Query 007746
Match_columns 591
No_of_seqs 267 out of 1679
Neff 5.6
Searched_HMMs 46136
Date Thu Mar 28 14:46:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/007746.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/007746hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03609 umuC DNA polymerase V 100.0 3.9E-44 8.5E-49 387.8 26.2 302 25-355 88-421 (422)
2 cd00424 PolY Y-family of DNA p 100.0 4.7E-44 1E-48 377.1 24.6 254 27-302 88-343 (343)
3 PTZ00205 DNA polymerase kappa; 100.0 3.4E-44 7.5E-49 394.7 24.5 253 26-307 218-487 (571)
4 cd01701 PolY_Rev1 DNA polymera 100.0 4.5E-44 9.7E-49 385.6 24.1 257 27-304 137-404 (404)
5 cd01703 PolY_Pol_iota DNA Poly 100.0 1.1E-43 2.3E-48 379.8 24.3 266 26-303 84-379 (379)
6 PRK03858 DNA polymerase IV; Va 100.0 2.1E-43 4.6E-48 378.3 24.8 265 27-320 89-354 (396)
7 PRK01216 DNA polymerase IV; Va 100.0 2.5E-43 5.4E-48 373.6 23.7 249 27-307 94-342 (351)
8 cd01702 PolY_Pol_eta DNA Polym 100.0 4.3E-43 9.3E-48 372.8 23.4 248 26-303 106-359 (359)
9 PRK03103 DNA polymerase IV; Re 100.0 7.8E-43 1.7E-47 375.8 25.4 264 27-320 94-362 (409)
10 PRK14133 DNA polymerase IV; Pr 100.0 1E-42 2.3E-47 367.4 24.5 257 26-318 91-347 (347)
11 PRK02794 DNA polymerase IV; Pr 100.0 1.3E-42 2.9E-47 375.6 23.6 262 27-320 124-386 (419)
12 PRK03348 DNA polymerase IV; Pr 100.0 3.7E-42 8E-47 375.8 27.0 263 26-322 94-357 (454)
13 PRK02406 DNA polymerase IV; Va 100.0 2.6E-42 5.6E-47 363.6 23.7 250 26-307 83-334 (343)
14 PRK01810 DNA polymerase IV; Va 100.0 4.4E-42 9.5E-47 369.8 24.4 261 27-319 96-358 (407)
15 cd03586 PolY_Pol_IV_kappa DNA 100.0 1.8E-41 3.9E-46 354.5 24.7 248 27-304 87-334 (334)
16 KOG2095 DNA polymerase iota/DN 100.0 4E-41 8.7E-46 368.5 25.0 232 1-232 144-375 (656)
17 cd01700 PolY_Pol_V_umuC umuC s 100.0 5.5E-41 1.2E-45 353.7 25.0 251 27-303 88-344 (344)
18 PRK03352 DNA polymerase IV; Va 100.0 5.6E-41 1.2E-45 353.9 23.4 247 27-307 98-345 (346)
19 COG0389 DinP Nucleotidyltransf 100.0 1.1E-38 2.4E-43 338.6 23.8 254 27-307 90-347 (354)
20 KOG2094 Predicted DNA damage i 100.0 9.4E-37 2E-41 313.8 19.1 252 25-308 187-447 (490)
21 KOG2093 Translesion DNA polyme 100.0 2E-36 4.3E-41 336.8 15.8 262 25-307 462-733 (1016)
22 cd03468 PolY_like DNA Polymera 100.0 4.5E-34 9.8E-39 298.6 21.5 244 25-302 85-334 (335)
23 PF11799 IMS_C: impB/mucB/samB 99.4 3.7E-13 8E-18 120.7 9.6 125 170-318 1-127 (127)
24 PF00817 IMS: impB/mucB/samB f 99.1 3.7E-11 8.1E-16 112.8 2.3 63 27-91 86-149 (149)
25 PF11798 IMS_HHH: IMS family H 98.5 5E-08 1.1E-12 69.3 1.7 32 103-135 1-32 (32)
26 PRK04301 radA DNA repair and r 98.0 5.3E-06 1.1E-10 87.4 4.8 80 109-189 2-88 (317)
27 TIGR02236 recomb_radA DNA repa 97.4 0.00017 3.7E-09 75.6 5.6 74 115-189 1-81 (310)
28 PF14520 HHH_5: Helix-hairpin- 96.9 0.0013 2.8E-08 52.9 4.0 50 116-166 8-59 (60)
29 PF11731 Cdd1: Pathogenicity l 96.4 0.0021 4.6E-08 56.6 2.6 41 114-155 13-53 (93)
30 PRK12766 50S ribosomal protein 95.0 0.043 9.3E-07 55.8 5.7 56 114-170 4-61 (232)
31 PF04994 TfoX_C: TfoX C-termin 93.0 0.12 2.6E-06 44.4 3.9 33 113-146 3-35 (81)
32 PRK02362 ski2-like helicase; P 92.8 0.12 2.5E-06 60.9 4.7 55 113-168 652-706 (737)
33 PF10391 DNA_pol_lambd_f: Fing 92.6 0.11 2.3E-06 41.1 2.8 27 116-143 5-31 (52)
34 COG3743 Uncharacterized conser 91.5 0.22 4.8E-06 46.5 4.0 37 114-151 68-104 (133)
35 PF03118 RNA_pol_A_CTD: Bacter 91.1 0.34 7.4E-06 40.0 4.3 46 107-154 6-51 (66)
36 PF14229 DUF4332: Domain of un 89.9 0.27 5.8E-06 45.4 3.0 54 101-155 41-94 (122)
37 PF12826 HHH_2: Helix-hairpin- 89.9 0.3 6.5E-06 39.9 3.0 47 118-166 8-56 (64)
38 PRK01172 ski2-like helicase; P 89.1 0.53 1.1E-05 54.8 5.3 53 113-166 612-666 (674)
39 PRK00254 ski2-like helicase; P 88.4 0.52 1.1E-05 55.4 4.7 53 113-166 645-699 (720)
40 PF14229 DUF4332: Domain of un 84.1 1.9 4.1E-05 39.7 5.1 43 119-163 1-48 (122)
41 PRK07758 hypothetical protein; 83.7 2.3 4.9E-05 37.8 5.1 41 118-159 39-81 (95)
42 COG2251 Predicted nuclease (Re 82.8 1.3 2.9E-05 49.1 4.1 68 102-170 214-283 (474)
43 smart00611 SEC63 Domain of unk 81.7 3.5 7.5E-05 43.1 6.6 62 112-174 150-213 (312)
44 PRK14667 uvrC excinuclease ABC 81.6 1.8 4E-05 49.8 4.8 54 112-167 513-567 (567)
45 PF02889 Sec63: Sec63 Brl doma 80.7 2.6 5.5E-05 44.0 5.2 61 113-174 148-210 (314)
46 PRK00116 ruvA Holliday junctio 79.4 1.9 4.2E-05 42.7 3.6 57 114-170 74-133 (192)
47 smart00483 POLXc DNA polymeras 78.8 1.6 3.4E-05 46.9 3.0 30 115-145 91-120 (334)
48 PRK08609 hypothetical protein; 78.6 1.9 4.1E-05 49.6 3.7 29 116-144 91-119 (570)
49 PF02961 BAF: Barrier to autoi 78.1 2 4.3E-05 37.7 2.8 33 110-143 16-48 (89)
50 TIGR00596 rad1 DNA repair prot 78.1 2.4 5.2E-05 50.8 4.4 52 115-168 759-811 (814)
51 TIGR03491 RecB family nuclease 77.5 1.9 4.2E-05 48.1 3.3 59 107-166 201-261 (457)
52 PF14377 DUF4414: Domain of un 75.5 1.3 2.8E-05 39.9 1.0 21 546-566 1-21 (108)
53 PTZ00035 Rad51 protein; Provis 74.7 4.3 9.4E-05 43.7 4.9 55 113-168 21-79 (337)
54 cd00141 NT_POLXc Nucleotidyltr 73.8 2.3 4.9E-05 45.2 2.5 28 116-144 88-115 (307)
55 PRK14671 uvrC excinuclease ABC 73.3 5.2 0.00011 46.6 5.4 51 113-165 569-619 (621)
56 PF14377 DUF4414: Domain of un 72.8 2.2 4.8E-05 38.4 1.8 25 543-567 42-66 (108)
57 PRK14672 uvrC excinuclease ABC 72.6 5.7 0.00012 46.6 5.5 63 112-176 607-671 (691)
58 PRK14670 uvrC excinuclease ABC 71.9 5.5 0.00012 46.0 5.2 54 112-167 513-568 (574)
59 PLN03186 DNA repair protein RA 71.2 2.7 5.8E-05 45.4 2.4 45 112-157 25-71 (342)
60 PRK07956 ligA NAD-dependent DN 71.2 5.4 0.00012 46.9 5.0 53 114-166 446-500 (665)
61 PRK14666 uvrC excinuclease ABC 70.6 5.4 0.00012 46.9 4.7 52 113-166 637-690 (694)
62 TIGR00575 dnlj DNA ligase, NAD 70.5 5.9 0.00013 46.5 5.1 54 113-166 432-487 (652)
63 TIGR00575 dnlj DNA ligase, NAD 70.3 11 0.00024 44.2 7.3 55 106-165 494-550 (652)
64 PLN03187 meiotic recombination 70.3 6.8 0.00015 42.4 5.2 56 112-168 28-87 (344)
65 PRK14669 uvrC excinuclease ABC 68.5 7.3 0.00016 45.5 5.2 54 113-168 552-605 (624)
66 PRK10917 ATP-dependent DNA hel 68.4 3.7 8.1E-05 48.2 2.9 31 113-144 9-39 (681)
67 TIGR02239 recomb_RAD51 DNA rep 66.7 7.2 0.00016 41.6 4.4 37 119-156 7-43 (316)
68 TIGR02238 recomb_DMC1 meiotic 66.1 11 0.00024 40.2 5.7 48 119-167 7-56 (313)
69 PRK12278 50S ribosomal protein 65.5 6.5 0.00014 40.1 3.6 36 114-150 159-194 (221)
70 TIGR01954 nusA_Cterm_rpt trans 65.4 14 0.0003 27.9 4.6 34 121-155 1-34 (50)
71 PRK14973 DNA topoisomerase I; 62.6 13 0.00028 45.5 6.0 105 55-167 825-932 (936)
72 PRK12311 rpsB 30S ribosomal pr 62.6 6 0.00013 42.6 2.9 36 114-150 264-299 (326)
73 PF00633 HHH: Helix-hairpin-he 62.4 3.9 8.5E-05 28.7 1.0 15 116-130 14-28 (30)
74 TIGR00084 ruvA Holliday juncti 61.9 9 0.00019 38.1 3.8 52 115-169 74-131 (191)
75 PRK14351 ligA NAD-dependent DN 61.8 11 0.00024 44.5 5.1 54 113-166 462-517 (689)
76 COG1200 RecG RecG-like helicas 58.9 6.8 0.00015 45.8 2.6 31 113-144 10-40 (677)
77 COG1948 MUS81 ERCC4-type nucle 54.4 15 0.00033 38.2 4.1 50 115-166 184-235 (254)
78 TIGR02027 rpoA DNA-directed RN 54.1 16 0.00035 38.8 4.3 54 110-165 232-287 (297)
79 PRK14605 ruvA Holliday junctio 53.9 13 0.00028 37.0 3.4 54 116-169 76-132 (194)
80 PRK12373 NADH dehydrogenase su 53.4 13 0.00028 41.1 3.5 36 114-150 324-359 (400)
81 COG0632 RuvA Holliday junction 53.0 6.8 0.00015 39.4 1.2 43 78-130 80-125 (201)
82 PRK14601 ruvA Holliday junctio 51.9 7 0.00015 38.7 1.2 56 63-130 67-125 (183)
83 PRK00558 uvrC excinuclease ABC 51.5 17 0.00037 42.3 4.3 53 112-166 542-596 (598)
84 PRK05182 DNA-directed RNA poly 51.1 19 0.00041 38.5 4.3 53 110-164 246-300 (310)
85 PRK14606 ruvA Holliday junctio 48.8 7.9 0.00017 38.4 1.0 55 64-130 68-125 (188)
86 PRK07956 ligA NAD-dependent DN 48.6 42 0.00091 39.7 6.9 55 106-165 507-563 (665)
87 PF07887 Calmodulin_bind: Calm 47.3 23 0.0005 37.7 4.2 41 115-156 164-209 (299)
88 smart00278 HhH1 Helix-hairpin- 45.8 14 0.0003 24.7 1.5 16 115-130 3-18 (26)
89 PRK13766 Hef nuclease; Provisi 45.7 25 0.00054 41.7 4.7 50 115-166 717-768 (773)
90 PRK14604 ruvA Holliday junctio 43.9 11 0.00024 37.6 1.2 55 64-130 68-125 (195)
91 TIGR00084 ruvA Holliday juncti 42.6 9.5 0.00021 37.9 0.4 55 64-130 67-124 (191)
92 PRK14603 ruvA Holliday junctio 42.3 12 0.00027 37.3 1.2 55 64-130 67-124 (197)
93 PRK13901 ruvA Holliday junctio 42.3 11 0.00024 37.7 0.9 58 61-130 64-124 (196)
94 PF00416 Ribosomal_S13: Riboso 42.0 22 0.00048 32.0 2.7 35 115-149 17-51 (107)
95 PRK08097 ligB NAD-dependent DN 41.5 36 0.00077 39.4 4.9 50 116-166 428-480 (562)
96 COG5018 KapD Inhibitor of the 40.9 8 0.00017 38.1 -0.4 39 540-578 24-62 (210)
97 TIGR03631 bact_S13 30S ribosom 40.5 27 0.00059 32.0 3.0 37 114-150 16-52 (113)
98 PRK14602 ruvA Holliday junctio 40.3 14 0.00031 37.0 1.3 58 61-130 66-126 (203)
99 TIGR00426 competence protein C 38.3 29 0.00062 28.3 2.6 30 115-144 18-52 (69)
100 PRK02515 psbU photosystem II c 37.9 61 0.0013 30.7 4.9 54 81-145 39-93 (132)
101 TIGR00615 recR recombination p 36.6 31 0.00067 34.7 3.0 16 115-130 13-28 (195)
102 PRK14604 ruvA Holliday junctio 36.4 41 0.00089 33.6 3.8 51 116-169 76-132 (195)
103 PTZ00134 40S ribosomal protein 36.1 33 0.00072 33.2 3.0 41 114-154 31-74 (154)
104 KOG2534 DNA polymerase IV (fam 35.6 40 0.00088 36.3 3.8 29 116-145 100-128 (353)
105 COG1796 POL4 DNA polymerase IV 35.4 25 0.00055 37.8 2.2 33 114-146 94-126 (326)
106 CHL00013 rpoA RNA polymerase a 35.4 44 0.00095 36.1 4.1 55 109-165 259-315 (327)
107 PRK00076 recR recombination pr 35.1 33 0.00072 34.4 3.0 16 115-130 13-28 (196)
108 PRK14602 ruvA Holliday junctio 34.8 39 0.00085 33.9 3.4 51 116-169 77-133 (203)
109 PRK13844 recombination protein 34.5 34 0.00075 34.4 2.9 16 115-130 17-32 (200)
110 PRK14351 ligA NAD-dependent DN 34.4 52 0.0011 39.1 4.8 46 118-165 533-580 (689)
111 PRK14668 uvrC excinuclease ABC 34.2 36 0.00078 39.5 3.4 50 112-163 524-575 (577)
112 PRK14600 ruvA Holliday junctio 33.3 23 0.00049 35.2 1.5 54 64-130 68-124 (186)
113 PRK14603 ruvA Holliday junctio 33.2 48 0.001 33.2 3.7 51 116-169 75-131 (197)
114 PRK05179 rpsM 30S ribosomal pr 32.2 46 0.001 30.9 3.2 36 114-149 18-53 (122)
115 CHL00137 rps13 ribosomal prote 31.8 46 0.001 30.9 3.1 36 114-149 18-53 (122)
116 PRK13901 ruvA Holliday junctio 31.4 58 0.0013 32.7 3.9 51 116-169 75-131 (196)
117 PRK14601 ruvA Holliday junctio 31.4 56 0.0012 32.4 3.8 51 116-169 76-132 (183)
118 PF07647 SAM_2: SAM domain (St 30.2 45 0.00098 26.5 2.5 46 102-156 5-50 (66)
119 COG0322 UvrC Nuclease subunit 30.1 50 0.0011 38.4 3.7 49 112-163 529-579 (581)
120 PRK14606 ruvA Holliday junctio 29.6 63 0.0014 32.1 3.8 51 116-169 76-132 (188)
121 TIGR03629 arch_S13P archaeal r 28.1 55 0.0012 31.3 3.0 39 114-152 22-63 (144)
122 cd00166 SAM Sterile alpha moti 27.9 1E+02 0.0023 23.6 4.2 46 102-157 3-48 (63)
123 PRK14350 ligA NAD-dependent DN 27.5 81 0.0018 37.4 4.9 51 115-166 438-491 (669)
124 PRK13482 DNA integrity scannin 27.1 87 0.0019 34.2 4.7 39 115-155 289-327 (352)
125 PRK04053 rps13p 30S ribosomal 26.8 62 0.0013 31.1 3.1 40 114-153 26-68 (149)
126 COG0099 RpsM Ribosomal protein 26.7 80 0.0017 29.4 3.7 39 114-152 18-56 (121)
127 COG2199 c-di-GMP synthetase (d 26.6 56 0.0012 30.8 2.8 47 32-82 95-148 (181)
128 PRK14600 ruvA Holliday junctio 25.6 54 0.0012 32.5 2.6 50 116-169 76-131 (186)
129 PRK07945 hypothetical protein; 24.9 1.2E+02 0.0027 32.6 5.4 57 106-167 42-98 (335)
130 cd00080 HhH2_motif Helix-hairp 24.3 57 0.0012 27.4 2.2 26 115-142 24-49 (75)
131 PF14716 HHH_8: Helix-hairpin- 23.4 51 0.0011 27.0 1.6 16 115-130 49-64 (68)
132 COG0353 RecR Recombinational D 23.1 71 0.0015 32.2 2.8 16 115-130 14-29 (198)
133 TIGR01448 recD_rel helicase, p 22.6 1.2E+02 0.0026 36.2 5.1 37 105-144 79-115 (720)
134 PRK05752 uroporphyrinogen-III 22.6 1.9E+02 0.0041 29.4 6.0 77 58-136 13-103 (255)
135 TIGR00677 fadh2_euk methylenet 22.0 3.7E+02 0.008 28.3 8.1 100 65-167 120-251 (281)
136 COG1555 ComEA DNA uptake prote 20.7 79 0.0017 30.2 2.6 29 116-144 100-132 (149)
137 TIGR01259 comE comEA protein. 20.5 86 0.0019 28.8 2.7 29 115-143 70-102 (120)
No 1
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=100.00 E-value=3.9e-44 Score=387.81 Aligned_cols=302 Identities=17% Similarity=0.177 Sum_probs=252.0
Q ss_pred cccCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCC-----CCEE
Q 007746 25 LESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKP-----AQQT 99 (591)
Q Consensus 25 ~~~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP-----~G~~ 99 (591)
+..+++..+.|||||+|+ |++++.++ +++..+|++||++|++++|||||||||+||++|||||+++|| +|++
T Consensus 88 l~~~tp~ve~~siDE~~l--Dvt~~~~l-~~~~~~a~~i~~~I~~~~gl~~siGia~n~~lAK~As~~~k~~~k~~~g~~ 164 (422)
T PRK03609 88 LEELSPRVEIYSIDEAFC--DLTGVRNC-RDLTDFGREIRATVLQRTHLTVGVGIAQTKTLAKLANHAAKKWQRQTGGVV 164 (422)
T ss_pred HHHhCCCceEecccccee--cCCCCcCC-CCHHHHHHHHHHHHHHHHCCceEEEecCCHHHHHHHHHHhCCCCCCCCcEE
Confidence 346889999999999998 99999776 467899999999999999999999999999999999988776 6888
Q ss_pred Ee-ccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccC
Q 007746 100 TV-PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL 178 (591)
Q Consensus 100 vl-~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~ 178 (591)
+| +++++.+||+++||++|||||+++.++|. .+||+|+|||++++...|+++||+ .|..+|+.|+|+++.++....+
T Consensus 165 ~i~~~~~~~~~L~~lPv~~l~GiG~~~~~~L~-~lGi~TigdL~~~~~~~L~~~fG~-~~~~l~~~a~G~~~~~~~~~~~ 242 (422)
T PRK03609 165 DLSNLERQRKLLSLQPVEEVWGVGRRISKKLN-AMGIKTALDLADTNIRFIRKHFNV-VLERTVRELRGEPCLSLEEFAP 242 (422)
T ss_pred EcCCHHHHHHHhhcCChhhcCCccHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCH-HHHHHHHHhCCCCCCCccccCC
Confidence 88 67899999999999999999999999996 999999999999999999999998 7999999999999999976655
Q ss_pred -CcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCC--CCcCceeeeCC
Q 007746 179 -PKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSR--KKFPSKSCPLR 255 (591)
Q Consensus 179 -~KSIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~--~~~~SrS~~L~ 255 (591)
+|+|+.+++|+ .++.+.+++..++..|+++|+.||+. +++.+++|+|++++. +|... .+..+++.+++
T Consensus 243 ~~ksi~~~~tf~--~~~~~~~~l~~~l~~l~~~l~~rLr~----~~~~~~~l~l~ir~~---~~~~~~~~~~~~~~~~l~ 313 (422)
T PRK03609 243 TKQEIVCSRSFG--ERITDYESMRQAICSYAARAAEKLRG----EHQYCRFISTFVKTS---PFALNEPYYGNSASVKLL 313 (422)
T ss_pred CCceEEEeeECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCcccEEEEEEEcC---CccccCCCcCceeEEeCC
Confidence 47999999998 78999999999999999999999997 799999999999985 34321 12357778899
Q ss_pred CcchhhHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCcccccccccCCCC--CCCC------
Q 007746 256 YGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNGPDK--FGST------ 327 (591)
Q Consensus 256 ~~T~~i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~LF~~~~~--~~~~------ 327 (591)
.||+ ++..|++.++++|.++|. .+.++|++||.+++|.+. ...|.+||+.... ....
T Consensus 314 ~pt~----d~~~l~~~a~~ll~~~~~--------~~~~~r~~GV~~~~l~~~---~~~q~~LF~~~~~~~~~~~l~~~iD 378 (422)
T PRK03609 314 TPTQ----DSRDIIAAATRALDAIWR--------DGHRYQKAGVMLGDFFSQ---GVAQLNLFDDNAPRPGSEQLMKVLD 378 (422)
T ss_pred CCCC----CHHHHHHHHHHHHHHHhC--------CCCceEEeeEEEEeeccC---CCcCccCccccccccchHHHHHHHH
Confidence 8984 778899999999987652 356899999999999864 3457899975211 1100
Q ss_pred -CccC--CC-----------ccccCCCC-CCCCCcccccCCCc
Q 007746 328 -SEQL--PD-----------NFIDAAPL-SPSGSESYSTLNST 355 (591)
Q Consensus 328 -~~~~--~d-----------~~i~~~~~-~ps~s~~c~~l~~~ 355 (591)
.+.+ .+ ...++..+ ||+|+|+..+||.+
T Consensus 379 ~i~~r~G~~~i~~a~~~~~~~w~~~~~~~s~~ytt~~~~l~~~ 421 (422)
T PRK03609 379 TLNAKSGKGTLYFAGQGIAQQWQMKREMLSPRYTTRWSDLLRV 421 (422)
T ss_pred HHHHhhCCCeEEECCCCCCCCccCchhhcCCCCCCCHHHccee
Confidence 0011 11 12233445 99999999988864
No 2
>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=4.7e-44 Score=377.07 Aligned_cols=254 Identities=26% Similarity=0.365 Sum_probs=227.3
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhC-CeEEEEecCCHHHHHHhccCCCCCCEEEecccc
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETE-FTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 105 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etG-Lt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~ 105 (591)
.+++..+.|||||+|+ |++++.++|+.+..+|++||++|++++| ||||||||+||++||||++++||+|++++++++
T Consensus 88 ~~sp~ve~~siDE~~l--dvt~~~~~~~~~~~la~~i~~~i~~~~ggl~~siGia~n~~lAKlAs~~~KP~g~~v~~~~~ 165 (343)
T cd00424 88 EVAPLVEVASIDELFL--DLTGSARLLGLGSEVALRIKRHIAEQLGGITASIGIASNKLLAKLAAKYAKPDGLTILDPED 165 (343)
T ss_pred HhCCcEEEccCCEEEE--ECCCchhccCCHHHHHHHHHHHHHHHhCCceEEEeecccHHHHHHHhccCCCCCEEEEcHHH
Confidence 5778899999999998 9999999999999999999999999998 999999999999999999999999999999999
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC-HHHHHHHhCcchHHHHHHHHcCCCCCccccccCCccccc
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS-EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGS 184 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~-~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~ 184 (591)
+.+||+++||++|||||+++.++|. .+||+|++||+.++ ...|+++||+ .|.++|+.|+|+|+++|.+..++|||+.
T Consensus 166 ~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~~~~~~~l~~~fg~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~ 243 (343)
T cd00424 166 LPGFLSKLPLTDLPGIGAVTAKRLE-AVGINPIGDLLAASPDALLALWGGV-SGERLWYALRGIDDEPLSPPRPRKSFSH 243 (343)
T ss_pred HHHHHhcCChhhcCCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHhhH-HHHHHHHHhCCcCCCCCCCCCCCCceee
Confidence 9999999999999999999999996 99999999999999 8889999997 7999999999999999988888999999
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHH
Q 007746 185 GKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQED 264 (591)
Q Consensus 185 e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~d 264 (591)
+++|+ .++.+.+++..+|..|+++|+.||+. .++.+++|+|++++.+. ....+....+++.+++.+| +
T Consensus 244 ~~tf~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~~~~l~l~lr~~~~-~~~~~~~~~~~~~~l~~~t-----~ 311 (343)
T cd00424 244 ERVLP--RDSRNAEDARPLLRLLLEKLARRLRR----DGRGATRLRLWLRTVDG-RWSGHADIPSRSAPRPIST-----E 311 (343)
T ss_pred eEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCceeEEEEEEEeCCC-cccccceeeeeeeeCCCCC-----C
Confidence 99998 78999999999999999999999997 69999999999998532 1001112468889999887 4
Q ss_pred HHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEec
Q 007746 265 TFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS 302 (591)
Q Consensus 265 a~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls 302 (591)
...|+++++++|.+.+. ...+.+||++||+++
T Consensus 312 ~~~l~~~~~~l~~~~~~------~~~~~~ir~~gv~~~ 343 (343)
T cd00424 312 DGELLHALDKLWRALLD------DKGPRRLRRLGVRLS 343 (343)
T ss_pred HHHHHHHHHHHHHhhhh------ccCCCCeeEEEEEeC
Confidence 46788888888887642 113678999999874
No 3
>PTZ00205 DNA polymerase kappa; Provisional
Probab=100.00 E-value=3.4e-44 Score=394.68 Aligned_cols=253 Identities=21% Similarity=0.210 Sum_probs=223.0
Q ss_pred ccCCCCCCccchhhhhhcCCCCchhhhc---chHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEe-
Q 007746 26 ESKDGNDSKATVKEWLCRCDADHRDKLL---ACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTV- 101 (591)
Q Consensus 26 ~~~~~~~~~ySIDE~fl~lDvt~~~~l~---~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl- 101 (591)
..+++..++|||||+|+ |+|++...| +.+..+|++||.+|+++||||||||||+||+||||||+++||||++++
T Consensus 218 ~~ysp~ve~~SIDEafL--DlT~~~~~~~~~~~~~~iA~~IR~~I~~~tgLt~SiGIA~NklLAKiASd~~KPnG~~vl~ 295 (571)
T PTZ00205 218 AEYDPNYISFGLDELTL--EVSAYIERFEGTKTAEDVASELRVRVFGETKLTASAGIGPTAALAKIASNINKPNGQHDLN 295 (571)
T ss_pred HhcCCcEEEeechhcee--ccCCchhhccCCCCHHHHHHHHHHHHHHHHCCcEEEEEcCCHHHHHHhhhccCCCCCeEEe
Confidence 46889999999999998 999986665 368899999999999999999999999999999999999999999986
Q ss_pred --ccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHH--------HHHHHhCcchHHHHHHHHcCCCCC
Q 007746 102 --PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSED--------KLQESYGFNTGTWLWNIARGISGE 171 (591)
Q Consensus 102 --~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~--------~L~k~FG~~~G~~L~~~arGid~~ 171 (591)
+++++.+||++|||++|||||++++++|. .+||+||+||++.+.. .|+..||...|.++|..++|+|.+
T Consensus 296 l~~~~~v~~fL~~LpV~ki~GIG~~t~~~L~-~~GI~TigDLa~~~~~l~~~f~~k~l~~llG~~~G~~l~~~a~G~d~~ 374 (571)
T PTZ00205 296 LHTRGDVMTYVRDLGLRSVPGVGKVTEALLK-GLGITTLSDIYNRRVELCYILHNNLFRFLLGASIGIMQWPDAATAANT 374 (571)
T ss_pred cCCHHHHHHHHhCCCcceeCCcCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHhHHHHHHHHhCchhhHHHHHHhcCCCCC
Confidence 67899999999999999999999999996 9999999999998876 477889976799999999999988
Q ss_pred c-ccc--ccCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcC
Q 007746 172 E-VQA--RLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 248 (591)
Q Consensus 172 ~-V~~--~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~ 248 (591)
+ +.. ...+|||++++||. . +.+.+++...|..||++|+.||++ .++.+++|+|++++. +|.. .
T Consensus 375 ~~v~~~~~~~rKSIg~ErTF~--~-~~d~~el~~~L~~L~~~v~~rLrk----~~l~artVtlKlK~~---dF~~----~ 440 (571)
T PTZ00205 375 ENCEGATGGQRKAISSERSFT--T-PRTKEGLQEMVDTVFNGAYEEMRK----SELMCRQISLTIRWA---SYRY----Q 440 (571)
T ss_pred CccCCCCCCCCceeEEeEeCC--C-CCCHHHHHHHHHHHHHHHHHHHHh----cCCCccEEEEEEEEC---CCCc----e
Confidence 4 432 34689999999998 3 679999999999999999999997 799999999999984 4543 4
Q ss_pred ceeeeCCCcchhhHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeec
Q 007746 249 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 307 (591)
Q Consensus 249 SrS~~L~~~T~~i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~ 307 (591)
+++.+|+.||+ +...|++++..+|...+ +.+.+||+|||++++|...
T Consensus 441 trs~tL~~pT~----d~~~I~~aa~~Ll~~~~--------~~~~~vRLlGV~ls~L~~~ 487 (571)
T PTZ00205 441 QYTKSLIQYSD----DSATLRRAVDGLLLPHA--------AKYSEMCLLGVRFLDLISA 487 (571)
T ss_pred EEEEECCCCcC----CHHHHHHHHHHHHHhcc--------ccCCCEEEEEEEEcccCcH
Confidence 78889999994 77889999988886532 2346899999999999875
No 4
>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=4.5e-44 Score=385.62 Aligned_cols=257 Identities=24% Similarity=0.254 Sum_probs=230.7
Q ss_pred cCCCCCCccchhhhhhcCCCCchhh-hcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecccc
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDK-LLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 105 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~-l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~ 105 (591)
.+++..+.|||||+|+ |++++.+ +|+++..+|++||++|++++|||||||||+||++||||++++||+|++++.+++
T Consensus 137 ~~s~~ve~~SiDE~~l--Dvt~~~~~~~~~~~~la~~ir~~I~~~~gl~~siGia~nk~lAKlAs~~aKP~g~~~i~~~~ 214 (404)
T cd01701 137 SYTDNIEAVSCDEALI--DITSLLEETYELPEELAEAIRNEIRETTGCSASVGIGPNILLARLATRKAKPDGQYHLSAEK 214 (404)
T ss_pred HhCCceEEcccceEEE--EcccccccccCCHHHHHHHHHHHHHHHHCCCEEEEEcCCHHHHHHHhcccCCCcEEEECHHH
Confidence 4677889999999998 9999985 788999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC--HHHHHHHhCcchHHHHHHHHcCCCCCccccccCCcccc
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS--EDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHG 183 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~--~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs 183 (591)
+.+||+++||++|||||++++++|. .+||+|++||+.++ ...|+++||...|.+||+.|+|+|+.+|.+..++|||+
T Consensus 215 ~~~~L~~lPv~~l~GIG~~~~~~L~-~~Gi~t~~dl~~~~~~~~~L~~~fG~~~g~~L~~~a~G~d~~~v~~~~~~ksi~ 293 (404)
T cd01701 215 VEEFLSQLKVGDLPGVGSSLAEKLV-KLFGDTCGGLELRSKTKEKLQKVLGPKTGEKLYDYCRGIDDRPVTGEKERKSVS 293 (404)
T ss_pred HHHHhhcCCHhHhCCCCHHHHHHHH-HcCCcchHHHHhCcccHHHHHHHHCHHHHHHHHHHhCCcCCCCCCCCCCCcccc
Confidence 9999999999999999999999996 99999999999999 99999999975799999999999999999888899999
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeeccc-CC-----CCCC--CCcCceeeeCC
Q 007746 184 SGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKS-SD-----SDSR--KKFPSKSCPLR 255 (591)
Q Consensus 184 ~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~-~~-----f~s~--~~~~SrS~~L~ 255 (591)
.+++|+ .++.+.+++..+|..|+++|+.||+. +++.+++|+|++++... .+ |..+ .+..+++.+|+
T Consensus 294 ~~~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~~~~~~~~~~~y~g~~~~~~~~~~~~l~ 367 (404)
T cd01701 294 AEINYG--IRFTNVDDVEQFLQRLSEELSKRLEE----SNVTGRQITLKLMKRAPGAPIEPPKYMGHGICDSFSKSSTLG 367 (404)
T ss_pred ceeeCC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCceeeEEEEEEeccccCccccccccccCCCcEEeeeeECC
Confidence 999998 78999999999999999999999998 79999999999997321 11 1111 12468899999
Q ss_pred CcchhhHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCC
Q 007746 256 YGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 304 (591)
Q Consensus 256 ~~T~~i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L 304 (591)
.||+ +...|+++++++|.+.+ ..+.+||+|||++++|
T Consensus 368 ~pT~----d~~~i~~~a~~ll~~~~--------~~~~~vR~lgv~~~~l 404 (404)
T cd01701 368 VATD----DSGVIGTEAKKLFRDLS--------IPPEELRGVGIQVTKL 404 (404)
T ss_pred CCCC----CHHHHHHHHHHHHHhcc--------CCCCCeeEEEEEEecC
Confidence 9995 77889999999998654 2356899999999886
No 5
>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=1.1e-43 Score=379.80 Aligned_cols=266 Identities=26% Similarity=0.362 Sum_probs=225.0
Q ss_pred ccCCC--CCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecc
Q 007746 26 ESKDG--NDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPF 103 (591)
Q Consensus 26 ~~~~~--~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~ 103 (591)
..+++ ..+.+||||+|+ |+|+...+++ ..+|++||++|+++||||||||||+||+|||||++++||+|++++.+
T Consensus 84 ~~~sp~~~ve~~SiDE~~l--Dvt~~~~~~g--~~la~~ir~~I~~~~Glt~siGIa~nk~lAKlas~~~KP~g~~~i~~ 159 (379)
T cd01703 84 RSYSWNDRVERLGFDENFM--DVTEMRLLVA--SHIAYEMRERIENELGLTCCAGIASNKLLAKLVGSVNKPNQQTTLLP 159 (379)
T ss_pred HHcCCHhhEEecCCCcEEE--EccCccchhH--HHHHHHHHHHHHHHhCCeEEEEEcCCHHHHHHHhhhcCCCCeEEEcC
Confidence 35777 889999999998 9999866553 78999999999999999999999999999999999999999999876
Q ss_pred ---ccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcC---------------HHHHHHHhCcchHHHHHHHH
Q 007746 104 ---SSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFS---------------EDKLQESYGFNTGTWLWNIA 165 (591)
Q Consensus 104 ---~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~---------------~~~L~k~FG~~~G~~L~~~a 165 (591)
+++.+||+++||++|||||++++++|. .+||+|+|||+.++ ...|+++||...|.+||+.|
T Consensus 160 ~~~~~~~~fl~~lpv~~l~GiG~~~~~kL~-~~GI~tigdl~~~~~~~~~~~~~~~~~~s~~~L~~~fG~~~g~~l~~~a 238 (379)
T cd01703 160 PSCADLMDFMDLHDLRKIPGIGYKTAAKLE-AHGISSVRDLQEFSNRNRQTVGAAPSLLELLLMVKEFGEGIGQRIWKLL 238 (379)
T ss_pred CchHHHHHHhccCCccccCCcCHHHHHHHH-HcCCCcHHHHHhCCcccccccccccccccHHHHHHHHCHHHHHHHHHHH
Confidence 467789999999999999999999996 99999999999999 99999999975699999999
Q ss_pred cCCCCCcc-ccccCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhh----cCceeeEEEEEEeecccCC
Q 007746 166 RGISGEEV-QARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQ----NKRIAHTLTLHASAFKSSD 240 (591)
Q Consensus 166 rGid~~~V-~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~----~~~~a~tLtL~ir~~~~~~ 240 (591)
+|+|+++| .+...+|||+.++||.. .++.+.+++..+|..|+++|+.||++++.+ .+..++||+|++|+.+.
T Consensus 239 ~G~d~~~V~~~~~~~ksis~e~tf~~-~~~~~~~~~~~~l~~l~~~l~~rl~~~l~~~~~~~~~~~~tv~l~vr~~~~-- 315 (379)
T cd01703 239 FGRDTSPVKPASDFPQQISIEDSYKK-CSLEEIREARNKIEELLASLLERMKQDLQEVKAGDGRRPHTLRLTLRRYTS-- 315 (379)
T ss_pred CCCCCCccCCCCCCCceeEEeeccCC-CCCCCHHHHHHHHHHHHHHHHHHHHhhhhccchhcCeeeeEEEEEEEECCC--
Confidence 99999999 45566899999999983 289999999999999999999999985533 68899999999998531
Q ss_pred CCCCCCcCceeeeCCCcchh-h---H-HHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecC
Q 007746 241 SDSRKKFPSKSCPLRYGTAK-I---Q-EDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 303 (591)
Q Consensus 241 f~s~~~~~SrS~~L~~~T~~-i---~-~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~ 303 (591)
...+..+.+++++++.+|+. + . .+...|++.++.+|.+.+.. ....+.+||++||++++
T Consensus 316 ~~~~~~~~sr~~~l~~~~~~~~~~~~~~~~~~i~~~~~~L~~~~~~~----~~~~~~~irl~gv~~~~ 379 (379)
T cd01703 316 TKKHYNRESKQAPIPSHVFQKLTGGNEIAARPIEKILMRLFRELVPP----KNVKGFNLTLLNVCFTN 379 (379)
T ss_pred CCCccceeeeccccCchhhccccccchhhHHHHHHHHHHHHHHhccc----ccCCCCceEEEEEEeeC
Confidence 11112346899999988841 1 0 14567899999998875421 01125689999999874
No 6
>PRK03858 DNA polymerase IV; Validated
Probab=100.00 E-value=2.1e-43 Score=378.34 Aligned_cols=265 Identities=22% Similarity=0.272 Sum_probs=238.2
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccH
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSV 106 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v 106 (591)
.+++..+.|||||+|+ |++++.++|+++..+|++||++|++++|||||||||+||++||||++++||+|+++++++++
T Consensus 89 ~~s~~ve~~siDe~~l--dvt~~~~~~~~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~~i~~~~~ 166 (396)
T PRK03858 89 DTTPLVEGLSIDEAFL--DVGGLRRISGTPVQIAARLRRRVREEVGLPITVGVARTKFLAKVASQVAKPDGLLVVPPDRE 166 (396)
T ss_pred HhCCceEEecCCeEEE--EccccccccCCHHHHHHHHHHHHHHHHCCCeEEEEcCChHHHHHhhcccCCCceEEECcHHH
Confidence 5778889999999998 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCccccccc
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGK 186 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~e~ 186 (591)
..||+++||++|||||++++++|+ .+||+|++||++++...|.++||...|.+||+.++|+|+.+|.+..++|||+.++
T Consensus 167 ~~~L~~lpl~~l~Gig~~~~~~L~-~~Gi~t~~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~v~~~~~~ksi~~~~ 245 (396)
T PRK03858 167 LAFLHPLPVRRLWGVGPVTAAKLR-AHGITTVGDVAELPESALVSLLGPAAGRHLHALAHNRDPRRVETGRRRRSVGAQR 245 (396)
T ss_pred HHHHhcCChhhcCCCCHHHHHHHH-HhCCCcHHHHhcCCHHHHHHHhCcHHHHHHHHHhCCCCCCCCCCCCCCcccccee
Confidence 999999999999999999999996 9999999999999999999999986799999999999999998888889999999
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHHHH
Q 007746 187 SFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTF 266 (591)
Q Consensus 187 tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~da~ 266 (591)
+|+ .++.+.+++..+|..|+++|+.||++ .++.+++|+|++++. +|.. .+++++++.+|+ +..
T Consensus 246 t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~---~~~~----~~~~~~l~~~t~----~~~ 308 (396)
T PRK03858 246 ALG--RGPNSPAEVDAVVVALVDRVARRMRA----AGRTGRTVVLRLRFD---DFTR----ATRSHTLPRPTA----STA 308 (396)
T ss_pred EcC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEeC---CCCE----EEEEEECCCCcC----CHH
Confidence 998 78999999999999999999999997 699999999999974 3332 477889998885 667
Q ss_pred HHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCccccccc-ccC
Q 007746 267 NLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKY-FNG 320 (591)
Q Consensus 267 ~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~L-F~~ 320 (591)
.|++.+..+|...+. ...+.+||++||.+++|.+. ...|.+| |+.
T Consensus 309 ~l~~l~~~ll~~~~~------~~~~~~irligv~~~~l~~~---~~~q~~L~f~~ 354 (396)
T PRK03858 309 TLLAAARDLVAAAAP------LIAERGLTLVGFAVSNLDDD---GAQQLELPFGL 354 (396)
T ss_pred HHHHHHHHHHHhhhh------ccCCCCeEEEEEEeecCCcc---cccccCCCccc
Confidence 788888888876431 11246899999999999864 3446778 753
No 7
>PRK01216 DNA polymerase IV; Validated
Probab=100.00 E-value=2.5e-43 Score=373.59 Aligned_cols=249 Identities=23% Similarity=0.319 Sum_probs=224.9
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccH
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSV 106 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v 106 (591)
.+++..+++||||+|+ |++++.++|+++..+|++||++|++++|||||||||+||++|||||+++||+|+++++++++
T Consensus 94 ~~tp~ve~~siDE~~L--Dvt~~~~l~g~~~~la~~ir~~I~~~~glt~siGia~nk~lAKlas~~~KP~g~~vi~~~~~ 171 (351)
T PRK01216 94 EYSEKIEIASIDEAYL--DISDKVKNYQDAYNLGLEIKNKILEKEKITVTVGISKNKVFAKIAADMAKPNGIKVIDDEEV 171 (351)
T ss_pred HhCCceEEccCCeEEE--EcccchhccCCHHHHHHHHHHHHHHHHCCcEEEEecCCHHHHHHHHhccCCCCEEEeCHHHH
Confidence 5788899999999998 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCccccccc
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGK 186 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~e~ 186 (591)
.+||++|||+++||||++++++|+ .+||+|+|||+++|...|.++||...|.+||+.++|+|.++|.+ ..+|||+.++
T Consensus 172 ~~~L~~LPi~~l~giG~~~~~~L~-~~Gi~TigdL~~~~~~~L~~rfG~~~~~~L~~~a~G~d~~pv~~-~~~ksi~~~~ 249 (351)
T PRK01216 172 KRFINELDIADIPGIGDITAEKLK-KLGVNKLVDTLRIEFDELKGIIGEAKAKYLFSLARNEYNEPVRA-RVRKSIGRYV 249 (351)
T ss_pred HHHHhcCCcccccCCCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHCHHHHHHHHHHhCCCCCCCCCC-CCCCCCcCeE
Confidence 999999999999999999999996 99999999999999999999999767999999999999999987 4569999999
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHHHH
Q 007746 187 SFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTF 266 (591)
Q Consensus 187 tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~da~ 266 (591)
+|. +++.+.+++...|..|+++++.||+. .++++++++++. +|.+ .+++.+++.+|+ ..
T Consensus 250 tl~--~di~~~~~l~~~l~~L~~~~~~rl~~-------~~~~~~~~~~~~---df~~----~t~~~tl~~~~~-----~~ 308 (351)
T PRK01216 250 TLP--RNTRDLEEIKPYLKRAIEEAYYKLDG-------IPKAIHVVAIME---DLDI----VSRGRTFTHGIS-----KE 308 (351)
T ss_pred ECC--CccCCHHHHHHHHHHHHHHHHHHHHh-------CCCEEEEEEEcC---CCCE----EEEEEECCCCCC-----HH
Confidence 998 79999999999999999999999984 467889999863 4543 689999998883 25
Q ss_pred HHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeec
Q 007746 267 NLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 307 (591)
Q Consensus 267 ~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~ 307 (591)
.+++++.++|.+... +.+.+||+|||++++|.+.
T Consensus 309 ~~~~~a~~Ll~~~~~-------~~~~~vRllGv~~~~l~~~ 342 (351)
T PRK01216 309 TAYREAVRLLQKILE-------EDERKIRRIGVRFSKIIEA 342 (351)
T ss_pred HHHHHHHHHHHhhhh-------cCCCCeeEEEEEEeccccc
Confidence 578888888875421 1245899999999999765
No 8
>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=4.3e-43 Score=372.84 Aligned_cols=248 Identities=42% Similarity=0.591 Sum_probs=216.6
Q ss_pred ccCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecccc
Q 007746 26 ESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 105 (591)
Q Consensus 26 ~~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~ 105 (591)
..+++..+.+||||+|+ |+ +..+|.+||++|++++|||||||||+||+||||||+++||+|++++++++
T Consensus 106 ~~~sp~vE~~SiDE~fl--Dv---------~~~la~~ir~~I~~~~glt~SiGIa~nk~lAKlAs~~~KP~g~~v~~~~~ 174 (359)
T cd01702 106 KRFGDVVEKASIDEAYL--DL---------GSRIVEEIRQQVYDELGYTCSAGIAHNKMLAKLASGMNKPNAQTILRNDA 174 (359)
T ss_pred HHcCCceEECcCCeeHH--HH---------HHHHHHHHHHHHHHHhCccEEeeecCCHHHHHHHhcccCCCCeEEECHHH
Confidence 35788899999999998 66 46799999999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc--CHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCcccc
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF--SEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHG 183 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~--~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs 183 (591)
+.+||+++||++|||||++++.+|.+.+||+|++||+++ +...|+++||.+.|.+||+.|+|+|+++|.+..++|||+
T Consensus 175 ~~~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~~~fG~~~g~~l~~~a~G~d~~~v~~~~~~ksi~ 254 (359)
T cd01702 175 VASFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQEHFGEKLGEWLYNLLRGIDHEPVKPRPLPKSMG 254 (359)
T ss_pred HHHHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCCCCCceee
Confidence 999999999999999999998775348999999999999 999999999965899999999999999999888899999
Q ss_pred cccccCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhH
Q 007746 184 SGKSFPGPRALKTV-ASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQ 262 (591)
Q Consensus 184 ~e~tF~~~~~i~~~-eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~ 262 (591)
.+++|+ .++.+. +++..+|..|+.+|+.||++++..+++.+++|+|++++. +| ....+++++++.++
T Consensus 255 ~~~tf~--~~~~~~~~~l~~~l~~L~~~l~~rL~~~~~~~~~~~~~v~v~lr~~---~~---~~~~sr~~~~~~~~---- 322 (359)
T cd01702 255 SSKNFP--GKTALSTEDVQHWLLVLASELNSRLEDDRYENNRRPKTLVLSLRQR---GD---GVRRSRSCALPRYD---- 322 (359)
T ss_pred eeeecC--CCCCChHHHHHHHHHHHHHHHHHHHHhhhhhcCceeeEEEEEEEEC---CC---cEEEEEEecCCCCC----
Confidence 999999 688887 999999999999999999986555699999999999985 33 12357777777665
Q ss_pred HHHHHHHHHHHHHHhhhccccccCCCCC---CcceeEEEEEecC
Q 007746 263 EDTFNLFQAGLREFLGSFGVKTQGSHYS---GWRITALSVSASK 303 (591)
Q Consensus 263 ~da~~L~~aal~ll~~~~~~~~~~~~~~---g~~iR~lGVsls~ 303 (591)
...|+++++++|.+++... .. +.+||++||++++
T Consensus 323 --~~~i~~~~~~l~~~~~~~~-----~~~~~~~~~rl~g~~~~~ 359 (359)
T cd01702 323 --AQKIVKDAFKLIKAINEEG-----LGLAWNYPLTLLSLSFTK 359 (359)
T ss_pred --HHHHHHHHHHHHHHhhhhc-----cccccCCCeEEEEEEecC
Confidence 3567778888887665311 11 4799999999875
No 9
>PRK03103 DNA polymerase IV; Reviewed
Probab=100.00 E-value=7.8e-43 Score=375.84 Aligned_cols=264 Identities=23% Similarity=0.364 Sum_probs=239.1
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccC---CCCCCEEEecc
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGM---NKPAQQTTVPF 103 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~---aKP~G~~vl~~ 103 (591)
.+++..+.|||||+|+ |++++.++|+++..+|++||++|++++|||||||||+||++||||+++ +||+|++++++
T Consensus 94 ~~sp~ve~~siDe~~l--Dvt~~~~~~~~~~~la~~ir~~i~~~~gl~~svGia~n~~lAklas~~~~k~kp~g~~v~~~ 171 (409)
T PRK03103 94 DFTDLVEPFSIDEQFL--DVTGSQKLFGSPLEIAQKIQQRIMRETGVYARVGIGPNKLLAKMACDNFAKKNPDGLFTLDK 171 (409)
T ss_pred HhCccceecCCCeeEe--eccchhhcCCCHHHHHHHHHHHHHHHHCceEEEeecCCHHHHHHHhcchhhcCCCcEEEECH
Confidence 5788899999999998 999999999999999999999999999999999999999999999998 99999999999
Q ss_pred ccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccC--Ccc
Q 007746 104 SSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKS 181 (591)
Q Consensus 104 ~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~--~KS 181 (591)
+++.+||+++||++|||||+++.++|. .+||+|+|||++++...|+++||. .|.++|+.++|+|+++|.+..+ +||
T Consensus 172 ~~~~~~L~~lpi~~l~gig~~~~~~L~-~~Gi~tigdl~~~~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~~~ks 249 (409)
T PRK03103 172 EDVPADLWPLPVRKLFGVGSRMEKHLR-RMGIRTIGQLANTPLERLKKRWGI-NGEVLWRTANGIDYSPVTPHSLDRQKA 249 (409)
T ss_pred HHHHHHHHcCCHhhcCCccHHHHHHHH-HcCCCCHHHHhcCCHHHHHHHHCH-HHHHHHHHhcCCCCCcCCcccCCCCCc
Confidence 999999999999999999999999996 999999999999999999999998 7999999999999999988643 589
Q ss_pred cccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhh
Q 007746 182 HGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKI 261 (591)
Q Consensus 182 Is~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i 261 (591)
|+.+.+|+ .++.+.+++...|..|+++|+.||++ .+..+++|+|++++. +++. .+..+++++++.||+
T Consensus 250 i~~~~t~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~lr~~---~~~~-~~~~~~~~~l~~pt~-- 317 (409)
T PRK03103 250 IGHQMTLP--RDYRGFEEIKVVLLELCEEVCRRARA----KGYMGRTVSVSLRGA---DFDW-PTGFSRQMTLPEPTN-- 317 (409)
T ss_pred cCCCeECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----hCCceeEEEEEEEeC---CCcC-CCCcceeeecCCCCC--
Confidence 99999998 78999999999999999999999997 699999999999975 3332 133578889998884
Q ss_pred HHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCcccccccccC
Q 007746 262 QEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 320 (591)
Q Consensus 262 ~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~LF~~ 320 (591)
+...|++.+..+|.+++ .+.+||+|||.+++|.+. ...|.+||+.
T Consensus 318 --~~~~l~~~~~~ll~~~~---------~~~~vr~lgv~~~~l~~~---~~~q~~LF~~ 362 (409)
T PRK03103 318 --LAMEVYEAACKLFHRHW---------DGKPVRRVGVTLSNLVSD---DVWQLSLFGD 362 (409)
T ss_pred --CHHHHHHHHHHHHHhcc---------cCCCceEEEEEEeCCCCC---cccCCCcccc
Confidence 77789998888887642 467999999999999875 3567899974
No 10
>PRK14133 DNA polymerase IV; Provisional
Probab=100.00 E-value=1e-42 Score=367.38 Aligned_cols=257 Identities=25% Similarity=0.296 Sum_probs=233.0
Q ss_pred ccCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecccc
Q 007746 26 ESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 105 (591)
Q Consensus 26 ~~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~ 105 (591)
.++++..+.|||||+|+ |++++. +++..+|++||++|++++|||||||||+||++||||++++||+|++++++++
T Consensus 91 ~~~s~~ve~~siDe~~l--dv~~~~---~~~~~la~~i~~~i~~~~gl~~siGia~n~~~Aklas~~~kp~g~~~~~~~~ 165 (347)
T PRK14133 91 YEVTPIVEPVSIDEAYL--DITNIK---EEPIKIAKYIKKKVKKETGLTLSVGISYNKFLAKLASDWNKPDGIKIITEDM 165 (347)
T ss_pred HHhCCceEEccCCeEEE--EccCCC---CCHHHHHHHHHHHHHHHHCCcEEEEEcCcHHHHHHHhccCCCCceEEECHHH
Confidence 35788899999999998 899875 6789999999999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCcccccc
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 185 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~e 185 (591)
+.+||+++||++|||||+++.++|. .+||+|++||+.++...|+++||. .|.++|+.++|+|+.+|.+..++|+|+.+
T Consensus 166 ~~~~L~~lpv~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~ 243 (347)
T PRK14133 166 IPDILKPLPISKVHGIGKKSVEKLN-NIGIYTIEDLLKLSREFLIEYFGK-FGVEIYERIRGIDYREVEVSRERKSIGKE 243 (347)
T ss_pred HHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCcceEee
Confidence 9999999999999999999999996 999999999999999999999997 79999999999999999988889999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHHH
Q 007746 186 KSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDT 265 (591)
Q Consensus 186 ~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~da 265 (591)
++|. .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++. ++.. .+++.+++.+|+ +.
T Consensus 244 ~~~~--~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~~~~l~l~l~~~---~~~~----~~~~~~l~~~t~----~~ 306 (347)
T PRK14133 244 TTLK--KDTKDKEELKKYLKDFSNIISEELKK----RNLYGKTVTVKIKTS---DFQT----HTKSKTLNDYIR----DK 306 (347)
T ss_pred EEcC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEEC---CCCe----eEEEEECCCCcC----CH
Confidence 9998 78999999999999999999999997 799999999999974 3333 467888998884 77
Q ss_pred HHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCcccccccc
Q 007746 266 FNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYF 318 (591)
Q Consensus 266 ~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~LF 318 (591)
..|++.+..+|.+++ .+.+||.|||.+++|.+. ...|.+||
T Consensus 307 ~~l~~l~~~lle~~~---------~~~~vr~lgl~~~~l~~~---~~~q~~l~ 347 (347)
T PRK14133 307 EEIYNVACEILEHIN---------IKEPIRLIGLSVSNLSEN---KIEQLSFL 347 (347)
T ss_pred HHHHHHHHHHHHhcc---------CCCCEEEEEEEEecCCCC---cccccCCC
Confidence 788888888887643 357999999999999865 34467776
No 11
>PRK02794 DNA polymerase IV; Provisional
Probab=100.00 E-value=1.3e-42 Score=375.56 Aligned_cols=262 Identities=22% Similarity=0.301 Sum_probs=236.5
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcch-HHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecccc
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLAC-GVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 105 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~-~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~ 105 (591)
.+++..+.|||||+|+ |++++.++|+. +..++++||++|++++|||||||||+||++||||++++||+|++++++++
T Consensus 124 ~~sp~ve~~siDe~~l--dvt~~~~l~g~~~~~~~~~i~~~i~~~~gl~~svGIa~n~~lAKlas~~~KP~g~~ii~~~~ 201 (419)
T PRK02794 124 ALTPLVEPLSIDEAFL--DLSGTERLHGAPPAVVLARFARRVEREIGITVSVGLSYNKFLAKIASDLDKPRGFSVIGRAE 201 (419)
T ss_pred HhCcceeeccCCeEEE--eccchhhhcCCCHHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHHhhhCCCCeEecCHHH
Confidence 5788899999999998 99999999985 45578999999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCcccccc
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 185 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~e 185 (591)
+.+||+++||++|||||+++.++|. .+||+|++||+.++...|+++||. .|.++|+.++|+|+.+|.+..++|||+.+
T Consensus 202 ~~~~L~~lPl~~L~GiG~~~~~~L~-~~GI~tigdL~~l~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~ksi~~~ 279 (419)
T PRK02794 202 ALAFLAPKPVGIIWGVGPATAARLA-RDGIRTIGDLQRADEADLMRRFGS-MGLRLWRLARGIDDRKVSPDREAKSVSAE 279 (419)
T ss_pred HHHHHhcCChhhhCCCCHHHHHHHH-HhccchHHHHhhCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCccCCCCceeeee
Confidence 9999999999999999999999996 999999999999999999999998 79999999999999999988889999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHHH
Q 007746 186 KSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDT 265 (591)
Q Consensus 186 ~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~da 265 (591)
++|. .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++. +|.. .+++.+++.||+ +.
T Consensus 280 ~tl~--~~~~~~~~l~~~l~~L~~~l~~rL~~----~~~~~~~l~l~l~~~---~~~~----~~~~~~l~~pt~----~~ 342 (419)
T PRK02794 280 TTFE--TDLSDFEDLEPILWRLSEKVSRRLKA----AGLAGRTVTLKLKTA---DFRL----RTRRRTLEDPTQ----LA 342 (419)
T ss_pred EECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCcceEEEEEEEC---CCCc----eEEEEECCCCcC----CH
Confidence 9998 78999999999999999999999997 799999999999974 3332 478888998884 77
Q ss_pred HHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCcccccccccC
Q 007746 266 FNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNG 320 (591)
Q Consensus 266 ~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~LF~~ 320 (591)
..|++.+..+|.+. +.+.+||.|||.+++|.+.. ...|.+||+.
T Consensus 343 ~~l~~~~~~ll~~~---------~~~~~vr~igv~~~~l~~~~--~~~q~~LF~~ 386 (419)
T PRK02794 343 DRIFRTARELLEKE---------TDGTAFRLIGIGVSDLSPAD--EADPPDLLDP 386 (419)
T ss_pred HHHHHHHHHHHHhc---------ccCCCEEEEEEEEecCCCcc--ccccccccCc
Confidence 78888888888754 24678999999999998752 1247889974
No 12
>PRK03348 DNA polymerase IV; Provisional
Probab=100.00 E-value=3.7e-42 Score=375.83 Aligned_cols=263 Identities=26% Similarity=0.316 Sum_probs=233.9
Q ss_pred ccCCCCCCccchhhhhhcCCCCchhh-hcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccc
Q 007746 26 ESKDGNDSKATVKEWLCRCDADHRDK-LLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFS 104 (591)
Q Consensus 26 ~~~~~~~~~ySIDE~fl~lDvt~~~~-l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~ 104 (591)
..+++..++|||||+|+ |+++... .+.....+|++||++|++++||+||||||+||+|||||++++||+|+++++++
T Consensus 94 ~~~sp~VE~~SiDE~fl--D~~~l~~~~~~~~~~~a~~lr~~I~~~~Gl~~SvGIa~nk~lAKlAs~~aKP~G~~vi~~~ 171 (454)
T PRK03348 94 RELSPVVEQLSFDEAFV--EPAELAGASAEEVEAFAERLRARVREETGLPASVGAGSGKQIAKIASGLAKPDGIRVVPPG 171 (454)
T ss_pred HHhCCceEEecCCeEEE--EccccccccCCCHHHHHHHHHHHHHHHHCCCeEEEEcCCHHHHHHhhccCCCCcEEEEEch
Confidence 36788899999999998 6665322 12367899999999999999999999999999999999999999999999999
Q ss_pred cHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCccccc
Q 007746 105 SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGS 184 (591)
Q Consensus 105 ~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~ 184 (591)
++.+||+++||++|||||+++.++|+ .+||+|++||+.++...|.++||...|.+||+.|+|+|+++|.+..++|+|+.
T Consensus 172 ~~~~~L~~LPv~~L~GIG~~t~~~L~-~lGI~TigDLa~l~~~~L~~~fG~~~g~~L~~~a~G~d~~pv~~~~~~ksis~ 250 (454)
T PRK03348 172 EERELLAPLPVRRLWGIGPVTEEKLH-RLGIETIGDLAALSEAEVANLLGATVGPALHRLARGIDDRPVAERAEAKQISA 250 (454)
T ss_pred HHHHHHHhCCccccCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHHCHHHHHHHHHHHcCCCCCCcccCCCCceEEE
Confidence 99999999999999999999999996 99999999999999999999999658999999999999999999888999999
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHH
Q 007746 185 GKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQED 264 (591)
Q Consensus 185 e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~d 264 (591)
+++|. .++.+.+++..+|..|+++|+.||++ .++.+++|+|++++. +|.. .+++.+++++|+ +
T Consensus 251 e~tf~--~~i~~~~~l~~~L~~L~~~l~~rL~~----~g~~~r~v~l~l~~~---d~~~----~srs~~l~~pt~----d 313 (454)
T PRK03348 251 ESTFA--VDLTTRAQLREAIERIAEHAHRRLLK----DGRGARTVTVKLRKS---DFST----LTRSATLPYATD----D 313 (454)
T ss_pred EEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCCccEEEEEEEeC---CCCc----cEEEEECCCCCC----C
Confidence 99998 78999999999999999999999997 699999999999874 3332 578999999985 6
Q ss_pred HHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCcccccccccCCC
Q 007746 265 TFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFNGPD 322 (591)
Q Consensus 265 a~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~LF~~~~ 322 (591)
...|++.+.++|...+ ...+||++||.+++|.+. .|.+||....
T Consensus 314 ~~~L~~la~~ll~~~~---------~~~~vRllgV~~s~l~~~-----~q~~LF~~~~ 357 (454)
T PRK03348 314 AAVLAATARRLLLDPD---------EIGPIRLVGVGFSGLSDV-----RQESLFPELD 357 (454)
T ss_pred HHHHHHHHHHHHHhhc---------cCCCeEEEEEEECCCCcc-----hhhccCCCcc
Confidence 7788888888887643 234899999999999752 5789997543
No 13
>PRK02406 DNA polymerase IV; Validated
Probab=100.00 E-value=2.6e-42 Score=363.65 Aligned_cols=250 Identities=25% Similarity=0.312 Sum_probs=224.4
Q ss_pred ccCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecccc
Q 007746 26 ESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSS 105 (591)
Q Consensus 26 ~~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~ 105 (591)
..+++..+.|||||+|+ |++++.++|+++..+|+.||++|++++|||||||||+||++||||++++||+|++++++++
T Consensus 83 ~~~sp~ve~~siDe~~l--dvt~~~~~~~~~~~la~~i~~~i~~~~gl~~siGia~n~~lAklas~~~Kp~g~~~~~~~~ 160 (343)
T PRK02406 83 RRYTDLIEPLSLDEAYL--DVTDNKLCIGSATLIAQEIRQDIFEELGLTASAGVAPNKFLAKIASDWNKPNGLFVITPEE 160 (343)
T ss_pred HHhCCceEEccCCeEEE--eccCccccCCCHHHHHHHHHHHHHHHHCCCeEEEeccCHHHHHHHhcCCCCCCEEEECHHH
Confidence 35788899999999998 9999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCcccccc
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSG 185 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~e 185 (591)
+.+||+++||++|||||+++.++|. .+||+|++||+.++...|+++||. .|.++|+.++|+|+.+|.+..++|+|+.+
T Consensus 161 ~~~~L~~lpi~~l~giG~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~-~~~~l~~~a~G~d~~~v~~~~~~ksi~~~ 238 (343)
T PRK02406 161 VDAFLATLPVEKIPGVGKVTAEKLH-ALGIYTCADLQKYDLAELIRHFGK-FGRRLYERARGIDERPVKPDRERKSVGVE 238 (343)
T ss_pred HHHHHHcCCcchhcCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhCCCCCCccccCCCCcceeee
Confidence 9999999999999999999999996 999999999999999999999997 79999999999999999988889999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC--ceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHH
Q 007746 186 KSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNK--RIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQE 263 (591)
Q Consensus 186 ~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~--~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~ 263 (591)
++|+ .++.+.+++..+|..|+++|+.||++ ++ +.+++|+|++++. ++.. .+++.+ ..++ +
T Consensus 239 ~~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~~~~~~l~l~l~~~---~~~~----~~~~~~-~~~~----~ 300 (343)
T PRK02406 239 RTFA--EDLYDLEACLAELPRLAEKLERRLER----AKPDKRIKTVGVKLKFA---DFQQ----TTKEHT-ADPL----D 300 (343)
T ss_pred eeCC--CCCCCHHHHHHHHHHHHHHHHHHHHh----cCCCccceeEEEEEEeC---CCCe----EEEecC-CCCC----C
Confidence 9998 78999999999999999999999997 68 9999999999974 3332 344554 4445 3
Q ss_pred HHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeec
Q 007746 264 DTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 307 (591)
Q Consensus 264 da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~ 307 (591)
+...|...+++++... + +.+||.|||++++|.+.
T Consensus 301 ~~~~l~~~~~~L~~~~---------~-~~~vr~lgv~~~~l~~~ 334 (343)
T PRK02406 301 KADLIELLAQALLRRL---------G-GRGVRLLGVGVTLLEPQ 334 (343)
T ss_pred cHHHHHHHHHHHHhhC---------c-CCCEEEEEEEEecCCcC
Confidence 5555666677666532 2 67899999999999865
No 14
>PRK01810 DNA polymerase IV; Validated
Probab=100.00 E-value=4.4e-42 Score=369.81 Aligned_cols=261 Identities=25% Similarity=0.348 Sum_probs=233.7
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccH
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSV 106 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v 106 (591)
.+++..+.|||||+|+ |+|++.+++ ++..+|++||++|++++|||||||||+||++||||++++||+|++++.++++
T Consensus 96 ~~sp~ve~~siDe~~l--dvt~~~~~~-~~~~~a~~i~~~i~~~~gl~~svGia~n~~lAklas~~~Kp~g~~vi~~~~~ 172 (407)
T PRK01810 96 EFTPLVQPVSIDEGYL--DITDCYALG-SPLEIAKMIQQRLLTELQLPCSIGIAPNKFLAKMASDMKKPLGITVLRKRDV 172 (407)
T ss_pred HhCCceEEecCCeEEE--eccCccccC-CHHHHHHHHHHHHHHHHCCceEEEEcCCHHHHHHHhcCCCCCCEEEECHHHH
Confidence 4678889999999998 999987765 5778999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccC--Cccccc
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLL--PKSHGS 184 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~--~KSIs~ 184 (591)
..||+++||++|||||+++.++|. .+||+|+|||+.+|...|+++||+ .|.++|+.|+|+|+.+|.+... +|||+.
T Consensus 173 ~~~L~~lpv~~l~giG~~~~~~L~-~~Gi~tigdL~~~~~~~L~~rfG~-~g~~l~~~a~G~d~~~v~~~~~~~~ksi~~ 250 (407)
T PRK01810 173 PEMLWPLPVGEMHGIGEKTAEKLK-DIGIQTIGDLAKADEHILRAKLGI-NGVRLQRRANGIDDRPVDPEAIYQFKSVGN 250 (407)
T ss_pred HHHHHhCCHhhcCCcCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHHhH-HHHHHHHHhcCCCCCCCCCCCCCCCceecc
Confidence 999999999999999999999996 999999999999999999999998 7999999999999999986543 699999
Q ss_pred ccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHH
Q 007746 185 GKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQED 264 (591)
Q Consensus 185 e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~d 264 (591)
+++|+ .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++. ++.. .+++.+++.||+ +
T Consensus 251 ~~~~~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~lr~~---~~~~----~~~~~~l~~pt~----~ 313 (407)
T PRK01810 251 STTLS--HDMDEEKELLDVLRRLSKSVSKRLQK----KTVVSYNVQIMIRYH---DRRT----ITRSKTLKNPIW----E 313 (407)
T ss_pred eEECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCccceeEEEEEEC---CCCc----eEEEEECCCCCC----C
Confidence 99999 78999999999999999999999997 799999999999985 3332 468888999984 7
Q ss_pred HHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecCCCccccccccc
Q 007746 265 TFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVLSGTCSIMKYFN 319 (591)
Q Consensus 265 a~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~~g~~sq~~LF~ 319 (591)
...|++.+..+|.+.+ .+.+||++||++++|.+... ...|.+||+
T Consensus 314 ~~~l~~~~~~ll~~~~---------~~~~vr~lgv~~~~l~~~~~-~~~q~~Lf~ 358 (407)
T PRK01810 314 KRDIFQAASRLFKQHW---------NGDPVRLLGVTATDLEWKTE-AVKQLDLFS 358 (407)
T ss_pred HHHHHHHHHHHHHhcc---------CCCCEEEEEEEEecCccccc-ccccccccc
Confidence 7789999998887643 35689999999999987521 245789997
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=1.8e-41 Score=354.50 Aligned_cols=248 Identities=30% Similarity=0.412 Sum_probs=229.4
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccH
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSV 106 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v 106 (591)
.+++..+.|||||+|+ |++++.++|+++..+|++||++|++++||+||||||+|+++||||++++||+|+++++++++
T Consensus 87 ~~~~~ve~~s~De~~l--dv~~~~~~~~~~~~la~~ir~~i~~~~g~~~siGia~n~~lAklaa~~~kp~g~~i~~~~~~ 164 (334)
T cd03586 87 EYTPLVEPLSIDEAYL--DVTDYVRLFGSATEIAKEIRARIREETGLTASAGIAPNKFLAKIASDLNKPNGLTVIPPEDV 164 (334)
T ss_pred HcCCceEEecccceeE--ccccccccCCCHHHHHHHHHHHHHHHHCCceEEEEhhcHHHHHHHhcCCCCCcEEEECHHHH
Confidence 5778899999999998 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCccccccc
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHGSGK 186 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs~e~ 186 (591)
.+||+++||+++||||+++.++|. .+||+|++||++++...|.++||. .|.++|+.++|+++.+|.+..++|+|+.++
T Consensus 165 ~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~~~G~~~~~v~~~~~~ks~~~~~ 242 (334)
T cd03586 165 EEFLAPLPVRKIPGVGKVTAEKLK-ELGIKTIGDLAKLDVELLKKLFGK-SGRRLYELARGIDNRPVEPDRERKSIGVER 242 (334)
T ss_pred HHHHhcCCchhhCCcCHHHHHHHH-HcCCcCHHHHHcCCHHHHHHHHhH-HHHHHHHHhCCCCCCCCCCCCCCCeeeeeE
Confidence 999999999999999999999996 999999999999999999999998 799999999999999999888899999999
Q ss_pred ccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHHHH
Q 007746 187 SFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDTF 266 (591)
Q Consensus 187 tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~da~ 266 (591)
+|+ .++.+.+++..+|..|+++|+.||+. .++.+++|+|++++.+ +. ..+++.+++.+|+ +..
T Consensus 243 ~~~--~~~~~~~~l~~~l~~l~~~l~~rL~~----~~~~~~~l~l~l~~~~---~~----~~~~~~~l~~~t~----~~~ 305 (334)
T cd03586 243 TFS--EDLTDPEELLEELLELAEELAERLRK----RGLKGRTVTVKLKYAD---FS----TRTRSRTLPEPTD----DAE 305 (334)
T ss_pred ECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----CCCCeEEEEEEEEECC---CC----eEEEEEECCCCCC----CHH
Confidence 998 78999999999999999999999998 6999999999999742 22 2578888988884 778
Q ss_pred HHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCC
Q 007746 267 NLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKI 304 (591)
Q Consensus 267 ~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L 304 (591)
.|++.+..+|.+++ .+.+||+|||++++|
T Consensus 306 ~l~~~~~~~l~~~~---------~~~~vr~igv~~~~l 334 (334)
T cd03586 306 DIYELALELLEELL---------DGRPIRLLGVRLSGL 334 (334)
T ss_pred HHHHHHHHHHHhcc---------CCCCEEEEEEEeecC
Confidence 89998888887653 247899999999876
No 16
>KOG2095 consensus DNA polymerase iota/DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=4e-41 Score=368.53 Aligned_cols=232 Identities=50% Similarity=0.709 Sum_probs=222.3
Q ss_pred CCCCCCCCCCCccchhhhhcceeccccCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEec
Q 007746 1 MLAETPPESLDEVDEEALKSHILGLESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIA 80 (591)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA 80 (591)
||++-||.......+.++..|..+++.++|.+....+-+||..+|+.+++.++..++.+|++||++|+++||||||+|||
T Consensus 144 ~~~~~~p~~~~~~~~s~~~~~~~~~~~e~~~~~ee~~~~~~~~~d~~~~d~~L~iGa~Iv~EiR~~i~~elg~tCSAGIa 223 (656)
T KOG2095|consen 144 MLLEEPPYGLIYGLPSALPNTREATNSENPLMREEIVSLWIENDDFDWDDVRLLIGAQIVKEIRDAIKLELGYTCSAGIA 223 (656)
T ss_pred hhhhccchhcccCCccccchhhhhhhhccccchhhHhhhhhhccccCchhhhhHHHHHHHHHHHHHHHHHhCceeecccc
Confidence 68888888888888888999999998899999999999999999999888888899999999999999999999999999
Q ss_pred CCHHHHHHhccCCCCCCEEEeccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHH
Q 007746 81 HNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTW 160 (591)
Q Consensus 81 ~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~ 160 (591)
+||+|||||+.++|||.||+|+...+++||..|||.++|++|+++++.|.+.|||.++|||+++++.+|++.||.++|.|
T Consensus 224 ~NKmLAKLvsg~nKPnqQTil~~~~v~~ll~slpi~k~~~lGGk~G~~lie~LGi~~vgdl~~fse~~L~~~fg~~~g~~ 303 (656)
T KOG2095|consen 224 HNKMLAKLVSGRNKPNQQTILPNTYVQDLLDSLPITKIRTLGGKLGEELIEVLGIDSVGDLQQFSETQLQKKFGEKNGTW 303 (656)
T ss_pred ccHHHHHHHhccCCCCcceecchHHHHHHHHhCCCceeeeccchHHHHHHHHhCCchHHHHHhcCHHHHHHhhCcchhHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999989999
Q ss_pred HHHHHcCCCCCccccccCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEE
Q 007746 161 LWNIARGISGEEVQARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLH 232 (591)
Q Consensus 161 L~~~arGid~~~V~~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ 232 (591)
||..|+|+|.++|.++..+|+|+++++|++...+.+.+++..||..++++++.||..+...+.+.+.+++++
T Consensus 304 l~~la~Gid~s~V~pr~~pkSig~~K~Fpg~~~~~~~~~l~~wl~~la~el~~Rl~~d~~en~r~as~l~~~ 375 (656)
T KOG2095|consen 304 LRNLARGIDNSPVRPRGLPKSIGSEKNFPGKRSRKSLEELQRWLNQLAEELAERLGKDRNENKRRASTLVVS 375 (656)
T ss_pred HHHHhcccCCCccccCCCCcchhhhhcCCCccccccHHHHHHHHHHHHHHHHHHHHhhhhhhccccceEEee
Confidence 999999999999999999999999999998788999999999999999999999999888889999999999
No 17
>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=5.5e-41 Score=353.71 Aligned_cols=251 Identities=24% Similarity=0.340 Sum_probs=221.8
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCC----CEEEec
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPA----QQTTVP 102 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~----G~~vl~ 102 (591)
.+++..+.+||||+|+ |++++.+ |+++..+|++||++|++++|||||||||+||++||||++++||+ |+++++
T Consensus 88 ~~~~~ve~~s~De~~l--dvt~~~~-~~~~~~la~~i~~~i~~~~gl~~s~Gia~~~~lAklas~~~kp~~~~~g~~~~~ 164 (344)
T cd01700 88 RFSPDVEVYSIDESFL--DLTGSLR-FGDLEELARKIRRRILQETGIPVTVGIGPTKTLAKLANDLAKKKNPYGGVVDLT 164 (344)
T ss_pred hcCCcceEeecchhhc--cCcCCCC-CCCHHHHHHHHHHHHHHHhCCceEEEecCCHHHHHHHHHHhcCCCCCCeEEEec
Confidence 5788899999999998 9999988 99999999999999999999999999999999999999999984 888887
Q ss_pred cccHH-hhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCcccccc-CCc
Q 007746 103 FSSVK-GLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARL-LPK 180 (591)
Q Consensus 103 ~~~v~-~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~-~~K 180 (591)
+++.. +||+++||++|||||+++.++|. .+||+|+|||++++...|.++||. .|.++|+.++|+|+.+|.+.. ++|
T Consensus 165 ~~~~~~~~l~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dL~~~~~~~L~~rfG~-~~~~l~~~a~G~d~~~v~~~~~~~k 242 (344)
T cd01700 165 DEEVRDKLLKILPVGDVWGIGRRTAKKLN-AMGIHTAGDLAQADPDLLRKKFGV-VGERLVRELNGIDCLPLEEYPPPKK 242 (344)
T ss_pred ChhHHHHHhccCChhhcCccCHHHHHHHH-HcCCCcHHHHhcCCHHHHHHHHHH-HHHHHHHHhCCCCCCcCCCCCCCCc
Confidence 76664 99999999999999999999996 999999999999999999999997 799999999999999997654 459
Q ss_pred ccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchh
Q 007746 181 SHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAK 260 (591)
Q Consensus 181 SIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~ 260 (591)
+|+.+.+|. .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++. +|.......+.+.+++.+|
T Consensus 243 s~~~~~~~~--~~~~~~~~l~~~l~~L~~~l~~~L~~----~~~~~~~l~l~l~~~---~~~~~~~~~~~~~~~~~~t-- 311 (344)
T cd01700 243 SIGSSRSFG--RDVTDLDELKQALAEYAERAAEKLRR----QKSVARTISVFIGTS---GFSRQPKYYSATNTLPYPT-- 311 (344)
T ss_pred EEEEeeEcC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCcccEEEEEEEcC---CCCCCCCccccccccCCcc--
Confidence 999999998 78999999999999999999999997 799999999999985 3333222233445677788
Q ss_pred hHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecC
Q 007746 261 IQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASK 303 (591)
Q Consensus 261 i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~ 303 (591)
++...|++.++.+|..++ ..+.+||+|||++++
T Consensus 312 --~~~~~l~~~~~~ll~~~~--------~~~~~iR~iGV~~~~ 344 (344)
T cd01700 312 --NDTREIVKAALRLLYAIY--------RPGYAYRKAGVMLSD 344 (344)
T ss_pred --hhHHHHHHHHHHHHHHHh--------CCCCcEEEEEEEeeC
Confidence 477889999998888765 236789999999875
No 18
>PRK03352 DNA polymerase IV; Validated
Probab=100.00 E-value=5.6e-41 Score=353.90 Aligned_cols=247 Identities=25% Similarity=0.306 Sum_probs=223.3
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccH
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSV 106 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v 106 (591)
.+++..+.+||||+|+ |+++. ++..+|+.||++|++++|||||||||+||++||||++.+||+|++++.++++
T Consensus 98 ~~s~~ve~~siDe~~l--d~t~~-----~~~~la~~ir~~i~~~~gl~~siGia~nk~lAklaa~~~Kp~g~~~~~~~~~ 170 (346)
T PRK03352 98 DLGVPVEVWGWDEAFL--GVDTD-----DPEALAEEIRAAVLERTGLSCSVGIGDNKLRAKIATGFAKPAGVFRLTDANW 170 (346)
T ss_pred HhCCceEEecCccEEE--eCCCC-----CHHHHHHHHHHHHHHHHCCCEEEeecCCHHHHHHHHhhcCCCcEEEECHHHH
Confidence 4778899999999998 88874 6789999999999999999999999999999999999999999999999999
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccc-cCCcccccc
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQAR-LLPKSHGSG 185 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~-~~~KSIs~e 185 (591)
.+||+++||++|||||+++.++|. .+||+|++||+.++...|.++||...|.+||+.++|+|.+++... ..+|+++.+
T Consensus 171 ~~~L~~lpl~~l~gig~~~~~~L~-~~Gi~ti~dl~~l~~~~L~~~fG~~~~~~l~~~a~G~d~~~~~~~~~~~ksi~~~ 249 (346)
T PRK03352 171 MAVMGDRPTDALWGVGPKTAKRLA-ALGITTVADLAAADPAELAATFGPTTGPWLLLLARGGGDTEVSAEPWVPRSRSRE 249 (346)
T ss_pred HHHHhcCCHHHcCCCCHHHHHHHH-HcCCccHHHHhcCCHHHHHHHhChHHHHHHHHHhCCCCCCCCCCCCCCCceEEEE
Confidence 999999999999999999999996 999999999999999999999997679999999999999998765 357999999
Q ss_pred cccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhHHHH
Q 007746 186 KSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQEDT 265 (591)
Q Consensus 186 ~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~~da 265 (591)
++|+ .++.+.+++..+|..|+++|+.||++ +++.+++|+|++++. +|.. .+++.+++.||+ +.
T Consensus 250 ~tf~--~~~~~~~~l~~~l~~L~~~l~~rLr~----~~~~~~~l~l~l~~~---~~~~----~~~~~~l~~pt~----d~ 312 (346)
T PRK03352 250 VTFP--QDLTDRAEVESAVRELARRVLDEVVA----EGRPVTRVAVKVRTA---TFYT----RTKIRKLPEPTT----DP 312 (346)
T ss_pred EECC--CCCCCHHHHHHHHHHHHHHHHHHHHH----cCCccceEEEEEEeC---CCce----eEEEEECCCCcC----CH
Confidence 9998 78999999999999999999999997 799999999999985 3322 477888998884 77
Q ss_pred HHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeec
Q 007746 266 FNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 307 (591)
Q Consensus 266 ~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~ 307 (591)
..|++.+..+|.+. +.+.+||.|||++.+|.+.
T Consensus 313 ~~l~~~~~~ll~~~---------~~~~~vr~igl~~~~~~~~ 345 (346)
T PRK03352 313 DVIEAAALDVLDRF---------ELDRPVRLLGVRLELAMPD 345 (346)
T ss_pred HHHHHHHHHHHHhc---------cCCCCEEEEEEEEeccCCC
Confidence 78888888888753 2356899999999999763
No 19
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.1e-38 Score=338.56 Aligned_cols=254 Identities=29% Similarity=0.390 Sum_probs=229.6
Q ss_pred cCCCCCCccchhhhhhcCCCCchhhhcc--hHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccc
Q 007746 27 SKDGNDSKATVKEWLCRCDADHRDKLLA--CGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFS 104 (591)
Q Consensus 27 ~~~~~~~~ySIDE~fl~lDvt~~~~l~~--~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~ 104 (591)
.+.+..+++||||+|+ |+|+.++.++ .+..+|.+||..|+.++|||||+|||+||++||||++++||+|++++.++
T Consensus 90 ~~~~~ve~lSIDE~~l--dvt~~~~~~g~~~~~~~a~~ir~~i~~~~~l~~s~Gi~~nk~laKiAs~~~kp~gi~~~~~~ 167 (354)
T COG0389 90 RYTPLVEPLSIDEAFL--DLTDALRLLGLADAPRIALEIRFGILLELGLTASVGISDNKFLAKIASDLNKPDGITVIEPE 167 (354)
T ss_pred hccccceeeeccceee--ecccccccCCcccHHHHHHHHHHHHHHhhCCEEEEEecCcHHHHHHHhcccCCCCEEEECHH
Confidence 4567789999999998 8999988888 68999999999999999999999999999999999999999999999999
Q ss_pred cHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCC-cccc
Q 007746 105 SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLP-KSHG 183 (591)
Q Consensus 105 ~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~-KSIs 183 (591)
++.+||++|||.++||||+.++++|. .+||+|++||+..+.+.|.++||. .|.+||+.++|+|.++|.....+ ||++
T Consensus 168 ~~~~~l~~Lpv~~~~GvG~~~~~~l~-~~Gi~ti~dl~~~~~~~L~~~~g~-~~~~l~~~a~Gid~~~v~~~~~~~ksi~ 245 (354)
T COG0389 168 EVPALLWQLPVLEFWGVGKVTAEKLR-RLGISTIGDLAETDLDALKKRFGK-LGERLYRLARGIDNRPVREQALRAKSIG 245 (354)
T ss_pred HHHHHHhcCChhhhCCCCHHHHHHHH-HcCChhHHHHHhcCHHHHHHHHhH-hHHHHHHHhcCCCccccccccccCcccc
Confidence 99999999999999999999999996 999999999999999999999998 68999999999999999998877 9999
Q ss_pred cccccCCCCCCCCHHHHHHHHHH-HHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhhH
Q 007746 184 SGKSFPGPRALKTVASVQHWLNQ-LCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKIQ 262 (591)
Q Consensus 184 ~e~tF~~~~~i~~~eel~~~L~~-LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i~ 262 (591)
.+.+|. .++.+.+++...|.. |+++++.||+. .+..+++|++++++. +|.. .+++.+|+.|++
T Consensus 246 ~~~t~~--~d~~~~~~~~~~l~~~l~e~~~~rl~~----~~~~~r~v~~~~~~~---df~~----~t~~~~l~~p~~--- 309 (354)
T COG0389 246 AESTFE--EDLTDAEELIERLRARLGEEVVSRLRK----SGRHGRTVSVKLKTA---DFPT----NTRSRKLAQPTS--- 309 (354)
T ss_pred ceeecc--ccccCHHHHHHHHHHHHHHHHHHHHHH----hCCCceEEEEEEEec---CCCc----ceeecccCCcCC---
Confidence 999999 799999988888888 99999999997 688899999999985 4533 578888988884
Q ss_pred HHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeec
Q 007746 263 EDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPV 307 (591)
Q Consensus 263 ~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~ 307 (591)
+..+++.+++.+|...+. .+.+.++|++||++++|.+.
T Consensus 310 -~~~~i~~~~~~l~~~~~~------~~~~~~~rl~gv~~~~~~~~ 347 (354)
T COG0389 310 -DPIEIYAAALPLLPPLLF------RGRGRRIRLLGVSGPELIDS 347 (354)
T ss_pred -CHHHHHHHHHHHHHHhhc------cCCCceEEEEEEEecCcccc
Confidence 567788888888876542 23367999999999999875
No 20
>KOG2094 consensus Predicted DNA damage inducible protein [Replication, recombination and repair]
Probab=100.00 E-value=9.4e-37 Score=313.75 Aligned_cols=252 Identities=24% Similarity=0.306 Sum_probs=215.2
Q ss_pred cccCCCCCCccchhhhhhcCCCCchhhhc--c-----hHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCC
Q 007746 25 LESKDGNDSKATVKEWLCRCDADHRDKLL--A-----CGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQ 97 (591)
Q Consensus 25 ~~~~~~~~~~ySIDE~fl~lDvt~~~~l~--~-----~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G 97 (591)
+.+||++.-+.||||+|+ |+|...+.- | +...++++||.+|+++||+|||+|||+|++|||++|+++||||
T Consensus 187 ~~~YDsn~~~~SlDEayl--nlT~~l~~~~~g~l~~nG~~evveeiR~rV~qeTglT~SaGIAaN~lLAKicSd~nKPNg 264 (490)
T KOG2094|consen 187 LAQYDSNFCAMSLDEAYL--NLTSHLRERELGFLVENGITEVVEEIRFRVEQETGLTCSAGIAANKLLAKICSDKNKPNG 264 (490)
T ss_pred HHHcCCccccchHHHHHH--hHHHHHHHhhcchhhhccHHHHHHHHHHHHHHhcCceeeccccHhHHHHHHhccccCCCC
Confidence 458999999999999998 788765432 3 2568999999999999999999999999999999999999999
Q ss_pred EEEeccc--cHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCcccc
Q 007746 98 QTTVPFS--SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQA 175 (591)
Q Consensus 98 ~~vl~~~--~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~ 175 (591)
|++|+++ .+.+||..|||+++-|||+.++..|. .|||.||||+.+. ...|--.|.+...+.+.+.+.|...++...
T Consensus 265 Qf~i~~dr~aim~F~kdLPvRkV~GIGrV~E~qLk-al~IkTcgdm~~k-~~ll~~lFsp~S~~~fLr~slG~g~t~~~~ 342 (490)
T KOG2094|consen 265 QFVIPNDRIAIMKFMKDLPVRKVSGIGRVTEQQLK-ALGIKTCGDMQQK-LVLLSLLFSPKSFQNFLRCSLGLGTTILDE 342 (490)
T ss_pred ceEecccHHHHHHHHhcCCcccccchhHHHHHHHH-hcCceeHHHHHHh-hhHHHHHhCchhHHHHHHHhhcCCCCcCcc
Confidence 9999776 48899999999999999999999996 9999999999875 456778899887888999999999999888
Q ss_pred ccCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCC
Q 007746 176 RLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLR 255 (591)
Q Consensus 176 ~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~ 255 (591)
...+|||++++||. ++.+...+...+.+||..|++-|+. .|++++||||++++. .|..+ +|+.++.
T Consensus 343 ~~eRKsis~ErTFs---~~sd~~il~~k~qel~~~lsedlqK----~glv~rtvtiKlK~s---sFev~----Tr~~t~s 408 (490)
T KOG2094|consen 343 DGERKSISSERTFS---STSDPSILYSKLQELCQMLSEDLQK----EGLVGRTVTIKLKTS---SFEVH----TRQKTIS 408 (490)
T ss_pred ccccccccceeeec---ccCCHHHHHHHHHHHHHHHHHHHHh----cCcccceEEEEEecc---ceeee----eccCchh
Confidence 88899999999998 6899999998888888887777775 799999999999974 45442 4544433
Q ss_pred CcchhhHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCeecC
Q 007746 256 YGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIVPVL 308 (591)
Q Consensus 256 ~~T~~i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~~~~ 308 (591)
.- -....+|++-|+++|...+ +..||++||.+++|....
T Consensus 409 ~v----v~S~edi~k~aleLLk~e~----------~~~iRLlGvR~sqlv~ee 447 (490)
T KOG2094|consen 409 QV----VHSEEDILKPALELLKQEY----------PMTIRLLGVRASQLVSEE 447 (490)
T ss_pred hh----hccHHHHHHHHHHHHHhhc----------CceEeeeeeeHhhccchh
Confidence 21 1355678888999888654 579999999999998763
No 21
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=100.00 E-value=2e-36 Score=336.82 Aligned_cols=262 Identities=21% Similarity=0.262 Sum_probs=224.9
Q ss_pred cccCCCCCCccchhhhhhcCCCCchhhhcc-hHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEecc
Q 007746 25 LESKDGNDSKATVKEWLCRCDADHRDKLLA-CGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPF 103 (591)
Q Consensus 25 ~~~~~~~~~~ySIDE~fl~lDvt~~~~l~~-~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~ 103 (591)
|.+|.-+.+..|+||+|+ |++.....+. .+..+|..||++|++.|||+||||||.|++||+||++.||||||+++.+
T Consensus 462 lasytl~I~aVSCDEa~v--d~s~~~~~~~~tp~~la~~IRqEI~e~TgC~aS~Gig~t~LLARlATr~AKP~Gq~~l~a 539 (1016)
T KOG2093|consen 462 LASYTLNIEAVSCDEAFV--DVSDLSDEENETPAVLAEHIRQEILEKTGCPASAGIGGTMLLARLATRVAKPNGQFYLSA 539 (1016)
T ss_pred HHhhccceeeecchhhhh--hhhhhhhhhccCHHHHHHHHHHHHHhccCCceeeccchHHHHHHHHHhhcCCCceeeecH
Confidence 345666677899999999 7775444443 6789999999999999999999999999999999999999999999999
Q ss_pred ccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccccccCCcccc
Q 007746 104 SSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQARLLPKSHG 183 (591)
Q Consensus 104 ~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~~~~~~KSIs 183 (591)
+.+.+||.+++|.+|||||..|..+|. .+||+|||||+.++...|++.||++.|..+|+.|||+|++|+.....|||++
T Consensus 540 ~~veeFis~~~v~~LPGVG~sm~~kL~-s~~i~tCgdLq~~T~~kl~k~~G~Klgq~i~~~CrG~Dd~P~~~~~~RKSvS 618 (1016)
T KOG2093|consen 540 EKVEEFISQLKVDDLPGVGSSMKSKLV-SQFIQTCGDLQLITLIKLRKVFGPKLGQKIYRGCRGIDDDPRSIEQVRKSVS 618 (1016)
T ss_pred HHHHHHhhhcccccCCCccHHHHHHHH-HhccchhHHHHHHHHHHHHhhhcccHHHHHHHhcCCCcCChHHHhhhhccee
Confidence 999999999999999999999999996 9999999999999999999999999999999999999999988777899999
Q ss_pred cccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecc------cCCCCCCC--CcCceeeeCC
Q 007746 184 SGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFK------SSDSDSRK--KFPSKSCPLR 255 (591)
Q Consensus 184 ~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~------~~~f~s~~--~~~SrS~~L~ 255 (591)
.+.+|+ .+++++.++...|..++++|-+||.+ -++.++.++|+++.+. ++.|.+++ ..++|++.|.
T Consensus 619 ~dIN~G--IRFtn~~ev~~fl~~~~eEl~rkL~e----i~k~~~sitLKlMvR~~~APietaK~mGhGiCD~~~rs~~l~ 692 (1016)
T KOG2093|consen 619 ADINYG--IRFTNIKEVEQFLCLLSEELRRKLLE----ISKTASSITLKLMVRTAKAPIETAKYMGHGICDDFVRSSKLR 692 (1016)
T ss_pred eeeecc--eeeccHHHHHHHHHHHHHHHHHHHHH----hhccccchhHHHHhhcCCCCCccccccceeeccchhhhhhcc
Confidence 999999 89999999999999999999999987 6888999999986531 13344443 3468999999
Q ss_pred CcchhhHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEec-CCeec
Q 007746 256 YGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSAS-KIVPV 307 (591)
Q Consensus 256 ~~T~~i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls-~L~~~ 307 (591)
++|+ ....|...+++|+... -.+...+|++||.+. +|.+.
T Consensus 693 ~~Td----~~~iItt~~~~L~~t~--------~~~~~elRG~gi~~ntkL~~~ 733 (1016)
T KOG2093|consen 693 EPTD----CNRIITTEVLRLYETN--------SEPPSELRGLGIHSNTKLMDV 733 (1016)
T ss_pred Cccc----cccchHHHHHHHHHhc--------CCChHHhccchhhcccccccc
Confidence 9995 4444555566665532 134667899999995 88765
No 22
>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=4.5e-34 Score=298.57 Aligned_cols=244 Identities=18% Similarity=0.085 Sum_probs=209.2
Q ss_pred cccCCCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccc
Q 007746 25 LESKDGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFS 104 (591)
Q Consensus 25 ~~~~~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~ 104 (591)
+.++++..+.+||||+|+ |++++.++|+++..+|+.||+.|. ++|++||||||+||++||||++.+||+|++.+...
T Consensus 85 l~~~s~~ve~~s~de~~l--dvs~~~~~~~~~~~~a~~i~~~~~-~~gl~~siGia~n~~~Aklas~~~kp~~~~~~~~~ 161 (335)
T cd03468 85 LLRFTPLVALDGPDGLLL--DVTGCLHLFGGEDALAASLRAALA-TLGLSARAGIADTPGAAWLLARAGGGRGVLRREAL 161 (335)
T ss_pred HHhcCCccccCCCCeEEE--EcccchhhcCCHHHHHHHHHHHHH-HcCCeEEEEecCCHHHHHHHhccCCCCccCCchHH
Confidence 346888899999999998 999999999999999999999995 78999999999999999999999999999877666
Q ss_pred cHHh-hcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCCCCCccc--cccCCcc
Q 007746 105 SVKG-LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGISGEEVQ--ARLLPKS 181 (591)
Q Consensus 105 ~v~~-fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGid~~~V~--~~~~~KS 181 (591)
.... ||+++|| ++||||+++.++|. .+||+|++||++++...|.++||. .|.++|+.++|+|+.++. ....+++
T Consensus 162 ~~~~~~l~~lp~-~~~gig~~~~~~L~-~~Gi~t~~dl~~~~~~~l~~rfG~-~~~~l~~~~~G~d~~~~~~~~~~~~~~ 238 (335)
T cd03468 162 AAALVLLAPLPV-AALRLPPETVELLA-RLGLRTLGDLAALPRAELARRFGL-ALLLRLDQAYGRDPEPLLFSPPPPAFD 238 (335)
T ss_pred HHHhhccCCCCh-hHhCCCHHHHHHHH-HhCcccHHHHHhCChHHHHhhcCH-HHHHHHHHHCCCCCCCCCCCCCCCChh
Confidence 6554 8999999 59999999999996 999999999999999999999998 699999999999999994 4556799
Q ss_pred cccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcCceeeeCCCcchhh
Q 007746 182 HGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFPSKSCPLRYGTAKI 261 (591)
Q Consensus 182 Is~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~SrS~~L~~~T~~i 261 (591)
++.+.+|+ .+..+.+ ...+..|+++++.||+. ++..+++|+|++++. ++.. .+.+.++..++.
T Consensus 239 ~~~~~~~~--~~~~~~~--~~~l~~l~~~l~~~L~~----~~~~~~~l~l~l~~~---~~~~----~~~~~~~~~~~~-- 301 (335)
T cd03468 239 FRLELQLE--EPIARGL--LFPLRRLLEQLCAFLAL----RGLGARRLSLTLFRE---DGRV----TRVLVGLARPSR-- 301 (335)
T ss_pred hhhhcCCC--CCcchhH--HHHHHHHHHHHHHHHHH----cCCeeeEEEEEEEEE---CCce----EEEEEeccCCcc--
Confidence 99999998 5666654 88999999999999997 799999999999974 2322 356777777774
Q ss_pred HHHHHHHHHHHHHHHhhhccccccCCCCCC---cceeEEEEEec
Q 007746 262 QEDTFNLFQAGLREFLGSFGVKTQGSHYSG---WRITALSVSAS 302 (591)
Q Consensus 262 ~~da~~L~~aal~ll~~~~~~~~~~~~~~g---~~iR~lGVsls 302 (591)
+...|++.+..+|.+. ..+ .+++.++|++.
T Consensus 302 --~~~~l~~l~~~~l~~~---------~~~~~~~~v~~~~v~~~ 334 (335)
T cd03468 302 --DDLPLLRLLRERLERL---------ALPRGIAPVRLLALTAE 334 (335)
T ss_pred --CHHHHHHHHHhhhhcc---------CCCCCeeeEEEEEeecc
Confidence 5555777777666542 234 68999999864
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=99.44 E-value=3.7e-13 Score=120.72 Aligned_cols=125 Identities=30% Similarity=0.413 Sum_probs=91.6
Q ss_pred CCccc-cccCCcccccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcCceeeEEEEEEeecccCCCCCCCCcC
Q 007746 170 GEEVQ-ARLLPKSHGSGKSFPGPRALKTVASVQHWLNQLCEELSERLCSDLEQNKRIAHTLTLHASAFKSSDSDSRKKFP 248 (591)
Q Consensus 170 ~~~V~-~~~~~KSIs~e~tF~~~~~i~~~eel~~~L~~LaeeLa~RLr~~l~~~~~~a~tLtL~ir~~~~~~f~s~~~~~ 248 (591)
++||. +...+|||+++++|+ .++.+.+++..+|..|+++|+.||++ +++.|++|+|+++|.+ +.. ....
T Consensus 1 ~~pV~~~~~~~ksi~~~~t~~--~~~~~~~~i~~~l~~l~~~l~~rL~~----~~~~~~~i~l~l~~~~---~~~-~~~~ 70 (127)
T PF11799_consen 1 DEPVQQPRPPPKSIGSERTFP--EPISDREEIEEWLRELAEELAERLRE----RGLAARTITLKLRYSD---FGR-CSSR 70 (127)
T ss_dssp ------SCSS-SEEEEEEEEC--EEESSHHHHHHHHHHHHHHHHHHHHH----CTEEEEEEEEEEEETT---SCS-CEEE
T ss_pred CCCCCCCCCCCCEEEEEEECC--CCCCCHHHHHHHHHHHHHHHHHHHHh----hCcCCceEEEEEEecC---Ccc-ccee
Confidence 46787 778899999999998 68999999999999999999999997 7999999999999853 321 1135
Q ss_pred ceeeeCCCcchhhHHHHHHHHHHHHHHHhhhccccccCCCCCCcceeEEEEEecCCe-ecCCCcccccccc
Q 007746 249 SKSCPLRYGTAKIQEDTFNLFQAGLREFLGSFGVKTQGSHYSGWRITALSVSASKIV-PVLSGTCSIMKYF 318 (591)
Q Consensus 249 SrS~~L~~~T~~i~~da~~L~~aal~ll~~~~~~~~~~~~~~g~~iR~lGVsls~L~-~~~~g~~sq~~LF 318 (591)
+++++++.|++ ++..|++++..+|.+... ..+++||+|||++++|. +. ...|.+||
T Consensus 71 ~~~~~l~~p~~----~~~~l~~~~~~l~~~~~~-------~~~~~vr~igv~~~~l~~~~---~~~q~~lF 127 (127)
T PF11799_consen 71 SRSIRLPFPTN----DADELLKAARELLERLLY-------DPGFPVRLIGVSASDLIEPA---GQRQLDLF 127 (127)
T ss_dssp EEEEEECCCEH----CHHHHHHHHHHHHHHHHH-------HTTCGEEEEEEEEEEEEEC-------B----
T ss_pred eEEEeccCCcC----CHHHHHHHHHHHHHHHhc-------CCCCCEEEEEEEECCCcCCC---CCcccccC
Confidence 77899999985 567788888888854420 12688999999999999 44 46688888
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=99.08 E-value=3.7e-11 Score=112.76 Aligned_cols=63 Identities=29% Similarity=0.296 Sum_probs=57.0
Q ss_pred cC-CCCCCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhcc
Q 007746 27 SK-DGNDSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLASG 91 (591)
Q Consensus 27 ~~-~~~~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~ 91 (591)
++ ++..+.+||||+|+ |++++.++|+....++++||++|++++||+||+|||+||++||||++
T Consensus 86 ~~~sp~ve~~s~de~~l--dv~~~~~l~~~~~~~~~~l~~~i~~~~gl~~s~Gia~~~~~Aklaa~ 149 (149)
T PF00817_consen 86 RFSSPRVEVYSPDELFL--DVTGSLRLFGGEEALARRLRQAIAEETGLTASIGIAPNPLLAKLAAD 149 (149)
T ss_dssp TTTCSEEEEEETTEEEE--EEHHHHHHHHHHHHHHHHHHHHHHHHHS--EEEEEESSHHHHHHHHH
T ss_pred hcccccceecccccccc--cCCcchhhcchHHHHHHHHHHHHHHHhCCEEEEEEeCCHHHHHHhcC
Confidence 45 56789999999998 99999999999999999999999999999999999999999999984
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=98.49 E-value=5e-08 Score=69.30 Aligned_cols=32 Identities=34% Similarity=0.513 Sum_probs=28.1
Q ss_pred cccHHhhcccCCCCcccCCcHHHHHHHHHhcCC
Q 007746 103 FSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGV 135 (591)
Q Consensus 103 ~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI 135 (591)
|+++.+||+++||+++||||++++++|. .+||
T Consensus 1 pe~v~~~l~~lpi~~~~GIG~kt~~kL~-~~GI 32 (32)
T PF11798_consen 1 PEDVPEFLWPLPIRKFWGIGKKTAKKLN-KLGI 32 (32)
T ss_dssp CHHHHHHHHCSBGGGSTTS-HHHHHHHH-CTT-
T ss_pred ChHHHHHHhcCCHHhhCCccHHHHHHHH-HccC
Confidence 4688999999999999999999999996 9997
No 26
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=98.01 E-value=5.3e-06 Score=87.38 Aligned_cols=80 Identities=20% Similarity=0.218 Sum_probs=66.8
Q ss_pred hcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc--chHHHHHHHHcC---CC--CCccccccCCcc
Q 007746 109 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG---IS--GEEVQARLLPKS 181 (591)
Q Consensus 109 fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~--~~G~~L~~~arG---id--~~~V~~~~~~KS 181 (591)
.|.++||.++||||++++++|. ..||+|++||+.++++.|.+.+|. +.|..++..++| .+ .+++.....+++
T Consensus 2 ~~~~~~l~~l~gIg~~~a~~L~-~~Gi~t~~dl~~~~~~~L~~~~g~~~~~a~~l~~~a~~~~~~~~~~t~~~l~~~~ks 80 (317)
T PRK04301 2 KMKEKDLEDLPGVGPATAEKLR-EAGYDTVEAIAVASPKELSEAAGIGESTAAKIIEAAREAADIGGFETALEVLERRKN 80 (317)
T ss_pred CcccccHhhcCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHHhcCCCHHHHHHHHHHHHHhhccccCccHHHHHHhhcc
Confidence 4789999999999999999996 999999999999999999999995 478999999998 53 444444445677
Q ss_pred cccccccC
Q 007746 182 HGSGKSFP 189 (591)
Q Consensus 182 Is~e~tF~ 189 (591)
++...|+.
T Consensus 81 ~~~~~Tg~ 88 (317)
T PRK04301 81 VGKITTGS 88 (317)
T ss_pred CCccCCCC
Confidence 77776664
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=97.44 E-value=0.00017 Score=75.58 Aligned_cols=74 Identities=19% Similarity=0.189 Sum_probs=61.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcc--hHHHHHHHHc---CCC--CCccccccCCcccccccc
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIAR---GIS--GEEVQARLLPKSHGSGKS 187 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~--~G~~L~~~ar---Gid--~~~V~~~~~~KSIs~e~t 187 (591)
|.++||||++++++|. ..||+|++||+.++.+.|.+.+|.. .|..++..++ |.+ .+.+.....+++++...|
T Consensus 1 l~~i~gig~~~~~~L~-~~Gi~ti~dl~~~~~~~L~~~~g~~~~~a~~l~~~~~~~~~~~~~~t~~~~~~~~~s~~~~~T 79 (310)
T TIGR02236 1 LEDLPGVGPATAEKLR-EAGYDTFEAIAVASPKELSEIAGISEGTAAKIIQAARKAADLGGFETADDVLERRKTIGKITT 79 (310)
T ss_pred CcccCCCCHHHHHHHH-HcCCCCHHHHHcCCHHHHHhccCCCHHHHHHHHHHHHHHhhccCCCCHHHHHHhhccCCeecC
Confidence 5689999999999996 9999999999999999999999963 5889999998 877 555554445677777776
Q ss_pred cC
Q 007746 188 FP 189 (591)
Q Consensus 188 F~ 189 (591)
+.
T Consensus 80 g~ 81 (310)
T TIGR02236 80 GS 81 (310)
T ss_pred CC
Confidence 64
No 28
>PF14520 HHH_5: Helix-hairpin-helix domain; PDB: 3AUO_B 3AU6_A 3AU2_A 3B0X_A 3B0Y_A 1SZP_C 3LDA_A 1WCN_A 2JZB_B 2ZTC_A ....
Probab=96.86 E-value=0.0013 Score=52.87 Aligned_cols=50 Identities=28% Similarity=0.349 Sum_probs=42.9
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
.+++|||++++.+|. ..||.|+.||+..+.+.|.+. +|.+.+..+...++
T Consensus 8 ~~I~Gig~~~a~~L~-~~G~~t~~~l~~a~~~~L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLY-EAGIKTLEDLANADPEELAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HTSTTCHHHHHHHHH-HTTCSSHHHHHTSHHHHHHTSTTSSHHHHHHHHHHHH
T ss_pred ccCCCCCHHHHHHHH-hcCCCcHHHHHcCCHHHHhcCCCCCHHHHHHHHHHHh
Confidence 368999999999997 899999999999999999888 66666777776654
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=96.41 E-value=0.0021 Score=56.60 Aligned_cols=41 Identities=20% Similarity=0.301 Sum_probs=36.1
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 155 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~ 155 (591)
.+.+|||||+++++-|. .+||+++.||+..++..|..++..
T Consensus 13 ~L~~iP~IG~a~a~DL~-~LGi~s~~~L~g~dP~~Ly~~lc~ 53 (93)
T PF11731_consen 13 DLTDIPNIGKATAEDLR-LLGIRSPADLKGRDPEELYERLCA 53 (93)
T ss_pred HHhcCCCccHHHHHHHH-HcCCCCHHHHhCCCHHHHHHHHHH
Confidence 46789999999999997 999999999999999887766553
No 30
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=94.97 E-value=0.043 Score=55.81 Aligned_cols=56 Identities=18% Similarity=0.262 Sum_probs=50.6
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHcCCCC
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISG 170 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~arGid~ 170 (591)
.+.+|+|||.+.+.+|. ..|+.|+.+|..++.+.|... +|.+.+..++..+.+.+.
T Consensus 4 ~L~~IpGIG~krakkLl-~~GF~Sve~Ik~AS~eEL~~V~GIg~k~AekI~e~l~~~~~ 61 (232)
T PRK12766 4 ELEDISGVGPSKAEALR-EAGFESVEDVRAADQSELAEVDGIGNALAARIKADVGGLEV 61 (232)
T ss_pred ccccCCCcCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHccCCCHHHHHHHHHHhccccc
Confidence 57789999999999997 999999999999999999999 887789999999886544
No 31
>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=93.00 E-value=0.12 Score=44.40 Aligned_cols=33 Identities=27% Similarity=0.439 Sum_probs=24.8
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCH
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 146 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~ 146 (591)
-.|+++|+||.++++.|. +.||+|+.||..+..
T Consensus 3 ~~l~~LpNig~~~e~~L~-~vGI~t~~~L~~~Ga 35 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLA-KVGIHTVEDLRELGA 35 (81)
T ss_dssp --GCGSTT--HHHHHHHH-HTT--SHHHHHHHHH
T ss_pred cchhhCCCCCHHHHHHHH-HcCCCCHHHHHHhCH
Confidence 368999999999999996 999999999999754
No 32
>PRK02362 ski2-like helicase; Provisional
Probab=92.78 E-value=0.12 Score=60.95 Aligned_cols=55 Identities=15% Similarity=0.151 Sum_probs=50.0
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCC
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 168 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGi 168 (591)
+|+..|||||++.+++|. .+||.|+.||+.+..+.|.+.||.+.+..++..++..
T Consensus 652 ~~L~~ip~i~~~~a~~l~-~~gi~s~~dl~~~~~~~l~~~~g~~~~~~i~~~~~~~ 706 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLY-NAGIESRADLRAADKSVVLAILGEKIAENILEQAGRR 706 (737)
T ss_pred HHHhCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHHCHHHHHHHHHHhCcc
Confidence 467779999999999997 8999999999999999999999999999999888844
No 33
>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=92.60 E-value=0.11 Score=41.13 Aligned_cols=27 Identities=26% Similarity=0.302 Sum_probs=20.7
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhh
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLK 143 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~ 143 (591)
..+||||+++++++- ..|++|+.||..
T Consensus 5 ~~I~GVG~~tA~~w~-~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWY-AKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHH-HTT--SHHHHHH
T ss_pred hhcccccHHHHHHHH-HhCCCCHHHHhh
Confidence 358999999999997 899999999975
No 34
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=91.54 E-value=0.22 Score=46.51 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=31.9
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE 151 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k 151 (591)
.|+.|-|||++++..|. .+||+|..||+.++...+..
T Consensus 68 DLt~I~GIGPk~e~~Ln-~~GI~tfaQIAAwt~~di~~ 104 (133)
T COG3743 68 DLTRISGIGPKLEKVLN-ELGIFTFAQIAAWTRADIAW 104 (133)
T ss_pred cchhhcccCHHHHHHHH-HcCCccHHHHHhcCHHHHHH
Confidence 46778999999999995 99999999999998765543
No 35
>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=91.05 E-value=0.34 Score=40.02 Aligned_cols=46 Identities=33% Similarity=0.476 Sum_probs=36.4
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhC
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG 154 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG 154 (591)
...+...||.++ |+..++...|. ..||+|++||..++...|.+.=|
T Consensus 6 ~~~~~~~~I~~L-~LS~Ra~n~L~-~~~I~tv~dL~~~s~~~L~~i~n 51 (66)
T PF03118_consen 6 EEELLDTPIEDL-GLSVRAYNCLK-RAGIHTVGDLVKYSEEDLLKIKN 51 (66)
T ss_dssp -HHHHCSBGGGS-TSBHHHHHHHH-CTT--BHHHHHCS-HHHHHTSTT
T ss_pred hHHHhcCcHHHh-CCCHHHHHHHH-HhCCcCHHHHHhCCHHHHHhCCC
Confidence 345667899998 79999999996 99999999999999999877644
No 36
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=89.92 E-value=0.27 Score=45.35 Aligned_cols=54 Identities=17% Similarity=0.306 Sum_probs=45.6
Q ss_pred eccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc
Q 007746 101 VPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 155 (591)
Q Consensus 101 l~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~ 155 (591)
++...+..+...-.+..++|||...+..|. ..||.|+.+|+..++..|...++.
T Consensus 41 i~~~~l~~w~~~AdL~ri~gi~~~~a~LL~-~AGv~Tv~~LA~~~p~~L~~~l~~ 94 (122)
T PF14229_consen 41 ISERNLLKWVNQADLMRIPGIGPQYAELLE-HAGVDTVEELAQRNPQNLHQKLGR 94 (122)
T ss_pred CCHHHHHHHHhHHHhhhcCCCCHHHHHHHH-HhCcCcHHHHHhCCHHHHHHHHHH
Confidence 455666666666666789999999999996 999999999999999999888774
No 37
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=89.89 E-value=0.3 Score=39.88 Aligned_cols=47 Identities=17% Similarity=0.314 Sum_probs=33.4
Q ss_pred ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 118 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 118 L~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
|+|||.++++.|.+.+| ++..|...+.+.|... +|...+..++.+..
T Consensus 8 I~~VG~~~ak~L~~~f~--sl~~l~~a~~e~L~~i~gIG~~~A~si~~ff~ 56 (64)
T PF12826_consen 8 IPGVGEKTAKLLAKHFG--SLEALMNASVEELSAIPGIGPKIAQSIYEFFQ 56 (64)
T ss_dssp STT--HHHHHHHHHCCS--CHHHHCC--HHHHCTSTT--HHHHHHHHHHHH
T ss_pred CCCccHHHHHHHHHHcC--CHHHHHHcCHHHHhccCCcCHHHHHHHHHHHC
Confidence 68999999999976666 9999999999999887 77767777776654
No 38
>PRK01172 ski2-like helicase; Provisional
Probab=89.07 E-value=0.53 Score=54.82 Aligned_cols=53 Identities=17% Similarity=0.263 Sum_probs=44.6
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
+|+..|||||+..+++|. ..||+|+.||+.++.+.+.+. ||.+.+..++..|+
T Consensus 612 ~~L~~ip~~~~~~a~~l~-~~g~~~~~di~~~~~~~~~~i~~~~~~~~~~i~~~~~ 666 (674)
T PRK01172 612 IDLVLIPKVGRVRARRLY-DAGFKTVDDIARSSPERIKKIYGFSDTLANAIVNRAM 666 (674)
T ss_pred HhhcCCCCCCHHHHHHHH-HcCCCCHHHHHhCCHHHHHHHhccCHHHHHHHHHHHH
Confidence 578889999999999996 999999999999999999888 56555666665543
No 39
>PRK00254 ski2-like helicase; Provisional
Probab=88.36 E-value=0.52 Score=55.44 Aligned_cols=53 Identities=15% Similarity=0.271 Sum_probs=48.5
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
+|+..+||||++.+++|. ..|+.|+.||..++.+.|.+. +|.+.|+.++..++
T Consensus 645 ~~L~~ipgig~~~~~~l~-~~g~~s~~~i~~a~~~el~~~~gi~~~~a~~i~~~~~ 699 (720)
T PRK00254 645 LELMRLPMIGRKRARALY-NAGFRSIEDIVNAKPSELLKVEGIGAKIVEGIFKHLG 699 (720)
T ss_pred hhhhcCCCCCHHHHHHHH-HccCCCHHHHHhCCHHHHhcCCCCCHHHHHHHHHHhc
Confidence 577789999999999997 999999999999999999998 78778999988877
No 40
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=84.13 E-value=1.9 Score=39.75 Aligned_cols=43 Identities=28% Similarity=0.458 Sum_probs=32.3
Q ss_pred cCCcHHHHHHHHHhcCCCcHHHHhhcCHH-----HHHHHhCcchHHHHHH
Q 007746 119 KQLGGKLGTSLQNELGVTTVGDLLKFSED-----KLQESYGFNTGTWLWN 163 (591)
Q Consensus 119 ~GIG~k~~~kL~~~lGI~TigDLa~~~~~-----~L~k~FG~~~G~~L~~ 163 (591)
||||++.+.+|. ..||+|++||...... .|....|. ....+..
T Consensus 1 pgi~~~~~~~L~-~~GI~t~~~Ll~~~~~~~~r~~La~~~~i-~~~~l~~ 48 (122)
T PF14229_consen 1 PGIGPKEAAKLK-AAGIKTTGDLLEAGDTPLGRKALAKKLGI-SERNLLK 48 (122)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHHcCCCHHHHHHHHHhcCC-CHHHHHH
Confidence 799999999995 9999999999987432 35566665 3444433
No 41
>PRK07758 hypothetical protein; Provisional
Probab=83.72 E-value=2.3 Score=37.83 Aligned_cols=41 Identities=24% Similarity=0.353 Sum_probs=33.7
Q ss_pred ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHH
Q 007746 118 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGT 159 (591)
Q Consensus 118 L~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~ 159 (591)
+++++-+....|. ..||+|++||..++.+.|.+. ||++.-.
T Consensus 39 ~~~LSvRA~N~Lk-~AGI~TL~dLv~~te~ELl~iknlGkKSL~ 81 (95)
T PRK07758 39 LSLLSAPARRALE-HHGIHTVEELSKYSEKEILKLHGMGPASLP 81 (95)
T ss_pred CccccHHHHHHHH-HcCCCcHHHHHcCCHHHHHHccCCCHHHHH
Confidence 4688989999996 999999999999999998666 6654333
No 42
>COG2251 Predicted nuclease (RecB family) [General function prediction only]
Probab=82.85 E-value=1.3 Score=49.05 Aligned_cols=68 Identities=21% Similarity=0.097 Sum_probs=56.3
Q ss_pred ccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhC--cchHHHHHHHHcCCCC
Q 007746 102 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG--FNTGTWLWNIARGISG 170 (591)
Q Consensus 102 ~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG--~~~G~~L~~~arGid~ 170 (591)
-+.-...++..-.+.=++||+......|+ ..||+|+.||++.+...+...+| ...+..+...|+-...
T Consensus 214 ~p~C~~~a~e~~~L~Lv~Gi~~~r~~~l~-~~GI~Ti~~LA~~~~~~~~~~~ga~~~~~~~l~~qa~~~~e 283 (474)
T COG2251 214 EPQCESEALEEDDLSLVPGITPSRYDVLE-EVGITTIEDLADASLPILELVAGALTALAAQLVLQARARVE 283 (474)
T ss_pred chhhhHHHhhccceeccCCCCHHHHHHHH-HcCcchHHHHHhccccchhhhhhhHHHHHHHHHHHHHhhcc
Confidence 35556778888889999999999999997 99999999999999888888888 4456777777776544
No 43
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=81.66 E-value=3.5 Score=43.09 Aligned_cols=62 Identities=16% Similarity=0.364 Sum_probs=52.4
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc--chHHHHHHHHcCCCCCccc
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEVQ 174 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~--~~G~~L~~~arGid~~~V~ 174 (591)
..|+..+|+||....++|. ..||.+++||..++.+.+...+|. ..|..+++.++....-.|.
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~-~~~i~s~~~l~~~~~~~~~~ll~~~~~~~~~i~~~~~~~P~l~v~ 213 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLE-KKKVLSLEDLLELEDEERGELLGLLDAEGERVYKVLSRLPKLNIE 213 (312)
T ss_pred CCccccCCCCCHHHHHHHH-hCCCCCHHHHHhcCHHHHHHHHcCCHHHHHHHHHHHHhCCcceeE
Confidence 3688899999999999996 899999999999999998888774 2588888888887665554
No 44
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=81.59 E-value=1.8 Score=49.77 Aligned_cols=54 Identities=17% Similarity=0.142 Sum_probs=46.0
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH-hCcchHHHHHHHHcC
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES-YGFNTGTWLWNIARG 167 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~-FG~~~G~~L~~~arG 167 (591)
.-.+.+|+|||++..++|. --+.++..+..++.++|.+. +|.+.|+.++..++|
T Consensus 513 ~S~Ld~I~GiG~kr~~~Ll--~~Fgs~~~ik~As~eeL~~vgi~~~~A~~I~~~l~~ 567 (567)
T PRK14667 513 KDILDKIKGIGEVKKEIIY--RNFKTLYDFLKADDEELKKLGIPPSVKQEVKKYLSG 567 (567)
T ss_pred cCccccCCCCCHHHHHHHH--HHhCCHHHHHhCCHHHHHHcCCCHHHHHHHHHHhcC
Confidence 3567899999999999996 44559999999999999998 566678999998877
No 45
>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=80.72 E-value=2.6 Score=44.02 Aligned_cols=61 Identities=23% Similarity=0.366 Sum_probs=45.2
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc--chHHHHHHHHcCCCCCccc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARGISGEEVQ 174 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~--~~G~~L~~~arGid~~~V~ 174 (591)
.|+..|||||....++|. ..||.|++||.+++.+.+...++. ..|..+...++.+..-.|.
T Consensus 148 ~~L~Qlp~i~~~~~~~l~-~~~i~~l~~l~~~~~~e~~~ll~~~~~~~~~i~~~~~~~P~~~i~ 210 (314)
T PF02889_consen 148 SPLLQLPHIGEESLKKLE-KRGIKTLQDLRDLSPEELEELLNRNPPFGKEILEVASRIPRLEIK 210 (314)
T ss_dssp -GGGGSTT--HHHHHHHH-HTT--SHHHHHHS-HHHHHHHH-S-HHHHHHHHHHHCCS--EEEE
T ss_pred ChhhcCCCCCHHHHHHHh-ccCCCcHHHHhhCCHHHHHHHHhhhhhhHHHHHHHHHHCCCEEEE
Confidence 588999999999999996 999999999999999999988862 3588899999988765553
No 46
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=79.38 E-value=1.9 Score=42.67 Aligned_cols=57 Identities=12% Similarity=0.076 Sum_probs=44.8
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHH-HHhhcCHHHHHHH--hCcchHHHHHHHHcCCCC
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVG-DLLKFSEDKLQES--YGFNTGTWLWNIARGISG 170 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~Tig-DLa~~~~~~L~k~--FG~~~G~~L~~~arGid~ 170 (591)
.+..++|||++++.++.+.+|..++- .+...+.+.|.+. +|.+.+++++..+++...
T Consensus 74 ~L~~i~GIGpk~A~~il~~fg~~~l~~~i~~~d~~~L~~v~Gig~k~A~~I~~~l~~~~~ 133 (192)
T PRK00116 74 LLISVSGVGPKLALAILSGLSPEELVQAIANGDVKALTKVPGIGKKTAERIVLELKDKLA 133 (192)
T ss_pred HHhcCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHhh
Confidence 45678999999999887678876653 4556688889887 778889999999887653
No 47
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=78.76 E-value=1.6 Score=46.92 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=26.2
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFS 145 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~ 145 (591)
+.+|||||++++.+|. .+||.|+.||....
T Consensus 91 l~~i~GiGpk~a~~l~-~lGi~tl~eL~~a~ 120 (334)
T smart00483 91 FTNVFGVGPKTAAKWY-RKGIRTLEELKKNK 120 (334)
T ss_pred HHccCCcCHHHHHHHH-HhCCCCHHHHHhcc
Confidence 3459999999999998 69999999998754
No 48
>PRK08609 hypothetical protein; Provisional
Probab=78.56 E-value=1.9 Score=49.64 Aligned_cols=29 Identities=38% Similarity=0.418 Sum_probs=26.3
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF 144 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~ 144 (591)
.++||||++++.+|.+.+||.|+.||...
T Consensus 91 ~~i~GiGpk~a~~l~~~lGi~tl~~L~~a 119 (570)
T PRK08609 91 LKLPGLGGKKIAKLYKELGVVDKESLKEA 119 (570)
T ss_pred hcCCCCCHHHHHHHHHHhCCCCHHHHHHH
Confidence 36999999999999878999999999975
No 49
>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=78.11 E-value=2 Score=37.74 Aligned_cols=33 Identities=24% Similarity=0.434 Sum_probs=23.3
Q ss_pred cccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhh
Q 007746 110 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLK 143 (591)
Q Consensus 110 L~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~ 143 (591)
|..-||++|+|||+.++.+|. ..|+..+..|..
T Consensus 16 MGeK~V~~laGIG~~lg~~L~-~~GfdKAy~vLG 48 (89)
T PF02961_consen 16 MGEKPVTELAGIGPVLGKRLE-EKGFDKAYVVLG 48 (89)
T ss_dssp -TT-BGGGSTT--HHHHHHHH-HTT--BHHHHHH
T ss_pred cCCCCccccCCcCHHHHHHHH-HCCCcHHHHHhh
Confidence 456799999999999999996 999998877654
No 50
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=78.09 E-value=2.4 Score=50.83 Aligned_cols=52 Identities=23% Similarity=0.314 Sum_probs=46.5
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhC-cchHHHHHHHHcCC
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYG-FNTGTWLWNIARGI 168 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG-~~~G~~L~~~arGi 168 (591)
|..|||||.+.+.+|. ..+.++.+|+.++.+.|....| .+.|..+|+.++..
T Consensus 759 L~~lPgI~~~~a~~ll--~~f~si~~l~~as~eeL~~~iG~~~~A~~i~~fl~~~ 811 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLR--KKVKSIRELAKLSQNELNELIGDEEAAKRLYDFLRTE 811 (814)
T ss_pred HHHCCCCCHHHHHHHH--HHcCCHHHHHhCCHHHHHHHhCCHHHHHHHHHHhccc
Confidence 4578999999999996 4689999999999999999999 88899999998864
No 51
>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=77.52 E-value=1.9 Score=48.11 Aligned_cols=59 Identities=24% Similarity=0.263 Sum_probs=42.2
Q ss_pred HhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH--HhCcchHHHHHHHHc
Q 007746 107 KGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 166 (591)
Q Consensus 107 ~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k--~FG~~~G~~L~~~ar 166 (591)
......-+|..|+|||++...+|+ ..||.|+.||+..+...|.. .++...+.+|...|+
T Consensus 201 ~~~~~~~~lslv~gi~~~~~~~L~-~~GI~ti~~La~~~~~~l~~~~~~~~~~~~~l~~qA~ 261 (457)
T TIGR03491 201 AVAKEEGHLSLVPGIGPSRYRLLQ-ELGIHTLEDLAAADPNDLEDFGEQGLGVAEQLVQQAR 261 (457)
T ss_pred HHHHhcCCeeecCCCCHHHHHHHH-HcCCCcHHHHhcCCccccccccccCHHHHHHHHHHHH
Confidence 344546789999999999999996 99999999999987544444 344334444444433
No 52
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=75.45 E-value=1.3 Score=39.93 Aligned_cols=21 Identities=38% Similarity=0.730 Sum_probs=18.4
Q ss_pred CCccccccCChHHHHHHHHhh
Q 007746 546 IDPSVIDELPKEIQDEIQAWL 566 (591)
Q Consensus 546 id~~~~~el~~ei~~e~~~~~ 566 (591)
|||+|+.+||.+|+.||-.=.
T Consensus 1 iDp~fLaaLPeDiR~Evl~~~ 21 (108)
T PF14377_consen 1 IDPEFLAALPEDIREEVLAQQ 21 (108)
T ss_pred CCHHHHHHCCHHHHHHHHHHH
Confidence 899999999999999994433
No 53
>PTZ00035 Rad51 protein; Provisional
Probab=74.72 E-value=4.3 Score=43.68 Aligned_cols=55 Identities=18% Similarity=0.177 Sum_probs=45.6
Q ss_pred CCCCcc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcc--hHHHHHHHHcCC
Q 007746 113 LPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 168 (591)
Q Consensus 113 LPI~kL--~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~--~G~~L~~~arGi 168 (591)
++|.++ +||+....++|+ ..||+|+.||+..+...|.+..|.. .++.+...++-.
T Consensus 21 ~~~~~l~~~g~~~~~~~kL~-~~g~~t~~~~~~~~~~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 21 QEIEKLQSAGINAADIKKLK-EAGICTVESVAYATKKDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred ccHHHHhcCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhhCCCHHHHHHHHHHHHHh
Confidence 367777 789999999996 9999999999999999999998853 245677666654
No 54
>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=73.82 E-value=2.3 Score=45.18 Aligned_cols=28 Identities=36% Similarity=0.477 Sum_probs=25.8
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF 144 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~ 144 (591)
.++||||++++++|. .+||.|+.||...
T Consensus 88 ~~i~GiGpk~a~~l~-~lGi~sl~dL~~a 115 (307)
T cd00141 88 LRVPGVGPKTARKLY-ELGIRTLEDLRKA 115 (307)
T ss_pred HcCCCCCHHHHHHHH-HcCCCCHHHHHHH
Confidence 459999999999998 9999999999975
No 55
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=73.27 E-value=5.2 Score=46.64 Aligned_cols=51 Identities=20% Similarity=0.285 Sum_probs=43.4
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHH
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIA 165 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~a 165 (591)
..+..|+|||.+++..|.+.+| |+.+|..++.+.|.+.+|.+.++.++.+.
T Consensus 569 s~L~~I~GIG~k~a~~Ll~~Fg--s~~~i~~As~eeL~~vig~k~A~~I~~~~ 619 (621)
T PRK14671 569 TELTDIAGIGEKTAEKLLEHFG--SVEKVAKASLEELAAVAGPKTAETIYRYY 619 (621)
T ss_pred hhhhcCCCcCHHHHHHHHHHcC--CHHHHHhCCHHHHHHHhCHHHHHHHHHHh
Confidence 3567899999999999975554 88999999999998889988899888765
No 56
>PF14377 DUF4414: Domain of unknown function (DUF4414)
Probab=72.79 E-value=2.2 Score=38.41 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=21.2
Q ss_pred cccCCccccccCChHHHHHHHHhhC
Q 007746 543 IEEIDPSVIDELPKEIQDEIQAWLR 567 (591)
Q Consensus 543 ~~~id~~~~~el~~ei~~e~~~~~~ 567 (591)
-.+|||.+++-||++||+||-+=.+
T Consensus 42 ~~~I~pefL~ALP~diR~EVl~qe~ 66 (108)
T PF14377_consen 42 PSQIDPEFLAALPPDIREEVLAQER 66 (108)
T ss_pred ccccCHHHHHhCCHHHHHHHHHHHH
Confidence 5689999999999999999865443
No 57
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=72.62 E-value=5.7 Score=46.63 Aligned_cols=63 Identities=10% Similarity=0.160 Sum_probs=52.4
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHcCCCCCccccc
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARGISGEEVQAR 176 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~arGid~~~V~~~ 176 (591)
...+.+|+|||++...+|.+.| .++..|..++.++|.+. ++.+.+..+++.+.--...||...
T Consensus 607 ~s~L~~IpGiG~kr~~~LL~~F--gS~~~i~~As~eel~~v~gi~~~~A~~i~~~~~~~~~~~~~~~ 671 (691)
T PRK14672 607 VLSFERLPHVGKVRAHRLLAHF--GSFRSLQSATPQDIATAIHIPLTQAHTILHAATRSTTAPVREE 671 (691)
T ss_pred ccccccCCCCCHHHHHHHHHHh--cCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHhhcccccchhHH
Confidence 4578899999999999996444 59999999999999998 777789999998887777777643
No 58
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=71.94 E-value=5.5 Score=45.99 Aligned_cols=54 Identities=22% Similarity=0.329 Sum_probs=44.7
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHcC
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIARG 167 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~arG 167 (591)
...+.+|+|||++..++|.+. +.++..+..++.++|.+. ++.+.|..++..++-
T Consensus 513 ~s~L~~I~GiG~kr~~~LL~~--Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~~ 568 (574)
T PRK14670 513 KLNYTKIKGIGEKKAKKILKS--LGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAEK 568 (574)
T ss_pred ccccccCCCCCHHHHHHHHHH--hCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHH
Confidence 347889999999999999644 459999999999999999 666678888887753
No 59
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=71.24 E-value=2.7 Score=45.43 Aligned_cols=45 Identities=20% Similarity=0.324 Sum_probs=39.9
Q ss_pred cCCCCcc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcch
Q 007746 112 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT 157 (591)
Q Consensus 112 ~LPI~kL--~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~ 157 (591)
..+|.+| .||+....++|+ .-||+|+.||+..++..|.+.+|...
T Consensus 25 ~~~~~~l~~~gi~~~~i~kL~-~~g~~T~~~~~~~~~~~L~~i~~is~ 71 (342)
T PLN03186 25 PFPIEQLQASGIAALDIKKLK-DAGIHTVESLAYAPKKDLLQIKGISE 71 (342)
T ss_pred CccHHHHHhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCH
Confidence 3478888 679999999996 99999999999999999999999743
No 60
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=71.20 E-value=5.4 Score=46.87 Aligned_cols=53 Identities=19% Similarity=0.259 Sum_probs=42.9
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH--HhCcchHHHHHHHHc
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIAR 166 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k--~FG~~~G~~L~~~ar 166 (591)
..-+|+|+|.++.++|-+..+|.++.||..+..+.|.. .||.+.+..|++...
T Consensus 446 ~al~I~GLG~k~i~~L~~~g~I~~i~DL~~L~~~~L~~l~gfG~Ksa~~ll~~Ie 500 (665)
T PRK07956 446 NAMDIDGLGEKIIEQLFEKGLIHDPADLFKLTAEDLLGLEGFGEKSAQNLLDAIE 500 (665)
T ss_pred cccCCCCcCHHHHHHHHHcCCCCCHHHHHhcCHHHHhcCcCcchHHHHHHHHHHH
Confidence 45678999999999998778899999999999888876 478777776655444
No 61
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=70.58 E-value=5.4 Score=46.93 Aligned_cols=52 Identities=13% Similarity=0.202 Sum_probs=43.2
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
-.+..+||||++..++|.+.|| ++.+|+..+.+.|.+. +|.+.++.++..++
T Consensus 637 s~L~~IPGIGpkr~k~LL~~FG--Sle~I~~AS~eELa~V~Gig~k~Ae~I~~~L~ 690 (694)
T PRK14666 637 GELQRVEGIGPATARLLWERFG--SLQAMAAAGEEGLAAVPGIGPARAAALHEHLK 690 (694)
T ss_pred hHHhhCCCCCHHHHHHHHHHhC--CHHHHHhcCHHHHHhcCCcCHHHHHHHHHHHH
Confidence 4577889999999999987777 9999999999999887 77767777776653
No 62
>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=70.53 E-value=5.9 Score=46.47 Aligned_cols=54 Identities=24% Similarity=0.288 Sum_probs=43.7
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
-.--+|+|+|.++.++|-+..+|+++.||..+..+.|... ||.+.+..|++...
T Consensus 432 r~al~I~GLG~k~i~~L~~~g~I~~~~Dl~~L~~~~L~~L~GfG~Ksa~nIl~~Ie 487 (652)
T TIGR00575 432 RNAMDIEGLGDKVIEQLFEKKLVRSVADLYALKKEDLLELEGFGEKSAQNLLNAIE 487 (652)
T ss_pred CCccCCCCcCHHHHHHHHHcCCcCCHHHHHhcCHHHHhhccCccHHHHHHHHHHHH
Confidence 3445789999999999986778999999999998888764 77777777766655
No 63
>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=70.30 E-value=11 Score=44.23 Aligned_cols=55 Identities=22% Similarity=0.276 Sum_probs=41.7
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHH
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 165 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~a 165 (591)
+.+||..+ .|||||.+++++|.+.+| ++.+|..++.+.|.+. ||.+.+..++.+.
T Consensus 494 l~r~L~aL---gIpgVG~~~ak~L~~~f~--sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 494 LARLLFAL---GIRHVGEVTAKNLAKHFG--TLDKLKAASLEELLSVEGVGPKVAESIVNFF 550 (652)
T ss_pred HHHHHhhc---cCCCcCHHHHHHHHHHhC--CHHHHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 34566655 359999999999986676 8999999988888777 7776666666554
No 64
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=70.28 E-value=6.8 Score=42.42 Aligned_cols=56 Identities=18% Similarity=0.229 Sum_probs=45.1
Q ss_pred cCCCCcc--cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcc--hHHHHHHHHcCC
Q 007746 112 SLPIKKM--KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARGI 168 (591)
Q Consensus 112 ~LPI~kL--~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~--~G~~L~~~arGi 168 (591)
..+|.++ .||+..+.++|+ ..||+|+.||+..+...|.+..|.. .+..+...++..
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~-~~g~~tv~~~~~~~~~~L~~~~g~s~~~~~ki~~~a~~~ 87 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQ-DAGIYTCNGLMMHTKKNLTGIKGLSEAKVDKICEAAEKL 87 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHHh
Confidence 5567777 679999999996 9999999999999999999988853 245555555543
No 65
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=68.48 E-value=7.3 Score=45.46 Aligned_cols=54 Identities=11% Similarity=0.054 Sum_probs=46.6
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcCC
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARGI 168 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arGi 168 (591)
-.+.+|+|||++...+|.+ -+.++..+..++.+.|.+.+|.+.++.++..++..
T Consensus 552 S~L~~IpGIG~kr~~~LL~--~FgSi~~I~~As~eeL~~vi~~k~A~~I~~~l~~~ 605 (624)
T PRK14669 552 SELLEIPGVGAKTVQRLLK--HFGSLERVRAATETQLAAVVGRAAAEAIIAHFTTE 605 (624)
T ss_pred HHHhcCCCCCHHHHHHHHH--HcCCHHHHHhCCHHHHHHHhCHHHHHHHHHHhcCc
Confidence 4677999999999999964 45599999999999999999988999999998743
No 66
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=68.40 E-value=3.7 Score=48.16 Aligned_cols=31 Identities=39% Similarity=0.618 Sum_probs=28.5
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 144 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~ 144 (591)
.||..+.|||++.+++|. ++||+|+.||...
T Consensus 9 ~~~~~l~gvg~~~~~~l~-~lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLA-KLGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHH-HcCCCCHHHHhhc
Confidence 489999999999999996 9999999999874
No 67
>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=66.69 E-value=7.2 Score=41.58 Aligned_cols=37 Identities=24% Similarity=0.240 Sum_probs=33.9
Q ss_pred cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcc
Q 007746 119 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 156 (591)
Q Consensus 119 ~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~ 156 (591)
.||+..+.++|+ ..||.|+.||+..++..|.+.+|..
T Consensus 7 ~~~~~~~~~~l~-~~g~~t~~~~~~~~~~~L~~i~~ls 43 (316)
T TIGR02239 7 NGITAADIKKLQ-EAGLHTVESVAYAPKKQLLEIKGIS 43 (316)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHHhCCC
Confidence 359999999996 9999999999999999999999963
No 68
>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=66.15 E-value=11 Score=40.18 Aligned_cols=48 Identities=15% Similarity=0.135 Sum_probs=39.2
Q ss_pred cCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcc--hHHHHHHHHcC
Q 007746 119 KQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN--TGTWLWNIARG 167 (591)
Q Consensus 119 ~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~--~G~~L~~~arG 167 (591)
.|||..+.++|+ ..||+|+.||+.++...|.+..|.. .+..+.+.++-
T Consensus 7 ~g~~~~~~~~L~-~~g~~t~~~~~~~~~~~L~~~~gls~~~~~~i~~~~~~ 56 (313)
T TIGR02238 7 HGINAADIKKLK-SAGICTVNGVIMTTRRALCKIKGLSEAKVDKIKEAASK 56 (313)
T ss_pred CCCCHHHHHHHH-HcCCCcHHHHHhCCHHHHHHhcCCCHHHHHHHHHHHHh
Confidence 579999999996 9999999999999999999998852 24555555543
No 69
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=65.55 E-value=6.5 Score=40.11 Aligned_cols=36 Identities=25% Similarity=0.481 Sum_probs=32.2
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 150 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 150 (591)
.+.++.|||+.++++|. ..||++..||+.++.+.+.
T Consensus 159 DL~~I~GIGp~~a~~L~-eaGi~tfaQIAa~t~a~ia 194 (221)
T PRK12278 159 DLTKITGVGPALAKKLN-EAGVTTFAQIAALTDADIA 194 (221)
T ss_pred hheeccccChHHHHHHH-HcCCCCHHHhhCCChhhhh
Confidence 47889999999999996 9999999999999887554
No 70
>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=65.37 E-value=14 Score=27.87 Aligned_cols=34 Identities=35% Similarity=0.422 Sum_probs=29.1
Q ss_pred CcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc
Q 007746 121 LGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 155 (591)
Q Consensus 121 IG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~ 155 (591)
|...++.+|. ..||.|+.+|+.++.+.|...-|.
T Consensus 1 i~~~~~~~L~-~~G~~s~e~la~~~~~eL~~i~g~ 34 (50)
T TIGR01954 1 IDEEIAQLLV-EEGFTTVEDLAYVPIDELLSIEGF 34 (50)
T ss_pred CCHHHHHHHH-HcCCCCHHHHHccCHHHHhcCCCC
Confidence 3467888996 999999999999999999888663
No 71
>PRK14973 DNA topoisomerase I; Provisional
Probab=62.60 E-value=13 Score=45.49 Aligned_cols=105 Identities=15% Similarity=0.016 Sum_probs=63.2
Q ss_pred hHHHHHHHHHHHHHHHhCCeEEEEecCCHHHHHHhc-cCCCCCCEEEeccccHHhhcccCCCCcccCCcHHHHHHHHHhc
Q 007746 55 CGVLIVTELRMQVLKETEFTCSAGIAHNKMLAKLAS-GMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNEL 133 (591)
Q Consensus 55 ~~~~lA~~IR~~I~~etGLt~SVGIA~NKlLAKLAS-~~aKP~G~~vl~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~l 133 (591)
.+.+++..==..+...|||. ...---++++|. ++.+|+-..+... ..--..-++..+.|||.++.++|. .-
T Consensus 825 ~~~d~~~a~p~~La~~~g~~----~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~el~~vkg~ge~t~~~l~-~a 896 (936)
T PRK14973 825 TPEDFCSVHPAYLALKTGIS----PETICRHAKLVCEKLGRPVPEKISKA---AFERGRAELLSVPGLGETTLEKLY-LA 896 (936)
T ss_pred CHHHHHhcCHHHHhcCCCCC----hhhHHHHHHHHHHHhcCCCchhhhhh---hhcccchhhhhccCCCHHHHHHHH-Hc
Confidence 34444444444444445542 222334555666 6667664332210 000011126678999999999995 99
Q ss_pred CCCcHHHHhhcCHHHHHHHhCc--chHHHHHHHHcC
Q 007746 134 GVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIARG 167 (591)
Q Consensus 134 GI~TigDLa~~~~~~L~k~FG~--~~G~~L~~~arG 167 (591)
||.++.||+..+++.|.+.=|+ +....+...+++
T Consensus 897 g~~~~e~l~~~d~~~la~~~~i~~k~~~~~~~~~~~ 932 (936)
T PRK14973 897 GVYDGDLLVSADPKKLAKVTGIDEKKLRNLQAYAKK 932 (936)
T ss_pred CCCCHHHhccCCHHHHhhhcCCCHHHHHHHHHHHhh
Confidence 9999999999999999887665 334455555543
No 72
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=62.56 E-value=6 Score=42.58 Aligned_cols=36 Identities=19% Similarity=0.373 Sum_probs=31.5
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 150 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 150 (591)
.+.++.|||++++++|. .+||++..||+.++.+.+.
T Consensus 264 dL~~I~GiGp~~e~~L~-~~Gi~~f~QiA~~t~~~~a 299 (326)
T PRK12311 264 DLKKLTGVSPQIEKKLN-DLGIFHFWQLAELDPDDAA 299 (326)
T ss_pred hhhhhccCChhhhhhhh-hcCCCCHHHhhCCChhhhh
Confidence 36789999999999995 9999999999999876443
No 73
>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=62.37 E-value=3.9 Score=28.73 Aligned_cols=15 Identities=20% Similarity=0.357 Sum_probs=11.8
Q ss_pred CcccCCcHHHHHHHH
Q 007746 116 KKMKQLGGKLGTSLQ 130 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~ 130 (591)
.+|||||++++..+.
T Consensus 14 ~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 14 MKLPGIGPKTANAIL 28 (30)
T ss_dssp HTSTT-SHHHHHHHH
T ss_pred HhCCCcCHHHHHHHH
Confidence 459999999998875
No 74
>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=61.91 E-value=9 Score=38.07 Aligned_cols=52 Identities=19% Similarity=0.201 Sum_probs=39.7
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHH--hCcchHHHHHHHHcCCC
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGIS 169 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~--FG~~~G~~L~~~arGid 169 (591)
+-.++|||+|++..+ +++.+..+|..+ +...|.+. ||+++++++.-++++.-
T Consensus 74 L~~V~GIGpK~Al~i---L~~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIileLk~k~ 131 (191)
T TIGR00084 74 LIKVNGVGPKLALAI---LSNMSPEEFVYAIETEEVKALVKIPGVGKKTAERLLLELKGKL 131 (191)
T ss_pred HhCCCCCCHHHHHHH---HhcCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHhhh
Confidence 457899999998766 778888888764 44667664 67788999988887753
No 75
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=61.75 E-value=11 Score=44.49 Aligned_cols=54 Identities=19% Similarity=0.172 Sum_probs=42.9
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
-..-+|.|+|.++.++|.+..+|+++.||..+..+.|... ||.+.+..|++...
T Consensus 462 r~al~I~GLG~k~i~~L~~~g~V~~~~Dl~~L~~~~L~~l~g~g~Ksa~~Ll~~Ie 517 (689)
T PRK14351 462 RDALDIEGLGEERVQQLVDAGLVESLADLYDLTVADLAELEGWGETSAENLLAELE 517 (689)
T ss_pred ccccCCCCcCHHHHHHHHHcCCCCCHHHHHHcCHHHHhcCcCcchhHHHHHHHHHH
Confidence 3445789999999999985556899999999998888765 78777777666554
No 76
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=58.85 E-value=6.8 Score=45.78 Aligned_cols=31 Identities=39% Similarity=0.734 Sum_probs=28.5
Q ss_pred CCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 007746 113 LPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 144 (591)
Q Consensus 113 LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~ 144 (591)
.|+..+.|||.+++++|. ++||+|+.||+-.
T Consensus 10 ~~l~~l~gig~~~a~~l~-~Lgi~tv~DLL~~ 40 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLK-KLGIHTVQDLLLY 40 (677)
T ss_pred cchhhhcCcCHHHHHHHH-HcCCCcHHHHHHh
Confidence 389999999999999996 9999999999874
No 77
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=54.41 E-value=15 Score=38.18 Aligned_cols=50 Identities=24% Similarity=0.387 Sum_probs=39.8
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc--chHHHHHHHHc
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWNIAR 166 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~--~~G~~L~~~ar 166 (591)
+..+||||.+++.+|. .-+.++++++.++...|.+.-|+ +.|..++...+
T Consensus 184 l~s~pgig~~~a~~ll--~~fgS~~~~~tas~~eL~~v~gig~k~A~~I~~~~~ 235 (254)
T COG1948 184 LESIPGIGPKLAERLL--KKFGSVEDVLTASEEELMKVKGIGEKKAREIYRFLR 235 (254)
T ss_pred HHcCCCccHHHHHHHH--HHhcCHHHHhhcCHHHHHHhcCccHHHHHHHHHHHh
Confidence 3456799999999996 45569999999999999999987 45666666655
No 78
>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=54.07 E-value=16 Score=38.76 Aligned_cols=54 Identities=26% Similarity=0.347 Sum_probs=42.2
Q ss_pred cccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHH
Q 007746 110 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 165 (591)
Q Consensus 110 L~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~a 165 (591)
+..++|.+| ++.-+...-|. +.||+|++||..++.+.|.+. ||++..+.+.+.+
T Consensus 232 ~~~~~I~~L-~LSvR~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~l 287 (297)
T TIGR02027 232 LLSIKIEEL-DLSVRSYNCLK-RAGIHTLGELVSKSEEELLKIKNFGKKSLTEIKEKL 287 (297)
T ss_pred hccccHHHh-CccHHHHhHHH-HcCCcCHHHHHhCCHHHHhhCCCCChhhHHHHHHHH
Confidence 455688888 58889999996 999999999999999987554 7776555554444
No 79
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=53.95 E-value=13 Score=37.00 Aligned_cols=54 Identities=13% Similarity=0.183 Sum_probs=41.3
Q ss_pred CcccCCcHHHHHHHHHhcCCCc-HHHHhhcCHHHHHHH--hCcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTT-VGDLLKFSEDKLQES--YGFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~T-igDLa~~~~~~L~k~--FG~~~G~~L~~~arGid 169 (591)
-.+.|||++++-.+.+.++... +..++.-+...|.+. .|+++++++.-+++|.-
T Consensus 76 i~V~GIGpK~Al~ILs~~~~~~l~~aI~~~D~~~L~~vpGIGkKtAerIilELk~Ki 132 (194)
T PRK14605 76 IDVSGIGPKLGLAMLSAMNAEALASAIISGNAELLSTIPGIGKKTASRIVLELKDKI 132 (194)
T ss_pred hCCCCCCHHHHHHHHHhCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHHHHH
Confidence 5789999999988876677776 444556688888886 45568899888888753
No 80
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=53.41 E-value=13 Score=41.14 Aligned_cols=36 Identities=22% Similarity=0.426 Sum_probs=31.5
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 150 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 150 (591)
.+.+|.|||.+++++|. .+||++..||+.++.+.+.
T Consensus 324 DLk~I~GIGpk~e~~Ln-~~Gi~~f~QIA~wt~~eia 359 (400)
T PRK12373 324 DLKLISGVGPKIEATLN-ELGIFTFDQVAAWKKAERA 359 (400)
T ss_pred hhhhccCCChHHHHHHH-hcCCCCHHHHhCCCHHHhH
Confidence 36788999999999995 9999999999999877543
No 81
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=53.00 E-value=6.8 Score=39.42 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=32.2
Q ss_pred EecCCHHHHHHhccCCCCCCEEEeccccHHhhcccCC---CCcccCCcHHHHHHHH
Q 007746 78 GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLP---IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 78 GIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~LP---I~kL~GIG~k~~~kL~ 130 (591)
|||+---||=|++ ++++++...+..-. +.++||||+|++++|-
T Consensus 80 GIGpK~ALaiLs~----------~~~~~l~~aI~~~d~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 80 GIGPKLALAILSN----------LDPEELAQAIANEDVKALSKIPGIGKKTAERIV 125 (201)
T ss_pred CccHHHHHHHHcC----------CCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHH
Confidence 9999888888875 24455555555433 5788999999999995
No 82
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=51.91 E-value=7 Score=38.69 Aligned_cols=56 Identities=20% Similarity=0.215 Sum_probs=37.4
Q ss_pred HHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 63 LRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 63 IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
-.+++++.+ +.++ ||||-.-||=|.+ ++++++...+..- -+.++||||+|+++|+-
T Consensus 67 ~Er~lF~~L-i~Vs-GIGpK~Al~ILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 67 DEQKMFEML-LKVN-GIGANTAMAVCSS----------LDVNSFYKALSLGDESVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 344555544 4455 8998777777653 3455666555544 35678999999999985
No 83
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=51.52 E-value=17 Score=42.29 Aligned_cols=53 Identities=9% Similarity=0.170 Sum_probs=43.4
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
..++..+||||.+...+|.+.+ .++..++.++.+.|.+. +|.+.+..++...+
T Consensus 542 ~s~L~~IpGIG~k~~k~Ll~~F--gS~~~i~~As~eeL~~v~Gig~~~A~~I~~~l~ 596 (598)
T PRK00558 542 TSALDDIPGIGPKRRKALLKHF--GSLKAIKEASVEELAKVPGISKKLAEAIYEALH 596 (598)
T ss_pred hhhHhhCCCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhhcCCcCHHHHHHHHHHhc
Confidence 3567889999999999997544 57999999999999988 77777887777654
No 84
>PRK05182 DNA-directed RNA polymerase subunit alpha; Provisional
Probab=51.14 E-value=19 Score=38.51 Aligned_cols=53 Identities=23% Similarity=0.355 Sum_probs=41.6
Q ss_pred cccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHH
Q 007746 110 LDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNI 164 (591)
Q Consensus 110 L~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ 164 (591)
+..++|.+| ++.-+...-|. +.||+|++||.+++.+.|.+. ||.+.-+.+.+.
T Consensus 246 ~l~~~I~~L-~LS~R~~n~Lk-~~~I~ti~dL~~~~~~~l~~~~n~G~ksl~ei~~~ 300 (310)
T PRK05182 246 ILLRPIEEL-ELSVRSYNCLK-RAGINTIGDLVQRTEEELLKTRNLGKKSLEEIKEK 300 (310)
T ss_pred cccccHHHh-ccchHHHHHHH-HcCCcCHHHHHhCCHHHHhcCCCCChhhHHHHHHH
Confidence 346788888 78889999996 999999999999999988655 676554444433
No 85
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=48.83 E-value=7.9 Score=38.44 Aligned_cols=55 Identities=9% Similarity=0.149 Sum_probs=36.5
Q ss_pred HHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 64 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 64 R~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
.+++++.+ +.++ ||||-.-||=|.+ ++++++.+.+..- -+.++||||+|++++|-
T Consensus 68 Er~lF~~L-i~V~-GIGpK~AL~iLs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 68 KKELFLSL-TKVS-RLGPKTALKIISN----------EDAETLVTMIASQDVEGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHHHHHH-hccC-CccHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 44445444 3444 8998887777653 2455555555543 36778999999999995
No 86
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=48.58 E-value=42 Score=39.66 Aligned_cols=55 Identities=18% Similarity=0.246 Sum_probs=38.0
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHH
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 165 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~a 165 (591)
+..||..+- ++|||.+++++|.+.+ .++.+|..++.+.|... +|.+.+..++.+.
T Consensus 507 l~R~l~alg---i~~IG~~~ak~L~~~f--~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff 563 (665)
T PRK07956 507 LARFLYALG---IRHVGEKAAKALARHF--GSLEALRAASEEELAAVEGVGEVVAQSIVEFF 563 (665)
T ss_pred HHHhhHhhh---ccCcCHHHHHHHHHHc--CCHHHHHhCCHHHHhccCCcCHHHHHHHHHHH
Confidence 345665553 5889999999886444 67888888888888776 6665566555543
No 87
>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=47.32 E-value=23 Score=37.73 Aligned_cols=41 Identities=29% Similarity=0.543 Sum_probs=31.3
Q ss_pred CCcccCCcH--HHHHHHHHhcCCCcHHHHhhc---CHHHHHHHhCcc
Q 007746 115 IKKMKQLGG--KLGTSLQNELGVTTVGDLLKF---SEDKLQESYGFN 156 (591)
Q Consensus 115 I~kL~GIG~--k~~~kL~~~lGI~TigDLa~~---~~~~L~k~FG~~ 156 (591)
|.+|-.||+ ..-++|. .-||+|++|++.+ ++..|++.||.+
T Consensus 164 VwRLe~Igk~G~~hk~L~-~~~I~tV~dFl~l~~~d~~~Lr~ilg~~ 209 (299)
T PF07887_consen 164 VWRLEKIGKDGAFHKRLK-KNGINTVEDFLKLLNKDPQKLREILGSG 209 (299)
T ss_pred hhhhhhccccCHHHHHHH-HcCCccHHHHHHHHhcCHHHHHHHHhcC
Confidence 455556665 4668885 8999999999874 778899999943
No 88
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=45.79 E-value=14 Score=24.72 Aligned_cols=16 Identities=19% Similarity=0.320 Sum_probs=14.0
Q ss_pred CCcccCCcHHHHHHHH
Q 007746 115 IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~ 130 (591)
+.+++|||.+++++|.
T Consensus 3 L~~i~GiG~k~A~~il 18 (26)
T smart00278 3 LLKVPGIGPKTAEKIL 18 (26)
T ss_pred hhhCCCCCHHHHHHHH
Confidence 4679999999999986
No 89
>PRK13766 Hef nuclease; Provisional
Probab=45.66 E-value=25 Score=41.66 Aligned_cols=50 Identities=22% Similarity=0.408 Sum_probs=41.4
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
+..+||||.+.+.+|.+.+| ++.++..++.+.|... +|.+.+..++..+.
T Consensus 717 L~~ipgig~~~a~~Ll~~fg--s~~~i~~as~~~L~~i~Gig~~~a~~i~~~~~ 768 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFG--SVEAVMTASEEELMEVEGIGEKTAKRIREVVT 768 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHh
Confidence 67789999999999975554 8999999999999988 78777887776654
No 90
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.95 E-value=11 Score=37.59 Aligned_cols=55 Identities=15% Similarity=0.178 Sum_probs=36.9
Q ss_pred HHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 64 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 64 R~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
-+++++.+ +.++ ||||-.-||=|.+ ++++++...+..- -+.++||||+|+++|+-
T Consensus 68 Er~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIi 125 (195)
T PRK14604 68 QRQLFELL-IGVS-GVGPKAALNLLSS----------GTPDELQLAIAGGDVARLARVPGIGKKTAERIV 125 (195)
T ss_pred HHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 44455544 4455 8998777776653 2455555555544 36778999999999995
No 91
>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=42.56 E-value=9.5 Score=37.91 Aligned_cols=55 Identities=18% Similarity=0.260 Sum_probs=35.6
Q ss_pred HHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhccc---CCCCcccCCcHHHHHHHH
Q 007746 64 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDS---LPIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 64 R~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~---LPI~kL~GIG~k~~~kL~ 130 (591)
-++++..+ +.++ ||||-+-+|-|. .++++++.+.+.. --+.++||||+|+++++-
T Consensus 67 Er~lF~~L-~~V~-GIGpK~Al~iL~----------~~~~~el~~aI~~~d~~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 67 ERELFKEL-IKVN-GVGPKLALAILS----------NMSPEEFVYAIETEEVKALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHHHHH-hCCC-CCCHHHHHHHHh----------cCCHHHHHHHHHhCCHHHHHhCCCCCHHHHHHHH
Confidence 34444444 3333 888877666543 2245566666554 457889999999999994
No 92
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.28 E-value=12 Score=37.32 Aligned_cols=55 Identities=18% Similarity=0.256 Sum_probs=37.9
Q ss_pred HHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 64 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 64 R~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
-+++++.+ ++++ ||||-.-||=|.+ ++++++...+..- -+.++||||+|+++++-
T Consensus 67 Er~lF~~L-~~V~-GIGpK~AL~iLs~----------~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 67 SLELFELL-LGVS-GVGPKLALALLSA----------LPPALLARALLEGDARLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 45555555 4555 8998777776653 2456666666554 36788999999999995
No 93
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.26 E-value=11 Score=37.74 Aligned_cols=58 Identities=21% Similarity=0.369 Sum_probs=37.7
Q ss_pred HHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 61 TELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 61 ~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
..-.+++++.+ +.++ ||||-.-||=|.+ ++++++...+..- .+.++||||+|+++|+-
T Consensus 64 t~~Er~lF~~L-isVs-GIGPK~ALaILs~----------~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 64 NSSEREVFEEL-IGVD-GIGPRAALRVLSG----------IKYNEFRDAIDREDIELISKVKGIGNKMAGKIF 124 (196)
T ss_pred CHHHHHHHHHH-hCcC-CcCHHHHHHHHcC----------CCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHH
Confidence 33345555555 4555 8988777776653 2445555555443 36778999999999995
No 94
>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=42.04 E-value=22 Score=31.95 Aligned_cols=35 Identities=14% Similarity=0.392 Sum_probs=24.8
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHH
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 149 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L 149 (591)
+.+++|||..++..+...+||..-.-+-.++.+++
T Consensus 17 Lt~IyGIG~~~A~~Ic~~lgi~~~~~~~~Ls~~~i 51 (107)
T PF00416_consen 17 LTKIYGIGRRKAKQICKKLGINPNKKVGDLSDEQI 51 (107)
T ss_dssp HTTSTTBCHHHHHHHHHHTTS-SSSBTTTSTHHHH
T ss_pred HhhhhccCHHHHHHHHHHcCCChhhhcccCCHHHH
Confidence 46899999999999888999965444444444433
No 95
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=41.50 E-value=36 Score=39.43 Aligned_cols=50 Identities=16% Similarity=0.287 Sum_probs=40.4
Q ss_pred CcccCCcHHHHHHHHHhcC-CCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 116 KKMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lG-I~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
-++-|+|.++.++|- ..| |+++.||..+..+.|... ||.+.+..|++...
T Consensus 428 mdI~GlGe~~i~~L~-~~G~i~~~~Diy~L~~~~l~~l~gfgeks~~nll~aIe 480 (562)
T PRK08097 428 LGLDGIGEGTWRALH-QTGLFEHLFSWLALTPEQLANTPGIGKARAEQLWHQFN 480 (562)
T ss_pred cCCCCcCHHHHHHHH-HcCCcCCHHHHhcCCHHHHhcCcCccHHHHHHHHHHHH
Confidence 457899999999998 677 699999999998888664 78777777766544
No 96
>COG5018 KapD Inhibitor of the KinA pathway to sporulation, predicted exonuclease [General function prediction only]
Probab=40.85 E-value=8 Score=38.09 Aligned_cols=39 Identities=26% Similarity=0.541 Sum_probs=35.0
Q ss_pred ccccccCCccccccCChHHHHHHHHhhCCCCCCCcccCC
Q 007746 540 KLRIEEIDPSVIDELPKEIQDEIQAWLRPSKRPHRVKQG 578 (591)
Q Consensus 540 ~~~~~~id~~~~~el~~ei~~e~~~~~~~~~~~~~~~~~ 578 (591)
.|.|.||..-+|+-.-.||-++++.++||.|.|.--++-
T Consensus 24 e~eiiei~a~lv~~id~~vvd~F~syVRP~~~P~Lt~~C 62 (210)
T COG5018 24 EFEIIEIEAGLVKSIDDEVVDTFSSYVRPKKFPKLTKRC 62 (210)
T ss_pred hceeeeehhhHHHHhhHHHHHHHHHhcCcccCchHHHHH
Confidence 466999999999999999999999999999999766653
No 97
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=40.47 E-value=27 Score=31.96 Aligned_cols=37 Identities=11% Similarity=0.278 Sum_probs=26.9
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQ 150 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~ 150 (591)
-+..+.|||..++..+...+||..-.-+-+++.+++.
T Consensus 16 aL~~i~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi~ 52 (113)
T TIGR03631 16 ALTYIYGIGRTRARKILEKAGIDPDKRVKDLTEEELN 52 (113)
T ss_pred eeeeeecccHHHHHHHHHHhCcCcccccccCCHHHHH
Confidence 3678999999999999989999744444444444443
No 98
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.31 E-value=14 Score=37.00 Aligned_cols=58 Identities=16% Similarity=0.160 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 61 TELRMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 61 ~~IR~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
..--++++..+ +.++ ||||-.-||=|.+ ++++++...+..- -+.++||||+|+++++-
T Consensus 66 ~~~Er~lF~~L-i~V~-GIGpK~Al~iLs~----------~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 66 TWDERQTFIVL-ISIS-KVGAKTALAILSQ----------FRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF 126 (203)
T ss_pred CHHHHHHHHHH-hCCC-CcCHHHHHHHHhh----------CCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHH
Confidence 33345555554 3455 8888777776653 2455555555543 36778999999999995
No 99
>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=38.34 E-value=29 Score=28.34 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=22.0
Q ss_pred CCc-ccCCcHHHHHHHHHh---c-CCCcHHHHhhc
Q 007746 115 IKK-MKQLGGKLGTSLQNE---L-GVTTVGDLLKF 144 (591)
Q Consensus 115 I~k-L~GIG~k~~~kL~~~---l-GI~TigDLa~~ 144 (591)
+.. ++|||.+.+++|-+. + ++.+..||..+
T Consensus 18 L~~~ipgig~~~a~~Il~~R~~~g~~~s~~dL~~v 52 (69)
T TIGR00426 18 LQRAMNGVGLKKAEAIVSYREEYGPFKTVEDLKQV 52 (69)
T ss_pred HHhHCCCCCHHHHHHHHHHHHHcCCcCCHHHHHcC
Confidence 445 899999999888733 3 47777777664
No 100
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=37.87 E-value=61 Score=30.66 Aligned_cols=54 Identities=20% Similarity=0.246 Sum_probs=38.5
Q ss_pred CCHHHHHHhccCCCCCCEEEeccccHHhhcccCCCCcccCCcHHHHHHHHHhcC-CCcHHHHhhcC
Q 007746 81 HNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELG-VTTVGDLLKFS 145 (591)
Q Consensus 81 ~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lG-I~TigDLa~~~ 145 (591)
.|..=|||+ .... ..-|....+.+|. .+||||+.+++++- ..| ..++.||.+.+
T Consensus 39 ~N~~d~kl~-~~~~---kIdiN~A~~~el~------~lpGigP~~A~~IV-~nGpf~sveDL~~V~ 93 (132)
T PRK02515 39 QNVADAKLG-EFGE---KIDLNNSSVRAFR------QFPGMYPTLAGKIV-KNAPYDSVEDVLNLP 93 (132)
T ss_pred cChhhHHHH-hcCC---cccCCccCHHHHH------HCCCCCHHHHHHHH-HCCCCCCHHHHHcCC
Confidence 377778888 3322 2234556666654 38999999999997 666 88999998763
No 101
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=36.63 E-value=31 Score=34.65 Aligned_cols=16 Identities=31% Similarity=0.488 Sum_probs=14.4
Q ss_pred CCcccCCcHHHHHHHH
Q 007746 115 IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~ 130 (591)
+++|||||+|+++||.
T Consensus 13 l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 13 LKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5679999999999995
No 102
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.37 E-value=41 Score=33.62 Aligned_cols=51 Identities=20% Similarity=0.129 Sum_probs=38.7
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHh--CcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~F--G~~~G~~L~~~arGid 169 (591)
..+.|||+|++-.+ |+-.+..+|+.+ +...|.+.- |+++|+++.-+++|.-
T Consensus 76 i~V~GIGpK~Al~i---Ls~~~~~el~~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~ 132 (195)
T PRK14604 76 IGVSGVGPKAALNL---LSSGTPDELQLAIAGGDVARLARVPGIGKKTAERIVLELKGKI 132 (195)
T ss_pred hCcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 46899999997665 455677777764 677887774 5678999999999863
No 103
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=36.09 E-value=33 Score=33.16 Aligned_cols=41 Identities=17% Similarity=0.334 Sum_probs=30.5
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHHhC
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESYG 154 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~k~FG 154 (591)
-++.|.|||..++..+...+||. +++||-.-....|...+.
T Consensus 31 aLt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~ 74 (154)
T PTZ00134 31 ALTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIA 74 (154)
T ss_pred eecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHh
Confidence 36789999999999998899996 566666555555555543
No 104
>KOG2534 consensus DNA polymerase IV (family X) [Replication, recombination and repair]
Probab=35.60 E-value=40 Score=36.28 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=25.6
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhcC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKFS 145 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~~ 145 (591)
+.+||||.+++++.- ..|++|+.|++.-+
T Consensus 100 tnifGvG~ktA~~Wy-~~GfrTled~Rk~~ 128 (353)
T KOG2534|consen 100 TNIFGVGLKTAEKWY-REGFRTLEDVRKKP 128 (353)
T ss_pred HHHhccCHHHHHHHH-HhhhhHHHHHHhCH
Confidence 568999999999995 99999999999544
No 105
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=35.40 E-value=25 Score=37.78 Aligned_cols=33 Identities=36% Similarity=0.469 Sum_probs=27.8
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSE 146 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~ 146 (591)
|+-+++|+|++...+|-..+||+++.+|+....
T Consensus 94 ~Ll~v~GlGpkKi~~Ly~elgi~~~e~l~~a~~ 126 (326)
T COG1796 94 PLLKVPGLGPKKIVSLYKELGIKDLEELQEALE 126 (326)
T ss_pred HHhhCCCCCcHHHHHHHHHHCcccHHHHHHHHH
Confidence 566799999987777777999999999998644
No 106
>CHL00013 rpoA RNA polymerase alpha subunit
Probab=35.38 E-value=44 Score=36.10 Aligned_cols=55 Identities=20% Similarity=0.357 Sum_probs=43.6
Q ss_pred hcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHH--HhCcchHHHHHHHH
Q 007746 109 LLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQE--SYGFNTGTWLWNIA 165 (591)
Q Consensus 109 fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k--~FG~~~G~~L~~~a 165 (591)
.+..++|.+| .+.-+...-|. +.||+|++||.+.+.+.|.+ -||.+....+...+
T Consensus 259 ~~~~~~Ie~L-~LSvRs~NcLk-~a~I~ti~dL~~~s~~dLl~ikN~GkKSl~EI~~~L 315 (327)
T CHL00013 259 ALKQIFIEQL-ELSVRAYNCLK-RANIHTLLDLLNYSQEDLLKIKNFGQKSAKEVLEAL 315 (327)
T ss_pred hhhceeHHhc-cCchhhhhhhh-hcCccCHHHHHhcCHHHHhhhhccCHhHHHHHHHHH
Confidence 4566788887 47778888895 99999999999999988744 48987766666665
No 107
>PRK00076 recR recombination protein RecR; Reviewed
Probab=35.14 E-value=33 Score=34.43 Aligned_cols=16 Identities=25% Similarity=0.478 Sum_probs=14.4
Q ss_pred CCcccCCcHHHHHHHH
Q 007746 115 IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~ 130 (591)
+++|||||+|+++||.
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5679999999999996
No 108
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.78 E-value=39 Score=33.90 Aligned_cols=51 Identities=14% Similarity=0.095 Sum_probs=37.6
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhh----cCHHHHHHHh--CcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLK----FSEDKLQESY--GFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~----~~~~~L~k~F--G~~~G~~L~~~arGid 169 (591)
..+.|||+|++-.+. +-.+..+|+. -+...|.+.- |+++|+++.-+++|.-
T Consensus 77 i~V~GIGpK~Al~iL---s~~~~~~l~~aI~~~D~~~L~~ipGIGkKtAerIilELkdK~ 133 (203)
T PRK14602 77 ISISKVGAKTALAIL---SQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIFLELKYKL 133 (203)
T ss_pred hCCCCcCHHHHHHHH---hhCCHHHHHHHHHhCCHHHHhcCCCcCHHHHHHHHHHHHHhh
Confidence 568999999987664 4446666655 3677787774 5678999999999863
No 109
>PRK13844 recombination protein RecR; Provisional
Probab=34.48 E-value=34 Score=34.45 Aligned_cols=16 Identities=25% Similarity=0.507 Sum_probs=14.4
Q ss_pred CCcccCCcHHHHHHHH
Q 007746 115 IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~ 130 (591)
+++|||||+|+++||.
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 5679999999999996
No 110
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=34.45 E-value=52 Score=39.07 Aligned_cols=46 Identities=15% Similarity=0.250 Sum_probs=31.2
Q ss_pred ccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHHHH
Q 007746 118 MKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWNIA 165 (591)
Q Consensus 118 L~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~~a 165 (591)
|||||.+++++|.+.+ .++.+|..++.+.|... +|.+.+..++.+.
T Consensus 533 IpgIG~~~ak~L~~~F--~si~~L~~As~eeL~~i~GIG~k~A~sI~~ff 580 (689)
T PRK14351 533 IPEVGPTTARNLAREF--GTFEAIMDADEEALRAVDDVGPTVAEEIREFF 580 (689)
T ss_pred CCCcCHHHHHHHHHHh--CCHHHHHhCCHHHHhccCCcCHHHHHHHHHHH
Confidence 5778888877775333 66777777777777666 6666666555553
No 111
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=34.17 E-value=36 Score=39.52 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=39.3
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH--hCcchHHHHHH
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES--YGFNTGTWLWN 163 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~--FG~~~G~~L~~ 163 (591)
.+.+..+||||.+...+|.+.+ .++.+++.++.+.|.+. +|.+.+..++.
T Consensus 524 ~~~L~~IpGIG~kr~~~LL~~F--GS~~~I~~As~eeL~~vpGi~~~~A~~I~~ 575 (577)
T PRK14668 524 STVLDDVPGVGPETRKRLLRRF--GSVEGVREASVEDLRDVPGVGEKTAETIRE 575 (577)
T ss_pred HhHHhcCCCCCHHHHHHHHHHc--CCHHHHHhCCHHHHHhCCCCCHHHHHHHHH
Confidence 4678899999999999996444 69999999999999888 55545555543
No 112
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.28 E-value=23 Score=35.18 Aligned_cols=54 Identities=15% Similarity=0.217 Sum_probs=33.7
Q ss_pred HHHHHHHhCCeEEEEecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC---CCCcccCCcHHHHHHHH
Q 007746 64 RMQVLKETEFTCSAGIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL---PIKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 64 R~~I~~etGLt~SVGIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L---PI~kL~GIG~k~~~kL~ 130 (591)
-+++++.+ +.++ ||||-.-||=|.+ ++++++...+..- -+ ++||||+|+++++-
T Consensus 68 Er~lF~~L-isV~-GIGpK~Al~iLs~----------~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 68 EQDCLRML-VKVS-GVNYKTAMSILSK----------LTPEQLFSAIVNEDKAAL-KVNGIGEKLINRII 124 (186)
T ss_pred HHHHHHHH-hCcC-CcCHHHHHHHHcc----------CCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHH
Confidence 45555555 4555 8888776666653 2334444443322 35 68999999999995
No 113
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=33.24 E-value=48 Score=33.17 Aligned_cols=51 Identities=18% Similarity=0.124 Sum_probs=38.5
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHh--CcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~F--G~~~G~~L~~~arGid 169 (591)
..+.|||+|++-.+ |+-.+..+|+.+ +...|.+.- |+++|+++.-+++|.-
T Consensus 75 ~~V~GIGpK~AL~i---Ls~~~~~~l~~aI~~~D~~~L~kvpGIGkKtAerIilELkdK~ 131 (197)
T PRK14603 75 LGVSGVGPKLALAL---LSALPPALLARALLEGDARLLTSASGVGKKLAERIALELKGKV 131 (197)
T ss_pred hCcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 46899999997655 555577777664 677787774 5678999999999864
No 114
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=32.21 E-value=46 Score=30.91 Aligned_cols=36 Identities=8% Similarity=0.253 Sum_probs=26.1
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 149 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L 149 (591)
-+..+.|||..++..+...+||..-.-+-+++.+++
T Consensus 18 aL~~I~GIG~~~a~~i~~~lgi~~~~~~~~L~~~qi 53 (122)
T PRK05179 18 ALTYIYGIGRTRAKEILAAAGIDPDTRVKDLTDEEL 53 (122)
T ss_pred eecccccccHHHHHHHHHHhCcCcccccccCCHHHH
Confidence 467899999999999988999974433444444444
No 115
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=31.82 E-value=46 Score=30.90 Aligned_cols=36 Identities=3% Similarity=0.119 Sum_probs=25.7
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKL 149 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L 149 (591)
-++.+.|||..++..+.+.+||.--.-+-+++.+++
T Consensus 18 aLt~i~GIG~~~A~~ic~~lgi~~~~~~~~Lt~~qi 53 (122)
T CHL00137 18 ALTYIYGIGLTSAKEILEKANIDPDIRTKDLTDEQI 53 (122)
T ss_pred eecccccccHHHHHHHHHHcCcCcCcCcccCCHHHH
Confidence 467899999999999998999964333333344443
No 116
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.41 E-value=58 Score=32.74 Aligned_cols=51 Identities=10% Similarity=0.100 Sum_probs=38.5
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHh--CcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~F--G~~~G~~L~~~arGid 169 (591)
-.+.|||+|++-.+ |.-.++.+|+.+ +...|.+.- |+++|+++.-+++|.-
T Consensus 75 isVsGIGPK~ALaI---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIIlELkdKl 131 (196)
T PRK13901 75 IGVDGIGPRAALRV---LSGIKYNEFRDAIDREDIELISKVKGIGNKMAGKIFLKLRGKL 131 (196)
T ss_pred hCcCCcCHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 46899999997555 555677777764 667787774 5678999999999863
No 117
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.39 E-value=56 Score=32.38 Aligned_cols=51 Identities=14% Similarity=0.175 Sum_probs=38.2
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHH--hCcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQES--YGFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~--FG~~~G~~L~~~arGid 169 (591)
..+.|||+|++-.+ |.-.++.+|+.+ +...|.+. .|+++|+++.-+++|.-
T Consensus 76 i~VsGIGpK~Al~I---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAeRIilELkdK~ 132 (183)
T PRK14601 76 LKVNGIGANTAMAV---CSSLDVNSFYKALSLGDESVLKKVPGIGPKSAKRIIAELSDAK 132 (183)
T ss_pred hccCCccHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHh
Confidence 46899999997544 555677777764 66778777 45678999999999863
No 118
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=30.18 E-value=45 Score=26.49 Aligned_cols=46 Identities=28% Similarity=0.484 Sum_probs=38.1
Q ss_pred ccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcc
Q 007746 102 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFN 156 (591)
Q Consensus 102 ~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~ 156 (591)
+++++.+||..+ |+ ......+. ..||..+..|..++.+.|. .+|+.
T Consensus 5 ~~~~v~~WL~~~------gl-~~y~~~f~-~~~i~g~~~L~~l~~~~L~-~lGI~ 50 (66)
T PF07647_consen 5 SPEDVAEWLKSL------GL-EQYADNFR-ENGIDGLEDLLQLTEEDLK-ELGIT 50 (66)
T ss_dssp CHHHHHHHHHHT------TC-GGGHHHHH-HTTCSHHHHHTTSCHHHHH-HTTTT
T ss_pred CHHHHHHHHHHC------Cc-HHHHHHHH-HcCCcHHHHHhhCCHHHHH-HcCCC
Confidence 567788888865 66 47778886 9999999999999999997 89984
No 119
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=30.08 E-value=50 Score=38.43 Aligned_cols=49 Identities=12% Similarity=0.232 Sum_probs=38.5
Q ss_pred cCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc--chHHHHHH
Q 007746 112 SLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF--NTGTWLWN 163 (591)
Q Consensus 112 ~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~--~~G~~L~~ 163 (591)
.-++.+|+|||.+..++|.. .+.++.++..++.+.|.+. |. +.++.++.
T Consensus 529 ~s~Ld~I~GiG~~r~~~LL~--~Fgs~~~i~~As~eel~~v-gi~~~~a~~i~~ 579 (581)
T COG0322 529 QSSLDDIPGIGPKRRKALLK--HFGSLKGIKSASVEELAKV-GISKKLAEKIYE 579 (581)
T ss_pred cCccccCCCcCHHHHHHHHH--HhhCHHHHHhcCHHHHHHc-CCCHHHHHHHHh
Confidence 44778999999999999964 4558999999999999998 65 34555554
No 120
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.60 E-value=63 Score=32.14 Aligned_cols=51 Identities=14% Similarity=0.121 Sum_probs=37.6
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHh--CcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~F--G~~~G~~L~~~arGid 169 (591)
..+.|||+|++-.+ ++-.++.+|+.+ +...|.+.- |+++|+++.-++++.-
T Consensus 76 i~V~GIGpK~AL~i---Ls~~~~~el~~aI~~~D~~~L~~vpGIGkKtAerIilELkdK~ 132 (188)
T PRK14606 76 TKVSRLGPKTALKI---ISNEDAETLVTMIASQDVEGLSKLPGISKKTAERIVMELKDEF 132 (188)
T ss_pred hccCCccHHHHHHH---HcCCCHHHHHHHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHhh
Confidence 46899999997655 455566666653 667787774 5678999999999853
No 121
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=28.13 E-value=55 Score=31.31 Aligned_cols=39 Identities=26% Similarity=0.475 Sum_probs=28.2
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQES 152 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~k~ 152 (591)
-+..|.|||.+++..+...+||. .++||-.-....|...
T Consensus 22 aLt~I~GIG~~~a~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~ 63 (144)
T TIGR03629 22 ALTGIKGIGRRFARAIARKLGVDPNAKLGYLDDEEIEKLEEA 63 (144)
T ss_pred eecceeccCHHHHHHHHHHcCcCCCCCcccCCHHHHHHHHHH
Confidence 46789999999999998899996 5566555444444443
No 122
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=27.87 E-value=1e+02 Score=23.55 Aligned_cols=46 Identities=28% Similarity=0.432 Sum_probs=35.8
Q ss_pred ccccHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcch
Q 007746 102 PFSSVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNT 157 (591)
Q Consensus 102 ~~~~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~ 157 (591)
+.+++.+||..+ |+ ......+. ..|| +..+|..++.+.|. .+|+..
T Consensus 3 ~~~~V~~wL~~~------~~-~~y~~~f~-~~~i-~g~~L~~l~~~dL~-~lgi~~ 48 (63)
T cd00166 3 SPEDVAEWLESL------GL-GQYADNFR-ENGI-DGDLLLLLTEEDLK-ELGITL 48 (63)
T ss_pred CHHHHHHHHHHc------Ch-HHHHHHHH-HcCC-CHHHHhHCCHHHHH-HcCCCC
Confidence 456677777654 33 57778885 8999 99999999999998 889865
No 123
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=27.48 E-value=81 Score=37.35 Aligned_cols=51 Identities=20% Similarity=0.073 Sum_probs=40.4
Q ss_pred CCcccCCcHHHHHHHHHhcC-CCcHHHHhhcCHHHHHHH--hCcchHHHHHHHHc
Q 007746 115 IKKMKQLGGKLGTSLQNELG-VTTVGDLLKFSEDKLQES--YGFNTGTWLWNIAR 166 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lG-I~TigDLa~~~~~~L~k~--FG~~~G~~L~~~ar 166 (591)
--+|-|+|.++.++|- ..| |.++.||..+..+.|... ||.+.+..|++...
T Consensus 438 aldI~GlG~~~i~~L~-~~G~i~~~~Dly~L~~~~l~~l~g~geksa~nl~~~Ie 491 (669)
T PRK14350 438 CMNIVGLSDKTIEFLF-EKKFISSEIDLYTFNFDRLINLKGFKDKRINNLKRSIE 491 (669)
T ss_pred cccccCcCHHHHHHHH-HcCCcCCHHHHhhCCHHHHhhccCccHHHHHHHHHHHH
Confidence 4478899999999998 555 789999999998888654 77767777776544
No 124
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=27.11 E-value=87 Score=34.25 Aligned_cols=39 Identities=26% Similarity=0.388 Sum_probs=33.6
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCc
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGF 155 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~ 155 (591)
+.++|+||+.++++|-+.|| ++..+..++.+.|.+.=|.
T Consensus 289 Ls~IPrl~k~iAk~Ll~~FG--SL~~Il~As~eeL~~VeGI 327 (352)
T PRK13482 289 LSKIPRLPSAVIENLVEHFG--SLQGLLAASIEDLDEVEGI 327 (352)
T ss_pred HhcCCCCCHHHHHHHHHHcC--CHHHHHcCCHHHHhhCCCc
Confidence 46789999999999987887 9999999999999887553
No 125
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=26.85 E-value=62 Score=31.14 Aligned_cols=40 Identities=20% Similarity=0.429 Sum_probs=30.4
Q ss_pred CCCcccCCcHHHHHHHHHhcCCC---cHHHHhhcCHHHHHHHh
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVT---TVGDLLKFSEDKLQESY 153 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~---TigDLa~~~~~~L~k~F 153 (591)
-++.|.|||..++..+.+.+||. +++||-.--...|...+
T Consensus 26 aLt~IyGIG~~~a~~Ic~~lgi~~~~~~~~Lt~~qi~~l~~~i 68 (149)
T PRK04053 26 ALTGIKGIGRRTARAIARKLGLDPNAKLGYLSDEEIEKIEEAL 68 (149)
T ss_pred eccccccccHHHHHHHHHHcCcCCCCccCcCCHHHHHHHHHHH
Confidence 46789999999999998899997 56666665555555554
No 126
>COG0099 RpsM Ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=26.72 E-value=80 Score=29.43 Aligned_cols=39 Identities=8% Similarity=0.252 Sum_probs=30.0
Q ss_pred CCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHH
Q 007746 114 PIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQES 152 (591)
Q Consensus 114 PI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~ 152 (591)
-++.|.|||..++..+.+.+||.--.-+-+++.+++.+.
T Consensus 18 ALt~IyGIG~~~a~~I~~~~gi~~~~r~~eLteeei~~i 56 (121)
T COG0099 18 ALTYIYGIGRRRAKEICKKAGIDPDKRVGELTEEEIERL 56 (121)
T ss_pred hhhhhccccHHHHHHHHHHcCCCHhHhhccCCHHHHHHH
Confidence 467789999999999888999976666666666666543
No 127
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=26.58 E-value=56 Score=30.79 Aligned_cols=47 Identities=15% Similarity=0.127 Sum_probs=30.6
Q ss_pred CCccchhhhhhcCCCCchhhhcchHHHHHHHHHHHHHHHh-------CCeEEEEecCC
Q 007746 32 DSKATVKEWLCRCDADHRDKLLACGVLIVTELRMQVLKET-------EFTCSAGIAHN 82 (591)
Q Consensus 32 ~~~ySIDE~fl~lDvt~~~~l~~~~~~lA~~IR~~I~~et-------GLt~SVGIA~N 82 (591)
...++=|||.+.+.-.. -.....+|++|+..|.... .+++|+||+..
T Consensus 95 ~~R~gGdEF~i~l~~~~----~~~~~~~~~~l~~~~~~~~~~~~~~~~~t~siGi~~~ 148 (181)
T COG2199 95 VARLGGDEFAVLLPGTS----LEEAARLAERIRAALEEPFFLGGEELRVTVSIGVALY 148 (181)
T ss_pred EEEeccceeEEEeCCCC----HHHHHHHHHHHHHHHHcccccCCceEEEEEEEEEEec
Confidence 44556677776543332 1245678888888886654 48999998743
No 128
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=25.61 E-value=54 Score=32.54 Aligned_cols=50 Identities=16% Similarity=0.040 Sum_probs=36.4
Q ss_pred CcccCCcHHHHHHHHHhcCCCcHHHHhhc----CHHHHHHHh--CcchHHHHHHHHcCCC
Q 007746 116 KKMKQLGGKLGTSLQNELGVTTVGDLLKF----SEDKLQESY--GFNTGTWLWNIARGIS 169 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~~lGI~TigDLa~~----~~~~L~k~F--G~~~G~~L~~~arGid 169 (591)
..+.|||+|++-.+ |.-.+..+|..+ +...| +.- |+++|+++.-+++|.-
T Consensus 76 isV~GIGpK~Al~i---Ls~~~~~~l~~aI~~~D~~~L-~vpGIGkKtAerIilELk~K~ 131 (186)
T PRK14600 76 VKVSGVNYKTAMSI---LSKLTPEQLFSAIVNEDKAAL-KVNGIGEKLINRIITELQYKV 131 (186)
T ss_pred hCcCCcCHHHHHHH---HccCCHHHHHHHHHcCCHhhe-ECCCCcHHHHHHHHHHHHHHh
Confidence 47899999997665 444566676653 56677 664 4678999999999853
No 129
>PRK07945 hypothetical protein; Provisional
Probab=24.90 E-value=1.2e+02 Score=32.56 Aligned_cols=57 Identities=16% Similarity=0.099 Sum_probs=35.9
Q ss_pred HHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhcCHHHHHHHhCcchHHHHHHHHcC
Q 007746 106 VKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKFSEDKLQESYGFNTGTWLWNIARG 167 (591)
Q Consensus 106 v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~~~~~L~k~FG~~~G~~L~~~arG 167 (591)
+.++...-.+.+|||||+.++.++.+-+-=-++.-| +.|+...++..|..|....+|
T Consensus 42 ~~~~~~~g~l~~~~giG~~~a~~i~e~~~tg~~~~l-----~~l~~~~~~~~g~~l~~~~~~ 98 (335)
T PRK07945 42 RARRARAGSLTSLPGIGPKTAKVIAQALAGRVPDYL-----AELRADAEPLGGGALRAALRG 98 (335)
T ss_pred HHHHHhcCCcccCCCcCHHHHHHHHHHHhcCCHHHH-----HHHHHhhcCCccHHHHHHHhh
Confidence 444443336889999999999999732222233322 445566666557777777776
No 130
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=24.28 E-value=57 Score=27.37 Aligned_cols=26 Identities=31% Similarity=0.480 Sum_probs=17.8
Q ss_pred CCcccCCcHHHHHHHHHhcCCCcHHHHh
Q 007746 115 IKKMKQLGGKLGTSLQNELGVTTVGDLL 142 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~lGI~TigDLa 142 (591)
+.-+||||.+++.+|-..+| ++..+.
T Consensus 24 i~gv~giG~k~A~~ll~~~~--~~~~~~ 49 (75)
T cd00080 24 IPGVPGIGPKTALKLLKEYG--SLENLL 49 (75)
T ss_pred CCCCCcccHHHHHHHHHHhC--CHHHHH
Confidence 34689999999999874444 444443
No 131
>PF14716 HHH_8: Helix-hairpin-helix domain; PDB: 2W9M_A 1HUZ_A 1HUO_A 2BPG_B 2BPF_A 1DK3_A 1BPE_A 1BNO_A 1BNP_A 1DK2_A ....
Probab=23.43 E-value=51 Score=26.99 Aligned_cols=16 Identities=19% Similarity=0.542 Sum_probs=14.3
Q ss_pred CCcccCCcHHHHHHHH
Q 007746 115 IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~ 130 (591)
+..|||||.+++.++.
T Consensus 49 ~~~l~gIG~~ia~kI~ 64 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKID 64 (68)
T ss_dssp HCTSTTTTHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHH
Confidence 5789999999999986
No 132
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=23.10 E-value=71 Score=32.17 Aligned_cols=16 Identities=31% Similarity=0.468 Sum_probs=14.4
Q ss_pred CCcccCCcHHHHHHHH
Q 007746 115 IKKMKQLGGKLGTSLQ 130 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~ 130 (591)
+++|||||.|++.|+.
T Consensus 14 l~kLPGvG~KsA~R~A 29 (198)
T COG0353 14 LKKLPGVGPKSAQRLA 29 (198)
T ss_pred HhhCCCCChhHHHHHH
Confidence 5689999999999996
No 133
>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=22.65 E-value=1.2e+02 Score=36.22 Aligned_cols=37 Identities=19% Similarity=0.276 Sum_probs=28.5
Q ss_pred cHHhhcccCCCCcccCCcHHHHHHHHHhcCCCcHHHHhhc
Q 007746 105 SVKGLLDSLPIKKMKQLGGKLGTSLQNELGVTTVGDLLKF 144 (591)
Q Consensus 105 ~v~~fL~~LPI~kL~GIG~k~~~kL~~~lGI~TigDLa~~ 144 (591)
.+..||. =..++|||++++++|-+.||..++.-|.+-
T Consensus 79 ~i~~yL~---s~~~~GIG~~~A~~iv~~fg~~~~~~i~~~ 115 (720)
T TIGR01448 79 GIVAYLS---SRSIKGVGKKLAQRIVKTFGEAAFDVLDDD 115 (720)
T ss_pred HHHHHHh---cCCCCCcCHHHHHHHHHHhCHhHHHHHHhC
Confidence 4556766 345899999999999889998877766554
No 134
>PRK05752 uroporphyrinogen-III synthase; Validated
Probab=22.60 E-value=1.9e+02 Score=29.37 Aligned_cols=77 Identities=16% Similarity=0.159 Sum_probs=45.4
Q ss_pred HHHHHHHHHHHHHhCCeEEE-------EecCCHHHHHHhccCCCCCCEEEeccccHHhhcccC-------CCCcccCCcH
Q 007746 58 LIVTELRMQVLKETEFTCSA-------GIAHNKMLAKLASGMNKPAQQTTVPFSSVKGLLDSL-------PIKKMKQLGG 123 (591)
Q Consensus 58 ~lA~~IR~~I~~etGLt~SV-------GIA~NKlLAKLAS~~aKP~G~~vl~~~~v~~fL~~L-------PI~kL~GIG~ 123 (591)
.-+.++.+.+ ++.|..+-. -+..+.-+.....+++.-+.+.+..+..++.|+..+ +-..+..||.
T Consensus 13 ~~~~~l~~~l-~~~G~~~~~~P~i~i~p~~~~~~~~~~l~~l~~~d~iifTS~naV~~~~~~l~~~~~~~~~~~~~aVG~ 91 (255)
T PRK05752 13 EECAALAASL-AEAGIFSSSLPLLAIEPLPETPEQRALLLELDRYCAVIVVSKPAARLGLELLDRYWPQPPQQPWFSVGA 91 (255)
T ss_pred HHHHHHHHHH-HHcCCCEEEcCcEEEeeCCCCHHHHHHHhcCCCCCEEEEECHHHHHHHHHHHHhhCCCCcCCEEEEECH
Confidence 3455555555 456765533 223333343433455555666666676666654322 1235668999
Q ss_pred HHHHHHHHhcCCC
Q 007746 124 KLGTSLQNELGVT 136 (591)
Q Consensus 124 k~~~kL~~~lGI~ 136 (591)
+|++.|+ .+||.
T Consensus 92 ~Ta~al~-~~G~~ 103 (255)
T PRK05752 92 ATAAILQ-DYGLD 103 (255)
T ss_pred HHHHHHH-HcCCC
Confidence 9999996 89984
No 135
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=21.98 E-value=3.7e+02 Score=28.27 Aligned_cols=100 Identities=9% Similarity=0.032 Sum_probs=51.5
Q ss_pred HHHHHHhCCeEEEEecCCH-----------HHHHHhccCCCCCCEE-----EeccccHHhhcc-------cCCCCcccCC
Q 007746 65 MQVLKETEFTCSAGIAHNK-----------MLAKLASGMNKPAQQT-----TVPFSSVKGLLD-------SLPIKKMKQL 121 (591)
Q Consensus 65 ~~I~~etGLt~SVGIA~NK-----------lLAKLAS~~aKP~G~~-----vl~~~~v~~fL~-------~LPI~kL~GI 121 (591)
+.|++..+-..+||+|-++ -+++|..... .+.-+ +.+.+.+.+|+. .+|| ++||
T Consensus 120 ~~i~~~~~~~f~igva~~Pe~Hp~~~~~~~d~~~L~~Ki~-aGA~f~iTQ~~Fd~~~~~~f~~~~~~~gi~~PI--i~GI 196 (281)
T TIGR00677 120 KYIRSKYGDYFCIGVAGYPEGHPEAESVELDLKYLKEKVD-AGADFIITQLFYDVDNFLKFVNDCRAIGIDCPI--VPGI 196 (281)
T ss_pred HHHHHhCCCceEEEEEECCCCCCCCCCHHHHHHHHHHHHH-cCCCEeeccceecHHHHHHHHHHHHHcCCCCCE--Eeec
Confidence 3344445545678888663 2344442221 12112 334455556655 3355 7887
Q ss_pred cH----HHHHHHHHhcCCCcHHHHhh----c-CHHHHHHHhCcchHHHHHHHHcC
Q 007746 122 GG----KLGTSLQNELGVTTVGDLLK----F-SEDKLQESYGFNTGTWLWNIARG 167 (591)
Q Consensus 122 G~----k~~~kL~~~lGI~TigDLa~----~-~~~~L~k~FG~~~G~~L~~~arG 167 (591)
-+ +...++.+..||.-..+|.+ . +.....+.+|.+.+..+.+.+.-
T Consensus 197 ~pi~s~~~~~~~~~~~Gi~vP~~l~~~l~~~~~~~~~~~~~gi~~a~~~~~~l~~ 251 (281)
T TIGR00677 197 MPINNYASFLRRAKWSKTKIPQEIMSRLEPIKDDDEAVRDYGIELIVEMCQKLLA 251 (281)
T ss_pred cccCCHHHHHHHHhcCCCCCCHHHHHHHHhccCCHHHHHHHHHHHHHHHHHHHHH
Confidence 44 33444433568876666554 2 23344556777666666666543
No 136
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=20.69 E-value=79 Score=30.25 Aligned_cols=29 Identities=28% Similarity=0.450 Sum_probs=21.9
Q ss_pred CcccCCcHHHHHHHHH---hcC-CCcHHHHhhc
Q 007746 116 KKMKQLGGKLGTSLQN---ELG-VTTVGDLLKF 144 (591)
Q Consensus 116 ~kL~GIG~k~~~kL~~---~lG-I~TigDLa~~ 144 (591)
..|||||.+.++++.. ..| ++++.||+..
T Consensus 100 ~~lpgIG~~kA~aIi~yRe~~G~f~sv~dL~~v 132 (149)
T COG1555 100 QALPGIGPKKAQAIIDYREENGPFKSVDDLAKV 132 (149)
T ss_pred HHCCCCCHHHHHHHHHHHHHcCCCCcHHHHHhc
Confidence 5689999999998862 233 7788888764
No 137
>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=20.54 E-value=86 Score=28.78 Aligned_cols=29 Identities=17% Similarity=0.292 Sum_probs=20.0
Q ss_pred CCcccCCcHHHHHHHHHhc----CCCcHHHHhh
Q 007746 115 IKKMKQLGGKLGTSLQNEL----GVTTVGDLLK 143 (591)
Q Consensus 115 I~kL~GIG~k~~~kL~~~l----GI~TigDLa~ 143 (591)
+..+||||.+.++++-... ++.++.||..
T Consensus 70 L~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL~~ 102 (120)
T TIGR01259 70 LQALPGIGPAKAKAIIEYREENGAFKSVDDLTK 102 (120)
T ss_pred HhcCCCCCHHHHHHHHHHHHhcCCcCCHHHHHc
Confidence 3468999999999987333 3556666544
Done!