Query psy6806
Match_columns 89
No_of_seqs 103 out of 105
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 18:51:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy6806.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/6806hhsearch_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 7.4E-63 1.6E-67 332.8 8.6 88 1-88 2-89 (89)
2 KOG4233|consensus 100.0 3E-58 6.5E-63 309.3 8.6 88 2-89 3-90 (90)
3 PF11798 IMS_HHH: IMS family H 97.1 0.00031 6.8E-09 38.9 1.7 29 7-39 4-32 (32)
4 PRK04301 radA DNA repair and r 96.6 0.0018 3.8E-08 49.8 2.9 35 13-47 1-35 (317)
5 PF14520 HHH_5: Helix-hairpin- 96.1 0.011 2.3E-07 35.7 3.7 54 19-82 6-59 (60)
6 PF11731 Cdd1: Pathogenicity l 95.4 0.0082 1.8E-07 40.9 1.4 31 18-48 12-42 (93)
7 COG3743 Uncharacterized conser 93.7 0.064 1.4E-06 38.9 2.8 37 9-45 57-94 (133)
8 cd01703 PolY_Pol_iota DNA Poly 92.9 0.086 1.9E-06 42.4 2.7 31 16-46 170-200 (379)
9 cd01701 PolY_Rev1 DNA polymera 92.6 0.079 1.7E-06 42.4 2.0 35 13-47 217-251 (404)
10 PRK03352 DNA polymerase IV; Va 92.5 0.088 1.9E-06 40.7 2.2 32 16-47 175-206 (346)
11 PRK02406 DNA polymerase IV; Va 92.4 0.077 1.7E-06 41.0 1.7 32 15-46 165-196 (343)
12 cd00424 PolY Y-family of DNA p 92.4 0.1 2.2E-06 40.3 2.4 32 15-46 170-201 (343)
13 PRK03858 DNA polymerase IV; Va 92.3 0.1 2.3E-06 40.9 2.4 32 16-47 171-202 (396)
14 cd01700 PolY_Pol_V_umuC umuC s 91.4 0.19 4E-06 38.9 2.8 35 13-47 171-205 (344)
15 PRK03609 umuC DNA polymerase V 91.1 0.17 3.8E-06 40.4 2.5 31 16-46 177-207 (422)
16 TIGR02236 recomb_radA DNA repa 91.0 0.21 4.4E-06 38.0 2.7 27 20-46 1-27 (310)
17 PF04994 TfoX_C: TfoX C-termin 90.7 0.24 5.1E-06 32.3 2.4 28 18-45 3-30 (81)
18 PF00633 HHH: Helix-hairpin-he 90.5 0.091 2E-06 28.8 0.3 18 18-35 11-28 (30)
19 smart00278 HhH1 Helix-hairpin- 90.2 0.21 4.6E-06 25.9 1.5 18 19-36 2-19 (26)
20 cd03586 PolY_Pol_IV_kappa DNA 90.2 0.24 5.1E-06 37.6 2.4 31 16-46 169-199 (334)
21 PRK01810 DNA polymerase IV; Va 90.1 0.24 5.1E-06 39.2 2.4 31 17-47 178-208 (407)
22 PTZ00205 DNA polymerase kappa; 89.9 0.23 5.1E-06 42.9 2.4 30 17-46 308-337 (571)
23 PRK03103 DNA polymerase IV; Re 89.9 0.25 5.4E-06 39.2 2.3 30 17-46 180-209 (409)
24 PRK02794 DNA polymerase IV; Pr 89.6 0.21 4.5E-06 39.9 1.8 34 14-47 205-238 (419)
25 PF14229 DUF4332: Domain of un 88.8 0.4 8.7E-06 33.0 2.5 24 24-47 1-24 (122)
26 PF10391 DNA_pol_lambd_f: Fing 88.3 0.32 7E-06 29.6 1.6 26 20-45 4-29 (52)
27 PRK03348 DNA polymerase IV; Pr 88.0 0.32 6.9E-06 39.8 1.8 32 15-46 177-208 (454)
28 cd01702 PolY_Pol_eta DNA Polym 87.7 0.37 8E-06 38.4 2.0 34 14-47 178-212 (359)
29 PRK12278 50S ribosomal protein 87.3 0.49 1.1E-05 36.4 2.4 29 17-45 157-185 (221)
30 PRK14133 DNA polymerase IV; Pr 87.2 0.56 1.2E-05 36.4 2.7 31 17-47 172-202 (347)
31 PRK01216 DNA polymerase IV; Va 86.0 0.52 1.1E-05 37.5 2.0 31 15-45 175-205 (351)
32 PF14716 HHH_8: Helix-hairpin- 85.4 0.55 1.2E-05 29.0 1.5 17 20-36 49-65 (68)
33 cd00141 NT_POLXc Nucleotidyltr 84.3 0.45 9.7E-06 37.2 0.9 44 3-46 69-113 (307)
34 PRK02515 psbU photosystem II c 83.5 1 2.2E-05 32.6 2.4 27 19-45 62-89 (132)
35 PRK12311 rpsB 30S ribosomal pr 83.1 0.83 1.8E-05 36.9 2.0 28 18-45 263-290 (326)
36 PRK12766 50S ribosomal protein 82.2 1.3 2.8E-05 34.7 2.6 28 18-45 3-30 (232)
37 PF02371 Transposase_20: Trans 81.1 1.2 2.6E-05 28.5 1.8 18 19-36 3-20 (87)
38 PF12826 HHH_2: Helix-hairpin- 80.7 0.81 1.8E-05 28.1 0.9 18 19-36 36-53 (64)
39 KOG1014|consensus 80.0 0.65 1.4E-05 37.6 0.4 19 22-40 57-75 (312)
40 cd00080 HhH2_motif Helix-hairp 78.8 3.4 7.4E-05 26.1 3.4 23 15-37 17-41 (75)
41 COG0389 DinP Nucleotidyltransf 77.3 1.9 4.1E-05 34.2 2.3 31 17-47 175-205 (354)
42 COG0353 RecR Recombinational D 76.8 1.5 3.2E-05 33.7 1.5 15 20-34 14-28 (198)
43 cd03468 PolY_like DNA Polymera 76.4 2.5 5.4E-05 32.0 2.6 32 15-47 168-199 (335)
44 PF14229 DUF4332: Domain of un 76.0 2.1 4.5E-05 29.4 1.9 24 19-42 54-77 (122)
45 PRK07945 hypothetical protein; 73.8 2.2 4.7E-05 33.8 1.8 18 19-36 50-67 (335)
46 PLN03187 meiotic recombination 73.4 2.8 6.1E-05 33.7 2.3 62 13-85 25-88 (344)
47 smart00279 HhH2 Helix-hairpin- 73.0 2.8 6E-05 23.6 1.6 17 20-36 18-34 (36)
48 KOG4305|consensus 72.9 3.6 7.8E-05 38.1 3.1 54 10-67 402-460 (1029)
49 PRK14601 ruvA Holliday junctio 72.9 1.4 3E-05 32.8 0.4 19 18-36 108-126 (183)
50 PRK10917 ATP-dependent DNA hel 72.7 3.1 6.7E-05 35.7 2.5 31 18-48 9-39 (681)
51 cd00008 53EXOc 5'-3' exonuclea 72.1 12 0.00025 28.2 5.3 57 15-79 178-236 (240)
52 KOG2094|consensus 71.1 5.3 0.00012 34.1 3.5 60 11-70 275-336 (490)
53 PTZ00035 Rad51 protein; Provis 69.9 4.1 8.8E-05 32.3 2.5 56 19-84 22-79 (337)
54 PRK13913 3-methyladenine DNA g 69.0 17 0.00037 27.7 5.6 50 18-67 121-178 (218)
55 PRK14604 ruvA Holliday junctio 68.6 2 4.2E-05 32.1 0.4 19 18-36 108-126 (195)
56 PRK14606 ruvA Holliday junctio 68.3 2 4.3E-05 31.9 0.4 19 18-36 108-126 (188)
57 PRK13901 ruvA Holliday junctio 68.2 2 4.3E-05 32.5 0.4 19 18-36 107-125 (196)
58 smart00611 SEC63 Domain of unk 66.9 19 0.00042 27.1 5.5 58 17-84 150-207 (312)
59 smart00483 POLXc DNA polymeras 65.6 2.8 6.2E-05 33.2 0.8 33 14-46 85-117 (334)
60 PRK12373 NADH dehydrogenase su 65.3 4.5 9.7E-05 33.8 2.0 27 19-45 324-350 (400)
61 PRK14602 ruvA Holliday junctio 64.5 2.7 5.8E-05 31.4 0.5 19 18-36 109-127 (203)
62 PRK14603 ruvA Holliday junctio 62.9 2.9 6.4E-05 31.2 0.4 19 18-36 107-125 (197)
63 PRK09482 flap endonuclease-lik 62.1 5.7 0.00012 30.9 1.9 23 14-36 176-200 (256)
64 TIGR00615 recR recombination p 61.7 4.3 9.2E-05 30.8 1.1 17 19-35 12-28 (195)
65 PRK13844 recombination protein 61.6 4.2 9.2E-05 31.0 1.1 17 19-35 16-32 (200)
66 PRK00076 recR recombination pr 60.7 4.5 9.8E-05 30.6 1.1 17 19-35 12-28 (196)
67 PRK02362 ski2-like helicase; P 60.0 6.9 0.00015 33.7 2.2 28 19-46 653-680 (737)
68 PF06844 DUF1244: Protein of u 59.6 6.9 0.00015 25.6 1.7 14 74-87 10-23 (68)
69 PRK08609 hypothetical protein; 59.2 5.4 0.00012 33.9 1.4 42 4-45 73-116 (570)
70 smart00483 POLXc DNA polymeras 58.5 5.8 0.00013 31.4 1.4 24 13-36 42-66 (334)
71 TIGR01259 comE comEA protein. 56.9 6.8 0.00015 26.9 1.4 19 19-37 69-87 (120)
72 COG0632 RuvA Holliday junction 56.6 5.5 0.00012 30.2 1.0 19 18-36 108-126 (201)
73 COG0300 DltE Short-chain dehyd 56.3 5.9 0.00013 31.1 1.1 18 23-40 15-32 (265)
74 TIGR02238 recomb_DMC1 meiotic 56.0 11 0.00024 29.6 2.6 52 24-85 7-58 (313)
75 PRK01172 ski2-like helicase; P 56.0 9.9 0.00021 32.2 2.5 55 19-83 613-667 (674)
76 PRK14600 ruvA Holliday junctio 55.3 6.3 0.00014 29.3 1.1 18 18-36 108-125 (186)
77 TIGR03491 RecB family nuclease 55.2 12 0.00026 30.6 2.8 30 17-46 206-235 (457)
78 PRK14605 ruvA Holliday junctio 55.1 4.5 9.7E-05 30.0 0.3 16 18-33 108-123 (194)
79 PF09288 UBA_3: Fungal ubiquit 55.1 10 0.00022 23.8 1.9 25 21-45 3-27 (55)
80 cd00141 NT_POLXc Nucleotidyltr 54.1 7.5 0.00016 30.4 1.4 18 19-36 46-63 (307)
81 TIGR00084 ruvA Holliday juncti 54.1 5.8 0.00013 29.3 0.7 18 18-35 107-124 (191)
82 PRK00116 ruvA Holliday junctio 53.3 7.4 0.00016 28.5 1.2 18 19-36 74-91 (192)
83 PLN03186 DNA repair protein RA 52.9 10 0.00022 30.4 2.0 56 19-84 27-84 (342)
84 PF12836 HHH_3: Helix-hairpin- 52.3 12 0.00026 22.7 1.8 28 19-46 15-47 (65)
85 COG1200 RecG RecG-like helicas 52.1 11 0.00025 33.6 2.3 32 18-49 10-41 (677)
86 PRK00254 ski2-like helicase; P 51.6 12 0.00027 32.0 2.4 28 19-46 646-673 (720)
87 PRK14976 5'-3' exonuclease; Pr 51.5 11 0.00023 29.4 1.9 22 15-36 186-209 (281)
88 PF02889 Sec63: Sec63 Brl doma 51.0 24 0.00052 26.4 3.6 55 17-81 147-201 (314)
89 smart00475 53EXOc 5'-3' exonuc 51.0 12 0.00026 28.8 2.1 34 15-48 181-218 (259)
90 TIGR00426 competence protein C 50.9 12 0.00026 22.7 1.6 19 19-37 17-36 (69)
91 TIGR01764 excise DNA binding d 50.6 5.8 0.00013 21.3 0.2 45 17-64 4-48 (49)
92 TIGR02239 recomb_RAD51 DNA rep 50.5 15 0.00032 28.9 2.5 52 24-85 7-58 (316)
93 TIGR01740 pyrF orotidine 5'-ph 49.3 11 0.00024 27.5 1.6 51 3-56 144-205 (213)
94 PRK14667 uvrC excinuclease ABC 47.8 28 0.0006 30.1 3.9 64 7-82 503-566 (567)
95 KOG2924|consensus 47.7 18 0.00039 30.0 2.7 58 6-67 115-187 (366)
96 PRK08609 hypothetical protein; 47.7 12 0.00025 31.9 1.6 18 19-36 49-66 (570)
97 COG5217 BIM1 Microtubule-bindi 46.6 32 0.0007 28.4 3.9 45 20-66 59-105 (342)
98 PF01367 5_3_exonuc: 5'-3' exo 46.3 3.4 7.4E-05 28.1 -1.4 22 15-36 13-36 (101)
99 COG3492 Uncharacterized protei 44.4 19 0.00041 25.2 2.0 15 73-87 40-54 (104)
100 TIGR01448 recD_rel helicase, p 44.3 24 0.00052 30.9 3.1 27 3-36 76-102 (720)
101 COG0258 Exo 5'-3' exonuclease 44.0 17 0.00037 28.1 2.0 23 15-37 193-217 (310)
102 PF11300 DUF3102: Protein of u 42.9 58 0.0013 23.3 4.4 39 46-84 28-69 (130)
103 smart00184 RING Ring finger. E 42.8 21 0.00046 17.5 1.6 11 76-86 20-30 (39)
104 PF13399 LytR_C: LytR cell env 42.6 18 0.0004 22.6 1.6 23 21-43 12-34 (90)
105 smart00478 ENDO3c endonuclease 41.6 15 0.00032 24.8 1.2 50 19-68 73-132 (149)
106 TIGR00596 rad1 DNA repair prot 41.2 46 0.001 30.0 4.4 51 20-82 759-809 (814)
107 PRK10702 endonuclease III; Pro 40.7 8.6 0.00019 28.8 -0.1 28 14-41 105-132 (211)
108 cd00056 ENDO3c endonuclease II 39.8 12 0.00027 25.4 0.5 25 16-40 81-105 (158)
109 KOG2093|consensus 39.6 19 0.00042 33.5 1.8 36 6-45 541-576 (1016)
110 KOG1209|consensus 39.2 18 0.00038 29.2 1.4 17 24-40 18-34 (289)
111 PRK10880 adenine DNA glycosyla 38.7 7.6 0.00016 31.5 -0.8 29 14-42 105-133 (350)
112 COG1796 POL4 DNA polymerase IV 38.3 20 0.00044 29.4 1.6 17 20-36 55-71 (326)
113 COG4221 Short-chain alcohol de 37.8 18 0.00038 28.6 1.2 38 23-69 15-52 (246)
114 TIGR01083 nth endonuclease III 37.5 18 0.00038 26.1 1.1 24 18-41 106-129 (191)
115 PRK13910 DNA glycosylase MutY; 36.9 12 0.00026 29.6 0.1 28 14-41 68-95 (289)
116 KOG2841|consensus 35.7 23 0.00049 28.3 1.5 28 7-36 218-245 (254)
117 TIGR00593 pola DNA polymerase 35.5 26 0.00056 31.8 2.0 22 15-36 180-203 (887)
118 cd00162 RING RING-finger (Real 34.5 27 0.00059 17.8 1.3 16 72-87 18-33 (45)
119 PF02330 MAM33: Mitochondrial 34.4 52 0.0011 23.9 3.1 38 28-66 162-200 (204)
120 COG1555 ComEA DNA uptake prote 33.9 20 0.00044 25.6 0.9 15 21-35 100-114 (149)
121 PF10691 DUF2497: Protein of u 33.4 24 0.00053 22.9 1.1 9 81-89 47-55 (73)
122 TIGR03252 uncharacterized HhH- 33.0 19 0.00042 26.9 0.7 15 18-32 115-129 (177)
123 PF02579 Nitro_FeMo-Co: Dinitr 32.7 43 0.00094 20.4 2.2 34 5-40 43-76 (94)
124 PF13639 zf-RING_2: Ring finge 32.2 24 0.00052 19.5 0.8 13 75-87 24-36 (44)
125 PRK07533 enoyl-(acyl carrier p 32.1 27 0.00058 25.2 1.3 16 25-40 23-38 (258)
126 PRK06079 enoyl-(acyl carrier p 32.1 27 0.00059 25.1 1.3 17 24-40 19-35 (252)
127 PRK08091 ribulose-phosphate 3- 31.9 89 0.0019 24.0 4.1 56 6-64 168-224 (228)
128 PRK06603 enoyl-(acyl carrier p 31.5 28 0.0006 25.3 1.3 16 25-40 21-36 (260)
129 cd00128 XPG Xeroderma pigmento 31.3 39 0.00083 26.0 2.1 23 15-37 220-242 (316)
130 cd01518 RHOD_YceA Member of th 31.3 22 0.00049 22.2 0.7 23 27-49 74-96 (101)
131 TIGR01084 mutY A/G-specific ad 30.7 26 0.00056 27.4 1.1 25 17-41 104-128 (275)
132 KOG0011|consensus 30.2 85 0.0018 26.1 4.0 36 29-65 300-335 (340)
133 cd00432 Ribosomal_L18_L5e Ribo 30.0 23 0.0005 23.3 0.6 34 17-50 53-86 (103)
134 KOG0317|consensus 30.0 30 0.00066 28.1 1.4 14 74-87 259-272 (293)
135 COG1948 MUS81 ERCC4-type nucle 29.4 28 0.0006 27.6 1.0 17 20-36 184-200 (254)
136 TIGR01684 viral_ppase viral ph 29.3 30 0.00066 28.0 1.3 32 55-88 69-109 (301)
137 PRK08690 enoyl-(acyl carrier p 29.2 31 0.00068 25.0 1.2 17 24-40 18-34 (261)
138 PF07535 zf-DBF: DBF zinc fing 29.0 33 0.00071 20.8 1.1 13 3-15 23-35 (49)
139 TIGR03674 fen_arch flap struct 29.0 44 0.00096 26.6 2.1 23 15-37 233-255 (338)
140 PRK08159 enoyl-(acyl carrier p 28.6 32 0.0007 25.3 1.2 17 24-40 22-38 (272)
141 PF00861 Ribosomal_L18p: Ribos 28.3 9.5 0.00021 26.2 -1.5 47 2-49 53-99 (119)
142 PRK12481 2-deoxy-D-gluconate 3 28.3 31 0.00067 24.7 1.1 17 24-40 18-34 (251)
143 PRK07370 enoyl-(acyl carrier p 28.2 35 0.00075 24.7 1.3 17 24-40 18-34 (258)
144 CHL00139 rpl18 ribosomal prote 28.1 26 0.00057 24.1 0.6 32 18-49 58-89 (109)
145 PRK08862 short chain dehydroge 28.0 32 0.00069 24.8 1.1 17 24-40 15-31 (227)
146 smart00450 RHOD Rhodanese Homo 27.8 27 0.0006 20.4 0.6 22 28-49 70-91 (100)
147 cd00853 NifX NifX belongs to a 27.2 41 0.00088 21.6 1.4 25 17-41 61-85 (102)
148 PRK05593 rplR 50S ribosomal pr 27.0 28 0.00061 24.2 0.6 33 17-49 65-97 (117)
149 PRK06505 enoyl-(acyl carrier p 27.0 36 0.00079 25.0 1.3 16 25-40 20-35 (271)
150 cd00158 RHOD Rhodanese Homolog 27.0 24 0.00052 20.6 0.2 24 26-49 62-85 (89)
151 KOG3242|consensus 26.7 41 0.0009 26.1 1.5 20 69-88 66-85 (208)
152 PRK07984 enoyl-(acyl carrier p 26.7 37 0.0008 25.0 1.2 16 25-40 19-34 (262)
153 PRK06997 enoyl-(acyl carrier p 26.7 38 0.00083 24.6 1.3 17 24-40 18-34 (260)
154 PRK08594 enoyl-(acyl carrier p 26.5 39 0.00084 24.5 1.3 17 24-40 19-35 (257)
155 PRK05755 DNA polymerase I; Pro 26.4 47 0.001 29.6 2.0 22 15-36 182-205 (880)
156 PF14579 HHH_6: Helix-hairpin- 26.3 50 0.0011 21.1 1.7 19 19-37 28-46 (90)
157 smart00586 ZnF_DBF Zinc finger 26.1 39 0.00085 20.5 1.1 12 3-14 23-34 (49)
158 PRK03980 flap endonuclease-1; 25.9 55 0.0012 25.7 2.1 22 15-36 186-207 (292)
159 PLN02780 ketoreductase/ oxidor 25.8 37 0.0008 26.0 1.1 17 24-40 63-79 (320)
160 PF09665 RE_Alw26IDE: Type II 25.7 91 0.002 27.2 3.5 41 30-70 128-177 (511)
161 PRK10308 3-methyl-adenine DNA 25.5 29 0.00064 27.0 0.6 28 18-45 207-234 (283)
162 PRK08415 enoyl-(acyl carrier p 25.5 41 0.00088 24.9 1.3 17 24-40 17-33 (274)
163 cd03572 ENTH_epsin_related ENT 25.3 35 0.00076 24.0 0.9 47 19-67 32-81 (122)
164 TIGR00588 ogg 8-oxoguanine DNA 25.2 38 0.00082 26.6 1.1 23 19-41 221-243 (310)
165 PRK06300 enoyl-(acyl carrier p 25.1 39 0.00084 26.1 1.2 17 24-40 20-36 (299)
166 PRK06483 dihydromonapterin red 25.0 38 0.00083 23.7 1.0 17 24-40 12-28 (236)
167 cd01523 RHOD_Lact_B Member of 24.8 29 0.00063 21.5 0.4 23 26-49 73-95 (100)
168 PRK14669 uvrC excinuclease ABC 24.7 27 0.00059 30.6 0.3 30 7-36 541-570 (624)
169 PF13788 DUF4180: Domain of un 24.7 48 0.0011 23.2 1.5 29 3-31 83-111 (113)
170 PRK05867 short chain dehydroge 24.6 39 0.00085 24.0 1.0 17 24-40 19-35 (253)
171 PF08933 DUF1864: Domain of un 24.5 27 0.00059 29.4 0.2 30 20-49 32-77 (387)
172 PF14359 DUF4406: Domain of un 24.4 31 0.00068 22.7 0.5 28 10-38 2-29 (92)
173 TIGR02867 spore_II_P stage II 24.3 37 0.0008 25.5 0.9 20 21-40 30-49 (196)
174 PRK08339 short chain dehydroge 24.3 43 0.00093 24.3 1.2 17 24-40 18-34 (263)
175 COG3079 Uncharacterized protei 24.0 40 0.00088 25.8 1.0 12 78-89 99-110 (186)
176 PRK06101 short chain dehydroge 23.8 40 0.00086 23.9 0.9 17 24-40 11-27 (240)
177 TIGR01613 primase_Cterm phage/ 23.8 1.2E+02 0.0026 23.1 3.6 65 21-88 220-294 (304)
178 PF12482 DUF3701: Phage integr 23.6 48 0.001 22.6 1.3 16 21-36 53-68 (96)
179 cd01532 4RHOD_Repeat_1 Member 23.6 39 0.00085 20.9 0.8 22 28-49 66-87 (92)
180 PF06135 DUF965: Bacterial pro 23.3 58 0.0013 21.8 1.6 21 29-49 23-43 (79)
181 PRK08416 7-alpha-hydroxysteroi 23.2 43 0.00094 24.0 1.0 17 24-40 18-34 (260)
182 TIGR00060 L18_bact ribosomal p 23.2 32 0.00069 24.0 0.3 35 16-50 61-95 (114)
183 PRK12747 short chain dehydroge 23.1 49 0.0011 23.4 1.3 17 24-40 14-30 (252)
184 PF00416 Ribosomal_S13: Riboso 23.1 66 0.0014 21.5 1.9 24 19-42 16-40 (107)
185 cd06578 HemD Uroporphyrinogen- 23.0 45 0.00097 23.1 1.1 24 21-44 203-226 (239)
186 COG5646 Uncharacterized conser 23.0 27 0.00058 25.3 -0.1 23 24-47 69-91 (126)
187 PF02184 HAT: HAT (Half-A-TPR) 23.0 82 0.0018 17.7 1.9 27 38-64 2-28 (32)
188 PRK07078 hypothetical protein; 22.6 1.8E+02 0.0038 26.2 4.8 71 18-88 633-709 (759)
189 PRK14670 uvrC excinuclease ABC 22.6 1.4E+02 0.0031 25.9 4.2 63 7-82 505-567 (574)
190 PRK12823 benD 1,6-dihydroxycyc 22.6 49 0.0011 23.4 1.2 17 24-40 18-34 (260)
191 TIGR00194 uvrC excinuclease AB 22.6 37 0.00079 29.4 0.6 30 7-36 530-559 (574)
192 PRK00558 uvrC excinuclease ABC 22.5 44 0.00096 28.8 1.1 64 7-81 532-595 (598)
193 cd01522 RHOD_1 Member of the R 22.4 32 0.0007 22.5 0.2 23 27-49 77-99 (117)
194 COG0322 UvrC Nuclease subunit 22.1 1.2E+02 0.0027 26.4 3.7 59 7-78 519-578 (581)
195 PRK06114 short chain dehydroge 22.1 47 0.001 23.6 1.1 17 24-40 18-34 (254)
196 PF09494 Slx4: Slx4 endonuclea 22.1 1.2E+02 0.0025 18.5 2.7 30 56-87 27-56 (64)
197 PF14098 SSPI: Small, acid-sol 22.0 37 0.00081 21.9 0.4 27 2-28 14-40 (65)
198 PRK12748 3-ketoacyl-(acyl-carr 21.9 56 0.0012 23.2 1.4 16 24-39 17-32 (256)
199 PF12728 HTH_17: Helix-turn-he 21.9 36 0.00079 19.1 0.3 45 18-65 5-49 (51)
200 PHA00439 exonuclease 21.7 57 0.0012 26.1 1.5 22 15-37 183-206 (286)
201 cd01444 GlpE_ST GlpE sulfurtra 21.7 40 0.00087 20.4 0.6 22 28-49 70-91 (96)
202 PTZ00217 flap endonuclease-1; 21.5 72 0.0016 26.2 2.1 21 16-36 233-253 (393)
203 KOG1811|consensus 21.4 49 0.0011 30.6 1.2 43 3-50 950-992 (1141)
204 PF00627 UBA: UBA/TS-N domain; 21.4 1.5E+02 0.0033 15.9 3.9 37 26-63 1-37 (37)
205 TIGR00575 dnlj DNA ligase, NAD 21.2 73 0.0016 27.9 2.2 31 6-41 425-455 (652)
206 PRK08340 glucose-1-dehydrogena 21.2 49 0.0011 23.6 1.0 17 24-40 10-26 (259)
207 PF00097 zf-C3HC4: Zinc finger 21.0 51 0.0011 17.5 0.8 11 76-86 21-31 (41)
208 PRK07063 short chain dehydroge 21.0 53 0.0012 23.3 1.1 17 24-40 17-33 (260)
209 KOG1205|consensus 21.0 48 0.001 26.3 1.0 19 22-40 20-38 (282)
210 PRK06463 fabG 3-ketoacyl-(acyl 21.0 55 0.0012 23.2 1.2 17 24-40 17-33 (255)
211 COG0177 Nth Predicted EndoIII- 21.0 34 0.00073 26.2 0.1 24 17-40 108-131 (211)
212 PRK07023 short chain dehydroge 20.8 58 0.0013 22.8 1.3 17 24-40 11-27 (243)
213 KOG1208|consensus 20.8 35 0.00077 27.0 0.2 20 24-46 45-64 (314)
214 PF05152 DUF705: Protein of un 20.7 54 0.0012 26.7 1.2 29 57-87 67-104 (297)
215 PRK08642 fabG 3-ketoacyl-(acyl 20.7 58 0.0013 22.7 1.2 17 24-40 15-31 (253)
216 TIGR02685 pter_reduc_Leis pter 20.6 63 0.0014 23.2 1.4 17 24-40 11-27 (267)
217 PF05186 Dpy-30: Dpy-30 motif; 20.6 1.2E+02 0.0026 17.5 2.4 28 26-53 10-40 (42)
218 PF02764 Diphtheria_T: Diphthe 20.4 32 0.00069 25.9 -0.2 13 21-33 106-118 (180)
219 PRK06523 short chain dehydroge 20.3 64 0.0014 22.8 1.4 17 24-40 19-35 (260)
220 PRK07523 gluconate 5-dehydroge 20.3 55 0.0012 23.2 1.1 17 24-40 20-36 (255)
221 cd04197 eIF-2B_epsilon_N The N 20.3 42 0.0009 23.9 0.5 30 30-65 37-66 (217)
222 PRK07478 short chain dehydroge 20.2 58 0.0013 23.0 1.2 17 24-40 16-32 (254)
223 PRK08993 2-deoxy-D-gluconate 3 20.2 56 0.0012 23.3 1.1 17 24-40 20-36 (253)
224 TIGR02114 coaB_strep phosphopa 20.1 51 0.0011 24.5 0.9 27 13-41 11-42 (227)
225 cd01527 RHOD_YgaP Member of th 20.1 40 0.00087 20.8 0.3 23 27-49 67-89 (99)
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=100.00 E-value=7.4e-63 Score=332.80 Aligned_cols=88 Identities=81% Similarity=1.397 Sum_probs=73.7
Q ss_pred CcchHHHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHH
Q psy6806 1 MSTSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNC 80 (89)
Q Consensus 1 ~~tS~Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~c 80 (89)
|||||||||||+||||||+|++||||||+||+||+++|||||||||||||+|+||++.|++||+++||||+|||+|||+|
T Consensus 2 sttSqKhr~Fv~EPMGeK~V~~laGIG~~lg~~L~~~GfdKAy~vLGqfLll~kde~~F~~WLk~~~gAn~kqa~dcy~c 81 (89)
T PF02961_consen 2 STTSQKHRNFVSEPMGEKPVTELAGIGPVLGKRLEEKGFDKAYVVLGQFLLLKKDEELFQDWLKDTCGANSKQAQDCYNC 81 (89)
T ss_dssp --S-HHHHHHTTS--TT-BGGGSTT--HHHHHHHHHTT--BHHHHHHHHHHTTT-HHHHHHHHHHHH---HHHHHHHHHH
T ss_pred CccCHHHHHHhcCccCCCCccccCCcCHHHHHHHHHCCCcHHHHHhhhhhhccCcHHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhc
Q psy6806 81 LKDWCGEF 88 (89)
Q Consensus 81 l~eWc~~f 88 (89)
|+|||++|
T Consensus 82 L~eWc~~F 89 (89)
T PF02961_consen 82 LKEWCDEF 89 (89)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHhC
Confidence 99999998
No 2
>KOG4233|consensus
Probab=100.00 E-value=3e-58 Score=309.31 Aligned_cols=88 Identities=66% Similarity=1.208 Sum_probs=87.1
Q ss_pred cchHHHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHH
Q psy6806 2 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCL 81 (89)
Q Consensus 2 ~tS~Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl 81 (89)
.||||||+||+||||+|+|++|+|||++||.+|.++||||||+||||||+|+|||++|++||+++||||+|||+|||+||
T Consensus 3 ~tS~khR~FvaEPmGeK~V~~laGIg~~lg~~L~~~GfdkAYvllGQfLllkKdE~lF~~Wlk~~~gat~~~a~~~~~CL 82 (90)
T KOG4233|consen 3 NTSQKHRAFVAEPMGEKDVTWLAGIGETLGIKLVDAGFDKAYVLLGQFLLLKKDEDLFQEWLKETCGATAKQAQDCFNCL 82 (90)
T ss_pred ccCHHHHHHhcCccCCCcceeeccccHHhhhhHHhccccHHHHHHHHHHHhcccHHHHHHHHHHHcCccHHHHHHHHHHH
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhcC
Q psy6806 82 KDWCGEFL 89 (89)
Q Consensus 82 ~eWc~~fl 89 (89)
+|||++||
T Consensus 83 ~eWc~~Fl 90 (90)
T KOG4233|consen 83 NEWCDCFL 90 (90)
T ss_pred HHHHHHhC
Confidence 99999997
No 3
>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=97.10 E-value=0.00031 Score=38.91 Aligned_cols=29 Identities=28% Similarity=0.637 Sum_probs=21.8
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHhcCC
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGF 39 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf 39 (89)
..+|+. || +|++++|||+.++++|.+.|+
T Consensus 4 v~~~l~-~l---pi~~~~GIG~kt~~kL~~~GI 32 (32)
T PF11798_consen 4 VPEFLW-PL---PIRKFWGIGKKTAKKLNKLGI 32 (32)
T ss_dssp HHHHHH-CS---BGGGSTTS-HHHHHHHHCTT-
T ss_pred HHHHHh-cC---CHHhhCCccHHHHHHHHHccC
Confidence 345554 33 899999999999999998875
No 4
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=96.60 E-value=0.0018 Score=49.81 Aligned_cols=35 Identities=31% Similarity=0.543 Sum_probs=32.1
Q ss_pred CCCCCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 13 EPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 13 ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
|.|+..++.++||||+.++.+|.+.||..+-.|+.
T Consensus 1 ~~~~~~~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~ 35 (317)
T PRK04301 1 EKMKEKDLEDLPGVGPATAEKLREAGYDTVEAIAV 35 (317)
T ss_pred CCcccccHhhcCCCCHHHHHHHHHcCCCCHHHHHc
Confidence 57999999999999999999999999999877754
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=96.08 E-value=0.011 Score=35.73 Aligned_cols=54 Identities=13% Similarity=0.187 Sum_probs=39.4
Q ss_pred CcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHH
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLK 82 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~ 82 (89)
++..+|||||..+.+|.+.||.....|.. . +.+. |...-|...+.+..-..-++
T Consensus 6 ~L~~I~Gig~~~a~~L~~~G~~t~~~l~~----a--~~~~----L~~i~Gig~~~a~~i~~~~~ 59 (60)
T PF14520_consen 6 DLLSIPGIGPKRAEKLYEAGIKTLEDLAN----A--DPEE----LAEIPGIGEKTAEKIIEAAR 59 (60)
T ss_dssp HHHTSTTCHHHHHHHHHHTTCSSHHHHHT----S--HHHH----HHTSTTSSHHHHHHHHHHHH
T ss_pred hhccCCCCCHHHHHHHHhcCCCcHHHHHc----C--CHHH----HhcCCCCCHHHHHHHHHHHh
Confidence 35679999999999999999998766654 2 2222 66678888888776554443
No 6
>PF11731 Cdd1: Pathogenicity locus; InterPro: IPR021725 Cdd1 is expressed as part of the pathogenicity locus operon in several different orders of bacteria []. Many members of the family are annotated as being putative mitomycin resistance proteins but this could not be confirmed.
Probab=95.39 E-value=0.0082 Score=40.89 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=28.0
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHhhhh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVVLGQ 48 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGq 48 (89)
++++.|||||+..++-|..-||..-.+|-|+
T Consensus 12 ~~L~~iP~IG~a~a~DL~~LGi~s~~~L~g~ 42 (93)
T PF11731_consen 12 SDLTDIPNIGKATAEDLRLLGIRSPADLKGR 42 (93)
T ss_pred HHHhcCCCccHHHHHHHHHcCCCCHHHHhCC
Confidence 4678999999999999999999999888664
No 7
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=93.70 E-value=0.064 Score=38.89 Aligned_cols=37 Identities=24% Similarity=0.314 Sum_probs=30.8
Q ss_pred hhhhCCCCCC-CcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 9 NFVSEPMGEK-PVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 9 ~Fv~ePMg~K-~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
.++-.|-+.+ ++|.|-||||++.+.|.+.|+..=-|+
T Consensus 57 ~~~~~~~~~~DDLt~I~GIGPk~e~~Ln~~GI~tfaQI 94 (133)
T COG3743 57 AGADAPAAPKDDLTRISGIGPKLEKVLNELGIFTFAQI 94 (133)
T ss_pred ccccCCCCCcccchhhcccCHHHHHHHHHcCCccHHHH
Confidence 5666677774 999999999999999999999875554
No 8
>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=92.94 E-value=0.086 Score=42.36 Aligned_cols=31 Identities=16% Similarity=0.319 Sum_probs=27.1
Q ss_pred CCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
..-||.+|||||+.++++|...|+.....+.
T Consensus 170 ~~lpv~~l~GiG~~~~~kL~~~GI~tigdl~ 200 (379)
T cd01703 170 DLHDLRKIPGIGYKTAAKLEAHGISSVRDLQ 200 (379)
T ss_pred ccCCccccCCcCHHHHHHHHHcCCCcHHHHH
Confidence 4458999999999999999999999877664
No 9
>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=92.58 E-value=0.079 Score=42.38 Aligned_cols=35 Identities=26% Similarity=0.174 Sum_probs=30.3
Q ss_pred CCCCCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 13 EPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 13 ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
+-|..-||++|||||+.++++|...|+.....+..
T Consensus 217 ~~L~~lPv~~l~GIG~~~~~~L~~~Gi~t~~dl~~ 251 (404)
T cd01701 217 EFLSQLKVGDLPGVGSSLAEKLVKLFGDTCGGLEL 251 (404)
T ss_pred HHhhcCCHhHhCCCCHHHHHHHHHcCCcchHHHHh
Confidence 34566799999999999999999999999877754
No 10
>PRK03352 DNA polymerase IV; Validated
Probab=92.54 E-value=0.088 Score=40.71 Aligned_cols=32 Identities=31% Similarity=0.502 Sum_probs=27.7
Q ss_pred CCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
...||.+|||||+.+..+|+..|+.+...|+.
T Consensus 175 ~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~~ 206 (346)
T PRK03352 175 GDRPTDALWGVGPKTAKRLAALGITTVADLAA 206 (346)
T ss_pred hcCCHHHcCCCCHHHHHHHHHcCCccHHHHhc
Confidence 46699999999999999999999998766643
No 11
>PRK02406 DNA polymerase IV; Validated
Probab=92.40 E-value=0.077 Score=40.98 Aligned_cols=32 Identities=25% Similarity=0.457 Sum_probs=27.5
Q ss_pred CCCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
+..-||++|||||+.+..+|...|+.+...|.
T Consensus 165 L~~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~ 196 (343)
T PRK02406 165 LATLPVEKIPGVGKVTAEKLHALGIYTCADLQ 196 (343)
T ss_pred HHcCCcchhcCCCHHHHHHHHHcCCCcHHHHH
Confidence 34569999999999999999999998876664
No 12
>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=92.40 E-value=0.1 Score=40.35 Aligned_cols=32 Identities=38% Similarity=0.646 Sum_probs=27.3
Q ss_pred CCCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
+..-||++|||||+.+.++|.+.|+.+...|.
T Consensus 170 L~~lpi~~l~giG~~~~~~L~~~Gi~ti~dl~ 201 (343)
T cd00424 170 LSKLPLTDLPGIGAVTAKRLEAVGINPIGDLL 201 (343)
T ss_pred HhcCChhhcCCCCHHHHHHHHHcCCCcHHHHh
Confidence 34558999999999999999999999876553
No 13
>PRK03858 DNA polymerase IV; Validated
Probab=92.29 E-value=0.1 Score=40.91 Aligned_cols=32 Identities=31% Similarity=0.385 Sum_probs=28.1
Q ss_pred CCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
..-||++|||||+.+..+|...|+.....|..
T Consensus 171 ~~lpl~~l~Gig~~~~~~L~~~Gi~t~~dl~~ 202 (396)
T PRK03858 171 HPLPVRRLWGVGPVTAAKLRAHGITTVGDVAE 202 (396)
T ss_pred hcCChhhcCCCCHHHHHHHHHhCCCcHHHHhc
Confidence 45599999999999999999999999877753
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=91.35 E-value=0.19 Score=38.88 Aligned_cols=35 Identities=23% Similarity=0.321 Sum_probs=29.9
Q ss_pred CCCCCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 13 EPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 13 ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
+-+..-||..|||||+.+..+|+..|+.....|..
T Consensus 171 ~~l~~lpl~~l~gig~~~~~~L~~~Gi~ti~dL~~ 205 (344)
T cd01700 171 KLLKILPVGDVWGIGRRTAKKLNAMGIHTAGDLAQ 205 (344)
T ss_pred HHhccCChhhcCccCHHHHHHHHHcCCCcHHHHhc
Confidence 44677799999999999999999999988766653
No 15
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=91.11 E-value=0.17 Score=40.43 Aligned_cols=31 Identities=32% Similarity=0.518 Sum_probs=26.9
Q ss_pred CCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
..-||.+|||||+.+.++|...|+.+...|.
T Consensus 177 ~~lPv~~l~GiG~~~~~~L~~lGi~TigdL~ 207 (422)
T PRK03609 177 SLQPVEEVWGVGRRISKKLNAMGIKTALDLA 207 (422)
T ss_pred hcCChhhcCCccHHHHHHHHHcCCCcHHHHh
Confidence 3448999999999999999999999976664
No 16
>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=91.05 E-value=0.21 Score=38.02 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=23.9
Q ss_pred cccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 20 VTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
+.++||||+..+++|.+.||.....|.
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~ 27 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIA 27 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHH
Confidence 468999999999999999999877664
No 17
>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=90.67 E-value=0.24 Score=32.31 Aligned_cols=28 Identities=14% Similarity=0.257 Sum_probs=20.1
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
+.++++|.||+++-+.|.+.|+.....+
T Consensus 3 ~~l~~LpNig~~~e~~L~~vGI~t~~~L 30 (81)
T PF04994_consen 3 NRLKDLPNIGPKSERMLAKVGIHTVEDL 30 (81)
T ss_dssp --GCGSTT--HHHHHHHHHTT--SHHHH
T ss_pred cchhhCCCCCHHHHHHHHHcCCCCHHHH
Confidence 4789999999999999999999987665
No 18
>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=90.45 E-value=0.091 Score=28.79 Aligned_cols=18 Identities=17% Similarity=0.385 Sum_probs=13.5
Q ss_pred CCcccccCccHHHHHhHH
Q psy6806 18 KPVTELAGVGDVLGKRLE 35 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~ 35 (89)
+++..||||||..+...-
T Consensus 11 eeL~~lpGIG~~tA~~I~ 28 (30)
T PF00633_consen 11 EELMKLPGIGPKTANAIL 28 (30)
T ss_dssp HHHHTSTT-SHHHHHHHH
T ss_pred HHHHhCCCcCHHHHHHHH
Confidence 357889999999987653
No 19
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=90.19 E-value=0.21 Score=25.91 Aligned_cols=18 Identities=11% Similarity=0.381 Sum_probs=15.8
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
.+..|||||+..+.+|.+
T Consensus 2 ~L~~i~GiG~k~A~~il~ 19 (26)
T smart00278 2 ELLKVPGIGPKTAEKILE 19 (26)
T ss_pred hhhhCCCCCHHHHHHHHH
Confidence 567899999999999876
No 20
>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=90.17 E-value=0.24 Score=37.62 Aligned_cols=31 Identities=26% Similarity=0.442 Sum_probs=27.2
Q ss_pred CCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
..-||+++||||+.++.+|...|+.+...|.
T Consensus 169 ~~lpl~~l~gig~~~~~~L~~~Gi~ti~dl~ 199 (334)
T cd03586 169 APLPVRKIPGVGKVTAEKLKELGIKTIGDLA 199 (334)
T ss_pred hcCCchhhCCcCHHHHHHHHHcCCcCHHHHH
Confidence 3458999999999999999999999877764
No 21
>PRK01810 DNA polymerase IV; Validated
Probab=90.15 E-value=0.24 Score=39.24 Aligned_cols=31 Identities=23% Similarity=0.402 Sum_probs=26.9
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
.-||++|||||+.+..+|..-|+.....|..
T Consensus 178 ~lpv~~l~giG~~~~~~L~~~Gi~tigdL~~ 208 (407)
T PRK01810 178 PLPVGEMHGIGEKTAEKLKDIGIQTIGDLAK 208 (407)
T ss_pred hCCHhhcCCcCHHHHHHHHHcCCCcHHHHHh
Confidence 3489999999999999999999998766653
No 22
>PTZ00205 DNA polymerase kappa; Provisional
Probab=89.94 E-value=0.23 Score=42.86 Aligned_cols=30 Identities=20% Similarity=0.302 Sum_probs=26.4
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
.-||++|||||++..++|...|+...-.|.
T Consensus 308 ~LpV~ki~GIG~~t~~~L~~~GI~TigDLa 337 (571)
T PTZ00205 308 DLGLRSVPGVGKVTEALLKGLGITTLSDIY 337 (571)
T ss_pred CCCcceeCCcCHHHHHHHHHcCCCcHHHHh
Confidence 448999999999999999999999876654
No 23
>PRK03103 DNA polymerase IV; Reviewed
Probab=89.87 E-value=0.25 Score=39.16 Aligned_cols=30 Identities=30% Similarity=0.407 Sum_probs=25.9
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
.-||++|||||+.+..+|..-|+.....|.
T Consensus 180 ~lpi~~l~gig~~~~~~L~~~Gi~tigdl~ 209 (409)
T PRK03103 180 PLPVRKLFGVGSRMEKHLRRMGIRTIGQLA 209 (409)
T ss_pred cCCHhhcCCccHHHHHHHHHcCCCCHHHHh
Confidence 349999999999999999999998766553
No 24
>PRK02794 DNA polymerase IV; Provisional
Probab=89.60 E-value=0.21 Score=39.93 Aligned_cols=34 Identities=26% Similarity=0.308 Sum_probs=28.6
Q ss_pred CCCCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 14 PMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 14 PMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
-+..-||++|||||+.+..+|+..|+.+...|..
T Consensus 205 ~L~~lPl~~L~GiG~~~~~~L~~~GI~tigdL~~ 238 (419)
T PRK02794 205 FLAPKPVGIIWGVGPATAARLARDGIRTIGDLQR 238 (419)
T ss_pred HHhcCChhhhCCCCHHHHHHHHHhccchHHHHhh
Confidence 3445589999999999999999999998776653
No 25
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=88.84 E-value=0.4 Score=33.02 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=21.5
Q ss_pred cCccHHHHHhHHhcCCchhhHhhh
Q psy6806 24 AGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
||||+....+|++.|+...-.||-
T Consensus 1 pgi~~~~~~~L~~~GI~t~~~Ll~ 24 (122)
T PF14229_consen 1 PGIGPKEAAKLKAAGIKTTGDLLE 24 (122)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHH
Confidence 899999999999999999866654
No 26
>PF10391 DNA_pol_lambd_f: Fingers domain of DNA polymerase lambda; InterPro: IPR018944 DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. This entry represents the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone []. ; GO: 0016779 nucleotidyltransferase activity; PDB: 1KDH_A 1KEJ_A 1JMS_A 2IHM_A 3OGU_A 1MQ2_A 2P66_A 7ICI_A 1ZQN_A 1ZQK_A ....
Probab=88.31 E-value=0.32 Score=29.57 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=19.1
Q ss_pred cccccCccHHHHHhHHhcCCchhhHh
Q psy6806 20 VTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
.+.|-||||+.|+++-++||..--.|
T Consensus 4 f~~I~GVG~~tA~~w~~~G~rtl~Dl 29 (52)
T PF10391_consen 4 FTGIWGVGPKTARKWYAKGIRTLEDL 29 (52)
T ss_dssp HHTSTT--HHHHHHHHHTT--SHHHH
T ss_pred hhhcccccHHHHHHHHHhCCCCHHHH
Confidence 46789999999999999999886666
No 27
>PRK03348 DNA polymerase IV; Provisional
Probab=87.99 E-value=0.32 Score=39.81 Aligned_cols=32 Identities=25% Similarity=0.402 Sum_probs=27.3
Q ss_pred CCCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
+..-||+.|||||+.+..+|...|+.....|.
T Consensus 177 L~~LPv~~L~GIG~~t~~~L~~lGI~TigDLa 208 (454)
T PRK03348 177 LAPLPVRRLWGIGPVTEEKLHRLGIETIGDLA 208 (454)
T ss_pred HHhCCccccCCCCHHHHHHHHHcCCccHHHHh
Confidence 34559999999999999999999999875553
No 28
>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=87.66 E-value=0.37 Score=38.37 Aligned_cols=34 Identities=26% Similarity=0.490 Sum_probs=26.9
Q ss_pred CCCCCCcccccCccHHHHHhH-HhcCCchhhHhhh
Q psy6806 14 PMGEKPVTELAGVGDVLGKRL-ESKGFDKAYVVLG 47 (89)
Q Consensus 14 PMg~K~Vt~l~GIG~~lg~~L-~~~Gf~kAy~lLG 47 (89)
-|..-||++|||||+.++++| +..|+.....|..
T Consensus 178 ~L~~lpv~~l~GiG~~~~~~ll~~~Gi~ti~dl~~ 212 (359)
T cd01702 178 FLSSLPITSIRGLGGKLGEEIIDLLGLPTEGDVAG 212 (359)
T ss_pred HhhcCcHHHhCCcCHHHHHHHHHHcCCcCHHHHHh
Confidence 344559999999999998875 8899998766543
No 29
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=87.35 E-value=0.49 Score=36.40 Aligned_cols=29 Identities=28% Similarity=0.503 Sum_probs=26.1
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
..+++.+.||||.+..+|.+.|+....|+
T Consensus 157 aDDL~~I~GIGp~~a~~L~eaGi~tfaQI 185 (221)
T PRK12278 157 ADDLTKITGVGPALAKKLNEAGVTTFAQI 185 (221)
T ss_pred cchheeccccChHHHHHHHHcCCCCHHHh
Confidence 35899999999999999999999987775
No 30
>PRK14133 DNA polymerase IV; Provisional
Probab=87.22 E-value=0.56 Score=36.37 Aligned_cols=31 Identities=19% Similarity=0.349 Sum_probs=26.6
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
.=||+.|||||+....+|..-|+.....|+.
T Consensus 172 ~lpv~~l~gig~~~~~~L~~~Gi~ti~dl~~ 202 (347)
T PRK14133 172 PLPISKVHGIGKKSVEKLNNIGIYTIEDLLK 202 (347)
T ss_pred hCCccccCCCCHHHHHHHHHcCCccHHHHhh
Confidence 4489999999999999999999998766643
No 31
>PRK01216 DNA polymerase IV; Validated
Probab=86.04 E-value=0.52 Score=37.50 Aligned_cols=31 Identities=23% Similarity=0.544 Sum_probs=26.3
Q ss_pred CCCCCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
+..-||+.+||||+....+|...|+...-.|
T Consensus 175 L~~LPi~~l~giG~~~~~~L~~~Gi~TigdL 205 (351)
T PRK01216 175 INELDIADIPGIGDITAEKLKKLGVNKLVDT 205 (351)
T ss_pred HhcCCcccccCCCHHHHHHHHHcCCCcHHHH
Confidence 4455899999999999999999999885444
No 32
>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=85.36 E-value=0.55 Score=29.00 Aligned_cols=17 Identities=24% Similarity=0.747 Sum_probs=15.2
Q ss_pred cccccCccHHHHHhHHh
Q psy6806 20 VTELAGVGDVLGKRLES 36 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~ 36 (89)
+..|||||+.++.+..|
T Consensus 49 ~~~l~gIG~~ia~kI~E 65 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKIDE 65 (68)
T ss_dssp HCTSTTTTHHHHHHHHH
T ss_pred HhhCCCCCHHHHHHHHH
Confidence 89999999999998765
No 33
>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=84.30 E-value=0.45 Score=37.21 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=33.4
Q ss_pred chHHHHhhhhC-CCCCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 3 TSQKHQNFVSE-PMGEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 3 tS~Khr~Fv~e-PMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
+++++.+...+ |-|=+..+.||||||..+++|-+.|+..---|.
T Consensus 69 ~~~~le~l~~~~~~~l~~l~~i~GiGpk~a~~l~~lGi~sl~dL~ 113 (307)
T cd00141 69 KLRKLEELREDVPPGLLLLLRVPGVGPKTARKLYELGIRTLEDLR 113 (307)
T ss_pred CHHHHHHHhccchHHHHHHHcCCCCCHHHHHHHHHcCCCCHHHHH
Confidence 44555555553 777778889999999999999999998755443
No 34
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=83.48 E-value=1 Score=32.65 Aligned_cols=27 Identities=15% Similarity=0.297 Sum_probs=20.9
Q ss_pred CcccccCccHHHHHhHHhcC-CchhhHh
Q psy6806 19 PVTELAGVGDVLGKRLESKG-FDKAYVV 45 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~G-f~kAy~l 45 (89)
....+|||||+++++....| |...-.|
T Consensus 62 el~~lpGigP~~A~~IV~nGpf~sveDL 89 (132)
T PRK02515 62 AFRQFPGMYPTLAGKIVKNAPYDSVEDV 89 (132)
T ss_pred HHHHCCCCCHHHHHHHHHCCCCCCHHHH
Confidence 34679999999999999865 6665444
No 35
>PRK12311 rpsB 30S ribosomal protein S2/unknown domain fusion protein; Provisional
Probab=83.13 E-value=0.83 Score=36.87 Aligned_cols=28 Identities=21% Similarity=0.391 Sum_probs=24.8
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
-+++.+.||||++.++|.+.|+..=.|+
T Consensus 263 DdL~~I~GiGp~~e~~L~~~Gi~~f~Qi 290 (326)
T PRK12311 263 DDLKKLTGVSPQIEKKLNDLGIFHFWQL 290 (326)
T ss_pred hhhhhhccCChhhhhhhhhcCCCCHHHh
Confidence 4789999999999999999999885554
No 36
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=82.17 E-value=1.3 Score=34.66 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=24.6
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
+++..|||||++-+++|-+.||.....|
T Consensus 3 ~~L~~IpGIG~krakkLl~~GF~Sve~I 30 (232)
T PRK12766 3 EELEDISGVGPSKAEALREAGFESVEDV 30 (232)
T ss_pred cccccCCCcCHHHHHHHHHcCCCCHHHH
Confidence 3688999999999999999999886655
No 37
>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=81.07 E-value=1.2 Score=28.53 Aligned_cols=18 Identities=22% Similarity=0.462 Sum_probs=15.4
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
-++.+||||++++..|-.
T Consensus 3 ~l~sipGig~~~a~~lla 20 (87)
T PF02371_consen 3 LLTSIPGIGPITAATLLA 20 (87)
T ss_pred hhcCCCCccHHHHHHHHH
Confidence 478899999999988765
No 38
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=80.67 E-value=0.81 Score=28.12 Aligned_cols=18 Identities=11% Similarity=0.458 Sum_probs=12.8
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
+++.+|||||+.+..+.+
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 578899999999888654
No 39
>KOG1014|consensus
Probab=79.95 E-value=0.65 Score=37.65 Aligned_cols=19 Identities=26% Similarity=0.728 Sum_probs=17.4
Q ss_pred cccCccHHHHHhHHhcCCc
Q psy6806 22 ELAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 22 ~l~GIG~~lg~~L~~~Gf~ 40 (89)
.=+|||+.++++|+.+||+
T Consensus 57 aTDGIGKayA~eLAkrG~n 75 (312)
T KOG1014|consen 57 ATDGIGKAYARELAKRGFN 75 (312)
T ss_pred CCCcchHHHHHHHHHcCCE
Confidence 3489999999999999998
No 40
>cd00080 HhH2_motif Helix-hairpin-helix class 2 (Pol1 family) motif. HhH2 domains are found in Rad2 family of prokaryotic and eukaryotic replication and repair nucleases, i.e., DNA polymerase I, Taq DNA polymerase, DNA repair protein Rad2 endonuclease, flap endonuclease, exonuclease I and IX, 5'-3' exonuclease and also bacteriophage Rnase H. These nucleases degrade RNA-DNA or DNA-DNA duplexes, or both and play essential roles in DNA duplication, repair, and recombination.
Probab=78.79 E-value=3.4 Score=26.11 Aligned_cols=23 Identities=17% Similarity=0.417 Sum_probs=18.0
Q ss_pred CC--CCCcccccCccHHHHHhHHhc
Q psy6806 15 MG--EKPVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 15 Mg--~K~Vt~l~GIG~~lg~~L~~~ 37 (89)
+| -.-+.-|||||+..+.+|-.+
T Consensus 17 ~GD~~D~i~gv~giG~k~A~~ll~~ 41 (75)
T cd00080 17 VGDKSDNIPGVPGIGPKTALKLLKE 41 (75)
T ss_pred cCCccccCCCCCcccHHHHHHHHHH
Confidence 56 335778999999999998864
No 41
>COG0389 DinP Nucleotidyltransferase/DNA polymerase involved in DNA repair [DNA replication, recombination, and repair]
Probab=77.34 E-value=1.9 Score=34.16 Aligned_cols=31 Identities=29% Similarity=0.402 Sum_probs=27.1
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
..+|++++|||++..++|...|+.+...+-.
T Consensus 175 ~Lpv~~~~GvG~~~~~~l~~~Gi~ti~dl~~ 205 (354)
T COG0389 175 QLPVLEFWGVGKVTAEKLRRLGISTIGDLAE 205 (354)
T ss_pred cCChhhhCCCCHHHHHHHHHcCChhHHHHHh
Confidence 3489999999999999999999988777655
No 42
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=76.80 E-value=1.5 Score=33.67 Aligned_cols=15 Identities=40% Similarity=0.671 Sum_probs=13.5
Q ss_pred cccccCccHHHHHhH
Q psy6806 20 VTELAGVGDVLGKRL 34 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L 34 (89)
...||||||.-+.|+
T Consensus 14 l~kLPGvG~KsA~R~ 28 (198)
T COG0353 14 LKKLPGVGPKSAQRL 28 (198)
T ss_pred HhhCCCCChhHHHHH
Confidence 567999999999997
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=76.45 E-value=2.5 Score=32.00 Aligned_cols=32 Identities=13% Similarity=0.038 Sum_probs=26.4
Q ss_pred CCCCCcccccCccHHHHHhHHhcCCchhhHhhh
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
+..-+| +++|||+....+|++.|+.+...+..
T Consensus 168 l~~lp~-~~~gig~~~~~~L~~~Gi~t~~dl~~ 199 (335)
T cd03468 168 LAPLPV-AALRLPPETVELLARLGLRTLGDLAA 199 (335)
T ss_pred cCCCCh-hHhCCCHHHHHHHHHhCcccHHHHHh
Confidence 345566 59999999999999999999876644
No 44
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=76.01 E-value=2.1 Score=29.44 Aligned_cols=24 Identities=25% Similarity=0.504 Sum_probs=21.0
Q ss_pred CcccccCccHHHHHhHHhcCCchh
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDKA 42 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~kA 42 (89)
++..+||||+..+.-|.+.|++..
T Consensus 54 dL~ri~gi~~~~a~LL~~AGv~Tv 77 (122)
T PF14229_consen 54 DLMRIPGIGPQYAELLEHAGVDTV 77 (122)
T ss_pred HhhhcCCCCHHHHHHHHHhCcCcH
Confidence 455799999999999999999863
No 45
>PRK07945 hypothetical protein; Provisional
Probab=73.81 E-value=2.2 Score=33.76 Aligned_cols=18 Identities=28% Similarity=0.492 Sum_probs=16.8
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
++++|||||+.++.+++|
T Consensus 50 ~l~~~~giG~~~a~~i~e 67 (335)
T PRK07945 50 SLTSLPGIGPKTAKVIAQ 67 (335)
T ss_pred CcccCCCcCHHHHHHHHH
Confidence 799999999999998887
No 46
>PLN03187 meiotic recombination protein DMC1 homolog; Provisional
Probab=73.37 E-value=2.8 Score=33.73 Aligned_cols=62 Identities=10% Similarity=0.119 Sum_probs=40.9
Q ss_pred CCCCCCCcccc--cCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHHHH
Q psy6806 13 EPMGEKPVTEL--AGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKDWC 85 (89)
Q Consensus 13 ePMg~K~Vt~l--~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~eWc 85 (89)
|+| -.++.+| +||+|...++|++.||..+.-|+- ..+. + |....|.+...+..-.+..++++
T Consensus 25 ~~~-~~~~~~l~~~g~~~~~~~kL~~~g~~tv~~~~~----~~~~-~-----L~~~~g~s~~~~~ki~~~a~~~~ 88 (344)
T PLN03187 25 EDL-FESIDKLISQGINAGDVKKLQDAGIYTCNGLMM----HTKK-N-----LTGIKGLSEAKVDKICEAAEKLL 88 (344)
T ss_pred hhc-ccCHHHHhhCCCCHHHHHHHHHcCCCcHHHHHh----CCHH-H-----HHHhcCCCHHHHHHHHHHHHHhh
Confidence 344 3478888 779999999999999999877642 2211 1 45556666666655444444443
No 47
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=72.97 E-value=2.8 Score=23.62 Aligned_cols=17 Identities=18% Similarity=0.364 Sum_probs=13.3
Q ss_pred cccccCccHHHHHhHHh
Q psy6806 20 VTELAGVGDVLGKRLES 36 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~ 36 (89)
+.-|||||+..+.+|-.
T Consensus 18 i~Gv~giG~ktA~~ll~ 34 (36)
T smart00279 18 IPGVKGIGPKTALKLLR 34 (36)
T ss_pred CCCCCcccHHHHHHHHH
Confidence 45799999998887754
No 48
>KOG4305|consensus
Probab=72.86 E-value=3.6 Score=38.15 Aligned_cols=54 Identities=20% Similarity=0.319 Sum_probs=41.4
Q ss_pred hhhCCCCCCCcccccCccHHHHHhHHh-cCCch--hhHhhhhhhhhhc--CHHHHHHHHHHhh
Q psy6806 10 FVSEPMGEKPVTELAGVGDVLGKRLES-KGFDK--AYVVLGQFLLLKQ--NEELFVDWMKETC 67 (89)
Q Consensus 10 Fv~ePMg~K~Vt~l~GIG~~lg~~L~~-~Gf~k--Ay~lLGqfL~l~k--~~~~F~~WLk~~~ 67 (89)
+++.-+++ -|.|||+.+.+-|-. +.|.+ |-|+.|++|+..| ..-.|++||++.-
T Consensus 402 ~~r~k~~G----~V~~IGdIll~~lp~~~~yi~Y~a~q~~ak~lie~k~k~n~~Fa~fl~~~~ 460 (1029)
T KOG4305|consen 402 RVRQKLSG----VVEGIGDILLAWLPKAEPYISYGANQAYAKALIEQKKKQNPRFARFLKECE 460 (1029)
T ss_pred HHhhccCC----ccchHHHHHHHHhhhhhHHHHHHhhhHHHHHHHHHHhccCchHHHHHHHHH
Confidence 34455555 789999999988866 44665 7789999999887 4459999999863
No 49
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=72.86 E-value=1.4 Score=32.77 Aligned_cols=19 Identities=21% Similarity=0.438 Sum_probs=15.6
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.++.+||||+..+.|+.-
T Consensus 108 ~~L~~vpGIGkKtAeRIil 126 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIA 126 (183)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 3567889999999999764
No 50
>PRK10917 ATP-dependent DNA helicase RecG; Provisional
Probab=72.74 E-value=3.1 Score=35.72 Aligned_cols=31 Identities=29% Similarity=0.440 Sum_probs=28.2
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHhhhh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVVLGQ 48 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGq 48 (89)
.+|+.|+||||..++.|+..|+....-||=.
T Consensus 9 ~~~~~l~gvg~~~~~~l~~lgi~t~~dll~~ 39 (681)
T PRK10917 9 APLTSLKGVGPKTAEKLAKLGIHTVQDLLLH 39 (681)
T ss_pred CChhhcCCCCHHHHHHHHHcCCCCHHHHhhc
Confidence 4899999999999999999999999988843
No 51
>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=72.13 E-value=12 Score=28.23 Aligned_cols=57 Identities=11% Similarity=0.205 Sum_probs=32.1
Q ss_pred CCC--CCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHH
Q psy6806 15 MGE--KPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYN 79 (89)
Q Consensus 15 Mg~--K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~ 79 (89)
||| ..+--||||||..+.+|-.+ |..-..++-..=.. .....+||. .+..++.-+++
T Consensus 178 ~GD~sDnipGv~GiG~ktA~~Ll~~-~gsle~i~~~~~~~---~~~~~~~l~----~~~~~~~~s~~ 236 (240)
T cd00008 178 MGDSSDNIPGVPGIGEKTAAKLLKE-YGSLEGILENLDKI---KGKLREKLE----EGKEMAFLSKR 236 (240)
T ss_pred cCCcccCCCCCCccCHHHHHHHHHH-hCCHHHHHHhHHHH---hHHHHHHHH----HhHHHHHHHHH
Confidence 664 46778899999999988864 33333333221111 125666666 34444444443
No 52
>KOG2094|consensus
Probab=71.09 E-value=5.3 Score=34.10 Aligned_cols=60 Identities=18% Similarity=0.331 Sum_probs=44.1
Q ss_pred hhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhh--hhhhhcCHHHHHHHHHHhhccc
Q psy6806 11 VSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQ--FLLLKQNEELFVDWMKETCQAN 70 (89)
Q Consensus 11 v~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGq--fL~l~k~~~~F~~WLk~~~gAn 70 (89)
|.+=|-+=||+.|.|||.|+-..|...|+...=-+--+ .|-+=-.+-.|+..|....|+-
T Consensus 275 im~F~kdLPvRkV~GIGrV~E~qLkal~IkTcgdm~~k~~ll~~lFsp~S~~~fLr~slG~g 336 (490)
T KOG2094|consen 275 IMKFMKDLPVRKVSGIGRVTEQQLKALGIKTCGDMQQKLVLLSLLFSPKSFQNFLRCSLGLG 336 (490)
T ss_pred HHHHHhcCCcccccchhHHHHHHHHhcCceeHHHHHHhhhHHHHHhCchhHHHHHHHhhcCC
Confidence 44446678999999999999999999999874322211 2222336778999999988876
No 53
>PTZ00035 Rad51 protein; Provisional
Probab=69.85 E-value=4.1 Score=32.34 Aligned_cols=56 Identities=13% Similarity=0.065 Sum_probs=37.7
Q ss_pred Ccccc--cCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHHH
Q psy6806 19 PVTEL--AGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKDW 84 (89)
Q Consensus 19 ~Vt~l--~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~eW 84 (89)
++.+| |||+|...++|++.||..+.-++- ..+ .=|....|.+...+..--+..++.
T Consensus 22 ~~~~l~~~g~~~~~~~kL~~~g~~t~~~~~~----~~~------~~L~~~~gis~~~~~~i~~~~~~~ 79 (337)
T PTZ00035 22 EIEKLQSAGINAADIKKLKEAGICTVESVAY----ATK------KDLCNIKGISEAKVEKIKEAASKL 79 (337)
T ss_pred cHHHHhcCCCCHHHHHHHHHcCCCcHHHHHh----CCH------HHHHHhhCCCHHHHHHHHHHHHHh
Confidence 68888 889999999999999999876643 221 123445666666555554444443
No 54
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=68.96 E-value=17 Score=27.67 Aligned_cols=50 Identities=10% Similarity=0.179 Sum_probs=34.9
Q ss_pred CCcccccCccHHHHHhHHhcCCch--------hhHhhhhhhhhhcCHHHHHHHHHHhh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDK--------AYVVLGQFLLLKQNEELFVDWMKETC 67 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~k--------Ay~lLGqfL~l~k~~~~F~~WLk~~~ 67 (89)
+.+..|||||+..+.-.---+|++ ++=|+.++=+...+-+..+.|+.+..
T Consensus 121 e~Ll~l~GIG~kTAd~iLlya~~rp~fvVDty~~Rv~~RlG~~~~~y~~~~~~~~~~l 178 (218)
T PRK13913 121 EWLLDQKGIGKESADAILCYVCAKEVMVVDKYSYLFLKKLGIEIEDYDELQHFFEKGV 178 (218)
T ss_pred HHHHcCCCccHHHHHHHHHHHcCCCccccchhHHHHHHHcCCCCCCHHHHHHHHHHhh
Confidence 458899999999998776666666 33455555444446677888888755
No 55
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.59 E-value=2 Score=32.10 Aligned_cols=19 Identities=16% Similarity=0.398 Sum_probs=15.8
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.++.+||||+..++|+.-
T Consensus 108 ~~L~kvpGIGkKtAerIil 126 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVL 126 (195)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 3567899999999999765
No 56
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.29 E-value=2 Score=31.87 Aligned_cols=19 Identities=16% Similarity=0.386 Sum_probs=15.6
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.++.+||||+..++|+.-
T Consensus 108 ~~L~~vpGIGkKtAerIil 126 (188)
T PRK14606 108 EGLSKLPGISKKTAERIVM 126 (188)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 3567899999999999764
No 57
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.16 E-value=2 Score=32.47 Aligned_cols=19 Identities=11% Similarity=0.433 Sum_probs=15.7
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.++.+||||+..+.|+.-
T Consensus 107 ~~L~~vpGIGkKtAeRIIl 125 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFL 125 (196)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 4567899999999999764
No 58
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=66.94 E-value=19 Score=27.06 Aligned_cols=58 Identities=21% Similarity=0.232 Sum_probs=40.8
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHHH
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKDW 84 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~eW 84 (89)
+-++..+|+||+..+++|++.|+..- +++.-+ +.+..... +|-+.+++.+.++.++.+
T Consensus 150 ~~~L~Qlp~i~~~~~~~l~~~~i~s~----~~l~~~--~~~~~~~l----l~~~~~~~~~i~~~~~~~ 207 (312)
T smart00611 150 DSPLLQLPHLPEEILKRLEKKKVLSL----EDLLEL--EDEERGEL----LGLLDAEGERVYKVLSRL 207 (312)
T ss_pred CCccccCCCCCHHHHHHHHhCCCCCH----HHHHhc--CHHHHHHH----HcCCHHHHHHHHHHHHhC
Confidence 34788899999999999999987543 333333 34444444 466778888888887654
No 59
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=65.62 E-value=2.8 Score=33.17 Aligned_cols=33 Identities=21% Similarity=0.139 Sum_probs=28.2
Q ss_pred CCCCCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 14 PMGEKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 14 PMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
|-|-...+.||||||..+++|-+.|+..--.|.
T Consensus 85 p~~l~~l~~i~GiGpk~a~~l~~lGi~tl~eL~ 117 (334)
T smart00483 85 YKSLKLFTNVFGVGPKTAAKWYRKGIRTLEELK 117 (334)
T ss_pred HHHHHHHHccCCcCHHHHHHHHHhCCCCHHHHH
Confidence 445667889999999999999999999877764
No 60
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=65.32 E-value=4.5 Score=33.81 Aligned_cols=27 Identities=22% Similarity=0.260 Sum_probs=25.0
Q ss_pred CcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
+++.+.||||.+..+|.+.||....|+
T Consensus 324 DLk~I~GIGpk~e~~Ln~~Gi~~f~QI 350 (400)
T PRK12373 324 DLKLISGVGPKIEATLNELGIFTFDQV 350 (400)
T ss_pred hhhhccCCChHHHHHHHhcCCCCHHHH
Confidence 789999999999999999999987776
No 61
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=64.53 E-value=2.7 Score=31.44 Aligned_cols=19 Identities=16% Similarity=0.364 Sum_probs=15.8
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.++.+||||+..+.|+.-
T Consensus 109 ~~L~~ipGIGkKtAerIil 127 (203)
T PRK14602 109 AALTRVSGIGKKTAQHIFL 127 (203)
T ss_pred HHHhcCCCcCHHHHHHHHH
Confidence 3578899999999999764
No 62
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=62.93 E-value=2.9 Score=31.15 Aligned_cols=19 Identities=32% Similarity=0.550 Sum_probs=15.8
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.++.+||||+..++|+.-
T Consensus 107 ~~L~kvpGIGkKtAerIil 125 (197)
T PRK14603 107 RLLTSASGVGKKLAERIAL 125 (197)
T ss_pred HHHhhCCCCCHHHHHHHHH
Confidence 3578899999999999764
No 63
>PRK09482 flap endonuclease-like protein; Provisional
Probab=62.06 E-value=5.7 Score=30.93 Aligned_cols=23 Identities=22% Similarity=0.312 Sum_probs=18.1
Q ss_pred CCCCC--CcccccCccHHHHHhHHh
Q psy6806 14 PMGEK--PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 14 PMg~K--~Vt~l~GIG~~lg~~L~~ 36 (89)
=|||. .+--||||||..|.+|-.
T Consensus 176 L~GD~sDnIpGVpGIG~KtA~~LL~ 200 (256)
T PRK09482 176 LAGISSSKIPGVAGIGPKSAAELLN 200 (256)
T ss_pred HhCCCccCCCCCCCcChHHHHHHHH
Confidence 46764 466789999999998876
No 64
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.67 E-value=4.3 Score=30.84 Aligned_cols=17 Identities=29% Similarity=0.595 Sum_probs=14.5
Q ss_pred CcccccCccHHHHHhHH
Q psy6806 19 PVTELAGVGDVLGKRLE 35 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~ 35 (89)
.+..|||||+.-+.||+
T Consensus 12 ~l~~LPGIG~KsA~RlA 28 (195)
T TIGR00615 12 SLKKLPGIGPKSAQRLA 28 (195)
T ss_pred HHHHCCCCCHHHHHHHH
Confidence 45789999999999974
No 65
>PRK13844 recombination protein RecR; Provisional
Probab=61.60 E-value=4.2 Score=31.00 Aligned_cols=17 Identities=24% Similarity=0.460 Sum_probs=14.6
Q ss_pred CcccccCccHHHHHhHH
Q psy6806 19 PVTELAGVGDVLGKRLE 35 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~ 35 (89)
....|||||+.-+.||+
T Consensus 16 ~l~~LPGIG~KsA~Rla 32 (200)
T PRK13844 16 SLRKLPTIGKKSSQRLA 32 (200)
T ss_pred HHHHCCCCCHHHHHHHH
Confidence 45789999999999974
No 66
>PRK00076 recR recombination protein RecR; Reviewed
Probab=60.68 E-value=4.5 Score=30.65 Aligned_cols=17 Identities=29% Similarity=0.587 Sum_probs=14.5
Q ss_pred CcccccCccHHHHHhHH
Q psy6806 19 PVTELAGVGDVLGKRLE 35 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~ 35 (89)
....|||||+.-+.||+
T Consensus 12 ~l~~LPGIG~KsA~Rla 28 (196)
T PRK00076 12 ALRKLPGIGPKSAQRLA 28 (196)
T ss_pred HHHHCCCCCHHHHHHHH
Confidence 45689999999999974
No 67
>PRK02362 ski2-like helicase; Provisional
Probab=60.00 E-value=6.9 Score=33.65 Aligned_cols=28 Identities=29% Similarity=0.420 Sum_probs=25.4
Q ss_pred CcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
++..|||||+..+++|-+.||+..+.+.
T Consensus 653 ~L~~ip~i~~~~a~~l~~~gi~s~~dl~ 680 (737)
T PRK02362 653 DLVGLRGVGRVRARRLYNAGIESRADLR 680 (737)
T ss_pred HHhCCCCCCHHHHHHHHHcCCCCHHHHH
Confidence 5678999999999999999999988875
No 68
>PF06844 DUF1244: Protein of unknown function (DUF1244); InterPro: IPR009654 This family consists of several short bacterial proteins of around 100 residues in length. The function of this family is unknown.; PDB: 2O35_A 3FYB_B.
Probab=59.62 E-value=6.9 Score=25.65 Aligned_cols=14 Identities=50% Similarity=1.168 Sum_probs=9.9
Q ss_pred HhHHHHHHHHHHHh
Q psy6806 74 SGDCYNCLKDWCGE 87 (89)
Q Consensus 74 a~dc~~cl~eWc~~ 87 (89)
|+-|-|||..|-.+
T Consensus 10 AgFCRNCLskWy~~ 23 (68)
T PF06844_consen 10 AGFCRNCLSKWYRE 23 (68)
T ss_dssp HS--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHHH
Confidence 56799999999753
No 69
>PRK08609 hypothetical protein; Provisional
Probab=59.15 E-value=5.4 Score=33.88 Aligned_cols=42 Identities=24% Similarity=0.258 Sum_probs=29.2
Q ss_pred hHHHHhhhh-CCCCCCCcccccCccHHHHHhHH-hcCCchhhHh
Q psy6806 4 SQKHQNFVS-EPMGEKPVTELAGVGDVLGKRLE-SKGFDKAYVV 45 (89)
Q Consensus 4 S~Khr~Fv~-ePMg~K~Vt~l~GIG~~lg~~L~-~~Gf~kAy~l 45 (89)
++++...-+ .|-|-..++.||||||..+++|- +.|++.--.|
T Consensus 73 ~~~le~l~~~~p~~~~~l~~i~GiGpk~a~~l~~~lGi~tl~~L 116 (570)
T PRK08609 73 SSVLQELKKEVPEGLLPLLKLPGLGGKKIAKLYKELGVVDKESL 116 (570)
T ss_pred hHHHHHHHhhCcHHHHHHhcCCCCCHHHHHHHHHHhCCCCHHHH
Confidence 444554443 35566678999999999999997 5788664443
No 70
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=58.53 E-value=5.8 Score=31.44 Aligned_cols=24 Identities=29% Similarity=0.606 Sum_probs=18.7
Q ss_pred CCCCCC-CcccccCccHHHHHhHHh
Q psy6806 13 EPMGEK-PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 13 ePMg~K-~Vt~l~GIG~~lg~~L~~ 36 (89)
+|+..- .++++||||+.++.+..|
T Consensus 42 ~~i~~~~~l~~lpgIG~~ia~kI~E 66 (334)
T smart00483 42 FPINSMKDLKGLPGIGDKIKKKIEE 66 (334)
T ss_pred CCCCCHHHHhcCCCccHHHHHHHHH
Confidence 344332 588999999999999887
No 71
>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=56.94 E-value=6.8 Score=26.89 Aligned_cols=19 Identities=21% Similarity=0.361 Sum_probs=16.0
Q ss_pred CcccccCccHHHHHhHHhc
Q psy6806 19 PVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~ 37 (89)
.+..|||||+..++++-+.
T Consensus 69 eL~~lpGIG~~~A~~Ii~~ 87 (120)
T TIGR01259 69 ELQALPGIGPAKAKAIIEY 87 (120)
T ss_pred HHhcCCCCCHHHHHHHHHH
Confidence 4667999999999998773
No 72
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=56.57 E-value=5.5 Score=30.20 Aligned_cols=19 Identities=21% Similarity=0.529 Sum_probs=16.2
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+-++.+||||+..+.|+.-
T Consensus 108 ~~L~k~PGIGkKtAerivl 126 (201)
T COG0632 108 KALSKIPGIGKKTAERIVL 126 (201)
T ss_pred HhhhcCCCCCHHHHHHHHH
Confidence 4678899999999999765
No 73
>COG0300 DltE Short-chain dehydrogenases of various substrate specificities [General function prediction only]
Probab=56.26 E-value=5.9 Score=31.09 Aligned_cols=18 Identities=33% Similarity=0.791 Sum_probs=16.3
Q ss_pred ccCccHHHHHhHHhcCCc
Q psy6806 23 LAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 23 l~GIG~~lg~~L~~~Gf~ 40 (89)
=.|||.+++++|+++|++
T Consensus 15 SsGIG~~~A~~lA~~g~~ 32 (265)
T COG0300 15 SSGIGAELAKQLARRGYN 32 (265)
T ss_pred CchHHHHHHHHHHHCCCE
Confidence 369999999999999986
No 74
>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=55.98 E-value=11 Score=29.63 Aligned_cols=52 Identities=12% Similarity=0.008 Sum_probs=34.1
Q ss_pred cCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHHHH
Q psy6806 24 AGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKDWC 85 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~eWc 85 (89)
+||++...++|++.||..+.-|+- .. ..=|...+|.+...+..--+.+...+
T Consensus 7 ~g~~~~~~~~L~~~g~~t~~~~~~----~~------~~~L~~~~gls~~~~~~i~~~~~~~~ 58 (313)
T TIGR02238 7 HGINAADIKKLKSAGICTVNGVIM----TT------RRALCKIKGLSEAKVDKIKEAASKII 58 (313)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHh----CC------HHHHHHhcCCCHHHHHHHHHHHHhhh
Confidence 679999999999999999876643 11 11244556666665555555544443
No 75
>PRK01172 ski2-like helicase; Provisional
Probab=55.96 E-value=9.9 Score=32.16 Aligned_cols=55 Identities=18% Similarity=0.196 Sum_probs=39.6
Q ss_pred CcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHH
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKD 83 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~e 83 (89)
++..|||||+..+++|.+.||...+-+.. -+.+. +.+..|.+.+|+..-..-++.
T Consensus 613 ~L~~ip~~~~~~a~~l~~~g~~~~~di~~------~~~~~----~~~i~~~~~~~~~~i~~~~~~ 667 (674)
T PRK01172 613 DLVLIPKVGRVRARRLYDAGFKTVDDIAR------SSPER----IKKIYGFSDTLANAIVNRAMK 667 (674)
T ss_pred hhcCCCCCCHHHHHHHHHcCCCCHHHHHh------CCHHH----HHHHhccCHHHHHHHHHHHHH
Confidence 56689999999999999999999988754 23333 233457777777765554443
No 76
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.30 E-value=6.3 Score=29.25 Aligned_cols=18 Identities=22% Similarity=0.525 Sum_probs=15.0
Q ss_pred CCcccccCccHHHHHhHHh
Q psy6806 18 KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~ 36 (89)
+.+ .+||||+..++|+.-
T Consensus 108 ~~L-~vpGIGkKtAerIil 125 (186)
T PRK14600 108 AAL-KVNGIGEKLINRIIT 125 (186)
T ss_pred hhe-ECCCCcHHHHHHHHH
Confidence 456 899999999999764
No 77
>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=55.18 E-value=12 Score=30.65 Aligned_cols=30 Identities=17% Similarity=0.209 Sum_probs=26.2
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
+.+|+.||||++.-..+|.+.||..--.|-
T Consensus 206 ~~~lslv~gi~~~~~~~L~~~GI~ti~~La 235 (457)
T TIGR03491 206 EGHLSLVPGIGPSRYRLLQELGIHTLEDLA 235 (457)
T ss_pred cCCeeecCCCCHHHHHHHHHcCCCcHHHHh
Confidence 568999999999999999999998865554
No 78
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=55.10 E-value=4.5 Score=29.99 Aligned_cols=16 Identities=19% Similarity=0.507 Sum_probs=14.0
Q ss_pred CCcccccCccHHHHHh
Q psy6806 18 KPVTELAGVGDVLGKR 33 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~ 33 (89)
+.++.+||||+..+.|
T Consensus 108 ~~L~~vpGIGkKtAer 123 (194)
T PRK14605 108 ELLSTIPGIGKKTASR 123 (194)
T ss_pred HHHHhCCCCCHHHHHH
Confidence 3467999999999999
No 79
>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=55.08 E-value=10 Score=23.75 Aligned_cols=25 Identities=32% Similarity=0.547 Sum_probs=16.0
Q ss_pred ccccCccHHHHHhHHhcCCchhhHh
Q psy6806 21 TELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 21 t~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
..+.||-+.+..+++..||++--+|
T Consensus 3 ~~~~Gi~~~lVd~F~~mGF~~dkVv 27 (55)
T PF09288_consen 3 AALYGIDKDLVDQFENMGFERDKVV 27 (55)
T ss_dssp SS----SHHHHHHHHHHT--HHHHH
T ss_pred HHHcCCCHHHHHHHHHcCCcHHHHH
Confidence 4678999999999999999986654
No 80
>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=54.13 E-value=7.5 Score=30.39 Aligned_cols=18 Identities=22% Similarity=0.632 Sum_probs=16.1
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
.++.+||||+.++.+..|
T Consensus 46 ~~~~ipgiG~~ia~kI~E 63 (307)
T cd00141 46 EAKKLPGIGKKIAEKIEE 63 (307)
T ss_pred HhcCCCCccHHHHHHHHH
Confidence 568999999999999887
No 81
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=54.10 E-value=5.8 Score=29.34 Aligned_cols=18 Identities=33% Similarity=0.580 Sum_probs=15.6
Q ss_pred CCcccccCccHHHHHhHH
Q psy6806 18 KPVTELAGVGDVLGKRLE 35 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~ 35 (89)
+.++.+||||+..+.|+-
T Consensus 107 ~~L~~ipGiGkKtAerIi 124 (191)
T TIGR00084 107 KALVKIPGVGKKTAERLL 124 (191)
T ss_pred HHHHhCCCCCHHHHHHHH
Confidence 468899999999999875
No 82
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=53.26 E-value=7.4 Score=28.50 Aligned_cols=18 Identities=28% Similarity=0.375 Sum_probs=14.4
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
.+..+|||||..+.++-+
T Consensus 74 ~L~~i~GIGpk~A~~il~ 91 (192)
T PRK00116 74 LLISVSGVGPKLALAILS 91 (192)
T ss_pred HHhcCCCCCHHHHHHHHH
Confidence 456799999999988755
No 83
>PLN03186 DNA repair protein RAD51 homolog; Provisional
Probab=52.91 E-value=10 Score=30.41 Aligned_cols=56 Identities=11% Similarity=0.148 Sum_probs=37.9
Q ss_pred Ccccc--cCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHHH
Q psy6806 19 PVTEL--AGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKDW 84 (89)
Q Consensus 19 ~Vt~l--~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~eW 84 (89)
++.+| +||++...++|++.||..+.-++- .. . .=|....|.+...+..=...+++.
T Consensus 27 ~~~~l~~~gi~~~~i~kL~~~g~~T~~~~~~----~~--~----~~L~~i~~is~~~~~~~~~~~~~~ 84 (342)
T PLN03186 27 PIEQLQASGIAALDIKKLKDAGIHTVESLAY----AP--K----KDLLQIKGISEAKVEKILEAASKL 84 (342)
T ss_pred cHHHHHhCCCCHHHHHHHHHcCCCcHHHHHh----CC--H----HHHHHhcCCCHHHHHHHHHHHHHh
Confidence 57788 779999999999999999876643 22 1 125556667666665444444443
No 84
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=52.30 E-value=12 Score=22.74 Aligned_cols=28 Identities=18% Similarity=0.239 Sum_probs=17.6
Q ss_pred CcccccCccHHHHHhHHh-----cCCchhhHhh
Q psy6806 19 PVTELAGVGDVLGKRLES-----KGFDKAYVVL 46 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~-----~Gf~kAy~lL 46 (89)
.+..+||||+.+++++.+ -+|.....|.
T Consensus 15 eL~~lpgi~~~~A~~Iv~~R~~~G~f~s~~dL~ 47 (65)
T PF12836_consen 15 ELQALPGIGPKQAKAIVEYREKNGPFKSLEDLK 47 (65)
T ss_dssp HHHTSTT--HHHHHHHHHHHHHH-S-SSGGGGG
T ss_pred HHHHcCCCCHHHHHHHHHHHHhCcCCCCHHHHh
Confidence 456789999999998877 2566655554
No 85
>COG1200 RecG RecG-like helicase [DNA replication, recombination, and repair / Transcription]
Probab=52.15 E-value=11 Score=33.55 Aligned_cols=32 Identities=22% Similarity=0.399 Sum_probs=28.2
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHhhhhh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
.+++.++||||..+.+|+.-|+...+-||=.|
T Consensus 10 ~~l~~l~gig~~~a~~l~~Lgi~tv~DLL~~~ 41 (677)
T COG1200 10 VPLSTLKGIGPKTAEKLKKLGIHTVQDLLLYL 41 (677)
T ss_pred cchhhhcCcCHHHHHHHHHcCCCcHHHHHHhC
Confidence 37999999999999999999999999876443
No 86
>PRK00254 ski2-like helicase; Provisional
Probab=51.59 E-value=12 Score=32.02 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=24.6
Q ss_pred CcccccCccHHHHHhHHhcCCchhhHhh
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
++..|||||+..+++|-+.||..-+.+.
T Consensus 646 ~L~~ipgig~~~~~~l~~~g~~s~~~i~ 673 (720)
T PRK00254 646 ELMRLPMIGRKRARALYNAGFRSIEDIV 673 (720)
T ss_pred hhhcCCCCCHHHHHHHHHccCCCHHHHH
Confidence 4568999999999999999999987764
No 87
>PRK14976 5'-3' exonuclease; Provisional
Probab=51.45 E-value=11 Score=29.39 Aligned_cols=22 Identities=18% Similarity=0.457 Sum_probs=17.5
Q ss_pred CCC--CCcccccCccHHHHHhHHh
Q psy6806 15 MGE--KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 15 Mg~--K~Vt~l~GIG~~lg~~L~~ 36 (89)
||| ..+--||||||..+.+|-.
T Consensus 186 ~GD~sDnipGVpGIG~KtA~~LL~ 209 (281)
T PRK14976 186 VGDSSDNIKGVKGIGPKTAIKLLN 209 (281)
T ss_pred hCCccCCCCCCCcccHHHHHHHHH
Confidence 564 3677789999999988876
No 88
>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=51.01 E-value=24 Score=26.43 Aligned_cols=55 Identities=18% Similarity=0.331 Sum_probs=31.7
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHH
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCL 81 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl 81 (89)
+-+...+||||+...++|+..|+.. |+++. +-+.+.....|. .+..++.+-.+.+
T Consensus 147 ~~~L~Qlp~i~~~~~~~l~~~~i~~----l~~l~--~~~~~e~~~ll~----~~~~~~~~i~~~~ 201 (314)
T PF02889_consen 147 DSPLLQLPHIGEESLKKLEKRGIKT----LQDLR--DLSPEELEELLN----RNPPFGKEILEVA 201 (314)
T ss_dssp S-GGGGSTT--HHHHHHHHHTT--S----HHHHH--HS-HHHHHHHH-----S-HHHHHHHHHHH
T ss_pred CChhhcCCCCCHHHHHHHhccCCCc----HHHHh--hCCHHHHHHHHh----hhhhhHHHHHHHH
Confidence 3478899999999999999988654 45553 336666666665 3335555544443
No 89
>smart00475 53EXOc 5'-3' exonuclease.
Probab=50.99 E-value=12 Score=28.78 Aligned_cols=34 Identities=18% Similarity=0.448 Sum_probs=22.3
Q ss_pred CCC--CCcccccCccHHHHHhHHhc--CCchhhHhhhh
Q psy6806 15 MGE--KPVTELAGVGDVLGKRLESK--GFDKAYVVLGQ 48 (89)
Q Consensus 15 Mg~--K~Vt~l~GIG~~lg~~L~~~--Gf~kAy~lLGq 48 (89)
||| ..+--||||||..+.+|-.+ .+++.|.-+.+
T Consensus 181 ~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~ 218 (259)
T smart00475 181 MGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDK 218 (259)
T ss_pred hCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHH
Confidence 564 35777899999999888763 34444444433
No 90
>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=50.86 E-value=12 Score=22.71 Aligned_cols=19 Identities=21% Similarity=0.267 Sum_probs=15.4
Q ss_pred Cccc-ccCccHHHHHhHHhc
Q psy6806 19 PVTE-LAGVGDVLGKRLESK 37 (89)
Q Consensus 19 ~Vt~-l~GIG~~lg~~L~~~ 37 (89)
.+.. +||||+..+++|-+.
T Consensus 17 ~L~~~ipgig~~~a~~Il~~ 36 (69)
T TIGR00426 17 ELQRAMNGVGLKKAEAIVSY 36 (69)
T ss_pred HHHhHCCCCCHHHHHHHHHH
Confidence 4556 899999999888774
No 91
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=50.62 E-value=5.8 Score=21.32 Aligned_cols=45 Identities=24% Similarity=0.267 Sum_probs=33.2
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHH
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMK 64 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk 64 (89)
-+.|.++=||++....++...|-=.+..+ |.- ..-+.+.+.+||+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~i~~~~~-g~~--~~~~~~~l~~~~~ 48 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGELPAYRV-GRH--YRIPREDVDEYLE 48 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCCCCeEEe-CCe--EEEeHHHHHHHHh
Confidence 34677788999999999999986555554 642 2337888888886
No 92
>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=50.51 E-value=15 Score=28.90 Aligned_cols=52 Identities=12% Similarity=0.066 Sum_probs=34.4
Q ss_pred cCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHHHHH
Q psy6806 24 AGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLKDWC 85 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~eWc 85 (89)
+||+|...++|++.||..+.-++- . +... |.+.+|.+...+..=...+.+++
T Consensus 7 ~~~~~~~~~~l~~~g~~t~~~~~~----~--~~~~----L~~i~~ls~~~~~~~~~~~~~~~ 58 (316)
T TIGR02239 7 NGITAADIKKLQEAGLHTVESVAY----A--PKKQ----LLEIKGISEAKADKILAEAAKLV 58 (316)
T ss_pred CCCCHHHHHHHHHcCCCcHHHHHh----C--CHHH----HHHHhCCCHHHHHHHHHHHHHhc
Confidence 459999999999999999876642 1 2221 33456666666665555555543
No 93
>TIGR01740 pyrF orotidine 5'-phosphate decarboxylase, subfamily 1. This model represents orotidine 5'-monophosphate decarboxylase, the PyrF protein of pyrimidine nucleotide biosynthesis. In many eukaryotes, the region hit by this model is part of a multifunctional protein.
Probab=49.35 E-value=11 Score=27.50 Aligned_cols=51 Identities=12% Similarity=0.183 Sum_probs=36.0
Q ss_pred chHHHHhhhhCCCCCCCcccccCccHHH---H--------HhHHhcCCchhhHhhhhhhhhhcCH
Q psy6806 3 TSQKHQNFVSEPMGEKPVTELAGVGDVL---G--------KRLESKGFDKAYVVLGQFLLLKQNE 56 (89)
Q Consensus 3 tS~Khr~Fv~ePMg~K~Vt~l~GIG~~l---g--------~~L~~~Gf~kAy~lLGqfL~l~k~~ 56 (89)
||+.....+++-.|+ -+.-.||||+.- . +.+.+.|-| +.|+|+++.-..|.
T Consensus 144 ~~~~~~~~ir~~~~~-~~~vtPGI~~~g~~~~dq~~~~~~~~~~~~Gad--~iVvGr~I~~~~d~ 205 (213)
T TIGR01740 144 CSAEEAKEIRKFTGD-FLILTPGIRLQSKGADDQQRVVTLEDAKEAGAD--VIIVGRGIYAAEDP 205 (213)
T ss_pred eCHHHHHHHHHhcCC-ceEEeCCcCCCCCCcCCccccCCHHHHHHcCCC--EEEEChhhcCCCCH
Confidence 455666667666663 688999999873 3 557778876 77899997654443
No 94
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=47.84 E-value=28 Score=30.11 Aligned_cols=64 Identities=11% Similarity=0.088 Sum_probs=39.6
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHH
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLK 82 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~ 82 (89)
||.--+.-|-.-.+.++|||||.-.+.|= -+|=-++.=...=.+=|... |.+.+.|..-++.|+
T Consensus 503 hR~~r~k~~~~S~Ld~I~GiG~kr~~~Ll-----------~~Fgs~~~ik~As~eeL~~v-gi~~~~A~~I~~~l~ 566 (567)
T PRK14667 503 NRKLREKEGLKDILDKIKGIGEVKKEIIY-----------RNFKTLYDFLKADDEELKKL-GIPPSVKQEVKKYLS 566 (567)
T ss_pred HHHHhhcccccCccccCCCCCHHHHHHHH-----------HHhCCHHHHHhCCHHHHHHc-CCCHHHHHHHHHHhc
Confidence 55555666666678899999999877754 44433333222112223445 888888887776653
No 95
>KOG2924|consensus
Probab=47.73 E-value=18 Score=29.95 Aligned_cols=58 Identities=29% Similarity=0.494 Sum_probs=45.1
Q ss_pred HHHhhhhCCCCCCCcccccCccHHH---------------HHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhh
Q psy6806 6 KHQNFVSEPMGEKPVTELAGVGDVL---------------GKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETC 67 (89)
Q Consensus 6 Khr~Fv~ePMg~K~Vt~l~GIG~~l---------------g~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~ 67 (89)
..|-.|---|-+--||.--||-+-+ |+.|.++|.++ +|..|+-+-|-..|++||....
T Consensus 115 tirylvqh~mVdviVttaGGvEEDlIKclaPTy~g~F~L~G~~LR~~GlNR----iGNllvPndNYckfEdWl~pIl 187 (366)
T KOG2924|consen 115 TIRYLVQHNMVDVIVTTAGGVEEDLIKCLAPTYLGDFSLDGKELRENGLNR----IGNLLVPNDNYCKFEDWLMPIL 187 (366)
T ss_pred HHHHHHHhcceeEEEecCCccHHHHHHHhCccceeeeecChHHHHhhhhhh----hccEecCCcchhhHHHHHHHHH
Confidence 4555666677777788888887766 56778888887 4777888888899999998764
No 96
>PRK08609 hypothetical protein; Provisional
Probab=47.66 E-value=12 Score=31.93 Aligned_cols=18 Identities=22% Similarity=0.433 Sum_probs=16.5
Q ss_pred CcccccCccHHHHHhHHh
Q psy6806 19 PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~ 36 (89)
.++.+||||+.++.+.+|
T Consensus 49 ~l~~ipgIG~~ia~kI~E 66 (570)
T PRK08609 49 DFTKLKGIGKGTAEVIQE 66 (570)
T ss_pred hhccCCCcCHHHHHHHHH
Confidence 689999999999998887
No 97
>COG5217 BIM1 Microtubule-binding protein involved in cell cycle control [Cell division and chromosome partitioning / Cytoskeleton]
Probab=46.55 E-value=32 Score=28.38 Aligned_cols=45 Identities=29% Similarity=0.479 Sum_probs=34.5
Q ss_pred cccccCccHHHHHhHHhcCCchhhHhhhhhhhhhc--CHHHHHHHHHHh
Q psy6806 20 VTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQ--NEELFVDWMKET 66 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k--~~~~F~~WLk~~ 66 (89)
+-+-||=|.+|..-..+.|+|||-.|+- |+.-| |.=.|..||++-
T Consensus 59 ey~~~~n~kILq~~Fs~~Gidk~v~v~~--lvrck~qdnLeflQwlk~h 105 (342)
T COG5217 59 EYKHPGNGKILQLLFSDYGIDKAVLVLV--LVRCKLQDNLEFLQWLKDH 105 (342)
T ss_pred heecCCchhHHHHHHHhcCcchhhhHHH--HHHHHHHHHHHHHHHHHHH
Confidence 4567888999999999999999977652 33333 556899999973
No 98
>PF01367 5_3_exonuc: 5'-3' exonuclease, C-terminal SAM fold; InterPro: IPR020045 This entry represents the C-terminal domain of 5' to 3' exonucleases. The 5'-3' exonucleases are conserved in organisms as diverse as bacteriophage and mammals. It adopts a SAM fold consisting of 4-5 helices packed into a bundle of two orthogonally packed alpha-hairpins. This domain is involved in interactions with DNA and proteins. 5' to 3' exonucleases that contain this domain include: Bacteriophage T4 RNase H, which has sequence similarity to the RAD2 family of eukaryotic proteins []. 5' to 3' exonuclease domain of DNA polymerase Taq, which is homologous to Escherichia coli DNA polymerase I (pol I) [, ]. Bacteriophage T5 5'-exonuclease, which are structure-specific endonucleases []. Flap endonuclease-1 (Fen-1 nuclease), a structure specific nuclease that is an essential enzyme for eukaryotic DNA replication and repair []. ; GO: 0003677 DNA binding, 0003824 catalytic activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B.
Probab=46.26 E-value=3.4 Score=28.06 Aligned_cols=22 Identities=18% Similarity=0.477 Sum_probs=12.0
Q ss_pred CCCC--CcccccCccHHHHHhHHh
Q psy6806 15 MGEK--PVTELAGVGDVLGKRLES 36 (89)
Q Consensus 15 Mg~K--~Vt~l~GIG~~lg~~L~~ 36 (89)
|||. .+--||||||..+.+|-.
T Consensus 13 ~GD~sDNIPGV~GIG~KtA~~LL~ 36 (101)
T PF01367_consen 13 VGDSSDNIPGVPGIGPKTAAKLLQ 36 (101)
T ss_dssp C-CCCCTB---TTSTCHCCCCCHH
T ss_pred cCCcccCCCCCCCCCHHHHHHHHH
Confidence 5552 355678889887777654
No 99
>COG3492 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.37 E-value=19 Score=25.20 Aligned_cols=15 Identities=47% Similarity=1.092 Sum_probs=12.3
Q ss_pred hHhHHHHHHHHHHHh
Q psy6806 73 QSGDCYNCLKDWCGE 87 (89)
Q Consensus 73 qa~dc~~cl~eWc~~ 87 (89)
-|+-|-|||..|-.+
T Consensus 40 LAgFCRNCLs~Wy~e 54 (104)
T COG3492 40 LAGFCRNCLSNWYRE 54 (104)
T ss_pred HHHHHHHHHHHHHHH
Confidence 367899999999754
No 100
>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=44.34 E-value=24 Score=30.88 Aligned_cols=27 Identities=22% Similarity=0.430 Sum_probs=20.8
Q ss_pred chHHHHhhhhCCCCCCCcccccCccHHHHHhHHh
Q psy6806 3 TSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 3 tS~Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~ 36 (89)
+..-...|+++++ +|||||+.++++.+
T Consensus 76 ~~~~i~~yL~s~~-------~~GIG~~~A~~iv~ 102 (720)
T TIGR01448 76 SKEGIVAYLSSRS-------IKGVGKKLAQRIVK 102 (720)
T ss_pred CHHHHHHHHhcCC-------CCCcCHHHHHHHHH
Confidence 3345677887654 89999999999976
No 101
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=44.02 E-value=17 Score=28.09 Aligned_cols=23 Identities=17% Similarity=0.408 Sum_probs=17.7
Q ss_pred CC--CCCcccccCccHHHHHhHHhc
Q psy6806 15 MG--EKPVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 15 Mg--~K~Vt~l~GIG~~lg~~L~~~ 37 (89)
|| -..+--||||||..+.+|-.+
T Consensus 193 ~Gd~sDnipGV~GIG~ktA~~Ll~~ 217 (310)
T COG0258 193 VGDSSDNIPGVKGIGPKTALKLLQE 217 (310)
T ss_pred hCCcccCCCCCCCcCHHHHHHHHHH
Confidence 55 335667999999999998773
No 102
>PF11300 DUF3102: Protein of unknown function (DUF3102); InterPro: IPR021451 This entry is represented by Streptococcus phage 7201, Orf2. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=42.88 E-value=58 Score=23.27 Aligned_cols=39 Identities=13% Similarity=0.311 Sum_probs=28.6
Q ss_pred hhhhhhhhc---CHHHHHHHHHHhhccchhhHhHHHHHHHHH
Q psy6806 46 LGQFLLLKQ---NEELFVDWMKETCQANAKQSGDCYNCLKDW 84 (89)
Q Consensus 46 LGqfL~l~k---~~~~F~~WLk~~~gAn~kqa~dc~~cl~eW 84 (89)
+|+-|.-=| .-..|..||++.++.+...|+..-+--.+|
T Consensus 28 IGrrL~eaK~~l~HGef~~Wle~~~~~s~rtA~~~M~va~~y 69 (130)
T PF11300_consen 28 IGRRLKEAKELLPHGEFGKWLEEEVGYSQRTAQRFMQVAEEY 69 (130)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHcCcCHHHHHHHHHHHHHh
Confidence 566665554 336899999999999999988765554444
No 103
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=42.81 E-value=21 Score=17.54 Aligned_cols=11 Identities=27% Similarity=1.065 Sum_probs=9.6
Q ss_pred HHHHHHHHHHH
Q psy6806 76 DCYNCLKDWCG 86 (89)
Q Consensus 76 dc~~cl~eWc~ 86 (89)
-|+.|+++|.+
T Consensus 20 ~c~~C~~~~~~ 30 (39)
T smart00184 20 FCRSCIRKWLK 30 (39)
T ss_pred HHHHHHHHHHH
Confidence 69999999975
No 104
>PF13399 LytR_C: LytR cell envelope-related transcriptional attenuator
Probab=42.60 E-value=18 Score=22.59 Aligned_cols=23 Identities=22% Similarity=0.446 Sum_probs=20.0
Q ss_pred ccccCccHHHHHhHHhcCCchhh
Q psy6806 21 TELAGVGDVLGKRLESKGFDKAY 43 (89)
Q Consensus 21 t~l~GIG~~lg~~L~~~Gf~kAy 43 (89)
+.++|.+...+..|+.+||....
T Consensus 12 t~~~GlA~~~a~~L~~~Gf~v~~ 34 (90)
T PF13399_consen 12 TGVSGLAARVADALRNRGFTVVE 34 (90)
T ss_pred cCCcCHHHHHHHHHHHCCCceee
Confidence 56799999999999999998743
No 105
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=41.63 E-value=15 Score=24.84 Aligned_cols=50 Identities=18% Similarity=0.211 Sum_probs=31.1
Q ss_pred CcccccCccHHHHHhHHhcCCch--------hhHhhhhhhhh--hcCHHHHHHHHHHhhc
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDK--------AYVVLGQFLLL--KQNEELFVDWMKETCQ 68 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~k--------Ay~lLGqfL~l--~k~~~~F~~WLk~~~g 68 (89)
.+..+|||||..+.-.---++.+ ..-++.++... +.+.+..+.++....+
T Consensus 73 ~L~~l~GIG~~tA~~~l~~~~~~~~~~~D~~v~r~~~rl~~~~~~~~~~~~~~~~~~~~p 132 (149)
T smart00478 73 ELLKLPGVGRKTANAVLSFALGKPFIPVDTHVLRIAKRLGLVDKKSTPEEVEKLLEKLLP 132 (149)
T ss_pred HHHcCCCCcHHHHHHHHHHHCCCCCCccchHHHHHHHHhCCCCCCCCHHHHHHHHHHHCC
Confidence 45689999999988777766665 23345554332 2235566666665543
No 106
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=41.17 E-value=46 Score=30.04 Aligned_cols=51 Identities=16% Similarity=0.217 Sum_probs=35.8
Q ss_pred cccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHH
Q psy6806 20 VTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLK 82 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~ 82 (89)
+..+||||+..+.+|-++ |..-..| .+-..+...+ ..| +.+.|...|+.|.
T Consensus 759 L~~lPgI~~~~a~~ll~~-f~si~~l------~~as~eeL~~----~iG-~~~~A~~i~~fl~ 809 (814)
T TIGR00596 759 LLKLPGVTKKNYRNLRKK-VKSIREL------AKLSQNELNE----LIG-DEEAAKRLYDFLR 809 (814)
T ss_pred HHHCCCCCHHHHHHHHHH-cCCHHHH------HhCCHHHHHH----HhC-CHHHHHHHHHHhc
Confidence 457999999999998875 5554443 3345555444 467 7888888888775
No 107
>PRK10702 endonuclease III; Provisional
Probab=40.66 E-value=8.6 Score=28.78 Aligned_cols=28 Identities=21% Similarity=0.343 Sum_probs=21.4
Q ss_pred CCCCCCcccccCccHHHHHhHHhcCCch
Q psy6806 14 PMGEKPVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 14 PMg~K~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
|-.-+.+..|||||+..+.-.---+|++
T Consensus 105 p~~~~~Ll~lpGVG~ktA~~ill~a~~~ 132 (211)
T PRK10702 105 PEDRAALEALPGVGRKTANVVLNTAFGW 132 (211)
T ss_pred CchHHHHhcCCcccHHHHHHHHHHHcCC
Confidence 4444567899999999998877666766
No 108
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=39.77 E-value=12 Score=25.43 Aligned_cols=25 Identities=16% Similarity=0.205 Sum_probs=18.7
Q ss_pred CCCCcccccCccHHHHHhHHhcCCc
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~ 40 (89)
-.+.++.+|||||..+.-..--+|.
T Consensus 81 ~~~~L~~l~GIG~~tA~~~l~~~~~ 105 (158)
T cd00056 81 AREELLALPGVGRKTANVVLLFALG 105 (158)
T ss_pred cHHHHHcCCCCCHHHHHHHHHHHCC
Confidence 3456789999999998877665554
No 109
>KOG2093|consensus
Probab=39.57 E-value=19 Score=33.50 Aligned_cols=36 Identities=28% Similarity=0.409 Sum_probs=29.3
Q ss_pred HHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 6 KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 6 Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
|-.+|+++ -+|+.|||+|..+-.||+..|+.+.=.|
T Consensus 541 ~veeFis~----~~v~~LPGVG~sm~~kL~s~~i~tCgdL 576 (1016)
T KOG2093|consen 541 KVEEFISQ----LKVDDLPGVGSSMKSKLVSQFIQTCGDL 576 (1016)
T ss_pred HHHHHhhh----cccccCCCccHHHHHHHHHhccchhHHH
Confidence 55677664 4899999999999999999998875444
No 110
>KOG1209|consensus
Probab=39.22 E-value=18 Score=29.25 Aligned_cols=17 Identities=29% Similarity=0.638 Sum_probs=15.5
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||.+|++++.++||-
T Consensus 18 GGIG~ala~ef~~~G~~ 34 (289)
T KOG1209|consen 18 GGIGYALAKEFARNGYL 34 (289)
T ss_pred cchhHHHHHHHHhCCeE
Confidence 58999999999999984
No 111
>PRK10880 adenine DNA glycosylase; Provisional
Probab=38.67 E-value=7.6 Score=31.50 Aligned_cols=29 Identities=28% Similarity=0.316 Sum_probs=24.2
Q ss_pred CCCCCCcccccCccHHHHHhHHhcCCchh
Q psy6806 14 PMGEKPVTELAGVGDVLGKRLESKGFDKA 42 (89)
Q Consensus 14 PMg~K~Vt~l~GIG~~lg~~L~~~Gf~kA 42 (89)
|..-+.+..|||||+..+.-...-+|++.
T Consensus 105 p~~~~~L~~LpGIG~~TA~aIl~~af~~~ 133 (350)
T PRK10880 105 PETFEEVAALPGVGRSTAGAILSLSLGKH 133 (350)
T ss_pred hhhHHHHhcCCCccHHHHHHHHHHHCCCC
Confidence 55567889999999999998888788874
No 112
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=38.34 E-value=20 Score=29.42 Aligned_cols=17 Identities=29% Similarity=0.708 Sum_probs=15.6
Q ss_pred cccccCccHHHHHhHHh
Q psy6806 20 VTELAGVGDVLGKRLES 36 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~ 36 (89)
.|.|||||+..+..+++
T Consensus 55 ~t~l~gIGk~ia~~I~e 71 (326)
T COG1796 55 LTELPGIGKGIAEKISE 71 (326)
T ss_pred cCCCCCccHHHHHHHHH
Confidence 78999999999999887
No 113
>COG4221 Short-chain alcohol dehydrogenase of unknown specificity [General function prediction only]
Probab=37.83 E-value=18 Score=28.55 Aligned_cols=38 Identities=21% Similarity=0.400 Sum_probs=25.9
Q ss_pred ccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhcc
Q psy6806 23 LAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQA 69 (89)
Q Consensus 23 l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gA 69 (89)
=.|||+..+++|.++|+. -++..+.+|+- ++|.+..++
T Consensus 15 SSGiG~A~A~~l~~~G~~--------vvl~aRR~drL-~~la~~~~~ 52 (246)
T COG4221 15 SSGIGEATARALAEAGAK--------VVLAARREERL-EALADEIGA 52 (246)
T ss_pred cchHHHHHHHHHHHCCCe--------EEEEeccHHHH-HHHHHhhcc
Confidence 379999999999999982 22334444443 466666663
No 114
>TIGR01083 nth endonuclease III. This equivalog model identifes nth members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=37.50 E-value=18 Score=26.14 Aligned_cols=24 Identities=21% Similarity=0.339 Sum_probs=19.0
Q ss_pred CCcccccCccHHHHHhHHhcCCch
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
+.++.+||||+..+.-.---+|.+
T Consensus 106 ~~L~~l~GIG~ktA~~ill~~~~~ 129 (191)
T TIGR01083 106 EELVKLPGVGRKTANVVLNVAFGI 129 (191)
T ss_pred HHHHhCCCCcHHHHHHHHHHHcCC
Confidence 357799999999988877766654
No 115
>PRK13910 DNA glycosylase MutY; Provisional
Probab=36.91 E-value=12 Score=29.64 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=22.4
Q ss_pred CCCCCCcccccCccHHHHHhHHhcCCch
Q psy6806 14 PMGEKPVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 14 PMg~K~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
|-.-+.+..|||||+..+.-.-.-+|++
T Consensus 68 P~~~~~L~~LpGIG~kTA~aIl~~af~~ 95 (289)
T PRK13910 68 PNDYQSLLKLPGIGAYTANAILCFGFRE 95 (289)
T ss_pred ChhHHHHHhCCCCCHHHHHHHHHHHCCC
Confidence 3345678899999999998888877776
No 116
>KOG2841|consensus
Probab=35.66 E-value=23 Score=28.32 Aligned_cols=28 Identities=29% Similarity=0.458 Sum_probs=23.5
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHh
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~ 36 (89)
++.++...+|+ +..+||+||.-+++|-+
T Consensus 218 Lq~~~~AS~~e--le~~~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 218 LQQISNASEGE--LEQCPGLGPAKAKRLHK 245 (254)
T ss_pred HHHHHhcCHhH--HHhCcCcCHHHHHHHHH
Confidence 56777888886 88999999999999865
No 117
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.49 E-value=26 Score=31.77 Aligned_cols=22 Identities=18% Similarity=0.524 Sum_probs=18.1
Q ss_pred CCC--CCcccccCccHHHHHhHHh
Q psy6806 15 MGE--KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 15 Mg~--K~Vt~l~GIG~~lg~~L~~ 36 (89)
||| ..+--||||||..+.+|-.
T Consensus 180 ~GD~sDnIpGVpGIG~KtA~kLL~ 203 (887)
T TIGR00593 180 VGDSSDNIPGVKGIGEKTAAKLLQ 203 (887)
T ss_pred cCCcccCCCCCCCcCHHHHHHHHH
Confidence 676 4677799999999998876
No 118
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=34.55 E-value=27 Score=17.84 Aligned_cols=16 Identities=19% Similarity=0.540 Sum_probs=11.9
Q ss_pred hhHhHHHHHHHHHHHh
Q psy6806 72 KQSGDCYNCLKDWCGE 87 (89)
Q Consensus 72 kqa~dc~~cl~eWc~~ 87 (89)
..-.-|+.|+++|...
T Consensus 18 C~H~~c~~C~~~~~~~ 33 (45)
T cd00162 18 CGHVFCRSCIDKWLKS 33 (45)
T ss_pred CCChhcHHHHHHHHHh
Confidence 3344699999999864
No 119
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=34.40 E-value=52 Score=23.88 Aligned_cols=38 Identities=21% Similarity=0.521 Sum_probs=26.0
Q ss_pred HHHHHhHHhcCCchhh-HhhhhhhhhhcCHHHHHHHHHHh
Q psy6806 28 DVLGKRLESKGFDKAY-VVLGQFLLLKQNEELFVDWMKET 66 (89)
Q Consensus 28 ~~lg~~L~~~Gf~kAy-~lLGqfL~l~k~~~~F~~WLk~~ 66 (89)
..+-.-|+++|++... ..|-.| +..|.......||++.
T Consensus 162 ~~~~~yLeeRGId~~la~fl~~y-~~~kEq~eYi~wL~~l 200 (204)
T PF02330_consen 162 DAFMNYLEERGIDEELANFLHDY-STDKEQREYIRWLKNL 200 (204)
T ss_dssp HHHHHHHHHTT-SHHHHHHHHHH-HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH-HHHHHHHHHHHHHHHH
Confidence 3455678889999853 334445 4666888999999864
No 120
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=33.92 E-value=20 Score=25.61 Aligned_cols=15 Identities=20% Similarity=0.392 Sum_probs=8.2
Q ss_pred ccccCccHHHHHhHH
Q psy6806 21 TELAGVGDVLGKRLE 35 (89)
Q Consensus 21 t~l~GIG~~lg~~L~ 35 (89)
..|||||+..+++..
T Consensus 100 ~~lpgIG~~kA~aIi 114 (149)
T COG1555 100 QALPGIGPKKAQAII 114 (149)
T ss_pred HHCCCCCHHHHHHHH
Confidence 445666666555543
No 121
>PF10691 DUF2497: Protein of unknown function (DUF2497) ; InterPro: IPR019632 Members of this family belong to the Alphaproteobacteria. The function of the family is not known.
Probab=33.40 E-value=24 Score=22.88 Aligned_cols=9 Identities=56% Similarity=1.007 Sum_probs=6.5
Q ss_pred HHHHHHhcC
Q psy6806 81 LKDWCGEFL 89 (89)
Q Consensus 81 l~eWc~~fl 89 (89)
|++|.|++|
T Consensus 47 LkeWLD~nL 55 (73)
T PF10691_consen 47 LKEWLDENL 55 (73)
T ss_pred HHHHHHhcc
Confidence 677777765
No 122
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=33.00 E-value=19 Score=26.92 Aligned_cols=15 Identities=27% Similarity=0.488 Sum_probs=12.5
Q ss_pred CCcccccCccHHHHH
Q psy6806 18 KPVTELAGVGDVLGK 32 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~ 32 (89)
+.+..|||||+..+.
T Consensus 115 e~Ll~LpGVG~KTAn 129 (177)
T TIGR03252 115 RRLKALPGFGKQKAK 129 (177)
T ss_pred HHHHcCCCCCHHHHH
Confidence 468999999998765
No 123
>PF02579 Nitro_FeMo-Co: Dinitrogenase iron-molybdenum cofactor; InterPro: IPR003731 This entry represents several Nif (B, X and Y) proteins, which are involved in the biosynthesis of the iron-molybdenum cofactor (FeMo-co) found in the dinitrogenase enzyme of the nitrogenase complex in nitrogen-fixing bacteria. The nitrogenase complex catalyses the reduction of atmospheric dinitrogen to ammonia, and is composed of an iron metalloprotein (dinitrogenase reductase; homodimer of NifH; IPR000392 from INTERPRO) and a Fe-Mo metalloprotein (dinitrogenase; heterotetramer of NifD and NifK; IPR000318 from INTERPRO). The pathway for the synthesis of the Fe-Mo cofactor involves several proteins, including NifB, NifE, NifH, NifN, NifQ, NifV and NifX. NifB appears to be an iron-sulphur source for FeMo-co biosynthesis, while NifX may be associated with the mature FeMo-co, in particular with the addition of homocitrate during the last step of biosynthesis []. The NifX protein shows sequence similarity with the C terminus of NifB [], as well as to the conserved protein MTH1175 from the archaeon Methanobacterium thermoautotrophicum, which displays a ribonuclease H-like motif of three layers, alpha/beta/alpha, with a single mixed beta-sheet [].; PDB: 2QTD_A 2KLA_A 1EO1_A 1P90_A 1RDU_A 2YX6_D 1O13_A 1T3V_A 2RE2_B 2WFB_A.
Probab=32.74 E-value=43 Score=20.41 Aligned_cols=34 Identities=26% Similarity=0.402 Sum_probs=26.0
Q ss_pred HHHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCc
Q psy6806 5 QKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 5 ~Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~ 40 (89)
.+...|+.+ .|- ++-=+.+||+....+|.++|+.
T Consensus 43 ~~~~~~l~~-~~v-~~li~~~iG~~~~~~L~~~gI~ 76 (94)
T PF02579_consen 43 DKIAKFLAE-EGV-DVLICGGIGEGAFRALKEAGIK 76 (94)
T ss_dssp THHHHHHHH-TTE-SEEEESCSCHHHHHHHHHTTSE
T ss_pred hhHHHHHHH-cCC-CEEEEeCCCHHHHHHHHHCCCE
Confidence 355667777 554 6666789999999999999885
No 124
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=32.19 E-value=24 Score=19.46 Aligned_cols=13 Identities=23% Similarity=0.570 Sum_probs=9.9
Q ss_pred hHHHHHHHHHHHh
Q psy6806 75 GDCYNCLKDWCGE 87 (89)
Q Consensus 75 ~dc~~cl~eWc~~ 87 (89)
.-|+.||.+|...
T Consensus 24 ~fh~~Ci~~~~~~ 36 (44)
T PF13639_consen 24 VFHRSCIKEWLKR 36 (44)
T ss_dssp EEEHHHHHHHHHH
T ss_pred eeCHHHHHHHHHh
Confidence 3478899999864
No 125
>PRK07533 enoyl-(acyl carrier protein) reductase; Provisional
Probab=32.08 E-value=27 Score=25.23 Aligned_cols=16 Identities=6% Similarity=0.106 Sum_probs=14.8
Q ss_pred CccHHHHHhHHhcCCc
Q psy6806 25 GVGDVLGKRLESKGFD 40 (89)
Q Consensus 25 GIG~~lg~~L~~~Gf~ 40 (89)
|||..++++|.+.|.+
T Consensus 23 GIG~a~a~~la~~G~~ 38 (258)
T PRK07533 23 SIAWGCARAFRALGAE 38 (258)
T ss_pred cHHHHHHHHHHHcCCE
Confidence 8999999999999974
No 126
>PRK06079 enoyl-(acyl carrier protein) reductase; Provisional
Probab=32.06 E-value=27 Score=25.13 Aligned_cols=17 Identities=6% Similarity=0.102 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|++
T Consensus 19 ~gIG~a~a~~la~~G~~ 35 (252)
T PRK06079 19 RSIAWGCAQAIKDQGAT 35 (252)
T ss_pred CchHHHHHHHHHHCCCE
Confidence 48999999999999975
No 127
>PRK08091 ribulose-phosphate 3-epimerase; Validated
Probab=31.88 E-value=89 Score=23.99 Aligned_cols=56 Identities=18% Similarity=0.200 Sum_probs=36.6
Q ss_pred HHHhhhhCCCCCCCcccccC-ccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHH
Q psy6806 6 KHQNFVSEPMGEKPVTELAG-VGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMK 64 (89)
Q Consensus 6 Khr~Fv~ePMg~K~Vt~l~G-IG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk 64 (89)
+.|.++.+ .|-+-.-+++| |.+...++|.+.|-| ..|.|.++--..|-....+=|+
T Consensus 168 ~lr~~~~~-~~~~~~IeVDGGI~~~ti~~l~~aGaD--~~V~GSalF~~~d~~~~i~~l~ 224 (228)
T PRK08091 168 QVENRLGN-RRVEKLISIDGSMTLELASYLKQHQID--WVVSGSALFSQGELKTTLKEWK 224 (228)
T ss_pred HHHHHHHh-cCCCceEEEECCCCHHHHHHHHHCCCC--EEEEChhhhCCCCHHHHHHHHH
Confidence 34455544 34334458887 999999999999999 4778998653334344433333
No 128
>PRK06603 enoyl-(acyl carrier protein) reductase; Provisional
Probab=31.48 E-value=28 Score=25.28 Aligned_cols=16 Identities=6% Similarity=0.192 Sum_probs=14.7
Q ss_pred CccHHHHHhHHhcCCc
Q psy6806 25 GVGDVLGKRLESKGFD 40 (89)
Q Consensus 25 GIG~~lg~~L~~~Gf~ 40 (89)
|||..++++|.++|.+
T Consensus 21 GIG~a~a~~la~~G~~ 36 (260)
T PRK06603 21 SISWAIAQLAKKHGAE 36 (260)
T ss_pred chHHHHHHHHHHcCCE
Confidence 8999999999999974
No 129
>cd00128 XPG Xeroderma pigmentosum G N- and I-regions (XPGN, XPGI); contains the HhH2 motif; domain in nucleases. XPG is a eukaryotic enzyme that functions in nucleotide-excision repair and transcription-coupled repair of oxidative DNA damage. Functionally/structurally related to FEN-1; divalent metal ion-dependent exo- and endonuclease, and bacterial and bacteriophage 5'3' exonucleases.
Probab=31.32 E-value=39 Score=26.05 Aligned_cols=23 Identities=26% Similarity=0.427 Sum_probs=18.6
Q ss_pred CCCCCcccccCccHHHHHhHHhc
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~ 37 (89)
+|..-..-|||||++.|-+|..+
T Consensus 220 ~G~Dy~~gv~giG~k~A~~li~~ 242 (316)
T cd00128 220 LGCDYTEGIPGIGPVTALKLIKK 242 (316)
T ss_pred cCCCCCCCCCCccHHHHHHHHHH
Confidence 45556678999999999999875
No 130
>cd01518 RHOD_YceA Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YceA, Bacillus subtilis YbfQ, and similar uncharacterized proteins.
Probab=31.31 E-value=22 Score=22.17 Aligned_cols=23 Identities=22% Similarity=0.460 Sum_probs=18.1
Q ss_pred cHHHHHhHHhcCCchhhHhhhhh
Q psy6806 27 GDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 27 G~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
+...+..|...||+++|.|-|=+
T Consensus 74 s~~a~~~L~~~G~~~v~~l~GG~ 96 (101)
T cd01518 74 CEKASAYLKERGFKNVYQLKGGI 96 (101)
T ss_pred HHHHHHHHHHhCCcceeeechhH
Confidence 45667788889999999887754
No 131
>TIGR01084 mutY A/G-specific adenine glycosylase. This equivalog model identifies mutY members of the pfam00730 superfamily (HhH-GPD: Helix-hairpin-helix and Gly/Pro rich loop followed by a conserved aspartate). The major members of the superfamily are nth and mutY.
Probab=30.75 E-value=26 Score=27.37 Aligned_cols=25 Identities=24% Similarity=0.305 Sum_probs=19.4
Q ss_pred CCCcccccCccHHHHHhHHhcCCch
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
-+.+..|||||+..+.-..--+|++
T Consensus 104 ~~~L~~LpGIG~~TA~~Il~~a~~~ 128 (275)
T TIGR01084 104 FEDLAALPGVGRYTAGAILSFALNK 128 (275)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHCCC
Confidence 3467899999999988777666665
No 132
>KOG0011|consensus
Probab=30.17 E-value=85 Score=26.08 Aligned_cols=36 Identities=31% Similarity=0.506 Sum_probs=29.9
Q ss_pred HHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHH
Q psy6806 29 VLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKE 65 (89)
Q Consensus 29 ~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~ 65 (89)
....||++-||++|.++ =-|+.-.|||++=-.+|.+
T Consensus 300 eAIeRL~alGF~ralVi-qayfACdKNEelAAN~Ll~ 335 (340)
T KOG0011|consen 300 EAIERLEALGFPRALVI-QAYFACDKNEELAANYLLS 335 (340)
T ss_pred HHHHHHHHhCCcHHHHH-HHHHhcCccHHHHHHHHHh
Confidence 45789999999999765 6788999999987777754
No 133
>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=30.04 E-value=23 Score=23.27 Aligned_cols=34 Identities=29% Similarity=0.312 Sum_probs=27.2
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhhhhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFL 50 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL 50 (89)
..++..-.-||..+|+|+.++|+.+++.=.|-|.
T Consensus 53 ~~n~~aA~~vG~~la~r~~~~gi~~vv~D~~~~~ 86 (103)
T cd00432 53 GNNVEAAYLVGRLLAKRALEKGIKKVVFDRGGYR 86 (103)
T ss_pred CCcHHHHHHHHHHHHHHHHHCCCCEEEEeCCCcc
Confidence 3466667789999999999999999877666554
No 134
>KOG0317|consensus
Probab=29.99 E-value=30 Score=28.10 Aligned_cols=14 Identities=36% Similarity=1.234 Sum_probs=10.0
Q ss_pred HhHHHHHHHHHHHh
Q psy6806 74 SGDCYNCLKDWCGE 87 (89)
Q Consensus 74 a~dc~~cl~eWc~~ 87 (89)
---|..|+.|||.+
T Consensus 259 HiFCWsCI~~w~~e 272 (293)
T KOG0317|consen 259 HIFCWSCILEWCSE 272 (293)
T ss_pred chHHHHHHHHHHcc
Confidence 34588888888864
No 135
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=29.36 E-value=28 Score=27.57 Aligned_cols=17 Identities=29% Similarity=0.601 Sum_probs=14.2
Q ss_pred cccccCccHHHHHhHHh
Q psy6806 20 VTELAGVGDVLGKRLES 36 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~ 36 (89)
|..+||||+.++.+|-.
T Consensus 184 l~s~pgig~~~a~~ll~ 200 (254)
T COG1948 184 LESIPGIGPKLAERLLK 200 (254)
T ss_pred HHcCCCccHHHHHHHHH
Confidence 56799999999888764
No 136
>TIGR01684 viral_ppase viral phosphatase. These proteins also include an N-terminal domain (ca. 125 aas) that is unique to this clade.
Probab=29.30 E-value=30 Score=27.98 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=20.9
Q ss_pred CHHHHHHHHHHhhcc---------chhhHhHHHHHHHHHHHhc
Q psy6806 55 NEELFVDWMKETCQA---------NAKQSGDCYNCLKDWCGEF 88 (89)
Q Consensus 55 ~~~~F~~WLk~~~gA---------n~kqa~dc~~cl~eWc~~f 88 (89)
|=..|..-||..... +.+.+ =|.||+||+-.+
T Consensus 69 ~m~~~R~~~k~~~k~~~lGh~~vl~~~~~--~y~~L~EW~v~~ 109 (301)
T TIGR01684 69 DMVDLRAHLKTAFKTSYFGHTFVLFHKPA--MYACLNEWYVFE 109 (301)
T ss_pred cHHHHHHHHHHHhcccccceEEEecCCcc--HHHHHHHHHccc
Confidence 334677777766543 33444 599999998653
No 137
>PRK08690 enoyl-(acyl carrier protein) reductase; Provisional
Probab=29.22 E-value=31 Score=25.00 Aligned_cols=17 Identities=12% Similarity=0.214 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|.+
T Consensus 18 ~GIG~a~a~~l~~~G~~ 34 (261)
T PRK08690 18 RSIAYGIAKACREQGAE 34 (261)
T ss_pred CcHHHHHHHHHHHCCCE
Confidence 48999999999999974
No 138
>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=29.03 E-value=33 Score=20.75 Aligned_cols=13 Identities=31% Similarity=0.552 Sum_probs=10.3
Q ss_pred chHHHHhhhhCCC
Q psy6806 3 TSQKHQNFVSEPM 15 (89)
Q Consensus 3 tS~Khr~Fv~ePM 15 (89)
.|.+||.|...+-
T Consensus 23 ~s~~Hr~FA~~~~ 35 (49)
T PF07535_consen 23 QSEKHRKFAENDS 35 (49)
T ss_pred CCHHHHHHHcCcc
Confidence 4889999987654
No 139
>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=29.01 E-value=44 Score=26.59 Aligned_cols=23 Identities=17% Similarity=0.293 Sum_probs=18.9
Q ss_pred CCCCCcccccCccHHHHHhHHhc
Q psy6806 15 MGEKPVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~~ 37 (89)
+|+-.-.-||||||+.|.+|-.+
T Consensus 233 ~G~dyn~Gv~GIG~ktA~kli~~ 255 (338)
T TIGR03674 233 VGTDYNEGVKGIGPKTALKLIKE 255 (338)
T ss_pred cCCCCCCCCCCccHHHHHHHHHH
Confidence 56666678999999999998864
No 140
>PRK08159 enoyl-(acyl carrier protein) reductase; Provisional
Probab=28.59 E-value=32 Score=25.31 Aligned_cols=17 Identities=12% Similarity=0.147 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|.+
T Consensus 22 ~GIG~aia~~la~~G~~ 38 (272)
T PRK08159 22 RSIAWGIAKACRAAGAE 38 (272)
T ss_pred CcHHHHHHHHHHHCCCE
Confidence 38999999999999974
No 141
>PF00861 Ribosomal_L18p: Ribosomal L18p/L5e family; InterPro: IPR005484 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes L18 from bacteria and L5 from eukaryotes. The ribosomal 5S RNA is the only known rRNA species to bind a ribosomal protein before its assembly into the ribosomal subunits []. In eukaryotes, the 5S rRNA molecule binds one protein species, a 34kDa protein which has been implicated in the intracellular transport of 5 S rRNA, while in bacteria it binds two or three different protein species []. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_M 4A1C_M 4A1A_M 4A17_M 3IZR_Q 3O58_E 1S1I_E 3IZS_Q 3O5H_E 1KQS_M ....
Probab=28.34 E-value=9.5 Score=26.18 Aligned_cols=47 Identities=26% Similarity=0.308 Sum_probs=29.5
Q ss_pred cchHHHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhh
Q psy6806 2 STSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 2 ~tS~Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
|.|..++.+.-.+ +.+.+..-.=+|..+|+++.++|+...+.=.|.|
T Consensus 53 t~~~~l~~~~~~~-~~~n~~aa~~vG~lla~ra~~~gi~~v~fdr~~~ 99 (119)
T PF00861_consen 53 TLSKELKKYGWKG-STKNVEAAYLVGELLAKRALEKGIAKVVFDRGGY 99 (119)
T ss_dssp EETTTGGGTT-SS-TTSSHHHHHHHHHHHHHHHHHTTSSEEEECTSTS
T ss_pred ecchhhhhhhhcc-CCCCEehHHHHHHHHHHHHHHcCCcEEEEcCCCC
Confidence 4444455543222 2235666677999999999999996655444444
No 142
>PRK12481 2-deoxy-D-gluconate 3-dehydrogenase; Provisional
Probab=28.31 E-value=31 Score=24.74 Aligned_cols=17 Identities=29% Similarity=0.513 Sum_probs=15.5
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|+.
T Consensus 18 ~gIG~aia~~l~~~G~~ 34 (251)
T PRK12481 18 TGLGQGMAIGLAKAGAD 34 (251)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 58999999999999975
No 143
>PRK07370 enoyl-(acyl carrier protein) reductase; Validated
Probab=28.20 E-value=35 Score=24.73 Aligned_cols=17 Identities=12% Similarity=0.263 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.+.|.+
T Consensus 18 ~GIG~aia~~la~~G~~ 34 (258)
T PRK07370 18 RSIAWGIAQQLHAAGAE 34 (258)
T ss_pred CchHHHHHHHHHHCCCE
Confidence 48999999999999975
No 144
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=28.15 E-value=26 Score=24.11 Aligned_cols=32 Identities=25% Similarity=0.194 Sum_probs=23.5
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHhhhhh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
+.+..-.=||..+|+++.++|++++..=-|-|
T Consensus 58 ~n~~aA~~vG~lla~ra~~~gi~~vvfDrgg~ 89 (109)
T CHL00139 58 STCDASKLVGQKLAKKSLKKGITKVVFDRGGK 89 (109)
T ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCC
Confidence 34445555999999999999999875544444
No 145
>PRK08862 short chain dehydrogenase; Provisional
Probab=27.97 E-value=32 Score=24.77 Aligned_cols=17 Identities=12% Similarity=0.216 Sum_probs=15.5
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|++
T Consensus 15 ~GIG~aia~~la~~G~~ 31 (227)
T PRK08862 15 SVLGRTISCHFARLGAT 31 (227)
T ss_pred cHHHHHHHHHHHHCCCE
Confidence 58999999999999975
No 146
>smart00450 RHOD Rhodanese Homology Domain. An alpha beta fold found duplicated in the Rhodanese protein. The 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 stress proteins such as Senesence specific protein 1 in plants, PspE and GlpE in bacteria and cyanide and arsenate resistance proteins. Inactive versions with a loss of the cysteine are also seen in Dual specificity phosphatases, ubiquitin hydrolases from yeast and in sulfuryltransferases. These are likely to play a role in protein interactions.
Probab=27.83 E-value=27 Score=20.36 Aligned_cols=22 Identities=23% Similarity=0.413 Sum_probs=18.5
Q ss_pred HHHHHhHHhcCCchhhHhhhhh
Q psy6806 28 DVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 28 ~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
...+..|.+.||+++|+|-|-|
T Consensus 70 ~~~~~~l~~~G~~~v~~l~GG~ 91 (100)
T smart00450 70 AKAAWLLRELGFKNVYLLDGGY 91 (100)
T ss_pred HHHHHHHHHcCCCceEEecCCH
Confidence 5678889999999999887765
No 147
>cd00853 NifX NifX belongs to a family of iron-molybdenum cluster-binding proteins that includes NifB, and NifY, all of which are involved in the synthesis of an iron-molybdenum cofactor (FeMo-co) that binds the active site of the dinitrogenase enzyme. The protein is part of the nitrogen fixation gene cluster in nitrogen-fixing bacteria and has sequence similarity to other members of the cluster.
Probab=27.24 E-value=41 Score=21.58 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=20.0
Q ss_pred CCCcccccCccHHHHHhHHhcCCch
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
+=+|-=..|||+....+|+++|+.=
T Consensus 61 ~~~vvi~~~iG~~a~~~L~~~GI~v 85 (102)
T cd00853 61 DCAILYCAAIGGPAAARLVRAGIHP 85 (102)
T ss_pred CCcEEEEhhcChhHHHHHHHcCCEE
Confidence 3355567899999999999999863
No 148
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=27.03 E-value=28 Score=24.20 Aligned_cols=33 Identities=18% Similarity=0.333 Sum_probs=25.2
Q ss_pred CCCcccccCccHHHHHhHHhcCCchhhHhhhhh
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
...+..-.=||..+|+++.++|+++++.=-|-|
T Consensus 65 ~~n~~aa~~vG~~la~ra~~~gi~~vvfDrg~~ 97 (117)
T PRK05593 65 GGNKEAAKKVGKLIAERAKAKGIKQVVFDRGGY 97 (117)
T ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEcCCCC
Confidence 346666777999999999999999965444444
No 149
>PRK06505 enoyl-(acyl carrier protein) reductase; Provisional
Probab=27.00 E-value=36 Score=25.02 Aligned_cols=16 Identities=19% Similarity=0.358 Sum_probs=14.9
Q ss_pred CccHHHHHhHHhcCCc
Q psy6806 25 GVGDVLGKRLESKGFD 40 (89)
Q Consensus 25 GIG~~lg~~L~~~Gf~ 40 (89)
|||..++++|.++|.+
T Consensus 20 GIG~aiA~~la~~Ga~ 35 (271)
T PRK06505 20 SIAWGIAKQLAAQGAE 35 (271)
T ss_pred cHHHHHHHHHHhCCCE
Confidence 8999999999999964
No 150
>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=26.97 E-value=24 Score=20.56 Aligned_cols=24 Identities=21% Similarity=0.205 Sum_probs=19.2
Q ss_pred ccHHHHHhHHhcCCchhhHhhhhh
Q psy6806 26 VGDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 26 IG~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
-....+..|.+.||++.|++-|-|
T Consensus 62 ~a~~~~~~l~~~G~~~v~~l~gG~ 85 (89)
T cd00158 62 RSARAAKLLRKAGGTNVYNLEGGM 85 (89)
T ss_pred hHHHHHHHHHHhCcccEEEecCCh
Confidence 346788899999999999876654
No 151
>KOG3242|consensus
Probab=26.74 E-value=41 Score=26.11 Aligned_cols=20 Identities=20% Similarity=0.526 Sum_probs=16.4
Q ss_pred cchhhHhHHHHHHHHHHHhc
Q psy6806 69 ANAKQSGDCYNCLKDWCGEF 88 (89)
Q Consensus 69 An~kqa~dc~~cl~eWc~~f 88 (89)
+--+|-.+|++=|+|||.++
T Consensus 66 ~vI~~~~evld~MneWc~eh 85 (208)
T KOG3242|consen 66 LVIHQPKEVLDKMNEWCIEH 85 (208)
T ss_pred chhcCCHHHHHHHHHHHHHh
Confidence 33578889999999999875
No 152
>PRK07984 enoyl-(acyl carrier protein) reductase; Provisional
Probab=26.73 E-value=37 Score=25.00 Aligned_cols=16 Identities=6% Similarity=0.279 Sum_probs=14.7
Q ss_pred CccHHHHHhHHhcCCc
Q psy6806 25 GVGDVLGKRLESKGFD 40 (89)
Q Consensus 25 GIG~~lg~~L~~~Gf~ 40 (89)
|||..++++|.+.|.+
T Consensus 19 GIG~aia~~la~~G~~ 34 (262)
T PRK07984 19 SIAYGIAQAMHREGAE 34 (262)
T ss_pred cHHHHHHHHHHHCCCE
Confidence 7999999999999964
No 153
>PRK06997 enoyl-(acyl carrier protein) reductase; Provisional
Probab=26.68 E-value=38 Score=24.59 Aligned_cols=17 Identities=12% Similarity=0.216 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|..
T Consensus 18 ~GIG~a~a~~l~~~G~~ 34 (260)
T PRK06997 18 RSIAYGIAKACKREGAE 34 (260)
T ss_pred CcHHHHHHHHHHHCCCe
Confidence 48999999999999965
No 154
>PRK08594 enoyl-(acyl carrier protein) reductase; Provisional
Probab=26.48 E-value=39 Score=24.54 Aligned_cols=17 Identities=12% Similarity=0.206 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|..
T Consensus 19 ~GIG~aia~~la~~G~~ 35 (257)
T PRK08594 19 RSIAWGIARSLHNAGAK 35 (257)
T ss_pred CCHHHHHHHHHHHCCCE
Confidence 49999999999999974
No 155
>PRK05755 DNA polymerase I; Provisional
Probab=26.43 E-value=47 Score=29.56 Aligned_cols=22 Identities=23% Similarity=0.575 Sum_probs=17.8
Q ss_pred CCC--CCcccccCccHHHHHhHHh
Q psy6806 15 MGE--KPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 15 Mg~--K~Vt~l~GIG~~lg~~L~~ 36 (89)
||| ..+--||||||..+.+|-.
T Consensus 182 ~GD~sDnipGv~GiG~ktA~~Ll~ 205 (880)
T PRK05755 182 MGDSSDNIPGVPGIGEKTAAKLLQ 205 (880)
T ss_pred hCCccCCCCCCCCccHHHHHHHHH
Confidence 564 3677789999999998876
No 156
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=26.32 E-value=50 Score=21.09 Aligned_cols=19 Identities=11% Similarity=0.499 Sum_probs=15.4
Q ss_pred CcccccCccHHHHHhHHhc
Q psy6806 19 PVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~ 37 (89)
+.+.|.|||+..++++.+.
T Consensus 28 gl~~Ikglg~~~a~~I~~~ 46 (90)
T PF14579_consen 28 GLSAIKGLGEEVAEKIVEE 46 (90)
T ss_dssp BGGGSTTS-HHHHHHHHHH
T ss_pred hHhhcCCCCHHHHHHHHHh
Confidence 5678999999999998873
No 157
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=26.06 E-value=39 Score=20.54 Aligned_cols=12 Identities=33% Similarity=0.581 Sum_probs=9.7
Q ss_pred chHHHHhhhhCC
Q psy6806 3 TSQKHQNFVSEP 14 (89)
Q Consensus 3 tS~Khr~Fv~eP 14 (89)
.|.+||.|...+
T Consensus 23 ~s~~Hr~FA~~~ 34 (49)
T smart00586 23 LSEKHRRFAENN 34 (49)
T ss_pred ccHHHHHHHcCc
Confidence 588999998754
No 158
>PRK03980 flap endonuclease-1; Provisional
Probab=25.93 E-value=55 Score=25.72 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=17.2
Q ss_pred CCCCCcccccCccHHHHHhHHh
Q psy6806 15 MGEKPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 15 Mg~K~Vt~l~GIG~~lg~~L~~ 36 (89)
+|---..-||||||..|.+|..
T Consensus 186 ~G~Dy~~GI~GIG~ktA~kLi~ 207 (292)
T PRK03980 186 VGTDYNPGIKGIGPKTALKLIK 207 (292)
T ss_pred cCCCCCCCCCCccHHHHHHHHH
Confidence 3444566899999999988876
No 159
>PLN02780 ketoreductase/ oxidoreductase
Probab=25.76 E-value=37 Score=26.03 Aligned_cols=17 Identities=29% Similarity=0.622 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|++
T Consensus 63 ~GIG~alA~~La~~G~~ 79 (320)
T PLN02780 63 DGIGKGFAFQLARKGLN 79 (320)
T ss_pred cHHHHHHHHHHHHCCCC
Confidence 68999999999999973
No 160
>PF09665 RE_Alw26IDE: Type II restriction endonuclease (RE_Alw26IDE); InterPro: IPR014328 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry represents type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family [], whose recognition sequences are 5'-GTCTC-3' (Alw26I), 5'-GGTCTC-3' (Eco31I) and 5'-CGTCTC-3' (Esp3I).
Probab=25.66 E-value=91 Score=27.24 Aligned_cols=41 Identities=27% Similarity=0.397 Sum_probs=34.5
Q ss_pred HHHhHHhcCCchhhHhhhhhhhhhc---------CHHHHHHHHHHhhccc
Q psy6806 30 LGKRLESKGFDKAYVVLGQFLLLKQ---------NEELFVDWMKETCQAN 70 (89)
Q Consensus 30 lg~~L~~~Gf~kAy~lLGqfL~l~k---------~~~~F~~WLk~~~gAn 70 (89)
+..+|.....+++|.=+..+|..+. +++.|..||.+++=.+
T Consensus 128 i~~~l~~~~gd~~~~~~~~~l~~k~~~~~~~~~~~~d~~i~~l~~~yi~~ 177 (511)
T PF09665_consen 128 IIERLKSLFGDNVYNDLPHFLFPKRIKDIPRLTSTLDEFIQWLYSEYIPK 177 (511)
T ss_pred HHHHHHHHhhhHHHHHHhHHHhhhhhcccCcCCchHHHHHHHHHHHhhcC
Confidence 5778999999999999999988766 6788999999886443
No 161
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=25.48 E-value=29 Score=27.01 Aligned_cols=28 Identities=18% Similarity=0.388 Sum_probs=21.5
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHh
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVV 45 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~l 45 (89)
+.++.||||||-.+.-..-.|+.+...+
T Consensus 207 ~~L~~LpGIGpwTA~~vllr~lg~~D~f 234 (283)
T PRK10308 207 KTLQTFPGIGRWTANYFALRGWQAKDVF 234 (283)
T ss_pred HHHhcCCCcCHHHHHHHHHHhCCCCCCC
Confidence 3578999999999987777677665554
No 162
>PRK08415 enoyl-(acyl carrier protein) reductase; Provisional
Probab=25.47 E-value=41 Score=24.93 Aligned_cols=17 Identities=12% Similarity=0.133 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.+.|.+
T Consensus 17 ~GIG~aiA~~la~~G~~ 33 (274)
T PRK08415 17 KSIAYGIAKACFEQGAE 33 (274)
T ss_pred CCHHHHHHHHHHHCCCE
Confidence 38999999999999974
No 163
>cd03572 ENTH_epsin_related ENTH domain, Epsin Related family; composed of hypothetical proteins containing an ENTH-like domain. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. ENTH and ANTH (E/ANTH) domains are structurally similar to the VHS domain and are composed of a superhelix of eight alpha helices. E/ANTH domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membranes. ENTH domains also function in the development of membrane curvature through lipid remodeling during the formation of clathrin-coated vesicles. E/ANTH-bearing proteins have recently been shown to function with adaptor protein-1 and GGA adaptors at the t
Probab=25.28 E-value=35 Score=23.95 Aligned_cols=47 Identities=19% Similarity=0.164 Sum_probs=34.2
Q ss_pred CcccccCccHHHHHhHHhcCCc---hhhHhhhhhhhhhcCHHHHHHHHHHhh
Q psy6806 19 PVTELAGVGDVLGKRLESKGFD---KAYVVLGQFLLLKQNEELFVDWMKETC 67 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~---kAy~lLGqfL~l~k~~~~F~~WLk~~~ 67 (89)
+.+++.-|.+.|.+||..+|-. ||.-|| +||+-+. .+.|+.|++..+
T Consensus 32 s~~~~~ei~d~L~kRL~~~~~hVK~K~Lril-k~l~~~G-~~~f~~~~~~~~ 81 (122)
T cd03572 32 SVGSCQELLEYLLKRLKRSSPHVKLKVLKII-KHLCEKG-NSDFKRELQRNS 81 (122)
T ss_pred CHHHHHHHHHHHHHHhcCCCCcchHHHHHHH-HHHHhhC-CHHHHHHHHHhH
Confidence 5566777889999999998832 233444 6766665 489999999764
No 164
>TIGR00588 ogg 8-oxoguanine DNA-glycosylase (ogg). All proteins in this family for which functions are known are 8-oxo-guanaine DNA glycosylases that function in base excision repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). This family is distantly realted to the Nth-MutY superfamily.
Probab=25.22 E-value=38 Score=26.63 Aligned_cols=23 Identities=35% Similarity=0.538 Sum_probs=18.3
Q ss_pred CcccccCccHHHHHhHHhcCCch
Q psy6806 19 PVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
.++.+|||||..+.-..--||.+
T Consensus 221 ~L~~l~GIG~~tAd~vll~~l~~ 243 (310)
T TIGR00588 221 ALCELPGVGPKVADCICLMGLDK 243 (310)
T ss_pred HHHhCCCccHHHHHHHHHHhCCC
Confidence 45789999999988777666665
No 165
>PRK06300 enoyl-(acyl carrier protein) reductase; Provisional
Probab=25.12 E-value=39 Score=26.05 Aligned_cols=17 Identities=29% Similarity=0.343 Sum_probs=15.5
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..+++.|+++|++
T Consensus 20 ~GIG~a~A~~la~~Ga~ 36 (299)
T PRK06300 20 QGYGWGIAKALAEAGAT 36 (299)
T ss_pred CCHHHHHHHHHHHCCCE
Confidence 59999999999999973
No 166
>PRK06483 dihydromonapterin reductase; Provisional
Probab=25.02 E-value=38 Score=23.66 Aligned_cols=17 Identities=24% Similarity=0.263 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|++
T Consensus 12 ~gIG~~ia~~l~~~G~~ 28 (236)
T PRK06483 12 QRIGLALAWHLLAQGQP 28 (236)
T ss_pred ChHHHHHHHHHHHCCCe
Confidence 58999999999999974
No 167
>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=24.82 E-value=29 Score=21.53 Aligned_cols=23 Identities=17% Similarity=0.421 Sum_probs=18.3
Q ss_pred ccHHHHHhHHhcCCchhhHhhhhh
Q psy6806 26 VGDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 26 IG~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
-+...+..|.+.||+ +|.|-|=|
T Consensus 73 rs~~aa~~L~~~G~~-~~~l~GG~ 95 (100)
T cd01523 73 SSQFVAELLAERGYD-VDYLAGGM 95 (100)
T ss_pred cHHHHHHHHHHcCce-eEEeCCcH
Confidence 346788899999999 88887754
No 168
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=24.72 E-value=27 Score=30.56 Aligned_cols=30 Identities=23% Similarity=0.252 Sum_probs=20.5
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHh
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~ 36 (89)
||.--+.-|-.-.+..+|||||.-.++|=+
T Consensus 541 hRk~R~k~~~~S~L~~IpGIG~kr~~~LL~ 570 (624)
T PRK14669 541 HRKRRETRDRTSELLEIPGVGAKTVQRLLK 570 (624)
T ss_pred hHHHhhHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 444444444444677899999999888765
No 169
>PF13788 DUF4180: Domain of unknown function (DUF4180)
Probab=24.72 E-value=48 Score=23.19 Aligned_cols=29 Identities=14% Similarity=0.181 Sum_probs=25.3
Q ss_pred chHHHHhhhhCCCCCCCcccccCccHHHH
Q psy6806 3 TSQKHQNFVSEPMGEKPVTELAGVGDVLG 31 (89)
Q Consensus 3 tS~Khr~Fv~ePMg~K~Vt~l~GIG~~lg 31 (89)
+|+.+++||.|---++.+..+|-..+.+.
T Consensus 83 ~S~~l~dfi~EsN~G~~~~F~~~~~eA~~ 111 (113)
T PF13788_consen 83 TSKSLRDFIYESNRGNHFFFVPDEEEAIA 111 (113)
T ss_pred cchhHHHHHHHhcCCCeEEEECCHHHHHh
Confidence 79999999999999999999988776654
No 170
>PRK05867 short chain dehydrogenase; Provisional
Probab=24.56 E-value=39 Score=23.96 Aligned_cols=17 Identities=18% Similarity=0.356 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.+.|++
T Consensus 19 ~gIG~~ia~~l~~~G~~ 35 (253)
T PRK05867 19 TGIGKRVALAYVEAGAQ 35 (253)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 58999999999999973
No 171
>PF08933 DUF1864: Domain of unknown function (DUF1864); InterPro: IPR015029 This protein has no known function. It is found in various hypothetical and conserved domain proteins. ; PDB: 2NWB_A 1ZEE_B 2X66_A 2V7L_A 2V7M_A 2V7K_A 2X67_A 2X68_A 2V7J_A 2V7I_A.
Probab=24.47 E-value=27 Score=29.37 Aligned_cols=30 Identities=37% Similarity=0.883 Sum_probs=22.2
Q ss_pred cccccCccHHHHHhHHh----------------cCCchhhHhhhhh
Q psy6806 20 VTELAGVGDVLGKRLES----------------KGFDKAYVVLGQF 49 (89)
Q Consensus 20 Vt~l~GIG~~lg~~L~~----------------~Gf~kAy~lLGqf 49 (89)
=..|+|||+.|-..|++ .||+-|.-+||..
T Consensus 32 ~~~v~gi~~~lk~~L~~~g~~~i~~ll~egntd~gFd~a~a~lgnv 77 (387)
T PF08933_consen 32 KADVPGIGELLKQQLEAEGRALISDLLAEGNTDEGFDSAFALLGNV 77 (387)
T ss_dssp TT-HCCCCHHHHCCCHCCHHHHHHCCCCCSSTTS-HHHHHHHHHHH
T ss_pred cccccchHHHHHHHHHhcCchHHHHHhhcCCcccCHHHHHHHHHhH
Confidence 35789999999888865 6788888887754
No 172
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=24.36 E-value=31 Score=22.71 Aligned_cols=28 Identities=29% Similarity=0.520 Sum_probs=17.9
Q ss_pred hhhCCCCCCCcccccCccHHHHHhHHhcC
Q psy6806 10 FVSEPMGEKPVTELAGVGDVLGKRLESKG 38 (89)
Q Consensus 10 Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~G 38 (89)
|||-||++.+=..-|-. ...+++|.++|
T Consensus 2 YIaGPmtG~~~~N~~~f-~~~a~~L~~~G 29 (92)
T PF14359_consen 2 YIAGPMTGLPDYNRPAF-NAAAKRLRAKG 29 (92)
T ss_pred eEeCCcCCCcchHHHHH-HHHHHHHHHCC
Confidence 68899998662222222 23677888888
No 173
>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=24.26 E-value=37 Score=25.50 Aligned_cols=20 Identities=45% Similarity=0.694 Sum_probs=17.2
Q ss_pred ccccCccHHHHHhHHhcCCc
Q psy6806 21 TELAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 21 t~l~GIG~~lg~~L~~~Gf~ 40 (89)
..|-+||..|++.|+++|+.
T Consensus 30 ~~V~~VG~~L~~~Le~~Gi~ 49 (196)
T TIGR02867 30 GNITKVGDRLAKELEEKGIG 49 (196)
T ss_pred CcHHHHHHHHHHHHHHCCCe
Confidence 46778999999999999873
No 174
>PRK08339 short chain dehydrogenase; Provisional
Probab=24.26 E-value=43 Score=24.31 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|.+
T Consensus 18 ~gIG~aia~~l~~~G~~ 34 (263)
T PRK08339 18 KGIGFGVARVLARAGAD 34 (263)
T ss_pred CcHHHHHHHHHHHCCCE
Confidence 48999999999999964
No 175
>COG3079 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.02 E-value=40 Score=25.81 Aligned_cols=12 Identities=42% Similarity=1.229 Sum_probs=10.3
Q ss_pred HHHHHHHHHhcC
Q psy6806 78 YNCLKDWCGEFL 89 (89)
Q Consensus 78 ~~cl~eWc~~fl 89 (89)
.+.|.+||+.||
T Consensus 99 ADAL~eW~nhFL 110 (186)
T COG3079 99 ADALAEWCNHFL 110 (186)
T ss_pred HHHHHHHHHHHH
Confidence 468999999996
No 176
>PRK06101 short chain dehydrogenase; Provisional
Probab=23.81 E-value=40 Score=23.87 Aligned_cols=17 Identities=24% Similarity=0.612 Sum_probs=15.5
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..+++.|.++|++
T Consensus 11 ~giG~~la~~L~~~G~~ 27 (240)
T PRK06101 11 SGIGKQLALDYAKQGWQ 27 (240)
T ss_pred cHHHHHHHHHHHhCCCE
Confidence 58999999999999975
No 177
>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain. This model represents a clade within a larger family of proteins from viruses of bacteria and animals. Members of this family are found in phage and plasmids of bacteria and archaea only. The model describes a domain of about 300 residues, found generally toward the protein C-terminus.
Probab=23.77 E-value=1.2e+02 Score=23.10 Aligned_cols=65 Identities=15% Similarity=0.293 Sum_probs=40.1
Q ss_pred ccccCccHHHHHh---HHhcC-Cch---hhHhhhhhhhhhcCHHHHHHHHHHhhcc---chhhHhHHHHHHHHHHHhc
Q psy6806 21 TELAGVGDVLGKR---LESKG-FDK---AYVVLGQFLLLKQNEELFVDWMKETCQA---NAKQSGDCYNCLKDWCGEF 88 (89)
Q Consensus 21 t~l~GIG~~lg~~---L~~~G-f~k---Ay~lLGqfL~l~k~~~~F~~WLk~~~gA---n~kqa~dc~~cl~eWc~~f 88 (89)
.|+|||=--+..- +.+.| |.. .-...-+|. ++.+-+.+|+.++|-. ..-...+=|+..++||++.
T Consensus 220 ~E~~~il~w~l~g~~~~~~~~~~~~p~~~~~~~~~~~---~~~d~v~~Fi~e~~~~~~~~~~~~~~ly~~y~~wc~~~ 294 (304)
T TIGR01613 220 NEKDVILYWAVEGIRLDQRIGDFSIPKAVLEATEEYK---EENDVVARFLEECCDDSEGEKVPVRFVYEAYKEWCEEG 294 (304)
T ss_pred HhHHHHHHHHHHHHHHHHhCCCcCCCHHHHHHHHHHH---HHCCcHHHHHHhheEeCCCcEEEHHHHHHHHHHHHHHc
Confidence 4677776543332 33355 542 233444443 4667888999988732 2235678999999999864
No 178
>PF12482 DUF3701: Phage integrase protein; InterPro: IPR022169 This domain family is found in bacteria, and is approximately 100 amino acids in length. The family is found in association with PF00589 from PFAM.
Probab=23.59 E-value=48 Score=22.55 Aligned_cols=16 Identities=25% Similarity=0.578 Sum_probs=13.6
Q ss_pred ccccCccHHHHHhHHh
Q psy6806 21 TELAGVGDVLGKRLES 36 (89)
Q Consensus 21 t~l~GIG~~lg~~L~~ 36 (89)
..|||||+.-+.+++.
T Consensus 53 r~vpglG~~~A~~I~a 68 (96)
T PF12482_consen 53 RAVPGLGAAGARRIEA 68 (96)
T ss_pred HhCcccchHHHHHHHH
Confidence 4689999999998875
No 179
>cd01532 4RHOD_Repeat_1 Member of the Rhodanese Homology Domain superfamily, repeat 1. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 1st repeat which does not contain the putative catalytic Cys residue.
Probab=23.57 E-value=39 Score=20.94 Aligned_cols=22 Identities=18% Similarity=0.377 Sum_probs=17.7
Q ss_pred HHHHHhHHhcCCchhhHhhhhh
Q psy6806 28 DVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 28 ~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
...+..|.+.||++.|+|-|=+
T Consensus 66 ~~aa~~L~~~G~~~v~~l~GG~ 87 (92)
T cd01532 66 PRAARRLSELGYTDVALLEGGL 87 (92)
T ss_pred HHHHHHHHHcCccCEEEccCCH
Confidence 5677889999999998876644
No 180
>PF06135 DUF965: Bacterial protein of unknown function (DUF965); InterPro: IPR009309 This family consists of several hypothetical bacterial proteins. The function of the family is unknown.
Probab=23.27 E-value=58 Score=21.81 Aligned_cols=21 Identities=24% Similarity=0.441 Sum_probs=17.2
Q ss_pred HHHHhHHhcCCchhhHhhhhh
Q psy6806 29 VLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 29 ~lg~~L~~~Gf~kAy~lLGqf 49 (89)
..-..|+|+|++-.-|+.|-.
T Consensus 23 ~Vy~AL~EKGYnPinQivGYl 43 (79)
T PF06135_consen 23 QVYAALEEKGYNPINQIVGYL 43 (79)
T ss_pred HHHHHHHHcCCChHHHHHhhe
Confidence 345679999999999999943
No 181
>PRK08416 7-alpha-hydroxysteroid dehydrogenase; Provisional
Probab=23.24 E-value=43 Score=23.97 Aligned_cols=17 Identities=18% Similarity=0.497 Sum_probs=15.7
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|..
T Consensus 18 ~gIG~~ia~~l~~~G~~ 34 (260)
T PRK08416 18 RGIGKAIVYEFAQSGVN 34 (260)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 79999999999999975
No 182
>TIGR00060 L18_bact ribosomal protein L18, bacterial type. The archaeal and eukaryotic type rpL18 is not detectable under this model.
Probab=23.24 E-value=32 Score=24.04 Aligned_cols=35 Identities=20% Similarity=0.285 Sum_probs=26.1
Q ss_pred CCCCcccccCccHHHHHhHHhcCCchhhHhhhhhh
Q psy6806 16 GEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFL 50 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL 50 (89)
+.+.+..-.=||..+|+++.++|++++..=-|-|+
T Consensus 61 ~~~n~~aA~~vG~~la~ra~~~gi~~vvfDrgg~~ 95 (114)
T TIGR00060 61 YTGNKDAAKKVGKLVAERLKEKGIKDVVFDRGGYK 95 (114)
T ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCEEEEeCCCCc
Confidence 44466667779999999999999998754444443
No 183
>PRK12747 short chain dehydrogenase; Provisional
Probab=23.14 E-value=49 Score=23.37 Aligned_cols=17 Identities=35% Similarity=0.636 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|.+
T Consensus 14 ~gIG~~ia~~l~~~G~~ 30 (252)
T PRK12747 14 RGIGRAIAKRLANDGAL 30 (252)
T ss_pred ChHHHHHHHHHHHCCCe
Confidence 58999999999999964
No 184
>PF00416 Ribosomal_S13: Ribosomal protein S13/S18; InterPro: IPR001892 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S13 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S13 is known to be involved in binding fMet-tRNA and, hence, in the initiation of translation. It is a basic protein of 115 to 177 amino-acid residues that contains thee helices and a beta-hairpin in the core of the protein, forming a helix-two turns-helix (H2TH) motif, and a non-globular C-terminal extension. This family of ribosomal proteins is present in prokaryotes, eukaryotes and archaea [, ].; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3BBN_M 2QBB_M 3I1M_M 3OFP_M 3OFX_M 3OFO_M 1VS5_M 3OAQ_M 2QAL_M 3J18_M ....
Probab=23.10 E-value=66 Score=21.49 Aligned_cols=24 Identities=21% Similarity=0.421 Sum_probs=18.4
Q ss_pred CcccccCccHHHHHhHHh-cCCchh
Q psy6806 19 PVTELAGVGDVLGKRLES-KGFDKA 42 (89)
Q Consensus 19 ~Vt~l~GIG~~lg~~L~~-~Gf~kA 42 (89)
.++.+.|||+..+..+-. .|++..
T Consensus 16 aLt~IyGIG~~~A~~Ic~~lgi~~~ 40 (107)
T PF00416_consen 16 ALTKIYGIGRRKAKQICKKLGINPN 40 (107)
T ss_dssp HHTTSTTBCHHHHHHHHHHTTS-SS
T ss_pred HHhhhhccCHHHHHHHHHHcCCChh
Confidence 357899999999999655 787763
No 185
>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=23.03 E-value=45 Score=23.06 Aligned_cols=24 Identities=21% Similarity=0.368 Sum_probs=20.3
Q ss_pred ccccCccHHHHHhHHhcCCchhhH
Q psy6806 21 TELAGVGDVLGKRLESKGFDKAYV 44 (89)
Q Consensus 21 t~l~GIG~~lg~~L~~~Gf~kAy~ 44 (89)
..+..||+..+..|.+.||...++
T Consensus 203 ~~~~aig~~t~~~l~~~g~~~~~~ 226 (239)
T cd06578 203 VKIAAIGPRTAEALRELGLKVVIV 226 (239)
T ss_pred CeEEEECHHHHHHHHHcCCCceee
Confidence 456789999999999999987653
No 186
>COG5646 Uncharacterized conserved protein [Function unknown]
Probab=23.00 E-value=27 Score=25.27 Aligned_cols=23 Identities=26% Similarity=0.531 Sum_probs=18.9
Q ss_pred cCccHHHHHhHHhcCCchhhHhhh
Q psy6806 24 AGVGDVLGKRLESKGFDKAYVVLG 47 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~kAy~lLG 47 (89)
+|| +..+.+|.+.|||.+|..++
T Consensus 69 ~gI-~~fa~~l~~~~yd~tkg~ir 91 (126)
T COG5646 69 AGI-DAFADELKEAGYDYTKGTIR 91 (126)
T ss_pred cch-HHHHHHHhhhcccccceeEe
Confidence 344 56889999999999998876
No 187
>PF02184 HAT: HAT (Half-A-TPR) repeat; InterPro: IPR003107 The HAT (Half A TPR) repeat has a repetitive pattern characterised by three aromatic residues with a conserved spacing. They are structurally and sequentially similar to TPRs (tetratricopeptide repeats), though they lack the highly conserved alanine and glycine residues found in TPRs. The number of HAT repeats found in different proteins varies between 9 and 12. HAT-repeat-containing proteins appear to be components of macromolecular complexes that are required for RNA processing []. The repeats may be involved in protein-protein interactions. The HAT motif has striking structural similarities to HEAT repeats (IPR000357 from INTERPRO), being of a similar length and consisting of two short helices connected by a loop domain, as in HEAT repeats.; GO: 0006396 RNA processing, 0005622 intracellular
Probab=22.99 E-value=82 Score=17.65 Aligned_cols=27 Identities=22% Similarity=0.532 Sum_probs=21.2
Q ss_pred CCchhhHhhhhhhhhhcCHHHHHHHHH
Q psy6806 38 GFDKAYVVLGQFLLLKQNEELFVDWMK 64 (89)
Q Consensus 38 Gf~kAy~lLGqfL~l~k~~~~F~~WLk 64 (89)
-||+|-.+.-+|+..+.+...+..|-+
T Consensus 2 E~dRAR~IyeR~v~~hp~~k~WikyAk 28 (32)
T PF02184_consen 2 EFDRARSIYERFVLVHPEVKNWIKYAK 28 (32)
T ss_pred hHHHHHHHHHHHHHhCCCchHHHHHHH
Confidence 378899999999999877776666643
No 188
>PRK07078 hypothetical protein; Validated
Probab=22.61 E-value=1.8e+02 Score=26.20 Aligned_cols=71 Identities=18% Similarity=0.339 Sum_probs=46.6
Q ss_pred CCcccccCccHHH---HHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccc---hhhHhHHHHHHHHHHHhc
Q psy6806 18 KPVTELAGVGDVL---GKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQAN---AKQSGDCYNCLKDWCGEF 88 (89)
Q Consensus 18 K~Vt~l~GIG~~l---g~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn---~kqa~dc~~cl~eWc~~f 88 (89)
|-..|+|||=.-+ ..++.+.||..-..|.--=--..++.+.+..||.++|-.. ...+.+=|+--++||++.
T Consensus 633 KL~~E~~GIL~WaieG~~~~~~~GL~~P~~V~~at~eY~~e~D~v~~Fl~e~c~~~~~~~~~~~~LY~~Y~~wc~~~ 709 (759)
T PRK07078 633 KLLAERDGILAWAVEGCLDWQRNGLDPPQSVVEATEEYFEAEDALGQWIEERCERGANAKELTAELFNDWKEWAERA 709 (759)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhCChHHHHHHHhceeCCCCceeHHHHHHHHHHHHHHc
Confidence 3345677764433 2455668877654443332233457899999999998432 235788999999999864
No 189
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=22.57 E-value=1.4e+02 Score=25.95 Aligned_cols=63 Identities=16% Similarity=0.154 Sum_probs=35.7
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHHH
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCLK 82 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl~ 82 (89)
||.--+. ..- .+.++|||||.-.+.|=+ +|=.+++=..+=.+=|....|.+.+-|..-++.|+
T Consensus 505 hRk~R~k-~~s-~L~~I~GiG~kr~~~LL~-----------~Fgs~~~I~~As~eeL~~v~gi~~~~A~~I~~~l~ 567 (574)
T PRK14670 505 NKKLREN-IKL-NYTKIKGIGEKKAKKILK-----------SLGTYKDILLLNEDEIAEKMKINIKMAKKIKKFAE 567 (574)
T ss_pred HHHhhcc-ccc-ccccCCCCCHHHHHHHHH-----------HhCCHHHHHhCCHHHHHhCCCCCHHHHHHHHHHHH
Confidence 4444444 333 778999999998777544 33333331111112234556777777777666654
No 190
>PRK12823 benD 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase; Provisional
Probab=22.57 E-value=49 Score=23.39 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|.+
T Consensus 18 ~gIG~~la~~l~~~G~~ 34 (260)
T PRK12823 18 QGIGRGVALRAAAEGAR 34 (260)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 58999999999999964
No 191
>TIGR00194 uvrC excinuclease ABC, C subunit. This family consists of the DNA repair enzyme UvrC, an ABC excinuclease subunit which interacts with the UvrA/UvrB complex to excise UV-damaged nucleotide segments.
Probab=22.56 E-value=37 Score=29.36 Aligned_cols=30 Identities=20% Similarity=0.317 Sum_probs=20.3
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHh
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~ 36 (89)
||.--+.-|-.-.+.+||||||.-.+.|-.
T Consensus 530 hR~~r~k~~~~S~Ld~I~GIG~kr~~~LL~ 559 (574)
T TIGR00194 530 HRKKRLKASLQSPLLKIPGVGEKRVQKLLK 559 (574)
T ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHH
Confidence 444444444444677899999998888754
No 192
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=22.45 E-value=44 Score=28.83 Aligned_cols=64 Identities=17% Similarity=0.223 Sum_probs=36.9
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHHhhccchhhHhHHHHHH
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKETCQANAKQSGDCYNCL 81 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~~~gAn~kqa~dc~~cl 81 (89)
||.--+.-+-.-.++.+||||+...++|-+. |.....+. .-..+. |...-|.+.+-|..-++-+
T Consensus 532 hR~~R~k~~~~s~L~~IpGIG~k~~k~Ll~~-FgS~~~i~------~As~ee----L~~v~Gig~~~A~~I~~~l 595 (598)
T PRK00558 532 HRKKRSKARLTSALDDIPGIGPKRRKALLKH-FGSLKAIK------EASVEE----LAKVPGISKKLAEAIYEAL 595 (598)
T ss_pred hccccccchhhhhHhhCCCcCHHHHHHHHHH-cCCHHHHH------hCCHHH----HhhcCCcCHHHHHHHHHHh
Confidence 4444444444456789999999999998873 22222221 112222 3455577777777655443
No 193
>cd01522 RHOD_1 Member of the Rhodanese Homology Domain superfamily, subgroup 1. This CD includes the putative rhodanese-related sulfurtransferases of several uncharacterized proteins.
Probab=22.43 E-value=32 Score=22.48 Aligned_cols=23 Identities=26% Similarity=0.405 Sum_probs=19.2
Q ss_pred cHHHHHhHHhcCCchhhHhhhhh
Q psy6806 27 GDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 27 G~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
....+..|.+.||+++|.++|=|
T Consensus 77 s~~aa~~L~~~G~~~v~~l~gG~ 99 (117)
T cd01522 77 SIAAAEAAAQAGFTNVYNVLEGF 99 (117)
T ss_pred HHHHHHHHHHCCCCeEEECcCce
Confidence 45677889999999999988866
No 194
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=22.13 E-value=1.2e+02 Score=26.43 Aligned_cols=59 Identities=22% Similarity=0.283 Sum_probs=35.7
Q ss_pred HHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHH-HHHHHHHHhhccchhhHhHHH
Q psy6806 7 HQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEE-LFVDWMKETCQANAKQSGDCY 78 (89)
Q Consensus 7 hr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~-~F~~WLk~~~gAn~kqa~dc~ 78 (89)
||.=-+.-|-.-++..+|||||.-.++| |-.|--++.=+. ..+++ ... |.|.+.|..-|
T Consensus 519 hR~~R~k~~~~s~Ld~I~GiG~~r~~~L-----------L~~Fgs~~~i~~As~eel-~~v-gi~~~~a~~i~ 578 (581)
T COG0322 519 HRKKRSKAMLQSSLDDIPGIGPKRRKAL-----------LKHFGSLKGIKSASVEEL-AKV-GISKKLAEKIY 578 (581)
T ss_pred HHHHhhhhhhcCccccCCCcCHHHHHHH-----------HHHhhCHHHHHhcCHHHH-HHc-CCCHHHHHHHH
Confidence 4554555555667789999999987764 555555544222 23333 334 77777766544
No 195
>PRK06114 short chain dehydrogenase; Provisional
Probab=22.10 E-value=47 Score=23.61 Aligned_cols=17 Identities=29% Similarity=0.575 Sum_probs=15.0
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|++
T Consensus 18 ~gIG~~ia~~l~~~G~~ 34 (254)
T PRK06114 18 SGIGQRIAIGLAQAGAD 34 (254)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 48999999999999964
No 196
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=22.08 E-value=1.2e+02 Score=18.53 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=15.1
Q ss_pred HHHHHHHHHHhhccchhhHhHHHHHHHHHHHh
Q psy6806 56 EELFVDWMKETCQANAKQSGDCYNCLKDWCGE 87 (89)
Q Consensus 56 ~~~F~~WLk~~~gAn~kqa~dc~~cl~eWc~~ 87 (89)
=+.|..||+ ..|. ..-..--..=|++|||.
T Consensus 27 L~el~~~L~-~~g~-~~~~~~~~~~l~~~lD~ 56 (64)
T PF09494_consen 27 LEELHAWLK-ASGI-GFDRKVDPSKLKEWLDS 56 (64)
T ss_pred HHHHHHHHH-HcCC-CccceeCHHHHHHHHHH
Confidence 367888888 1111 00001122347888875
No 197
>PF14098 SSPI: Small, acid-soluble spore protein I
Probab=22.00 E-value=37 Score=21.90 Aligned_cols=27 Identities=15% Similarity=0.338 Sum_probs=22.9
Q ss_pred cchHHHHhhhhCCCCCCCcccccCccH
Q psy6806 2 STSQKHQNFVSEPMGEKPVTELAGVGD 28 (89)
Q Consensus 2 ~tS~Khr~Fv~ePMg~K~Vt~l~GIG~ 28 (89)
++.+-.+++|.+.+..++=..|||.|-
T Consensus 14 ~s~~el~~~I~daI~sgEE~~LPGLGV 40 (65)
T PF14098_consen 14 SSKEELKDTIEDAIQSGEEKALPGLGV 40 (65)
T ss_pred CCHHHHHHHHHHHHhccchhcCCchHH
Confidence 356778999999999889999999984
No 198
>PRK12748 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=21.88 E-value=56 Score=23.18 Aligned_cols=16 Identities=38% Similarity=0.810 Sum_probs=14.6
Q ss_pred cCccHHHHHhHHhcCC
Q psy6806 24 AGVGDVLGKRLESKGF 39 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf 39 (89)
.|||..++++|.++|+
T Consensus 17 ~giG~~la~~l~~~G~ 32 (256)
T PRK12748 17 NGIGAAVCRRLAAKGI 32 (256)
T ss_pred CCHHHHHHHHHHHcCC
Confidence 4799999999999996
No 199
>PF12728 HTH_17: Helix-turn-helix domain
Probab=21.87 E-value=36 Score=19.05 Aligned_cols=45 Identities=18% Similarity=0.288 Sum_probs=32.7
Q ss_pred CCcccccCccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHH
Q psy6806 18 KPVTELAGVGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKE 65 (89)
Q Consensus 18 K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~ 65 (89)
+++.++=||++....++...|-=+++. .|.- ..-+.+.+.+|+..
T Consensus 5 ~e~a~~l~is~~tv~~~~~~g~i~~~~-~g~~--~~~~~~~l~~~~~~ 49 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIRQGKIPPFK-IGRK--WRIPKSDLDRWLER 49 (51)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCCCeEE-eCCE--EEEeHHHHHHHHHh
Confidence 467788899999999999887666665 5542 22267788888864
No 200
>PHA00439 exonuclease
Probab=21.74 E-value=57 Score=26.08 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=15.7
Q ss_pred CCCC--CcccccCccHHHHHhHHhc
Q psy6806 15 MGEK--PVTELAGVGDVLGKRLESK 37 (89)
Q Consensus 15 Mg~K--~Vt~l~GIG~~lg~~L~~~ 37 (89)
|||. .+--||||| ..+.+|-++
T Consensus 183 ~GDsSDNIPGVpGIG-KTA~kLL~~ 206 (286)
T PHA00439 183 KGDSTDGYSGIPGWG-DTAEAFLEN 206 (286)
T ss_pred ccccccCCCCCCCcC-HHHHHHHhC
Confidence 6663 356678899 888887776
No 201
>cd01444 GlpE_ST GlpE sulfurtransferase (ST) and homologs are members of the Rhodanese Homology Domain superfamily. Unlike other rhodanese sulfurtransferases, GlpE is a single domain protein but indications are that it functions as a dimer. The active site contains a catalytically active cysteine.
Probab=21.72 E-value=40 Score=20.36 Aligned_cols=22 Identities=27% Similarity=0.492 Sum_probs=17.2
Q ss_pred HHHHHhHHhcCCchhhHhhhhh
Q psy6806 28 DVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 28 ~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
...+..|.+.||++.|.|-|-+
T Consensus 70 ~~a~~~l~~~G~~~v~~l~gG~ 91 (96)
T cd01444 70 AQLAQALREAGFTDVRSLAGGF 91 (96)
T ss_pred HHHHHHHHHcCCceEEEcCCCH
Confidence 4567788999999998777644
No 202
>PTZ00217 flap endonuclease-1; Provisional
Probab=21.52 E-value=72 Score=26.17 Aligned_cols=21 Identities=19% Similarity=0.294 Sum_probs=16.0
Q ss_pred CCCCcccccCccHHHHHhHHh
Q psy6806 16 GEKPVTELAGVGDVLGKRLES 36 (89)
Q Consensus 16 g~K~Vt~l~GIG~~lg~~L~~ 36 (89)
|-.-.--||||||+.|-+|-.
T Consensus 233 G~Dy~pgi~GIG~ktA~~Li~ 253 (393)
T PTZ00217 233 GCDYCDTIKGIGPKTAYKLIK 253 (393)
T ss_pred CCCCCCCCCCccHHHHHHHHH
Confidence 333556799999999888875
No 203
>KOG1811|consensus
Probab=21.44 E-value=49 Score=30.62 Aligned_cols=43 Identities=28% Similarity=0.359 Sum_probs=28.2
Q ss_pred chHHHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCchhhHhhhhhh
Q psy6806 3 TSQKHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDKAYVVLGQFL 50 (89)
Q Consensus 3 tS~Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~kAy~lLGqfL 50 (89)
+-+||--|=.--|-+ ++..- -.+|.+|.|+|||-||-||-.|-
T Consensus 950 a~~khsLFGN~~dke-~s~~k----cei~eklVE~~FdiAf~Vi~dFk 992 (1141)
T KOG1811|consen 950 ALPKHSLFGNNHDKE-DSACK----CEIGEKLVEDGFDIAFRVIQDFK 992 (1141)
T ss_pred CCCcccccCCCccch-hhhhe----eehhhhhhhcCcchHHHHHHHhc
Confidence 344566665555555 22222 24667889999999999998883
No 204
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=21.36 E-value=1.5e+02 Score=15.85 Aligned_cols=37 Identities=22% Similarity=0.340 Sum_probs=19.9
Q ss_pred ccHHHHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHH
Q psy6806 26 VGDVLGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWM 63 (89)
Q Consensus 26 IG~~lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WL 63 (89)
|-+.....|.+-||++.-.. =-...-+.|-+.=.+||
T Consensus 1 i~~~~v~~L~~mGf~~~~~~-~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 1 IDEEKVQQLMEMGFSREQAR-EALRACNGNVERAVDWL 37 (37)
T ss_dssp SHHHHHHHHHHHTS-HHHHH-HHHHHTTTSHHHHHHHH
T ss_pred CCHHHHHHHHHcCCCHHHHH-HHHHHcCCCHHHHHHhC
Confidence 44667788999999987332 22222233444444443
No 205
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=21.22 E-value=73 Score=27.88 Aligned_cols=31 Identities=23% Similarity=0.447 Sum_probs=22.9
Q ss_pred HHHhhhhCCCCCCCcccccCccHHHHHhHHhcCCch
Q psy6806 6 KHQNFVSEPMGEKPVTELAGVGDVLGKRLESKGFDK 41 (89)
Q Consensus 6 Khr~Fv~ePMg~K~Vt~l~GIG~~lg~~L~~~Gf~k 41 (89)
+..-|+| |+.-.++|+||....+|-++|+-+
T Consensus 425 ~l~hf~s-----r~al~I~GLG~k~i~~L~~~g~I~ 455 (652)
T TIGR00575 425 RIKHFAS-----RNAMDIEGLGDKVIEQLFEKKLVR 455 (652)
T ss_pred HhHHhhc-----CCccCCCCcCHHHHHHHHHcCCcC
Confidence 3445555 455679999999999999988643
No 206
>PRK08340 glucose-1-dehydrogenase; Provisional
Probab=21.17 E-value=49 Score=23.62 Aligned_cols=17 Identities=29% Similarity=0.450 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|+.
T Consensus 10 ~gIG~aia~~l~~~G~~ 26 (259)
T PRK08340 10 RGIGFNVARELLKKGAR 26 (259)
T ss_pred cHHHHHHHHHHHHcCCE
Confidence 68999999999999964
No 207
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=21.03 E-value=51 Score=17.55 Aligned_cols=11 Identities=36% Similarity=1.150 Sum_probs=9.3
Q ss_pred HHHHHHHHHHH
Q psy6806 76 DCYNCLKDWCG 86 (89)
Q Consensus 76 dc~~cl~eWc~ 86 (89)
-|+.||.+|.+
T Consensus 21 fC~~C~~~~~~ 31 (41)
T PF00097_consen 21 FCRDCLRKWLE 31 (41)
T ss_dssp EEHHHHHHHHH
T ss_pred chHHHHHHHHH
Confidence 58899999976
No 208
>PRK07063 short chain dehydrogenase; Provisional
Probab=21.01 E-value=53 Score=23.29 Aligned_cols=17 Identities=18% Similarity=0.556 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|++
T Consensus 17 ~gIG~~~a~~l~~~G~~ 33 (260)
T PRK07063 17 QGIGAAIARAFAREGAA 33 (260)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 58999999999999974
No 209
>KOG1205|consensus
Probab=20.98 E-value=48 Score=26.30 Aligned_cols=19 Identities=26% Similarity=0.571 Sum_probs=16.2
Q ss_pred cccCccHHHHHhHHhcCCc
Q psy6806 22 ELAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 22 ~l~GIG~~lg~~L~~~Gf~ 40 (89)
.=.|||+.++..|...|-.
T Consensus 20 ASsGIG~~lA~~la~~G~~ 38 (282)
T KOG1205|consen 20 ASSGIGEALAYELAKRGAK 38 (282)
T ss_pred CCcHHHHHHHHHHHhCCCc
Confidence 3479999999999999863
No 210
>PRK06463 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=20.97 E-value=55 Score=23.21 Aligned_cols=17 Identities=18% Similarity=0.479 Sum_probs=15.5
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|.+
T Consensus 17 ~gIG~~~a~~l~~~G~~ 33 (255)
T PRK06463 17 RGIGRAIAEAFLREGAK 33 (255)
T ss_pred ChHHHHHHHHHHHCCCE
Confidence 68999999999999974
No 211
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=20.96 E-value=34 Score=26.22 Aligned_cols=24 Identities=25% Similarity=0.338 Sum_probs=16.2
Q ss_pred CCCcccccCccHHHHHhHHhcCCc
Q psy6806 17 EKPVTELAGVGDVLGKRLESKGFD 40 (89)
Q Consensus 17 ~K~Vt~l~GIG~~lg~~L~~~Gf~ 40 (89)
-+.+..|||||+..|.---..+|.
T Consensus 108 ~~eL~~LPGVGrKTAnvVL~~a~g 131 (211)
T COG0177 108 REELLSLPGVGRKTANVVLSFAFG 131 (211)
T ss_pred HHHHHhCCCcchHHHHHHHHhhcC
Confidence 345889999999876554444343
No 212
>PRK07023 short chain dehydrogenase; Provisional
Probab=20.82 E-value=58 Score=22.83 Aligned_cols=17 Identities=29% Similarity=0.579 Sum_probs=15.1
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|+.
T Consensus 11 ggiG~~ia~~l~~~G~~ 27 (243)
T PRK07023 11 RGLGAALAEQLLQPGIA 27 (243)
T ss_pred cchHHHHHHHHHhCCCE
Confidence 48999999999999965
No 213
>KOG1208|consensus
Probab=20.81 E-value=35 Score=27.01 Aligned_cols=20 Identities=40% Similarity=0.592 Sum_probs=16.8
Q ss_pred cCccHHHHHhHHhcCCchhhHhh
Q psy6806 24 AGVGDVLGKRLESKGFDKAYVVL 46 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~kAy~lL 46 (89)
-|||-..++.|++.| |.+++
T Consensus 45 sGIG~eta~~La~~G---a~Vv~ 64 (314)
T KOG1208|consen 45 SGIGFETARELALRG---AHVVL 64 (314)
T ss_pred CchHHHHHHHHHhCC---CEEEE
Confidence 399999999999999 55554
No 214
>PF05152 DUF705: Protein of unknown function (DUF705); InterPro: IPR007827 This family contains uncharacterised baculoviral proteins.
Probab=20.66 E-value=54 Score=26.71 Aligned_cols=29 Identities=28% Similarity=0.452 Sum_probs=18.8
Q ss_pred HHHHHHHHHhhcc---------chhhHhHHHHHHHHHHHh
Q psy6806 57 ELFVDWMKETCQA---------NAKQSGDCYNCLKDWCGE 87 (89)
Q Consensus 57 ~~F~~WLk~~~gA---------n~kqa~dc~~cl~eWc~~ 87 (89)
..|..-||.+... +.+.+ =|+||+||+-.
T Consensus 67 ~diR~~lK~~fk~s~lGh~fvl~~~~~--~y~~L~EW~v~ 104 (297)
T PF05152_consen 67 RDIRKNLKTAFKTSYLGHVFVLNEKPP--MYNFLKEWYVQ 104 (297)
T ss_pred HHHHHHHHHHhcccccCcEEEecCCcc--HHHHHHHHhcC
Confidence 4566666665543 33443 59999999854
No 215
>PRK08642 fabG 3-ketoacyl-(acyl-carrier-protein) reductase; Provisional
Probab=20.65 E-value=58 Score=22.71 Aligned_cols=17 Identities=18% Similarity=0.522 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|.+
T Consensus 15 ~gIG~~la~~l~~~G~~ 31 (253)
T PRK08642 15 RGLGAAIARAFAREGAR 31 (253)
T ss_pred CcHHHHHHHHHHHCCCe
Confidence 68999999999999964
No 216
>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=20.59 E-value=63 Score=23.24 Aligned_cols=17 Identities=18% Similarity=0.511 Sum_probs=15.3
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|..
T Consensus 11 ~gIG~~~a~~l~~~G~~ 27 (267)
T TIGR02685 11 KRIGSSIAVALHQEGYR 27 (267)
T ss_pred CcHHHHHHHHHHhCCCe
Confidence 59999999999999864
No 217
>PF05186 Dpy-30: Dpy-30 motif; InterPro: IPR007858 This motif is about 40 residues long and is probably formed of two alpha-helices. It is found in the Dpy-30 proteins, hence the motifs name. Dpy-30 from Caenorhabditis elegans is an essential component of dosage compensation machinery and loss of dpy-30 activity results in XX-specific lethality; in XO animals, Dpy-30 is required for developmental processes other than dosage compensation []. In yeast, the homologue of DPY-30, Saf19p, functions as part of the Set1 complex that is necessary for the methylation of histone H3 at lysine residue 4; Set1 is a key part of epigenetic developmental control []. There is also a human homologue of Dpy-30 []. This Dpy-30 region may be a dimerisation motif analogous that found in the cAMP-dependent protein kinase regulator, type II PKA, R subunit IPR003117 from INTERPRO.; PDB: 3G36_D.
Probab=20.56 E-value=1.2e+02 Score=17.48 Aligned_cols=28 Identities=29% Similarity=0.420 Sum_probs=16.1
Q ss_pred ccHHHHHhHHh---cCCchhhHhhhhhhhhh
Q psy6806 26 VGDVLGKRLES---KGFDKAYVVLGQFLLLK 53 (89)
Q Consensus 26 IG~~lg~~L~~---~Gf~kAy~lLGqfL~l~ 53 (89)
|+++|.+-|++ .-=+.---.||+||+.+
T Consensus 10 v~p~L~~gL~~l~~~rP~DPi~~La~~Ll~~ 40 (42)
T PF05186_consen 10 VGPVLTEGLAELAKERPEDPIEFLAEYLLKH 40 (42)
T ss_dssp THHHHHHHHHHHHHH--SSHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHCCCChHHHHHHHHHHh
Confidence 56677666665 11133455678887654
No 218
>PF02764 Diphtheria_T: Diphtheria toxin, T domain; InterPro: IPR022405 Diphtheria toxin (2.4.2.36 from EC) is a 58 kDa protein secreted by lysogenic strains of Corynebacterium diphtheriae. The toxin causes the disease diphtheria in humans by gaining entry into the cell cytoplasm and inhibiting protein synthesis []. The mechanism of inhibition involves transfer of the ADP-ribose group of NAD to elongation factor-2 (EF-2), rendering EF-2 inactive. The catalysed reaction is as follows: NAD+ + peptide diphthamide = nicotinamide + peptide N-(ADP-D-ribosyl)diphthamide The crystal structure of the diphtheria toxin homodimer has been determined to 2.5A resolution []. The structure reveals a Y-shaped molecule of 3 domains, a catalytic domain (fragment A), whose fold is of the alpha + beta type; a transmembrane (TM) domain, which consists of 9 alpha-helices, 2 pairs of which may participate in pH-triggered membrane insertion and translocation; and a receptor-binding domain, which forms a flattened beta-barrel with a jelly-roll-like topology []. The TM- and receptor binding-domains together constitute fragment B. This entry represents the translocation domain (also known as the T domain) found as the central domain in the Diphtheria toxin protein. The T domain has a multi-helical globin-like fold with two additional helices at N-termini, but which has no counterpart to the first globin helix. This domain is thought to unfold in the membrane []. pH-induced conformational change in the T domain triggers insertion into the endosomal membrane and facilitates the transfer of the catalytic domain into the cytoplasm [, ].; PDB: 1MDT_B 1SGK_A 1F0L_B 1DDT_A 1TOX_B 4AE0_A 1XDT_T 4AE1_A.
Probab=20.35 E-value=32 Score=25.86 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=8.7
Q ss_pred ccccCccHHHHHh
Q psy6806 21 TELAGVGDVLGKR 33 (89)
Q Consensus 21 t~l~GIG~~lg~~ 33 (89)
.=|||||.++|..
T Consensus 106 sivPGiG~~mGiA 118 (180)
T PF02764_consen 106 SIVPGIGSVMGIA 118 (180)
T ss_dssp TT-S-HHHHHTEE
T ss_pred Hhcccchhhhhhc
Confidence 3489999999865
No 219
>PRK06523 short chain dehydrogenase; Provisional
Probab=20.35 E-value=64 Score=22.81 Aligned_cols=17 Identities=29% Similarity=0.401 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|++
T Consensus 19 ~gIG~~ia~~l~~~G~~ 35 (260)
T PRK06523 19 KGIGAATVARLLEAGAR 35 (260)
T ss_pred CchhHHHHHHHHHCCCE
Confidence 48999999999999974
No 220
>PRK07523 gluconate 5-dehydrogenase; Provisional
Probab=20.29 E-value=55 Score=23.17 Aligned_cols=17 Identities=29% Similarity=0.567 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|+.
T Consensus 20 g~iG~~ia~~l~~~G~~ 36 (255)
T PRK07523 20 QGIGYALAEGLAQAGAE 36 (255)
T ss_pred chHHHHHHHHHHHcCCE
Confidence 58999999999999974
No 221
>cd04197 eIF-2B_epsilon_N The N-terminal domain of epsilon subunit of the eIF-2B is a subfamily of glycosyltransferase 2. N-terminal domain of epsilon subunit of the eukaryotic translation initiation factor 2B (eIF-2B): eIF-2B is a guanine nucleotide-exchange factor which mediates the exchange of GDP (bound to initiation factor eIF2) for GTP, generating active eIF2.GTP complex. EIF2B is a complex multimeric protein consisting of five subunits named alpha, beta, gamma, delta and epsilon. Subunit epsilon shares sequence similarity with gamma subunit, and with a family of bifunctional nucleotide-binding enzymes such as ADP-glucose pyrophosphorylase, suggesting that epsilon subunit may play roles in nucleotide binding activity. In yeast, eIF2B gamma enhances the activity of eIF2B-epsilon leading to the idea that these subunits form the catalytic subcomplex.
Probab=20.28 E-value=42 Score=23.86 Aligned_cols=30 Identities=10% Similarity=0.241 Sum_probs=21.4
Q ss_pred HHHhHHhcCCchhhHhhhhhhhhhcCHHHHHHHHHH
Q psy6806 30 LGKRLESKGFDKAYVVLGQFLLLKQNEELFVDWMKE 65 (89)
Q Consensus 30 lg~~L~~~Gf~kAy~lLGqfL~l~k~~~~F~~WLk~ 65 (89)
.-..|.+.|+++.+++.+ | +.+.+.+++.+
T Consensus 37 ~l~~l~~~Gi~~I~iv~~-~-----~~~~i~~~l~~ 66 (217)
T cd04197 37 TLEFLALNGVEEVFVFCC-S-----HSDQIKEYIEK 66 (217)
T ss_pred HHHHHHHCCCCeEEEEeC-C-----CHHHHHHHHhh
Confidence 345667799999888776 3 44667777765
No 222
>PRK07478 short chain dehydrogenase; Provisional
Probab=20.24 E-value=58 Score=23.01 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=15.2
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
.|||..++++|.++|..
T Consensus 16 ~giG~~ia~~l~~~G~~ 32 (254)
T PRK07478 16 SGIGRAAAKLFAREGAK 32 (254)
T ss_pred ChHHHHHHHHHHHCCCE
Confidence 58999999999999973
No 223
>PRK08993 2-deoxy-D-gluconate 3-dehydrogenase; Validated
Probab=20.18 E-value=56 Score=23.30 Aligned_cols=17 Identities=29% Similarity=0.544 Sum_probs=15.1
Q ss_pred cCccHHHHHhHHhcCCc
Q psy6806 24 AGVGDVLGKRLESKGFD 40 (89)
Q Consensus 24 ~GIG~~lg~~L~~~Gf~ 40 (89)
-|||..++++|.++|.+
T Consensus 20 ~gIG~a~a~~l~~~G~~ 36 (253)
T PRK08993 20 TGLGQGMALGLAEAGCD 36 (253)
T ss_pred chHHHHHHHHHHHCCCE
Confidence 48999999999999965
No 224
>TIGR02114 coaB_strep phosphopantothenate--cysteine ligase, streptococcal. In most bacteria, a single bifunctional protein catalyses phosphopantothenoylcysteine decarboxylase and phosphopantothenate--cysteine ligase activities, sequential steps in coenzyme A biosynthesis (see TIGR00521). These activities reside in separate proteins encoded by tandem genes in some bacterial lineages. This model describes proteins from the genera Streptococcus and Enterococcus homologous to the C-terminal region of TIGR00521, corresponding to phosphopantothenate--cysteine ligase activity.
Probab=20.15 E-value=51 Score=24.51 Aligned_cols=27 Identities=22% Similarity=0.529 Sum_probs=20.1
Q ss_pred CCCCCCCccccc-----CccHHHHHhHHhcCCch
Q psy6806 13 EPMGEKPVTELA-----GVGDVLGKRLESKGFDK 41 (89)
Q Consensus 13 ePMg~K~Vt~l~-----GIG~~lg~~L~~~Gf~k 41 (89)
||+. +|+.+- |||..++++|.++|.+=
T Consensus 11 e~iD--~VR~itN~SSGgIG~AIA~~la~~Ga~V 42 (227)
T TIGR02114 11 EPID--SVRSITNHSTGHLGKIITETFLSAGHEV 42 (227)
T ss_pred CCCC--CceeecCCcccHHHHHHHHHHHHCCCEE
Confidence 5554 455442 89999999999999754
No 225
>cd01527 RHOD_YgaP Member of the Rhodanese Homology Domain superfamily. This CD includes Escherichia coli YgaP, and similar uncharacterized putative rhodanese-related sulfurtransferases.
Probab=20.08 E-value=40 Score=20.78 Aligned_cols=23 Identities=26% Similarity=0.354 Sum_probs=18.1
Q ss_pred cHHHHHhHHhcCCchhhHhhhhh
Q psy6806 27 GDVLGKRLESKGFDKAYVVLGQF 49 (89)
Q Consensus 27 G~~lg~~L~~~Gf~kAy~lLGqf 49 (89)
....+..|.+.||+++|.+-|-+
T Consensus 67 s~~~~~~L~~~g~~~v~~l~gG~ 89 (99)
T cd01527 67 TQQNAERLAAISAGEAYVLEGGL 89 (99)
T ss_pred HHHHHHHHHHcCCccEEEeeCCH
Confidence 35677789999999998887744
Done!