p~~s~~~~~QriGR~~R~~~~K 443 (501)
T PHA02558 409 ISIKNLHHVIFAHPSKSKIIVLQSIGRVLRKHGSK 443 (501)
T ss_pred cccccccEEEEecCCcchhhhhhhhhccccCCCCC
Confidence 45678899999999999999999999999876554
No 166
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.74 E-value=1.7e+02 Score=27.71 Aligned_cols=20 Identities=5% Similarity=0.006 Sum_probs=14.7
Q ss_pred cHHHHHHHHcCCCCchhhhh
Q psy11328 288 NAAIEDFISKLPGMAEWSRA 307 (410)
Q Consensus 288 ~~~~~~~l~~lPgi~~~~~~ 307 (410)
+...-..|.++.||+.+.+=
T Consensus 68 Er~lF~~Li~V~GIGpK~AL 87 (188)
T PRK14606 68 KKELFLSLTKVSRLGPKTAL 87 (188)
T ss_pred HHHHHHHHhccCCccHHHHH
Confidence 45566788999999876543
No 167
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=22.67 E-value=1.2e+02 Score=34.20 Aligned_cols=50 Identities=16% Similarity=0.107 Sum_probs=42.3
Q ss_pred CCCcCHHHHHHHHhc--CCCHHHHHcCCHHHHHHhhC-CchhHHHHHHHhccC
Q psy11328 353 RPRVTSKNKAAVLNR--GSSLPALCKLSEQELCSLVE-NTTLGNALYKALHTR 402 (410)
Q Consensus 353 ~~~v~~~n~~~ll~~--~~sl~~l~~~s~eeL~~~~g-~~~~a~~ly~fl~~~ 402 (410)
..|++++....|+++ ++++.||..++.++|.++-| .+..|+.|++.+...
T Consensus 441 I~GlG~~~i~~L~~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie~s 493 (669)
T PRK14350 441 IVGLSDKTIEFLFEKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSIEAS 493 (669)
T ss_pred ccCcCHHHHHHHHHcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHHHHH
Confidence 467999999999975 69999999999999998854 357899999888754
No 168
>COG0553 HepA Superfamily II DNA/RNA helicases, SNF2 family [Transcription / DNA replication, recombination, and repair]
Probab=22.39 E-value=1.3e+02 Score=33.37 Aligned_cols=49 Identities=14% Similarity=0.157 Sum_probs=34.5
Q ss_pred hCCCEEEEEcCCchhhhhhhhhhc---ccCCCceEEEEEEeCCcHHHHHHHH
Q psy11328 13 LKPTSVIFYNADVAAIRQVEVYQC---AQSEVKVKVFFMQYGESVEEQAYLS 61 (410)
Q Consensus 13 ~~p~~VI~Yep~~s~IR~IE~y~~---~~~~~~~~Vy~L~y~~S~EE~~yl~ 61 (410)
...+.||+|||.----...|.-.+ .+...+++||=++.++|.||.-.-.
T Consensus 780 t~a~~vi~~d~~wnp~~~~Qa~dRa~RigQ~~~v~v~r~i~~~tiEe~i~~~ 831 (866)
T COG0553 780 TGADTVILFDPWWNPAVELQAIDRAHRIGQKRPVKVYRLITRGTIEEKILEL 831 (866)
T ss_pred cccceEEEeccccChHHHHHHHHHHHHhcCcceeEEEEeecCCcHHHHHHHH
Confidence 367899999996433333333322 2556799999999999999985443
No 169
>COG1194 MutY A/G-specific DNA glycosylase [DNA replication, recombination, and repair]
Probab=22.31 E-value=1.2e+02 Score=31.61 Aligned_cols=40 Identities=23% Similarity=0.179 Sum_probs=33.6
Q ss_pred HHHHHHhcCCCHHHHHcCCHHHHHHh---hCCchhHHHHHHHh
Q psy11328 360 NKAAVLNRGSSLPALCKLSEQELCSL---VENTTLGNALYKAL 399 (410)
Q Consensus 360 n~~~ll~~~~sl~~l~~~s~eeL~~~---~g~~~~a~~ly~fl 399 (410)
-+.+-+++|.+++.|++++++|+.++ +|--+.|+.|++.-
T Consensus 55 yy~~fl~rfPti~~LA~A~~~evl~~W~gLGYysRArnL~~~A 97 (342)
T COG1194 55 YYERFLERFPTIKALAAAPEDEVLKAWEGLGYYSRARNLHKAA 97 (342)
T ss_pred hHHHHHHhCCCHHHHhcCCHHHHHHHHHhcChHHHHHHHHHHH
Confidence 47889999999999999999999988 55346788887654
No 170
>KOG0389|consensus
Probab=21.75 E-value=1.7e+02 Score=34.19 Aligned_cols=46 Identities=20% Similarity=0.132 Sum_probs=35.2
Q ss_pred CCEEEEEcCC--chhhhhhhhhh-cccCCCceEEEEEEeCCcHHHHHHH
Q psy11328 15 PTSVIFYNAD--VAAIRQVEVYQ-CAQSEVKVKVFFMQYGESVEEQAYL 60 (410)
Q Consensus 15 p~~VI~Yep~--~s~IR~IE~y~-~~~~~~~~~Vy~L~y~~S~EE~~yl 60 (410)
-+.||+||-+ |--=||-|-++ |.|...++.||=|++++|+||..+-
T Consensus 848 An~VIihD~dFNP~dD~QAEDRcHRvGQtkpVtV~rLItk~TIEE~I~~ 896 (941)
T KOG0389|consen 848 ANTVIIHDIDFNPYDDKQAEDRCHRVGQTKPVTVYRLITKSTIEEGILR 896 (941)
T ss_pred cceEEEeecCCCCcccchhHHHHHhhCCcceeEEEEEEecCcHHHHHHH
Confidence 4789999976 55556666543 3455679999999999999998654
No 171
>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=21.45 E-value=1.7e+02 Score=33.24 Aligned_cols=87 Identities=18% Similarity=0.210 Sum_probs=0.0
Q ss_pred HHHHHHHHc--CCCCchhhhhhhhhhhhccCCCCCCCCchhhhhhhhhhhhhhhhcCCCCCCCCCCCCCcCHHHHHHHHh
Q psy11328 289 AAIEDFISK--LPGMAEWSRARTLNLEVLGLNPGQGGNFLTELFRASSFFLLLFRIKPAPGRESNPRPRVTSKNKAAVLN 366 (410)
Q Consensus 289 ~~~~~~l~~--lPgi~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~n~~~ll~ 366 (410)
.....+|++ +|||+...+.+....+ |.+.++-+.+. -..|..| ||++++.+..+.+
T Consensus 78 ~~i~~yL~s~~~~GIG~~~A~~iv~~f--------g~~~~~~i~~~---~~~L~~v-----------~gi~~~~~~~i~~ 135 (720)
T TIGR01448 78 EGIVAYLSSRSIKGVGKKLAQRIVKTF--------GEAAFDVLDDD---PEKLLEV-----------PGISKANLEKFVS 135 (720)
T ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHHh--------CHhHHHHHHhC---HHHHhcC-----------CCCCHHHHHHHHH
Q ss_pred cCCCHHHHHcCCHHHHHHh-hCCchhHHHHHHHh
Q psy11328 367 RGSSLPALCKLSEQELCSL-VENTTLGNALYKAL 399 (410)
Q Consensus 367 ~~~sl~~l~~~s~eeL~~~-~g~~~~a~~ly~fl 399 (410)
......+..++- .-|.++ ++. ..|.+||+++
T Consensus 136 ~~~~~~~~~~~~-~~L~~~gi~~-~~a~ki~~~y 167 (720)
T TIGR01448 136 QWSQQGDERRLL-AGLQGLGIGI-KLAQRIYKFY 167 (720)
T ss_pred HHHHhHHHHHHH-HHHHHcCCCH-HHHHHHHHHH
No 172
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=21.42 E-value=1.4e+02 Score=28.90 Aligned_cols=24 Identities=17% Similarity=0.169 Sum_probs=14.2
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHh
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSL 385 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~ 385 (410)
||+|.|.++.- +|++...+++.++
T Consensus 20 vG~KsA~R~Af------hLL~~~~~~~~~l 43 (198)
T COG0353 20 VGPKSAQRLAF------HLLQRDREDVERL 43 (198)
T ss_pred CChhHHHHHHH------HHHccCHHHHHHH
Confidence 66666666643 4556666665544
No 173
>cd08541 SAM_PNT-FLI-1 Sterile alpha motif (SAM)/Pointed domain of friend leukemia integration 1 transcription activator. SAM Pointed domain of FLI-1 (Friend Leukemia Integration) subfamily of ETS transcriptional regulators is a putative protein-protein interaction domain. The FLI-1 protein participates in regulation of cellular differentiation, proliferation, and survival. The Fli-1 gene was initially described in Friend virus-induced erythroleukemias as a site for virus integration. It is highly expressed in hematopoietic tissues and at lower level in lungs, heart, and ovaries. Fli-1 is a proto-oncogene implicated in Ewing's sarcoma and erythroleukemia. Members of this subfamily are potential targets for cancer therapy.
Probab=21.24 E-value=1.1e+02 Score=26.06 Aligned_cols=35 Identities=14% Similarity=0.123 Sum_probs=28.6
Q ss_pred hcCC--CHHHHHcCCHHHHHHhhCCchhHHHHHHHhcc
Q psy11328 366 NRGS--SLPALCKLSEQELCSLVENTTLGNALYKALHT 401 (410)
Q Consensus 366 ~~~~--sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~ 401 (410)
.+|. +=++||.+|.|++....+. ..|.-|+..|..
T Consensus 44 ~~F~~m~Gk~LC~LskedF~~~~p~-~~gdiLw~HL~~ 80 (91)
T cd08541 44 SFFQNMDGKELCKMNKEDFLRATSL-YNTEVLLSHLSY 80 (91)
T ss_pred hhccCCCHHHHHhCCHHHHHHHcCC-CccHHHHHHHHH
Confidence 4563 7789999999999998865 689999887754
No 174
>cd08543 SAM_PNT-ETS-2 Sterile alpha motif (SAM)/Pointed domain of ETS-2. SAM Pointed domain of ETS-2 subfamily of ETS transcriptional regulators is a protein-protein interaction domain. It contains a docking site for Cdk10 (cyclin-dependent kinase 10), a member of the Cdc2 kinase family. The interaction between ETS-2 and Cdk10 kinase inhibits ETS-2 transactivation activity in mammals. ETS-2 is also regulated by ERK2 MAP kinase. ETS-2, which is phosphorylated by ERK2, can interact with coactivators and enhance transactivation. ETS-2 transcriptional activators are involved in embryonic development and cell cycle control. The Ets-2 gene is a proto-oncogene. It is overexpressed in breast and prostate cancer cells and its overexpression is necessary for transformation of such cells. Members of ETS-2 subfamily are potential molecular targets for selective cancer therapy.
Probab=21.07 E-value=91 Score=26.54 Aligned_cols=29 Identities=24% Similarity=0.534 Sum_probs=24.7
Q ss_pred HHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 371 LPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 371 l~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
=++||.+|.|+.....++ -.|.-||..|.
T Consensus 52 Gk~LC~Ls~edF~~~ap~-~~GdIL~~HL~ 80 (89)
T cd08543 52 GQELCNLGKERFLELAPD-FVGDILWEHLE 80 (89)
T ss_pred hHHHHcCCHHHHHhHcCC-CcchHHHHHHH
Confidence 379999999999999974 47999998775
No 175
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=20.99 E-value=78 Score=30.25 Aligned_cols=26 Identities=15% Similarity=0.129 Sum_probs=17.7
Q ss_pred CCCCCcCHHHHHHHHh-----cCCCHHHHHc
Q psy11328 351 NPRPRVTSKNKAAVLN-----RGSSLPALCK 376 (410)
Q Consensus 351 ~~~~~v~~~n~~~ll~-----~~~sl~~l~~ 376 (410)
+-+||||.|.+..+|. .|.|.+|+-+
T Consensus 119 eLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 119 ELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp GGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred hhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 5678999999999997 5999888765
No 176
>COG1498 SIK1 Protein implicated in ribosomal biogenesis, Nop56p homolog [Translation, ribosomal structure and biogenesis]
Probab=20.90 E-value=1.1e+02 Score=32.70 Aligned_cols=44 Identities=23% Similarity=0.354 Sum_probs=38.8
Q ss_pred cCHHHHHHHHhcCCCHHHHHcCCHHHHHHhhCCchhHHHHHHHhccCC
Q psy11328 356 VTSKNKAAVLNRGSSLPALCKLSEQELCSLVENTTLGNALYKALHTRP 403 (410)
Q Consensus 356 v~~~n~~~ll~~~~sl~~l~~~s~eeL~~~~g~~~~a~~ly~fl~~~~ 403 (410)
||+.-+.+|+.+-|+|.+|+.++...++ ++|- =|.||..|+++-
T Consensus 248 VG~~lgARLIs~AGgL~~LAk~PASTIQ-vLGA---EKALFraL~~~~ 291 (395)
T COG1498 248 VGPVLGARLISHAGGLTRLAKMPASTIQ-VLGA---EKALFRALKTGA 291 (395)
T ss_pred HhHHHHHHHHHHhcCHHHHHhCccchhh-hhhh---hHHHHHHHhCCC
Confidence 8999999999999999999999999886 7874 467999998754
No 177
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.85 E-value=2e+02 Score=27.65 Aligned_cols=23 Identities=13% Similarity=0.216 Sum_probs=15.6
Q ss_pred cHHHHHHHHcCCCCchhhhhhhh
Q psy11328 288 NAAIEDFISKLPGMAEWSRARTL 310 (410)
Q Consensus 288 ~~~~~~~l~~lPgi~~~~~~~~~ 310 (410)
....-+.|.++.||+.+.+-..+
T Consensus 67 Er~lF~~LisVsGIGPK~ALaIL 89 (196)
T PRK13901 67 EREVFEELIGVDGIGPRAALRVL 89 (196)
T ss_pred HHHHHHHHhCcCCcCHHHHHHHH
Confidence 45566788899998876553333
No 178
>KOG0384|consensus
Probab=20.83 E-value=1.5e+02 Score=36.08 Aligned_cols=48 Identities=17% Similarity=0.254 Sum_probs=33.1
Q ss_pred CCEEEEEcCCchhhhhhhhhh---cccCCCceEEEEEEeCCcHHHHHHHHH
Q psy11328 15 PTSVIFYNADVAAIRQVEVYQ---CAQSEVKVKVFFMQYGESVEEQAYLSD 62 (410)
Q Consensus 15 p~~VI~Yep~~s~IR~IE~y~---~~~~~~~~~Vy~L~y~~S~EE~~yl~s 62 (410)
-|-||+||.|=--==-+|.-- |.|....++||=|++++|+||..+-.+
T Consensus 771 ADTVIIFDSDWNPQNDLQAqARaHRIGQkk~VnVYRLVTk~TvEeEilERA 821 (1373)
T KOG0384|consen 771 ADTVIIFDSDWNPQNDLQAQARAHRIGQKKHVNVYRLVTKNTVEEEILERA 821 (1373)
T ss_pred cceEEEeCCCCCcchHHHHHHHHHhhcccceEEEEEEecCCchHHHHHHHH
Confidence 478999998732222344333 345567899999999999999865443
No 179
>PRK00099 rplJ 50S ribosomal protein L10; Reviewed
Probab=20.32 E-value=3.3e+02 Score=24.88 Aligned_cols=52 Identities=15% Similarity=0.253 Sum_probs=34.6
Q ss_pred CeEEEec-CChhhHHHHHHHHhcCCCCCCcccccccCCCCCCCccccccHHHHHHHHcCCC
Q psy11328 241 KLRLIWS-SGPYNTAQLFFELKQGRDEPSAEVASSIGQTPNEDYTDRYNAAIEDFISKLPG 300 (410)
Q Consensus 241 ~l~IiwS-~s~~eTA~ll~~Lk~~~eepd~~~a~~i~~~~~~~~~~~~~~~~~~~l~~lPg 300 (410)
..-++|| .||.+.+.+|..+.+..+.....-+. +. ..-++....+.|.+||+
T Consensus 77 ~~al~fs~~d~~~~~k~l~~f~K~~~~~~l~gg~-~e-------g~~l~~~~i~~la~LPs 129 (172)
T PRK00099 77 PTAIAFSYEDPVAAAKVLKDFAKDNKKLEIKGGA-IE-------GKVLDAEEVKALAKLPS 129 (172)
T ss_pred CeEEEEeCCChHHHHHHHHHHHhhCcCceEEEEE-EC-------CEEcCHHHHHHHhcCCC
Confidence 3567898 68999999999987744333221111 11 12457788889999999
No 180
>cd08542 SAM_PNT-ETS-1 Sterile alpha motif (SAM)/Pointed domain of ETS-1. SAM Pointed domain of ETS-1 subfamily of ETS transcriptional activators is a protein-protein interaction domain. The ETS-1 activator is regulated by phosphorylation. It contains a docking site for the ERK2 MAP (Mitogen Activated Protein) kinase, while the ERK2 phosphorylation site is located in the N-terminal disordered region upstream of the SAM Pointed domain. Mutations of the kinase docking site residues inhibit phosphorylation. ETS-1 activators play role in a number of different physiological processes, and they are expressed during embryonic development, including blood vessel formation, hematopoietic, lymphoid, neuronal and osteogenic differentiation. The Ets-1 gene is a proto-oncogene involved in progression of different tumors (including breast cancer, meningioma, and prostate cancer). Members of this subfamily are potential molecular targets for selective cancer therapy.
Probab=20.10 E-value=1e+02 Score=26.13 Aligned_cols=29 Identities=28% Similarity=0.515 Sum_probs=24.4
Q ss_pred HHHHHcCCHHHHHHhhCCchhHHHHHHHhc
Q psy11328 371 LPALCKLSEQELCSLVENTTLGNALYKALH 400 (410)
Q Consensus 371 l~~l~~~s~eeL~~~~g~~~~a~~ly~fl~ 400 (410)
=++||.+|.|+......+ -.|.-||..|.
T Consensus 52 Gk~LC~Ls~edF~~~~P~-~~GdIL~~HL~ 80 (88)
T cd08542 52 GAALCALGKECFLELAPD-FVGDILWEHLE 80 (88)
T ss_pred HHHHHcCCHHHHHhHcCC-CccHHHHHHHH
Confidence 379999999999999964 47999998764
Done!