Query psy14489
Match_columns 284
No_of_seqs 142 out of 1188
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 21:05:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14489.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14489hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14976 5'-3' exonuclease; Pr 100.0 1.6E-76 3.5E-81 541.1 29.7 272 1-277 1-281 (281)
2 PRK09482 flap endonuclease-lik 100.0 5.2E-75 1.1E-79 522.1 25.7 250 1-259 1-254 (256)
3 smart00475 53EXOc 5'-3' exonuc 100.0 1.8E-73 3.9E-78 515.5 26.7 250 4-258 2-257 (259)
4 TIGR00593 pola DNA polymerase 100.0 6E-71 1.3E-75 567.8 27.5 274 5-283 1-282 (887)
5 cd00008 53EXOc 5'-3' exonuclea 100.0 3.8E-68 8.2E-73 476.8 26.9 237 3-240 1-240 (240)
6 PRK05755 DNA polymerase I; Pro 100.0 2.9E-67 6.4E-72 544.6 29.8 276 1-282 1-282 (880)
7 COG0258 Exo 5'-3' exonuclease 100.0 5.6E-60 1.2E-64 438.6 23.8 275 4-283 12-297 (310)
8 PHA00439 exonuclease 100.0 6.6E-56 1.4E-60 401.5 21.2 197 3-212 6-219 (286)
9 PHA02567 rnh RnaseH; Provision 100.0 2.5E-49 5.4E-54 360.1 18.9 260 3-283 14-301 (304)
10 PTZ00217 flap endonuclease-1; 100.0 3.3E-46 7.1E-51 355.1 21.5 253 3-277 28-319 (393)
11 PF02739 5_3_exonuc_N: 5'-3' e 100.0 6.3E-47 1.4E-51 322.5 13.6 161 3-164 1-169 (169)
12 TIGR03674 fen_arch flap struct 100.0 3.8E-45 8.3E-50 342.5 20.1 247 2-278 20-313 (338)
13 cd00128 XPG Xeroderma pigmento 100.0 1.7E-40 3.8E-45 308.8 19.4 252 3-277 24-306 (316)
14 PRK03980 flap endonuclease-1; 100.0 2E-40 4.2E-45 304.5 19.4 223 26-277 2-265 (292)
15 PF01367 5_3_exonuc: 5'-3' exo 100.0 5.3E-32 1.2E-36 211.0 -3.6 99 166-268 1-100 (101)
16 KOG2519|consensus 99.9 3.8E-25 8.2E-30 208.8 19.2 253 4-277 29-315 (449)
17 KOG2518|consensus 99.9 1.4E-21 3E-26 186.8 15.4 195 4-211 25-253 (556)
18 TIGR00600 rad2 DNA excision re 99.9 4.1E-21 8.8E-26 198.8 17.4 178 88-277 774-974 (1034)
19 cd00080 HhH2_motif Helix-hairp 99.8 1.1E-21 2.4E-26 145.5 5.4 73 163-237 2-74 (75)
20 smart00279 HhH2 Helix-hairpin- 99.6 1.1E-16 2.3E-21 101.8 3.5 36 168-203 1-36 (36)
21 KOG2520|consensus 99.5 8.5E-14 1.8E-18 140.9 14.1 128 72-208 453-585 (815)
22 PF00867 XPG_I: XPG I-region; 99.0 5.3E-10 1.2E-14 86.3 6.3 79 97-183 2-94 (94)
23 PF05991 NYN_YacP: YacP-like N 98.3 1.5E-06 3.3E-11 73.9 5.6 123 6-163 1-126 (166)
24 smart00484 XPGI Xeroderma pigm 98.1 1.7E-05 3.6E-10 58.4 7.3 64 97-166 2-73 (73)
25 smart00485 XPGN Xeroderma pigm 97.9 1.3E-05 2.9E-10 62.1 4.4 69 3-74 24-93 (99)
26 PF00752 XPG_N: XPG N-terminal 97.8 2.1E-05 4.6E-10 61.0 4.5 60 3-65 26-86 (101)
27 PF12813 XPG_I_2: XPG domain c 97.6 0.00036 7.8E-09 63.1 8.6 79 89-176 7-107 (246)
28 COG3688 Predicted RNA-binding 97.3 0.0012 2.7E-08 55.2 8.4 102 1-136 1-109 (173)
29 TIGR00600 rad2 DNA excision re 97.1 0.00041 8.8E-09 73.5 4.1 74 3-79 24-97 (1034)
30 PF12826 HHH_2: Helix-hairpin- 97.1 0.00033 7.1E-09 50.1 2.0 26 187-212 7-32 (64)
31 PF09293 RNaseH_C: T4 RNase H, 96.8 0.00019 4E-09 57.5 -1.2 103 167-283 2-119 (122)
32 TIGR00084 ruvA Holliday juncti 95.6 0.039 8.5E-07 48.0 6.9 70 134-214 31-102 (191)
33 PRK00116 ruvA Holliday junctio 95.3 0.044 9.6E-07 47.7 6.2 25 187-211 77-104 (192)
34 PF11977 RNase_Zc3h12a: Zc3h12 95.0 0.17 3.7E-06 42.3 8.8 101 3-136 2-110 (155)
35 PF14520 HHH_5: Helix-hairpin- 95.0 0.026 5.7E-07 39.5 3.1 27 186-212 8-35 (60)
36 cd06167 LabA_like LabA_like pr 94.9 0.2 4.3E-06 40.9 8.6 54 90-143 56-117 (149)
37 PF04599 Pox_G5: Poxvirus G5 p 94.3 0.2 4.4E-06 48.3 8.2 115 92-213 149-272 (425)
38 PHA03065 Hypothetical protein; 94.1 0.2 4.4E-06 48.2 7.8 194 4-213 28-274 (438)
39 PRK14605 ruvA Holliday junctio 94.0 0.067 1.4E-06 46.7 4.1 69 134-213 31-102 (194)
40 PRK14602 ruvA Holliday junctio 93.7 0.073 1.6E-06 46.8 3.8 45 161-214 59-104 (203)
41 PRK14600 ruvA Holliday junctio 93.5 0.1 2.2E-06 45.2 4.3 48 158-214 55-103 (186)
42 PRK14601 ruvA Holliday junctio 93.5 0.082 1.8E-06 45.7 3.7 45 161-214 58-103 (183)
43 PF00633 HHH: Helix-hairpin-he 93.4 0.053 1.1E-06 32.9 1.6 18 184-201 12-29 (30)
44 PRK12766 50S ribosomal protein 93.3 0.092 2E-06 46.8 3.8 29 184-212 4-33 (232)
45 PRK14669 uvrC excinuclease ABC 93.3 0.055 1.2E-06 55.1 2.6 30 184-213 553-582 (624)
46 PRK14666 uvrC excinuclease ABC 93.1 0.091 2E-06 53.9 3.8 30 184-213 638-667 (694)
47 PRK14670 uvrC excinuclease ABC 93.1 0.087 1.9E-06 53.2 3.7 30 184-213 515-544 (574)
48 PF10391 DNA_pol_lambd_f: Fing 93.1 0.083 1.8E-06 36.2 2.4 26 186-211 5-31 (52)
49 TIGR00194 uvrC excinuclease AB 92.8 0.076 1.6E-06 53.7 2.8 47 163-212 524-570 (574)
50 PRK14667 uvrC excinuclease ABC 92.8 0.078 1.7E-06 53.5 2.9 48 163-213 497-544 (567)
51 PRK14604 ruvA Holliday junctio 92.6 0.13 2.7E-06 45.0 3.6 70 134-214 31-103 (195)
52 PRK14671 uvrC excinuclease ABC 91.9 0.11 2.4E-06 53.0 2.7 28 185-212 571-598 (621)
53 smart00278 HhH1 Helix-hairpin- 91.6 0.11 2.5E-06 30.1 1.4 18 185-202 3-20 (26)
54 PRK13901 ruvA Holliday junctio 91.3 0.28 6.1E-06 42.9 4.2 45 161-214 57-102 (196)
55 PRK14668 uvrC excinuclease ABC 91.1 0.14 3.1E-06 51.8 2.5 31 183-213 525-555 (577)
56 PRK14606 ruvA Holliday junctio 91.1 0.29 6.3E-06 42.5 4.1 45 161-214 58-103 (188)
57 PRK14603 ruvA Holliday junctio 90.9 0.31 6.6E-06 42.7 4.1 45 161-214 57-102 (197)
58 PRK00558 uvrC excinuclease ABC 90.6 0.18 3.9E-06 51.3 2.7 29 185-213 545-573 (598)
59 PRK14672 uvrC excinuclease ABC 90.2 0.22 4.8E-06 51.1 2.9 48 163-213 591-638 (691)
60 TIGR00575 dnlj DNA ligase, NAD 89.7 0.34 7.5E-06 49.8 3.9 43 186-228 501-550 (652)
61 TIGR00596 rad1 DNA repair prot 89.2 3.8 8.3E-05 43.3 11.1 137 38-212 646-786 (814)
62 PRK02515 psbU photosystem II c 88.9 0.41 8.8E-06 39.0 3.0 42 188-230 66-109 (132)
63 PRK14351 ligA NAD-dependent DN 88.1 0.54 1.2E-05 48.7 4.0 91 187-277 532-639 (689)
64 PRK07956 ligA NAD-dependent DN 87.1 0.6 1.3E-05 48.1 3.7 89 187-277 515-620 (665)
65 PF03159 XRN_N: XRN 5'-3' exon 85.5 1.6 3.5E-05 39.3 5.2 143 5-150 32-234 (237)
66 COG0322 UvrC Nuclease subunit 84.9 0.66 1.4E-05 47.0 2.6 48 163-213 513-560 (581)
67 COG1948 MUS81 ERCC4-type nucle 84.9 0.71 1.5E-05 41.9 2.6 27 187-213 186-212 (254)
68 PF02371 Transposase_20: Trans 84.2 0.67 1.5E-05 34.8 1.8 25 185-209 4-28 (87)
69 cd00141 NT_POLXc Nucleotidyltr 83.7 1.3 2.8E-05 41.3 3.9 27 186-213 88-116 (307)
70 COG0632 RuvA Holliday junction 83.1 2.8 6E-05 36.8 5.5 49 157-214 54-103 (201)
71 TIGR01259 comE comEA protein. 81.9 1.3 2.8E-05 35.5 2.7 24 186-209 71-100 (120)
72 PF01936 NYN: NYN domain; Int 81.1 3.3 7.1E-05 33.2 5.0 54 90-143 51-113 (146)
73 PF11798 IMS_HHH: IMS family H 80.4 1 2.2E-05 27.6 1.2 16 184-199 12-27 (32)
74 smart00483 POLXc DNA polymeras 79.1 1.5 3.2E-05 41.4 2.6 27 186-213 92-120 (334)
75 PRK13766 Hef nuclease; Provisi 78.7 1.5 3.3E-05 45.7 2.8 29 185-213 717-745 (773)
76 PRK14602 ruvA Holliday junctio 78.6 0.77 1.7E-05 40.3 0.4 30 176-205 102-131 (203)
77 PRK08609 hypothetical protein; 78.0 2.5 5.5E-05 42.8 4.0 28 187-214 92-121 (570)
78 PRK14601 ruvA Holliday junctio 77.8 0.79 1.7E-05 39.6 0.3 37 166-204 93-129 (183)
79 PF01927 Mut7-C: Mut7-C RNAse 77.6 4.8 0.0001 33.3 4.9 72 90-168 11-85 (147)
80 PRK14600 ruvA Holliday junctio 77.4 1.6 3.4E-05 37.9 2.1 36 166-204 93-128 (186)
81 PRK13901 ruvA Holliday junctio 75.9 0.93 2E-05 39.6 0.2 37 167-205 93-129 (196)
82 TIGR01448 recD_rel helicase, p 75.3 3.3 7.1E-05 43.2 4.0 38 168-213 77-116 (720)
83 TIGR00426 competence protein C 74.5 3.6 7.7E-05 29.3 3.0 22 188-209 22-49 (69)
84 TIGR00288 conserved hypothetic 73.5 6 0.00013 33.5 4.5 50 92-143 72-123 (160)
85 COG1555 ComEA DNA uptake prote 71.0 4.2 9.1E-05 33.9 3.0 23 187-209 101-129 (149)
86 PRK14604 ruvA Holliday junctio 70.4 1.6 3.4E-05 38.2 0.3 37 167-205 94-130 (195)
87 PF11731 Cdd1: Pathogenicity l 70.3 4 8.7E-05 31.4 2.5 24 186-209 15-39 (93)
88 COG0272 Lig NAD-dependent DNA 69.7 3 6.5E-05 42.8 2.1 91 186-276 514-623 (667)
89 PRK14606 ruvA Holliday junctio 68.7 1.8 3.9E-05 37.6 0.3 37 167-205 94-130 (188)
90 PRK13482 DNA integrity scannin 68.5 4 8.6E-05 38.9 2.6 27 187-213 291-317 (352)
91 PTZ00349 dehydrodolichyl dipho 67.4 19 0.00041 33.9 6.8 92 41-140 9-122 (322)
92 PF12826 HHH_2: Helix-hairpin- 66.3 1.3 2.8E-05 31.4 -0.9 35 174-208 26-60 (64)
93 PRK14603 ruvA Holliday junctio 65.8 2.7 5.8E-05 36.8 0.8 37 167-205 93-129 (197)
94 PF14520 HHH_5: Helix-hairpin- 64.2 5.2 0.00011 27.6 1.9 21 182-202 37-57 (60)
95 KOG2841|consensus 64.0 4.9 0.00011 36.1 2.1 28 186-213 198-225 (254)
96 PRK14350 ligA NAD-dependent DN 63.6 6.5 0.00014 40.7 3.2 26 186-211 505-531 (669)
97 PF14229 DUF4332: Domain of un 63.4 10 0.00022 30.4 3.7 52 189-241 1-56 (122)
98 cd01015 CSHase N-carbamoylsarc 62.2 18 0.0004 30.4 5.3 43 90-133 104-146 (179)
99 KOG2841|consensus 61.3 6.6 0.00014 35.3 2.4 13 189-201 233-245 (254)
100 TIGR00615 recR recombination p 61.1 7.3 0.00016 34.0 2.6 18 184-201 12-29 (195)
101 PRK00076 recR recombination pr 61.0 7.5 0.00016 34.0 2.7 17 185-201 13-29 (196)
102 PRK07956 ligA NAD-dependent DN 60.9 26 0.00056 36.4 7.0 26 186-211 448-475 (665)
103 PRK13844 recombination protein 60.0 8.1 0.00018 33.9 2.7 18 184-201 16-33 (200)
104 PRK00254 ski2-like helicase; P 58.9 8 0.00017 40.2 3.0 27 186-212 648-675 (720)
105 cd00431 cysteine_hydrolases Cy 58.8 21 0.00045 29.1 5.0 43 90-133 100-142 (161)
106 PRK11440 putative hydrolase; P 57.0 26 0.00056 29.7 5.4 43 90-133 111-153 (188)
107 PRK14605 ruvA Holliday junctio 56.3 6.9 0.00015 34.1 1.7 26 178-204 104-129 (194)
108 cd01012 YcaC_related YcaC rela 56.0 26 0.00056 28.8 5.1 43 90-133 78-120 (157)
109 COG4365 Uncharacterized protei 55.5 36 0.00079 33.2 6.4 138 53-212 224-403 (537)
110 TIGR03252 uncharacterized HhH- 55.5 5.6 0.00012 34.2 1.0 22 184-205 116-137 (177)
111 PF13052 DUF3913: Protein of u 55.2 6 0.00013 26.5 0.9 14 182-195 18-31 (57)
112 PF05889 SLA_LP_auto_ag: Solub 55.1 34 0.00073 33.1 6.2 88 40-144 142-231 (389)
113 TIGR00084 ruvA Holliday juncti 55.1 6.9 0.00015 34.0 1.5 24 178-202 103-126 (191)
114 COG0353 RecR Recombinational D 55.0 6.3 0.00014 34.4 1.2 18 183-200 12-29 (198)
115 KOG1602|consensus 54.7 28 0.0006 31.8 5.3 87 48-140 34-139 (271)
116 TIGR03614 RutB pyrimidine util 54.2 28 0.00061 30.7 5.3 43 90-133 141-183 (226)
117 COG1412 Uncharacterized protei 53.3 14 0.0003 30.4 2.9 41 98-144 75-115 (136)
118 COG1948 MUS81 ERCC4-type nucle 52.9 32 0.00069 31.4 5.4 122 80-212 118-243 (254)
119 PF14579 HHH_6: Helix-hairpin- 52.8 18 0.00039 27.2 3.3 30 185-214 29-63 (90)
120 COG0632 RuvA Holliday junction 52.3 8 0.00017 34.0 1.5 24 182-205 107-130 (201)
121 cd01013 isochorismatase Isocho 52.2 26 0.00055 30.4 4.6 43 90-133 132-174 (203)
122 TIGR02236 recomb_radA DNA repa 52.2 12 0.00026 34.5 2.7 28 185-212 1-29 (310)
123 TIGR00305 probable toxin-antit 51.4 15 0.00033 28.5 2.8 28 108-140 86-113 (114)
124 PF14716 HHH_8: Helix-hairpin- 50.3 11 0.00023 26.8 1.6 15 185-199 49-63 (68)
125 TIGR00575 dnlj DNA ligase, NAD 49.0 43 0.00093 34.7 6.3 26 186-211 435-462 (652)
126 PLN02621 nicotinamidase 47.9 39 0.00085 29.0 5.1 43 90-133 117-159 (197)
127 cd01014 nicotinamidase_related 47.2 39 0.00085 27.7 4.8 43 90-133 89-131 (155)
128 PRK14172 bifunctional 5,10-met 47.1 19 0.00042 33.2 3.1 73 125-202 181-272 (278)
129 PRK01229 N-glycosylase/DNA lya 45.9 13 0.00028 32.8 1.7 18 187-204 123-140 (208)
130 PRK14827 undecaprenyl pyrophos 45.1 50 0.0011 30.8 5.6 65 49-119 66-141 (296)
131 PF00857 Isochorismatase: Isoc 44.7 28 0.00061 28.7 3.6 43 90-133 102-144 (174)
132 COG1656 Uncharacterized conser 43.0 48 0.001 28.2 4.6 47 88-141 15-61 (165)
133 PRK14175 bifunctional 5,10-met 42.3 18 0.00039 33.5 2.2 75 125-202 181-273 (286)
134 KOG4700|consensus 41.4 54 0.0012 28.4 4.7 79 125-214 59-139 (207)
135 COG1936 Predicted nucleotide k 40.1 17 0.00038 31.3 1.6 21 185-205 5-25 (180)
136 COG1335 PncA Amidases related 39.8 70 0.0015 27.2 5.4 43 90-133 123-165 (205)
137 PRK13913 3-methyladenine DNA g 39.5 17 0.00037 32.3 1.5 20 185-204 123-143 (218)
138 PRK10702 endonuclease III; Pro 39.5 16 0.00035 32.2 1.4 17 185-201 111-127 (211)
139 cd00475 CIS_IPPS Cis (Z)-Isopr 39.5 20 0.00044 31.9 2.0 66 51-122 1-77 (221)
140 PRK00116 ruvA Holliday junctio 39.3 18 0.00039 31.3 1.6 23 183-205 108-130 (192)
141 cd00056 ENDO3c endonuclease II 39.2 18 0.00038 29.7 1.5 18 185-202 85-102 (158)
142 PRK11609 nicotinamidase/pyrazi 38.6 62 0.0013 28.0 4.9 43 90-133 132-174 (212)
143 PRK10792 bifunctional 5,10-met 38.3 23 0.00051 32.7 2.3 75 125-202 182-274 (285)
144 PRK14837 undecaprenyl pyrophos 38.2 22 0.00049 31.8 2.1 65 50-120 6-81 (230)
145 PRK14351 ligA NAD-dependent DN 38.1 66 0.0014 33.6 5.7 26 186-211 465-492 (689)
146 PRK14831 undecaprenyl pyrophos 37.9 22 0.00047 32.3 2.0 66 49-120 19-95 (249)
147 PF14229 DUF4332: Domain of un 37.6 73 0.0016 25.4 4.8 49 156-209 31-80 (122)
148 TIGR01370 cysRS possible cyste 37.4 3.2E+02 0.0069 25.7 9.7 55 83-140 249-311 (315)
149 cd01011 nicotinamidase Nicotin 37.3 70 0.0015 27.4 5.0 43 90-133 128-170 (196)
150 PF14097 SpoVAE: Stage V sporu 37.0 44 0.00095 28.6 3.5 55 4-61 2-62 (180)
151 PRK14839 undecaprenyl pyrophos 36.7 22 0.00047 32.1 1.7 68 47-120 6-84 (239)
152 PF00416 Ribosomal_S13: Riboso 36.6 28 0.00061 27.2 2.2 19 186-204 18-36 (107)
153 PRK14832 undecaprenyl pyrophos 36.5 24 0.00053 32.1 2.1 66 50-121 18-94 (253)
154 PRK14829 undecaprenyl pyrophos 36.2 25 0.00053 31.8 2.0 65 49-119 13-88 (243)
155 PRK14841 undecaprenyl pyrophos 36.1 26 0.00056 31.5 2.2 65 50-120 3-78 (233)
156 smart00478 ENDO3c endonuclease 35.9 21 0.00046 29.0 1.5 17 185-201 74-90 (149)
157 PF15632 ATPgrasp_Ter: ATP-gra 35.8 2.3E+02 0.005 26.8 8.5 98 42-149 14-112 (329)
158 COG5049 XRN1 5'-3' exonuclease 35.7 5.6E+02 0.012 27.2 12.0 45 105-150 186-238 (953)
159 PRK14833 undecaprenyl pyrophos 35.7 27 0.0006 31.3 2.2 66 50-121 4-80 (233)
160 TIGR01083 nth endonuclease III 35.4 21 0.00046 30.7 1.5 18 184-201 107-124 (191)
161 PRK08097 ligB NAD-dependent DN 35.2 30 0.00066 35.1 2.7 31 184-214 460-495 (562)
162 TIGR00264 alpha-NAC-related pr 35.1 2E+02 0.0044 23.0 6.8 43 88-150 11-53 (116)
163 PF00875 DNA_photolyase: DNA p 35.0 1.1E+02 0.0024 25.1 5.8 50 84-138 51-100 (165)
164 PRK14176 bifunctional 5,10-met 35.0 25 0.00055 32.5 2.0 107 90-202 150-278 (287)
165 PF07131 DUF1382: Protein of u 34.8 1.4E+02 0.003 21.0 5.1 44 76-122 2-45 (61)
166 PF13419 HAD_2: Haloacid dehal 34.8 9.3 0.0002 30.7 -0.9 34 157-194 139-172 (176)
167 COG1796 POL4 DNA polymerase IV 34.7 38 0.00082 31.9 3.0 19 184-202 129-147 (326)
168 PRK14178 bifunctional 5,10-met 34.6 28 0.00061 32.1 2.2 106 91-202 139-266 (279)
169 PTZ00331 alpha/beta hydrolase; 34.4 80 0.0017 27.5 5.0 43 90-133 136-178 (212)
170 COG3743 Uncharacterized conser 34.2 25 0.00055 28.7 1.6 26 183-209 67-94 (133)
171 PRK14838 undecaprenyl pyrophos 33.7 29 0.00064 31.3 2.1 66 50-121 10-86 (242)
172 PRK14842 undecaprenyl pyrophos 33.4 30 0.00064 31.3 2.1 66 50-121 8-84 (241)
173 PRK14180 bifunctional 5,10-met 33.0 25 0.00055 32.5 1.6 73 125-202 181-272 (282)
174 PRK14834 undecaprenyl pyrophos 32.8 37 0.00081 30.8 2.6 65 50-120 14-89 (249)
175 COG0177 Nth Predicted EndoIII- 32.3 29 0.00062 30.8 1.8 20 187-206 113-133 (211)
176 TIGR00028 Mtu_PIN_fam Mycobact 31.7 43 0.00094 26.3 2.6 28 109-142 105-132 (142)
177 PRK14828 undecaprenyl pyrophos 31.6 36 0.00078 31.0 2.3 66 50-121 26-103 (256)
178 cd01080 NAD_bind_m-THF_DH_Cycl 30.7 37 0.00081 28.7 2.2 20 183-202 142-162 (168)
179 PF04900 Fcf1: Fcf1; InterPro 30.2 31 0.00067 26.4 1.5 38 107-149 50-89 (101)
180 PRK14835 undecaprenyl pyrophos 30.1 43 0.00093 30.9 2.6 67 50-122 41-118 (275)
181 PRK14840 undecaprenyl pyrophos 29.7 45 0.00098 30.3 2.6 65 50-120 18-97 (250)
182 PRK04301 radA DNA repair and r 28.8 44 0.00095 31.0 2.5 29 184-212 7-36 (317)
183 COG2454 Uncharacterized conser 28.8 4.1E+02 0.0089 23.5 8.7 80 4-102 67-160 (211)
184 cd05212 NAD_bind_m-THF_DH_Cycl 28.3 2.2E+02 0.0048 23.2 6.3 104 90-202 14-134 (140)
185 PRK14194 bifunctional 5,10-met 27.9 35 0.00075 31.9 1.6 109 90-202 145-277 (301)
186 PRK14169 bifunctional 5,10-met 27.8 55 0.0012 30.3 2.9 75 125-202 179-271 (282)
187 TIGR02247 HAD-1A3-hyp Epoxide 27.7 69 0.0015 27.2 3.4 32 157-192 158-189 (211)
188 PRK10736 hypothetical protein; 27.5 42 0.00091 32.3 2.1 22 187-208 12-33 (374)
189 COG1423 ATP-dependent DNA liga 26.9 1.7E+02 0.0038 28.0 6.0 46 93-140 189-238 (382)
190 PF00702 Hydrolase: haloacid d 26.9 69 0.0015 26.8 3.2 66 108-182 130-205 (215)
191 PRK13366 protocatechuate 4,5-d 26.8 2.8E+02 0.006 25.6 7.3 76 33-111 31-124 (284)
192 TIGR03556 photolyase_8HDF deox 26.6 4.9E+02 0.011 25.6 9.6 51 84-139 53-103 (471)
193 PRK13910 DNA glycosylase MutY; 26.4 38 0.00083 31.4 1.6 22 183-204 72-94 (289)
194 PRK14181 bifunctional 5,10-met 26.2 41 0.0009 31.2 1.8 75 126-202 181-277 (287)
195 COG3852 NtrB Signal transducti 26.0 43 0.00094 31.6 1.9 25 182-206 293-336 (363)
196 PRK14830 undecaprenyl pyrophos 25.9 52 0.0011 29.9 2.3 64 50-119 22-96 (251)
197 TIGR01084 mutY A/G-specific ad 25.9 38 0.00082 31.1 1.5 19 183-201 105-123 (275)
198 PF09550 DUF2376: Conserved hy 25.7 1.5E+02 0.0032 19.4 3.8 27 174-204 16-42 (43)
199 PRK14836 undecaprenyl pyrophos 25.5 43 0.00094 30.4 1.7 65 50-120 14-89 (253)
200 PRK14177 bifunctional 5,10-met 25.4 70 0.0015 29.6 3.1 71 125-202 182-270 (284)
201 TIGR01428 HAD_type_II 2-haloal 25.3 34 0.00074 28.8 1.0 33 159-195 156-188 (198)
202 PF14635 HHH_7: Helix-hairpin- 24.8 47 0.001 26.1 1.6 19 186-204 53-71 (104)
203 PRK08609 hypothetical protein; 24.6 85 0.0018 31.9 3.8 15 184-198 49-63 (570)
204 PRK13482 DNA integrity scannin 24.6 53 0.0011 31.4 2.2 26 173-198 309-334 (352)
205 TIGR02853 spore_dpaA dipicolin 23.5 59 0.0013 29.9 2.3 24 185-210 261-285 (287)
206 CHL00137 rps13 ribosomal prote 23.4 53 0.0011 26.5 1.7 19 186-204 20-38 (122)
207 cd01702 PolY_Pol_eta DNA Polym 23.1 71 0.0015 30.4 2.8 27 185-211 184-212 (359)
208 PTZ00134 40S ribosomal protein 22.7 54 0.0012 27.6 1.7 18 187-204 34-51 (154)
209 PF13638 PIN_4: PIN domain; PD 22.5 81 0.0018 24.7 2.7 34 108-141 87-121 (133)
210 PRK05628 coproporphyrinogen II 22.4 3.3E+02 0.0071 25.8 7.2 76 29-107 168-245 (375)
211 TIGR03631 bact_S13 30S ribosom 22.4 51 0.0011 26.1 1.4 20 186-205 18-37 (113)
212 PRK14192 bifunctional 5,10-met 22.3 53 0.0012 30.3 1.7 19 184-202 254-273 (283)
213 smart00670 PINc Large family o 22.0 71 0.0015 23.9 2.2 25 110-139 86-110 (111)
214 PF12836 HHH_3: Helix-hairpin- 21.9 61 0.0013 22.7 1.6 16 186-201 17-32 (65)
215 PRK10880 adenine DNA glycosyla 21.9 52 0.0011 31.4 1.6 21 185-205 111-132 (350)
216 PRK05179 rpsM 30S ribosomal pr 21.8 58 0.0013 26.2 1.6 19 186-204 20-38 (122)
217 PRK10853 putative reductase; P 21.6 87 0.0019 24.8 2.6 28 254-281 29-56 (118)
218 cd03035 ArsC_Yffb Arsenate Red 21.5 85 0.0018 24.2 2.5 28 254-281 28-55 (105)
219 PRK11587 putative phosphatase; 21.5 2.1E+02 0.0046 24.4 5.3 32 159-194 146-177 (218)
220 COG1011 Predicted hydrolase (H 21.3 46 0.001 28.4 1.1 42 156-203 159-201 (229)
221 PF06574 FAD_syn: FAD syntheta 21.1 4.8E+02 0.01 21.6 7.2 92 28-135 15-115 (157)
222 PRK10308 3-methyl-adenine DNA 21.0 54 0.0012 30.2 1.5 24 185-208 209-233 (283)
223 COG1569 Predicted nucleic acid 20.9 90 0.0019 25.9 2.6 34 126-163 103-136 (142)
224 TIGR01662 HAD-SF-IIIA HAD-supe 20.8 2.5E+02 0.0054 21.7 5.2 36 156-195 90-127 (132)
225 PRK14188 bifunctional 5,10-met 20.8 59 0.0013 30.3 1.7 108 91-202 145-280 (296)
226 PRK14171 bifunctional 5,10-met 20.7 60 0.0013 30.1 1.7 75 125-202 182-274 (288)
227 PRK07379 coproporphyrinogen II 20.6 3.8E+02 0.0082 25.7 7.3 74 29-105 175-250 (400)
228 KOG1921|consensus 20.6 37 0.0008 30.9 0.3 25 185-209 161-186 (286)
229 PRK10563 6-phosphogluconate ph 20.5 78 0.0017 27.1 2.3 26 158-187 149-174 (221)
230 PF14582 Metallophos_3: Metall 20.4 2.6E+02 0.0057 25.4 5.5 83 37-120 19-109 (255)
231 PF01850 PIN: PIN domain; Int 20.1 63 0.0014 24.3 1.5 30 108-142 90-119 (121)
No 1
>PRK14976 5'-3' exonuclease; Provisional
Probab=100.00 E-value=1.6e-76 Score=541.08 Aligned_cols=272 Identities=40% Similarity=0.613 Sum_probs=261.0
Q ss_pred CCCcEEEEecchHHHHHhccC----CCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhC
Q psy14489 1 MQNTLLLVDGSSCIYRAFYAL----PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKAT 76 (284)
Q Consensus 1 m~~~~llIDg~~l~~r~~~a~----~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~ 76 (284)
|.++++||||++++||+||+. +.+++++|.+|+|++||++++.++++.++|+|+++|||+++++||+++||+||+|
T Consensus 1 m~~~~lliDg~~~~~ra~~a~~~~~~~l~~~~G~~t~a~~gf~~~l~~ll~~~~p~~~~v~fD~~~~~~R~~l~p~YKan 80 (281)
T PRK14976 1 MMKKALLIDGNSLIFRSYYATLKQGPKLKNNKGLPTNAIHTFLTMIFKILKKLNPSYILIAFDAGRKTFRHQLYDEYKQG 80 (281)
T ss_pred CCCcEEEEeCcHHHHHHHHccCccCCCccCCCCCCchHHHHHHHHHHHHHHhcCCCEEEEEEECCCCcccccccHHHhcC
Confidence 777899999999999999996 4577899999999999999999999999999999999998899999999999999
Q ss_pred CCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--Cc--
Q psy14489 77 RKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NN-- 152 (284)
Q Consensus 77 R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~~-- 152 (284)
|+++|++|.+|++.++++++.+||+++.++|+||||+||++|+++.. .|..++|+|+|||++||++++|.+|+ +.
T Consensus 81 R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDviatla~~~~~-~g~~v~IvS~DkDl~ql~~~~v~~~~~~~~~~ 159 (281)
T PRK14976 81 RKKTPESLISQIPLLKKILKLAGIKWEEQPGYEADDLIGSLAKKLSK-QNITVLIYSSDKDLLQLVNENTDVLLKKKGTS 159 (281)
T ss_pred CCCCCHHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH-CCCeEEEEeCCCCcCccCCCCeEEEEecCCCC
Confidence 99999999999999999999999999999999999999999999887 88899999999999999999999887 33
Q ss_pred -EeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhc
Q psy14489 153 -KIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWL 231 (284)
Q Consensus 153 -~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~ 231 (284)
+.++.+.|.++||++|+||+|+++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|.++++++
T Consensus 160 ~~~~~~~~v~~~~gv~p~q~~d~~aL~GD~sDnipGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~~ 239 (281)
T PRK14976 160 HFILNTNNFFELYGIEPKQIIDYKGLVGDSSDNIKGVKGIGPKTAIKLLNKYGNIENIYENIDKIKKKIKNKLSEAKEKA 239 (281)
T ss_pred cEEEcHHHHHHHhCcCHHHHHHHHHHhCCccCCCCCCCcccHHHHHHHHHHcCCHHHHHHhHHHHhHHHHHHHHHhHHHH
Confidence 6899999999999999999999999999999999999999999999999999999999999999888999999999999
Q ss_pred hhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHHHHcCch
Q psy14489 232 PKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLN 277 (284)
Q Consensus 232 ~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~ 277 (284)
++|++|++|++|+|++.+ ++++.+.+++.+++.++|+++||+
T Consensus 240 ~~s~~L~~l~~d~~l~~~----l~~~~~~~~~~~~l~~~~~~~e~~ 281 (281)
T PRK14976 240 LLSKKLATIKTDVPLDFQ----IEDIKLKKLDQPELKKIFEELELK 281 (281)
T ss_pred HHhhhhhEEeecCCCCCC----HHHhccCCCCHHHHHHHHHHcCCC
Confidence 999999999999999998 899999999999999999999984
No 2
>PRK09482 flap endonuclease-like protein; Provisional
Probab=100.00 E-value=5.2e-75 Score=522.15 Aligned_cols=250 Identities=32% Similarity=0.463 Sum_probs=237.9
Q ss_pred CCCcEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCc--cccccCchhhhCCC
Q psy14489 1 MQNTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKN--FRNILYPSYKATRK 78 (284)
Q Consensus 1 m~~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~--~R~~l~~~YKa~R~ 78 (284)
|.++++||||++++||+||+.+ +++|. |||++||++++.++++.++|+|+++|||+++++ ||+++||+||+||+
T Consensus 1 ~~~~llLiDg~~l~~R~~~a~~---~~~g~-t~av~gf~~~l~~ll~~~~p~~i~v~fD~~~~~~~fR~~l~p~YKa~R~ 76 (256)
T PRK09482 1 MMNHLLIIDALNLIRRIHAVQP---SPNDI-NACVETCQHALDKLIRHSQPTHAVAVFDGDARSSGWRHQLLPDYKAGRK 76 (256)
T ss_pred CCCeEEEEeCcHHHHHHHhCCC---CCCCc-chHHHHHHHHHHHHHHHcCCCEEEEEEeCCCCCcccHHHHhHHHhcCCC
Confidence 5667999999999999999975 36787 999999999999999999999999999997777 99999999999999
Q ss_pred CCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--CcEeee
Q psy14489 79 KMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHD 156 (284)
Q Consensus 79 ~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~~~~~~ 156 (284)
++|++|..|++.++++++.+||+++..+||||||+||++|+++.+ .+.+|+|+|+|||++||++++|++|+ +.++++
T Consensus 77 ~~Pe~l~~Q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~-~~~~v~I~S~DKDl~Qlv~~~v~~~~~~~~~~~~ 155 (256)
T PRK09482 77 PMPEALQQGLPAIRAAFEELGIDSWHADGNEADDLIATLAVKVAQ-AGHQATIVSTDKGYCQLLSPTIQIRDYFQKRWLD 155 (256)
T ss_pred CCcHHHHHHHHHHHHHHHhCCCCEeccCCcCHHHHHHHHHHHHHH-CCCeEEEEECCCCccccCCCCeEEEeccccccCC
Confidence 999999999999999999999999999999999999999999887 88899999999999999999999997 556799
Q ss_pred HhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhhhh
Q psy14489 157 RTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKK 236 (284)
Q Consensus 157 ~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~~~ 236 (284)
.+.+.++||++|+|++||++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|.++++++++||+
T Consensus 156 ~~~v~~~~Gv~P~q~~D~~aL~GD~sDnIpGVpGIG~KtA~~LL~~~gsle~i~~~~~~~~~~~~~~L~~~~~~a~lsr~ 235 (256)
T PRK09482 156 APFIEQEFGVEPQQLPDYWGLAGISSSKIPGVAGIGPKSAAELLNQFRSLENIYESLDALPEKWRKKLEEHKEMARLCRK 235 (256)
T ss_pred HHHHHHHhCCCHHHHHHHHHHhCCCccCCCCCCCcChHHHHHHHHHhCCHHHHHHhHHHhhHHHHHHHHHhHHHHHHHHh
Confidence 99999999999999999999999999999999999999999999999999999999999988999999999999999999
Q ss_pred hhhhccccCCCCCcCCCcccccc
Q psy14489 237 ILTIKTDCDLTKNIVSIPESLIL 259 (284)
Q Consensus 237 L~~l~~d~~~~~~~~~~~~~l~~ 259 (284)
|++|++|+|++.+ ++++.+
T Consensus 236 L~~l~~dv~l~~~----l~~l~~ 254 (256)
T PRK09482 236 LAQLQTDLPLGGN----LQQLRL 254 (256)
T ss_pred hheEeeCCCCCCC----HHHhcc
Confidence 9999999999888 777766
No 3
>smart00475 53EXOc 5'-3' exonuclease.
Probab=100.00 E-value=1.8e-73 Score=515.52 Aligned_cols=250 Identities=46% Similarity=0.735 Sum_probs=238.9
Q ss_pred cEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCChh
Q psy14489 4 TLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYN 83 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~~ 83 (284)
+++||||++++||+||+.+.+++++|.+|+|++||++++.++++.++|+|+++|||+++++||+++||+||+||+++|++
T Consensus 2 ~lllIDg~~~i~R~~~a~~~l~~~~G~~t~a~~g~~~~l~~l~~~~~p~~~~~~fD~~~~~~R~~l~p~YKa~R~~~pe~ 81 (259)
T smart00475 2 KLLLVDGSSLAFRAYFALPPLKNSKGEPTNAVYGFLRMLLKLIKEEKPTYVAVVFDAKGKTFRHELYPEYKANRPKTPDE 81 (259)
T ss_pred cEEEEeCcHHHHHHHHCCCcccCCCCCcccHHHHHHHHHHHHHHHcCCCeEEEEEeCCCCccccchhHHHHhCCCCCCHH
Confidence 58999999999999999988889999999999999999999999999999999999988999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--C----cEeeeH
Q psy14489 84 LILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--N----NKIHDR 157 (284)
Q Consensus 84 l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~----~~~~~~ 157 (284)
|.+|++.++++|+.+||+++..+||||||+||++|++... .|..++|+|+|||++||++++|.+|. + .+.++.
T Consensus 82 L~~q~~~~~~~l~~~gi~~i~~~g~EADD~iatla~~~~~-~g~~~~IvS~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~ 160 (259)
T smart00475 82 LLEQIPLIKELLDALGIPVLEVEGYEADDVIATLAKKAEA-EGYEVRIVSGDKDLLQLVSDKVSVLDPTKGIKEFELYTP 160 (259)
T ss_pred HHHHHHHHHHHHHHCCCCEEeeCCcCHHHHHHHHHHHHHh-CCCeEEEEeCCCcHhhcCCCCEEEEeccCCCCccEEEcH
Confidence 9999999999999999999999999999999999999887 78999999999999999999999887 3 267999
Q ss_pred hHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhhhhh
Q psy14489 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKI 237 (284)
Q Consensus 158 ~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~~~L 237 (284)
+++.++||++|+||+|+++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|.++++++++|++|
T Consensus 161 ~~v~~~~Gv~p~q~~d~~aL~GD~sDnipGV~GIG~KtA~~Ll~~ygsle~i~~~~~~~~~~~~~~l~~~~~~~~ls~~L 240 (259)
T smart00475 161 ENVIEKYGLTPEQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEFGSLENILENLDKLKKKLREKLLAHKEDAKLSRKL 240 (259)
T ss_pred HHHHHHhCcCHHHHHHHHHHhCCcccCCCCCCCCCHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhcHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999999999999999999889999999999999999999
Q ss_pred hhhccccCCCCCcCCCccccc
Q psy14489 238 LTIKTDCDLTKNIVSIPESLI 258 (284)
Q Consensus 238 ~~l~~d~~~~~~~~~~~~~l~ 258 (284)
++|++|+|++.+ ++++.
T Consensus 241 ~~l~~d~~l~~~----~~~~~ 257 (259)
T smart00475 241 ATIETDVPLEVD----LEDLR 257 (259)
T ss_pred heeeeCCCCCCC----HHHhc
Confidence 999999998877 66554
No 4
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=6e-71 Score=567.77 Aligned_cols=274 Identities=41% Similarity=0.595 Sum_probs=262.7
Q ss_pred EEEEecchHHHHHhccCC--CccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCCh
Q psy14489 5 LLLVDGSSCIYRAFYALP--DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPY 82 (284)
Q Consensus 5 ~llIDg~~l~~r~~~a~~--~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~ 82 (284)
++||||++++||+|||.+ ++++++|.||||++||++++.++++.++|+|++||||+++++||+++||+||+||+++|+
T Consensus 1 l~lIDg~~l~~Ra~~a~~~~~l~~~~G~~t~av~Gf~~~l~~ll~~~~p~~i~v~FD~~~~tfR~~~~~~YKa~R~~~Pe 80 (887)
T TIGR00593 1 LLLIDGHSLAFRAYFALKNKPLTNSKGEPTNAVYGFTKMLLKLLKEEKPTYVAVAFDSGTPTFRHEAYAEYKANRAPTPE 80 (887)
T ss_pred CEEEeCcHHHHHHHHCCCcccCcCCCCCEecHHHHHHHHHHHHHHhcCCCEEEEEEcCCCCcchHHHHHHHHhCCCCChH
Confidence 589999999999999997 488999999999999999999999999999999999998899999999999999999999
Q ss_pred hHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--C---cEeeeH
Q psy14489 83 NLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--N---NKIHDR 157 (284)
Q Consensus 83 ~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~---~~~~~~ 157 (284)
+|..|++.++++|+.+|||++..+||||||+||++|+++.+ .|.+|+|+|+|||++||++++|++++ + ...++.
T Consensus 81 ~l~~Q~~~i~~~l~~~gi~~i~~~g~EADDiIatla~~~~~-~g~~v~IvS~DkDllQLv~~~v~~~~~~~~~~~~~~~~ 159 (887)
T TIGR00593 81 ELIEQIPLIKELLDALGIPILEVEGYEADDVIATLAKQAEK-EGYEVRIISGDKDLLQLVSDNVKVLIPKGKTSFTEITP 159 (887)
T ss_pred HHHHHHHHHHHHHHHCCCcEEeeCCccHHHHHHHHHHHHHh-CCCcEEEEECCCChhhcCCCCEEEEeccCCCCceEEcH
Confidence 99999999999999999999999999999999999999887 88999999999999999999999997 2 257999
Q ss_pred hHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhh-hhhccHHHhHhhchhhhh
Q psy14489 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG-VIGKNLRFALNWLPKLKK 236 (284)
Q Consensus 158 ~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~-~~~~~l~~~~~~~~l~~~ 236 (284)
+.|.++||++|+||+|+++|+||+|||||||||||||||.+||++|||+|+|+++++++++ +++++|.++++++++|++
T Consensus 160 ~~v~~~~Gv~p~q~~D~~aL~GD~sDnIpGVpGIG~KtA~kLL~~ygsle~i~~~~~~i~~~k~~~~L~~~~e~a~ls~~ 239 (887)
T TIGR00593 160 EYVVEKYGVTPDQLVDLKALVGDSSDNIPGVKGIGEKTAAKLLQEFGSLENIYENLDQIKSAKMREKLIAHKEDAFLSKE 239 (887)
T ss_pred HHHHHHhCCCHHHHHHHHHHcCCcccCCCCCCCcCHHHHHHHHHHcCCHHHHHHHHHHhccHHHHHHHHHhHHHHHHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999975 699999999999999999
Q ss_pred hhhhccccCCCCCcCCCccccccCCCCHHHHHHHHHHcCchhHHhhc
Q psy14489 237 ILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFLM 283 (284)
Q Consensus 237 L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~ 283 (284)
|++|++|+|++.+ ++++.+.++|.+++.++|+++||+++++++
T Consensus 240 L~ti~~d~~l~~~----~~~~~~~~~~~~~l~~~~~~lef~~l~~~~ 282 (887)
T TIGR00593 240 LATIVTDVPLEVD----LEDLRLSEPDRERLYALLQELEFKSLLDRL 282 (887)
T ss_pred hheeecCCCCCCC----HHHhccCCCCHHHHHHHHHHhCCccHHHHh
Confidence 9999999999998 889999999999999999999999988765
No 5
>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=100.00 E-value=3.8e-68 Score=476.75 Aligned_cols=237 Identities=49% Similarity=0.815 Sum_probs=227.3
Q ss_pred CcEEEEecchHHHHHhccCCCccCC-CCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCC
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNI-DNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP 81 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~-~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p 81 (284)
++++||||++++||+||+.+...++ +|.+|++++||++++.++++.++|+++++|||+++++||++++|+||+||+++|
T Consensus 1 ~~~llIDg~~l~yr~~~a~~~~~~~~~g~~t~ai~g~~~~l~~~~~~~~p~~~~~~fD~~~~~~R~~l~p~YK~~R~~~p 80 (240)
T cd00008 1 KRLLLIDGSSLAYRAYFALPPLKNSPKGLPTNAVYGFLNMLLKLIKEYKPTYVAVVFDAGGKTFRHELYPEYKANRKKMP 80 (240)
T ss_pred CcEEEEEChHHHHHHHHCCCCcCCCCCCcCchHHHHHHHHHHHHHHhcCCCeEEEEEeCCCCcccccccHHHHcCCCCCC
Confidence 3699999999999999999866666 899999999999999999999999999999999889999999999999999999
Q ss_pred hhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--CcEeeeHhH
Q psy14489 82 YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTT 159 (284)
Q Consensus 82 ~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~~~~~~~~~ 159 (284)
++|..|++.++++|+.+||+++.++|+||||+||++|++... .|.+++|+|+|||++||++++|.+++ +.++++.+.
T Consensus 81 ~~l~~q~~~~~~~l~~~gi~~i~~~~~EADD~ia~la~~~~~-~g~~~~I~S~DkD~~ql~~~~v~~~~~~~~~~i~~~~ 159 (240)
T cd00008 81 EELREQIPLIKELLEALGIPVLEIEGYEADDVIGTLAKKAEA-EGYKVVIVSGDKDLLQLVSDNVKVVSPMKKKLVTEEN 159 (240)
T ss_pred HHHHHHHHHHHHHHHHCCCCEEecCCcCHHHHHHHHHHHHHH-cCCeEEEEeCCCChhhhCCCCEEEEeCCCceEEeHHH
Confidence 999999999999999999999999999999999999999887 78999999999999999999999997 567899999
Q ss_pred HHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhhhhhhh
Q psy14489 160 IISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILT 239 (284)
Q Consensus 160 ~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~~~L~~ 239 (284)
+.+++|++|+|++++++|+||+|||||||||||||||.+||++|||+|+|+++++.++++++++|.++.+++++|++|++
T Consensus 160 v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~~s~~L~~ 239 (240)
T cd00008 160 VIEKYGVTPAQIIDYKALMGDSSDNIPGVPGIGEKTAAKLLKEYGSLEGILENLDKIKGKLREKLEEGKEMAFLSKRLAT 239 (240)
T ss_pred HHHHhCcCHHHHHHHHHHcCCcccCCCCCCccCHHHHHHHHHHhCCHHHHHHhHHHHhHHHHHHHHHhHHHHHHHHHhhc
Confidence 99999999999999999999999999999999999999999999999999999999888999999999999999999998
Q ss_pred h
Q psy14489 240 I 240 (284)
Q Consensus 240 l 240 (284)
|
T Consensus 240 l 240 (240)
T cd00008 240 I 240 (240)
T ss_pred C
Confidence 5
No 6
>PRK05755 DNA polymerase I; Provisional
Probab=100.00 E-value=2.9e-67 Score=544.59 Aligned_cols=276 Identities=49% Similarity=0.766 Sum_probs=263.7
Q ss_pred CCCcEEEEecchHHHHHhccC-CCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCC
Q psy14489 1 MQNTLLLVDGSSCIYRAFYAL-PDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK 79 (284)
Q Consensus 1 m~~~~llIDg~~l~~r~~~a~-~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~ 79 (284)
|+ +++||||++++||+||+. +.+++++|.+|+|++||++++.++++.++|+|++||||+++++||+++||+||+||++
T Consensus 1 ~~-~~~liDg~~~~~r~~~a~~~~~~~~~g~~~~a~~g~~~~l~~~~~~~~p~~~~v~fD~~~~~~R~~~~~~YK~~R~~ 79 (880)
T PRK05755 1 MK-TLLLIDGSSLLFRAFYALLPTLRNSDGLPTGAVYGFLNMLLKLLKEEKPTHVAVAFDAKGKTFRHELYPEYKANRPP 79 (880)
T ss_pred CC-eEEEEeCcHHHHHHHHCCCCcccCCCCCcccHHHHHHHHHHHHHHhcCCCEEEEEEECCCCccccccCHHHhCCCCC
Confidence 54 599999999999999998 6678899999999999999999999999999999999998899999999999999999
Q ss_pred CChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe-----CcEe
Q psy14489 80 MPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN-----NNKI 154 (284)
Q Consensus 80 ~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~-----~~~~ 154 (284)
+|++|..|++.++++|+.+||+++..|||||||+||++|++... .|..++|+|+|||++||++++|++|+ +...
T Consensus 80 ~p~~l~~q~~~~~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~-~~~~~~i~S~DkD~~ql~~~~v~~~~~~~~~~~~~ 158 (880)
T PRK05755 80 MPEDLREQIPLIRELLRALGIPLLELEGYEADDVIGTLAKQAEA-AGYEVLIVTGDKDLLQLVDDNVTLLDTMGVSKNEE 158 (880)
T ss_pred CcHHHHHHHHHHHHHHHHCCCCEEeeCCccHHHHHHHHHHHHHh-CCCcEEEEcCCCChhhhCCCCEEEeeccCCCCCeE
Confidence 99999999999999999999999999999999999999998877 78899999999999999999999887 2467
Q ss_pred eeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhh
Q psy14489 155 HDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKL 234 (284)
Q Consensus 155 ~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~ 234 (284)
++.+.|.++||++|+||+|+++|+||+|||||||||||||||.+||++|||+|+|++++++++++++++|.++++++++|
T Consensus 159 ~~~~~v~~~~g~~p~q~~d~~~L~GD~sDnipGv~GiG~ktA~~Ll~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~ls 238 (880)
T PRK05755 159 LDPEEVVEKYGVTPEQIIDYLALMGDSSDNIPGVPGIGEKTAAKLLQEYGSLEGLYENLDEIKGKKKEKLRENKEQAFLS 238 (880)
T ss_pred EcHHHHHHHHCcCHHHHHHHHHHhCCccCCCCCCCCccHHHHHHHHHHcCCHHHHHHhHHHhchHHHHHHHHhHHHHHhh
Confidence 99999999999999999999999999999999999999999999999999999999999999888899999999999999
Q ss_pred hhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHHHHcCchhHHhh
Q psy14489 235 KKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFNKYKLNKLNFL 282 (284)
Q Consensus 235 ~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~~~~~~~~~~~~ 282 (284)
++|++|++|+|++.+ ++++.+.++|.+++.+||+++||++++++
T Consensus 239 ~~l~~l~~d~~~~~~----~~~~~~~~~~~~~l~~~~~~~~~~~~~~~ 282 (880)
T PRK05755 239 RKLATIKTDVPLEVD----LEDLELQPPDREKLIALFKELEFKSLLRR 282 (880)
T ss_pred hhhheeeeCCCCCCC----HHHhccCCCCHHHHHHHHHHhCcHHHHHH
Confidence 999999999999988 78899999999999999999999998875
No 7
>COG0258 Exo 5'-3' exonuclease (including N-terminal domain of PolI) [DNA replication, recombination, and repair]
Probab=100.00 E-value=5.6e-60 Score=438.63 Aligned_cols=275 Identities=39% Similarity=0.562 Sum_probs=256.7
Q ss_pred cEEEEecchHHHHHhccCCC-ccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCC-CC
Q psy14489 4 TLLLVDGSSCIYRAFYALPD-IRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK-MP 81 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~~~-l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~-~p 81 (284)
++++|||++++||+|||.+. +.+..|.+||++++|..++.++++..+|+|+++|||+++++||+++++.||++|.+ +|
T Consensus 12 ~l~~IDg~~~lyr~~~a~~~~~~~~~g~~~~~~~~~~~~l~~~~~~~~~~~~~~vFD~~~~tfR~~~~~~yK~~R~~~~p 91 (310)
T COG0258 12 KLLLIDGSSLLYRALHALPQPLGNPLGDPTGAVSGFLGMLYRLIRLLEPTHPVVVFDGKPPTFRHELLEEYKANREKEMP 91 (310)
T ss_pred cEEEEechHHHHHHHHhcchhcCCCCCCCccHHHHHHHHHHHHHHhcCCCcEEEEEcCCCCcchHHHHHHHHhCCCccCH
Confidence 69999999999999999964 67889999999999999999999999999999999999999999999999999999 99
Q ss_pred hhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe--CcE---eee
Q psy14489 82 YNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN--NNK---IHD 156 (284)
Q Consensus 82 ~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~--~~~---~~~ 156 (284)
++|..|++.+.+++..+|++.+..+|+||||+|+++|+...+ .|..+.|+|+|||++||+++++.+++ +.. .++
T Consensus 92 ~~l~~q~~~i~~~~~~~~~~~l~~~G~eadd~i~t~A~~a~~-~g~~~~I~S~DkD~lql~~~~~~~~~~~~~~~~~~~~ 170 (310)
T COG0258 92 DELAPQIPILTELLVALGIPLLELMGIEADDPIETLAQKAYK-KGDVVLIISGDKDLLQLVSPNVLVINGKKGEPEKFLD 170 (310)
T ss_pred HHHHHHHHHHHHHHHHhCcHhhhcCCCCcchhHHHHHHHHHh-cCCeEEEEeCCcchhhhcCCCcEEEeccCCCCcccCC
Confidence 999999999999999999999999999999999999999887 89999999999999999999998887 222 479
Q ss_pred HhHHHHHh-CCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhhh
Q psy14489 157 RTTIISRF-GVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLK 235 (284)
Q Consensus 157 ~~~~~~~~-G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~~ 235 (284)
...+.++| |++|+|++|+++|+||+|||+|||+|||||||.+||++|||+|.++++++.++++.++++.++++.+++++
T Consensus 171 ~~~~~e~~~g~~p~qliD~~~L~Gd~sDnipGV~GIG~ktA~~Ll~~~gs~e~i~~~~~~~~~~~~~~l~~~~~~afl~~ 250 (310)
T COG0258 171 LEEVEEKFKGLTPEQLIDLKALVGDSSDNIPGVKGIGPKTALKLLQEYGSLEGLYENLDIIKKKTREKLLEDKEKAFLSK 250 (310)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHhCCcccCCCCCCCcCHHHHHHHHHHhCCHHHHHHhhhhhcchhhHHHHHHHHHHhcCc
Confidence 99999999 99999999999999999999999999999999999999999999999999888888999999999999999
Q ss_pred hhhhhccccCCCCCcCCCccc---cccCCCCHHHHHHHHHHcCchhHHhhc
Q psy14489 236 KILTIKTDCDLTKNIVSIPES---LILQPKDEKLLMQLFNKYKLNKLNFLM 283 (284)
Q Consensus 236 ~L~~l~~d~~~~~~~~~~~~~---l~~~~~~~~~l~~~~~~~~~~~~~~~~ 283 (284)
.|+++.+|+++..+ .++ +.....|.+.+..++.+++|.++.+.+
T Consensus 251 ~l~t~~~d~~l~~~----~~~~~~~~~~~~d~~~~~~~~~~~~~~~l~~~~ 297 (310)
T COG0258 251 PLATIKTDVPLEFD----LEDILELLVPEHDFSKLLEERVELGFKRLLKAI 297 (310)
T ss_pred ccccccccccCCcC----ccchhhhccCcccHHHHHHHHHHHhHHHHHHHH
Confidence 99999999999877 555 444455888999999999999988654
No 8
>PHA00439 exonuclease
Probab=100.00 E-value=6.6e-56 Score=401.54 Aligned_cols=197 Identities=20% Similarity=0.366 Sum_probs=175.8
Q ss_pred CcEEEEecchHHHHHhccC-------CCccCCCCcchhHHHHHHHHHHHHHHh---cCCCEEEEEEeCCCCccccccCch
Q psy14489 3 NTLLLVDGSSCIYRAFYAL-------PDIRNIDNFPVGALYGTIKMLRKLYKN---YRATYIACIFDAKGKNFRNILYPS 72 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~-------~~l~~~~g~~t~ai~gf~~~l~~l~~~---~~~~~~i~~fD~~~~~~R~~l~~~ 72 (284)
++++||||++++||+|||. +++++++|.||||++||++++.++++. ++|+++++||| ++++|||++||+
T Consensus 6 ~~llLIDG~~l~fRA~~A~~~~~~~~~~l~~~~G~~t~A~~gf~~~L~kl~~~~k~~~p~~i~vaFD-~~~tfR~elyp~ 84 (286)
T PHA00439 6 KGVLVMDGDYLVFQAMAAAEVETDWGEDIWTLECDHAKARQILEDSIKSYKTRKKAWKDAPIVLAFT-DSVNWRKEVVPT 84 (286)
T ss_pred CcEEEEeCcHHHHHHHHccCcccccCCCCCCCCCeeccHHHHHHHHHHHHHHhhccCCCCeEEEEEC-CCCChHhhhhhH
Confidence 3799999999999999999 357899999999999999999999999 89999999999 689999999999
Q ss_pred hhhCCCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCC-eEEEEcCCCccccccCCCeEEEe-
Q psy14489 73 YKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNL-KVIISTNDKDMAQLVSNKIALIN- 150 (284)
Q Consensus 73 YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~-~v~I~S~DkDl~ql~~~~v~~~~- 150 (284)
||+||+++|++ ..|++.++++++.+|++++..+|+||||+||++|++..+ .|. +++|+|+||||+||++. +.+|.
T Consensus 85 YKanR~~~p~~-~~~~~~i~el~~~~gi~~i~~~G~EADDvIgtla~~~~~-~g~~~vvIvS~DKDl~QLv~~-~~~~~~ 161 (286)
T PHA00439 85 YKANRKAKRKP-VGYRKFLEELMAREEWKSILEPGLEGDDVMGIIGTNPSL-FGFKKAVLVSCDKDFKTIPNC-DFLWCT 161 (286)
T ss_pred hcCCCCCCCCc-hhhHHHHHHHHHhCCCCEEeeCCccHHHHHHHHHHHHHH-CCCCeEEEEeCCCCHhhcCcc-eEEEcc
Confidence 99999999999 778999999999999999999999999999999999877 777 99999999999999876 33444
Q ss_pred -CcEe-eeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHh---cCCHHHHHHh
Q psy14489 151 -NNKI-HDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQ---YNSLENIINN 212 (284)
Q Consensus 151 -~~~~-~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~---~gsle~i~~~ 212 (284)
+... ++.+ .|+||+++++|+||+||||||||||| |||.+||++ +-.++..+.+
T Consensus 162 ~~~~~~~~~~--------~p~~~~d~~AL~GDsSDNIPGVpGIG-KTA~kLL~~~~~~~~~~~~~~s 219 (286)
T PHA00439 162 TGNILTQTPE--------TADRWHLFQTIKGDSTDGYSGIPGWG-DTAEAFLENPYIFEQVEKVLKS 219 (286)
T ss_pred CCceEEcCcc--------cHHHHHhhhhcccccccCCCCCCCcC-HHHHHHHhCccccchhhHHhhc
Confidence 2211 3322 38999999999999999999999999 999999999 6666776665
No 9
>PHA02567 rnh RnaseH; Provisional
Probab=100.00 E-value=2.5e-49 Score=360.11 Aligned_cols=260 Identities=20% Similarity=0.221 Sum_probs=205.4
Q ss_pred CcEEEEecchHHHHHhccCCCccCCCCcchhHHHH-HHHHHHHHHHhcCC--CEEEEEEeCCC-CccccccCchhhhCCC
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYG-TIKMLRKLYKNYRA--TYIACIFDAKG-KNFRNILYPSYKATRK 78 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~g-f~~~l~~l~~~~~~--~~~i~~fD~~~-~~~R~~l~~~YKa~R~ 78 (284)
..++|||||+++||+|||. +.+++|.+|+++++ +++++.++++.+++ +++++|||+++ ++|||++||+||+||+
T Consensus 14 ~~~~LiDgs~i~~~~~~a~--l~~~~~~~~~~ir~~v~nsL~~~v~~~k~~~~~i~vaFD~~~~~tfR~elyp~YKAnR~ 91 (304)
T PHA02567 14 EGVNLIDFSQIIIATIMAN--FKPKDKINEAMVRHLVLNSIRYNVKKFKEEYPEIVLAFDNSKSGYWRRDIAWYYKKNRK 91 (304)
T ss_pred CCEEEEehHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHHHHHhcCCCCeEEEEEeCCCCCCchhhhhhHhhcCCC
Confidence 3699999999999999995 78889999999955 89999999988655 55999999864 7999999999999999
Q ss_pred CCChhHHHHH--------HHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccC-CCeEEE
Q psy14489 79 KMPYNLILQI--------NLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVS-NKIALI 149 (284)
Q Consensus 79 ~~p~~l~~q~--------~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~-~~v~~~ 149 (284)
++|++|..|+ +.++++++.+||+++..+|+||||+||++|+++.+ .|.+|+|+|+|||++||+. ++|.+|
T Consensus 92 ~~Peel~~q~~~l~~~l~~ii~el~~~~gi~~l~~~g~EADDvIgTLA~k~~~-~g~~VvIvS~DKDl~QLv~~~~v~~~ 170 (304)
T PHA02567 92 KDREESPWDWEGLFEAINKIVDEIKENMPYKVMKIDKAEADDIIAVLTKKFSA-EGRPVLIVSSDGDFTQLHKYPGVKQW 170 (304)
T ss_pred CCChHHHHHHHHhhhhHHHHHHHHHHHCCCCEEEeCCccHHHHHHHHHHHHHh-CCCcEEEEeCCCChhhccCCCCeEEe
Confidence 9999987776 56788889999999999999999999999999887 7899999999999999995 889988
Q ss_pred eCcEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccCh------------hhHHHHHHhcCCHHHHHHhhhhhh
Q psy14489 150 NNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGP------------KTAVKLLNQYNSLENIINNANNIK 217 (284)
Q Consensus 150 ~~~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~------------ktA~~LL~~~gsle~i~~~~~~~~ 217 (284)
+ .++.++|.++||. |+|++++++|+||+||||||||--|. -...+.|. .++++
T Consensus 171 ~---~~~~~~V~~k~G~-P~q~iD~kaL~GDsSDNIPGVp~~~d~~~~~~~ger~~~~~~~~~~------~~~~~----- 235 (304)
T PHA02567 171 S---PMQKKWVKPKYGS-PEKDLMTKIIKGDKKDGVASIKVRSDYILTRVEGERAPSISTKELE------AIADA----- 235 (304)
T ss_pred e---cCCHHHHHHHhCC-HHHHHHHHHhCCcccCCcCCCCCCCCeEEEecccccCCcccHHHHH------HHhcc-----
Confidence 7 3456889999995 99999999999999999999985332 22333333 22211
Q ss_pred hhhhccHHHhH--hhchhhhhhhhhccccCCCCCcCCCccccc-cCCCCHHHHHHHHHHcCchhHHhhc
Q psy14489 218 GVIGKNLRFAL--NWLPKLKKILTIKTDCDLTKNIVSIPESLI-LQPKDEKLLMQLFNKYKLNKLNFLM 283 (284)
Q Consensus 218 ~~~~~~l~~~~--~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~-~~~~~~~~l~~~~~~~~~~~~~~~~ 283 (284)
.-.+.+.... +.-..|++|+.+.. +|-... .+|++++. +.++...++..+|.+.++++++..+
T Consensus 236 -~~~~~~~~~e~~~r~~~n~~l~d~~~-ip~~i~-~~i~~~~~~~~~~~~~k~~~yf~~~~l~~~~~~~ 301 (304)
T PHA02567 236 -EDPKVLLTEEEYERYDENRELIDFDF-IPDDIA-DKIIEAYNSYKPPPRGKIYSYFVKNGLSKLLQKV 301 (304)
T ss_pred -cchhhhcCHHHHHHhhccceeecccc-CcHHHH-HHHHHHHhcCCCCCccchHHHHHHhhHHHHHHhh
Confidence 1112222222 23334555555432 332221 25667776 6788899999999999999998754
No 10
>PTZ00217 flap endonuclease-1; Provisional
Probab=100.00 E-value=3.3e-46 Score=355.10 Aligned_cols=253 Identities=20% Similarity=0.285 Sum_probs=210.0
Q ss_pred CcEEEEecchHHHHHhccCC------CccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhC
Q psy14489 3 NTLLLVDGSSCIYRAFYALP------DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKAT 76 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~------~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~ 76 (284)
.++++|||++|+||++|+++ ++.+++|.+|++++||+.++.++++. +. .+++||||.++.+|++.++.||++
T Consensus 28 gk~vaIDa~~~lyr~~~a~~~~~~~~~l~~~~G~~t~~l~g~~~r~~~Ll~~-gi-kPv~VFDG~~p~~K~~~~~~Rk~~ 105 (393)
T PTZ00217 28 GRVIAIDASMALYQFLIAIRDDSQGGNLTNEAGEVTSHISGLFNRTIRLLEA-GI-KPVYVFDGKPPELKSGELEKRRER 105 (393)
T ss_pred CcEEEEeHHHHHHHHHHHcccccccccchhccCCccHHHHHHHHHHHHHHHC-CC-CEEEEEcCCCchhhHHHHHHHHHH
Confidence 46899999999999999885 36788999999999999999999973 22 348999998899999999999999
Q ss_pred CCCCChhH-----------------------HHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 77 RKKMPYNL-----------------------ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 77 R~~~p~~l-----------------------~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
|..+|+++ ..|++.++++|+.+|||++.+|+ ||||+||+|++ .|..+.|+|
T Consensus 106 R~~a~~~l~~a~~~g~~~~a~k~~~r~~~vt~~~~~~~~~lL~~~Gip~i~AP~-EAdaq~A~L~~-----~g~v~~ViS 179 (393)
T PTZ00217 106 REEAEEELEKAIEEGDDEEIKKQSKRTVRVTKEQNEDAKKLLRLMGIPVIEAPC-EAEAQCAELVK-----KGKVYAVAT 179 (393)
T ss_pred HHHhHHHHHHHHhcCCHHHHHHHHhhcccCCHHHHHHHHHHHHHcCCceEECCc-CHHHHHHHHHH-----CCCeEEEeC
Confidence 99988877 56788999999999999999997 99999999986 577888999
Q ss_pred CCCccccccCCCeE-EEe-------CcEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCC
Q psy14489 134 NDKDMAQLVSNKIA-LIN-------NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 134 ~DkDl~ql~~~~v~-~~~-------~~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
+|+|++|++++.+. .++ ...+++.+.+.+.+|++|+||+|+++|+| |||+|||||||||||.+||++|||
T Consensus 180 ~D~D~l~fg~~~vi~~l~~~~~~~~~~~~~~~~~v~~~~gl~~~q~id~~iL~G--~Dy~pgi~GIG~ktA~~Li~~~gs 257 (393)
T PTZ00217 180 EDMDALTFGTPVLLRNLNFSEAKKRPIQEINLSTVLEELGLSMDQFIDLCILCG--CDYCDTIKGIGPKTAYKLIKKYKS 257 (393)
T ss_pred CCcCeeecCCcEEEEcccccccCCCCeEEEEHHHHHHHhCCCHHHHHHHHHHhC--CCCCCCCCCccHHHHHHHHHHcCC
Confidence 99999999987541 122 13579999999999999999999999999 999999999999999999999999
Q ss_pred HHHHHHhhhhhhhhhhccHH-HhHhhchhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHH-HHcCch
Q psy14489 206 LENIINNANNIKGVIGKNLR-FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYKLN 277 (284)
Q Consensus 206 le~i~~~~~~~~~~~~~~l~-~~~~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~-~~~~~~ 277 (284)
+|+|+++++..+..+.+.+. .....++++..+.+ +.+ . ++.|++||.+.|.+|| +++||+
T Consensus 258 le~il~~~~~~k~~~p~~~~~~~~~~~f~~p~V~~-------~~~----~-~l~w~~pD~~~l~~fl~~e~~f~ 319 (393)
T PTZ00217 258 IEEILEHLDKTKYPVPENFDYKEARELFLNPEVTP-------AEE----I-DLKWNEPDEEGLKKFLVKEKNFN 319 (393)
T ss_pred HHHHHHHHHhcCCCCCCCCChHHHHHHhcCCCcCC-------CCC----C-CCCCCCCCHHHHHHHHHhccCCC
Confidence 99999998865433333222 22334444433221 112 2 6889999999999997 689986
No 11
>PF02739 5_3_exonuc_N: 5'-3' exonuclease, N-terminal resolvase-like domain; InterPro: IPR020046 The N-terminal and internal 5'3'-exonuclease domains are commonly found together, and are most often associated with 5' to 3' nuclease activities. The XPG protein signatures (PDOC00658 from PROSITEDOC) are never found outside the '53EXO' domains. The latter are found in more diverse proteins [, , ]. The number of amino acids that separate the two 53EXO domains, and the presence of accompanying motifs allow the diagnosis of several protein families. In the eubacterial type A DNA-polymerases, the N-terminal and internal domains are separated by a few amino acids, usually four. The pattern DNA_POLYMERASE_A (IPR001098 from INTERPRO) is always present towards the C terminus. Several eukaryotic structure-dependent endonucleases and exonucleases have the 53EXO domains separated by 24 to 27 amino acids, and the XPG protein signatures are always present. In several proteins from herpesviridae, the two 53EXO domains are separated by 50 to 120 amino acids. These proteins are implicated in the inhibition of the expression of the host genes. Eukaryotic DNA repair proteins with 600 to 700 amino acids between the 53_EXO domains all carry the XPG protein signatures. This entry represents the N-terminal resolvase-like domain, which has a 3-layer alpha/beta/alpha core structure and contains an alpha-helical arch [, ].; GO: 0003677 DNA binding, 0008409 5'-3' exonuclease activity; PDB: 1TAQ_A 1BGX_T 1TAU_A 1XO1_B 1EXN_A 1UT8_A 1UT5_B 3H7I_A 3H8J_A 3H8S_A ....
Probab=100.00 E-value=6.3e-47 Score=322.46 Aligned_cols=161 Identities=45% Similarity=0.805 Sum_probs=147.7
Q ss_pred CcEEEEecchHHHHHhccCC--CccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCC
Q psy14489 3 NTLLLVDGSSCIYRAFYALP--DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKM 80 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~--~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~ 80 (284)
++++||||++++||+|||.+ ++.+++|.||++++||++++.++++.++|+++++|||+++++||++++|+||+||+++
T Consensus 1 k~llLIDg~~l~~Ra~~a~~~~~l~~~~G~~t~ai~g~~~~l~~l~~~~~p~~~vv~fD~~~~~fR~~l~p~YKanR~~~ 80 (169)
T PF02739_consen 1 KKLLLIDGNSLLFRAYYALPKDPLRNSDGEPTNAIYGFLRMLLKLLKDFKPDYVVVAFDSKGPTFRKELYPEYKANRKPM 80 (169)
T ss_dssp -EEEEEEHHHHHHHCCCCCTTST-BETTSEB-HHHHHHHHHHHHHHHHTTEEEEEEEEEBSSCHHHHHCCTTTTHHHHHH
T ss_pred CeEEEEechHHHHHHHHhhccCCCcCCCCCChHHHHHHHHHHHHHHHHcCCceEEEEecCCCcchHHHHHHHHHhCCCCC
Confidence 47999999999999999998 7889999999999999999999999999999999999988899999999999999999
Q ss_pred ChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCC--CeEEEe----CcEe
Q psy14489 81 PYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSN--KIALIN----NNKI 154 (284)
Q Consensus 81 p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~--~v~~~~----~~~~ 154 (284)
|++|..|++.++++++.+||+++..+|+||||+||++|++... .|.+|+|+|+||||+||+++ +|.+|+ +.+.
T Consensus 81 p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADDvIatla~~~~~-~~~~v~IvS~DkD~~QLv~~~~~V~~~~~~~~~~~~ 159 (169)
T PF02739_consen 81 PEELIPQLPYIKELLEALGIPVLEVPGYEADDVIATLAKKASE-EGFEVIIVSGDKDLLQLVDENVNVYLLDPGKKKFKV 159 (169)
T ss_dssp HHHHHHHHHHHHHHHHHTTSEEEEETTB-HHHHHHHHHHHHHH-TTCEEEEE-SSGGGGGGTCS-TSEEEEETTTTCS-E
T ss_pred CHHHHHHHHHHHHHHHHCCCCEecCCCCcHHHHHHHHHhhhcc-CCCEEEEEcCCCCHHHhcCCCceEEEeecCCCCCEE
Confidence 9999999999999999999999999999999999999999988 88999999999999999999 777777 4688
Q ss_pred eeHhHHHHHh
Q psy14489 155 HDRTTIISRF 164 (284)
Q Consensus 155 ~~~~~~~~~~ 164 (284)
++.+.|.|+|
T Consensus 160 ~~~~~v~eky 169 (169)
T PF02739_consen 160 YDPEEVEEKY 169 (169)
T ss_dssp B-HHHHHHHT
T ss_pred EcHHHHhhcC
Confidence 9999999986
No 12
>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=100.00 E-value=3.8e-45 Score=342.47 Aligned_cols=247 Identities=17% Similarity=0.277 Sum_probs=209.8
Q ss_pred CCcEEEEecchHHHHHhccCC-----CccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhC
Q psy14489 2 QNTLLLVDGSSCIYRAFYALP-----DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKAT 76 (284)
Q Consensus 2 ~~~~llIDg~~l~~r~~~a~~-----~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~ 76 (284)
..++++|||++|+||++++++ ++.+++|.+|++++||+.++.++++. + ..+++||||+++++|++.++.||+.
T Consensus 20 ~gk~vaIDas~~L~r~~~a~~~~~g~~l~~~~G~~t~~l~g~~~~~~~ll~~-~-i~Pv~VFDG~~p~~K~~~~~~R~~~ 97 (338)
T TIGR03674 20 SGKVVAVDAFNALYQFLSSIRQPDGTPLMDSRGRITSHLSGLFYRTINLLEN-G-IKPVYVFDGKPPELKAETLEERREI 97 (338)
T ss_pred CCCEEEEeHHHHHHHHHHHHhccccchhhhccCCCcHHHHHHHHHHHHHHHC-C-CeEEEEECCCChhhhHhhHHHHHHH
Confidence 457999999999999999864 47789999999999999999999864 3 3459999999899999999999998
Q ss_pred CCCCChhHHH-----------------------HHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 77 RKKMPYNLIL-----------------------QINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 77 R~~~p~~l~~-----------------------q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
|...++.+.. |++.++++|+.+|||++.+|| |||+++|+|++ .|....|+|
T Consensus 98 r~~a~~~~~~~~~~g~~~~a~~~~~r~~~~~~~~~~~~k~lL~~~Gip~i~AP~-EAeaq~a~L~~-----~g~vd~v~S 171 (338)
T TIGR03674 98 REEAEEKWEEALEKGDLEEARKYAQRSSRLTSEIVESSKKLLDLMGIPYVQAPS-EGEAQAAYMAK-----KGDVDYVGS 171 (338)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHhhcCCCCHHHHHHHHHHHHHcCCeEEECCc-cHHHHHHHHHH-----CCCeeEEec
Confidence 8876666543 377899999999999999998 99999999996 466679999
Q ss_pred CCCccccccCCCeEEEe----C--------------cEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhh
Q psy14489 134 NDKDMAQLVSNKIALIN----N--------------NKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKT 195 (284)
Q Consensus 134 ~DkDl~ql~~~~v~~~~----~--------------~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~kt 195 (284)
+|+|++|+++++| +.+ . .+.++.+.+.+++|++|+||+|+++|+|| +|| ||||||||||
T Consensus 172 ~D~D~l~fg~~~v-i~~~~~~~~~~~~~~~~~~~~~~e~~~~~~v~~~lgl~~~q~id~~iL~G~-dyn-~Gv~GIG~kt 248 (338)
T TIGR03674 172 QDYDSLLFGAPRL-VRNLTISGKRKLPGKNIYVEVKPELIELEEVLSELGITREQLIDIAILVGT-DYN-EGVKGIGPKT 248 (338)
T ss_pred CCcCeeeecCCEE-EEecccccccCCCcccccccccceeeeHHHHHHHhCCCHHHHHHHHHhcCC-CCC-CCCCCccHHH
Confidence 9999999999876 332 1 12489999999999999999999999998 667 9999999999
Q ss_pred HHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHH-HHHc
Q psy14489 196 AVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQL-FNKY 274 (284)
Q Consensus 196 A~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~-~~~~ 274 (284)
|.+||++|||+|+|+++++.. + +. + +++.++.+++++..+ .++.|..||.+++.+| |+++
T Consensus 249 A~kli~~~gsie~il~~~~~~-------~----~~--~-~~~~~~f~~~~v~~~-----~~~~~~~pd~e~l~~fl~~e~ 309 (338)
T TIGR03674 249 ALKLIKEHGDLEKVLKARGED-------I----EN--Y-DEIREFFLNPPVTDD-----YELKWRKPDKEGIIEFLCDEH 309 (338)
T ss_pred HHHHHHHcCCHHHHHHhhcCC-------C----CC--H-HHHHHHhCCCCCCCC-----CCccCCCCCHHHHHHHHhhcC
Confidence 999999999999999986522 1 11 2 578888888887665 4788999999999995 6999
Q ss_pred Cchh
Q psy14489 275 KLNK 278 (284)
Q Consensus 275 ~~~~ 278 (284)
+|+.
T Consensus 310 ~~~~ 313 (338)
T TIGR03674 310 DFSE 313 (338)
T ss_pred CCCH
Confidence 9973
No 13
>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=100.00 E-value=1.7e-40 Score=308.84 Aligned_cols=252 Identities=20% Similarity=0.231 Sum_probs=199.2
Q ss_pred CcEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCcc-------ccccCchhhh
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNF-------RNILYPSYKA 75 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~-------R~~l~~~YKa 75 (284)
.++++|||++|+||++++++....+.|.+++++.+|++++.++++ ++ .++++||||..+.+ |++..++||+
T Consensus 24 gk~laID~~~~l~r~~~a~~~~~~~~g~~~~~l~~~~~rl~~L~~-~~-i~pvfVFDG~~~~~K~~~~~~R~~~r~~~~~ 101 (316)
T cd00128 24 GKKVAIDASIWLYQFLKACRQELGSGGETTSHLQGFFYRTCRLLE-LG-IKPVFVFDGKPPPLKAETLAKRRERREEAEE 101 (316)
T ss_pred CcEEEecHHHHHHHHHHHhhhhccCCCCCcHHHHHHHHHHHHHHH-CC-CEEEEEEcCCCchhhHHHHHHHHHHHHHHHH
Confidence 468999999999999999864334689999999999999998886 44 57899999977665 8888899999
Q ss_pred CCCCCCh----------------hHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccc
Q psy14489 76 TRKKMPY----------------NLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMA 139 (284)
Q Consensus 76 ~R~~~p~----------------~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ 139 (284)
+|..+++ ....|++.++++|+.+||+++.+| +||||+||+|++ .+....|+|+|+|++
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lL~~~gi~~i~ap-~EAdaq~a~l~~-----~g~v~~i~S~DsD~l 175 (316)
T cd00128 102 EAKEALEKGLEEEAKKLERRAVRVTPQMIEEAKELLRLMGIPYIVAP-YEAEAQCAYLAK-----KGLVDAIITEDSDLL 175 (316)
T ss_pred HHHHHHHhCCHHHHHHHHhccCcCCHHHHHHHHHHHHHcCCCEEECC-cCHHHHHHHHHh-----CCCeeEEEecCCCee
Confidence 8887765 125667889999999999999988 699999999987 466779999999999
Q ss_pred cccCCCeEE-Ee-----CcEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 140 QLVSNKIAL-IN-----NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 140 ql~~~~v~~-~~-----~~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
|+++++|.. ++ +...++.+.+.+++|++|+||+++++|+| |||+|||||||+|||.+||++|||++++++++
T Consensus 176 ~fg~~~vi~~~~~~~~~~~~~~~~~~~~~~lgl~~~q~id~~~L~G--~Dy~~gv~giG~k~A~~li~~~~~~~~~~~~l 253 (316)
T cd00128 176 LFGAPRVYRNLFDSGAKPVEEIDLEKILKELGLTREKLIDLAILLG--CDYTEGIPGIGPVTALKLIKKYGDIEKDIERL 253 (316)
T ss_pred eecCceEEEecccCCCCceEEEEHHHHHHHcCCCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHcCChHHHHHHH
Confidence 999886533 22 23579999999999999999999999999 99999999999999999999999999998877
Q ss_pred hhhhhhhhccH-HHhHhhchhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHH-HHcCch
Q psy14489 214 NNIKGVIGKNL-RFALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYKLN 277 (284)
Q Consensus 214 ~~~~~~~~~~l-~~~~~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~-~~~~~~ 277 (284)
..-........ ......+++ .+++..+ ...+.|..|+.+.+.+|+ .+.+|+
T Consensus 254 ~~~~~~~~~~~~~~~~~~~f~---------~p~~~~~----~~~~~~~~p~~~~l~~~~~~~~~~~ 306 (316)
T cd00128 254 KKKLYRSPEDFPLKEAREFFL---------NPEVTDD----FIDLRWRDPDEEGIIEFLCKEHGFN 306 (316)
T ss_pred HHhCccCCCcCChHHHHHHHc---------CCCCCCC----CCceeecCCCHHHHHHHccCCCCCC
Confidence 53211111001 011122221 2222222 245779999999999998 577776
No 14
>PRK03980 flap endonuclease-1; Provisional
Probab=100.00 E-value=2e-40 Score=304.52 Aligned_cols=223 Identities=18% Similarity=0.288 Sum_probs=185.6
Q ss_pred CCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCChhHHH-------------------
Q psy14489 26 NIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLIL------------------- 86 (284)
Q Consensus 26 ~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~~l~~------------------- 86 (284)
+++|.+|++++||+.++.++++. + ..+++||||.++++|++.++.||++|..+|+.+..
T Consensus 2 ~~~G~~Ts~l~g~~~r~~~ll~~-g-i~PvfVFDG~~p~~K~~~~~~rk~~R~~a~~~~~~~~~~g~~~~a~k~~~~~~~ 79 (292)
T PRK03980 2 DSKGRITSHLSGIFYRTINLLEN-G-IKPVYVFDGKPPELKAEEIEERREVREEAEEKYEEAKEEGDLEEARKYAQRSSR 79 (292)
T ss_pred CCCCcCcHHHHHHHHHHHHHHHC-C-CEEEEEECCCCchHHHHHHHHHHHHHHHhHHHHHHHHHcCCHHHHHHHHhcccc
Confidence 68999999999999999999875 3 34599999999999999999999999999888765
Q ss_pred ----HHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeE-EEe---C-------
Q psy14489 87 ----QINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIA-LIN---N------- 151 (284)
Q Consensus 87 ----q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~-~~~---~------- 151 (284)
|++.++++|+.+|||++.+|| |||..||+|++ .|..+.|+|+|+|++|+++++|. .+. +
T Consensus 80 vt~~~~~~~k~lL~~~GIp~i~AP~-EAEAq~A~L~~-----~g~vd~V~S~D~D~l~fg~~~vir~l~~~~~~~~p~~~ 153 (292)
T PRK03980 80 LTDEIVEDSKKLLDLMGIPYVQAPS-EGEAQAAYMAK-----KGDAWAVGSQDYDSLLFGAPRLVRNLTISGKRKLPGKN 153 (292)
T ss_pred CCHHHHHHHHHHHHHCCCCEEecCc-hHHHHHHHHHH-----CCCeEEEecCCcCeeeecCCEEEEeecccccccCcccc
Confidence 788999999999999999997 99999999996 57778999999999999998752 111 1
Q ss_pred ------cEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHH
Q psy14489 152 ------NKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLR 225 (284)
Q Consensus 152 ------~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~ 225 (284)
.+.++.+.+.+++|++|+||+|+++|+| |||+|||||||||||.+||++|||+|+|+++.+.- +. ..
T Consensus 154 ~~~~~~~e~~~~~~vl~~lgl~~~q~id~~iL~G--~Dy~~GI~GIG~ktA~kLi~~~~sle~i~~~~~~~---~~-~~- 226 (292)
T PRK03980 154 VYVEVKPELIELEEVLKELGITREQLIDIAILVG--TDYNPGIKGIGPKTALKLIKKHGDLEKVLEERGFE---IE-NY- 226 (292)
T ss_pred ccccccceeeeHHHHHHHhCCCHHHHHHHHHhcC--CCCCCCCCCccHHHHHHHHHHCCCHHHHHHhccCC---CC-CH-
Confidence 1368999999999999999999999999 99999999999999999999999999999865411 00 11
Q ss_pred HhHhhchhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHH-HHcCch
Q psy14489 226 FALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYKLN 277 (284)
Q Consensus 226 ~~~~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~-~~~~~~ 277 (284)
.+.-.+..++++..+ ..++|+.||.+.|.+|| ++.+|+
T Consensus 227 ---------~~~r~~f~~p~v~~~-----~~~~~~~pd~~~l~~fl~~e~~f~ 265 (292)
T PRK03980 227 ---------DEIREFFLNPPVTDD-----YELKWKEPDKEGIIEFLVEEHDFS 265 (292)
T ss_pred ---------HHHHHHhcCCCCCCC-----CCccCCCCCHHHHHHHHhccCCCC
Confidence 111122233444333 47899999999999997 699986
No 15
>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=99.96 E-value=5.3e-32 Score=211.03 Aligned_cols=99 Identities=51% Similarity=0.718 Sum_probs=69.4
Q ss_pred CChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhh-hhhccHHHhHhhchhhhhhhhhcccc
Q psy14489 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKG-VIGKNLRFALNWLPKLKKILTIKTDC 244 (284)
Q Consensus 166 ~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~-~~~~~l~~~~~~~~l~~~L~~l~~d~ 244 (284)
|+|+|++||++|+||+|||||||||||+|||.+||++|||+|+|+++++++++ +++++|.++++++++||+|++|++|+
T Consensus 1 V~P~q~~D~~aL~GD~sDNIPGV~GIG~KtA~~LL~~ygsle~i~~~~~~~~~~k~~~~l~~~~e~a~ls~~L~tl~~dv 80 (101)
T PF01367_consen 1 VPPEQIADYKALVGDSSDNIPGVPGIGPKTAAKLLQEYGSLENILANLDEIKGKKIREKLRENKEQALLSRKLATLKTDV 80 (101)
T ss_dssp --GHHHHHHCCCC-CCCCTB---TTSTCHCCCCCHHHHTSCHCCCCC-SSS-TSCCCHHHHTSCCCCCCHHHHH-H-S--
T ss_pred CCHHHHHHHHHHcCCcccCCCCCCCCCHHHHHHHHHHcCCHHHHHHhHHhccccHHHHHHHHHHHHHHHhHHHhhhhcCC
Confidence 57999999999999999999999999999999999999999999999999988 89999999999999999999999999
Q ss_pred CCCCCcCCCccccccCCCCHHHHH
Q psy14489 245 DLTKNIVSIPESLILQPKDEKLLM 268 (284)
Q Consensus 245 ~~~~~~~~~~~~l~~~~~~~~~l~ 268 (284)
|++.+ ++++.+..+|.+++.
T Consensus 81 ~l~~~----l~~l~~~~~d~~~l~ 100 (101)
T PF01367_consen 81 PLPFS----LEDLRLQPPDREKLI 100 (101)
T ss_dssp -------------------HHHH-
T ss_pred CCCCC----cchhccCCCCHHHhc
Confidence 99999 999999999998875
No 16
>KOG2519|consensus
Probab=99.93 E-value=3.8e-25 Score=208.80 Aligned_cols=253 Identities=22% Similarity=0.292 Sum_probs=185.2
Q ss_pred cEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCC----
Q psy14489 4 TLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK---- 79 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~---- 79 (284)
+-+.||||.|+||..-+...-.+..|.+|..+.|++....+++ .++ ..+|+||||.+|.+..+.+.....-|..
T Consensus 29 kkVAID~s~~lyqfl~~v~~~~~~~~~~~~HL~g~f~Rt~~l~-~~g-i~Pv~VfDG~pP~lKs~e~~kR~~rr~~a~~~ 106 (449)
T KOG2519|consen 29 KKVAIDASMWLYQFLIVVRSCRNEAGEPTSHLMGMFYRTIRLI-ENG-IKPVYVFDGKPPDLKSQELAKRSERRSEADKE 106 (449)
T ss_pred ceEEEecceeHhhHhhhhccccccCCCchHHHHHHHHHHHHHH-HcC-CcEEEEECCCCCCcchHHHHHHHHHhhhhhhh
Confidence 4689999999999988765334667889999999999999999 455 4679999997766543333222222211
Q ss_pred -CCh-------hH-----------HHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCcccc
Q psy14489 80 -MPY-------NL-----------ILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQ 140 (284)
Q Consensus 80 -~p~-------~l-----------~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~q 140 (284)
.|+ ++ .++-+.++.+|..+|||++.+|+ ||..+||.|++ .|.-..++|.|.|.+.
T Consensus 107 ~~~~~e~~~~~~~~k~~~r~vkvtk~~~dEak~LL~lmGIp~i~ap~-EAEAqCA~Lnk-----~g~V~~~at~DsD~l~ 180 (449)
T KOG2519|consen 107 LKPAKEAGAKENMEKFFSRLVKVTKQHNDEAKRLLSLMGIPVLDAPG-EAEAQCAALNK-----AGKVYAVATEDSDALT 180 (449)
T ss_pred hhhHHHhhhHHHHHHHHHHHhhhcchhhHHHHHHHHHcCCeeecCCc-hHHHHHHHHhh-----cCceeeeeccccchhh
Confidence 111 11 12234789999999999999886 99999999998 4567889999999999
Q ss_pred ccCCCe-E--EE-e----CcEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHH-
Q psy14489 141 LVSNKI-A--LI-N----NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN- 211 (284)
Q Consensus 141 l~~~~v-~--~~-~----~~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~- 211 (284)
+..+.+ + .. . -..+|+...+.+.+|++-++|+|+++|+| ||++++|.|||+++|.+||++|+++++|++
T Consensus 181 fg~~~~lr~l~~s~~~~~pv~e~~~~~il~~l~l~~~~fidL~lLlG--CDYc~~I~Gig~~~al~lir~~~~i~~ile~ 258 (449)
T KOG2519|consen 181 FGAPVKLRHLIHSLASGLPVSEYDMSRILEGLGLSRESFIDLCLLLG--CDYCPTIRGIGPKKALKLIRQHGDIENILEI 258 (449)
T ss_pred ccCHHHHHHhccchhcCCCeEEeeHHHHHHHhcccHHHHHHHHHHhc--CcccccccccChHHHHHHHHHhcCHHHHhhh
Confidence 987632 1 11 1 24678999999999999999999999999 999999999999999999999999999998
Q ss_pred hhhhhhhhhhccHHH-hHhhchhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHHH-HcCch
Q psy14489 212 NANNIKGVIGKNLRF-ALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLFN-KYKLN 277 (284)
Q Consensus 212 ~~~~~~~~~~~~l~~-~~~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~~-~~~~~ 277 (284)
+.+..+-++.+++.- ..+.++++ .+++.+.. .-++.|..||.+.+.+|+. +.+|.
T Consensus 259 ~~~~~~~~ip~~w~~~~~r~~f~~-------p~~~~~~~----~~~i~w~~pd~~~li~fl~~~~~f~ 315 (449)
T KOG2519|consen 259 NSDLKEYPIPEDWSYKLARKLFLE-------PEFPNPES----ILDLKWKTPDTEGLIQFLVGEKQFN 315 (449)
T ss_pred ccchhhcCCCCCccHHHHHHHhcC-------cccCCccc----eeecccCCCChHHHHHHHHhhhccC
Confidence 543211123333221 12222222 12232222 2478999999999999986 77775
No 17
>KOG2518|consensus
Probab=99.87 E-value=1.4e-21 Score=186.82 Aligned_cols=195 Identities=21% Similarity=0.225 Sum_probs=151.5
Q ss_pred cEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCC-------CccccccCchhhhC
Q psy14489 4 TLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKG-------KNFRNILYPSYKAT 76 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~-------~~~R~~l~~~YKa~ 76 (284)
..+.|||+.|+||+.++|.. ....|.||.-...|+..-.+++..++. .+|+||||+. ..-|++ .+|+|
T Consensus 25 ~tvavD~y~WLhrg~~~Ca~-el~~~~pT~ryi~y~ik~v~lL~~~gi-kPilVFDG~~LP~K~~te~~Rr~---~R~~n 99 (556)
T KOG2518|consen 25 KTVAVDGYCWLHRGALACAE-KLAKGKPTDRYIQFFIKRVKLLLSYGI-KPILVFDGDPLPSKKETERKRRE---RRKKN 99 (556)
T ss_pred ceEEEehhhHHhhhHHhHHH-HHhcCCChHHHHHHHHHHHHHHHhcCC-eEEEEecCCCcccccccchHHHH---HHHHh
Confidence 57899999999999999863 346789999999999999999999885 6799999863 122333 23333
Q ss_pred CCCC------------ChhHHHH-------HHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCc
Q psy14489 77 RKKM------------PYNLILQ-------INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKD 137 (284)
Q Consensus 77 R~~~------------p~~l~~q-------~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkD 137 (284)
+... -+-+... ...+.++|+..|+.++++| ||||.++++|.+ .|.--.|+|.|+|
T Consensus 100 ~~~a~~ll~~G~~~~A~~~fqr~VdIT~~ma~~lI~~~r~~nVe~IVAP-yEADAQlayL~~-----~~~i~~IITEDSD 173 (556)
T KOG2518|consen 100 LDAAEQLLAEGKESNARECFQRCVDITPEMAHKLIQYLRSQNVEYIVAP-YEADAQLAYLER-----EGIVDAIITEDSD 173 (556)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHhccCcHHHHHHHHHHHHHcCCceEecC-ccccchhHHHHh-----cCcceEEEecccc
Confidence 3221 1112211 1245677888899999776 999999999986 5677899999999
Q ss_pred cccccCCCeEE-Ee---CcEeeeHhHHHHHhCC----ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHH
Q psy14489 138 MAQLVSNKIAL-IN---NNKIHDRTTIISRFGV----SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENI 209 (284)
Q Consensus 138 l~ql~~~~v~~-~~---~~~~~~~~~~~~~~G~----~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i 209 (284)
|+++++..|.. ++ +..+++.....+.+++ +-++|..+|+|.| ||+.+||||||-+||.++|.+|.+.|.+
T Consensus 174 Ll~fGc~~vifK~d~~G~~le~~~~~l~~~~~l~~~~~~ekfr~mciLSG--CDYl~slpGvGl~tA~k~l~k~~~~d~v 251 (556)
T KOG2518|consen 174 LLVFGCKKVIFKMDSFGNGLEINRSKLPECKPLGDKFTEEKFRRMCILSG--CDYLSSLPGVGLATAHKLLSKYNTPDRV 251 (556)
T ss_pred ccccCchhheeeccCCCCcccccHhhhhhccccccccCHHHHHHHHHhcC--CcccccCccccHHHHHHHHHhcCcHHHH
Confidence 99999987633 33 4566777766666655 4688999999999 9999999999999999999999999999
Q ss_pred HH
Q psy14489 210 IN 211 (284)
Q Consensus 210 ~~ 211 (284)
+.
T Consensus 252 i~ 253 (556)
T KOG2518|consen 252 II 253 (556)
T ss_pred HH
Confidence 74
No 18
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=99.86 E-value=4.1e-21 Score=198.84 Aligned_cols=178 Identities=16% Similarity=0.231 Sum_probs=130.6
Q ss_pred HHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeE-EE-e--C-cEeeeHhHHHH
Q psy14489 88 INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIA-LI-N--N-NKIHDRTTIIS 162 (284)
Q Consensus 88 ~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~-~~-~--~-~~~~~~~~~~~ 162 (284)
+..++++|+.+|||++.+| +|||++||.|++ .|....|+|.|+|++.+++++|. -+ + + ...|+.+.+.+
T Consensus 774 ~~~~~~LL~~~GIP~i~AP-~EAEAqcA~L~~-----~G~vd~V~TeDsD~llFGa~~v~rn~~~~~~~ve~~~~~~i~~ 847 (1034)
T TIGR00600 774 ILESQELLRLFGIPYIVAP-MEAEAQCAILDL-----LDQTSGTITDDSDIWLFGARHVYKNFFNQNKFVEYYQYVDIHN 847 (1034)
T ss_pred HHHHHHHHHHCCCCeeeCC-ccHHHHHHHHHh-----CCCeEEEEccccceeccCCceeeecccCCCCceEEeeHHHHHH
Confidence 4578999999999999998 599999999987 68889999999999999887653 11 2 1 45789999999
Q ss_pred HhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcC--CHHHHHHhhh---hhhh-h-hh-------ccHHH--
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYN--SLENIINNAN---NIKG-V-IG-------KNLRF-- 226 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~g--sle~i~~~~~---~~~~-~-~~-------~~l~~-- 226 (284)
.+|+++++|+++++|+| |||.+||||||||||.+||++|| +++++++-.+ .+.. . .. .+...
T Consensus 848 ~lglt~~qli~laiL~G--~DY~~GI~GIGpktAl~li~~~~~~~le~L~~f~~w~~~~~~~~~~~~~~~~~~~~~~~~~ 925 (1034)
T TIGR00600 848 QLGLDRNKLINLAYLLG--SDYTEGIPTVGPVSAMEILNEFPGDGLEPLLKFKEWWHEAQKDKKKRENPNDTKVKKKLRL 925 (1034)
T ss_pred HhCCCHHHHHHHHHeeC--CCCCCCCCcccHHHHHHHHHHcCCCCHHHHHHHHHHHHHhhhccccccccchhhhhhcccc
Confidence 99999999999999999 99999999999999999999999 4777764221 1100 0 00 00000
Q ss_pred -hHhhchhhhhhhhhccccCCCCCcCCCccccccCCCCHHHHHHHH-HHcCch
Q psy14489 227 -ALNWLPKLKKILTIKTDCDLTKNIVSIPESLILQPKDEKLLMQLF-NKYKLN 277 (284)
Q Consensus 227 -~~~~~~l~~~L~~l~~d~~~~~~~~~~~~~l~~~~~~~~~l~~~~-~~~~~~ 277 (284)
....-+=+..+..+..++.+..+ ...+.|+.||.+.|+.|| .++||+
T Consensus 926 ~~lp~~FP~~~V~~~yl~P~V~~~----~~~f~W~~PD~e~L~~Fl~~~~gws 974 (1034)
T TIGR00600 926 LQLTPGFPNPAVADAYLRPVVDDS----KGSFLWGKPDLDKIREFCQRYFGWN 974 (1034)
T ss_pred cccCCCCCcHHHHHHhcCCCCCCC----cCCCCCCCCCHHHHHHHHHHccCCC
Confidence 01111111223333333334333 357899999999999997 588886
No 19
>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=99.85 E-value=1.1e-21 Score=145.53 Aligned_cols=73 Identities=44% Similarity=0.722 Sum_probs=66.8
Q ss_pred HhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhhhhhhhhhccHHHhHhhchhhhhh
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNANNIKGVIGKNLRFALNWLPKLKKI 237 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~~~~~~~~l~~~L 237 (284)
++|++|+||+++++|+||+|||+|||||||+|||.+||++|||+++++++++.++ .++++.++.+.+++++.|
T Consensus 2 ~~g~~~~q~~d~~~L~GD~~D~i~gv~giG~k~A~~ll~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~l 74 (75)
T cd00080 2 KLGLTPEQFIDLAILVGDKSDNIPGVPGIGPKTALKLLKEYGSLENLLENLDKIK--LREKLLEHKELAKLSKLL 74 (75)
T ss_pred CCCcCHHHHHHHHHHcCCccccCCCCCcccHHHHHHHHHHhCCHHHHHHHHHHHh--HHHhhhccHHHHHHHHhh
Confidence 5899999999999999999999999999999999999999999999999998774 677788888888887765
No 20
>smart00279 HhH2 Helix-hairpin-helix class 2 (Pol1 family) motifs.
Probab=99.65 E-value=1.1e-16 Score=101.84 Aligned_cols=36 Identities=64% Similarity=1.154 Sum_probs=34.9
Q ss_pred hhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhc
Q psy14489 168 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQY 203 (284)
Q Consensus 168 p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~ 203 (284)
|+||+++++|+||++||||||||||+|||.+||++|
T Consensus 1 p~q~~~~~~L~GD~~dni~Gv~giG~ktA~~ll~~~ 36 (36)
T smart00279 1 PEQLIDYAILVGDYSDNIPGVKGIGPKTALKLLREF 36 (36)
T ss_pred CHHHHHHHHHhCcCCCCCCCCCcccHHHHHHHHHhC
Confidence 689999999999999999999999999999999986
No 21
>KOG2520|consensus
Probab=99.53 E-value=8.5e-14 Score=140.87 Aligned_cols=128 Identities=23% Similarity=0.340 Sum_probs=106.0
Q ss_pred hhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeE--EE
Q psy14489 72 SYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIA--LI 149 (284)
Q Consensus 72 ~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~--~~ 149 (284)
.|+..|-... --...+..|+++|+.+|||+|.+|+ ||+.+||.|-. .+....|+|.|.|.+.+++-+|+ +|
T Consensus 453 k~~~~r~~~e-vt~~m~~e~QElL~~fGIPyI~APm-EAEAQCa~Le~-----~~LvdGiITDDSDV~LFGg~~VYrn~F 525 (815)
T KOG2520|consen 453 KYIQSRGADE-VTSDMFKELQELLRLFGIPYIIAPM-EAEAQCAFLEQ-----LNLVDGIITDDSDVFLFGGTRVYRNFF 525 (815)
T ss_pred HHHHhccCch-hHHHHHHHHHHHHHHcCCceecccc-cHHHHHHHHHH-----cCCcceeecccccceeeccchhhHHHh
Confidence 5666665543 2223356799999999999999996 99999999876 56678899999999999986653 22
Q ss_pred e--C-cEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHH
Q psy14489 150 N--N-NKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLEN 208 (284)
Q Consensus 150 ~--~-~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~ 208 (284)
+ + ...|....+...||+....++.+..|.| ||+..|++||||.+|..+|.+|+.-++
T Consensus 526 ~knk~ve~y~~~di~kel~l~R~~lI~lA~LlG--sDYt~Gl~giGpV~AlEil~Efp~~~~ 585 (815)
T KOG2520|consen 526 NKNKYVEKYQLDDIEKELGLDRPNLISLAQLLG--SDYTEGLKGIGPVSALEILAEFPGDEN 585 (815)
T ss_pred hcCccceeeehHHHHHHHccCchhhHHHHHhcc--cccccCCCcccchHHHHHHHHcCCcch
Confidence 3 2 3678899999999999999999999999 999999999999999999999994444
No 22
>PF00867 XPG_I: XPG I-region; InterPro: IPR006086 This entry represents endonucleases that cleave 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. The endonuclease binds 2 magnesium ions per subunit. which probably participate in the reaction catalyzed by the enzyme. May bind an additional third magnesium ion after substrate binding.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A 2IZO_A 1A77_A 1A76_A 3QEA_Z 3QE9_Y 3QEB_Z ....
Probab=99.03 E-value=5.3e-10 Score=86.29 Aligned_cols=79 Identities=23% Similarity=0.400 Sum_probs=61.2
Q ss_pred hcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCe-EEEe--C-----------cEeeeHhHHHH
Q psy14489 97 AIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKI-ALIN--N-----------NKIHDRTTIIS 162 (284)
Q Consensus 97 ~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v-~~~~--~-----------~~~~~~~~~~~ 162 (284)
.+|+|++.+| +|||.++|.|.+ .|.-..|+|+|+|++.++.+.| +-++ + ...++.+.+.+
T Consensus 2 ~~gv~~i~AP-~EAeAq~A~L~~-----~g~vd~V~t~DsD~l~fG~~~vi~~~~~~~~~~~~~~~~~~~~~~~~~~i~~ 75 (94)
T PF00867_consen 2 LMGVPYIVAP-YEAEAQCAYLER-----NGLVDAVITEDSDLLLFGAPKVIRKLSDKSSGKCSSKSEKEVEVIDLDDILK 75 (94)
T ss_dssp HHT-EEEE-S-S-HHHHHHHHHH-----TTSSSEEE-SSSHHHHTT-SEEEESST-CSCCSTS-CCESEEEEEEHHHHHH
T ss_pred CCCCeEEEcC-chHHHHHHHHHH-----hcceeEEEecCCCEEeeCCCEEEEeccccccCCcccccccceEEEEHHHHHH
Confidence 5799999999 699999999997 5667789999999999977643 2111 1 24788999999
Q ss_pred HhCCChhHHHhhhhhcCCCCC
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSD 183 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sD 183 (284)
..|++.+||+++++|+| ||
T Consensus 76 ~l~l~~~~fi~~~iL~G--~D 94 (94)
T PF00867_consen 76 ELGLTREQFIDLCILCG--CD 94 (94)
T ss_dssp HHTTSHHHHHHHHHHHH--ET
T ss_pred HcCCCHHHHHHHheecC--CC
Confidence 99999999999999999 65
No 23
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=98.25 E-value=1.5e-06 Score=73.92 Aligned_cols=123 Identities=21% Similarity=0.306 Sum_probs=75.4
Q ss_pred EEEecchHHHHHhccCCCccCC--CCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCChh
Q psy14489 6 LLVDGSSCIYRAFYALPDIRNI--DNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYN 83 (284)
Q Consensus 6 llIDg~~l~~r~~~a~~~l~~~--~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~~ 83 (284)
|||||+|++|. +|.+... ++....|-..++..|..... +....++||||+... +.-... ++.
T Consensus 1 LlIDGYNli~~----~~~l~~~~~~~~l~~aR~~Li~~L~~y~~-~~~~~v~VVFDa~~~-------~~~~~~----~~~ 64 (166)
T PF05991_consen 1 LLIDGYNLIHA----WPELRSLAERGDLEAARERLIEMLSEYAQ-FSGYEVIVVFDAYKV-------PGGSEE----REE 64 (166)
T ss_pred CeEcchhhhCC----CHHHHhhcCcCCHHHHHHHHHHHHHHHhc-ccCCEEEEEEeCCcC-------CCCCce----eee
Confidence 68999999975 3433221 23333444455555554443 445789999998320 000000 000
Q ss_pred HHHHHHHHHHHHHhcCCcEEe-eCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEeCcEeeeHhHHHH
Q psy14489 84 LILQINLIHQMVKAIGWPILI-IKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIIS 162 (284)
Q Consensus 84 l~~q~~~i~~~l~~~gi~~~~-~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~~~~~~~~~~~~~ 162 (284)
.-|+.++. ..|-.||++|--++..... .+..++|+|+|....+.+... ....++.+.+..
T Consensus 65 -------------~~gi~Vvft~~~~tAD~~Ie~~v~~~~~-~~~~v~VVTSD~~iq~~~~~~-----GA~~iss~ef~~ 125 (166)
T PF05991_consen 65 -------------YGGIEVVFTKEGETADDYIERLVRELKN-RPRQVTVVTSDREIQRAARGR-----GAKRISSEEFLR 125 (166)
T ss_pred -------------eCceEEEECCCCCCHHHHHHHHHHHhcc-CCCeEEEEeCCHHHHHHHhhC-----CCEEEcHHHHHH
Confidence 13676644 5578999999999998765 578999999999998876320 334555555544
Q ss_pred H
Q psy14489 163 R 163 (284)
Q Consensus 163 ~ 163 (284)
.
T Consensus 126 ~ 126 (166)
T PF05991_consen 126 E 126 (166)
T ss_pred H
Confidence 3
No 24
>smart00484 XPGI Xeroderma pigmentosum G I-region. domain in nucleases
Probab=98.08 E-value=1.7e-05 Score=58.44 Aligned_cols=64 Identities=23% Similarity=0.339 Sum_probs=50.3
Q ss_pred hcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCe-EEEe---C----cEeeeHhHHHHHhCC
Q psy14489 97 AIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKI-ALIN---N----NKIHDRTTIISRFGV 166 (284)
Q Consensus 97 ~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v-~~~~---~----~~~~~~~~~~~~~G~ 166 (284)
.+|||++.+|+ ||+.++|.|.+ .|.-..|+|.|.|++.++.+++ +-++ + ...++.+.+.+++|+
T Consensus 2 ~~gi~~i~AP~-eAeAq~A~L~~-----~g~vdav~s~D~D~llfG~~~vi~~~~~~~~~~~~~~~i~~~~vl~~L~l 73 (73)
T smart00484 2 LMGIPYIVAPY-EAEAQCAYLAK-----SGLVDAIITEDSDLLLFGAPRLYRNLFFSGKKKLEFRIIDLESVLKELGL 73 (73)
T ss_pred cCCCeEEEcCC-cHHHHHHHHHh-----CCCeeEEEcCccceEecCCcEEEEecccCCCcccCeEEEEHHHHHHHcCC
Confidence 47999999996 99999999997 4667799999999999988864 3333 2 346777777777663
No 25
>smart00485 XPGN Xeroderma pigmentosum G N-region. domain in nucleases
Probab=97.92 E-value=1.3e-05 Score=62.07 Aligned_cols=69 Identities=17% Similarity=0.242 Sum_probs=46.1
Q ss_pred CcEEEEecchHHHHHhccCCCccCCCCcchh-HHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhh
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVG-ALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYK 74 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~-ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YK 74 (284)
.+.+.||+++|+||+++++.. ....+.++. .+.+++..+.++++ ++ ..+|+||||..+....+....-+
T Consensus 24 g~~vaIDa~~wl~~~~~~~~~-~~~~~~~~~~~l~~~~~rl~~L~~-~~-I~PifVFDG~~~~~K~~t~~~R~ 93 (99)
T smart00485 24 GKTLAIDASIWLYQFLTACRE-KLGTPLPNSKHLMGLFYRTCRLLE-FG-IKPIFVFDGKPPPLKSETLAKRR 93 (99)
T ss_pred CceEeccHHHHHHHHHHHHhh-hhcCCCCchHHHHHHHHHHHHHHH-CC-CeEEEEECCCCchhhHHHHHHHH
Confidence 468999999999999998742 111122333 78888888888875 45 45799999965544443333333
No 26
>PF00752 XPG_N: XPG N-terminal domain; InterPro: IPR006085 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. People's skin cells with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-G is one of the most rare and phenotypically heterogeneous of XP, showing anything from slight to extreme dysfunction in DNA excision repair [, ]. XP-G can be corrected by a 133 Kd nuclear protein, XPGC []. XPGC is an acidic protein that confers normal UV resistance in expressing cells []. It is a magnesium-dependent, single-strand DNA endonuclease that makes structure-specific endonucleolytic incisions in a DNA substrate containing a duplex region and single-stranded arms [, ]. XPGC cleaves one strand of the duplex at the border with the single-stranded region []. XPG belongs to a family of proteins that includes RAD2 from Saccharomyces cerevisiae (Baker's yeast) and rad13 from Schizosaccharomyces pombe (Fission yeast), which are single-stranded DNA endonucleases [, ]; mouse and human FEN-1, a structure-specific endonuclease; RAD2 from fission yeast and RAD27 from budding yeast; fission yeast exo1, a 5'-3' double-stranded DNA exonuclease that may act in a pathway that corrects mismatched base pairs; yeast DHS1, and yeast DIN7. Sequence alignment of this family of proteins reveals that similarities are largely confined to two regions. The first is located at the N-terminal extremity (N-region) and corresponds to the first 95 to 105 amino acids. The second region is internal (I-region) and found towards the C terminus; it spans about 140 residues and contains a highly conserved core of 27 amino acids that includes a conserved pentapeptide (E-A-[DE]-A-[QS]). It is possible that the conserved acidic residues are involved in the catalytic mechanism of DNA excision repair in XPG. The amino acids linking the N- and I-regions are not conserved. This entry represents the N-terminal of XPG.; GO: 0004518 nuclease activity, 0006281 DNA repair; PDB: 1A77_A 1A76_A 1MC8_B 3QEB_Z 3QEA_Z 3QE9_Y 1UL1_Z 3Q8K_A 3Q8M_A 3Q8L_A ....
Probab=97.85 E-value=2.1e-05 Score=61.03 Aligned_cols=60 Identities=15% Similarity=0.152 Sum_probs=40.0
Q ss_pred CcEEEEecchHHHHHhccCCCccCCCCcc-hhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCcc
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFP-VGALYGTIKMLRKLYKNYRATYIACIFDAKGKNF 65 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~~g~~-t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~ 65 (284)
.+.+.|||+.|+||+++++..- ...+.. +..+.+++..+..++. ++ ..+||||||..+..
T Consensus 26 g~~vaID~s~wl~~~~~~~~~~-~~~~~~~~~~~~~~~~r~~~L~~-~g-I~PifVFDG~~~~~ 86 (101)
T PF00752_consen 26 GKRVAIDASCWLHQFLFSCREE-LGQGVGTDSHLRGLFSRLCRLLE-HG-IKPIFVFDGKPPPL 86 (101)
T ss_dssp TCEEEEEHHHHHHHHHHHSBCT-TSCB-BS-HHHHHHHHHHHHHHH-TT-EEEEEEE--STTGG
T ss_pred CCEEEEEcHHHHHHHHHHhHHH-hccccchHHHHHHHHHHHHHHHH-CC-CEEEEEECCCCchh
Confidence 4689999999999999987531 122222 4677888888887765 45 46799999965433
No 27
>PF12813 XPG_I_2: XPG domain containing
Probab=97.56 E-value=0.00036 Score=63.08 Aligned_cols=79 Identities=20% Similarity=0.238 Sum_probs=59.3
Q ss_pred HHHHHHHHhc---CCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccC--C-CeEEEe------------
Q psy14489 89 NLIHQMVKAI---GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVS--N-KIALIN------------ 150 (284)
Q Consensus 89 ~~i~~~l~~~---gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~--~-~v~~~~------------ 150 (284)
+.+.+.|+.+ |++++.++| |||.-||.+|++. | ..|+|+|+||+-+-- . ++.-++
T Consensus 7 ~~~~e~L~~~~~~~~~~~~~~~-EAD~~~A~~A~~~----~--~~VLt~DSDf~I~dlg~~~~yipl~~l~~~~~~~~~~ 79 (246)
T PF12813_consen 7 PAFIEALRESWRYGVPVVQCPG-EADRECAALARKW----G--CPVLTNDSDFLIHDLGQKGGYIPLDSLEWDSVPKTGS 79 (246)
T ss_pred HHHHHHHHHHhhcCCcEEEcCc-cchHHHHHHHHHc----C--CeEEccCCCEEEeccCCCceEEEeeeeEeecccccCC
Confidence 5677888888 999999998 9999999999763 3 489999999998643 1 222222
Q ss_pred ----CcEeeeHhHHHHHhCCChhHHHhhhh
Q psy14489 151 ----NNKIHDRTTIISRFGVSPEKIVDYFS 176 (284)
Q Consensus 151 ----~~~~~~~~~~~~~~G~~p~q~~~~~~ 176 (284)
....|+++.+..++|+. .++.+.+
T Consensus 80 ~~~i~~~~y~~~~i~~~l~l~--~Lp~lA~ 107 (246)
T PF12813_consen 80 GSYISAKVYSPDKICKRLGLP--LLPLLAY 107 (246)
T ss_pred CCeeEEEEEcHHHHHHHcCCc--hhHHHHH
Confidence 13568999999999986 5544444
No 28
>COG3688 Predicted RNA-binding protein containing a PIN domain [General function prediction only]
Probab=97.34 E-value=0.0012 Score=55.18 Aligned_cols=102 Identities=25% Similarity=0.364 Sum_probs=59.2
Q ss_pred CCCcEEEEecchHHHHHhccCCCc---cCCCCcchhHHHHHHHHHHHHHH---hcCCCEEEEEEeCCC-CccccccCchh
Q psy14489 1 MQNTLLLVDGSSCIYRAFYALPDI---RNIDNFPVGALYGTIKMLRKLYK---NYRATYIACIFDAKG-KNFRNILYPSY 73 (284)
Q Consensus 1 m~~~~llIDg~~l~~r~~~a~~~l---~~~~g~~t~ai~gf~~~l~~l~~---~~~~~~~i~~fD~~~-~~~R~~l~~~Y 73 (284)
|++.+|||||+|++= +.|.+ ...+|.. .|-. .|..-+- ++....++||||.-- +. +-..|
T Consensus 1 ~~~~iLLVDGYNmIg----aWp~Lk~lkd~~~LE-~AR~----~LIe~l~~Y~s~~g~~iivVFDA~~v~g----~~~~~ 67 (173)
T COG3688 1 MKMRILLVDGYNMIG----AWPELKQLKDRNGLE-AARD----KLIEALAEYQSFTGYKIIVVFDAHYVPG----VGREY 67 (173)
T ss_pred CCceEEEeccchhcc----ccHHHHHHHhhccHH-HHHH----HHHHHHHHhhcccCceEEEEEEcccccc----ccccc
Confidence 677899999999972 22322 1222221 1212 2222222 345578999999721 11 12233
Q ss_pred hhCCCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCC
Q psy14489 74 KATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDK 136 (284)
Q Consensus 74 Ka~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~Dk 136 (284)
+.+|-. .++...|--||--|-.+|.......-..|+|+|+|.
T Consensus 68 ~~~~vs---------------------vvyT~~~ETADs~IEr~~~el~~~~t~~V~VaTSD~ 109 (173)
T COG3688 68 KNHRVS---------------------VVYTKEGETADSFIERYVAELRNAATHQVIVATSDR 109 (173)
T ss_pred cccceE---------------------EEEecCCccHHHHHHHHHHHHhccccceEEEEeCch
Confidence 333221 146678888999999999877631334889999874
No 29
>TIGR00600 rad2 DNA excision repair protein (rad2). All proteins in this family for which functions are known are flap endonucleases that generate the 3' incision next to DNA damage as part of nucleotide excision repair. This family is related to many other flap endonuclease families including the fen1 family. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.11 E-value=0.00041 Score=73.53 Aligned_cols=74 Identities=20% Similarity=0.202 Sum_probs=54.8
Q ss_pred CcEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCC
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKK 79 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~ 79 (284)
.+.+.||+++|+||+.+++.. ..........+.||+..+.+|+. ++ ..+|+||||+.+..++......+..|..
T Consensus 24 Gk~vAIDasiWL~q~l~~vr~-~~g~~l~n~hl~g~f~Ri~~Ll~-~g-I~PVfVFDG~~p~lK~~t~~~R~~rR~~ 97 (1034)
T TIGR00600 24 GKRLAVDISIWLNQALKGVRD-REGNAIKNSHLLTLFHRLCKLLF-FR-IRPIFVFDGGAPLLKRQTLAKRRQRRDG 97 (1034)
T ss_pred CeEEEechHHHHHHHHHHHHh-ccCCccCCHHHHHHHHHHHHHHH-CC-CeEEEEECCCCchHhHHHHHHHHHHHHH
Confidence 478999999999999988742 11222345788999999999987 44 4679999998777666666566655544
No 30
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=97.07 E-value=0.00033 Score=50.12 Aligned_cols=26 Identities=38% Similarity=0.643 Sum_probs=21.8
Q ss_pred CCCccChhhHHHHHHhcCCHHHHHHh
Q psy14489 187 GVKKIGPKTAVKLLNQYNSLENIINN 212 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gsle~i~~~ 212 (284)
||||||+++|..|+++|||++++..+
T Consensus 7 GI~~VG~~~ak~L~~~f~sl~~l~~a 32 (64)
T PF12826_consen 7 GIPGVGEKTAKLLAKHFGSLEALMNA 32 (64)
T ss_dssp TSTT--HHHHHHHHHCCSCHHHHCC-
T ss_pred CCCCccHHHHHHHHHHcCCHHHHHHc
Confidence 89999999999999999999998754
No 31
>PF09293 RNaseH_C: T4 RNase H, C terminal; 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: 1TFR_A 3H8S_A 2IHN_A 3H7I_A 3H8W_A 3H8J_A.
Probab=96.81 E-value=0.00019 Score=57.55 Aligned_cols=103 Identities=20% Similarity=0.166 Sum_probs=57.1
Q ss_pred ChhHHHhhhhhcCCCCCCCCCCCccCh------------hhHHHHHHhcCCHHHHHHhhhhhhhhhhccHH--HhHhhch
Q psy14489 167 SPEKIVDYFSLIGDMSDNLPGVKKIGP------------KTAVKLLNQYNSLENIINNANNIKGVIGKNLR--FALNWLP 232 (284)
Q Consensus 167 ~p~q~~~~~~L~GD~sDni~Gv~giG~------------ktA~~LL~~~gsle~i~~~~~~~~~~~~~~l~--~~~~~~~ 232 (284)
+|+.-+-.+++-||.+|||++|.-.+. .+..++|++..+-|+. +.+. +....-.
T Consensus 2 s~~~d~~~KiiKGDkkDgVa~Ik~r~D~~~t~vegeR~p~~~~~~l~~~~~~ed~------------~~llt~e~~~Rf~ 69 (122)
T PF09293_consen 2 SPEMDLMTKIIKGDKKDGVASIKVRSDFIVTRVEGERTPPISTKWLESIFDMEDP------------KKLLTEEQYKRFK 69 (122)
T ss_dssp HHHHHHHHHHHHEBGGGTBE-TTS-TTHHHH--TT-------HHHHHHHH-GGGH------------HHHS-HHHHHHHH
T ss_pred ChhHHHHHHHHcCCccCCcCceeeccCeeEeccccccCCcccHHHHHHHhCcchH------------HHhcCHHHHHHHh
Confidence 367778899999999999999976543 3344444433111111 1111 1133444
Q ss_pred hhhhhhhhccccCCCCCcCCCccccc-cCCCCHHHHHHHHHHcCchhHHhhc
Q psy14489 233 KLKKILTIKTDCDLTKNIVSIPESLI-LQPKDEKLLMQLFNKYKLNKLNFLM 283 (284)
Q Consensus 233 l~~~L~~l~~d~~~~~~~~~~~~~l~-~~~~~~~~l~~~~~~~~~~~~~~~~ 283 (284)
.|+.|+.++. +|-... .+|++.+. ..++....+..+|.+.|+..++..+
T Consensus 70 eN~~LIDFd~-IPd~I~-~~Iie~yn~~k~~~rgk~y~YFvk~~L~kL~~~i 119 (122)
T PF09293_consen 70 ENRVLIDFDY-IPDDIR-DSIIEEYNNYKPPPRGKMYKYFVKNGLSKLLDKI 119 (122)
T ss_dssp HHHHHH-GGG-S-HHHH-HHHHHHHHT-----TTHHHHHHHHTT-CCGCCGG
T ss_pred hhhhhhcHhh-chHHHH-HHHHHHHhcCCCCCccchHHHHHHhhHHHHHHHh
Confidence 6667777653 332221 25677777 5677789999999999999988765
No 32
>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=95.63 E-value=0.039 Score=48.02 Aligned_cols=70 Identities=23% Similarity=0.265 Sum_probs=44.2
Q ss_pred CCCcccccc-CCCeEEEeCcEeeeHhHHHHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHH
Q psy14489 134 NDKDMAQLV-SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIIN 211 (284)
Q Consensus 134 ~DkDl~ql~-~~~v~~~~~~~~~~~~~~~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~ 211 (284)
+...+.++. +..+++|. . .+-.++-..-||+ +.+.--.|..|.+ |+|||||+|..+|..+ +++++.+
T Consensus 31 ~~~~~~~l~~g~~v~l~t-~-~~vred~~~LyGF~~~~Er~lF~~L~~--------V~GIGpK~Al~iL~~~-~~~el~~ 99 (191)
T TIGR00084 31 PMTCAYELNLEQKAQVFT-H-LVVREDAELLFGFNTLEERELFKELIK--------VNGVGPKLALAILSNM-SPEEFVY 99 (191)
T ss_pred cHHHHHhcCCCCeEEEEE-E-EEEecCCceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHhcC-CHHHHHH
Confidence 344555542 34566664 0 0112233446788 5666667777754 8999999999999975 5777777
Q ss_pred hhh
Q psy14489 212 NAN 214 (284)
Q Consensus 212 ~~~ 214 (284)
++.
T Consensus 100 aI~ 102 (191)
T TIGR00084 100 AIE 102 (191)
T ss_pred HHH
Confidence 664
No 33
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=95.33 E-value=0.044 Score=47.66 Aligned_cols=25 Identities=32% Similarity=0.587 Sum_probs=20.5
Q ss_pred CCCccChhhHHHHHHhcCC---HHHHHH
Q psy14489 187 GVKKIGPKTAVKLLNQYNS---LENIIN 211 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gs---le~i~~ 211 (284)
.|||||||||.++|+.||+ .+.|.+
T Consensus 77 ~i~GIGpk~A~~il~~fg~~~l~~~i~~ 104 (192)
T PRK00116 77 SVSGVGPKLALAILSGLSPEELVQAIAN 104 (192)
T ss_pred cCCCCCHHHHHHHHHhCCHHHHHHHHHh
Confidence 3899999999999999998 444444
No 34
>PF11977 RNase_Zc3h12a: Zc3h12a-like Ribonuclease NYN domain; InterPro: IPR021869 This domain is found in the Zc3h12a protein which has shown to be a ribonuclease that controls the stability of a set of inflammatory genes []. It has been suggested that this domain belongs to the PIN domain superfamily []. ; PDB: 3V33_A 3V34_B 3V32_B.
Probab=95.04 E-value=0.17 Score=42.29 Aligned_cols=101 Identities=20% Similarity=0.236 Sum_probs=47.7
Q ss_pred CcEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCCh
Q psy14489 3 NTLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPY 82 (284)
Q Consensus 3 ~~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~ 82 (284)
.+.++|||+|++|.... .+.....+|.. .+.. ++..+. .++++|+. ++|... .+.+...++
T Consensus 2 ~r~VVIDG~NVA~~~~~-------~~~f~~~~i~~---~v~~-~~~rG~-~~v~v~~~---~~~~~~----~~~~~~~~~ 62 (155)
T PF11977_consen 2 LRPVVIDGSNVAYSHGN-------QKFFSVRGIQI---AVEY-FKSRGH-EVVVVFPP---NYRYKK----LAKKSDDQE 62 (155)
T ss_dssp B--EEEEHHHHHHHHTT-------TTSEEHHHHHH---HHHH-HHHTT----EEEEEE---GGGGS-----TTS-EESTC
T ss_pred CCEEEEeCHHHHhhcCC-------CCCcCHHHHHH---HHHH-HHHcCC-CeEEEEcc---hhhhcc----ccCCCChHH
Confidence 46899999999883321 11233334332 2333 333342 35778873 444333 111111233
Q ss_pred hHHHHHHHHHHHHHhcCCcEEeeCCch--------HHHHHHHHHHHhhHhCCCeEEEEcCCC
Q psy14489 83 NLILQINLIHQMVKAIGWPILIIKGVE--------ADDVIGTLAKQAVTKHNLKVIISTNDK 136 (284)
Q Consensus 83 ~l~~q~~~i~~~l~~~gi~~~~~~g~E--------ADD~ia~la~~~~~~~~~~v~I~S~Dk 136 (284)
.|. + |...|.-++...|.. +|-.|-++|... ..+|||+|+
T Consensus 63 ~L~-------~-l~~~~~i~~tp~~~~~g~~~~~ydD~~il~~A~~~------~a~IVSND~ 110 (155)
T PF11977_consen 63 ELE-------K-LIRKGIIYFTPSGSNYGSRSRNYDDRYILYYAEEK------DAVIVSNDR 110 (155)
T ss_dssp HHH-------H-HHHTTSEEEE-EEEETTEEEEB-HHHHHHHHHHHT------T-EEE-S--
T ss_pred HHH-------H-HHHCCeEEEcCCCCCCCCcccccchHHHHHHHHHc------CCEEEeCch
Confidence 332 2 233787667666666 777777777642 457889995
No 35
>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=94.97 E-value=0.026 Score=39.49 Aligned_cols=27 Identities=37% Similarity=0.568 Sum_probs=24.0
Q ss_pred CCCCccChhhHHHHHHh-cCCHHHHHHh
Q psy14489 186 PGVKKIGPKTAVKLLNQ-YNSLENIINN 212 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~-~gsle~i~~~ 212 (284)
..||||||++|.+|.+. |+|++++...
T Consensus 8 ~~I~Gig~~~a~~L~~~G~~t~~~l~~a 35 (60)
T PF14520_consen 8 LSIPGIGPKRAEKLYEAGIKTLEDLANA 35 (60)
T ss_dssp HTSTTCHHHHHHHHHHTTCSSHHHHHTS
T ss_pred ccCCCCCHHHHHHHHhcCCCcHHHHHcC
Confidence 36899999999999999 9999999764
No 36
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=94.86 E-value=0.2 Score=40.93 Aligned_cols=54 Identities=13% Similarity=0.153 Sum_probs=37.9
Q ss_pred HHHHHHHhcCCcEEeeCCc-------hHHHHHHHHHHHhhH-hCCCeEEEEcCCCccccccC
Q psy14489 90 LIHQMVKAIGWPILIIKGV-------EADDVIGTLAKQAVT-KHNLKVIISTNDKDMAQLVS 143 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~-------EADD~ia~la~~~~~-~~~~~v~I~S~DkDl~ql~~ 143 (284)
...+.|+..|+.++..+.. .+|--|+.-+-.... +.-+.++++|+|+|+..++.
T Consensus 56 ~~~~~L~~~g~~~~~~~~~~~~~~~~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~i~ 117 (149)
T cd06167 56 GFLDALRRLGFEPIQKPLRTRGSGKKGVDVALAIDALELAYKRRIDTIVLVSGDSDFVPLVE 117 (149)
T ss_pred HHHHHHHHCCcEEEEEcceecCCcccCccHHHHHHHHHHhhhcCCCEEEEEECCccHHHHHH
Confidence 3456677899988877742 377777765544332 13568999999999999864
No 37
>PF04599 Pox_G5: Poxvirus G5 protein; InterPro: IPR007678 Protein G5 is found in a number of Poxviruses.
Probab=94.27 E-value=0.2 Score=48.34 Aligned_cols=115 Identities=21% Similarity=0.321 Sum_probs=70.2
Q ss_pred HHHHHhc--CCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEeCcEeeeHhHHHHHhCCChh
Q psy14489 92 HQMVKAI--GWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPE 169 (284)
Q Consensus 92 ~~~l~~~--gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~G~~p~ 169 (284)
.+.|..+ ++..+.++|.-|+=++..-|+......|.=-+++|.|.|.+.+.+-+. ..+. .....+-|-+.|.
T Consensus 149 ~~~L~~~~~~V~IvyCDgvDAEFvMC~~Ak~~a~~~g~WPlliStDQDtllfss~D~----~~Ki--I~t~~~~Y~~~P~ 222 (425)
T PF04599_consen 149 ESSLSRLKEDVEIVYCDGVDAEFVMCARAKKLAAKNGRWPLLISTDQDTLLFSSCDT----PPKI--IKTMNQLYKFIPC 222 (425)
T ss_pred HHHHHhccCCceEEEECCcChhHHHHHHHHHHHHhcCCCceEEeeccceeeeeecCc----hHHH--HHhHHhHeeecCC
Confidence 4455554 789999999999999999998766535555689999999999865321 1111 1122233444443
Q ss_pred H---HHhhhhhcCCCCCCCCCCCccC--hhhH--HHHHHhcCCHHHHHHhh
Q psy14489 170 K---IVDYFSLIGDMSDNLPGVKKIG--PKTA--VKLLNQYNSLENIINNA 213 (284)
Q Consensus 170 q---~~~~~~L~GD~sDni~Gv~giG--~ktA--~~LL~~~gsle~i~~~~ 213 (284)
. ++.-.++.=..||+-||+.|+- +++- .+|+.+| |+++++..+
T Consensus 223 ~~s~YL~kL~~L~NGCDfFpGLyG~~it~~~l~~i~LF~dF-ti~Ni~~SL 272 (425)
T PF04599_consen 223 SKSRYLSKLTALVNGCDFFPGLYGISITKKSLNRIKLFEDF-TIDNILQSL 272 (425)
T ss_pred chHHHHHHHHHHHhcccccCCcceeEechhhccceeccccc-cHHHHHHHH
Confidence 2 2222333334599999999953 3332 2333332 567777655
No 38
>PHA03065 Hypothetical protein; Provisional
Probab=94.14 E-value=0.2 Score=48.19 Aligned_cols=194 Identities=17% Similarity=0.247 Sum_probs=109.5
Q ss_pred cEEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCC----Cc---cccc-cCchhhh
Q psy14489 4 TLLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKG----KN---FRNI-LYPSYKA 75 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~----~~---~R~~-l~~~YKa 75 (284)
+-+-||+.++..-..|++..+ ..-...|...+..+.+. ...+++..|.|. .. -|++ ....||.
T Consensus 28 ~~iFVD~ms~fmsiAysv~~~-------~eL~~~~~~~iq~w~~~--~gkVtlFvDRG~I~IK~~lReKRr~a~~~~~kR 98 (438)
T PHA03065 28 NGIFVDTMSVFMSIAYSVNNL-------DELRSTFEEYVQQWVKK--AGKVTLFVDRGSIPIKQSLREKRRKASKNTIKR 98 (438)
T ss_pred ceEEEechhhhhhhhhhhCCH-------HHHHHHHHHHHHHHHhc--CCcEEEEEecCccchhhHHHHHHHHHHHHHHHH
Confidence 357899999988888876421 11122334455555433 457788888653 11 2333 2344555
Q ss_pred CCCCC------------C----hhH------HH-------------HHH-HHHHHHHhc--CCcEEeeCCchHHHHHHHH
Q psy14489 76 TRKKM------------P----YNL------IL-------------QIN-LIHQMVKAI--GWPILIIKGVEADDVIGTL 117 (284)
Q Consensus 76 ~R~~~------------p----~~l------~~-------------q~~-~i~~~l~~~--gi~~~~~~g~EADD~ia~l 117 (284)
+|... . |+. +- ++. .+.+.|..+ ++..+.++|..|+=++..-
T Consensus 99 K~~ei~~l~~~i~~ld~~d~~yEEikt~~~lrI~Kl~F~~fLa~~~nlk~~l~~~L~~~~~~v~I~yCdgvDAEfvMC~~ 178 (438)
T PHA03065 99 KREEIEKLEDDIKNLDVDDEMYEEIKTDLELKIDKLSFQLFLANSNNLKRLLESALARLGENVEIVYCDGVDAEFVMCAR 178 (438)
T ss_pred HHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHHHHHHHHHHcchhhHHHHHHHHHHhccCCceEEEECCcchhHHHHHH
Confidence 44421 0 111 11 111 233456666 7999999999999999999
Q ss_pred HHHhhHhCCCeEEEEcCCCccccccCCCeEEEeCcEeeeHhHHHHHhCCChhHH---HhhhhhcCCCCCCCCCCCccC--
Q psy14489 118 AKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKI---VDYFSLIGDMSDNLPGVKKIG-- 192 (284)
Q Consensus 118 a~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~G~~p~q~---~~~~~L~GD~sDni~Gv~giG-- 192 (284)
|+......|.=-+++|.|.|.+.+.+-.- ..+. .....+-|-+.|... +.-.+..=..||+-||+.|+-
T Consensus 179 ak~~a~~~g~WPl~iStDQDtllf~s~D~----~~Ki--I~t~~~~Y~~~P~~~t~YL~kL~~L~NGCDfFpGLyG~~it 252 (438)
T PHA03065 179 AKELAATTGEWPLLISTDQDTLLFSSCDR----LPKI--IKTANQLYKFIPCAKTRYLSKLVALVNGCDFFPGLYGISIT 252 (438)
T ss_pred HHHHHhhcCCCceEEeccCCeeEEEecCc----HHHH--HHhHHHHheeCCChhHHHHHHHHHHHhcccccCccceEEec
Confidence 98765535555689999999999865321 1111 112334455545333 222333334599999999954
Q ss_pred hhhH--HHHHHhcCCHHHHHHhh
Q psy14489 193 PKTA--VKLLNQYNSLENIINNA 213 (284)
Q Consensus 193 ~ktA--~~LL~~~gsle~i~~~~ 213 (284)
+++- .+|+.+| |.+|++.++
T Consensus 253 ~~~l~r~~LF~dF-t~~Nv~~SL 274 (438)
T PHA03065 253 PKSLNRIQLFDDF-TIDNVVRSL 274 (438)
T ss_pred hhhccceechhhh-hHHHHHHHH
Confidence 3332 2334443 456666655
No 39
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=94.02 E-value=0.067 Score=46.68 Aligned_cols=69 Identities=25% Similarity=0.430 Sum_probs=43.1
Q ss_pred CCCcccccc--CCCeEEEeCcEeeeHhHHHHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHH
Q psy14489 134 NDKDMAQLV--SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 210 (284)
Q Consensus 134 ~DkDl~ql~--~~~v~~~~~~~~~~~~~~~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~ 210 (284)
+.+.+.++. ++.+++|. . .+-.++-..-||+ +.+.--.|..|.+ |+|||||+|..+|..++ .+++.
T Consensus 31 s~~~~~~l~~~g~~~~l~t-~-~~vrEd~~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~ILs~~~-~~~l~ 99 (194)
T PRK14605 31 PATSPALIGGLGQRVRVFT-H-LHVREDALSLFGFATTEELSLFETLID--------VSGIGPKLGLAMLSAMN-AEALA 99 (194)
T ss_pred CHHHHHhcccCCCeEEEEE-E-EEEecCCceeeCCCCHHHHHHHHHHhC--------CCCCCHHHHHHHHHhCC-HHHHH
Confidence 344444443 33455554 0 1112233446788 5666667777754 88999999999999886 56666
Q ss_pred Hhh
Q psy14489 211 NNA 213 (284)
Q Consensus 211 ~~~ 213 (284)
.++
T Consensus 100 ~aI 102 (194)
T PRK14605 100 SAI 102 (194)
T ss_pred HHH
Confidence 555
No 40
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.74 E-value=0.073 Score=46.76 Aligned_cols=45 Identities=24% Similarity=0.488 Sum_probs=34.1
Q ss_pred HHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 161 ISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 161 ~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
..-||+ +.++--.|..|.+ |.|||||+|..+|..+ +.+++..++.
T Consensus 59 ~~LyGF~~~~Er~lF~~Li~--------V~GIGpK~Al~iLs~~-~~~~l~~aI~ 104 (203)
T PRK14602 59 LELFGFATWDERQTFIVLIS--------ISKVGAKTALAILSQF-RPDDLRRLVA 104 (203)
T ss_pred ceeeCCCCHHHHHHHHHHhC--------CCCcCHHHHHHHHhhC-CHHHHHHHHH
Confidence 346788 5566667777754 8899999999999985 6677777663
No 41
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.52 E-value=0.1 Score=45.21 Aligned_cols=48 Identities=19% Similarity=0.263 Sum_probs=35.9
Q ss_pred hHHHHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 158 TTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 158 ~~~~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
++-..-||+ ++++--.|..|.+ |.|||||+|..+|+.+ +.+++..++.
T Consensus 55 Ed~~~LyGF~~~~Er~lF~~Lis--------V~GIGpK~Al~iLs~~-~~~~l~~aI~ 103 (186)
T PRK14600 55 DNVTQLYGFLNREEQDCLRMLVK--------VSGVNYKTAMSILSKL-TPEQLFSAIV 103 (186)
T ss_pred cCCceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHccC-CHHHHHHHHH
Confidence 344456888 6666677777754 8899999999999985 6677777664
No 42
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=93.50 E-value=0.082 Score=45.72 Aligned_cols=45 Identities=16% Similarity=0.272 Sum_probs=34.1
Q ss_pred HHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 161 ISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 161 ~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
..-||+ +.++--.|..|.+ |.|||||+|..+|..+ +.+++..++.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li~--------VsGIGpK~Al~ILs~~-~~~el~~aI~ 103 (183)
T PRK14601 58 NKLYGFLDKDEQKMFEMLLK--------VNGIGANTAMAVCSSL-DVNSFYKALS 103 (183)
T ss_pred ceeeCCCCHHHHHHHHHHhc--------cCCccHHHHHHHHcCC-CHHHHHHHHH
Confidence 446788 5666667777754 8899999999999985 6678887764
No 43
>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=93.38 E-value=0.053 Score=32.86 Aligned_cols=18 Identities=44% Similarity=0.610 Sum_probs=13.3
Q ss_pred CCCCCCccChhhHHHHHH
Q psy14489 184 NLPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~ 201 (284)
-+..+||||++||..++.
T Consensus 12 eL~~lpGIG~~tA~~I~~ 29 (30)
T PF00633_consen 12 ELMKLPGIGPKTANAILS 29 (30)
T ss_dssp HHHTSTT-SHHHHHHHHH
T ss_pred HHHhCCCcCHHHHHHHHh
Confidence 345689999999988764
No 44
>PRK12766 50S ribosomal protein L32e; Provisional
Probab=93.33 E-value=0.092 Score=46.83 Aligned_cols=29 Identities=24% Similarity=0.491 Sum_probs=25.8
Q ss_pred CCCCCCccChhhHHHHHHh-cCCHHHHHHh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQ-YNSLENIINN 212 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~-~gsle~i~~~ 212 (284)
.+..|||||+++|.+|++. |+|+++|-.+
T Consensus 4 ~L~~IpGIG~krakkLl~~GF~Sve~Ik~A 33 (232)
T PRK12766 4 ELEDISGVGPSKAEALREAGFESVEDVRAA 33 (232)
T ss_pred ccccCCCcCHHHHHHHHHcCCCCHHHHHhC
Confidence 4567899999999999999 9999999765
No 45
>PRK14669 uvrC excinuclease ABC subunit C; Provisional
Probab=93.26 E-value=0.055 Score=55.14 Aligned_cols=30 Identities=30% Similarity=0.517 Sum_probs=26.5
Q ss_pred CCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
-+.+|||||+|++.+||+.|||+++|..+-
T Consensus 553 ~L~~IpGIG~kr~~~LL~~FgSi~~I~~As 582 (624)
T PRK14669 553 ELLEIPGVGAKTVQRLLKHFGSLERVRAAT 582 (624)
T ss_pred HHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 356899999999999999999999998754
No 46
>PRK14666 uvrC excinuclease ABC subunit C; Provisional
Probab=93.10 E-value=0.091 Score=53.92 Aligned_cols=30 Identities=33% Similarity=0.514 Sum_probs=27.1
Q ss_pred CCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
-+..|||||++++.+||+.|||+++|.++.
T Consensus 638 ~L~~IPGIGpkr~k~LL~~FGSle~I~~AS 667 (694)
T PRK14666 638 ELQRVEGIGPATARLLWERFGSLQAMAAAG 667 (694)
T ss_pred HHhhCCCCCHHHHHHHHHHhCCHHHHHhcC
Confidence 467899999999999999999999999854
No 47
>PRK14670 uvrC excinuclease ABC subunit C; Provisional
Probab=93.10 E-value=0.087 Score=53.21 Aligned_cols=30 Identities=30% Similarity=0.433 Sum_probs=27.1
Q ss_pred CCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
-+.+|||||||+..+||+.|||+++|-++-
T Consensus 515 ~L~~I~GiG~kr~~~LL~~Fgs~~~I~~As 544 (574)
T PRK14670 515 NYTKIKGIGEKKAKKILKSLGTYKDILLLN 544 (574)
T ss_pred ccccCCCCCHHHHHHHHHHhCCHHHHHhCC
Confidence 567899999999999999999999998754
No 48
>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=93.07 E-value=0.083 Score=36.22 Aligned_cols=26 Identities=35% Similarity=0.538 Sum_probs=18.4
Q ss_pred CCCCccChhhHHHHHH-hcCCHHHHHH
Q psy14489 186 PGVKKIGPKTAVKLLN-QYNSLENIIN 211 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~-~~gsle~i~~ 211 (284)
.+|.||||+||.++.. .+.|++++-.
T Consensus 5 ~~I~GVG~~tA~~w~~~G~rtl~Dl~~ 31 (52)
T PF10391_consen 5 TGIWGVGPKTARKWYAKGIRTLEDLRK 31 (52)
T ss_dssp HTSTT--HHHHHHHHHTT--SHHHHHH
T ss_pred hhcccccHHHHHHHHHhCCCCHHHHhh
Confidence 3689999999999998 4568998844
No 49
>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=92.83 E-value=0.076 Score=53.71 Aligned_cols=47 Identities=26% Similarity=0.346 Sum_probs=32.9
Q ss_pred HhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHh
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINN 212 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~ 212 (284)
+|.++-++=..-+.+.. .-+.+|||||||+..+||+.|||+++|-++
T Consensus 524 RFAi~~hR~~r~k~~~~---S~Ld~I~GIG~kr~~~LL~~Fgs~~~i~~A 570 (574)
T TIGR00194 524 RFAISFHRKKRLKASLQ---SPLLKIPGVGEKRVQKLLKYFGSLKGIKKA 570 (574)
T ss_pred HHHHHHHHHHHHHHHHH---HHHhcCCCCCHHHHHHHHHHcCCHHHHHhC
Confidence 45554444333343333 234578899999999999999999998654
No 50
>PRK14667 uvrC excinuclease ABC subunit C; Provisional
Probab=92.82 E-value=0.078 Score=53.50 Aligned_cols=48 Identities=19% Similarity=0.277 Sum_probs=33.6
Q ss_pred HhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
+|+++-++=..-+.+.. --+.+|||||||+..+||+.|||+++|-++-
T Consensus 497 RFAi~~hR~~r~k~~~~---S~Ld~I~GiG~kr~~~Ll~~Fgs~~~ik~As 544 (567)
T PRK14667 497 RFALSYNRKLREKEGLK---DILDKIKGIGEVKKEIIYRNFKTLYDFLKAD 544 (567)
T ss_pred HHHHHHHHHHhhccccc---CccccCCCCCHHHHHHHHHHhCCHHHHHhCC
Confidence 45554444333333332 2356788999999999999999999998753
No 51
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=92.64 E-value=0.13 Score=45.03 Aligned_cols=70 Identities=21% Similarity=0.357 Sum_probs=44.0
Q ss_pred CCCcccccc--CCCeEEEeCcEeeeHhHHHHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHH
Q psy14489 134 NDKDMAQLV--SNKIALINNNKIHDRTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENII 210 (284)
Q Consensus 134 ~DkDl~ql~--~~~v~~~~~~~~~~~~~~~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~ 210 (284)
+.+.+.++. +..+++|. . .+-.++-..-||+ +.++--.|..|. +|.|||||+|..+|+.+ +.+++.
T Consensus 31 s~~~~~~l~~~g~~v~l~t-~-~~vrEd~~~LyGF~~~~Er~lF~~Li--------~V~GIGpK~Al~iLs~~-~~~el~ 99 (195)
T PRK14604 31 PRSVLAAIGAIGDEVFLYT-H-LIVREDALTLYGFSTPAQRQLFELLI--------GVSGVGPKAALNLLSSG-TPDELQ 99 (195)
T ss_pred CHHHHHHhccCCCeEEEEE-E-EEEecCCceeeCCCCHHHHHHHHHHh--------CcCCcCHHHHHHHHcCC-CHHHHH
Confidence 455566553 34455554 0 0112223345787 555556666775 48899999999999974 677888
Q ss_pred Hhhh
Q psy14489 211 NNAN 214 (284)
Q Consensus 211 ~~~~ 214 (284)
.++.
T Consensus 100 ~aI~ 103 (195)
T PRK14604 100 LAIA 103 (195)
T ss_pred HHHH
Confidence 7764
No 52
>PRK14671 uvrC excinuclease ABC subunit C; Provisional
Probab=91.89 E-value=0.11 Score=53.01 Aligned_cols=28 Identities=39% Similarity=0.621 Sum_probs=24.7
Q ss_pred CCCCCccChhhHHHHHHhcCCHHHHHHh
Q psy14489 185 LPGVKKIGPKTAVKLLNQYNSLENIINN 212 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~~gsle~i~~~ 212 (284)
+.||||||+|+|..|++.|||+++|..+
T Consensus 571 L~~I~GIG~k~a~~Ll~~Fgs~~~i~~A 598 (621)
T PRK14671 571 LTDIAGIGEKTAEKLLEHFGSVEKVAKA 598 (621)
T ss_pred hhcCCCcCHHHHHHHHHHcCCHHHHHhC
Confidence 3578999999999999999999998664
No 53
>smart00278 HhH1 Helix-hairpin-helix DNA-binding motif class 1.
Probab=91.58 E-value=0.11 Score=30.09 Aligned_cols=18 Identities=56% Similarity=0.693 Sum_probs=15.6
Q ss_pred CCCCCccChhhHHHHHHh
Q psy14489 185 LPGVKKIGPKTAVKLLNQ 202 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~ 202 (284)
+..|||||+|+|.++++.
T Consensus 3 L~~i~GiG~k~A~~il~~ 20 (26)
T smart00278 3 LLKVPGIGPKTAEKILEA 20 (26)
T ss_pred hhhCCCCCHHHHHHHHHh
Confidence 567999999999999873
No 54
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.27 E-value=0.28 Score=42.88 Aligned_cols=45 Identities=24% Similarity=0.489 Sum_probs=33.6
Q ss_pred HHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 161 ISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 161 ~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
..-||+ +.++--.|..|.+ |.|||||+|..+|..+ +.+++..++.
T Consensus 57 ~~LYGF~t~~Er~lF~~Lis--------VsGIGPK~ALaILs~~-~~~el~~aI~ 102 (196)
T PRK13901 57 LKLFGFLNSSEREVFEELIG--------VDGIGPRAALRVLSGI-KYNEFRDAID 102 (196)
T ss_pred ceeeCCCCHHHHHHHHHHhC--------cCCcCHHHHHHHHcCC-CHHHHHHHHH
Confidence 345788 5666666777754 8899999999999985 6677777663
No 55
>PRK14668 uvrC excinuclease ABC subunit C; Provisional
Probab=91.13 E-value=0.14 Score=51.78 Aligned_cols=31 Identities=29% Similarity=0.538 Sum_probs=27.9
Q ss_pred CCCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 183 DNLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 183 Dni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
--+..|||||++++.+||+.|||+++|+.+-
T Consensus 525 ~~L~~IpGIG~kr~~~LL~~FGS~~~I~~As 555 (577)
T PRK14668 525 TVLDDVPGVGPETRKRLLRRFGSVEGVREAS 555 (577)
T ss_pred hHHhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 4567899999999999999999999999864
No 56
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=91.07 E-value=0.29 Score=42.49 Aligned_cols=45 Identities=29% Similarity=0.519 Sum_probs=33.6
Q ss_pred HHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 161 ISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 161 ~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
..-||+ +.++--.|..|. +|.|||||+|..+|..+ +.+++.+++.
T Consensus 58 ~~LyGF~~~~Er~lF~~Li--------~V~GIGpK~AL~iLs~~-~~~el~~aI~ 103 (188)
T PRK14606 58 ITLYGFSNERKKELFLSLT--------KVSRLGPKTALKIISNE-DAETLVTMIA 103 (188)
T ss_pred ceeeCCCCHHHHHHHHHHh--------ccCCccHHHHHHHHcCC-CHHHHHHHHH
Confidence 345788 556666677775 48899999999999875 6677777664
No 57
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=90.88 E-value=0.31 Score=42.66 Aligned_cols=45 Identities=24% Similarity=0.400 Sum_probs=33.1
Q ss_pred HHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 161 ISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 161 ~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
..-||+ +.++--.|..|. +|.|||||+|..+|..+ +.+++.+++.
T Consensus 57 ~~LyGF~~~~Er~lF~~L~--------~V~GIGpK~AL~iLs~~-~~~~l~~aI~ 102 (197)
T PRK14603 57 LSLYGFPDEDSLELFELLL--------GVSGVGPKLALALLSAL-PPALLARALL 102 (197)
T ss_pred ceeeCcCCHHHHHHHHHHh--------CcCCcCHHHHHHHHcCC-CHHHHHHHHH
Confidence 345777 445555666665 48899999999999985 6678877764
No 58
>PRK00558 uvrC excinuclease ABC subunit C; Validated
Probab=90.60 E-value=0.18 Score=51.27 Aligned_cols=29 Identities=34% Similarity=0.570 Sum_probs=25.9
Q ss_pred CCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 185 LPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
+.+|||||++++.+||+.|||+++|+++-
T Consensus 545 L~~IpGIG~k~~k~Ll~~FgS~~~i~~As 573 (598)
T PRK00558 545 LDDIPGIGPKRRKALLKHFGSLKAIKEAS 573 (598)
T ss_pred HhhCCCcCHHHHHHHHHHcCCHHHHHhCC
Confidence 46789999999999999999999998753
No 59
>PRK14672 uvrC excinuclease ABC subunit C; Provisional
Probab=90.17 E-value=0.22 Score=51.08 Aligned_cols=48 Identities=15% Similarity=0.292 Sum_probs=33.2
Q ss_pred HhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
+|.++-.+=..-+.+.- --+..|||||+|++.+||+.|||+++|-++-
T Consensus 591 RFAIt~hR~~R~k~~~~---s~L~~IpGiG~kr~~~LL~~FgS~~~i~~As 638 (691)
T PRK14672 591 RFAITRNRHLRTKKELV---LSFERLPHVGKVRAHRLLAHFGSFRSLQSAT 638 (691)
T ss_pred HHHHHHHHHHhhhhhcc---cccccCCCCCHHHHHHHHHHhcCHHHHHhCC
Confidence 45554333333333332 2345788999999999999999999998754
No 60
>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=89.72 E-value=0.34 Score=49.79 Aligned_cols=43 Identities=14% Similarity=0.330 Sum_probs=31.2
Q ss_pred CCCCccChhhHHHHHHhcCCHHHHHHhhh-h---h---hhhhhccHHHhH
Q psy14489 186 PGVKKIGPKTAVKLLNQYNSLENIINNAN-N---I---KGVIGKNLRFAL 228 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~gsle~i~~~~~-~---~---~~~~~~~l~~~~ 228 (284)
=||||||+++|..|++.|+|++++..+-. + + ..+..+++.++.
T Consensus 501 LgIpgVG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~~I~~ff 550 (652)
T TIGR00575 501 LGIRHVGEVTAKNLAKHFGTLDKLKAASLEELLSVEGVGPKVAESIVNFF 550 (652)
T ss_pred ccCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhcCCCcCHHHHHHHHHHH
Confidence 36899999999999999999999876431 2 2 225555665543
No 61
>TIGR00596 rad1 DNA repair protein (rad1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford Universit
Probab=89.18 E-value=3.8 Score=43.31 Aligned_cols=137 Identities=11% Similarity=0.102 Sum_probs=70.9
Q ss_pred HHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCC--hhHHHHHHHHHHHHHhc-CCcEEeeCC-chHHHH
Q psy14489 38 TIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP--YNLILQINLIHQMVKAI-GWPILIIKG-VEADDV 113 (284)
Q Consensus 38 f~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p--~~l~~q~~~i~~~l~~~-gi~~~~~~g-~EADD~ 113 (284)
++..+.+|.+.|+-.-+++=||. .+.|..+-+.++ +|.-.| ..+.. .+-.+.-.+ |+++++..+ +|.=.+
T Consensus 646 L~~Q~~~m~~~Y~~PvLLIE~d~-~~~f~l~~~~~~--~~~~~~~~~~i~~---~L~~L~l~fP~l~IiwS~s~~~TA~i 719 (814)
T TIGR00596 646 LYNQCEKMLRYYAYPVLLIEFDQ-NKSFSLEPRNDL--SQEISSVNNDIQQ---KLALLTLHFPKLRIIWSSSPYATAEI 719 (814)
T ss_pred HHHHHHHHHHhcCCcEEEEEecC-Cccccccccccc--ccccCccHHHHHH---HHHHHHHhcCCceEEecCCHHHHHHH
Confidence 34455567777766566777774 445554444343 223234 33322 122222335 899988665 556667
Q ss_pred HHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEeCcEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccCh
Q psy14489 114 IGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGP 193 (284)
Q Consensus 114 ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ 193 (284)
+..|+++..+ ++....+.-+ .|- + . ..+. ....+ ...++ +-++||||+
T Consensus 720 ~~~Lk~~e~e-pd~~~~v~i~-~~~-----~-~----~~k~---------~~~~~-~~q~~----------L~~lPgI~~ 767 (814)
T TIGR00596 720 FEELKLGKEE-PDPATAAALG-SDE-----N-T----TAEG---------LKFND-GPQDF----------LLKLPGVTK 767 (814)
T ss_pred HHHHHhcCCC-CCcccceecC-ccc-----c-c----cccc---------ccccH-HHHHH----------HHHCCCCCH
Confidence 7777765432 2211111110 000 0 0 0000 00011 11122 235889999
Q ss_pred hhHHHHHHhcCCHHHHHHh
Q psy14489 194 KTAVKLLNQYNSLENIINN 212 (284)
Q Consensus 194 ktA~~LL~~~gsle~i~~~ 212 (284)
+.|..||.+|||++++..+
T Consensus 768 ~~a~~ll~~f~si~~l~~a 786 (814)
T TIGR00596 768 KNYRNLRKKVKSIRELAKL 786 (814)
T ss_pred HHHHHHHHHcCCHHHHHhC
Confidence 9999999999999999764
No 62
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=88.93 E-value=0.41 Score=39.04 Aligned_cols=42 Identities=21% Similarity=0.305 Sum_probs=28.8
Q ss_pred CCccChhhHHHHHH--hcCCHHHHHHhhhhhhhhhhccHHHhHhh
Q psy14489 188 VKKIGPKTAVKLLN--QYNSLENIINNANNIKGVIGKNLRFALNW 230 (284)
Q Consensus 188 v~giG~ktA~~LL~--~~gsle~i~~~~~~~~~~~~~~l~~~~~~ 230 (284)
+|||||++|.++++ .|.|+|++++ +.-+..+..+.++++++.
T Consensus 66 lpGigP~~A~~IV~nGpf~sveDL~~-V~GIgekqk~~l~k~~~~ 109 (132)
T PRK02515 66 FPGMYPTLAGKIVKNAPYDSVEDVLN-LPGLSERQKELLEANLDN 109 (132)
T ss_pred CCCCCHHHHHHHHHCCCCCCHHHHHc-CCCCCHHHHHHHHHhhcc
Confidence 68999999999997 5778888865 333444444455554443
No 63
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=88.09 E-value=0.54 Score=48.65 Aligned_cols=91 Identities=15% Similarity=0.240 Sum_probs=50.1
Q ss_pred CCCccChhhHHHHHHhcCCHHHHHHhh-hhh------hhhhhccHHHhH---hhchhhhhhhhhccccC-CCCCcCCCcc
Q psy14489 187 GVKKIGPKTAVKLLNQYNSLENIINNA-NNI------KGVIGKNLRFAL---NWLPKLKKILTIKTDCD-LTKNIVSIPE 255 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gsle~i~~~~-~~~------~~~~~~~l~~~~---~~~~l~~~L~~l~~d~~-~~~~~~~~~~ 255 (284)
||||||+++|.+|++.|+|++++..+- +++ ..+..+++.++. ++..+-.+|...--+.. ........+.
T Consensus 532 gIpgIG~~~ak~L~~~F~si~~L~~As~eeL~~i~GIG~k~A~sI~~ff~~~~n~~~i~~L~~~Gv~~~~~~~~~~~~l~ 611 (689)
T PRK14351 532 GIPEVGPTTARNLAREFGTFEAIMDADEEALRAVDDVGPTVAEEIREFFDSERNRAVIDDLLDHGVDPQPAESEGGDALD 611 (689)
T ss_pred CCCCcCHHHHHHHHHHhCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhHHHHHHHHHHhcccccccccccCCCCCC
Confidence 689999999999999999999987643 222 224555555543 23333333433211100 0000000011
Q ss_pred c--cc----cCCCCHHHHHHHHHHcCch
Q psy14489 256 S--LI----LQPKDEKLLMQLFNKYKLN 277 (284)
Q Consensus 256 ~--l~----~~~~~~~~l~~~~~~~~~~ 277 (284)
. +. +...+++.+.++.+++|-.
T Consensus 612 g~~~v~TG~l~~~~R~~~~~~i~~~Gg~ 639 (689)
T PRK14351 612 GLTFVFTGSLSGYTRSEAQELVEAHGGN 639 (689)
T ss_pred CcEEEEccCCCCCCHHHHHHHHHHcCCE
Confidence 2 21 2234788899998888863
No 64
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=87.06 E-value=0.6 Score=48.13 Aligned_cols=89 Identities=12% Similarity=0.199 Sum_probs=51.0
Q ss_pred CCCccChhhHHHHHHhcCCHHHHHHhh-hh---h---hhhhhccHHHhHhh---chhhhhhhhhccccCCCCCcC-CCcc
Q psy14489 187 GVKKIGPKTAVKLLNQYNSLENIINNA-NN---I---KGVIGKNLRFALNW---LPKLKKILTIKTDCDLTKNIV-SIPE 255 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gsle~i~~~~-~~---~---~~~~~~~l~~~~~~---~~l~~~L~~l~~d~~~~~~~~-~~~~ 255 (284)
||||||+++|..|++.|+|++++..+- ++ + ..++.+++.++..+ ..+-.+|...- +.+....+ ..+.
T Consensus 515 gi~~IG~~~ak~L~~~f~sl~~l~~As~eeL~~i~GIG~~~A~sI~~ff~~~~~~~~i~~L~~~g--v~~~~~~~~~~~~ 592 (665)
T PRK07956 515 GIRHVGEKAAKALARHFGSLEALRAASEEELAAVEGVGEVVAQSIVEFFAVEENRELIDELLEAG--VNMEYKGEEVDLA 592 (665)
T ss_pred hccCcCHHHHHHHHHHcCCHHHHHhCCHHHHhccCCcCHHHHHHHHHHHhhhhHHHHHHHHHHcC--CCccccccCCCcc
Confidence 789999999999999999999987642 22 2 23555666655432 22323333211 11110000 0011
Q ss_pred c--cc----cCCCCHHHHHHHHHHcCch
Q psy14489 256 S--LI----LQPKDEKLLMQLFNKYKLN 277 (284)
Q Consensus 256 ~--l~----~~~~~~~~l~~~~~~~~~~ 277 (284)
. +. ....+++.+.++.+++|..
T Consensus 593 g~~~v~TG~l~~~~R~e~~~~i~~~G~~ 620 (665)
T PRK07956 593 GKTVVLTGTLEQLSRDEAKEKLEALGAK 620 (665)
T ss_pred ccEEEEeCCCCCCCHHHHHHHHHHcCCE
Confidence 1 11 2234789999999999874
No 65
>PF03159 XRN_N: XRN 5'-3' exonuclease N-terminus; InterPro: IPR004859 Signatures of this entry align residues towards the N terminus of several proteins with multiple functions. The members of this family all appear to possess 5'-3' exonuclease activity 3.1.11 from EC. Thus, the aligned region may be necessary for 5'-3' exonuclease function.; GO: 0003676 nucleic acid binding, 0004527 exonuclease activity, 0005622 intracellular; PDB: 2Y35_A 3PIE_B 3PIF_C 3FQD_A.
Probab=85.49 E-value=1.6 Score=39.26 Aligned_cols=143 Identities=15% Similarity=0.189 Sum_probs=69.7
Q ss_pred EEEEecchHHHHHhccCCCccCCCCcchhHHHHHHHHHHHHHHhcCCCEE-EEEEeCCCCc-----cccccC--------
Q psy14489 5 LLLVDGSSCIYRAFYALPDIRNIDNFPVGALYGTIKMLRKLYKNYRATYI-ACIFDAKGKN-----FRNILY-------- 70 (284)
Q Consensus 5 ~llIDg~~l~~r~~~a~~~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~-i~~fD~~~~~-----~R~~l~-------- 70 (284)
-|.||.|+++|.+.+.... .........+..++..+..++...+|... ++++||.+|. -|..-+
T Consensus 32 ~LYiDmN~IIH~~~~~~~~--~~~~~~~~~~~~i~~~id~l~~~v~P~k~l~iavDGvaP~AKm~qQR~RRf~~~~~~~~ 109 (237)
T PF03159_consen 32 NLYIDMNGIIHNCIHPNDS--SIPKTEEEIFQRIFNYIDRLVRIVRPRKLLYIAVDGVAPRAKMNQQRSRRFKSAKESEE 109 (237)
T ss_dssp EEEEETHHHHHHHHS-SSS------SHHHHHHHHHHHHHHHHHHH-ESSEEEEE---S--HHHHHHHHHHHHHHHHHHHH
T ss_pred EEEEEcchhhhHhcCCccc--CCCccHHHHHHHHHHHHHHhheeecCceEEEEEcCCCCCchHHHHHHHHHHHHhhcchh
Confidence 5889999999999886542 11111123444556677777777778554 6999997652 111111
Q ss_pred --chhhhCC----------------CC------CC-----hhHHHHHH-HHHHHHHh----cCCcEEe----eCCchHHH
Q psy14489 71 --PSYKATR----------------KK------MP-----YNLILQIN-LIHQMVKA----IGWPILI----IKGVEADD 112 (284)
Q Consensus 71 --~~YKa~R----------------~~------~p-----~~l~~q~~-~i~~~l~~----~gi~~~~----~~g~EADD 112 (284)
..+++.+ .. +| ..|...+. ++..-+.. -++.++. +|| |++-
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~~fdsn~ITPGT~FM~~l~~~L~~~~~~k~~~~~~~~~~~vi~S~~~vpG-EGE~ 188 (237)
T PF03159_consen 110 NNKEESEIKEEIDEEGEQLPPEDQEEKFDSNCITPGTEFMEKLSDALRYYIKKKLNSDPKWQNLKVIFSGSDVPG-EGEH 188 (237)
T ss_dssp HHHHHHHHHHHHHHHT--B-HHHHS----GGGSSTTSHHHHHHHHHHHHHHHHHHHH-GGGCCSEEEEE-TTSSS--HHH
T ss_pred HHHHHHHHhhhhhhccccccccccccccccceeccCCHHHHHHHHHHHHHHHHHhcCCCCcCceEEEEeCCCCCC-ccHH
Confidence 0000000 00 12 11222222 22222221 1345544 567 9998
Q ss_pred HHHHHHHHhhH----hCCCeEEEEcCCCcccccc----CCCeEEEe
Q psy14489 113 VIGTLAKQAVT----KHNLKVIISTNDKDMAQLV----SNKIALIN 150 (284)
Q Consensus 113 ~ia~la~~~~~----~~~~~v~I~S~DkDl~ql~----~~~v~~~~ 150 (284)
=|-...|.... .+...++|+|.|.|+..|. .+++.++.
T Consensus 189 KI~~~IR~~~~~~~~~~n~~h~i~g~DaDlIll~L~~~~~~~~ilr 234 (237)
T PF03159_consen 189 KIMDFIRSQRSQPDYDPNTSHCIYGSDADLILLSLATHEPNIYILR 234 (237)
T ss_dssp HHHHHHHHHHHSTTS-TT--EEEE-SSTHHHHHHHHTT-SSEEEEE
T ss_pred HHHHHHHHhhhcCCCCCCceEEEEecCHhHHHHHHccCCCeEEEEe
Confidence 88877776443 1456899999999998753 34666654
No 66
>COG0322 UvrC Nuclease subunit of the excinuclease complex [DNA replication, recombination, and repair]
Probab=84.90 E-value=0.66 Score=47.01 Aligned_cols=48 Identities=25% Similarity=0.451 Sum_probs=34.2
Q ss_pred HhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 163 RFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 163 ~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
+|.++-++-...+...=. -.-+|||||+++..+||+.|||+++|.++.
T Consensus 513 rfAi~~hR~~R~k~~~~s---~Ld~I~GiG~~r~~~LL~~Fgs~~~i~~As 560 (581)
T COG0322 513 RFAITYHRKKRSKAMLQS---SLDDIPGIGPKRRKALLKHFGSLKGIKSAS 560 (581)
T ss_pred HHHHHHHHHHhhhhhhcC---ccccCCCcCHHHHHHHHHHhhCHHHHHhcC
Confidence 455554444445554432 245677889999999999999999998764
No 67
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=84.88 E-value=0.71 Score=41.87 Aligned_cols=27 Identities=33% Similarity=0.715 Sum_probs=24.1
Q ss_pred CCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 187 GVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
++||||++.|..||..|||+++++.+-
T Consensus 186 s~pgig~~~a~~ll~~fgS~~~~~tas 212 (254)
T COG1948 186 SIPGIGPKLAERLLKKFGSVEDVLTAS 212 (254)
T ss_pred cCCCccHHHHHHHHHHhcCHHHHhhcC
Confidence 467999999999999999999998764
No 68
>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=84.22 E-value=0.67 Score=34.81 Aligned_cols=25 Identities=32% Similarity=0.547 Sum_probs=21.9
Q ss_pred CCCCCccChhhHHHHHHhcCCHHHH
Q psy14489 185 LPGVKKIGPKTAVKLLNQYNSLENI 209 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~~gsle~i 209 (284)
+..|||||+.||..+|.+.|+++..
T Consensus 4 l~sipGig~~~a~~llaeigd~~rF 28 (87)
T PF02371_consen 4 LTSIPGIGPITAATLLAEIGDISRF 28 (87)
T ss_pred hcCCCCccHHHHHHHHHHHcCchhc
Confidence 4679999999999999999998663
No 69
>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=83.68 E-value=1.3 Score=41.32 Aligned_cols=27 Identities=41% Similarity=0.565 Sum_probs=22.6
Q ss_pred CCCCccChhhHHHHHHhcC--CHHHHHHhh
Q psy14489 186 PGVKKIGPKTAVKLLNQYN--SLENIINNA 213 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g--sle~i~~~~ 213 (284)
-+|+|||||||.+|. +.| |++++..+.
T Consensus 88 ~~i~GiGpk~a~~l~-~lGi~sl~dL~~a~ 116 (307)
T cd00141 88 LRVPGVGPKTARKLY-ELGIRTLEDLRKAA 116 (307)
T ss_pred HcCCCCCHHHHHHHH-HcCCCCHHHHHHHh
Confidence 368999999999999 544 899998875
No 70
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=83.15 E-value=2.8 Score=36.82 Aligned_cols=49 Identities=27% Similarity=0.350 Sum_probs=34.4
Q ss_pred HhHHHHHhCC-ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHhhh
Q psy14489 157 RTTIISRFGV-SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINNAN 214 (284)
Q Consensus 157 ~~~~~~~~G~-~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~~~ 214 (284)
.++-..-||+ +.+.=-.|.-|. .|.|||||+|..+|+- .+++++..++.
T Consensus 54 REd~~~LyGF~~~~ER~lF~~Li--------sVnGIGpK~ALaiLs~-~~~~~l~~aI~ 103 (201)
T COG0632 54 REDAHLLYGFLTEEERELFRLLI--------SVNGIGPKLALAILSN-LDPEELAQAIA 103 (201)
T ss_pred hhhHHHHcCCCCHHHHHHHHHHH--------ccCCccHHHHHHHHcC-CCHHHHHHHHH
Confidence 3445667899 444445556664 3779999999999996 46677777664
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=81.85 E-value=1.3 Score=35.54 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=18.7
Q ss_pred CCCCccChhhHHHHHHhc------CCHHHH
Q psy14489 186 PGVKKIGPKTAVKLLNQY------NSLENI 209 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~------gsle~i 209 (284)
..+||||+++|.++|..+ .|++++
T Consensus 71 ~~lpGIG~~~A~~Ii~~R~~~g~f~s~eeL 100 (120)
T TIGR01259 71 QALPGIGPAKAKAIIEYREENGAFKSVDDL 100 (120)
T ss_pred hcCCCCCHHHHHHHHHHHHhcCCcCCHHHH
Confidence 457899999999999974 455555
No 72
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=81.11 E-value=3.3 Score=33.16 Aligned_cols=54 Identities=13% Similarity=0.148 Sum_probs=28.4
Q ss_pred HHHHHHHhcCCcEEeeCC--------chHHHHHHHHHHHhh-HhCCCeEEEEcCCCccccccC
Q psy14489 90 LIHQMVKAIGWPILIIKG--------VEADDVIGTLAKQAV-TKHNLKVIISTNDKDMAQLVS 143 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g--------~EADD~ia~la~~~~-~~~~~~v~I~S~DkDl~ql~~ 143 (284)
.+.+.|+..|+++...+. -.+|-.|+.-+.... ......++|+|+|+|+..++.
T Consensus 51 ~~~~~L~~~g~~v~~~~~~~~~~~~k~~~D~~l~~d~~~~~~~~~~d~ivLvSgD~Df~~~v~ 113 (146)
T PF01936_consen 51 SFQEALQRAGIKVRHFPLRKRGGGGKKGVDVALAVDILELAYENPPDTIVLVSGDSDFAPLVR 113 (146)
T ss_dssp HHHHHHHHHT-EEEE------S---S---HHHHHHHHHHHG--GG-SEEEEE---GGGHHHHH
T ss_pred hHHHHHHhCeeeEEeeecccccccccCCcHHHHHHHHHHHhhccCCCEEEEEECcHHHHHHHH
Confidence 344666778986655432 236766765544332 113478999999999999875
No 73
>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=80.44 E-value=1 Score=27.55 Aligned_cols=16 Identities=44% Similarity=0.397 Sum_probs=11.8
Q ss_pred CCCCCCccChhhHHHH
Q psy14489 184 NLPGVKKIGPKTAVKL 199 (284)
Q Consensus 184 ni~Gv~giG~ktA~~L 199 (284)
.|.-++|||+||+.+|
T Consensus 12 pi~~~~GIG~kt~~kL 27 (32)
T PF11798_consen 12 PIRKFWGIGKKTAKKL 27 (32)
T ss_dssp BGGGSTTS-HHHHHHH
T ss_pred CHHhhCCccHHHHHHH
Confidence 3566899999998884
No 74
>smart00483 POLXc DNA polymerase X family. includes vertebrate polymerase beta and terminal deoxynucleotidyltransferases
Probab=79.13 E-value=1.5 Score=41.40 Aligned_cols=27 Identities=37% Similarity=0.507 Sum_probs=23.0
Q ss_pred CCCCccChhhHHHHHHhcC--CHHHHHHhh
Q psy14489 186 PGVKKIGPKTAVKLLNQYN--SLENIINNA 213 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g--sle~i~~~~ 213 (284)
-.|||||||||..|.+ .| |++++.++.
T Consensus 92 ~~i~GiGpk~a~~l~~-lGi~tl~eL~~a~ 120 (334)
T smart00483 92 TNVFGVGPKTAAKWYR-KGIRTLEELKKNK 120 (334)
T ss_pred HccCCcCHHHHHHHHH-hCCCCHHHHHhcc
Confidence 4689999999999998 66 899997754
No 75
>PRK13766 Hef nuclease; Provisional
Probab=78.73 E-value=1.5 Score=45.70 Aligned_cols=29 Identities=24% Similarity=0.560 Sum_probs=25.8
Q ss_pred CCCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 185 LPGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
+.++||||+++|.+|+++|||+++++.+-
T Consensus 717 L~~ipgig~~~a~~Ll~~fgs~~~i~~as 745 (773)
T PRK13766 717 VESLPDVGPVLARNLLEHFGSVEAVMTAS 745 (773)
T ss_pred HhcCCCCCHHHHHHHHHHcCCHHHHHhCC
Confidence 46799999999999999999999998643
No 76
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=78.60 E-value=0.77 Score=40.34 Aligned_cols=30 Identities=23% Similarity=0.238 Sum_probs=22.9
Q ss_pred hhcCCCCCCCCCCCccChhhHHHHHHhcCC
Q psy14489 176 SLIGDMSDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 176 ~L~GD~sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
++......-+..|||||+|||.+++-+..+
T Consensus 102 aI~~~D~~~L~~ipGIGkKtAerIilELkd 131 (203)
T PRK14602 102 LVAEEDVAALTRVSGIGKKTAQHIFLELKY 131 (203)
T ss_pred HHHhCCHHHHhcCCCcCHHHHHHHHHHHHH
Confidence 444444678899999999999999876443
No 77
>PRK08609 hypothetical protein; Provisional
Probab=78.05 E-value=2.5 Score=42.82 Aligned_cols=28 Identities=18% Similarity=0.300 Sum_probs=23.3
Q ss_pred CCCccChhhHHHHHHhcC--CHHHHHHhhh
Q psy14489 187 GVKKIGPKTAVKLLNQYN--SLENIINNAN 214 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~g--sle~i~~~~~ 214 (284)
.|||||||||.+|-++.| |++++.+++.
T Consensus 92 ~i~GiGpk~a~~l~~~lGi~tl~~L~~a~~ 121 (570)
T PRK08609 92 KLPGLGGKKIAKLYKELGVVDKESLKEACE 121 (570)
T ss_pred cCCCCCHHHHHHHHHHhCCCCHHHHHHHHH
Confidence 589999999999997655 8999887664
No 78
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.75 E-value=0.79 Score=39.65 Aligned_cols=37 Identities=24% Similarity=0.417 Sum_probs=25.7
Q ss_pred CChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcC
Q psy14489 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 166 ~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~g 204 (284)
++|+++.. .+..|| ..-+..|||||+|||.+++-+..
T Consensus 93 ~~~~el~~-aI~~~D-~~~L~~vpGIGkKtAeRIilELk 129 (183)
T PRK14601 93 LDVNSFYK-ALSLGD-ESVLKKVPGIGPKSAKRIIAELS 129 (183)
T ss_pred CCHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHHH
Confidence 34554433 344455 56788999999999999987644
No 79
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=77.58 E-value=4.8 Score=33.30 Aligned_cols=72 Identities=22% Similarity=0.397 Sum_probs=46.7
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCC--eEEEe-CcEeeeHhHHHHHhCC
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNK--IALIN-NNKIHDRTTIISRFGV 166 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~--v~~~~-~~~~~~~~~~~~~~G~ 166 (284)
.+-..|..+|+.++..++. .|+-|..+|+. ..=+|+|.|+++....... +.... ....-....+.+.||+
T Consensus 11 ~Lar~LR~lG~Dt~~~~~~-~D~~il~~A~~------e~RillTrd~~l~~~~~~~~~~~li~~~~~~~QL~ev~~~~~l 83 (147)
T PF01927_consen 11 RLARWLRLLGYDTLYSRDI-DDDEILELARE------EGRILLTRDRDLLKRRRVSGGVILIRSDDPEEQLREVLERFGL 83 (147)
T ss_pred HHHHHHHHCCCcEEEeCCC-ChHHHHHHhhh------CCeEEEECCHHHHHHhhccCCEEEEcCCCHHHHHHHHHHHcCC
Confidence 4667889999999988865 66666666753 2458999999999876532 12222 2222234455667777
Q ss_pred Ch
Q psy14489 167 SP 168 (284)
Q Consensus 167 ~p 168 (284)
.+
T Consensus 84 ~~ 85 (147)
T PF01927_consen 84 KL 85 (147)
T ss_pred cc
Confidence 54
No 80
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=77.44 E-value=1.6 Score=37.86 Aligned_cols=36 Identities=22% Similarity=0.394 Sum_probs=26.2
Q ss_pred CChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcC
Q psy14489 166 VSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 166 ~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~g 204 (284)
++|+++.. .+-.||. .-+ .|||||+|||.+++-+..
T Consensus 93 ~~~~~l~~-aI~~~D~-~~L-~vpGIGkKtAerIilELk 128 (186)
T PRK14600 93 LTPEQLFS-AIVNEDK-AAL-KVNGIGEKLINRIITELQ 128 (186)
T ss_pred CCHHHHHH-HHHcCCH-hhe-ECCCCcHHHHHHHHHHHH
Confidence 35555544 3456786 678 899999999999987644
No 81
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=75.88 E-value=0.93 Score=39.63 Aligned_cols=37 Identities=24% Similarity=0.185 Sum_probs=25.8
Q ss_pred ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCC
Q psy14489 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 167 ~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
+|+++.. .+..|| ..-+..|||||+|||.+++-+..+
T Consensus 93 ~~~el~~-aI~~~D-~~~L~~vpGIGkKtAeRIIlELkd 129 (196)
T PRK13901 93 KYNEFRD-AIDRED-IELISKVKGIGNKMAGKIFLKLRG 129 (196)
T ss_pred CHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 4444433 234555 567889999999999999876443
No 82
>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=75.29 E-value=3.3 Score=43.22 Aligned_cols=38 Identities=24% Similarity=0.490 Sum_probs=25.9
Q ss_pred hhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCC--HHHHHHhh
Q psy14489 168 PEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS--LENIINNA 213 (284)
Q Consensus 168 p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gs--le~i~~~~ 213 (284)
.+.+..|.. . +-+||||||||.++.+.||. ++-|.++.
T Consensus 77 ~~~i~~yL~-s-------~~~~GIG~~~A~~iv~~fg~~~~~~i~~~~ 116 (720)
T TIGR01448 77 KEGIVAYLS-S-------RSIKGVGKKLAQRIVKTFGEAAFDVLDDDP 116 (720)
T ss_pred HHHHHHHHh-c-------CCCCCcCHHHHHHHHHHhCHhHHHHHHhCH
Confidence 355666654 2 23788899999999999994 44444443
No 83
>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=74.52 E-value=3.6 Score=29.30 Aligned_cols=22 Identities=23% Similarity=0.546 Sum_probs=17.2
Q ss_pred CCccChhhHHHHHHh---cC---CHHHH
Q psy14489 188 VKKIGPKTAVKLLNQ---YN---SLENI 209 (284)
Q Consensus 188 v~giG~ktA~~LL~~---~g---sle~i 209 (284)
+||+|+++|.++|+. +| +++++
T Consensus 22 ipgig~~~a~~Il~~R~~~g~~~s~~dL 49 (69)
T TIGR00426 22 MNGVGLKKAEAIVSYREEYGPFKTVEDL 49 (69)
T ss_pred CCCCCHHHHHHHHHHHHHcCCcCCHHHH
Confidence 788999999999998 56 44444
No 84
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=73.53 E-value=6 Score=33.48 Aligned_cols=50 Identities=20% Similarity=0.303 Sum_probs=36.8
Q ss_pred HHHHHhcCCcEEeeCCchHHHHHHHHHHHhh--HhCCCeEEEEcCCCccccccC
Q psy14489 92 HQMVKAIGWPILIIKGVEADDVIGTLAKQAV--TKHNLKVIISTNDKDMAQLVS 143 (284)
Q Consensus 92 ~~~l~~~gi~~~~~~g~EADD~ia~la~~~~--~~~~~~v~I~S~DkDl~ql~~ 143 (284)
.+.|...|+..+...| -.|=-++.=|-... . .-+.++++|+|.||..|+.
T Consensus 72 ~~~l~~~Gf~pv~~kG-~~Dv~laIDame~~~~~-~iD~~vLvSgD~DF~~Lv~ 123 (160)
T TIGR00288 72 IEAVVNQGFEPIIVAG-DVDVRMAVEAMELIYNP-NIDAVALVTRDADFLPVIN 123 (160)
T ss_pred HHHHHHCCceEEEecC-cccHHHHHHHHHHhccC-CCCEEEEEeccHhHHHHHH
Confidence 5677789998877788 66666665554332 2 4468999999999999874
No 85
>COG1555 ComEA DNA uptake protein and related DNA-binding proteins [DNA replication, recombination, and repair]
Probab=71.03 E-value=4.2 Score=33.94 Aligned_cols=23 Identities=26% Similarity=0.693 Sum_probs=16.4
Q ss_pred CCCccChhhHHHHHH------hcCCHHHH
Q psy14489 187 GVKKIGPKTAVKLLN------QYNSLENI 209 (284)
Q Consensus 187 Gv~giG~ktA~~LL~------~~gsle~i 209 (284)
.+||||+|+|.+++. .|.|+|++
T Consensus 101 ~lpgIG~~kA~aIi~yRe~~G~f~sv~dL 129 (149)
T COG1555 101 ALPGIGPKKAQAIIDYREENGPFKSVDDL 129 (149)
T ss_pred HCCCCCHHHHHHHHHHHHHcCCCCcHHHH
Confidence 467889999888886 24566664
No 86
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=70.37 E-value=1.6 Score=38.17 Aligned_cols=37 Identities=27% Similarity=0.355 Sum_probs=26.1
Q ss_pred ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCC
Q psy14489 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 167 ~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
+|+++.. .+-.|| ..-+..|||||+|||.+++-+..+
T Consensus 94 ~~~el~~-aI~~~D-~~~L~kvpGIGkKtAerIilELk~ 130 (195)
T PRK14604 94 TPDELQL-AIAGGD-VARLARVPGIGKKTAERIVLELKG 130 (195)
T ss_pred CHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 4555543 244455 467889999999999999876544
No 87
>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=70.26 E-value=4 Score=31.40 Aligned_cols=24 Identities=25% Similarity=0.264 Sum_probs=18.1
Q ss_pred CCCCccChhhHHHHHH-hcCCHHHH
Q psy14489 186 PGVKKIGPKTAVKLLN-QYNSLENI 209 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~-~~gsle~i 209 (284)
..|||||+++|.+|.. .+.|++++
T Consensus 15 ~~iP~IG~a~a~DL~~LGi~s~~~L 39 (93)
T PF11731_consen 15 TDIPNIGKATAEDLRLLGIRSPADL 39 (93)
T ss_pred hcCCCccHHHHHHHHHcCCCCHHHH
Confidence 4589999999999986 44455554
No 88
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=69.67 E-value=3 Score=42.76 Aligned_cols=91 Identities=15% Similarity=0.217 Sum_probs=53.1
Q ss_pred CCCCccChhhHHHHHHhcCCHHHHHHhhhh----h---hhhhhccHHHhHh---hchhhhhhhhhccccCCC-CCcC--C
Q psy14489 186 PGVKKIGPKTAVKLLNQYNSLENIINNANN----I---KGVIGKNLRFALN---WLPKLKKILTIKTDCDLT-KNIV--S 252 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~gsle~i~~~~~~----~---~~~~~~~l~~~~~---~~~l~~~L~~l~~d~~~~-~~~~--~ 252 (284)
=|||.||+++|..|-+.|+|+++++++-.+ + .+.+.+++.++.. ...+..+|.+.-....-. .... +
T Consensus 514 LGIr~VG~~~Ak~La~~f~sl~~l~~a~~e~l~~i~giG~~vA~si~~ff~~~~~~~li~~L~~~g~~~~~~~~~~~~~~ 593 (667)
T COG0272 514 LGIRHVGETTAKSLARHFGTLEALLAASEEELASIPGIGEVVARSIIEFFANEENRELIDELLAAGVKWEEEEKISIETS 593 (667)
T ss_pred cCCchhhHHHHHHHHHHhhhHHHHHhcCHHHHhhccchhHHHHHHHHHHHcCHHHHHHHHHHHHcCCCcccccccccccc
Confidence 589999999999999999999999876422 2 2255566665433 222344443332111100 0000 0
Q ss_pred Ccccc------ccCCCCHHHHHHHHHHcCc
Q psy14489 253 IPESL------ILQPKDEKLLMQLFNKYKL 276 (284)
Q Consensus 253 ~~~~l------~~~~~~~~~l~~~~~~~~~ 276 (284)
.+... .+....++..++.++.+|=
T Consensus 594 ~l~gkt~V~TGtL~~~sR~eak~~le~lGa 623 (667)
T COG0272 594 PLAGKTFVLTGTLEGMSRDEAKALLEALGA 623 (667)
T ss_pred ccCCCEEEEeccCCCCCHHHHHHHHHHcCC
Confidence 01111 1244678889999998875
No 89
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.68 E-value=1.8 Score=37.59 Aligned_cols=37 Identities=22% Similarity=0.315 Sum_probs=25.7
Q ss_pred ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCC
Q psy14489 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 167 ~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
+|+++.. .+..|| ..-+..|||||+|||.+++-+..+
T Consensus 94 ~~~el~~-aI~~~D-~~~L~~vpGIGkKtAerIilELkd 130 (188)
T PRK14606 94 DAETLVT-MIASQD-VEGLSKLPGISKKTAERIVMELKD 130 (188)
T ss_pred CHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 4444433 344555 567889999999999999876443
No 90
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=68.49 E-value=4 Score=38.86 Aligned_cols=27 Identities=11% Similarity=0.386 Sum_probs=24.7
Q ss_pred CCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 187 GVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
.||++|++.|..|+++|||+.+++++-
T Consensus 291 ~IPrl~k~iAk~Ll~~FGSL~~Il~As 317 (352)
T PRK13482 291 KIPRLPSAVIENLVEHFGSLQGLLAAS 317 (352)
T ss_pred cCCCCCHHHHHHHHHHcCCHHHHHcCC
Confidence 479999999999999999999999854
No 91
>PTZ00349 dehydrodolichyl diphosphate synthetase; Provisional
Probab=67.36 E-value=19 Score=33.91 Aligned_cols=92 Identities=14% Similarity=0.092 Sum_probs=54.5
Q ss_pred HHHHHHHh-cCCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCc
Q psy14489 41 MLRKLYKN-YRATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGV 108 (284)
Q Consensus 41 ~l~~l~~~-~~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~ 108 (284)
.+.+.++. .-|.|++|+.|| ...| |+.-.+...+||... +.+ ..+-+++..+||+++.. +..
T Consensus 9 ~~~~~l~~g~iP~HVAiIMDG-NrRwAk~~gl~~~~GH~~G~-~~l----~~il~~c~~lGIk~lTlYAFStENwkRp~~ 82 (322)
T PTZ00349 9 FITSLLRDFINIKHISIIMDG-NRRFAKEKGLHSAIGHFMGS-KAL----IQIIEICIKLKIKILSVFSFSLLNYNRSPE 82 (322)
T ss_pred HHHHHhhcCCCCCcEEEEcCC-CHHHHHHCCCCHHHHHHHHH-HHH----HHHHHHHHHcCCCEEEEEEeehhhhCCCHH
Confidence 44455554 237999999997 4444 333345666666653 223 24556666789999873 566
Q ss_pred hHHHHHHHHHH----------HhhHhCCCeEEEEcCCCcccc
Q psy14489 109 EADDVIGTLAK----------QAVTKHNLKVIISTNDKDMAQ 140 (284)
Q Consensus 109 EADD~ia~la~----------~~~~~~~~~v~I~S~DkDl~q 140 (284)
|=+.++.-+.. ...+ .|.++-++ +|.|.+.
T Consensus 83 EV~~Lm~L~~~~l~~~~~~~~~l~~-~~irirvi-Gd~~~Lp 122 (322)
T PTZ00349 83 EIHFLFYLNLLILINEDFFFKFIKD-NKIKIKII-GNLSYIN 122 (322)
T ss_pred HHHHHHHHHHHHHHHhhhhHHHHHH-CCCEEEEE-eChhhCC
Confidence 88877755422 1223 45565554 5776643
No 92
>PF12826 HHH_2: Helix-hairpin-helix motif; PDB: 1X2I_B 1DGS_A 1V9P_B.
Probab=66.30 E-value=1.3 Score=31.41 Aligned_cols=35 Identities=26% Similarity=0.435 Sum_probs=21.9
Q ss_pred hhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHH
Q psy14489 174 YFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLEN 208 (284)
Q Consensus 174 ~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~ 208 (284)
+..|.--+.+-+.-||||||++|..+.+=|.+.++
T Consensus 26 l~~l~~a~~e~L~~i~gIG~~~A~si~~ff~~~~n 60 (64)
T PF12826_consen 26 LEALMNASVEELSAIPGIGPKIAQSIYEFFQDPEN 60 (64)
T ss_dssp HHHHCC--HHHHCTSTT--HHHHHHHHHHHH-HHH
T ss_pred HHHHHHcCHHHHhccCCcCHHHHHHHHHHHCCHHh
Confidence 33444445566788999999999998887766544
No 93
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.84 E-value=2.7 Score=36.76 Aligned_cols=37 Identities=22% Similarity=0.306 Sum_probs=25.4
Q ss_pred ChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCC
Q psy14489 167 SPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 167 ~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
+|+++.. .+..|| ..-+..|||||+|||.+++-+..+
T Consensus 93 ~~~~l~~-aI~~~D-~~~L~kvpGIGkKtAerIilELkd 129 (197)
T PRK14603 93 PPALLAR-ALLEGD-ARLLTSASGVGKKLAERIALELKG 129 (197)
T ss_pred CHHHHHH-HHHhCC-HHHHhhCCCCCHHHHHHHHHHHHH
Confidence 4554433 244555 456789999999999999876443
No 94
>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=64.20 E-value=5.2 Score=27.64 Aligned_cols=21 Identities=33% Similarity=0.552 Sum_probs=17.5
Q ss_pred CCCCCCCCccChhhHHHHHHh
Q psy14489 182 SDNLPGVKKIGPKTAVKLLNQ 202 (284)
Q Consensus 182 sDni~Gv~giG~ktA~~LL~~ 202 (284)
.+-+-.|||||+++|.+++..
T Consensus 37 ~~~L~~i~Gig~~~a~~i~~~ 57 (60)
T PF14520_consen 37 PEELAEIPGIGEKTAEKIIEA 57 (60)
T ss_dssp HHHHHTSTTSSHHHHHHHHHH
T ss_pred HHHHhcCCCCCHHHHHHHHHH
Confidence 455778899999999999875
No 95
>KOG2841|consensus
Probab=64.00 E-value=4.9 Score=36.10 Aligned_cols=28 Identities=25% Similarity=0.398 Sum_probs=22.4
Q ss_pred CCCCccChhhHHHHHHhcCCHHHHHHhh
Q psy14489 186 PGVKKIGPKTAVKLLNQYNSLENIINNA 213 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~gsle~i~~~~ 213 (284)
.-||||+..-|..||.+|||+++|+.+-
T Consensus 198 t~i~~VnKtda~~LL~~FgsLq~~~~AS 225 (254)
T KOG2841|consen 198 TTIPGVNKTDAQLLLQKFGSLQQISNAS 225 (254)
T ss_pred HhCCCCCcccHHHHHHhcccHHHHHhcC
Confidence 4577788888888999999998887653
No 96
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=63.60 E-value=6.5 Score=40.69 Aligned_cols=26 Identities=35% Similarity=0.611 Sum_probs=22.8
Q ss_pred CCCCccChhhHHHHH-HhcCCHHHHHH
Q psy14489 186 PGVKKIGPKTAVKLL-NQYNSLENIIN 211 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL-~~~gsle~i~~ 211 (284)
=|||+||+++|..|. +.|++++++.+
T Consensus 505 LGI~~vG~~~ak~La~~~f~~~~~l~~ 531 (669)
T PRK14350 505 MGIKDLGENTILLLINNNLNSFDKIST 531 (669)
T ss_pred cCCCchhHHHHHHHHHHhhCCHHHHHh
Confidence 378999999999999 89999998865
No 97
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=63.40 E-value=10 Score=30.43 Aligned_cols=52 Identities=23% Similarity=0.302 Sum_probs=30.0
Q ss_pred CccChhhHHHHHHhcC--CHHHHHHhhhhhhhh--hhccHHHhHhhchhhhhhhhhc
Q psy14489 189 KKIGPKTAVKLLNQYN--SLENIINNANNIKGV--IGKNLRFALNWLPKLKKILTIK 241 (284)
Q Consensus 189 ~giG~ktA~~LL~~~g--sle~i~~~~~~~~~~--~~~~l~~~~~~~~l~~~L~~l~ 241 (284)
||||++++.+| ++.| |.+++++..+.-.++ +..++.-..+.+...+.+++|.
T Consensus 1 pgi~~~~~~~L-~~~GI~t~~~Ll~~~~~~~~r~~La~~~~i~~~~l~~w~~~AdL~ 56 (122)
T PF14229_consen 1 PGIGPKEAAKL-KAAGIKTTGDLLEAGDTPLGRKALAKKLGISERNLLKWVNQADLM 56 (122)
T ss_pred CCCCHHHHHHH-HHcCCCcHHHHHHcCCCHHHHHHHHHhcCCCHHHHHHHHhHHHhh
Confidence 79999999988 4444 788888876543332 3322222334444444444444
No 98
>cd01015 CSHase N-carbamoylsarcosine amidohydrolase (CSHase) hydrolyzes N-carbamoylsarcosine to sarcosine, carbon dioxide and ammonia. CSHase is involved in one of the two alternative pathways for creatinine degradation to glycine in microorganisms.This CSHase-containing pathway degrades creatinine via N-methylhydantoin N-carbamoylsarcosine and sarcosine to glycine. Enzymes of this pathway are used in the diagnosis for renal disfunction, for determining creatinine levels in urine and serum.
Probab=62.19 E-value=18 Score=30.43 Aligned_cols=43 Identities=23% Similarity=0.354 Sum_probs=38.5
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|.++|=-+-+-|+...+ .|++|+|++
T Consensus 104 ~L~~~L~~~gi~~vvi~G~~t~~CV~~Ta~~A~~-~Gy~v~vv~ 146 (179)
T cd01015 104 SLAATLTARGVDTLIVAGCSTSGCIRATAVDAMQ-HGFRPIVVR 146 (179)
T ss_pred cHHHHHHHcCCCEEEEeeecccHhHHHHHHHHHH-CCCeEEEee
Confidence 4667888999999999999999999999998888 899998886
No 99
>KOG2841|consensus
Probab=61.27 E-value=6.6 Score=35.26 Aligned_cols=13 Identities=31% Similarity=0.547 Sum_probs=8.6
Q ss_pred CccChhhHHHHHH
Q psy14489 189 KKIGPKTAVKLLN 201 (284)
Q Consensus 189 ~giG~ktA~~LL~ 201 (284)
||+||..|.+|.+
T Consensus 233 ~G~G~~kak~l~~ 245 (254)
T KOG2841|consen 233 PGLGPAKAKRLHK 245 (254)
T ss_pred cCcCHHHHHHHHH
Confidence 5777777766654
No 100
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.14 E-value=7.3 Score=34.05 Aligned_cols=18 Identities=39% Similarity=0.547 Sum_probs=14.1
Q ss_pred CCCCCCccChhhHHHHHH
Q psy14489 184 NLPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~ 201 (284)
.+.-.||||+|+|.++--
T Consensus 12 ~l~~LPGIG~KsA~RlA~ 29 (195)
T TIGR00615 12 SLKKLPGIGPKSAQRLAF 29 (195)
T ss_pred HHHHCCCCCHHHHHHHHH
Confidence 345689999999988743
No 101
>PRK00076 recR recombination protein RecR; Reviewed
Probab=61.04 E-value=7.5 Score=34.01 Aligned_cols=17 Identities=41% Similarity=0.556 Sum_probs=13.9
Q ss_pred CCCCCccChhhHHHHHH
Q psy14489 185 LPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~ 201 (284)
+.-.||||+|+|.++--
T Consensus 13 l~~LPGIG~KsA~Rla~ 29 (196)
T PRK00076 13 LRKLPGIGPKSAQRLAF 29 (196)
T ss_pred HHHCCCCCHHHHHHHHH
Confidence 45689999999998754
No 102
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=60.92 E-value=26 Score=36.36 Aligned_cols=26 Identities=12% Similarity=0.218 Sum_probs=21.4
Q ss_pred CCCCccChhhHHHHHHhcC--CHHHHHH
Q psy14489 186 PGVKKIGPKTAVKLLNQYN--SLENIIN 211 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g--sle~i~~ 211 (284)
-.|+|+|||++.+|.++.+ +++++++
T Consensus 448 l~I~GLG~k~i~~L~~~g~I~~i~DL~~ 475 (665)
T PRK07956 448 MDIDGLGEKIIEQLFEKGLIHDPADLFK 475 (665)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHh
Confidence 3468999999999998754 8899984
No 103
>PRK13844 recombination protein RecR; Provisional
Probab=59.96 E-value=8.1 Score=33.90 Aligned_cols=18 Identities=28% Similarity=0.390 Sum_probs=14.2
Q ss_pred CCCCCCccChhhHHHHHH
Q psy14489 184 NLPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~ 201 (284)
.+.-.||||+|+|.++--
T Consensus 16 ~l~~LPGIG~KsA~Rla~ 33 (200)
T PRK13844 16 SLRKLPTIGKKSSQRLAL 33 (200)
T ss_pred HHHHCCCCCHHHHHHHHH
Confidence 346689999999988754
No 104
>PRK00254 ski2-like helicase; Provisional
Probab=58.88 E-value=8 Score=40.20 Aligned_cols=27 Identities=37% Similarity=0.538 Sum_probs=24.7
Q ss_pred CCCCccChhhHHHHHHh-cCCHHHHHHh
Q psy14489 186 PGVKKIGPKTAVKLLNQ-YNSLENIINN 212 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~-~gsle~i~~~ 212 (284)
..|||+|+++|.+|++. |+|+++|.++
T Consensus 648 ~~ipgig~~~~~~l~~~g~~s~~~i~~a 675 (720)
T PRK00254 648 MRLPMIGRKRARALYNAGFRSIEDIVNA 675 (720)
T ss_pred hcCCCCCHHHHHHHHHccCCCHHHHHhC
Confidence 56899999999999999 9999999775
No 105
>cd00431 cysteine_hydrolases Cysteine hydrolases; This family contains amidohydrolases, like CSHase (N-carbamoylsarcosine amidohydrolase), involved in creatine metabolism and nicotinamidase, converting nicotinamide to nicotinic acid and ammonia in the pyridine nucleotide cycle. It also contains isochorismatase, an enzyme that catalyzes the conversion of isochorismate to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of the vinyl ether bond, and other related enzymes with unknown function.
Probab=58.81 E-value=21 Score=29.10 Aligned_cols=43 Identities=19% Similarity=0.363 Sum_probs=38.3
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|.++|--+.+-++...+ .|++++|++
T Consensus 100 ~l~~~L~~~~i~~vil~G~~t~~CV~~T~~~a~~-~G~~v~vi~ 142 (161)
T cd00431 100 DLDELLRERGIDTLVVCGIATDICVLATARDALD-LGYRVIVVE 142 (161)
T ss_pred CHHHHHHHCCCCEEEEEecCcChhHHHHHHHHHH-CCCEEEEeh
Confidence 4667888899999999999999999999998888 899999986
No 106
>PRK11440 putative hydrolase; Provisional
Probab=57.04 E-value=26 Score=29.74 Aligned_cols=43 Identities=12% Similarity=0.252 Sum_probs=38.0
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|.+++=-+.+-|+.... .|++++|++
T Consensus 111 ~L~~~L~~~gi~~lii~Gv~T~~CV~~Ta~~A~~-~gy~v~vv~ 153 (188)
T PRK11440 111 DLELQLRRRGIDTIVLCGISTNIGVESTARNAWE-LGFNLVIAE 153 (188)
T ss_pred CHHHHHHHCCCCEEEEeeechhHHHHHHHHHHHH-CCCEEEEec
Confidence 3566788899999999999999999999998888 899999986
No 107
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=56.26 E-value=6.9 Score=34.05 Aligned_cols=26 Identities=27% Similarity=0.445 Sum_probs=20.1
Q ss_pred cCCCCCCCCCCCccChhhHHHHHHhcC
Q psy14489 178 IGDMSDNLPGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 178 ~GD~sDni~Gv~giG~ktA~~LL~~~g 204 (284)
.||. .-+..|||||+|||.+++-+..
T Consensus 104 ~~D~-~~L~~vpGIGkKtAerIilELk 129 (194)
T PRK14605 104 SGNA-ELLSTIPGIGKKTASRIVLELK 129 (194)
T ss_pred hCCH-HHHHhCCCCCHHHHHHHHHHHH
Confidence 5664 4578899999999999776533
No 108
>cd01012 YcaC_related YcaC related amidohydrolases; E.coli YcaC is an homooctameric hydrolase with unknown specificity. Despite its weak sequence similarity, it is structurally related to other amidohydrolases and shares conserved active site residues with them. Multimerisation interface seems not to be conserved in all members.
Probab=55.96 E-value=26 Score=28.84 Aligned_cols=43 Identities=16% Similarity=0.281 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|..+|--+.+.++.... .|+++++++
T Consensus 78 ~L~~~L~~~gi~~lii~G~~T~~CV~~Ta~~a~~-~g~~v~v~~ 120 (157)
T cd01012 78 AFRKALKATGRKQVVLAGLETHVCVLQTALDLLE-EGYEVFVVA 120 (157)
T ss_pred HHHHHHHhcCCCEEEEEEeeccHHHHHHHHHHHH-CCCEEEEEe
Confidence 4667888899999999999999999999998887 899998876
No 109
>COG4365 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.54 E-value=36 Score=33.25 Aligned_cols=138 Identities=20% Similarity=0.320 Sum_probs=80.4
Q ss_pred EEEEEEeCCCCccccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCC-cEEeeCCchHHHHHHHHHHHhhHhCCCeEEE
Q psy14489 53 YIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGW-PILIIKGVEADDVIGTLAKQAVTKHNLKVII 131 (284)
Q Consensus 53 ~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi-~~~~~~g~EADD~ia~la~~~~~~~~~~v~I 131 (284)
.-+++||++.|.+|+-..|-++.--. .|..+..++..-.+-+++.|+ +.+..+. ..+-+
T Consensus 224 eGllvlds~~p~lrkLeapmf~kiL~-k~~~l~~af~dqq~rl~qaGy~~~I~~~~-------------------tnanL 283 (537)
T COG4365 224 EGLLVLDSGDPALRKLEAPMFAKILE-KPLALSAAFEDQQERLSQAGYTPPIIRPA-------------------TNANL 283 (537)
T ss_pred cceEEecCCChHHHHHHHHHHHHHHh-hhHhHHHHHHHHHHHHHhCCCCCccccCc-------------------cccee
Confidence 44888999889999988777654322 377788888888888888888 4443221 12334
Q ss_pred EcCCCccccccCCCeEEE--e-CcEeeeHhHHHHHhCCChhHH---------------------------------Hhhh
Q psy14489 132 STNDKDMAQLVSNKIALI--N-NNKIHDRTTIISRFGVSPEKI---------------------------------VDYF 175 (284)
Q Consensus 132 ~S~DkDl~ql~~~~v~~~--~-~~~~~~~~~~~~~~G~~p~q~---------------------------------~~~~ 175 (284)
+-.+-|..+|+.-.-.-| + +.+.++.+++.+.....|+.| -+..
T Consensus 284 F~eeEdsR~li~ydg~~f~ln~~d~tytReELl~~le~hPerfSnnvvtrplmqe~lfptlafvagP~ei~YWaeLkrvf 363 (537)
T COG4365 284 FYEEEDSRRLIRYDGQSFSLNTHDKTYTREELLAHLEAHPERFSNNVVTRPLMQERLFPTLAFVAGPGEIKYWAELKRVF 363 (537)
T ss_pred EEeecCceeeeeecCceeEeecccccccHHHHHHHHhhCHHhcCCcccccHHHHhhccCccccccCcchhhHHHHHHHHH
Confidence 445666788776322222 2 344555555544333333322 2223
Q ss_pred hhcCCCCCCCCCCCccCh----hhHHHHHHhcC-CHHHHHHh
Q psy14489 176 SLIGDMSDNLPGVKKIGP----KTAVKLLNQYN-SLENIINN 212 (284)
Q Consensus 176 ~L~GD~sDni~Gv~giG~----ktA~~LL~~~g-sle~i~~~ 212 (284)
.+|| ----|-+|.+|. ..-.|+|.+|. |+|+.+..
T Consensus 364 ~~c~--~kmp~vmPrl~it~l~~~ieK~lae~nisle~ai~~ 403 (537)
T COG4365 364 KTCG--RKMPPVMPRLGITYLNDRIEKLLAEYNISLEKAIVD 403 (537)
T ss_pred HHhc--ccCCCCccccchhhhhHHHHHHHHHcCCCHHHHHHh
Confidence 4444 223345577764 34568888887 67776653
No 110
>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=55.46 E-value=5.6 Score=34.22 Aligned_cols=22 Identities=18% Similarity=0.246 Sum_probs=17.9
Q ss_pred CCCCCCccChhhHHHHHHhcCC
Q psy14489 184 NLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~~gs 205 (284)
-+-.+||||+|||-=.|..+|+
T Consensus 116 ~Ll~LpGVG~KTAnvVL~~l~~ 137 (177)
T TIGR03252 116 RLKALPGFGKQKAKIFLALLGK 137 (177)
T ss_pred HHHcCCCCCHHHHHHHHHHHHH
Confidence 3567999999999988886655
No 111
>PF13052 DUF3913: Protein of unknown function (DUF3913)
Probab=55.22 E-value=6 Score=26.45 Aligned_cols=14 Identities=43% Similarity=0.762 Sum_probs=12.8
Q ss_pred CCCCCCCCccChhh
Q psy14489 182 SDNLPGVKKIGPKT 195 (284)
Q Consensus 182 sDni~Gv~giG~kt 195 (284)
.||+|-||.||+|.
T Consensus 18 wdnvptiprigekv 31 (57)
T PF13052_consen 18 WDNVPTIPRIGEKV 31 (57)
T ss_pred hccCCCccccchhh
Confidence 69999999999985
No 112
>PF05889 SLA_LP_auto_ag: Soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen); InterPro: IPR008829 This family consists of several eukaryotic and archaeal proteins which are related to the Homo sapiens soluble liver antigen/liver pancreas antigen (SLA/LP autoantigen). Autoantibodies are a hallmark of autoimmune hepatitis, but most are not disease specific. Autoantibodies to soluble liver antigen (SLA) and to liver and pancreas antigen (LP) have been described as disease specific, occurring in about 30% of all patients with autoimmune hepatitis []. The function of SLA/LP is unknown, however, it has been suggested that the protein may function as a serine hydroxymethyltransferase and may be an important enzyme in the thus far poorly understood selenocysteine pathway []. The archaeal sequences Q8TXK0 from SWISSPROT and Q8TYR3 from SWISSPROT are annotated as being pyridoxal phosphate-dependent enzymes.; GO: 0016740 transferase activity; PDB: 2E7J_B 2E7I_B 2Z67_C 3HL2_D 3BC8_A 3BCA_A 3BCB_A.
Probab=55.10 E-value=34 Score=33.13 Aligned_cols=88 Identities=18% Similarity=0.301 Sum_probs=57.0
Q ss_pred HHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEe--eCCchHHHHHHHH
Q psy14489 40 KMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILI--IKGVEADDVIGTL 117 (284)
Q Consensus 40 ~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~--~~g~EADD~ia~l 117 (284)
..+.+.+++.+++.+.++++. .++-+.|. |+++. .+-++++..|||.+. +-|.-.-..+..+
T Consensus 142 ~~ie~~i~~~G~~~iLcvltt----------tscfapr~--~D~i~----~IakiC~~~~IPhlvNnAYgvQ~~~~~~~i 205 (389)
T PF05889_consen 142 EAIEAKIEELGADNILCVLTT----------TSCFAPRL--PDDIE----EIAKICKEYDIPHLVNNAYGVQSSKCMHLI 205 (389)
T ss_dssp HHHHHHHHHHCGGGEEEEEEE----------SSTTTTB------HH----HHHHHHHHHT--EEEEGTTTTT-HHHHHHH
T ss_pred HHHHHHHHHhCCCCeEEEEEe----------cCccCCCC--CccHH----HHHHHHHHcCCceEEccchhhhHHHHHHHH
Confidence 356666677888888888875 45556555 55554 577788889999987 4455556666666
Q ss_pred HHHhhHhCCCeEEEEcCCCccccccCC
Q psy14489 118 AKQAVTKHNLKVIISTNDKDMAQLVSN 144 (284)
Q Consensus 118 a~~~~~~~~~~v~I~S~DkDl~ql~~~ 144 (284)
.+..+. --.++.+-|.||||+-=++.
T Consensus 206 ~~a~~~-GRvda~vqS~dkNF~VPvGg 231 (389)
T PF05889_consen 206 QQAWRV-GRVDAFVQSTDKNFMVPVGG 231 (389)
T ss_dssp HHHHHH-STCSEEEEEHHHHHCEESSH
T ss_pred HHHHhc-CCcceeeeecCCCEEecCCC
Confidence 554443 34589999999999886654
No 113
>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=55.10 E-value=6.9 Score=33.99 Aligned_cols=24 Identities=29% Similarity=0.422 Sum_probs=19.0
Q ss_pred cCCCCCCCCCCCccChhhHHHHHHh
Q psy14489 178 IGDMSDNLPGVKKIGPKTAVKLLNQ 202 (284)
Q Consensus 178 ~GD~sDni~Gv~giG~ktA~~LL~~ 202 (284)
.||. .-+..|||||+|||.+++-+
T Consensus 103 ~~d~-~~L~~ipGiGkKtAerIile 126 (191)
T TIGR00084 103 TEEV-KALVKIPGVGKKTAERLLLE 126 (191)
T ss_pred hCCH-HHHHhCCCCCHHHHHHHHHH
Confidence 3664 45788999999999999843
No 114
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=54.99 E-value=6.3 Score=34.39 Aligned_cols=18 Identities=39% Similarity=0.652 Sum_probs=14.2
Q ss_pred CCCCCCCccChhhHHHHH
Q psy14489 183 DNLPGVKKIGPKTAVKLL 200 (284)
Q Consensus 183 Dni~Gv~giG~ktA~~LL 200 (284)
|.+.-+||||||+|.++-
T Consensus 12 ~~l~kLPGvG~KsA~R~A 29 (198)
T COG0353 12 DALKKLPGVGPKSAQRLA 29 (198)
T ss_pred HHHhhCCCCChhHHHHHH
Confidence 445678999999998864
No 115
>KOG1602|consensus
Probab=54.71 E-value=28 Score=31.79 Aligned_cols=87 Identities=11% Similarity=0.156 Sum_probs=52.4
Q ss_pred hcCCCEEEEEEeCCCCccccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHH
Q psy14489 48 NYRATYIACIFDAKGKNFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTL 117 (284)
Q Consensus 48 ~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~l 117 (284)
..-|.|++++.||.+..-|+.-.+.-+++++.. .++-.+-++|..+||+.+++ +..|-|-++.-.
T Consensus 34 g~~P~HVaFIMDGNRR~AKk~~L~~~~GH~aGf-----~~l~~ile~C~~lGI~~vT~fAFSieNFkRs~eEVd~LM~L~ 108 (271)
T KOG1602|consen 34 GPMPRHVAFIMDGNRRYAKKRGLETSEGHEAGF-----EALKEILELCKELGIKEVTVFAFSIENFKRSPEEVDGLMDLA 108 (271)
T ss_pred CCCcceeEEEecCchHHHHhcCCCcccchHHHH-----HHHHHHHHHHHHcCCcEEEEEEEehhhhCCCHHHHHHHHHHH
Confidence 456899999999854333444445566666542 23345666777799999874 456887777643
Q ss_pred HHHhhH---------hCCCeEEEEcCCCcccc
Q psy14489 118 AKQAVT---------KHNLKVIISTNDKDMAQ 140 (284)
Q Consensus 118 a~~~~~---------~~~~~v~I~S~DkDl~q 140 (284)
-.+... +.|.++.|+ +|.++++
T Consensus 109 ~~k~~~~~~~~~~~~~~gvririi-GdlslL~ 139 (271)
T KOG1602|consen 109 LEKIERLLEQGEKLDKYGVRIRVI-GDLSLLP 139 (271)
T ss_pred HHHHHHHHHHhhhhhhcCeEEEEE-cchhhCC
Confidence 332221 134454444 5766665
No 116
>TIGR03614 RutB pyrimidine utilization protein B. RL Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5114-9. Epub 2006 Mar 15.
Probab=54.17 E-value=28 Score=30.65 Aligned_cols=43 Identities=12% Similarity=0.237 Sum_probs=38.9
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..||..+..-|..+|=-+-+-++...+ .|++++|++
T Consensus 141 ~L~~~Lr~~gI~~lvi~Gv~T~~CV~sTar~A~~-~Gy~v~vv~ 183 (226)
T TIGR03614 141 PLDSMLRARGIRNLVFTGIATNVCVESTLRDGFH-LEYFGVVLE 183 (226)
T ss_pred CHHHHHHHCCCCEEEEeccCccHhHHHHHHHHHH-CCCEEEEec
Confidence 4677889999999999999999999999998888 899999986
No 117
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=53.27 E-value=14 Score=30.44 Aligned_cols=41 Identities=24% Similarity=0.330 Sum_probs=32.0
Q ss_pred cCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCC
Q psy14489 98 IGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSN 144 (284)
Q Consensus 98 ~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~ 144 (284)
.+++++.. +-.|||.|-..|.+ .+ +++|+|+|+.|.+-+..
T Consensus 75 er~~~~~~-~~~aDe~i~~~a~~----~~-~~iVaTnD~eLk~rlr~ 115 (136)
T COG1412 75 ERLECIHK-GRYADECLLEAALK----HG-RYIVATNDKELKRRLRE 115 (136)
T ss_pred hccCcccc-CCChHHHHHHHHHH----cC-CEEEEeCCHHHHHHHHH
Confidence 35667766 66899999988875 23 69999999999997653
No 118
>COG1948 MUS81 ERCC4-type nuclease [DNA replication, recombination, and repair]
Probab=52.89 E-value=32 Score=31.35 Aligned_cols=122 Identities=16% Similarity=0.246 Sum_probs=59.0
Q ss_pred CChhHHHHHHHHHHHHHhcCCcEEee-CCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe---CcEee
Q psy14489 80 MPYNLILQINLIHQMVKAIGWPILII-KGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN---NNKIH 155 (284)
Q Consensus 80 ~p~~l~~q~~~i~~~l~~~gi~~~~~-~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~---~~~~~ 155 (284)
.|+.+..++-.+ .-.+|++++.. ...|--.+|..||++... ++...+..+..+-...+-.....+.. .....
T Consensus 118 ~~~av~~al~s~---~vdfg~~vi~t~~~~~Ta~~i~~la~req~-e~~r~v~~~~~~~~~t~~e~q~~il~s~pgig~~ 193 (254)
T COG1948 118 HPNAVRGALASL---AVDFGLPVIWTRSPEETAELIHELARREQE-ERKRSVNPHGKKKAKTLKELQLYILESIPGIGPK 193 (254)
T ss_pred CHHHHHHHHHHH---HhhcCceEEEeCCHHHHHHHHHHHHHHHHH-hccccccccccccccchHHHHHHHHHcCCCccHH
Confidence 366665544322 12278999876 446777788888887663 22222222211111111100000000 11222
Q ss_pred eHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHhcCCHHHHHHh
Q psy14489 156 DRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQYNSLENIINN 212 (284)
Q Consensus 156 ~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~~gsle~i~~~ 212 (284)
....+..+||- .+.+ .-++ -.-+.-|.|||+++|..+=.-|.|.-..+..
T Consensus 194 ~a~~ll~~fgS-~~~~----~tas--~~eL~~v~gig~k~A~~I~~~~~t~~~~~~~ 243 (254)
T COG1948 194 LAERLLKKFGS-VEDV----LTAS--EEELMKVKGIGEKKAREIYRFLRTEYKLIEA 243 (254)
T ss_pred HHHHHHHHhcC-HHHH----hhcC--HHHHHHhcCccHHHHHHHHHHHhchhhhhcc
Confidence 33334444442 1100 0111 1334668999999999888777776555443
No 119
>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=52.85 E-value=18 Score=27.17 Aligned_cols=30 Identities=30% Similarity=0.567 Sum_probs=22.1
Q ss_pred CCCCCccChhhHHHHHH-----hcCCHHHHHHhhh
Q psy14489 185 LPGVKKIGPKTAVKLLN-----QYNSLENIINNAN 214 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~-----~~gsle~i~~~~~ 214 (284)
...|+|+|+++|.++++ .|.|+++++..++
T Consensus 29 l~~Ikglg~~~a~~I~~~R~~g~f~s~~df~~R~~ 63 (90)
T PF14579_consen 29 LSAIKGLGEEVAEKIVEERENGPFKSLEDFIQRLP 63 (90)
T ss_dssp GGGSTTS-HHHHHHHHHHHHCSS-SSHHHHHHHS-
T ss_pred HhhcCCCCHHHHHHHHHhHhcCCCCCHHHHHHHHh
Confidence 35689999999999996 4678888887764
No 120
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=52.33 E-value=8 Score=33.96 Aligned_cols=24 Identities=25% Similarity=0.380 Sum_probs=19.7
Q ss_pred CCCCCCCCccChhhHHHHHHhcCC
Q psy14489 182 SDNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 182 sDni~Gv~giG~ktA~~LL~~~gs 205 (284)
...+..+||||.|||.+++-+..+
T Consensus 107 ~~~L~k~PGIGkKtAerivleLk~ 130 (201)
T COG0632 107 VKALSKIPGIGKKTAERIVLELKG 130 (201)
T ss_pred hHhhhcCCCCCHHHHHHHHHHHhh
Confidence 456788999999999999876554
No 121
>cd01013 isochorismatase Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase, catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate, via the hydrolysis of a vinyl ether, an uncommon reaction in biological systems. Isochorismatase is part of the phenazine biosynthesis pathway. Phenazines are antimicrobial compounds that provide the competitive advantage for certain bacteria.
Probab=52.21 E-value=26 Score=30.36 Aligned_cols=43 Identities=23% Similarity=0.207 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|.++|--+-+-|+...+ .|++++|++
T Consensus 132 ~L~~~Lr~~gi~~lii~Gv~T~~CV~~Ta~~A~~-~Gy~v~vv~ 174 (203)
T cd01013 132 PLLERLKESGRDQLIITGVYAHIGCLSTAVDAFM-RDIQPFVVA 174 (203)
T ss_pred CHHHHHHHcCCCEEEEEEeccChhHHHHHHHHHH-CCCeEEEec
Confidence 4567788999999999999999999999998887 899998876
No 122
>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=52.16 E-value=12 Score=34.49 Aligned_cols=28 Identities=36% Similarity=0.558 Sum_probs=24.2
Q ss_pred CCCCCccChhhHHHHHHh-cCCHHHHHHh
Q psy14489 185 LPGVKKIGPKTAVKLLNQ-YNSLENIINN 212 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~-~gsle~i~~~ 212 (284)
+..+||||+++|.+|.+. +.|++++...
T Consensus 1 l~~i~gig~~~~~~L~~~Gi~ti~dl~~~ 29 (310)
T TIGR02236 1 LEDLPGVGPATAEKLREAGYDTFEAIAVA 29 (310)
T ss_pred CcccCCCCHHHHHHHHHcCCCCHHHHHcC
Confidence 356899999999999998 9999998664
No 123
>TIGR00305 probable toxin-antitoxin system toxin component, PIN family. This uncharacterized protein family, part of the PIN domain superfamily, is restricted to bacteria and archaea. A comprehensive in silico study of toxin-antitoxin systems by Makarova, et al. (2009) finds evidence this family represents the toxin-like component of one class of type 2 toxin-antitoxin systems.
Probab=51.38 E-value=15 Score=28.49 Aligned_cols=28 Identities=18% Similarity=0.096 Sum_probs=20.8
Q ss_pred chHHHHHHHHHHHhhHhCCCeEEEEcCCCcccc
Q psy14489 108 VEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQ 140 (284)
Q Consensus 108 ~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~q 140 (284)
-..|+.+..+|.. +...+|+|+|||++-
T Consensus 86 D~~D~~~l~~A~~-----~~ad~iVT~Dkdll~ 113 (114)
T TIGR00305 86 DKKDNKFLNTAYA-----SKANALITGDTDLLV 113 (114)
T ss_pred CchhHHHHHHHHh-----cCCCEEEECCHHHhh
Confidence 3668888877764 334689999999874
No 124
>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=50.34 E-value=11 Score=26.85 Aligned_cols=15 Identities=33% Similarity=0.414 Sum_probs=13.1
Q ss_pred CCCCCccChhhHHHH
Q psy14489 185 LPGVKKIGPKTAVKL 199 (284)
Q Consensus 185 i~Gv~giG~ktA~~L 199 (284)
+.++||||+++|.++
T Consensus 49 ~~~l~gIG~~ia~kI 63 (68)
T PF14716_consen 49 LKKLPGIGKSIAKKI 63 (68)
T ss_dssp HCTSTTTTHHHHHHH
T ss_pred HhhCCCCCHHHHHHH
Confidence 588999999998876
No 125
>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=49.01 E-value=43 Score=34.66 Aligned_cols=26 Identities=15% Similarity=0.295 Sum_probs=21.0
Q ss_pred CCCCccChhhHHHHHHhcC--CHHHHHH
Q psy14489 186 PGVKKIGPKTAVKLLNQYN--SLENIIN 211 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g--sle~i~~ 211 (284)
-.|+|+|+|++.+|.++.+ +++++++
T Consensus 435 l~I~GLG~k~i~~L~~~g~I~~~~Dl~~ 462 (652)
T TIGR00575 435 MDIEGLGDKVIEQLFEKKLVRSVADLYA 462 (652)
T ss_pred cCCCCcCHHHHHHHHHcCCcCCHHHHHh
Confidence 3468999999999998654 7888884
No 126
>PLN02621 nicotinamidase
Probab=47.85 E-value=39 Score=29.00 Aligned_cols=43 Identities=26% Similarity=0.389 Sum_probs=37.5
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|.++|=-+-+-++...+ .|++++|++
T Consensus 117 ~L~~~L~~~gi~~lvi~Gv~T~~CV~~Ta~~a~~-~gy~v~v~~ 159 (197)
T PLN02621 117 RLEERLRKIGVKEVIVTGVMTNLCCETTAREAFV-RGFRVFFST 159 (197)
T ss_pred cHHHHHHHCCCCEEEEEecccchhHHHHHHHHHH-CCCEEEEec
Confidence 4667788999999999999999999998988887 899988875
No 127
>cd01014 nicotinamidase_related Nicotinamidase_ related amidohydrolases. Cysteine hydrolases of unknown function that share the catalytic triad with other amidohydrolases, like nicotinamidase, which converts nicotinamide to nicotinic acid and ammonia.
Probab=47.17 E-value=39 Score=27.69 Aligned_cols=43 Identities=16% Similarity=0.259 Sum_probs=37.1
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.+.|+..|+..+..-|.++|=-+.+-|+...+ .|++++|++
T Consensus 89 ~l~~~L~~~gi~~viv~G~~td~CV~~Ta~~a~~-~g~~v~vi~ 131 (155)
T cd01014 89 DLEEWLREAGIDHLVICGAMTEMCVDTTVRSAFD-LGYDVTVVA 131 (155)
T ss_pred CHHHHHHHCCCCEEEEEeeccchhHHHHHHHHHH-CCCcEEEec
Confidence 4677888999999999999999888888888777 899998865
No 128
>PRK14172 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=47.10 E-value=19 Score=33.18 Aligned_cols=73 Identities=21% Similarity=0.357 Sum_probs=44.2
Q ss_pred CCCeEEEEcCC-CccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCCC---------CCC
Q psy14489 125 HNLKVIISTND-KDMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMSD---------NLP 186 (284)
Q Consensus 125 ~~~~v~I~S~D-kDl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~sD---------ni~ 186 (284)
.+..|.+|.+. +|+..+... .+-+-- +...++.+++++- .|+++. +- -++||- | .|.
T Consensus 181 ~~AtVt~chs~T~~l~~~~~~ADIvIsAvGkp~~i~~~~ik~gavVIDvGin~~---~g-kl~GDv-d~~~v~~~a~~iT 255 (278)
T PRK14172 181 ENATVTICHSKTKNLKEVCKKADILVVAIGRPKFIDEEYVKEGAIVIDVGTSSV---NG-KITGDV-NFDKVIDKASYIT 255 (278)
T ss_pred CCCEEEEeCCCCCCHHHHHhhCCEEEEcCCCcCccCHHHcCCCcEEEEeecccc---CC-ceeeec-cHHHHHhhccEec
Confidence 56677777544 455444332 333333 5667888877652 465542 11 388874 4 355
Q ss_pred CCC-ccChhhHHHHHHh
Q psy14489 187 GVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 187 Gv~-giG~ktA~~LL~~ 202 (284)
.|| |+||-|.+-|++.
T Consensus 256 PVPGGVGp~T~a~L~~N 272 (278)
T PRK14172 256 PVPGGVGSLTTTLLIKN 272 (278)
T ss_pred CCCCCccHHHHHHHHHH
Confidence 565 5999999999873
No 129
>PRK01229 N-glycosylase/DNA lyase; Provisional
Probab=45.87 E-value=13 Score=32.85 Aligned_cols=18 Identities=33% Similarity=0.455 Sum_probs=14.7
Q ss_pred CCCccChhhHHHHHHhcC
Q psy14489 187 GVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~g 204 (284)
.+||||+|||--.|.-.+
T Consensus 123 ~lpGIG~KTAd~vL~~~~ 140 (208)
T PRK01229 123 NIKGIGYKEASHFLRNVG 140 (208)
T ss_pred cCCCCcHHHHHHHHHHcc
Confidence 789999999999885333
No 130
>PRK14827 undecaprenyl pyrophosphate synthase; Provisional
Probab=45.12 E-value=50 Score=30.77 Aligned_cols=65 Identities=11% Similarity=0.029 Sum_probs=41.0
Q ss_pred cCCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEeeCCc----------hHHHHHHHH
Q psy14489 49 YRATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGV----------EADDVIGTL 117 (284)
Q Consensus 49 ~~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~----------EADD~ia~l 117 (284)
.-|.|++|+.|| +..| |+.-.+...++|.... .+ ..+.+++..+||++++.-.+ |=+.++.-+
T Consensus 66 ~iP~HVAiIMDG-NrRwAk~~gl~~~~GH~~G~~-~l----~~v~~~c~~lGI~~lTvYaFStEN~kR~~~EV~~Lm~L~ 139 (296)
T PRK14827 66 RLPNHVAIVMDG-NGRWATQRGLARTEGHKMGEA-VV----IDIACGAIELGIKWLSLYAFSTENWKRSPEEVRFLMGFN 139 (296)
T ss_pred CCCCeEEEeccC-chHHHHHCCCCHhHHHHHHHH-HH----HHHHHHHHHcCCCEEEEeeecchhhcCCHHHHHHHHHHH
Confidence 348999999997 4444 3334566677766531 22 23555666789999886444 766666554
Q ss_pred HH
Q psy14489 118 AK 119 (284)
Q Consensus 118 a~ 119 (284)
..
T Consensus 140 ~~ 141 (296)
T PRK14827 140 RD 141 (296)
T ss_pred HH
Confidence 43
No 131
>PF00857 Isochorismatase: Isochorismatase family; InterPro: IPR000868 This is a family of hydrolase enzymes. Isochorismatase, also known as 2,3 dihydro-2,3 dihydroxybenzoate synthase catalyses the conversion of isochorismate, in the presence of water, to 2,3-dihydroxybenzoate and pyruvate (3.3.2.1 from EC).; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1XN4_A 3KL2_F 1YZV_A 3IRV_A 1IM5_A 1ILW_A 3PL1_A 1NF9_A 1NF8_A 1X9G_A ....
Probab=44.69 E-value=28 Score=28.67 Aligned_cols=43 Identities=21% Similarity=0.361 Sum_probs=37.1
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|..+|=-+-+-++.+.+ .|++|+|++
T Consensus 102 ~L~~~L~~~gi~~vil~G~~t~~CV~~Ta~~a~~-~g~~v~v~~ 144 (174)
T PF00857_consen 102 DLDEILRKRGIDTVILCGVATDVCVLATARDAFD-RGYRVIVVE 144 (174)
T ss_dssp SHHHHHHHTTESEEEEEEESTTTHHHHHHHHHHH-TT-EEEEEE
T ss_pred cccccccccccceEEEcccccCcEEehhHHHHHH-CCCEEEEEC
Confidence 4567888899999999999999999999998888 899988875
No 132
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=42.99 E-value=48 Score=28.19 Aligned_cols=47 Identities=21% Similarity=0.343 Sum_probs=36.9
Q ss_pred HHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccc
Q psy14489 88 INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQL 141 (284)
Q Consensus 88 ~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql 141 (284)
+-.+-.+|..+|++++... -|.||-|..++.. ..-+|+|.|.-++.-
T Consensus 15 LG~LARwLRllGydt~~~~-~~~d~~i~~i~~~------e~rIllTRDr~L~~r 61 (165)
T COG1656 15 LGKLARWLRLLGYDTVYSS-NESDDEIILIAKK------EGRILLTRDRELYKR 61 (165)
T ss_pred HHHHHHHHHHcCCceeeec-cCCcHHHHHHHhc------CCeEEEeccHHHHHH
Confidence 3456789999999998765 5888888888763 346899999988875
No 133
>PRK14175 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=42.26 E-value=18 Score=33.54 Aligned_cols=75 Identities=23% Similarity=0.382 Sum_probs=43.2
Q ss_pred CCCeEEEEcCCC-ccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCC--------CCCCC
Q psy14489 125 HNLKVIISTNDK-DMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMS--------DNLPG 187 (284)
Q Consensus 125 ~~~~v~I~S~Dk-Dl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~s--------Dni~G 187 (284)
.+..|.++.+.+ |+.+.... .+.+-- +...++.+++.+. .|.++. .+- -++||-. -.|.+
T Consensus 181 ~gatVtv~~s~t~~l~~~~~~ADIVIsAvg~p~~i~~~~vk~gavVIDvGi~~~--~~g-kl~GDvd~~~~~~~a~~iTP 257 (286)
T PRK14175 181 KNASVTILHSRSKDMASYLKDADVIVSAVGKPGLVTKDVVKEGAVIIDVGNTPD--ENG-KLKGDVDYDAVKEIAGAITP 257 (286)
T ss_pred CCCeEEEEeCCchhHHHHHhhCCEEEECCCCCcccCHHHcCCCcEEEEcCCCcC--CCC-CeecCccHHHHHhhccCcCC
Confidence 567777776654 34444333 232222 4446777766431 355441 111 3778732 26777
Q ss_pred CCc-cChhhHHHHHHh
Q psy14489 188 VKK-IGPKTAVKLLNQ 202 (284)
Q Consensus 188 v~g-iG~ktA~~LL~~ 202 (284)
||| +||.|.+.|++.
T Consensus 258 VPGGVGp~T~a~L~~n 273 (286)
T PRK14175 258 VPGGVGPLTITMVLNN 273 (286)
T ss_pred CCCCCHHHHHHHHHHH
Confidence 875 999999999884
No 134
>KOG4700|consensus
Probab=41.36 E-value=54 Score=28.41 Aligned_cols=79 Identities=14% Similarity=0.262 Sum_probs=47.8
Q ss_pred CCCeEEEEcCCCccccccCCCeEEEe--CcEeeeHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHHh
Q psy14489 125 HNLKVIISTNDKDMAQLVSNKIALIN--NNKIHDRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLNQ 202 (284)
Q Consensus 125 ~~~~v~I~S~DkDl~ql~~~~v~~~~--~~~~~~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~~ 202 (284)
.+..+--|+-++||-|+ +|+|.. ..+--..+++.++.--.-.....-+.++| ++|.|+=||.|+-.-|=+
T Consensus 59 l~vqiS~V~vt~dFS~~---~vYWm~~~~geN~e~e~~L~rs~~~~rh~l~~~~~~g----~vP~IkFV~DK~~~~l~e- 130 (207)
T KOG4700|consen 59 LQVQISRVRVTRDFSQV---SVYWMCRGDGENSEIEDFLERSKHQIRHRLEESIGIG----TVPEIKFVGDKALLMLQE- 130 (207)
T ss_pred cceeEEEEEeccchhhh---eeEEEecCCccHHHHHHHHHHHHHHHHHHHHHHhccc----cCCceEEecchHHHHHHH-
Confidence 56778889999999997 677776 22212234444432111112233455666 899999999998554422
Q ss_pred cCCHHHHHHhhh
Q psy14489 203 YNSLENIINNAN 214 (284)
Q Consensus 203 ~gsle~i~~~~~ 214 (284)
++++++.++
T Consensus 131 ---~d~ll~~aD 139 (207)
T KOG4700|consen 131 ---MDKLLREAD 139 (207)
T ss_pred ---HHHHHHHhc
Confidence 456665544
No 135
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=40.14 E-value=17 Score=31.27 Aligned_cols=21 Identities=29% Similarity=0.498 Sum_probs=18.8
Q ss_pred CCCCCccChhhHHHHHHhcCC
Q psy14489 185 LPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~~gs 205 (284)
|.|-||+|..|+.++|+++|-
T Consensus 5 ITGTPGvGKTT~~~~L~~lg~ 25 (180)
T COG1936 5 ITGTPGVGKTTVCKLLRELGY 25 (180)
T ss_pred EeCCCCCchHHHHHHHHHhCC
Confidence 578999999999999998775
No 136
>COG1335 PncA Amidases related to nicotinamidase [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=39.82 E-value=70 Score=27.23 Aligned_cols=43 Identities=14% Similarity=0.315 Sum_probs=37.7
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+..+|+..||..+..-|..+|--+-+-++.... .|+++++++
T Consensus 123 ~L~~~Lr~~~i~~l~v~G~~td~CV~~T~~~A~~-~gy~v~v~~ 165 (205)
T COG1335 123 DLDDILRNLGIDTVVVCGIATDICVLATARDAFD-LGYQVTLVE 165 (205)
T ss_pred CHHHHHHHCCCCEEEEeeeehhHHHHHHHHHHHH-CCCeEEEeh
Confidence 3677888899999999999999999998988887 899988876
No 137
>PRK13913 3-methyladenine DNA glycosylase; Provisional
Probab=39.54 E-value=17 Score=32.30 Aligned_cols=20 Identities=30% Similarity=0.283 Sum_probs=15.7
Q ss_pred CCCCCccChhhHHHHHH-hcC
Q psy14489 185 LPGVKKIGPKTAVKLLN-QYN 204 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~-~~g 204 (284)
+-.+||||++||--+|. .++
T Consensus 123 Ll~l~GIG~kTAd~iLlya~~ 143 (218)
T PRK13913 123 LLDQKGIGKESADAILCYVCA 143 (218)
T ss_pred HHcCCCccHHHHHHHHHHHcC
Confidence 45699999999988776 444
No 138
>PRK10702 endonuclease III; Provisional
Probab=39.49 E-value=16 Score=32.18 Aligned_cols=17 Identities=41% Similarity=0.524 Sum_probs=13.4
Q ss_pred CCCCCccChhhHHHHHH
Q psy14489 185 LPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~ 201 (284)
+--+||||+|||--.|.
T Consensus 111 Ll~lpGVG~ktA~~ill 127 (211)
T PRK10702 111 LEALPGVGRKTANVVLN 127 (211)
T ss_pred HhcCCcccHHHHHHHHH
Confidence 34579999999988764
No 139
>cd00475 CIS_IPPS Cis (Z)-Isoprenyl Diphosphate Synthases (cis-IPPS); homodimers which catalyze the successive 1'-4 condensation of the isopentenyl diphosphate (IPP) molecule to trans,trans-farnesyl diphosphate (FPP) or to cis,trans-FPP to form long-chain polyprenyl diphosphates. A few can also catalyze the condensation of IPP to trans-geranyl diphosphate to form the short-chain cis,trans- FPP. In prokaryotes, the cis-IPPS, undecaprenyl diphosphate synthase (UPP synthase) catalyzes the formation of the carrier lipid UPP in bacterial cell wall peptidooglycan biosynthesis. Similarly, in eukaryotes, the cis-IPPS, dehydrodolichyl diphosphate (dedol-PP) synthase catalyzes the formation of the polyisoprenoid glycosyl carrier lipid dolichyl monophosphate. cis-IPPS are mechanistically and structurally distinct from trans-IPPS, lacking the DDXXD motifs, yet requiring Mg2+ for activity.
Probab=39.48 E-value=20 Score=31.89 Aligned_cols=66 Identities=11% Similarity=0.117 Sum_probs=42.1
Q ss_pred CCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHHH
Q psy14489 51 ATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLAK 119 (284)
Q Consensus 51 ~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la~ 119 (284)
|.|++|+.||. ..| |+.-.+...++|... +. +..+.+++..+||++++. |.-|=+.++.-+..
T Consensus 1 P~HvaiImDGN-rRwA~~~gl~~~~GH~~G~-~~----~~~i~~~~~~~gI~~lTvyaFS~eN~~R~~~EV~~Lm~l~~~ 74 (221)
T cd00475 1 PKHVAFIMDGN-RRWAKQRGMDRIEGHKAGA-EK----LRDILRWCLELGVKEVTLYAFSTENWKRPKEEVDFLMELFRD 74 (221)
T ss_pred CCeEEEecCCC-HHHHHHCCCChhHhHHHHH-HH----HHHHHHHHHHcCCCEEEEEeechhhhCcCHHHHHHHHHHHHH
Confidence 68999999973 344 333346666666653 12 234556677789999875 34487777777665
Q ss_pred Hhh
Q psy14489 120 QAV 122 (284)
Q Consensus 120 ~~~ 122 (284)
...
T Consensus 75 ~l~ 77 (221)
T cd00475 75 VLR 77 (221)
T ss_pred HHH
Confidence 543
No 140
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=39.33 E-value=18 Score=31.28 Aligned_cols=23 Identities=30% Similarity=0.413 Sum_probs=18.7
Q ss_pred CCCCCCCccChhhHHHHHHhcCC
Q psy14489 183 DNLPGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 183 Dni~Gv~giG~ktA~~LL~~~gs 205 (284)
.-+..|||||+|+|.+++.++..
T Consensus 108 ~~L~~v~Gig~k~A~~I~~~l~~ 130 (192)
T PRK00116 108 KALTKVPGIGKKTAERIVLELKD 130 (192)
T ss_pred HHHHhCCCCCHHHHHHHHHHHHH
Confidence 34678999999999999987543
No 141
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=39.24 E-value=18 Score=29.71 Aligned_cols=18 Identities=33% Similarity=0.289 Sum_probs=14.4
Q ss_pred CCCCCccChhhHHHHHHh
Q psy14489 185 LPGVKKIGPKTAVKLLNQ 202 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~ 202 (284)
+..+|||||+||.-.+.-
T Consensus 85 L~~l~GIG~~tA~~~l~~ 102 (158)
T cd00056 85 LLALPGVGRKTANVVLLF 102 (158)
T ss_pred HHcCCCCCHHHHHHHHHH
Confidence 356899999999887764
No 142
>PRK11609 nicotinamidase/pyrazinamidase; Provisional
Probab=38.56 E-value=62 Score=27.97 Aligned_cols=43 Identities=19% Similarity=0.262 Sum_probs=38.1
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..||..+..-|...|=-+-+-|+.+.. .|++|+|++
T Consensus 132 ~L~~~L~~~gi~~lii~G~~T~~CV~~Ta~dA~~-~gy~v~v~~ 174 (212)
T PRK11609 132 ALDDWLREHGITELIVMGLATDYCVKFTVLDALA-LGYQVNVIT 174 (212)
T ss_pred cHHHHHHHcCCCEEEEEEeccCHHHHHHHHHHHH-CCCEEEEEe
Confidence 4667888999999999999999999999998887 899999886
No 143
>PRK10792 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=38.31 E-value=23 Score=32.75 Aligned_cols=75 Identities=20% Similarity=0.291 Sum_probs=42.1
Q ss_pred CCCeEEEEcCCC-ccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCC--------CCCCC
Q psy14489 125 HNLKVIISTNDK-DMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMS--------DNLPG 187 (284)
Q Consensus 125 ~~~~v~I~S~Dk-Dl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~s--------Dni~G 187 (284)
.+..|.++.+.+ |+...... .+.+-- +...++.+++.+. -|+++- .+- -++||-. -.|.+
T Consensus 182 ~~atVtv~hs~T~~l~~~~~~ADIvi~avG~p~~v~~~~vk~gavVIDvGin~~--~~g-k~~GDvd~~~~~~~a~~itP 258 (285)
T PRK10792 182 AGCTVTVCHRFTKNLRHHVRNADLLVVAVGKPGFIPGEWIKPGAIVIDVGINRL--EDG-KLVGDVEFETAAERASWITP 258 (285)
T ss_pred CCCeEEEEECCCCCHHHHHhhCCEEEEcCCCcccccHHHcCCCcEEEEcccccc--cCC-CcCCCcCHHHHHhhccCcCC
Confidence 566777776544 33333322 232222 4556777766542 344331 011 4778731 25778
Q ss_pred CCc-cChhhHHHHHHh
Q psy14489 188 VKK-IGPKTAVKLLNQ 202 (284)
Q Consensus 188 v~g-iG~ktA~~LL~~ 202 (284)
||| +||.|.+-|++.
T Consensus 259 vPGGVGp~T~a~L~~N 274 (285)
T PRK10792 259 VPGGVGPMTVATLLEN 274 (285)
T ss_pred CCCCChHHHHHHHHHH
Confidence 875 999999999984
No 144
>PRK14837 undecaprenyl pyrophosphate synthase; Provisional
Probab=38.15 E-value=22 Score=31.83 Aligned_cols=65 Identities=11% Similarity=0.165 Sum_probs=41.4
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++++.|| ...| |+.-.|...++|... +. +..+.+++..+||++++. |..|=+.++.-+.
T Consensus 6 ~P~HVAiImDG-NrRwAk~~gl~~~~GH~~G~-~~----~~~i~~~c~~~GI~~lT~YaFS~EN~~Rp~~EV~~Lm~L~~ 79 (230)
T PRK14837 6 LPSHVGIIMDG-NRRWALKKGLSFFEGHKEGL-KR----AKEIVKHSLKLGIKYLSLYVFSTENWNRTDSEIEHLMFLIA 79 (230)
T ss_pred CCCeEEEEccC-CHHHHHHCCCchhhhHHHHH-HH----HHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHH
Confidence 37999999997 4444 333346666666653 12 234555666789999874 4567777776655
Q ss_pred HH
Q psy14489 119 KQ 120 (284)
Q Consensus 119 ~~ 120 (284)
..
T Consensus 80 ~~ 81 (230)
T PRK14837 80 DY 81 (230)
T ss_pred HH
Confidence 43
No 145
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=38.15 E-value=66 Score=33.57 Aligned_cols=26 Identities=15% Similarity=0.316 Sum_probs=21.0
Q ss_pred CCCCccChhhHHHHHHhcC--CHHHHHH
Q psy14489 186 PGVKKIGPKTAVKLLNQYN--SLENIIN 211 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g--sle~i~~ 211 (284)
-.|+|+|++|..+|.+... ++.++|.
T Consensus 465 l~I~GLG~k~i~~L~~~g~V~~~~Dl~~ 492 (689)
T PRK14351 465 LDIEGLGEERVQQLVDAGLVESLADLYD 492 (689)
T ss_pred cCCCCcCHHHHHHHHHcCCCCCHHHHHH
Confidence 4578999999999998754 7777776
No 146
>PRK14831 undecaprenyl pyrophosphate synthase; Provisional
Probab=37.85 E-value=22 Score=32.27 Aligned_cols=66 Identities=14% Similarity=0.140 Sum_probs=41.6
Q ss_pred cCCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHH
Q psy14489 49 YRATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTL 117 (284)
Q Consensus 49 ~~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~l 117 (284)
.-|.|++|+.||- ..| |+.-.+...++|... +. +..+.+++..+||++++. +.-|=++++.-+
T Consensus 19 ~~P~HVaiImDGN-rRwA~~~gl~~~~GH~~G~-~~----l~~i~~~c~~~GI~~vT~yaFS~eN~kR~~~Ev~~Lm~L~ 92 (249)
T PRK14831 19 RLPKHVAVIMDGN-GRWAKRRGLPRIMGHRRGV-DA----LKDLLRCCKDWGIGALTAYAFSTENWSRPLEEVNFLMTLF 92 (249)
T ss_pred CCCCeEEEecCCc-HHHHHHCCCchhhhHHHHH-HH----HHHHHHHHHHcCCCEEEEeecchhhhCcCHHHHHHHHHHH
Confidence 3489999999973 344 444445666666653 12 234556777799999874 345666666655
Q ss_pred HHH
Q psy14489 118 AKQ 120 (284)
Q Consensus 118 a~~ 120 (284)
...
T Consensus 93 ~~~ 95 (249)
T PRK14831 93 ERV 95 (249)
T ss_pred HHH
Confidence 443
No 147
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=37.63 E-value=73 Score=25.40 Aligned_cols=49 Identities=20% Similarity=0.469 Sum_probs=36.3
Q ss_pred eHhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhhHHHHHH-hcCCHHHH
Q psy14489 156 DRTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKTAVKLLN-QYNSLENI 209 (284)
Q Consensus 156 ~~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~ktA~~LL~-~~gsle~i 209 (284)
.......+.|+++..+..+..+ +|-. -|||||+..|.-|.. .+.|++++
T Consensus 31 ~r~~La~~~~i~~~~l~~w~~~----AdL~-ri~gi~~~~a~LL~~AGv~Tv~~L 80 (122)
T PF14229_consen 31 GRKALAKKLGISERNLLKWVNQ----ADLM-RIPGIGPQYAELLEHAGVDTVEEL 80 (122)
T ss_pred HHHHHHHhcCCCHHHHHHHHhH----HHhh-hcCCCCHHHHHHHHHhCcCcHHHH
Confidence 3344667789999999999888 4555 899999999776665 34477665
No 148
>TIGR01370 cysRS possible cysteinyl-tRNA synthetase, Methanococcus type. Assignment of this protein family as cysteinyl-tRNA synthetase is controversial, supported by PubMed:11333988 but challenged by PubMed:14679218. Members of this family from Deinococcus radiodurans (bacterial) and Methanococcus jannaschii (archaeal), species lacking a conventional cysteinyl-tRNA synthetase (Cys--tRNA ligase), have been indicated to be a novel form of that enzyme, perhaps distantly related to class I tRNA ligases. The member from Thermotoga maritima is presumed to be a second isozyme of cysteinyl-tRNA synthetase. A number of homologous but more distantly related proteins are annotated as alpha-1,4 polygalactosaminidases.
Probab=37.41 E-value=3.2e+02 Score=25.67 Aligned_cols=55 Identities=13% Similarity=0.153 Sum_probs=36.0
Q ss_pred hHHHHHHHHHHHHHhcCCcEEeeCCchHH--------HHHHHHHHHhhHhCCCeEEEEcCCCcccc
Q psy14489 83 NLILQINLIHQMVKAIGWPILIIKGVEAD--------DVIGTLAKQAVTKHNLKVIISTNDKDMAQ 140 (284)
Q Consensus 83 ~l~~q~~~i~~~l~~~gi~~~~~~g~EAD--------D~ia~la~~~~~~~~~~v~I~S~DkDl~q 140 (284)
+....+..++++.+ .|++++..+ |=++ +.+..++++..+ .|..-+|...|-++.-
T Consensus 249 dr~~~l~~L~~~~~-~G~~Vl~ID-Y~~~~~~~~~n~~~~~~~~~~~~~-~Gf~pYVsd~~l~l~~ 311 (315)
T TIGR01370 249 ERQRRLLALYRLWQ-QGKFVLTVD-YVDDGTKTNENPARMKDAAEKARA-AGLIPYVAESDLELDE 311 (315)
T ss_pred HHHHHHHHHHHHHH-CCCcEEEEE-ecCCcccchhhHHHHHHHHHHHHH-cCCeeeecCchhcccc
Confidence 33333455665544 499998866 4333 566777777777 8888777776777644
No 149
>cd01011 nicotinamidase Nicotinamidase/pyrazinamidase (PZase). Nicotinamidase, a ubiquitous enzyme in prokaryotes, converts nicotinamide to nicotinic acid (niacin) and ammonia, which in turn can be recycled to make nicotinamide adenine dinucleotide (NAD). The same enzyme is also called pyrazinamidase, because in converts the tuberculosis drug pyrazinamide (PZA) into its active form pyrazinoic acid (POA).
Probab=37.33 E-value=70 Score=27.38 Aligned_cols=43 Identities=14% Similarity=0.193 Sum_probs=37.8
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..||..+..-|..+|=-+.+-++.... .|++++|++
T Consensus 128 ~L~~~L~~~~i~~lii~G~~t~~CV~~T~~~a~~-~g~~v~v~~ 170 (196)
T cd01011 128 GLAEYLRERGIDRVDVVGLATDYCVKATALDALK-AGFEVRVLE 170 (196)
T ss_pred hHHHHHHHCCCCEEEEEEecccHHHHHHHHHHHH-CCCEEEEec
Confidence 5678888999999999999999999999988887 888988886
No 150
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=36.96 E-value=44 Score=28.65 Aligned_cols=55 Identities=27% Similarity=0.316 Sum_probs=38.8
Q ss_pred cEEEEecchHHHHHhccC-C-----CccCCCCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCC
Q psy14489 4 TLLLVDGSSCIYRAFYAL-P-----DIRNIDNFPVGALYGTIKMLRKLYKNYRATYIACIFDAK 61 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~-~-----~l~~~~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~ 61 (284)
.+|+-||+..+.|+--.. . -.+.|.|+||. +.| ..+.+++++...+.+++-||-+
T Consensus 2 VIlvTDGD~~A~ravE~aa~~iGgRCIS~S~GNPT~-lsG--~elV~lIk~a~~DPV~VMfDD~ 62 (180)
T PF14097_consen 2 VILVTDGDEYAKRAVEIAAKNIGGRCISQSAGNPTP-LSG--EELVELIKQAPHDPVLVMFDDK 62 (180)
T ss_pred EEEEECChHHHHHHHHHHHHHhCcEEEeccCCCCCc-CCH--HHHHHHHHhCCCCCEEEEEeCC
Confidence 357779999999984321 1 13568899872 222 4678888888888899999963
No 151
>PRK14839 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.74 E-value=22 Score=32.14 Aligned_cols=68 Identities=15% Similarity=0.189 Sum_probs=43.4
Q ss_pred HhcCCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHH
Q psy14489 47 KNYRATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIG 115 (284)
Q Consensus 47 ~~~~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia 115 (284)
....|.|++|+.|| ...| |+.-.+...++|... +. +..+.+++..+||++++. +.-|=+.++.
T Consensus 6 ~~~~P~HVAiImDG-NrRwAk~~gl~~~~GH~~G~-~~----l~~i~~~c~~~GI~~lTvYaFS~EN~~R~~~EV~~Lm~ 79 (239)
T PRK14839 6 DRRSGLHVAIIMDG-NGRWATARGLPRLAGHRAGV-EA----IRRVVEAAPDLGIGTLTLYAFSSDNWRRPAAEVGGLMR 79 (239)
T ss_pred CCCCCCEEEEEcCC-CHHHHHHCCCCHHHHHHHHH-HH----HHHHHHHHHHcCCCEEEEEEechhhcCCCHHHHHHHHH
Confidence 34568999999997 3444 444456666776653 12 234556677789999874 3457777776
Q ss_pred HHHHH
Q psy14489 116 TLAKQ 120 (284)
Q Consensus 116 ~la~~ 120 (284)
-+.+.
T Consensus 80 L~~~~ 84 (239)
T PRK14839 80 LLRAY 84 (239)
T ss_pred HHHHH
Confidence 55543
No 152
>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=36.60 E-value=28 Score=27.16 Aligned_cols=19 Identities=16% Similarity=0.310 Sum_probs=16.7
Q ss_pred CCCCccChhhHHHHHHhcC
Q psy14489 186 PGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g 204 (284)
..|.|||+.+|..+..+.|
T Consensus 18 t~IyGIG~~~A~~Ic~~lg 36 (107)
T PF00416_consen 18 TKIYGIGRRKAKQICKKLG 36 (107)
T ss_dssp TTSTTBCHHHHHHHHHHTT
T ss_pred hhhhccCHHHHHHHHHHcC
Confidence 4589999999999999877
No 153
>PRK14832 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.53 E-value=24 Score=32.07 Aligned_cols=66 Identities=17% Similarity=0.138 Sum_probs=43.3
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.|| ...| |+.-.|...++|... +. +..+.+++..+||++++. |.-|=+.++.-+.
T Consensus 18 iP~HVAiImDG-NrRwAk~~gl~~~~GH~~G~-~~----l~~i~~~c~~~gI~~lTvyaFS~EN~~Rp~~EV~~Lm~L~~ 91 (253)
T PRK14832 18 IPQHIAVIMDG-NGRWATSQGLPRIAGHRQGA-RT----LKELLRCCKDWGIKALTAYAFSTENWQRPIEEVDFLMLLFE 91 (253)
T ss_pred CCCEEEEECCC-CHHHHHHCCCCHHHHHHHHH-HH----HHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHH
Confidence 48999999997 3344 444456677776653 22 234556667789998874 4458888887665
Q ss_pred HHh
Q psy14489 119 KQA 121 (284)
Q Consensus 119 ~~~ 121 (284)
+..
T Consensus 92 ~~l 94 (253)
T PRK14832 92 RLL 94 (253)
T ss_pred HHH
Confidence 443
No 154
>PRK14829 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.20 E-value=25 Score=31.80 Aligned_cols=65 Identities=12% Similarity=0.025 Sum_probs=40.9
Q ss_pred cCCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEeeC----------CchHHHHHHHH
Q psy14489 49 YRATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIK----------GVEADDVIGTL 117 (284)
Q Consensus 49 ~~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~----------g~EADD~ia~l 117 (284)
.-|.|++++.|| ...| |+.-.+...++|... +. +..+.+++..+||++++.- .-|=+.++.-+
T Consensus 13 ~~P~HvaiImDG-NrRwAk~~g~~~~~GH~~G~-~~----l~~iv~~c~~~gI~~vTvYaFS~eN~kR~~~Ev~~lm~L~ 86 (243)
T PRK14829 13 KLPRHIAVVMDG-NGRWATQRGLKRTEGHKAGE-PV----LFDVVAGAIEAGVPYLSLYTFSTENWKRSPDEVRFLMGFS 86 (243)
T ss_pred CCCCeEEEecCC-CHHHHHHCCCChhHHHHHHH-HH----HHHHHHHHHHcCCCEEEEeeecchhhCCCHHHHHHHHHHH
Confidence 348999999997 4444 333346666766653 12 2345567777999998853 34666666554
Q ss_pred HH
Q psy14489 118 AK 119 (284)
Q Consensus 118 a~ 119 (284)
..
T Consensus 87 ~~ 88 (243)
T PRK14829 87 RD 88 (243)
T ss_pred HH
Confidence 43
No 155
>PRK14841 undecaprenyl pyrophosphate synthase; Provisional
Probab=36.13 E-value=26 Score=31.48 Aligned_cols=65 Identities=12% Similarity=0.141 Sum_probs=42.2
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.|| ...| |+.-.+.+.+++... +. +..+.+++..+||++++. |..|=+.++.-+.
T Consensus 3 ~P~HVaiImDG-NrRwAk~~g~~~~~GH~~G~-~~----l~~i~~~~~~lgIk~lTvYaFS~eN~~R~~~Ev~~Lm~L~~ 76 (233)
T PRK14841 3 IPQHVAIIMDG-NGRWAKKRGLPRIKGHQRGA-EV----LHNTVKWSLELGIKYLTAFSFSTENWKRPKEEVEFLMDLFV 76 (233)
T ss_pred CCCEEEEEccC-CHHHHHHCCCchhhhHHHHH-HH----HHHHHHHHHHcCCCEEEEEeeeHhhcCCCHHHHHHHHHHHH
Confidence 38999999997 3344 443456666666542 12 234555666789999874 4568888887766
Q ss_pred HH
Q psy14489 119 KQ 120 (284)
Q Consensus 119 ~~ 120 (284)
..
T Consensus 77 ~~ 78 (233)
T PRK14841 77 QM 78 (233)
T ss_pred HH
Confidence 54
No 156
>smart00478 ENDO3c endonuclease III. includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=35.91 E-value=21 Score=28.97 Aligned_cols=17 Identities=35% Similarity=0.427 Sum_probs=12.9
Q ss_pred CCCCCccChhhHHHHHH
Q psy14489 185 LPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~ 201 (284)
+..+||||++||--++.
T Consensus 74 L~~l~GIG~~tA~~~l~ 90 (149)
T smart00478 74 LLKLPGVGRKTANAVLS 90 (149)
T ss_pred HHcCCCCcHHHHHHHHH
Confidence 34689999999866554
No 157
>PF15632 ATPgrasp_Ter: ATP-grasp in the biosynthetic pathway with Ter operon
Probab=35.80 E-value=2.3e+02 Score=26.79 Aligned_cols=98 Identities=8% Similarity=0.122 Sum_probs=59.1
Q ss_pred HHHHHHhcCCCEEEEEEeCCCCc-cccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHH
Q psy14489 42 LRKLYKNYRATYIACIFDAKGKN-FRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQ 120 (284)
Q Consensus 42 l~~l~~~~~~~~~i~~fD~~~~~-~R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~ 120 (284)
+.+.+++. ...-+++=|..+.. ....--..|+.-+ .++++ ++.+.++|+..||.++ .|+++...+.+.-. .
T Consensus 14 ~i~~lr~~-~~~~i~~sh~~~~~~~~~~aD~~~~eP~--~~~~y---v~~~l~~C~~~~Idv~-~P~~~~~~l~~~r~-~ 85 (329)
T PF15632_consen 14 IIRSLRAN-RDFTIIASHRDPRAPILYAADEAYLEPA--DGEEY---VDWCLDFCKEHGIDVF-VPGRNRELLAAHRD-E 85 (329)
T ss_pred HHHHHHcC-CCeEEEEEeCCCCchHHhcCceeeecCC--CHHHH---HHHHHHHHHHhCCeEE-EcCccHHHHHHHHH-H
Confidence 33334443 34446666653211 1111223355443 34454 4578888889999988 69999999555433 4
Q ss_pred hhHhCCCeEEEEcCCCccccccCCCeEEE
Q psy14489 121 AVTKHNLKVIISTNDKDMAQLVSNKIALI 149 (284)
Q Consensus 121 ~~~~~~~~v~I~S~DkDl~ql~~~~v~~~ 149 (284)
+.+ .|.++.+ ++|.+.+.+..+....+
T Consensus 86 F~a-~Gv~l~~-~~~~~~l~~~~dK~~~y 112 (329)
T PF15632_consen 86 FEA-LGVKLLT-ASSAETLELADDKAAFY 112 (329)
T ss_pred HHH-hCCEEEe-cCCHHHHHHHhhHHHHH
Confidence 555 6877666 68999999887654433
No 158
>COG5049 XRN1 5'-3' exonuclease [DNA replication, recombination, and repair / Cell division and chromosome partitioning / Translation]
Probab=35.74 E-value=5.6e+02 Score=27.17 Aligned_cols=45 Identities=18% Similarity=0.262 Sum_probs=31.7
Q ss_pred eCCchHHHHHHHHHHHhhHh----CCCeEEEEcCCCcccccc----CCCeEEEe
Q psy14489 105 IKGVEADDVIGTLAKQAVTK----HNLKVIISTNDKDMAQLV----SNKIALIN 150 (284)
Q Consensus 105 ~~g~EADD~ia~la~~~~~~----~~~~v~I~S~DkDl~ql~----~~~v~~~~ 150 (284)
+|| |.+-=|-...|.-+.+ ++.+..|.+-|-||..|+ .+++.++.
T Consensus 186 vPG-EGEHKIM~FIRsqkaqp~ynpNT~HciYGLDADLImLGLstH~PHF~iLR 238 (953)
T COG5049 186 VPG-EGEHKIMNFIRSQKAQPSYNPNTRHCIYGLDADLIMLGLSTHEPHFLILR 238 (953)
T ss_pred CCC-ccHHHHHHHHHhcccCCCcCCCceeEEeccCccceeeecccCCCeeEEee
Confidence 688 8888777666643221 345788999999999975 45666665
No 159
>PRK14833 undecaprenyl pyrophosphate synthase; Provisional
Probab=35.67 E-value=27 Score=31.31 Aligned_cols=66 Identities=17% Similarity=0.091 Sum_probs=43.8
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.||- ..| |+.-.+...++|... +.+ ..+.+++..+||.+++. |.-|=++++.-+.
T Consensus 4 ~P~HVaiImDGN-rRwA~~~gl~~~~GH~~G~-~~l----~~~~~~c~~~gI~~lTvyaFS~eN~~R~~~Ev~~Lm~L~~ 77 (233)
T PRK14833 4 TLKHLAIIMDGN-GRWAKLRGKARAAGHKKGV-KTL----REITIWCANHKLECLTLYAFSTENWKRPKSEVDFLMKLLK 77 (233)
T ss_pred CCCeEEEEccCC-HHHHHHCCCChhhhHHHHH-HHH----HHHHHHHHHcCCCEEEEeecchhhcCcCHHHHHHHHHHHH
Confidence 378999999984 344 444456677777653 222 24556667789998874 4558888877766
Q ss_pred HHh
Q psy14489 119 KQA 121 (284)
Q Consensus 119 ~~~ 121 (284)
+..
T Consensus 78 ~~l 80 (233)
T PRK14833 78 KYL 80 (233)
T ss_pred HHH
Confidence 644
No 160
>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=35.41 E-value=21 Score=30.65 Aligned_cols=18 Identities=39% Similarity=0.458 Sum_probs=14.3
Q ss_pred CCCCCCccChhhHHHHHH
Q psy14489 184 NLPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~ 201 (284)
.+.-+||||+|||--+|.
T Consensus 107 ~L~~l~GIG~ktA~~ill 124 (191)
T TIGR01083 107 ELVKLPGVGRKTANVVLN 124 (191)
T ss_pred HHHhCCCCcHHHHHHHHH
Confidence 344789999999988775
No 161
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=35.16 E-value=30 Score=35.10 Aligned_cols=31 Identities=23% Similarity=0.376 Sum_probs=22.5
Q ss_pred CCCCCCccChhhHHHHHHhcC-----CHHHHHHhhh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQYN-----SLENIINNAN 214 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~~g-----sle~i~~~~~ 214 (284)
.+-.++|+|+|.|.+|++... +++.++.++.
T Consensus 460 ~l~~l~gfgeks~~nll~aIe~sk~~~l~r~l~aLG 495 (562)
T PRK08097 460 QLANTPGIGKARAEQLWHQFNLARQQPFSRWLKALG 495 (562)
T ss_pred HHhcCcCccHHHHHHHHHHHHHHcCCCHHHHHHHcC
Confidence 456678888888888876543 6777777764
No 162
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=35.15 E-value=2e+02 Score=22.99 Aligned_cols=43 Identities=19% Similarity=0.381 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccCCCeEEEe
Q psy14489 88 INLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVSNKIALIN 150 (284)
Q Consensus 88 ~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~~~v~~~~ 150 (284)
+..++++++.+|+.+...+ -..|+|-+.|+++. +-.+.|.++.
T Consensus 11 ~~~mkkmMk~MGi~~~eid-------------------V~~ViIk~~~k~iv-f~~p~V~~m~ 53 (116)
T TIGR00264 11 LKQMQKMMKQMGMEMEDLD-------------------VEEVIIVFDDEEWI-FENPKVQVMD 53 (116)
T ss_pred HHHHHHHHHHcCCCccccc-------------------cEEEEEEeCCceEE-EecCeeEEEe
Confidence 3457788899998744221 02589999999998 7788888887
No 163
>PF00875 DNA_photolyase: DNA photolyase from Prosite.; InterPro: IPR006050 DNA photolyases are enzymes that bind to DNA containing pyrimidine dimers: on absorption of visible light, they catalyse dimer splitting into the constituent monomers, a process called photoreactivation []. This is a DNA repair mechanism, repairing mismatched pyrimidine dimers induced by exposure to ultra-violet light []. The precise mechanisms involved in substrate binding, conversion of light energy to the mechanical energy needed to rupture the cyclobutane ring, and subsequent release of the product are uncertain []. Analysis of DNA lyases has revealed the presence of an intrinsic chromophore, all monomers containing a reduced FAD moiety, and, in addition, either a reduced pterin or 8-hydroxy-5-diazaflavin as a second chromophore [, ]. Either chromophore may act as the primary photon acceptor, peak absorptions occurring in the blue region of the spectrum and in the UV-B region, at a wavelength around 290nm []. This domain binds a light harvesting cofactor.; GO: 0003913 DNA photolyase activity, 0006281 DNA repair; PDB: 3UMV_A 2J07_A 1IQU_A 2J09_A 2J08_A 1IQR_A 1DNP_A 3FY4_B 2VTB_A 2J4D_B ....
Probab=35.03 E-value=1.1e+02 Score=25.09 Aligned_cols=50 Identities=18% Similarity=0.460 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCcc
Q psy14489 84 LILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDM 138 (284)
Q Consensus 84 l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl 138 (284)
+.+.+..+++-|...|++.+...| ++.+++..+++.. +...++++.|-..
T Consensus 51 l~~sL~~L~~~L~~~g~~L~v~~g-~~~~~l~~l~~~~----~~~~V~~~~~~~~ 100 (165)
T PF00875_consen 51 LLESLADLQESLRKLGIPLLVLRG-DPEEVLPELAKEY----GATAVYFNEEYTP 100 (165)
T ss_dssp HHHHHHHHHHHHHHTTS-EEEEES-SHHHHHHHHHHHH----TESEEEEE---SH
T ss_pred HHHHHHHHHHHHHhcCcceEEEec-chHHHHHHHHHhc----CcCeeEeccccCH
Confidence 456677888889999999998888 7889999888754 3355666555443
No 164
>PRK14176 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=34.96 E-value=25 Score=32.55 Aligned_cols=107 Identities=18% Similarity=0.288 Sum_probs=55.2
Q ss_pred HHHHHHHhcCCcE----EeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCC-ccccccCC-CeEEEe--CcEeeeHhHHH
Q psy14489 90 LIHQMVKAIGWPI----LIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDK-DMAQLVSN-KIALIN--NNKIHDRTTII 161 (284)
Q Consensus 90 ~i~~~l~~~gi~~----~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~Dk-Dl~ql~~~-~v~~~~--~~~~~~~~~~~ 161 (284)
.+.++|+..||+. +.+-| -..-+=.-++..... .+..|.++...+ |+...... .+-+-- +...++.+++.
T Consensus 150 av~~ll~~~~i~l~Gk~vvViG-rs~iVGkPla~lL~~-~~atVtv~hs~T~~l~~~~~~ADIvv~AvG~p~~i~~~~vk 227 (287)
T PRK14176 150 GVIRALEEYGVDIEGKNAVIVG-HSNVVGKPMAAMLLN-RNATVSVCHVFTDDLKKYTLDADILVVATGVKHLIKADMVK 227 (287)
T ss_pred HHHHHHHHcCCCCCCCEEEEEC-CCcccHHHHHHHHHH-CCCEEEEEeccCCCHHHHHhhCCEEEEccCCccccCHHHcC
Confidence 3566777766532 11222 111111223333333 566777776654 44444332 332222 44566766665
Q ss_pred HH-----hCCChhHHHhhhhhcCCCC--------CCCCCCC-ccChhhHHHHHHh
Q psy14489 162 SR-----FGVSPEKIVDYFSLIGDMS--------DNLPGVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 162 ~~-----~G~~p~q~~~~~~L~GD~s--------Dni~Gv~-giG~ktA~~LL~~ 202 (284)
+. .|++.. +- -++||-. -.|.+|| |+||.|.+-|++.
T Consensus 228 ~gavVIDvGin~~---~g-kl~GDvd~~~~~~~a~~iTPVPGGVGp~T~a~L~~n 278 (287)
T PRK14176 228 EGAVIFDVGITKE---ED-KVYGDVDFENVIKKASLITPVPGGVGPLTIAMLMKH 278 (287)
T ss_pred CCcEEEEeccccc---CC-CccCCcCHHHHHhhceEcCCCCCCChHHHHHHHHHH
Confidence 42 344321 11 3678732 2467776 5999999999874
No 165
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=34.83 E-value=1.4e+02 Score=21.02 Aligned_cols=44 Identities=27% Similarity=0.374 Sum_probs=31.6
Q ss_pred CCCCCChhHHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhh
Q psy14489 76 TRKKMPYNLILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAV 122 (284)
Q Consensus 76 ~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~ 122 (284)
||. .|.+|.+.++... .|.+.||.++-.| .++|.-..+|+....
T Consensus 2 nra-sPv~LR~~lE~A~-~La~~GIRFVpiP-v~~dee~~~L~s~~~ 45 (61)
T PF07131_consen 2 NRA-SPVDLRKALEMAH-SLAHIGIRFVPIP-VVTDEEFHTLSSQLS 45 (61)
T ss_pred CCc-cHHHHHHHHHHHH-HHHHcCceeeccc-cccHHHHHHHHHHHH
Confidence 444 4888988887665 6778999888666 688877777766543
No 166
>PF13419 HAD_2: Haloacid dehalogenase-like hydrolase; PDB: 2FI1_A 2I6X_A 3SD7_A 4F71_A 4DFD_B 4F72_B 4DCC_A 3DDH_A 3KZX_A 2B0C_A ....
Probab=34.76 E-value=9.3 Score=30.70 Aligned_cols=34 Identities=24% Similarity=0.559 Sum_probs=22.9
Q ss_pred HhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChh
Q psy14489 157 RTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPK 194 (284)
Q Consensus 157 ~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~k 194 (284)
...+.+++|+.|++ ++++||+..++.+....|.+
T Consensus 139 ~~~~~~~~~~~p~~----~~~vgD~~~d~~~A~~~G~~ 172 (176)
T PF13419_consen 139 YRRALEKLGIPPEE----ILFVGDSPSDVEAAKEAGIK 172 (176)
T ss_dssp HHHHHHHHTSSGGG----EEEEESSHHHHHHHHHTTSE
T ss_pred HHHHHHHcCCCcce----EEEEeCCHHHHHHHHHcCCe
Confidence 34567788998855 68899887666554444443
No 167
>COG1796 POL4 DNA polymerase IV (family X) [DNA replication, recombination, and repair]
Probab=34.75 E-value=38 Score=31.89 Aligned_cols=19 Identities=26% Similarity=0.634 Sum_probs=16.0
Q ss_pred CCCCCCccChhhHHHHHHh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQ 202 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~ 202 (284)
.+.+++|+|+|.|.++|+.
T Consensus 129 ~~~~l~GfG~kse~~il~~ 147 (326)
T COG1796 129 KIRGLRGFGKKSEAKILEN 147 (326)
T ss_pred CccccCCccchhHHHHHHH
Confidence 6788899999999888874
No 168
>PRK14178 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=34.61 E-value=28 Score=32.11 Aligned_cols=106 Identities=17% Similarity=0.288 Sum_probs=53.5
Q ss_pred HHHHHHhcCCcE----EeeCCchHHHHHHHHHHHhhHhCCCeEEEEcC-CCccccccCC-CeEEEe--CcEeeeHhHHHH
Q psy14489 91 IHQMVKAIGWPI----LIIKGVEADDVIGTLAKQAVTKHNLKVIISTN-DKDMAQLVSN-KIALIN--NNKIHDRTTIIS 162 (284)
Q Consensus 91 i~~~l~~~gi~~----~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~-DkDl~ql~~~-~v~~~~--~~~~~~~~~~~~ 162 (284)
+.++|+..|++. +.+-|. .--+-..+|..... .+..|.++.+ .+|+.+.... .+-+-- +...++.+++++
T Consensus 139 v~~ll~~~~i~l~Gk~V~ViGr-s~~vGrpla~lL~~-~~atVtv~hs~t~~L~~~~~~ADIvI~Avgk~~lv~~~~vk~ 216 (279)
T PRK14178 139 IMTLLHEYKISIAGKRAVVVGR-SIDVGRPMAALLLN-ADATVTICHSKTENLKAELRQADILVSAAGKAGFITPDMVKP 216 (279)
T ss_pred HHHHHHHcCCCCCCCEEEEECC-CccccHHHHHHHHh-CCCeeEEEecChhHHHHHHhhCCEEEECCCcccccCHHHcCC
Confidence 566777776533 112221 11222333333333 4566655544 4455555443 232222 345667666643
Q ss_pred H-----hCCChhHHHhhhhhcCCCC--------CCCCCCCc-cChhhHHHHHHh
Q psy14489 163 R-----FGVSPEKIVDYFSLIGDMS--------DNLPGVKK-IGPKTAVKLLNQ 202 (284)
Q Consensus 163 ~-----~G~~p~q~~~~~~L~GD~s--------Dni~Gv~g-iG~ktA~~LL~~ 202 (284)
. .|++. . +- -++||-. -.|.+||| +||.|.+-|++.
T Consensus 217 GavVIDVgi~~--~-~g-kl~GDvdf~~~~~~a~~iTPVPGGVGp~T~a~L~~N 266 (279)
T PRK14178 217 GATVIDVGINQ--V-NG-KLCGDVDFDAVKEIAGAITPVPGGVGPMTIATLMEN 266 (279)
T ss_pred CcEEEEeeccc--c-CC-CCcCCccHHHHHhhccCcCCCCCCCHHHHHHHHHHH
Confidence 1 23322 1 11 3777632 25677874 999999999884
No 169
>PTZ00331 alpha/beta hydrolase; Provisional
Probab=34.42 E-value=80 Score=27.53 Aligned_cols=43 Identities=28% Similarity=0.253 Sum_probs=37.2
Q ss_pred HHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEc
Q psy14489 90 LIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIIST 133 (284)
Q Consensus 90 ~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S 133 (284)
.+.++|+..|+..+..-|.++|=-+.+-++.... .|++++|++
T Consensus 136 ~L~~~L~~~gi~~lvi~G~~t~~CV~~Ta~~a~~-~g~~v~vv~ 178 (212)
T PTZ00331 136 GLAQILKAHGVRRVFICGLAFDFCVLFTALDAVK-LGFKVVVLE 178 (212)
T ss_pred hHHHHHHHCCCCEEEEEEeccCHHHHHHHHHHHH-CCCEEEEeC
Confidence 4667888899999999999999999888888777 899988886
No 170
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=34.16 E-value=25 Score=28.74 Aligned_cols=26 Identities=38% Similarity=0.685 Sum_probs=20.1
Q ss_pred CCCCCCCccChhhHHHHHHhcC--CHHHH
Q psy14489 183 DNLPGVKKIGPKTAVKLLNQYN--SLENI 209 (284)
Q Consensus 183 Dni~Gv~giG~ktA~~LL~~~g--sle~i 209 (284)
|++.-|.|||||. .+.|+..| +..+|
T Consensus 67 DDLt~I~GIGPk~-e~~Ln~~GI~tfaQI 94 (133)
T COG3743 67 DDLTRISGIGPKL-EKVLNELGIFTFAQI 94 (133)
T ss_pred ccchhhcccCHHH-HHHHHHcCCccHHHH
Confidence 9999999999988 56677777 44444
No 171
>PRK14838 undecaprenyl pyrophosphate synthase; Provisional
Probab=33.74 E-value=29 Score=31.32 Aligned_cols=66 Identities=14% Similarity=0.155 Sum_probs=42.3
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.|| ...| |+.-.+...++|... +. +..+.+++..+||++++. |.-|=+.++.-+.
T Consensus 10 ~P~HVAiImDG-NrRwA~~~gl~~~~GH~~G~-~~----l~~i~~~~~~~gI~~lT~YaFS~EN~kR~~~Ev~~Lm~l~~ 83 (242)
T PRK14838 10 IPQHIAIIMDG-NGRWAKERGKERSFGHQAGA-ET----VHIITEEAARLGVKFLTLYTFSTENWNRPSDEVAALMSLLL 83 (242)
T ss_pred CCCEEEEeccC-CHHHHHHCCCCHHHHHHHHH-HH----HHHHHHHHHHcCCCEEEEEeechhhcCCCHHHHHHHHHHHH
Confidence 48999999997 3344 333345566666542 12 234555667789998874 4467787777766
Q ss_pred HHh
Q psy14489 119 KQA 121 (284)
Q Consensus 119 ~~~ 121 (284)
...
T Consensus 84 ~~l 86 (242)
T PRK14838 84 DSI 86 (242)
T ss_pred HHH
Confidence 544
No 172
>PRK14842 undecaprenyl pyrophosphate synthase; Provisional
Probab=33.45 E-value=30 Score=31.29 Aligned_cols=66 Identities=14% Similarity=0.140 Sum_probs=42.7
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.||- ..| |+.=.+...++|... +.+ ..+.+++..+||++++. |.-|=+.++.-+.
T Consensus 8 ~P~HVaiImDGN-rRwAk~~gl~~~~GH~~G~-~~l----~~i~~~c~~lgI~~vTvYaFS~eN~~R~~~EV~~Lm~L~~ 81 (241)
T PRK14842 8 IPAHIAVIMDGN-GRWAESQGKKRSEGHREGA-NAI----DRLMDASLEYGLKNISLYAFSTENWKRPITEIRSIFGLLV 81 (241)
T ss_pred CCCeEEEEcCCC-HHHHHHCCCChhHhHHHHH-HHH----HHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHHHHHH
Confidence 489999999973 344 333346666666653 122 24556677789999874 4457777777666
Q ss_pred HHh
Q psy14489 119 KQA 121 (284)
Q Consensus 119 ~~~ 121 (284)
...
T Consensus 82 ~~l 84 (241)
T PRK14842 82 EFI 84 (241)
T ss_pred HHH
Confidence 543
No 173
>PRK14180 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=32.97 E-value=25 Score=32.47 Aligned_cols=73 Identities=19% Similarity=0.333 Sum_probs=45.1
Q ss_pred CCCeEEEEcCC-CccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCCC---------CCC
Q psy14489 125 HNLKVIISTND-KDMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMSD---------NLP 186 (284)
Q Consensus 125 ~~~~v~I~S~D-kDl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~sD---------ni~ 186 (284)
.+..|.+|.+- +|+...... .+-+-- +...++.+++.+- -|++.. +- -++||- | .|.
T Consensus 181 ~~ATVt~chs~T~dl~~~~k~ADIvIsAvGkp~~i~~~~vk~gavVIDvGin~~---~g-kl~GDv-d~~~v~~~a~~iT 255 (282)
T PRK14180 181 AKATVTTCHRFTTDLKSHTTKADILIVAVGKPNFITADMVKEGAVVIDVGINHV---DG-KIVGDV-DFAAVKDKVAAIT 255 (282)
T ss_pred CCCEEEEEcCCCCCHHHHhhhcCEEEEccCCcCcCCHHHcCCCcEEEEeccccc---CC-ceeCCc-CHHHHHhhccEec
Confidence 56677777443 566554433 333332 5667787777652 355431 11 388883 3 567
Q ss_pred CCC-ccChhhHHHHHHh
Q psy14489 187 GVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 187 Gv~-giG~ktA~~LL~~ 202 (284)
.|| |+||-|.+-|++.
T Consensus 256 PVPGGVGp~T~a~L~~N 272 (282)
T PRK14180 256 PVPGGVGPMTITELLYN 272 (282)
T ss_pred cCCCChhHHHHHHHHHH
Confidence 788 8999999999873
No 174
>PRK14834 undecaprenyl pyrophosphate synthase; Provisional
Probab=32.80 E-value=37 Score=30.80 Aligned_cols=65 Identities=17% Similarity=0.233 Sum_probs=39.6
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.||. ..| |+.-.+...++|... +. +..+.+++..+||++++. |--|-+.++.-+.
T Consensus 14 ~P~HVAiImDGN-rRwAk~~g~~~~~GH~~G~-~~----l~~i~~~c~~lgI~~lTvYaFS~eN~~R~~~EV~~Lm~L~~ 87 (249)
T PRK14834 14 VPRHVAIIMDGN-GRWAKARGLPRAAGHRAGV-EA----LRRVVRAAGELGIGYLTLFAFSSENWSRPASEVSDLFGLLR 87 (249)
T ss_pred CCCeEEEEecCc-hHHHHHCCCchhhhHHHHH-HH----HHHHHHHHHHcCCCEEEEEEEeccccCCCHHHHHHHHHHHH
Confidence 389999999973 344 333345566665542 12 234556667789998774 2356777666554
Q ss_pred HH
Q psy14489 119 KQ 120 (284)
Q Consensus 119 ~~ 120 (284)
..
T Consensus 88 ~~ 89 (249)
T PRK14834 88 LF 89 (249)
T ss_pred HH
Confidence 43
No 175
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=32.29 E-value=29 Score=30.75 Aligned_cols=20 Identities=25% Similarity=0.318 Sum_probs=15.8
Q ss_pred CCCccChhhHHHHHHh-cCCH
Q psy14489 187 GVKKIGPKTAVKLLNQ-YNSL 206 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~-~gsl 206 (284)
..||||+|||-=.|+. ||-.
T Consensus 113 ~LPGVGrKTAnvVL~~a~g~p 133 (211)
T COG0177 113 SLPGVGRKTANVVLSFAFGIP 133 (211)
T ss_pred hCCCcchHHHHHHHHhhcCCC
Confidence 3689999999988886 5543
No 176
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=31.72 E-value=43 Score=26.27 Aligned_cols=28 Identities=25% Similarity=0.429 Sum_probs=20.5
Q ss_pred hHHHHHHHHHHHhhHhCCCeEEEEcCCCcccccc
Q psy14489 109 EADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLV 142 (284)
Q Consensus 109 EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~ 142 (284)
-+|.+|+..|.. .+ ..++|.|+|+.++.
T Consensus 105 ~~D~~i~a~A~~----~~--~~lvT~D~~f~~~~ 132 (142)
T TIGR00028 105 VTDAHLAALARE----HG--AELVTFDRGFARFA 132 (142)
T ss_pred chHHHHHHHHHH----cC--CEEEecCCCccccC
Confidence 478888887764 34 46779999986653
No 177
>PRK14828 undecaprenyl pyrophosphate synthase; Provisional
Probab=31.62 E-value=36 Score=31.00 Aligned_cols=66 Identities=8% Similarity=0.158 Sum_probs=39.8
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchh-hhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSY-KATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTL 117 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~Y-Ka~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~l 117 (284)
-|.|++|+.||. ..| |+.-.+.. .++|... +.+ ..+.+++..+||+++.. |.-|=+.++.-+
T Consensus 26 ~P~HvAiImDGN-rRwA~~~gl~~~~~GH~~G~-~~l----~~~~~~~~~~gIk~lTvYaFS~eN~~R~~~Ev~~Lm~L~ 99 (256)
T PRK14828 26 VPGHVGIIVDGN-RRWARKAGFTDVSQGHRAGA-AKI----GEFLGWCDETDVNVVTLYLLSTDNLGRPSEELNPLLDII 99 (256)
T ss_pred CCCEEEEEecCC-hHHHHHcCCCchHHHHHHHH-HHH----HHHHHHHHHcCCCEEEEEEEEhhhcCCCHHHHHHHHHHH
Confidence 479999999973 344 33334555 5555542 222 24555666789998875 345666666555
Q ss_pred HHHh
Q psy14489 118 AKQA 121 (284)
Q Consensus 118 a~~~ 121 (284)
....
T Consensus 100 ~~~l 103 (256)
T PRK14828 100 EDVV 103 (256)
T ss_pred HHHH
Confidence 4443
No 178
>cd01080 NAD_bind_m-THF_DH_Cyclohyd NADP binding domain of methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NADP binding domain of the Methylene-Tetrahydrofolate Dehydrogenase/cyclohydrolase (m-THF DH/cyclohydrolase) bifunctional enzyme. Tetrahydrofolate is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional DH/cyclodrolase form. In bacteria, monofucntional DH, as well a
Probab=30.73 E-value=37 Score=28.71 Aligned_cols=20 Identities=25% Similarity=0.479 Sum_probs=16.1
Q ss_pred CCCCCCC-ccChhhHHHHHHh
Q psy14489 183 DNLPGVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 183 Dni~Gv~-giG~ktA~~LL~~ 202 (284)
-+++++| |+||.|++.|++.
T Consensus 142 ~~~~~~pggvgp~t~a~l~~n 162 (168)
T cd01080 142 SAITPVPGGVGPMTVAMLMKN 162 (168)
T ss_pred cCcCCCCCcChHHHHHHHHHH
Confidence 4567776 5999999999875
No 179
>PF04900 Fcf1: Fcf1; InterPro: IPR006984 This family is comprises of uncharacterised eukaryotic proteins.
Probab=30.25 E-value=31 Score=26.36 Aligned_cols=38 Identities=32% Similarity=0.419 Sum_probs=27.7
Q ss_pred CchHHHHHHHHHHHhhHhCCCeEEEEcCCCccccccC--CCeEEE
Q psy14489 107 GVEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLVS--NKIALI 149 (284)
Q Consensus 107 g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~~--~~v~~~ 149 (284)
+.-|||-|-.++.. .+. .+|+|.|+++..-+. ++|.+.
T Consensus 50 ~~~addci~~~~~~----~~~-~~VaT~D~~Lr~~lr~~~GvPvi 89 (101)
T PF04900_consen 50 PGSADDCILDLAGK----NNK-YIVATQDKELRRRLRKIPGVPVI 89 (101)
T ss_pred CcCHHHHHHHHhcc----CCe-EEEEecCHHHHHHHhcCCCCCEE
Confidence 35699999998863 232 899999999998655 455443
No 180
>PRK14835 undecaprenyl pyrophosphate synthase; Provisional
Probab=30.12 E-value=43 Score=30.87 Aligned_cols=67 Identities=13% Similarity=0.235 Sum_probs=43.3
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee-----CC-----chHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII-----KG-----VEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~-----~g-----~EADD~ia~la 118 (284)
-|.|++|+.|| +..| |+.-.+...++|... +.+. .+.+++..+||++++. ++ .|-+.++.-+.
T Consensus 41 ~P~HVAiImDG-NrRwAk~~g~~~~~GH~~G~-~~l~----~i~~~c~~lGIk~lTvYaFS~EN~~R~~~EV~~Lm~L~~ 114 (275)
T PRK14835 41 LPRHLGLILDG-NRRFARALGLQREMGHEFGV-QKAY----EVLEWCLELGIPTVTIWVFSTDNFSRSPAEVETLMNLFE 114 (275)
T ss_pred CCCEEEEEecC-chHHHHHCCCCHHHHHHHHH-HHHH----HHHHHHHHcCCCEEEEEEEEccccCCCHHHHHHHHHHHH
Confidence 47999999997 4444 444455666666542 2232 4556666789998774 33 38888877776
Q ss_pred HHhh
Q psy14489 119 KQAV 122 (284)
Q Consensus 119 ~~~~ 122 (284)
+...
T Consensus 115 ~~l~ 118 (275)
T PRK14835 115 REAR 118 (275)
T ss_pred HHHH
Confidence 6544
No 181
>PRK14840 undecaprenyl pyrophosphate synthase; Provisional
Probab=29.75 E-value=45 Score=30.29 Aligned_cols=65 Identities=12% Similarity=0.151 Sum_probs=41.2
Q ss_pred CCCEEEEEEeCCCCcccccc-----CchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHH
Q psy14489 50 RATYIACIFDAKGKNFRNIL-----YPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVI 114 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~R~~l-----~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~i 114 (284)
-|.|++|+.|| ...|=+.- .+...++|... +. +..+.+++..+||++++. +.-|=+.++
T Consensus 18 ~P~HVaiImDG-NrRwAk~~~~~~gl~~~~GH~~G~-~~----l~~v~~~c~~~GIk~lTvYaFS~EN~~R~~~EV~~Lm 91 (250)
T PRK14840 18 LPRHVAIIMDG-NRRWYRKHEQFCQKRAISGHYYGA-KS----LPQIVDTALHLGIEVLTLFAFSTENFSRSKEEVAELF 91 (250)
T ss_pred CCCeEEEEcCC-ChHHHhhCCCccCCCHHHHHHHHH-HH----HHHHHHHHHHcCCCEEEEEEeehhhcCCCHHHHHHHH
Confidence 47999999997 44452221 36666776653 12 224555666789998874 445777777
Q ss_pred HHHHHH
Q psy14489 115 GTLAKQ 120 (284)
Q Consensus 115 a~la~~ 120 (284)
.-+...
T Consensus 92 ~L~~~~ 97 (250)
T PRK14840 92 SLFNSQ 97 (250)
T ss_pred HHHHHH
Confidence 666554
No 182
>PRK04301 radA DNA repair and recombination protein RadA; Validated
Probab=28.80 E-value=44 Score=30.98 Aligned_cols=29 Identities=34% Similarity=0.562 Sum_probs=24.0
Q ss_pred CCCCCCccChhhHHHHHHh-cCCHHHHHHh
Q psy14489 184 NLPGVKKIGPKTAVKLLNQ-YNSLENIINN 212 (284)
Q Consensus 184 ni~Gv~giG~ktA~~LL~~-~gsle~i~~~ 212 (284)
.+..+||||+++|.+|.+. +.|++++...
T Consensus 7 ~l~~l~gIg~~~a~~L~~~Gi~t~~dl~~~ 36 (317)
T PRK04301 7 DLEDLPGVGPATAEKLREAGYDTVEAIAVA 36 (317)
T ss_pred cHhhcCCCCHHHHHHHHHcCCCCHHHHHcC
Confidence 3556899999999999986 8899998653
No 183
>COG2454 Uncharacterized conserved protein [Function unknown]
Probab=28.80 E-value=4.1e+02 Score=23.47 Aligned_cols=80 Identities=23% Similarity=0.273 Sum_probs=47.1
Q ss_pred cEEEEecchHHHHHhccCC-------C--ccCC---CCcc--hhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCcccccc
Q psy14489 4 TLLLVDGSSCIYRAFYALP-------D--IRNI---DNFP--VGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNIL 69 (284)
Q Consensus 4 ~~llIDg~~l~~r~~~a~~-------~--l~~~---~g~~--t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l 69 (284)
..+.|||+|++----.... + ++.- .|.. ..-+...+.++...+++++|..+++.||..
T Consensus 67 ~~l~iDGyNvLItleSl~~g~~vlcdDg~iRDl~~~~gkyk~~E~t~~Al~lil~~lk~~~~k~vi~L~d~~-------- 138 (211)
T COG2454 67 QDLVIDGYNVLITLESLLKGEAVLCDDGVIRDLRGVQGKYKINEKTDKALDLLLEFLKDVEPKSVIFLFDAP-------- 138 (211)
T ss_pred ceEEEechhhhhhHHHHhcCcEEEecCchhhhhhhhccchhhhhHHHHHHHHHHHHHHHcCCceEEEEeCCC--------
Confidence 5789999999754322111 0 1110 1111 122334567888889999999999999852
Q ss_pred CchhhhCCCCCChhHHHHHHHHHHHHHhcCCcE
Q psy14489 70 YPSYKATRKKMPYNLILQINLIHQMVKAIGWPI 102 (284)
Q Consensus 70 ~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~ 102 (284)
.-| ..+|.. .+++.++..||+.
T Consensus 139 --vs~------SGel~~---~i~~~mK~~~I~g 160 (211)
T COG2454 139 --VSK------SGELAG---RIEEKMKSLGIPG 160 (211)
T ss_pred --CCc------cHHHHH---HHHHHHHhcCCCc
Confidence 111 234442 5677778888873
No 184
>cd05212 NAD_bind_m-THF_DH_Cyclohyd_like NAD(P) binding domain of methylene-tetrahydrofolate dehydrogenase and methylene-tetrahydrofolate dehydrogenase/cyclohydrolase. NAD(P) binding domains of methylene-tetrahydrofolate dehydrogenase (m-THF DH) and m-THF DH/cyclohydrolase bifunctional enzymes (m-THF DH/cyclohydrolase). M-THF is a versatile carrier of activated one-carbon units. The major one-carbon folate donors are N-5 methyltetrahydrofolate, N5,N10-m-THF, and N10-formayltetrahydrofolate. The oxidation of metabolic intermediate m-THF to m-THF requires the enzyme m-THF DH. In addition, most DHs also have an associated cyclohydrolase activity which catalyzes its hydrolysis to N10-formyltetrahydrofolate. m-THF DH is typically found as part of a multifunctional protein in eukaryotes. NADP-dependent m-THF DH in mammals, birds and yeast are components of a trifunctional enzyme with DH, cyclohydrolase, and synthetase activities. Certain eukaryotic cells also contain homodimeric bifunctional
Probab=28.30 E-value=2.2e+02 Score=23.24 Aligned_cols=104 Identities=9% Similarity=0.048 Sum_probs=50.7
Q ss_pred HHHHHHHhcCCcE-------EeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCC-ccccccCC-CeEEEe--CcEeeeHh
Q psy14489 90 LIHQMVKAIGWPI-------LIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDK-DMAQLVSN-KIALIN--NNKIHDRT 158 (284)
Q Consensus 90 ~i~~~l~~~gi~~-------~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~Dk-Dl~ql~~~-~v~~~~--~~~~~~~~ 158 (284)
.+.++++..|++. +...+.-+.-+...| .+ .+..+.++..+. |+...+.. .+-+-- +...++.+
T Consensus 14 a~~~ll~~~~~~~~gk~v~VvGrs~~vG~pla~lL----~~-~gatV~~~~~~t~~l~~~v~~ADIVvsAtg~~~~i~~~ 88 (140)
T cd05212 14 AVKELLNKEGVRLDGKKVLVVGRSGIVGAPLQCLL----QR-DGATVYSCDWKTIQLQSKVHDADVVVVGSPKPEKVPTE 88 (140)
T ss_pred HHHHHHHHcCCCCCCCEEEEECCCchHHHHHHHHH----HH-CCCEEEEeCCCCcCHHHHHhhCCEEEEecCCCCccCHH
Confidence 4566777666532 222232333333333 23 577777776444 55544433 232222 34556777
Q ss_pred HHHH-----HhCCChhHHHhhhhhcCCCCCCCCCC-CccChhhHHHHHHh
Q psy14489 159 TIIS-----RFGVSPEKIVDYFSLIGDMSDNLPGV-KKIGPKTAVKLLNQ 202 (284)
Q Consensus 159 ~~~~-----~~G~~p~q~~~~~~L~GD~sDni~Gv-~giG~ktA~~LL~~ 202 (284)
++++ .+|.+.+.+.+..-. +..+-.+ -|+||-|.+-|++.
T Consensus 89 ~ikpGa~Vidvg~~~~~~~~~~~~----a~~~tPvpgGVGp~T~a~L~~n 134 (140)
T cd05212 89 WIKPGATVINCSPTKLSGDDVKES----ASLYVPMTGGVGKLTVAMRMQN 134 (140)
T ss_pred HcCCCCEEEEcCCCcccchhhHhh----ceEEcCCCCCchHHHHHHHHHH
Confidence 6654 234433221111111 1223333 48999999999864
No 185
>PRK14194 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.89 E-value=35 Score=31.89 Aligned_cols=109 Identities=18% Similarity=0.268 Sum_probs=53.9
Q ss_pred HHHHHHHhcCCcE----EeeCCchHHHHHHHHHHHhhHhCCCeEEEEc-CCCccccccCC-CeEEEe--CcEeeeHhHHH
Q psy14489 90 LIHQMVKAIGWPI----LIIKGVEADDVIGTLAKQAVTKHNLKVIIST-NDKDMAQLVSN-KIALIN--NNKIHDRTTII 161 (284)
Q Consensus 90 ~i~~~l~~~gi~~----~~~~g~EADD~ia~la~~~~~~~~~~v~I~S-~DkDl~ql~~~-~v~~~~--~~~~~~~~~~~ 161 (284)
.+.++|+..|++. +..-|. ..-+=.-+|....+ .|..+.++. .-+++..+... .+.+.- +...++..++.
T Consensus 145 aii~lL~~~~i~l~Gk~V~vIG~-s~ivG~PmA~~L~~-~gatVtv~~~~t~~l~e~~~~ADIVIsavg~~~~v~~~~ik 222 (301)
T PRK14194 145 GCLRLLEDTCGDLTGKHAVVIGR-SNIVGKPMAALLLQ-AHCSVTVVHSRSTDAKALCRQADIVVAAVGRPRLIDADWLK 222 (301)
T ss_pred HHHHHHHHhCCCCCCCEEEEECC-CCccHHHHHHHHHH-CCCEEEEECCCCCCHHHHHhcCCEEEEecCChhcccHhhcc
Confidence 3566777766532 222221 01122234444544 678888883 33444444432 332222 33344444333
Q ss_pred H-----HhCCChhHHHh--hhhhcCCCC-C-------CCCCCC-ccChhhHHHHHHh
Q psy14489 162 S-----RFGVSPEKIVD--YFSLIGDMS-D-------NLPGVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 162 ~-----~~G~~p~q~~~--~~~L~GD~s-D-------ni~Gv~-giG~ktA~~LL~~ 202 (284)
+ ..|+++ ..+ ..-|+||-. | .|..|| |+||-|.+-|++.
T Consensus 223 ~GaiVIDvgin~--~~~~g~~kl~GDvdf~~~~~~a~~iTPVPGGVGp~Tva~L~~N 277 (301)
T PRK14194 223 PGAVVIDVGINR--IDDDGRSRLVGDVDFDSALPVVSAITPVPGGVGPMTIAFLMKN 277 (301)
T ss_pred CCcEEEEecccc--cCCCCCcceecccchHHHHhhcceecCCCCchhHHHHHHHHHH
Confidence 2 123332 001 013888843 1 356677 8999999999873
No 186
>PRK14169 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=27.85 E-value=55 Score=30.28 Aligned_cols=75 Identities=24% Similarity=0.414 Sum_probs=43.9
Q ss_pred CCCeEEEEcCC-CccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCC-C-------CCCC
Q psy14489 125 HNLKVIISTND-KDMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMS-D-------NLPG 187 (284)
Q Consensus 125 ~~~~v~I~S~D-kDl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~s-D-------ni~G 187 (284)
.+..|.++.+. +|+...... .+.+-- +...++.+++++- .|+++ ..+- -++||-. + .|..
T Consensus 179 ~~atVtichs~T~~l~~~~~~ADIvI~AvG~p~~i~~~~vk~GavVIDvGin~--~~~g-kl~GDVd~~~v~~~a~~iTP 255 (282)
T PRK14169 179 HDATVTIAHSKTRNLKQLTKEADILVVAVGVPHFIGADAVKPGAVVIDVGISR--GADG-KLLGDVDEAAVAPIASAITP 255 (282)
T ss_pred CCCEEEEECCCCCCHHHHHhhCCEEEEccCCcCccCHHHcCCCcEEEEeeccc--cCCC-CeeecCcHHHHHhhccEecC
Confidence 56778888544 455444332 343333 5667788877652 35543 1111 3888732 1 2345
Q ss_pred CC-ccChhhHHHHHHh
Q psy14489 188 VK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 188 v~-giG~ktA~~LL~~ 202 (284)
|| |+||-|.+-|++.
T Consensus 256 VPGGVGp~T~a~L~~N 271 (282)
T PRK14169 256 VPGGVGPMTIASLMAQ 271 (282)
T ss_pred CCCCcHHHHHHHHHHH
Confidence 55 6999999999874
No 187
>TIGR02247 HAD-1A3-hyp Epoxide hydrolase N-terminal domain-like phosphatase. These appear to be members of the haloacid dehalogenase (HAD) superfamily of aspartate-nucleophile hydrolases by general homology and the conservation of all of the recognized catalytic motifs (although the first motif is unusual in the replacement of the more common aspartate with glycine...). The variable domain is found in between motifs 1 and 2, indicating membership in subfamily I and phylogeny and prediction of the alpha helical nature of the variable domain (by PSI-PRED) indicate membership in subfamily IA.
Probab=27.72 E-value=69 Score=27.22 Aligned_cols=32 Identities=28% Similarity=0.609 Sum_probs=20.7
Q ss_pred HhHHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccC
Q psy14489 157 RTTIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIG 192 (284)
Q Consensus 157 ~~~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG 192 (284)
...+.+++|+.|++ ++++||+.-++.+....|
T Consensus 158 ~~~~~~~~g~~~~~----~l~i~D~~~di~aA~~aG 189 (211)
T TIGR02247 158 YQLMLERLGVAPEE----CVFLDDLGSNLKPAAALG 189 (211)
T ss_pred HHHHHHHcCCCHHH----eEEEcCCHHHHHHHHHcC
Confidence 34556788998855 566799877774433333
No 188
>PRK10736 hypothetical protein; Provisional
Probab=27.47 E-value=42 Score=32.34 Aligned_cols=22 Identities=9% Similarity=0.137 Sum_probs=19.9
Q ss_pred CCCccChhhHHHHHHhcCCHHH
Q psy14489 187 GVKKIGPKTAVKLLNQYNSLEN 208 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~gsle~ 208 (284)
.+||||+++..+|++.||+.++
T Consensus 12 ~~~giG~~~~~~L~~~~~~~~~ 33 (374)
T PRK10736 12 SVSSLYGDKMVRIAHRLLAQSQ 33 (374)
T ss_pred hCCCCCHHHHHHHHHHhcChhh
Confidence 4789999999999999999875
No 189
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=26.93 E-value=1.7e+02 Score=27.96 Aligned_cols=46 Identities=22% Similarity=0.343 Sum_probs=33.4
Q ss_pred HHHHhcCCcEEeeCC-chHHHH---HHHHHHHhhHhCCCeEEEEcCCCcccc
Q psy14489 93 QMVKAIGWPILIIKG-VEADDV---IGTLAKQAVTKHNLKVIISTNDKDMAQ 140 (284)
Q Consensus 93 ~~l~~~gi~~~~~~g-~EADD~---ia~la~~~~~~~~~~v~I~S~DkDl~q 140 (284)
++++..|++.+.+-| +.|||. |+.+.++..+ .|..-+|+ .|.|+.-
T Consensus 189 ~l~ekYgl~~V~~fg~~~~~e~~eei~eIve~L~k-eGREGVV~-Kdpdm~~ 238 (382)
T COG1423 189 ELAEKYGLPHVEIFGEFPADEAGEEIYEIVERLNK-EGREGVVM-KDPDMRV 238 (382)
T ss_pred HHHHHcCCCceEEeeeechhHhHHHHHHHHHHHhh-cCCcceEe-cCccccc
Confidence 466789999988765 777777 7777877776 66665555 5777754
No 190
>PF00702 Hydrolase: haloacid dehalogenase-like hydrolase; InterPro: IPR005834 This group of hydrolase enzymes is structurally different from the alpha/beta hydrolase family (abhydrolase). This group includes L-2-haloacid dehalogenase, epoxide hydrolases and phosphatases. The structure consists of two domains. One is an inserted four helix bundle, which is the least well conserved region of the alignment, between residues 16 and 96 of HAD1_PSESP. The rest of the fold is composed of the core alpha/beta domain.; GO: 0003824 catalytic activity, 0008152 metabolic process; PDB: 1TE2_A 3NAL_A 3NAM_A 3NAN_A 3A1D_B 3J09_A 3J08_A 2B8E_C 3A1E_A 2VOY_J ....
Probab=26.91 E-value=69 Score=26.79 Aligned_cols=66 Identities=21% Similarity=0.305 Sum_probs=39.8
Q ss_pred chHHHHHHHHHHHhhHhCCCeEEEEcCCCccc-----cccC-CCeEEEeCc--EeeeH--hHHHHHhCCChhHHHhhhhh
Q psy14489 108 VEADDVIGTLAKQAVTKHNLKVIISTNDKDMA-----QLVS-NKIALINNN--KIHDR--TTIISRFGVSPEKIVDYFSL 177 (284)
Q Consensus 108 ~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~-----ql~~-~~v~~~~~~--~~~~~--~~~~~~~G~~p~q~~~~~~L 177 (284)
-+|-+.|..|.. .|.++.|+|+|.... +.++ +...++... ++-.. ..+.+.+++.|+ -.++
T Consensus 130 ~~~~~~l~~L~~-----~Gi~~~i~TGD~~~~a~~~~~~lgi~~~~v~a~~~~kP~~k~~~~~i~~l~~~~~----~v~~ 200 (215)
T PF00702_consen 130 PGAKEALQELKE-----AGIKVAILTGDNESTASAIAKQLGIFDSIVFARVIGKPEPKIFLRIIKELQVKPG----EVAM 200 (215)
T ss_dssp TTHHHHHHHHHH-----TTEEEEEEESSEHHHHHHHHHHTTSCSEEEEESHETTTHHHHHHHHHHHHTCTGG----GEEE
T ss_pred hhhhhhhhhhhc-----cCcceeeeeccccccccccccccccccccccccccccccchhHHHHHHHHhcCCC----EEEE
Confidence 367777777654 678999999994332 2222 233344322 22222 456677787664 6788
Q ss_pred cCCCC
Q psy14489 178 IGDMS 182 (284)
Q Consensus 178 ~GD~s 182 (284)
+||+.
T Consensus 201 vGDg~ 205 (215)
T PF00702_consen 201 VGDGV 205 (215)
T ss_dssp EESSG
T ss_pred EccCH
Confidence 99765
No 191
>PRK13366 protocatechuate 4,5-dioxygenase subunit beta; Provisional
Probab=26.80 E-value=2.8e+02 Score=25.59 Aligned_cols=76 Identities=14% Similarity=0.302 Sum_probs=43.6
Q ss_pred hHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhh--------hCC-----CCCC-----hhHHHHHHHHHHH
Q psy14489 33 GALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYK--------ATR-----KKMP-----YNLILQINLIHQM 94 (284)
Q Consensus 33 ~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YK--------a~R-----~~~p-----~~l~~q~~~i~~~ 94 (284)
..+..-+..+.+.+++.+|+.+|+++|.-..+|+-+..|.+. ... ...| .+|.. .+.+.
T Consensus 31 ~~~~~a~~~i~~~i~~~~PDvvVii~~dH~~~f~~d~~P~f~Ig~~~~~~~~~~~~g~~~v~~~~g~~eLA~---~i~~~ 107 (284)
T PRK13366 31 QPVFKGYEFSKQWEKEEKPDVIFLVYNDHATAFSLDIIPTFAIGTAAEYQPADEGWGPRPVPKVIGHPDLAA---HIAQS 107 (284)
T ss_pred HHHHHHHHHHHHHHHHhCCCEEEEEcCCcHHhhcccCCCceEEeeCceecCcccccCCCCCCCCCCCHHHHH---HHHHH
Confidence 344555667777778899998887766544666665444332 211 1123 44543 34455
Q ss_pred HHhcCCcEEeeCCchHH
Q psy14489 95 VKAIGWPILIIKGVEAD 111 (284)
Q Consensus 95 l~~~gi~~~~~~g~EAD 111 (284)
+...|+++......+-|
T Consensus 108 l~~~g~~~~~~~~~~lD 124 (284)
T PRK13366 108 VIQDDFDLTIVNKMDVD 124 (284)
T ss_pred HHHCCCCEeecCCCCCC
Confidence 55677877655544444
No 192
>TIGR03556 photolyase_8HDF deoxyribodipyrimidine photo-lyase, 8-HDF type. This model describes a narrow clade of cyanobacterial deoxyribodipyrimidine photo-lyase. This group, in contrast to several closely related proteins, uses a chromophore that, in other lineages is modified further to become coenzyme F420. This chromophore is called 8-HDF in most articles on the DNA photolyase and FO in most literature on coenzyme F420.
Probab=26.64 E-value=4.9e+02 Score=25.58 Aligned_cols=51 Identities=25% Similarity=0.297 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHhcCCcEEeeCCchHHHHHHHHHHHhhHhCCCeEEEEcCCCccc
Q psy14489 84 LILQINLIHQMVKAIGWPILIIKGVEADDVIGTLAKQAVTKHNLKVIISTNDKDMA 139 (284)
Q Consensus 84 l~~q~~~i~~~l~~~gi~~~~~~g~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ 139 (284)
+.+.+..+.+-|..+|++.+...| +..+++..++++ .+...++++.|-+..
T Consensus 53 l~esL~~L~~~L~~~G~~L~v~~G-~p~~vl~~l~~~----~~~~~V~~~~~~~~~ 103 (471)
T TIGR03556 53 LIGCLQELQQRYQQAGSQLLILQG-DPVQLIPQLAQQ----LGAKAVYWNLDVEPY 103 (471)
T ss_pred HHHHHHHHHHHHHHCCCCeEEEEC-CHHHHHHHHHHH----cCCCEEEEecccCHH
Confidence 445566788888889999998888 788888888865 344566666665543
No 193
>PRK13910 DNA glycosylase MutY; Provisional
Probab=26.36 E-value=38 Score=31.38 Aligned_cols=22 Identities=27% Similarity=0.350 Sum_probs=16.2
Q ss_pred CCCCCCCccChhhHHHHHH-hcC
Q psy14489 183 DNLPGVKKIGPKTAVKLLN-QYN 204 (284)
Q Consensus 183 Dni~Gv~giG~ktA~~LL~-~~g 204 (284)
+-+-.+||||++||.-.+. .||
T Consensus 72 ~~L~~LpGIG~kTA~aIl~~af~ 94 (289)
T PRK13910 72 QSLLKLPGIGAYTANAILCFGFR 94 (289)
T ss_pred HHHHhCCCCCHHHHHHHHHHHCC
Confidence 3345688999999988776 444
No 194
>PRK14181 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=26.21 E-value=41 Score=31.17 Aligned_cols=75 Identities=19% Similarity=0.381 Sum_probs=43.1
Q ss_pred CCeEEEEcCC-CccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHh----hhhhcCCCC-C-------C
Q psy14489 126 NLKVIISTND-KDMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVD----YFSLIGDMS-D-------N 184 (284)
Q Consensus 126 ~~~v~I~S~D-kDl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~----~~~L~GD~s-D-------n 184 (284)
+..|.++.+- +|+..+... .+.+-- +...++.+++++- .|+++ ..+ -.-|+||-. + .
T Consensus 181 ~AtVtvchs~T~~l~~~~~~ADIvV~AvG~p~~i~~~~ik~GavVIDvGin~--~~~~~~~g~kl~GDVd~e~~~~~a~~ 258 (287)
T PRK14181 181 NATVTLLHSQSENLTEILKTADIIIAAIGVPLFIKEEMIAEKAVIVDVGTSR--VPAANPKGYILVGDVDFNNVVPKCRA 258 (287)
T ss_pred CCEEEEeCCCCCCHHHHHhhCCEEEEccCCcCccCHHHcCCCCEEEEecccc--cccccCCCCeeEeccchHHHHhhccc
Confidence 4567777543 444444332 333332 5566777777652 45543 101 013888732 1 4
Q ss_pred CCCCC-ccChhhHHHHHHh
Q psy14489 185 LPGVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 185 i~Gv~-giG~ktA~~LL~~ 202 (284)
|..|| |+||-|.+-|++.
T Consensus 259 iTPVPGGVGp~T~a~L~~N 277 (287)
T PRK14181 259 ITPVPGGVGPMTVAMLMRN 277 (287)
T ss_pred ccCCCCchHHHHHHHHHHH
Confidence 67788 8999999999874
No 195
>COG3852 NtrB Signal transduction histidine kinase, nitrogen specific [Signal transduction mechanisms]
Probab=26.01 E-value=43 Score=31.61 Aligned_cols=25 Identities=36% Similarity=0.448 Sum_probs=21.8
Q ss_pred CCCCCCCC-------------------ccChhhHHHHHHhcCCH
Q psy14489 182 SDNLPGVK-------------------KIGPKTAVKLLNQYNSL 206 (284)
Q Consensus 182 sDni~Gv~-------------------giG~ktA~~LL~~~gsl 206 (284)
-||-|||| |.|-.-|.+++.+||.+
T Consensus 293 iDNGPGVP~~L~~~lF~P~Vs~r~~GsGLGLala~~li~qH~G~ 336 (363)
T COG3852 293 IDNGPGVPPDLQDHLFYPMVSGREGGTGLGLALAQNLIDQHGGK 336 (363)
T ss_pred ecCCCCCChHHhhhccccccccCCCCccccHHHHHHHHHhcCCE
Confidence 57888886 89999999999999974
No 196
>PRK14830 undecaprenyl pyrophosphate synthase; Provisional
Probab=25.91 E-value=52 Score=29.88 Aligned_cols=64 Identities=16% Similarity=0.246 Sum_probs=38.8
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.||. ..| |+.-.+...++|... ..+..+.+++..+||+.++. +--|=++++.-+.
T Consensus 22 ~P~HVAiImDGN-rRwAk~~gl~~~~Gh~~G~-----~~l~~~l~~c~~~GI~~vTvYaFS~eN~~R~~~Ev~~Lm~l~~ 95 (251)
T PRK14830 22 IPKHIAIIMDGN-GRWAKKRMLPRIAGHKAGM-----DTVKKITKAASELGVKVLTLYAFSTENWKRPKDEVKFLMNLPV 95 (251)
T ss_pred CCCeEEEEecCc-hHHHHHCCCchhhhHHHHH-----HHHHHHHHHHHHcCCCEEEEEEEehhhcCCCHHHHHHHHHHHH
Confidence 489999999973 333 333345555555432 12334666777799998763 3456667765444
Q ss_pred H
Q psy14489 119 K 119 (284)
Q Consensus 119 ~ 119 (284)
.
T Consensus 96 ~ 96 (251)
T PRK14830 96 E 96 (251)
T ss_pred H
Confidence 3
No 197
>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=25.91 E-value=38 Score=31.12 Aligned_cols=19 Identities=26% Similarity=0.447 Sum_probs=14.6
Q ss_pred CCCCCCCccChhhHHHHHH
Q psy14489 183 DNLPGVKKIGPKTAVKLLN 201 (284)
Q Consensus 183 Dni~Gv~giG~ktA~~LL~ 201 (284)
+-+-.+||||++||.-.+.
T Consensus 105 ~~L~~LpGIG~~TA~~Il~ 123 (275)
T TIGR01084 105 EDLAALPGVGRYTAGAILS 123 (275)
T ss_pred HHHHhCCCCCHHHHHHHHH
Confidence 3455689999999977665
No 198
>PF09550 DUF2376: Conserved hypothetical phage protein (DUF2376); InterPro: IPR019056 Gene transfer agents belong to a group of unusual genetic exchange elements []. GTAs are unusual in the sense they have the structure of a small tailed phage, which do not possess typical phage traits such as host cell lysis and infectious transmission of the GTA genes. In the Rhodobacter capsulatus GTA the GTA particles contain random 4.5 kb DNA fragments of the R.capsulatus genome. These DNA fragments can be transmitted to other cells where allelic conversion may occur via homologous recombination. The genes coding for the GTA particles are of two distinct types: the first is a cluster of genes reminiscent of a cryptyic prophage, where a number of the genes have similarity to known phage structural genes; the second type consists of two genes coding for a cellular two-component signal transduction system, which regulates the transcription of the GTA structural gene cluster in a growth phase dependent manner []. This entry is represented by ORFg10.1 (RCAP_rcc01693) of the Gene Transfer Agent (GTA) of Rhodobacter capsulatus [see Fig.1, in ]. The function is not known.
Probab=25.72 E-value=1.5e+02 Score=19.45 Aligned_cols=27 Identities=15% Similarity=0.385 Sum_probs=18.4
Q ss_pred hhhhcCCCCCCCCCCCccChhhHHHHHHhcC
Q psy14489 174 YFSLIGDMSDNLPGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 174 ~~~L~GD~sDni~Gv~giG~ktA~~LL~~~g 204 (284)
+.++.| .+. |...++...-.+|+..|.
T Consensus 16 l~a~~g--~~~--~~~pl~R~~L~~Lm~~~P 42 (43)
T PF09550_consen 16 LRAMLG--ADA--GAAPLDRAELDALMRRFP 42 (43)
T ss_pred HHHhcC--ccc--CCCCCCHHHHHHHHHHCc
Confidence 478888 333 457777777777777765
No 199
>PRK14836 undecaprenyl pyrophosphate synthase; Provisional
Probab=25.50 E-value=43 Score=30.43 Aligned_cols=65 Identities=15% Similarity=0.197 Sum_probs=40.4
Q ss_pred CCCEEEEEEeCCCCcc-ccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee----------CCchHHHHHHHHH
Q psy14489 50 RATYIACIFDAKGKNF-RNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII----------KGVEADDVIGTLA 118 (284)
Q Consensus 50 ~~~~~i~~fD~~~~~~-R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~----------~g~EADD~ia~la 118 (284)
-|.|++|+.||. ..| |+.-.+...++|.... .+..+.+++..+||++++. +.-|=+.++.-+.
T Consensus 14 ~P~HVAiImDGN-rRwA~~~gl~~~~GH~~G~~-----~~~~iv~~c~~~gI~~lTvYaFS~eN~~R~~~EV~~Lm~l~~ 87 (253)
T PRK14836 14 IPRHIAIIMDGN-GRWAKRRGKPRVEGHRAGVR-----AVRRTIEFCLEKGIEMLTLFAFSSENWLRPADEVSALMELFL 87 (253)
T ss_pred CCCeEEEecCCc-HHHHHHCCCchhhhHHHHHH-----HHHHHHHHHHHcCCCEEehhHhhhhhcCCCHHHHHHHHHHHH
Confidence 489999999973 333 3333455666665431 2334566777799998874 3456677666555
Q ss_pred HH
Q psy14489 119 KQ 120 (284)
Q Consensus 119 ~~ 120 (284)
..
T Consensus 88 ~~ 89 (253)
T PRK14836 88 KA 89 (253)
T ss_pred HH
Confidence 43
No 200
>PRK14177 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=25.39 E-value=70 Score=29.62 Aligned_cols=71 Identities=23% Similarity=0.313 Sum_probs=42.3
Q ss_pred CCCeEEEEcCCC-ccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCC--------CCCCC
Q psy14489 125 HNLKVIISTNDK-DMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMS--------DNLPG 187 (284)
Q Consensus 125 ~~~~v~I~S~Dk-Dl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~s--------Dni~G 187 (284)
.+..|.+|.+.+ |+..+... .+-+-- +...++.+++++- .|++. -++||-. -.|..
T Consensus 182 ~~atVt~chs~T~~l~~~~~~ADIvIsAvGk~~~i~~~~ik~gavVIDvGin~-------~~~GDVd~~~v~~~a~~iTP 254 (284)
T PRK14177 182 MNATVTLCHSKTQNLPSIVRQADIIVGAVGKPEFIKADWISEGAVLLDAGYNP-------GNVGDIEISKAKDKSSFYTP 254 (284)
T ss_pred CCCEEEEeCCCCCCHHHHHhhCCEEEEeCCCcCccCHHHcCCCCEEEEecCcc-------cccCCcCHHHHhhhccEecC
Confidence 456677765443 34333322 333322 5667888877652 46654 1689832 13455
Q ss_pred CC-ccChhhHHHHHHh
Q psy14489 188 VK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 188 v~-giG~ktA~~LL~~ 202 (284)
|| |+||-|.+-|++.
T Consensus 255 VPGGVGp~T~a~L~~N 270 (284)
T PRK14177 255 VPGGVGPMTIAVLLLQ 270 (284)
T ss_pred CCCCChHHHHHHHHHH
Confidence 65 5999999999884
No 201
>TIGR01428 HAD_type_II 2-haloalkanoic acid dehalogenase, type II. Note that the Type I HAD enzymes have not yet been fully characterized, but clearly utilize a substantially different catalytic mechanism and are thus unlikely to be related.
Probab=25.26 E-value=34 Score=28.82 Aligned_cols=33 Identities=30% Similarity=0.491 Sum_probs=22.8
Q ss_pred HHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChhh
Q psy14489 159 TIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPKT 195 (284)
Q Consensus 159 ~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~kt 195 (284)
.+.+++|+.|++ ++++||+.-++.|....|..+
T Consensus 156 ~~~~~~~~~p~~----~~~vgD~~~Di~~A~~~G~~~ 188 (198)
T TIGR01428 156 LALEALGVPPDE----VLFVASNPWDLGGAKKFGFKT 188 (198)
T ss_pred HHHHHhCCChhh----EEEEeCCHHHHHHHHHCCCcE
Confidence 455788998855 568998876666665566544
No 202
>PF14635 HHH_7: Helix-hairpin-helix motif ; PDB: 3PSI_A 3PSF_A.
Probab=24.77 E-value=47 Score=26.07 Aligned_cols=19 Identities=32% Similarity=0.419 Sum_probs=13.6
Q ss_pred CCCCccChhhHHHHHHhcC
Q psy14489 186 PGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g 204 (284)
+=|.|.||.+|..|++...
T Consensus 53 qfV~GLGPRKA~~Ll~~l~ 71 (104)
T PF14635_consen 53 QFVCGLGPRKAQALLKALK 71 (104)
T ss_dssp GGSTT--HHHHHHHHHHHH
T ss_pred hHhcCCChHHHHHHHHHHH
Confidence 5578999999999998643
No 203
>PRK08609 hypothetical protein; Provisional
Probab=24.60 E-value=85 Score=31.92 Aligned_cols=15 Identities=33% Similarity=0.386 Sum_probs=12.5
Q ss_pred CCCCCCccChhhHHH
Q psy14489 184 NLPGVKKIGPKTAVK 198 (284)
Q Consensus 184 ni~Gv~giG~ktA~~ 198 (284)
-..++||||++.|.+
T Consensus 49 ~l~~ipgIG~~ia~k 63 (570)
T PRK08609 49 DFTKLKGIGKGTAEV 63 (570)
T ss_pred hhccCCCcCHHHHHH
Confidence 367899999999875
No 204
>PRK13482 DNA integrity scanning protein DisA; Provisional
Probab=24.59 E-value=53 Score=31.39 Aligned_cols=26 Identities=23% Similarity=0.274 Sum_probs=22.8
Q ss_pred hhhhhcCCCCCCCCCCCccChhhHHH
Q psy14489 173 DYFSLIGDMSDNLPGVKKIGPKTAVK 198 (284)
Q Consensus 173 ~~~~L~GD~sDni~Gv~giG~ktA~~ 198 (284)
.++.++.-+.+.+..|+|||+++|..
T Consensus 309 SL~~Il~As~eeL~~VeGIGe~rA~~ 334 (352)
T PRK13482 309 SLQGLLAASIEDLDEVEGIGEVRARA 334 (352)
T ss_pred CHHHHHcCCHHHHhhCCCcCHHHHHH
Confidence 67788888888899999999999987
No 205
>TIGR02853 spore_dpaA dipicolinic acid synthetase, A subunit. This predicted Rossman fold-containing protein is the A subunit of dipicolinic acid synthetase as found in most, though not all, endospore-forming low-GC Gram-positive bacteria; it is absent in Clostridium. The B subunit is represented by TIGR02852. This protein is also known as SpoVFA.
Probab=23.49 E-value=59 Score=29.90 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=17.2
Q ss_pred CCCCCc-cChhhHHHHHHhcCCHHHHH
Q psy14489 185 LPGVKK-IGPKTAVKLLNQYNSLENII 210 (284)
Q Consensus 185 i~Gv~g-iG~ktA~~LL~~~gsle~i~ 210 (284)
.||+|| ++|+||.++|.+ .+.+++
T Consensus 261 ~~glPg~~ap~ta~~i~~~--~~~~~~ 285 (287)
T TIGR02853 261 APGLPGIVAPKTAGKILAN--VLSELL 285 (287)
T ss_pred eCCCCcccCchhHHHHHHH--HHHHHh
Confidence 377776 789999999975 444443
No 206
>CHL00137 rps13 ribosomal protein S13; Validated
Probab=23.38 E-value=53 Score=26.47 Aligned_cols=19 Identities=26% Similarity=0.328 Sum_probs=16.2
Q ss_pred CCCCccChhhHHHHHHhcC
Q psy14489 186 PGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g 204 (284)
..|.|||+.+|..+.++.|
T Consensus 20 t~i~GIG~~~A~~ic~~lg 38 (122)
T CHL00137 20 TYIYGIGLTSAKEILEKAN 38 (122)
T ss_pred cccccccHHHHHHHHHHcC
Confidence 3478999999999998876
No 207
>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=23.07 E-value=71 Score=30.40 Aligned_cols=27 Identities=7% Similarity=0.334 Sum_probs=21.3
Q ss_pred CCCCCccChhhHHHHHHhcC--CHHHHHH
Q psy14489 185 LPGVKKIGPKTAVKLLNQYN--SLENIIN 211 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~~~g--sle~i~~ 211 (284)
+.-++|||++++.++|+.+| |+.++.+
T Consensus 184 v~~l~GiG~~~~~~ll~~~Gi~ti~dl~~ 212 (359)
T cd01702 184 ITSIRGLGGKLGEEIIDLLGLPTEGDVAG 212 (359)
T ss_pred HHHhCCcCHHHHHHHHHHcCCcCHHHHHh
Confidence 45578999999999998777 6677654
No 208
>PTZ00134 40S ribosomal protein S18; Provisional
Probab=22.73 E-value=54 Score=27.56 Aligned_cols=18 Identities=22% Similarity=0.296 Sum_probs=16.3
Q ss_pred CCCccChhhHHHHHHhcC
Q psy14489 187 GVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 187 Gv~giG~ktA~~LL~~~g 204 (284)
.|.|||+.+|..++.+.|
T Consensus 34 ~I~GIG~~~A~~I~~~lg 51 (154)
T PTZ00134 34 AIKGIGRRFAYLVCKKAG 51 (154)
T ss_pred ccccccHHHHHHHHHHcC
Confidence 378999999999999887
No 209
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=22.52 E-value=81 Score=24.73 Aligned_cols=34 Identities=29% Similarity=0.270 Sum_probs=24.3
Q ss_pred chHHHHHHHHHHHhhHhC-CCeEEEEcCCCccccc
Q psy14489 108 VEADDVIGTLAKQAVTKH-NLKVIISTNDKDMAQL 141 (284)
Q Consensus 108 ~EADD~ia~la~~~~~~~-~~~v~I~S~DkDl~ql 141 (284)
-..||.|-..|..+.+.. +.+|+++|.|+.+..-
T Consensus 87 ~~~D~~Il~~a~~~~~~~~~~~vvLvT~D~~l~~~ 121 (133)
T PF13638_consen 87 QRNDDRILNCALYLQEENPGRKVVLVTNDKNLRLK 121 (133)
T ss_dssp -HHHHHHHHHHHHHHHHCGCEEEEEEE--HHHHHH
T ss_pred cccHHHHHHHHHHHHHhcCCCeEEEEeCCHHHHHH
Confidence 378998888888776633 6789999999987654
No 210
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=22.42 E-value=3.3e+02 Score=25.76 Aligned_cols=76 Identities=11% Similarity=-0.005 Sum_probs=40.1
Q ss_pred CcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCC--hhHHHHHHHHHHHHHhcCCcEEeeC
Q psy14489 29 NFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP--YNLILQINLIHQMVKAIGWPILIIK 106 (284)
Q Consensus 29 g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p--~~l~~q~~~i~~~l~~~gi~~~~~~ 106 (284)
|.|......+...+..+. ..+|+++.+ +.- .......++..++.+.-+.| +.+..++..+.+.|+..|+..++..
T Consensus 168 GlPgqt~~~~~~tl~~~~-~l~~~~i~~-y~l-~~~~gT~l~~~~~~g~~~~~~~~~~~~~~~~~~~~l~~~G~~~ye~s 244 (375)
T PRK05628 168 GTPGESDDDWRASLDAAL-EAGVDHVSA-YAL-IVEDGTALARRVRRGELPAPDDDVLADRYELADARLSAAGFDWYEVS 244 (375)
T ss_pred cCCCCCHHHHHHHHHHHH-hcCCCEEEe-eee-ecCCCChHHHHhhcCCCCCCChHHHHHHHHHHHHHHHHcCCCeeeec
Confidence 334444445555555444 467777533 211 01111122334443333334 3466778889999999998877654
Q ss_pred C
Q psy14489 107 G 107 (284)
Q Consensus 107 g 107 (284)
+
T Consensus 245 ~ 245 (375)
T PRK05628 245 N 245 (375)
T ss_pred c
Confidence 3
No 211
>TIGR03631 bact_S13 30S ribosomal protein S13. This model describes bacterial ribosomal protein S13, to the exclusion of the homologous archaeal S13P and eukaryotic ribosomal protein S18. This model identifies some (but not all) instances of chloroplast and mitochondrial S13, which is of bacterial type.
Probab=22.37 E-value=51 Score=26.13 Aligned_cols=20 Identities=25% Similarity=0.248 Sum_probs=17.1
Q ss_pred CCCCccChhhHHHHHHhcCC
Q psy14489 186 PGVKKIGPKTAVKLLNQYNS 205 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~gs 205 (284)
..|.|||+.+|..+..+.|-
T Consensus 18 ~~i~GIG~~~a~~i~~~lgi 37 (113)
T TIGR03631 18 TYIYGIGRTRARKILEKAGI 37 (113)
T ss_pred eeeecccHHHHHHHHHHhCc
Confidence 45889999999999998873
No 212
>PRK14192 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=22.28 E-value=53 Score=30.26 Aligned_cols=19 Identities=32% Similarity=0.443 Sum_probs=15.2
Q ss_pred CCCCCC-ccChhhHHHHHHh
Q psy14489 184 NLPGVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 184 ni~Gv~-giG~ktA~~LL~~ 202 (284)
.|..|| |+||-|.+-|++.
T Consensus 254 ~itPvPGGVGp~T~a~L~~n 273 (283)
T PRK14192 254 AYTPVPGGVGPMTINTLIRQ 273 (283)
T ss_pred EeCCCCCcChHHHHHHHHHH
Confidence 456676 5999999999874
No 213
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=22.04 E-value=71 Score=23.89 Aligned_cols=25 Identities=36% Similarity=0.484 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHhhHhCCCeEEEEcCCCccc
Q psy14489 110 ADDVIGTLAKQAVTKHNLKVIISTNDKDMA 139 (284)
Q Consensus 110 ADD~ia~la~~~~~~~~~~v~I~S~DkDl~ 139 (284)
.|+.+..+|... ..++++|.|+++.
T Consensus 86 ~D~~il~~a~~~-----~~~~lvT~D~~l~ 110 (111)
T smart00670 86 NDALILATAKEL-----GNVVLVTNDRDLR 110 (111)
T ss_pred ChHHHHHHHHHC-----CCCEEEeCCcccC
Confidence 577888777643 1579999999975
No 214
>PF12836 HHH_3: Helix-hairpin-helix motif; PDB: 2EDU_A 2OCE_A 3BZK_A 3BZC_A 2DUY_A.
Probab=21.95 E-value=61 Score=22.66 Aligned_cols=16 Identities=31% Similarity=0.576 Sum_probs=11.6
Q ss_pred CCCCccChhhHHHHHH
Q psy14489 186 PGVKKIGPKTAVKLLN 201 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~ 201 (284)
..+||+|++.|..+++
T Consensus 17 ~~lpgi~~~~A~~Iv~ 32 (65)
T PF12836_consen 17 QALPGIGPKQAKAIVE 32 (65)
T ss_dssp HTSTT--HHHHHHHHH
T ss_pred HHcCCCCHHHHHHHHH
Confidence 4578999999998887
No 215
>PRK10880 adenine DNA glycosylase; Provisional
Probab=21.92 E-value=52 Score=31.39 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=16.1
Q ss_pred CCCCCccChhhHHHHHH-hcCC
Q psy14489 185 LPGVKKIGPKTAVKLLN-QYNS 205 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~-~~gs 205 (284)
+-.+||||++||..++. .|+-
T Consensus 111 L~~LpGIG~~TA~aIl~~af~~ 132 (350)
T PRK10880 111 VAALPGVGRSTAGAILSLSLGK 132 (350)
T ss_pred HhcCCCccHHHHHHHHHHHCCC
Confidence 45689999999998876 4543
No 216
>PRK05179 rpsM 30S ribosomal protein S13; Validated
Probab=21.77 E-value=58 Score=26.20 Aligned_cols=19 Identities=21% Similarity=0.212 Sum_probs=16.5
Q ss_pred CCCCccChhhHHHHHHhcC
Q psy14489 186 PGVKKIGPKTAVKLLNQYN 204 (284)
Q Consensus 186 ~Gv~giG~ktA~~LL~~~g 204 (284)
..|.|||+.+|..++.+.|
T Consensus 20 ~~I~GIG~~~a~~i~~~lg 38 (122)
T PRK05179 20 TYIYGIGRTRAKEILAAAG 38 (122)
T ss_pred cccccccHHHHHHHHHHhC
Confidence 4578999999999999877
No 217
>PRK10853 putative reductase; Provisional
Probab=21.57 E-value=87 Score=24.80 Aligned_cols=28 Identities=14% Similarity=0.107 Sum_probs=22.2
Q ss_pred ccccccCCCCHHHHHHHHHHcCchhHHh
Q psy14489 254 PESLILQPKDEKLLMQLFNKYKLNKLNF 281 (284)
Q Consensus 254 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~ 281 (284)
.-++.-.+|+.+.|..++.++|+..+++
T Consensus 29 ~~d~~k~p~s~~eL~~~l~~~g~~~l~n 56 (118)
T PRK10853 29 FHDYRVDGLDSELLQGFIDELGWEALLN 56 (118)
T ss_pred EeehccCCcCHHHHHHHHHHcCHHHHHh
Confidence 3466677899999999999999877664
No 218
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=21.51 E-value=85 Score=24.23 Aligned_cols=28 Identities=14% Similarity=-0.039 Sum_probs=21.2
Q ss_pred ccccccCCCCHHHHHHHHHHcCchhHHh
Q psy14489 254 PESLILQPKDEKLLMQLFNKYKLNKLNF 281 (284)
Q Consensus 254 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~ 281 (284)
.-++.-.+++.+.|..++.++|...+++
T Consensus 28 ~~di~~~p~s~~eL~~~l~~~g~~~li~ 55 (105)
T cd03035 28 FHDYRKDGLDAATLERWLAKVGWETLLN 55 (105)
T ss_pred EEecccCCCCHHHHHHHHHHhChHHHHc
Confidence 3455667889999999999888766653
No 219
>PRK11587 putative phosphatase; Provisional
Probab=21.49 E-value=2.1e+02 Score=24.45 Aligned_cols=32 Identities=13% Similarity=0.185 Sum_probs=21.0
Q ss_pred HHHHHhCCChhHHHhhhhhcCCCCCCCCCCCccChh
Q psy14489 159 TIISRFGVSPEKIVDYFSLIGDMSDNLPGVKKIGPK 194 (284)
Q Consensus 159 ~~~~~~G~~p~q~~~~~~L~GD~sDni~Gv~giG~k 194 (284)
...+++|+.|++ ++++||+.-++.+....|.+
T Consensus 146 ~~~~~~g~~p~~----~l~igDs~~di~aA~~aG~~ 177 (218)
T PRK11587 146 LGAQLLGLAPQE----CVVVEDAPAGVLSGLAAGCH 177 (218)
T ss_pred HHHHHcCCCccc----EEEEecchhhhHHHHHCCCE
Confidence 345678888744 78899988776544444443
No 220
>COG1011 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=21.25 E-value=46 Score=28.40 Aligned_cols=42 Identities=26% Similarity=0.396 Sum_probs=32.3
Q ss_pred eHhHHHHHhCCChhHHHhhhhhcCCCCCCC-CCCCccChhhHHHHHHhc
Q psy14489 156 DRTTIISRFGVSPEKIVDYFSLIGDMSDNL-PGVKKIGPKTAVKLLNQY 203 (284)
Q Consensus 156 ~~~~~~~~~G~~p~q~~~~~~L~GD~sDni-~Gv~giG~ktA~~LL~~~ 203 (284)
-.+.+.+++|+.| .-.+.+||+-.|. -|....|.+|. +++..
T Consensus 159 ~f~~~~~~~g~~p----~~~l~VgD~~~~di~gA~~~G~~~v--wi~~~ 201 (229)
T COG1011 159 IFEYALEKLGVPP----EEALFVGDSLENDILGARALGMKTV--WINRG 201 (229)
T ss_pred HHHHHHHHcCCCc----ceEEEECCChhhhhHHHHhcCcEEE--EECCC
Confidence 3445678899986 5578899999999 89999999886 55543
No 221
>PF06574 FAD_syn: FAD synthetase; InterPro: IPR015864 Riboflavin is converted into catalytically active cofactors (FAD and FMN) by the actions of riboflavin kinase (2.7.1.26 from EC), which converts it into FMN, and FAD synthetase (2.7.7.2 from EC), which adenylates FMN to FAD. Eukaryotes usually have two separate enzymes, while most prokaryotes have a single bifunctional protein that can carry out both catalyses, although exceptions occur in both cases. While eukaryotic monofunctional riboflavin kinase is orthologous to the bifunctional prokaryotic enzyme [], the monofunctional FAD synthetase differs from its prokaryotic counterpart, and is instead related to the PAPS-reductase family []. The bacterial FAD synthetase that is part of the bifunctional enzyme has remote similarity to nucleotidyl transferases and, hence, it may be involved in the adenylylation reaction of FAD synthetases []. This entry represents prokaryotic-type FAD synthetase, which occurs primarily as part of a bifunctional enzyme.; GO: 0003919 FMN adenylyltransferase activity, 0009231 riboflavin biosynthetic process; PDB: 2X0K_B 3OP1_B 1T6Z_A 2I1L_A 1T6Y_B 1T6X_B 1S4M_A 1MRZ_A.
Probab=21.09 E-value=4.8e+02 Score=21.58 Aligned_cols=92 Identities=23% Similarity=0.346 Sum_probs=48.8
Q ss_pred CCcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCC-ccccccCchhhhCCCCCChhHHHHHHHHHHHHHhcCCcEEee-
Q psy14489 28 DNFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGK-NFRNILYPSYKATRKKMPYNLILQINLIHQMVKAIGWPILII- 105 (284)
Q Consensus 28 ~g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~-~~R~~l~~~YKa~R~~~p~~l~~q~~~i~~~l~~~gi~~~~~- 105 (284)
||...+.- ..+..+.+.-+..+...+++.||..+. .++ | ...|..|. ..+.=.++|+.+|+.++..
T Consensus 15 DGvH~GHq-~Li~~~~~~a~~~~~~~~v~tF~~~P~~~~~----~------~~~~~~l~-s~~ek~~~l~~~Gvd~~~~~ 82 (157)
T PF06574_consen 15 DGVHLGHQ-KLIKKAVEIAKEKGLKSVVLTFDPHPKEVLN----P------DKPPKLLT-SLEEKLELLESLGVDYVIVI 82 (157)
T ss_dssp TT--HHHH-HHHHHHHHHHHHCT-EEEEEEESS-CHHHHS----C------TCCGGBSS--HHHHHHHHHHTTESEEEEE
T ss_pred CCccHHHH-HHHHHHhhhhhhcccceEEEEcccCHHHHhc----C------CCcccCCC-CHHHHHHHHHHcCCCEEEEe
Confidence 45555442 234555666666777788999985321 122 1 11122222 1223345678899887542
Q ss_pred ------CCchHHHHHHHHHH-HhhHhCCCeEEEEcCC
Q psy14489 106 ------KGVEADDVIGTLAK-QAVTKHNLKVIISTND 135 (284)
Q Consensus 106 ------~g~EADD~ia~la~-~~~~~~~~~v~I~S~D 135 (284)
...+|+|-+-.+-. + .+.+.+|+-.|
T Consensus 83 ~F~~~~~~ls~~~Fi~~iL~~~----l~~~~ivvG~D 115 (157)
T PF06574_consen 83 PFTEEFANLSPEDFIEKILKEK----LNVKHIVVGED 115 (157)
T ss_dssp -CCCHHCCS-HHHHHHHHCCCH----CTEEEEEEETT
T ss_pred cchHHHHcCCHHHHHHHHHHhc----CCccEEEEccC
Confidence 36789999987432 3 45577787666
No 222
>PRK10308 3-methyl-adenine DNA glycosylase II; Provisional
Probab=20.98 E-value=54 Score=30.21 Aligned_cols=24 Identities=21% Similarity=0.173 Sum_probs=16.3
Q ss_pred CCCCCccChhhHHHHH-HhcCCHHH
Q psy14489 185 LPGVKKIGPKTAVKLL-NQYNSLEN 208 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL-~~~gsle~ 208 (284)
+-.+|||||+||--.+ ..+|-.|.
T Consensus 209 L~~LpGIGpwTA~~vllr~lg~~D~ 233 (283)
T PRK10308 209 LQTFPGIGRWTANYFALRGWQAKDV 233 (283)
T ss_pred HhcCCCcCHHHHHHHHHHhCCCCCC
Confidence 3558999999995544 45665543
No 223
>COG1569 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=20.91 E-value=90 Score=25.88 Aligned_cols=34 Identities=15% Similarity=0.173 Sum_probs=22.6
Q ss_pred CCeEEEEcCCCccccccCCCeEEEeCcEeeeHhHHHHH
Q psy14489 126 NLKVIISTNDKDMAQLVSNKIALINNNKIHDRTTIISR 163 (284)
Q Consensus 126 ~~~v~I~S~DkDl~ql~~~~v~~~~~~~~~~~~~~~~~ 163 (284)
+-.-+++|+|+|++-+-+++= ..+..|+..|.++
T Consensus 103 ~kA~~lvTgD~dLL~lr~~n~----~~~Iltp~eF~~~ 136 (142)
T COG1569 103 SKADYLVTGDQDLLVLRDENK----RVEILTPQEFLEE 136 (142)
T ss_pred ccCCEEEEcchhhheecccCC----cEEEcCHHHHHHH
Confidence 334689999999999876541 1335566666553
No 224
>TIGR01662 HAD-SF-IIIA HAD-superfamily hydrolase, subfamily IIIA. In the case of histidinol phosphatase and PNK-3'-phosphatase, this model represents a domain of a bifunctional system. In the histidinol phosphatase HisB, a C-terminal domain is an imidazoleglycerol-phosphate dehydratase which catalyzes a related step in histidine biosynthesis. In PNK-3'-phosphatase, N- and C-terminal domains constitute the polynucleotide kinase and DNA-binding components of the enzyme.
Probab=20.81 E-value=2.5e+02 Score=21.71 Aligned_cols=36 Identities=25% Similarity=0.374 Sum_probs=23.5
Q ss_pred eHhHHHHHh-CCChhHHHhhhhhcCC-CCCCCCCCCccChhh
Q psy14489 156 DRTTIISRF-GVSPEKIVDYFSLIGD-MSDNLPGVKKIGPKT 195 (284)
Q Consensus 156 ~~~~~~~~~-G~~p~q~~~~~~L~GD-~sDni~Gv~giG~kt 195 (284)
....+.+++ |+.|++ .+++|| +..++.+....|.++
T Consensus 90 ~~~~~~~~~~~~~~~~----~v~IGD~~~~Di~~A~~~Gi~~ 127 (132)
T TIGR01662 90 MFLEALKRFNEIDPEE----SVYVGDQDLTDLQAAKRAGLAF 127 (132)
T ss_pred HHHHHHHHcCCCChhh----eEEEcCCCcccHHHHHHCCCeE
Confidence 334677888 588865 567999 566666555555443
No 225
>PRK14188 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.81 E-value=59 Score=30.26 Aligned_cols=108 Identities=19% Similarity=0.305 Sum_probs=54.6
Q ss_pred HHHHHHhcCCcE----EeeCCchHHHHHHHHHHHhhHhCCCeEEEE-cCCCccccccCC-CeEEEe--CcEeeeHhHHHH
Q psy14489 91 IHQMVKAIGWPI----LIIKGVEADDVIGTLAKQAVTKHNLKVIIS-TNDKDMAQLVSN-KIALIN--NNKIHDRTTIIS 162 (284)
Q Consensus 91 i~~~l~~~gi~~----~~~~g~EADD~ia~la~~~~~~~~~~v~I~-S~DkDl~ql~~~-~v~~~~--~~~~~~~~~~~~ 162 (284)
+.++|+..|++. +.+-| --.-+=.-+|+...+ .|..|.++ |..+|+..+... .+.+.- +...++..++.+
T Consensus 145 i~~ll~~~~i~~~Gk~V~viG-rs~~mG~PmA~~L~~-~g~tVtv~~~rT~~l~e~~~~ADIVIsavg~~~~v~~~~lk~ 222 (296)
T PRK14188 145 CMMLLRRVHGDLSGLNAVVIG-RSNLVGKPMAQLLLA-ANATVTIAHSRTRDLPAVCRRADILVAAVGRPEMVKGDWIKP 222 (296)
T ss_pred HHHHHHHhCCCCCCCEEEEEc-CCcchHHHHHHHHHh-CCCEEEEECCCCCCHHHHHhcCCEEEEecCChhhcchheecC
Confidence 566777665422 11112 111222344555555 68888888 566676655533 333322 223333333222
Q ss_pred -----HhCCChhHHH--h---h-hhhcCCCC-C-------CCCCCC-ccChhhHHHHHHh
Q psy14489 163 -----RFGVSPEKIV--D---Y-FSLIGDMS-D-------NLPGVK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 163 -----~~G~~p~q~~--~---~-~~L~GD~s-D-------ni~Gv~-giG~ktA~~LL~~ 202 (284)
..|+++ .. + - .-++||-. + .|..|| |+||-|.+-|++.
T Consensus 223 GavVIDvGin~--~~~~~~~~g~~~l~GDvd~~~v~~~a~~iTPVPGGVGp~T~a~L~~N 280 (296)
T PRK14188 223 GATVIDVGINR--IPAPEKGEGKTRLVGDVAFAEAAEVAGAITPVPGGVGPMTIACLLAN 280 (296)
T ss_pred CCEEEEcCCcc--cCCccccCCCceeeCCCCHHHHHhhccEecCCCCChhHHHHHHHHHH
Confidence 234432 11 1 1 13888832 1 455565 5999999999874
No 226
>PRK14171 bifunctional 5,10-methylene-tetrahydrofolate dehydrogenase/ 5,10-methylene-tetrahydrofolate cyclohydrolase; Provisional
Probab=20.73 E-value=60 Score=30.14 Aligned_cols=75 Identities=21% Similarity=0.317 Sum_probs=42.7
Q ss_pred CCCeEEEEcCC-CccccccCC-CeEEEe--CcEeeeHhHHHHH-----hCCChhHHHhhhhhcCCCC--------CCCCC
Q psy14489 125 HNLKVIISTND-KDMAQLVSN-KIALIN--NNKIHDRTTIISR-----FGVSPEKIVDYFSLIGDMS--------DNLPG 187 (284)
Q Consensus 125 ~~~~v~I~S~D-kDl~ql~~~-~v~~~~--~~~~~~~~~~~~~-----~G~~p~q~~~~~~L~GD~s--------Dni~G 187 (284)
.+..|.+|.+- +|+..+... .+-+-- +...++.+++++- .|+++. ..- =++||-. -+|..
T Consensus 182 ~~ATVtichs~T~~L~~~~~~ADIvV~AvGkp~~i~~~~vk~GavVIDvGin~~--~~g-kl~GDVd~~~v~~~a~~iTP 258 (288)
T PRK14171 182 ENCSVTICHSKTHNLSSITSKADIVVAAIGSPLKLTAEYFNPESIVIDVGINRI--SGN-KIIGDVDFENVKSKVKYITP 258 (288)
T ss_pred CCCEEEEeCCCCCCHHHHHhhCCEEEEccCCCCccCHHHcCCCCEEEEeecccc--CCC-CeECCccHHHHHhhceEeCC
Confidence 45667766543 444443332 333332 5567787777652 455431 111 3788832 14455
Q ss_pred CC-ccChhhHHHHHHh
Q psy14489 188 VK-KIGPKTAVKLLNQ 202 (284)
Q Consensus 188 v~-giG~ktA~~LL~~ 202 (284)
|| |+||-|.+-|++.
T Consensus 259 VPGGVGp~T~a~L~~N 274 (288)
T PRK14171 259 VPGGIGPMTIAFLLKN 274 (288)
T ss_pred CCCCcHHHHHHHHHHH
Confidence 65 6999999999874
No 227
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=20.58 E-value=3.8e+02 Score=25.73 Aligned_cols=74 Identities=15% Similarity=0.196 Sum_probs=39.9
Q ss_pred CcchhHHHHHHHHHHHHHHhcCCCEEEEEEeCCCCccccccCchhhhCCCCCC--hhHHHHHHHHHHHHHhcCCcEEee
Q psy14489 29 NFPVGALYGTIKMLRKLYKNYRATYIACIFDAKGKNFRNILYPSYKATRKKMP--YNLILQINLIHQMVKAIGWPILII 105 (284)
Q Consensus 29 g~~t~ai~gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~~~YKa~R~~~p--~~l~~q~~~i~~~l~~~gi~~~~~ 105 (284)
|.|......+...+..+.+ .+|+|+-+. -- ...--..++..|+.++...| ++...++..+.+.|+..|+..++.
T Consensus 175 GlPgqt~e~~~~tl~~~~~-l~p~~is~y-~L-~~~pgT~l~~~~~~g~~~~~~~~~~~~~~~~~~~~L~~~Gy~~yei 250 (400)
T PRK07379 175 GLPHQTLEDWQASLEAAIA-LNPTHLSCY-DL-VLEPGTAFGKQYQPGKAPLPSDETTAAMYRLAQEILTQAGYEHYEI 250 (400)
T ss_pred CCCCCCHHHHHHHHHHHHc-CCCCEEEEe-cc-eecCCchhHHHhhcCCCCCCCHHHHHHHHHHHHHHHHHcCCceeee
Confidence 3443444455555555553 567775432 10 01111123445655554444 344556778899999999877764
No 228
>KOG1921|consensus
Probab=20.57 E-value=37 Score=30.90 Aligned_cols=25 Identities=28% Similarity=0.477 Sum_probs=18.0
Q ss_pred CCCCCccChhhHHHHHH-hcCCHHHH
Q psy14489 185 LPGVKKIGPKTAVKLLN-QYNSLENI 209 (284)
Q Consensus 185 i~Gv~giG~ktA~~LL~-~~gsle~i 209 (284)
+-+.||||||.|.-.++ .+|.+.+|
T Consensus 161 LlsLPGVGPKMa~L~m~~AWn~i~GI 186 (286)
T KOG1921|consen 161 LLSLPGVGPKMAHLTMQVAWNKIVGI 186 (286)
T ss_pred HhcCCCCchHHHHHHHHHHhccceeE
Confidence 34569999999988877 45555554
No 229
>PRK10563 6-phosphogluconate phosphatase; Provisional
Probab=20.45 E-value=78 Score=27.10 Aligned_cols=26 Identities=19% Similarity=0.176 Sum_probs=19.0
Q ss_pred hHHHHHhCCChhHHHhhhhhcCCCCCCCCC
Q psy14489 158 TTIISRFGVSPEKIVDYFSLIGDMSDNLPG 187 (284)
Q Consensus 158 ~~~~~~~G~~p~q~~~~~~L~GD~sDni~G 187 (284)
....+++|+.|++ ++++||+..+|-+
T Consensus 149 ~~a~~~~~~~p~~----~l~igDs~~di~a 174 (221)
T PRK10563 149 FHAAEAMNVNVEN----CILVDDSSAGAQS 174 (221)
T ss_pred HHHHHHcCCCHHH----eEEEeCcHhhHHH
Confidence 4556789998864 6788998777643
No 230
>PF14582 Metallophos_3: Metallophosphoesterase, calcineurin superfamily; PDB: 1UF3_B 2YVT_A.
Probab=20.36 E-value=2.6e+02 Score=25.36 Aligned_cols=83 Identities=11% Similarity=0.187 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHhcCCCEEEEEEeCCCCccccccC-chhhhCCCCCChhH-------HHHHHHHHHHHHhcCCcEEeeCCc
Q psy14489 37 GTIKMLRKLYKNYRATYIACIFDAKGKNFRNILY-PSYKATRKKMPYNL-------ILQINLIHQMVKAIGWPILIIKGV 108 (284)
Q Consensus 37 gf~~~l~~l~~~~~~~~~i~~fD~~~~~~R~~l~-~~YKa~R~~~p~~l-------~~q~~~i~~~l~~~gi~~~~~~g~ 108 (284)
..+..+.+.+.+.+++-++++=|--.+.-|.+-| ..-.++|.+..++. ...+..+-+.|..+|+|++..||
T Consensus 19 e~l~~l~~~~~e~~~D~~v~~G~~~~~~a~~~e~~~a~~~~r~p~k~~i~~e~~~~~e~~~~ff~~L~~~~~p~~~vPG- 97 (255)
T PF14582_consen 19 ELLERLVEVIPEKGPDAVVFVGDLLKAEARSDEYERAQEEQREPDKSEINEEECYDSEALDKFFRILGELGVPVFVVPG- 97 (255)
T ss_dssp HHHHHHHHHHHHHT-SEEEEES-SS-TCHHHHHHHHHHHTT----THHHHHHHHHHHHHHHHHHHHHHCC-SEEEEE---
T ss_pred HHHHHHHhhccccCCCEEEEeccccccchhhhHHHHHhhhccCcchhhhhhhhhhhHHHHHHHHHHHHhcCCcEEEecC-
Confidence 3456677777778898777666542344444333 23345666543322 22244555677778999999998
Q ss_pred hHHHHHHHHHHH
Q psy14489 109 EADDVIGTLAKQ 120 (284)
Q Consensus 109 EADD~ia~la~~ 120 (284)
--|.-+-..-+.
T Consensus 98 ~~Dap~~~~lr~ 109 (255)
T PF14582_consen 98 NMDAPERFFLRE 109 (255)
T ss_dssp TTS-SHHHHHHH
T ss_pred CCCchHHHHHHH
Confidence 555544444443
No 231
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=20.13 E-value=63 Score=24.28 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=19.9
Q ss_pred chHHHHHHHHHHHhhHhCCCeEEEEcCCCcccccc
Q psy14489 108 VEADDVIGTLAKQAVTKHNLKVIISTNDKDMAQLV 142 (284)
Q Consensus 108 ~EADD~ia~la~~~~~~~~~~v~I~S~DkDl~ql~ 142 (284)
--+|-+++.+|.... -..++|.|+|+..+.
T Consensus 90 ~~~Da~~~a~A~~~~-----~~~v~T~D~~f~~~a 119 (121)
T PF01850_consen 90 DFADALIAATAKENG-----APLVVTFDKDFRKVA 119 (121)
T ss_dssp SHHHHHHHHHHHHHT------EEE-ESSHHHHHHH
T ss_pred ChhHHHHHHHHHHcC-----CEEEEECCcCHHhcc
Confidence 367888888887532 235669999987653
Done!