Query 011631
Match_columns 481
No_of_seqs 179 out of 1384
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 03:30:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011631.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011631hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00205 DNA polymerase kappa; 100.0 1.7E-48 3.8E-53 417.1 28.4 269 2-271 226-513 (571)
2 PRK01216 DNA polymerase IV; Va 100.0 3.1E-45 6.8E-50 378.1 29.7 238 2-248 101-343 (351)
3 cd01701 PolY_Rev1 DNA polymera 100.0 3.6E-45 7.8E-50 384.2 28.9 239 2-244 144-404 (404)
4 KOG2094 Predicted DNA damage i 100.0 1.9E-46 4.1E-51 374.3 18.2 257 1-261 195-457 (490)
5 PRK03858 DNA polymerase IV; Va 100.0 7.8E-45 1.7E-49 380.0 29.5 242 2-247 96-343 (396)
6 cd00424 PolY Y-family of DNA p 100.0 6.2E-45 1.4E-49 374.3 28.1 235 2-242 95-343 (343)
7 PRK02406 DNA polymerase IV; Va 100.0 2E-44 4.3E-49 370.4 27.8 240 2-247 91-334 (343)
8 PRK14133 DNA polymerase IV; Pr 100.0 3.1E-44 6.7E-49 369.7 29.3 239 2-248 99-340 (347)
9 PRK02794 DNA polymerase IV; Pr 100.0 3.6E-44 7.7E-49 378.2 28.5 243 2-248 131-376 (419)
10 PRK03352 DNA polymerase IV; Va 100.0 5.8E-44 1.3E-48 367.4 28.9 237 2-247 105-345 (346)
11 cd01703 PolY_Pol_iota DNA Poly 100.0 3.6E-44 7.9E-49 373.5 26.8 238 2-243 94-379 (379)
12 PRK03348 DNA polymerase IV; Pr 100.0 1.2E-43 2.5E-48 377.7 29.4 242 2-246 102-346 (454)
13 PRK03103 DNA polymerase IV; Re 100.0 1.4E-43 3.1E-48 372.2 27.8 241 2-247 101-352 (409)
14 PRK01810 DNA polymerase IV; Va 100.0 2.2E-43 4.8E-48 370.6 28.9 240 2-247 103-347 (407)
15 cd03586 PolY_Pol_IV_kappa DNA 100.0 2.7E-43 5.9E-48 359.5 28.4 238 2-244 94-334 (334)
16 cd01702 PolY_Pol_eta DNA Polym 100.0 5.7E-43 1.2E-47 362.3 24.8 227 2-243 114-359 (359)
17 PRK03609 umuC DNA polymerase V 100.0 1.1E-42 2.4E-47 367.1 27.1 241 2-247 97-353 (422)
18 cd01700 PolY_Pol_V_umuC umuC s 100.0 8.7E-42 1.9E-46 351.0 24.7 237 2-243 95-344 (344)
19 COG0389 DinP Nucleotidyltransf 100.0 5.6E-40 1.2E-44 339.5 26.3 242 2-247 97-347 (354)
20 cd03468 PolY_like DNA Polymera 100.0 1.9E-36 4.1E-41 309.0 24.6 233 2-242 94-334 (335)
21 KOG2093 Translesion DNA polyme 100.0 1.9E-36 4.2E-41 328.0 12.5 263 2-271 471-753 (1016)
22 KOG2095 DNA polymerase iota/DN 100.0 3.2E-29 7E-34 267.7 11.9 169 23-193 199-375 (656)
23 PF11799 IMS_C: impB/mucB/samB 99.5 5.3E-14 1.1E-18 123.1 10.9 107 139-245 2-116 (127)
24 PF00817 IMS: impB/mucB/samB f 99.2 1.4E-11 3E-16 112.6 3.3 56 2-58 94-149 (149)
25 PF11798 IMS_HHH: IMS family H 98.5 5.7E-08 1.2E-12 66.5 3.1 31 73-104 2-32 (32)
26 PRK04301 radA DNA repair and r 97.8 1.7E-05 3.6E-10 81.4 3.9 79 78-157 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 97.0 0.00074 1.6E-08 68.9 4.6 73 84-157 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.6 0.003 6.5E-08 49.1 4.2 49 84-133 7-58 (60)
29 PF11731 Cdd1: Pathogenicity l 95.9 0.0077 1.7E-07 51.3 3.4 37 83-120 13-50 (93)
30 PF04994 TfoX_C: TfoX C-termin 94.6 0.061 1.3E-06 44.6 4.9 50 82-132 3-57 (81)
31 PF10391 DNA_pol_lambd_f: Fing 94.1 0.036 7.8E-07 42.2 2.3 29 84-113 4-32 (52)
32 PRK12766 50S ribosomal protein 93.2 0.18 3.8E-06 49.8 5.9 53 83-136 4-59 (232)
33 PF03118 RNA_pol_A_CTD: Bacter 92.5 0.27 5.8E-06 39.2 5.0 51 77-129 7-60 (66)
34 COG3743 Uncharacterized conser 91.4 0.23 5.1E-06 44.8 3.8 31 83-114 68-98 (133)
35 PRK02362 ski2-like helicase; P 91.0 0.3 6.5E-06 55.9 5.3 52 82-134 652-704 (737)
36 PRK01172 ski2-like helicase; P 85.8 1.1 2.5E-05 50.6 5.5 50 81-131 611-663 (674)
37 PF14229 DUF4332: Domain of un 85.2 1.1 2.5E-05 39.8 4.1 49 74-123 45-94 (122)
38 PRK08609 hypothetical protein; 82.9 1.1 2.4E-05 50.0 3.6 30 84-113 90-119 (570)
39 PRK00254 ski2-like helicase; P 82.7 1.6 3.6E-05 49.8 5.0 53 81-134 644-699 (720)
40 PF02961 BAF: Barrier to autoi 82.1 1.4 3E-05 37.3 3.0 32 79-111 16-47 (89)
41 smart00483 POLXc DNA polymeras 81.8 1 2.2E-05 46.9 2.6 30 83-113 90-119 (334)
42 PF12826 HHH_2: Helix-hairpin- 79.8 2.3 4.9E-05 33.5 3.4 44 87-132 8-54 (64)
43 cd00141 NT_POLXc Nucleotidyltr 79.8 1.4 3E-05 45.4 2.8 29 84-113 87-115 (307)
44 PF14229 DUF4332: Domain of un 79.1 1.9 4.1E-05 38.4 3.1 36 88-124 1-42 (122)
45 COG2251 Predicted nuclease (Re 75.3 4.6 0.0001 43.5 5.2 47 75-122 218-265 (474)
46 PF00633 HHH: Helix-hairpin-he 75.1 1.6 3.4E-05 29.5 1.1 16 84-99 13-28 (30)
47 PRK10917 ATP-dependent DNA hel 74.5 2.4 5.1E-05 48.3 3.0 31 82-113 9-39 (681)
48 PRK07758 hypothetical protein; 74.5 6.5 0.00014 33.7 4.9 44 86-130 38-84 (95)
49 PF02889 Sec63: Sec63 Brl doma 73.8 7.2 0.00016 39.5 6.1 61 75-136 139-204 (314)
50 PRK14667 uvrC excinuclease ABC 73.7 5.2 0.00011 44.7 5.3 53 81-135 513-567 (567)
51 PF13878 zf-C2H2_3: zinc-finge 72.2 1.6 3.5E-05 31.5 0.7 26 394-419 14-39 (41)
52 PRK14669 uvrC excinuclease ABC 67.9 9.6 0.00021 43.2 5.9 52 82-135 552-604 (624)
53 COG1200 RecG RecG-like helicas 67.9 3.9 8.4E-05 46.2 2.8 31 82-113 10-40 (677)
54 PTZ00035 Rad51 protein; Provis 67.2 5.4 0.00012 41.6 3.6 54 81-135 20-78 (337)
55 TIGR00596 rad1 DNA repair prot 64.5 9.2 0.0002 44.6 5.0 50 84-135 759-810 (814)
56 PLN03187 meiotic recombination 64.4 6.9 0.00015 41.1 3.7 54 80-134 27-85 (344)
57 TIGR03491 RecB family nuclease 63.9 8.5 0.00019 41.7 4.4 37 77-114 202-238 (457)
58 smart00611 SEC63 Domain of unk 61.3 17 0.00037 36.8 5.9 55 81-136 150-207 (312)
59 PRK07956 ligA NAD-dependent DN 60.8 12 0.00026 42.8 5.0 48 83-130 446-496 (665)
60 PRK12278 50S ribosomal protein 59.3 9.6 0.00021 37.6 3.4 32 82-114 158-189 (221)
61 TIGR02239 recomb_RAD51 DNA rep 59.3 11 0.00025 38.9 4.2 35 89-124 8-43 (316)
62 PRK00116 ruvA Holliday junctio 59.3 10 0.00022 36.3 3.6 53 83-135 74-130 (192)
63 PLN03186 DNA repair protein RA 58.8 9.2 0.0002 40.1 3.4 43 81-124 25-70 (342)
64 TIGR02238 recomb_DMC1 meiotic 58.5 12 0.00026 38.7 4.2 48 85-133 2-54 (313)
65 TIGR00575 dnlj DNA ligase, NAD 57.7 15 0.00032 41.9 5.1 50 82-131 432-484 (652)
66 smart00278 HhH1 Helix-hairpin- 56.8 7.6 0.00017 24.9 1.5 17 84-100 3-19 (26)
67 PRK14672 uvrC excinuclease ABC 56.3 18 0.0004 41.3 5.4 59 81-141 607-668 (691)
68 PRK12311 rpsB 30S ribosomal pr 56.2 9.2 0.0002 39.9 2.8 31 83-114 264-294 (326)
69 PRK14671 uvrC excinuclease ABC 54.4 20 0.00044 40.6 5.4 49 82-132 569-618 (621)
70 PRK14670 uvrC excinuclease ABC 53.1 20 0.00044 40.2 5.1 50 81-132 513-565 (574)
71 PF04475 DUF555: Protein of un 52.1 5.8 0.00013 34.2 0.5 35 391-430 45-96 (102)
72 PRK03922 hypothetical protein; 51.9 5.7 0.00012 34.8 0.5 43 391-438 47-106 (113)
73 KOG3014 Protein involved in es 49.4 6.9 0.00015 39.1 0.6 29 394-422 38-66 (257)
74 TIGR01448 recD_rel helicase, p 49.2 30 0.00065 39.9 5.8 48 68-118 73-120 (720)
75 COG0632 RuvA Holliday junction 48.6 11 0.00024 36.6 1.9 43 45-99 80-125 (201)
76 PRK14351 ligA NAD-dependent DN 47.1 27 0.00058 40.2 4.9 49 82-130 462-513 (689)
77 PRK14666 uvrC excinuclease ABC 46.6 27 0.00058 40.0 4.8 49 82-132 637-688 (694)
78 PRK00558 uvrC excinuclease ABC 46.1 28 0.00061 39.3 4.9 50 81-132 542-594 (598)
79 TIGR02027 rpoA DNA-directed RN 45.8 24 0.00052 36.3 4.0 51 79-131 232-285 (297)
80 PF13894 zf-C2H2_4: C2H2-type 44.8 6.7 0.00014 23.5 -0.2 12 394-405 1-12 (24)
81 PRK12373 NADH dehydrogenase su 43.9 22 0.00047 38.1 3.4 31 83-114 324-354 (400)
82 COG5540 RING-finger-containing 43.8 8.5 0.00019 39.6 0.3 17 389-405 355-373 (374)
83 PRK05182 DNA-directed RNA poly 43.3 27 0.00059 36.1 3.9 50 79-130 246-298 (310)
84 KOG2534 DNA polymerase IV (fam 40.6 34 0.00073 35.6 4.0 32 84-116 99-130 (353)
85 PRK14601 ruvA Holliday junctio 40.4 15 0.00032 35.2 1.4 56 30-99 67-125 (183)
86 PF02591 DUF164: Putative zinc 40.1 9.6 0.00021 29.0 0.0 25 386-410 15-39 (56)
87 TIGR00615 recR recombination p 38.6 16 0.00034 35.4 1.2 16 84-99 13-28 (195)
88 TIGR00426 competence protein C 38.4 40 0.00086 26.5 3.3 31 83-113 17-52 (69)
89 PRK00076 recR recombination pr 38.2 16 0.00035 35.4 1.2 16 84-99 13-28 (196)
90 PRK14973 DNA topoisomerase I; 38.0 85 0.0018 37.5 7.3 103 22-134 825-931 (936)
91 PRK14606 ruvA Holliday junctio 37.6 18 0.00038 34.8 1.4 55 31-99 68-125 (188)
92 PF14716 HHH_8: Helix-hairpin- 36.9 21 0.00045 28.2 1.5 18 83-100 48-65 (68)
93 PRK13901 ruvA Holliday junctio 36.2 19 0.00041 34.9 1.4 58 28-99 64-124 (196)
94 PRK13844 recombination protein 36.0 18 0.00039 35.2 1.2 16 84-99 17-32 (200)
95 PRK02515 psbU photosystem II c 35.3 33 0.00073 31.2 2.7 54 48-114 39-93 (132)
96 PRK14604 ruvA Holliday junctio 35.2 20 0.00044 34.6 1.4 56 30-99 67-125 (195)
97 CHL00013 rpoA RNA polymerase a 35.1 45 0.00097 34.9 4.0 54 77-132 258-314 (327)
98 PRK14602 ruvA Holliday junctio 35.0 21 0.00046 34.6 1.5 57 29-99 67-126 (203)
99 TIGR01954 nusA_Cterm_rpt trans 34.6 52 0.0011 23.7 3.3 32 90-122 1-33 (50)
100 COG1885 Uncharacterized protei 34.2 16 0.00035 31.9 0.5 43 391-438 47-106 (115)
101 PRK14603 ruvA Holliday junctio 33.8 22 0.00048 34.3 1.4 56 30-99 66-124 (197)
102 COG0177 Nth Predicted EndoIII- 33.5 32 0.00069 33.8 2.5 52 43-105 78-133 (211)
103 PF01246 Ribosomal_L24e: Ribos 33.1 14 0.00031 30.0 -0.0 14 393-406 3-16 (71)
104 COG2075 RPL24A Ribosomal prote 32.2 21 0.00045 28.6 0.8 13 394-406 4-16 (66)
105 PRK14668 uvrC excinuclease ABC 31.4 60 0.0013 36.6 4.5 87 36-130 464-574 (577)
106 COG0353 RecR Recombinational D 30.7 24 0.00052 34.2 1.1 16 84-99 14-29 (198)
107 PRK14600 ruvA Holliday junctio 30.4 28 0.00061 33.4 1.5 15 84-99 110-124 (186)
108 COG1948 MUS81 ERCC4-type nucle 30.2 69 0.0015 32.3 4.3 47 84-132 184-233 (254)
109 PF13240 zinc_ribbon_2: zinc-r 30.1 26 0.00057 22.1 0.8 12 395-406 1-12 (23)
110 TIGR00575 dnlj DNA ligase, NAD 29.4 72 0.0016 36.4 4.8 18 83-100 467-484 (652)
111 TIGR01259 comE comEA protein. 28.0 50 0.0011 29.2 2.6 30 83-113 69-103 (120)
112 COG1796 POL4 DNA polymerase IV 27.3 26 0.00057 36.4 0.8 33 82-114 93-125 (326)
113 KOG2894 Uncharacterized conser 27.0 1.8E+02 0.0039 29.8 6.4 117 149-271 147-263 (331)
114 PRK08097 ligB NAD-dependent DN 26.9 89 0.0019 35.1 4.8 45 85-130 428-476 (562)
115 COG1555 ComEA DNA uptake prote 26.2 58 0.0013 30.0 2.8 29 85-114 100-133 (149)
116 COG0322 UvrC Nuclease subunit 25.8 91 0.002 35.2 4.7 49 81-131 529-579 (581)
117 PF06397 Desulfoferrod_N: Desu 25.6 24 0.00051 25.0 0.1 9 393-401 6-14 (36)
118 COG2199 c-di-GMP synthetase (d 25.4 63 0.0014 29.4 2.9 41 6-49 101-148 (181)
119 PRK05752 uroporphyrinogen-III 25.1 2E+02 0.0044 28.2 6.6 79 23-105 11-103 (255)
120 PRK00807 50S ribosomal protein 24.8 30 0.00066 26.3 0.5 14 394-407 2-15 (52)
121 PF13909 zf-H2C2_5: C2H2-type 24.4 27 0.00059 21.5 0.2 11 394-404 1-11 (24)
122 COG4071 Uncharacterized protei 24.4 95 0.002 30.7 3.9 50 7-56 122-175 (278)
123 smart00279 HhH2 Helix-hairpin- 23.6 60 0.0013 22.7 1.8 17 84-100 18-34 (36)
124 PRK14891 50S ribosomal protein 23.3 35 0.00077 30.9 0.7 15 393-407 4-18 (131)
125 PRK13766 Hef nuclease; Provisi 23.0 1.1E+02 0.0023 35.4 4.7 47 84-132 717-766 (773)
126 cd00472 Ribosomal_L24e_L24 Rib 23.0 34 0.00074 26.3 0.5 14 393-406 3-16 (54)
127 PF07887 Calmodulin_bind: Calm 22.8 1.2E+02 0.0026 31.3 4.6 51 84-135 164-224 (299)
128 PRK13293 F420-0--gamma-glutamy 22.5 1.2E+02 0.0025 30.6 4.2 47 4-51 107-153 (245)
129 PRK07945 hypothetical protein; 21.8 1.3E+02 0.0029 31.2 4.8 26 75-100 42-67 (335)
130 smart00355 ZnF_C2H2 zinc finge 21.7 39 0.00084 20.1 0.5 12 394-405 1-12 (26)
131 PHA02768 hypothetical protein; 21.6 36 0.00077 26.4 0.4 27 391-419 3-29 (55)
132 TIGR00084 ruvA Holliday juncti 21.1 50 0.0011 31.7 1.4 43 45-99 79-124 (191)
133 PRK14605 ruvA Holliday junctio 20.9 48 0.001 31.9 1.2 15 84-98 110-124 (194)
134 PF00416 Ribosomal_S13: Riboso 20.6 65 0.0014 27.9 1.8 23 84-106 17-39 (107)
135 PF09889 DUF2116: Uncharacteri 20.6 44 0.00096 26.2 0.7 12 395-406 5-16 (59)
136 PF05715 zf-piccolo: Piccolo Z 20.6 46 0.00099 26.2 0.7 16 395-410 32-47 (61)
137 COG2888 Predicted Zn-ribbon RN 20.3 46 0.00099 26.2 0.7 13 392-404 49-61 (61)
No 1
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=1.7e-48 Score=417.10 Aligned_cols=269 Identities=28% Similarity=0.401 Sum_probs=240.4
Q ss_pred CCccceEEEecCCcccccC--CCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEec-CChhHHHHh
Q 011631 2 AASLDEAYLDITEVCRERG--ISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLP-NDRMAVMTF 78 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g--~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~-~~~~~v~~f 78 (481)
+|||||||||+|++...|+ .++.++|++||++|+++||||||||||+||+||||||+++||||+++++ ...+++.+|
T Consensus 226 ~~SIDEafLDlT~~~~~~~~~~~~~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~l~~~~~v~~f 305 (571)
T PTZ00205 226 SFGLDELTLEVSAYIERFEGTKTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLNLHTRGDVMTY 305 (571)
T ss_pred EeechhceeccCCchhhccCCCCHHHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEecCCHHHHHHH
Confidence 6899999999999876552 3789999999999999999999999999999999999999999999874 233589999
Q ss_pred hccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhchH---------HHHHHhcHhHHHHHHHHhcCCCCCC-CC--CCCC
Q 011631 79 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGS---------LLCAVFSHSTADFFLSVGLGLGSTN-TP--QARF 146 (481)
Q Consensus 79 L~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~~---------~L~~~fG~~~~~~l~~~a~Gid~~~-v~--~~~~ 146 (481)
|++|||++|||||++++++|+. +||+||+||++.+. .+..+||...|.++|..++|+|..+ +. ....
T Consensus 306 L~~LpV~ki~GIG~~t~~~L~~-~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~~~v~~~~~~~ 384 (571)
T PTZ00205 306 VRDLGLRSVPGVGKVTEALLKG-LGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANTENCEGATGGQ 384 (571)
T ss_pred HhCCCcceeCCcCHHHHHHHHH-cCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCCCccCCCCCCC
Confidence 9999999999999999999997 99999999998773 3567788767888999999999874 33 2346
Q ss_pred CcccccccccCccCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHH
Q 011631 147 RKSISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLL 226 (481)
Q Consensus 147 ~KSIs~e~tF~~~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL 226 (481)
+||||+++||+...+.+++...|..|+++|+.||++.++.+++|+|++++.+|...+++.+++.||++...|+++|..||
T Consensus 385 rKSIg~ErTF~~~~d~~el~~~L~~L~~~v~~rLrk~~l~artVtlKlK~~dF~~~trs~tL~~pT~d~~~I~~aa~~Ll 464 (571)
T PTZ00205 385 RKAISSERSFTTPRTKEGLQEMVDTVFNGAYEEMRKSELMCRQISLTIRWASYRYQQYTKSLIQYSDDSATLRRAVDGLL 464 (571)
T ss_pred CceeEEeEeCCCCCCHHHHHHHHHHHHHHHHHHHHhcCCCccEEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHH
Confidence 89999999999888999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhh-C-CCCEEEEEEEEecCCCCccc--CCCCcccchHHHHhccCccCc
Q 011631 227 KAE-L-PVSLRLIGLRVTQFNEDKVR--APSDPTQKTLTNFMTSGHASK 271 (481)
Q Consensus 227 ~~~-~-~~~VR~IGV~vs~L~~~~~~--~~~~~~q~si~~Ff~s~~~~~ 271 (481)
+.. + ..+||+|||++++|...+.. ..+++.|.+|.+|.+.+.+..
T Consensus 465 ~~~~~~~~~vRLlGV~ls~L~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 513 (571)
T PTZ00205 465 LPHAAKYSEMCLLGVRFLDLISAKDFHMKRKGGNQLSISQFIRPKKPGE 513 (571)
T ss_pred HhccccCCCEEEEEEEEcccCcHHHHHHHhcCCceeeHHHHcCCCCCCc
Confidence 876 4 37899999999999987642 356799999999998877554
No 2
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=3.1e-45 Score=378.07 Aligned_cols=238 Identities=26% Similarity=0.394 Sum_probs=222.7
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|++.++|| ++..+|++||++|++++|+|||||||+||++|||||+.+||+|+++++++ ++.+||++
T Consensus 101 ~~siDE~~LDvt~~~~l~g-~~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~--~~~~~L~~ 177 (351)
T PRK01216 101 IASIDEAYLDISDKVKNYQ-DAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDE--EVKRFINE 177 (351)
T ss_pred EccCCeEEEEcccchhccC-CHHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHH--HHHHHHhc
Confidence 5899999999999999998 89999999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
|||++|||||++++++|++ +||+|+|||++++ ..|.++||...+.++|.+++|++..++.+. .+|||+++++|.. +
T Consensus 178 LPi~~l~giG~~~~~~L~~-~Gi~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~~pv~~~-~~ksi~~~~tl~~di 255 (351)
T PRK01216 178 LDIADIPGIGDITAEKLKK-LGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYNEPVRAR-VRKSIGRYVTLPRNT 255 (351)
T ss_pred CCcccccCCCHHHHHHHHH-cCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCCCC-CCCCCcCeEECCCcc
Confidence 9999999999999999997 9999999999999 899999998778899999999999998774 5699999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC--C-CCEEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL--P-VSLRL 236 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~--~-~~VR~ 236 (481)
.+.+++...|.+|+++++.||+. .++++++++++.+|.+.+++.+++.||+ ..+|++.+..||++++ . .+||+
T Consensus 256 ~~~~~l~~~l~~L~~~~~~rl~~---~~~~~~~~~~~~df~~~t~~~tl~~~~~-~~~~~~~a~~Ll~~~~~~~~~~vRl 331 (351)
T PRK01216 256 RDLEEIKPYLKRAIEEAYYKLDG---IPKAIHVVAIMEDLDIVSRGRTFTHGIS-KETAYREAVRLLQKILEEDERKIRR 331 (351)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHh---CCCEEEEEEEcCCCCEEEEEEECCCCCC-HHHHHHHHHHHHHhhhhcCCCCeeE
Confidence 89999999999999999999996 6889999999999999999999999997 6889999999999874 2 58999
Q ss_pred EEEEEecCCCCc
Q 011631 237 IGLRVTQFNEDK 248 (481)
Q Consensus 237 IGV~vs~L~~~~ 248 (481)
|||++++|.+..
T Consensus 332 lGv~~~~l~~~~ 343 (351)
T PRK01216 332 IGVRFSKIIEAI 343 (351)
T ss_pred EEEEEecccccc
Confidence 999999998763
No 3
>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=3.6e-45 Score=384.21 Aligned_cols=239 Identities=28% Similarity=0.392 Sum_probs=223.4
Q ss_pred CCccceEEEecCCccc-ccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhc
Q 011631 2 AASLDEAYLDITEVCR-ERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFIS 80 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~-l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~ 80 (481)
++||||+|||+|++.+ +++ ++..+|++||++|++++|||||||||+||++|||||+.+||+|+++++++ ++.+||+
T Consensus 144 ~~SiDE~~lDvt~~~~~~~~-~~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~--~~~~~L~ 220 (404)
T cd01701 144 AVSCDEALIDITSLLEETYE-LPEELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAE--KVEEFLS 220 (404)
T ss_pred EcccceEEEEcccccccccC-CHHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHH--HHHHHhh
Confidence 5899999999999985 677 89999999999999999999999999999999999999999999999875 7899999
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch---HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccC
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG---SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFS 157 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~---~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~ 157 (481)
++||++|||||++++++|++ +||+|++||++++ ..|.++||...+.++|..++|+|..++.+..++|||+++++|+
T Consensus 221 ~lPv~~l~GIG~~~~~~L~~-~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~~~~tf~ 299 (404)
T cd01701 221 QLKVGDLPGVGSSLAEKLVK-LFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVSAEINYG 299 (404)
T ss_pred cCCHhHhCCCCHHHHHHHHH-cCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCccccceeeCC
Confidence 99999999999999999997 9999999999986 5899999987789999999999999998878899999999999
Q ss_pred c-cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEec---------------CCeeeEEEEEcCCCCCCHHHHHHH
Q 011631 158 V-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTA---------------SFEVRTRAVTLQKYISSSEDILKH 221 (481)
Q Consensus 158 ~-~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~---------------~f~~~srs~~l~~pt~d~~~L~~~ 221 (481)
. ..+.+++..+|..|+++|+.||+++++.+++|+|++++. +|...+++++++.||++...|++.
T Consensus 300 ~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~~pT~d~~~i~~~ 379 (404)
T cd01701 300 IRFTNVDDVEQFLQRLSEELSKRLEESNVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLGVATDDSGVIGTE 379 (404)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHcCCceeeEEEEEEeccccCccccccccccCCCcEEeeeeECCCCCCCHHHHHHH
Confidence 7 689999999999999999999999999999999999972 256789999999999999999999
Q ss_pred HHHHHHhhC-C-CCEEEEEEEEecC
Q 011631 222 ASVLLKAEL-P-VSLRLIGLRVTQF 244 (481)
Q Consensus 222 a~~LL~~~~-~-~~VR~IGV~vs~L 244 (481)
+..||++++ + .+||+|||++++|
T Consensus 380 a~~ll~~~~~~~~~vR~lgv~~~~l 404 (404)
T cd01701 380 AKKLFRDLSIPPEELRGVGIQVTKL 404 (404)
T ss_pred HHHHHHhccCCCCCeeEEEEEEecC
Confidence 999999985 3 6999999999986
No 4
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=1.9e-46 Score=374.30 Aligned_cols=257 Identities=54% Similarity=0.827 Sum_probs=238.8
Q ss_pred CCCccceEEEecCCccccc--C----CCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhH
Q 011631 1 MAASLDEAYLDITEVCRER--G----ISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMA 74 (481)
Q Consensus 1 ~~~SIDEafLDiTg~~~l~--g----~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~ 74 (481)
++.|+||||||+|..++.. | .+..+++++||.+|+++||+|||+|||+|++|||+||+.+|||||++|++++..
T Consensus 195 ~~~SlDEaylnlT~~l~~~~~g~l~~nG~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nKPNgQf~i~~dr~a 274 (490)
T KOG2094|consen 195 CAMSLDEAYLNLTSHLRERELGFLVENGITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNKPNGQFVIPNDRIA 274 (490)
T ss_pred ccchHHHHHHhHHHHHHHhhcchhhhccHHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccCCCCceEecccHHH
Confidence 5789999999999987654 3 127899999999999999999999999999999999999999999999999889
Q ss_pred HHHhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhchHHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCccccccc
Q 011631 75 VMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSER 154 (481)
Q Consensus 75 v~~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~ 154 (481)
+++||..|||+++.|||+.++..|+. +||.||||+.+.-..|...|.+..++.+.+.+.|.+.++.+....+|||++|+
T Consensus 275 im~F~kdLPvRkV~GIGrV~E~qLka-l~IkTcgdm~~k~~ll~~lFsp~S~~~fLr~slG~g~t~~~~~~eRKsis~Er 353 (490)
T KOG2094|consen 275 IMKFMKDLPVRKVSGIGRVTEQQLKA-LGIKTCGDMQQKLVLLSLLFSPKSFQNFLRCSLGLGTTILDEDGERKSISSER 353 (490)
T ss_pred HHHHHhcCCcccccchhHHHHHHHHh-cCceeHHHHHHhhhHHHHHhCchhHHHHHHHhhcCCCCcCcccccccccccee
Confidence 99999999999999999999999996 99999999988778888999999899998999999999988888899999999
Q ss_pred ccCccCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCCCCE
Q 011631 155 TFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSL 234 (481)
Q Consensus 155 tF~~~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~~~~V 234 (481)
||..+.+...+...+++||..|+..|++.|+.+++|+|+++++.|+..+|+.++.....+.++|+..|.+||++.+|..|
T Consensus 354 TFs~~sd~~il~~k~qel~~~lsedlqK~glv~rtvtiKlK~ssFev~Tr~~t~s~vv~S~edi~k~aleLLk~e~~~~i 433 (490)
T KOG2094|consen 354 TFSSTSDPSILYSKLQELCQMLSEDLQKEGLVGRTVTIKLKTSSFEVHTRQKTISQVVHSEEDILKPALELLKQEYPMTI 433 (490)
T ss_pred eecccCCHHHHHHHHHHHHHHHHHHHHhcCcccceEEEEEeccceeeeeccCchhhhhccHHHHHHHHHHHHHhhcCceE
Confidence 99999999999999999999999999999999999999999999999999999999899999999999999999999999
Q ss_pred EEEEEEEecCCCCcccCCCCcccchHH
Q 011631 235 RLIGLRVTQFNEDKVRAPSDPTQKTLT 261 (481)
Q Consensus 235 R~IGV~vs~L~~~~~~~~~~~~q~si~ 261 (481)
|++||++++|...+ ....+|+++.
T Consensus 434 RLlGvR~sqlv~ee---d~~~~~~tv~ 457 (490)
T KOG2094|consen 434 RLLGVRASQLVSEE---DRKLAQQTVS 457 (490)
T ss_pred eeeeeeHhhccchh---ccchhhcchh
Confidence 99999999999985 2344555554
No 5
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=7.8e-45 Score=380.03 Aligned_cols=242 Identities=30% Similarity=0.504 Sum_probs=229.8
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
+|||||+|||+|++.++|| ++..+|++||++|++++|+|||||||+||++||||++.+||+|+++++++ ++.+||++
T Consensus 96 ~~siDe~~ldvt~~~~~~~-~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~--~~~~~L~~ 172 (396)
T PRK03858 96 GLSIDEAFLDVGGLRRISG-TPVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPD--RELAFLHP 172 (396)
T ss_pred EecCCeEEEEccccccccC-CHHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcH--HHHHHHhc
Confidence 5799999999999999898 89999999999999999999999999999999999999999999999886 67899999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
+||++|||||++++++|++ +||+|++||++++ ..|.++||...++++|.+++|+|..++.+..++|||+++++|+. .
T Consensus 173 lpl~~l~Gig~~~~~~L~~-~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~t~~~~~ 251 (396)
T PRK03858 173 LPVRRLWGVGPVTAAKLRA-HGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQRALGRGP 251 (396)
T ss_pred CChhhcCCCCHHHHHHHHH-hCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCccccceeEcCCCC
Confidence 9999999999999999997 9999999999998 78999999877899999999999999987778899999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC----CCCEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PVSLR 235 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~----~~~VR 235 (481)
.+.+++..+|+.|+++|+.||+++++.+++|+|++++.+|...+++++++.||++...|++.+..+|++++ +.+||
T Consensus 252 ~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~l~~~ll~~~~~~~~~~~ir 331 (396)
T PRK03858 252 NSPAEVDAVVVALVDRVARRMRAAGRTGRTVVLRLRFDDFTRATRSHTLPRPTASTATLLAAARDLVAAAAPLIAERGLT 331 (396)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEeCCCCEEEEEEECCCCcCCHHHHHHHHHHHHHhhhhccCCCCeE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999864 35799
Q ss_pred EEEEEEecCCCC
Q 011631 236 LIGLRVTQFNED 247 (481)
Q Consensus 236 ~IGV~vs~L~~~ 247 (481)
++||++++|.+.
T Consensus 332 ligv~~~~l~~~ 343 (396)
T PRK03858 332 LVGFAVSNLDDD 343 (396)
T ss_pred EEEEEeecCCcc
Confidence 999999999865
No 6
>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=6.2e-45 Score=374.33 Aligned_cols=235 Identities=29% Similarity=0.429 Sum_probs=220.5
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhC-CceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAG-LTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFIS 80 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etG-lt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~ 80 (481)
++||||+|||+|++.++|+ ++..+|+.||++|++++| +|||||||+||++||||++.+||||+++++++ ++.+||+
T Consensus 95 ~~siDE~~ldvt~~~~~~~-~~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~--~~~~~L~ 171 (343)
T cd00424 95 VASIDELFLDLTGSARLLG-LGSEVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPE--DLPGFLS 171 (343)
T ss_pred EccCCEEEEECCCchhccC-CHHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHH--HHHHHHh
Confidence 5899999999999998888 899999999999999998 99999999999999999999999999999875 6889999
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch--HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG--SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV 158 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~--~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~ 158 (481)
++||++|||||+++.++|++ +||+|++||++++ ..+.++||.. +.++|..++|+|..++.+..++|||+++++|+.
T Consensus 172 ~lpi~~l~giG~~~~~~L~~-~Gi~ti~dl~~~~~~~~l~~~fg~~-~~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~~ 249 (343)
T cd00424 172 KLPLTDLPGIGAVTAKRLEA-VGINPIGDLLAASPDALLALWGGVS-GERLWYALRGIDDEPLSPPRPRKSFSHERVLPR 249 (343)
T ss_pred cCChhhcCCCCHHHHHHHHH-cCCCcHHHHhcCCHHHHHHHHhhHH-HHHHHHHhCCcCCCCCCCCCCCCceeeeEECCC
Confidence 99999999999999999997 9999999999998 4677888875 788999999999999988888999999999987
Q ss_pred -cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecC------CeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCC
Q 011631 159 -TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTAS------FEVRTRAVTLQKYISSSEDILKHASVLLKAELP 231 (481)
Q Consensus 159 -~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~------f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~~ 231 (481)
..+.+++..+|..|+++|+.||+++++.+++|+|++++.+ |...+++.+++.|| +...|++.+..||++++.
T Consensus 250 ~~~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~lr~~~~~~~~~~~~~~~~~~l~~~t-~~~~l~~~~~~l~~~~~~ 328 (343)
T cd00424 250 DSRNAEDARPLLRLLLEKLARRLRRDGRGATRLRLWLRTVDGRWSGHADIPSRSAPRPIST-EDGELLHALDKLWRALLD 328 (343)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHcCCceeEEEEEEEeCCCcccccceeeeeeeeCCCCC-CHHHHHHHHHHHHHhhhh
Confidence 6899999999999999999999999999999999999998 67899999999999 999999999999999863
Q ss_pred ----CCEEEEEEEEe
Q 011631 232 ----VSLRLIGLRVT 242 (481)
Q Consensus 232 ----~~VR~IGV~vs 242 (481)
.+||+|||+++
T Consensus 329 ~~~~~~ir~~gv~~~ 343 (343)
T cd00424 329 DKGPRRLRRLGVRLS 343 (343)
T ss_pred ccCCCCeeEEEEEeC
Confidence 68999999975
No 7
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=2e-44 Score=370.43 Aligned_cols=240 Identities=37% Similarity=0.522 Sum_probs=227.0
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|++.++|| ++..+|+.||++|++++|+|||||||+||++||||++.+||+|+++++++ ++.+||++
T Consensus 91 ~~siDe~~ldvt~~~~~~~-~~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~--~~~~~L~~ 167 (343)
T PRK02406 91 PLSLDEAYLDVTDNKLCIG-SATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPE--EVDAFLAT 167 (343)
T ss_pred EccCCeEEEeccCccccCC-CHHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHH--HHHHHHHc
Confidence 4799999999999999998 89999999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
+||++|||||+++.++|++ +||+|++||++++ ..|.++||.. +.++|+.++|+|..++.+..++|||+++++|+. .
T Consensus 168 lpi~~l~giG~~~~~~L~~-~Gi~ti~dl~~l~~~~L~~~fG~~-~~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~~~ 245 (343)
T PRK02406 168 LPVEKIPGVGKVTAEKLHA-LGIYTCADLQKYDLAELIRHFGKF-GRRLYERARGIDERPVKPDRERKSVGVERTFAEDL 245 (343)
T ss_pred CCcchhcCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHHHhHH-HHHHHHHhCCCCCCccccCCCCcceeeeeeCCCCC
Confidence 9999999999999999997 9999999999998 7999999985 788999999999999988788999999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhC--CcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCCCCEEEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEG--LRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELPVSLRLI 237 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~--~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~~~~VR~I 237 (481)
.+.+++..+|++|+++|+.||++++ +.+++|+|++++.++...+++.+ ..++++...|+..+..|++..++.+||+|
T Consensus 246 ~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~~~l~l~l~~~~~~~~~~~~~-~~~~~~~~~l~~~~~~L~~~~~~~~vr~l 324 (343)
T PRK02406 246 YDLEACLAELPRLAEKLERRLERAKPDKRIKTVGVKLKFADFQQTTKEHT-ADPLDKADLIELLAQALLRRLGGRGVRLL 324 (343)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCccceeEEEEEEeCCCCeEEEecC-CCCCCcHHHHHHHHHHHHhhCcCCCEEEE
Confidence 8999999999999999999999999 99999999999999998888888 77888889999999999998888899999
Q ss_pred EEEEecCCCC
Q 011631 238 GLRVTQFNED 247 (481)
Q Consensus 238 GV~vs~L~~~ 247 (481)
||++++|.+.
T Consensus 325 gv~~~~l~~~ 334 (343)
T PRK02406 325 GVGVTLLEPQ 334 (343)
T ss_pred EEEEecCCcC
Confidence 9999999965
No 8
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.1e-44 Score=369.72 Aligned_cols=239 Identities=36% Similarity=0.549 Sum_probs=226.2
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|++. + ++..+|++||++|++++|||||||||+||++||||++.+||+|+++++++ ++.+||++
T Consensus 99 ~~siDe~~ldv~~~~---~-~~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~--~~~~~L~~ 172 (347)
T PRK14133 99 PVSIDEAYLDITNIK---E-EPIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITED--MIPDILKP 172 (347)
T ss_pred EccCCeEEEEccCCC---C-CHHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHH--HHHHHHHh
Confidence 489999999999985 4 78999999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
+||++|||||+++.++|++ +||+|++||++++ ..|.++||.. +..+|..++|+|..++.+..++|||+.+++|+. .
T Consensus 173 lpv~~l~gig~~~~~~L~~-~Gi~ti~dl~~l~~~~L~~rfG~~-g~~l~~~a~G~d~~~v~~~~~~ksi~~~~~~~~~~ 250 (347)
T PRK14133 173 LPISKVHGIGKKSVEKLNN-IGIYTIEDLLKLSREFLIEYFGKF-GVEIYERIRGIDYREVEVSRERKSIGKETTLKKDT 250 (347)
T ss_pred CCccccCCCCHHHHHHHHH-cCCccHHHHhhCCHHHHHHHHhHH-HHHHHHHhCCCCCCCCCCCCCCcceEeeEEcCCCC
Confidence 9999999999999999997 9999999999998 8999999974 788889999999999988888999999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIG 238 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~-~~~VR~IG 238 (481)
.+.+.+..+|..|+++|+.||+.+++.+++++|++++.++...+++++++.||++.+.|++.+..+|++++ +.+||.||
T Consensus 251 ~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~l~~~lle~~~~~~~vr~lg 330 (347)
T PRK14133 251 KDKEELKKYLKDFSNIISEELKKRNLYGKTVTVKIKTSDFQTHTKSKTLNDYIRDKEEIYNVACEILEHINIKEPIRLIG 330 (347)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEECCCCeeEEEEECCCCcCCHHHHHHHHHHHHHhccCCCCEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999985 58999999
Q ss_pred EEEecCCCCc
Q 011631 239 LRVTQFNEDK 248 (481)
Q Consensus 239 V~vs~L~~~~ 248 (481)
|++++|.+..
T Consensus 331 l~~~~l~~~~ 340 (347)
T PRK14133 331 LSVSNLSENK 340 (347)
T ss_pred EEEecCCCCc
Confidence 9999999753
No 9
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.6e-44 Score=378.20 Aligned_cols=243 Identities=32% Similarity=0.451 Sum_probs=229.5
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|++.++||..+..++++||++|++++|+|||||||+||++||||++.+||||++++.++ ++.+||++
T Consensus 131 ~~siDe~~ldvt~~~~l~g~~~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~--~~~~~L~~ 208 (419)
T PRK02794 131 PLSIDEAFLDLSGTERLHGAPPAVVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRA--EALAFLAP 208 (419)
T ss_pred eccCCeEEEeccchhhhcCCCHHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHH--HHHHHHhc
Confidence 5799999999999999998556678999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
+||++|||||+++.++|++ +||+|++||++++ ..|.++||.. +..+|..++|+|..++.+..++|||+++++|+. .
T Consensus 209 lPl~~L~GiG~~~~~~L~~-~GI~tigdL~~l~~~~L~~rfG~~-g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tl~~~~ 286 (419)
T PRK02794 209 KPVGIIWGVGPATAARLAR-DGIRTIGDLQRADEADLMRRFGSM-GLRLWRLARGIDDRKVSPDREAKSVSAETTFETDL 286 (419)
T ss_pred CChhhhCCCCHHHHHHHHH-hccchHHHHhhCCHHHHHHHHhHH-HHHHHHHhCCCCCCCCccCCCCceeeeeEECCCCC
Confidence 9999999999999999997 9999999999998 7999999985 788999999999999988788999999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIG 238 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~-~~~VR~IG 238 (481)
.+.+++..+|..|+++|+.||+++++.+++|+|++++.+|...+++++++.||++...|++.+..+|++++ +.+||+||
T Consensus 287 ~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~l~l~l~~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~ig 366 (419)
T PRK02794 287 SDFEDLEPILWRLSEKVSRRLKAAGLAGRTVTLKLKTADFRLRTRRRTLEDPTQLADRIFRTARELLEKETDGTAFRLIG 366 (419)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCcceEEEEEEECCCCceEEEEECCCCcCCHHHHHHHHHHHHHhcccCCCEEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999986 58999999
Q ss_pred EEEecCCCCc
Q 011631 239 LRVTQFNEDK 248 (481)
Q Consensus 239 V~vs~L~~~~ 248 (481)
|++++|.+..
T Consensus 367 v~~~~l~~~~ 376 (419)
T PRK02794 367 IGVSDLSPAD 376 (419)
T ss_pred EEEecCCCcc
Confidence 9999999753
No 10
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=5.8e-44 Score=367.41 Aligned_cols=237 Identities=28% Similarity=0.408 Sum_probs=223.2
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|+. ++..+|+.||++|++++|+|||||||+||++||||++.+||+|++++.++ ++.+||++
T Consensus 105 ~~siDe~~ld~t~~------~~~~la~~ir~~i~~~~gl~~siGia~nk~lAklaa~~~Kp~g~~~~~~~--~~~~~L~~ 176 (346)
T PRK03352 105 VWGWDEAFLGVDTD------DPEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDA--NWMAVMGD 176 (346)
T ss_pred EecCccEEEeCCCC------CHHHHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHHhhcCCCcEEEECHH--HHHHHHhc
Confidence 47999999999985 68999999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCC-CCcccccccccCc-
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQAR-FRKSISSERTFSV- 158 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~-~~KSIs~e~tF~~- 158 (481)
+||++|||||+++.++|++ +||+|++||+.++ ..|.++||...+.++|.+++|+|..+++... .+||++.+++|+.
T Consensus 177 lpl~~l~gig~~~~~~L~~-~Gi~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~~tf~~~ 255 (346)
T PRK03352 177 RPTDALWGVGPKTAKRLAA-LGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSREVTFPQD 255 (346)
T ss_pred CCHHHcCCCCHHHHHHHHH-cCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEEEECCCC
Confidence 9999999999999999997 9999999999998 8999999987789999999999999987543 4799999999987
Q ss_pred cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEE
Q 011631 159 TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLI 237 (481)
Q Consensus 159 ~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~-~~~VR~I 237 (481)
+.+.+++..+|+.|+++|+.||+++++.+++|+|++++.+|...+++++++.||++...|++++..+|++++ +.+||+|
T Consensus 256 ~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~l~~~~~~~~~~~~~l~~pt~d~~~l~~~~~~ll~~~~~~~~vr~i 335 (346)
T PRK03352 256 LTDRAEVESAVRELARRVLDEVVAEGRPVTRVAVKVRTATFYTRTKIRKLPEPTTDPDVIEAAALDVLDRFELDRPVRLL 335 (346)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHcCCccceEEEEEEeCCCceeEEEEECCCCcCCHHHHHHHHHHHHHhccCCCCEEEE
Confidence 689999999999999999999999999999999999999999899999999999999999999999999985 5899999
Q ss_pred EEEEecCCCC
Q 011631 238 GLRVTQFNED 247 (481)
Q Consensus 238 GV~vs~L~~~ 247 (481)
||++++|.+.
T Consensus 336 gl~~~~~~~~ 345 (346)
T PRK03352 336 GVRLELAMPD 345 (346)
T ss_pred EEEEeccCCC
Confidence 9999999875
No 11
>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=3.6e-44 Score=373.50 Aligned_cols=238 Identities=28% Similarity=0.427 Sum_probs=217.1
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecC-ChhHHHHhhc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPN-DRMAVMTFIS 80 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~-~~~~v~~fL~ 80 (481)
++||||+|||+|++..++ +.++|++||++|+++||||||||||+||++||||++.+||+|+++|.+ +.+++.+||+
T Consensus 94 ~~SiDE~~lDvt~~~~~~---g~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~~~~~~~~~fl~ 170 (379)
T cd01703 94 RLGFDENFMDVTEMRLLV---ASHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLPPSCADLMDFMD 170 (379)
T ss_pred ecCCCcEEEEccCccchh---HHHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcCCchHHHHHHhc
Confidence 589999999999986544 388999999999999999999999999999999999999999998865 3235788999
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch---------------H-HHHHHhcHhHHHHHHHHhcCCCCCCC-CC
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG---------------S-LLCAVFSHSTADFFLSVGLGLGSTNT-PQ 143 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~---------------~-~L~~~fG~~~~~~l~~~a~Gid~~~v-~~ 143 (481)
++||++|||||++++++|++ +||.|+|||++.+ . .|+++||...+.++|+.|+|+|.+++ .+
T Consensus 171 ~lpv~~l~GiG~~~~~kL~~-~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a~G~d~~~V~~~ 249 (379)
T cd01703 171 LHDLRKIPGIGYKTAAKLEA-HGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLLFGRDTSPVKPA 249 (379)
T ss_pred cCCccccCCcCHHHHHHHHH-cCCCcHHHHHhCCcccccccccccccccHHHHHHHHCHHHHHHHHHHHCCCCCCccCCC
Confidence 99999999999999999997 9999999999876 3 79999998778999999999999999 55
Q ss_pred CCCCcccccccccCc--cCCHHHHHHHHHHHHHHHHHHHHH--------hCCcccEEEEEEEecC-----CeeeEEEEEc
Q 011631 144 ARFRKSISSERTFSV--TEDKALLYRKLAEIAEMLSADMQK--------EGLRGRTLTLKLKTAS-----FEVRTRAVTL 208 (481)
Q Consensus 144 ~~~~KSIs~e~tF~~--~~d~e~L~~~L~~La~eL~~RLr~--------~~~~artltL~lr~~~-----f~~~srs~~l 208 (481)
...+|||+.++||.. ..+..++..+|..|+++|+.||++ .+..+++|+|++++.+ |.+.+++.++
T Consensus 250 ~~~~ksis~e~tf~~~~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~~~~~~~~~sr~~~l 329 (379)
T cd01703 250 SDFPQQISIEDSYKKCSLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTSTKKHYNRESKQAPI 329 (379)
T ss_pred CCCCceeEEeeccCCCCCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCCCCCccceeeecccc
Confidence 567899999999986 468899999999999999999999 9999999999999999 9999999999
Q ss_pred CCCCC---------CHHHHHHHHHHHHHhhCC------CCEEEEEEEEec
Q 011631 209 QKYIS---------SSEDILKHASVLLKAELP------VSLRLIGLRVTQ 243 (481)
Q Consensus 209 ~~pt~---------d~~~L~~~a~~LL~~~~~------~~VR~IGV~vs~ 243 (481)
+.|++ +...|++.+..||+++++ .+||++||++++
T Consensus 330 ~~~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~~~~~~~~irl~gv~~~~ 379 (379)
T cd01703 330 PSHVFQKLTGGNEIAARPIEKILMRLFRELVPPKNVKGFNLTLLNVCFTN 379 (379)
T ss_pred CchhhccccccchhhHHHHHHHHHHHHHHhcccccCCCCceEEEEEEeeC
Confidence 99998 678999999999998753 279999999975
No 12
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.2e-43 Score=377.74 Aligned_cols=242 Identities=28% Similarity=0.418 Sum_probs=226.9
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+++.......++..+|++||++|++++|||||||||+||++|||||+.+||||+++++++ ++.+||++
T Consensus 102 ~~SiDE~flD~~~l~~~~~~~~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~--~~~~~L~~ 179 (454)
T PRK03348 102 QLSFDEAFVEPAELAGASAEEVEAFAERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIRVVPPG--EERELLAP 179 (454)
T ss_pred EecCCeEEEEccccccccCCCHHHHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHhhccCCCCcEEEEEch--HHHHHHHh
Confidence 5899999999887654222368999999999999999999999999999999999999999999999886 68999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
+||++|||||+++.++|++ +||+||+||++++ ..|.++||...+.+||.+|+|+|..++.+..++|+|+.+.+|+. +
T Consensus 180 LPv~~L~GIG~~t~~~L~~-lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~e~tf~~~i 258 (454)
T PRK03348 180 LPVRRLWGIGPVTEEKLHR-LGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISAESTFAVDL 258 (454)
T ss_pred CCccccCCCCHHHHHHHHH-cCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEEEEECCCCC
Confidence 9999999999999999997 9999999999998 89999999877999999999999999988888999999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIG 238 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~-~~~VR~IG 238 (481)
.+.+.+..+|+.|+++|+.||+++++.+++|+|++++.+|...+++++++.||++...|+++++.+|++.+ ..+||++|
T Consensus 259 ~~~~~l~~~L~~L~~~l~~rL~~~g~~~r~v~l~l~~~d~~~~srs~~l~~pt~d~~~L~~la~~ll~~~~~~~~vRllg 338 (454)
T PRK03348 259 TTRAQLREAIERIAEHAHRRLLKDGRGARTVTVKLRKSDFSTLTRSATLPYATDDAAVLAATARRLLLDPDEIGPIRLVG 338 (454)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHcCCCccEEEEEEEeCCCCccEEEEECCCCCCCHHHHHHHHHHHHHhhccCCCeEEEE
Confidence 89999999999999999999999999999999999999999999999999999999999999999999875 47899999
Q ss_pred EEEecCCC
Q 011631 239 LRVTQFNE 246 (481)
Q Consensus 239 V~vs~L~~ 246 (481)
|++++|.+
T Consensus 339 V~~s~l~~ 346 (454)
T PRK03348 339 VGFSGLSD 346 (454)
T ss_pred EEECCCCc
Confidence 99999974
No 13
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=1.4e-43 Score=372.22 Aligned_cols=241 Identities=25% Similarity=0.416 Sum_probs=227.1
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhc---CCCCcEEEecCChhHHHHh
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDI---NKPNGQFVLPNDRMAVMTF 78 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~---aKPnG~~vI~~~~~~v~~f 78 (481)
++||||+|||+|++.++|| ++..+|++||++|++++|||||||||+|+++||||++. +||+|++++.++ ++.+|
T Consensus 101 ~~siDe~~lDvt~~~~~~~-~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~~--~~~~~ 177 (409)
T PRK03103 101 PFSIDEQFLDVTGSQKLFG-SPLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDKE--DVPAD 177 (409)
T ss_pred ecCCCeeEeeccchhhcCC-CHHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECHH--HHHHH
Confidence 5899999999999999998 89999999999999999999999999999999999998 999999999875 78999
Q ss_pred hccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCC--Ccccccccc
Q 011631 79 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARF--RKSISSERT 155 (481)
Q Consensus 79 L~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~--~KSIs~e~t 155 (481)
|+++||++|||||+++.++|++ +||+|+|||++++ ..|.++||.. +..+|..++|+|.+++.+..+ +|||+.+.+
T Consensus 178 L~~lpi~~l~gig~~~~~~L~~-~Gi~tigdl~~~~~~~L~~~fG~~-~~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~t 255 (409)
T PRK03103 178 LWPLPVRKLFGVGSRMEKHLRR-MGIRTIGQLANTPLERLKKRWGIN-GEVLWRTANGIDYSPVTPHSLDRQKAIGHQMT 255 (409)
T ss_pred HHcCCHhhcCCccHHHHHHHHH-cCCCCHHHHhcCCHHHHHHHHCHH-HHHHHHHhcCCCCCcCCcccCCCCCccCCCeE
Confidence 9999999999999999999997 9999999999999 7899999985 788999999999999877643 589999999
Q ss_pred cCc-cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCee---eEEEEEcCCCCCCHHHHHHHHHHHHHhhC-
Q 011631 156 FSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEV---RTRAVTLQKYISSSEDILKHASVLLKAEL- 230 (481)
Q Consensus 156 F~~-~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~---~srs~~l~~pt~d~~~L~~~a~~LL~~~~- 230 (481)
|+. ..+.++|...|..|+++|+.||++.++.+++|+|++++.+++. .+++++++.||++...|++.+..+|++++
T Consensus 256 ~~~~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~lr~~~~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~ 335 (409)
T PRK03103 256 LPRDYRGFEEIKVVLLELCEEVCRRARAKGYMGRTVSVSLRGADFDWPTGFSRQMTLPEPTNLAMEVYEAACKLFHRHWD 335 (409)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHhCCceeEEEEEEEeCCCcCCCCcceeeecCCCCCCHHHHHHHHHHHHHhccc
Confidence 987 6899999999999999999999999999999999999999988 99999999999999999999999999986
Q ss_pred CCCEEEEEEEEecCCCC
Q 011631 231 PVSLRLIGLRVTQFNED 247 (481)
Q Consensus 231 ~~~VR~IGV~vs~L~~~ 247 (481)
+.+||+|||++++|.+.
T Consensus 336 ~~~vr~lgv~~~~l~~~ 352 (409)
T PRK03103 336 GKPVRRVGVTLSNLVSD 352 (409)
T ss_pred CCCceEEEEEEeCCCCC
Confidence 47999999999999975
No 14
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=2.2e-43 Score=370.57 Aligned_cols=240 Identities=29% Similarity=0.416 Sum_probs=224.9
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|++.+++ ++.++|++||++|++++|+|||||||+||++||||++.+||+|++++.++ ++.+||++
T Consensus 103 ~~siDe~~ldvt~~~~~~--~~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~--~~~~~L~~ 178 (407)
T PRK01810 103 PVSIDEGYLDITDCYALG--SPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKR--DVPEMLWP 178 (407)
T ss_pred EecCCeEEEeccCccccC--CHHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHH--HHHHHHHh
Confidence 589999999999988765 58999999999999999999999999999999999999999999999875 78899999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCC--CCcccccccccCc
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQAR--FRKSISSERTFSV 158 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~--~~KSIs~e~tF~~ 158 (481)
+||++|||||+++.++|++ +||+|++||+.++ ..|.++||.. +.++|+.++|+|..++.+.. .+|||+++++|+.
T Consensus 179 lpv~~l~giG~~~~~~L~~-~Gi~tigdL~~~~~~~L~~rfG~~-g~~l~~~a~G~d~~~v~~~~~~~~ksi~~~~~~~~ 256 (407)
T PRK01810 179 LPVGEMHGIGEKTAEKLKD-IGIQTIGDLAKADEHILRAKLGIN-GVRLQRRANGIDDRPVDPEAIYQFKSVGNSTTLSH 256 (407)
T ss_pred CCHhhcCCcCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHHHhHH-HHHHHHHhcCCCCCCCCCCCCCCCceecceEECCC
Confidence 9999999999999999997 9999999999998 8999999985 78899999999999987544 3699999999998
Q ss_pred -cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCC-CCEEE
Q 011631 159 -TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELP-VSLRL 236 (481)
Q Consensus 159 -~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~~-~~VR~ 236 (481)
..+.+++..+|..|+++|+.||+++++.+++|+|++++.++...+++++++.||++...|++.+..+|++++. .+||+
T Consensus 257 ~~~~~~~l~~~l~~L~~~l~~rLr~~~~~~~~l~l~lr~~~~~~~~~~~~l~~pt~~~~~l~~~~~~ll~~~~~~~~vr~ 336 (407)
T PRK01810 257 DMDEEKELLDVLRRLSKSVSKRLQKKTVVSYNVQIMIRYHDRRTITRSKTLKNPIWEKRDIFQAASRLFKQHWNGDPVRL 336 (407)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHcCCccceeEEEEEECCCCceEEEEECCCCCCCHHHHHHHHHHHHHhccCCCCEEE
Confidence 6899999999999999999999999999999999999999999999999999999999999999999999864 78999
Q ss_pred EEEEEecCCCC
Q 011631 237 IGLRVTQFNED 247 (481)
Q Consensus 237 IGV~vs~L~~~ 247 (481)
+||++++|.+.
T Consensus 337 lgv~~~~l~~~ 347 (407)
T PRK01810 337 LGVTATDLEWK 347 (407)
T ss_pred EEEEEecCccc
Confidence 99999999975
No 15
>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=2.7e-43 Score=359.51 Aligned_cols=238 Identities=44% Similarity=0.670 Sum_probs=226.5
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+|++.++|+ ++..+|+.||++|++++|++||+|||+|+++||||++.+||+|+++++++ ++.+||++
T Consensus 94 ~~s~De~~ldv~~~~~~~~-~~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~--~~~~~L~~ 170 (334)
T cd03586 94 PLSIDEAYLDVTDYVRLFG-SATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPE--DVEEFLAP 170 (334)
T ss_pred EecccceeEccccccccCC-CHHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHH--HHHHHHhc
Confidence 5899999999999998888 89999999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
+||++|||||+++.++|++ +||+|++||++++ ..|.++||.. +.++|+.++|++..++.+..++|||+++++|+. .
T Consensus 171 lpl~~l~gig~~~~~~L~~-~Gi~ti~dl~~~~~~~L~~~~g~~-~~~l~~~~~G~~~~~v~~~~~~ks~~~~~~~~~~~ 248 (334)
T cd03586 171 LPVRKIPGVGKVTAEKLKE-LGIKTIGDLAKLDVELLKKLFGKS-GRRLYELARGIDNRPVEPDRERKSIGVERTFSEDL 248 (334)
T ss_pred CCchhhCCcCHHHHHHHHH-cCCcCHHHHHcCCHHHHHHHHhHH-HHHHHHHhCCCCCCCCCCCCCCCeeeeeEECCCCC
Confidence 9999999999999999997 9999999999998 7899999985 788889999999999988788999999999987 6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC-CCCEEEEE
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL-PVSLRLIG 238 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~-~~~VR~IG 238 (481)
.+.+++..+|..|+++|+.||+.+++.+++++|++++.++...+++.+++.||++...|++.+..+|++++ +.+||+||
T Consensus 249 ~~~~~l~~~l~~l~~~l~~rL~~~~~~~~~l~l~l~~~~~~~~~~~~~l~~~t~~~~~l~~~~~~~l~~~~~~~~vr~ig 328 (334)
T cd03586 249 TDPEELLEELLELAEELAERLRKRGLKGRTVTVKLKYADFSTRTRSRTLPEPTDDAEDIYELALELLEELLDGRPIRLLG 328 (334)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCCCeEEEEEEEEECCCCeEEEEEECCCCCCCHHHHHHHHHHHHHhccCCCCEEEEE
Confidence 88999999999999999999999999999999999999999999999999999999999999999999985 57999999
Q ss_pred EEEecC
Q 011631 239 LRVTQF 244 (481)
Q Consensus 239 V~vs~L 244 (481)
|++++|
T Consensus 329 v~~~~l 334 (334)
T cd03586 329 VRLSGL 334 (334)
T ss_pred EEeecC
Confidence 999986
No 16
>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=5.7e-43 Score=362.33 Aligned_cols=227 Identities=35% Similarity=0.504 Sum_probs=206.3
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||+|||+ +..+|++||++|++++|||||||||+||++|||||+.+||+|+++++++ ++.+||++
T Consensus 114 ~~SiDE~flDv----------~~~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~--~~~~~L~~ 181 (359)
T cd01702 114 KASIDEAYLDL----------GSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRND--AVASFLSS 181 (359)
T ss_pred ECcCCeeHHHH----------HHHHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHH--HHHHHhhc
Confidence 58999999999 4679999999999999999999999999999999999999999999875 78999999
Q ss_pred CCCcccCCCCHHHHHH-HhhccCCCcHHHHHhc--h-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccC
Q 011631 82 LPIRKIGGIGKVTEHI-LRDVFGINTCEEMLQK--G-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFS 157 (481)
Q Consensus 82 LPI~~LpGIG~kt~~k-L~~~lGI~TigDL~~~--~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~ 157 (481)
+||++|||||++++.+ |++ +||+|++||+++ + ..|.++||...+.++|+.++|+|..++.+..++|||+++++|+
T Consensus 182 lpv~~l~GiG~~~~~~ll~~-~Gi~ti~dl~~~~~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~~~~tf~ 260 (359)
T cd01702 182 LPITSIRGLGGKLGEEIIDL-LGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMGSSKNFP 260 (359)
T ss_pred CcHHHhCCcCHHHHHHHHHH-cCCcCHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCceeeeeeecC
Confidence 9999999999999776 576 999999999999 7 7899999977799999999999999998877899999999999
Q ss_pred c-cCCH-HHHHHHHHHHHHHHHHHHHHh----CCcccEEEEEEEecC-CeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC
Q 011631 158 V-TEDK-ALLYRKLAEIAEMLSADMQKE----GLRGRTLTLKLKTAS-FEVRTRAVTLQKYISSSEDILKHASVLLKAEL 230 (481)
Q Consensus 158 ~-~~d~-e~L~~~L~~La~eL~~RLr~~----~~~artltL~lr~~~-f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~ 230 (481)
. ..+. +++..+|..|+.+|+.||++. ++.+++|+|++++.+ +...+++.+++.|+ ...|++.+..||++++
T Consensus 261 ~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~~~~~~~sr~~~~~~~~--~~~i~~~~~~l~~~~~ 338 (359)
T cd01702 261 GKTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQRGDGVRRSRSCALPRYD--AQKIVKDAFKLIKAIN 338 (359)
T ss_pred CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEECCCcEEEEEEecCCCCC--HHHHHHHHHHHHHHhh
Confidence 7 5666 999999999999999999997 999999999999999 55566666665544 9999999999999875
Q ss_pred --------CCCEEEEEEEEec
Q 011631 231 --------PVSLRLIGLRVTQ 243 (481)
Q Consensus 231 --------~~~VR~IGV~vs~ 243 (481)
..+||+|||++++
T Consensus 339 ~~~~~~~~~~~~rl~g~~~~~ 359 (359)
T cd01702 339 EEGLGLAWNYPLTLLSLSFTK 359 (359)
T ss_pred hhccccccCCCeEEEEEEecC
Confidence 2689999999875
No 17
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=1.1e-42 Score=367.12 Aligned_cols=241 Identities=21% Similarity=0.266 Sum_probs=218.9
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCC-----CcEEEecCChhHHH
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKP-----NGQFVLPNDRMAVM 76 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKP-----nG~~vI~~~~~~v~ 76 (481)
+|||||+|||+|++.++ + ++..+|++||++|++++|||||||||+||++|||||+.+|| +|+++|.+. +++.
T Consensus 97 ~~siDE~~lDvt~~~~l-~-~~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~~i~~~-~~~~ 173 (422)
T PRK03609 97 IYSIDEAFCDLTGVRNC-R-DLTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVVDLSNL-ERQR 173 (422)
T ss_pred EeccccceecCCCCcCC-C-CHHHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEEEcCCH-HHHH
Confidence 58999999999999775 3 68999999999999999999999999999999999998876 688887422 3789
Q ss_pred HhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCC-Cccccccc
Q 011631 77 TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARF-RKSISSER 154 (481)
Q Consensus 77 ~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~-~KSIs~e~ 154 (481)
+||+++||++|||||+++.++|++ +||+|+|||++++ ..|+++||.. +..+|..++|++..++....+ +|+|++++
T Consensus 174 ~~L~~lPv~~l~GiG~~~~~~L~~-lGi~TigdL~~~~~~~L~~~fG~~-~~~l~~~a~G~~~~~~~~~~~~~ksi~~~~ 251 (422)
T PRK03609 174 KLLSLQPVEEVWGVGRRISKKLNA-MGIKTALDLADTNIRFIRKHFNVV-LERTVRELRGEPCLSLEEFAPTKQEIVCSR 251 (422)
T ss_pred HHhhcCChhhcCCccHHHHHHHHH-cCCCcHHHHhcCCHHHHHHHHCHH-HHHHHHHhCCCCCCCccccCCCCceEEEee
Confidence 999999999999999999999997 9999999999998 8999999986 677888999999888865555 47999999
Q ss_pred ccCc-cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCe------eeEEEEEcCCCCCCHHHHHHHHHHHHH
Q 011631 155 TFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFE------VRTRAVTLQKYISSSEDILKHASVLLK 227 (481)
Q Consensus 155 tF~~-~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~------~~srs~~l~~pt~d~~~L~~~a~~LL~ 227 (481)
+|+. ..+.+++..++..|+++|+.||+++++.+++|+|++++++|. ..+++.+++.||++...|++.+..+|+
T Consensus 252 tf~~~~~~~~~l~~~l~~l~~~l~~rLr~~~~~~~~l~l~ir~~~~~~~~~~~~~~~~~~l~~pt~d~~~l~~~a~~ll~ 331 (422)
T PRK03609 252 SFGERITDYESMRQAICSYAARAAEKLRGEHQYCRFISTFVKTSPFALNEPYYGNSASVKLLTPTQDSRDIIAAATRALD 331 (422)
T ss_pred ECCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccEEEEEEEcCCccccCCCcCceeEEeCCCCCCCHHHHHHHHHHHHH
Confidence 9987 689999999999999999999999999999999999999986 357888899999999999999999999
Q ss_pred hhCC--CCEEEEEEEEecCCCC
Q 011631 228 AELP--VSLRLIGLRVTQFNED 247 (481)
Q Consensus 228 ~~~~--~~VR~IGV~vs~L~~~ 247 (481)
+++. .++|++||.+++|.+.
T Consensus 332 ~~~~~~~~~r~~GV~~~~l~~~ 353 (422)
T PRK03609 332 AIWRDGHRYQKAGVMLGDFFSQ 353 (422)
T ss_pred HHhCCCCceEEeeEEEEeeccC
Confidence 9863 5799999999999865
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=8.7e-42 Score=350.99 Aligned_cols=237 Identities=27% Similarity=0.408 Sum_probs=214.7
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCC----cEEEecCChhHHHH
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPN----GQFVLPNDRMAVMT 77 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPn----G~~vI~~~~~~v~~ 77 (481)
++||||+|||+|++.+ |+ ++..+|++||++|++++|+|||+|||+||++|||||+.+||+ |++++++. ....+
T Consensus 95 ~~s~De~~ldvt~~~~-~~-~~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~~~-~~~~~ 171 (344)
T cd01700 95 VYSIDESFLDLTGSLR-FG-DLEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLTDE-EVRDK 171 (344)
T ss_pred EeecchhhccCcCCCC-CC-CHHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEecCh-hHHHH
Confidence 5799999999999988 87 899999999999999999999999999999999999999984 88888664 12348
Q ss_pred hhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCC-CCcccccccc
Q 011631 78 FISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQAR-FRKSISSERT 155 (481)
Q Consensus 78 fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~-~~KSIs~e~t 155 (481)
||+++||++|||||+++.++|++ +||+|++||++++ ..|.++||.. +.++|..++|+|..++.+.. ++|||+.+.+
T Consensus 172 ~l~~lpl~~l~gig~~~~~~L~~-~Gi~ti~dL~~~~~~~L~~rfG~~-~~~l~~~a~G~d~~~v~~~~~~~ks~~~~~~ 249 (344)
T cd01700 172 LLKILPVGDVWGIGRRTAKKLNA-MGIHTAGDLAQADPDLLRKKFGVV-GERLVRELNGIDCLPLEEYPPPKKSIGSSRS 249 (344)
T ss_pred HhccCChhhcCccCHHHHHHHHH-cCCCcHHHHhcCCHHHHHHHHHHH-HHHHHHHhCCCCCCcCCCCCCCCcEEEEeeE
Confidence 99999999999999999999997 9999999999998 7999999984 78889999999999996544 4599999999
Q ss_pred cCc-cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEE----EEEcCCCCCCHHHHHHHHHHHHHhhC
Q 011631 156 FSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTR----AVTLQKYISSSEDILKHASVLLKAEL 230 (481)
Q Consensus 156 F~~-~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~sr----s~~l~~pt~d~~~L~~~a~~LL~~~~ 230 (481)
|.. ..+.+++..+|++|+++|+.||+++++.+++|+|++++++|...++ +.+++.||++...|++.+..+|++++
T Consensus 250 ~~~~~~~~~~l~~~l~~L~~~l~~~L~~~~~~~~~l~l~l~~~~~~~~~~~~~~~~~~~~~t~~~~~l~~~~~~ll~~~~ 329 (344)
T cd01700 250 FGRDVTDLDELKQALAEYAERAAEKLRRQKSVARTISVFIGTSGFSRQPKYYSATNTLPYPTNDTREIVKAALRLLYAIY 329 (344)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHHHHHcCCcccEEEEEEEcCCCCCCCCccccccccCCcchhHHHHHHHHHHHHHHHh
Confidence 987 6899999999999999999999999999999999999998876444 35778999999999999999999986
Q ss_pred -C-CCEEEEEEEEec
Q 011631 231 -P-VSLRLIGLRVTQ 243 (481)
Q Consensus 231 -~-~~VR~IGV~vs~ 243 (481)
+ .+||+|||++++
T Consensus 330 ~~~~~iR~iGV~~~~ 344 (344)
T cd01700 330 RPGYAYRKAGVMLSD 344 (344)
T ss_pred CCCCcEEEEEEEeeC
Confidence 3 589999999875
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.6e-40 Score=339.46 Aligned_cols=242 Identities=33% Similarity=0.501 Sum_probs=226.6
Q ss_pred CCccceEEEecCCcccccCC-CHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhc
Q 011631 2 AASLDEAYLDITEVCRERGI-SGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFIS 80 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~-s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~ 80 (481)
++||||+|||+|+....+|. ++..+|.+||..|+.++|+|||+|||+||++|||||+++||+|++++.+. ++.+|||
T Consensus 97 ~lSIDE~~ldvt~~~~~~g~~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~--~~~~~l~ 174 (354)
T COG0389 97 PLSIDEAFLDLTDALRLLGLADAPRIALEIRFGILLELGLTASVGISDNKFLAKIASDLNKPDGITVIEPE--EVPALLW 174 (354)
T ss_pred eeeccceeeecccccccCCcccHHHHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHhcccCCCCEEEECHH--HHHHHHh
Confidence 68999999999998887764 68999999999999999999999999999999999999999999999964 8999999
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCC-cccccccccCc
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFR-KSISSERTFSV 158 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~-KSIs~e~tF~~ 158 (481)
+||+.++||||+.++.+|+. +||.|++||+..+ ..|.++||... +++|..++|+|.+++.....+ ||++++.||+.
T Consensus 175 ~Lpv~~~~GvG~~~~~~l~~-~Gi~ti~dl~~~~~~~L~~~~g~~~-~~l~~~a~Gid~~~v~~~~~~~ksi~~~~t~~~ 252 (354)
T COG0389 175 QLPVLEFWGVGKVTAEKLRR-LGISTIGDLAETDLDALKKRFGKLG-ERLYRLARGIDNRPVREQALRAKSIGAESTFEE 252 (354)
T ss_pred cCChhhhCCCCHHHHHHHHH-cCChhHHHHHhcCHHHHHHHHhHhH-HHHHHHhcCCCccccccccccCccccceeeccc
Confidence 99999999999999999997 9999999999976 78999999986 999999999999999888777 99999999998
Q ss_pred -cCCHHHHHHHHHH-HHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhC----CC
Q 011631 159 -TEDKALLYRKLAE-IAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAEL----PV 232 (481)
Q Consensus 159 -~~d~e~L~~~L~~-La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~----~~ 232 (481)
..+.+.+...|.. |+++++.||+..+..++++++++++++|...+++.+++.|+++..+++..+..+|++++ +.
T Consensus 253 d~~~~~~~~~~l~~~l~e~~~~rl~~~~~~~r~v~~~~~~~df~~~t~~~~l~~p~~~~~~i~~~~~~l~~~~~~~~~~~ 332 (354)
T COG0389 253 DLTDAEELIERLRARLGEEVVSRLRKSGRHGRTVSVKLKTADFPTNTRSRKLAQPTSDPIEIYAAALPLLPPLLFRGRGR 332 (354)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHhCCCceEEEEEEEecCCCcceeecccCCcCCCHHHHHHHHHHHHHHhhccCCCc
Confidence 4788877777777 99999999999999999999999999999999999999999999999999999999875 35
Q ss_pred CEEEEEEEEecCCCC
Q 011631 233 SLRLIGLRVTQFNED 247 (481)
Q Consensus 233 ~VR~IGV~vs~L~~~ 247 (481)
.+|++||++++|.+.
T Consensus 333 ~~rl~gv~~~~~~~~ 347 (354)
T COG0389 333 RIRLLGVSGPELIDS 347 (354)
T ss_pred eEEEEEEEecCcccc
Confidence 899999999999976
No 20
>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=1.9e-36 Score=309.02 Aligned_cols=233 Identities=20% Similarity=0.180 Sum_probs=209.9
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHH-Hhhc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVM-TFIS 80 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~-~fL~ 80 (481)
++||||+|||+|++.++|| ++..+|+.|++++ .++|++||||||+|+++||||++.+||+|++.+... ... .|++
T Consensus 94 ~~s~de~~ldvs~~~~~~~-~~~~~a~~i~~~~-~~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~--~~~~~~l~ 169 (335)
T cd03468 94 LDGPDGLLLDVTGCLHLFG-GEDALAASLRAAL-ATLGLSARAGIADTPGAAWLLARAGGGRGVLRREAL--AAALVLLA 169 (335)
T ss_pred cCCCCeEEEEcccchhhcC-CHHHHHHHHHHHH-HHcCCeEEEEecCCHHHHHHHhccCCCCccCCchHH--HHHhhccC
Confidence 5899999999999999998 8999999999999 478999999999999999999999999999876553 333 3889
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCC--CCCCCCcccccccccC
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNT--PQARFRKSISSERTFS 157 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v--~~~~~~KSIs~e~tF~ 157 (481)
++|+ ++||||+++.++|++ +||+|++||++++ ..|.++||.. +..+|..++|+|..++ .+.+.+++++.+.+|+
T Consensus 170 ~lp~-~~~gig~~~~~~L~~-~Gi~t~~dl~~~~~~~l~~rfG~~-~~~l~~~~~G~d~~~~~~~~~~~~~~~~~~~~~~ 246 (335)
T cd03468 170 PLPV-AALRLPPETVELLAR-LGLRTLGDLAALPRAELARRFGLA-LLLRLDQAYGRDPEPLLFSPPPPAFDFRLELQLE 246 (335)
T ss_pred CCCh-hHhCCCHHHHHHHHH-hCcccHHHHHhCChHHHHhhcCHH-HHHHHHHHCCCCCCCCCCCCCCCChhhhhhcCCC
Confidence 9999 599999999999997 9999999999998 8999999986 5667899999999998 4556689999999999
Q ss_pred ccCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHhhCC----CC
Q 011631 158 VTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKAELP----VS 233 (481)
Q Consensus 158 ~~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~~~~----~~ 233 (481)
....... ...+..|+++|+.+|+.+++.+++|+|++++.++...+++.++..|+++...|++.++.+|+++.. .+
T Consensus 247 ~~~~~~~-~~~l~~l~~~l~~~L~~~~~~~~~l~l~l~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~l~~~~~~~~~~~ 325 (335)
T cd03468 247 EPIARGL-LFPLRRLLEQLCAFLALRGLGARRLSLTLFREDGRVTRVLVGLARPSRDDLPLLRLLRERLERLALPRGIAP 325 (335)
T ss_pred CCcchhH-HHHHHHHHHHHHHHHHHcCCeeeEEEEEEEEECCceEEEEEeccCCccCHHHHHHHHHhhhhccCCCCCeee
Confidence 7433233 899999999999999999999999999999999999999999999999999999999999998753 68
Q ss_pred EEEEEEEEe
Q 011631 234 LRLIGLRVT 242 (481)
Q Consensus 234 VR~IGV~vs 242 (481)
||.+||++.
T Consensus 326 v~~~~v~~~ 334 (335)
T cd03468 326 VRLLALTAE 334 (335)
T ss_pred EEEEEeecc
Confidence 999999874
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=1.9e-36 Score=327.96 Aligned_cols=263 Identities=23% Similarity=0.341 Sum_probs=236.7
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS 81 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~ 81 (481)
++||||||+|+++.+..+..++..+|..||++|++.|||+||||||.|++||+||++.||||||+++.+. .+.+||++
T Consensus 471 aVSCDEa~vd~s~~~~~~~~tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a~--~veeFis~ 548 (1016)
T KOG2093|consen 471 AVSCDEAFVDVSDLSDEENETPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSAE--KVEEFISQ 548 (1016)
T ss_pred eecchhhhhhhhhhhhhhccCHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecHH--HHHHHhhh
Confidence 6899999999999998888889999999999999999999999999999999999999999999999886 79999999
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc-c
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV-T 159 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~-~ 159 (481)
++|.+|||||..|..+|.. +||+|||||+.+. ..|++.||++.|..+|..|+|+|++|......|||++++++|+. .
T Consensus 549 ~~v~~LPGVG~sm~~kL~s-~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS~dIN~GIRF 627 (1016)
T KOG2093|consen 549 LKVDDLPGVGSSMKSKLVS-QFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVSADINYGIRF 627 (1016)
T ss_pred cccccCCCccHHHHHHHHH-hccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhcceeeeeecceee
Confidence 9999999999999999997 9999999999887 88999999999999999999999998876667999999999997 5
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecC---------------CeeeEEEEEcCCCCCCHHHHHHHHHH
Q 011631 160 EDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTAS---------------FEVRTRAVTLQKYISSSEDILKHASV 224 (481)
Q Consensus 160 ~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~---------------f~~~srs~~l~~pt~d~~~L~~~a~~ 224 (481)
....++..+|..++++|-.||.+-++.+++++|+++.+. ++..+++.++..||+....|...+..
T Consensus 628 tn~~ev~~fl~~~~eEl~rkL~ei~k~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~~~Td~~~iItt~~~~ 707 (1016)
T KOG2093|consen 628 TNIKEVEQFLCLLSEELRRKLLEISKTASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLREPTDCNRIITTEVLR 707 (1016)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHhhccccchhHHHHhhcCCCCCccccccceeeccchhhhhhccCccccccchHHHHHH
Confidence 788999999999999999999999999999999986542 23367889999999999999999999
Q ss_pred HHHhhC--CCCEEEEEEEEe-cCCCCcccCCCCcccchHHHHhccCccCc
Q 011631 225 LLKAEL--PVSLRLIGLRVT-QFNEDKVRAPSDPTQKTLTNFMTSGHASK 271 (481)
Q Consensus 225 LL~~~~--~~~VR~IGV~vs-~L~~~~~~~~~~~~q~si~~Ff~s~~~~~ 271 (481)
|++..- +..+|++||.+. +|.+.. ....+.-+..+|.....++
T Consensus 708 L~~t~~~~~~elRG~gi~~ntkL~~~~----~~~~~~~l~e~Fgt~s~~~ 753 (1016)
T KOG2093|consen 708 LYETNSEPPSELRGLGIHSNTKLMDVL----ENLPPELLSEMFGTYSGKR 753 (1016)
T ss_pred HHHhcCCChHHhccchhhccccccccc----cCCcHHHHHhhcccccccc
Confidence 998864 367999999995 888764 2344566777887766554
No 22
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=99.96 E-value=3.2e-29 Score=267.73 Aligned_cols=169 Identities=34% Similarity=0.506 Sum_probs=158.1
Q ss_pred HHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccCCCcccCCCCHHHHHHHhhcc
Q 011631 23 GIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVF 102 (481)
Q Consensus 23 ~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~LPI~~LpGIG~kt~~kL~~~l 102 (481)
+..||++||++|+.+||||||+|||+||+||||||.++|||.|+||+.. .+.+||..|||.+++++|.++.+.|...+
T Consensus 199 Ga~Iv~EiR~~i~~elg~tCSAGIa~NKmLAKLvsg~nKPnqQTil~~~--~v~~ll~slpi~k~~~lGGk~G~~lie~L 276 (656)
T KOG2095|consen 199 GAQIVKEIRDAIKLELGYTCSAGIAHNKMLAKLVSGRNKPNQQTILPNT--YVQDLLDSLPITKIRTLGGKLGEELIEVL 276 (656)
T ss_pred HHHHHHHHHHHHHHHhCceeeccccccHHHHHHHhccCCCCcceecchH--HHHHHHHhCCCceeeeccchHHHHHHHHh
Confidence 4899999999999999999999999999999999999999999999986 79999999999999999988888887789
Q ss_pred CCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcCCCCCCCCCCCCCcccccccccCc---cCCHHHHHHHHHHHHHHHHH
Q 011631 103 GINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLGLGSTNTPQARFRKSISSERTFSV---TEDKALLYRKLAEIAEMLSA 178 (481)
Q Consensus 103 GI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~Gid~~~v~~~~~~KSIs~e~tF~~---~~d~e~L~~~L~~La~eL~~ 178 (481)
||.++|||++.. .+|++.||...+.|+|.+|+|+|.++|.++..+|||+++++|+. ..+.+++..||..++.++..
T Consensus 277 Gi~~vgdl~~fse~~L~~~fg~~~g~~l~~la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~ 356 (656)
T KOG2095|consen 277 GIDSVGDLQQFSETQLQKKFGEKNGTWLRNLARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAE 356 (656)
T ss_pred CCchHHHHHhcCHHHHHHhhCcchhHHHHHHhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHH
Confidence 999999999998 89999999999999999999999999999999999999999995 47888999999999999999
Q ss_pred HHHHh----CCcccEEEEE
Q 011631 179 DMQKE----GLRGRTLTLK 193 (481)
Q Consensus 179 RLr~~----~~~artltL~ 193 (481)
||..+ ...+.++.++
T Consensus 357 Rl~~d~~en~r~as~l~~~ 375 (656)
T KOG2095|consen 357 RLGKDRNENKRRASTLVVS 375 (656)
T ss_pred HHHhhhhhhccccceEEee
Confidence 99776 4667788887
No 23
>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=99.53 E-value=5.3e-14 Score=123.09 Aligned_cols=107 Identities=33% Similarity=0.457 Sum_probs=96.0
Q ss_pred CCCC-CCCCCcccccccccCc-cCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCe---eeEEEEEcCCCCC
Q 011631 139 TNTP-QARFRKSISSERTFSV-TEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFE---VRTRAVTLQKYIS 213 (481)
Q Consensus 139 ~~v~-~~~~~KSIs~e~tF~~-~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~---~~srs~~l~~pt~ 213 (481)
+||. +..++|||+++++|+. ..+.+.+..+|..|+++|+.||++.++.+++|+|++++.++. ..+++.+++.|++
T Consensus 2 ~pV~~~~~~~ksi~~~~t~~~~~~~~~~i~~~l~~l~~~l~~rL~~~~~~~~~i~l~l~~~~~~~~~~~~~~~~l~~p~~ 81 (127)
T PF11799_consen 2 EPVQQPRPPPKSIGSERTFPEPISDREEIEEWLRELAEELAERLRERGLAARTITLKLRYSDFGRCSSRSRSIRLPFPTN 81 (127)
T ss_dssp -----SCSS-SEEEEEEEECEEESSHHHHHHHHHHHHHHHHHHHHHCTEEEEEEEEEEEETTSCSCEEEEEEEEECCCEH
T ss_pred CCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHhhCcCCceEEEEEEecCCcccceeeEEEeccCCcC
Confidence 4566 6778999999999997 689999999999999999999999999999999999999998 8999999999999
Q ss_pred CHHHHHHHHHHHHHhh-C--CCCEEEEEEEEecCC
Q 011631 214 SSEDILKHASVLLKAE-L--PVSLRLIGLRVTQFN 245 (481)
Q Consensus 214 d~~~L~~~a~~LL~~~-~--~~~VR~IGV~vs~L~ 245 (481)
+...|+..+..+|++. + ..+||+|||++++|.
T Consensus 82 ~~~~l~~~~~~l~~~~~~~~~~~vr~igv~~~~l~ 116 (127)
T PF11799_consen 82 DADELLKAARELLERLLYDPGFPVRLIGVSASDLI 116 (127)
T ss_dssp CHHHHHHHHHHHHHHHHHHTTCGEEEEEEEEEEEE
T ss_pred CHHHHHHHHHHHHHHHhcCCCCCEEEEEEEECCCc
Confidence 9999999999999665 4 478999999999999
No 24
>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=99.17 E-value=1.4e-11 Score=112.59 Aligned_cols=56 Identities=46% Similarity=0.637 Sum_probs=51.4
Q ss_pred CCccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhhh
Q 011631 2 AASLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCSD 58 (481)
Q Consensus 2 ~~SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~ 58 (481)
.+|+||+|+|+|++.++|| +...++++||++|++++|++||+|||+|+++||||++
T Consensus 94 ~~s~de~~ldv~~~~~l~~-~~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 94 VYSPDELFLDVTGSLRLFG-GEEALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp EEETTEEEEEEHHHHHHHH-HHHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred ecccccccccCCcchhhcc-hHHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 4799999999999999998 7899999999999999999999999999999999985
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=98.55 E-value=5.7e-08 Score=66.54 Aligned_cols=31 Identities=48% Similarity=0.679 Sum_probs=27.3
Q ss_pred hHHHHhhccCCCcccCCCCHHHHHHHhhccCC
Q 011631 73 MAVMTFISSLPIRKIGGIGKVTEHILRDVFGI 104 (481)
Q Consensus 73 ~~v~~fL~~LPI~~LpGIG~kt~~kL~~~lGI 104 (481)
+++.+||+++||+++||||++|+++|++ +||
T Consensus 2 e~v~~~l~~lpi~~~~GIG~kt~~kL~~-~GI 32 (32)
T PF11798_consen 2 EDVPEFLWPLPIRKFWGIGKKTAKKLNK-LGI 32 (32)
T ss_dssp HHHHHHHHCSBGGGSTTS-HHHHHHHHC-TT-
T ss_pred hHHHHHHhcCCHHhhCCccHHHHHHHHH-ccC
Confidence 3789999999999999999999999997 997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=97.79 E-value=1.7e-05 Score=81.36 Aligned_cols=79 Identities=23% Similarity=0.244 Sum_probs=62.0
Q ss_pred hhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcH--hHHHHHHHHhcC---CC--CCCCCCCCCCcc
Q 011631 78 FISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVGLG---LG--STNTPQARFRKS 149 (481)
Q Consensus 78 fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~--~~~~~l~~~a~G---id--~~~v~~~~~~KS 149 (481)
.|.++||.++||||++++++|.+ .||.|++||+..+ ..|.+++|. ..++.++..++| .+ .+.+.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~L~~-~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEKLRE-AGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHHHHH-cCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 47899999999999999999997 9999999999998 789999994 467888888887 42 222222234577
Q ss_pred cccccccC
Q 011631 150 ISSERTFS 157 (481)
Q Consensus 150 Is~e~tF~ 157 (481)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 77666654
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=96.99 E-value=0.00074 Score=68.86 Aligned_cols=73 Identities=27% Similarity=0.310 Sum_probs=55.7
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHh--HHHHHHHHhc---CCC--CCCCCCCCCCcccccccc
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVGL---GLG--STNTPQARFRKSISSERT 155 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~--~~~~l~~~a~---Gid--~~~v~~~~~~KSIs~e~t 155 (481)
|.++||||++++++|.+ .||.|++||+..+ ..|.+++|.. .++.++..+. |.+ .+.+.....+++++...|
T Consensus 1 l~~i~gig~~~~~~L~~-~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~T 79 (310)
T TIGR02236 1 LEDLPGVGPATAEKLRE-AGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKTIGKITT 79 (310)
T ss_pred CcccCCCCHHHHHHHHH-cCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhccCCeecC
Confidence 56899999999999997 9999999999998 7999999953 5777777776 766 333332234677776666
Q ss_pred cC
Q 011631 156 FS 157 (481)
Q Consensus 156 F~ 157 (481)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 54
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=96.58 E-value=0.003 Score=49.05 Aligned_cols=49 Identities=24% Similarity=0.377 Sum_probs=39.5
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVG 133 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~a 133 (481)
+.+|+|||++++.+|.+ .|+.|+.||+..+ ..|..+ +|...++.+...+
T Consensus 7 L~~I~Gig~~~a~~L~~-~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~ 58 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLYE-AGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAA 58 (60)
T ss_dssp HHTSTTCHHHHHHHHHH-TTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHH
T ss_pred hccCCCCCHHHHHHHHh-cCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHH
Confidence 34689999999999998 8999999999987 677766 6666676665443
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=95.88 E-value=0.0077 Score=51.28 Aligned_cols=37 Identities=27% Similarity=0.346 Sum_probs=31.2
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV 120 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~ 120 (481)
.+.+|||||+++++-|.. +||+++.||+..+ ..|..+
T Consensus 13 ~L~~iP~IG~a~a~DL~~-LGi~s~~~L~g~dP~~Ly~~ 50 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLRL-LGIRSPADLKGRDPEELYER 50 (93)
T ss_pred HHhcCCCccHHHHHHHHH-cCCCCHHHHhCCCHHHHHHH
Confidence 378999999999999997 9999999999876 444433
No 30
>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=94.65 E-value=0.061 Score=44.64 Aligned_cols=50 Identities=22% Similarity=0.365 Sum_probs=31.1
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch---H--HHHHHhcHhHHHHHHHH
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG---S--LLCAVFSHSTADFFLSV 132 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~---~--~L~~~fG~~~~~~l~~~ 132 (481)
-.|++||+||+++++.|.+ .||+|+.||..+- . .|++.-.......||.+
T Consensus 3 ~~l~~LpNig~~~e~~L~~-vGI~t~~~L~~~Ga~~a~~~Lk~~~~~~~~~~L~aL 57 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAK-VGIHTVEDLRELGAVEAYLRLKASGPSVCLNLLYAL 57 (81)
T ss_dssp --GCGSTT--HHHHHHHHH-TT--SHHHHHHHHHHHHHHHHHHH-TT--HHHHHHH
T ss_pred cchhhCCCCCHHHHHHHHH-cCCCCHHHHHHhCHHHHHHHHHHHCCCCCHHHHHHH
Confidence 3589999999999999998 8999999998874 2 34444222334556654
No 31
>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=94.14 E-value=0.036 Score=42.22 Aligned_cols=29 Identities=28% Similarity=0.335 Sum_probs=21.6
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhc
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 113 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~ 113 (481)
+..|||||+++|+++-. .|++|+.||...
T Consensus 4 f~~I~GVG~~tA~~w~~-~G~rtl~Dl~~~ 32 (52)
T PF10391_consen 4 FTGIWGVGPKTARKWYA-KGIRTLEDLRKS 32 (52)
T ss_dssp HHTSTT--HHHHHHHHH-TT--SHHHHHHG
T ss_pred hhhcccccHHHHHHHHH-hCCCCHHHHhhh
Confidence 35689999999999997 999999999753
No 32
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=93.23 E-value=0.18 Score=49.76 Aligned_cols=53 Identities=25% Similarity=0.347 Sum_probs=45.8
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHHhcCC
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGLGL 136 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~a~Gi 136 (481)
+|.+|+|||++.+.+|.+ .|+.|+.+|+..+ ..|.++ +|...+..++..+.+.
T Consensus 4 ~L~~IpGIG~krakkLl~-~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~ 59 (232)
T PRK12766 4 ELEDISGVGPSKAEALRE-AGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGL 59 (232)
T ss_pred ccccCCCcCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccc
Confidence 578999999999999997 8999999999987 788888 8888888888775543
No 33
>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=92.50 E-value=0.27 Score=39.21 Aligned_cols=51 Identities=18% Similarity=0.291 Sum_probs=37.4
Q ss_pred HhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHH--HHhcHhHHHHH
Q 011631 77 TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFF 129 (481)
Q Consensus 77 ~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~--~~fG~~~~~~l 129 (481)
..+...||.+| |+..++...|++ .||+|++||..++ ..|. +-||.+..+-+
T Consensus 7 ~~~~~~~I~~L-~LS~Ra~n~L~~-~~I~tv~dL~~~s~~~L~~i~n~G~ksl~EI 60 (66)
T PF03118_consen 7 EELLDTPIEDL-GLSVRAYNCLKR-AGIHTVGDLVKYSEEDLLKIKNFGKKSLEEI 60 (66)
T ss_dssp HHHHCSBGGGS-TSBHHHHHHHHC-TT--BHHHHHCS-HHHHHTSTTSHHHHHHHH
T ss_pred HHHhcCcHHHh-CCCHHHHHHHHH-hCCcCHHHHHhCCHHHHHhCCCCCHhHHHHH
Confidence 45678999999 899999999997 9999999999997 5555 34555544433
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.38 E-value=0.23 Score=44.76 Aligned_cols=31 Identities=29% Similarity=0.499 Sum_probs=29.0
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhch
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 114 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~ 114 (481)
.|+.|-|||++.+..|+. +||.|..||+.+.
T Consensus 68 DLt~I~GIGPk~e~~Ln~-~GI~tfaQIAAwt 98 (133)
T COG3743 68 DLTRISGIGPKLEKVLNE-LGIFTFAQIAAWT 98 (133)
T ss_pred cchhhcccCHHHHHHHHH-cCCccHHHHHhcC
Confidence 588899999999999998 9999999999986
No 35
>PRK02362 ski2-like helicase; Provisional
Probab=90.96 E-value=0.3 Score=55.90 Aligned_cols=52 Identities=21% Similarity=0.353 Sum_probs=46.0
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhc
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGL 134 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~ 134 (481)
+|+..|||||++.+++|.+ .||.|+.||+... ..|.++||.+.++.+...+.
T Consensus 652 ~~L~~ip~i~~~~a~~l~~-~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~ 704 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYN-AGIESRADLRAADKSVVLAILGEKIAENILEQAG 704 (737)
T ss_pred HHHhCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhC
Confidence 5777899999999999997 9999999999886 78888899998888877654
No 36
>PRK01172 ski2-like helicase; Provisional
Probab=85.82 E-value=1.1 Score=50.60 Aligned_cols=50 Identities=20% Similarity=0.365 Sum_probs=40.6
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHH
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLS 131 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~ 131 (481)
.+|+..|||||+..+++|.+ .||+|+.||+.++ ..+.++ +|...++.+..
T Consensus 611 ~~~L~~ip~~~~~~a~~l~~-~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~ 663 (674)
T PRK01172 611 LIDLVLIPKVGRVRARRLYD-AGFKTVDDIARSSPERIKKIYGFSDTLANAIVN 663 (674)
T ss_pred HHhhcCCCCCCHHHHHHHHH-cCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHH
Confidence 36888999999999999997 9999999999986 677777 55555555544
No 37
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=85.23 E-value=1.1 Score=39.83 Aligned_cols=49 Identities=22% Similarity=0.446 Sum_probs=40.4
Q ss_pred HHHHhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcH
Q 011631 74 AVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH 123 (481)
Q Consensus 74 ~v~~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~ 123 (481)
.+.++...-.+-.++|||+..+..|.. .||.|+.+|+..+ ..|...++.
T Consensus 45 ~l~~w~~~AdL~ri~gi~~~~a~LL~~-AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 45 NLLKWVNQADLMRIPGIGPQYAELLEH-AGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred HHHHHHhHHHhhhcCCCCHHHHHHHHH-hCcCcHHHHHhCCHHHHHHHHHH
Confidence 566666666677999999999999997 8999999999987 667666554
No 38
>PRK08609 hypothetical protein; Provisional
Probab=82.89 E-value=1.1 Score=50.05 Aligned_cols=30 Identities=20% Similarity=0.290 Sum_probs=26.3
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhc
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 113 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~ 113 (481)
+..|||||++++.+|.+.+||.|+.||...
T Consensus 90 l~~i~GiGpk~a~~l~~~lGi~tl~~L~~a 119 (570)
T PRK08609 90 LLKLPGLGGKKIAKLYKELGVVDKESLKEA 119 (570)
T ss_pred HhcCCCCCHHHHHHHHHHhCCCCHHHHHHH
Confidence 458999999999999855999999999864
No 39
>PRK00254 ski2-like helicase; Provisional
Probab=82.67 E-value=1.6 Score=49.83 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=46.0
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHHhc
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGL 134 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~a~ 134 (481)
.+|+..|||||++.+++|.+ .|+.|+.|+...+ ..|.+. +|.+.++.++....
T Consensus 644 ~~~L~~ipgig~~~~~~l~~-~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 644 LLELMRLPMIGRKRARALYN-AGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred HhhhhcCCCCCHHHHHHHHH-ccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 36788999999999999997 8999999999987 788888 78888888877643
No 40
>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=82.14 E-value=1.4 Score=37.26 Aligned_cols=32 Identities=25% Similarity=0.494 Sum_probs=22.7
Q ss_pred hccCCCcccCCCCHHHHHHHhhccCCCcHHHHH
Q 011631 79 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEML 111 (481)
Q Consensus 79 L~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~ 111 (481)
|...||++|+|||+..+.+|.. -|+..+..|+
T Consensus 16 MGeK~V~~laGIG~~lg~~L~~-~GfdKAy~vL 47 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLEE-KGFDKAYVVL 47 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHHH-TT--BHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHHH-CCCcHHHHHh
Confidence 4567999999999999999997 8999877664
No 41
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=81.78 E-value=1 Score=46.94 Aligned_cols=30 Identities=27% Similarity=0.299 Sum_probs=27.0
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhc
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQK 113 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~ 113 (481)
.+..|||||++++.+|.+ +||+|+.||...
T Consensus 90 ~l~~i~GiGpk~a~~l~~-lGi~tl~eL~~a 119 (334)
T smart00483 90 LFTNVFGVGPKTAAKWYR-KGIRTLEELKKN 119 (334)
T ss_pred HHHccCCcCHHHHHHHHH-hCCCCHHHHHhc
Confidence 367899999999999998 999999999764
No 42
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=79.77 E-value=2.3 Score=33.47 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=27.5
Q ss_pred cCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHH
Q 011631 87 IGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 132 (481)
Q Consensus 87 LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~ 132 (481)
|||||.++++.|.+ ...|+..|.+.+ ..|... +|+..++.++.+
T Consensus 8 I~~VG~~~ak~L~~--~f~sl~~l~~a~~e~L~~i~gIG~~~A~si~~f 54 (64)
T PF12826_consen 8 IPGVGEKTAKLLAK--HFGSLEALMNASVEELSAIPGIGPKIAQSIYEF 54 (64)
T ss_dssp STT--HHHHHHHHH--CCSCHHHHCC--HHHHCTSTT--HHHHHHHHHH
T ss_pred CCCccHHHHHHHHH--HcCCHHHHHHcCHHHHhccCCcCHHHHHHHHHH
Confidence 58999999999987 455888888776 666655 666666655543
No 43
>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=79.75 E-value=1.4 Score=45.36 Aligned_cols=29 Identities=28% Similarity=0.536 Sum_probs=26.0
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhc
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQK 113 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~ 113 (481)
+..|||||++++++|.. +||.|+.||...
T Consensus 87 l~~i~GiGpk~a~~l~~-lGi~sl~dL~~a 115 (307)
T cd00141 87 LLRVPGVGPKTARKLYE-LGIRTLEDLRKA 115 (307)
T ss_pred HHcCCCCCHHHHHHHHH-cCCCCHHHHHHH
Confidence 56899999999999995 999999999764
No 44
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=79.11 E-value=1.9 Score=38.42 Aligned_cols=36 Identities=31% Similarity=0.449 Sum_probs=28.8
Q ss_pred CCCCHHHHHHHhhccCCCcHHHHHhch----H--HHHHHhcHh
Q 011631 88 GGIGKVTEHILRDVFGINTCEEMLQKG----S--LLCAVFSHS 124 (481)
Q Consensus 88 pGIG~kt~~kL~~~lGI~TigDL~~~~----~--~L~~~fG~~ 124 (481)
||||++++.+|++ .||+|.+||.... . .|....|..
T Consensus 1 pgi~~~~~~~L~~-~GI~t~~~Ll~~~~~~~~r~~La~~~~i~ 42 (122)
T PF14229_consen 1 PGIGPKEAAKLKA-AGIKTTGDLLEAGDTPLGRKALAKKLGIS 42 (122)
T ss_pred CCCCHHHHHHHHH-cCCCcHHHHHHcCCCHHHHHHHHHhcCCC
Confidence 7999999999997 9999999998874 1 355555543
No 45
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=75.31 E-value=4.6 Score=43.53 Aligned_cols=47 Identities=19% Similarity=0.259 Sum_probs=40.0
Q ss_pred HHHhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhc
Q 011631 75 VMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 122 (481)
Q Consensus 75 v~~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG 122 (481)
..++...-.|.-+|||++...+.|.. .||+|+.+|+..+ ..+...+|
T Consensus 218 ~~~a~e~~~L~Lv~Gi~~~r~~~l~~-~GI~Ti~~LA~~~~~~~~~~~g 265 (474)
T COG2251 218 ESEALEEDDLSLVPGITPSRYDVLEE-VGITTIEDLADASLPILELVAG 265 (474)
T ss_pred hHHHhhccceeccCCCCHHHHHHHHH-cCcchHHHHHhccccchhhhhh
Confidence 45677888899999999999999997 8999999999976 55566666
No 46
>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=75.07 E-value=1.6 Score=29.50 Aligned_cols=16 Identities=31% Similarity=0.499 Sum_probs=12.7
Q ss_pred CcccCCCCHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILR 99 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~ 99 (481)
|.+|||||++++..+.
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 5678999999998875
No 47
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=74.50 E-value=2.4 Score=48.34 Aligned_cols=31 Identities=29% Similarity=0.603 Sum_probs=28.5
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhc
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQK 113 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~ 113 (481)
.||..|.|||++.+++|++ +||.|+.||+..
T Consensus 9 ~~~~~l~gvg~~~~~~l~~-lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLAK-LGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHHH-cCCCCHHHHhhc
Confidence 5899999999999999997 999999999764
No 48
>PRK07758 hypothetical protein; Provisional
Probab=74.45 E-value=6.5 Score=33.73 Aligned_cols=44 Identities=14% Similarity=0.128 Sum_probs=33.8
Q ss_pred ccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHH--HHhcHhHHHHHH
Q 011631 86 KIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFL 130 (481)
Q Consensus 86 ~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~--~~fG~~~~~~l~ 130 (481)
-+|+++-+...-|++ .||+|++||..++ .+|. +-||++..+.|.
T Consensus 38 ~~~~LSvRA~N~Lk~-AGI~TL~dLv~~te~ELl~iknlGkKSL~EIk 84 (95)
T PRK07758 38 FLSLLSAPARRALEH-HGIHTVEELSKYSEKEILKLHGMGPASLPKLR 84 (95)
T ss_pred CCccccHHHHHHHHH-cCCCcHHHHHcCCHHHHHHccCCCHHHHHHHH
Confidence 346889999999997 8999999999997 5554 457776555443
No 49
>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=73.80 E-value=7.2 Score=39.46 Aligned_cols=61 Identities=16% Similarity=0.227 Sum_probs=40.5
Q ss_pred HHHhhc--cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhc--HhHHHHHHHHhcCC
Q 011631 75 VMTFIS--SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS--HSTADFFLSVGLGL 136 (481)
Q Consensus 75 v~~fL~--~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG--~~~~~~l~~~a~Gi 136 (481)
+.+-+| +.|+..|||||...+.+|.+ .||.|+++|+.++ ..+...++ ...+..+.+.+..+
T Consensus 139 i~q~~w~~~~~L~Qlp~i~~~~~~~l~~-~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~ 204 (314)
T PF02889_consen 139 IVQALWDSDSPLLQLPHIGEESLKKLEK-RGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRI 204 (314)
T ss_dssp HHHTS-TTS-GGGGSTT--HHHHHHHHH-TT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS
T ss_pred HHhhcCCCCChhhcCCCCCHHHHHHHhc-cCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHC
Confidence 334444 36899999999999999997 8999999999997 67777776 23456666666654
No 50
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=73.68 E-value=5.2 Score=44.74 Aligned_cols=53 Identities=23% Similarity=0.231 Sum_probs=43.0
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH-hcHhHHHHHHHHhcC
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV-FSHSTADFFLSVGLG 135 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~-fG~~~~~~l~~~a~G 135 (481)
.-.+.+|||||+++..+|-+ .+.|+..+...+ .+|.+. ++...++.++....|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll~--~Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIYR--NFKTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHHH--HhCCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 35789999999999999876 667999999988 889888 666778878776554
No 51
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=72.20 E-value=1.6 Score=31.50 Aligned_cols=26 Identities=27% Similarity=0.583 Sum_probs=24.2
Q ss_pred ccccccccCCCCCcHhhhhcccchhH
Q 011631 394 YKCSLCGTEMPPSFIEERQEHSDFHL 419 (481)
Q Consensus 394 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 419 (481)
-+|+.||..--|+=.|.+..|.-||=
T Consensus 14 ~~C~~CgM~Y~~~~~eD~~~H~~yH~ 39 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSPEDEKLHKKYHD 39 (41)
T ss_pred cCCCCCCCEECCCCHHHHHHHHHHHh
Confidence 58999999999999999999999993
No 52
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=67.90 E-value=9.6 Score=43.16 Aligned_cols=52 Identities=19% Similarity=0.196 Sum_probs=43.4
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHHhcC
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSVGLG 135 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~a~G 135 (481)
-.|.+|||||+++..+|-+ -+.++..+...+ .+|.+.+|.+.++.++.....
T Consensus 552 S~L~~IpGIG~kr~~~LL~--~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~ 604 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK--HFGSLERVRAATETQLAAVVGRAAAEAIIAHFTT 604 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcC
Confidence 4688999999999999876 667999998887 788888999888888876543
No 53
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=67.89 E-value=3.9 Score=46.24 Aligned_cols=31 Identities=32% Similarity=0.651 Sum_probs=28.5
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhc
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQK 113 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~ 113 (481)
.|+..+.|||++++++|++ +||+|+.||+..
T Consensus 10 ~~l~~l~gig~~~a~~l~~-Lgi~tv~DLL~~ 40 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLKK-LGIHTVQDLLLY 40 (677)
T ss_pred cchhhhcCcCHHHHHHHHH-cCCCcHHHHHHh
Confidence 4899999999999999997 999999999764
No 54
>PTZ00035 Rad51 protein; Provisional
Probab=67.23 E-value=5.4 Score=41.59 Aligned_cols=54 Identities=22% Similarity=0.246 Sum_probs=41.9
Q ss_pred cCCCccc--CCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHh--HHHHHHHHhcC
Q 011631 81 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVGLG 135 (481)
Q Consensus 81 ~LPI~~L--pGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~--~~~~l~~~a~G 135 (481)
..+|.+| +||++.+..+|++ .||+|+.||+..+ ..|.+..|.. .++.+...++-
T Consensus 20 ~~~~~~l~~~g~~~~~~~kL~~-~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~ 78 (337)
T PTZ00035 20 FQEIEKLQSAGINAADIKKLKE-AGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASK 78 (337)
T ss_pred CccHHHHhcCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHH
Confidence 3478888 7899999999997 8999999999987 7888888853 34455444443
No 55
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=64.50 E-value=9.2 Score=44.60 Aligned_cols=50 Identities=16% Similarity=0.187 Sum_probs=43.2
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhc-HhHHHHHHHHhcC
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS-HSTADFFLSVGLG 135 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG-~~~~~~l~~~a~G 135 (481)
|..|||||++.+..|-. .+.++.+|++++ ..|....| ...+..+|...+.
T Consensus 759 L~~lPgI~~~~a~~ll~--~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~ 810 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRK--KVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRT 810 (814)
T ss_pred HHHCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhcc
Confidence 55789999999999985 799999999998 78999999 8888988876543
No 56
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=64.44 E-value=6.9 Score=41.07 Aligned_cols=54 Identities=24% Similarity=0.257 Sum_probs=41.8
Q ss_pred ccCCCccc--CCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHh--HHHHHHHHhc
Q 011631 80 SSLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVGL 134 (481)
Q Consensus 80 ~~LPI~~L--pGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~--~~~~l~~~a~ 134 (481)
+..+|.+| .||++.+.++|+. .||+|+.||+..+ ..|.+..|.. .++.+...++
T Consensus 27 ~~~~~~~l~~~g~~~~~~~kL~~-~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~ 85 (344)
T PLN03187 27 LFESIDKLISQGINAGDVKKLQD-AGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAE 85 (344)
T ss_pred cccCHHHHhhCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHH
Confidence 36778888 6799999999997 8999999999987 7888777743 3444444443
No 57
>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=63.93 E-value=8.5 Score=41.72 Aligned_cols=37 Identities=22% Similarity=0.353 Sum_probs=32.3
Q ss_pred HhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch
Q 011631 77 TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 114 (481)
Q Consensus 77 ~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~ 114 (481)
.....-+|..|+||+++....|++ .||.|+.||+...
T Consensus 202 ~~~~~~~lslv~gi~~~~~~~L~~-~GI~ti~~La~~~ 238 (457)
T TIGR03491 202 VAKEEGHLSLVPGIGPSRYRLLQE-LGIHTLEDLAAAD 238 (457)
T ss_pred HHHhcCCeeecCCCCHHHHHHHHH-cCCCcHHHHhcCC
Confidence 344467899999999999999997 8999999999875
No 58
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=61.31 E-value=17 Score=36.77 Aligned_cols=55 Identities=11% Similarity=0.077 Sum_probs=42.2
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcH--hHHHHHHHHhcCC
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVGLGL 136 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~--~~~~~l~~~a~Gi 136 (481)
..|+..||+||+..+++|.+ .||.+++||..++ ..+...+|. ..+..++..+...
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~~-~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~ 207 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLEK-KKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRL 207 (312)
T ss_pred CCccccCCCCCHHHHHHHHh-CCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhC
Confidence 35899999999999999997 8999999999987 666666553 3455555555443
No 59
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=60.77 E-value=12 Score=42.77 Aligned_cols=48 Identities=19% Similarity=0.165 Sum_probs=37.8
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHH--HhcHhHHHHHH
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFL 130 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~--~fG~~~~~~l~ 130 (481)
.-=+|+|+|+++.++|-+..+|.++.||..+. ..|.. .||.+.++.++
T Consensus 446 ~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll 496 (665)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLL 496 (665)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHH
Confidence 45678999999999999867899999999876 55654 57887666554
No 60
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=59.32 E-value=9.6 Score=37.60 Aligned_cols=32 Identities=22% Similarity=0.347 Sum_probs=29.3
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 114 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~ 114 (481)
=.+..|.|||+..+++|+. .||.|..||+.+.
T Consensus 158 DDL~~I~GIGp~~a~~L~e-aGi~tfaQIAa~t 189 (221)
T PRK12278 158 DDLTKITGVGPALAKKLNE-AGVTTFAQIAALT 189 (221)
T ss_pred chheeccccChHHHHHHHH-cCCCCHHHhhCCC
Confidence 3488999999999999997 9999999999986
No 61
>TIGR02239 recomb_RAD51 DNA repair protein RAD51. This eukaryotic sequence family consists of RAD51, a protein involved in DNA homologous recombination and repair. It is similar in sequence the exclusively meiotic recombinase DMC1 (TIGR02238), to archaeal families RadA (TIGR02236) and RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Probab=59.29 E-value=11 Score=38.85 Aligned_cols=35 Identities=23% Similarity=0.246 Sum_probs=31.2
Q ss_pred CCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHh
Q 011631 89 GIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 124 (481)
Q Consensus 89 GIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~ 124 (481)
||++.+..+|++ .||.|+.||+..+ ..|.+.+|..
T Consensus 8 ~~~~~~~~~l~~-~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 8 GITAADIKKLQE-AGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHHhCCC
Confidence 599999999997 8999999999987 7888888854
No 62
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=59.26 E-value=10 Score=36.34 Aligned_cols=53 Identities=11% Similarity=0.068 Sum_probs=35.6
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHH-Hhch-HHHHHH--hcHhHHHHHHHHhcC
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEM-LQKG-SLLCAV--FSHSTADFFLSVGLG 135 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL-~~~~-~~L~~~--fG~~~~~~l~~~a~G 135 (481)
.+..++|||++++.++-+.+|..++-+. ...+ ..|.+. +|++.++.++....+
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 4677999999999977665787665433 2333 567666 677777777644443
No 63
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=58.81 E-value=9.2 Score=40.07 Aligned_cols=43 Identities=28% Similarity=0.397 Sum_probs=37.4
Q ss_pred cCCCccc--CCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHh
Q 011631 81 SLPIRKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS 124 (481)
Q Consensus 81 ~LPI~~L--pGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~ 124 (481)
..+|.+| .||+.....+|++ -||.|+.|++..+ ..|.+++|..
T Consensus 25 ~~~~~~l~~~gi~~~~i~kL~~-~g~~T~~~~~~~~~~~L~~i~~is 70 (342)
T PLN03186 25 PFPIEQLQASGIAALDIKKLKD-AGIHTVESLAYAPKKDLLQIKGIS 70 (342)
T ss_pred CccHHHHHhCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCCC
Confidence 4578888 6799999999997 8999999999987 7888888864
No 64
>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=58.46 E-value=12 Score=38.65 Aligned_cols=48 Identities=23% Similarity=0.314 Sum_probs=36.5
Q ss_pred ccc--CCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHh--HHHHHHHHh
Q 011631 85 RKI--GGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHS--TADFFLSVG 133 (481)
Q Consensus 85 ~~L--pGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~--~~~~l~~~a 133 (481)
.+| .||++.+.++|++ .||+|+.|++..+ ..|.++.|.. .++.+...+
T Consensus 2 ~~~~~~g~~~~~~~~L~~-~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~ 54 (313)
T TIGR02238 2 DKLQAHGINAADIKKLKS-AGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAA 54 (313)
T ss_pred chhhcCCCCHHHHHHHHH-cCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHH
Confidence 445 4799999999997 8999999999987 7888887743 344444433
No 65
>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=57.74 E-value=15 Score=41.86 Aligned_cols=50 Identities=16% Similarity=0.147 Sum_probs=38.1
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHH--HhcHhHHHHHHH
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCA--VFSHSTADFFLS 131 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~--~fG~~~~~~l~~ 131 (481)
..-=+|+|+|+++.++|-+..+|+++.||..+. ..|.. .||.+.++.+++
T Consensus 432 r~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~ 484 (652)
T TIGR00575 432 RNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLN 484 (652)
T ss_pred CCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHH
Confidence 344578999999999999866789999999876 55554 477776666644
No 66
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=56.75 E-value=7.6 Score=24.91 Aligned_cols=17 Identities=29% Similarity=0.477 Sum_probs=14.7
Q ss_pred CcccCCCCHHHHHHHhh
Q 011631 84 IRKIGGIGKVTEHILRD 100 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~ 100 (481)
+..+||||++++++|..
T Consensus 3 L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 3 LLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhCCCCCHHHHHHHHH
Confidence 56899999999999874
No 67
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=56.29 E-value=18 Score=41.26 Aligned_cols=59 Identities=14% Similarity=0.186 Sum_probs=45.2
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHHhcCCCCCCC
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSVGLGLGSTNT 141 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~a~Gid~~~v 141 (481)
...+.+|||||++...+|-+ -+.++..|...+ .+|.+. ++...+..+++.+.--...|+
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~--~FgS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~ 668 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLA--HFGSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPV 668 (691)
T ss_pred ccccccCCCCCHHHHHHHHH--HhcCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccch
Confidence 45799999999999998876 566899998887 788888 777778888776544333343
No 68
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=56.17 E-value=9.2 Score=39.89 Aligned_cols=31 Identities=23% Similarity=0.381 Sum_probs=28.7
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhch
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 114 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~ 114 (481)
.++.|.|||++.+++|+. +||.+..|++.+.
T Consensus 264 dL~~I~GiGp~~e~~L~~-~Gi~~f~QiA~~t 294 (326)
T PRK12311 264 DLKKLTGVSPQIEKKLND-LGIFHFWQLAELD 294 (326)
T ss_pred hhhhhccCChhhhhhhhh-cCCCCHHHhhCCC
Confidence 488899999999999997 9999999999886
No 69
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=54.39 E-value=20 Score=40.62 Aligned_cols=49 Identities=24% Similarity=0.314 Sum_probs=40.4
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcHhHHHHHHHH
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSHSTADFFLSV 132 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~~~~~~l~~~ 132 (481)
..+..|+|||++++..|-. .+.|+.+|...+ ..|.+.+|...++.++..
T Consensus 569 s~L~~I~GIG~k~a~~Ll~--~Fgs~~~i~~As~eeL~~vig~k~A~~I~~~ 618 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLE--HFGSVEKVAKASLEELAAVAGPKTAETIYRY 618 (621)
T ss_pred hhhhcCCCcCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHH
Confidence 4578999999999999986 666899998887 778877999888877654
No 70
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=53.07 E-value=20 Score=40.22 Aligned_cols=50 Identities=18% Similarity=0.233 Sum_probs=40.2
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHH
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 132 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~ 132 (481)
...+.+|||||+++..+|-+ ...++..+...+ .+|.+. ++...+..++..
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~--~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~ 565 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILK--SLGTYKDILLLNEDEIAEKMKINIKMAKKIKKF 565 (574)
T ss_pred ccccccCCCCCHHHHHHHHH--HhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 34789999999999998876 566899998888 788888 666677777654
No 71
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=52.10 E-value=5.8 Score=34.19 Aligned_cols=35 Identities=43% Similarity=0.834 Sum_probs=25.7
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhcccchhHHHHhhhhhccC
Q 011631 391 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGS 430 (481)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~ 430 (481)
+....|.-||.||+|-|+ .|.-|| |+|+-|-|-+-
T Consensus 45 vG~~~cP~Cge~~~~a~vva~taLVgL~l~mkVfnAes~EH-----A~RIAKs~iGk 96 (102)
T PF04475_consen 45 VGDTICPKCGEELDSAFVVADTALVGLILEMKVFNAESEEH-----AERIAKSEIGK 96 (102)
T ss_pred cCcccCCCCCCccCceEEEeccceEEEEEEEEEeecCCHHH-----HHHHHHHHHhH
Confidence 346789999999999875 567777 56666655443
No 72
>PRK03922 hypothetical protein; Provisional
Probab=51.92 E-value=5.7 Score=34.84 Aligned_cols=43 Identities=33% Similarity=0.591 Sum_probs=33.4
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhcccchhHHHHhhhhhccCcccccccc
Q 011631 391 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGSDLRILTHR 438 (481)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (481)
+....|.-||.+++|-|+ .|+-|| |+|+-|-|-+-..+.+|-+
T Consensus 47 vG~~~cP~cge~~~~afvvA~taLVgL~lemkVFnAes~EH-----A~RIAK~eIG~aL~dvPL~ 106 (113)
T PRK03922 47 VGLTICPKCGEPFDSAFVVADTALVGLLLEMKVFNAESEEH-----ASRIAKSEIGKALRDIPLE 106 (113)
T ss_pred cCcccCCCCCCcCCcEEEEeccceEEEEEEEEEeecCCHHH-----HHHHHHHHHhhHHhcCCce
Confidence 346789999999999864 678888 7888888877666666654
No 73
>KOG3014 consensus Protein involved in establishing cohesion between sister chromatids during DNA replication [Replication, recombination and repair]
Probab=49.42 E-value=6.9 Score=39.14 Aligned_cols=29 Identities=28% Similarity=0.432 Sum_probs=26.4
Q ss_pred ccccccccCCCCCcHhhhhcccchhHHHH
Q 011631 394 YKCSLCGTEMPPSFIEERQEHSDFHLAER 422 (481)
Q Consensus 394 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 422 (481)
-+|.-||-.--++=+|++.+|..||=+.+
T Consensus 38 ~~C~~Cgm~Yt~~s~EDe~~H~~fH~~~l 66 (257)
T KOG3014|consen 38 VKCKECGMKYTVTSPEDEALHEKFHNRFL 66 (257)
T ss_pred eehhhcCceecCCCHHHHHHHHHHHHhhc
Confidence 47999999999999999999999997654
No 74
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=49.16 E-value=30 Score=39.90 Aligned_cols=48 Identities=23% Similarity=0.424 Sum_probs=34.6
Q ss_pred ecCChhHHHHhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhchHHHH
Q 011631 68 LPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKGSLLC 118 (481)
Q Consensus 68 I~~~~~~v~~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~~~L~ 118 (481)
+|+..+.+..||+. ..++|||+++++++-+.||..++.-|.+-+..|.
T Consensus 73 ~p~~~~~i~~yL~s---~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~~~L~ 120 (720)
T TIGR01448 73 APTSKEGIVAYLSS---RSIKGVGKKLAQRIVKTFGEAAFDVLDDDPEKLL 120 (720)
T ss_pred CCCCHHHHHHHHhc---CCCCCcCHHHHHHHHHHhCHhHHHHHHhCHHHHh
Confidence 34444467778873 4589999999999988899888877765554344
No 75
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=48.64 E-value=11 Score=36.61 Aligned_cols=43 Identities=28% Similarity=0.364 Sum_probs=28.2
Q ss_pred eccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC---CCcccCCCCHHHHHHHh
Q 011631 45 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 99 (481)
Q Consensus 45 GIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L---PI~~LpGIG~kt~~kL~ 99 (481)
||||.--||=|++-- ++ ++...+..- -+.++||||+++++++-
T Consensus 80 GIGpK~ALaiLs~~~----------~~--~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSNLD----------PE--ELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcCCC----------HH--HHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 888888777666521 11 233333332 27788999999999985
No 76
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=47.10 E-value=27 Score=40.16 Aligned_cols=49 Identities=16% Similarity=0.230 Sum_probs=37.4
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHH
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFL 130 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~ 130 (481)
...=+|.|+|+++.++|-+..+|+++.||..+. ..|... ||.+.++.++
T Consensus 462 r~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll 513 (689)
T PRK14351 462 RDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLL 513 (689)
T ss_pred ccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHH
Confidence 345578999999999999855579999999987 556554 7877666554
No 77
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=46.64 E-value=27 Score=40.02 Aligned_cols=49 Identities=27% Similarity=0.409 Sum_probs=38.0
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHH
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 132 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~ 132 (481)
-.+..|||||+++..+|-+.|| ++.++...+ ..|.+. +|...++.++..
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~ 688 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEH 688 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHH
Confidence 4688999999999988876566 999998877 678776 677766666543
No 78
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=46.11 E-value=28 Score=39.27 Aligned_cols=50 Identities=18% Similarity=0.250 Sum_probs=40.1
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHH
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 132 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~ 132 (481)
..++..|||||++++.+|-+ .+.++..+...+ ..|.+. +|...+..++.+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~--~FgS~~~i~~As~eeL~~v~Gig~~~A~~I~~~ 594 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLK--HFGSLKAIKEASVEELAKVPGISKKLAEAIYEA 594 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHH--HcCCHHHHHhCCHHHHhhcCCcCHHHHHHHHHH
Confidence 35788999999999999986 566899998887 778887 777777766654
No 79
>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=45.81 E-value=24 Score=36.28 Aligned_cols=51 Identities=20% Similarity=0.270 Sum_probs=40.1
Q ss_pred hccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHH--HHhcHhHHHHHHH
Q 011631 79 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFLS 131 (481)
Q Consensus 79 L~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~--~~fG~~~~~~l~~ 131 (481)
+..+||.+| ++.-++..-|++ .||+|++||.+++ ..|. +-||++..+-+.+
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk~-~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~ 285 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLKR-AGIHTLGELVSKSEEELLKIKNFGKKSLTEIKE 285 (297)
T ss_pred hccccHHHh-CccHHHHhHHHH-cCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHH
Confidence 566789999 799999999997 8999999999987 4443 5677775554443
No 80
>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=44.78 E-value=6.7 Score=23.48 Aligned_cols=12 Identities=25% Similarity=1.132 Sum_probs=8.2
Q ss_pred ccccccccCCCC
Q 011631 394 YKCSLCGTEMPP 405 (481)
Q Consensus 394 ~~~~~~~~~~~~ 405 (481)
|+|.+||...+-
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 789999988764
No 81
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=43.93 E-value=22 Score=38.13 Aligned_cols=31 Identities=26% Similarity=0.441 Sum_probs=28.7
Q ss_pred CCcccCCCCHHHHHHHhhccCCCcHHHHHhch
Q 011631 83 PIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 114 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~ 114 (481)
.++.|.|||++++++|+. +||.+..|++.+.
T Consensus 324 DLk~I~GIGpk~e~~Ln~-~Gi~~f~QIA~wt 354 (400)
T PRK12373 324 DLKLISGVGPKIEATLNE-LGIFTFDQVAAWK 354 (400)
T ss_pred hhhhccCCChHHHHHHHh-cCCCCHHHHhCCC
Confidence 478899999999999997 9999999999886
No 82
>COG5540 RING-finger-containing ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.77 E-value=8.5 Score=39.56 Aligned_cols=17 Identities=53% Similarity=1.323 Sum_probs=15.8
Q ss_pred eeecCc--cccccccCCCC
Q 011631 389 IWLDDY--KCSLCGTEMPP 405 (481)
Q Consensus 389 ~~~~~~--~~~~~~~~~~~ 405 (481)
-|+.|| +|..|-.++||
T Consensus 355 kW~~~y~~~CPvCrt~iPP 373 (374)
T COG5540 355 KWLLGYSNKCPVCRTAIPP 373 (374)
T ss_pred HHHhhhcccCCccCCCCCC
Confidence 599999 59999999999
No 83
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=43.25 E-value=27 Score=36.13 Aligned_cols=50 Identities=20% Similarity=0.269 Sum_probs=39.2
Q ss_pred hccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHH--HHhcHhHHHHHH
Q 011631 79 ISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFL 130 (481)
Q Consensus 79 L~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~--~~fG~~~~~~l~ 130 (481)
+-.+||.+| ++.-++..-|++ .||+|++||.+++ ..|. +-||++..+-+.
T Consensus 246 ~l~~~I~~L-~LS~R~~n~Lk~-~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~ 298 (310)
T PRK05182 246 ILLRPIEEL-ELSVRSYNCLKR-AGINTIGDLVQRTEEELLKTRNLGKKSLEEIK 298 (310)
T ss_pred cccccHHHh-ccchHHHHHHHH-cCCcCHHHHHhCCHHHHhcCCCCChhhHHHHH
Confidence 447889999 799999999998 8999999999987 5544 457766544443
No 84
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=40.56 E-value=34 Score=35.63 Aligned_cols=32 Identities=25% Similarity=0.242 Sum_probs=27.2
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhchHH
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQKGSL 116 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~~~~ 116 (481)
.+.++|||.+++++-.+ .|++|+.|++..+..
T Consensus 99 FtnifGvG~ktA~~Wy~-~GfrTled~Rk~~~k 130 (353)
T KOG2534|consen 99 FTNIFGVGLKTAEKWYR-EGFRTLEDVRKKPDK 130 (353)
T ss_pred HHHHhccCHHHHHHHHH-hhhhHHHHHHhCHHH
Confidence 45679999999999997 899999999965533
No 85
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.41 E-value=15 Score=35.16 Aligned_cols=56 Identities=20% Similarity=0.300 Sum_probs=32.1
Q ss_pred HHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC---CCcccCCCCHHHHHHHh
Q 011631 30 LRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 99 (481)
Q Consensus 30 IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L---PI~~LpGIG~kt~~kL~ 99 (481)
--+++++.+ +++| ||||-.-||-|.+ + +++ ++...+..- .+..+||||++|++++-
T Consensus 67 ~Er~lF~~L-i~Vs-GIGpK~Al~ILs~-~---------~~~--el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 67 DEQKMFEML-LKVN-GIGANTAMAVCSS-L---------DVN--SFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHHHH-hccC-CccHHHHHHHHcC-C---------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 334444444 3333 8887766664432 2 221 233333332 37788999999999974
No 86
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=40.11 E-value=9.6 Score=29.03 Aligned_cols=25 Identities=28% Similarity=0.525 Sum_probs=19.7
Q ss_pred CcceeecCccccccccCCCCCcHhh
Q 011631 386 DQFIWLDDYKCSLCGTEMPPSFIEE 410 (481)
Q Consensus 386 ~~~~~~~~~~~~~~~~~~~~~~~~~ 410 (481)
..+-=|++-.|+-|+.+|||....+
T Consensus 15 ~~va~v~~~~C~gC~~~l~~~~~~~ 39 (56)
T PF02591_consen 15 VAVARVEGGTCSGCHMELPPQELNE 39 (56)
T ss_pred cEEEEeeCCccCCCCEEcCHHHHHH
Confidence 3445577889999999999987654
No 87
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=38.58 E-value=16 Score=35.44 Aligned_cols=16 Identities=31% Similarity=0.594 Sum_probs=14.7
Q ss_pred CcccCCCCHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILR 99 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~ 99 (481)
+++|||||++++++|.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6789999999999996
No 88
>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=38.36 E-value=40 Score=26.48 Aligned_cols=31 Identities=16% Similarity=0.405 Sum_probs=23.1
Q ss_pred CCcc-cCCCCHHHHHHHhhc---c-CCCcHHHHHhc
Q 011631 83 PIRK-IGGIGKVTEHILRDV---F-GINTCEEMLQK 113 (481)
Q Consensus 83 PI~~-LpGIG~kt~~kL~~~---l-GI~TigDL~~~ 113 (481)
.+.. +||||.+.++++-.. . ++.+..||...
T Consensus 17 ~L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v 52 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQV 52 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcC
Confidence 3556 899999998887762 2 48888888764
No 89
>PRK00076 recR recombination protein RecR; Reviewed
Probab=38.20 E-value=16 Score=35.41 Aligned_cols=16 Identities=38% Similarity=0.636 Sum_probs=14.7
Q ss_pred CcccCCCCHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILR 99 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~ 99 (481)
++.|||||+|++++|.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6789999999999996
No 90
>PRK14973 DNA topoisomerase I; Provisional
Probab=37.97 E-value=85 Score=37.45 Aligned_cols=103 Identities=11% Similarity=0.067 Sum_probs=60.2
Q ss_pred CHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHhh-hcCCCCcEEEecCChhHHHHhhccCCCcccCCCCHHHHHHHhh
Q 011631 22 SGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVCS-DINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRD 100 (481)
Q Consensus 22 s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLAS-~~aKPnG~~vI~~~~~~v~~fL~~LPI~~LpGIG~kt~~kL~~ 100 (481)
+++++|..==..+...+|+. ...-.-++++|+ ++.+|+-..+.... .--..-.+..++|+|++|.++|.+
T Consensus 825 ~~~d~~~a~p~~La~~~g~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~el~~vkg~ge~t~~~l~~ 895 (936)
T PRK14973 825 TPEDFCSVHPAYLALKTGIS----PETICRHAKLVCEKLGRPVPEKISKAA-----FERGRAELLSVPGLGETTLEKLYL 895 (936)
T ss_pred CHHHHHhcCHHHHhcCCCCC----hhhHHHHHHHHHHHhcCCCchhhhhhh-----hcccchhhhhccCCCHHHHHHHHH
Confidence 34555544444444444442 222233455666 77777644332110 001122278889999999999997
Q ss_pred ccCCCcHHHHHhch-HHHHHHhcH--hHHHHHHHHhc
Q 011631 101 VFGINTCEEMLQKG-SLLCAVFSH--STADFFLSVGL 134 (481)
Q Consensus 101 ~lGI~TigDL~~~~-~~L~~~fG~--~~~~~l~~~a~ 134 (481)
.||.++.||++.+ ..|.+.=|. +....+.+.++
T Consensus 896 -ag~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~ 931 (936)
T PRK14973 896 -AGVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAK 931 (936)
T ss_pred -cCCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHh
Confidence 8999999999987 677765554 33444444443
No 91
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.63 E-value=18 Score=34.78 Aligned_cols=55 Identities=20% Similarity=0.323 Sum_probs=31.6
Q ss_pred HHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC---CCcccCCCCHHHHHHHh
Q 011631 31 RTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 99 (481)
Q Consensus 31 R~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L---PI~~LpGIG~kt~~kL~ 99 (481)
-+++++.+ +.++ ||||-.-||=|.. + +++ ++...+..- .+..+||||++|++++-
T Consensus 68 Er~lF~~L-i~V~-GIGpK~AL~iLs~-~---------~~~--el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 68 KKELFLSL-TKVS-RLGPKTALKIISN-E---------DAE--TLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHHHHHH-hccC-CccHHHHHHHHcC-C---------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 34444444 2333 8887776664432 2 121 233333332 37788999999999975
No 92
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=36.87 E-value=21 Score=28.24 Aligned_cols=18 Identities=28% Similarity=0.588 Sum_probs=15.5
Q ss_pred CCcccCCCCHHHHHHHhh
Q 011631 83 PIRKIGGIGKVTEHILRD 100 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~ 100 (481)
.+..|||||++++.++.+
T Consensus 48 ~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHCTSTTTTHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHH
Confidence 368899999999998875
No 93
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.19 E-value=19 Score=34.90 Aligned_cols=58 Identities=22% Similarity=0.327 Sum_probs=32.7
Q ss_pred HHHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc---CCCcccCCCCHHHHHHHh
Q 011631 28 EELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS---LPIRKIGGIGKVTEHILR 99 (481)
Q Consensus 28 ~~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~---LPI~~LpGIG~kt~~kL~ 99 (481)
..--+++++.+ +++| ||||-.-||=|.+ + +++ ++...+.. -.+..+||||++|++++-
T Consensus 64 t~~Er~lF~~L-isVs-GIGPK~ALaILs~-~---------~~~--el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 64 NSSEREVFEEL-IGVD-GIGPRAALRVLSG-I---------KYN--EFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred CHHHHHHHHHH-hCcC-CcCHHHHHHHHcC-C---------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 33444555554 3444 7887666664432 2 121 23333332 237788999999999974
No 94
>PRK13844 recombination protein RecR; Provisional
Probab=35.96 E-value=18 Score=35.16 Aligned_cols=16 Identities=38% Similarity=0.559 Sum_probs=14.7
Q ss_pred CcccCCCCHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILR 99 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~ 99 (481)
++.|||||++++++|.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 6789999999999996
No 95
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=35.34 E-value=33 Score=31.16 Aligned_cols=54 Identities=19% Similarity=0.201 Sum_probs=36.1
Q ss_pred CCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccCCCcccCCCCHHHHHHHhhccC-CCcHHHHHhch
Q 011631 48 PNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRDVFG-INTCEEMLQKG 114 (481)
Q Consensus 48 ~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~LPI~~LpGIG~kt~~kL~~~lG-I~TigDL~~~~ 114 (481)
.|+.=|||+ ....+ .-|... .+.+ +..+||||+..++++-. .| ..++.||.+.+
T Consensus 39 ~N~~d~kl~-~~~~k---IdiN~A--~~~e------l~~lpGigP~~A~~IV~-nGpf~sveDL~~V~ 93 (132)
T PRK02515 39 QNVADAKLG-EFGEK---IDLNNS--SVRA------FRQFPGMYPTLAGKIVK-NAPYDSVEDVLNLP 93 (132)
T ss_pred cChhhHHHH-hcCCc---ccCCcc--CHHH------HHHCCCCCHHHHHHHHH-CCCCCCHHHHHcCC
Confidence 377777887 44221 112332 3444 34589999999999886 55 89999998875
No 96
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.22 E-value=20 Score=34.57 Aligned_cols=56 Identities=25% Similarity=0.339 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC---CCcccCCCCHHHHHHHh
Q 011631 30 LRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 99 (481)
Q Consensus 30 IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L---PI~~LpGIG~kt~~kL~ 99 (481)
--++++..+ ++++ ||||-.-||=|.. . +++ ++...+..- -+.++||||++|++++-
T Consensus 67 ~Er~lF~~L-i~V~-GIGpK~Al~iLs~-~---------~~~--el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 67 AQRQLFELL-IGVS-GVGPKAALNLLSS-G---------TPD--ELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHHHH-hCcC-CcCHHHHHHHHcC-C---------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 334444444 3333 7777666654432 1 121 333334332 37788999999999985
No 97
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=35.11 E-value=45 Score=34.85 Aligned_cols=54 Identities=17% Similarity=0.191 Sum_probs=42.1
Q ss_pred HhhccCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHH--HHhcHhHHHHHHHH
Q 011631 77 TFISSLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLC--AVFSHSTADFFLSV 132 (481)
Q Consensus 77 ~fL~~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~--~~fG~~~~~~l~~~ 132 (481)
..+..++|.+| .+.-+...-|++ .||+|+|||.+.. ..|. +-||++..+-+.+.
T Consensus 258 ~~~~~~~Ie~L-~LSvRs~NcLk~-a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~ 314 (327)
T CHL00013 258 IALKQIFIEQL-ELSVRAYNCLKR-ANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEA 314 (327)
T ss_pred hhhhceeHHhc-cCchhhhhhhhh-cCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHH
Confidence 35677889999 689899999998 8999999999987 4433 67998766555443
No 98
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.00 E-value=21 Score=34.64 Aligned_cols=57 Identities=18% Similarity=0.246 Sum_probs=31.8
Q ss_pred HHHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC---CCcccCCCCHHHHHHHh
Q 011631 29 ELRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 99 (481)
Q Consensus 29 ~IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L---PI~~LpGIG~kt~~kL~ 99 (481)
.--++++..+ ++++ ||||-.-+|=|.+ + +++ ++...+..- -|..+||||++|++++-
T Consensus 67 ~~Er~lF~~L-i~V~-GIGpK~Al~iLs~-~---------~~~--~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 67 WDERQTFIVL-ISIS-KVGAKTALAILSQ-F---------RPD--DLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHHHHHHHH-hCCC-CcCHHHHHHHHhh-C---------CHH--HHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 3344455553 2333 7777666554432 2 121 233333322 37788999999999985
No 99
>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=34.58 E-value=52 Score=23.74 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=25.6
Q ss_pred CCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhc
Q 011631 90 IGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFS 122 (481)
Q Consensus 90 IG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG 122 (481)
|+..++.+|.. .|+.|+.+|+..+ ..|..+-|
T Consensus 1 i~~~~~~~L~~-~G~~s~e~la~~~~~eL~~i~g 33 (50)
T TIGR01954 1 IDEEIAQLLVE-EGFTTVEDLAYVPIDELLSIEG 33 (50)
T ss_pred CCHHHHHHHHH-cCCCCHHHHHccCHHHHhcCCC
Confidence 35678889987 8999999999986 67776644
No 100
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.17 E-value=16 Score=31.86 Aligned_cols=43 Identities=33% Similarity=0.648 Sum_probs=34.3
Q ss_pred ecCccccccccCCCCCcH-----------------hhhhcccchhHHHHhhhhhccCcccccccc
Q 011631 391 LDDYKCSLCGTEMPPSFI-----------------EERQEHSDFHLAERLQKEESGSDLRILTHR 438 (481)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 438 (481)
+-.++|.-||..+-+-|+ .|+.|| |+|+-|-|-+-..+.+|-+
T Consensus 47 ~G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFNaes~EH-----A~RIAK~eIGk~L~~iPL~ 106 (115)
T COG1885 47 VGSTSCPKCGEPFESAFVVANTALVGLILSMKVFNAESDEH-----AERIAKAEIGKALKDIPLE 106 (115)
T ss_pred cccccCCCCCCccceeEEEecceeEEEEEEEEEecCCCHHH-----HHHHHHHHHhhHhhcCCce
Confidence 346899999999998765 577777 8999998888777777765
No 101
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.81 E-value=22 Score=34.35 Aligned_cols=56 Identities=21% Similarity=0.293 Sum_probs=32.6
Q ss_pred HHHHHHHHhCCceEEeccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC---CCcccCCCCHHHHHHHh
Q 011631 30 LRTSVYEEAGLTCSAGVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL---PIRKIGGIGKVTEHILR 99 (481)
Q Consensus 30 IR~~I~~etGlt~SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L---PI~~LpGIG~kt~~kL~ 99 (481)
--++++..+ ++++ ||||-.-||=|.+ . +++ ++...+..- -+.++||||++|++++-
T Consensus 66 ~Er~lF~~L-~~V~-GIGpK~AL~iLs~-~---------~~~--~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 66 DSLELFELL-LGVS-GVGPKLALALLSA-L---------PPA--LLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHHHHH-hCcC-CcCHHHHHHHHcC-C---------CHH--HHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 344445554 3443 8887666664432 1 221 334444432 37788999999999985
No 102
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=33.50 E-value=32 Score=33.76 Aligned_cols=52 Identities=23% Similarity=0.402 Sum_probs=29.0
Q ss_pred EEeccCCHHHHHHhhh---cCCCCcEEEecCChhHHHHhhccCCCcccCCCCHHHHHHHhh-ccCCC
Q 011631 43 SAGVAPNRLLAKVCSD---INKPNGQFVLPNDRMAVMTFISSLPIRKIGGIGKVTEHILRD-VFGIN 105 (481)
Q Consensus 43 SiGIA~NKlLAKLAS~---~aKPnG~~vI~~~~~~v~~fL~~LPI~~LpGIG~kt~~kL~~-~lGI~ 105 (481)
++|.-.||.-.=++.. ..+.+|. +|.. ..+ |.+|||||++|+...-. .||+.
T Consensus 78 ~iGlyr~KAk~I~~~~~~l~e~~~g~--vP~~---~~e------L~~LPGVGrKTAnvVL~~a~g~p 133 (211)
T COG0177 78 SIGLYRNKAKNIKELARILLEKFGGE--VPDT---REE------LLSLPGVGRKTANVVLSFAFGIP 133 (211)
T ss_pred hcCCcHHHHHHHHHHHHHHHHHcCCC--CCch---HHH------HHhCCCcchHHHHHHHHhhcCCC
Confidence 6677777743222211 1355663 4443 222 56789999999876432 35543
No 103
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=33.09 E-value=14 Score=30.03 Aligned_cols=14 Identities=36% Similarity=0.705 Sum_probs=9.6
Q ss_pred CccccccccCCCCC
Q 011631 393 DYKCSLCGTEMPPS 406 (481)
Q Consensus 393 ~~~~~~~~~~~~~~ 406 (481)
-++|+.||.+++|+
T Consensus 3 ~~~C~Fsg~~I~PG 16 (71)
T PF01246_consen 3 TEKCSFSGYKIYPG 16 (71)
T ss_dssp SEE-TTT-SEE-SS
T ss_pred eEEecccCCccCCC
Confidence 36899999999998
No 104
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=32.20 E-value=21 Score=28.62 Aligned_cols=13 Identities=38% Similarity=1.065 Sum_probs=12.0
Q ss_pred ccccccccCCCCC
Q 011631 394 YKCSLCGTEMPPS 406 (481)
Q Consensus 394 ~~~~~~~~~~~~~ 406 (481)
..||.||.+++|+
T Consensus 4 ~~CsFcG~~I~PG 16 (66)
T COG2075 4 RVCSFCGKKIEPG 16 (66)
T ss_pred eEecCcCCccCCC
Confidence 5799999999998
No 105
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=31.44 E-value=60 Score=36.58 Aligned_cols=87 Identities=20% Similarity=0.254 Sum_probs=56.5
Q ss_pred HHhCCce-EEeccCCHHHHHHhhhcCCCCcEEEecCCh----------hHHHHh----------hccCCCcccCCCCHHH
Q 011631 36 EEAGLTC-SAGVAPNRLLAKVCSDINKPNGQFVLPNDR----------MAVMTF----------ISSLPIRKIGGIGKVT 94 (481)
Q Consensus 36 ~etGlt~-SiGIA~NKlLAKLAS~~aKPnG~~vI~~~~----------~~v~~f----------L~~LPI~~LpGIG~kt 94 (481)
+++|+.+ =+|+|-+. -..-.|++-..++.+. +++..| ...+.+..|||||+++
T Consensus 464 ~elg~~i~v~glaK~~------e~i~~~~~~~~l~~~~~~l~lL~~irDEaHRFAi~~hR~~r~~~~~~L~~IpGIG~kr 537 (577)
T PRK14668 464 AETGWDVPAIALAKAE------ELVVTPDRTYDWPDDAPQLHLLQRVRDEAHRFAVQYHQTLRDDVSTVLDDVPGVGPET 537 (577)
T ss_pred HHcCCCCcEEEEEcCC------eEEEcCCCeeecCCCCHHHHHHHHHHHHHHHHHhhHHHHHHHHHHhHHhcCCCCCHHH
Confidence 6888743 56777654 2344566654455441 111111 1246788999999999
Q ss_pred HHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHH
Q 011631 95 EHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFL 130 (481)
Q Consensus 95 ~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~ 130 (481)
..+|-+ ...++.++...+ ..|.+. +|...+..+.
T Consensus 538 ~~~LL~--~FGS~~~I~~As~eeL~~vpGi~~~~A~~I~ 574 (577)
T PRK14668 538 RKRLLR--RFGSVEGVREASVEDLRDVPGVGEKTAETIR 574 (577)
T ss_pred HHHHHH--HcCCHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 999876 567899998887 678777 5666555554
No 106
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=30.68 E-value=24 Score=34.18 Aligned_cols=16 Identities=25% Similarity=0.576 Sum_probs=14.5
Q ss_pred CcccCCCCHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILR 99 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~ 99 (481)
+++|||||+++++++.
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 6789999999999996
No 107
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.44 E-value=28 Score=33.36 Aligned_cols=15 Identities=27% Similarity=0.476 Sum_probs=13.3
Q ss_pred CcccCCCCHHHHHHHh
Q 011631 84 IRKIGGIGKVTEHILR 99 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~ 99 (481)
+ ++||||++|++++-
T Consensus 110 L-~vpGIGkKtAerIi 124 (186)
T PRK14600 110 L-KVNGIGEKLINRII 124 (186)
T ss_pred e-ECCCCcHHHHHHHH
Confidence 6 78999999999975
No 108
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=30.24 E-value=69 Score=32.32 Aligned_cols=47 Identities=21% Similarity=0.222 Sum_probs=36.3
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHHhcH--hHHHHHHHH
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAVFSH--STADFFLSV 132 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~fG~--~~~~~l~~~ 132 (481)
+..+||||..+++.|-. -+.++++++... ..|.+..|. +.+..++.+
T Consensus 184 l~s~pgig~~~a~~ll~--~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~ 233 (254)
T COG1948 184 LESIPGIGPKLAERLLK--KFGSVEDVLTASEEELMKVKGIGEKKAREIYRF 233 (254)
T ss_pred HHcCCCccHHHHHHHHH--HhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHH
Confidence 55678999999999986 666999998887 778887776 455656554
No 109
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=30.10 E-value=26 Score=22.10 Aligned_cols=12 Identities=33% Similarity=0.858 Sum_probs=9.8
Q ss_pred cccccccCCCCC
Q 011631 395 KCSLCGTEMPPS 406 (481)
Q Consensus 395 ~~~~~~~~~~~~ 406 (481)
+|.-||.|+++.
T Consensus 1 ~Cp~CG~~~~~~ 12 (23)
T PF13240_consen 1 YCPNCGAEIEDD 12 (23)
T ss_pred CCcccCCCCCCc
Confidence 588999999874
No 110
>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=29.42 E-value=72 Score=36.44 Aligned_cols=18 Identities=17% Similarity=0.385 Sum_probs=11.6
Q ss_pred CCcccCCCCHHHHHHHhh
Q 011631 83 PIRKIGGIGKVTEHILRD 100 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~ 100 (481)
.|..|+|+|.+++++|.+
T Consensus 467 ~L~~L~GfG~Ksa~nIl~ 484 (652)
T TIGR00575 467 DLLELEGFGEKSAQNLLN 484 (652)
T ss_pred HHhhccCccHHHHHHHHH
Confidence 355667777777666654
No 111
>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=28.05 E-value=50 Score=29.23 Aligned_cols=30 Identities=10% Similarity=0.444 Sum_probs=22.8
Q ss_pred CCcccCCCCHHHHHHHhhcc-----CCCcHHHHHhc
Q 011631 83 PIRKIGGIGKVTEHILRDVF-----GINTCEEMLQK 113 (481)
Q Consensus 83 PI~~LpGIG~kt~~kL~~~l-----GI~TigDL~~~ 113 (481)
.+..|||||++.++++-+ + ++.++.||...
T Consensus 69 eL~~lpGIG~~~A~~Ii~-~R~~~g~f~s~eeL~~V 103 (120)
T TIGR01259 69 ELQALPGIGPAKAKAIIE-YREENGAFKSVDDLTKV 103 (120)
T ss_pred HHhcCCCCCHHHHHHHHH-HHHhcCCcCCHHHHHcC
Confidence 356789999999988876 4 46777777654
No 112
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=27.34 E-value=26 Score=36.40 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=25.1
Q ss_pred CCCcccCCCCHHHHHHHhhccCCCcHHHHHhch
Q 011631 82 LPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG 114 (481)
Q Consensus 82 LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~ 114 (481)
.|+-++||+|++...+|-..+||+++.+|....
T Consensus 93 ~~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~ 125 (326)
T COG1796 93 EPLLKVPGLGPKKIVSLYKELGIKDLEELQEAL 125 (326)
T ss_pred HHHhhCCCCCcHHHHHHHHHHCcccHHHHHHHH
Confidence 356788999986555555559999999997754
No 113
>KOG2894 consensus Uncharacterized conserved protein XAP-5 [Function unknown]
Probab=26.99 E-value=1.8e+02 Score=29.83 Aligned_cols=117 Identities=16% Similarity=0.203 Sum_probs=71.7
Q ss_pred ccccccccCccCCHHHHHHHHHHHHHHHHHHHHHhCCcccEEEEEEEecCCeeeEEEEEcCCCCCCHHHHHHHHHHHHHh
Q 011631 149 SISSERTFSVTEDKALLYRKLAEIAEMLSADMQKEGLRGRTLTLKLKTASFEVRTRAVTLQKYISSSEDILKHASVLLKA 228 (481)
Q Consensus 149 SIs~e~tF~~~~d~e~L~~~L~~La~eL~~RLr~~~~~artltL~lr~~~f~~~srs~~l~~pt~d~~~L~~~a~~LL~~ 228 (481)
.-++..+|-++.++++-...+++-+.. .-++++.....--++|.+.|-++..+.+.+.+.. -|.....++.|...|..
T Consensus 147 dP~VDTSFLPDrEREeeEnr~RE~L~~-eW~~~qe~~K~Eei~it~sYWDGsgHRr~v~~rK-Gnti~qfL~~~~e~L~k 224 (331)
T KOG2894|consen 147 DPDVDTSFLPDREREEEENRLREELRQ-EWEAKQEKIKNEEIEITFSYWDGSGHRRNVKVRK-GNTIQQFLQKALEQLRK 224 (331)
T ss_pred CCCcccccCCchhhHHHHHHHHHHHHH-HHHHHHHHhcCCceEEEEEeecCCCcceeeeecC-CChHHHHHHHHHHHHHH
Confidence 334567787766666655666553332 2234455666778899998888888778777654 34566677777777665
Q ss_pred hCCCCEEEEEEEEecCCCCcccCCCCcccchHHHHhccCccCc
Q 011631 229 ELPVSLRLIGLRVTQFNEDKVRAPSDPTQKTLTNFMTSGHASK 271 (481)
Q Consensus 229 ~~~~~VR~IGV~vs~L~~~~~~~~~~~~q~si~~Ff~s~~~~~ 271 (481)
-+. .+|..| +.+|.-.+. +.--|++.+.-+|+-.....+
T Consensus 225 dF~-Elrs~~--~e~LmyvKE-DLIiPH~~sFydfIvtkArGK 263 (331)
T KOG2894|consen 225 DFR-ELRSAG--VEQLMYVKE-DLIIPHHHSFYDFIVTKARGK 263 (331)
T ss_pred HHH-HHHHhh--HHHhhhhhh-heecccchhHHHHHHHHhccC
Confidence 321 233333 334433321 344588999999987655444
No 114
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=26.89 E-value=89 Score=35.11 Aligned_cols=45 Identities=20% Similarity=0.186 Sum_probs=35.0
Q ss_pred cccCCCCHHHHHHHhhccC-CCcHHHHHhch-HHHHH--HhcHhHHHHHH
Q 011631 85 RKIGGIGKVTEHILRDVFG-INTCEEMLQKG-SLLCA--VFSHSTADFFL 130 (481)
Q Consensus 85 ~~LpGIG~kt~~kL~~~lG-I~TigDL~~~~-~~L~~--~fG~~~~~~l~ 130 (481)
=+|-|+|.++.++|-+ .| |+++.||..+. ..|.. .||.+.++.++
T Consensus 428 mdI~GlGe~~i~~L~~-~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll 476 (562)
T PRK08097 428 LGLDGIGEGTWRALHQ-TGLFEHLFSWLALTPEQLANTPGIGKARAEQLW 476 (562)
T ss_pred cCCCCcCHHHHHHHHH-cCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHH
Confidence 4567999999999997 67 69999999987 45554 47887666554
No 115
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=26.18 E-value=58 Score=30.05 Aligned_cols=29 Identities=14% Similarity=0.407 Sum_probs=23.6
Q ss_pred cccCCCCHHHHHHHhhcc-----CCCcHHHHHhch
Q 011631 85 RKIGGIGKVTEHILRDVF-----GINTCEEMLQKG 114 (481)
Q Consensus 85 ~~LpGIG~kt~~kL~~~l-----GI~TigDL~~~~ 114 (481)
..|||||++.++++-. + ...+++||+..+
T Consensus 100 ~~lpgIG~~kA~aIi~-yRe~~G~f~sv~dL~~v~ 133 (149)
T COG1555 100 QALPGIGPKKAQAIID-YREENGPFKSVDDLAKVK 133 (149)
T ss_pred HHCCCCCHHHHHHHHH-HHHHcCCCCcHHHHHhcc
Confidence 7889999999988765 4 378999998754
No 116
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=25.79 E-value=91 Score=35.19 Aligned_cols=49 Identities=18% Similarity=0.224 Sum_probs=36.3
Q ss_pred cCCCcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH-hcHhHHHHHHH
Q 011631 81 SLPIRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV-FSHSTADFFLS 131 (481)
Q Consensus 81 ~LPI~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~-fG~~~~~~l~~ 131 (481)
.-++.+|+|||++...+|-+ ...|+..+...+ .+|.+. .+...++.++.
T Consensus 529 ~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~~As~eel~~vgi~~~~a~~i~~ 579 (581)
T COG0322 529 QSSLDDIPGIGPKRRKALLK--HFGSLKGIKSASVEELAKVGISKKLAEKIYE 579 (581)
T ss_pred cCccccCCCcCHHHHHHHHH--HhhCHHHHHhcCHHHHHHcCCCHHHHHHHHh
Confidence 34789999999999988876 566888888877 778877 33345555543
No 117
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=25.61 E-value=24 Score=25.00 Aligned_cols=9 Identities=56% Similarity=1.291 Sum_probs=5.3
Q ss_pred Ccccccccc
Q 011631 393 DYKCSLCGT 401 (481)
Q Consensus 393 ~~~~~~~~~ 401 (481)
=|||..||-
T Consensus 6 ~YkC~~CGn 14 (36)
T PF06397_consen 6 FYKCEHCGN 14 (36)
T ss_dssp EEE-TTT--
T ss_pred EEEccCCCC
Confidence 499999995
No 118
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=25.43 E-value=63 Score=29.44 Aligned_cols=41 Identities=27% Similarity=0.253 Sum_probs=28.2
Q ss_pred ceEEEecCCcccccCCCHHHHHHHHHHHHHHHh-------CCceEEeccCC
Q 011631 6 DEAYLDITEVCRERGISGIEIAEELRTSVYEEA-------GLTCSAGVAPN 49 (481)
Q Consensus 6 DEafLDiTg~~~l~g~s~~~iA~~IR~~I~~et-------Glt~SiGIA~N 49 (481)
||+-+=+.+... ..+..+|++|+..|.... .+|+|+||+..
T Consensus 101 dEF~i~l~~~~~---~~~~~~~~~l~~~~~~~~~~~~~~~~~t~siGi~~~ 148 (181)
T COG2199 101 DEFAVLLPGTSL---EEAARLAERIRAALEEPFFLGGEELRVTVSIGVALY 148 (181)
T ss_pred ceeEEEeCCCCH---HHHHHHHHHHHHHHHcccccCCceEEEEEEEEEEec
Confidence 565555555431 257889999988886654 37999998743
No 119
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=25.14 E-value=2e+02 Score=28.23 Aligned_cols=79 Identities=20% Similarity=0.257 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHhCCceEE-------eccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhccC-----C--CcccC
Q 011631 23 GIEIAEELRTSVYEEAGLTCSA-------GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISSL-----P--IRKIG 88 (481)
Q Consensus 23 ~~~iA~~IR~~I~~etGlt~Si-------GIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~L-----P--I~~Lp 88 (481)
+..-+..+.+.+ ++.|..+-. -...+.-+.....++..-+.+.+..+. .|..|+..+ . -..+.
T Consensus 11 p~~~~~~l~~~l-~~~G~~~~~~P~i~i~p~~~~~~~~~~l~~l~~~d~iifTS~n--aV~~~~~~l~~~~~~~~~~~~~ 87 (255)
T PRK05752 11 PAEECAALAASL-AEAGIFSSSLPLLAIEPLPETPEQRALLLELDRYCAVIVVSKP--AARLGLELLDRYWPQPPQQPWF 87 (255)
T ss_pred cHHHHHHHHHHH-HHcCCCEEEcCcEEEeeCCCCHHHHHHHhcCCCCCEEEEECHH--HHHHHHHHHHhhCCCCcCCEEE
Confidence 445556666666 577865443 233333333333445544555544443 566554322 1 12455
Q ss_pred CCCHHHHHHHhhccCCC
Q 011631 89 GIGKVTEHILRDVFGIN 105 (481)
Q Consensus 89 GIG~kt~~kL~~~lGI~ 105 (481)
-||++|++.|++ +|+.
T Consensus 88 aVG~~Ta~al~~-~G~~ 103 (255)
T PRK05752 88 SVGAATAAILQD-YGLD 103 (255)
T ss_pred EECHHHHHHHHH-cCCC
Confidence 899999999997 8985
No 120
>PRK00807 50S ribosomal protein L24e; Validated
Probab=24.82 E-value=30 Score=26.29 Aligned_cols=14 Identities=43% Similarity=1.037 Sum_probs=12.1
Q ss_pred ccccccccCCCCCc
Q 011631 394 YKCSLCGTEMPPSF 407 (481)
Q Consensus 394 ~~~~~~~~~~~~~~ 407 (481)
++|+-||.++.|+-
T Consensus 2 ~~C~fcG~~I~pg~ 15 (52)
T PRK00807 2 RTCSFCGKEIEPGT 15 (52)
T ss_pred cccCCCCCeEcCCC
Confidence 57999999999874
No 121
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=24.45 E-value=27 Score=21.50 Aligned_cols=11 Identities=36% Similarity=0.939 Sum_probs=7.1
Q ss_pred ccccccccCCC
Q 011631 394 YKCSLCGTEMP 404 (481)
Q Consensus 394 ~~~~~~~~~~~ 404 (481)
|+|+.|.+.-.
T Consensus 1 y~C~~C~y~t~ 11 (24)
T PF13909_consen 1 YKCPHCSYSTS 11 (24)
T ss_dssp EE-SSSS-EES
T ss_pred CCCCCCCCcCC
Confidence 79999987653
No 122
>COG4071 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.43 E-value=95 Score=30.70 Aligned_cols=50 Identities=24% Similarity=0.208 Sum_probs=37.6
Q ss_pred eEEEecCCccccc----CCCHHHHHHHHHHHHHHHhCCceEEeccCCHHHHHHh
Q 011631 7 EAYLDITEVCRER----GISGIEIAEELRTSVYEEAGLTCSAGVAPNRLLAKVC 56 (481)
Q Consensus 7 EafLDiTg~~~l~----g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKlLAKLA 56 (481)
|+=+|+|...-.| ..++..+|+.|+.+|++++|..+++=|+.+--.=.+.
T Consensus 122 EaG~Dl~NVPGtya~plPenp~~vA~el~~Ei~rr~GvDV~v~v~DTDaTY~iL 175 (278)
T COG4071 122 EAGVDLTNVPGTYACPLPENPKKVAEELYKEIKRRLGVDVVVMVADTDATYRIL 175 (278)
T ss_pred hcCccccCCCcceeccCCCChHHHHHHHHHHHHHHhCCceEEEEecCchHHHHH
Confidence 6667776653222 1378999999999999999999999999886444433
No 123
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=23.57 E-value=60 Score=22.72 Aligned_cols=17 Identities=35% Similarity=0.372 Sum_probs=13.5
Q ss_pred CcccCCCCHHHHHHHhh
Q 011631 84 IRKIGGIGKVTEHILRD 100 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~ 100 (481)
|.-+||||++++.+|-+
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 55789999999987743
No 124
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=23.31 E-value=35 Score=30.86 Aligned_cols=15 Identities=27% Similarity=0.616 Sum_probs=13.1
Q ss_pred CccccccccCCCCCc
Q 011631 393 DYKCSLCGTEMPPSF 407 (481)
Q Consensus 393 ~~~~~~~~~~~~~~~ 407 (481)
-++|+.||..+.|+-
T Consensus 4 ~e~CsFcG~kIyPG~ 18 (131)
T PRK14891 4 TRTCDYTGEEIEPGT 18 (131)
T ss_pred eeeecCcCCcccCCC
Confidence 468999999999983
No 125
>PRK13766 Hef nuclease; Provisional
Probab=23.03 E-value=1.1e+02 Score=35.35 Aligned_cols=47 Identities=19% Similarity=0.273 Sum_probs=37.2
Q ss_pred CcccCCCCHHHHHHHhhccCCCcHHHHHhch-HHHHHH--hcHhHHHHHHHH
Q 011631 84 IRKIGGIGKVTEHILRDVFGINTCEEMLQKG-SLLCAV--FSHSTADFFLSV 132 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~TigDL~~~~-~~L~~~--fG~~~~~~l~~~ 132 (481)
+..|||||++++.+|-+ .+.++.++...+ ..|... +|...+..++..
T Consensus 717 L~~ipgig~~~a~~Ll~--~fgs~~~i~~as~~~L~~i~Gig~~~a~~i~~~ 766 (773)
T PRK13766 717 VESLPDVGPVLARNLLE--HFGSVEAVMTASEEELMEVEGIGEKTAKRIREV 766 (773)
T ss_pred HhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHH
Confidence 77899999999988876 445899998887 678877 787777776654
No 126
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=22.96 E-value=34 Score=26.32 Aligned_cols=14 Identities=43% Similarity=0.975 Sum_probs=12.4
Q ss_pred CccccccccCCCCC
Q 011631 393 DYKCSLCGTEMPPS 406 (481)
Q Consensus 393 ~~~~~~~~~~~~~~ 406 (481)
-..|+-||..++|+
T Consensus 3 ~~~C~f~g~~I~PG 16 (54)
T cd00472 3 TEKCSFCGYKIYPG 16 (54)
T ss_pred EEEecCcCCeecCC
Confidence 35899999999998
No 127
>PF07887 Calmodulin_bind: Calmodulin binding protein-like; InterPro: IPR012416 The members of this family are putative or actual calmodulin binding proteins expressed by various plant species. Some members (for example, Q8H6T7 from SWISSPROT), are known to be involved in the induction of plant defence responses []. However, their precise function in this regard is as yet unknown.
Probab=22.81 E-value=1.2e+02 Score=31.33 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=35.2
Q ss_pred CcccCCCCHH--HHHHHhhccCCCcHHHHHhch----HHHHHHhcH----hHHHHHHHHhcC
Q 011631 84 IRKIGGIGKV--TEHILRDVFGINTCEEMLQKG----SLLCAVFSH----STADFFLSVGLG 135 (481)
Q Consensus 84 I~~LpGIG~k--t~~kL~~~lGI~TigDL~~~~----~~L~~~fG~----~~~~~l~~~a~G 135 (481)
|..|-.||+. .-.+|.. -||.|++|++.+- ..|+.+||. +.|+.+..+|+-
T Consensus 164 VwRLe~Igk~G~~hk~L~~-~~I~tV~dFl~l~~~d~~~Lr~ilg~~ms~k~We~~v~HA~t 224 (299)
T PF07887_consen 164 VWRLEKIGKDGAFHKRLKK-NGINTVEDFLKLLNKDPQKLREILGSGMSNKMWETTVEHAKT 224 (299)
T ss_pred hhhhhhccccCHHHHHHHH-cCCccHHHHHHHHhcCHHHHHHHHhcCCChhhHHHHHHHHHh
Confidence 4555566653 4577886 7999999998762 678899983 245555566653
No 128
>PRK13293 F420-0--gamma-glutamyl ligase; Reviewed
Probab=22.54 E-value=1.2e+02 Score=30.60 Aligned_cols=47 Identities=17% Similarity=0.029 Sum_probs=35.0
Q ss_pred ccceEEEecCCcccccCCCHHHHHHHHHHHHHHHhCCceEEeccCCHH
Q 011631 4 SLDEAYLDITEVCRERGISGIEIAEELRTSVYEEAGLTCSAGVAPNRL 51 (481)
Q Consensus 4 SIDEafLDiTg~~~l~g~s~~~iA~~IR~~I~~etGlt~SiGIA~NKl 51 (481)
.||+.-.+- ++..++-.+|..-|++||++|++.+|..+.|=|..+.-
T Consensus 107 GID~SNv~~-g~~~LLP~DPd~SA~~ir~~l~~~~g~~v~VIItDt~g 153 (245)
T PRK13293 107 GIDESNVPD-GDLLLLPENPDESAERIREGLEELTGKKVGVIITDTNG 153 (245)
T ss_pred ccccccCCC-CeEEecCCCHHHHHHHHHHHHHHHHCCCEEEEEEcCCC
Confidence 455554432 33334456899999999999999999999888887754
No 129
>PRK07945 hypothetical protein; Provisional
Probab=21.84 E-value=1.3e+02 Score=31.24 Aligned_cols=26 Identities=15% Similarity=0.234 Sum_probs=20.1
Q ss_pred HHHhhccCCCcccCCCCHHHHHHHhh
Q 011631 75 VMTFISSLPIRKIGGIGKVTEHILRD 100 (481)
Q Consensus 75 v~~fL~~LPI~~LpGIG~kt~~kL~~ 100 (481)
+.+....-.+++|||||+.++.++.+
T Consensus 42 ~~~~~~~g~l~~~~giG~~~a~~i~e 67 (335)
T PRK07945 42 RARRARAGSLTSLPGIGPKTAKVIAQ 67 (335)
T ss_pred HHHHHhcCCcccCCCcCHHHHHHHHH
Confidence 44444333789999999999999887
No 130
>smart00355 ZnF_C2H2 zinc finger.
Probab=21.70 E-value=39 Score=20.08 Aligned_cols=12 Identities=33% Similarity=1.035 Sum_probs=9.6
Q ss_pred ccccccccCCCC
Q 011631 394 YKCSLCGTEMPP 405 (481)
Q Consensus 394 ~~~~~~~~~~~~ 405 (481)
|+|..||...+-
T Consensus 1 ~~C~~C~~~f~~ 12 (26)
T smart00355 1 YRCPECGKVFKS 12 (26)
T ss_pred CCCCCCcchhCC
Confidence 789999987753
No 131
>PHA02768 hypothetical protein; Provisional
Probab=21.62 E-value=36 Score=26.38 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=17.2
Q ss_pred ecCccccccccCCCCCcHhhhhcccchhH
Q 011631 391 LDDYKCSLCGTEMPPSFIEERQEHSDFHL 419 (481)
Q Consensus 391 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 419 (481)
+-||.|+.||....-+ ..-+.|...|.
T Consensus 3 ~~~y~C~~CGK~Fs~~--~~L~~H~r~H~ 29 (55)
T PHA02768 3 LLGYECPICGEIYIKR--KSMITHLRKHN 29 (55)
T ss_pred ccccCcchhCCeeccH--HHHHHHHHhcC
Confidence 4589999999876532 23355555554
No 132
>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=21.11 E-value=50 Score=31.68 Aligned_cols=43 Identities=30% Similarity=0.439 Sum_probs=27.2
Q ss_pred eccCCHHHHHHhhhcCCCCcEEEecCChhHHHHhhcc---CCCcccCCCCHHHHHHHh
Q 011631 45 GVAPNRLLAKVCSDINKPNGQFVLPNDRMAVMTFISS---LPIRKIGGIGKVTEHILR 99 (481)
Q Consensus 45 GIA~NKlLAKLAS~~aKPnG~~vI~~~~~~v~~fL~~---LPI~~LpGIG~kt~~kL~ 99 (481)
||||-.-+|-|. .. .++ ++.+.+.. --|..+||||+++++++-
T Consensus 79 GIGpK~Al~iL~-~~---------~~~--el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 79 GVGPKLALAILS-NM---------SPE--EFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred CCCHHHHHHHHh-cC---------CHH--HHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 888766655422 11 221 34444443 448889999999999874
No 133
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.92 E-value=48 Score=31.89 Aligned_cols=15 Identities=40% Similarity=0.589 Sum_probs=13.4
Q ss_pred CcccCCCCHHHHHHH
Q 011631 84 IRKIGGIGKVTEHIL 98 (481)
Q Consensus 84 I~~LpGIG~kt~~kL 98 (481)
+..+||||+++++++
T Consensus 110 L~~vpGIGkKtAerI 124 (194)
T PRK14605 110 LSTIPGIGKKTASRI 124 (194)
T ss_pred HHhCCCCCHHHHHHH
Confidence 778999999999994
No 134
>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=20.63 E-value=65 Score=27.90 Aligned_cols=23 Identities=35% Similarity=0.557 Sum_probs=18.7
Q ss_pred CcccCCCCHHHHHHHhhccCCCc
Q 011631 84 IRKIGGIGKVTEHILRDVFGINT 106 (481)
Q Consensus 84 I~~LpGIG~kt~~kL~~~lGI~T 106 (481)
+..|.|||+.++..+-..+||..
T Consensus 17 Lt~IyGIG~~~A~~Ic~~lgi~~ 39 (107)
T PF00416_consen 17 LTKIYGIGRRKAKQICKKLGINP 39 (107)
T ss_dssp HTTSTTBCHHHHHHHHHHTTS-S
T ss_pred HhhhhccCHHHHHHHHHHcCCCh
Confidence 67899999999999777789853
No 135
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=20.62 E-value=44 Score=26.21 Aligned_cols=12 Identities=42% Similarity=1.392 Sum_probs=10.6
Q ss_pred cccccccCCCCC
Q 011631 395 KCSLCGTEMPPS 406 (481)
Q Consensus 395 ~~~~~~~~~~~~ 406 (481)
.|..||..+||+
T Consensus 5 HC~~CG~~Ip~~ 16 (59)
T PF09889_consen 5 HCPVCGKPIPPD 16 (59)
T ss_pred cCCcCCCcCCcc
Confidence 599999999984
No 136
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=20.59 E-value=46 Score=26.23 Aligned_cols=16 Identities=38% Similarity=0.827 Sum_probs=13.3
Q ss_pred cccccccCCCCCcHhh
Q 011631 395 KCSLCGTEMPPSFIEE 410 (481)
Q Consensus 395 ~~~~~~~~~~~~~~~~ 410 (481)
-|++|||-=.|...|-
T Consensus 32 VCnlCGFNP~Phl~E~ 47 (61)
T PF05715_consen 32 VCNLCGFNPTPHLTEV 47 (61)
T ss_pred hhcccCCCCCcccccc
Confidence 6999999988877753
No 137
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=20.28 E-value=46 Score=26.24 Aligned_cols=13 Identities=46% Similarity=1.163 Sum_probs=11.2
Q ss_pred cCccccccccCCC
Q 011631 392 DDYKCSLCGTEMP 404 (481)
Q Consensus 392 ~~~~~~~~~~~~~ 404 (481)
+-|+|.-||||=|
T Consensus 49 ~~Y~Cp~CGF~GP 61 (61)
T COG2888 49 NPYRCPKCGFEGP 61 (61)
T ss_pred CceECCCcCccCC
Confidence 5799999999865
Done!