Query psy16215
Match_columns 1041
No_of_seqs 288 out of 1612
Neff 4.9
Searched_HMMs 46136
Date Fri Aug 16 23:46:34 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16215hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2095|consensus 100.0 1.6E-73 3.5E-78 657.8 27.9 403 2-429 14-431 (656)
2 PRK01810 DNA polymerase IV; Va 100.0 2.4E-71 5.3E-76 632.2 37.8 384 2-474 3-388 (407)
3 PRK02794 DNA polymerase IV; Pr 100.0 4.7E-70 1E-74 624.5 37.7 382 1-474 33-414 (419)
4 PRK03103 DNA polymerase IV; Re 100.0 3.2E-70 6.9E-75 623.5 35.5 382 3-475 2-390 (409)
5 PRK03858 DNA polymerase IV; Va 100.0 9.7E-70 2.1E-74 616.4 37.3 378 2-473 2-380 (396)
6 cd01701 PolY_Rev1 DNA polymera 100.0 5.1E-69 1.1E-73 613.8 41.2 343 3-424 46-404 (404)
7 PRK14133 DNA polymerase IV; Pr 100.0 1.3E-68 2.9E-73 598.2 41.6 346 3-437 2-347 (347)
8 PTZ00205 DNA polymerase kappa; 100.0 5.6E-69 1.2E-73 624.7 39.8 354 4-440 133-509 (571)
9 cd01702 PolY_Pol_eta DNA Polym 100.0 5.5E-69 1.2E-73 605.3 37.6 340 7-423 1-359 (359)
10 PRK01216 DNA polymerase IV; Va 100.0 2.3E-68 5E-73 598.6 42.0 345 5-438 2-350 (351)
11 PRK03348 DNA polymerase IV; Pr 100.0 6.3E-68 1.4E-72 612.8 44.0 356 1-442 2-358 (454)
12 PRK03609 umuC DNA polymerase V 100.0 7.6E-69 1.7E-73 615.0 33.8 389 5-484 1-404 (422)
13 PRK03352 DNA polymerase IV; Va 100.0 4.7E-67 1E-71 585.1 41.1 339 3-427 4-345 (346)
14 cd00424 PolY Y-family of DNA p 100.0 3.9E-67 8.4E-72 585.5 40.4 336 7-422 1-343 (343)
15 cd01703 PolY_Pol_iota DNA Poly 100.0 7.1E-67 1.5E-71 591.7 38.9 341 7-423 1-379 (379)
16 cd03586 PolY_Pol_IV_kappa DNA 100.0 3.3E-66 7.1E-71 573.2 40.6 334 7-424 1-334 (334)
17 PRK02406 DNA polymerase IV; Va 100.0 1.5E-64 3.3E-69 564.4 40.2 333 11-429 1-336 (343)
18 cd01700 PolY_Pol_V_umuC umuC s 100.0 1.5E-64 3.2E-69 564.6 34.2 333 7-423 1-344 (344)
19 COG0389 DinP Nucleotidyltransf 100.0 1.5E-59 3.3E-64 527.9 38.6 346 4-428 1-348 (354)
20 KOG2094|consensus 100.0 7.4E-61 1.6E-65 518.7 25.1 341 3-427 102-446 (490)
21 cd03468 PolY_like DNA Polymera 100.0 1.1E-53 2.3E-58 473.1 34.3 331 7-422 1-334 (335)
22 KOG2093|consensus 100.0 1.9E-52 4.1E-57 489.3 17.1 356 7-440 374-749 (1016)
23 PF00817 IMS: impB/mucB/samB f 100.0 2.8E-35 6E-40 293.2 15.1 148 9-223 1-149 (149)
24 PF11799 IMS_C: impB/mucB/samB 99.4 2.8E-12 6E-17 122.5 11.8 123 302-437 1-127 (127)
25 PF11798 IMS_HHH: IMS family H 98.2 1.1E-06 2.4E-11 67.3 2.8 32 235-267 1-32 (32)
26 PRK04301 radA DNA repair and r 97.5 5.3E-05 1.2E-09 85.2 3.6 80 241-321 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 96.8 0.0012 2.6E-08 74.0 4.5 74 247-321 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.2 0.0038 8.3E-08 53.9 3.2 51 247-298 7-59 (60)
29 PF11731 Cdd1: Pathogenicity l 95.0 0.018 3.9E-07 54.6 2.9 41 246-287 13-53 (93)
30 PRK12766 50S ribosomal protein 92.3 0.22 4.8E-06 54.4 5.6 56 246-302 4-61 (232)
31 PF03118 RNA_pol_A_CTD: Bacter 90.3 0.54 1.2E-05 42.0 5.0 55 239-295 6-62 (66)
32 PRK02362 ski2-like helicase; P 90.2 0.32 6.9E-06 61.3 5.0 55 245-300 652-706 (737)
33 PF08827 DUF1805: Domain of un 89.9 0.18 3.8E-06 44.3 1.7 27 42-68 32-58 (59)
34 COG3743 Uncharacterized conser 89.5 0.35 7.7E-06 48.6 3.6 38 246-284 68-105 (133)
35 PF04994 TfoX_C: TfoX C-termin 89.3 0.35 7.5E-06 44.9 3.2 35 245-280 3-37 (81)
36 PF12826 HHH_2: Helix-hairpin- 89.1 0.39 8.5E-06 42.3 3.3 47 250-298 8-56 (64)
37 PF10391 DNA_pol_lambd_f: Fing 88.4 0.28 6E-06 42.0 1.8 27 248-275 5-31 (52)
38 PF14229 DUF4332: Domain of un 87.3 0.62 1.3E-05 46.2 3.8 53 234-287 42-94 (122)
39 PRK14667 uvrC excinuclease ABC 85.1 1.1 2.5E-05 55.0 5.2 53 245-299 514-567 (567)
40 COG2251 Predicted nuclease (Re 82.3 1.6 3.5E-05 51.8 4.7 68 233-301 213-282 (474)
41 PRK00116 ruvA Holliday junctio 81.6 1.4 3.1E-05 46.9 3.7 57 246-302 74-133 (192)
42 PF00096 zf-C2H2: Zinc finger, 81.1 0.25 5.5E-06 34.4 -1.4 22 952-973 1-23 (23)
43 PRK01172 ski2-like helicase; P 80.5 2 4.4E-05 53.6 5.1 52 245-297 612-665 (674)
44 PRK00254 ski2-like helicase; P 80.1 1.9 4.1E-05 54.4 4.7 54 244-298 644-699 (720)
45 PF12230 PRP21_like_P: Pre-mRN 77.1 0.77 1.7E-05 49.9 0.0 26 950-975 167-192 (229)
46 PRK14669 uvrC excinuclease ABC 76.4 4 8.6E-05 50.9 5.8 54 245-300 552-605 (624)
47 TIGR00596 rad1 DNA repair prot 75.0 3.6 7.8E-05 52.8 5.0 52 247-300 759-811 (814)
48 PRK14671 uvrC excinuclease ABC 74.6 4.3 9.3E-05 50.7 5.5 52 245-298 569-620 (621)
49 PF14229 DUF4332: Domain of un 73.9 4.5 9.8E-05 40.2 4.4 44 251-296 1-49 (122)
50 PRK08609 hypothetical protein; 72.5 2.8 6.2E-05 51.7 3.3 79 188-292 57-138 (570)
51 PRK14670 uvrC excinuclease ABC 72.2 4.8 0.0001 49.8 5.0 53 245-299 514-568 (574)
52 PRK14666 uvrC excinuclease ABC 72.2 4.2 9.1E-05 51.1 4.6 52 245-298 637-690 (694)
53 PRK07758 hypothetical protein; 71.4 7.3 0.00016 37.5 5.0 47 250-297 39-87 (95)
54 KOG2093|consensus 71.4 0.87 1.9E-05 57.4 -1.5 31 6-36 330-360 (1016)
55 PF02889 Sec63: Sec63 Brl doma 70.2 7.8 0.00017 43.4 5.9 68 237-305 138-209 (314)
56 smart00483 POLXc DNA polymeras 70.1 3.5 7.6E-05 47.6 3.1 30 247-277 91-120 (334)
57 PF02961 BAF: Barrier to autoi 69.5 2.6 5.6E-05 40.0 1.5 34 240-274 14-47 (89)
58 PRK14672 uvrC excinuclease ABC 69.5 6.5 0.00014 49.4 5.3 60 245-306 608-669 (691)
59 TIGR03491 RecB family nuclease 69.4 4.6 9.9E-05 48.4 4.0 61 237-298 199-261 (457)
60 PTZ00035 Rad51 protein; Provis 68.8 6.2 0.00013 45.6 4.7 55 245-300 21-79 (337)
61 PRK07956 ligA NAD-dependent DN 67.6 6.6 0.00014 49.4 5.0 53 246-298 446-500 (665)
62 smart00611 SEC63 Domain of unk 66.0 11 0.00023 42.4 5.8 59 244-303 150-210 (312)
63 PLN03187 meiotic recombination 63.1 8.1 0.00018 44.9 4.3 56 244-300 28-87 (344)
64 TIGR00575 dnlj DNA ligase, NAD 61.7 10 0.00023 47.6 5.1 53 246-298 433-487 (652)
65 TIGR02238 recomb_DMC1 meiotic 59.7 14 0.0003 42.4 5.3 51 248-299 2-56 (313)
66 cd00141 NT_POLXc Nucleotidyltr 59.3 6 0.00013 45.1 2.3 29 247-276 87-115 (307)
67 PF00633 HHH: Helix-hairpin-he 57.0 6.3 0.00014 30.2 1.3 16 247-262 13-28 (30)
68 PF13894 zf-C2H2_4: C2H2-type 56.9 2.3 4.9E-05 29.0 -1.0 22 952-973 1-23 (24)
69 PRK14973 DNA topoisomerase I; 55.9 15 0.00032 48.1 5.2 52 247-299 879-932 (936)
70 COG3377 Uncharacterized conser 55.6 3.9 8.4E-05 38.9 0.0 26 43-68 69-94 (95)
71 PRK00558 uvrC excinuclease ABC 54.9 15 0.00033 45.8 4.9 53 245-299 543-597 (598)
72 TIGR00084 ruvA Holliday juncti 54.8 12 0.00026 40.1 3.5 52 247-301 74-131 (191)
73 PRK12278 50S ribosomal protein 53.8 12 0.00025 41.2 3.2 39 245-284 158-196 (221)
74 PRK14605 ruvA Holliday junctio 53.8 13 0.00028 39.9 3.6 63 237-301 67-132 (194)
75 TIGR02239 recomb_RAD51 DNA rep 53.7 20 0.00044 41.1 5.4 45 252-297 8-54 (316)
76 PLN03186 DNA repair protein RA 53.5 12 0.00026 43.5 3.5 53 244-297 25-81 (342)
77 COG1948 MUS81 ERCC4-type nucle 50.1 22 0.00047 39.9 4.7 51 247-299 184-236 (254)
78 PHA02768 hypothetical protein; 49.8 4.5 9.7E-05 35.3 -0.5 23 952-974 6-29 (55)
79 PRK14351 ligA NAD-dependent DN 49.3 22 0.00047 45.2 5.1 53 246-298 463-517 (689)
80 PF13912 zf-C2H2_6: C2H2-type 49.1 2.8 6E-05 30.3 -1.6 23 951-973 1-24 (27)
81 PRK13766 Hef nuclease; Provisi 49.0 20 0.00043 45.6 4.7 51 247-299 717-769 (773)
82 PRK12311 rpsB 30S ribosomal pr 48.4 13 0.00027 43.2 2.6 36 246-282 264-299 (326)
83 smart00355 ZnF_C2H2 zinc finge 47.8 5.3 0.00012 27.3 -0.3 23 952-974 1-24 (26)
84 PRK10917 ATP-dependent DNA hel 47.4 12 0.00027 47.1 2.6 31 245-276 9-39 (681)
85 TIGR00426 competence protein C 46.6 22 0.00047 31.5 3.3 45 246-296 17-66 (69)
86 TIGR00575 dnlj DNA ligase, NAD 44.6 26 0.00057 44.2 4.7 17 109-125 268-284 (652)
87 COG0322 UvrC Nuclease subunit 42.3 26 0.00057 43.6 4.2 50 245-296 530-580 (581)
88 TIGR01954 nusA_Cterm_rpt trans 42.1 49 0.0011 27.0 4.5 43 254-297 2-46 (50)
89 KOG2071|consensus 42.1 11 0.00023 46.5 0.8 31 952-982 419-454 (579)
90 PF00416 Ribosomal_S13: Riboso 40.6 29 0.00063 33.8 3.4 40 247-286 17-59 (107)
91 PRK12373 NADH dehydrogenase su 39.6 24 0.00053 41.9 3.2 36 246-282 324-359 (400)
92 TIGR02027 rpoA DNA-directed RN 39.5 31 0.00068 39.4 4.0 55 242-298 232-288 (297)
93 PF13438 DUF4113: Domain of un 39.5 3.8 8.2E-05 35.0 -2.5 34 449-485 2-36 (52)
94 KOG3905|consensus 39.3 30 0.00066 40.2 3.8 98 924-1036 324-421 (473)
95 PRK13482 DNA integrity scannin 37.5 42 0.00092 39.4 4.6 48 247-296 289-338 (352)
96 PRK14668 uvrC excinuclease ABC 37.2 35 0.00076 42.5 4.2 50 244-295 524-575 (577)
97 PTZ00134 40S ribosomal protein 37.1 32 0.0007 35.9 3.3 41 246-286 31-74 (154)
98 PRK05182 DNA-directed RNA poly 36.9 36 0.00079 39.2 4.0 54 243-298 247-302 (310)
99 TIGR03631 bact_S13 30S ribosom 36.8 33 0.00072 34.0 3.2 40 246-285 16-58 (113)
100 smart00278 HhH1 Helix-hairpin- 36.6 25 0.00054 25.7 1.7 17 247-263 3-19 (26)
101 KOG2534|consensus 35.1 37 0.00081 39.3 3.6 33 248-282 100-132 (353)
102 COG1200 RecG RecG-like helicas 34.9 24 0.00052 44.4 2.3 31 245-276 10-40 (677)
103 TIGR01259 comE comEA protein. 34.2 33 0.00071 34.1 2.7 30 247-276 70-103 (120)
104 smart00734 ZnF_Rad18 Rad18-lik 32.4 12 0.00027 27.7 -0.4 22 952-973 2-23 (26)
105 COG1796 POL4 DNA polymerase IV 30.5 26 0.00056 40.5 1.5 50 245-294 93-145 (326)
106 cd00080 HhH2_motif Helix-hairp 30.5 47 0.001 30.3 2.9 26 247-274 24-49 (75)
107 COG0632 RuvA Holliday junction 30.2 37 0.00079 37.0 2.5 43 210-262 80-125 (201)
108 KOG3993|consensus 29.8 20 0.00042 42.7 0.4 23 952-974 296-319 (500)
109 PRK14602 ruvA Holliday junctio 29.6 48 0.001 35.9 3.3 54 248-301 77-133 (203)
110 CHL00137 rps13 ribosomal prote 29.5 54 0.0012 33.0 3.3 41 245-285 17-60 (122)
111 PRK02515 psbU photosystem II c 29.1 41 0.00089 34.3 2.4 54 214-277 40-93 (132)
112 PRK05179 rpsM 30S ribosomal pr 29.1 54 0.0012 33.0 3.3 40 246-285 18-60 (122)
113 PRK14601 ruvA Holliday junctio 28.9 34 0.00074 36.6 2.0 54 197-262 69-125 (183)
114 PRK14351 ligA NAD-dependent DN 27.5 72 0.0016 40.7 4.7 45 250-296 533-579 (689)
115 TIGR03629 arch_S13P archaeal r 27.0 60 0.0013 33.6 3.3 42 245-286 21-65 (144)
116 PRK14606 ruvA Holliday junctio 26.9 55 0.0012 35.1 3.1 63 237-301 67-132 (188)
117 PRK14604 ruvA Holliday junctio 26.8 55 0.0012 35.3 3.1 63 237-301 67-132 (195)
118 PF12171 zf-C2H2_jaz: Zinc-fin 26.4 25 0.00054 25.7 0.3 21 951-971 1-22 (27)
119 PRK14603 ruvA Holliday junctio 25.9 57 0.0012 35.3 3.0 63 237-301 66-131 (197)
120 PRK14601 ruvA Holliday junctio 25.1 64 0.0014 34.6 3.1 63 237-301 67-132 (183)
121 KOG2841|consensus 24.8 78 0.0017 35.4 3.7 50 247-298 197-248 (254)
122 PRK04053 rps13p 30S ribosomal 24.6 73 0.0016 33.2 3.3 41 246-286 26-69 (149)
123 PRK13901 ruvA Holliday junctio 24.4 67 0.0015 34.8 3.2 63 237-301 66-131 (196)
124 PRK14606 ruvA Holliday junctio 23.9 46 0.001 35.7 1.8 53 198-262 70-125 (188)
125 PRK08097 ligB NAD-dependent DN 23.5 1.1E+02 0.0023 38.4 5.0 49 248-297 428-479 (562)
126 PRK07956 ligA NAD-dependent DN 23.1 98 0.0021 39.4 4.7 20 246-265 480-499 (665)
127 PRK14600 ruvA Holliday junctio 22.6 54 0.0012 35.1 2.1 62 237-301 67-131 (186)
128 COG0632 RuvA Holliday junction 22.5 69 0.0015 34.9 2.8 56 247-302 75-133 (201)
129 PRK13901 ruvA Holliday junctio 22.4 49 0.0011 35.8 1.7 55 196-262 67-124 (196)
130 COG0099 RpsM Ribosomal protein 22.2 90 0.0019 31.5 3.3 38 245-282 17-54 (121)
131 PRK14604 ruvA Holliday junctio 22.1 55 0.0012 35.3 2.0 54 197-262 69-125 (195)
132 PF05605 zf-Di19: Drought indu 22.1 26 0.00056 29.8 -0.4 25 951-975 2-27 (54)
133 TIGR00084 ruvA Holliday juncti 21.5 52 0.0011 35.3 1.7 43 210-262 79-124 (191)
134 PF01367 5_3_exonuc: 5'-3' exo 21.5 19 0.0004 35.1 -1.5 34 233-266 1-39 (101)
135 PRK14603 ruvA Holliday junctio 20.9 61 0.0013 35.0 2.0 53 198-262 69-124 (197)
136 PF09237 GAGA: GAGA factor; I 20.6 20 0.00043 31.1 -1.3 29 948-976 21-51 (54)
137 PF08004 DUF1699: Protein of u 20.6 1.6E+02 0.0034 30.2 4.6 36 59-101 30-65 (131)
138 PF12836 HHH_3: Helix-hairpin- 20.1 77 0.0017 27.9 2.2 30 247-276 16-49 (65)
No 1
>KOG2095|consensus
Probab=100.00 E-value=1.6e-73 Score=657.80 Aligned_cols=403 Identities=42% Similarity=0.636 Sum_probs=343.6
Q ss_pred CCcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCC
Q psy16215 2 TSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVR 81 (1041)
Q Consensus 2 ~~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~ 81 (1041)
..|||+||||||||||||++++|+|+++||||+||+ +||||||+||++||+++|++.||+++||+|+++|||...
T Consensus 14 ~~RVIahVDMDcFyaQVEq~r~P~lr~~PlaVvQ~n-----gIIAVsYeARa~GV~R~M~v~EAK~kCPqLvlv~v~~~~ 88 (656)
T KOG2095|consen 14 SLRVIAHVDMDCFYAQVEQRRNPELRSKPLAVVQYN-----GIIAVSYEARAFGVKRLMTVDEAKKKCPQLVLVHVPVAR 88 (656)
T ss_pred ccceEEEecchhhHHHHHhhcCchhccCceEEEEee-----eEEEEehhhhhhCCchhhhHHHHHhhCCceEEeeccccc
Confidence 469999999999999999999999999999999997 699999999999999999999999999999999999988
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhh----ccccccccccccccccCCCCCCc-----
Q psy16215 82 GKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKS----IGHIAASQLSNTFVVGFGPDNND----- 152 (1041)
Q Consensus 82 ~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~----~~~~~~~~L~~~~~~g~~~~~~~----- 152 (1041)
+++|...||.++.+|+++|..|.|+||++++||+|||+|.++.+++.+ .++.....+..+++.++++...-
T Consensus 89 ~ka~~~~YR~as~ev~~~L~~y~~viek~~~dea~ld~tasvder~q~L~s~~~~~~~~~~p~~~~~~~~s~~~~~~~~~ 168 (656)
T KOG2095|consen 89 EKADLPKYREASEEVKESLEPYRPVIEKASKDEAFLDLTASVDERLQDLQSDEFNMLLEEPPYGLIYGLPSALPNTREAT 168 (656)
T ss_pred ccchhhhhhhhHHHHHHHHhhhHHHHHHHhhhhhhhhHHHHHHHHHHHHhhhhhhhhhhccchhcccCCccccchhhhhh
Confidence 999999999999999999999999999999999999999999988765 34556666666777777763311
Q ss_pred ----hhhhhhcchhhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCC
Q psy16215 153 ----EDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQ 228 (1041)
Q Consensus 153 ----e~~r~~g~~~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPn 228 (1041)
+..+-+.+..|+... ..+|++++|++|+.||++||++|+.+||||||+|||+||+|||||+.++|||
T Consensus 169 ~~e~~~~~ee~~~~~~~~~---------d~~~~d~~L~iGa~Iv~EiR~~i~~elg~tCSAGIa~NKmLAKLvsg~nKPn 239 (656)
T KOG2095|consen 169 NSENPLMREEIVSLWIEND---------DFDWDDVRLLIGAQIVKEIRDAIKLELGYTCSAGIAHNKMLAKLVSGRNKPN 239 (656)
T ss_pred hhccccchhhHhhhhhhcc---------ccCchhhhhHHHHHHHHHHHHHHHHHhCceeeccccccHHHHHHHhccCCCC
Confidence 111223334454221 1248999999999999999999999999999999999999999999999999
Q ss_pred ceEEeccchHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccc
Q psy16215 229 KQSILPQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNAR 308 (1041)
Q Consensus 229 Gqtvl~p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~ 308 (1041)
.||||+...+++||..|||.++|++|+++++.+++.|||.++|||++++...|++.||.+.|.|||..++|+|.++|.++
T Consensus 240 qQTil~~~~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse~~L~~~fg~~~g~~l~~la~Gid~s~V~pr 319 (656)
T KOG2095|consen 240 QQTILPNTYVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSETQLQKKFGEKNGTWLRNLARGIDNSPVRPR 319 (656)
T ss_pred cceecchHHHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCHHHHHHhhCcchhHHHHHHhcccCCCccccC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cCCcceeeEEeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEE--EEEcCCCCceeEEEEEeCCCCc
Q psy16215 309 LVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVS--FTQETDGKVNSCSRSIALASYK 386 (1041)
Q Consensus 309 ~ppKSIssErTF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLk--LR~sd~g~~~s~SRSl~LpT~D 386 (1041)
..||||+++++|++...+.+.+++..||.+++.++..||-.++.++.+.+.++.++ +... -++...+..++
T Consensus 320 ~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~as~l~~~~~~~~~-------ss~~~~~~~~d 392 (656)
T KOG2095|consen 320 GLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRASTLVVSRSLFKL-------SSQITGLVDYD 392 (656)
T ss_pred CCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccccceEEeecccccc-------ccccccccchh
Confidence 99999999999998667899999999999999999999999988999999999998 2211 12333333455
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcCCCCCCC
Q psy16215 387 LQDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSASKFSPLGS 429 (1041)
Q Consensus 387 ae~L~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSdLvp~~~ 429 (1041)
...++.....++..+. +..+...+..+++.+..|.....
T Consensus 393 ~~~~~~~~~~~ir~~~----~~~~~~~~~~l~~~~~sf~~~~~ 431 (656)
T KOG2095|consen 393 DHKKVYDKLVKIRNIV----DVSFSFKLTLLSVYFKSFQAKNE 431 (656)
T ss_pred hhhhhhhhhhhcccch----hcccchhHHHHHHHHhccccccc
Confidence 5555555555444111 12245556667777777765443
No 2
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=2.4e-71 Score=632.24 Aligned_cols=384 Identities=26% Similarity=0.408 Sum_probs=343.8
Q ss_pred CCcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCC
Q psy16215 2 TSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVR 81 (1041)
Q Consensus 2 ~~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~ 81 (1041)
.+|+|+||||||||||||++++|+|+++||||++.+.++++.|+||||+||++||++||++++|+++||++++++
T Consensus 3 ~~r~i~hiD~d~Fyasve~~~~p~l~~~Pv~V~~~~~~~~~~v~a~ny~Ar~~GV~~Gm~~~~A~~lcP~l~~~~----- 77 (407)
T PRK01810 3 KGRVIFHVDMNSFFASVEIAYDPSLQGKPLAVAGNEKERKGIIVTCSYEARAYGIRTTMPLWEAKRLCPQLIVRR----- 77 (407)
T ss_pred CCCEEEEEecCcHHHhHHhhhCccccCCcEEEeCCCCCCCeEEEEcCHHHHHhCCCCCChHHHHHHHCCCeEEEC-----
Confidence 579999999999999999999999999999998754335688999999999999999999999999999999987
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcch
Q psy16215 82 GKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVM 161 (1041)
Q Consensus 82 ~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~ 161 (1041)
+|++.|+++|++|++++++|+|.||++||||+|||||++.+
T Consensus 78 --~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~------------------------------------- 118 (407)
T PRK01810 78 --PNFDRYREASRQMFQILSEFTPLVQPVSIDEGYLDITDCYA------------------------------------- 118 (407)
T ss_pred --CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEeccCccc-------------------------------------
Confidence 89999999999999999999999999999999999998743
Q ss_pred hhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHh
Q psy16215 162 EWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSML 241 (1041)
Q Consensus 162 ~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~f 241 (1041)
+|+ +..+|++||++|++++|++||||||+||++||||++.+||+|++++.++++..|
T Consensus 119 -----~~~------------------~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~~~~~~ 175 (407)
T PRK01810 119 -----LGS------------------PLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKRDVPEM 175 (407)
T ss_pred -----cCC------------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHHHHHHH
Confidence 221 246899999999999999999999999999999999999999999999999999
Q ss_pred hhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccC--CcceeeEEe
Q psy16215 242 YANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLV--SKSIGCCKR 319 (1041)
Q Consensus 242 L~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~p--pKSIssErT 319 (1041)
|+++||++|||||+++.++ |..+||+|++||+++|...|+++|| ..|.++|+.++|+|.++|.+..+ ++||+.+++
T Consensus 176 L~~lpv~~l~giG~~~~~~-L~~~Gi~tigdL~~~~~~~L~~rfG-~~g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~ 253 (407)
T PRK01810 176 LWPLPVGEMHGIGEKTAEK-LKDIGIQTIGDLAKADEHILRAKLG-INGVRLQRRANGIDDRPVDPEAIYQFKSVGNSTT 253 (407)
T ss_pred HHhCCHhhcCCcCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHHHh-HHHHHHHHHhcCCCCCCCCCCCCCCCceecceEE
Confidence 9999999999999999998 7999999999999999999999999 68999999999999999987543 599999999
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHH
Q psy16215 320 FPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVIN 399 (1041)
Q Consensus 320 F~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~ 399 (1041)
|+. ++.+.++|..+|..|+.+|+.||+++ ++.|++|+|++++.++. ..+.++++..|+++...|+..+..+|+
T Consensus 254 ~~~--~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~lr~~~~~-~~~~~~~l~~pt~~~~~l~~~~~~ll~ 326 (407)
T PRK01810 254 LSH--DMDEEKELLDVLRRLSKSVSKRLQKK----TVVSYNVQIMIRYHDRR-TITRSKTLKNPIWEKRDIFQAASRLFK 326 (407)
T ss_pred CCC--CCCCHHHHHHHHHHHHHHHHHHHHHc----CCccceeEEEEEECCCC-ceEEEEECCCCCCCHHHHHHHHHHHHH
Confidence 996 68999999999999999999999998 99999999999998863 344555566678999999999999999
Q ss_pred HhccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcCCCCCCCCCCCCCCCCCCcCcCCCCCcccCccccccCC
Q psy16215 400 KTNSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFFKPQDHPEPMTSEHSSLPEQSTNHDSKKRDKTLLNFNQ 474 (1041)
Q Consensus 400 rL~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLFd~~~~~e~~~se~lS~a~D~iN~~s~k~gktll~~g~ 474 (1041)
+++. ..+||++||++++|.+...+..|.+||+.... .....++..+|.+| .++|...+..|.
T Consensus 327 ~~~~-------~~~vr~lgv~~~~l~~~~~~~~q~~Lf~~~~~---~~~~~l~~~id~l~---~r~G~~ai~~a~ 388 (407)
T PRK01810 327 QHWN-------GDPVRLLGVTATDLEWKTEAVKQLDLFSFEED---AKEEPLLAVIDQIN---DKYGMPLLQRGS 388 (407)
T ss_pred hccC-------CCCEEEEEEEEecCccccccccccccccchhh---hhHHHHHHHHHHHH---HhcCcchhhhHH
Confidence 9873 56899999999999976433357899973211 23456788899999 899999998773
No 3
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=4.7e-70 Score=624.50 Aligned_cols=382 Identities=23% Similarity=0.341 Sum_probs=342.7
Q ss_pred CCCcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCC
Q psy16215 1 MTSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSV 80 (1041)
Q Consensus 1 ~~~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~ 80 (1041)
|..|+|+||||||||||||++++|+|+++||||+.. .++.|++|||+||++||++||++++|+++||++++++
T Consensus 33 ~~~~~i~hiD~d~Fyasve~~~~p~l~~~Pv~v~~~---~~~~V~a~ny~Ar~~GV~~GM~~~~A~~lcP~l~~v~---- 105 (419)
T PRK02794 33 LYTLSIAHIDCDAFYASVEKRDNPELRDKPVIIGGG---KRGVVSTACYIARIHGVRSAMPMFKALKLCPDAVVIK---- 105 (419)
T ss_pred ccCCEEEEEcCCcHHHHHHhhhCccccCCcEEEecC---CCeEEEecCHHHHHhCCCcCCHHHHHHHHCCCcEEEC----
Confidence 456899999999999999999999999999999763 3688999999999999999999999999999999987
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcc
Q psy16215 81 RGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGV 160 (1041)
Q Consensus 81 ~~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~ 160 (1041)
+|++.|+++|++|++++++|+|.||++||||+|||||++.+
T Consensus 106 ---~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~------------------------------------ 146 (419)
T PRK02794 106 ---PDMEKYVRVGREVRAMMQALTPLVEPLSIDEAFLDLSGTER------------------------------------ 146 (419)
T ss_pred ---CCHHHHHHHHHHHHHHHHHhCcceeeccCCeEEEeccchhh------------------------------------
Confidence 89999999999999999999999999999999999998754
Q ss_pred hhhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHH
Q psy16215 161 MEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSM 240 (1041)
Q Consensus 161 ~~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~ 240 (1041)
+|+.. ...++++||++|++++||+||+|||+||++||||++.+||+|++++.++++.+
T Consensus 147 ------l~g~~----------------~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~~~~~ 204 (419)
T PRK02794 147 ------LHGAP----------------PAVVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRAEALA 204 (419)
T ss_pred ------hcCCC----------------HHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHHHHHH
Confidence 45432 13467899999999999999999999999999999999999999999999999
Q ss_pred hhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeC
Q psy16215 241 LYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRF 320 (1041)
Q Consensus 241 fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF 320 (1041)
||+++||++|||||+++.++ |.++||+|++||+++|...|+++|| ..|.++|+.++|+|.++|.+..++|||+.+++|
T Consensus 205 ~L~~lPl~~L~GiG~~~~~~-L~~~GI~tigdL~~l~~~~L~~rfG-~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl 282 (419)
T PRK02794 205 FLAPKPVGIIWGVGPATAAR-LARDGIRTIGDLQRADEADLMRRFG-SMGLRLWRLARGIDDRKVSPDREAKSVSAETTF 282 (419)
T ss_pred HHhcCChhhhCCCCHHHHHH-HHHhccchHHHHhhCCHHHHHHHHh-HHHHHHHHHhCCCCCCCCccCCCCceeeeeEEC
Confidence 99999999999999999998 7999999999999999999999999 589999999999999999988889999999999
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHHH
Q psy16215 321 PGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINK 400 (1041)
Q Consensus 321 ~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~r 400 (1041)
+. ++.+.++|..+|..|+.+|+.||+++ ++.+++|+|++++.++. ..+.+.++..|+++.+.|+..+..+|++
T Consensus 283 ~~--~~~~~~~l~~~l~~L~~~l~~rL~~~----~~~~~~l~l~l~~~~~~-~~~~~~~l~~pt~~~~~l~~~~~~ll~~ 355 (419)
T PRK02794 283 ET--DLSDFEDLEPILWRLSEKVSRRLKAA----GLAGRTVTLKLKTADFR-LRTRRRTLEDPTQLADRIFRTARELLEK 355 (419)
T ss_pred CC--CCCCHHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEECCCC-ceEEEEECCCCcCCHHHHHHHHHHHHHh
Confidence 86 68999999999999999999999998 99999999999988762 2344555555788999999999999999
Q ss_pred hccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcCCCCCCCCCCCCCCCCCCcCcCCCCCcccCccccccCC
Q psy16215 401 TNSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFFKPQDHPEPMTSEHSSLPEQSTNHDSKKRDKTLLNFNQ 474 (1041)
Q Consensus 401 L~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLFd~~~~~e~~~se~lS~a~D~iN~~s~k~gktll~~g~ 474 (1041)
++. ..+||+|||++++|.+... ..+.+||+... .+...++..+|.+| .|+|+..+..|.
T Consensus 356 ~~~-------~~~vr~igv~~~~l~~~~~-~~q~~LF~~~~----~~~~~l~~~id~l~---~r~G~~ai~~a~ 414 (419)
T PRK02794 356 ETD-------GTAFRLIGIGVSDLSPADE-ADPPDLLDPQA----TRRAAAERAIDALR---AKFGAAAVETGR 414 (419)
T ss_pred ccc-------CCCEEEEEEEEecCCCccc-cccccccCcch----hhHHHHHHHHHHHH---HhhCcchhhhHh
Confidence 863 5689999999999997543 13688997431 23446788899999 899999888774
No 4
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=3.2e-70 Score=623.45 Aligned_cols=382 Identities=22% Similarity=0.352 Sum_probs=341.8
Q ss_pred CcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCC
Q psy16215 3 SRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRG 82 (1041)
Q Consensus 3 ~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~ 82 (1041)
.|+|+||||||||||||+..+|+|+++||||++.....+++|+||||+||++||++||++++|+++||++++++
T Consensus 2 ~r~i~hiD~d~Ffasve~~~~P~l~~~Pv~V~~~~~~~~~~v~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~------ 75 (409)
T PRK03103 2 ERVILLVDMQSFYASVEKAANPELKGRPVIVSGDPERRSGVVLAACPLAKAYGVKTAERLWEAQQKCPDLVVVK------ 75 (409)
T ss_pred CCEEEEEecchHHHhHhcccChhhcCCcEEEeccCCCCCEEEEEcCHHHHHhCCCCCChHHHHHHHCCCeEEEC------
Confidence 69999999999999999999999999999998753234578999999999999999999999999999999987
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchh
Q psy16215 83 KADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVME 162 (1041)
Q Consensus 83 k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~ 162 (1041)
+|++.|+++|++|++++++|+|.||++||||+|||||++..
T Consensus 76 -~d~~~y~~~s~~i~~~l~~~sp~ve~~siDe~~lDvt~~~~-------------------------------------- 116 (409)
T PRK03103 76 -PRMQRYIDVSLQITRILEDFTDLVEPFSIDEQFLDVTGSQK-------------------------------------- 116 (409)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCccceecCCCeeEeeccchhh--------------------------------------
Confidence 89999999999999999999999999999999999999854
Q ss_pred hcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccC---CCCCceEEeccchHH
Q psy16215 163 WLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGL---HKPQKQSILPQSSVS 239 (1041)
Q Consensus 163 W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~---aKPnGqtvl~p~~v~ 239 (1041)
+|++ ...+|++||++|++++||+||||||+|+++||||++. +||+|++++.++++.
T Consensus 117 ----~~~~-----------------~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~~~~ 175 (409)
T PRK03103 117 ----LFGS-----------------PLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKEDVP 175 (409)
T ss_pred ----cCCC-----------------HHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHHHHH
Confidence 3442 2468999999999999999999999999999999998 999999999999999
Q ss_pred HhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccC--CcceeeE
Q psy16215 240 MLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLV--SKSIGCC 317 (1041)
Q Consensus 240 ~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~p--pKSIssE 317 (1041)
.||+++||++|||||+++.++ |+.+||+|+|||+++|...|+++|| ..|.++|+.++|+|.++|.+..+ +|||+.+
T Consensus 176 ~~L~~lpi~~l~gig~~~~~~-L~~~Gi~tigdl~~~~~~~L~~~fG-~~~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~ 253 (409)
T PRK03103 176 ADLWPLPVRKLFGVGSRMEKH-LRRMGIRTIGQLANTPLERLKKRWG-INGEVLWRTANGIDYSPVTPHSLDRQKAIGHQ 253 (409)
T ss_pred HHHHcCCHhhcCCccHHHHHH-HHHcCCCCHHHHhcCCHHHHHHHHC-HHHHHHHHHhcCCCCCcCCcccCCCCCccCCC
Confidence 999999999999999999998 8999999999999999999999999 68999999999999999998754 5899999
Q ss_pred EeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCc--eeEEEEEeCCCCcHHHHHHHHH
Q psy16215 318 KRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKV--NSCSRSIALASYKLQDIVEVSM 395 (1041)
Q Consensus 318 rTF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~--~s~SRSl~LpT~Dae~L~~~A~ 395 (1041)
.+|+. ++.+.++|..+|..|+.+|+.||++. +..+++|+|++++.++... .+.+..+..|+++.+.|+..+.
T Consensus 254 ~t~~~--~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~lr~~~~~~~~~~~~~~~l~~pt~~~~~l~~~~~ 327 (409)
T PRK03103 254 MTLPR--DYRGFEEIKVVLLELCEEVCRRARAK----GYMGRTVSVSLRGADFDWPTGFSRQMTLPEPTNLAMEVYEAAC 327 (409)
T ss_pred eECCC--CCCCHHHHHHHHHHHHHHHHHHHHHh----CCceeEEEEEEEeCCCcCCCCcceeeecCCCCCCHHHHHHHHH
Confidence 99986 68999999999999999999999998 9999999999999875321 3344455557889999999999
Q ss_pred HHHHHhccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcCCCCCCCCCCCCCCCCCCcCcCCCCCcccCccccccCCC
Q psy16215 396 QVINKTNSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFFKPQDHPEPMTSEHSSLPEQSTNHDSKKRDKTLLNFNQQ 475 (1041)
Q Consensus 396 ~LL~rL~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLFd~~~~~e~~~se~lS~a~D~iN~~s~k~gktll~~g~~ 475 (1041)
.+|++++. ..+||+|||++++|.+... .|.+||+... ....++..+|.+| .++|...+..+..
T Consensus 328 ~ll~~~~~-------~~~vr~lgv~~~~l~~~~~--~q~~LF~~~~-----~~~~l~~~ld~l~---~r~G~~av~~~~~ 390 (409)
T PRK03103 328 KLFHRHWD-------GKPVRRVGVTLSNLVSDDV--WQLSLFGDRE-----RKRSLGYVMDDIK---NRFGPTAILRASS 390 (409)
T ss_pred HHHHhccc-------CCCceEEEEEEeCCCCCcc--cCCCcccchh-----hHHHHHHHHHHHH---HhhChhHHhhHHh
Confidence 99999873 5689999999999997533 4789997531 2346778899999 8999999987743
No 5
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=9.7e-70 Score=616.43 Aligned_cols=378 Identities=19% Similarity=0.310 Sum_probs=338.3
Q ss_pred CCcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCC
Q psy16215 2 TSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVR 81 (1041)
Q Consensus 2 ~~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~ 81 (1041)
+.|+|+||||||||||||++.+|+|+++||||++ ++|+||||+||++||++||++++|+++||++++++
T Consensus 2 ~~~~i~hiD~d~Fyas~e~~~~p~l~~~Pv~V~~------~~V~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~----- 70 (396)
T PRK03858 2 ADASILHADLDSFYASVEQRDDPALRGRPVIVGG------GVVLAASYEAKAYGVRTAMGGRQARRLCPQAVVVP----- 70 (396)
T ss_pred CCCEEEEEccChHHHHHHhhhCccccCCcEEEeC------CEEEEeCHHHHHhCCCCCChHHHHHHHCCCeEEEC-----
Confidence 5789999999999999999999999999999963 68999999999999999999999999999999987
Q ss_pred CCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcch
Q psy16215 82 GKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVM 161 (1041)
Q Consensus 82 ~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~ 161 (1041)
+|++.|+++|++|++++.+|+|.||++||||+|||||++.+
T Consensus 71 --~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldvt~~~~------------------------------------- 111 (396)
T PRK03858 71 --PRMSAYSRASKAVFEVFRDTTPLVEGLSIDEAFLDVGGLRR------------------------------------- 111 (396)
T ss_pred --CCHHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEcccccc-------------------------------------
Confidence 89999999999999999999999999999999999999753
Q ss_pred hhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHh
Q psy16215 162 EWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSML 241 (1041)
Q Consensus 162 ~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~f 241 (1041)
+|++ +..+|++||++|++++|++||||||+||++||||++.+||+|++++.++++..|
T Consensus 112 -----~~~~-----------------~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~~~~~~ 169 (396)
T PRK03858 112 -----ISGT-----------------PVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPDRELAF 169 (396)
T ss_pred -----ccCC-----------------HHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcHHHHHH
Confidence 3443 246899999999999999999999999999999999999999999999999999
Q ss_pred hhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCC
Q psy16215 242 YANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFP 321 (1041)
Q Consensus 242 L~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~ 321 (1041)
|+++||++|||||+++.++ |+++||+|++||+++|+..|.++||...|.+||++++|+|.++|.+..++|||+.+++|+
T Consensus 170 L~~lpl~~l~Gig~~~~~~-L~~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~t~~ 248 (396)
T PRK03858 170 LHPLPVRRLWGVGPVTAAK-LRAHGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALG 248 (396)
T ss_pred HhcCChhhcCCCCHHHHHH-HHHhCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcC
Confidence 9999999999999999998 799999999999999999999999966899999999999999998888899999999998
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHHHh
Q psy16215 322 GKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKT 401 (1041)
Q Consensus 322 ~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~rL 401 (1041)
. ++.+.+++..+|..|+.+|+.||+++ ++.+++|+|++++.++. ..+.+.++..|+++...|++.+..+|+++
T Consensus 249 ~--~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~-~~~~~~~l~~~t~~~~~l~~l~~~ll~~~ 321 (396)
T PRK03858 249 R--GPNSPAEVDAVVVALVDRVARRMRAA----GRTGRTVVLRLRFDDFT-RATRSHTLPRPTASTATLLAAARDLVAAA 321 (396)
T ss_pred C--CCCCHHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEeCCCC-EEEEEEECCCCcCCHHHHHHHHHHHHHhh
Confidence 5 68999999999999999999999998 99999999999998863 23334445556889999999999999997
Q ss_pred ccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhc-CCCCCCCCCCCCCCCCCCcCcCCCCCcccCccccccC
Q psy16215 402 NSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQF-FKPQDHPEPMTSEHSSLPEQSTNHDSKKRDKTLLNFN 473 (1041)
Q Consensus 402 ~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DL-Fd~~~~~e~~~se~lS~a~D~iN~~s~k~gktll~~g 473 (1041)
+.. ....+||++||.+++|.+... .|.+| |+.. .....++..+|.+| .++|...+..+
T Consensus 322 ~~~----~~~~~irligv~~~~l~~~~~--~q~~L~f~~~-----~~~~~l~~~id~l~---~r~G~~~i~~~ 380 (396)
T PRK03858 322 APL----IAERGLTLVGFAVSNLDDDGA--QQLELPFGLR-----RPGSALDAALDAVR---DRFGNAAVTRA 380 (396)
T ss_pred hhc----cCCCCeEEEEEEeecCCcccc--cccCCCccch-----hhHHHHHHHHHHHH---HhhCchhhhhH
Confidence 521 013589999999999987543 35677 7542 12346788899999 89999988876
No 6
>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=100.00 E-value=5.1e-69 Score=613.77 Aligned_cols=343 Identities=28% Similarity=0.415 Sum_probs=311.8
Q ss_pred CcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCC
Q psy16215 3 SRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRG 82 (1041)
Q Consensus 3 ~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~ 82 (1041)
.|+|+||||||||||||++++|+|+++||||++++ .++++|+||||+||++||++||++++|+++||++++++
T Consensus 46 ~r~i~hiD~d~FyasvE~~~~p~L~~kPv~V~~~~-~~~~~V~a~sy~AR~~GV~~gM~~~~A~~lcP~l~vv~------ 118 (404)
T cd01701 46 QRIIMHVDFDCFFVSVSIRNRPDLKGKPVAVCHGK-GPNSEIASCNYEARSYGIKNGMWVGQAKKLCPQLVTLP------ 118 (404)
T ss_pred CcEEEEEeCchHHHHHHhhhCccccCCCEEEecCC-CCCeEEEecCHHHHhcCCCCCCcHHHHHHHCCCcEEEC------
Confidence 58999999999999999999999999999999864 34688999999999999999999999999999999987
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchh
Q psy16215 83 KADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVME 162 (1041)
Q Consensus 83 k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~ 162 (1041)
+|++.|+++|++|+++|++|+|.||++||||+|||||+..+.
T Consensus 119 -~~~~~Y~~~s~~i~~il~~~s~~ve~~SiDE~~lDvt~~~~~------------------------------------- 160 (404)
T cd01701 119 -YDFEAYEEVSLTFYEILASYTDNIEAVSCDEALIDITSLLEE------------------------------------- 160 (404)
T ss_pred -CChHHHHHHHHHHHHHHHHhCCceEEcccceEEEEccccccc-------------------------------------
Confidence 899999999999999999999999999999999999987520
Q ss_pred hcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhh
Q psy16215 163 WLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLY 242 (1041)
Q Consensus 163 W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL 242 (1041)
+|++ +..+|++||++|++++||+||||||+||++||||++.+||+|++++.++++..||
T Consensus 161 ----~~~~-----------------~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~~~~~~L 219 (404)
T cd01701 161 ----TYEL-----------------PEELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEKVEEFL 219 (404)
T ss_pred ----ccCC-----------------HHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHHHHHHHh
Confidence 2322 2578999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccCCHHHHHHHHHhCCCccchhhhhCC--HHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeC
Q psy16215 243 ANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFS--LKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRF 320 (1041)
Q Consensus 243 ~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp--~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF 320 (1041)
+++||++|||||++++++ |..+||.|++||+++| ...|+++||...|.+||+.++|+|.++|.+..++|||+.+++|
T Consensus 220 ~~lPv~~l~GIG~~~~~~-L~~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf 298 (404)
T cd01701 220 SQLKVGDLPGVGSSLAEK-LVKLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINY 298 (404)
T ss_pred hcCCHhHhCCCCHHHHHH-HHHcCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeC
Confidence 999999999999999998 8999999999999999 9999999997689999999999999999988889999999999
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCC------------CCceeEEEEEeC--CCCc
Q psy16215 321 PGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETD------------GKVNSCSRSIAL--ASYK 386 (1041)
Q Consensus 321 ~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~------------g~~~s~SRSl~L--pT~D 386 (1041)
+. ++.+.+++..+|..|+++|+.||+++ +..|++|+|++++... +.+.+++++.++ |+++
T Consensus 299 ~~--~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~d 372 (404)
T cd01701 299 GI--RFTNVDDVEQFLQRLSEELSKRLEES----NVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATDD 372 (404)
T ss_pred CC--CCCCHHHHHHHHHHHHHHHHHHHHHc----CCceeeEEEEEEeccccCccccccccccCCCcEEeeeeECCCCCCC
Confidence 85 68899999999999999999999998 9999999999997221 012355565555 6889
Q ss_pred HHHHHHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcCC
Q psy16215 387 LQDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSASKF 424 (1041)
Q Consensus 387 ae~L~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSdL 424 (1041)
...|+..+..+|++++. ...+||+|||++++|
T Consensus 373 ~~~i~~~a~~ll~~~~~------~~~~vR~lgv~~~~l 404 (404)
T cd01701 373 SGVIGTEAKKLFRDLSI------PPEELRGVGIQVTKL 404 (404)
T ss_pred HHHHHHHHHHHHHhccC------CCCCeeEEEEEEecC
Confidence 99999999999999863 135899999999886
No 7
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.3e-68 Score=598.19 Aligned_cols=346 Identities=27% Similarity=0.402 Sum_probs=317.6
Q ss_pred CcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCC
Q psy16215 3 SRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRG 82 (1041)
Q Consensus 3 ~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~ 82 (1041)
+|+|+||||||||||||+..+|+|+++||||.+.. .++.|++|||+||++||++||++++|+++||++++++
T Consensus 2 ~r~i~hiD~d~F~as~e~~~~p~l~~~Pvvv~~~~--~~~~V~a~n~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~------ 73 (347)
T PRK14133 2 DRVIIHVDMDAFFASVEQMDNPKLKGKPVIVGGIS--ERGVVSTCSYEARKYGVHSAMPVFMAKKRCPHGIFLP------ 73 (347)
T ss_pred CCEEEEEecChHHHHHHhhhCccccCCCEEEecCC--CCcEEEECCHHHHhcCCCCCChHHHHHHHCCCcEEEC------
Confidence 69999999999999999999999999999998643 4678999999999999999999999999999999987
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchh
Q psy16215 83 KADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVME 162 (1041)
Q Consensus 83 k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~ 162 (1041)
+|++.|+++|++|++++++|+|.||++||||+||||++...
T Consensus 74 -~d~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ldv~~~~~-------------------------------------- 114 (347)
T PRK14133 74 -VRHERYKEVSKNIFKILYEVTPIVEPVSIDEAYLDITNIKE-------------------------------------- 114 (347)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEccCCCC--------------------------------------
Confidence 89999999999999999999999999999999999997520
Q ss_pred hcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhh
Q psy16215 163 WLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLY 242 (1041)
Q Consensus 163 W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL 242 (1041)
+ +..+|++||++|++++||+||+|||+||++||||++++||+|++++.++++..||
T Consensus 115 -------~-----------------~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~~~~~~L 170 (347)
T PRK14133 115 -------E-----------------PIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDMIPDIL 170 (347)
T ss_pred -------C-----------------HHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHHHHHHHH
Confidence 0 2468999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCCC
Q psy16215 243 ANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPG 322 (1041)
Q Consensus 243 ~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~~ 322 (1041)
+++||+++||||+++.++ |+++||+|++||+++|...|+++|| ..|.++|+.++|+|.+++.+..++|||+.+++|+.
T Consensus 171 ~~lpv~~l~gig~~~~~~-L~~~Gi~ti~dl~~l~~~~L~~rfG-~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~ 248 (347)
T PRK14133 171 KPLPISKVHGIGKKSVEK-LNNIGIYTIEDLLKLSREFLIEYFG-KFGVEIYERIRGIDYREVEVSRERKSIGKETTLKK 248 (347)
T ss_pred HhCCccccCCCCHHHHHH-HHHcCCccHHHHhhCCHHHHHHHHh-HHHHHHHHHhCCCCCCCCCCCCCCcceEeeEEcCC
Confidence 999999999999999998 8999999999999999999999999 68999999999999999999889999999999986
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHHHhc
Q psy16215 323 KTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKTN 402 (1041)
Q Consensus 323 r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~rL~ 402 (1041)
++.+.+++..+|..|+++|+.||+++ ++.+++|+|++++.++. ..+.+++++.|+++.+.|+..+..+|++++
T Consensus 249 --~~~~~~~l~~~l~~L~~~l~~rL~~~----~~~~~~l~l~l~~~~~~-~~~~~~~l~~~t~~~~~l~~l~~~lle~~~ 321 (347)
T PRK14133 249 --DTKDKEELKKYLKDFSNIISEELKKR----NLYGKTVTVKIKTSDFQ-THTKSKTLNDYIRDKEEIYNVACEILEHIN 321 (347)
T ss_pred --CCCCHHHHHHHHHHHHHHHHHHHHhc----CCCcceEEEEEEECCCC-eeEEEEECCCCcCCHHHHHHHHHHHHHhcc
Confidence 79999999999999999999999998 99999999999988752 233445555578899999999999999987
Q ss_pred cCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcC
Q psy16215 403 SAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFF 437 (1041)
Q Consensus 403 ~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLF 437 (1041)
. ..+||.|||++++|.+... .+.+||
T Consensus 322 ~-------~~~vr~lgl~~~~l~~~~~--~q~~l~ 347 (347)
T PRK14133 322 I-------KEPIRLIGLSVSNLSENKI--EQLSFL 347 (347)
T ss_pred C-------CCCEEEEEEEEecCCCCcc--cccCCC
Confidence 3 5689999999999997543 356776
No 8
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=5.6e-69 Score=624.74 Aligned_cols=354 Identities=19% Similarity=0.278 Sum_probs=310.5
Q ss_pred cEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCC
Q psy16215 4 RIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGK 83 (1041)
Q Consensus 4 RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k 83 (1041)
++|+||||||||||||++++|+|+++||||++ +|+|+||||+||+|||+.|||+++|+++||+|++++
T Consensus 133 ~~I~HVDmDaFYASVE~~~~PeLrgkPvaVg~-----~gvV~TaSYeARk~GVrsgMp~~~AkkLCP~Liivp------- 200 (571)
T PTZ00205 133 GTYIHLDMDMFYAAVEIKKHPEYAAIPLAIGT-----MTMLQTANYVARGRGIRQGMPGFLALKICPNLLILP------- 200 (571)
T ss_pred CeEEEEecCcHhhhhheccCccccCCcEEEcc-----CCEEEEcCHHHHhhCCCcCCcHHHHHHhCCCCcEec-------
Confidence 48999999999999999999999999999975 378999999999999999999999999999999987
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhh
Q psy16215 84 ADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEW 163 (1041)
Q Consensus 84 ~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W 163 (1041)
+||+.|+++|++|+++|.+|+|.||++||||+|||||++..
T Consensus 201 ~d~~~Y~~~S~~I~~il~~ysp~ve~~SIDEafLDlT~~~~--------------------------------------- 241 (571)
T PTZ00205 201 PDFDAYNEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIE--------------------------------------- 241 (571)
T ss_pred CCHHHHHHHHHHHHHHHHhcCCcEEEeechhceeccCCchh---------------------------------------
Confidence 89999999999999999999999999999999999998753
Q ss_pred cccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEe---ccchHHH
Q psy16215 164 LGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSIL---PQSSVSM 240 (1041)
Q Consensus 164 ~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl---~p~~v~~ 240 (1041)
.|... ..+..+|++||++|++++|||||||||+||+||||||+++||+|++++ .++++..
T Consensus 242 ---~~~~~--------------~~~~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~ 304 (571)
T PTZ00205 242 ---RFEGT--------------KTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMT 304 (571)
T ss_pred ---hccCC--------------CCHHHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHH
Confidence 11100 003578999999999999999999999999999999999999999987 6789999
Q ss_pred hhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHH--------HHHHHhhhhhHHHHHHHHcCCCCcc-ccc--cc
Q psy16215 241 LYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLK--------QLQSHFEEKTASWLYYIARGIDHEP-VNA--RL 309 (1041)
Q Consensus 241 fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~--------~L~krFG~k~G~~L~~~aRGiD~ep-V~p--~~ 309 (1041)
||++|||++|||||++++++ |..+||+|++||++.+.. .|+..||...|.++|..++|+|.++ +.+ ..
T Consensus 305 fL~~LpV~ki~GIG~~t~~~-L~~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~ 383 (571)
T PTZ00205 305 YVRDLGLRSVPGVGKVTEAL-LKGLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGG 383 (571)
T ss_pred HHhCCCcceeCCcCHHHHHH-HHHcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCC
Confidence 99999999999999999987 899999999999998876 4778889668999999999999884 332 44
Q ss_pred CCcceeeEEeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHH
Q psy16215 310 VSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQD 389 (1041)
Q Consensus 310 ppKSIssErTF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~ 389 (1041)
.+|||++++||+. +.+.++|...|..|+++|+.||+++ +..|++|+|++++.+|. ..+.+++++.|+++...
T Consensus 384 ~rKSIg~ErTF~~---~~d~~el~~~L~~L~~~v~~rLrk~----~l~artVtlKlK~~dF~-~~trs~tL~~pT~d~~~ 455 (571)
T PTZ00205 384 QRKAISSERSFTT---PRTKEGLQEMVDTVFNGAYEEMRKS----ELMCRQISLTIRWASYR-YQQYTKSLIQYSDDSAT 455 (571)
T ss_pred CCceeEEeEeCCC---CCCHHHHHHHHHHHHHHHHHHHHhc----CCCccEEEEEEEECCCC-ceEEEEECCCCcCCHHH
Confidence 6899999999985 5799999999999999999999998 99999999999999983 33455666667899999
Q ss_pred HHHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcCCCCCCC---------CcchhhcCCCC
Q psy16215 390 IVEVSMQVINKTNSAPPISDLTPPLLFLGLSASKFSPLGS---------HPSIQQFFKPQ 440 (1041)
Q Consensus 390 L~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSdLvp~~~---------q~sI~DLFd~~ 440 (1041)
|+..+..||.+... ...+||+|||++++|..... |.++..|..+.
T Consensus 456 I~~aa~~Ll~~~~~------~~~~vRLlGV~ls~L~~~~~~~~~~~~~~~~~~~~~~~~~ 509 (571)
T PTZ00205 456 LRRAVDGLLLPHAA------KYSEMCLLGVRFLDLISAKDFHMKRKGGNQLSISQFIRPK 509 (571)
T ss_pred HHHHHHHHHHhccc------cCCCEEEEEEEEcccCcHHHHHHHhcCCceeeHHHHcCCC
Confidence 99999999987631 13589999999999988554 34555555444
No 9
>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=100.00 E-value=5.5e-69 Score=605.28 Aligned_cols=340 Identities=46% Similarity=0.708 Sum_probs=311.0
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeecc--------
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVP-------- 78 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP-------- 78 (1041)
+||||||||||||++++|+|+++||||++++ .|+||||+||++||++||++++|+++||++++++++
T Consensus 1 ~hiD~D~FfasvE~~~~p~l~~~PvvV~~~~-----~V~a~syeAR~~GV~~gm~~~~A~~lcP~l~~v~~~~~~~~~~~ 75 (359)
T cd01702 1 AHIDMDAFFAQVEQVRLGLLRNDPVAVVQWN-----SIIAVSYAARAFGVTRFMTIDEAKKKCPDLILAHVATYKKGEDE 75 (359)
T ss_pred CccccchHHHHHHhHhcccccCCcEEEecCC-----cEEEECHHHHhcCCCCCCcHHHHHHHCCCcEEECCccccccccc
Confidence 5999999999999999999999999999864 399999999999999999999999999999998753
Q ss_pred --------CCCCCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCC
Q psy16215 79 --------SVRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDN 150 (1041)
Q Consensus 79 --------~~~~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~ 150 (1041)
...++++++.|+++|++|++++.+|+|.||++||||+|||+.
T Consensus 76 ~~~~~~~~~~~~~~~~~~Y~~~S~~i~~~l~~~sp~vE~~SiDE~flDv~------------------------------ 125 (359)
T cd01702 76 ADYHENPSPARHKVSLDPYRRASRKILNILKRFGDVVEKASIDEAYLDLG------------------------------ 125 (359)
T ss_pred cccccccccccccccHHHHHHHHHHHHHHHHHcCCceEECcCCeeHHHHH------------------------------
Confidence 223567899999999999999999999999999999999992
Q ss_pred CchhhhhhcchhhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCce
Q psy16215 151 NDEDARKAGVMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQ 230 (1041)
Q Consensus 151 ~~e~~r~~g~~~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGq 230 (1041)
..+|++||++|++++|||||||||+||++||||++++||+|+
T Consensus 126 --------------------------------------~~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~ 167 (359)
T cd01702 126 --------------------------------------SRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQ 167 (359)
T ss_pred --------------------------------------HHHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCe
Confidence 136889999999999999999999999999999999999999
Q ss_pred EEeccchHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhC--CHHHHHHHhhhhhHHHHHHHHcCCCCcccccc
Q psy16215 231 SILPQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKF--SLKQLQSHFEEKTASWLYYIARGIDHEPVNAR 308 (1041)
Q Consensus 231 tvl~p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~L--p~~~L~krFG~k~G~~L~~~aRGiD~epV~p~ 308 (1041)
++++++++.+||+++||++|||||+++++++|+.+||+|++||+++ +...|+++||.+.|.+||+.++|+|.++|.+.
T Consensus 168 ~v~~~~~~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~ 247 (359)
T cd01702 168 TILRNDAVASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPR 247 (359)
T ss_pred EEECHHHHHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCC
Confidence 9999999999999999999999999998887799999999999999 99999999997789999999999999999988
Q ss_pred cCCcceeeEEeCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcH
Q psy16215 309 LVSKSIGCCKRFPGKTCLATR-QDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKL 387 (1041)
Q Consensus 309 ~ppKSIssErTF~~r~dLtd~-eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Da 387 (1041)
.++|||+.+++|+. ++.+. +++..+|..|+.+|+.||++++..+++.+++|+|++++.++ +.+.++++++|+++.
T Consensus 248 ~~~ksi~~~~tf~~--~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~~~--~~~~sr~~~~~~~~~ 323 (359)
T cd01702 248 PLPKSMGSSKNFPG--KTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGD--GVRRSRSCALPRYDA 323 (359)
T ss_pred CCCceeeeeeecCC--CCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEECCC--cEEEEEEecCCCCCH
Confidence 88999999999996 57777 99999999999999999998655568999999999999885 367889999998889
Q ss_pred HHHHHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcC
Q psy16215 388 QDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSASK 423 (1041)
Q Consensus 388 e~L~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSd 423 (1041)
+.|+..+..||++++..+....|..|||+|||++++
T Consensus 324 ~~i~~~~~~l~~~~~~~~~~~~~~~~~rl~g~~~~~ 359 (359)
T cd01702 324 QKIVKDAFKLIKAINEEGLGLAWNYPLTLLSLSFTK 359 (359)
T ss_pred HHHHHHHHHHHHHhhhhccccccCCCeEEEEEEecC
Confidence 999999999999988532212356899999999875
No 10
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=2.3e-68 Score=598.55 Aligned_cols=345 Identities=28% Similarity=0.436 Sum_probs=308.5
Q ss_pred EEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCC--CCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCC
Q psy16215 5 IIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNT--WKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRG 82 (1041)
Q Consensus 5 vI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~--~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~ 82 (1041)
+|+||||||||||||++++|+|+++||||+++.+ ..+|.|++|||+||++||+.||++++|+++||++++++
T Consensus 2 ~i~hiD~daFfasve~~~~P~L~~kPv~V~~~~~~~~~~gvV~aasy~Ar~~GV~sgM~~~~A~~lcP~li~v~------ 75 (351)
T PRK01216 2 IILFVDFDYFFAQVEEVLNPSLKGKPVVVCVYSGRFEDSGAVATANYEARKLGIKAGMPIVEAKKILPNAVYLP------ 75 (351)
T ss_pred EEEEEecchHHHHHHhHhChhhcCCcEEEEecCCCCCCCeEEEECCHHHHHhCCCCCCcHHHHHHHCCCeEEEC------
Confidence 7999999999999999999999999999986431 13578999999999999999999999999999999987
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchh
Q psy16215 83 KADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVME 162 (1041)
Q Consensus 83 k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~ 162 (1041)
+|++.|+.+|++|++++++|+|.||++||||+|||||++.+
T Consensus 76 -~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~LDvt~~~~-------------------------------------- 116 (351)
T PRK01216 76 -MRKEVYQQVSNRIMKLLREYSEKIEIASIDEAYLDISDKVK-------------------------------------- 116 (351)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCceEEccCCeEEEEcccchh--------------------------------------
Confidence 89999999999999999999999999999999999999864
Q ss_pred hcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhh
Q psy16215 163 WLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLY 242 (1041)
Q Consensus 163 W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL 242 (1041)
+|++ +..+|++||++|++++|+|||+|||+||++|||||+++||+|++++.++++.+||
T Consensus 117 ----l~g~-----------------~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~~~~~~L 175 (351)
T PRK01216 117 ----NYQD-----------------AYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEVKRFI 175 (351)
T ss_pred ----ccCC-----------------HHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHHHHHHHH
Confidence 4543 3578999999999999999999999999999999999999999999999999999
Q ss_pred hcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCCC
Q psy16215 243 ANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPG 322 (1041)
Q Consensus 243 ~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~~ 322 (1041)
++|||+++||||+++.++ |+++||+|+|||+++|.+.|+++||...|.+||++++|+|.++|.+. ++|||+.+++|+.
T Consensus 176 ~~LPi~~l~giG~~~~~~-L~~~Gi~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~~pv~~~-~~ksi~~~~tl~~ 253 (351)
T PRK01216 176 NELDIADIPGIGDITAEK-LKKLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYNEPVRAR-VRKSIGRYVTLPR 253 (351)
T ss_pred hcCCcccccCCCHHHHHH-HHHcCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCCCC-CCCCCcCeEECCC
Confidence 999999999999999987 89999999999999999999999996679999999999999999884 5699999999986
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeC--CCCcHHHHHHHHHHHHHH
Q psy16215 323 KTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIAL--ASYKLQDIVEVSMQVINK 400 (1041)
Q Consensus 323 r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~L--pT~Dae~L~~~A~~LL~r 400 (1041)
++.+.+++...|..|+.+++.||+. .++++++++++.++ .+.+|+.++ +++ .+.+++.+..||++
T Consensus 254 --di~~~~~l~~~l~~L~~~~~~rl~~-------~~~~~~~~~~~~df---~~~t~~~tl~~~~~-~~~~~~~a~~Ll~~ 320 (351)
T PRK01216 254 --NTRDLEEIKPYLKRAIEEAYYKLDG-------IPKAIHVVAIMEDL---DIVSRGRTFTHGIS-KETAYREAVRLLQK 320 (351)
T ss_pred --ccCCHHHHHHHHHHHHHHHHHHHHh-------CCCEEEEEEEcCCC---CEEEEEEECCCCCC-HHHHHHHHHHHHHh
Confidence 7999999999999999999999986 36788899998887 456666665 454 58899999999998
Q ss_pred hccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcCC
Q psy16215 401 TNSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFFK 438 (1041)
Q Consensus 401 L~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLFd 438 (1041)
++.. ...+||+|||++++|.+.-. .+.||.
T Consensus 321 ~~~~-----~~~~vRllGv~~~~l~~~~~---~~~~~~ 350 (351)
T PRK01216 321 ILEE-----DERKIRRIGVRFSKIIEAIG---LDKFFD 350 (351)
T ss_pred hhhc-----CCCCeeEEEEEEeccccccc---HHHhhc
Confidence 7520 02489999999999987632 455553
No 11
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=6.3e-68 Score=612.83 Aligned_cols=356 Identities=25% Similarity=0.375 Sum_probs=321.7
Q ss_pred CCCcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCC-cEEeeccC
Q psy16215 1 MTSRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPE-IELCRVPS 79 (1041)
Q Consensus 1 ~~~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPd-LvvV~VP~ 79 (1041)
|+.|+|+||||||||||||++.+|+|+++||+|.+.. .++.|++|||+||++||++||++.+|+++||+ +++++
T Consensus 2 ~~~r~I~hiDmDaFfasvE~~~~P~L~g~PvvV~~~~--~~gvV~aasyeAR~~GVrsgMp~~~A~~lcP~~lv~v~--- 76 (454)
T PRK03348 2 RAQRWVLHLDMDAFFASVEQLTRPTLRGRPVLVGGLG--GRGVVAGASYEARVFGARSAMPMHQARRLVGNGAVVLP--- 76 (454)
T ss_pred CCCCEEEEEecChHHHhhhhhhCccccCCcEEEEcCC--CCeEEEeCCHHHHhcCCCCCCcHHHHHHhCCCCEEEEC---
Confidence 6789999999999999999999999999999997642 46888999999999999999999999999999 99986
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhc
Q psy16215 80 VRGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAG 159 (1041)
Q Consensus 80 ~~~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g 159 (1041)
+|++.|+.+|++|++++.+|+|.||++||||+|||+++....
T Consensus 77 ----~d~~~Y~~~s~~i~~~l~~~sp~VE~~SiDE~flD~~~l~~~---------------------------------- 118 (454)
T PRK03348 77 ----PRFVVYRAASRRVFDTLRELSPVVEQLSFDEAFVEPAELAGA---------------------------------- 118 (454)
T ss_pred ----CChHHHHHHHHHHHHHHHHhCCceEEecCCeEEEEccccccc----------------------------------
Confidence 899999999999999999999999999999999997764210
Q ss_pred chhhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHH
Q psy16215 160 VMEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVS 239 (1041)
Q Consensus 160 ~~~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~ 239 (1041)
.++. +..+|++||++|++++||+||||||+||++||||++++||+|+++++++.+.
T Consensus 119 -------~~~~-----------------~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~~~~ 174 (454)
T PRK03348 119 -------SAEE-----------------VEAFAERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIRVVPPGEER 174 (454)
T ss_pred -------cCCC-----------------HHHHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHhhccCCCCcEEEEEchHHH
Confidence 0000 2468999999999999999999999999999999999999999999999999
Q ss_pred HhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEe
Q psy16215 240 MLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKR 319 (1041)
Q Consensus 240 ~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErT 319 (1041)
+||++|||++|||||+++.++ |+++||+|++||++++...|+++||...|.+||++++|+|.++|.+..++|+|+.+++
T Consensus 175 ~~L~~LPv~~L~GIG~~t~~~-L~~lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~e~t 253 (454)
T PRK03348 175 ELLAPLPVRRLWGIGPVTEEK-LHRLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAEST 253 (454)
T ss_pred HHHHhCCccccCCCCHHHHHH-HHHcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEE
Confidence 999999999999999999998 8999999999999999999999999778999999999999999999889999999999
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHH
Q psy16215 320 FPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVIN 399 (1041)
Q Consensus 320 F~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~ 399 (1041)
|+. ++.+.++|..+|..|+.+|+.||+++ ++.+++|+|++++.++. ..+.+.+++.|+++...|++.+..+|+
T Consensus 254 f~~--~i~~~~~l~~~L~~L~~~l~~rL~~~----g~~~r~v~l~l~~~d~~-~~srs~~l~~pt~d~~~L~~la~~ll~ 326 (454)
T PRK03348 254 FAV--DLTTRAQLREAIERIAEHAHRRLLKD----GRGARTVTVKLRKSDFS-TLTRSATLPYATDDAAVLAATARRLLL 326 (454)
T ss_pred CCC--CCCCHHHHHHHHHHHHHHHHHHHHHc----CCCccEEEEEEEeCCCC-ccEEEEECCCCCCCHHHHHHHHHHHHH
Confidence 985 69999999999999999999999998 99999999999998762 233444455568899999999999999
Q ss_pred HhccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcCCCCCC
Q psy16215 400 KTNSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFFKPQDH 442 (1041)
Q Consensus 400 rL~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLFd~~~~ 442 (1041)
++.. ..+||++||++++|.+. .|.+||...+.
T Consensus 327 ~~~~-------~~~vRllgV~~s~l~~~----~q~~LF~~~~~ 358 (454)
T PRK03348 327 DPDE-------IGPIRLVGVGFSGLSDV----RQESLFPELDL 358 (454)
T ss_pred hhcc-------CCCeEEEEEEECCCCcc----hhhccCCCccc
Confidence 9763 45899999999999753 47889976543
No 12
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=7.6e-69 Score=615.03 Aligned_cols=389 Identities=23% Similarity=0.282 Sum_probs=340.9
Q ss_pred EEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCC--CcEEeeccCCCC
Q psy16215 5 IIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCP--EIELCRVPSVRG 82 (1041)
Q Consensus 5 vI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCP--dLvvV~VP~~~~ 82 (1041)
+|+||||||||||||++.+|+|+|+||||++.+ +|+|+||||+||++||+.|||+++|+++|| ++++++
T Consensus 1 ~~~hvD~d~FfaS~E~~~~p~l~g~Pv~V~~~~---~g~V~aasyeAr~~GV~~gmp~~~a~~l~~~~~l~~~~------ 71 (422)
T PRK03609 1 MFALCDVNSFYASCETVFRPDLRGKPVVVLSNN---DGCVIARSAEAKALGIKMGDPWFKQKDLFRRCGVVCFS------ 71 (422)
T ss_pred CEEEEecCcceeeeeeccCccccCCcEEEEECC---CcEEEEcCHHHHHhCCCCCCcHHHHHHHhccCCeEEeC------
Confidence 499999999999999999999999999999753 589999999999999999999999999994 378876
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchh
Q psy16215 83 KADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVME 162 (1041)
Q Consensus 83 k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~ 162 (1041)
+|++.|.++|++|++++.+|+|.||++||||+|||||++.+
T Consensus 72 -~d~~~y~~~s~~i~~~l~~~tp~ve~~siDE~~lDvt~~~~-------------------------------------- 112 (422)
T PRK03609 72 -SNYELYADMSNRVMSTLEELSPRVEIYSIDEAFCDLTGVRN-------------------------------------- 112 (422)
T ss_pred -CCHHHHHHHHHHHHHHHHHhCCCceEeccccceecCCCCcC--------------------------------------
Confidence 89999999999999999999999999999999999998743
Q ss_pred hcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCC-----CceEEe-ccc
Q psy16215 163 WLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKP-----QKQSIL-PQS 236 (1041)
Q Consensus 163 W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKP-----nGqtvl-~p~ 236 (1041)
+++ ...+|++||++|++++||+||||||+||++||||+.++|| +|++++ .++
T Consensus 113 ----l~~------------------~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~~ 170 (422)
T PRK03609 113 ----CRD------------------LTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNLE 170 (422)
T ss_pred ----CCC------------------HHHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCHH
Confidence 111 2468999999999999999999999999999999988776 688877 688
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCC-ccee
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVS-KSIG 315 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~pp-KSIs 315 (1041)
.+.+||+++||++|||||+++.++ |+++||+|+|||+++|+..|+++|| ..|.++|+.++|++.+++.+..++ |+|+
T Consensus 171 ~~~~~L~~lPv~~l~GiG~~~~~~-L~~lGi~TigdL~~~~~~~L~~~fG-~~~~~l~~~a~G~~~~~~~~~~~~~ksi~ 248 (422)
T PRK03609 171 RQRKLLSLQPVEEVWGVGRRISKK-LNAMGIKTALDLADTNIRFIRKHFN-VVLERTVRELRGEPCLSLEEFAPTKQEIV 248 (422)
T ss_pred HHHHHhhcCChhhcCCccHHHHHH-HHHcCCCcHHHHhcCCHHHHHHHHC-HHHHHHHHHhCCCCCCCccccCCCCceEE
Confidence 999999999999999999999998 8999999999999999999999999 689999999999999998776554 7999
Q ss_pred eEEeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCC-----ceeEEEEEeCCCCcHHHH
Q psy16215 316 CCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGK-----VNSCSRSIALASYKLQDI 390 (1041)
Q Consensus 316 sErTF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~-----~~s~SRSl~LpT~Dae~L 390 (1041)
.+++|+. ++.+.++|..+|..|+++|+.||+++ ++.+++|+|++++.++.. ..+.+.++..|+++...|
T Consensus 249 ~~~tf~~--~~~~~~~l~~~l~~l~~~l~~rLr~~----~~~~~~l~l~ir~~~~~~~~~~~~~~~~~~l~~pt~d~~~l 322 (422)
T PRK03609 249 CSRSFGE--RITDYESMRQAICSYAARAAEKLRGE----HQYCRFISTFVKTSPFALNEPYYGNSASVKLLTPTQDSRDI 322 (422)
T ss_pred EeeECCC--CCCCHHHHHHHHHHHHHHHHHHHHHc----CCcccEEEEEEEcCCccccCCCcCceeEEeCCCCCCCHHHH
Confidence 9999986 68999999999999999999999998 999999999999988631 123344455578999999
Q ss_pred HHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcCCCCCCCCcchhhcCCCCCCCCCCCCCCCCCCcCcCCCCCcccCcccc
Q psy16215 391 VEVSMQVINKTNSAPPISDLTPPLLFLGLSASKFSPLGSHPSIQQFFKPQDHPEPMTSEHSSLPEQSTNHDSKKRDKTLL 470 (1041)
Q Consensus 391 ~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSdLvp~~~q~sI~DLFd~~~~~e~~~se~lS~a~D~iN~~s~k~gktll 470 (1041)
+..+..+|++++. +..++|++||.+++|.+... .|.+||+.... ....+.++.++|.+| .++|+..+
T Consensus 323 ~~~a~~ll~~~~~------~~~~~r~~GV~~~~l~~~~~--~q~~LF~~~~~--~~~~~~l~~~iD~i~---~r~G~~~i 389 (422)
T PRK03609 323 IAAATRALDAIWR------DGHRYQKAGVMLGDFFSQGV--AQLNLFDDNAP--RPGSEQLMKVLDTLN---AKSGKGTL 389 (422)
T ss_pred HHHHHHHHHHHhC------CCCceEEeeEEEEeeccCCC--cCccCcccccc--ccchHHHHHHHHHHH---HhhCCCeE
Confidence 9999999999874 24579999999999997543 47889975321 123457888999999 89999999
Q ss_pred ccCCC-ChHHHHHHH
Q psy16215 471 NFNQQ-TPFQLALNR 484 (1041)
Q Consensus 471 ~~g~~-tp~q~~~~~ 484 (1041)
..|.. ....|.|++
T Consensus 390 ~~a~~~~~~~w~~~~ 404 (422)
T PRK03609 390 YFAGQGIAQQWQMKR 404 (422)
T ss_pred EECCCCCCCCccCch
Confidence 98866 444599875
No 13
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=4.7e-67 Score=585.13 Aligned_cols=339 Identities=27% Similarity=0.361 Sum_probs=311.2
Q ss_pred CcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCC--CCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCC
Q psy16215 3 SRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNT--WKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSV 80 (1041)
Q Consensus 3 ~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~--~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~ 80 (1041)
+|+|+||||||||||||++.+|+|+++||||++... ..++.|++|||+||++||++||++++|+++||++++++
T Consensus 4 ~r~i~hiD~d~F~as~e~~~~p~l~~~Pvvv~~~~~~~~~~~~V~~~sy~Ar~~GV~~gM~~~~A~~lcP~l~~v~---- 79 (346)
T PRK03352 4 PRWVLHVDLDQFIAAVELLRRPELAGLPVIVGGNGDPTEPRKVVTCASYEARAFGVRAGMPLRTAARRCPDAVFLP---- 79 (346)
T ss_pred CcEEEEEccchHHHHHHhhhCccccCCCEEEecCCCCCCCceEEEECCHHHHHhCCCcCChHHHHHHHCCCeEEEC----
Confidence 699999999999999999999999999999986431 12678999999999999999999999999999999987
Q ss_pred CCCCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcc
Q psy16215 81 RGKADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGV 160 (1041)
Q Consensus 81 ~~k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~ 160 (1041)
+|++.|+.+|++|++++++|+|.||++||||+|||+|+.-
T Consensus 80 ---~~~~~y~~~s~~i~~~l~~~s~~ve~~siDe~~ld~t~~~------------------------------------- 119 (346)
T PRK03352 80 ---SDPAAYDAASEEVMATLRDLGVPVEVWGWDEAFLGVDTDD------------------------------------- 119 (346)
T ss_pred ---CCcHHHHHHHHHHHHHHHHhCCceEEecCccEEEeCCCCC-------------------------------------
Confidence 8999999999999999999999999999999999999640
Q ss_pred hhhcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHH
Q psy16215 161 MEWLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSM 240 (1041)
Q Consensus 161 ~~W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~ 240 (1041)
...+|+.||++|++++||+||+|||+||++||||++.+||+|++++.++.+.+
T Consensus 120 ---------------------------~~~la~~ir~~i~~~~gl~~siGia~nk~lAklaa~~~Kp~g~~~~~~~~~~~ 172 (346)
T PRK03352 120 ---------------------------PEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDANWMA 172 (346)
T ss_pred ---------------------------HHHHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHHhhcCCCcEEEECHHHHHH
Confidence 13589999999999999999999999999999999999999999999999999
Q ss_pred hhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccc-cCCcceeeEEe
Q psy16215 241 LYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNAR-LVSKSIGCCKR 319 (1041)
Q Consensus 241 fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~-~ppKSIssErT 319 (1041)
||+++||++|||||+++.++ |+++||+|++||+++|...|.++||...|.+||++++|+|.+++... ..|||++.+++
T Consensus 173 ~L~~lpl~~l~gig~~~~~~-L~~~Gi~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~~t 251 (346)
T PRK03352 173 VMGDRPTDALWGVGPKTAKR-LAALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVT 251 (346)
T ss_pred HHhcCCHHHcCCCCHHHHHH-HHHcCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEE
Confidence 99999999999999999998 89999999999999999999999996679999999999999998764 35799999999
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHH
Q psy16215 320 FPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVIN 399 (1041)
Q Consensus 320 F~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~ 399 (1041)
|+. ++.+.+++..+|..|+.+|+.||+++ ++.+++|+|++++.++. ..+.++++..|+++.+.|+..+..+|+
T Consensus 252 f~~--~~~~~~~l~~~l~~L~~~l~~rLr~~----~~~~~~l~l~l~~~~~~-~~~~~~~l~~pt~d~~~l~~~~~~ll~ 324 (346)
T PRK03352 252 FPQ--DLTDRAEVESAVRELARRVLDEVVAE----GRPVTRVAVKVRTATFY-TRTKIRKLPEPTTDPDVIEAAALDVLD 324 (346)
T ss_pred CCC--CCCCHHHHHHHHHHHHHHHHHHHHHc----CCccceEEEEEEeCCCc-eeEEEEECCCCcCCHHHHHHHHHHHHH
Confidence 985 69999999999999999999999998 99999999999998863 234455566678999999999999999
Q ss_pred HhccCCCCCCCCCCEEEEEEEEcCCCCC
Q psy16215 400 KTNSAPPISDLTPPLLFLGLSASKFSPL 427 (1041)
Q Consensus 400 rL~~~~~~~a~~~pVRlIGVsLSdLvp~ 427 (1041)
++.. ..+||+|||++.+|.+.
T Consensus 325 ~~~~-------~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 325 RFEL-------DRPVRLLGVRLELAMPD 345 (346)
T ss_pred hccC-------CCCEEEEEEEEeccCCC
Confidence 9863 56899999999999864
No 14
>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=100.00 E-value=3.9e-67 Score=585.50 Aligned_cols=336 Identities=27% Similarity=0.377 Sum_probs=306.3
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCCCH
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADI 86 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~Dl 86 (1041)
+||||||||||||++.+|+|+++||||++++. .+++|+||||+||++||++||++++|+++||++++++ +|+
T Consensus 1 ~hiD~d~F~as~e~~~~p~l~~~Pv~V~~~~~-~~~~V~a~sy~Ar~~GV~~gm~~~~A~~lcP~l~~~~-------~~~ 72 (343)
T cd00424 1 LHIDFDNFFASVEQLARPELKGRPVVVVPFNS-DSTCVIACSYEARKYGVKRGMPVREARKMCPNLILVP-------ARL 72 (343)
T ss_pred CeEecchHHHHHHhhhCccccCCCEEEecCCC-CCeEEEEeCHHHHHhCCCCCCcHHHHHHhCCCeEEEC-------CCc
Confidence 69999999999999999999999999998753 4578999999999999999999999999999999987 899
Q ss_pred HHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhccc
Q psy16215 87 SKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQ 166 (1041)
Q Consensus 87 d~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~~~ 166 (1041)
+.|+++|++|++++.+|+|.||++||||+|||||+..+
T Consensus 73 ~~y~~~s~~i~~~l~~~sp~ve~~siDE~~ldvt~~~~------------------------------------------ 110 (343)
T cd00424 73 DLYRRLSERLLSELEEVAPLVEVASIDELFLDLTGSAR------------------------------------------ 110 (343)
T ss_pred HHHHHHHHHHHHHHHHhCCcEEEccCCEEEEECCCchh------------------------------------------
Confidence 99999999999999999999999999999999999854
Q ss_pred ccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhC-CceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC
Q psy16215 167 VYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQ-FHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL 245 (1041)
Q Consensus 167 LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elG-lt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L 245 (1041)
+|++ +..+|++||++|++++| +|||||||+||++||||++++||+|+++++++++.+||+++
T Consensus 111 ~~~~-----------------~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~~~~~~L~~l 173 (343)
T cd00424 111 LLGL-----------------GSEVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPEDLPGFLSKL 173 (343)
T ss_pred ccCC-----------------HHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHHHHHHHHhcC
Confidence 3332 35789999999999998 99999999999999999999999999999999999999999
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCC-HHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCCCCC
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFS-LKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPGKT 324 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp-~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~~r~ 324 (1041)
||+++||||+++.++ |+.+||+|++||+++| ...|+++|| +.|.++|+.++|+|.++|.+..++|||+.+++|+.
T Consensus 174 pi~~l~giG~~~~~~-L~~~Gi~ti~dl~~~~~~~~l~~~fg-~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~~-- 249 (343)
T cd00424 174 PLTDLPGIGAVTAKR-LEAVGINPIGDLLAASPDALLALWGG-VSGERLWYALRGIDDEPLSPPRPRKSFSHERVLPR-- 249 (343)
T ss_pred ChhhcCCCCHHHHHH-HHHcCCCcHHHHhcCCHHHHHHHHhh-HHHHHHHHHhCCcCCCCCCCCCCCCceeeeEECCC--
Confidence 999999999999998 7999999999999999 888999999 68999999999999999998888999999999986
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCC---CceeEEEEEeC--CCCcHHHHHHHHHHHHH
Q psy16215 325 CLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDG---KVNSCSRSIAL--ASYKLQDIVEVSMQVIN 399 (1041)
Q Consensus 325 dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g---~~~s~SRSl~L--pT~Dae~L~~~A~~LL~ 399 (1041)
++.+.+++..+|..|+.+|+.||+++ ++.+++|+|++++.++. .+..++++.++ |+ +...|+..+..+|+
T Consensus 250 ~~~~~~~l~~~l~~l~~~l~~rL~~~----~~~~~~l~l~lr~~~~~~~~~~~~~~~~~~l~~~t-~~~~l~~~~~~l~~ 324 (343)
T cd00424 250 DSRNAEDARPLLRLLLEKLARRLRRD----GRGATRLRLWLRTVDGRWSGHADIPSRSAPRPIST-EDGELLHALDKLWR 324 (343)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHc----CCceeEEEEEEEeCCCcccccceeeeeeeeCCCCC-CHHHHHHHHHHHHH
Confidence 69999999999999999999999998 99999999999998742 13456666555 57 88999999999999
Q ss_pred HhccCCCCCCCCCCEEEEEEEEc
Q psy16215 400 KTNSAPPISDLTPPLLFLGLSAS 422 (1041)
Q Consensus 400 rL~~~~~~~a~~~pVRlIGVsLS 422 (1041)
+++.. ....+||++||+++
T Consensus 325 ~~~~~----~~~~~ir~~gv~~~ 343 (343)
T cd00424 325 ALLDD----KGPRRLRRLGVRLS 343 (343)
T ss_pred hhhhc----cCCCCeeEEEEEeC
Confidence 98731 01458999999975
No 15
>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=100.00 E-value=7.1e-67 Score=591.72 Aligned_cols=341 Identities=28% Similarity=0.439 Sum_probs=301.4
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCCCH
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADI 86 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~Dl 86 (1041)
+||||||||||||++.+|+|+++||||++ +++|+||||+||++||++|||+++|+++||++++++ ..|+
T Consensus 1 ~HiD~DaFyasve~~~~P~L~~kPv~V~~-----~~~V~aasy~AR~~GV~~gm~~~~A~~lcP~li~v~------~~~~ 69 (379)
T cd01703 1 IHLDLDCFYAQVEEIRDPSLKSKPLGIQQ-----KYIVVTCNYEARRLGVKKLMSIKDAKEICPDLVLVN------GEDL 69 (379)
T ss_pred CeeecccHHHHHHhhhccccCCCcEEECC-----CCEEEEcCHHHHHhCCCCCCcHHHHHHhCCCeEEEc------CCCh
Confidence 69999999999999999999999999965 478999999999999999999999999999999886 1489
Q ss_pred HHHHHHHHHHHHHHHhcCC--cEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhc
Q psy16215 87 SKYRNAGREVIAVLSEFSN--IVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWL 164 (1041)
Q Consensus 87 d~Yr~aS~kI~eIL~~fSP--~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~ 164 (1041)
+.|+++|++|++++.+|+| .||++||||+|||+|+...
T Consensus 70 ~~Y~~~S~~i~~~l~~~sp~~~ve~~SiDE~~lDvt~~~~---------------------------------------- 109 (379)
T cd01703 70 TPFRDMSKKVYRLLRSYSWNDRVERLGFDENFMDVTEMRL---------------------------------------- 109 (379)
T ss_pred HHHHHHHHHHHHHHHHcCCHhhEEecCCCcEEEEccCccc----------------------------------------
Confidence 9999999999999999999 9999999999999998621
Q ss_pred ccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEecc---chHHHh
Q psy16215 165 GQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQ---SSVSML 241 (1041)
Q Consensus 165 ~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p---~~v~~f 241 (1041)
+| |..+|++||++|++++||+||||||+||+|||||++.+||+|++++.+ +++.+|
T Consensus 110 --~~-------------------g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~f 168 (379)
T cd01703 110 --LV-------------------ASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDF 168 (379)
T ss_pred --hh-------------------HHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHH
Confidence 11 356899999999999999999999999999999999999999999977 467889
Q ss_pred hhcCCccccccCCHHHHHHHHHhCCCccchhhhhCC---------------HHHHHHHhhhhhHHHHHHHHcCCCCccc-
Q psy16215 242 YANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFS---------------LKQLQSHFEEKTASWLYYIARGIDHEPV- 305 (1041)
Q Consensus 242 L~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp---------------~~~L~krFG~k~G~~L~~~aRGiD~epV- 305 (1041)
|+++||++|||||++++++ |..+||.|++||++++ ...|+++||...|.+||+.|+|+|.++|
T Consensus 169 l~~lpv~~l~GiG~~~~~k-L~~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a~G~d~~~V~ 247 (379)
T cd01703 169 MDLHDLRKIPGIGYKTAAK-LEAHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVK 247 (379)
T ss_pred hccCCccccCCcCHHHHHH-HHHcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCHHHHHHHHHHHCCCCCCccC
Confidence 9999999999999999998 7999999999999999 9999999997679999999999999999
Q ss_pred ccccCCcceeeEEeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhc----cCceeeEEEEEEEEcCCC--CceeEEEE
Q psy16215 306 NARLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTL----NKRRAQLLTVSFTQETDG--KVNSCSRS 379 (1041)
Q Consensus 306 ~p~~ppKSIssErTF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~----ngr~artLTLkLR~sd~g--~~~s~SRS 379 (1041)
.+...+|||+.+++|+. .++.+..++..+|..|+++|+.||++++.+ ++..+++|+|++|+.+.. .+.+++|+
T Consensus 248 ~~~~~~ksis~e~tf~~-~~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~~~~~~~~~sr~ 326 (379)
T cd01703 248 PASDFPQQISIEDSYKK-CSLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTSTKKHYNRESKQ 326 (379)
T ss_pred CCCCCCceeEEeeccCC-CCCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCCCCCccceeeec
Confidence 55667899999999986 268899999999999999999999994322 488999999999998810 12567888
Q ss_pred EeCC--CC---------cHHHHHHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcC
Q psy16215 380 IALA--SY---------KLQDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSASK 423 (1041)
Q Consensus 380 l~Lp--T~---------Dae~L~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSd 423 (1041)
.+++ ++ +.+.|++.+..||++++.. ......+||++||++++
T Consensus 327 ~~l~~~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~--~~~~~~~irl~gv~~~~ 379 (379)
T cd01703 327 APIPSHVFQKLTGGNEIAARPIEKILMRLFRELVPP--KNVKGFNLTLLNVCFTN 379 (379)
T ss_pred cccCchhhccccccchhhHHHHHHHHHHHHHHhccc--ccCCCCceEEEEEEeeC
Confidence 7776 44 4679999999999998741 00013489999999975
No 16
>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=100.00 E-value=3.3e-66 Score=573.20 Aligned_cols=334 Identities=34% Similarity=0.536 Sum_probs=309.2
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCCCH
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADI 86 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~Dl 86 (1041)
+||||||||||||++.+|+|+++||||++++ .+++|++|||+||++||++||++++|+++||++++++ +|+
T Consensus 1 ~hiD~d~Ffas~e~~~~p~l~~~Pv~V~~~~--~~~~v~a~n~~Ar~~GV~~Gm~~~~A~~lcp~l~~~~-------~~~ 71 (334)
T cd03586 1 IHIDMDAFYASVEQRDNPELKGKPVAVGGSS--DRGVVSTASYEARKFGVRSAMPIFQAKKLCPNLIFVP-------PRF 71 (334)
T ss_pred CeeccchHHHHHHhhhCccccCCCEEEEeCC--CCeEEEEcCHHHHhcCCCcCCcHHHHHHHCCCeEEEC-------CCc
Confidence 6999999999999999999999999999875 3679999999999999999999999999999999987 899
Q ss_pred HHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhccc
Q psy16215 87 SKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQ 166 (1041)
Q Consensus 87 d~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~~~ 166 (1041)
+.|+++|++|++++++|+|.||++||||+|||+|++..
T Consensus 72 ~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldv~~~~~------------------------------------------ 109 (334)
T cd03586 72 DKYREVSRQIMEILREYTPLVEPLSIDEAYLDVTDYVR------------------------------------------ 109 (334)
T ss_pred HHHHHHHHHHHHHHHHcCCceEEecccceeEccccccc------------------------------------------
Confidence 99999999999999999999999999999999998743
Q ss_pred ccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcCC
Q psy16215 167 VYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLS 246 (1041)
Q Consensus 167 LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~LP 246 (1041)
+|++ +..+|++||++|++++||+||+|||+|+++||||++.+||+|+++++++++.+||+++|
T Consensus 110 ~~~~-----------------~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~~~~~~L~~lp 172 (334)
T cd03586 110 LFGS-----------------ATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDVEEFLAPLP 172 (334)
T ss_pred cCCC-----------------HHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHHHHHHHHhcCC
Confidence 3432 35789999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCCCCCCC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPGKTCL 326 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~~r~dL 326 (1041)
|+++||||+++.++ |..+||+|++||+++|...|.++|| ..|.++|+.++|+|.+++.+..++|||+++++|+. ++
T Consensus 173 l~~l~gig~~~~~~-L~~~Gi~ti~dl~~~~~~~L~~~~g-~~~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~~--~~ 248 (334)
T cd03586 173 VRKIPGVGKVTAEK-LKELGIKTIGDLAKLDVELLKKLFG-KSGRRLYELARGIDNRPVEPDRERKSIGVERTFSE--DL 248 (334)
T ss_pred chhhCCcCHHHHHH-HHHcCCcCHHHHHcCCHHHHHHHHh-HHHHHHHHHhCCCCCCCCCCCCCCCeeeeeEECCC--CC
Confidence 99999999999987 8999999999999999999999999 68999999999999999998889999999999986 68
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHHHhccCCC
Q psy16215 327 ATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKTNSAPP 406 (1041)
Q Consensus 327 td~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~rL~~~~~ 406 (1041)
.+.+++..+|..|+.+|+.||+.+ ++.+++|+|++++.++. ..+.+..+..|+++...|++.+..+|+++..
T Consensus 249 ~~~~~l~~~l~~l~~~l~~rL~~~----~~~~~~l~l~l~~~~~~-~~~~~~~l~~~t~~~~~l~~~~~~~l~~~~~--- 320 (334)
T cd03586 249 TDPEELLEELLELAEELAERLRKR----GLKGRTVTVKLKYADFS-TRTRSRTLPEPTDDAEDIYELALELLEELLD--- 320 (334)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhC----CCCeEEEEEEEEECCCC-eEEEEEECCCCCCCHHHHHHHHHHHHHhccC---
Confidence 899999999999999999999998 99999999999998762 2334444445688999999999999999884
Q ss_pred CCCCCCCEEEEEEEEcCC
Q psy16215 407 ISDLTPPLLFLGLSASKF 424 (1041)
Q Consensus 407 ~~a~~~pVRlIGVsLSdL 424 (1041)
..+||+|||++++|
T Consensus 321 ----~~~vr~igv~~~~l 334 (334)
T cd03586 321 ----GRPIRLLGVRLSGL 334 (334)
T ss_pred ----CCCEEEEEEEeecC
Confidence 46899999999876
No 17
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=1.5e-64 Score=564.37 Aligned_cols=333 Identities=29% Similarity=0.455 Sum_probs=303.5
Q ss_pred CCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCCCHHHHH
Q psy16215 11 MDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADISKYR 90 (1041)
Q Consensus 11 mD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~Dld~Yr 90 (1041)
|||||||||++.+|+|+++||||+++. ..+++|++|||+||++||++||++++|+++||+|++++ +|++.|+
T Consensus 1 ~d~Ffasve~~~~p~l~~~Pv~v~~~~-~~~~~v~a~n~~Ar~~GV~~gm~~~~A~~lcP~l~~~~-------~d~~~y~ 72 (343)
T PRK02406 1 MDCFYAAVEMRDNPELRGKPVAVGGSP-GRRGVISTCNYEARKFGVRSAMPTAQALKLCPDLIFVP-------GRFDVYK 72 (343)
T ss_pred CCchHHHHHhhhCccccCCCEEEecCC-CCCeEEEecCHHHHHhCCCCCCcHHHHHHHCCCeEEEC-------CChHHHH
Confidence 899999999999999999999998763 35688999999999999999999999999999999987 8999999
Q ss_pred HHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhcccccCC
Q psy16215 91 NAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQVYSD 170 (1041)
Q Consensus 91 ~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~~~LFg~ 170 (1041)
++|++|++++++|+|.||++||||+|||+|++.+ +|++
T Consensus 73 ~~s~~i~~~l~~~sp~ve~~siDe~~ldvt~~~~------------------------------------------~~~~ 110 (343)
T PRK02406 73 EVSRQIREIFRRYTDLIEPLSLDEAYLDVTDNKL------------------------------------------CIGS 110 (343)
T ss_pred HHHHHHHHHHHHhCCceEEccCCeEEEeccCccc------------------------------------------cCCC
Confidence 9999999999999999999999999999999854 3443
Q ss_pred CcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcCCcccc
Q psy16215 171 TDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSIKKV 250 (1041)
Q Consensus 171 ~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~LPI~kI 250 (1041)
+..+|+.||++|++++|++||||||+||++||||++++||+|++++.++++.+||+++||++|
T Consensus 111 -----------------~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~~~~~~L~~lpi~~l 173 (343)
T PRK02406 111 -----------------ATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEEVDAFLATLPVEKI 173 (343)
T ss_pred -----------------HHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHHHHHHHHHcCCcchh
Confidence 246899999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCCCCCCCCCHH
Q psy16215 251 RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPGKTCLATRQ 330 (1041)
Q Consensus 251 pGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~~r~dLtd~e 330 (1041)
||||+++.++ |+++||+|++||+++|...|+++|| ..|.++|+.++|+|.++|.+..++|||+.+++|+. ++.+.+
T Consensus 174 ~giG~~~~~~-L~~~Gi~ti~dl~~l~~~~L~~~fG-~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~--~~~~~~ 249 (343)
T PRK02406 174 PGVGKVTAEK-LHALGIYTCADLQKYDLAELIRHFG-KFGRRLYERARGIDERPVKPDRERKSVGVERTFAE--DLYDLE 249 (343)
T ss_pred cCCCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHHHh-HHHHHHHHHhCCCCCCccccCCCCcceeeeeeCCC--CCCCHH
Confidence 9999999998 8999999999999999999999999 68999999999999999999888999999999985 689999
Q ss_pred HHHHHHHHHHHHHHHHHHhchhccC--ceeeEEEEEEEEcCCCCceeEEEEEeC-CCCcHHHHHHHHHHHHHHhccCCCC
Q psy16215 331 DVSHWIQELADEVCERLEDDLTLNK--RRAQLLTVSFTQETDGKVNSCSRSIAL-ASYKLQDIVEVSMQVINKTNSAPPI 407 (1041)
Q Consensus 331 eL~~~L~~LaeELaeRLRr~~~~ng--r~artLTLkLR~sd~g~~~s~SRSl~L-pT~Dae~L~~~A~~LL~rL~~~~~~ 407 (1041)
++..+|..|+.+|+.||+++ + +.+++|+|++++.++ ...+++.+- ++++...+...+..|++..+
T Consensus 250 ~l~~~l~~l~~~l~~rL~~~----~~~~~~~~l~l~l~~~~~---~~~~~~~~~~~~~~~~~l~~~~~~L~~~~~----- 317 (343)
T PRK02406 250 ACLAELPRLAEKLERRLERA----KPDKRIKTVGVKLKFADF---QQTTKEHTADPLDKADLIELLAQALLRRLG----- 317 (343)
T ss_pred HHHHHHHHHHHHHHHHHHhc----CCCccceeEEEEEEeCCC---CeEEEecCCCCCCcHHHHHHHHHHHHhhCc-----
Confidence 99999999999999999998 8 999999999999886 334444443 35566777777778877755
Q ss_pred CCCCCCEEEEEEEEcCCCCCCC
Q psy16215 408 SDLTPPLLFLGLSASKFSPLGS 429 (1041)
Q Consensus 408 ~a~~~pVRlIGVsLSdLvp~~~ 429 (1041)
..+||+|||++++|.+...
T Consensus 318 ---~~~vr~lgv~~~~l~~~~~ 336 (343)
T PRK02406 318 ---GRGVRLLGVGVTLLEPQLE 336 (343)
T ss_pred ---CCCEEEEEEEEecCCcCch
Confidence 5689999999999997643
No 18
>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=100.00 E-value=1.5e-64 Score=564.61 Aligned_cols=333 Identities=23% Similarity=0.333 Sum_probs=297.9
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCc--EEeeccCCCCCC
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEI--ELCRVPSVRGKA 84 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdL--vvV~VP~~~~k~ 84 (1041)
+||||||||||||++++|+|+++||||+++. ++.|++|||+||++||++||++.+|+++||++ ++++ +
T Consensus 1 ~hiD~d~Ffasve~~~~p~l~~~Pv~V~~~~---~~~i~~~ny~Ar~~GV~~gm~~~~A~~lcP~l~~~~v~-------~ 70 (344)
T cd01700 1 ALVDCNSFYASCERVFRPLLLGRPLVVLSNN---DGCVIARSPEAKALGIKMGSPYFKVPDLLERHGVAVFS-------S 70 (344)
T ss_pred CccccccceeeehhhhCCCcCCCeEEEEECC---CCEEEECCHHHHHhCCCCCCcHHHhHhhccccCeEEEc-------C
Confidence 6999999999999999999999999998853 46799999999999999999999999999999 6665 8
Q ss_pred CHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhc
Q psy16215 85 DISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWL 164 (1041)
Q Consensus 85 Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~ 164 (1041)
|++.|+++|++|++++++|+|.||++||||+|||||++.+
T Consensus 71 ~~~~y~~~s~~i~~~l~~~~~~ve~~s~De~~ldvt~~~~---------------------------------------- 110 (344)
T cd01700 71 NYALYGDMSRRIMSILERFSPDVEVYSIDESFLDLTGSLR---------------------------------------- 110 (344)
T ss_pred chHHHHHHHHHHHHHHHhcCCcceEeecchhhccCcCCCC----------------------------------------
Confidence 9999999999999999999999999999999999998732
Q ss_pred ccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCC----ceEEeccchHH-
Q psy16215 165 GQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQ----KQSILPQSSVS- 239 (1041)
Q Consensus 165 ~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPn----Gqtvl~p~~v~- 239 (1041)
|++ +..+|++||++|++++|++||+|||+||++||||++++||+ |++++.+++..
T Consensus 111 ---~~~-----------------~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~~~~~ 170 (344)
T cd01700 111 ---FGD-----------------LEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDEEVRD 170 (344)
T ss_pred ---CCC-----------------HHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecChhHHH
Confidence 111 24689999999999999999999999999999999999984 77788766664
Q ss_pred HhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccC-CcceeeEE
Q psy16215 240 MLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLV-SKSIGCCK 318 (1041)
Q Consensus 240 ~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~p-pKSIssEr 318 (1041)
+||+++||++|||||+++.++ |+++||+|++||+++|.+.|.++|| ..|.++|+.++|+|.++|.+..+ +|||+.+.
T Consensus 171 ~~l~~lpl~~l~gig~~~~~~-L~~~Gi~ti~dL~~~~~~~L~~rfG-~~~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~ 248 (344)
T cd01700 171 KLLKILPVGDVWGIGRRTAKK-LNAMGIHTAGDLAQADPDLLRKKFG-VVGERLVRELNGIDCLPLEEYPPPKKSIGSSR 248 (344)
T ss_pred HHhccCChhhcCccCHHHHHH-HHHcCCCcHHHHhcCCHHHHHHHHH-HHHHHHHHHhCCCCCCcCCCCCCCCcEEEEee
Confidence 999999999999999999998 8999999999999999999999999 58999999999999999976544 59999999
Q ss_pred eCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCcee-E--EEEEeCCCCcHHHHHHHHH
Q psy16215 319 RFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNS-C--SRSIALASYKLQDIVEVSM 395 (1041)
Q Consensus 319 TF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s-~--SRSl~LpT~Dae~L~~~A~ 395 (1041)
+|+. ++.+.+++..+|..|+++|+.||+++ ++.|++|+|++++.+++.... . +..+..|+++.+.|+..+.
T Consensus 249 ~~~~--~~~~~~~l~~~l~~L~~~l~~~L~~~----~~~~~~l~l~l~~~~~~~~~~~~~~~~~~~~~t~~~~~l~~~~~ 322 (344)
T cd01700 249 SFGR--DVTDLDELKQALAEYAERAAEKLRRQ----KSVARTISVFIGTSGFSRQPKYYSATNTLPYPTNDTREIVKAAL 322 (344)
T ss_pred EcCC--CCCCHHHHHHHHHHHHHHHHHHHHHc----CCcccEEEEEEEcCCCCCCCCccccccccCCcchhHHHHHHHHH
Confidence 9985 68999999999999999999999998 999999999999987642211 1 2244567889999999999
Q ss_pred HHHHHhccCCCCCCCCCCEEEEEEEEcC
Q psy16215 396 QVINKTNSAPPISDLTPPLLFLGLSASK 423 (1041)
Q Consensus 396 ~LL~rL~~~~~~~a~~~pVRlIGVsLSd 423 (1041)
.+|++++. ...+||+|||++++
T Consensus 323 ~ll~~~~~------~~~~iR~iGV~~~~ 344 (344)
T cd01700 323 RLLYAIYR------PGYAYRKAGVMLSD 344 (344)
T ss_pred HHHHHHhC------CCCcEEEEEEEeeC
Confidence 99999873 24589999999975
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.5e-59 Score=527.92 Aligned_cols=346 Identities=31% Similarity=0.443 Sum_probs=314.8
Q ss_pred cEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCC
Q psy16215 4 RIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGK 83 (1041)
Q Consensus 4 RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k 83 (1041)
|+|+||||||||||||++.+|+|+++||||++. . .+|.|++|||+||+|||+.|||+++|+++||++++++
T Consensus 1 ~~i~hvD~Daf~Asve~~~~p~l~~~Pvvv~~~-~-~~gvV~~~sy~Ar~~Gv~sam~~~~A~~~cp~~~~~~------- 71 (354)
T COG0389 1 RKILHVDMDAFYASVEERDNPELKGKPVVVGGG-A-PRGVVLAASYEARAFGVRSAMPLFEALKLCPRAIVAP------- 71 (354)
T ss_pred CeEEEEeccchhhhhhhhcCccccCCCeEEEec-C-CCCEEEecCHHHHHhCCcccChHHHHHHHCCCCEEeC-------
Confidence 689999999999999999999999999999985 1 4789999999999999999999999999999999987
Q ss_pred CCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhh
Q psy16215 84 ADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEW 163 (1041)
Q Consensus 84 ~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W 163 (1041)
++++.|+.+|.+|++++.+|+|.||++||||+|||+|+...
T Consensus 72 ~~~~~y~~~s~~i~~i~~~~~~~ve~lSIDE~~ldvt~~~~--------------------------------------- 112 (354)
T COG0389 72 PNFAAYRLASAEIRAILERYTPLVEPLSIDEAFLDLTDALR--------------------------------------- 112 (354)
T ss_pred CcHHHHHHHHHHHHHHHHhccccceeeeccceeeecccccc---------------------------------------
Confidence 89999999999999999999999999999999999998753
Q ss_pred cccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhh
Q psy16215 164 LGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYA 243 (1041)
Q Consensus 164 ~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~ 243 (1041)
.+|. ..+..+|..||+.|+.++|++||+|||+||++||+|++++||+|++++.+..+..||+
T Consensus 113 ---~~g~---------------~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~~~~~~l~ 174 (354)
T COG0389 113 ---LLGL---------------ADAPRIALEIRFGILLELGLTASVGISDNKFLAKIASDLNKPDGITVIEPEEVPALLW 174 (354)
T ss_pred ---cCCc---------------ccHHHHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHhcccCCCCEEEECHHHHHHHHh
Confidence 1221 0145799999999999999999999999999999999999999999999999999999
Q ss_pred cCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCC-cceeeEEeCCC
Q psy16215 244 NLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVS-KSIGCCKRFPG 322 (1041)
Q Consensus 244 ~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~pp-KSIssErTF~~ 322 (1041)
+|||.++||||+.++++ |+.+||.|++||+..+...|.++|| ..+.+||+.++|+|.++|.+.... ||++.+.+|+.
T Consensus 175 ~Lpv~~~~GvG~~~~~~-l~~~Gi~ti~dl~~~~~~~L~~~~g-~~~~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~~ 252 (354)
T COG0389 175 QLPVLEFWGVGKVTAEK-LRRLGISTIGDLAETDLDALKKRFG-KLGERLYRLARGIDNRPVREQALRAKSIGAESTFEE 252 (354)
T ss_pred cCChhhhCCCCHHHHHH-HHHcCChhHHHHHhcCHHHHHHHHh-HhHHHHHHHhcCCCccccccccccCccccceeeccc
Confidence 99999999999988887 8999999999999999999999999 677999999999999999998887 99999999997
Q ss_pred CCCCCCHHHHHHHHHH-HHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHHHh
Q psy16215 323 KTCLATRQDVSHWIQE-LADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKT 401 (1041)
Q Consensus 323 r~dLtd~eeL~~~L~~-LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~rL 401 (1041)
++.+.+++...|.. |+++++.||+.. +..++++++++++.++ ...+.++.+..|+.+..+++..+..++.++
T Consensus 253 --d~~~~~~~~~~l~~~l~e~~~~rl~~~----~~~~r~v~~~~~~~df-~~~t~~~~l~~p~~~~~~i~~~~~~l~~~~ 325 (354)
T COG0389 253 --DLTDAEELIERLRARLGEEVVSRLRKS----GRHGRTVSVKLKTADF-PTNTRSRKLAQPTSDPIEIYAAALPLLPPL 325 (354)
T ss_pred --cccCHHHHHHHHHHHHHHHHHHHHHHh----CCCceEEEEEEEecCC-CcceeecccCCcCCCHHHHHHHHHHHHHHh
Confidence 68889988888888 999999999997 8899999999999997 345566667777888999999999999988
Q ss_pred ccCCCCCCCCCCEEEEEEEEcCCCCCC
Q psy16215 402 NSAPPISDLTPPLLFLGLSASKFSPLG 428 (1041)
Q Consensus 402 ~~~~~~~a~~~pVRlIGVsLSdLvp~~ 428 (1041)
+.. .+..++|++||++++|....
T Consensus 326 ~~~----~~~~~~rl~gv~~~~~~~~~ 348 (354)
T COG0389 326 LFR----GRGRRIRLLGVSGPELIDSE 348 (354)
T ss_pred hcc----CCCceEEEEEEEecCccccc
Confidence 742 11457889999999998765
No 20
>KOG2094|consensus
Probab=100.00 E-value=7.4e-61 Score=518.73 Aligned_cols=341 Identities=28% Similarity=0.412 Sum_probs=305.5
Q ss_pred CcEEEEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCC
Q psy16215 3 SRIIALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRG 82 (1041)
Q Consensus 3 ~RvI~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~ 82 (1041)
+|+|+|||||+|||+||++++|.|+++|+||++. +++.++||.||++||+.+||.+-|+++||+|++||
T Consensus 102 sr~~vhvDmDAfyAaVE~~dnP~lk~~PmAVGs~-----smlsTaNY~ARkFGVRaaMPgFIarklCPdLiiVP------ 170 (490)
T KOG2094|consen 102 SRIIVHVDMDAFYAAVEMLDNPKLKSKPMAVGSK-----SMLSTANYVARKFGVRAAMPGFIARKLCPDLIIVP------ 170 (490)
T ss_pred cceEEEechHHHHHHHHhccCcccccCCccccch-----hhhhhhhHHHHHhhhhhcCchHHHhccCCceEEeC------
Confidence 5899999999999999999999999999999754 57889999999999999999999999999999987
Q ss_pred CCCHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchh
Q psy16215 83 KADISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVME 162 (1041)
Q Consensus 83 k~Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~ 162 (1041)
.+|..|+.+|+++-++|.+|.|.+-..|+||+|||+|..++.+-
T Consensus 171 -~n~~kYt~~Ske~~~v~~~YDsn~~~~SlDEaylnlT~~l~~~~----------------------------------- 214 (490)
T KOG2094|consen 171 -LNFSKYTIVSKEIQNVLAQYDSNFCAMSLDEAYLNLTSHLRERE----------------------------------- 214 (490)
T ss_pred -CCcHHHHHHHHHHHHHHHHcCCccccchHHHHHHhHHHHHHHhh-----------------------------------
Confidence 89999999999999999999999999999999999999987430
Q ss_pred hcccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccc--hHHH
Q psy16215 163 WLGQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQS--SVSM 240 (1041)
Q Consensus 163 W~~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~--~v~~ 240 (1041)
||. ++. + -...++++||.+|.+++|+|||+|||+|++|||+||+.+|||||++++++ .+..
T Consensus 215 -----~g~----l~~-n-------G~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~aim~ 277 (490)
T KOG2094|consen 215 -----LGF----LVE-N-------GITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIAIMK 277 (490)
T ss_pred -----cch----hhh-c-------cHHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHHHHH
Confidence 110 000 0 02478999999999999999999999999999999999999999999875 6799
Q ss_pred hhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeC
Q psy16215 241 LYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRF 320 (1041)
Q Consensus 241 fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF 320 (1041)
||.+|||+++-|||+.+... |..|||.||||+.+- ...|--.|.+...+.+++-+.|...++......+|||+.++||
T Consensus 278 F~kdLPvRkV~GIGrV~E~q-Lkal~IkTcgdm~~k-~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~ErTF 355 (490)
T KOG2094|consen 278 FMKDLPVRKVSGIGRVTEQQ-LKALGIKTCGDMQQK-LVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSERTF 355 (490)
T ss_pred HHhcCCcccccchhHHHHHH-HHhcCceeHHHHHHh-hhHHHHHhCchhHHHHHHHhhcCCCCcCccccccccccceeee
Confidence 99999999999999877765 789999999999875 6778888988777888999999999988888889999999999
Q ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCC--CcHHHHHHHHHHHH
Q psy16215 321 PGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALAS--YKLQDIVEVSMQVI 398 (1041)
Q Consensus 321 ~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT--~Dae~L~~~A~~LL 398 (1041)
.. +.+...+...+..||+.|++-|++. |.++++|+|++++..| ..++|+.+... ...++|+..|.+||
T Consensus 356 s~---~sd~~il~~k~qel~~~lsedlqK~----glv~rtvtiKlK~ssF---ev~Tr~~t~s~vv~S~edi~k~aleLL 425 (490)
T KOG2094|consen 356 SS---TSDPSILYSKLQELCQMLSEDLQKE----GLVGRTVTIKLKTSSF---EVHTRQKTISQVVHSEEDILKPALELL 425 (490)
T ss_pred cc---cCCHHHHHHHHHHHHHHHHHHHHhc----CcccceEEEEEeccce---eeeeccCchhhhhccHHHHHHHHHHHH
Confidence 84 7889999999999999999999998 9999999999999987 67787776643 57899999999999
Q ss_pred HHhccCCCCCCCCCCEEEEEEEEcCCCCC
Q psy16215 399 NKTNSAPPISDLTPPLLFLGLSASKFSPL 427 (1041)
Q Consensus 399 ~rL~~~~~~~a~~~pVRlIGVsLSdLvp~ 427 (1041)
++.+ +..||++||+++.|+..
T Consensus 426 k~e~--------~~~iRLlGvR~sqlv~e 446 (490)
T KOG2094|consen 426 KQEY--------PMTIRLLGVRASQLVSE 446 (490)
T ss_pred Hhhc--------CceEeeeeeeHhhccch
Confidence 9977 56899999999999865
No 21
>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=100.00 E-value=1.1e-53 Score=473.10 Aligned_cols=331 Identities=20% Similarity=0.211 Sum_probs=291.2
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCCCH
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADI 86 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~Dl 86 (1041)
+.|+|++||++|+.+.+|+|+++||||++.+. +++|++|||+||++||+.||++++|+++||++++++ +|+
T Consensus 1 l~~~~p~~~l~~~~~~~p~l~~~Pv~V~~~~~--~~~V~~~s~~Ar~~GV~~Gm~~~~A~~lcP~l~~~~-------~~~ 71 (335)
T cd03468 1 LALWFPRLPLDALLRNRPADDEAPLAVVERKK--AGRILACNAAARAAGVRPGMPLAEALALCPNLQVVE-------YDP 71 (335)
T ss_pred CeeeCCcCHHHHHhhcCCcccCCCeEEEEeCC--CCEEEecCHHHHHcCCCCCCcHHHHHHhCCCCeeec-------CCh
Confidence 47899999999999999999999999988642 689999999999999999999999999999999987 899
Q ss_pred HHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhccc
Q psy16215 87 SKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQ 166 (1041)
Q Consensus 87 d~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~~~ 166 (1041)
+.|.++|++|++++++|+|.||.+||||+|||+|+..+
T Consensus 72 ~~y~~~s~~i~~~l~~~s~~ve~~s~de~~ldvs~~~~------------------------------------------ 109 (335)
T cd03468 72 EADARALQELALWLLRFTPLVALDGPDGLLLDVTGCLH------------------------------------------ 109 (335)
T ss_pred HHHHHHHHHHHHHHHhcCCccccCCCCeEEEEcccchh------------------------------------------
Confidence 99999999999999999999999999999999998854
Q ss_pred ccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHH-hhhcC
Q psy16215 167 VYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSM-LYANL 245 (1041)
Q Consensus 167 LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~-fL~~L 245 (1041)
+|++ ...+++.|++.+. ++|++||+|||+||++||||++.+||+|++.+.+..... ||+++
T Consensus 110 ~~~~-----------------~~~~a~~i~~~~~-~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~~~~~~~l~~l 171 (335)
T cd03468 110 LFGG-----------------EDALAASLRAALA-TLGLSARAGIADTPGAAWLLARAGGGRGVLRREALAAALVLLAPL 171 (335)
T ss_pred hcCC-----------------HHHHHHHHHHHHH-HcCCeEEEEecCCHHHHHHHhccCCCCccCCchHHHHHhhccCCC
Confidence 3432 2468999999996 689999999999999999999999999998877666654 89999
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCccc--ccccCCcceeeEEeCCCC
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPV--NARLVSKSIGCCKRFPGK 323 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV--~p~~ppKSIssErTF~~r 323 (1041)
|+ ++||||+++.++ |+++||+|++||+++|...|+++|| ..|.++|+.++|+|..++ .+..++++++.+.+|+.
T Consensus 172 p~-~~~gig~~~~~~-L~~~Gi~t~~dl~~~~~~~l~~rfG-~~~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~~- 247 (335)
T cd03468 172 PV-AALRLPPETVEL-LARLGLRTLGDLAALPRAELARRFG-LALLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLEE- 247 (335)
T ss_pred Ch-hHhCCCHHHHHH-HHHhCcccHHHHHhCChHHHHhhcC-HHHHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCCC-
Confidence 99 599999999987 8999999999999999999999999 578999999999999999 45567899999999986
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEEeCCCCcHHHHHHHHHHHHHHhcc
Q psy16215 324 TCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSIALASYKLQDIVEVSMQVINKTNS 403 (1041)
Q Consensus 324 ~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl~LpT~Dae~L~~~A~~LL~rL~~ 403 (1041)
+..+.+ ...|..|+.+|+.||+.+ +..+++|+|++++.++ ...+.+.....|+++...|++.+..+|+++..
T Consensus 248 -~~~~~~--~~~l~~l~~~l~~~L~~~----~~~~~~l~l~l~~~~~-~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~~ 319 (335)
T cd03468 248 -PIARGL--LFPLRRLLEQLCAFLALR----GLGARRLSLTLFREDG-RVTRVLVGLARPSRDDLPLLRLLRERLERLAL 319 (335)
T ss_pred -CcchhH--HHHHHHHHHHHHHHHHHc----CCeeeEEEEEEEEECC-ceEEEEEeccCCccCHHHHHHHHHhhhhccCC
Confidence 344433 899999999999999998 9999999999999876 33445555566788899999999999998762
Q ss_pred CCCCCCCCCCEEEEEEEEc
Q psy16215 404 APPISDLTPPLLFLGLSAS 422 (1041)
Q Consensus 404 ~~~~~a~~~pVRlIGVsLS 422 (1041)
.....+||++||++.
T Consensus 320 ----~~~~~~v~~~~v~~~ 334 (335)
T cd03468 320 ----PRGIAPVRLLALTAE 334 (335)
T ss_pred ----CCCeeeEEEEEeecc
Confidence 001168999999874
No 22
>KOG2093|consensus
Probab=100.00 E-value=1.9e-52 Score=489.32 Aligned_cols=356 Identities=24% Similarity=0.365 Sum_probs=312.0
Q ss_pred EEEeCCchhHHhHhhhCCCCCCCcEEEEecCC--CCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCC
Q psy16215 7 ALIDMDCFYCQVECKLNPSLHGKPLAVVQYNT--WKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKA 84 (1041)
Q Consensus 7 ~HIDmD~FYASVE~~~~PeLrgkPVaV~q~n~--~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~ 84 (1041)
+|+++||||.+|+...+++++++|++|+++.+ .+.+.|.+|||+||+||||+||.+.+|++|||+|+++| |
T Consensus 374 ~~v~~dcf~~sv~~~n~~D~k~kpvav~hg~d~~~s~sEIASCsY~AR~~GIKNGMfV~~A~klCPqL~~lP-------Y 446 (1016)
T KOG2093|consen 374 VKVELDCFFVSVVIKNRLDLKDKPVAVCHGSDNPKSTSEIASCSYEARAYGIKNGMFVRHAKKLCPQLVILP-------Y 446 (1016)
T ss_pred hHHHHHHhhhhheeccccccccCcceeeccCCCCcchhhhhccccHHHHhCcccceeHHHHHHhCcccEeec-------c
Confidence 45556677777777788999999999998422 24567899999999999999999999999999999987 9
Q ss_pred CHHHHHHHHHHHHHHHHhcCCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhc
Q psy16215 85 DISKYRNAGREVIAVLSEFSNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWL 164 (1041)
Q Consensus 85 Dld~Yr~aS~kI~eIL~~fSP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~ 164 (1041)
||+.|.++|+.++++|++|+-.|+.+|+||+|+|+++....
T Consensus 447 ~FE~Ykevs~tlYetlasytl~I~aVSCDEa~vd~s~~~~~--------------------------------------- 487 (1016)
T KOG2093|consen 447 DFEAYKEVSETLYETLASYTLNIEAVSCDEAFVDVSDLSDE--------------------------------------- 487 (1016)
T ss_pred cHHHHHHHHHHHHHHHHhhccceeeecchhhhhhhhhhhhh---------------------------------------
Confidence 99999999999999999999999999999999999987541
Q ss_pred ccccCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhc
Q psy16215 165 GQVYSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYAN 244 (1041)
Q Consensus 165 ~~LFg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~ 244 (1041)
+.- ....+|..||+.|++.|||+||||||.|++||+||++.+|||||+++.++.+.+||..
T Consensus 488 ---~~~----------------tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~~veeFis~ 548 (1016)
T KOG2093|consen 488 ---ENE----------------TPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAEKVEEFISQ 548 (1016)
T ss_pred ---hcc----------------CHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecHHHHHHHhhh
Confidence 000 0246899999999999999999999999999999999999999999999999999999
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCCCCcccccccCCcceeeEEeCCCCC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGIDHEPVNARLVSKSIGCCKRFPGKT 324 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGiD~epV~p~~ppKSIssErTF~~r~ 324 (1041)
++|.+|||+|..|..+ |..+||+|||||+......|++.||++.|..+|+.|||+|++|+.....+||++++.+|+.|
T Consensus 549 ~~v~~LPGVG~sm~~k-L~s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~GIR- 626 (1016)
T KOG2093|consen 549 LKVDDLPGVGSSMKSK-LVSQFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYGIR- 626 (1016)
T ss_pred cccccCCCccHHHHHH-HHHhccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeeccee-
Confidence 9999999999999998 79999999999999999999999999999999999999999998887789999999999985
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEE------------EcCCCCceeEEEEEeC--CCCcHHHH
Q psy16215 325 CLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFT------------QETDGKVNSCSRSIAL--ASYKLQDI 390 (1041)
Q Consensus 325 dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR------------~sd~g~~~s~SRSl~L--pT~Dae~L 390 (1041)
++...++...|..++++|-+||-+- ++.++.++|++. |.++|.|..+.|+..+ ||.+...|
T Consensus 627 -Ftn~~ev~~fl~~~~eEl~rkL~ei----~k~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~~~Td~~~iI 701 (1016)
T KOG2093|consen 627 -FTNIKEVEQFLCLLSEELRRKLLEI----SKTASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLREPTDCNRII 701 (1016)
T ss_pred -eccHHHHHHHHHHHHHHHHHHHHHh----hccccchhHHHHhhcCCCCCccccccceeeccchhhhhhccCccccccch
Confidence 8899999999999999999999886 888999998875 3334556667777655 67888899
Q ss_pred HHHHHHHHHHhccCCCCCCCCCCEEEEEEEEc-CCCCCCC---CcchhhcCCCC
Q psy16215 391 VEVSMQVINKTNSAPPISDLTPPLLFLGLSAS-KFSPLGS---HPSIQQFFKPQ 440 (1041)
Q Consensus 391 ~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLS-dLvp~~~---q~sI~DLFd~~ 440 (1041)
...++.|.+.+.. ....+|++||.+. .|.+... +..+..||+..
T Consensus 702 tt~~~~L~~t~~~------~~~elRG~gi~~ntkL~~~~~~~~~~~l~e~Fgt~ 749 (1016)
T KOG2093|consen 702 TTEVLRLYETNSE------PPSELRGLGIHSNTKLMDVLENLPPELLSEMFGTY 749 (1016)
T ss_pred HHHHHHHHHhcCC------ChHHhccchhhccccccccccCCcHHHHHhhcccc
Confidence 9999999999874 2456899999994 8887655 33567788654
No 23
>PF00817 IMS: impB/mucB/samB family; InterPro: IPR001126 In Escherichia coli, UV and many chemicals appear to cause mutagenesis by a process of translesion synthesis that requires DNA polymerase III and the SOS-regulated proteins UmuD, UmuC and RecA. This machinery allows the replication to continue through DNA lesion, and therefore avoid lethal interruption of DNA replication after DNA damage []. UmuC is a well conserved protein in prokaryotes, with a homologue in yeast species. Proteins currently known to belong to this family are listed below: E. coli MucB protein. Plasmid-born analogue of the UmuC protein. Saccharomyces cerevisiae (Baker's yeast) Rev1 protein. Homologue of UmuC also required for normal induction of mutations by physical and chemical agents. Salmonella typhimurium ImpB protein. Plasmid-born analogue of the UmuC protein. Bacterial UmuC protein. E. coli DNA-damage-inducible protein P (DinP). S. typhimurium SamB homologue of UmuC plasmid associated. ; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3BJY_A 2AQ4_A 3OSP_A 4DL7_A 4DL6_A 3TQ1_A 3MR2_A 4EEY_A 3MR3_A 4DL4_A ....
Probab=100.00 E-value=2.8e-35 Score=293.18 Aligned_cols=148 Identities=37% Similarity=0.597 Sum_probs=133.7
Q ss_pred EeCCchhHHhHhhhCCCCCCCcEEEEecCCCCCcEEEEcCHHHHHcCCCCCCCHHHHHhhCCCcEEeeccCCCCCCCHHH
Q psy16215 9 IDMDCFYCQVECKLNPSLHGKPLAVVQYNTWKGGGIIAVNYEARHKGVTRHMRGDEAKQHCPEIELCRVPSVRGKADISK 88 (1041)
Q Consensus 9 IDmD~FYASVE~~~~PeLrgkPVaV~q~n~~~~g~VIAvNYeARa~GVK~GMpl~eArkLCPdLvvV~VP~~~~k~Dld~ 88 (1041)
|||||||||||++++|+|+++||||+++++ .+++|++|||+||++||++||++.+|+++||++++++ +|++.
T Consensus 1 iD~~~F~as~e~~~~p~L~~~PvaV~~~~~-~~~~V~a~n~~Ar~~GV~~Gm~~~~A~~lcp~l~~~~-------~d~~~ 72 (149)
T PF00817_consen 1 IDMDAFFASVERRRDPELRGRPVAVVSGQG-NRGRVIAANYEARAAGVRPGMPLAEALALCPDLVVVP-------PDPER 72 (149)
T ss_dssp EEETTHHHHHHHHHSGGGTTSSEEEEECTS-STCEEEEE-HHHHTTTSTTTSBHHHHHHHSTTSEEEE-------EEHHH
T ss_pred CccccHHHHHHhhhCccccCCCEEEEeccc-ccchhhhhHHHHHhhccccchhhhhHhhhccceeecc-------ccHHH
Confidence 799999999999999999999999999752 4589999999999999999999999999999999987 89999
Q ss_pred HHHHHHHHHHHHHhc-CCcEEEeccceEEEEcchhHHHHHhhccccccccccccccccCCCCCCchhhhhhcchhhcccc
Q psy16215 89 YRNAGREVIAVLSEF-SNIVERASIDEAYIDLTDVVHERMKSIGHIAASQLSNTFVVGFGPDNNDEDARKAGVMEWLGQV 167 (1041)
Q Consensus 89 Yr~aS~kI~eIL~~f-SP~VE~aSIDEafLDLT~~v~~~L~~~~~~~~~~L~~~~~~g~~~~~~~e~~r~~g~~~W~~~L 167 (1041)
|++++++|++++.+| +|.||.+|+||+|||+|++.+ +
T Consensus 73 ~~~~~~~l~~~l~~~~sp~ve~~s~de~~ldv~~~~~------------------------------------------l 110 (149)
T PF00817_consen 73 YREASERLAEILYRFSSPRVEVYSPDELFLDVTGSLR------------------------------------------L 110 (149)
T ss_dssp HHHHHHHHHHHHHTTTCSEEEEEETTEEEEEEHHHHH------------------------------------------H
T ss_pred HHHHHHHHHHHHHhcccccceecccccccccCCcchh------------------------------------------h
Confidence 999999999999999 789999999999999999765 3
Q ss_pred cCCCcccccccchhHHhhhHHHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhcc
Q psy16215 168 YSDTDTSLMENTEDFQELAIAGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCG 223 (1041)
Q Consensus 168 Fg~~d~p~v~~~~~~~~L~~g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~ 223 (1041)
|++ ...++++||++|.+++|++||+|||+|+++||||++
T Consensus 111 ~~~-----------------~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 111 FGG-----------------EEALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp HHH-----------------HHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred cch-----------------HHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 322 146899999999999999999999999999999984
No 24
>PF11799 IMS_C: impB/mucB/samB family C-terminal domain; InterPro: IPR017961 This entry represents the little finger domain found in Y-family (lesion bypass) DNA polymerases. Y-family polymerases were originally known as UmuC/DinB/Rev1/Rad30 after each branch of the family. These enzymes are characterised by their low-fidelity synthesis on undamaged DNA templates and by their ability to traverse replication-blocking lesions. By contrast, high-fidelity polymerases (such as DNA polymerase III) are sensitive to distortions in the DNA template. As a result, Y-family polymerases can extend primer strands across DNA strand lesions that would otherwise stall replicative polymerases. To minimize mutations through their low fidelity synthesis, these enzymes are regulated, and are thought to interact with processivity factors, beta-clamp or proliferating cell nuclear antigen (PCNA), which are also essential for the function of replicative DNA polymerases []. Organisms can contain more than one Y-family polymerase, each with a unique DNA damage bypass and fidelity profile. For example, humans posses four Y-family polymerases: DNA polymerases kappa, iota, eta and Rev1. Y-family polymerases show no homology to DNA polymerases from the A-, B-, C-, D- or X-families []. The Y-family of DNA polymerases includes the following enzymes: Prokaryotic DNA polymerase IV (DinB) []. Archaeal DinB homologue DNA polymerase IV []. Eukaryotic DinB homologue DNA polymerase kappa []. Prokarytoic DNA repair proteins UmuC and UmuD []. Eukaryotic Rad30 homologues DNA polymerase eta and iota [, ]. Eukaryotic DNA repair protein Rev1 []. Human DNA polymerase kappa is a right-handed shaped molecule with palm, fingers, thumb, little finger and wrist subdomains []. This entry represents the little finger domain.; GO: 0003684 damaged DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006281 DNA repair; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 3GV8_B 3G6V_A 4EBC_A 3GV5_B ....
Probab=99.38 E-value=2.8e-12 Score=122.49 Aligned_cols=123 Identities=29% Similarity=0.522 Sum_probs=92.7
Q ss_pred Ccccc-cccCCcceeeEEeCCCCCCCCCHHHHHHHHHHHHHHHHHHHHhchhccCceeeEEEEEEEEcCCCCceeEEEEE
Q psy16215 302 HEPVN-ARLVSKSIGCCKRFPGKTCLATRQDVSHWIQELADEVCERLEDDLTLNKRRAQLLTVSFTQETDGKVNSCSRSI 380 (1041)
Q Consensus 302 ~epV~-p~~ppKSIssErTF~~r~dLtd~eeL~~~L~~LaeELaeRLRr~~~~ngr~artLTLkLR~sd~g~~~s~SRSl 380 (1041)
++||. +..++|||+++++|+. ++.+.+++..+|..|+.+|+.||++. ++.|++|+|+++|.+++.+...+++.
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~~--~~~~~~~i~~~l~~l~~~l~~rL~~~----~~~~~~i~l~l~~~~~~~~~~~~~~~ 74 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFPE--PISDREEIEEWLRELAEELAERLRER----GLAARTITLKLRYSDFGRCSSRSRSI 74 (127)
T ss_dssp ------SCSS-SEEEEEEEECE--EESSHHHHHHHHHHHHHHHHHHHHHC----TEEEEEEEEEEEETTSCSCEEEEEEE
T ss_pred CCCCCCCCCCCCEEEEEEECCC--CCCCHHHHHHHHHHHHHHHHHHHHhh----CcCCceEEEEEEecCCcccceeeEEE
Confidence 36787 7889999999999985 68899999999999999999999987 99999999999999875444555555
Q ss_pred eC--CCCcHHHHHHHHHHHHHHhccCCCCCCCCCCEEEEEEEEcCCC-CCCCCcchhhcC
Q psy16215 381 AL--ASYKLQDIVEVSMQVINKTNSAPPISDLTPPLLFLGLSASKFS-PLGSHPSIQQFF 437 (1041)
Q Consensus 381 ~L--pT~Dae~L~~~A~~LL~rL~~~~~~~a~~~pVRlIGVsLSdLv-p~~~q~sI~DLF 437 (1041)
.+ |+++...|+..+..+|+++... ...++|+|||++++|. +.+ ..|.+||
T Consensus 75 ~l~~p~~~~~~l~~~~~~l~~~~~~~-----~~~~vr~igv~~~~l~~~~~--~~q~~lF 127 (127)
T PF11799_consen 75 RLPFPTNDADELLKAARELLERLLYD-----PGFPVRLIGVSASDLIEPAG--QRQLDLF 127 (127)
T ss_dssp EECCCEHCHHHHHHHHHHHHHHHHHH-----TTCGEEEEEEEEEEEEEC------B----
T ss_pred eccCCcCCHHHHHHHHHHHHHHHhcC-----CCCCEEEEEEEECCCcCCCC--CcccccC
Confidence 55 6778899999999999665321 1467999999999999 443 3577777
No 25
>PF11798 IMS_HHH: IMS family HHH motif; InterPro: IPR024728 This helix-hairpin-helix motif is found in proteins belonging to the type-Y family of DNA polymerases []. This type of polymerases are thought to be involved in UV protection and mutation [, ]. ; PDB: 3PZP_B 2OH2_B 2W7O_B 3IN5_B 1T94_A 2W7P_B 2W8K_A 2AGQ_A 1RYR_A 3RAX_A ....
Probab=98.18 E-value=1.1e-06 Score=67.27 Aligned_cols=32 Identities=22% Similarity=0.296 Sum_probs=28.3
Q ss_pred cchHHHhhhcCCccccccCCHHHHHHHHHhCCC
Q psy16215 235 QSSVSMLYANLSIKKVRHLGGKLGDEVVETLQC 267 (1041)
Q Consensus 235 p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI 267 (1041)
|+++.+||+++||+++||||++++++ |+++||
T Consensus 1 pe~v~~~l~~lpi~~~~GIG~kt~~k-L~~~GI 32 (32)
T PF11798_consen 1 PEDVPEFLWPLPIRKFWGIGKKTAKK-LNKLGI 32 (32)
T ss_dssp CHHHHHHHHCSBGGGSTTS-HHHHHH-HHCTT-
T ss_pred ChHHHHHHhcCCHHhhCCccHHHHHH-HHHccC
Confidence 57899999999999999999999998 899997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.54 E-value=5.3e-05 Score=85.20 Aligned_cols=80 Identities=16% Similarity=0.135 Sum_probs=65.4
Q ss_pred hhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcC---CC--CcccccccCCcc
Q psy16215 241 LYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARG---ID--HEPVNARLVSKS 313 (1041)
Q Consensus 241 fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRG---iD--~epV~p~~ppKS 313 (1041)
-|.++||.++||||++++++ |...||.|++||+.+++..|.+.+| +..|..+|+.++| .+ .+++.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~-L~~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEK-LREAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHH-HHHcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 47899999999999999998 8999999999999999999999999 4588999999998 43 344443344577
Q ss_pred eeeEEeCC
Q psy16215 314 IGCCKRFP 321 (1041)
Q Consensus 314 IssErTF~ 321 (1041)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 77665553
No 27
>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=96.79 E-value=0.0012 Score=73.97 Aligned_cols=74 Identities=18% Similarity=0.144 Sum_probs=60.9
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHc---CCC--CcccccccCCcceeeEEe
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIAR---GID--HEPVNARLVSKSIGCCKR 319 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aR---GiD--~epV~p~~ppKSIssErT 319 (1041)
|.++||||++++++ |...||.|++||+.+++..|.+.+| ...+..+|..++ |.+ .+++.....+++++...+
T Consensus 1 l~~i~gig~~~~~~-L~~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~T 79 (310)
T TIGR02236 1 LEDLPGVGPATAEK-LREAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKTIGKITT 79 (310)
T ss_pred CcccCCCCHHHHHH-HHHcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhccCCeecC
Confidence 56899999999998 7999999999999999999999998 346899999998 877 555554445677777766
Q ss_pred CC
Q psy16215 320 FP 321 (1041)
Q Consensus 320 F~ 321 (1041)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 64
No 28
>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=96.24 E-value=0.0038 Score=53.93 Aligned_cols=51 Identities=22% Similarity=0.234 Sum_probs=43.7
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
+.+|+|||++++.+ |...|+.|+.||+..+++.|.+. +|++.+..+...++
T Consensus 7 L~~I~Gig~~~a~~-L~~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 7 LLSIPGIGPKRAEK-LYEAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHTSTTCHHHHHHH-HHHTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred hccCCCCCHHHHHH-HHhcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 34789999999998 67779999999999999999987 67888888877664
No 29
>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=94.99 E-value=0.018 Score=54.65 Aligned_cols=41 Identities=10% Similarity=0.222 Sum_probs=36.7
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhh
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEE 287 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~ 287 (1041)
.+++|||||+++++- |..+||+++.||+..++..|-.++..
T Consensus 13 ~L~~iP~IG~a~a~D-L~~LGi~s~~~L~g~dP~~Ly~~lc~ 53 (93)
T PF11731_consen 13 DLTDIPNIGKATAED-LRLLGIRSPADLKGRDPEELYERLCA 53 (93)
T ss_pred HHhcCCCccHHHHHH-HHHcCCCCHHHHhCCCHHHHHHHHHH
Confidence 568999999999997 78999999999999999988877764
No 30
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=92.26 E-value=0.22 Score=54.38 Aligned_cols=56 Identities=7% Similarity=0.144 Sum_probs=50.0
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHcCCCC
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIARGIDH 302 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aRGiD~ 302 (1041)
.|.+|+|||++.+++ |...|+.|+.+|...+...|.+. +|...+..++..+.+.+.
T Consensus 4 ~L~~IpGIG~krakk-Ll~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 4 ELEDISGVGPSKAEA-LREAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred ccccCCCcCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc
Confidence 578999999999988 56789999999999999999999 888899999999986543
No 31
>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=90.25 E-value=0.54 Score=41.99 Aligned_cols=55 Identities=16% Similarity=0.112 Sum_probs=40.2
Q ss_pred HHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHH
Q psy16215 239 SMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYY 295 (1041)
Q Consensus 239 ~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~ 295 (1041)
...+...||..+ |+..+.... |.+.||+|++||..++...|.+. ||.+....+..
T Consensus 6 ~~~~~~~~I~~L-~LS~Ra~n~-L~~~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI~~ 62 (66)
T PF03118_consen 6 EEELLDTPIEDL-GLSVRAYNC-LKRAGIHTVGDLVKYSEEDLLKIKNFGKKSLEEIKE 62 (66)
T ss_dssp -HHHHCSBGGGS-TSBHHHHHH-HHCTT--BHHHHHCS-HHHHHTSTTSHHHHHHHHHH
T ss_pred hHHHhcCcHHHh-CCCHHHHHH-HHHhCCcCHHHHHhCCHHHHHhCCCCCHhHHHHHHH
Confidence 345667899999 899988876 89999999999999999998765 66555444433
No 32
>PRK02362 ski2-like helicase; Provisional
Probab=90.20 E-value=0.32 Score=61.29 Aligned_cols=55 Identities=15% Similarity=0.074 Sum_probs=50.4
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGI 300 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGi 300 (1041)
+|+-.|||||++.+++ |..+||+++.||+++....|.+.||.+.+..++..++..
T Consensus 652 ~~L~~ip~i~~~~a~~-l~~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 652 LDLVGLRGVGRVRARR-LYNAGIESRADLRAADKSVVLAILGEKIAENILEQAGRR 706 (737)
T ss_pred HHHhCCCCCCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhCcc
Confidence 5888999999999987 678999999999999999999999999999999998854
No 33
>PF08827 DUF1805: Domain of unknown function (DUF1805); InterPro: IPR014931 This protein is found in bacteria and archaea and has an N-terminal tetramerisation region that is composed of beta sheets. ; PDB: 1QW2_A.
Probab=89.92 E-value=0.18 Score=44.29 Aligned_cols=27 Identities=26% Similarity=0.342 Sum_probs=19.6
Q ss_pred cEEEEcCHHHHHcCCCCCCCHHHHHhh
Q psy16215 42 GGIIAVNYEARHKGVTRHMRGDEAKQH 68 (1041)
Q Consensus 42 g~VIAvNYeARa~GVK~GMpl~eArkL 68 (1041)
+.|.++|+.|+++||+.||+..+|+.+
T Consensus 32 a~v~~vt~~A~~lGI~~Gm~g~eAL~~ 58 (59)
T PF08827_consen 32 APVESVTSAAEELGIKPGMTGREALEK 58 (59)
T ss_dssp SB-SEE-HHHHHTT--TT-BHHHHGGG
T ss_pred ChHHHHHHHHHHhCCCCCCCHHHHHHh
Confidence 357899999999999999999999875
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=89.46 E-value=0.35 Score=48.62 Aligned_cols=38 Identities=13% Similarity=0.261 Sum_probs=33.6
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH 284 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr 284 (1041)
.|+.|-|||+++... |+.+||+|..||+.++...+...
T Consensus 68 DLt~I~GIGPk~e~~-Ln~~GI~tfaQIAAwt~~di~~i 105 (133)
T COG3743 68 DLTRISGIGPKLEKV-LNELGIFTFAQIAAWTRADIAWI 105 (133)
T ss_pred cchhhcccCHHHHHH-HHHcCCccHHHHHhcCHHHHHHH
Confidence 578899999999987 89999999999999998876654
No 35
>PF04994 TfoX_C: TfoX C-terminal domain; InterPro: IPR007077 This domain is found in a number of bacterial proteins including the TfoX gene product of Haemophilus influenzae. TfoX may play a key role in the development of genetic competence by regulating the expression of late competence-specific genes []. This family corresponds to the C-terminal presumed domain of TfoX. The domain is found in association with the N-terminal domain in some, but not all members of this group, suggesting this is an autonomous and functionally unrelated domain. For example it is found associated with Q9JZR1 from SWISSPROT in IPR002125 from INTERPRO.; PDB: 3BQT_A 3MAB_A.
Probab=89.28 E-value=0.35 Score=44.88 Aligned_cols=35 Identities=14% Similarity=0.225 Sum_probs=25.3
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHH
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQ 280 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~ 280 (1041)
-.|+++|+||+++.+. |.+.||+|+.||.++....
T Consensus 3 ~~l~~LpNig~~~e~~-L~~vGI~t~~~L~~~Ga~~ 37 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERM-LAKVGIHTVEDLRELGAVE 37 (81)
T ss_dssp --GCGSTT--HHHHHH-HHHTT--SHHHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHH-HHHcCCCCHHHHHHhCHHH
Confidence 3689999999998876 8999999999999986543
No 36
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.14 E-value=0.39 Score=42.33 Aligned_cols=47 Identities=17% Similarity=0.243 Sum_probs=35.6
Q ss_pred cccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 250 VRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 250 IpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
|||||.+.++.|++.+| ++..|.+.+.+.|... +|+..+..++.+.+
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHHHC
Confidence 68999999999888887 8999999999999887 88888888888765
No 37
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=88.44 E-value=0.28 Score=41.99 Aligned_cols=27 Identities=19% Similarity=0.161 Sum_probs=20.3
Q ss_pred cccccCCHHHHHHHHHhCCCccchhhhh
Q psy16215 248 KKVRHLGGKLGDEVVETLQCSTMLELEK 275 (1041)
Q Consensus 248 ~kIpGIG~K~a~rLL~~LGI~TIGDLa~ 275 (1041)
..|||||++++++ +-..|++|+.||..
T Consensus 5 ~~I~GVG~~tA~~-w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARK-WYAKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHH-HHHTT--SHHHHHH
T ss_pred hhcccccHHHHHH-HHHhCCCCHHHHhh
Confidence 4799999999998 67899999999965
No 38
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=87.33 E-value=0.62 Score=46.21 Aligned_cols=53 Identities=11% Similarity=0.236 Sum_probs=44.5
Q ss_pred ccchHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhh
Q psy16215 234 PQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEE 287 (1041)
Q Consensus 234 ~p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~ 287 (1041)
+...+..+...-.+-.|+|||+..+. ||...||.|+.+|+..++..|...++.
T Consensus 42 ~~~~l~~w~~~AdL~ri~gi~~~~a~-LL~~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 42 SERNLLKWVNQADLMRIPGIGPQYAE-LLEHAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred CHHHHHHHHhHHHhhhcCCCCHHHHH-HHHHhCcCcHHHHHhCCHHHHHHHHHH
Confidence 44556666666667789999999987 589999999999999999999999984
No 39
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=85.07 E-value=1.1 Score=54.99 Aligned_cols=53 Identities=11% Similarity=0.154 Sum_probs=47.3
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH-hhhhhHHHHHHHHcC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH-FEEKTASWLYYIARG 299 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr-FG~k~G~~L~~~aRG 299 (1041)
-.+.+|||||++..+.||..+| ++..+.+.+.++|.+. +|...|..++..++|
T Consensus 514 S~Ld~I~GiG~kr~~~Ll~~Fg--s~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 514 DILDKIKGIGEVKKEIIYRNFK--TLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred CccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 4788999999999999888776 8899999999999999 667889999999887
No 40
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=82.30 E-value=1.6 Score=51.78 Aligned_cols=68 Identities=19% Similarity=0.066 Sum_probs=56.8
Q ss_pred eccchHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcCCC
Q psy16215 233 LPQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARGID 301 (1041)
Q Consensus 233 l~p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRGiD 301 (1041)
..|.+...++..-.|.-+|||++...+. |+.+||+|+.||+..+...+...+| ...+..+-..++-..
T Consensus 213 f~p~C~~~a~e~~~L~Lv~Gi~~~r~~~-l~~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~ 282 (474)
T COG2251 213 FEPQCESEALEEDDLSLVPGITPSRYDV-LEEVGITTIEDLADASLPILELVAGALTALAAQLVLQARARV 282 (474)
T ss_pred cchhhhHHHhhccceeccCCCCHHHHHH-HHHcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHhhc
Confidence 3577889999999999999999998886 8999999999999999998888888 455666666666543
No 41
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=81.64 E-value=1.4 Score=46.90 Aligned_cols=57 Identities=18% Similarity=0.168 Sum_probs=46.6
Q ss_pred CccccccCCHHHHHHHHHhCCCccch-hhhhCCHHHHHHH--hhhhhHHHHHHHHcCCCC
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTML-ELEKFSLKQLQSH--FEEKTASWLYYIARGIDH 302 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIG-DLa~Lp~~~L~kr--FG~k~G~~L~~~aRGiD~ 302 (1041)
.+..|+|||++++.++|..+|..++- .+..-++..|.+. +|++.+++++..+++...
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 35579999999999999999987764 4556688899887 778999999999887653
No 42
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=81.10 E-value=0.25 Score=34.38 Aligned_cols=22 Identities=23% Similarity=0.534 Sum_probs=19.6
Q ss_pred ccccccCCCCCccc-ccccchhh
Q psy16215 952 IICDKCSQPIDINE-LQEHQDYH 973 (1041)
Q Consensus 952 ~~C~rC~~~v~~~E-~~EH~DyH 973 (1041)
|.|+.|++.|..+. |..|+..|
T Consensus 1 y~C~~C~~~f~~~~~l~~H~~~H 23 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNLKRHMRRH 23 (23)
T ss_dssp EEETTTTEEESSHHHHHHHHHHH
T ss_pred CCCCCCCCccCCHHHHHHHHhHC
Confidence 57999999999977 99998876
No 43
>PRK01172 ski2-like helicase; Provisional
Probab=80.53 E-value=2 Score=53.58 Aligned_cols=52 Identities=12% Similarity=0.158 Sum_probs=44.8
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHH
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIA 297 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~a 297 (1041)
+|+-.|||+|+..+++ |...|++|+.||+.++.+.+.+. +|++.+..++..+
T Consensus 612 ~~L~~ip~~~~~~a~~-l~~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~ 665 (674)
T PRK01172 612 IDLVLIPKVGRVRARR-LYDAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRA 665 (674)
T ss_pred HhhcCCCCCCHHHHHH-HHHcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHH
Confidence 6889999999999988 79999999999999999999888 5666666666654
No 44
>PRK00254 ski2-like helicase; Provisional
Probab=80.13 E-value=1.9 Score=54.38 Aligned_cols=54 Identities=9% Similarity=0.094 Sum_probs=49.4
Q ss_pred cCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 244 NLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 244 ~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
.+|+..|||||++.+++ |...|+.++.||...+.+.|.+. +|++.|..++..++
T Consensus 644 ~~~L~~ipgig~~~~~~-l~~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 644 LLELMRLPMIGRKRARA-LYNAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred HhhhhcCCCCCHHHHHH-HHHccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 36888999999999988 67899999999999999999999 88899999999877
No 45
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=77.09 E-value=0.77 Score=49.93 Aligned_cols=26 Identities=27% Similarity=0.455 Sum_probs=0.0
Q ss_pred CcccccccCCCCCcccccccchhhHH
Q psy16215 950 TKIICDKCSQPIDINELQEHQDYHFA 975 (1041)
Q Consensus 950 d~~~C~rC~~~v~~~E~~EH~DyHfA 975 (1041)
..+.|+-||+.||+.+|+|||.+.+-
T Consensus 167 ~~~~cPitGe~IP~~e~~eHmRi~Ll 192 (229)
T PF12230_consen 167 KMIICPITGEMIPADEMDEHMRIELL 192 (229)
T ss_dssp --------------------------
T ss_pred cccccccccccccccccccccccccc
Confidence 34679999999999999999998763
No 46
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=76.38 E-value=4 Score=50.94 Aligned_cols=54 Identities=9% Similarity=0.071 Sum_probs=47.9
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHcCC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIARGI 300 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aRGi 300 (1041)
-.|..|||||++...+||+.+| ++..+...+.++|.+.+|.+.|..++..++..
T Consensus 552 S~L~~IpGIG~kr~~~LL~~Fg--Si~~I~~As~eeL~~vi~~k~A~~I~~~l~~~ 605 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLKHFG--SLERVRAATETQLAAVVGRAAAEAIIAHFTTE 605 (624)
T ss_pred HHHhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHHHhCHHHHHHHHHHhcCc
Confidence 4778999999999999888776 88899999999999999999999999999854
No 47
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=74.99 E-value=3.6 Score=52.80 Aligned_cols=52 Identities=23% Similarity=0.245 Sum_probs=47.1
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh-hhhHHHHHHHHcCC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE-EKTASWLYYIARGI 300 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG-~k~G~~L~~~aRGi 300 (1041)
|..|||||++.+.+||.. +.++.+|+.++.++|....| ++.|..+|+.++..
T Consensus 759 L~~lPgI~~~~a~~ll~~--f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRKK--VKSIRELAKLSQNELNELIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHHCCCCCHHHHHHHHHH--cCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhccc
Confidence 568999999999998775 77999999999999999999 99999999999864
No 48
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=74.62 E-value=4.3 Score=50.66 Aligned_cols=52 Identities=21% Similarity=0.323 Sum_probs=45.6
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhhhhhHHHHHHHHc
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFEEKTASWLYYIAR 298 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG~k~G~~L~~~aR 298 (1041)
-.+..|+|||++++..||..+| ++.+|...+.+.|.+.+|++.|+.++.+++
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fg--s~~~i~~As~eeL~~vig~k~A~~I~~~~~ 620 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFG--SVEKVAKASLEELAAVAGPKTAETIYRYYH 620 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcC--CHHHHHhCCHHHHHHHhCHHHHHHHHHHhC
Confidence 4678999999999999888877 778999999999998899999999987753
No 49
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=73.86 E-value=4.5 Score=40.21 Aligned_cols=44 Identities=14% Similarity=0.046 Sum_probs=32.1
Q ss_pred ccCCHHHHHHHHHhCCCccchhhhhCCHH-----HHHHHhhhhhHHHHHHH
Q psy16215 251 RHLGGKLGDEVVETLQCSTMLELEKFSLK-----QLQSHFEEKTASWLYYI 296 (1041)
Q Consensus 251 pGIG~K~a~rLL~~LGI~TIGDLa~Lp~~-----~L~krFG~k~G~~L~~~ 296 (1041)
||||++.+.+ |...||.|.+||...... .|....| .....+..+
T Consensus 1 pgi~~~~~~~-L~~~GI~t~~~Ll~~~~~~~~r~~La~~~~-i~~~~l~~w 49 (122)
T PF14229_consen 1 PGIGPKEAAK-LKAAGIKTTGDLLEAGDTPLGRKALAKKLG-ISERNLLKW 49 (122)
T ss_pred CCCCHHHHHH-HHHcCCCcHHHHHHcCCCHHHHHHHHHhcC-CCHHHHHHH
Confidence 7999999998 799999999999987543 3555555 333444333
No 50
>PRK08609 hypothetical protein; Provisional
Probab=72.54 E-value=2.8 Score=51.65 Aligned_cols=79 Identities=23% Similarity=0.190 Sum_probs=50.0
Q ss_pred HHHHHHHHHHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcCCccccccCCHHHHHHHHHhCCC
Q psy16215 188 AGVIVEEIRAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQC 267 (1041)
Q Consensus 188 g~~IA~~IR~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI 267 (1041)
|..+|..|++-+ ++| .-..|-+|... .|..+.+|+ +|||||++++.++.+.+||
T Consensus 57 G~~ia~kI~Eil--~tG--------~~~~le~l~~~----------~p~~~~~l~------~i~GiGpk~a~~l~~~lGi 110 (570)
T PRK08609 57 GKGTAEVIQEYR--ETG--------ESSVLQELKKE----------VPEGLLPLL------KLPGLGGKKIAKLYKELGV 110 (570)
T ss_pred CHHHHHHHHHHH--HhC--------ChHHHHHHHhh----------CcHHHHHHh------cCCCCCHHHHHHHHHHhCC
Confidence 567888887777 344 22334444432 123333444 8999999999997668999
Q ss_pred ccchhhhhCCHH-HHHH--HhhhhhHHH
Q psy16215 268 STMLELEKFSLK-QLQS--HFEEKTASW 292 (1041)
Q Consensus 268 ~TIGDLa~Lp~~-~L~k--rFG~k~G~~ 292 (1041)
+|+.||.+.-.. .|+. .||+++.+.
T Consensus 111 ~tl~~L~~a~~~~~~~~~~gfg~k~~~~ 138 (570)
T PRK08609 111 VDKESLKEACENGKVQALAGFGKKTEEK 138 (570)
T ss_pred CCHHHHHHHHHhCChhhccCcchhHHHH
Confidence 999999875322 3443 367655443
No 51
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=72.24 E-value=4.8 Score=49.81 Aligned_cols=53 Identities=17% Similarity=0.272 Sum_probs=46.1
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHcC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIARG 299 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aRG 299 (1041)
..+.+|||||++..+.||+.+| ++..+.+.+.++|.+. ++.+.|..++..++-
T Consensus 514 s~L~~I~GiG~kr~~~LL~~Fg--s~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 514 LNYTKIKGIGEKKAKKILKSLG--TYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred cccccCCCCCHHHHHHHHHHhC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 4788999999999999888776 8899999999999999 777888988888753
No 52
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=72.22 E-value=4.2 Score=51.10 Aligned_cols=52 Identities=12% Similarity=0.087 Sum_probs=45.3
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
-.+..|||||++..++||+.+| ++.++...+.+.|.+. +|.+.+..+++.++
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~ 690 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEHLK 690 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHH
Confidence 4678899999999999999999 9999999999999887 78888888877654
No 53
>PRK07758 hypothetical protein; Provisional
Probab=71.45 E-value=7.3 Score=37.51 Aligned_cols=47 Identities=19% Similarity=0.135 Sum_probs=35.3
Q ss_pred cccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHH
Q psy16215 250 VRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIA 297 (1041)
Q Consensus 250 IpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~a 297 (1041)
+++++-+.... |.+.||.|++||..++.++|.+. ||++....|...+
T Consensus 39 ~~~LSvRA~N~-Lk~AGI~TL~dLv~~te~ELl~iknlGkKSL~EIkekL 87 (95)
T PRK07758 39 LSLLSAPARRA-LEHHGIHTVEELSKYSEKEILKLHGMGPASLPKLRKAL 87 (95)
T ss_pred CccccHHHHHH-HHHcCCCcHHHHHcCCHHHHHHccCCCHHHHHHHHHHH
Confidence 35677666665 78999999999999999998755 7765555554443
No 54
>KOG2093|consensus
Probab=71.41 E-value=0.87 Score=57.36 Aligned_cols=31 Identities=32% Similarity=0.474 Sum_probs=29.0
Q ss_pred EEEEeCCchhHHhHhhhCCCCCCCcEEEEec
Q psy16215 6 IALIDMDCFYCQVECKLNPSLHGKPLAVVQY 36 (1041)
Q Consensus 6 I~HIDmD~FYASVE~~~~PeLrgkPVaV~q~ 36 (1041)
++|+||||||++|-.+..|.+++.|.|+...
T Consensus 330 ~~~~dmk~fF~nv~l~~k~~~kg~~~a~~~d 360 (1016)
T KOG2093|consen 330 TWHNDMKDFFVNVGLRLKPALKGQPTAETAD 360 (1016)
T ss_pred HHHHhhhhhhhcccccCCccccCCceeeecc
Confidence 6899999999999999999999999999764
No 55
>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=70.22 E-value=7.8 Score=43.39 Aligned_cols=68 Identities=13% Similarity=0.180 Sum_probs=47.6
Q ss_pred hHHHhhh--cCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcCCCCccc
Q psy16215 237 SVSMLYA--NLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARGIDHEPV 305 (1041)
Q Consensus 237 ~v~~fL~--~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRGiD~epV 305 (1041)
.+.+-+| +.|+..|||||....++ |...||.++++|.+++..++...++ +..|..+...++.+..-.+
T Consensus 138 ~i~q~~w~~~~~L~Qlp~i~~~~~~~-l~~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~P~~~i 209 (314)
T PF02889_consen 138 CIVQALWDSDSPLLQLPHIGEESLKK-LEKRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRIPRLEI 209 (314)
T ss_dssp HHHHTS-TTS-GGGGSTT--HHHHHH-HHHTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS--EEE
T ss_pred HHHhhcCCCCChhhcCCCCCHHHHHH-HhccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHCCCEEE
Confidence 3444444 36999999999999988 7899999999999999999999986 4578889999998754433
No 56
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=70.11 E-value=3.5 Score=47.56 Aligned_cols=30 Identities=23% Similarity=0.140 Sum_probs=25.4
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFS 277 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp 277 (1041)
+..|||||++++.++ ..+||+|+.||.+..
T Consensus 91 l~~i~GiGpk~a~~l-~~lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKW-YRKGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHH-HHhCCCCHHHHHhcc
Confidence 448999999999985 559999999998754
No 57
>PF02961 BAF: Barrier to autointegration factor; InterPro: IPR004122 Barrier-to-autointegration factor (BAF) is an essential protein that is highly conserved in metazoan evolution, and which may act as a DNA-bridging protein []. BAF binds directly to double-stranded DNA, to transcription activators, and to inner nuclear membrane proteins, including lamin A filament proteins that anchor nuclear-pore complexes in place, and nuclear LEM-domain proteins that bind to laminins filaments and chromatin. New findings suggest that BAF has structural roles in nuclear assembly and chromatin organisation, represses gene expression and might interlink chromatin structure, nuclear architecture and gene regulation in metazoans []. BAF can be exploited by retroviruses to act as a host component of pre-integration complexes, which promote the integration of the retroviral DNA into the host chromosome by preventing autointegration of retroviral DNA []. BAF might contribute to the assembly or activity of retroviral pre-integration complexes through direct binding to the retroviral proteins p55 Gag and matrix, as well as to DNA.; GO: 0003677 DNA binding; PDB: 2ODG_A 2BZF_A 2EZX_B 2EZY_B 1QCK_B 1CI4_B 2EZZ_B.
Probab=69.54 E-value=2.6 Score=40.01 Aligned_cols=34 Identities=12% Similarity=0.153 Sum_probs=22.6
Q ss_pred HhhhcCCccccccCCHHHHHHHHHhCCCccchhhh
Q psy16215 240 MLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELE 274 (1041)
Q Consensus 240 ~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa 274 (1041)
+-|..-||+.|+|||+.++.+ |...|+..+..|.
T Consensus 14 EPMGeK~V~~laGIG~~lg~~-L~~~GfdKAy~vL 47 (89)
T PF02961_consen 14 EPMGEKPVTELAGIGPVLGKR-LEEKGFDKAYVVL 47 (89)
T ss_dssp S--TT-BGGGSTT--HHHHHH-HHHTT--BHHHHH
T ss_pred CccCCCCccccCCcCHHHHHH-HHHCCCcHHHHHh
Confidence 345667999999999999999 7999998865553
No 58
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=69.49 E-value=6.5 Score=49.41 Aligned_cols=60 Identities=15% Similarity=0.242 Sum_probs=51.4
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHcCCCCcccc
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIARGIDHEPVN 306 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aRGiD~epV~ 306 (1041)
..+.+|||||++...+||+.+| ++..|...+.++|.+. ++...|..++..+.---..||.
T Consensus 608 s~L~~IpGiG~kr~~~LL~~Fg--S~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~ 669 (691)
T PRK14672 608 LSFERLPHVGKVRAHRLLAHFG--SFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVR 669 (691)
T ss_pred cccccCCCCCHHHHHHHHHHhc--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchh
Confidence 5889999999999999888776 8899999999999998 7788899999888766666664
No 59
>TIGR03491 RecB family nuclease, putative, TM0106 family. Members of this uncharacterized protein family are found broadly but sporadically among bacteria. The N-terminal region is homologous to the Cas4 protein of CRISPR systems, although this protein family shows no signs of association with CRISPR repeats.
Probab=69.40 E-value=4.6 Score=48.42 Aligned_cols=61 Identities=16% Similarity=0.065 Sum_probs=45.4
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHH--HhhhhhHHHHHHHHc
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQS--HFEEKTASWLYYIAR 298 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~k--rFG~k~G~~L~~~aR 298 (1041)
+.+.....-+|+.|+||+++...+ |...||.|+.||+..++..|.. .+|...+.+|...++
T Consensus 199 C~~~~~~~~~lslv~gi~~~~~~~-L~~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~ 261 (457)
T TIGR03491 199 CEAVAKEEGHLSLVPGIGPSRYRL-LQELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQAR 261 (457)
T ss_pred HHHHHHhcCCeeecCCCCHHHHHH-HHHcCCCcHHHHhcCCccccccccccCHHHHHHHHHHHH
Confidence 456666678999999999998887 8999999999999997655555 344444555544443
No 60
>PTZ00035 Rad51 protein; Provisional
Probab=68.78 E-value=6.2 Score=45.62 Aligned_cols=55 Identities=13% Similarity=0.020 Sum_probs=45.8
Q ss_pred CCcccc--ccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcCC
Q psy16215 245 LSIKKV--RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARGI 300 (1041)
Q Consensus 245 LPI~kI--pGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRGi 300 (1041)
++|.++ +||++...++ |+..||.|+.||+..++..|.+..| ...+..+...++-.
T Consensus 21 ~~~~~l~~~g~~~~~~~k-L~~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKK-LKEAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred ccHHHHhcCCCCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 478888 6899999988 8999999999999999999999987 44566777666654
No 61
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=67.62 E-value=6.6 Score=49.41 Aligned_cols=53 Identities=23% Similarity=0.230 Sum_probs=44.2
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHH--HhhhhhHHHHHHHHc
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQS--HFEEKTASWLYYIAR 298 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~k--rFG~k~G~~L~~~aR 298 (1041)
..=+|+|+|+++.++|.+..+|.++.||..+....|.. .||++.+..|++...
T Consensus 446 ~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie 500 (665)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIE 500 (665)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHH
Confidence 45679999999999988888999999999999888876 588888877765544
No 62
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=66.03 E-value=11 Score=42.43 Aligned_cols=59 Identities=8% Similarity=0.160 Sum_probs=49.6
Q ss_pred cCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcCCCCc
Q psy16215 244 NLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARGIDHE 303 (1041)
Q Consensus 244 ~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRGiD~e 303 (1041)
..|+..+|++|...+++ |...||.+++||..++...+...+| +..|..++..++....-
T Consensus 150 ~~~L~Qlp~i~~~~~~~-l~~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l 210 (312)
T smart00611 150 DSPLLQLPHLPEEILKR-LEKKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKL 210 (312)
T ss_pred CCccccCCCCCHHHHHH-HHhCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCcc
Confidence 46999999999999988 7889999999999999999888876 34678888888776433
No 63
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=63.06 E-value=8.1 Score=44.94 Aligned_cols=56 Identities=16% Similarity=0.030 Sum_probs=46.4
Q ss_pred cCCcccc--ccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcCC
Q psy16215 244 NLSIKKV--RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARGI 300 (1041)
Q Consensus 244 ~LPI~kI--pGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRGi 300 (1041)
..+|.++ .||++...++ |+..||+|+.||+..++.+|.+..| +..+..+...++-.
T Consensus 28 ~~~~~~l~~~g~~~~~~~k-L~~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~ 87 (344)
T PLN03187 28 FESIDKLISQGINAGDVKK-LQDAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL 87 (344)
T ss_pred ccCHHHHhhCCCCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 6678888 5799999998 8999999999999999999999887 45566666666654
No 64
>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=61.70 E-value=10 Score=47.62 Aligned_cols=53 Identities=21% Similarity=0.268 Sum_probs=44.6
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHH--HhhhhhHHHHHHHHc
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQS--HFEEKTASWLYYIAR 298 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~k--rFG~k~G~~L~~~aR 298 (1041)
.--+|+|+|+++.++|.+..+|+++.||..+....|.. .||++.+..|++...
T Consensus 433 ~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 433 NAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred CccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 44578999999999988888899999999999888876 478888887777665
No 65
>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=59.73 E-value=14 Score=42.40 Aligned_cols=51 Identities=10% Similarity=-0.035 Sum_probs=41.4
Q ss_pred ccc--ccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcC
Q psy16215 248 KKV--RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARG 299 (1041)
Q Consensus 248 ~kI--pGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRG 299 (1041)
.++ .|||+...++ |+..||.|+.||+..++.+|.+..| ...+..+.+.++-
T Consensus 2 ~~~~~~g~~~~~~~~-L~~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~ 56 (313)
T TIGR02238 2 DKLQAHGINAADIKK-LKSAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASK 56 (313)
T ss_pred chhhcCCCCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 445 4799999998 8999999999999999999999987 4455666665554
No 66
>cd00141 NT_POLXc Nucleotidyltransferase (NT) domain of family X DNA Polymerases. X family polymerases fill in short gaps during DNA repair. They are relatively inaccurate enzymes and play roles in base excision repair, in non-homologous end joining (NHEJ) which acts mainly to repair damage due to ionizing radiation, and in V(D)J recombination. This family includes eukaryotic Pol beta, Pol lambda, Pol mu, and terminal deoxyribonucleotidyl transferase (TdT). Pol beta and Pol lambda are primarily DNA template-dependent polymerases. TdT is a DNA template-independent polymerase. Pol mu has both template dependent and template independent activities. This subgroup belongs to the Pol beta-like NT superfamily. In the majority of enzymes in this superfamily, two carboxylates, Dx[D/E], together with a third more distal carboxylate, coordinate two divalent metal cations involved in a two-metal ion mechanism of nucleotide addition. These three carboxylate residues are fairly well conserved in this
Probab=59.32 E-value=6 Score=45.13 Aligned_cols=29 Identities=24% Similarity=0.298 Sum_probs=25.2
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKF 276 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~L 276 (1041)
+..|||||+++++++ ..+||.|+.||...
T Consensus 87 l~~i~GiGpk~a~~l-~~lGi~sl~dL~~a 115 (307)
T cd00141 87 LLRVPGVGPKTARKL-YELGIRTLEDLRKA 115 (307)
T ss_pred HHcCCCCCHHHHHHH-HHcCCCCHHHHHHH
Confidence 347999999999985 59999999999874
No 67
>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=57.02 E-value=6.3 Score=30.21 Aligned_cols=16 Identities=19% Similarity=0.447 Sum_probs=12.3
Q ss_pred ccccccCCHHHHHHHH
Q psy16215 247 IKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL 262 (1041)
|.+|||||++++..++
T Consensus 13 L~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 13 LMKLPGIGPKTANAIL 28 (30)
T ss_dssp HHTSTT-SHHHHHHHH
T ss_pred HHhCCCcCHHHHHHHH
Confidence 3479999999999865
No 68
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=56.85 E-value=2.3 Score=29.05 Aligned_cols=22 Identities=27% Similarity=0.622 Sum_probs=16.1
Q ss_pred ccccccCCCCCc-ccccccchhh
Q psy16215 952 IICDKCSQPIDI-NELQEHQDYH 973 (1041)
Q Consensus 952 ~~C~rC~~~v~~-~E~~EH~DyH 973 (1041)
+.|+.|+..+.. ++|..|+.-|
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~~~ 23 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMRTH 23 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHHhh
Confidence 579999999999 5598887654
No 69
>PRK14973 DNA topoisomerase I; Provisional
Probab=55.86 E-value=15 Score=48.14 Aligned_cols=52 Identities=19% Similarity=0.005 Sum_probs=43.4
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARG 299 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRG 299 (1041)
+..|+|+|+++.++ |...||.++.||+..+++.|.++=| .+....+..++++
T Consensus 879 l~~vkg~ge~t~~~-l~~ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~~ 932 (936)
T PRK14973 879 LLSVPGLGETTLEK-LYLAGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAKK 932 (936)
T ss_pred hhhccCCCHHHHHH-HHHcCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHhh
Confidence 77899999999987 8999999999999999999998866 4455556665554
No 70
>COG3377 Uncharacterized conserved protein [Function unknown]
Probab=55.58 E-value=3.9 Score=38.92 Aligned_cols=26 Identities=35% Similarity=0.529 Sum_probs=23.2
Q ss_pred EEEEcCHHHHHcCCCCCCCHHHHHhh
Q psy16215 43 GIIAVNYEARHKGVTRHMRGDEAKQH 68 (1041)
Q Consensus 43 ~VIAvNYeARa~GVK~GMpl~eArkL 68 (1041)
-|..++++|-+.||++||.+++|+.+
T Consensus 69 ~i~evT~~Ae~lGI~~Gm~~r~aL~k 94 (95)
T COG3377 69 PIVEVTSAAEELGIKRGMKGREALEK 94 (95)
T ss_pred hHHHHHHHHHHhCCCccchHHHHHhc
Confidence 46679999999999999999999864
No 71
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=54.88 E-value=15 Score=45.80 Aligned_cols=53 Identities=13% Similarity=0.253 Sum_probs=45.6
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHcC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIARG 299 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aRG 299 (1041)
.++..|||||++.+.+||+.+| ++..++..+.+.|.+. +|+..+..++.+++.
T Consensus 543 s~L~~IpGIG~k~~k~Ll~~Fg--S~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~~ 597 (598)
T PRK00558 543 SALDDIPGIGPKRRKALLKHFG--SLKAIKEASVEELAKVPGISKKLAEAIYEALHK 597 (598)
T ss_pred hhHhhCCCcCHHHHHHHHHHcC--CHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhcc
Confidence 5788999999999999888876 5899999999999988 888888888887653
No 72
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=54.85 E-value=12 Score=40.12 Aligned_cols=52 Identities=27% Similarity=0.199 Sum_probs=38.4
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhh----CCHHHHHHH--hhhhhHHHHHHHHcCCC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEK----FSLKQLQSH--FEEKTASWLYYIARGID 301 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~----Lp~~~L~kr--FG~k~G~~L~~~aRGiD 301 (1041)
+-.++|||+|++..+ +++.+..+|.. -+...|.+. ||+++++++.-.+++.-
T Consensus 74 L~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 74 LIKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred HhCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhh
Confidence 358999999999875 55556666654 355677764 77899999988887764
No 73
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=53.75 E-value=12 Score=41.25 Aligned_cols=39 Identities=10% Similarity=0.225 Sum_probs=33.7
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH 284 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr 284 (1041)
=.+..|.|||+.+.++ |..+||++..||+.++.+.+...
T Consensus 158 DDL~~I~GIGp~~a~~-L~eaGi~tfaQIAa~t~a~ia~i 196 (221)
T PRK12278 158 DDLTKITGVGPALAKK-LNEAGVTTFAQIAALTDADIAKI 196 (221)
T ss_pred chheeccccChHHHHH-HHHcCCCCHHHhhCCChhhhhhh
Confidence 4578899999999998 89999999999999988765533
No 74
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.75 E-value=13 Score=39.89 Aligned_cols=63 Identities=19% Similarity=0.187 Sum_probs=47.4
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCcc-chhhhhCCHHHHHHH--hhhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCST-MLELEKFSLKQLQSH--FEEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~T-IGDLa~Lp~~~L~kr--FG~k~G~~L~~~aRGiD 301 (1041)
...+++..| -.++|||++++..+|..++... +..++.-+...|.+. .|+++|+++.-.++|.-
T Consensus 67 ~Er~lF~~L--i~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~Ki 132 (194)
T PRK14605 67 EELSLFETL--IDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDKI 132 (194)
T ss_pred HHHHHHHHH--hCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 334444443 5889999999999999999888 445557788889886 56889999887777753
No 75
>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=53.66 E-value=20 Score=41.07 Aligned_cols=45 Identities=16% Similarity=-0.031 Sum_probs=36.3
Q ss_pred cCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHH
Q psy16215 252 HLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIA 297 (1041)
Q Consensus 252 GIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~a 297 (1041)
||++.+..+ |+..||.|+.||+..++..|.+.+| ...+..+...+
T Consensus 8 ~~~~~~~~~-l~~~g~~t~~~~~~~~~~~L~~i~~ls~~~~~~~~~~~ 54 (316)
T TIGR02239 8 GITAADIKK-LQEAGLHTVESVAYAPKKQLLEIKGISEAKADKILAEA 54 (316)
T ss_pred CCCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 599999988 8999999999999999999999998 23334444433
No 76
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=53.53 E-value=12 Score=43.53 Aligned_cols=53 Identities=13% Similarity=0.030 Sum_probs=42.0
Q ss_pred cCCcccc--ccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHH
Q psy16215 244 NLSIKKV--RHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIA 297 (1041)
Q Consensus 244 ~LPI~kI--pGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~a 297 (1041)
..+|+++ .||+....++ |+..||.|+.||+..++..|.+.+| ...+..+...+
T Consensus 25 ~~~~~~l~~~gi~~~~i~k-L~~~g~~T~~~~~~~~~~~L~~i~~is~~~~~~~~~~~ 81 (342)
T PLN03186 25 PFPIEQLQASGIAALDIKK-LKDAGIHTVESLAYAPKKDLLQIKGISEAKVEKILEAA 81 (342)
T ss_pred CccHHHHHhCCCCHHHHHH-HHHcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 3478888 5799999987 8999999999999999999999998 22334444443
No 77
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=50.14 E-value=22 Score=39.94 Aligned_cols=51 Identities=20% Similarity=0.299 Sum_probs=41.2
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHHcC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIARG 299 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~aRG 299 (1041)
+..+||||..++.++|..+| ++++++.++...|.+..| ++.|..+++.++-
T Consensus 184 l~s~pgig~~~a~~ll~~fg--S~~~~~tas~~eL~~v~gig~k~A~~I~~~~~t 236 (254)
T COG1948 184 LESIPGIGPKLAERLLKKFG--SVEDVLTASEEELMKVKGIGEKKAREIYRFLRT 236 (254)
T ss_pred HHcCCCccHHHHHHHHHHhc--CHHHHhhcCHHHHHHhcCccHHHHHHHHHHHhc
Confidence 55677999999999887665 889999999999999987 4667777776653
No 78
>PHA02768 hypothetical protein; Provisional
Probab=49.79 E-value=4.5 Score=35.33 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=21.3
Q ss_pred ccccccCCCCCccc-ccccchhhH
Q psy16215 952 IICDKCSQPIDINE-LQEHQDYHF 974 (1041)
Q Consensus 952 ~~C~rC~~~v~~~E-~~EH~DyHf 974 (1041)
|.|+.||+.|.... |+.|+--|-
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcC
Confidence 78999999999966 999999998
No 79
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=49.30 E-value=22 Score=45.17 Aligned_cols=53 Identities=15% Similarity=0.202 Sum_probs=43.2
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
..=+|.|+|+++.++|.+..+|.++.||..+....|... ||++.+..|++...
T Consensus 463 ~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie 517 (689)
T PRK14351 463 DALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELE 517 (689)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHH
Confidence 456789999999999777667899999999999888764 88888777766543
No 80
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=49.15 E-value=2.8 Score=30.30 Aligned_cols=23 Identities=30% Similarity=0.665 Sum_probs=19.5
Q ss_pred cccccccCCCCCccc-ccccchhh
Q psy16215 951 KIICDKCSQPIDINE-LQEHQDYH 973 (1041)
Q Consensus 951 ~~~C~rC~~~v~~~E-~~EH~DyH 973 (1041)
++.|+.|++.|..-. |.+|+-.|
T Consensus 1 ~~~C~~C~~~F~~~~~l~~H~~~h 24 (27)
T PF13912_consen 1 PFECDECGKTFSSLSALREHKRSH 24 (27)
T ss_dssp SEEETTTTEEESSHHHHHHHHCTT
T ss_pred CCCCCccCCccCChhHHHHHhHHh
Confidence 368999999999955 99998776
No 81
>PRK13766 Hef nuclease; Provisional
Probab=49.02 E-value=20 Score=45.62 Aligned_cols=51 Identities=18% Similarity=0.246 Sum_probs=44.2
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHcC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIARG 299 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aRG 299 (1041)
+..|||||++.+.+|++.+| ++.++..++...|... +|++.+..++..++.
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~~ 769 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMTASEEELMEVEGIGEKTAKRIREVVTS 769 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHhh
Confidence 67899999999999988876 7999999999999988 888888888876653
No 82
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=48.39 E-value=13 Score=43.19 Aligned_cols=36 Identities=11% Similarity=0.235 Sum_probs=31.9
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHH
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQ 282 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~ 282 (1041)
.+.+|.|||+++.++ |..+||++..|+++++.+.+.
T Consensus 264 dL~~I~GiGp~~e~~-L~~~Gi~~f~QiA~~t~~~~a 299 (326)
T PRK12311 264 DLKKLTGVSPQIEKK-LNDLGIFHFWQLAELDPDDAA 299 (326)
T ss_pred hhhhhccCChhhhhh-hhhcCCCCHHHhhCCChhhhh
Confidence 578899999999987 899999999999999877554
No 83
>smart00355 ZnF_C2H2 zinc finger.
Probab=47.84 E-value=5.3 Score=27.35 Aligned_cols=23 Identities=26% Similarity=0.572 Sum_probs=19.4
Q ss_pred ccccccCCCCCccc-ccccchhhH
Q psy16215 952 IICDKCSQPIDINE-LQEHQDYHF 974 (1041)
Q Consensus 952 ~~C~rC~~~v~~~E-~~EH~DyHf 974 (1041)
+.|+.|+..+..+. |..|+.-|.
T Consensus 1 ~~C~~C~~~f~~~~~l~~H~~~H~ 24 (26)
T smart00355 1 YRCPECGKVFKSKSALKEHMRTHX 24 (26)
T ss_pred CCCCCCcchhCCHHHHHHHHHHhc
Confidence 47999999999966 999988764
No 84
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=47.38 E-value=12 Score=47.07 Aligned_cols=31 Identities=16% Similarity=0.283 Sum_probs=28.0
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKF 276 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~L 276 (1041)
.||+.+.|||++.++. |+++||.|+.||...
T Consensus 9 ~~~~~l~gvg~~~~~~-l~~lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEK-LAKLGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHH-HHHcCCCCHHHHhhc
Confidence 4899999999999886 899999999999864
No 85
>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=46.62 E-value=22 Score=31.51 Aligned_cols=45 Identities=11% Similarity=0.176 Sum_probs=30.3
Q ss_pred Cccc-cccCCHHHHHHHHHh---CC-CccchhhhhCCHHHHHHHhhhhhHHHHHHH
Q psy16215 246 SIKK-VRHLGGKLGDEVVET---LQ-CSTMLELEKFSLKQLQSHFEEKTASWLYYI 296 (1041)
Q Consensus 246 PI~k-IpGIG~K~a~rLL~~---LG-I~TIGDLa~Lp~~~L~krFG~k~G~~L~~~ 296 (1041)
.|.. +||||.+.+++++.. .| +.+..||.+.+ -+|.+.+.+++..
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v~------gi~~~~~~~i~~~ 66 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQVP------GIGNSLVEKNLAV 66 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcCC------CCCHHHHHHHHhh
Confidence 3455 899999999998776 55 77777776643 3555555555443
No 86
>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=44.60 E-value=26 Score=44.20 Aligned_cols=17 Identities=18% Similarity=0.311 Sum_probs=11.3
Q ss_pred EeccceEEEEcchhHHH
Q psy16215 109 RASIDEAYIDLTDVVHE 125 (1041)
Q Consensus 109 ~aSIDEafLDLT~~v~~ 125 (1041)
.+.||.+.+-+.+....
T Consensus 268 ~y~iDGiViKvn~~~~~ 284 (652)
T TIGR00575 268 PYEIDGVVVKVDDLALQ 284 (652)
T ss_pred CCCCCcEEEEecCHHHH
Confidence 46778887777665443
No 87
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=42.33 E-value=26 Score=43.59 Aligned_cols=50 Identities=16% Similarity=0.275 Sum_probs=40.3
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH-hhhhhHHHHHHH
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH-FEEKTASWLYYI 296 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr-FG~k~G~~L~~~ 296 (1041)
-++.+|+|||++..++||..+| ++..+...+.++|.+. .+...++.++..
T Consensus 530 s~Ld~I~GiG~~r~~~LL~~Fg--s~~~i~~As~eel~~vgi~~~~a~~i~~~ 580 (581)
T COG0322 530 SSLDDIPGIGPKRRKALLKHFG--SLKGIKSASVEELAKVGISKKLAEKIYEA 580 (581)
T ss_pred CccccCCCcCHHHHHHHHHHhh--CHHHHHhcCHHHHHHcCCCHHHHHHHHhh
Confidence 4889999999999999888776 7888999999999999 334556666543
No 88
>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=42.12 E-value=49 Score=27.03 Aligned_cols=43 Identities=21% Similarity=0.119 Sum_probs=31.7
Q ss_pred CHHHHHHHHHhCCCccchhhhhCCHHHHHHHhh--hhhHHHHHHHH
Q psy16215 254 GGKLGDEVVETLQCSTMLELEKFSLKQLQSHFE--EKTASWLYYIA 297 (1041)
Q Consensus 254 G~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krFG--~k~G~~L~~~a 297 (1041)
+..++.+ |..-|+.|+.+|+.+++..|...-| +..+..+...+
T Consensus 2 ~~~~~~~-L~~~G~~s~e~la~~~~~eL~~i~g~~~e~a~~ii~~a 46 (50)
T TIGR01954 2 DEEIAQL-LVEEGFTTVEDLAYVPIDELLSIEGFDEETAKELINRA 46 (50)
T ss_pred CHHHHHH-HHHcCCCCHHHHHccCHHHHhcCCCCCHHHHHHHHHHH
Confidence 4456666 7889999999999999999998865 33444444433
No 89
>KOG2071|consensus
Probab=42.09 E-value=11 Score=46.51 Aligned_cols=31 Identities=23% Similarity=0.439 Sum_probs=25.2
Q ss_pred ccccccCCCCCccc-----ccccchhhHHhhhhccc
Q psy16215 952 IICDKCSQPIDINE-----LQEHQDYHFALELSTTS 982 (1041)
Q Consensus 952 ~~C~rC~~~v~~~E-----~~EH~DyHfAkdLQ~s~ 982 (1041)
..|.-||..+...| |+.|+||||=+..-...
T Consensus 419 nqC~~CG~R~~~~ee~sk~md~H~dwh~r~n~~~r~ 454 (579)
T KOG2071|consen 419 NQCKSCGLRFDDSEERSKHMDIHDDWHRRKNTTIRG 454 (579)
T ss_pred chhcccccccccchhhhhHhhhhhhhhhhhhhhccc
Confidence 57999999998833 99999999987766544
No 90
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=40.58 E-value=29 Score=33.78 Aligned_cols=40 Identities=15% Similarity=0.324 Sum_probs=27.2
Q ss_pred ccccccCCHHHHHHHHHhCCCcc---chhhhhCCHHHHHHHhh
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCST---MLELEKFSLKQLQSHFE 286 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~T---IGDLa~Lp~~~L~krFG 286 (1041)
++.|.|||..++..++..+||.. +++|-.-....|...+.
T Consensus 17 Lt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i~~l~~~i~ 59 (107)
T PF00416_consen 17 LTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQIDKLRKIIE 59 (107)
T ss_dssp HTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHHHHHHHHHH
T ss_pred HhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHHHHHHHHHH
Confidence 57899999999999999999975 44444333334444443
No 91
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=39.56 E-value=24 Score=41.93 Aligned_cols=36 Identities=14% Similarity=0.214 Sum_probs=32.0
Q ss_pred CccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHH
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQ 282 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~ 282 (1041)
.+..|.|||+++.++ |+.+||++..|++.++...+.
T Consensus 324 DLk~I~GIGpk~e~~-Ln~~Gi~~f~QIA~wt~~eia 359 (400)
T PRK12373 324 DLKLISGVGPKIEAT-LNELGIFTFDQVAAWKKAERA 359 (400)
T ss_pred hhhhccCCChHHHHH-HHhcCCCCHHHHhCCCHHHhH
Confidence 577899999999987 899999999999999877554
No 92
>TIGR02027 rpoA DNA-directed RNA polymerase, alpha subunit, bacterial and chloroplast-type. This family consists of the bacterial (and chloroplast) DNA-directed RNA polymerase alpha subunit, encoded by the rpoA gene. The RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. The amino terminal domain is involved in dimerizing and assembling the other RNA polymerase subunits into a transcriptionally active enzyme. The carboxy-terminal domain contains determinants for interaction with DNA and with transcriptional activator proteins.
Probab=39.52 E-value=31 Score=39.41 Aligned_cols=55 Identities=16% Similarity=0.097 Sum_probs=43.4
Q ss_pred hhcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 242 YANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 242 L~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
+-.+||.++ ++.-+...- |++.||.|++||.+++.+.|.+. ||.+....+.+.+.
T Consensus 232 ~~~~~I~~L-~LSvR~~n~-Lk~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l~ 288 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNC-LKRAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKLA 288 (297)
T ss_pred hccccHHHh-CccHHHHhH-HHHcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHHH
Confidence 455688888 688777766 89999999999999999998644 88776666666554
No 93
>PF13438 DUF4113: Domain of unknown function (DUF4113)
Probab=39.46 E-value=3.8 Score=35.03 Aligned_cols=34 Identities=6% Similarity=0.047 Sum_probs=27.1
Q ss_pred CCCCCCcCcCCCCCcccCccccccCC-CChHHHHHHHH
Q psy16215 449 EHSSLPEQSTNHDSKKRDKTLLNFNQ-QTPFQLALNRI 485 (1041)
Q Consensus 449 e~lS~a~D~iN~~s~k~gktll~~g~-~tp~q~~~~~~ 485 (1041)
+.||.++|.|| .+||+..+.+|. .....|+|++=
T Consensus 2 ~~LM~~iD~iN---~r~G~~~i~~a~~g~~~~W~mr~~ 36 (52)
T PF13438_consen 2 QRLMQAIDAIN---RRFGRGTIRLASQGFRRSWKMRRE 36 (52)
T ss_pred hHHHHHHHHHH---HhcCCCEEEEeECCCCcchHHHHH
Confidence 56899999999 899999888774 34468888763
No 94
>KOG3905|consensus
Probab=39.29 E-value=30 Score=40.25 Aligned_cols=98 Identities=16% Similarity=0.154 Sum_probs=55.0
Q ss_pred CCccccccccccCCCCCCCccCCCCCCcccccccCCCCCcccccccchhhHHhhhhcccCCCCCCCCCCCCCCccccccc
Q psy16215 924 PMDTVDIINTIADSSTVDSAINIADPTKIICDKCSQPIDINELQEHQDYHFALELSTTSEPPNSTSNISNSSSSSKILNK 1003 (1041)
Q Consensus 924 ~~~~~~~~k~~~~~~~~~~~~~~~~~d~~~C~rC~~~v~~~E~~EH~DyHfAkdLQ~s~~~~~s~~~~~~~s~~~~~~~~ 1003 (1041)
||+.+..+....+-.... .-.+.+...|++--.|--|-++||.=+-+.++++...|..++.. .+.
T Consensus 324 n~~~vkaed~y~d~itkp--------------p~Rk~v~ekei~aEddQaFL~k~q~iLak~~~t~a~rp~~sq~~-~~~ 388 (473)
T KOG3905|consen 324 NFPTVKAEDNYEDIITKP--------------PVRKVVHEKEIEAEDDQAFLMKLQSILAKQPTTAAPRPRTSQER-GPD 388 (473)
T ss_pred cCCCCCccccccccccCC--------------cchhhhhhhhhhcchHHHHHHHHHHHHhcCCCCCCCCcccccCC-CCC
Confidence 566666655554433332 22333444566777788999999998766554433222211111 122
Q ss_pred CCCCCCCCCCCCCCccccccccccchhcccccC
Q psy16215 1004 KSSKRGRPSKLNSFKNSENFKKLKTIDQFFKPK 1036 (1041)
Q Consensus 1004 ~~~k~~r~~~~~~~~~~~~~~~~~tl~sFFk~~ 1036 (1041)
|+.+.|+.++++++.++.++..-+-|.+||..+
T Consensus 389 ksprtpg~~g~sSP~k~~~P~segVlasffnsl 421 (473)
T KOG3905|consen 389 KSPRTPGRSGSSSPLKKSDPTSEGVLASFFNSL 421 (473)
T ss_pred CCCCCCCCCCCCCCCCCCCCchhHHHHHHHHHH
Confidence 233344444555666666666777799999764
No 95
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=37.46 E-value=42 Score=39.37 Aligned_cols=48 Identities=19% Similarity=0.187 Sum_probs=39.2
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHH
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYI 296 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~ 296 (1041)
+.+||+||+.++++|+..+| ++..+...+.+.|.+. .|+..+..+...
T Consensus 289 Ls~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGIGe~rA~~I~e~ 338 (352)
T PRK13482 289 LSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGIGEVRARAIREG 338 (352)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCcCHHHHHHHHHH
Confidence 56899999999999999998 9999999999999875 566555554443
No 96
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=37.25 E-value=35 Score=42.54 Aligned_cols=50 Identities=16% Similarity=0.222 Sum_probs=41.6
Q ss_pred cCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHH
Q psy16215 244 NLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYY 295 (1041)
Q Consensus 244 ~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~ 295 (1041)
.+.+..|||||++...+||+.+ .++.+++..+.++|.+. +|...+..++.
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~F--GS~~~I~~As~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRF--GSVEGVREASVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 4678899999999999988877 48899999999999888 66666666654
No 97
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=37.13 E-value=32 Score=35.91 Aligned_cols=41 Identities=10% Similarity=0.179 Sum_probs=32.4
Q ss_pred CccccccCCHHHHHHHHHhCCCc---cchhhhhCCHHHHHHHhh
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCS---TMLELEKFSLKQLQSHFE 286 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~---TIGDLa~Lp~~~L~krFG 286 (1041)
-|+.|.|||..++..++..+||. +++||-.-....|...+.
T Consensus 31 aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 31 ALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred eecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence 46889999999999999999996 567776655566666665
No 98
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=36.90 E-value=36 Score=39.17 Aligned_cols=54 Identities=11% Similarity=0.023 Sum_probs=42.2
Q ss_pred hcCCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHHHc
Q psy16215 243 ANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYIAR 298 (1041)
Q Consensus 243 ~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~aR 298 (1041)
-.+||.++ ++.-+...- |++.||+|++||.+++.+.|.+. ||.+....+.+.+.
T Consensus 247 l~~~I~~L-~LS~R~~n~-Lk~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~L~ 302 (310)
T PRK05182 247 LLRPIEEL-ELSVRSYNC-LKRAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEKLA 302 (310)
T ss_pred ccccHHHh-ccchHHHHH-HHHcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHHHHH
Confidence 36789998 788887776 89999999999999999998654 77666555555443
No 99
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=36.82 E-value=33 Score=33.99 Aligned_cols=40 Identities=10% Similarity=0.248 Sum_probs=28.2
Q ss_pred CccccccCCHHHHHHHHHhCCCcc---chhhhhCCHHHHHHHh
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCST---MLELEKFSLKQLQSHF 285 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~T---IGDLa~Lp~~~L~krF 285 (1041)
.|+.|.|||..++..++..+||.. +++|-.-....|...+
T Consensus 16 aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~l 58 (113)
T TIGR03631 16 ALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELNAIREEI 58 (113)
T ss_pred eeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHH
Confidence 468999999999999999999974 4555443333333333
No 100
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=36.57 E-value=25 Score=25.70 Aligned_cols=17 Identities=29% Similarity=0.542 Sum_probs=14.3
Q ss_pred ccccccCCHHHHHHHHH
Q psy16215 247 IKKVRHLGGKLGDEVVE 263 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~ 263 (1041)
+..|||||++++++++.
T Consensus 3 L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 3 LLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhCCCCCHHHHHHHHH
Confidence 56899999999998664
No 101
>KOG2534|consensus
Probab=35.14 E-value=37 Score=39.26 Aligned_cols=33 Identities=12% Similarity=0.087 Sum_probs=27.6
Q ss_pred cccccCCHHHHHHHHHhCCCccchhhhhCCHHHHH
Q psy16215 248 KKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQ 282 (1041)
Q Consensus 248 ~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~ 282 (1041)
+.|+|||.+++++ ..++|++|+.|++.- ++.+.
T Consensus 100 tnifGvG~ktA~~-Wy~~GfrTled~Rk~-~~kft 132 (353)
T KOG2534|consen 100 TNIFGVGLKTAEK-WYREGFRTLEDVRKK-PDKFT 132 (353)
T ss_pred HHHhccCHHHHHH-HHHhhhhHHHHHHhC-HHHHH
Confidence 5789999999998 799999999999954 44443
No 102
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=34.90 E-value=24 Score=44.39 Aligned_cols=31 Identities=16% Similarity=0.395 Sum_probs=28.0
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhC
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKF 276 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~L 276 (1041)
.|+..+.|||++.++. |+++||+|+.||.-+
T Consensus 10 ~~l~~l~gig~~~a~~-l~~Lgi~tv~DLL~~ 40 (677)
T COG1200 10 VPLSTLKGIGPKTAEK-LKKLGIHTVQDLLLY 40 (677)
T ss_pred cchhhhcCcCHHHHHH-HHHcCCCcHHHHHHh
Confidence 3899999999999987 899999999999764
No 103
>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=34.15 E-value=33 Score=34.10 Aligned_cols=30 Identities=13% Similarity=0.263 Sum_probs=21.6
Q ss_pred ccccccCCHHHHHHHHHhC----CCccchhhhhC
Q psy16215 247 IKKVRHLGGKLGDEVVETL----QCSTMLELEKF 276 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~L----GI~TIGDLa~L 276 (1041)
+..|||||++.+++++... ++.++.||.+.
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~V 103 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTKV 103 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHcC
Confidence 4578999999999988765 35555566443
No 104
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=32.40 E-value=12 Score=27.70 Aligned_cols=22 Identities=23% Similarity=0.460 Sum_probs=19.1
Q ss_pred ccccccCCCCCcccccccchhh
Q psy16215 952 IICDKCSQPIDINELQEHQDYH 973 (1041)
Q Consensus 952 ~~C~rC~~~v~~~E~~EH~DyH 973 (1041)
+.|+-|++.++...+.+|.|..
T Consensus 2 v~CPiC~~~v~~~~in~HLD~C 23 (26)
T smart00734 2 VQCPVCFREVPENLINSHLDSC 23 (26)
T ss_pred CcCCCCcCcccHHHHHHHHHHh
Confidence 4799999999888899999954
No 105
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=30.53 E-value=26 Score=40.51 Aligned_cols=50 Identities=20% Similarity=0.187 Sum_probs=35.2
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHH-HHHH--hhhhhHHHHH
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQ-LQSH--FEEKTASWLY 294 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~-L~kr--FG~k~G~~L~ 294 (1041)
.|+-++||+|++-..+|-+.+||+++.+|+...... ++.. ||++.+..++
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~~~~~~~l~GfG~kse~~il 145 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEALENGKIRGLRGFGKKSEAKIL 145 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHHhCCccccCCccchhHHHHH
Confidence 467789999997666778899999999998765433 2333 4554444443
No 106
>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=30.52 E-value=47 Score=30.33 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=19.7
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhh
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELE 274 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa 274 (1041)
+.-|||||++++.+++..+| ++..+.
T Consensus 24 i~gv~giG~k~A~~ll~~~~--~~~~~~ 49 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG--SLENLL 49 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC--CHHHHH
Confidence 45789999999999888866 444443
No 107
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=30.18 E-value=37 Score=36.95 Aligned_cols=43 Identities=26% Similarity=0.320 Sum_probs=29.8
Q ss_pred EEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC---CccccccCCHHHHHHHH
Q psy16215 210 GIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL---SIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 210 GIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L---PI~kIpGIG~K~a~rLL 262 (1041)
|||+---||-|.+- +++.+...+..- -|.++||||+|+++|++
T Consensus 80 GIGpK~ALaiLs~~----------~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSNL----------DPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcCC----------CHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 88888888866652 344555555542 45788999999999864
No 108
>KOG3993|consensus
Probab=29.79 E-value=20 Score=42.67 Aligned_cols=23 Identities=22% Similarity=0.553 Sum_probs=21.6
Q ss_pred ccccccCCCCCccc-ccccchhhH
Q psy16215 952 IICDKCSQPIDINE-LQEHQDYHF 974 (1041)
Q Consensus 952 ~~C~rC~~~v~~~E-~~EH~DyHf 974 (1041)
|.|+.|++.|.... |-.|-.||=
T Consensus 296 YrCPEC~KVFsCPANLASHRRWHK 319 (500)
T KOG3993|consen 296 YRCPECDKVFSCPANLASHRRWHK 319 (500)
T ss_pred ecCCcccccccCchhhhhhhcccC
Confidence 88999999999977 999999994
No 109
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.63 E-value=48 Score=35.92 Aligned_cols=54 Identities=13% Similarity=0.140 Sum_probs=40.9
Q ss_pred cccccCCHHHHHHHHHhCCCccchhh-hhCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 248 KKVRHLGGKLGDEVVETLQCSTMLEL-EKFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 248 ~kIpGIG~K~a~rLL~~LGI~TIGDL-a~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
..+.|||+|++-.+|..++...+.+. +.-+...|.+.- |+++|+++.-.++|.-
T Consensus 77 i~V~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK~ 133 (203)
T PRK14602 77 ISISKVGAKTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYKL 133 (203)
T ss_pred hCCCCcCHHHHHHHHhhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHhh
Confidence 57889999999887777766555433 344778888774 5899999999999863
No 110
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=29.49 E-value=54 Score=32.99 Aligned_cols=41 Identities=12% Similarity=0.202 Sum_probs=29.4
Q ss_pred CCccccccCCHHHHHHHHHhCCCc---cchhhhhCCHHHHHHHh
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCS---TMLELEKFSLKQLQSHF 285 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~---TIGDLa~Lp~~~L~krF 285 (1041)
.-|+.|.|||..++..++..+||. .+++|-.-....|...+
T Consensus 17 ~aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi~~l~~~i 60 (122)
T CHL00137 17 YALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQISALREII 60 (122)
T ss_pred eeecccccccHHHHHHHHHHcCcCcCcCcccCCHHHHHHHHHHH
Confidence 346889999999999999999997 45555544344444444
No 111
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=29.14 E-value=41 Score=34.35 Aligned_cols=54 Identities=19% Similarity=0.154 Sum_probs=37.0
Q ss_pred CHHHHHHhccCCCCCceEEeccchHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhhhCC
Q psy16215 214 NKVLAKLVCGLHKPQKQSILPQSSVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELEKFS 277 (1041)
Q Consensus 214 NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp 277 (1041)
|..=|||+ ....+ .-+....+.+|. .+||||+.+++++...=...++.||.+.+
T Consensus 40 N~~d~kl~-~~~~k---IdiN~A~~~el~------~lpGigP~~A~~IV~nGpf~sveDL~~V~ 93 (132)
T PRK02515 40 NVADAKLG-EFGEK---IDLNNSSVRAFR------QFPGMYPTLAGKIVKNAPYDSVEDVLNLP 93 (132)
T ss_pred ChhhHHHH-hcCCc---ccCCccCHHHHH------HCCCCCHHHHHHHHHCCCCCCHHHHHcCC
Confidence 66778887 33221 113344555543 58999999999988665689999998874
No 112
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=29.13 E-value=54 Score=32.99 Aligned_cols=40 Identities=10% Similarity=0.254 Sum_probs=29.3
Q ss_pred CccccccCCHHHHHHHHHhCCCcc---chhhhhCCHHHHHHHh
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCST---MLELEKFSLKQLQSHF 285 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~T---IGDLa~Lp~~~L~krF 285 (1041)
.|+.|.|||..++..++..+||.. +++|-.-....|...+
T Consensus 18 aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~~l~~~i 60 (122)
T PRK05179 18 ALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEELDKIREEI 60 (122)
T ss_pred eecccccccHHHHHHHHHHhCcCcccccccCCHHHHHHHHHHH
Confidence 468899999999999999999974 5555544444444444
No 113
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=28.88 E-value=34 Score=36.58 Aligned_cols=54 Identities=20% Similarity=0.245 Sum_probs=32.8
Q ss_pred HHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC---CccccccCCHHHHHHHH
Q psy16215 197 AAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL---SIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 197 ~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L---PI~kIpGIG~K~a~rLL 262 (1041)
+.+|..+ +.++ |||+-.-||-|.+ ++|+++...+..= -++++||||+|+++|++
T Consensus 69 r~lF~~L-i~Vs-GIGpK~Al~ILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 69 QKMFEML-LKVN-GIGANTAMAVCSS----------LDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3344433 3444 8887777765543 2455555555432 45678999999998863
No 114
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.52 E-value=72 Score=40.70 Aligned_cols=45 Identities=9% Similarity=0.106 Sum_probs=26.6
Q ss_pred cccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHH--hhhhhHHHHHHH
Q psy16215 250 VRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSH--FEEKTASWLYYI 296 (1041)
Q Consensus 250 IpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~kr--FG~k~G~~L~~~ 296 (1041)
|||||.+.+++|++.+ .++.+|..++.+.|.+. +|++.+..++.+
T Consensus 533 IpgIG~~~ak~L~~~F--~si~~L~~As~eeL~~i~GIG~k~A~sI~~f 579 (689)
T PRK14351 533 IPEVGPTTARNLAREF--GTFEAIMDADEEALRAVDDVGPTVAEEIREF 579 (689)
T ss_pred CCCcCHHHHHHHHHHh--CCHHHHHhCCHHHHhccCCcCHHHHHHHHHH
Confidence 5666766666655544 45566666666666655 555555555444
No 115
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=27.03 E-value=60 Score=33.56 Aligned_cols=42 Identities=12% Similarity=0.330 Sum_probs=31.6
Q ss_pred CCccccccCCHHHHHHHHHhCCCc---cchhhhhCCHHHHHHHhh
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCS---TMLELEKFSLKQLQSHFE 286 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~---TIGDLa~Lp~~~L~krFG 286 (1041)
.-|+.|.|||++++..++..+||. .++||-.-....|...+.
T Consensus 21 ~aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 65 (144)
T TIGR03629 21 YALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEAVE 65 (144)
T ss_pred EeecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHHHH
Confidence 346899999999999999999996 566665554555555554
No 116
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.87 E-value=55 Score=35.12 Aligned_cols=63 Identities=19% Similarity=0.200 Sum_probs=43.3
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhh-hCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELE-KFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa-~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
...+++..| -.+.|||+|++-.+|..++...+.+.. .-+...|.+.- |+++|+++.-.+++.-
T Consensus 67 ~Er~lF~~L--i~V~GIGpK~AL~iLs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK~ 132 (188)
T PRK14606 67 RKKELFLSL--TKVSRLGPKTALKIISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDEF 132 (188)
T ss_pred HHHHHHHHH--hccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 334444443 478899999987776666555544432 34677888774 5899999999998864
No 117
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.76 E-value=55 Score=35.32 Aligned_cols=63 Identities=16% Similarity=0.065 Sum_probs=42.9
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhh-hhCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLEL-EKFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDL-a~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
...+++..| ..+.|||+|++-.+|..+....+.+. +.-+...|.+.- |+++|+++.-.++|.-
T Consensus 67 ~Er~lF~~L--i~V~GIGpK~Al~iLs~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~ 132 (195)
T PRK14604 67 AQRQLFELL--IGVSGVGPKAALNLLSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGKI 132 (195)
T ss_pred HHHHHHHHH--hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 344444444 47889999999777665544443333 234677888774 5899999999999864
No 118
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=26.37 E-value=25 Score=25.69 Aligned_cols=21 Identities=24% Similarity=0.670 Sum_probs=17.5
Q ss_pred cccccccCCCCCccc-ccccch
Q psy16215 951 KIICDKCSQPIDINE-LQEHQD 971 (1041)
Q Consensus 951 ~~~C~rC~~~v~~~E-~~EH~D 971 (1041)
++.|+-|+..|.... +..|+.
T Consensus 1 q~~C~~C~k~f~~~~~~~~H~~ 22 (27)
T PF12171_consen 1 QFYCDACDKYFSSENQLKQHMK 22 (27)
T ss_dssp -CBBTTTTBBBSSHHHHHCCTT
T ss_pred CCCcccCCCCcCCHHHHHHHHc
Confidence 478999999999966 999975
No 119
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.94 E-value=57 Score=35.26 Aligned_cols=63 Identities=19% Similarity=0.112 Sum_probs=43.1
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhh-hhCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLEL-EKFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDL-a~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
...+++..| ..+.|||+|++-.+|..++...+.+. +.-+...|.+.- |+++|+++.-.++|.-
T Consensus 66 ~Er~lF~~L--~~V~GIGpK~AL~iLs~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 66 DSLELFELL--LGVSGVGPKLALALLSALPPALLARALLEGDARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred HHHHHHHHH--hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 334444444 47889999998776665555444333 234777888774 5899999999998864
No 120
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.06 E-value=64 Score=34.59 Aligned_cols=63 Identities=14% Similarity=0.094 Sum_probs=43.0
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhh-hCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELE-KFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa-~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
...+++..| ..+.|||+|++-.+|..+....+.+.. .=+...|.+.= |+++|+++.-.++|.-
T Consensus 67 ~Er~lF~~L--i~VsGIGpK~Al~ILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 67 DEQKMFEML--LKVNGIGANTAMAVCSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred HHHHHHHHH--hccCCccHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 344444443 478899999997766665554443332 33677787774 5899999999999864
No 121
>KOG2841|consensus
Probab=24.78 E-value=78 Score=35.39 Aligned_cols=50 Identities=8% Similarity=0.083 Sum_probs=41.4
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHHHHh--hhhhHHHHHHHHc
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQSHF--EEKTASWLYYIAR 298 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~krF--G~k~G~~L~~~aR 298 (1041)
|+.||||+..-+..||..+| +++++...+..+|.+.- |+..+.+||..++
T Consensus 197 Lt~i~~VnKtda~~LL~~Fg--sLq~~~~AS~~ele~~~G~G~~kak~l~~~l~ 248 (254)
T KOG2841|consen 197 LTTIPGVNKTDAQLLLQKFG--SLQQISNASEGELEQCPGLGPAKAKRLHKFLH 248 (254)
T ss_pred HHhCCCCCcccHHHHHHhcc--cHHHHHhcCHhHHHhCcCcCHHHHHHHHHHHh
Confidence 46788999888888777766 78889899999999886 7778888988775
No 122
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=24.56 E-value=73 Score=33.20 Aligned_cols=41 Identities=10% Similarity=0.285 Sum_probs=32.4
Q ss_pred CccccccCCHHHHHHHHHhCCCc---cchhhhhCCHHHHHHHhh
Q psy16215 246 SIKKVRHLGGKLGDEVVETLQCS---TMLELEKFSLKQLQSHFE 286 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~LGI~---TIGDLa~Lp~~~L~krFG 286 (1041)
-|+.|.|||..++..++..+||. .++||-.-....|...+.
T Consensus 26 aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 69 (149)
T PRK04053 26 ALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEALE 69 (149)
T ss_pred eccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHHH
Confidence 46889999999999999999997 567776655566666664
No 123
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.42 E-value=67 Score=34.85 Aligned_cols=63 Identities=14% Similarity=0.205 Sum_probs=42.9
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhh-hhCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLEL-EKFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDL-a~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
...+++..| -.+.|||+|++-.+|..++...+.+. ..-+...|.+.- |+++|+++.-.++|.-
T Consensus 66 ~Er~lF~~L--isVsGIGPK~ALaILs~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdKl 131 (196)
T PRK13901 66 SEREVFEEL--IGVDGIGPRAALRVLSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKL 131 (196)
T ss_pred HHHHHHHHH--hCcCCcCHHHHHHHHcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 344444443 47889999999777666655444333 234677787774 5899999999999863
No 124
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.85 E-value=46 Score=35.69 Aligned_cols=53 Identities=11% Similarity=0.171 Sum_probs=34.0
Q ss_pred HHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC---CccccccCCHHHHHHHH
Q psy16215 198 AVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL---SIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 198 ~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L---PI~kIpGIG~K~a~rLL 262 (1041)
.+|..+ +.++ |||+-.-||-|.. ++++++...+..- -++++||||+|+++|+.
T Consensus 70 ~lF~~L-i~V~-GIGpK~AL~iLs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 70 ELFLSL-TKVS-RLGPKTALKIISN----------EDAETLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 334433 3444 8888877775543 1345555555543 56789999999999964
No 125
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=23.48 E-value=1.1e+02 Score=38.36 Aligned_cols=49 Identities=10% Similarity=0.052 Sum_probs=39.2
Q ss_pred cccccCCHHHHHHHHHhCC-CccchhhhhCCHHHHHH--HhhhhhHHHHHHHH
Q psy16215 248 KKVRHLGGKLGDEVVETLQ-CSTMLELEKFSLKQLQS--HFEEKTASWLYYIA 297 (1041)
Q Consensus 248 ~kIpGIG~K~a~rLL~~LG-I~TIGDLa~Lp~~~L~k--rFG~k~G~~L~~~a 297 (1041)
=+|-|+|.++.++|+ ..| |.++.||..|....|.. .||++.+..|++..
T Consensus 428 mdI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aI 479 (562)
T PRK08097 428 LGLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQF 479 (562)
T ss_pred cCCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHH
Confidence 457899999999855 456 69999999999888876 58888777776653
No 126
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=23.10 E-value=98 Score=39.38 Aligned_cols=20 Identities=10% Similarity=0.365 Sum_probs=12.8
Q ss_pred CccccccCCHHHHHHHHHhC
Q psy16215 246 SIKKVRHLGGKLGDEVVETL 265 (1041)
Q Consensus 246 PI~kIpGIG~K~a~rLL~~L 265 (1041)
.|..++|+|.+.++.||+.+
T Consensus 480 ~L~~l~gfG~Ksa~~ll~~I 499 (665)
T PRK07956 480 DLLGLEGFGEKSAQNLLDAI 499 (665)
T ss_pred HHhcCcCcchHHHHHHHHHH
Confidence 45666777777766655543
No 127
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.61 E-value=54 Score=35.15 Aligned_cols=62 Identities=13% Similarity=-0.054 Sum_probs=42.0
Q ss_pred hHHHhhhcCCccccccCCHHHHHHHHHhCCCccchhhh-hCCHHHHHHHh--hhhhHHHHHHHHcCCC
Q psy16215 237 SVSMLYANLSIKKVRHLGGKLGDEVVETLQCSTMLELE-KFSLKQLQSHF--EEKTASWLYYIARGID 301 (1041)
Q Consensus 237 ~v~~fL~~LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa-~Lp~~~L~krF--G~k~G~~L~~~aRGiD 301 (1041)
...+++..| -.+.|||+|++-.+|..++...+.+.. +-+...| +.- |+++|+++.-.++|.-
T Consensus 67 ~Er~lF~~L--isV~GIGpK~Al~iLs~~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~K~ 131 (186)
T PRK14600 67 EEQDCLRML--VKVSGVNYKTAMSILSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYKV 131 (186)
T ss_pred HHHHHHHHH--hCcCCcCHHHHHHHHccCCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHHHh
Confidence 334444443 478899999998777666555444332 3366777 664 5889999999999864
No 128
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=22.46 E-value=69 Score=34.91 Aligned_cols=56 Identities=20% Similarity=0.198 Sum_probs=41.9
Q ss_pred ccccccCCHHHHHHHHHhCCCccchhhhh-CCHHHHHHH--hhhhhHHHHHHHHcCCCC
Q psy16215 247 IKKVRHLGGKLGDEVVETLQCSTMLELEK-FSLKQLQSH--FEEKTASWLYYIARGIDH 302 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~LGI~TIGDLa~-Lp~~~L~kr--FG~k~G~~L~~~aRGiD~ 302 (1041)
+-++.|||+|++-.+|..+....+.+... -+...|.+. .|+++|+++.-.+.|.-.
T Consensus 75 LisVnGIGpK~ALaiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~~ 133 (201)
T COG0632 75 LISVNGIGPKLALAILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKLA 133 (201)
T ss_pred HHccCCccHHHHHHHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhhh
Confidence 45688999999988777777766655544 356667766 468999999999999643
No 129
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.37 E-value=49 Score=35.85 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=35.0
Q ss_pred HHHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC---CccccccCCHHHHHHHH
Q psy16215 196 RAAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL---SIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 196 R~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L---PI~kIpGIG~K~a~rLL 262 (1041)
-+.+|..+ +.++ |||+-..+|-|.+ ++++++...+..= .+.++||||+|+++|+.
T Consensus 67 Er~lF~~L-isVs-GIGPK~ALaILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 67 EREVFEEL-IGVD-GIGPRAALRVLSG----------IKYNEFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 34445444 4555 8888777775543 2445555544432 56789999999999964
No 130
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=22.25 E-value=90 Score=31.54 Aligned_cols=38 Identities=5% Similarity=0.225 Sum_probs=27.7
Q ss_pred CCccccccCCHHHHHHHHHhCCCccchhhhhCCHHHHH
Q psy16215 245 LSIKKVRHLGGKLGDEVVETLQCSTMLELEKFSLKQLQ 282 (1041)
Q Consensus 245 LPI~kIpGIG~K~a~rLL~~LGI~TIGDLa~Lp~~~L~ 282 (1041)
+.|+.|.|||..++..++..+||.--.-+-.|+.+++.
T Consensus 17 iALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~ 54 (121)
T COG0099 17 IALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIE 54 (121)
T ss_pred ehhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHH
Confidence 34678999999999999999999754444444444443
No 131
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=22.13 E-value=55 Score=35.33 Aligned_cols=54 Identities=17% Similarity=0.247 Sum_probs=34.4
Q ss_pred HHHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC---CccccccCCHHHHHHHH
Q psy16215 197 AAVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL---SIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 197 ~~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L---PI~kIpGIG~K~a~rLL 262 (1041)
+.+|..+ +.++ |||+-.-||-|.. .+++++...+..- -++++||||+|+++|++
T Consensus 69 r~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 69 RQLFELL-IGVS-GVGPKAALNLLSS----------GTPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 3344443 3444 8888777775543 2455555555543 56788999999999963
No 132
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=22.11 E-value=26 Score=29.82 Aligned_cols=25 Identities=28% Similarity=0.542 Sum_probs=19.8
Q ss_pred cccccccCCCCCccccccc-chhhHH
Q psy16215 951 KIICDKCSQPIDINELQEH-QDYHFA 975 (1041)
Q Consensus 951 ~~~C~rC~~~v~~~E~~EH-~DyHfA 975 (1041)
.|.|+=||+.+...+|.+| ++.|..
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~ 27 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRS 27 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcC
Confidence 4789999998777779999 666653
No 133
>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=21.54 E-value=52 Score=35.29 Aligned_cols=43 Identities=16% Similarity=0.264 Sum_probs=29.8
Q ss_pred EEeCCHHHHHHhccCCCCCceEEeccchHHHhhhc---CCccccccCCHHHHHHHH
Q psy16215 210 GIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYAN---LSIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 210 GIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~---LPI~kIpGIG~K~a~rLL 262 (1041)
||++-..+|-|. ...++++...+.. --|.++||||+|++++++
T Consensus 79 GIGpK~Al~iL~----------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 79 GVGPKLALAILS----------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCCHHHHHHHHh----------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 888777666432 2245555555554 467899999999999974
No 134
>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=21.48 E-value=19 Score=35.05 Aligned_cols=34 Identities=18% Similarity=0.291 Sum_probs=22.9
Q ss_pred eccchHHHhhhcC-----CccccccCCHHHHHHHHHhCC
Q psy16215 233 LPQSSVSMLYANL-----SIKKVRHLGGKLGDEVVETLQ 266 (1041)
Q Consensus 233 l~p~~v~~fL~~L-----PI~kIpGIG~K~a~rLL~~LG 266 (1041)
|+|+.+..|++-+ -|-=|||||+|++..||+.+|
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~yg 39 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYG 39 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHT
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcC
Confidence 4577777777755 334466899999998888887
No 135
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.93 E-value=61 Score=35.05 Aligned_cols=53 Identities=19% Similarity=0.288 Sum_probs=34.6
Q ss_pred HHHhhhCCceeEEEeCCHHHHHHhccCCCCCceEEeccchHHHhhhcC---CccccccCCHHHHHHHH
Q psy16215 198 AVLSKTQFHCSAGIAHNKVLAKLVCGLHKPQKQSILPQSSVSMLYANL---SIKKVRHLGGKLGDEVV 262 (1041)
Q Consensus 198 ~I~~elGlt~SVGIA~NKlLAKLAS~~aKPnGqtvl~p~~v~~fL~~L---PI~kIpGIG~K~a~rLL 262 (1041)
.+|..+ ++++ |||+-.-||-|.+ +.++++...+..= -+.++||||+|+++|+.
T Consensus 69 ~lF~~L-~~V~-GIGpK~AL~iLs~----------~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 69 ELFELL-LGVS-GVGPKLALALLSA----------LPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 344444 3455 8888777775543 2455555555543 56789999999999963
No 136
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=20.58 E-value=20 Score=31.10 Aligned_cols=29 Identities=24% Similarity=0.402 Sum_probs=19.6
Q ss_pred CCCcccccccCCCCCccc-ccccc-hhhHHh
Q psy16215 948 DPTKIICDKCSQPIDINE-LQEHQ-DYHFAL 976 (1041)
Q Consensus 948 ~~d~~~C~rC~~~v~~~E-~~EH~-DyHfAk 976 (1041)
++.+-+|+.|+..+.... |--|+ -+||+|
T Consensus 21 S~~PatCP~C~a~~~~srnLrRHle~~H~~k 51 (54)
T PF09237_consen 21 SEQPATCPICGAVIRQSRNLRRHLEIRHFKK 51 (54)
T ss_dssp TS--EE-TTT--EESSHHHHHHHHHHHTTTS
T ss_pred cCCCCCCCcchhhccchhhHHHHHHHHhccc
Confidence 344568999999999966 99999 678876
No 137
>PF08004 DUF1699: Protein of unknown function (DUF1699); InterPro: IPR012546 This family contains many archaeal proteins which have very conserved sequences.
Probab=20.56 E-value=1.6e+02 Score=30.16 Aligned_cols=36 Identities=17% Similarity=0.364 Sum_probs=28.3
Q ss_pred CCCHHHHHhhCCCcEEeeccCCCCCCCHHHHHHHHHHHHHHHH
Q psy16215 59 HMRGDEAKQHCPEIELCRVPSVRGKADISKYRNAGREVIAVLS 101 (1041)
Q Consensus 59 GMpl~eArkLCPdLvvV~VP~~~~k~Dld~Yr~aS~kI~eIL~ 101 (1041)
.+-++...+.||++.++++| ...|+.+|..+--.|.
T Consensus 30 N~Dif~Lv~~CP~lk~iqiP-------~SY~~t~Sksi~mfL~ 65 (131)
T PF08004_consen 30 NKDIFSLVERCPNLKAIQIP-------PSYYKTLSKSIKMFLE 65 (131)
T ss_pred chHHHHHHHhCCCCeEEeCC-------hHHHHHHhHHHHHHHH
Confidence 34578889999999999987 3478888888776664
No 138
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=20.07 E-value=77 Score=27.95 Aligned_cols=30 Identities=17% Similarity=0.330 Sum_probs=20.4
Q ss_pred ccccccCCHHHHHHHHHhC----CCccchhhhhC
Q psy16215 247 IKKVRHLGGKLGDEVVETL----QCSTMLELEKF 276 (1041)
Q Consensus 247 I~kIpGIG~K~a~rLL~~L----GI~TIGDLa~L 276 (1041)
+..+||||+++++++++-= ++.++.||...
T Consensus 16 L~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v 49 (65)
T PF12836_consen 16 LQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEV 49 (65)
T ss_dssp HHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGS
T ss_pred HHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhC
Confidence 3467899999998865533 67889998876
Done!