Query psy6808
Match_columns 132
No_of_seqs 85 out of 87
Neff 1.9
Searched_HMMs 46136
Date Fri Aug 16 18:53:49 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6808.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6808hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02961 BAF: Barrier to autoi 100.0 2.4E-30 5.3E-35 185.9 2.5 47 27-73 1-47 (89)
2 KOG4233|consensus 99.9 2.6E-26 5.6E-31 166.2 2.3 47 27-73 1-47 (90)
3 PRK04301 radA DNA repair and r 96.3 0.0013 2.8E-08 52.4 0.8 43 40-82 1-43 (317)
4 PF11798 IMS_HHH: IMS family H 96.0 0.0043 9.2E-08 36.5 1.7 23 44-66 10-32 (32)
5 PF14520 HHH_5: Helix-hairpin- 91.9 0.092 2E-06 33.1 1.4 28 47-74 7-34 (60)
6 TIGR02236 recomb_radA DNA repa 90.6 0.098 2.1E-06 41.2 0.6 36 47-82 1-36 (310)
7 cd00424 PolY Y-family of DNA p 88.7 0.24 5.1E-06 39.8 1.5 36 41-76 169-204 (343)
8 PRK02406 DNA polymerase IV; Va 88.6 0.13 2.8E-06 41.2 -0.1 41 41-81 164-204 (343)
9 cd01703 PolY_Pol_iota DNA Poly 87.9 0.3 6.6E-06 41.1 1.7 35 42-76 169-203 (379)
10 PRK03352 DNA polymerase IV; Va 87.8 0.24 5.2E-06 39.7 1.0 39 42-80 174-212 (346)
11 COG3743 Uncharacterized conser 87.7 0.42 9.2E-06 37.1 2.2 46 35-80 56-102 (133)
12 cd01701 PolY_Rev1 DNA polymera 85.9 0.38 8.2E-06 40.2 1.2 37 40-76 217-253 (404)
13 PRK03858 DNA polymerase IV; Va 85.5 0.38 8.3E-06 39.2 1.1 36 42-77 170-205 (396)
14 cd01700 PolY_Pol_V_umuC umuC s 85.3 0.54 1.2E-05 37.7 1.8 41 40-80 171-211 (344)
15 cd03586 PolY_Pol_IV_kappa DNA 84.2 0.56 1.2E-05 36.8 1.4 39 42-80 168-206 (334)
16 PRK03609 umuC DNA polymerase V 82.4 0.76 1.7E-05 38.3 1.6 36 42-77 176-211 (422)
17 PRK03103 DNA polymerase IV; Re 80.8 0.51 1.1E-05 38.8 0.0 39 43-81 179-217 (409)
18 PRK12311 rpsB 30S ribosomal pr 80.2 0.88 1.9E-05 38.8 1.2 37 45-81 263-299 (326)
19 PRK02794 DNA polymerase IV; Pr 80.1 0.86 1.9E-05 38.0 1.1 38 41-78 205-242 (419)
20 PF11731 Cdd1: Pathogenicity l 79.9 0.73 1.6E-05 33.4 0.6 28 45-72 12-39 (93)
21 PRK01810 DNA polymerase IV; Va 78.8 0.56 1.2E-05 38.6 -0.4 38 43-80 177-214 (407)
22 PTZ00205 DNA polymerase kappa; 77.7 1.2 2.5E-05 40.9 1.3 34 42-75 306-339 (571)
23 smart00278 HhH1 Helix-hairpin- 77.1 1.8 3.9E-05 23.8 1.5 18 46-63 2-19 (26)
24 PRK02515 psbU photosystem II c 76.8 0.83 1.8E-05 35.4 0.1 44 47-92 63-109 (132)
25 PRK03348 DNA polymerase IV; Pr 76.3 1.4 3E-05 37.7 1.4 39 41-79 176-214 (454)
26 cd01702 PolY_Pol_eta DNA Polym 76.1 0.6 1.3E-05 38.9 -0.9 42 40-81 177-221 (359)
27 PRK01216 DNA polymerase IV; Va 74.6 1.9 4.1E-05 35.9 1.7 41 40-80 173-213 (351)
28 KOG1014|consensus 74.4 2.2 4.8E-05 36.8 2.1 27 49-78 57-83 (312)
29 PF14716 HHH_8: Helix-hairpin- 74.4 2 4.4E-05 27.8 1.4 18 46-63 48-65 (68)
30 COG5608 LEA14-like dessication 74.1 2.2 4.8E-05 34.2 1.9 26 72-97 27-68 (161)
31 PRK12278 50S ribosomal protein 73.5 1.9 4.1E-05 35.2 1.4 39 43-81 156-194 (221)
32 PF04994 TfoX_C: TfoX C-termin 73.2 2 4.4E-05 29.5 1.3 27 45-71 3-29 (81)
33 PF00633 HHH: Helix-hairpin-he 73.2 2.6 5.7E-05 24.6 1.6 17 46-62 12-28 (30)
34 PRK14133 DNA polymerase IV; Pr 72.4 1.5 3.2E-05 35.3 0.6 38 43-80 171-208 (347)
35 PRK10917 ATP-dependent DNA hel 70.8 2.4 5.2E-05 38.0 1.6 39 45-83 9-47 (681)
36 PF10391 DNA_pol_lambd_f: Fing 70.4 3 6.5E-05 26.9 1.5 25 48-72 5-29 (52)
37 PLN03187 meiotic recombination 67.4 1.8 3.9E-05 36.6 0.0 38 44-81 28-67 (344)
38 PRK12766 50S ribosomal protein 63.7 5.4 0.00012 33.2 2.2 32 45-76 3-34 (232)
39 PF14229 DUF4332: Domain of un 63.6 4.1 8.8E-05 29.5 1.3 32 51-82 1-32 (122)
40 PF03625 DUF302: Domain of unk 61.5 2.6 5.7E-05 26.6 -0.0 42 57-98 4-47 (65)
41 COG0389 DinP Nucleotidyltransf 61.3 2.5 5.5E-05 35.0 -0.1 40 44-84 175-214 (354)
42 PTZ00035 Rad51 protein; Provis 61.0 2.5 5.5E-05 35.1 -0.2 37 46-82 22-60 (337)
43 cd03468 PolY_like DNA Polymera 60.9 3.8 8.3E-05 32.1 0.8 39 41-80 167-205 (335)
44 PF09288 UBA_3: Fungal ubiquit 58.8 3 6.6E-05 28.2 -0.1 28 48-75 3-30 (55)
45 PRK03980 flap endonuclease-1; 55.3 6 0.00013 32.7 1.1 56 39-94 183-240 (292)
46 COG0300 DltE Short-chain dehyd 54.6 5.9 0.00013 32.8 0.9 19 49-67 14-32 (265)
47 PF12826 HHH_2: Helix-hairpin- 54.6 8.8 0.00019 24.8 1.6 18 46-63 36-53 (64)
48 cd00080 HhH2_motif Helix-hairp 53.9 11 0.00023 25.1 1.9 24 41-64 16-41 (75)
49 TIGR02238 recomb_DMC1 meiotic 52.8 5.3 0.00012 33.0 0.4 32 51-82 7-38 (313)
50 cd00141 NT_POLXc Nucleotidyltr 52.3 6.2 0.00014 32.3 0.7 42 30-71 69-111 (307)
51 smart00279 HhH2 Helix-hairpin- 51.2 14 0.00031 22.2 2.0 23 42-64 11-35 (36)
52 PRK07945 hypothetical protein; 51.1 11 0.00023 31.3 1.9 19 46-64 50-68 (335)
53 PF02371 Transposase_20: Trans 50.4 10 0.00022 25.3 1.4 18 46-63 3-20 (87)
54 COG1200 RecG RecG-like helicas 47.8 15 0.00033 34.8 2.5 43 45-87 10-52 (677)
55 PF13399 LytR_C: LytR cell env 47.2 29 0.00062 22.7 3.2 39 48-88 12-50 (90)
56 PF14229 DUF4332: Domain of un 46.3 15 0.00032 26.6 1.8 28 46-73 54-81 (122)
57 PLN03186 DNA repair protein RA 45.5 7 0.00015 33.0 0.0 36 46-81 27-64 (342)
58 TIGR02239 recomb_RAD51 DNA rep 42.3 9.2 0.0002 31.5 0.2 32 51-82 7-38 (316)
59 PRK14601 ruvA Holliday junctio 42.0 10 0.00022 29.7 0.5 18 45-62 108-125 (183)
60 KOG2093|consensus 40.5 13 0.00027 36.9 0.9 39 33-75 541-579 (1016)
61 PRK12373 NADH dehydrogenase su 39.6 13 0.00028 33.1 0.7 36 46-81 324-359 (400)
62 PRK07533 enoyl-(acyl carrier p 37.0 21 0.00045 26.7 1.4 16 52-67 23-38 (258)
63 PRK14604 ruvA Holliday junctio 36.8 14 0.0003 29.1 0.5 19 45-63 108-126 (195)
64 cd00432 Ribosomal_L18_L5e Ribo 36.0 20 0.00044 24.8 1.1 27 43-69 52-78 (103)
65 smart00483 POLXc DNA polymeras 35.7 21 0.00046 29.7 1.4 18 46-63 49-66 (334)
66 PRK14606 ruvA Holliday junctio 35.5 15 0.00033 28.7 0.5 18 45-62 108-125 (188)
67 TIGR00426 competence protein C 35.4 12 0.00027 23.8 -0.0 18 47-64 18-36 (69)
68 PRK13844 recombination protein 35.3 21 0.00046 28.9 1.3 16 47-62 17-32 (200)
69 TIGR00615 recR recombination p 34.7 22 0.00048 28.7 1.3 26 47-79 13-38 (195)
70 PRK13901 ruvA Holliday junctio 34.7 16 0.00034 29.3 0.5 18 45-62 107-124 (196)
71 KOG0011|consensus 34.6 13 0.00029 32.8 0.0 27 56-82 300-326 (340)
72 PRK00076 recR recombination pr 34.3 23 0.00049 28.5 1.3 16 47-62 13-28 (196)
73 cd00008 53EXOc 5'-3' exonuclea 33.5 33 0.00072 27.0 2.1 26 39-64 175-202 (240)
74 CHL00139 rpl18 ribosomal prote 31.9 25 0.00055 25.7 1.1 25 45-69 58-82 (109)
75 PRK14602 ruvA Holliday junctio 31.8 19 0.00042 28.3 0.5 18 45-62 109-126 (203)
76 cd00141 NT_POLXc Nucleotidyltr 31.7 30 0.00064 28.4 1.6 18 46-63 46-63 (307)
77 KOG1332|consensus 31.4 28 0.0006 30.5 1.4 40 7-54 181-220 (299)
78 TIGR03491 RecB family nuclease 31.4 38 0.00083 29.0 2.3 26 44-69 206-231 (457)
79 TIGR01259 comE comEA protein. 31.3 32 0.0007 24.8 1.6 19 46-64 69-87 (120)
80 PRK05593 rplR 50S ribosomal pr 31.2 26 0.00057 25.8 1.1 26 44-69 65-90 (117)
81 COG0632 RuvA Holliday junction 31.0 24 0.00053 28.3 1.0 19 44-62 107-125 (201)
82 smart00541 FYRN "FY-rich" doma 30.8 31 0.00067 21.6 1.2 15 11-25 22-36 (44)
83 PRK14603 ruvA Holliday junctio 30.7 20 0.00044 28.1 0.5 18 45-62 107-124 (197)
84 PF11810 DUF3332: Domain of un 30.3 62 0.0013 25.6 3.1 65 12-96 69-133 (176)
85 TIGR03674 fen_arch flap struct 29.9 27 0.00059 29.2 1.1 52 39-91 230-284 (338)
86 PRK09482 flap endonuclease-lik 29.5 41 0.00089 27.7 2.1 31 33-64 169-201 (256)
87 COG3294 HD supefamily hydrolas 29.1 34 0.00073 29.6 1.6 38 88-126 160-198 (269)
88 KOG1209|consensus 29.0 31 0.00066 30.0 1.3 17 50-66 17-33 (289)
89 KOG4303|consensus 28.8 41 0.00089 31.2 2.1 26 81-106 292-317 (524)
90 PRK06079 enoyl-(acyl carrier p 28.8 31 0.00067 25.7 1.2 17 51-67 19-35 (252)
91 PRK06603 enoyl-(acyl carrier p 28.8 31 0.00066 26.0 1.1 16 52-67 21-36 (260)
92 PF08869 XisI: XisI protein; 28.5 44 0.00096 24.9 1.9 33 50-82 72-104 (111)
93 COG0353 RecR Recombinational D 28.5 31 0.00067 28.4 1.2 24 48-78 15-38 (198)
94 PRK00254 ski2-like helicase; P 28.2 21 0.00045 32.0 0.2 35 46-80 646-680 (720)
95 COG1555 ComEA DNA uptake prote 27.4 39 0.00084 25.6 1.5 16 48-63 100-115 (149)
96 PRK01172 ski2-like helicase; P 26.9 36 0.00077 30.1 1.4 35 46-80 613-647 (674)
97 smart00475 53EXOc 5'-3' exonuc 26.9 49 0.0011 26.8 2.1 25 40-64 179-205 (259)
98 PRK07370 enoyl-(acyl carrier p 26.9 35 0.00076 25.6 1.2 17 51-67 18-34 (258)
99 PF12836 HHH_3: Helix-hairpin- 26.8 45 0.00097 21.3 1.5 29 47-75 16-49 (65)
100 smart00769 WHy Water Stress an 26.8 34 0.00075 23.1 1.0 13 85-97 21-33 (100)
101 PRK08690 enoyl-(acyl carrier p 26.6 35 0.00075 25.7 1.1 17 51-67 18-34 (261)
102 PRK12481 2-deoxy-D-gluconate 3 26.5 32 0.00068 25.6 0.9 18 50-67 17-34 (251)
103 smart00483 POLXc DNA polymeras 26.1 46 0.001 27.7 1.8 34 41-74 85-118 (334)
104 PRK14600 ruvA Holliday junctio 26.0 35 0.00076 26.7 1.1 17 45-62 108-124 (186)
105 PRK08862 short chain dehydroge 26.0 33 0.00072 25.7 0.9 17 51-67 15-31 (227)
106 PTZ00134 40S ribosomal protein 25.9 27 0.00058 27.2 0.4 50 47-96 32-82 (154)
107 PF03807 F420_oxidored: NADP o 25.8 44 0.00095 21.3 1.3 28 53-81 10-37 (96)
108 PRK06101 short chain dehydroge 25.8 31 0.00067 25.3 0.7 18 50-67 10-27 (240)
109 PRK08159 enoyl-(acyl carrier p 25.5 36 0.00079 26.0 1.1 17 51-67 22-38 (272)
110 PRK06483 dihydromonapterin red 25.4 34 0.00073 24.7 0.8 16 51-66 12-27 (236)
111 PRK10702 endonuclease III; Pro 25.3 28 0.00061 27.4 0.4 29 41-69 105-133 (211)
112 PLN02780 ketoreductase/ oxidor 25.2 35 0.00075 27.3 0.9 26 50-78 62-87 (320)
113 COG4221 Short-chain alcohol de 24.9 37 0.00081 28.5 1.1 18 49-66 14-31 (246)
114 PRK02362 ski2-like helicase; P 24.8 37 0.00081 30.6 1.1 31 45-75 652-682 (737)
115 PRK06505 enoyl-(acyl carrier p 24.8 39 0.00085 25.8 1.1 16 52-67 20-35 (271)
116 PRK08609 hypothetical protein; 24.7 45 0.00097 29.9 1.6 19 46-64 49-67 (570)
117 KOG2094|consensus 24.6 35 0.00076 31.4 1.0 35 35-69 272-306 (490)
118 PRK12748 3-ketoacyl-(acyl-carr 24.4 45 0.00096 24.5 1.3 16 51-66 17-32 (256)
119 cd06578 HemD Uroporphyrinogen- 24.1 54 0.0012 23.3 1.7 25 48-72 203-227 (239)
120 PRK05867 short chain dehydroge 23.9 37 0.0008 24.9 0.8 25 51-78 19-43 (253)
121 PF05822 UMPH-1: Pyrimidine 5' 23.8 39 0.00085 28.1 1.0 41 50-90 113-155 (246)
122 PRK08594 enoyl-(acyl carrier p 23.8 43 0.00094 25.2 1.2 17 51-67 19-35 (257)
123 TIGR00601 rad23 UV excision re 23.7 20 0.00044 31.0 -0.7 27 56-82 339-365 (378)
124 COG0258 Exo 5'-3' exonuclease 23.6 59 0.0013 26.3 2.0 26 39-64 190-217 (310)
125 PRK14976 5'-3' exonuclease; Pr 23.5 60 0.0013 26.6 2.0 26 39-64 183-210 (281)
126 PRK06997 enoyl-(acyl carrier p 23.5 45 0.00098 25.2 1.2 17 51-67 18-34 (260)
127 TIGR02867 spore_II_P stage II 23.3 35 0.00075 27.2 0.6 20 48-67 30-49 (196)
128 TIGR00084 ruvA Holliday juncti 23.2 37 0.00081 26.4 0.7 18 45-62 107-124 (191)
129 PRK07023 short chain dehydroge 23.2 46 0.00099 24.1 1.2 17 51-67 11-27 (243)
130 PRK08642 fabG 3-ketoacyl-(acyl 23.1 45 0.00097 24.0 1.1 18 50-67 14-31 (253)
131 PRK10880 adenine DNA glycosyla 23.0 29 0.00063 29.7 0.1 32 41-72 105-136 (350)
132 PRK07984 enoyl-(acyl carrier p 22.8 45 0.00097 25.5 1.1 16 52-67 19-34 (262)
133 cd00158 RHOD Rhodanese Homolog 22.7 66 0.0014 19.3 1.6 19 54-72 63-81 (89)
134 PRK08415 enoyl-(acyl carrier p 22.6 46 0.001 25.6 1.2 17 51-67 17-33 (274)
135 PRK08339 short chain dehydroge 22.5 45 0.00097 25.1 1.0 16 51-66 18-33 (263)
136 TIGR00060 L18_bact ribosomal p 22.5 47 0.001 24.7 1.1 27 43-69 61-87 (114)
137 COG0456 RimI Acetyltransferase 22.5 26 0.00056 23.9 -0.2 51 51-115 106-160 (177)
138 PRK12827 short chain dehydroge 22.4 47 0.001 23.6 1.1 18 50-67 15-32 (249)
139 PRK06114 short chain dehydroge 22.3 43 0.00092 24.7 0.9 16 51-66 18-33 (254)
140 PRK08416 7-alpha-hydroxysteroi 22.2 42 0.00091 24.9 0.8 19 49-67 16-34 (260)
141 PRK12823 benD 1,6-dihydroxycyc 22.2 47 0.001 24.3 1.1 17 51-67 18-34 (260)
142 PRK06523 short chain dehydroge 22.1 53 0.0011 24.0 1.3 17 51-67 19-35 (260)
143 PRK12747 short chain dehydroge 22.0 50 0.0011 24.1 1.1 17 51-67 14-30 (252)
144 PRK06463 fabG 3-ketoacyl-(acyl 21.8 48 0.001 24.3 1.0 18 50-67 16-33 (255)
145 PF13207 AAA_17: AAA domain; P 21.7 69 0.0015 20.9 1.7 21 47-67 4-26 (121)
146 PRK06924 short chain dehydroge 21.6 45 0.00097 24.1 0.9 17 50-66 10-26 (251)
147 PRK07523 gluconate 5-dehydroge 21.3 46 0.001 24.3 0.9 17 50-66 19-35 (255)
148 PRK07063 short chain dehydroge 20.9 49 0.0011 24.2 1.0 18 50-67 16-33 (260)
149 TIGR01832 kduD 2-deoxy-D-gluco 20.9 49 0.0011 23.9 0.9 16 51-66 15-30 (248)
150 PRK06550 fabG 3-ketoacyl-(acyl 20.7 54 0.0012 23.5 1.1 16 51-66 15-30 (235)
151 TIGR01448 recD_rel helicase, p 20.7 71 0.0015 29.4 2.1 31 27-64 73-103 (720)
152 TIGR02685 pter_reduc_Leis pter 20.7 56 0.0012 24.3 1.2 17 51-67 11-27 (267)
153 PRK05653 fabG 3-ketoacyl-(acyl 20.5 52 0.0011 23.2 1.0 26 51-79 15-40 (246)
154 PF07535 zf-DBF: DBF zinc fing 20.5 57 0.0012 21.2 1.1 14 30-43 23-36 (49)
155 smart00478 ENDO3c endonuclease 20.5 67 0.0014 22.6 1.5 22 47-68 74-95 (149)
156 KOG1205|consensus 20.5 47 0.001 27.9 0.8 18 49-66 20-37 (282)
157 KOG1811|consensus 20.5 26 0.00056 34.6 -0.7 47 28-79 948-994 (1141)
158 PRK00116 ruvA Holliday junctio 20.4 66 0.0014 24.7 1.6 19 46-64 74-92 (192)
159 PRK08340 glucose-1-dehydrogena 20.3 47 0.001 24.5 0.7 17 50-66 9-25 (259)
160 PRK06300 enoyl-(acyl carrier p 20.3 50 0.0011 26.6 1.0 16 51-66 20-35 (299)
161 PRK14605 ruvA Holliday junctio 20.2 39 0.00085 26.4 0.3 16 45-60 108-123 (194)
162 cd01523 RHOD_Lact_B Member of 20.1 73 0.0016 20.5 1.5 18 54-72 74-91 (100)
163 PF02889 Sec63: Sec63 Brl doma 20.0 26 0.00057 27.2 -0.7 32 44-75 147-178 (314)
No 1
>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=99.96 E-value=2.4e-30 Score=185.87 Aligned_cols=47 Identities=74% Similarity=1.066 Sum_probs=35.5
Q ss_pred cccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceee
Q psy6808 27 KMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQ 73 (132)
Q Consensus 27 MstTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl 73 (132)
||+|||||||||+||||||+|++|||||++||+||+++|||||||||
T Consensus 1 MsttSqKhr~Fv~EPMGeK~V~~laGIG~~lg~~L~~~GfdKAy~vL 47 (89)
T PF02961_consen 1 MSTTSQKHRNFVSEPMGEKPVTELAGIGPVLGKRLEEKGFDKAYVVL 47 (89)
T ss_dssp ---S-HHHHHHTTS--TT-BGGGSTT--HHHHHHHHHTT--BHHHHH
T ss_pred CCccCHHHHHHhcCccCCCCccccCCcCHHHHHHHHHCCCcHHHHHh
Confidence 89999999999999999999999999999999999999999999996
No 2
>KOG4233|consensus
Probab=99.92 E-value=2.6e-26 Score=166.23 Aligned_cols=47 Identities=55% Similarity=0.793 Sum_probs=45.8
Q ss_pred cccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceee
Q psy6808 27 KMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQ 73 (132)
Q Consensus 27 MstTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl 73 (132)
|+.||||||+||+||||||+|++|||||++||.+|.++||||||+|+
T Consensus 1 Ms~tS~khR~FvaEPmGeK~V~~laGIg~~lg~~L~~~GfdkAYvll 47 (90)
T KOG4233|consen 1 MSNTSQKHRAFVAEPMGEKDVTWLAGIGETLGIKLVDAGFDKAYVLL 47 (90)
T ss_pred CCccCHHHHHHhcCccCCCcceeeccccHHhhhhHHhccccHHHHHH
Confidence 78899999999999999999999999999999999999999999986
No 3
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=96.33 E-value=0.0013 Score=52.41 Aligned_cols=43 Identities=28% Similarity=0.479 Sum_probs=37.4
Q ss_pred CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
|-|+..++.++||||++++++|.+.||..+-.++.....++++
T Consensus 1 ~~~~~~~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~~~~~L~~ 43 (317)
T PRK04301 1 EKMKEKDLEDLPGVGPATAEKLREAGYDTVEAIAVASPKELSE 43 (317)
T ss_pred CCcccccHhhcCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHH
Confidence 5699999999999999999999999999999998875545433
No 4
>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=96.03 E-value=0.0043 Score=36.52 Aligned_cols=23 Identities=26% Similarity=0.554 Sum_probs=19.1
Q ss_pred CCCccccCCCchHHHHhHHhcCC
Q psy6808 44 EKPVTELAGVGDVLGKRLESKGF 66 (132)
Q Consensus 44 EK~Vt~LAGIGpvLGkrLeekGF 66 (132)
+-+|++++|||+..+++|++.|.
T Consensus 10 ~lpi~~~~GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 10 PLPIRKFWGIGKKTAKKLNKLGI 32 (32)
T ss_dssp CSBGGGSTTS-HHHHHHHHCTT-
T ss_pred cCCHHhhCCccHHHHHHHHHccC
Confidence 34999999999999999999873
No 5
>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=91.89 E-value=0.092 Score=33.11 Aligned_cols=28 Identities=14% Similarity=0.262 Sum_probs=23.2
Q ss_pred ccccCCCchHHHHhHHhcCCCccceeee
Q psy6808 47 VTELAGVGDVLGKRLESKGFDKSINPQM 74 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLeekGFDKAYvVl~ 74 (132)
...++|||+..+.+|.+.||.....+..
T Consensus 7 L~~I~Gig~~~a~~L~~~G~~t~~~l~~ 34 (60)
T PF14520_consen 7 LLSIPGIGPKRAEKLYEAGIKTLEDLAN 34 (60)
T ss_dssp HHTSTTCHHHHHHHHHHTTCSSHHHHHT
T ss_pred hccCCCCCHHHHHHHHhcCCCcHHHHHc
Confidence 3578999999999999999987655543
No 6
>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=90.58 E-value=0.098 Score=41.19 Aligned_cols=36 Identities=22% Similarity=0.442 Sum_probs=30.6
Q ss_pred ccccCCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 47 VTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
+.+++|||+..+++|.+.||.....++.....++.+
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L~~ 36 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIAVASPKELSE 36 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHHcCCHHHHHh
Confidence 467999999999999999999999988876666544
No 7
>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=88.73 E-value=0.24 Score=39.84 Aligned_cols=36 Identities=31% Similarity=0.459 Sum_probs=32.5
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFP 76 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~ 76 (132)
=+..-||.+|+|||+.+.++|++.|.....+++-.+
T Consensus 169 ~L~~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~~~ 204 (343)
T cd00424 169 FLSKLPLTDLPGIGAVTAKRLEAVGINPIGDLLAAS 204 (343)
T ss_pred HHhcCChhhcCCCCHHHHHHHHHcCCCcHHHHhcCC
Confidence 356679999999999999999999999999998776
No 8
>PRK02406 DNA polymerase IV; Validated
Probab=88.55 E-value=0.13 Score=41.20 Aligned_cols=41 Identities=22% Similarity=0.395 Sum_probs=34.8
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
-+..-||++|+|||+.++++|+..|+.....+.-.+...+.
T Consensus 164 ~L~~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~~l~~~~L~ 204 (343)
T PRK02406 164 FLATLPVEKIPGVGKVTAEKLHALGIYTCADLQKYDLAELI 204 (343)
T ss_pred HHHcCCcchhcCCCHHHHHHHHHcCCCcHHHHHhCCHHHHH
Confidence 44567999999999999999999999999999887654443
No 9
>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=87.85 E-value=0.3 Score=41.08 Aligned_cols=35 Identities=23% Similarity=0.409 Sum_probs=31.1
Q ss_pred CCCCCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808 42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFP 76 (132)
Q Consensus 42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~ 76 (132)
|..-+|.+|+|||+.++++|.+.|.....++.-.+
T Consensus 169 l~~lpv~~l~GiG~~~~~kL~~~GI~tigdl~~~~ 203 (379)
T cd01703 169 MDLHDLRKIPGIGYKTAAKLEAHGISSVRDLQEFS 203 (379)
T ss_pred hccCCccccCCcCHHHHHHHHHcCCCcHHHHHhCC
Confidence 45678999999999999999999999988887665
No 10
>PRK03352 DNA polymerase IV; Validated
Probab=87.82 E-value=0.24 Score=39.74 Aligned_cols=39 Identities=28% Similarity=0.476 Sum_probs=33.4
Q ss_pred CCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
+.+.||.+|+|||+....+|++.|+.+..+++--+...+
T Consensus 174 L~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L 212 (346)
T PRK03352 174 MGDRPTDALWGVGPKTAKRLAALGITTVADLAAADPAEL 212 (346)
T ss_pred HhcCCHHHcCCCCHHHHHHHHHcCCccHHHHhcCCHHHH
Confidence 457899999999999999999999999999887654433
No 11
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=87.65 E-value=0.42 Score=37.07 Aligned_cols=46 Identities=24% Similarity=0.316 Sum_probs=35.6
Q ss_pred HhhhcCCCCCC-CccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 35 QNFVSEPMGEK-PVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 35 RnFVsEPMGEK-~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
..++--|-+.| +.+.+-||||++.+.|.+.|.-.--|+--.-.-||
T Consensus 56 p~~~~~~~~~~DDLt~I~GIGPk~e~~Ln~~GI~tfaQIAAwt~~di 102 (133)
T COG3743 56 PAGADAPAAPKDDLTRISGIGPKLEKVLNELGIFTFAQIAAWTRADI 102 (133)
T ss_pred cccccCCCCCcccchhhcccCHHHHHHHHHcCCccHHHHHhcCHHHH
Confidence 46788888885 99999999999999999999866555544443333
No 12
>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=85.91 E-value=0.38 Score=40.15 Aligned_cols=37 Identities=24% Similarity=0.233 Sum_probs=33.1
Q ss_pred CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808 40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFP 76 (132)
Q Consensus 40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~ 76 (132)
+-|..-||++|+|||+.++++|...|+....++.-.+
T Consensus 217 ~~L~~lPv~~l~GIG~~~~~~L~~~Gi~t~~dl~~~~ 253 (404)
T cd01701 217 EFLSQLKVGDLPGVGSSLAEKLVKLFGDTCGGLELRS 253 (404)
T ss_pred HHhhcCCHhHhCCCCHHHHHHHHHcCCcchHHHHhCc
Confidence 3467779999999999999999999999999888776
No 13
>PRK03858 DNA polymerase IV; Validated
Probab=85.53 E-value=0.38 Score=39.16 Aligned_cols=36 Identities=28% Similarity=0.464 Sum_probs=31.5
Q ss_pred CCCCCccccCCCchHHHHhHHhcCCCccceeeecCC
Q psy6808 42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPD 77 (132)
Q Consensus 42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~ 77 (132)
|..-||++|+|||+.+.++|++.|+....++.-.+.
T Consensus 170 L~~lpl~~l~Gig~~~~~~L~~~Gi~t~~dl~~l~~ 205 (396)
T PRK03858 170 LHPLPVRRLWGVGPVTAAKLRAHGITTVGDVAELPE 205 (396)
T ss_pred HhcCChhhcCCCCHHHHHHHHHhCCCcHHHHhcCCH
Confidence 456699999999999999999999999999876543
No 14
>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=85.33 E-value=0.54 Score=37.71 Aligned_cols=41 Identities=17% Similarity=0.230 Sum_probs=35.0
Q ss_pred CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
+-|..-|+..|+|||+.+.++|+..|+....+++-.+..++
T Consensus 171 ~~l~~lpl~~l~gig~~~~~~L~~~Gi~ti~dL~~~~~~~L 211 (344)
T cd01700 171 KLLKILPVGDVWGIGRRTAKKLNAMGIHTAGDLAQADPDLL 211 (344)
T ss_pred HHhccCChhhcCccCHHHHHHHHHcCCCcHHHHhcCCHHHH
Confidence 45688899999999999999999999999999887754333
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=84.22 E-value=0.56 Score=36.80 Aligned_cols=39 Identities=21% Similarity=0.340 Sum_probs=33.1
Q ss_pred CCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
|..-||++|+|||+.++.+|...|+.+..++.-.+...+
T Consensus 168 L~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~~~~~~L 206 (334)
T cd03586 168 LAPLPVRKIPGVGKVTAEKLKELGIKTIGDLAKLDVELL 206 (334)
T ss_pred HhcCCchhhCCcCHHHHHHHHHcCCcCHHHHHcCCHHHH
Confidence 345699999999999999999999999999887765444
No 16
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=82.37 E-value=0.76 Score=38.28 Aligned_cols=36 Identities=25% Similarity=0.413 Sum_probs=31.7
Q ss_pred CCCCCccccCCCchHHHHhHHhcCCCccceeeecCC
Q psy6808 42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPD 77 (132)
Q Consensus 42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~ 77 (132)
+..-||.+|+|||+...++|+..|+....++.-.+.
T Consensus 176 L~~lPv~~l~GiG~~~~~~L~~lGi~TigdL~~~~~ 211 (422)
T PRK03609 176 LSLQPVEEVWGVGRRISKKLNAMGIKTALDLADTNI 211 (422)
T ss_pred hhcCChhhcCCccHHHHHHHHHcCCCcHHHHhcCCH
Confidence 355699999999999999999999999999887653
No 17
>PRK03103 DNA polymerase IV; Reviewed
Probab=80.77 E-value=0.51 Score=38.82 Aligned_cols=39 Identities=26% Similarity=0.279 Sum_probs=33.0
Q ss_pred CCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 43 GEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 43 GEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
..-||++|+|||+.+.++|+..|+....++.-.+...+.
T Consensus 179 ~~lpi~~l~gig~~~~~~L~~~Gi~tigdl~~~~~~~L~ 217 (409)
T PRK03103 179 WPLPVRKLFGVGSRMEKHLRRMGIRTIGQLANTPLERLK 217 (409)
T ss_pred HcCCHhhcCCccHHHHHHHHHcCCCCHHHHhcCCHHHHH
Confidence 445999999999999999999999999998877654443
No 18
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=80.18 E-value=0.88 Score=38.78 Aligned_cols=37 Identities=19% Similarity=0.236 Sum_probs=33.1
Q ss_pred CCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
.+.+.+.||||.+.++|.+.|+..-.|+--+.+-|++
T Consensus 263 DdL~~I~GiGp~~e~~L~~~Gi~~f~QiA~~t~~~~a 299 (326)
T PRK12311 263 DDLKKLTGVSPQIEKKLNDLGIFHFWQLAELDPDDAA 299 (326)
T ss_pred hhhhhhccCChhhhhhhhhcCCCCHHHhhCCChhhhh
Confidence 5678899999999999999999999999888888765
No 19
>PRK02794 DNA polymerase IV; Provisional
Probab=80.08 E-value=0.86 Score=37.96 Aligned_cols=38 Identities=26% Similarity=0.303 Sum_probs=32.5
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCC
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDP 78 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~ 78 (132)
-|.+-||++|+|||+...++|+..|+....++.-.+..
T Consensus 205 ~L~~lPl~~L~GiG~~~~~~L~~~GI~tigdL~~l~~~ 242 (419)
T PRK02794 205 FLAPKPVGIIWGVGPATAARLARDGIRTIGDLQRADEA 242 (419)
T ss_pred HHhcCChhhhCCCCHHHHHHHHHhccchHHHHhhCCHH
Confidence 45566999999999999999999999999988766533
No 20
>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=79.90 E-value=0.73 Score=33.42 Aligned_cols=28 Identities=14% Similarity=0.328 Sum_probs=23.7
Q ss_pred CCccccCCCchHHHHhHHhcCCCcccee
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSINP 72 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYvV 72 (132)
+..+.|||||+..++-|...|+..-.+|
T Consensus 12 ~~L~~iP~IG~a~a~DL~~LGi~s~~~L 39 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLRLLGIRSPADL 39 (93)
T ss_pred HHHhcCCCccHHHHHHHHHcCCCCHHHH
Confidence 4568999999999999999999765544
No 21
>PRK01810 DNA polymerase IV; Validated
Probab=78.78 E-value=0.56 Score=38.59 Aligned_cols=38 Identities=18% Similarity=0.274 Sum_probs=32.5
Q ss_pred CCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 43 GEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 43 GEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
..-||++|+|||+.+.++|+..|+....++.-.+...+
T Consensus 177 ~~lpv~~l~giG~~~~~~L~~~Gi~tigdL~~~~~~~L 214 (407)
T PRK01810 177 WPLPVGEMHGIGEKTAEKLKDIGIQTIGDLAKADEHIL 214 (407)
T ss_pred HhCCHhhcCCcCHHHHHHHHHcCCCcHHHHHhCCHHHH
Confidence 44599999999999999999999999999887765444
No 22
>PTZ00205 DNA polymerase kappa; Provisional
Probab=77.65 E-value=1.2 Score=40.90 Aligned_cols=34 Identities=18% Similarity=0.189 Sum_probs=29.3
Q ss_pred CCCCCccccCCCchHHHHhHHhcCCCccceeeec
Q psy6808 42 MGEKPVTELAGVGDVLGKRLESKGFDKSINPQMF 75 (132)
Q Consensus 42 MGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f 75 (132)
|..-||++++|||++..++|...|....-.+.-.
T Consensus 306 L~~LpV~ki~GIG~~t~~~L~~~GI~TigDLa~~ 339 (571)
T PTZ00205 306 VRDLGLRSVPGVGKVTEALLKGLGITTLSDIYNR 339 (571)
T ss_pred HhCCCcceeCCcCHHHHHHHHHcCCCcHHHHhcC
Confidence 3455999999999999999999999988877654
No 23
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=77.13 E-value=1.8 Score=23.80 Aligned_cols=18 Identities=11% Similarity=0.381 Sum_probs=15.5
Q ss_pred CccccCCCchHHHHhHHh
Q psy6808 46 PVTELAGVGDVLGKRLES 63 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLee 63 (132)
.+..++|||+..+.+|.+
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 356899999999999986
No 24
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=76.82 E-value=0.83 Score=35.37 Aligned_cols=44 Identities=20% Similarity=0.339 Sum_probs=31.1
Q ss_pred ccccCCCchHHHHhHHhcC-CCccceeeecCCCChhh--eeeeccCCCC
Q psy6808 47 VTELAGVGDVLGKRLESKG-FDKSINPQMFPDPDIEE--KVLLFKNPNS 92 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLeekG-FDKAYvVl~f~~~~~~~--~~~~~~~~~~ 92 (132)
...||||||++|++....| |...-.|+-- |.|-| |-++=||-..
T Consensus 63 l~~lpGigP~~A~~IV~nGpf~sveDL~~V--~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 63 FRQFPGMYPTLAGKIVKNAPYDSVEDVLNL--PGLSERQKELLEANLDN 109 (132)
T ss_pred HHHCCCCCHHHHHHHHHCCCCCCHHHHHcC--CCCCHHHHHHHHHhhcc
Confidence 3679999999999999887 7777766654 34544 3455555544
No 25
>PRK03348 DNA polymerase IV; Provisional
Probab=76.30 E-value=1.4 Score=37.74 Aligned_cols=39 Identities=21% Similarity=0.378 Sum_probs=33.0
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD 79 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~ 79 (132)
-|..-+|.+|+|||+....+|+..|+....++.-.+...
T Consensus 176 ~L~~LPv~~L~GIG~~t~~~L~~lGI~TigDLa~l~~~~ 214 (454)
T PRK03348 176 LLAPLPVRRLWGIGPVTEEKLHRLGIETIGDLAALSEAE 214 (454)
T ss_pred HHHhCCccccCCCCHHHHHHHHHcCCccHHHHhcCCHHH
Confidence 345669999999999999999999999999888765433
No 26
>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=76.12 E-value=0.6 Score=38.87 Aligned_cols=42 Identities=21% Similarity=0.480 Sum_probs=32.1
Q ss_pred CCCCCCCccccCCCchHHHHhH-HhcCCCccceeeec--CCCChh
Q psy6808 40 EPMGEKPVTELAGVGDVLGKRL-ESKGFDKSINPQMF--PDPDIE 81 (132)
Q Consensus 40 EPMGEK~Vt~LAGIGpvLGkrL-eekGFDKAYvVl~f--~~~~~~ 81 (132)
+-|..-+|.+|+|||+.++++| ++.|....-++.-. +..++.
T Consensus 177 ~~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~~~~~~~~L~ 221 (359)
T cd01702 177 SFLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAGFRSSESDLQ 221 (359)
T ss_pred HHhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHhccCCHHHHH
Confidence 3445669999999999998875 89999988888766 444443
No 27
>PRK01216 DNA polymerase IV; Validated
Probab=74.63 E-value=1.9 Score=35.95 Aligned_cols=41 Identities=17% Similarity=0.433 Sum_probs=33.5
Q ss_pred CCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 40 EPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 40 EPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
+-+..-||+.|+|||+....+|++.|+...-+++-.+...+
T Consensus 173 ~~L~~LPi~~l~giG~~~~~~L~~~Gi~TigdL~~~~~~~L 213 (351)
T PRK01216 173 RFINELDIADIPGIGDITAEKLKKLGVNKLVDTLRIEFDEL 213 (351)
T ss_pred HHHhcCCcccccCCCHHHHHHHHHcCCCcHHHHhcCCHHHH
Confidence 34456699999999999999999999998888877664333
No 28
>KOG1014|consensus
Probab=74.38 E-value=2.2 Score=36.78 Aligned_cols=27 Identities=19% Similarity=0.427 Sum_probs=22.1
Q ss_pred ccCCCchHHHHhHHhcCCCccceeeecCCC
Q psy6808 49 ELAGVGDVLGKRLESKGFDKSINPQMFPDP 78 (132)
Q Consensus 49 ~LAGIGpvLGkrLeekGFDKAYvVl~f~~~ 78 (132)
.=+|||+.++++|+.+||+ ++|.=-+.
T Consensus 57 aTDGIGKayA~eLAkrG~n---vvLIsRt~ 83 (312)
T KOG1014|consen 57 ATDGIGKAYARELAKRGFN---VVLISRTQ 83 (312)
T ss_pred CCCcchHHHHHHHHHcCCE---EEEEeCCH
Confidence 4589999999999999997 66655554
No 29
>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=74.38 E-value=2 Score=27.84 Aligned_cols=18 Identities=22% Similarity=0.693 Sum_probs=15.9
Q ss_pred CccccCCCchHHHHhHHh
Q psy6808 46 PVTELAGVGDVLGKRLES 63 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLee 63 (132)
.+..|||||+.++.++.|
T Consensus 48 ~~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 48 DLKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HHCTSTTTTHHHHHHHHH
T ss_pred HHhhCCCCCHHHHHHHHH
Confidence 379999999999999875
No 30
>COG5608 LEA14-like dessication related protein [Defense mechanisms]
Probab=74.07 E-value=2.2 Score=34.20 Aligned_cols=26 Identities=35% Similarity=0.556 Sum_probs=19.9
Q ss_pred eeecCCCChhh--------------eeeec--cCCCCccccc
Q psy6808 72 PQMFPDPDIEE--------------KVLLF--KNPNSLPIPI 97 (132)
Q Consensus 72 Vl~f~~~~~~~--------------~~~~~--~~~~~~~~~~ 97 (132)
++-|.+|++|+ -|..+ -|||+.|||+
T Consensus 27 ~i~~~~p~ve~~ka~wGkvt~s~~EiV~t~KiyNPN~fPipV 68 (161)
T COG5608 27 MIPVKKPGVESMKAKWGKVTNSETEIVGTLKIYNPNPFPIPV 68 (161)
T ss_pred ceEcCCCCceEEEEEEEEEeccceEEEEEEEecCCCCcceee
Confidence 67899999874 34444 4999999996
No 31
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=73.54 E-value=1.9 Score=35.20 Aligned_cols=39 Identities=31% Similarity=0.536 Sum_probs=33.9
Q ss_pred CCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 43 GEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 43 GEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
+..+++.+.||||.+.++|.+.|.....|+-=+.+-|+.
T Consensus 156 ~aDDL~~I~GIGp~~a~~L~eaGi~tfaQIAa~t~a~ia 194 (221)
T PRK12278 156 GADDLTKITGVGPALAKKLNEAGVTTFAQIAALTDADIA 194 (221)
T ss_pred CcchheeccccChHHHHHHHHcCCCCHHHhhCCChhhhh
Confidence 457789999999999999999999999998887777654
No 32
>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=73.19 E-value=2 Score=29.53 Aligned_cols=27 Identities=15% Similarity=0.293 Sum_probs=18.4
Q ss_pred CCccccCCCchHHHHhHHhcCCCccce
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSIN 71 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYv 71 (132)
+.+++||.||+++.+.|.+.|...+-.
T Consensus 3 ~~l~~LpNig~~~e~~L~~vGI~t~~~ 29 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVGIHTVED 29 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT--SHHH
T ss_pred cchhhCCCCCHHHHHHHHHcCCCCHHH
Confidence 567899999999999999999876543
No 33
>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=73.17 E-value=2.6 Score=24.63 Aligned_cols=17 Identities=18% Similarity=0.384 Sum_probs=12.7
Q ss_pred CccccCCCchHHHHhHH
Q psy6808 46 PVTELAGVGDVLGKRLE 62 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLe 62 (132)
....|||||+..|....
T Consensus 12 eL~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAIL 28 (30)
T ss_dssp HHHTSTT-SHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHH
Confidence 45789999999988754
No 34
>PRK14133 DNA polymerase IV; Provisional
Probab=72.44 E-value=1.5 Score=35.35 Aligned_cols=38 Identities=13% Similarity=0.223 Sum_probs=31.9
Q ss_pred CCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 43 GEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 43 GEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
..=||.+|+|||+...++|+..|+....+++-.+...+
T Consensus 171 ~~lpv~~l~gig~~~~~~L~~~Gi~ti~dl~~l~~~~L 208 (347)
T PRK14133 171 KPLPISKVHGIGKKSVEKLNNIGIYTIEDLLKLSREFL 208 (347)
T ss_pred HhCCccccCCCCHHHHHHHHHcCCccHHHHhhCCHHHH
Confidence 45589999999999999999999999988876654433
No 35
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=70.85 E-value=2.4 Score=37.99 Aligned_cols=39 Identities=23% Similarity=0.385 Sum_probs=33.8
Q ss_pred CCccccCCCchHHHHhHHhcCCCccceeeecCCCChhhe
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEK 83 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~~ 83 (132)
.+|+.|.||||..++.|+..|......+++++--..|..
T Consensus 9 ~~~~~l~gvg~~~~~~l~~lgi~t~~dll~~~P~~y~d~ 47 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLAKLGIHTVQDLLLHLPRRYEDR 47 (681)
T ss_pred CChhhcCCCCHHHHHHHHHcCCCCHHHHhhcCCCceEEc
Confidence 589999999999999999999999999998876555543
No 36
>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=70.36 E-value=3 Score=26.95 Aligned_cols=25 Identities=24% Similarity=0.310 Sum_probs=17.0
Q ss_pred cccCCCchHHHHhHHhcCCCcccee
Q psy6808 48 TELAGVGDVLGKRLESKGFDKSINP 72 (132)
Q Consensus 48 t~LAGIGpvLGkrLeekGFDKAYvV 72 (132)
+.+-|||+.-|+++-++||..--.|
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl 29 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDL 29 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHH
Confidence 5688999999999999999654433
No 37
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=67.36 E-value=1.8 Score=36.63 Aligned_cols=38 Identities=16% Similarity=0.222 Sum_probs=33.6
Q ss_pred CCCcccc--CCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 44 EKPVTEL--AGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 44 EK~Vt~L--AGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
-.++.+| .||++...++|+++||..+..+++.+..++-
T Consensus 28 ~~~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~~~~~~L~ 67 (344)
T PLN03187 28 FESIDKLISQGINAGDVKKLQDAGIYTCNGLMMHTKKNLT 67 (344)
T ss_pred ccCHHHHhhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHH
Confidence 5668888 7799999999999999999999999877764
No 38
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=63.71 E-value=5.4 Score=33.19 Aligned_cols=32 Identities=19% Similarity=0.397 Sum_probs=26.4
Q ss_pred CCccccCCCchHHHHhHHhcCCCccceeeecC
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFP 76 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~ 76 (132)
+....++|||++-+++|-+.||.-...+..-.
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~Sve~Ik~AS 34 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFESVEDVRAAD 34 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCCHHHHHhCC
Confidence 35678999999999999999998777665543
No 39
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=63.56 E-value=4.1 Score=29.48 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=26.2
Q ss_pred CCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 51 AGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 51 AGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
||||+..+.+|++.|+...-.++---+-.+..
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~~~~~~~~r 32 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLEAGDTPLGR 32 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHHcCCCHHHH
Confidence 79999999999999999888877665554444
No 40
>PF03625 DUF302: Domain of unknown function DUF302 ; InterPro: IPR005180 This domain is found in an undescribed set of proteins. It normally occurs uniquely within a sequence, but is found as a tandem repeat (Q9X8B8 from SWISSPROT). It has an interesting phylogenetic distribution with the majority of examples in bacteria and archaea, but it is also found in Drosophila melanogaster (e.g. Q9VA18 from SWISSPROT). The hypothetical protein TT1751 from Thermus thermophilus has a beta-alpha-beta(4)-alpha structural fold [].; PDB: 1Q9U_A 1J3M_B.
Probab=61.53 E-value=2.6 Score=26.55 Aligned_cols=42 Identities=21% Similarity=0.237 Sum_probs=29.1
Q ss_pred HHHhHHhcCCC--ccceeeecCCCChhheeeeccCCCCccccce
Q psy6808 57 LGKRLESKGFD--KSINPQMFPDPDIEEKVLLFKNPNSLPIPIG 98 (132)
Q Consensus 57 LGkrLeekGFD--KAYvVl~f~~~~~~~~~~~~~~~~~~~~~~~ 98 (132)
+++.|+++|++ ..+.++.|-+|.+..+++-..---++-.|.-
T Consensus 4 ~~~~~~~~g~~~~~~~~i~~~cnp~~a~~ll~~~p~~~~~lPcr 47 (65)
T PF03625_consen 4 HSEELKEKGGEDLPPYRILEFCNPKIAYQLLKADPEIGLFLPCR 47 (65)
T ss_dssp HHHHHHCCC-S--S-EEEEEEE-HHHHHHHHCC-GGGGGC-SEE
T ss_pred HHHHHHHcCCccCCCeEEEEECChHHHHHHHHhhHHHHHhCCeE
Confidence 46789999999 8999999999999998877544445566653
No 41
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=61.35 E-value=2.5 Score=34.96 Aligned_cols=40 Identities=30% Similarity=0.356 Sum_probs=34.3
Q ss_pred CCCccccCCCchHHHHhHHhcCCCccceeeecCCCChhhee
Q psy6808 44 EKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKV 84 (132)
Q Consensus 44 EK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~~~ 84 (132)
+.+|.++.|||+...++|+..|+....++.= .++|+..+.
T Consensus 175 ~Lpv~~~~GvG~~~~~~l~~~Gi~ti~dl~~-~~~~~L~~~ 214 (354)
T COG0389 175 QLPVLEFWGVGKVTAEKLRRLGISTIGDLAE-TDLDALKKR 214 (354)
T ss_pred cCChhhhCCCCHHHHHHHHHcCChhHHHHHh-cCHHHHHHH
Confidence 4599999999999999999999999998888 777774443
No 42
>PTZ00035 Rad51 protein; Provisional
Probab=60.98 E-value=2.5 Score=35.10 Aligned_cols=37 Identities=19% Similarity=0.227 Sum_probs=32.1
Q ss_pred Ccccc--CCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 46 PVTEL--AGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 46 ~Vt~L--AGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
++.+| +||++...++|+++||..+..+++....++.+
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~~~~~~L~~ 60 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAYATKKDLCN 60 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHH
Confidence 57888 88999999999999999999999887766643
No 43
>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=60.90 E-value=3.8 Score=32.06 Aligned_cols=39 Identities=13% Similarity=0.135 Sum_probs=31.7
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
-+..-++ +++|||+....+|++.|+....++.-.+..++
T Consensus 167 ~l~~lp~-~~~gig~~~~~~L~~~Gi~t~~dl~~~~~~~l 205 (335)
T cd03468 167 LLAPLPV-AALRLPPETVELLARLGLRTLGDLAALPRAEL 205 (335)
T ss_pred ccCCCCh-hHhCCCHHHHHHHHHhCcccHHHHHhCChHHH
Confidence 3566677 59999999999999999999988877655444
No 44
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=58.83 E-value=3 Score=28.17 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=18.7
Q ss_pred cccCCCchHHHHhHHhcCCCccceeeec
Q psy6808 48 TELAGVGDVLGKRLESKGFDKSINPQMF 75 (132)
Q Consensus 48 t~LAGIGpvLGkrLeekGFDKAYvVl~f 75 (132)
.++.||-+.+..+++..||++--++..|
T Consensus 3 ~~~~Gi~~~lVd~F~~mGF~~dkVvevl 30 (55)
T PF09288_consen 3 AALYGIDKDLVDQFENMGFERDKVVEVL 30 (55)
T ss_dssp SS----SHHHHHHHHHHT--HHHHHHHH
T ss_pred HHHcCCCHHHHHHHHHcCCcHHHHHHHH
Confidence 4688999999999999999998777654
No 45
>PRK03980 flap endonuclease-1; Provisional
Probab=55.34 E-value=6 Score=32.66 Aligned_cols=56 Identities=21% Similarity=0.309 Sum_probs=36.6
Q ss_pred cCCCCCCCccccCCCchHHHHhHHhc-C-CCccceeeecCCCChhheeeeccCCCCcc
Q psy6808 39 SEPMGEKPVTELAGVGDVLGKRLESK-G-FDKSINPQMFPDPDIEEKVLLFKNPNSLP 94 (132)
Q Consensus 39 sEPMGEK~Vt~LAGIGpvLGkrLeek-G-FDKAYvVl~f~~~~~~~~~~~~~~~~~~~ 94 (132)
+-=+|-.-..-++|||++-|.+|..+ | .++.+...-..-|+.+|-.-+|+||+-..
T Consensus 183 ~iL~G~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~~~~~~~~~~r~~f~~p~v~~ 240 (292)
T PRK03980 183 AILVGTDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGFEIENYDEIREFFLNPPVTD 240 (292)
T ss_pred HHhcCCCCCCCCCCccHHHHHHHHHHCCCHHHHHHhccCCCCCHHHHHHHhcCCCCCC
Confidence 34577777889999999999988754 2 23333322223345566677899998653
No 46
>COG0300 DltE Short-chain dehydrogenases of various substrate specificities [General function prediction only]
Probab=54.64 E-value=5.9 Score=32.82 Aligned_cols=19 Identities=32% Similarity=0.749 Sum_probs=16.8
Q ss_pred ccCCCchHHHHhHHhcCCC
Q psy6808 49 ELAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 49 ~LAGIGpvLGkrLeekGFD 67 (132)
.=.|||..++++|+++|++
T Consensus 14 ASsGIG~~~A~~lA~~g~~ 32 (265)
T COG0300 14 ASSGIGAELAKQLARRGYN 32 (265)
T ss_pred CCchHHHHHHHHHHHCCCE
Confidence 3479999999999999985
No 47
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=54.63 E-value=8.8 Score=24.80 Aligned_cols=18 Identities=11% Similarity=0.458 Sum_probs=12.7
Q ss_pred CccccCCCchHHHHhHHh
Q psy6808 46 PVTELAGVGDVLGKRLES 63 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLee 63 (132)
....++|||++.+..+.+
T Consensus 36 ~L~~i~gIG~~~A~si~~ 53 (64)
T PF12826_consen 36 ELSAIPGIGPKIAQSIYE 53 (64)
T ss_dssp HHCTSTT--HHHHHHHHH
T ss_pred HHhccCCcCHHHHHHHHH
Confidence 457899999999988754
No 48
>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=53.91 E-value=11 Score=25.15 Aligned_cols=24 Identities=17% Similarity=0.368 Sum_probs=19.6
Q ss_pred CCC--CCCccccCCCchHHHHhHHhc
Q psy6808 41 PMG--EKPVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 41 PMG--EK~Vt~LAGIGpvLGkrLeek 64 (132)
=+| -.-+.-+||||++.|.+|-.+
T Consensus 16 L~GD~~D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 16 LVGDKSDNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred HcCCccccCCCCCcccHHHHHHHHHH
Confidence 467 445778999999999999865
No 49
>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=52.78 E-value=5.3 Score=32.96 Aligned_cols=32 Identities=19% Similarity=0.133 Sum_probs=27.7
Q ss_pred CCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 51 AGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 51 AGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
.|||+...++|+++||..+..+++....++-+
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~~~~~~L~~ 38 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIMTTRRALCK 38 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHH
Confidence 67999999999999999999999887666543
No 50
>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=52.34 E-value=6.2 Score=32.32 Aligned_cols=42 Identities=19% Similarity=0.294 Sum_probs=31.7
Q ss_pred ccHHHHhhhcC-CCCCCCccccCCCchHHHHhHHhcCCCccce
Q psy6808 30 TSQKHQNFVSE-PMGEKPVTELAGVGDVLGKRLESKGFDKSIN 71 (132)
Q Consensus 30 TSqKHRnFVsE-PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYv 71 (132)
++.++.+.-++ |-|=+....++|||+..+++|-+.|+.---.
T Consensus 69 ~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~~lGi~sl~d 111 (307)
T cd00141 69 KLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYELGIRTLED 111 (307)
T ss_pred CHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHHHcCCCCHHH
Confidence 45556665554 6666777899999999999999999975433
No 51
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=51.25 E-value=14 Score=22.20 Aligned_cols=23 Identities=17% Similarity=0.420 Sum_probs=16.7
Q ss_pred CCCCC--ccccCCCchHHHHhHHhc
Q psy6808 42 MGEKP--VTELAGVGDVLGKRLESK 64 (132)
Q Consensus 42 MGEK~--Vt~LAGIGpvLGkrLeek 64 (132)
+||+. +.-++|||++-|.+|-.+
T Consensus 11 ~GD~~dni~Gv~giG~ktA~~ll~~ 35 (36)
T smart00279 11 VGDYSDNIPGVKGIGPKTALKLLRE 35 (36)
T ss_pred hCcCCCCCCCCCcccHHHHHHHHHh
Confidence 45432 357999999999988653
No 52
>PRK07945 hypothetical protein; Provisional
Probab=51.08 E-value=11 Score=31.34 Aligned_cols=19 Identities=26% Similarity=0.459 Sum_probs=16.1
Q ss_pred CccccCCCchHHHHhHHhc
Q psy6808 46 PVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeek 64 (132)
..++|||||+-++.+++|-
T Consensus 50 ~l~~~~giG~~~a~~i~e~ 68 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQA 68 (335)
T ss_pred CcccCCCcCHHHHHHHHHH
Confidence 7899999999999877653
No 53
>PF02371 Transposase_20: Transposase IS116/IS110/IS902 family; InterPro: IPR003346 Transposases are needed for efficient transposition of the insertion sequence or transposon DNA. This family includes transposases for IS116, IS110 and IS902. It is often found with the transposase IS111A/IS1328/IS1533 family (see IPR002525 from INTERPRO) [, ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated
Probab=50.44 E-value=10 Score=25.34 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=15.0
Q ss_pred CccccCCCchHHHHhHHh
Q psy6808 46 PVTELAGVGDVLGKRLES 63 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLee 63 (132)
-++.+||||++.+..|-.
T Consensus 3 ~l~sipGig~~~a~~lla 20 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLA 20 (87)
T ss_pred hhcCCCCccHHHHHHHHH
Confidence 467899999999988765
No 54
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=47.75 E-value=15 Score=34.84 Aligned_cols=43 Identities=21% Similarity=0.409 Sum_probs=37.3
Q ss_pred CCccccCCCchHHHHhHHhcCCCccceeeecCCCChhheeeec
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLF 87 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~~~~~~ 87 (132)
.+++.+.|||+..+++|+..|......++.++--+.|.+-.+.
T Consensus 10 ~~l~~l~gig~~~a~~l~~Lgi~tv~DLL~~~P~~YeD~~~~~ 52 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLKKLGIHTVQDLLLYLPRRYEDRTLLP 52 (677)
T ss_pred cchhhhcCcCHHHHHHHHHcCCCcHHHHHHhCccchhhccccC
Confidence 4789999999999999999999999999888877777665544
No 55
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=47.24 E-value=29 Score=22.70 Aligned_cols=39 Identities=21% Similarity=0.385 Sum_probs=27.5
Q ss_pred cccCCCchHHHHhHHhcCCCccceeeecCCCChhheeeecc
Q psy6808 48 TELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFK 88 (132)
Q Consensus 48 t~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~~~~~~~ 88 (132)
+..+|.....+..|+++||.....- -.+..+ ++-+++|.
T Consensus 12 t~~~GlA~~~a~~L~~~Gf~v~~~~-n~~~~~-~~t~I~y~ 50 (90)
T PF13399_consen 12 TGVSGLAARVADALRNRGFTVVEVG-NAPSSD-ETTTIYYG 50 (90)
T ss_pred cCCcCHHHHHHHHHHHCCCceeecC-CCCCCC-CCEEEEEC
Confidence 4568999999999999999885543 334444 55555553
No 56
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=46.26 E-value=15 Score=26.62 Aligned_cols=28 Identities=21% Similarity=0.368 Sum_probs=23.2
Q ss_pred CccccCCCchHHHHhHHhcCCCccceee
Q psy6808 46 PVTELAGVGDVLGKRLESKGFDKSINPQ 73 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeekGFDKAYvVl 73 (132)
+...++|||+..+.-|.+.|++-...+-
T Consensus 54 dL~ri~gi~~~~a~LL~~AGv~Tv~~LA 81 (122)
T PF14229_consen 54 DLMRIPGIGPQYAELLEHAGVDTVEELA 81 (122)
T ss_pred HhhhcCCCCHHHHHHHHHhCcCcHHHHH
Confidence 3457899999999999999998766553
No 57
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=45.50 E-value=7 Score=32.96 Aligned_cols=36 Identities=22% Similarity=0.411 Sum_probs=31.1
Q ss_pred Ccccc--CCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 46 PVTEL--AGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 46 ~Vt~L--AGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
++.+| .||++...++|+++||..+..+++....++.
T Consensus 27 ~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~~~~~~L~ 64 (342)
T PLN03186 27 PIEQLQASGIAALDIKKLKDAGIHTVESLAYAPKKDLL 64 (342)
T ss_pred cHHHHHhCCCCHHHHHHHHHcCCCcHHHHHhCCHHHHH
Confidence 57888 7799999999999999999999988766553
No 58
>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=42.27 E-value=9.2 Score=31.48 Aligned_cols=32 Identities=19% Similarity=0.260 Sum_probs=27.5
Q ss_pred CCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 51 AGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 51 AGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
.||++...++|+++||..+..++....+++.+
T Consensus 7 ~~~~~~~~~~l~~~g~~t~~~~~~~~~~~L~~ 38 (316)
T TIGR02239 7 NGITAADIKKLQEAGLHTVESVAYAPKKQLLE 38 (316)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHhCCHHHHHH
Confidence 35999999999999999999998887666644
No 59
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.95 E-value=10 Score=29.72 Aligned_cols=18 Identities=22% Similarity=0.442 Sum_probs=14.7
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
|..+.+||||+..|+|+.
T Consensus 108 ~~L~~vpGIGkKtAeRIi 125 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRII 125 (183)
T ss_pred HHHhhCCCCCHHHHHHHH
Confidence 456788999999999864
No 60
>KOG2093|consensus
Probab=40.48 E-value=13 Score=36.93 Aligned_cols=39 Identities=28% Similarity=0.434 Sum_probs=33.2
Q ss_pred HHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeec
Q psy6808 33 KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMF 75 (132)
Q Consensus 33 KHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f 75 (132)
|-.+|++ .-+|+.|||+|..+-.||+..|..+.-+||+.
T Consensus 541 ~veeFis----~~~v~~LPGVG~sm~~kL~s~~i~tCgdLq~~ 579 (1016)
T KOG2093|consen 541 KVEEFIS----QLKVDDLPGVGSSMKSKLVSQFIQTCGDLQLI 579 (1016)
T ss_pred HHHHHhh----hcccccCCCccHHHHHHHHHhccchhHHHHHH
Confidence 5556655 46899999999999999999999999888874
No 61
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=39.64 E-value=13 Score=33.06 Aligned_cols=36 Identities=14% Similarity=0.183 Sum_probs=31.7
Q ss_pred CccccCCCchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 46 PVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
+.+.+.|||+.+.++|.+.|+....|+-=+.+-++.
T Consensus 324 DLk~I~GIGpk~e~~Ln~~Gi~~f~QIA~wt~~eia 359 (400)
T PRK12373 324 DLKLISGVGPKIEATLNELGIFTFDQVAAWKKAERA 359 (400)
T ss_pred hhhhccCCChHHHHHHHhcCCCCHHHHhCCCHHHhH
Confidence 678899999999999999999999998887776654
No 62
>PRK07533 enoyl-(acyl carrier protein) reductase; Provisional
Probab=36.96 E-value=21 Score=26.72 Aligned_cols=16 Identities=6% Similarity=0.106 Sum_probs=14.8
Q ss_pred CCchHHHHhHHhcCCC
Q psy6808 52 GVGDVLGKRLESKGFD 67 (132)
Q Consensus 52 GIGpvLGkrLeekGFD 67 (132)
|||..++++|.++|++
T Consensus 23 GIG~a~a~~la~~G~~ 38 (258)
T PRK07533 23 SIAWGCARAFRALGAE 38 (258)
T ss_pred cHHHHHHHHHHHcCCE
Confidence 8999999999999964
No 63
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=36.83 E-value=14 Score=29.06 Aligned_cols=19 Identities=16% Similarity=0.398 Sum_probs=15.1
Q ss_pred CCccccCCCchHHHHhHHh
Q psy6808 45 KPVTELAGVGDVLGKRLES 63 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLee 63 (132)
+..+.+||||+..|+|+.-
T Consensus 108 ~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 4457889999999998653
No 64
>cd00432 Ribosomal_L18_L5e Ribosomal L18/L5e: L18 (L5e) is a ribosomal protein found in the central protuberance (CP) of the large subunit. L18 binds 5S rRNA and induces a conformational change that stimulates the binding of L5 to 5S rRNA. Association of 5S rRNA with 23S rRNA depends on the binding of L18 and L5 to 5S rRNA. L18/L5e is generally described as L18 in prokaryotes and archaea, and as L5e (or L5) in eukaryotes. In bacteria, the CP proteins L5, L18, and L25 are required for the ribosome to incorporate 5S rRNA into the large subunit, one of the last steps in ribosome assembly. In archaea, both L18 and L5 bind 5S rRNA; in eukaryotes, only the L18 homolog (L5e) binds 5S rRNA but a homolog to L5 is also identified.
Probab=35.99 E-value=20 Score=24.81 Aligned_cols=27 Identities=33% Similarity=0.355 Sum_probs=22.1
Q ss_pred CCCCccccCCCchHHHHhHHhcCCCcc
Q psy6808 43 GEKPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 43 GEK~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
+.+.+..-.-||+.||+|+.++|..++
T Consensus 52 ~~~n~~aA~~vG~~la~r~~~~gi~~v 78 (103)
T cd00432 52 SGNNVEAAYLVGRLLAKRALEKGIKKV 78 (103)
T ss_pred CCCcHHHHHHHHHHHHHHHHHCCCCEE
Confidence 445567778899999999999998774
No 65
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=35.73 E-value=21 Score=29.67 Aligned_cols=18 Identities=33% Similarity=0.708 Sum_probs=15.7
Q ss_pred CccccCCCchHHHHhHHh
Q psy6808 46 PVTELAGVGDVLGKRLES 63 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLee 63 (132)
.+++|||||+.++.+..|
T Consensus 49 ~l~~lpgIG~~ia~kI~E 66 (334)
T smart00483 49 DLKGLPGIGDKIKKKIEE 66 (334)
T ss_pred HHhcCCCccHHHHHHHHH
Confidence 578999999999998774
No 66
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.48 E-value=15 Score=28.72 Aligned_cols=18 Identities=17% Similarity=0.433 Sum_probs=14.6
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
+..+.+||||+..|+||.
T Consensus 108 ~~L~~vpGIGkKtAerIi 125 (188)
T PRK14606 108 EGLSKLPGISKKTAERIV 125 (188)
T ss_pred HHHhhCCCCCHHHHHHHH
Confidence 445788999999999864
No 67
>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=35.39 E-value=12 Score=23.79 Aligned_cols=18 Identities=22% Similarity=0.290 Sum_probs=13.9
Q ss_pred ccc-cCCCchHHHHhHHhc
Q psy6808 47 VTE-LAGVGDVLGKRLESK 64 (132)
Q Consensus 47 Vt~-LAGIGpvLGkrLeek 64 (132)
... ++|||+..+++|-+.
T Consensus 18 L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 18 LQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHhHCCCCCHHHHHHHHHH
Confidence 345 789999888888766
No 68
>PRK13844 recombination protein RecR; Provisional
Probab=35.28 E-value=21 Score=28.91 Aligned_cols=16 Identities=25% Similarity=0.480 Sum_probs=13.9
Q ss_pred ccccCCCchHHHHhHH
Q psy6808 47 VTELAGVGDVLGKRLE 62 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLe 62 (132)
...|||||+.-|.||+
T Consensus 17 l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 17 LRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4689999999999983
No 69
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.75 E-value=22 Score=28.66 Aligned_cols=26 Identities=19% Similarity=0.340 Sum_probs=18.9
Q ss_pred ccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808 47 VTELAGVGDVLGKRLESKGFDKSINPQMFPDPD 79 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~ 79 (132)
...|||||+.-|.|| ||.++.-++.+
T Consensus 13 l~~LPGIG~KsA~Rl-------A~~ll~~~~~~ 38 (195)
T TIGR00615 13 LKKLPGIGPKSAQRL-------AFHLLKRDPSE 38 (195)
T ss_pred HHHCCCCCHHHHHHH-------HHHHHcCCHHH
Confidence 467999999999998 55555544433
No 70
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=34.70 E-value=16 Score=29.33 Aligned_cols=18 Identities=11% Similarity=0.495 Sum_probs=14.9
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
|..+.+||||+..|+|+.
T Consensus 107 ~~L~~vpGIGkKtAeRII 124 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIF 124 (196)
T ss_pred HHHhhCCCCCHHHHHHHH
Confidence 456788999999999864
No 71
>KOG0011|consensus
Probab=34.59 E-value=13 Score=32.77 Aligned_cols=27 Identities=30% Similarity=0.330 Sum_probs=22.5
Q ss_pred HHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 56 VLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 56 vLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
.--.||++.||++|-+++-||-=|-.|
T Consensus 300 eAIeRL~alGF~ralViqayfACdKNE 326 (340)
T KOG0011|consen 300 EAIERLEALGFPRALVIQAYFACDKNE 326 (340)
T ss_pred HHHHHHHHhCCcHHHHHHHHHhcCccH
Confidence 345799999999999999999766544
No 72
>PRK00076 recR recombination protein RecR; Reviewed
Probab=34.33 E-value=23 Score=28.51 Aligned_cols=16 Identities=31% Similarity=0.617 Sum_probs=13.8
Q ss_pred ccccCCCchHHHHhHH
Q psy6808 47 VTELAGVGDVLGKRLE 62 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLe 62 (132)
...|||||+.-|.||+
T Consensus 13 l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 13 LRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHCCCCCHHHHHHHH
Confidence 4679999999999983
No 73
>cd00008 53EXOc 5'-3' exonuclease; T5 type 5'-3' exonuclease domains may co-occur with DNA polymerase I (Pol I) domains, or be part of Pol I containing complexes. They digest dsDNA and ssDNA, releasing mono-,di- and tri-nucleotides, as well as oligonucleotides, and have also been reported to possess RNase H activity. Also called 5' nuclease family, involved in structure-specific cleavage of flaps formed by Pol I activity (similar to mammalian flap endonuclease I, FEN-1). A single nucleic acid strand may be threaded through the 5' nuclease enzyme before cleavage occurs. The domain binds two divalent metal ions which are necessary for activity.
Probab=33.46 E-value=33 Score=27.02 Aligned_cols=26 Identities=19% Similarity=0.473 Sum_probs=21.1
Q ss_pred cCCCCC--CCccccCCCchHHHHhHHhc
Q psy6808 39 SEPMGE--KPVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 39 sEPMGE--K~Vt~LAGIGpvLGkrLeek 64 (132)
.-=||| .-+--+||||++-|.+|-.+
T Consensus 175 ~~L~GD~sDnipGv~GiG~ktA~~Ll~~ 202 (240)
T cd00008 175 KALMGDSSDNIPGVPGIGEKTAAKLLKE 202 (240)
T ss_pred HHHcCCcccCCCCCCccCHHHHHHHHHH
Confidence 345886 56788999999999999876
No 74
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=31.91 E-value=25 Score=25.71 Aligned_cols=25 Identities=28% Similarity=0.283 Sum_probs=19.5
Q ss_pred CCccccCCCchHHHHhHHhcCCCcc
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
+.+..-.=||..+|+|+.++|++++
T Consensus 58 ~n~~aA~~vG~lla~ra~~~gi~~v 82 (109)
T CHL00139 58 STCDASKLVGQKLAKKSLKKGITKV 82 (109)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCEE
Confidence 3344555599999999999998774
No 75
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=31.80 E-value=19 Score=28.32 Aligned_cols=18 Identities=17% Similarity=0.423 Sum_probs=14.9
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
+..+.+||||+..|+|+.
T Consensus 109 ~~L~~ipGIGkKtAerIi 126 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIF 126 (203)
T ss_pred HHHhcCCCcCHHHHHHHH
Confidence 456789999999999865
No 76
>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=31.66 E-value=30 Score=28.41 Aligned_cols=18 Identities=22% Similarity=0.632 Sum_probs=15.3
Q ss_pred CccccCCCchHHHHhHHh
Q psy6808 46 PVTELAGVGDVLGKRLES 63 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLee 63 (132)
.++.+||||+.++.+..|
T Consensus 46 ~~~~ipgiG~~ia~kI~E 63 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEE 63 (307)
T ss_pred HhcCCCCccHHHHHHHHH
Confidence 458999999999988765
No 77
>KOG1332|consensus
Probab=31.43 E-value=28 Score=30.46 Aligned_cols=40 Identities=28% Similarity=0.477 Sum_probs=31.6
Q ss_pred ccccceeeeeecCCcccccccccccHHHHhhhcCCCCCCCccccCCCc
Q psy6808 7 HWCNSTVHFWPFTSPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGVG 54 (132)
Q Consensus 7 ~~~~~~~~f~~~~~~~~~~~MstTSqKHRnFVsEPMGEK~Vt~LAGIG 54 (132)
-=|..+||.|-|.+-. =-|..|-.+|.+||. +|.+-|-+|
T Consensus 181 gGcDn~VkiW~~~~~~--w~~e~~l~~H~dwVR------DVAwaP~~g 220 (299)
T KOG1332|consen 181 GGCDNLVKIWKFDSDS--WKLERTLEGHKDWVR------DVAWAPSVG 220 (299)
T ss_pred cCCccceeeeecCCcc--hhhhhhhhhcchhhh------hhhhccccC
Confidence 3589999999999872 236778999999995 677777765
No 78
>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=31.35 E-value=38 Score=29.02 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=23.5
Q ss_pred CCCccccCCCchHHHHhHHhcCCCcc
Q psy6808 44 EKPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 44 EK~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
+.++..|+||+..-..+|.++|+..-
T Consensus 206 ~~~lslv~gi~~~~~~~L~~~GI~ti 231 (457)
T TIGR03491 206 EGHLSLVPGIGPSRYRLLQELGIHTL 231 (457)
T ss_pred cCCeeecCCCCHHHHHHHHHcCCCcH
Confidence 68999999999999999999999544
No 79
>TIGR01259 comE comEA protein. This model describes the ComEA protein in bacteria. The com E locus is obligatory for bacterial cell competence - the process of internalizing the exogenous added DNA. Lesions in the loci has been variously described for the appearance of competence-related pheonotypes and impairment of competence, suggesting their intimate functional role in bacterial transformation.
Probab=31.33 E-value=32 Score=24.82 Aligned_cols=19 Identities=21% Similarity=0.361 Sum_probs=15.7
Q ss_pred CccccCCCchHHHHhHHhc
Q psy6808 46 PVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeek 64 (132)
....|||||+..++++-+.
T Consensus 69 eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 69 ELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHhcCCCCCHHHHHHHHHH
Confidence 4467999999999998765
No 80
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=31.18 E-value=26 Score=25.84 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=21.1
Q ss_pred CCCccccCCCchHHHHhHHhcCCCcc
Q psy6808 44 EKPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 44 EK~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
.+.+..-.=||+.+|+|+.++|++++
T Consensus 65 ~~n~~aa~~vG~~la~ra~~~gi~~v 90 (117)
T PRK05593 65 GGNKEAAKKVGKLIAERAKAKGIKQV 90 (117)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEE
Confidence 34456666799999999999999884
No 81
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=30.99 E-value=24 Score=28.35 Aligned_cols=19 Identities=21% Similarity=0.532 Sum_probs=15.7
Q ss_pred CCCccccCCCchHHHHhHH
Q psy6808 44 EKPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 44 EK~Vt~LAGIGpvLGkrLe 62 (132)
.+.++.+||||+..|+||.
T Consensus 107 ~~~L~k~PGIGkKtAeriv 125 (201)
T COG0632 107 VKALSKIPGIGKKTAERIV 125 (201)
T ss_pred hHhhhcCCCCCHHHHHHHH
Confidence 3567889999999999964
No 82
>smart00541 FYRN "FY-rich" domain, N-terminal region. is sometimes closely juxtaposed with the C-terminal region (FYRC), but sometimes is far distant. Unknown function, but occurs frequently in chromatin-associated proteins.
Probab=30.81 E-value=31 Score=21.61 Aligned_cols=15 Identities=27% Similarity=0.716 Sum_probs=12.8
Q ss_pred ceeeeeecCCccccc
Q psy6808 11 STVHFWPFTSPTQEL 25 (132)
Q Consensus 11 ~~~~f~~~~~~~~~~ 25 (132)
|+++|||..+|...-
T Consensus 22 s~R~y~S~~dp~~~c 36 (44)
T smart00541 22 STRKYWSVKDPNRRC 36 (44)
T ss_pred EEEEEecccCCCCEE
Confidence 688999999998764
No 83
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=30.74 E-value=20 Score=28.15 Aligned_cols=18 Identities=33% Similarity=0.619 Sum_probs=14.8
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
+..+.+||||+..|+|+.
T Consensus 107 ~~L~kvpGIGkKtAerIi 124 (197)
T PRK14603 107 RLLTSASGVGKKLAERIA 124 (197)
T ss_pred HHHhhCCCCCHHHHHHHH
Confidence 456789999999999864
No 84
>PF11810 DUF3332: Domain of unknown function (DUF3332); InterPro: IPR021768 This family of proteins are functionally uncharacterised. This family is only found in bacteria.
Probab=30.26 E-value=62 Score=25.56 Aligned_cols=65 Identities=15% Similarity=0.247 Sum_probs=46.5
Q ss_pred eeeeeecCCcccccccccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCChhheeeeccCCC
Q psy6808 12 TVHFWPFTSPTQELAKMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDIEEKVLLFKNPN 91 (132)
Q Consensus 12 ~~~f~~~~~~~~~~~MstTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~~~~~~~~~~ 91 (132)
++.||+=..|.+.. -.|+|.++..+.+++..|..++.+.|+.-. ..-.++++.+-+...+
T Consensus 69 sIEFWTG~NPi~g~--------------~~v~d~~~~~v~~~n~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~ 128 (176)
T PF11810_consen 69 SIEFWTGSNPITGK--------------PSVVDTPTKTVIKVNGKLDVSLTENPYSIT------VFREIEGKTMEQIDDK 128 (176)
T ss_pred eeeeecCCCCcCCC--------------CcccCCcccEEecCCceeehhhhhCcccee------eccCCCCceEEEecCC
Confidence 57899988888432 247888889999999999999999998654 2334555555555555
Q ss_pred Ccccc
Q psy6808 92 SLPIP 96 (132)
Q Consensus 92 ~~~~~ 96 (132)
..-.-
T Consensus 129 ~~~~~ 133 (176)
T PF11810_consen 129 TEQMW 133 (176)
T ss_pred cceeE
Confidence 54443
No 85
>TIGR03674 fen_arch flap structure-specific endonuclease. Endonuclease that cleaves the 5'-overhanging flap structure that is generated by displacement synthesis when DNA polymerase encounters the 5'-end of a downstream Okazaki fragment. Has 5'-endo-/exonuclease and 5'-pseudo-Y-endonuclease activities. Cleaves the junction between single and double-stranded regions of flap DNA
Probab=29.85 E-value=27 Score=29.15 Aligned_cols=52 Identities=15% Similarity=0.147 Sum_probs=32.3
Q ss_pred cCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCC---ChhheeeeccCCC
Q psy6808 39 SEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDP---DIEEKVLLFKNPN 91 (132)
Q Consensus 39 sEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~---~~~~~~~~~~~~~ 91 (132)
+-=||+..-.-++|||++-|.+|..+ |.....++-..+- +.+|-.-+|.||+
T Consensus 230 ~iL~G~dyn~Gv~GIG~ktA~kli~~-~gsie~il~~~~~~~~~~~~~~~~f~~~~ 284 (338)
T TIGR03674 230 AILVGTDYNEGVKGIGPKTALKLIKE-HGDLEKVLKARGEDIENYDEIREFFLNPP 284 (338)
T ss_pred HHhcCCCCCCCCCCccHHHHHHHHHH-cCCHHHHHHhhcCCCCCHHHHHHHhCCCC
Confidence 45588887889999999999999866 2222222111111 2234456788885
No 86
>PRK09482 flap endonuclease-like protein; Provisional
Probab=29.45 E-value=41 Score=27.70 Aligned_cols=31 Identities=16% Similarity=0.283 Sum_probs=22.6
Q ss_pred HHHhhhcCCCCCC--CccccCCCchHHHHhHHhc
Q psy6808 33 KHQNFVSEPMGEK--PVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 33 KHRnFVsEPMGEK--~Vt~LAGIGpvLGkrLeek 64 (132)
.-.+|. -=|||. -+--+|||||+-|.+|-.+
T Consensus 169 q~~D~~-aL~GD~sDnIpGVpGIG~KtA~~LL~~ 201 (256)
T PRK09482 169 QLPDYW-GLAGISSSKIPGVAGIGPKSAAELLNQ 201 (256)
T ss_pred HHHHHH-HHhCCCccCCCCCCCcChHHHHHHHHH
Confidence 334443 358877 4678999999999998764
No 87
>COG3294 HD supefamily hydrolase [General function prediction only]
Probab=29.10 E-value=34 Score=29.55 Aligned_cols=38 Identities=37% Similarity=0.538 Sum_probs=29.9
Q ss_pred cCCCCccccceeE-EeeeeeeecCCccCCccccccccccc
Q psy6808 88 KNPNSLPIPIGVE-VLGYTKIKNNKSRYPYLDYGCTEIHN 126 (132)
Q Consensus 88 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~ 126 (132)
.|++.|.|--|+- |---|.+..++||+||. -||-.||.
T Consensus 160 ~~~~~LTiEagvi~VADgtDmt~GRsR~py~-~g~~dIhs 198 (269)
T COG3294 160 ENETPLTIEAGVIAVADGTDMTKGRSRIPYE-KGKRDIHS 198 (269)
T ss_pred CCCCceeeeeeeEEecccccccccccccchh-hcCCchhh
Confidence 3777777777763 55678899999999997 58888885
No 88
>KOG1209|consensus
Probab=28.98 E-value=31 Score=30.02 Aligned_cols=17 Identities=29% Similarity=0.675 Sum_probs=15.6
Q ss_pred cCCCchHHHHhHHhcCC
Q psy6808 50 LAGVGDVLGKRLESKGF 66 (132)
Q Consensus 50 LAGIGpvLGkrLeekGF 66 (132)
--|||..|++++.++||
T Consensus 17 ~GGIG~ala~ef~~~G~ 33 (289)
T KOG1209|consen 17 SGGIGYALAKEFARNGY 33 (289)
T ss_pred CcchhHHHHHHHHhCCe
Confidence 35999999999999998
No 89
>KOG4303|consensus
Probab=28.82 E-value=41 Score=31.16 Aligned_cols=26 Identities=35% Similarity=0.539 Sum_probs=23.8
Q ss_pred hheeeeccCCCCccccceeEEeeeee
Q psy6808 81 EEKVLLFKNPNSLPIPIGVEVLGYTK 106 (132)
Q Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (132)
-+||-..-|-|.+||.+|+-|.+||.
T Consensus 292 wskv~Fsidi~~fPisvG~iVFsYTS 317 (524)
T KOG4303|consen 292 WSKVTFSIDINTFPISVGMIVFSYTS 317 (524)
T ss_pred ceeEEEEEEcccCceEEEEEEEeeec
Confidence 47888889999999999999999995
No 90
>PRK06079 enoyl-(acyl carrier protein) reductase; Provisional
Probab=28.80 E-value=31 Score=25.73 Aligned_cols=17 Identities=6% Similarity=0.102 Sum_probs=15.3
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
.|||..++++|.++|+.
T Consensus 19 ~gIG~a~a~~la~~G~~ 35 (252)
T PRK06079 19 RSIAWGCAQAIKDQGAT 35 (252)
T ss_pred CchHHHHHHHHHHCCCE
Confidence 48999999999999974
No 91
>PRK06603 enoyl-(acyl carrier protein) reductase; Provisional
Probab=28.77 E-value=31 Score=25.97 Aligned_cols=16 Identities=6% Similarity=0.192 Sum_probs=14.7
Q ss_pred CCchHHHHhHHhcCCC
Q psy6808 52 GVGDVLGKRLESKGFD 67 (132)
Q Consensus 52 GIGpvLGkrLeekGFD 67 (132)
|||..++++|.++|.+
T Consensus 21 GIG~a~a~~la~~G~~ 36 (260)
T PRK06603 21 SISWAIAQLAKKHGAE 36 (260)
T ss_pred chHHHHHHHHHHcCCE
Confidence 8999999999999974
No 92
>PF08869 XisI: XisI protein; InterPro: IPR014968 The fdxN element, along with two other DNA elements, is excised from the chromosome during heterocyst differentiation in cyanobacteria. The xisH as well as the xisF and xisI genes are required []. ; PDB: 3D7Q_A 2NWV_A 2NVM_A 2NLV_B.
Probab=28.48 E-value=44 Score=24.94 Aligned_cols=33 Identities=21% Similarity=0.286 Sum_probs=25.1
Q ss_pred cCCCchHHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 50 LAGVGDVLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
-.|.-.-++..|.++|..|-..||-|-.|+..+
T Consensus 72 ~d~TE~gIa~eLve~GVpk~dIVLgF~~P~~R~ 104 (111)
T PF08869_consen 72 RDGTEDGIAEELVEAGVPKEDIVLGFHPPEVRQ 104 (111)
T ss_dssp EESSSSHHHHHHHHTT--GGGEEETTS-GGGGC
T ss_pred cCchhhHHHHHHHHcCCCHHHEEEccCCccccc
Confidence 456667789999999999999999999987654
No 93
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=28.48 E-value=31 Score=28.36 Aligned_cols=24 Identities=25% Similarity=0.308 Sum_probs=17.6
Q ss_pred cccCCCchHHHHhHHhcCCCccceeeecCCC
Q psy6808 48 TELAGVGDVLGKRLESKGFDKSINPQMFPDP 78 (132)
Q Consensus 48 t~LAGIGpvLGkrLeekGFDKAYvVl~f~~~ 78 (132)
..|||||+.-|.|+ ||.++--.+-
T Consensus 15 ~kLPGvG~KsA~R~-------AfhLL~~~~~ 38 (198)
T COG0353 15 KKLPGVGPKSAQRL-------AFHLLQRDRE 38 (198)
T ss_pred hhCCCCChhHHHHH-------HHHHHccCHH
Confidence 57999999999997 5655544333
No 94
>PRK00254 ski2-like helicase; Provisional
Probab=28.18 E-value=21 Score=32.04 Aligned_cols=35 Identities=14% Similarity=0.182 Sum_probs=27.2
Q ss_pred CccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 46 PVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
+...+||||++.+++|-++||.--+.+.---+.+|
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~~a~~~el 680 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIVNAKPSEL 680 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHHhCCHHHH
Confidence 34579999999999999999998877665443333
No 95
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=27.36 E-value=39 Score=25.55 Aligned_cols=16 Identities=19% Similarity=0.378 Sum_probs=13.5
Q ss_pred cccCCCchHHHHhHHh
Q psy6808 48 TELAGVGDVLGKRLES 63 (132)
Q Consensus 48 t~LAGIGpvLGkrLee 63 (132)
..|||||+..|+++.+
T Consensus 100 ~~lpgIG~~kA~aIi~ 115 (149)
T COG1555 100 QALPGIGPKKAQAIID 115 (149)
T ss_pred HHCCCCCHHHHHHHHH
Confidence 6799999999988754
No 96
>PRK01172 ski2-like helicase; Provisional
Probab=26.92 E-value=36 Score=30.10 Aligned_cols=35 Identities=23% Similarity=0.266 Sum_probs=27.8
Q ss_pred CccccCCCchHHHHhHHhcCCCccceeeecCCCCh
Q psy6808 46 PVTELAGVGDVLGKRLESKGFDKSINPQMFPDPDI 80 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~~ 80 (132)
+...|||||+..+++|.++||.-.+.+.---|.++
T Consensus 613 ~L~~ip~~~~~~a~~l~~~g~~~~~di~~~~~~~~ 647 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDAGFKTVDDIARSSPERI 647 (674)
T ss_pred hhcCCCCCCHHHHHHHHHcCCCCHHHHHhCCHHHH
Confidence 34579999999999999999999888766443333
No 97
>smart00475 53EXOc 5'-3' exonuclease.
Probab=26.92 E-value=49 Score=26.79 Aligned_cols=25 Identities=20% Similarity=0.490 Sum_probs=20.0
Q ss_pred CCCCC--CCccccCCCchHHHHhHHhc
Q psy6808 40 EPMGE--KPVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 40 EPMGE--K~Vt~LAGIGpvLGkrLeek 64 (132)
-=||| .-+--+||||++-|.+|-++
T Consensus 179 aL~GD~sDnipGV~GIG~KtA~~Ll~~ 205 (259)
T smart00475 179 ALMGDSSDNIPGVPGIGEKTAAKLLKE 205 (259)
T ss_pred HHhCCcccCCCCCCCCCHHHHHHHHHH
Confidence 35786 45778999999999988765
No 98
>PRK07370 enoyl-(acyl carrier protein) reductase; Validated
Probab=26.90 E-value=35 Score=25.61 Aligned_cols=17 Identities=12% Similarity=0.263 Sum_probs=15.4
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|.+
T Consensus 18 ~GIG~aia~~la~~G~~ 34 (258)
T PRK07370 18 RSIAWGIAQQLHAAGAE 34 (258)
T ss_pred CchHHHHHHHHHHCCCE
Confidence 48999999999999974
No 99
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=26.84 E-value=45 Score=21.33 Aligned_cols=29 Identities=17% Similarity=0.245 Sum_probs=18.5
Q ss_pred ccccCCCchHHHHhHHhc-----CCCccceeeec
Q psy6808 47 VTELAGVGDVLGKRLESK-----GFDKSINPQMF 75 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLeek-----GFDKAYvVl~f 75 (132)
...+||||+.+++++.+- +|.....++-.
T Consensus 16 L~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~~v 49 (65)
T PF12836_consen 16 LQALPGIGPKQAKAIVEYREKNGPFKSLEDLKEV 49 (65)
T ss_dssp HHTSTT--HHHHHHHHHHHHHH-S-SSGGGGGGS
T ss_pred HHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHhhC
Confidence 357899999999987542 67776666644
No 100
>smart00769 WHy Water Stress and Hypersensitive response.
Probab=26.82 E-value=34 Score=23.06 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=10.7
Q ss_pred eeccCCCCccccc
Q psy6808 85 LLFKNPNSLPIPI 97 (132)
Q Consensus 85 ~~~~~~~~~~~~~ 97 (132)
+...|||..|+++
T Consensus 21 l~v~NPN~~~l~~ 33 (100)
T smart00769 21 VKVQNPNPFPIPV 33 (100)
T ss_pred EEEECCCCCcccc
Confidence 4568999999887
No 101
>PRK08690 enoyl-(acyl carrier protein) reductase; Provisional
Probab=26.61 E-value=35 Score=25.70 Aligned_cols=17 Identities=12% Similarity=0.214 Sum_probs=15.3
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|.+
T Consensus 18 ~GIG~a~a~~l~~~G~~ 34 (261)
T PRK08690 18 RSIAYGIAKACREQGAE 34 (261)
T ss_pred CcHHHHHHHHHHHCCCE
Confidence 48999999999999974
No 102
>PRK12481 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=26.50 E-value=32 Score=25.58 Aligned_cols=18 Identities=28% Similarity=0.429 Sum_probs=16.0
Q ss_pred cCCCchHHHHhHHhcCCC
Q psy6808 50 LAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFD 67 (132)
-.|||..++++|.++|+.
T Consensus 17 s~gIG~aia~~l~~~G~~ 34 (251)
T PRK12481 17 NTGLGQGMAIGLAKAGAD 34 (251)
T ss_pred CchHHHHHHHHHHHCCCE
Confidence 369999999999999974
No 103
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=26.08 E-value=46 Score=27.69 Aligned_cols=34 Identities=21% Similarity=0.135 Sum_probs=27.4
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCccceeee
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINPQM 74 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~ 74 (132)
|-|-.....++|||+.-+++|-+.|+..--.|.-
T Consensus 85 p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~~ 118 (334)
T smart00483 85 YKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELKK 118 (334)
T ss_pred HHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHHh
Confidence 4456667899999999999999999987665543
No 104
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=26.02 E-value=35 Score=26.74 Aligned_cols=17 Identities=24% Similarity=0.526 Sum_probs=14.1
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
+.. .+||||+..|+|+.
T Consensus 108 ~~L-~vpGIGkKtAerIi 124 (186)
T PRK14600 108 AAL-KVNGIGEKLINRII 124 (186)
T ss_pred hhe-ECCCCcHHHHHHHH
Confidence 455 89999999999865
No 105
>PRK08862 short chain dehydrogenase; Provisional
Probab=26.00 E-value=33 Score=25.69 Aligned_cols=17 Identities=12% Similarity=0.216 Sum_probs=15.5
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
.|||..++++|.++|++
T Consensus 15 ~GIG~aia~~la~~G~~ 31 (227)
T PRK08862 15 SVLGRTISCHFARLGAT 31 (227)
T ss_pred cHHHHHHHHHHHHCCCE
Confidence 68999999999999974
No 106
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=25.90 E-value=27 Score=27.21 Aligned_cols=50 Identities=24% Similarity=0.438 Sum_probs=40.2
Q ss_pred ccccCCCchHHHHhH-HhcCCCccceeeecCCCChhheeeeccCCCCcccc
Q psy6808 47 VTELAGVGDVLGKRL-ESKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIP 96 (132)
Q Consensus 47 Vt~LAGIGpvLGkrL-eekGFDKAYvVl~f~~~~~~~~~~~~~~~~~~~~~ 96 (132)
.+.+-|||...+..+ ...|+|.-.-+-...+.+++.-.-+..||..+.||
T Consensus 32 Lt~I~GIG~~~A~~I~~~lgi~~~~~~~~Lt~~qi~~l~~~i~~~~~~~iP 82 (154)
T PTZ00134 32 LTAIKGIGRRFAYLVCKKAGIDVTKRAGELTAEEIEKIVEIIANPLQFKIP 82 (154)
T ss_pred ecccccccHHHHHHHHHHcCcCcCCCcccCCHHHHHHHHHHHhccccCCCC
Confidence 478899999999875 56799988888888888888777777888666665
No 107
>PF03807 F420_oxidored: NADP oxidoreductase coenzyme F420-dependent; InterPro: IPR004455 The function of F420-dependent NADP reductase is the transfer of electrons from reduced coenzyme F420 into an electron transport chain. It catalyses the reduction of F420 with NADP(+) and the reduction of NADP(+) with F420H(2).; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process; PDB: 2IZZ_B 2GR9_B 2GRA_B 2GER_C 2AMF_E 2AHR_C 2VQ3_B 2VNS_B 2RCY_D 2YJZ_D ....
Probab=25.79 E-value=44 Score=21.34 Aligned_cols=28 Identities=21% Similarity=0.331 Sum_probs=20.6
Q ss_pred CchHHHHhHHhcCCCccceeeecCCCChh
Q psy6808 53 VGDVLGKRLESKGFDKSINPQMFPDPDIE 81 (132)
Q Consensus 53 IGpvLGkrLeekGFDKAYvVl~f~~~~~~ 81 (132)
+|..|++.|.+.|+ +...+.+..+++-|
T Consensus 10 mg~al~~~l~~~g~-~~~~v~~~~~r~~~ 37 (96)
T PF03807_consen 10 MGSALARGLLASGI-KPHEVIIVSSRSPE 37 (96)
T ss_dssp HHHHHHHHHHHTTS--GGEEEEEEESSHH
T ss_pred HHHHHHHHHHHCCC-CceeEEeeccCcHH
Confidence 57889999999999 77777766455543
No 108
>PRK06101 short chain dehydrogenase; Provisional
Probab=25.78 E-value=31 Score=25.28 Aligned_cols=18 Identities=22% Similarity=0.554 Sum_probs=15.9
Q ss_pred cCCCchHHHHhHHhcCCC
Q psy6808 50 LAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFD 67 (132)
-.|||..++++|.++|++
T Consensus 10 s~giG~~la~~L~~~G~~ 27 (240)
T PRK06101 10 TSGIGKQLALDYAKQGWQ 27 (240)
T ss_pred CcHHHHHHHHHHHhCCCE
Confidence 469999999999999974
No 109
>PRK08159 enoyl-(acyl carrier protein) reductase; Provisional
Probab=25.47 E-value=36 Score=26.00 Aligned_cols=17 Identities=12% Similarity=0.147 Sum_probs=15.2
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|.+
T Consensus 22 ~GIG~aia~~la~~G~~ 38 (272)
T PRK08159 22 RSIAWGIAKACRAAGAE 38 (272)
T ss_pred CcHHHHHHHHHHHCCCE
Confidence 38999999999999973
No 110
>PRK06483 dihydromonapterin reductase; Provisional
Probab=25.40 E-value=34 Score=24.72 Aligned_cols=16 Identities=25% Similarity=0.293 Sum_probs=14.9
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
-|||..++++|.++|+
T Consensus 12 ~gIG~~ia~~l~~~G~ 27 (236)
T PRK06483 12 QRIGLALAWHLLAQGQ 27 (236)
T ss_pred ChHHHHHHHHHHHCCC
Confidence 5899999999999997
No 111
>PRK10702 endonuclease III; Provisional
Probab=25.26 E-value=28 Score=27.43 Aligned_cols=29 Identities=21% Similarity=0.336 Sum_probs=23.0
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCcc
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
|-..+...+|||||+..|.-.---+|++.
T Consensus 105 p~~~~~Ll~lpGVG~ktA~~ill~a~~~~ 133 (211)
T PRK10702 105 PEDRAALEALPGVGRKTANVVLNTAFGWP 133 (211)
T ss_pred CchHHHHhcCCcccHHHHHHHHHHHcCCC
Confidence 44455677899999999998888888874
No 112
>PLN02780 ketoreductase/ oxidoreductase
Probab=25.18 E-value=35 Score=27.26 Aligned_cols=26 Identities=23% Similarity=0.414 Sum_probs=19.3
Q ss_pred cCCCchHHHHhHHhcCCCccceeeecCCC
Q psy6808 50 LAGVGDVLGKRLESKGFDKSINPQMFPDP 78 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFDKAYvVl~f~~~ 78 (132)
-.|||..++++|.++|++ +++.--++
T Consensus 62 s~GIG~alA~~La~~G~~---Vil~~R~~ 87 (320)
T PLN02780 62 TDGIGKGFAFQLARKGLN---LVLVARNP 87 (320)
T ss_pred CcHHHHHHHHHHHHCCCC---EEEEECCH
Confidence 469999999999999973 44444343
No 113
>COG4221 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]
Probab=24.90 E-value=37 Score=28.48 Aligned_cols=18 Identities=22% Similarity=0.510 Sum_probs=16.3
Q ss_pred ccCCCchHHHHhHHhcCC
Q psy6808 49 ELAGVGDVLGKRLESKGF 66 (132)
Q Consensus 49 ~LAGIGpvLGkrLeekGF 66 (132)
.=+|||+..+++|.++|+
T Consensus 14 ASSGiG~A~A~~l~~~G~ 31 (246)
T COG4221 14 ASSGIGEATARALAEAGA 31 (246)
T ss_pred CcchHHHHHHHHHHHCCC
Confidence 347999999999999998
No 114
>PRK02362 ski2-like helicase; Provisional
Probab=24.83 E-value=37 Score=30.55 Aligned_cols=31 Identities=26% Similarity=0.395 Sum_probs=26.6
Q ss_pred CCccccCCCchHHHHhHHhcCCCccceeeec
Q psy6808 45 KPVTELAGVGDVLGKRLESKGFDKSINPQMF 75 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f 75 (132)
=+...|||||+.-+++|-+.|+...+.+.--
T Consensus 652 ~~L~~ip~i~~~~a~~l~~~gi~s~~dl~~~ 682 (737)
T PRK02362 652 LDLVGLRGVGRVRARRLYNAGIESRADLRAA 682 (737)
T ss_pred HHHhCCCCCCHHHHHHHHHcCCCCHHHHHhC
Confidence 3456799999999999999999999988743
No 115
>PRK06505 enoyl-(acyl carrier protein) reductase; Provisional
Probab=24.80 E-value=39 Score=25.81 Aligned_cols=16 Identities=19% Similarity=0.358 Sum_probs=14.8
Q ss_pred CCchHHHHhHHhcCCC
Q psy6808 52 GVGDVLGKRLESKGFD 67 (132)
Q Consensus 52 GIGpvLGkrLeekGFD 67 (132)
|||..++++|.++|.+
T Consensus 20 GIG~aiA~~la~~Ga~ 35 (271)
T PRK06505 20 SIAWGIAKQLAAQGAE 35 (271)
T ss_pred cHHHHHHHHHHhCCCE
Confidence 8999999999999963
No 116
>PRK08609 hypothetical protein; Provisional
Probab=24.71 E-value=45 Score=29.86 Aligned_cols=19 Identities=21% Similarity=0.373 Sum_probs=15.7
Q ss_pred CccccCCCchHHHHhHHhc
Q psy6808 46 PVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeek 64 (132)
.++.+||||+.++++.+|-
T Consensus 49 ~l~~ipgIG~~ia~kI~Ei 67 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQEY 67 (570)
T ss_pred hhccCCCcCHHHHHHHHHH
Confidence 5789999999999876653
No 117
>KOG2094|consensus
Probab=24.62 E-value=35 Score=31.43 Aligned_cols=35 Identities=23% Similarity=0.449 Sum_probs=29.2
Q ss_pred HhhhcCCCCCCCccccCCCchHHHHhHHhcCCCcc
Q psy6808 35 QNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 35 RnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
|+=|.+=|-+=||+.+.|||.|.-..|.+.|....
T Consensus 272 r~aim~F~kdLPvRkV~GIGrV~E~qLkal~IkTc 306 (490)
T KOG2094|consen 272 RIAIMKFMKDLPVRKVSGIGRVTEQQLKALGIKTC 306 (490)
T ss_pred HHHHHHHHhcCCcccccchhHHHHHHHHhcCceeH
Confidence 44455567788999999999999999999998655
No 118
>PRK12748 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=24.38 E-value=45 Score=24.51 Aligned_cols=16 Identities=38% Similarity=0.810 Sum_probs=14.7
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
.|||..++++|.++|+
T Consensus 17 ~giG~~la~~l~~~G~ 32 (256)
T PRK12748 17 NGIGAAVCRRLAAKGI 32 (256)
T ss_pred CCHHHHHHHHHHHcCC
Confidence 4899999999999995
No 119
>cd06578 HemD Uroporphyrinogen-III synthase (HemD) catalyzes the asymmetrical cyclization of tetrapyrrole (linear) to uroporphyrinogen-III, the fourth step in the biosynthesis of heme. This ubiquitous enzyme is present in eukaryotes, bacteria and archaea. Mutations in the human uroporphyrinogen-III synthase gene cause congenital erythropoietic porphyria, a recessive inborn error of metabolism also known as Gunther disease.
Probab=24.09 E-value=54 Score=23.35 Aligned_cols=25 Identities=20% Similarity=0.331 Sum_probs=21.2
Q ss_pred cccCCCchHHHHhHHhcCCCcccee
Q psy6808 48 TELAGVGDVLGKRLESKGFDKSINP 72 (132)
Q Consensus 48 t~LAGIGpvLGkrLeekGFDKAYvV 72 (132)
..+.-||+..++.|++.||...++.
T Consensus 203 ~~~~aig~~t~~~l~~~g~~~~~~~ 227 (239)
T cd06578 203 VKIAAIGPRTAEALRELGLKVVIVA 227 (239)
T ss_pred CeEEEECHHHHHHHHHcCCCceeee
Confidence 4677899999999999999877654
No 120
>PRK05867 short chain dehydrogenase; Provisional
Probab=23.94 E-value=37 Score=24.90 Aligned_cols=25 Identities=12% Similarity=0.116 Sum_probs=18.9
Q ss_pred CCCchHHHHhHHhcCCCccceeeecCCC
Q psy6808 51 AGVGDVLGKRLESKGFDKSINPQMFPDP 78 (132)
Q Consensus 51 AGIGpvLGkrLeekGFDKAYvVl~f~~~ 78 (132)
-|||..++++|.++|+. +++..-++
T Consensus 19 ~gIG~~ia~~l~~~G~~---V~~~~r~~ 43 (253)
T PRK05867 19 TGIGKRVALAYVEAGAQ---VAIAARHL 43 (253)
T ss_pred chHHHHHHHHHHHCCCE---EEEEcCCH
Confidence 58999999999999973 44444443
No 121
>PF05822 UMPH-1: Pyrimidine 5'-nucleotidase (UMPH-1); InterPro: IPR006434 This family is a small group of metazoan sequences with sequences from Arabidopsis thaliana (Mouse-ear cress) and rice. The sequences represent pyrimidine 5-nucleotidases, apparently in reference to HSPC233, the Homo sapiens (Human) homologue []. The structure of mouse sequence has been reported []. This group of sequences was originally found during searches for members of the haloacid dehalogenase (HAD) superfamily (IPR005834 from INTERPRO). All of the conserved catalytic motifs [] are found. The placement of the variable domain between motifs 1 and 2 indicates membership in subfamily I of the superfamily, but these sequences are sufficiently different from any of the branches of that subfamily (IA-ID) as to constitute a separate branch to now be called IE. Considering that the closest identifiable hit outside of the noise range is to a phosphoserine phosphatase, this group may be considered to be most closely allied to subfamily IB.; GO: 0000287 magnesium ion binding, 0008253 5'-nucleotidase activity, 0005737 cytoplasm; PDB: 2BDU_B 2G07_A 2G06_A 2G0A_A 2Q4T_A 2G09_A 2G08_A 2VKQ_A 2CN1_A 2JGA_A.
Probab=23.84 E-value=39 Score=28.06 Aligned_cols=41 Identities=32% Similarity=0.419 Sum_probs=27.1
Q ss_pred cCCCchHHHHhHHhcC--CCccceeeecCCCChhheeeeccCC
Q psy6808 50 LAGVGDVLGKRLESKG--FDKSINPQMFPDPDIEEKVLLFKNP 90 (132)
Q Consensus 50 LAGIGpvLGkrLeekG--FDKAYvVl~f~~~~~~~~~~~~~~~ 90 (132)
=||||+++-.-|+.+| ++..-+|-=|-+-|-+.++.-|+.|
T Consensus 113 SAGlgdvI~~vL~q~~~~~~Nv~VvSN~M~Fd~~g~l~gF~~~ 155 (246)
T PF05822_consen 113 SAGLGDVIEEVLRQAGVFHPNVKVVSNFMDFDEDGVLVGFKGP 155 (246)
T ss_dssp EEEEHHHHHHHHHHTT--BTTEEEEEE-EEE-TTSBEEEE-SS
T ss_pred eCCcHHHHHHHHHHcCCCCCCeEEEeeeEEECCcceEeecCCC
Confidence 3899999999999997 3344445445445545677778876
No 122
>PRK08594 enoyl-(acyl carrier protein) reductase; Provisional
Probab=23.78 E-value=43 Score=25.20 Aligned_cols=17 Identities=12% Similarity=0.206 Sum_probs=15.3
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
.|||..++++|.++|..
T Consensus 19 ~GIG~aia~~la~~G~~ 35 (257)
T PRK08594 19 RSIAWGIARSLHNAGAK 35 (257)
T ss_pred CCHHHHHHHHHHHCCCE
Confidence 49999999999999973
No 123
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.69 E-value=20 Score=31.04 Aligned_cols=27 Identities=30% Similarity=0.306 Sum_probs=22.2
Q ss_pred HHHHhHHhcCCCccceeeecCCCChhh
Q psy6808 56 VLGKRLESKGFDKSINPQMFPDPDIEE 82 (132)
Q Consensus 56 vLGkrLeekGFDKAYvVl~f~~~~~~~ 82 (132)
.--+||++.||++.-+++-|+-=|-.|
T Consensus 339 ~AIeRL~~LGF~r~~viqaY~ACdKNE 365 (378)
T TIGR00601 339 EAIERLCALGFDRGLVIQAYFACDKNE 365 (378)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhcCCcH
Confidence 456899999999999999998666544
No 124
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=23.60 E-value=59 Score=26.32 Aligned_cols=26 Identities=15% Similarity=0.334 Sum_probs=20.6
Q ss_pred cCCCC--CCCccccCCCchHHHHhHHhc
Q psy6808 39 SEPMG--EKPVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 39 sEPMG--EK~Vt~LAGIGpvLGkrLeek 64 (132)
.-=|| -.-+--++|||++-|.+|-.+
T Consensus 190 ~~L~Gd~sDnipGV~GIG~ktA~~Ll~~ 217 (310)
T COG0258 190 KALVGDSSDNIPGVKGIGPKTALKLLQE 217 (310)
T ss_pred HHHhCCcccCCCCCCCcCHHHHHHHHHH
Confidence 34578 455778999999999998765
No 125
>PRK14976 5'-3' exonuclease; Provisional
Probab=23.51 E-value=60 Score=26.61 Aligned_cols=26 Identities=19% Similarity=0.390 Sum_probs=20.4
Q ss_pred cCCCCC--CCccccCCCchHHHHhHHhc
Q psy6808 39 SEPMGE--KPVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 39 sEPMGE--K~Vt~LAGIGpvLGkrLeek 64 (132)
.-=||| .-+--+||||++-|.+|-.+
T Consensus 183 ~aL~GD~sDnipGVpGIG~KtA~~LL~~ 210 (281)
T PRK14976 183 KGLVGDSSDNIKGVKGIGPKTAIKLLNK 210 (281)
T ss_pred HHHhCCccCCCCCCCcccHHHHHHHHHH
Confidence 345886 55778999999999988754
No 126
>PRK06997 enoyl-(acyl carrier protein) reductase; Provisional
Probab=23.46 E-value=45 Score=25.15 Aligned_cols=17 Identities=12% Similarity=0.216 Sum_probs=15.2
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|..
T Consensus 18 ~GIG~a~a~~l~~~G~~ 34 (260)
T PRK06997 18 RSIAYGIAKACKREGAE 34 (260)
T ss_pred CcHHHHHHHHHHHCCCe
Confidence 48999999999999964
No 127
>TIGR02867 spore_II_P stage II sporulation protein P. Stage II sporulation protein P is a protein of the endospore formation program in a number of lineages in the Firmicutes (low-GC Gram-positive bacteria). It is expressed in the mother cell compartment, under control of Sigma-E. SpoIIP, along with SpoIIM and SpoIID, is one of three major proteins involved in engulfment of the forespore by the mother cell. This protein family is named for the single member in Bacillus subtilis, although most sporulating bacteria have two members.
Probab=23.32 E-value=35 Score=27.15 Aligned_cols=20 Identities=45% Similarity=0.694 Sum_probs=17.4
Q ss_pred cccCCCchHHHHhHHhcCCC
Q psy6808 48 TELAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 48 t~LAGIGpvLGkrLeekGFD 67 (132)
..+-++|+.|++.|+++|+.
T Consensus 30 ~~V~~VG~~L~~~Le~~Gi~ 49 (196)
T TIGR02867 30 GNITKVGDRLAKELEEKGIG 49 (196)
T ss_pred CcHHHHHHHHHHHHHHCCCe
Confidence 56778999999999999973
No 128
>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=23.19 E-value=37 Score=26.42 Aligned_cols=18 Identities=33% Similarity=0.580 Sum_probs=15.5
Q ss_pred CCccccCCCchHHHHhHH
Q psy6808 45 KPVTELAGVGDVLGKRLE 62 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkrLe 62 (132)
+.++.+||||+.-++|+.
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 567899999999999874
No 129
>PRK07023 short chain dehydrogenase; Provisional
Probab=23.16 E-value=46 Score=24.15 Aligned_cols=17 Identities=29% Similarity=0.579 Sum_probs=15.2
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|+.
T Consensus 11 ggiG~~ia~~l~~~G~~ 27 (243)
T PRK07023 11 RGLGAALAEQLLQPGIA 27 (243)
T ss_pred cchHHHHHHHHHhCCCE
Confidence 58999999999999973
No 130
>PRK08642 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=23.12 E-value=45 Score=24.00 Aligned_cols=18 Identities=17% Similarity=0.455 Sum_probs=15.7
Q ss_pred cCCCchHHHHhHHhcCCC
Q psy6808 50 LAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFD 67 (132)
=-|||..++++|.++|++
T Consensus 14 s~gIG~~la~~l~~~G~~ 31 (253)
T PRK08642 14 SRGLGAAIARAFAREGAR 31 (253)
T ss_pred CCcHHHHHHHHHHHCCCe
Confidence 369999999999999963
No 131
>PRK10880 adenine DNA glycosylase; Provisional
Probab=23.03 E-value=29 Score=29.74 Aligned_cols=32 Identities=25% Similarity=0.267 Sum_probs=26.9
Q ss_pred CCCCCCccccCCCchHHHHhHHhcCCCcccee
Q psy6808 41 PMGEKPVTELAGVGDVLGKRLESKGFDKSINP 72 (132)
Q Consensus 41 PMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvV 72 (132)
|.-.+...+|||||+.-|.-...-+|++..-+
T Consensus 105 p~~~~~L~~LpGIG~~TA~aIl~~af~~~~~i 136 (350)
T PRK10880 105 PETFEEVAALPGVGRSTAGAILSLSLGKHFPI 136 (350)
T ss_pred hhhHHHHhcCCCccHHHHHHHHHHHCCCCeec
Confidence 55557789999999999999999999996554
No 132
>PRK07984 enoyl-(acyl carrier protein) reductase; Provisional
Probab=22.78 E-value=45 Score=25.53 Aligned_cols=16 Identities=6% Similarity=0.279 Sum_probs=14.7
Q ss_pred CCchHHHHhHHhcCCC
Q psy6808 52 GVGDVLGKRLESKGFD 67 (132)
Q Consensus 52 GIGpvLGkrLeekGFD 67 (132)
|||..++++|.++|..
T Consensus 19 GIG~aia~~la~~G~~ 34 (262)
T PRK07984 19 SIAYGIAQAMHREGAE 34 (262)
T ss_pred cHHHHHHHHHHHCCCE
Confidence 7999999999999963
No 133
>cd00158 RHOD Rhodanese Homology Domain (RHOD); an alpha beta fold domain found duplicated in the rhodanese protein. The cysteine containing enzymatically active version of the domain is also found in the Cdc25 class of protein phosphatases and a variety of proteins such as sulfide dehydrogenases and certain stress proteins such as senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions (no active site cysteine) are also seen in dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases, where they are believed to play a regulatory role in multidomain proteins.
Probab=22.67 E-value=66 Score=19.28 Aligned_cols=19 Identities=21% Similarity=0.081 Sum_probs=15.8
Q ss_pred chHHHHhHHhcCCCcccee
Q psy6808 54 GDVLGKRLESKGFDKSINP 72 (132)
Q Consensus 54 GpvLGkrLeekGFDKAYvV 72 (132)
....+..|.+.||++.|.+
T Consensus 63 a~~~~~~l~~~G~~~v~~l 81 (89)
T cd00158 63 SARAAKLLRKAGGTNVYNL 81 (89)
T ss_pred HHHHHHHHHHhCcccEEEe
Confidence 3678899999999988754
No 134
>PRK08415 enoyl-(acyl carrier protein) reductase; Provisional
Probab=22.57 E-value=46 Score=25.62 Aligned_cols=17 Identities=12% Similarity=0.133 Sum_probs=15.3
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
.|||..++++|.++|+.
T Consensus 17 ~GIG~aiA~~la~~G~~ 33 (274)
T PRK08415 17 KSIAYGIAKACFEQGAE 33 (274)
T ss_pred CCHHHHHHHHHHHCCCE
Confidence 48999999999999973
No 135
>PRK08339 short chain dehydrogenase; Provisional
Probab=22.52 E-value=45 Score=25.12 Aligned_cols=16 Identities=25% Similarity=0.393 Sum_probs=15.0
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
-|||..++++|.++|+
T Consensus 18 ~gIG~aia~~l~~~G~ 33 (263)
T PRK08339 18 KGIGFGVARVLARAGA 33 (263)
T ss_pred CcHHHHHHHHHHHCCC
Confidence 5899999999999996
No 136
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=22.48 E-value=47 Score=24.69 Aligned_cols=27 Identities=22% Similarity=0.325 Sum_probs=22.3
Q ss_pred CCCCccccCCCchHHHHhHHhcCCCcc
Q psy6808 43 GEKPVTELAGVGDVLGKRLESKGFDKS 69 (132)
Q Consensus 43 GEK~Vt~LAGIGpvLGkrLeekGFDKA 69 (132)
+.+.+..-.=+|..+|+++.++|..++
T Consensus 61 ~~~n~~aA~~vG~~la~ra~~~gi~~v 87 (114)
T TIGR00060 61 YTGNKDAAKKVGKLVAERLKEKGIKDV 87 (114)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCEE
Confidence 555566777799999999999998875
No 137
>COG0456 RimI Acetyltransferases [General function prediction only]
Probab=22.47 E-value=26 Score=23.88 Aligned_cols=51 Identities=22% Similarity=0.346 Sum_probs=28.5
Q ss_pred CCCchHHHHhHH----hcCCCccceeeecCCCChhheeeeccCCCCccccceeEEeeeeeeecCCccCC
Q psy6808 51 AGVGDVLGKRLE----SKGFDKSINPQMFPDPDIEEKVLLFKNPNSLPIPIGVEVLGYTKIKNNKSRYP 115 (132)
Q Consensus 51 AGIGpvLGkrLe----ekGFDKAYvVl~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (132)
.|||..|-..+. ++|+. -.+.+.-.++-+.-+-||+. +||..++--+..|+
T Consensus 106 ~Gig~~Ll~~~~~~~~~~~~~--~~~~L~V~~~N~~Ai~lY~~------------~GF~~~~~~~~yy~ 160 (177)
T COG0456 106 RGIGRALLDEALERLRERGLA--DKIVLEVRESNEAAIGLYRK------------LGFEVVKIRKNYYA 160 (177)
T ss_pred CCHHHHHHHHHHHHHHhcCCC--ceEEEEEecCChHHHHHHHH------------cCCEEEeeehhhcc
Confidence 489999888544 44442 23333344444444444443 78887776665544
No 138
>PRK12827 short chain dehydrogenase; Provisional
Probab=22.44 E-value=47 Score=23.63 Aligned_cols=18 Identities=33% Similarity=0.632 Sum_probs=16.0
Q ss_pred cCCCchHHHHhHHhcCCC
Q psy6808 50 LAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFD 67 (132)
-.|||..+++.|.++|++
T Consensus 15 sg~iG~~la~~l~~~g~~ 32 (249)
T PRK12827 15 SGGLGRAIAVRLAADGAD 32 (249)
T ss_pred CChHHHHHHHHHHHCCCe
Confidence 368999999999999975
No 139
>PRK06114 short chain dehydrogenase; Provisional
Probab=22.32 E-value=43 Score=24.67 Aligned_cols=16 Identities=25% Similarity=0.513 Sum_probs=14.8
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
-|||..++++|.++|+
T Consensus 18 ~gIG~~ia~~l~~~G~ 33 (254)
T PRK06114 18 SGIGQRIAIGLAQAGA 33 (254)
T ss_pred chHHHHHHHHHHHCCC
Confidence 4899999999999996
No 140
>PRK08416 7-alpha-hydroxysteroid dehydrogenase; Provisional
Probab=22.22 E-value=42 Score=24.87 Aligned_cols=19 Identities=16% Similarity=0.408 Sum_probs=16.7
Q ss_pred ccCCCchHHHHhHHhcCCC
Q psy6808 49 ELAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 49 ~LAGIGpvLGkrLeekGFD 67 (132)
.-.|||..++++|.++|+.
T Consensus 16 as~gIG~~ia~~l~~~G~~ 34 (260)
T PRK08416 16 GTRGIGKAIVYEFAQSGVN 34 (260)
T ss_pred CCchHHHHHHHHHHHCCCE
Confidence 3479999999999999974
No 141
>PRK12823 benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional
Probab=22.16 E-value=47 Score=24.26 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=15.3
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|+.
T Consensus 18 ~gIG~~la~~l~~~G~~ 34 (260)
T PRK12823 18 QGIGRGVALRAAAEGAR 34 (260)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 68999999999999963
No 142
>PRK06523 short chain dehydrogenase; Provisional
Probab=22.06 E-value=53 Score=23.99 Aligned_cols=17 Identities=29% Similarity=0.401 Sum_probs=15.4
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
-|||..++++|.++|++
T Consensus 19 ~gIG~~ia~~l~~~G~~ 35 (260)
T PRK06523 19 KGIGAATVARLLEAGAR 35 (260)
T ss_pred CchhHHHHHHHHHCCCE
Confidence 59999999999999974
No 143
>PRK12747 short chain dehydrogenase; Provisional
Probab=21.97 E-value=50 Score=24.11 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=15.4
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
.|||..++++|.++|.+
T Consensus 14 ~gIG~~ia~~l~~~G~~ 30 (252)
T PRK12747 14 RGIGRAIAKRLANDGAL 30 (252)
T ss_pred ChHHHHHHHHHHHCCCe
Confidence 59999999999999964
No 144
>PRK06463 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=21.85 E-value=48 Score=24.33 Aligned_cols=18 Identities=17% Similarity=0.429 Sum_probs=15.9
Q ss_pred cCCCchHHHHhHHhcCCC
Q psy6808 50 LAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFD 67 (132)
-.|||..++++|.++|++
T Consensus 16 s~gIG~~~a~~l~~~G~~ 33 (255)
T PRK06463 16 TRGIGRAIAEAFLREGAK 33 (255)
T ss_pred CChHHHHHHHHHHHCCCE
Confidence 369999999999999963
No 145
>PF13207 AAA_17: AAA domain; PDB: 3AKC_A 3AKE_A 3AKD_A 2QL6_G 2QT1_A 2QSZ_A 2QSY_A 2QT0_A 2QG6_A 2P0E_A ....
Probab=21.75 E-value=69 Score=20.87 Aligned_cols=21 Identities=33% Similarity=0.673 Sum_probs=16.0
Q ss_pred ccccCCCch-HHHHhHHhc-CCC
Q psy6808 47 VTELAGVGD-VLGKRLESK-GFD 67 (132)
Q Consensus 47 Vt~LAGIGp-vLGkrLeek-GFD 67 (132)
|.-.||.|+ +++++|+++ ||.
T Consensus 4 I~G~~gsGKST~a~~La~~~~~~ 26 (121)
T PF13207_consen 4 ISGPPGSGKSTLAKELAERLGFP 26 (121)
T ss_dssp EEESTTSSHHHHHHHHHHHHTCE
T ss_pred EECCCCCCHHHHHHHHHHHHCCe
Confidence 345688997 588999997 874
No 146
>PRK06924 short chain dehydrogenase; Provisional
Probab=21.61 E-value=45 Score=24.14 Aligned_cols=17 Identities=29% Similarity=0.591 Sum_probs=15.3
Q ss_pred cCCCchHHHHhHHhcCC
Q psy6808 50 LAGVGDVLGKRLESKGF 66 (132)
Q Consensus 50 LAGIGpvLGkrLeekGF 66 (132)
--|||..++++|.++|+
T Consensus 10 sggiG~~ia~~l~~~g~ 26 (251)
T PRK06924 10 SQGLGEAIANQLLEKGT 26 (251)
T ss_pred CchHHHHHHHHHHhcCC
Confidence 35899999999999997
No 147
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=21.29 E-value=46 Score=24.33 Aligned_cols=17 Identities=29% Similarity=0.474 Sum_probs=15.3
Q ss_pred cCCCchHHHHhHHhcCC
Q psy6808 50 LAGVGDVLGKRLESKGF 66 (132)
Q Consensus 50 LAGIGpvLGkrLeekGF 66 (132)
--|||..++++|.++|+
T Consensus 19 ~g~iG~~ia~~l~~~G~ 35 (255)
T PRK07523 19 SQGIGYALAEGLAQAGA 35 (255)
T ss_pred cchHHHHHHHHHHHcCC
Confidence 36899999999999997
No 148
>PRK07063 short chain dehydrogenase; Provisional
Probab=20.90 E-value=49 Score=24.24 Aligned_cols=18 Identities=17% Similarity=0.503 Sum_probs=15.8
Q ss_pred cCCCchHHHHhHHhcCCC
Q psy6808 50 LAGVGDVLGKRLESKGFD 67 (132)
Q Consensus 50 LAGIGpvLGkrLeekGFD 67 (132)
--|||..++++|.++|++
T Consensus 16 s~gIG~~~a~~l~~~G~~ 33 (260)
T PRK07063 16 AQGIGAAIARAFAREGAA 33 (260)
T ss_pred CchHHHHHHHHHHHCCCE
Confidence 369999999999999973
No 149
>TIGR01832 kduD 2-deoxy-D-gluconate 3-dehydrogenase. This model describes 2-deoxy-D-gluconate 3-dehydrogenase (also called 2-keto-3-deoxygluconate oxidoreductase), a member of the family of short-chain-alcohol dehydrogenases (pfam00106). This protein has been characterized in Erwinia chrysanthemi as an enzyme of pectin degradation.
Probab=20.89 E-value=49 Score=23.91 Aligned_cols=16 Identities=25% Similarity=0.457 Sum_probs=14.9
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
.|||..++++|.++|+
T Consensus 15 ~gIG~~ia~~l~~~G~ 30 (248)
T TIGR01832 15 TGLGQGIAVGLAEAGA 30 (248)
T ss_pred chHHHHHHHHHHHCCC
Confidence 5899999999999996
No 150
>PRK06550 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=20.71 E-value=54 Score=23.49 Aligned_cols=16 Identities=19% Similarity=0.430 Sum_probs=14.8
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
.|||..++++|.++|.
T Consensus 15 ~~iG~~ia~~l~~~G~ 30 (235)
T PRK06550 15 SGIGLAQARAFLAQGA 30 (235)
T ss_pred chHHHHHHHHHHHCCC
Confidence 5899999999999996
No 151
>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=20.68 E-value=71 Score=29.40 Aligned_cols=31 Identities=19% Similarity=0.362 Sum_probs=23.5
Q ss_pred cccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhc
Q psy6808 27 KMSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 27 MstTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeek 64 (132)
+.++..--..|++.++ ++|||++.+++|.++
T Consensus 73 ~p~~~~~i~~yL~s~~-------~~GIG~~~A~~iv~~ 103 (720)
T TIGR01448 73 APTSKEGIVAYLSSRS-------IKGVGKKLAQRIVKT 103 (720)
T ss_pred CCCCHHHHHHHHhcCC-------CCCcCHHHHHHHHHH
Confidence 4445556678988654 899999999999765
No 152
>TIGR02685 pter_reduc_Leis pteridine reductase. Pteridine reductase is an enzyme used by trypanosomatids (including Trypanosoma cruzi and Leishmania major) to obtain reduced pteridines by salvage rather than biosynthetic pathways. Enzymes in T. cruzi described as pteridine reductase 1 (PTR1) and pteridine reductase 2 (PTR2) have different activity profiles. PTR1 is more active with with fully oxidized biopterin and folate than with reduced forms, while PTR2 reduces dihydrobiopterin and dihydrofolate but not oxidized pteridines. T. cruzi PTR1 and PTR2 are more similar to each other in sequence than either is to the pteridine reductase of Leishmania major, and all are included in this family.
Probab=20.67 E-value=56 Score=24.32 Aligned_cols=17 Identities=18% Similarity=0.511 Sum_probs=15.4
Q ss_pred CCCchHHHHhHHhcCCC
Q psy6808 51 AGVGDVLGKRLESKGFD 67 (132)
Q Consensus 51 AGIGpvLGkrLeekGFD 67 (132)
.|||..++++|.++|.+
T Consensus 11 ~gIG~~~a~~l~~~G~~ 27 (267)
T TIGR02685 11 KRIGSSIAVALHQEGYR 27 (267)
T ss_pred CcHHHHHHHHHHhCCCe
Confidence 69999999999999973
No 153
>PRK05653 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Validated
Probab=20.50 E-value=52 Score=23.19 Aligned_cols=26 Identities=19% Similarity=0.335 Sum_probs=19.7
Q ss_pred CCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808 51 AGVGDVLGKRLESKGFDKSINPQMFPDPD 79 (132)
Q Consensus 51 AGIGpvLGkrLeekGFDKAYvVl~f~~~~ 79 (132)
-|||..+++.|.++|+. ++++--+++
T Consensus 15 g~iG~~l~~~l~~~g~~---v~~~~r~~~ 40 (246)
T PRK05653 15 RGIGRAIALRLAADGAK---VVIYDSNEE 40 (246)
T ss_pred cHHHHHHHHHHHHCCCE---EEEEeCChh
Confidence 57999999999999985 455555544
No 154
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=20.46 E-value=57 Score=21.19 Aligned_cols=14 Identities=29% Similarity=0.522 Sum_probs=10.6
Q ss_pred ccHHHHhhhcCCCC
Q psy6808 30 TSQKHQNFVSEPMG 43 (132)
Q Consensus 30 TSqKHRnFVsEPMG 43 (132)
.|.+||.|+..+--
T Consensus 23 ~s~~Hr~FA~~~~N 36 (49)
T PF07535_consen 23 QSEKHRKFAENDSN 36 (49)
T ss_pred CCHHHHHHHcCccc
Confidence 46799999976543
No 155
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=20.46 E-value=67 Score=22.55 Aligned_cols=22 Identities=27% Similarity=0.360 Sum_probs=19.0
Q ss_pred ccccCCCchHHHHhHHhcCCCc
Q psy6808 47 VTELAGVGDVLGKRLESKGFDK 68 (132)
Q Consensus 47 Vt~LAGIGpvLGkrLeekGFDK 68 (132)
...++|||+.-+.-+.--||.+
T Consensus 74 L~~l~GIG~~tA~~~l~~~~~~ 95 (149)
T smart00478 74 LLKLPGVGRKTANAVLSFALGK 95 (149)
T ss_pred HHcCCCCcHHHHHHHHHHHCCC
Confidence 4579999999998888888887
No 156
>KOG1205|consensus
Probab=20.46 E-value=47 Score=27.92 Aligned_cols=18 Identities=28% Similarity=0.593 Sum_probs=16.2
Q ss_pred ccCCCchHHHHhHHhcCC
Q psy6808 49 ELAGVGDVLGKRLESKGF 66 (132)
Q Consensus 49 ~LAGIGpvLGkrLeekGF 66 (132)
+=.|||+.++..|..+|-
T Consensus 20 ASsGIG~~lA~~la~~G~ 37 (282)
T KOG1205|consen 20 ASSGIGEALAYELAKRGA 37 (282)
T ss_pred CCcHHHHHHHHHHHhCCC
Confidence 457999999999999995
No 157
>KOG1811|consensus
Probab=20.45 E-value=26 Score=34.59 Aligned_cols=47 Identities=21% Similarity=0.214 Sum_probs=36.2
Q ss_pred ccccHHHHhhhcCCCCCCCccccCCCchHHHHhHHhcCCCccceeeecCCCC
Q psy6808 28 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKSINPQMFPDPD 79 (132)
Q Consensus 28 stTSqKHRnFVsEPMGEK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f~~~~ 79 (132)
.++-.||.-|=.--|-+.....+ .+|++|.|+|||-||.|++=|.-|
T Consensus 948 ega~~khsLFGN~~dke~s~~kc-----ei~eklVE~~FdiAf~Vi~dFkL~ 994 (1141)
T KOG1811|consen 948 EGALPKHSLFGNNHDKEDSACKC-----EIGEKLVEDGFDIAFRVIQDFKLD 994 (1141)
T ss_pred cCCCCcccccCCCccchhhhhee-----ehhhhhhhcCcchHHHHHHHhccc
Confidence 35667899887777776655554 577889999999999999877654
No 158
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=20.40 E-value=66 Score=24.74 Aligned_cols=19 Identities=26% Similarity=0.337 Sum_probs=15.0
Q ss_pred CccccCCCchHHHHhHHhc
Q psy6808 46 PVTELAGVGDVLGKRLESK 64 (132)
Q Consensus 46 ~Vt~LAGIGpvLGkrLeek 64 (132)
....++||||..+.+|-+.
T Consensus 74 ~L~~i~GIGpk~A~~il~~ 92 (192)
T PRK00116 74 LLISVSGVGPKLALAILSG 92 (192)
T ss_pred HHhcCCCCCHHHHHHHHHh
Confidence 3456999999999988653
No 159
>PRK08340 glucose-1-dehydrogenase; Provisional
Probab=20.34 E-value=47 Score=24.53 Aligned_cols=17 Identities=29% Similarity=0.415 Sum_probs=15.3
Q ss_pred cCCCchHHHHhHHhcCC
Q psy6808 50 LAGVGDVLGKRLESKGF 66 (132)
Q Consensus 50 LAGIGpvLGkrLeekGF 66 (132)
-.|||..++++|.++|+
T Consensus 9 s~gIG~aia~~l~~~G~ 25 (259)
T PRK08340 9 SRGIGFNVARELLKKGA 25 (259)
T ss_pred CcHHHHHHHHHHHHcCC
Confidence 36899999999999996
No 160
>PRK06300 enoyl-(acyl carrier protein) reductase; Provisional
Probab=20.25 E-value=50 Score=26.63 Aligned_cols=16 Identities=31% Similarity=0.364 Sum_probs=15.2
Q ss_pred CCCchHHHHhHHhcCC
Q psy6808 51 AGVGDVLGKRLESKGF 66 (132)
Q Consensus 51 AGIGpvLGkrLeekGF 66 (132)
.|||..+++.|+++|+
T Consensus 20 ~GIG~a~A~~la~~Ga 35 (299)
T PRK06300 20 QGYGWGIAKALAEAGA 35 (299)
T ss_pred CCHHHHHHHHHHHCCC
Confidence 6999999999999996
No 161
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=20.19 E-value=39 Score=26.36 Aligned_cols=16 Identities=19% Similarity=0.507 Sum_probs=13.8
Q ss_pred CCccccCCCchHHHHh
Q psy6808 45 KPVTELAGVGDVLGKR 60 (132)
Q Consensus 45 K~Vt~LAGIGpvLGkr 60 (132)
+..+.+||||+..++|
T Consensus 108 ~~L~~vpGIGkKtAer 123 (194)
T PRK14605 108 ELLSTIPGIGKKTASR 123 (194)
T ss_pred HHHHhCCCCCHHHHHH
Confidence 4467899999999999
No 162
>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily. This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.
Probab=20.11 E-value=73 Score=20.53 Aligned_cols=18 Identities=17% Similarity=0.326 Sum_probs=14.4
Q ss_pred chHHHHhHHhcCCCcccee
Q psy6808 54 GDVLGKRLESKGFDKSINP 72 (132)
Q Consensus 54 GpvLGkrLeekGFDKAYvV 72 (132)
....+..|.+.||+ +|.+
T Consensus 74 s~~aa~~L~~~G~~-~~~l 91 (100)
T cd01523 74 SQFVAELLAERGYD-VDYL 91 (100)
T ss_pred HHHHHHHHHHcCce-eEEe
Confidence 46788899999998 7654
No 163
>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=20.01 E-value=26 Score=27.16 Aligned_cols=32 Identities=22% Similarity=0.422 Sum_probs=20.8
Q ss_pred CCCccccCCCchHHHHhHHhcCCCccceeeec
Q psy6808 44 EKPVTELAGVGDVLGKRLESKGFDKSINPQMF 75 (132)
Q Consensus 44 EK~Vt~LAGIGpvLGkrLeekGFDKAYvVl~f 75 (132)
+-+...|||||+...++|+.+|..--.++.-+
T Consensus 147 ~~~L~Qlp~i~~~~~~~l~~~~i~~l~~l~~~ 178 (314)
T PF02889_consen 147 DSPLLQLPHIGEESLKKLEKRGIKTLQDLRDL 178 (314)
T ss_dssp S-GGGGSTT--HHHHHHHHHTT--SHHHHHHS
T ss_pred CChhhcCCCCCHHHHHHHhccCCCcHHHHhhC
Confidence 35778999999999999999995544444433
Done!