Query 001045
Match_columns 1176
No_of_seqs 562 out of 4207
Neff 6.5
Searched_HMMs 46136
Date Thu Mar 28 14:17:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001045.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001045hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0967 ATP-dependent DNA liga 100.0 9E-106 2E-110 922.9 44.8 502 646-1176 45-546 (714)
2 PLN03113 DNA ligase 1; Provisi 100.0 4.1E-90 9E-95 845.2 53.3 464 693-1176 109-572 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 1.1E-77 2.5E-82 733.4 46.7 421 713-1176 1-426 (590)
4 PRK09247 ATP-dependent DNA lig 100.0 6.3E-68 1.4E-72 640.2 43.2 396 716-1176 2-402 (539)
5 PRK03180 ligB ATP-dependent DN 100.0 2.9E-68 6.4E-73 638.3 39.1 376 713-1176 1-376 (508)
6 TIGR00574 dnl1 DNA ligase I, A 100.0 8.6E-66 1.9E-70 622.1 40.4 364 772-1176 1-366 (514)
7 KOG0966 ATP-dependent DNA liga 100.0 1.7E-61 3.7E-66 567.9 31.3 413 711-1176 3-432 (881)
8 cd07900 Adenylation_DNA_ligase 100.0 1.8E-45 4E-50 399.0 25.1 211 950-1176 2-212 (219)
9 COG1793 CDC9 ATP-dependent DNA 100.0 1.8E-43 3.9E-48 416.7 24.9 307 782-1176 2-308 (444)
10 PHA02587 30 DNA ligase; Provis 100.0 1.2E-41 2.5E-46 407.5 30.8 328 719-1176 3-357 (488)
11 KOG1361 Predicted hydrolase in 100.0 1.2E-40 2.5E-45 384.7 27.5 330 35-373 86-433 (481)
12 cd07901 Adenylation_DNA_ligase 100.0 1.2E-40 2.7E-45 359.0 24.2 201 954-1176 1-201 (207)
13 cd07903 Adenylation_DNA_ligase 100.0 3.2E-40 6.9E-45 360.4 22.7 208 949-1176 3-216 (225)
14 cd07897 Adenylation_DNA_ligase 100.0 4.7E-40 1E-44 354.3 22.7 197 956-1176 3-199 (207)
15 cd07902 Adenylation_DNA_ligase 100.0 1.1E-39 2.4E-44 352.8 23.0 200 949-1173 5-205 (213)
16 cd08039 Adenylation_DNA_ligase 100.0 9E-39 1.9E-43 349.0 24.1 201 967-1176 10-228 (235)
17 cd07898 Adenylation_DNA_ligase 100.0 1.3E-38 2.9E-43 341.8 23.7 195 958-1176 1-195 (201)
18 cd07905 Adenylation_DNA_ligase 100.0 9.6E-38 2.1E-42 333.2 20.6 187 958-1176 1-187 (194)
19 PF01068 DNA_ligase_A_M: ATP d 100.0 1.3E-37 2.9E-42 333.7 20.7 198 960-1176 1-198 (202)
20 COG1782 Predicted metal-depend 100.0 7.2E-37 1.6E-41 345.5 25.1 309 35-353 191-607 (637)
21 cd07906 Adenylation_DNA_ligase 100.0 1.1E-36 2.4E-41 324.1 20.3 184 958-1176 1-184 (190)
22 PRK08224 ligC ATP-dependent DN 100.0 3.2E-36 7E-41 346.2 21.6 193 951-1176 2-194 (350)
23 TIGR03675 arCOG00543 arCOG0054 100.0 3E-33 6.6E-38 343.1 33.9 307 35-351 185-598 (630)
24 PRK07636 ligB ATP-dependent DN 100.0 2E-34 4.4E-39 322.4 20.2 180 957-1176 2-181 (275)
25 PRK09633 ligD ATP-dependent DN 100.0 2.6E-34 5.6E-39 349.4 20.5 191 958-1176 1-203 (610)
26 PRK09632 ATP-dependent DNA lig 100.0 9.3E-34 2E-38 348.4 21.3 183 952-1176 455-637 (764)
27 COG0595 mRNA degradation ribon 100.0 6.2E-33 1.3E-37 331.6 22.8 311 35-376 44-410 (555)
28 PF04675 DNA_ligase_A_N: DNA l 100.0 1E-32 2.2E-37 290.4 18.0 176 713-891 1-177 (177)
29 TIGR02779 NHEJ_ligase_lig DNA 100.0 1.8E-32 3.8E-37 310.9 20.4 169 977-1176 10-178 (298)
30 PRK05972 ligD ATP-dependent DN 100.0 1.4E-32 3E-37 340.9 21.0 182 956-1176 232-413 (860)
31 TIGR00649 MG423 conserved hypo 100.0 3E-31 6.5E-36 315.5 29.1 314 35-372 11-396 (422)
32 COG1236 YSH1 Predicted exonucl 100.0 3.2E-31 6.9E-36 313.5 26.4 318 35-376 11-410 (427)
33 KOG1136 Predicted cleavage and 100.0 1.5E-29 3.4E-34 273.2 23.1 304 35-352 14-415 (501)
34 cd07896 Adenylation_kDNA_ligas 100.0 3.5E-29 7.5E-34 263.0 16.4 169 958-1176 1-169 (174)
35 PHA00454 ATP-dependent DNA lig 100.0 1.5E-28 3.2E-33 280.7 21.6 190 959-1176 7-216 (315)
36 KOG1137 mRNA cleavage and poly 100.0 2.9E-28 6.4E-33 278.0 22.0 335 34-391 23-452 (668)
37 cd06846 Adenylation_DNA_ligase 100.0 1.3E-27 2.8E-32 252.8 18.3 173 959-1176 1-177 (182)
38 PRK09125 DNA ligase; Provision 99.9 2.6E-27 5.6E-32 265.8 18.4 169 958-1176 28-196 (282)
39 cd07895 Adenylation_mRNA_cappi 99.9 5.6E-24 1.2E-28 231.0 15.6 157 974-1176 36-210 (215)
40 TIGR02776 NHEJ_ligase_prk DNA 99.9 4E-23 8.7E-28 249.4 15.0 139 1006-1176 1-139 (552)
41 KOG4437 ATP-dependent DNA liga 99.8 3.6E-19 7.7E-24 192.7 17.9 333 690-1087 139-482 (482)
42 TIGR02651 RNase_Z ribonuclease 99.8 1.8E-18 3.8E-23 197.0 16.0 179 23-208 3-257 (299)
43 TIGR02649 true_RNase_BN ribonu 99.8 3.2E-18 6.9E-23 195.5 15.3 179 23-208 2-259 (303)
44 PRK11244 phnP carbon-phosphoru 99.7 1.7E-17 3.6E-22 184.4 16.5 177 23-208 4-211 (250)
45 cd07894 Adenylation_RNA_ligase 99.7 1E-16 2.2E-21 184.0 16.7 144 979-1162 48-194 (342)
46 PRK02113 putative hydrolase; P 99.7 7E-16 1.5E-20 171.5 17.5 158 34-208 31-213 (252)
47 TIGR03307 PhnP phosphonate met 99.7 1.5E-15 3.2E-20 167.6 18.6 168 32-208 21-201 (238)
48 PRK05184 pyrroloquinoline quin 99.7 1E-15 2.2E-20 174.7 15.4 144 34-184 35-222 (302)
49 COG1234 ElaC Metal-dependent h 99.6 1.7E-15 3.8E-20 171.7 14.6 210 23-248 5-282 (292)
50 PRK00055 ribonuclease Z; Revie 99.6 2E-15 4.4E-20 168.8 10.7 175 22-208 4-223 (270)
51 TIGR02108 PQQ_syn_pqqB coenzym 99.6 2.7E-14 5.8E-19 162.7 16.8 145 33-184 33-222 (302)
52 PRK02126 ribonuclease Z; Provi 99.5 1.2E-13 2.6E-18 159.3 17.4 174 32-208 10-303 (334)
53 PF12706 Lactamase_B_2: Beta-l 99.5 3.5E-14 7.6E-19 150.5 12.0 136 60-208 29-184 (194)
54 KOG1135 mRNA cleavage and poly 99.5 2.2E-13 4.8E-18 160.9 17.3 194 35-242 12-249 (764)
55 TIGR02650 RNase_Z_T_toga ribon 99.4 2.1E-12 4.6E-17 143.3 14.2 161 41-208 13-234 (277)
56 PRK00685 metal-dependent hydro 99.4 8.8E-12 1.9E-16 136.3 18.0 184 38-248 8-219 (228)
57 PRK04286 hypothetical protein; 99.3 4.2E-11 9.2E-16 136.6 16.6 208 22-249 3-276 (298)
58 KOG2121 Predicted metal-depend 99.2 2.9E-12 6.3E-17 153.7 1.3 179 21-208 444-676 (746)
59 smart00849 Lactamase_B Metallo 99.2 9.1E-11 2E-15 122.3 10.1 120 36-162 4-148 (183)
60 PF07522 DRMBL: DNA repair met 99.1 2.7E-10 5.8E-15 111.1 9.0 90 264-353 4-109 (110)
61 PRK11709 putative L-ascorbate 99.0 3E-09 6.5E-14 123.8 16.4 138 59-208 108-273 (355)
62 PRK11921 metallo-beta-lactamas 99.0 2E-09 4.3E-14 127.8 11.1 113 37-157 32-163 (394)
63 PRK05452 anaerobic nitric oxid 98.9 4.5E-09 9.9E-14 127.3 10.9 114 37-157 34-167 (479)
64 PF02112 PDEase_II: cAMP phosp 98.9 2.9E-08 6.2E-13 114.0 15.2 147 59-208 78-281 (335)
65 COG1423 ATP-dependent DNA liga 98.9 3.4E-08 7.4E-13 110.1 14.9 168 950-1162 62-235 (382)
66 TIGR03413 GSH_gloB hydroxyacyl 98.8 1.3E-08 2.7E-13 113.5 9.1 98 47-160 21-130 (248)
67 PF01331 mRNA_cap_enzyme: mRNA 98.7 1.3E-08 2.9E-13 109.0 6.9 155 975-1171 12-184 (192)
68 COG1235 PhnP Metal-dependent h 98.7 2.8E-08 6E-13 112.1 9.6 157 44-208 38-225 (269)
69 PF13483 Lactamase_B_3: Beta-l 98.7 1.7E-07 3.7E-12 97.5 12.4 118 38-184 7-138 (163)
70 PLN02398 hydroxyacylglutathion 98.6 6.8E-08 1.5E-12 111.1 9.0 100 47-160 99-210 (329)
71 TIGR01209 RNA ligase, Pab1020 98.6 3.5E-07 7.5E-12 105.4 14.6 170 950-1162 53-227 (374)
72 PLN02469 hydroxyacylglutathion 98.6 1.9E-07 4E-12 104.7 10.5 101 47-159 24-138 (258)
73 PLN02962 hydroxyacylglutathion 98.6 1.6E-07 3.4E-12 104.7 8.7 120 30-160 15-154 (251)
74 PRK10241 hydroxyacylglutathion 98.5 2.4E-07 5.1E-12 103.5 8.0 97 46-160 22-131 (251)
75 PF07521 RMMBL: RNA-metabolisi 98.4 2.7E-07 5.8E-12 74.6 3.9 37 315-351 4-40 (43)
76 PF00753 Lactamase_B: Metallo- 98.4 4.5E-07 9.7E-12 94.2 5.7 119 39-162 7-151 (194)
77 COG5212 PDE1 Low-affinity cAMP 98.4 1.5E-06 3.2E-11 94.2 9.6 126 59-187 111-271 (356)
78 KOG1138 Predicted cleavage and 98.2 9E-05 2E-09 86.3 21.2 173 59-248 95-329 (653)
79 COG2220 Predicted Zn-dependent 98.2 1.4E-05 3.1E-10 89.6 12.7 140 37-185 13-184 (258)
80 COG0426 FpaA Uncharacterized f 98.1 8.3E-06 1.8E-10 94.7 9.5 115 36-158 34-167 (388)
81 COG0491 GloB Zn-dependent hydr 98.1 4.3E-06 9.3E-11 91.4 7.0 108 47-161 36-172 (252)
82 TIGR00361 ComEC_Rec2 DNA inter 97.9 8.8E-05 1.9E-09 94.0 14.8 125 40-180 452-605 (662)
83 KOG0813 Glyoxylase [General fu 97.9 2.6E-05 5.5E-10 86.4 7.1 89 59-160 50-143 (265)
84 PRK01109 ATP-dependent DNA lig 97.8 4.4E-05 9.5E-10 95.2 9.5 94 711-814 113-211 (590)
85 COG5226 CEG1 mRNA capping enzy 97.8 1.7E-05 3.8E-10 87.0 3.7 166 977-1174 60-239 (404)
86 cd00114 LIGANc NAD+ dependent 97.7 0.00043 9.4E-09 79.5 13.7 177 959-1162 72-283 (307)
87 PRK11539 ComEC family competen 97.7 0.0003 6.6E-09 90.4 13.7 101 44-161 518-644 (755)
88 COG1237 Metal-dependent hydrol 97.6 0.00024 5.2E-09 78.1 9.9 63 32-94 14-96 (259)
89 PF01653 DNA_ligase_aden: NAD- 97.6 6.6E-05 1.4E-09 86.4 5.9 178 959-1162 77-290 (315)
90 COG2333 ComEC Predicted hydrol 97.6 0.00055 1.2E-08 77.9 12.8 112 44-162 61-196 (293)
91 PRK08097 ligB NAD-dependent DN 97.5 0.0025 5.3E-08 78.4 17.6 180 959-1176 96-300 (562)
92 smart00532 LIGANc Ligase N fam 97.5 0.00072 1.6E-08 81.2 12.7 178 959-1162 74-287 (441)
93 COG2248 Predicted hydrolase (m 97.4 0.0042 9.1E-08 67.7 15.5 124 108-248 134-274 (304)
94 cd09232 Snurportin-1_C C-termi 97.2 0.0023 4.9E-08 68.4 10.7 145 978-1174 20-178 (186)
95 PRK14351 ligA NAD-dependent DN 97.1 0.0044 9.4E-08 78.4 13.5 177 959-1162 104-314 (689)
96 TIGR00575 dnlj DNA ligase, NAD 97.0 0.0026 5.5E-08 80.2 11.0 177 959-1162 67-280 (652)
97 PRK07956 ligA NAD-dependent DN 96.9 0.0078 1.7E-07 76.0 14.1 178 959-1162 78-292 (665)
98 PRK14350 ligA NAD-dependent DN 96.8 0.0098 2.1E-07 74.9 13.7 178 959-1162 78-289 (669)
99 PF09414 RNA_ligase: RNA ligas 96.4 0.0061 1.3E-07 64.9 6.9 110 979-1108 1-129 (186)
100 TIGR02307 RNA_lig_RNL2 RNA lig 96.1 0.036 7.7E-07 63.8 10.9 109 976-1108 22-145 (325)
101 PF14555 UBA_4: UBA-like domai 96.0 0.0059 1.3E-07 49.5 3.0 42 590-634 1-42 (43)
102 KOG0814 Glyoxylase [General fu 95.9 0.016 3.4E-07 59.9 6.3 84 60-157 57-141 (237)
103 COG0272 Lig NAD-dependent DNA 95.7 0.08 1.7E-06 65.7 12.5 155 979-1162 109-292 (667)
104 PF14597 Lactamase_B_5: Metall 94.4 0.037 7.9E-07 58.1 3.6 107 37-160 22-140 (199)
105 PHA02142 putative RNA ligase 94.3 0.51 1.1E-05 55.3 13.2 152 968-1161 157-343 (366)
106 PRK09247 ATP-dependent DNA lig 93.9 0.2 4.4E-06 62.3 9.6 89 828-940 2-91 (539)
107 PF04675 DNA_ligase_A_N: DNA l 93.6 0.22 4.8E-06 52.6 8.0 91 827-941 3-100 (177)
108 COG2015 Alkyl sulfatase and re 93.6 0.2 4.4E-06 59.2 8.1 59 37-95 124-206 (655)
109 PRK03180 ligB ATP-dependent DN 93.1 0.39 8.5E-06 59.3 10.1 92 712-813 72-166 (508)
110 KOG3798 Predicted Zn-dependent 92.4 0.7 1.5E-05 50.8 9.5 159 59-232 131-307 (343)
111 PLN03113 DNA ligase 1; Provisi 90.3 1.4 2.9E-05 56.7 10.7 93 823-939 127-229 (744)
112 TIGR00574 dnl1 DNA ligase I, A 88.0 2.1 4.5E-05 53.2 9.8 92 712-813 54-148 (514)
113 KOG3132 m3G-cap-specific nucle 85.0 2.9 6.3E-05 45.7 7.6 145 978-1171 115-269 (325)
114 KOG2386 mRNA capping enzyme, g 83.2 0.77 1.7E-05 54.2 2.6 103 976-1109 282-385 (393)
115 cd00194 UBA Ubiquitin Associat 82.7 1.4 2.9E-05 34.4 3.1 36 590-629 2-37 (38)
116 KOG4736 Uncharacterized conser 82.1 4.5 9.8E-05 45.9 7.9 106 45-162 103-216 (302)
117 TIGR02306 RNA_lig_DRB0094 RNA 81.9 19 0.00042 42.3 13.4 105 978-1108 158-277 (341)
118 PF02845 CUE: CUE domain; Int 80.0 2.6 5.7E-05 33.8 3.9 39 455-494 2-40 (42)
119 smart00165 UBA Ubiquitin assoc 78.4 2.2 4.8E-05 33.1 2.9 35 590-628 2-36 (37)
120 PF00627 UBA: UBA/TS-N domain; 73.3 4.5 9.8E-05 31.5 3.4 35 589-627 2-36 (37)
121 PF13691 Lactamase_B_4: tRNase 71.3 7 0.00015 34.6 4.5 39 38-76 12-63 (63)
122 PF00627 UBA: UBA/TS-N domain; 70.3 6.2 0.00013 30.8 3.6 34 454-490 2-35 (37)
123 KOG0967 ATP-dependent DNA liga 67.5 35 0.00075 42.7 10.7 92 823-938 97-198 (714)
124 PF14555 UBA_4: UBA-like domai 66.9 8 0.00017 31.3 3.7 37 456-494 2-38 (43)
125 PF13483 Lactamase_B_3: Beta-l 60.8 11 0.00023 39.2 4.4 34 317-350 128-163 (163)
126 smart00546 CUE Domain that may 56.3 16 0.00035 29.4 3.7 40 454-494 2-41 (43)
127 cd00194 UBA Ubiquitin Associat 53.0 20 0.00043 27.8 3.7 35 456-493 3-37 (38)
128 smart00165 UBA Ubiquitin assoc 51.9 21 0.00046 27.5 3.6 34 456-492 3-36 (37)
129 KOG1135 mRNA cleavage and poly 48.0 26 0.00056 44.1 5.2 65 315-391 534-598 (764)
130 PF12706 Lactamase_B_2: Beta-l 42.2 21 0.00045 37.5 3.0 25 326-350 169-193 (194)
131 COG4566 TtrR Response regulato 38.7 84 0.0018 34.0 6.7 85 801-886 84-175 (202)
132 PF02845 CUE: CUE domain; Int 31.9 41 0.0009 26.9 2.5 40 589-630 1-40 (42)
133 KOG1137 mRNA cleavage and poly 28.9 23 0.00049 43.5 0.7 97 59-162 206-323 (668)
134 PRK00685 metal-dependent hydro 27.2 75 0.0016 34.6 4.4 34 319-352 159-194 (228)
135 KOG3592 Microtubule-associated 24.0 36 0.00079 42.9 1.2 37 44-80 55-101 (934)
136 smart00546 CUE Domain that may 23.7 99 0.0021 24.8 3.3 39 590-630 3-41 (43)
137 PRK11709 putative L-ascorbate 23.2 97 0.0021 36.9 4.5 25 327-351 259-283 (355)
138 PF00701 DHDPS: Dihydrodipicol 21.8 2.5E+02 0.0053 32.1 7.4 67 1084-1161 37-105 (289)
139 cd00408 DHDPS-like Dihydrodipi 21.7 2.1E+02 0.0046 32.4 6.9 66 1085-1161 34-101 (281)
140 cd00950 DHDPS Dihydrodipicolin 21.3 2E+02 0.0044 32.7 6.6 67 1084-1161 36-104 (284)
141 PRK00055 ribonuclease Z; Revie 20.8 99 0.0021 34.4 3.9 29 325-353 207-235 (270)
142 PRK03170 dihydrodipicolinate s 20.1 2.2E+02 0.0047 32.6 6.5 65 1086-1161 39-105 (292)
143 TIGR02313 HpaI-NOT-DapA 2,4-di 20.0 2.3E+02 0.005 32.7 6.7 65 1086-1161 38-104 (294)
No 1
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=9.3e-106 Score=922.90 Aligned_cols=502 Identities=45% Similarity=0.793 Sum_probs=472.7
Q ss_pred ccCccccCccccccchhhhhhhhhhhccccccccccccccccCcccccCCCCCCCcccccccCCCCCcchHHHHHHHHHH
Q 001045 646 SKSSVQSDSCNKDCSSALEKIVSEELQHITDMSVQRPSKELMDPTLVSLPPEKYDPIEHACWSSGQPAPYIHLARTFDLV 725 (1176)
Q Consensus 646 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~F~~l~~~~~~i 725 (1176)
++...+...|...|++.+. .+++......+......+|..|+|..+|||+.|+.+||++||++|+.|
T Consensus 45 ~~~~~~v~~~~~~~~~~s~-------------~~s~~~~~~~~~~~~~~~~~~y~~~~~a~wk~~~~~py~~~a~tF~kI 111 (714)
T KOG0967|consen 45 TDTFEVVKDSTLGSSDSSI-------------TLSSNADSKSDSGLLKKSPEDYLPSENACWKDGSKVPYLELARTFEKI 111 (714)
T ss_pred ccceeeccccccCcccccc-------------cccccccccccccccCCCccccchhhhhhccccCcCcHHHHHHHHHHH
Confidence 4556666777777766553 556666666666667788999999999999999999999999999999
Q ss_pred HhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHhCCChHHHHHHHHhcCCh
Q 001045 726 EAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKIRDMYNRLGDL 805 (1176)
Q Consensus 726 ~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~g~~~~~i~~~~~~~GDl 805 (1176)
++|++|++++++|+|||+.+++++|+|++|+|||++|+|+|+|++.|||||+++|+|||++++|.+.+.++..|++.|||
T Consensus 112 e~~s~Rl~i~~il~n~f~~v~~~sP~dLlp~vYLsiN~l~P~yeGlELGvGes~l~KAi~EatGrt~~~vk~~~~~~GDL 191 (714)
T KOG0967|consen 112 EETSGRLEIIDILSNFLRSVLATSPDDLLPTVYLSINKLAPDYEGLELGVGESLLMKAIAEATGRTLSHVKNQYNKLGDL 191 (714)
T ss_pred HhhccceeHHHHHHHHHHHHHhcCchhhhhHHHHhhhccCccccCccccccHHHHHHHHHHHhCccHHHHHHHHHhcCcH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHHHhhccccCcchhhH
Q 001045 806 GDVAQECRQTQALLAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTI 885 (1176)
Q Consensus 806 G~va~~~~~~q~~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiIlk~LRiG~~~~tv 885 (1176)
|+||+.++.+|++|++|+||||.+||..|++||..+|++|+.+|..+++.||.+|++.|+|||+|.|.++||||++++||
T Consensus 192 G~VA~~sR~sQ~~m~~P~pLtV~~VF~~Lr~IAk~sG~~S~~kK~~lik~Llvac~~~E~kyLiRsL~gkLRiGlaeqTv 271 (714)
T KOG0967|consen 192 GLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVACRGIEAKYLIRSLEGKLRIGLAEQTV 271 (714)
T ss_pred HHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhcccccHHHHHHHHHhhhhhhhhHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhccccCCCccccCcCCCCCccCCCCcc
Q 001045 886 LPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMNKGIGFSASTLSMVPGVPIKPMLAKI 965 (1176)
Q Consensus 886 l~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~~g~~~~~~~~~l~~g~Pi~PMLA~~ 965 (1176)
|.||++|+.++......+..+...+++.++.....++++|+++|||+.+++.|+++|++.+...|.++||+|++||||+|
T Consensus 272 L~AL~~A~~~~~~~~~~~~~~~d~~kd~le~~~~ivk~afcq~P~ydiivp~lL~~Gie~L~e~c~l~PGIPlKPMLAkp 351 (714)
T KOG0967|consen 272 LAALGQAFVLNDNNDEEKSKKPDSLKDPLEEAAQIVKQAFCQLPDYDIIVPALLEHGIENLPETCKLTPGIPLKPMLAKP 351 (714)
T ss_pred HHHHHHHHhccCchhhhccCCcchhhhhhHHHHHHHHHHHhcCCchhhhHHHHHHhhhhhccccCccCCCCCCcchhcCc
Confidence 99999999988654334555667789999999999999999999999999999999999999999999999999999999
Q ss_pred cCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEec
Q 001045 966 TNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDR 1045 (1176)
Q Consensus 966 ~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~ 1045 (1176)
++++.+++++|++..|+|||||||||+|||+..+|.|.|||||+++.|.+||||...+..+.++.+.+||||||+||||+
T Consensus 352 TK~i~evl~rf~~~~FTCEyKYDGeRAQIH~~edG~v~IfSRN~E~~T~kYPDi~~~~~~~~kp~v~sFIlD~EvVA~Dr 431 (714)
T KOG0967|consen 352 TKGIQEVLERFQDKAFTCEYKYDGERAQIHKLEDGTVEIFSRNSENNTGKYPDIIEVISKLKKPSVKSFILDCEVVAWDR 431 (714)
T ss_pred chhHHHHHHHhhCceeEEEeecCceeeeeEEccCCcEEEEecccccccccCccHHHHHHHhhCCccceeEEeeeEEEEec
Confidence 99999999999999999999999999999999999999999999999999999999999998899999999999999999
Q ss_pred CCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEE
Q 001045 1046 KNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTV 1125 (1176)
Q Consensus 1046 ~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v 1125 (1176)
+.| +++|||.|++|.|+. +...++++.||+|+|||||+||++|+++||++||++|.+.| .+.+|+|+++....
T Consensus 432 ~~~-~IlpFQvLSTRkRk~----v~v~dikV~Vcvf~FDily~ng~~Li~~pL~eRR~~l~e~f-~e~~g~f~fat~~~- 504 (714)
T KOG0967|consen 432 EKG-KILPFQVLSTRKRKN----VDVNDIKVKVCVFVFDILYLNGESLIQEPLRERRELLHESF-KEIPGEFQFATSLD- 504 (714)
T ss_pred cCC-ccCchhhhhhhhccc----cchhhceEEEEEEEEeeeeeCChhhhhhhHHHHHHHHHhhc-ccCCCceeEeeeec-
Confidence 986 999999999999884 44678899999999999999999999999999999999999 78899999999876
Q ss_pred cCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1126 EGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1126 ~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
+++.++|++||+++++.+|||+|||.+|.++.|+|.|||++|
T Consensus 505 ---------tn~~~eiq~Fl~~sv~~~cEGlMvKtLd~~atYep~kRs~~W 546 (714)
T KOG0967|consen 505 ---------TNDIDEIQEFLEESVQNSCEGLMVKTLDTNATYEPSKRSNNW 546 (714)
T ss_pred ---------cCCHHHHHHHHHHhhccCcceeEEEeeccccccCchhhccch
Confidence 368999999999999999999999999999999999999999
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=4.1e-90 Score=845.24 Aligned_cols=464 Identities=40% Similarity=0.749 Sum_probs=425.1
Q ss_pred cCCCCCCCcccccccCCCCCcchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccc
Q 001045 693 SLPPEKYDPIEHACWSSGQPAPYIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIE 772 (1176)
Q Consensus 693 ~~~~~~~~~~~~~~~~~g~~~~F~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~e 772 (1176)
...+..|+|..+++|..|.+|||.+||++|++|+.|++|++|+++|+|||+.++..+|+|+.+++||++|+|+|+|++.|
T Consensus 109 ~~~~~~~~~~~~~~w~~~~~~~f~~l~~~~~~Ie~tt~rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~e 188 (744)
T PLN03113 109 KKKPNDFDPEKVAYWEKGERVPFLFVALAFDLISNETGRIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVE 188 (744)
T ss_pred cCCccccCcchhhcccCCCCccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcc
Confidence 34577899999999999999999999999999999999999999999999999888999999999999999999999999
Q ss_pred cccchhhHHHHHHHHhCCChHHHHHHHHhcCChHHHHHHHHhhccccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHH
Q 001045 773 LNIGGSLVTSAIEEACGTNRSKIRDMYNRLGDLGDVAQECRQTQALLAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSL 852 (1176)
Q Consensus 773 lgige~~L~kal~~~~g~~~~~i~~~~~~~GDlG~va~~~~~~q~~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~i 852 (1176)
||||+++|+|+|++++|++.+.+++.|++.||||+||+.++++|.+++.+++|||.+||+.|.+||..+|++|+.+|..+
T Consensus 189 lgige~~L~kai~e~~g~~~~~ik~~y~~~GDlG~vA~~~~~~q~~~~~~~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~ 268 (744)
T PLN03113 189 LGIGEATIIKALAEAFGRTEKQVKKQYKELGDLGLVAKASRSSQSMMRKPEPLTVVKVFNTFQQIAKESGKDSQEKKKNR 268 (744)
T ss_pred cCcCHHHHHHHHHHHHCcCHHHHHHHHHHhCCHHHHHHhhhcccccccCCCCCCHHHHHHHHHHHHhhhCccCHHHHHHH
Confidence 99999999999999999999999999999999999999999888887778999999999999999999999999999999
Q ss_pred HHHHHhhcchhhHHHHHHHHhhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChH
Q 001045 853 IVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLD 932 (1176)
Q Consensus 853 l~~Ll~~~~~~E~k~LvRiIlk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~ 932 (1176)
|..||..|++.|+|||+|+|+++||||++++||+.|||+||..+.... .........|++....++++|+.+|||+
T Consensus 269 i~~Ll~~~~~~E~k~liR~l~g~LRIGv~e~tVl~ALa~a~~~~~~~~----~~~~~~~~~l~~~~~~v~~a~~~~p~~~ 344 (744)
T PLN03113 269 IKALLVAATDCEPLYLIRLLQTKLRIGLAGQTLLAALGQAAVYNEEHS----TPPPNIQSPLEEAAKIVKQVYSVLPVYD 344 (744)
T ss_pred HHHHHHhCCHHHHHHHHHHHhccccccccHHHHHHHHHHHhccccccc----ccccccchhhHHHHHHHHHHhccCCCHH
Confidence 999999999999999999999999999999999999999997654211 1112234456777788999999999999
Q ss_pred HHHHHHhccccCCCccccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccC
Q 001045 933 LLIPSLMNKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDET 1012 (1176)
Q Consensus 933 ~v~~~L~~~g~~~~~~~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~ 1012 (1176)
.|++.|+..|+..+...|.++||+||+||||++++++++++++|++.+|+||+||||+|||||+..+|.|++||||++|+
T Consensus 345 ~i~~~ll~~g~~~l~~~~~i~~g~Pi~PMLA~~~~~~~eil~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~ 424 (744)
T PLN03113 345 KIVPALLSGGVWNLPKTCSFTPGVPVGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERN 424 (744)
T ss_pred HHHHHHHhCCcccccccccccCCCCCCCccCCCCCChHHHhhccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcc
Confidence 99999999998777788999999999999999999999999999999999999999999999985578999999999999
Q ss_pred CCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcc
Q 001045 1013 TSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQ 1092 (1176)
Q Consensus 1013 T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~ 1092 (1176)
|.+|||++..+..++.+.+.+||||||+|+||+.++ +++|||.|++|.|+.. .....++|+||++|||||+||++
T Consensus 425 T~~fPel~~~~~~~~~~~~~~~ILDGEiVa~d~~~~-~~lpFq~Lq~R~rk~~----~~~~~~~pv~~~aFDlLylnG~~ 499 (744)
T PLN03113 425 TGKYPDVVVAISRLKKPSVKSFILDCELVAYDREKK-KILPFQILSTRARKNV----VMSDIKVDVCIFAFDMLYLNGQP 499 (744)
T ss_pred cccchhHHHHHHHhccccCCCEEEEeEEEEEECCCC-CcCCHHHHHhhhcccc----chhccccceEEEEEeccccCccC
Confidence 999999999998876566789999999999998764 8999999999977532 23345689999999999999999
Q ss_pred cccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCC
Q 001045 1093 LLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKR 1172 (1176)
Q Consensus 1093 Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkR 1172 (1176)
|+++||.+||++|+++| .+.++++++++.... ++.++++++|+++++.|+||||+|+++.+|+|+||+|
T Consensus 500 L~~~PL~eRR~~L~~~~-~~~~~~i~~~~~~~~----------~~~ee~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkR 568 (744)
T PLN03113 500 LIQEQLKIRREHLYESF-EEDPGFFQFATAITS----------NDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKR 568 (744)
T ss_pred hhcCCHHHHHHHHHHHh-ccCCCcEEEeeeecc----------CCHHHHHHHHHHHHHcCCceEEEeccCCCCCccCCCC
Confidence 99999999999999999 566788999988753 5789999999999999999999999866699999999
Q ss_pred CCCC
Q 001045 1173 SDSW 1176 (1176)
Q Consensus 1173 s~~W 1176 (1176)
+.+|
T Consensus 569 s~~W 572 (744)
T PLN03113 569 SNNW 572 (744)
T ss_pred CCCe
Confidence 9999
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=1.1e-77 Score=733.38 Aligned_cols=421 Identities=31% Similarity=0.514 Sum_probs=380.8
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHhCCCh
Q 001045 713 APYIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNR 792 (1176)
Q Consensus 713 ~~F~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~g~~~ 792 (1176)
|||..||.+|++|++|++|++|+++|+|||+.+ +|+++.+++||++|+++|+|++++||||+++|.++|++++|++.
T Consensus 1 m~f~~l~~~~~~i~~t~~r~~k~~~l~~~~~~~---~~~~~~~~~~l~~~~~~p~~~~~~~gi~~~~l~k~i~~~~g~~~ 77 (590)
T PRK01109 1 MEFSELAEYFERLEKTTSRTQLTKLLADLLKKT---PPEIIDKVVYLIQGKLWPDWLGLELGVGEKLLIKAISMATGISE 77 (590)
T ss_pred CcHHHHHHHHHHHHhhhchHHHHHHHHHHHHhC---CHHhhhhhHHHHhCCcCccccCcccCcCHHHHHHHHHHHHCcCH
Confidence 689999999999999999999999999999996 78999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhcc--c---cCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHH
Q 001045 793 SKIRDMYNRLGDLGDVAQECRQTQA--L---LAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKF 867 (1176)
Q Consensus 793 ~~i~~~~~~~GDlG~va~~~~~~q~--~---l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~ 867 (1176)
+.++++|++.||+|++|+.+++.+. + +..+++||+.+|++.|++||+.+|.+|+..|..+|..||.+|++.|++|
T Consensus 78 ~~~~~~~~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~~~~E~k~ 157 (590)
T PRK01109 78 KEVENLYKKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDASPLEAKY 157 (590)
T ss_pred HHHHHHHHhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhCCHHHHHH
Confidence 9999999999999999999987543 2 2457889999999999999999999999999999999999999999999
Q ss_pred HHHHHhhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhccccCCCc
Q 001045 868 LVRTLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMNKGIGFSA 947 (1176)
Q Consensus 868 LvRiIlk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~~g~~~~~ 947 (1176)
|+|+|+++||||+++++|+.|||+||+... .++.++++|+.+||++.|+..+..+|++. .
T Consensus 158 iirli~g~lriGv~e~~il~ALa~A~~~~~-------------------~~~~ve~~y~~~~Dlg~va~~l~~~g~~~-~ 217 (590)
T PRK01109 158 IARFVEGRLRLGVGDATILDALAIAFGGAV-------------------ARELVERAYNLRADLGYIAKILAEGGIEA-L 217 (590)
T ss_pred HHHHHhhhhhcCccHHHHHHHHHHHHhccc-------------------chHHHHHHHHhCCCHHHHHHHHHhcchhh-h
Confidence 999999999999999999999999986211 24789999999999999999999888743 3
Q ss_pred cccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhc
Q 001045 948 STLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFC 1027 (1176)
Q Consensus 948 ~~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~ 1027 (1176)
..+.++||+|++||||+++++++++++++++ .|++|+||||+|||+|++ ++.|++||||++|+|..||+|++.+...+
T Consensus 218 ~~~~i~~~~Pv~PmLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~-~~~v~l~SR~~~d~T~~~pel~~~~~~~~ 295 (590)
T PRK01109 218 KKVKPQVGIPIRPMLAERLSSPKEILKKMGG-EALVEYKYDGERAQIHKK-GDKVKIFSRRLENITHQYPDVVEYAKEAI 295 (590)
T ss_pred ccCcccCCCCCCcccCCccCCHHHHHHHcCC-CeEEEecCCceEEEEEEc-CCEEEEEeCCchhhccccchHHHHHHHhc
Confidence 6799999999999999999999999999864 689999999999999994 89999999999999999999999988754
Q ss_pred CCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHH
Q 001045 1028 KPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKD 1107 (1176)
Q Consensus 1028 ~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~ 1107 (1176)
...+||||||||+||+++| +++|||.|++|.|+. .+......+|+||++|||||+||++|+++||.+||++|++
T Consensus 296 --~~~~~ILDGElv~~d~~~g-~~~~F~~l~~R~r~~---~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~ 369 (590)
T PRK01109 296 --KAEEAIVEGEIVAVDPETG-EMRPFQELMHRKRKY---DIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEE 369 (590)
T ss_pred --CccceEEeeeEEEEECCCC-cccChHHHhhccccc---chhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHH
Confidence 3579999999999997665 789999999994432 1222335678999999999999999999999999999999
Q ss_pred hhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1108 LFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1108 ~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
++ .+. +.+.++++..+ ++.++++++|++++++|+||||+|+++.+|+|+||+|+.+|
T Consensus 370 ~~-~~~-~~~~~~~~~~~----------~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~W 426 (590)
T PRK01109 370 IV-KEN-DKVKLAERIIT----------DDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLW 426 (590)
T ss_pred hc-CCC-CceEEeeeEec----------CCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccH
Confidence 99 443 45888887753 57899999999999999999999999434999999999999
No 4
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=6.3e-68 Score=640.19 Aligned_cols=396 Identities=20% Similarity=0.262 Sum_probs=344.4
Q ss_pred HHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHhCCChHHH
Q 001045 716 IHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKI 795 (1176)
Q Consensus 716 ~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~g~~~~~i 795 (1176)
..||++|++|++|++|++|+++|++||+++ +|+|+.+++||++|.+++ +||++++|.+++++++|++++.+
T Consensus 2 ~~fa~~~~~i~~t~~~~ek~~~l~~~~~~~---~~~d~~~~~~ll~g~~~~------~~i~~~~l~k~~~~~~g~~~~~~ 72 (539)
T PRK09247 2 KAFAELLDRLDLTTSTNAKLALLADYFRSA---PDPDRAWALALLTGGLPR------RLVKTRLLRELAAERADLPPWLF 72 (539)
T ss_pred hHHHHHHHHHHhccCHHHHHHHHHHHHHhC---CHHHHHHHHHHhcCCccc------CCCCHHHHHHHHHHHHCcCHHHH
Confidence 579999999999999999999999999997 788999999999999984 79999999999999999999999
Q ss_pred HHHHHhcCChHHHHHHHHhhccc--cCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHHHh
Q 001045 796 RDMYNRLGDLGDVAQECRQTQAL--LAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLV 873 (1176)
Q Consensus 796 ~~~~~~~GDlG~va~~~~~~q~~--l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiIl 873 (1176)
++.|++.||+|++|+.+++.+.. .+.+.++||.+|+..|.+|+.. .|...|.+||.+|++.|++||+|+|+
T Consensus 73 ~~~~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~-------~k~~~l~~ll~~~~~~e~~~i~rli~ 145 (539)
T PRK09247 73 EESYDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE-------ELRAALADLWDRLDEDGRFALNKLIT 145 (539)
T ss_pred HHHHHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH-------HHHHHHHHHHHhCCHHHHHHHHHHhh
Confidence 99999999999999999654322 2234679999999999999753 36788999999999999999999999
Q ss_pred hccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhh--CCChHHHHHHHhccccCCCccccC
Q 001045 874 RNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNI--LPSLDLLIPSLMNKGIGFSASTLS 951 (1176)
Q Consensus 874 k~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~--~pdl~~v~~~L~~~g~~~~~~~~~ 951 (1176)
++||||+++++|+.|||+||..+. +.+.++|+. .|+++.+...+.. |. ..+.
T Consensus 146 g~lRiG~~~~~v~~ala~a~~~~~---------------------~~v~~~~~~~~~~~~~~~~~~~~~-~~----~~~~ 199 (539)
T PRK09247 146 GGFRVGVSARLVTRALAELGGVDE---------------------ARIAQRLMGLWPPYADLFAWLIGP-EE----DPLP 199 (539)
T ss_pred CccccchhHHHHHHHHHHHhCCCH---------------------HHHHHHHhCCCCCcHHHHHHHhhC-Cc----cccC
Confidence 999999999999999999996542 577888988 7888887755543 44 5788
Q ss_pred cCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCC
Q 001045 952 MVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAA 1031 (1176)
Q Consensus 952 l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~ 1031 (1176)
++||+|++||||+++++..+. .+...+|++|+||||+|||+|+ .++.|++|||||+++|..||++.+.+... +
T Consensus 200 ~~~~~P~~pMLA~~~~~~~~~--~~~~~~~~~E~K~DG~R~qih~-~~~~v~lfSR~g~d~t~~fPei~~~~~~l----~ 272 (539)
T PRK09247 200 ADPGQPYPFFLAHPLEDEDLT--LGDPADWQAEWKWDGIRVQLVR-RGGEVRLWSRGEELITERFPELAEAAEAL----P 272 (539)
T ss_pred CCCCCcCCCeeCCcCCCchhh--hcCCCcEEEEEeEcceEEEEEE-eCCEEEEEeCCCccchhhhHHHHHHHHhC----C
Confidence 999999999999999887653 3344689999999999999999 58899999999999999999999987652 3
Q ss_pred CCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcc
Q 001045 1032 GTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYD 1111 (1176)
Q Consensus 1032 ~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~ 1111 (1176)
.+||||||+|+||++++ .++|||.|++|.+++... .......|+||++|||||+||++|+++||.+||++|++++ .
T Consensus 273 ~~~ILDGElv~~~~~~~-~~~~F~~l~~R~~rk~~~--~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~-~ 348 (539)
T PRK09247 273 DGTVLDGELLVWRPEDG-RPQPFADLQQRIGRKTVG--KKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALI-A 348 (539)
T ss_pred CCEEEEeEEEEEECCCC-CcCCHHHHHHHhcccccc--hhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHh-c
Confidence 68999999999997664 789999999995432221 1122357899999999999999999999999999999999 4
Q ss_pred cC-CCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1112 EK-MGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1112 ~~-~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
+. ++++.+++...+ .+.++++++|++++++|+||||+|+++ |+|+||+|+..|
T Consensus 349 ~~~~~~i~~~~~~~~----------~~~~e~~~~~~~a~~~g~EGlm~K~~~--s~Y~~Grr~~~W 402 (539)
T PRK09247 349 RLPDPRLDLSPLVPF----------SDWDELAALRAAARERGVEGLMLKRRD--SPYLVGRKKGPW 402 (539)
T ss_pred ccCCCeEEecCceec----------CCHHHHHHHHHHHHHCCCceEEEecCC--CCcCCCCCcchh
Confidence 43 458888887763 578999999999999999999999998 999999999988
No 5
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.9e-68 Score=638.26 Aligned_cols=376 Identities=27% Similarity=0.433 Sum_probs=332.0
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHhCCCh
Q 001045 713 APYIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNR 792 (1176)
Q Consensus 713 ~~F~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~g~~~ 792 (1176)
|+|..||++|++|+.|++|++|+++|++||+.+ +|+|+.+++||++|+++ ++++|++++.+.++++.
T Consensus 1 m~f~~~~~~~~~l~~tt~r~~k~~~l~~~~~~~---~~~d~~~~~~~~~g~~~----~~~l~~~~~~v~~~~~~------ 67 (508)
T PRK03180 1 MLLADVAATSAAVAATSSRLAKVARLAELLRRA---DPAEVAIVVAWLSGELR----QRRIGVGWATLRSLPAP------ 67 (508)
T ss_pred CcHHHHHHHHHHHHhccCHHHHHHHHHHHHHhC---CHHHHHHHHHHhcCCCC----CCccCccHHHHHhcccc------
Confidence 689999999999999999999999999999997 78999999999999997 46899998777776432
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhccccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHHH
Q 001045 793 SKIRDMYNRLGDLGDVAQECRQTQALLAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTL 872 (1176)
Q Consensus 793 ~~i~~~~~~~GDlG~va~~~~~~q~~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiI 872 (1176)
..+++|||.+||+.|++||..+|.+|+..|..+|..||.+|++.|+|||+|+|
T Consensus 68 ---------------------------~~~~~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~~~~E~~~l~r~i 120 (508)
T PRK03180 68 ---------------------------AAEPTLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAATEDEQRFLRRLL 120 (508)
T ss_pred ---------------------------cCCCCCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 11367999999999999999999999999999999999999999999999999
Q ss_pred hhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhccccCCCccccCc
Q 001045 873 VRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMNKGIGFSASTLSM 952 (1176)
Q Consensus 873 lk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~~g~~~~~~~~~l 952 (1176)
+++||||+++++|+.|||+||..+. ++++++|+.|+|++.+++.++..|... ...|.+
T Consensus 121 ~~~lRiGv~~~~v~~Ala~a~~~~~---------------------~~v~~a~~~~~dl~~v~~~~l~~~~~~-~~~~~i 178 (508)
T PRK03180 121 TGELRQGALDGVMADAVARAAGVPA---------------------AAVRRAAMLAGDLPAVAAAALTGGAAA-LARFRL 178 (508)
T ss_pred hCCCcccccHHHHHHHHHHHhCCCH---------------------HHHHHHHHHcCCHHHHHHHHHhcCccc-cccCCC
Confidence 9999999999999999999996543 689999999999999999988877643 478999
Q ss_pred CCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCC
Q 001045 953 VPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAG 1032 (1176)
Q Consensus 953 ~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~ 1032 (1176)
+||+|++||||++++++++++++++ .+|++|+||||+|||+|+ .+++|++||||++++|..||++.+.+... ..+
T Consensus 179 ~~~~P~~PMLA~~~~~~~~~~~~~~-~~~~~E~K~DG~R~qih~-~~~~v~l~SR~~~d~T~~fPei~~~~~~~---~~~ 253 (508)
T PRK03180 179 EVGRPVRPMLAQTATSVAEALARLG-GPAAVEAKLDGARVQVHR-DGDDVRVYTRTLDDITARLPEVVEAVRAL---PVR 253 (508)
T ss_pred CCCCCCCCccCCcCCChHHHHHHhC-CCeEEEEEEceeEEEEEE-ECCEEEEEeCCCCcchhhhHHHHHHHHhC---CCc
Confidence 9999999999999999988888885 589999999999999999 58899999999999999999999887763 357
Q ss_pred CeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhccc
Q 001045 1033 TFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDE 1112 (1176)
Q Consensus 1033 ~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~ 1112 (1176)
+||||||||+||+ +| +++|||.+++|.++... +......+|++|++|||||+||++|+++||.+||++|++++ .+
T Consensus 254 ~~ILDGElv~~d~-~g-~~~~F~~l~~R~~~k~~--~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~-~~ 328 (508)
T PRK03180 254 SLVLDGEAIALRP-DG-RPRPFQVTASRFGRRVD--VAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALV-PA 328 (508)
T ss_pred ceeecceEEEECC-CC-CcCCHHHHHHHhccccc--hhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhh-cc
Confidence 9999999999997 34 78999999999654322 22233468999999999999999999999999999999999 32
Q ss_pred CCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1113 KMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1113 ~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
. ..++... ..+.++++++|++++++|+||||+|+++ |+|+||+|+.+|
T Consensus 329 ~----~~~~~~~----------~~~~~~~~~~~~~a~~~g~EGlm~K~~d--s~Y~~GrR~~~W 376 (508)
T PRK03180 329 A----HRVPRLV----------TADPAAAAAFLAAALAAGHEGVMVKSLD--APYAAGRRGAGW 376 (508)
T ss_pred c----cccccee----------cCCHHHHHHHHHHHHHcCCceEEEeCCC--CCcCCCCCCCCc
Confidence 1 1122222 3568999999999999999999999998 999999999998
No 6
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=8.6e-66 Score=622.11 Aligned_cols=364 Identities=35% Similarity=0.571 Sum_probs=330.7
Q ss_pred ccccchhhHHHHHHHHhCCChHHHHHHHHhcCChHHHHHHHHhhcc-ccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHH
Q 001045 772 ELNIGGSLVTSAIEEACGTNRSKIRDMYNRLGDLGDVAQECRQTQA-LLAPPPPLLIKDVYSMLCKISVQTGSGSTARKK 850 (1176)
Q Consensus 772 elgige~~L~kal~~~~g~~~~~i~~~~~~~GDlG~va~~~~~~q~-~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~ 850 (1176)
+||||+++|.|++++++|++.+.+++.|.+.||+|++++.+++.+. ....+.+|||.+|++.|++||+.+|.+|+.+|.
T Consensus 1 ~~gi~~~~l~k~~~~~~~~~~~~~~~~~~~~gd~g~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~ia~~~g~~s~~~k~ 80 (514)
T TIGR00574 1 EYGIGEKLLIKAISKALGIPKDEIEEKVKEDGDLGEVIEGLFSKQKQTSFFSAPLTVKEVYETLKNIAETSGEGSQDKKI 80 (514)
T ss_pred CCCCcHHHHHHHHHHHHCcCHHHHHHHHHhcCCHHHHHHHHhccccccccCCCCcCHHHHHHHHHHHHHhhCCCcHHHHH
Confidence 6999999999999999999999999999999999999999987655 445678999999999999999999999999999
Q ss_pred HHHHHHHhhcchhhHHHHHHHHhhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCC
Q 001045 851 SLIVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPS 930 (1176)
Q Consensus 851 ~il~~Ll~~~~~~E~k~LvRiIlk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pd 930 (1176)
.+|..||++|++.|+|||+|+|+++||||+++++|+.||+.++..+ |+++.++|+.|||
T Consensus 81 ~~l~~ll~~~~~~e~k~l~r~i~~~lriG~~~~~il~al~~~~~~~---------------------~~~~~~~~~~~~d 139 (514)
T TIGR00574 81 KLLKSLLKRASPLEAKYLIRTILGDLRIGIAEKTILDALAKAFLLS---------------------HPDVERAFNLTND 139 (514)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHhhhcccCccHHHHHHHHHHHhccc---------------------hHHHHHHHHhCCC
Confidence 9999999999999999999999999999999999999999988643 4789999999999
Q ss_pred hHHHHHHHhccccCCCccccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCc
Q 001045 931 LDLLIPSLMNKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGD 1010 (1176)
Q Consensus 931 l~~v~~~L~~~g~~~~~~~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~ 1010 (1176)
++.||+.|.++|.+.....+.++||+|++||||+++++++++++++++ +|++|+||||+|||+|+ .+++|++|||||+
T Consensus 140 l~~v~~~l~~~~~~~~~~~~~i~~~~p~~PMLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~-~~~~v~l~SR~g~ 217 (514)
T TIGR00574 140 LGKVAKILLEPGLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-KFYVEYKYDGERVQIHK-DGDKFKIFSRRLE 217 (514)
T ss_pred HHHHHHHHHhcChhhhcccceeecCCcCccccCCccCCHHHHHHHhCC-ceEEEEeecceEEEEEE-cCCEEEEEcCCCc
Confidence 999999999988866656789999999999999999999988888764 89999999999999999 5889999999999
Q ss_pred cCCCCchhH-HHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeC
Q 001045 1011 ETTSRFPDL-ISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFAN 1089 (1176)
Q Consensus 1011 d~T~~ypdl-~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~ln 1089 (1176)
++|..||++ .+.+...+. ...+||||||||+||.++| +++||+.|++|.++ . ++.......++||++|||||+|
T Consensus 218 ~~t~~~pei~~~~~~~~~~-~~~~~ILDGElv~~d~~~g-~~~~F~~l~~r~~~-~--~~~~~~~~~~~~~~vFDiL~l~ 292 (514)
T TIGR00574 218 NYTYAYPEIFTEFIKEAFP-GIKSCILDGEMVAIDPETG-KILPFQTLLRRKRR-Y--DIDSMEKKVPVCLFVFDILYLN 292 (514)
T ss_pred ccccccchhHHHHHHHhcC-ccceeeecceEEEEEcCCC-CCcCcHhHHhhhhh-c--cccccccccceEEEEEEEEEEC
Confidence 999999999 887877653 3578999999999998775 78999999999764 1 1222334678999999999999
Q ss_pred CcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCccc
Q 001045 1090 GEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSP 1169 (1176)
Q Consensus 1090 G~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~p 1169 (1176)
|++++++||.+||++|++++ .+.++.+.+++.+.+ ++.+++.++|++++++|+||||+|+++ |+|+|
T Consensus 293 g~~l~~~pl~eRr~~L~~~~-~~~~~~i~~~~~~~~----------~~~e~~~~~~~~~~~~g~EGlv~K~~d--s~Y~~ 359 (514)
T TIGR00574 293 GESLIDEPLIERREILESIL-KPIPNRIEIAEMKIT----------SNVEELEKFLNEAISEGCEGLMLKDLK--SIYEP 359 (514)
T ss_pred CcchhcCcHHHHHHHHHHhc-cCCCCcEEEEEEEec----------CCHHHHHHHHHHHHHcCCceEEEecCC--CcccC
Confidence 99999999999999999999 666788999998764 478999999999999999999999998 99999
Q ss_pred CCCCCCC
Q 001045 1170 SKRSDSW 1176 (1176)
Q Consensus 1170 GkRs~~W 1176 (1176)
|+|+.+|
T Consensus 360 G~Rs~~W 366 (514)
T TIGR00574 360 GKRGWLW 366 (514)
T ss_pred CCCCCcc
Confidence 9999999
No 7
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-61 Score=567.88 Aligned_cols=413 Identities=24% Similarity=0.387 Sum_probs=359.7
Q ss_pred CCcchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCccc--ccccchhhHHHHHHHHh
Q 001045 711 QPAPYIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENI--ELNIGGSLVTSAIEEAC 788 (1176)
Q Consensus 711 ~~~~F~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~--elgige~~L~kal~~~~ 788 (1176)
.|+-|+.+|++|+.|+.|...+.|++.+..++.+. ..|-+.++.+|.+++++.|.+|+. .|||++..|++.+++++
T Consensus 3 ~~~~F~~~~~~f~~i~~t~~~~~k~~~~~k~~~s~--~~~~e~~sd~y~~lRL~lp~lDReR~~Yglket~La~l~i~~l 80 (881)
T KOG0966|consen 3 SPQNFSEVVDFFNKIRRTSNVKSKQAKFRKNFESW--CRPCEVGSDMYVALRLILPDLDRERGSYGLKETVLARLYIRAL 80 (881)
T ss_pred CccccchHHHHHHHHHHhhhhHhHHHHHhhccccc--cccccCCcchhhhhhhcccchhhcccccCchHHHHHHHHHHHh
Confidence 47889999999999999999999999999999886 356677888899999999999974 99999999999999999
Q ss_pred CCChHHH---H-HHHH----hcCChHHHHHHHHhhccccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhc
Q 001045 789 GTNRSKI---R-DMYN----RLGDLGDVAQECRQTQALLAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSC 860 (1176)
Q Consensus 789 g~~~~~i---~-~~~~----~~GDlG~va~~~~~~q~~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~ 860 (1176)
+++++.- + ..|+ ..||++.+++.+.+.+.....++.|||++||+.||.||..... ..++...|..|.++|
T Consensus 81 ~lprds~Da~rL~nwr~~~~~~Gdfs~i~~~vl~~R~~~~~s~alTi~evN~lLD~LA~~~~~--~~~~~~~l~~lv~~~ 158 (881)
T KOG0966|consen 81 HLPRDSADAVRLKNWRASTGARGDFSLILYEVLQRRCENPSSGALTIKEVNDLLDSLASGPSE--DGKKFKKLSQLVEQC 158 (881)
T ss_pred cCCCCcHHHHHHHhhccCCCcCccHHHHHHHHHHHHhcCCCCCceeHHHHHHHHHHHcCCchh--hhhhhHHHHHHHHhC
Confidence 9987432 2 1254 2489999999998876554444559999999999999964432 223337899999999
Q ss_pred chhhHHHHHHHHhhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhc
Q 001045 861 REKEMKFLVRTLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMN 940 (1176)
Q Consensus 861 ~~~E~k~LvRiIlk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~ 940 (1176)
++.|+|||+|+|+|++.+|+++++|+.. |||+|.+.|++|.||+.||+.|.+
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~v----------------------------fHPdA~dl~~vtsDLk~Vc~~L~D 210 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSV----------------------------FHPDAQDLYNVTSDLKAVCKKLYD 210 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhh----------------------------cCccHHHHHHHhhhHHHHHHHhcC
Confidence 9999999999999999999999999875 679999999999999999999999
Q ss_pred cccCCCccccCcCCCCCccCCCCcccCChh-HHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchh-
Q 001045 941 KGIGFSASTLSMVPGVPIKPMLAKITNGVP-QVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPD- 1018 (1176)
Q Consensus 941 ~g~~~~~~~~~l~~g~Pi~PMLA~~~~~~~-~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypd- 1018 (1176)
+..........+.+|..++||||+..+... +++++|++++|++|+|+||||+|+|+ .+|.+++|||||.|+|..|..
T Consensus 211 p~~~l~~~~~~i~lfsa~~PqLa~~~~~~~~~~~e~m~~~~f~lEtK~DGERiQlHk-~g~~~~yfSRNg~dyT~~yg~s 289 (881)
T KOG0966|consen 211 PSVGLKELDEDIELFSAFRPQLAQKQKLGDWAIIEKMGGQDFYLETKFDGERIQLHK-DGGEYKYFSRNGNDYTYEYGAS 289 (881)
T ss_pred CccCccccccceeehhhcCHHHHhhhccchHHHHHHhcCCceEEEeeccCceEEEEe-cCCEEEEEecCCcchhhhcCcc
Confidence 887655555569999999999999887655 78899999999999999999999999 599999999999999987743
Q ss_pred -----HHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCccc
Q 001045 1019 -----LISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQL 1093 (1176)
Q Consensus 1019 -----l~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~L 1093 (1176)
+...|+.+|...+.+||||||||+||+.+ .+++||+..+...+.... ....++||++|||||+||++|
T Consensus 290 ~~~g~lt~~i~~~f~~~v~~cILDGEMm~wD~~~-~~f~~~G~~~dik~~~~~------~~~~qp~yvvfDLLylNgksL 362 (881)
T KOG0966|consen 290 YAHGTLTQRIHGAFNKEVESCILDGEMMTWDTKT-KRFCPFGSNSDIKELSSR------DGSQQPCYVVFDLLYLNGKSL 362 (881)
T ss_pred cccccccHHHHhhhhhcchheEecceEEEeecch-hhhccCCchhhHHHhhcc------ccCCCceEEEeeeeeecCccc
Confidence 67788888877899999999999999998 599999998865443221 234579999999999999999
Q ss_pred ccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCC
Q 001045 1094 LGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRS 1173 (1176)
Q Consensus 1094 l~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs 1173 (1176)
.+.||.+|++.|++++ .+.+++++++++..+ .+.++|+++|++|++.|.||||+|.++ |.|.||.|+
T Consensus 363 ~~~~l~qR~e~L~~v~-~p~~~~iei~~~~~~----------~~~edi~~~f~~ai~~~~EGIVlK~~~--S~Y~pg~R~ 429 (881)
T KOG0966|consen 363 FGAPLHQRLEILKKVI-VPKSGRIEIVRSEVG----------STKEDIEQFFEEAIDNGEEGIVLKKPD--SSYVPGQRS 429 (881)
T ss_pred CCccHHHHHHHHHhcc-cCCCCeeEEeehhhc----------ccHHHHHHHHHHHHhcCCCceEEeccC--cccCccccC
Confidence 9999999999999999 788899999988764 578999999999999999999999998 999999999
Q ss_pred CCC
Q 001045 1174 DSW 1176 (1176)
Q Consensus 1174 ~~W 1176 (1176)
++|
T Consensus 430 ~gW 432 (881)
T KOG0966|consen 430 NGW 432 (881)
T ss_pred CCc
Confidence 999
No 8
>cd07900 Adenylation_DNA_ligase_I_Euk Adenylation domain of eukaryotic DNA Ligase I. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and C-terminal oligonucleotide/oligo
Probab=100.00 E-value=1.8e-45 Score=399.03 Aligned_cols=211 Identities=52% Similarity=0.934 Sum_probs=189.4
Q ss_pred cCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCC
Q 001045 950 LSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKP 1029 (1176)
Q Consensus 950 ~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~ 1029 (1176)
+.++||+|++||||+++.+++++++.+++.+|++|+||||+|||+|+..+|.|++|||||+++|..||+|++.+...+.+
T Consensus 2 ~~~~~~~pi~PMLA~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~~~t~~~pel~~~~~~~~~~ 81 (219)
T cd07900 2 CKLTPGIPVKPMLAKPTKGVSEVLDRFEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKSLKP 81 (219)
T ss_pred ceeecCCccccccCCccCCHHHHHHHhCCCeEEEEEeecceEEEEEEcCCCeEEEECCCCccccchhhHHHHHHHHHhcc
Confidence 57899999999999999999999999998899999999999999999645899999999999999999999999988766
Q ss_pred CCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhh
Q 001045 1030 AAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLF 1109 (1176)
Q Consensus 1030 ~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~ 1109 (1176)
.+.+||||||||+||..+| .+.||+.|++|.++.... .....+++|++|||||+||++|+++||.+||++|++++
T Consensus 82 ~~~~~iLDGElv~~~~~~g-~~~~F~~l~~r~~~~~~~----~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~ 156 (219)
T cd07900 82 SVKSFILDSEIVAYDRETG-KILPFQVLSTRKRKDVDA----NDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLF 156 (219)
T ss_pred cCccEEEeeEEEEEEcCCC-CCcChHHHhhhccccccc----ccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhc
Confidence 6789999999999998765 688999999997654321 23467899999999999999999999999999999999
Q ss_pred cccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1110 YDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1110 ~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.+.++++.++++..+ ++.++++++|++++++|+||||+|+++++|+|.||+||.+|
T Consensus 157 -~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~g~EGiv~K~~~~~s~Y~~g~Rs~~W 212 (219)
T cd07900 157 -KEVPGRFQFATSKDS----------EDTEEIQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNW 212 (219)
T ss_pred -CCCCCeEEEEEEEec----------CCHHHHHHHHHHHHHcCCceEEEecCCCCCccCCCCcCCCc
Confidence 566788999988764 57899999999999999999999998755899999999998
No 9
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.8e-43 Score=416.67 Aligned_cols=307 Identities=33% Similarity=0.520 Sum_probs=261.5
Q ss_pred HHHHHHhCCChHHHHHHHHhcCChHHHHHHHHhhccccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcc
Q 001045 782 SAIEEACGTNRSKIRDMYNRLGDLGDVAQECRQTQALLAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCR 861 (1176)
Q Consensus 782 kal~~~~g~~~~~i~~~~~~~GDlG~va~~~~~~q~~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~ 861 (1176)
+++....| ...+.+.|...||+|.++..++. +.+|+..|.+++...| +. .++..|+..++
T Consensus 2 ~av~~~~~--~~~~~~~~~~~Gdlg~~~~~~~~------------v~~v~~~~~~~~~~~g---~~---~~~~~L~~~~~ 61 (444)
T COG1793 2 KAVSEEDG--EYEIFEGYIPQGDLGEGAVLLWD------------VEGVYLTLSKVAERTG---QE---RLLWLLLDEAD 61 (444)
T ss_pred cchhhhcc--chhhhhcccccCccchhheeeee------------cccchhhHHHHHhhcC---ch---hHHHHHHHhcc
Confidence 35556666 56677889999999999988775 8999999999999988 22 78888888888
Q ss_pred hhhHHHHHHHHhhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhcc
Q 001045 862 EKEMKFLVRTLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMNK 941 (1176)
Q Consensus 862 ~~E~k~LvRiIlk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~~ 941 (1176)
+|+++++++.||+.| ++++|+.+||+..++..++..
T Consensus 62 ----------------~gv~~~~~~~ala~~----------------------------~~~~~~~~~d~g~~a~~~~~~ 97 (444)
T COG1793 62 ----------------IGVSEGTVLDALAEA----------------------------VERAYLWHNDLGALAKILLTL 97 (444)
T ss_pred ----------------cchhhHHHHHHHHHH----------------------------hhhhhccCCCchhhhhhhhhc
Confidence 999999999999853 578999999999999998887
Q ss_pred ccCCCccccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHH
Q 001045 942 GIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLIS 1021 (1176)
Q Consensus 942 g~~~~~~~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~ 1021 (1176)
+.... ..+.+.+|.|++|||+.....+.+...+..+ .|++|+||||+|+|+|+ .++.|++|||||+|+|.+||++..
T Consensus 98 ~~~~~-~~~~~~~~~p~~~~la~~~~~~~~~~~~~~~-~w~~E~K~DG~R~q~h~-~~~~vrl~SR~g~d~T~~fP~~~~ 174 (444)
T COG1793 98 GAEAL-DKATLLPGRPLPPMLAPMLASLEEALPRDGG-DWAYEEKFDGYRVQIHI-DGGKVRLYSRNGEDWTGRFPDILE 174 (444)
T ss_pred ccccc-cccccccCCccchhhccccccccccCCCCCC-CEEEEEeeceEEEEEEE-cCCEEEEEeCCCccchhhChHHHH
Confidence 76544 6677899999999999998887776666543 49999999999999999 588999999999999999998766
Q ss_pred HHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHH
Q 001045 1022 IINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQR 1101 (1176)
Q Consensus 1022 ~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eR 1101 (1176)
.+...+ ...++|||||+|++|++ .+.|||.|++|.+.+.+ +.......+++|++|||||+||++|+++||.+|
T Consensus 175 ~~~~~l--~~~~~iiDGE~V~~~~~---~~~~F~~Lq~r~~~k~~--v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eR 247 (444)
T COG1793 175 AAAEAL--PADDFILDGEIVVLDEE---GRLDFQALQQRLRRKYD--VAKLRRETPLVLFAFDLLYLDGEDLRGLPLEER 247 (444)
T ss_pred HHHhcC--CCCceEEeeeEEEECCC---CCCCHHHHHHHhhhccc--hhhhccCCceEEEEEEEEeECCcccccCchHHH
Confidence 666543 55699999999999974 57899999999876543 455567889999999999999999999999999
Q ss_pred HHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1102 RKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1102 r~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
|++|++++ ... +++.+++.+.+ .+.++++.+|+.+++.|+||||+|..+ |+|+||+|+++|
T Consensus 248 r~~Le~lv-~~~-~~~~~~~~i~~----------~~~~~~~~~~~~a~~~g~EGvv~K~~d--s~Y~~g~R~~~W 308 (444)
T COG1793 248 RALLEELV-KSS-DKIEIAERIPF----------SDAEEGEAFLEAAIELGLEGVVAKRPD--SPYRAGGRSNKW 308 (444)
T ss_pred HHHHHHHh-ccc-cccccccceec----------cChhhHHHHHHHHHhcCceEEEEeCCC--CCcCCCCCCCcc
Confidence 99999999 332 55666666654 467899999999999999999999887 999999999999
No 10
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=1.2e-41 Score=407.48 Aligned_cols=328 Identities=19% Similarity=0.248 Sum_probs=244.4
Q ss_pred HHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHhCCChHHHHHH
Q 001045 719 ARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNRSKIRDM 798 (1176)
Q Consensus 719 ~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~g~~~~~i~~~ 798 (1176)
=+++++|++|.++++|.++|.+. . +.+.+...++|+.+.+. .|||+ .
T Consensus 3 ~~il~~~~~~~~~~~k~~il~~~-~-----~n~~l~~~~~~~~~~~~------~~~~~---------------~------ 49 (488)
T PHA02587 3 LDILNELASTDSTKEKEAILKEN-K-----DNELLKEVFRLTYNKQI------NFGIK---------------K------ 49 (488)
T ss_pred HHHHHHHHhccCcchHHHHHHhc-c-----cChHHHHHHHHHhCcce------eEeee---------------E------
Confidence 36789999999999999999765 1 33445555566544432 23322 0
Q ss_pred HHhcCChHHHHHHHHhhccccCCCCCCcHHH-HHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHHHhhccc
Q 001045 799 YNRLGDLGDVAQECRQTQALLAPPPPLLIKD-VYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNLR 877 (1176)
Q Consensus 799 ~~~~GDlG~va~~~~~~q~~l~~~~~LTi~e-V~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiIlk~LR 877 (1176)
|.+.| ..-..+.++++.+ +...+.++|+..-.+ ......|..+|.+|++.|++||+|+|+++||
T Consensus 50 ~~~~~-------------~~~~~~~~~~~~~~~~~~~~~l~~r~~~~--~~~~~~l~~ll~~~~~~e~~~l~rli~~~lr 114 (488)
T PHA02587 50 WPKPG-------------HVEGSDGMLSLEDLLDFLEFDLATRKLTG--NAAIEELAQILSSMNEDDAEVLRRVLMRDLE 114 (488)
T ss_pred cCCCc-------------cccCCCCceeHHHHHHHHHHHHHHhhcch--hHHHHHHHHHHHhCCHHHHHHHHHHHhcccC
Confidence 11111 0011235577777 555666888765554 3446889999999999999999999999999
Q ss_pred cCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhccccCCCccccCcCCCCC
Q 001045 878 IGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMNKGIGFSASTLSMVPGVP 957 (1176)
Q Consensus 878 iG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~~g~~~~~~~~~l~~g~P 957 (1176)
||+++++|+.||+ +++|
T Consensus 115 iGvs~~~i~~~~~---------------------------------------------------------------~~~P 131 (488)
T PHA02587 115 CGASEKIANKVWK---------------------------------------------------------------GLIP 131 (488)
T ss_pred CCccHHHHHHHhc---------------------------------------------------------------CCcc
Confidence 9999999987641 1589
Q ss_pred ccC-CCCcccCChhHHHHh-ccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcC---CCCC
Q 001045 958 IKP-MLAKITNGVPQVLKL-FQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCK---PAAG 1032 (1176)
Q Consensus 958 i~P-MLA~~~~~~~~~~~~-~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~---~~~~ 1032 (1176)
++| |||++... +.+++ ++ .+|++|+||||+|||+|+ .++.|++|||||++++. ||+|.+.+..... ..+.
T Consensus 132 ~~p~mLA~~~~~--~~~~~~~~-~~~~~E~K~DG~R~q~h~-~~~~v~l~SR~g~~~~~-~p~i~~~l~~~~~~~~~~~~ 206 (488)
T PHA02587 132 EQPQMLASSFSE--KLIKKNIK-FPAYAQLKADGARCFADI-DADGIEIRSRNGNEYLG-LDLLKEELKKMTAEARQRPG 206 (488)
T ss_pred CCCCccCCCCCH--HHHHhhcc-CcEEEEEccCceEEEEEE-eCCEEEEEecCCccccC-ChhHHHHHHHHhhhhcccCC
Confidence 987 99998543 45655 54 489999999999999999 48999999999999974 8999988876532 1247
Q ss_pred CeEEEEEEEEEecCCCCcccCh-------------HHHhhhhcCCCCchhhh-----cccccceEEEEEEeeeeC---Cc
Q 001045 1033 TFILDAEVVAIDRKNGCKIMSF-------------QELSSRERGGKDSVITI-----KSVKVDICVFVFDIMFAN---GE 1091 (1176)
Q Consensus 1033 ~~ILDGElVa~d~~~g~~~~pF-------------q~L~~R~r~~~~~~i~~-----~~~~~~v~~~vFDiL~ln---G~ 1091 (1176)
+||||||+|+||..++ .+.+| |.++.|.++..-..... .....+++|++||||+++ |.
T Consensus 207 ~~VLDGElv~~~~~~~-~~~~~~f~~~~~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~ 285 (488)
T PHA02587 207 GVVIDGELVYVEVETK-KPNGLSFLFDDSKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGK 285 (488)
T ss_pred cEEEEeEEEEEecccC-CCccchhhcccccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCC
Confidence 8999999999987653 44454 78888864321110000 134578999999999653 44
Q ss_pred ccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCC
Q 001045 1092 QLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSK 1171 (1176)
Q Consensus 1092 ~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGk 1171 (1176)
.+++.||.+||++|++++.....+++.+++...+ ++.++++++|+++++.|+||||+|+++ |+|+||
T Consensus 286 ~~~~~pl~eRr~~L~~l~~~~~~~~i~l~~~~~~----------~~~ee~~~~~~~a~~~G~EGimlK~~d--s~Y~~G- 352 (488)
T PHA02587 286 EKSDMPYDDRFSKLAQMFEDCGYDRVELIENQVV----------NNLEEAKEIYKRYVDQGLEGIILKNTD--GLWEDG- 352 (488)
T ss_pred ccccCCHHHHHHHHHHHHhhcCCCcEEEEeeEEc----------CCHHHHHHHHHHHHhCCCCeEEEECCC--CCCCCC-
Confidence 5788999999999999994344568888887764 468999999999999999999999998 999999
Q ss_pred CCCCC
Q 001045 1172 RSDSW 1176 (1176)
Q Consensus 1172 Rs~~W 1176 (1176)
|+.+|
T Consensus 353 Rs~~W 357 (488)
T PHA02587 353 RSKDQ 357 (488)
T ss_pred CCCCc
Confidence 88888
No 11
>KOG1361 consensus Predicted hydrolase involved in interstrand cross-link repair [Replication, recombination and repair]
Probab=100.00 E-value=1.2e-40 Score=384.69 Aligned_cols=330 Identities=43% Similarity=0.703 Sum_probs=280.7
Q ss_pred CCCCCCeeEeCCccEEEecCCcCC-CCccEEEeccCChhhhCCcccCCCCceEEeCHHHHHHHHHhhccCCCceEEeCCC
Q 001045 35 PRTFPPSKHVPNTRFLIDAFRYAA-DFSVSYFLSHFHSDHYTGLSPSWSKGIIFCSEITSRLLSQILNINPKFIYPLPIK 113 (1176)
Q Consensus 35 ~r~~p~~~~ipg~~~liD~~~~~~-~~i~avfITHaH~DHiggL~~l~~~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~ 113 (1176)
+..++-|.+.||..|.||+|++.. ..+.++|+||+|+||+.||...|.+++|||++.|+.++...++++...++.++.+
T Consensus 86 ~~p~~~~~~~p~~~f~VD~f~~~~~~~~s~yFLsHFHSDHy~GL~~sW~~p~lYCS~ita~Lv~~~~~v~~~~i~~l~l~ 165 (481)
T KOG1361|consen 86 RIPLHVIKVLPGGEFSVDAFRYGHIEGCSAYFLSHFHSDHYIGLTKSWSHPPLYCSPITARLVPLKVSVTKQSIQALDLN 165 (481)
T ss_pred CCCCcceeecCCCcEEEehhhcCCccccceeeeecccccccccccccccCCcccccccchhhhhhhcccChhhceeecCC
Confidence 345566777899999999998866 6789999999999999999999999999999999999999999998899999999
Q ss_pred ceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCC
Q 001045 114 IPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPL 193 (1176)
Q Consensus 114 ~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~ 193 (1176)
+++.+.++.|++++|+||||++||+|+...+ ..+|||||||+...+...|++.....+|.|++|+||+++.+.||+
T Consensus 166 ~~~~i~~~~vt~ldAnHCPGa~mf~F~~~~~----~~~lhtGDFR~s~~m~~~p~~~~~~~i~~lyLDtTycnp~y~Fps 241 (481)
T KOG1361|consen 166 QPLEIPGIQVTLLDANHCPGAVMFLFELSFG----PCILHTGDFRASADMSKEPALTLEQTIDILYLDTTYCNPKYDFPS 241 (481)
T ss_pred CceeecceEEEEeccccCCCceEEEeecCCC----ceEEecCCcccChhhhhChHHhcCCccceEEEeecccCCCCCCcc
Confidence 9999999999999999999999999998763 699999999999999888865555799999999999999999999
Q ss_pred hHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccchHHHHHHHHHHcCCcEEEccchHHHHHHhCCCCCCccc-cCCC
Q 001045 194 QEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIGKEKILIEIFKKCGRKVCVDSRKMEVLRVLGYGDSGVFT-EDES 272 (1176)
Q Consensus 194 ~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slGR~q~ll~ia~~~g~~I~vdg~~~~il~~lg~~~~~~~t-~d~~ 272 (1176)
++++++.+++++...... +.++|+++++|++|++..++++|+.++.+|++..+.+.+++.+|..+...++ .+..
T Consensus 242 q~esvq~v~~~i~~~~~~-----~~~~Li~v~~ysiGkE~l~~eia~~l~~kI~v~~~~~~~~~~lg~~d~~~~~s~d~~ 316 (481)
T KOG1361|consen 242 QEESVQEVVDVIRSHASK-----NDRVLIVVGTYSIGKEKLLLEIARILNSKIWVEPRRLRLLQCLGFDDESKLLSIDVD 316 (481)
T ss_pred HHHHHHHHHHHHHhhhhh-----CCceEEEEEEEecchhHHHHHHHHHhCCceEEehhhchhhhhcCCCChhhhhccccc
Confidence 999999999999987665 3689999999999999999999999999999999999999999977544444 4777
Q ss_pred CCeEEEecChHH-----------HHhcCCCceEEEEeccceeecccCcee----eeccCCeeEEEEeecCCCCHHHHHHH
Q 001045 273 ETDVHVVGWNEI-----------MVERGYDKVVGFVPTGWTYEVKRNKFA----VRSKDAFEIHLVPYSEHSNYDELREY 337 (1176)
Q Consensus 273 ~~~I~v~~~~~~-----------~~~~g~~~~v~i~ptGw~~~~~~~~~~----v~~~~~~~v~~i~~SgHAs~~EL~~~ 337 (1176)
+..+|+.+++.. ....++..++++.|+||+.....+... ......+.++.+|||.|++|.||.+|
T Consensus 317 ~ssvhv~~~~~l~~~~~l~~~~~~~~~~~s~~v~~~~tgwt~~~~~s~~~~~~~~~~~~~i~~~~vpYseHSs~~el~~f 396 (481)
T KOG1361|consen 317 ESSVHVVPMNSLASSPSLKEYESQYEDGYSKLVGFSPTGWTKGKLVSLDKENSRPQSGSKIPISLVPYSEHSSYTELSEF 396 (481)
T ss_pred cCceeEeehhhhccccchhhhhcccccCcceeEeecccccccccccccCccccccccccccccccccccccCCHHHHHHH
Confidence 888999887722 122456789999999999654322211 11222467789999999999999999
Q ss_pred HHHcCCCEEEEEecCCCCcCchHHH-HHHHHHHHHHH
Q 001045 338 VKFLKPKRVIPTVGMDIEKLDSKHA-NKMRKYFAGLV 373 (1176)
Q Consensus 338 V~~lrPk~VIPvHG~~~e~~~~~E~-~~m~k~f~~l~ 373 (1176)
++.++|+.|||+++.+++..+..+. ..|...+..+.
T Consensus 397 ~~~lk~k~iiptv~~~~~~~~~~~~~~~k~s~~~~~~ 433 (481)
T KOG1361|consen 397 LSKLKPKTIIPTVNEDTELSDATEVPEEKSSLLLSWP 433 (481)
T ss_pred HHhcCCCeeecCccCCccccchhhhhhhhhhhhccch
Confidence 9999999999999999866666555 45555444333
No 12
>cd07901 Adenylation_DNA_ligase_Arch_LigB Adenylation domain of archaeal and bacterial LigB-like DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of archaeal DNA ligases and bacterial proteins similar to Mycobacterium tuberculosis LigB. Members of this group contain adeny
Probab=100.00 E-value=1.2e-40 Score=359.01 Aligned_cols=201 Identities=36% Similarity=0.609 Sum_probs=173.8
Q ss_pred CCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCC
Q 001045 954 PGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGT 1033 (1176)
Q Consensus 954 ~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~ 1033 (1176)
||.|++||||+++.++++++++. +.+|++|+||||+|||+|+ .++.|++|||||+++|..||+|.+.+...+ ...+
T Consensus 1 ~~~p~~PmLA~~~~~~~~~~~~~-~~~~~~E~K~DG~R~~~~~-~~~~v~~~SR~~~~~t~~~pel~~~~~~~~--~~~~ 76 (207)
T cd07901 1 VGRPVRPMLAQRAPSVEEALIKE-GGEAAVEYKYDGIRVQIHK-DGDEVRIFSRRLEDITNALPEVVEAVRELV--KAED 76 (207)
T ss_pred CCCCCccccCCCCCCHHHHHHhc-CCcEEEEEeEcceeEEEEE-eCCEEEEEeCCCccccchhhHHHHHHHhcC--CCCC
Confidence 68999999999998888776665 5789999999999999999 488999999999999999999999888753 2478
Q ss_pred eEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccC
Q 001045 1034 FILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEK 1113 (1176)
Q Consensus 1034 ~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~ 1113 (1176)
||||||||+||+ +| .+.+|+.|++|.++... +.......+++|+|||||++||++++++||.+||++|++++ ...
T Consensus 77 ~iLDGElv~~~~-~g-~~~~F~~l~~r~~~~~~--~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~-~~~ 151 (207)
T cd07901 77 AILDGEAVAYDP-DG-RPLPFQETLRRFRRKYD--VEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIV-PET 151 (207)
T ss_pred EEEeCEEEEECC-CC-CccCHHHHHHHhccccc--hhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhc-CcC
Confidence 999999999996 54 67899999999654322 22222356899999999999999999999999999999999 443
Q ss_pred CCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1114 MGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1114 ~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
+.+.++++..+ .+.+++.++|++++++|+||||+|+++ |+|.||+||.+|
T Consensus 152 -~~i~~~~~~~~----------~~~~~~~~~~~~~~~~g~EGiv~K~~~--s~Y~~g~Rs~~w 201 (207)
T cd07901 152 -EAILLAPRIVT----------DDPEEAEEFFEEALEAGHEGVMVKSLD--SPYQAGRRGKNW 201 (207)
T ss_pred -CcEEEEEEEec----------CCHHHHHHHHHHHHHcCCceEEEeCCC--CCcCCCCCCCCe
Confidence 67888887764 467999999999999999999999998 999999999999
No 13
>cd07903 Adenylation_DNA_ligase_IV Adenylation domain of DNA Ligase IV. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligase in eukaryotic cells (I, III and IV). DNA ligase IV is required for DNA non-homologous end joining pathways, including recombination of the V(D)J immunoglobulin gene segments in cells of the mammalian immune system. DNA ligase IV is stabilized by forming a complex with XRCC4, a nuclear phosphoprotein, which is phosphorylated by DNA-dependent protein kinase. DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more di
Probab=100.00 E-value=3.2e-40 Score=360.41 Aligned_cols=208 Identities=31% Similarity=0.495 Sum_probs=179.8
Q ss_pred ccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHH-----
Q 001045 949 TLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISII----- 1023 (1176)
Q Consensus 949 ~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l----- 1023 (1176)
.+.++||.||+||||+++++....+..+.+.+|++|+||||+|||+|++ ++.|++|||||+++|..||++....
T Consensus 3 ~~~~~~~~p~~PmLa~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~i~~~-~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~ 81 (225)
T cd07903 3 DLSIELFSPFRPMLAERLNIGYVEIKLLKGKPFYIETKLDGERIQLHKD-GNEFKYFSRNGNDYTYLYGASLTPGSLTPY 81 (225)
T ss_pred CceeecCCcCccccCCCCCCHHHHHHhhcCCeEEEEEeeCceEEEEEec-CCEEEEEeCCCccccccccccccccccchh
Confidence 4678999999999999999877766788889999999999999999994 8999999999999999999987653
Q ss_pred -HhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHH
Q 001045 1024 -NEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRR 1102 (1176)
Q Consensus 1024 -~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr 1102 (1176)
...+.....+||||||||+||..+ +.+.||+.|+++.+.... .....+++|++||||++||++++++||.+|+
T Consensus 82 l~~~~~~~~~~~iLDGElv~~~~~~-~~~~~f~~l~~~~~~~~~-----~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~ 155 (225)
T cd07903 82 IHLAFNPKVKSCILDGEMVVWDKET-KRFLPFGTLKDVAKLREV-----EDSDLQPCFVVFDILYLNGKSLTNLPLHERK 155 (225)
T ss_pred hhhhccccCcEEEeceEEEEEEcCc-CeeccchHHHHHHhhccc-----ccCCccEEEEEEEEEEECCeecccCcHHHHH
Confidence 233445678999999999999765 478999999876543210 1235679999999999999999999999999
Q ss_pred HHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1103 KYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1103 ~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
++|++++ .+.++++.++++..+ ++.+++.++|++++++|+||||+|+++ |+|+||+||.+|
T Consensus 156 ~~L~~~~-~~~~~~i~~~~~~~~----------~~~~~~~~~~~~~~~~g~EGlv~K~~~--s~Y~~g~Rs~~w 216 (225)
T cd07903 156 KLLEKII-TPIPGRLEVVKRTEA----------STKEEIEEALNEAIDNREEGIVVKDLD--SKYKPGKRGGGW 216 (225)
T ss_pred HHHHHhc-CCCCCeEEEEEEEeC----------CCHHHHHHHHHHHHHcCCceEEEecCC--CCCccCCcCCCc
Confidence 9999999 556678999888764 467899999999999999999999998 999999999998
No 14
>cd07897 Adenylation_DNA_ligase_Bac1 Adenylation domain of putative bacterial ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of predicted bacterial ATP-dependent DNA ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. The adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family, including this group. The adenylation domain binds ATP and contains many of the active site residues.
Probab=100.00 E-value=4.7e-40 Score=354.27 Aligned_cols=197 Identities=22% Similarity=0.360 Sum_probs=168.7
Q ss_pred CCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeE
Q 001045 956 VPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFI 1035 (1176)
Q Consensus 956 ~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~I 1035 (1176)
+|++||||+++.+..+.+ .....|++|+||||+|||+|+ .++.|++|||||+++|..||++...+.. .+.+||
T Consensus 3 ~~~~pmLA~~~~~~~~~~--~~~~~~~~E~K~DG~R~~~~~-~~~~v~l~SR~g~~~t~~~p~l~~~~~~----l~~~~i 75 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDL--GDPSDWQAEWKWDGIRGQLIR-RGGEVFLWSRGEELITGSFPELLAAAEA----LPDGTV 75 (207)
T ss_pred CCCCceeCCcCCCchhhh--cCcccEEEEEeEceEEEEEEE-cCCEEEEEeCCCCcccccchHHHHHHHh----CCCCeE
Confidence 799999999999877654 345689999999999999999 5889999999999999999999987765 246899
Q ss_pred EEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCC
Q 001045 1036 LDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMG 1115 (1176)
Q Consensus 1036 LDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~ 1115 (1176)
||||||+||. +...||+.|++|.+..... .......+++|++|||||+||++++++||.+||++|++++.....+
T Consensus 76 LDGElv~~~~---~~~~~F~~l~~r~~~~~~~--~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~ 150 (207)
T cd07897 76 LDGELLVWRD---GRPLPFNDLQQRLGRKTVG--KKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPP 150 (207)
T ss_pred EEeEEEEecC---CCccCHHHHHHHhcccccc--hhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCC
Confidence 9999999985 2679999999996533221 1112357899999999999999999999999999999999332247
Q ss_pred cEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1116 YFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1116 ~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
++.++++..+ .+.+++.++|++++++|+||||+|+++ |+|+||+|+.+|
T Consensus 151 ~i~~~~~~~~----------~~~~~~~~~~~~~~~~g~EGiv~K~~~--s~Y~~Grr~~~W 199 (207)
T cd07897 151 RLDLSPLIAF----------ADWEELAALRAQSRERGAEGLMLKRRD--SPYLVGRKKGDW 199 (207)
T ss_pred ceeecceEec----------CCHHHHHHHHHHHHHcCCeEEEEeCCC--CCcCCCCcCCCe
Confidence 7888887764 478999999999999999999999998 999999999998
No 15
>cd07902 Adenylation_DNA_ligase_III Adenylation domain of DNA Ligase III. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three-step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). DNA ligase III is not found in lower eukaryotes and is present both in the nucleus and mitochondria. It has several isoforms; two splice forms, III-alpha and III-beta, differ in their carboxy-terminal sequences. DNA ligase III-beta is believed to play a role in homologous recombination during meiotic prophase. DNA ligase III-alpha interacts with X-ray Cross Complementing factor 1 (XRCC1) and functions in single nuc
Probab=100.00 E-value=1.1e-39 Score=352.80 Aligned_cols=200 Identities=29% Similarity=0.502 Sum_probs=173.4
Q ss_pred ccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCC-CchhHHHHHHhhc
Q 001045 949 TLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTS-RFPDLISIINEFC 1027 (1176)
Q Consensus 949 ~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~-~ypdl~~~l~~~~ 1027 (1176)
.+.+++|.|++||||+++++++++++++. ..|++|+||||+|||+|+ .++.|++|||||+++|. .||++.+.+.+.+
T Consensus 5 ~~~~~~~~p~~PmLA~~~~~~~~~i~~~~-~~~~~E~K~DG~R~~i~~-~~~~v~l~SR~g~~~t~~~~~~~~~~~~~~~ 82 (213)
T cd07902 5 SVRASLMTPVKPMLAEACKSVEDAMKKCP-NGMYAEIKYDGERVQVHK-QGDNFKFFSRSLKPVLPHKVAHFKDYIPKAF 82 (213)
T ss_pred eEEeEcCCcccCccCCcCCCHHHHHHhcC-CceEEEeccCCEEEEEEE-cCCEEEEEcCCCcccccchhHHHHHHHHHhc
Confidence 46789999999999999988887777653 469999999999999999 47899999999999996 6899988888765
Q ss_pred CCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHH
Q 001045 1028 KPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKD 1107 (1176)
Q Consensus 1028 ~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~ 1107 (1176)
. ...+||||||||+||.++| .+++|+.++.|.+... ...+++|++||||++||.+++++||.+||++|++
T Consensus 83 ~-~~~~~iLDGEiv~~d~~~g-~~~~F~~l~~~~~~~~--------~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~ 152 (213)
T cd07902 83 P-HGHSMILDSEVLLVDTKTG-KPLPFGTLGIHKKSAF--------KDANVCLFVFDCLYYNGESLMDKPLRERRKILED 152 (213)
T ss_pred c-cccceeeeeEEEEEECCCC-cccccchhhhhhcccc--------ccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHH
Confidence 3 3689999999999998775 7789999998755311 2347999999999999999999999999999999
Q ss_pred hhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCC
Q 001045 1108 LFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRS 1173 (1176)
Q Consensus 1108 ~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs 1173 (1176)
++ .+.++++.++++..+ .+.+++.++|++++++|+||||+|+++ |+|.||+|+
T Consensus 153 ~~-~~~~~~~~~~~~~~~----------~~~~~l~~~~~~~~~~g~EGvV~K~~~--s~Y~~G~r~ 205 (213)
T cd07902 153 NM-VEIPNRIMLSEMKFV----------KKADDLSAMIARVIKEGLEGLVLKDLK--SVYEPGKRH 205 (213)
T ss_pred hc-cCCCCeEEEEEEEEc----------CCHHHHHHHHHHHHHCCCCeEEEeCCC--CCccCCCCC
Confidence 99 555667888887764 467899999999999999999999998 999999983
No 16
>cd08039 Adenylation_DNA_ligase_Fungal Adenylation domain of uncharacterized fungal ATP-dependent DNA ligase-like proteins. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. This group is composed of uncharacterized fungal proteins with similarity to ATP-dependent DNA ligases. ATP dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site res
Probab=100.00 E-value=9e-39 Score=348.98 Aligned_cols=201 Identities=22% Similarity=0.375 Sum_probs=165.9
Q ss_pred CChhHHHHhccCceEEEEEecceeEEEEEEe---eCCeEEEEcCCCccCCCCchhHHHHHHhhcC------CCCCCeEEE
Q 001045 967 NGVPQVLKLFQNKAFTCEYKYDGQRAQIHKL---VDGTVRIFSRNGDETTSRFPDLISIINEFCK------PAAGTFILD 1037 (1176)
Q Consensus 967 ~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~---~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~------~~~~~~ILD 1037 (1176)
+++..+++.+++..|++|+||||+|||+|+. .++.|++|||||+++|..||++.+.+...+. +.+++||||
T Consensus 10 ~~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILD 89 (235)
T cd08039 10 RSIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILE 89 (235)
T ss_pred cCHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEE
Confidence 3577888999999999999999999999984 1789999999999999999999988776542 236799999
Q ss_pred EEEEEEecCCCCcccChHHHhhhhcCCCC----chhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccC
Q 001045 1038 AEVVAIDRKNGCKIMSFQELSSRERGGKD----SVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEK 1113 (1176)
Q Consensus 1038 GElVa~d~~~g~~~~pFq~L~~R~r~~~~----~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~ 1113 (1176)
||||+||+.+| ++.|||.|++|.+.... ..........++||++|||||+||++|++.||.+||++|++++ .+.
T Consensus 90 GEiVv~d~~~g-~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~-~~~ 167 (235)
T cd08039 90 GEMVVWSDRQG-KIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLV-HVI 167 (235)
T ss_pred eEEEEEECCCC-ccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhc-ccC
Confidence 99999998665 78999999988542210 0011123457899999999999999999999999999999999 666
Q ss_pred CCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCC-----CCCC
Q 001045 1114 MGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKR-----SDSW 1176 (1176)
Q Consensus 1114 ~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkR-----s~~W 1176 (1176)
++++.+++...+... ...+.++++++|++++++|+||||+|+++ |+|.||+| +..|
T Consensus 168 ~~~~~~~~~~~i~~~-----~~~~~~~l~~~~~~a~~~g~EGIv~K~~~--S~Y~pgr~~~~~r~~~W 228 (235)
T cd08039 168 PGYAGLSERFPIDFS-----RSSGYERLRQIFARAIAERWEGLVLKGDE--EPYFDLFLEQGSFSGCW 228 (235)
T ss_pred CCcEEEEEEEeeccc-----CCCCHHHHHHHHHHHHHcCCceEEEecCC--CCcccCcccccccCCCe
Confidence 788888887765321 12467899999999999999999999998 99999854 5788
No 17
>cd07898 Adenylation_DNA_ligase Adenylation domain of ATP-dependent DNA Ligases. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent ligases are present in many organisms such as viruses, bacteriophages, eukarya, archaea and bacteria. Some organisms express a variety of different ligases which appear to be targeted to specific functions. ATP-dependent DNA ligases have a highly modular architecture consisting of a unique arrangement of two or more discrete domains including a DNA-binding domain, an adenylation (nucleotidyltransferase (NTase)) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many of the active-site residues. The adenylation and C-terminal OB-f
Probab=100.00 E-value=1.3e-38 Score=341.80 Aligned_cols=195 Identities=35% Similarity=0.541 Sum_probs=168.7
Q ss_pred ccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEE
Q 001045 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILD 1037 (1176)
Q Consensus 958 i~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILD 1037 (1176)
|+||||+++++++++ .++.+..|++|+||||+|||+|+ .++.|++|||+|+++|..||++...+.. .+.+||||
T Consensus 1 i~pmLa~~~~~~~~~-~~~~~~~~~~E~K~DG~R~~~~~-~~~~v~l~SR~g~~~t~~~p~i~~~~~~----~~~~~vLD 74 (201)
T cd07898 1 IKPMLAHPEESAEAA-KAKKPAAAWVEDKYDGIRAQVHK-DGGRVEIFSRSLEDITDQFPELAAAAKA----LPHEFILD 74 (201)
T ss_pred CCCeecCcCCChHHH-HhhCCCeEEEEEeeceEEEEEEE-eCCEEEEEcCCChhchhhhhhHHHHHHh----CCCCEEEE
Confidence 689999999988765 66778899999999999999999 4789999999999999999999987764 35899999
Q ss_pred EEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcE
Q 001045 1038 AEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYF 1117 (1176)
Q Consensus 1038 GElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i 1117 (1176)
||||+||.. ...||+.+++|.++.... .......+++|++||||++||++++++||.||+++|++++ ...++.+
T Consensus 75 GElv~~~~~---~~~~f~~~~~~~~~~~~~--~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~-~~~~~~i 148 (201)
T cd07898 75 GEILAWDDN---RGLPFSELFKRLGRKFRD--KFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELF-VEIPGRI 148 (201)
T ss_pred EEEEEEeCC---CCCcHHHHHHHhcccccc--hhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhh-cCCCCcE
Confidence 999999863 346999999885432221 1113457899999999999999999999999999999999 5567889
Q ss_pred EEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1118 QYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1118 ~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.+++...+ ++.+++.++|++++++|+||||+|+++ |+|+||+||.+|
T Consensus 149 ~~~~~~~~----------~~~~~~~~~~~~~~~~g~EGim~K~~~--s~Y~~g~Rs~~w 195 (201)
T cd07898 149 RIAPALPV----------ESAEELEAAFARARARGNEGLMLKDPD--SPYEPGRRGLAW 195 (201)
T ss_pred EEeeeEEc----------CCHHHHHHHHHHHHHcCCceEEEeCCC--CCcCCCCcCCCc
Confidence 99888764 467899999999999999999999998 999999999999
No 18
>cd07905 Adenylation_DNA_ligase_LigC Adenylation domain of Mycobacterium tuberculosis LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic core unit that is
Probab=100.00 E-value=9.6e-38 Score=333.21 Aligned_cols=187 Identities=26% Similarity=0.430 Sum_probs=158.2
Q ss_pred ccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEE
Q 001045 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILD 1037 (1176)
Q Consensus 958 i~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILD 1037 (1176)
|+||||..+.++++ +.+|++|+||||+|||+|+ .++.|++|||||+++|..||++.+++... .+.+||||
T Consensus 1 i~PmLa~~~~~~~~------~~~~~~E~K~DG~R~~~~~-~~~~v~l~SR~g~~~t~~~p~~~~~~~~~---~~~~~iLD 70 (194)
T cd07905 1 VEPMLARAVDALPE------PGGWQYEPKWDGFRCLAFR-DGDEVRLQSRSGKPLTRYFPELVAAARAL---LPPGCVLD 70 (194)
T ss_pred CCceeCCccCCCCC------CCceEEEeeeceEEEEEEE-eCCEEEEEeCCCCchhhhhHHHHHHHHhh---CCCCEEEE
Confidence 68999999876654 5789999999999999999 58899999999999999999999988874 35689999
Q ss_pred EEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcE
Q 001045 1038 AEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYF 1117 (1176)
Q Consensus 1038 GElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i 1117 (1176)
||||+||.. . .+|+.|++|.+.... .+.......+++|++|||||+||+++++.||.+||++|++++ ....+.+
T Consensus 71 GElv~~~~~---~-~~F~~l~~r~~~~~~-~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~-~~~~~~i 144 (194)
T cd07905 71 GELVVWRGG---R-LDFDALQQRIHPAAS-RVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALL-AGWGPPL 144 (194)
T ss_pred eEEEEEcCC---C-CCHHHHHHHhccccc-chhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHh-cccCCCe
Confidence 999999852 2 499999999754322 122334567899999999999999999999999999999999 4445677
Q ss_pred EEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1118 QYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1118 ~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.+++.. .+.+++.++|++++++|+||||+|+++ |+|+||+| +|
T Consensus 145 ~~~~~~------------~~~~~~~~~~~~~~~~g~EGiv~K~~~--s~Y~~Gr~--~W 187 (194)
T cd07905 145 HLSPAT------------TDRAEAREWLEEFEGAGLEGVVAKRLD--GPYRPGER--AM 187 (194)
T ss_pred EECCcc------------CCHHHHHHHHHHHHHCCCceEEEeCCC--CCcCCCCC--cE
Confidence 776642 356799999999999999999999998 99999974 46
No 19
>PF01068 DNA_ligase_A_M: ATP dependent DNA ligase domain; InterPro: IPR012310 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This domain belongs to a more diverse superfamily, including catalytic domain of the mRNA capping enzyme (IPR001339 from INTERPRO) and NAD-dependent DNA ligase (IPR001679 from INTERPRO) []. ; GO: 0003910 DNA ligase (ATP) activity, 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 1X9N_A 2CFM_A 3QWU_B 3GDE_A 2Q2U_C 2Q2T_A 1FVI_A 1P8L_A 2VUG_A ....
Probab=100.00 E-value=1.3e-37 Score=333.72 Aligned_cols=198 Identities=36% Similarity=0.636 Sum_probs=174.0
Q ss_pred CCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEE
Q 001045 960 PMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAE 1039 (1176)
Q Consensus 960 PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGE 1039 (1176)
||||+++.+++++++++ +.+|++|+||||+|||||+ .++.|++|||+|+++|..||++...+...+.+...+||||||
T Consensus 1 PmLA~~~~~~~~~~~~~-~~~~~~e~K~DG~R~~i~~-~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~~~vLDGE 78 (202)
T PF01068_consen 1 PMLAQPFDSIEKALKKF-GGPWYVEPKYDGVRCQIHK-DGGGVRLFSRNGKDITSQFPELAEALRELLFPDGPDFVLDGE 78 (202)
T ss_dssp -EEEEEESSHHHHHHHT-TSCEEEEEEESSEEEEEEE-ETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCTEEEEEEE
T ss_pred CcCCccccCHHHHHHhc-CCCeEEEEeEeeEEeeeee-ccccceeecccccchhhHHHHHHHHHHHHhcCCCCceEEEEE
Confidence 99999999999999998 7899999999999999999 699999999999999999999999999987777778999999
Q ss_pred EEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcEEE
Q 001045 1040 VVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQY 1119 (1176)
Q Consensus 1040 lVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~ 1119 (1176)
||+||+.++ ...||+.++.+.++.... + .....+++|++||||++||.+++++||.+|+++|++++ ....+.+.+
T Consensus 79 lv~~d~~~~-~~~~f~~~~~~~~~~~~~-~--~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~-~~~~~~i~~ 153 (202)
T PF01068_consen 79 LVVLDPNTG-SPLPFQELSGRLNRRSKK-I--PEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELL-EPPPPRIRI 153 (202)
T ss_dssp EEEBETTTS-SBCCHHHHHHHHBHSSSC-H--HHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHB-G-BTSSEEE
T ss_pred EEEEecCCC-cchhHHHHhhhhhhhccc-c--hhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhh-ccCCCceeE
Confidence 999999875 889999999997432211 1 11267899999999999999999999999999999999 666788999
Q ss_pred eEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1120 AKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1120 ~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
++...+ .+.++++++|+++++.|+||||+|+++ ++|+||+|+.+|
T Consensus 154 ~~~~~~----------~~~~~~~~~~~~~~~~g~EG~v~K~~~--~~Y~~Gkrs~~w 198 (202)
T PF01068_consen 154 VESYVV----------NSKEELEELFEEAIDQGFEGLVLKDPD--SPYEPGKRSSGW 198 (202)
T ss_dssp EEEEEE----------SSHHHHHHHHHHHHHTTSSEEEEEETT--SSC-TTEEEEEE
T ss_pred eeeecC----------CCHHHHHHHHHHHHHcCCceEEEECCC--CccCCCCcCCCc
Confidence 998775 468999999999999999999999988 999999998887
No 20
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=100.00 E-value=7.2e-37 Score=345.50 Aligned_cols=309 Identities=21% Similarity=0.324 Sum_probs=235.4
Q ss_pred CCCCCCeeE-eCCccEEEecCCc-----------------CCCCccEEEeccCChhhhCCcccCCC---CceEEeCHHHH
Q 001045 35 PRTFPPSKH-VPNTRFLIDAFRY-----------------AADFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCSEITS 93 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~~~-----------------~~~~i~avfITHaH~DHiggL~~l~~---~~pIY~s~~T~ 93 (1176)
+.+.+|.++ .|..++|+||+-. ....+|||+|||||.||+|-||.++. .+|||||++|.
T Consensus 191 EVGRSa~lv~T~eSrVLlDcG~n~a~~~~~~~Pyl~vpE~~~~~lDAViiTHAHLDH~G~lP~LfkYgy~GPVY~T~PTR 270 (637)
T COG1782 191 EVGRSALLVSTPESRVLLDCGVNVAGNGEDAFPYLDVPEFQPDELDAVIITHAHLDHCGFLPLLFKYGYDGPVYCTPPTR 270 (637)
T ss_pred hccceeEEEecCCceEEEeccccCCCCccccCcccccccccccccceEEEeecccccccchhhhhhcCCCCCeeeCCCcH
Confidence 567788888 8999999999811 11359999999999999999998764 89999999999
Q ss_pred HHHHHhh----------ccCC-----------CceEEeCCCceEEE-CCEEEEEEecCCCcCceEEEEEEcCCCCcccEE
Q 001045 94 RLLSQIL----------NINP-----------KFIYPLPIKIPVLI-DGCEVVLVGANHCPGAVQFLFKVPGRNGGFERY 151 (1176)
Q Consensus 94 ~ll~~~l----------~~~~-----------~~i~~l~~~~~~~i-~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~I 151 (1176)
+++-... |-.+ ....++++|+..+| .++++||+.|||+.||+|..++..+ |. .+|
T Consensus 271 Dlm~LLq~Dyi~va~keg~~ppY~~k~v~~~lkhtItldYgevTDIaPDirLTf~NAGHILGSA~~HlHIGd--Gl-yNi 347 (637)
T COG1782 271 DLMVLLQLDYIEVAEKEGGEPPYESKDVRKVLKHTITLDYGEVTDIAPDIRLTFYNAGHILGSAMAHLHIGD--GL-YNI 347 (637)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHheeeeeccCcccccCCccEEEEecccchhcceeeEEEecC--Cc-eeE
Confidence 9987543 1111 23678999999998 5899999999999999999999965 32 799
Q ss_pred EEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccch
Q 001045 152 VHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIGK 231 (1176)
Q Consensus 152 lYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slGR 231 (1176)
+|||||++..+.+.+++...|++++.||+|+||+.+...+|+++++++++.+.+.+++.+ ||+ ||||+|++||
T Consensus 348 ~yTGDfk~~~trLl~~A~n~FpRvEtlimEsTYGg~~d~q~~R~eaE~~L~~vi~~t~~r-----GGK--vLIP~fAVGR 420 (637)
T COG1782 348 VYTGDFKFEKTRLLEPANNKFPRVETLIMESTYGGRDDVQPPREEAEKELIKVINDTLKR-----GGK--VLIPVFAVGR 420 (637)
T ss_pred EEecccccceeeecChhhccCcchhheeeeeccCCccccCccHHHHHHHHHHHHHHHHhc-----CCe--EEEEeeeccc
Confidence 999999999999999998888999999999999988888999999999999999999888 788 7999999999
Q ss_pred HHHHHHHHHHc---C----CcEEEccchHHHHHHh-CCC---------------C----CCccccC-----------CCC
Q 001045 232 EKILIEIFKKC---G----RKVCVDSRKMEVLRVL-GYG---------------D----SGVFTED-----------ESE 273 (1176)
Q Consensus 232 ~q~ll~ia~~~---g----~~I~vdg~~~~il~~l-g~~---------------~----~~~~t~d-----------~~~ 273 (1176)
.|+++-++++. | .|||+||+.++..... .|| . ...|..- ..+
T Consensus 421 ~QEvM~VLee~mr~g~ipe~PVYlDGMI~EatAIhtaYPEyL~~~lr~~I~~~g~NPF~se~f~~V~~~~~r~~i~~~~e 500 (637)
T COG1782 421 SQEVMIVLEEAMRKGLIPEVPVYLDGMIWEATAIHTAYPEYLNKELRERIFHEGENPFLSEIFKRVEGSDERQEIIESDE 500 (637)
T ss_pred cceehhHHHHHHhcCCCCCCceeeeeeeeehhhhhhcCHHhhhHHHHHHHhcCCCCCccccceeecCChhHHHHHhcCCC
Confidence 99999888764 2 6999999988643211 111 1 1111100 002
Q ss_pred CeEEEecCh--------HHHHhcCCCceEEEEeccceeecccCce------ee----------eccCCeeEEEE-eecCC
Q 001045 274 TDVHVVGWN--------EIMVERGYDKVVGFVPTGWTYEVKRNKF------AV----------RSKDAFEIHLV-PYSEH 328 (1176)
Q Consensus 274 ~~I~v~~~~--------~~~~~~g~~~~v~i~ptGw~~~~~~~~~------~v----------~~~~~~~v~~i-~~SgH 328 (1176)
..|++..++ +.+.+...++...++..||+++.+.|+- .+ ..+.++.|+.+ .||||
T Consensus 501 p~iIlaTSGMlnGGPvveyfk~lA~DprntliFVgYQAeGTLGRriq~G~kEipi~~~~G~te~i~inMeV~tieGFSGH 580 (637)
T COG1782 501 PAIILATSGMLNGGPVVEYFKHLAPDPKNTLIFVGYQAEGTLGRRIQSGAKEIPIPGEDGKTEVIKVNMEVETIEGFSGH 580 (637)
T ss_pred CeEEEeccccccCCcHHHHHHHhCCCCCceEEEEEeccCcchhhhhhcCceecccccCCCCeEEEEEEEEEEEecCcCCC
Confidence 234444333 2222333344444555788887654431 01 13345666666 59999
Q ss_pred CCHHHHHHHHHHcCC--CEEEEEecCC
Q 001045 329 SNYDELREYVKFLKP--KRVIPTVGMD 353 (1176)
Q Consensus 329 As~~EL~~~V~~lrP--k~VIPvHG~~ 353 (1176)
|+..+|.+||+.++| ++|+.+||..
T Consensus 581 sdrrqL~~yvr~~~PkP~ki~~~HGe~ 607 (637)
T COG1782 581 SDRRQLMKYVRRMNPKPEKILLNHGEP 607 (637)
T ss_pred ccHHHHHHHHHhcCCCCceeEeecCCh
Confidence 999999999999955 7999999943
No 21
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor
Probab=100.00 E-value=1.1e-36 Score=324.11 Aligned_cols=184 Identities=30% Similarity=0.520 Sum_probs=158.7
Q ss_pred ccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEE
Q 001045 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILD 1037 (1176)
Q Consensus 958 i~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILD 1037 (1176)
|+||||+++.++.+ +.+|++|+||||+|||+|+. ++.|++|||+|+++|..||+|...+.+. ...++|||
T Consensus 1 i~pmLa~~~~~~~~------~~~~~~e~K~DG~R~~i~~~-~~~v~~~SR~g~~~t~~~p~l~~~~~~~---~~~~~iLD 70 (190)
T cd07906 1 IEPMLATLVDEPPD------GEDWLYEIKWDGYRALARVD-GGRVRLYSRNGLDWTARFPELAEALAAL---PVRDAVLD 70 (190)
T ss_pred CCCeECCcCCCCCC------CCCeEEEEeEceEEEEEEEE-CCEEEEEcCCCCcchhhhHHHHHHHHhc---CCCCEEEE
Confidence 68999999987643 67899999999999999994 7899999999999999999999887763 46899999
Q ss_pred EEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcE
Q 001045 1038 AEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYF 1117 (1176)
Q Consensus 1038 GElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i 1117 (1176)
||||+||.. ...+|+.+++|.+... ......+++|+|||||++||++++++||.||+++|++++ .+.++++
T Consensus 71 GElv~~~~~---~~~~F~~l~~~~~~~~-----~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~-~~~~~~i 141 (190)
T cd07906 71 GEIVVLDEG---GRPDFQALQNRLRLRR-----RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELL-PAGSPRL 141 (190)
T ss_pred eEEEEECCC---CCCCHHHHHHhhcccc-----hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHh-ccCCCcE
Confidence 999999964 2479999999976532 123456899999999999999999999999999999999 5556788
Q ss_pred EEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1118 QYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1118 ~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.++++... +.+++|++++++|+||||+|+++ |+|+||+||..|
T Consensus 142 ~~~~~~~~--------------~~~~~~~~~~~~g~EGiv~K~~~--s~Y~~g~rs~~w 184 (190)
T cd07906 142 RVSEHFEG--------------GGAALFAAACELGLEGIVAKRAD--SPYRSGRRSRDW 184 (190)
T ss_pred EECceEcC--------------CHHHHHHHHHHcCCcEEEEecCC--CCcCCCCCCCcc
Confidence 88776532 23789999999999999999998 999999999999
No 22
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.2e-36 Score=346.15 Aligned_cols=193 Identities=25% Similarity=0.418 Sum_probs=162.0
Q ss_pred CcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCC
Q 001045 951 SMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPA 1030 (1176)
Q Consensus 951 ~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~ 1030 (1176)
.+.+|.|++||||..+..++ .+.+|++|+||||+|||+|+ .+++|++|||||+++|..||+|.+.+... .
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~-~~~~v~l~SRng~d~t~~fPel~~~~~~~---~ 71 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFR-DGDEVELGSRNGKPLTRYFPELVAALRAE---L 71 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEE-ECCEEEEEeCCCCCchhhhHHHHHHHHhh---C
Confidence 35788999999999876544 24679999999999999999 48899999999999999999999888764 3
Q ss_pred CCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhc
Q 001045 1031 AGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFY 1110 (1176)
Q Consensus 1031 ~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~ 1110 (1176)
+.+||||||||+||. + . .+|+.|++|.+.... .+.......+++|++|||||+||++|+++||.+||++|++++
T Consensus 72 ~~~~vLDGEiVv~~~--~-~-~~F~~Lq~r~~~~~~-~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~- 145 (350)
T PRK08224 72 PERCVLDGEIVVARD--G-G-LDFEALQQRIHPAAS-RVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAA- 145 (350)
T ss_pred CCCEEEeeEEEEeCC--C-C-CCHHHHHhhhhcccc-chhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhc-
Confidence 579999999999983 2 3 899999999653222 233334567899999999999999999999999999999999
Q ss_pred ccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1111 DEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1111 ~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.. .+.+++++.+ .+.++++++|+++++.|+||||+|+++ |+|+||+|+ |
T Consensus 146 ~~-~~~i~~~~~~------------~~~~~~~~~~~~a~~~G~EGIV~Kr~d--S~Y~~Grr~--W 194 (350)
T PRK08224 146 AG-SGPVHLTPAT------------TDPATARRWFEEFEGAGLDGVIAKPLD--GPYQPGKRA--M 194 (350)
T ss_pred CC-CCcEEEeccc------------CCHHHHHHHHHHHHhCCCcEEEEeCCC--CCcCCCCcC--E
Confidence 33 3456666542 346789999999999999999999998 999999998 7
No 23
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=100.00 E-value=3e-33 Score=343.09 Aligned_cols=307 Identities=21% Similarity=0.319 Sum_probs=228.6
Q ss_pred CCCCCCeeE-eCCccEEEecCCcC-----------------CCCccEEEeccCChhhhCCcccCC---CCceEEeCHHHH
Q 001045 35 PRTFPPSKH-VPNTRFLIDAFRYA-----------------ADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSEITS 93 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~~~~-----------------~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~~T~ 93 (1176)
+.+.+|+.+ .++..+++|||-.. ..++++|||||+|.||+|+||.+. +.+|||||+.|+
T Consensus 185 eVG~Sc~Ll~~~~~~ILIDcG~~~~~~~~~~~p~l~~~~~~~~~IDaVlITHaH~DHiG~LP~L~k~g~~gpIY~T~pT~ 264 (630)
T TIGR03675 185 EVGRSALLLSTPESRILLDCGVNVGANGDNAYPYLDVPEFQLDELDAVVITHAHLDHSGLVPLLFKYGYDGPVYCTPPTR 264 (630)
T ss_pred ccCCCEEEEEECCCEEEEECCCCccccchhhcccccccCCCHHHCcEEEECCCCHHHHhhHHHHHHhCCCCceeecHHHH
Confidence 345578888 78999999998221 146899999999999999999753 368999999999
Q ss_pred HHHHHhh----------ccCC-----------CceEEeCCCceEEE-CCEEEEEEecCCCcCceEEEEEEcCCCCcccEE
Q 001045 94 RLLSQIL----------NINP-----------KFIYPLPIKIPVLI-DGCEVVLVGANHCPGAVQFLFKVPGRNGGFERY 151 (1176)
Q Consensus 94 ~ll~~~l----------~~~~-----------~~i~~l~~~~~~~i-~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~I 151 (1176)
+++...+ +..+ ..+.++++++++.+ ++++|+++++||++||+++.|+..++ + .+|
T Consensus 265 ~l~~~ll~D~~~i~~~~g~~~~y~~~dv~~~~~~~~~l~yg~~~~i~~~i~vt~~~AGHilGsa~~~~~i~dg-~--~~I 341 (630)
T TIGR03675 265 DLMTLLQLDYIDVAQREGKKPPYSSKDVREALKHTITLDYGEVTDIAPDIKLTFYNAGHILGSAIAHLHIGDG-L--YNI 341 (630)
T ss_pred HHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHhccEEeCCCCeEEecCCEEEEEecCccccCceEEEEEECCC-C--EEE
Confidence 9876543 1111 23678999999999 58999999999999999999987542 2 589
Q ss_pred EEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccch
Q 001045 152 VHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIGK 231 (1176)
Q Consensus 152 lYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slGR 231 (1176)
+|||||++....+..+....+.++|+||+||||+++.+.++++.+..+++.+.+.+++.+ +|+ |+||+|++||
T Consensus 342 vYTGD~~~~~~~ll~~a~~~~~~vD~LI~ESTYg~~~~~~~~r~~~e~~l~~~I~~tl~~-----gG~--VLIP~favGR 414 (630)
T TIGR03675 342 VYTGDFKYEKTRLLDPAVNKFPRVETLIMESTYGGRDDYQPSREEAEKELIKVVNETIKR-----GGK--VLIPVFAVGR 414 (630)
T ss_pred EEeCCCCCCCCcCccchhhcCCCCCEEEEeCccCCCCCCCCCHHHHHHHHHHHHHHHHhC-----CCE--EEEEechhHH
Confidence 999999998877666554445789999999999998777899999999999999999876 788 7999999999
Q ss_pred HHHHHHHHHHc-------CCcEEEccchHHHHHHh----CCC------------CC----Cccc--cC---------CCC
Q 001045 232 EKILIEIFKKC-------GRKVCVDSRKMEVLRVL----GYG------------DS----GVFT--ED---------ESE 273 (1176)
Q Consensus 232 ~q~ll~ia~~~-------g~~I~vdg~~~~il~~l----g~~------------~~----~~~t--~d---------~~~ 273 (1176)
.|+++.++.++ ..|||+|++..++...+ .+. .. ..|. .+ ...
T Consensus 415 ~QEll~~L~~~~~~g~lp~~pIy~dg~~~~~t~i~~~~~e~l~~~~~~~i~~~~~npf~~~~~~~v~~~~~~~~i~~~~~ 494 (630)
T TIGR03675 415 AQEVMLVLEEAMRKGLIPEVPVYLDGMIWEATAIHTAYPEYLNKELRERIFHEGENPFLSEIFVRVEGSDERREIIESDE 494 (630)
T ss_pred HHHHHHHHHHHHHhCCCCCCcEEEEchHHHHHHHHHHhHHHhCHHHHHHHhhcCCCcccCCceEEeCCHHHHHHHhcCCC
Confidence 99999888753 36999999766543221 000 00 0010 00 113
Q ss_pred CeEEEecCh--------HHHHhcCCCceEEEEeccceeecccCc--------eee-------eccCCeeEEEEe-ecCCC
Q 001045 274 TDVHVVGWN--------EIMVERGYDKVVGFVPTGWTYEVKRNK--------FAV-------RSKDAFEIHLVP-YSEHS 329 (1176)
Q Consensus 274 ~~I~v~~~~--------~~~~~~g~~~~v~i~ptGw~~~~~~~~--------~~v-------~~~~~~~v~~i~-~SgHA 329 (1176)
..|++++.+ ..+.....++...+..+||+.+.+.++ +.+ ....+++|+.+. |||||
T Consensus 495 p~VIiatsGMl~gG~~~~~l~~l~~d~kn~IifvGyqa~gTlGr~l~~g~~~i~i~g~~~~~~i~v~~~V~~~~gfSaHa 574 (630)
T TIGR03675 495 PAIILATSGMLNGGPVVEYLKLLAPDPRNSLVFVGYQAEGTLGRRIQSGWREIPLTDEGKTETIKINMEVETVEGFSGHS 574 (630)
T ss_pred CEEEEECCCCCCcchHHHHHHHHcCCCCCeEEEeCCCCCCchHHHHhcCCcEEEecCCCCceEEEEEEEEEEeCCccccC
Confidence 446665544 122223334444555689998765432 111 123457788887 99999
Q ss_pred CHHHHHHHHHHcCC--CEEEEEec
Q 001045 330 NYDELREYVKFLKP--KRVIPTVG 351 (1176)
Q Consensus 330 s~~EL~~~V~~lrP--k~VIPvHG 351 (1176)
|+.||.+|++.++| ++|+.+||
T Consensus 575 D~~~L~~~v~~~~p~p~~v~lvHG 598 (630)
T TIGR03675 575 DRRQLMNYVRRMQPKPEKILLNHG 598 (630)
T ss_pred CHHHHHHHHHhcCCCCCEEEEEcC
Confidence 99999999999966 99999999
No 24
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2e-34 Score=322.43 Aligned_cols=180 Identities=26% Similarity=0.478 Sum_probs=150.7
Q ss_pred CccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEE
Q 001045 957 PIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFIL 1036 (1176)
Q Consensus 957 Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~IL 1036 (1176)
.++||||...... +++.+|++|+||||+|||+|+ .++.|++|||||+++|..||++.... .+.+|||
T Consensus 2 ~~~PmLa~~~~~~------~~~~~~~~E~K~DG~R~~~~~-~~~~v~l~SR~g~~~t~~fPe~~~~~------~~~~~vL 68 (275)
T PRK07636 2 FISPMLLESAKEP------FNSENYITEPKFDGIRLIASK-NNGLIRLYTRHNNEVTAKFPELLNLD------IPDGTVL 68 (275)
T ss_pred CcCCccCCcCCCC------CCCCcEEEEEEEceeEEEEEE-eCCEEEEEeCCCCCchhhhhhHHhhh------cCCCEEE
Confidence 3789999876533 356789999999999999999 58899999999999999999998743 1357999
Q ss_pred EEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCc
Q 001045 1037 DAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGY 1116 (1176)
Q Consensus 1037 DGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~ 1116 (1176)
|||||+||.. ...+|+.|++|.+.... ....+++|++|||||+||++|+++||.+||++|++++ .+ .+.
T Consensus 69 DGElv~~d~~---g~~~F~~l~~r~~~~~~------~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~-~~-~~~ 137 (275)
T PRK07636 69 DGELIVLGST---GAPDFEAVMERFQSKKS------TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLL-LP-HPN 137 (275)
T ss_pred EeEEEEECCC---CCCCHHHHHHHhccccc------cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhc-CC-CCC
Confidence 9999999963 34699999999664321 1246899999999999999999999999999999999 43 345
Q ss_pred EEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1117 FQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1117 i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
+.++++.. ++.+++|+++++.|.||||+|+++ |+|.||+||.+|
T Consensus 138 ~~~~~~~~--------------~~~~~~~~~~~~~g~EGiV~K~~d--s~Y~~g~Rs~~W 181 (275)
T PRK07636 138 VKIIEGIE--------------GHGTAYFELVEERELEGIVIKKAN--SPYEINKRSDNW 181 (275)
T ss_pred EEEccccc--------------ccHHHHHHHHHHcCCcEEEEeCCC--CCCCCCCCCCCe
Confidence 66555432 356789999999999999999998 999999999999
No 25
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.6e-34 Score=349.43 Aligned_cols=191 Identities=26% Similarity=0.410 Sum_probs=156.3
Q ss_pred ccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcC--CCCCCeE
Q 001045 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCK--PAAGTFI 1035 (1176)
Q Consensus 958 i~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~--~~~~~~I 1035 (1176)
++||||..+..++ .+..|++|+||||+|||+|+ .++.|++|||||+++|.+||+|.+.+..+.. ....+||
T Consensus 1 ~~PMLa~~~~~~p------~g~~w~~E~K~DG~R~~~h~-~~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~~~~~~I 73 (610)
T PRK09633 1 MKPMQPTLTTSIP------IGDEWRYEVKYDGFRCLLII-DETGITLISRNGRELTNTFPEIIEFCESNFEHLKEELPLT 73 (610)
T ss_pred CCCCcCCcCCCCC------CCCcEEEEEeEcceEEEEEE-ECCEEEEEeCCCCcchhhhhHHHHHHHhhhhccccCCcee
Confidence 5799998877654 36789999999999999999 5889999999999999999999988776432 1224799
Q ss_pred EEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCC-
Q 001045 1036 LDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKM- 1114 (1176)
Q Consensus 1036 LDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~- 1114 (1176)
||||||+||.. ...+|+.|++|.+......+.......+++|++|||||+||++|+++||.+||++|++++. ..+
T Consensus 74 LDGEiVvld~~---g~~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~-~~~~ 149 (610)
T PRK09633 74 LDGELVCLVNP---YRSDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMK-AAKL 149 (610)
T ss_pred eeeEEEEecCC---CCCCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhh-hccc
Confidence 99999999853 2469999999965433222333345678999999999999999999999999999999993 321
Q ss_pred ---------CcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1115 ---------GYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1115 ---------~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
..+.+ ..+.++++++|+++++.|+||||+|+++ |+|+||+||.+|
T Consensus 150 ~~~~~~~~~~~i~~---------------~~~~~~~~~l~~~a~~~g~EGIV~Kr~d--S~Y~~G~Rs~~W 203 (610)
T PRK09633 150 PASPDPYAKARIQY---------------IPSTTDFDALWEAVKRYDGEGIVAKKKT--SKWLENKRSKDW 203 (610)
T ss_pred ccccccccccceEE---------------cCCHHHHHHHHHHHHHcCCceEEEeCCC--CCCCCCCCCCCe
Confidence 12222 2345689999999999999999999998 999999999999
No 26
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=9.3e-34 Score=348.44 Aligned_cols=183 Identities=28% Similarity=0.480 Sum_probs=156.6
Q ss_pred cCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCC
Q 001045 952 MVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAA 1031 (1176)
Q Consensus 952 l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~ 1031 (1176)
..++.|++||||+.+... .+.+..|++|+||||+|||+|+ .++.|++|||||+++|.+||+|.+....+ ..
T Consensus 455 ~~~~~~v~PMLA~~~~~~-----~~~~~~w~~E~K~DG~R~~~~~-~~g~vrL~SRnG~d~T~~fPel~~~~~~l---~~ 525 (764)
T PRK09632 455 AEEADDLAPMLATAGTVA-----GLKASQWAFEGKWDGYRLLAEA-DHGALRLRSRSGRDVTAEYPELAALAEDL---AD 525 (764)
T ss_pred CCCCCCCcCccCCcCCCC-----CCCCCCEEEEEEECceeEEEEE-eCCEEEEEeCCCCCccccchhHHHHHhhC---CC
Confidence 467899999999976422 2456789999999999999999 58999999999999999999999865553 34
Q ss_pred CCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcc
Q 001045 1032 GTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYD 1111 (1176)
Q Consensus 1032 ~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~ 1111 (1176)
.+||||||||+||.. ...+|+.|++|.+ ..+++|++|||||+||++|+++||.+||++|++++ .
T Consensus 526 ~~~ILDGEiVvld~~---G~~~F~~Lq~r~~------------~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~-~ 589 (764)
T PRK09632 526 HHVVLDGEIVALDDS---GVPSFGLLQNRGR------------DTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALA-P 589 (764)
T ss_pred cceeeeeEEEEeCCC---CCCCHHHHhhhhh------------cCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhh-C
Confidence 699999999999974 3469999999832 24699999999999999999999999999999999 3
Q ss_pred cCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1112 EKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1112 ~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
..+.+.+++++. .+++++|+.++++|+||||+|+++ |+|+||+||.+|
T Consensus 590 -~~~~i~~s~~~~--------------~~~~~~l~~a~~~GlEGIVaKr~d--S~Y~pGrRs~~W 637 (764)
T PRK09632 590 -SGGSLTVPPLLP--------------GDGAEALAYSRELGWEGVVAKRRD--STYQPGRRSSSW 637 (764)
T ss_pred -CCCcEEecceec--------------ccHHHHHHHHHHcCCcEEEEeCCC--CCCCCCCcCCCe
Confidence 345677776653 246789999999999999999998 999999999999
No 27
>COG0595 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]
Probab=100.00 E-value=6.2e-33 Score=331.65 Aligned_cols=311 Identities=25% Similarity=0.332 Sum_probs=228.4
Q ss_pred CCCCCCeeE-eCCccEEEecCCcCCCCccEEEeccCChhhhCCcccCCC--C-ceEEeCHHHHHHHHHhhc---cCC--C
Q 001045 35 PRTFPPSKH-VPNTRFLIDAFRYAADFSVSYFLSHFHSDHYTGLSPSWS--K-GIIFCSEITSRLLSQILN---INP--K 105 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~~~~~~~i~avfITHaH~DHiggL~~l~~--~-~pIY~s~~T~~ll~~~l~---~~~--~ 105 (1176)
+...+|.++ +|+..++.+. ..+++++||||+|.||+||+|+++. . .|||+|+.|+.+++..+. ... .
T Consensus 44 ~~~~~gvDliIPd~~yl~~n----~~kvkgI~lTHgHeDHIGaip~ll~~~~~~piy~s~lt~~Li~~k~~~~~~~~~~~ 119 (555)
T COG0595 44 EDDLLGVDLIIPDFSYLEEN----KDKVKGIFLTHGHEDHIGALPYLLKQVLFAPIYASPLTAALIKEKLKEHGLFKNEN 119 (555)
T ss_pred ccccccccEEecChHHhhhc----cccceEEEecCCchhhccchHHHHhcCCcCceecCHhhHHHHHHHHHHhccccccC
Confidence 446777766 6777777776 4689999999999999999999876 3 899999999999998874 112 3
Q ss_pred ceEEeCCCceEEECCEEEEEEecCC-CcCceEEEEEEcCCCCcccEEEEECCCCCcccccchh-h----hhcc--CCCcE
Q 001045 106 FIYPLPIKIPVLIDGCEVVLVGANH-CPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQP-V----MNEF--AGCDA 177 (1176)
Q Consensus 106 ~i~~l~~~~~~~i~~~~Vt~~~a~H-~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~-~----l~~~--~~vDv 177 (1176)
.++.++.+..++++++.|+++++.| ||+|+++.++++. +.|+|||||++++...... . +.++ .++++
T Consensus 120 ~~~ev~~~~~i~~~~~~v~f~~vtHSIPds~g~~i~Tp~-----G~Iv~TGDFk~d~~~~~g~~~d~~r~~~~g~eGVl~ 194 (555)
T COG0595 120 ELHEVKPGSEIKFGSFEVEFFPVTHSIPDSLGIVIKTPE-----GNIVYTGDFKFDPTPVDGEPTDLARLAEIGKEGVLA 194 (555)
T ss_pred ceEEeCCCCeEEeCcEEEEEEeecccCccceEEEEECCC-----ccEEEeCCEEecCCcCCCCcCCHHHHHHhccCCcEE
Confidence 5889999999999999999999999 9999999999987 4899999999998765522 1 2222 68999
Q ss_pred EEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccc--cchHHHHHHHHHHcCCcEEEccchHHH
Q 001045 178 VFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYV--IGKEKILIEIFKKCGRKVCVDSRKMEV 255 (1176)
Q Consensus 178 LI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~s--lGR~q~ll~ia~~~g~~I~vdg~~~~i 255 (1176)
||+|||++......++++++.+.+.++++.+ +|+ |++.+|+ ++|.|.++++|.++||++++.|+.|..
T Consensus 195 LisdsTna~~pg~t~SE~~v~~~l~~i~~~a--------~gr--VIv~tfaSni~Ri~~i~~~A~~~gR~vvv~GrSm~~ 264 (555)
T COG0595 195 LISDSTNAENPGFTPSESEVGENLEDIIRNA--------KGR--VIVTTFASNIERIQTIIDAAEKLGRKVVVTGRSMER 264 (555)
T ss_pred EEeCCcccCCCCCCCCHHHHHHHHHHHHHhC--------CCc--EEEEEchhhHHHHHHHHHHHHHcCCeEEEEcHhHHH
Confidence 9999999997777899999888888888766 567 5566666 999999999999999999999999865
Q ss_pred H----HHhCCC---CCCccccCC------CCCeEEEecChHH------HHhcCC--------CceEEEE--e-cc--cee
Q 001045 256 L----RVLGYG---DSGVFTEDE------SETDVHVVGWNEI------MVERGY--------DKVVGFV--P-TG--WTY 303 (1176)
Q Consensus 256 l----~~lg~~---~~~~~t~d~------~~~~I~v~~~~~~------~~~~g~--------~~~v~i~--p-tG--w~~ 303 (1176)
+ +.+|+. +..++.... .+..|.++|.+.. .+..+. ...+.|. | +| |..
T Consensus 265 ~~~~a~~lg~~~~~~~~~i~~~~~~~~~~~~~lii~TG~qgep~aaL~r~a~~~h~~~~i~~gD~vIfss~~ipgne~~~ 344 (555)
T COG0595 265 LIAIARRLGYLKLPDESFIEIREVKRYPDEEVLIICTGSQGEPMAALSRMANGEHRYVKIKEGDTVIFSSSPIPGNEAAV 344 (555)
T ss_pred HHHHHhhcccccCccccccCHHHhccccccceEEEEeCCCCCchhhhhHhhcCCccceecCCCCeEEEeccCcCCcHHHH
Confidence 4 445543 222332211 1234667777721 111111 1222222 1 34 221
Q ss_pred ecccCceeeeccCCeeE-----EEEeecCCCCHHHHHHHHHHcCCCEEEEEecCCCCcCchHHHHHHHHHHHHHHHHh
Q 001045 304 EVKRNKFAVRSKDAFEI-----HLVPYSEHSNYDELREYVKFLKPKRVIPTVGMDIEKLDSKHANKMRKYFAGLVDEM 376 (1176)
Q Consensus 304 ~~~~~~~~v~~~~~~~v-----~~i~~SgHAs~~EL~~~V~~lrPk~VIPvHG~~~e~~~~~E~~~m~k~f~~l~~~~ 376 (1176)
....+.+ .+.+.++ ..+|.|||++.+||+.|++.++|+++||+|| |++++.+|.+-....+
T Consensus 345 ~~~~n~l---~~~g~~i~~~~~~~~hvSGHas~eel~~mi~~l~Pky~iPvHG---------eyr~~~~~a~la~~~G 410 (555)
T COG0595 345 YRLLNRL---YKAGAKVITGGDKKVHVSGHASREELKLMINLLRPKYLIPVHG---------EYRMLVAHAKLAEEEG 410 (555)
T ss_pred HHHHHHH---HhcCcEEeecccceeEecCCCChHHHHHHHHhhCCceecccCC---------CcHHHHHHHHHHHhcC
Confidence 1111111 1111111 4579999999999999999999999999999 7777777765544443
No 28
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=100.00 E-value=1e-32 Score=290.44 Aligned_cols=176 Identities=33% Similarity=0.590 Sum_probs=147.4
Q ss_pred cchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHhCCCh
Q 001045 713 APYIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEACGTNR 792 (1176)
Q Consensus 713 ~~F~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~g~~~ 792 (1176)
|+|.+||++|+.|++|++|++|+++|++||+.+ .++++.+++|+++++++|+|++|+||||++.|.+++++++|+++
T Consensus 1 m~F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~---~~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~ 77 (177)
T PF04675_consen 1 MPFSDLCELFEKLESTSSRLEKIAILSNFFRSW---REEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPE 77 (177)
T ss_dssp GBHHHHHHHHHHHHT---HHHHHHHHHHHHHTS---HCCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-H
T ss_pred CcHHHHHHHHHHHHhccCHHHHHHHHHHHHHHc---ccchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCH
Confidence 799999999999999999999999999999997 45559999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCChHHHHHHHHhhcc-ccCCCCCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHH
Q 001045 793 SKIRDMYNRLGDLGDVAQECRQTQA-LLAPPPPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRT 871 (1176)
Q Consensus 793 ~~i~~~~~~~GDlG~va~~~~~~q~-~l~~~~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRi 871 (1176)
+.+++.|++.||+|.+|+.+++++. ....+++|||.+||+.|++||..+|.+|+..|..+|..|+++|+|.|++||+|+
T Consensus 78 ~~~~~~~~~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~~E~k~i~Ri 157 (177)
T PF04675_consen 78 KSIDESYKKVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSPEEAKWIVRI 157 (177)
T ss_dssp HHHHHHHHHHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHHhcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCHHHHHHHHHH
Confidence 9999999999999999999987655 334578999999999999999999999999999999999999999999999999
Q ss_pred HhhccccCcchhhHHHHHHH
Q 001045 872 LVRNLRIGAMMRTILPALAQ 891 (1176)
Q Consensus 872 Ilk~LRiG~~~~tvl~aLa~ 891 (1176)
|+|+||||+++++|+.|||+
T Consensus 158 il~~lriG~~~~~il~ala~ 177 (177)
T PF04675_consen 158 ILKDLRIGVSEKTILDALAP 177 (177)
T ss_dssp HTT--SSS--HHHHHHHHHH
T ss_pred HhCCCeeCccHHHHHHHhCc
Confidence 99999999999999999874
No 29
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.
Probab=100.00 E-value=1.8e-32 Score=310.94 Aligned_cols=169 Identities=28% Similarity=0.483 Sum_probs=142.9
Q ss_pred cCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHH
Q 001045 977 QNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQE 1056 (1176)
Q Consensus 977 ~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~ 1056 (1176)
.+..|++|+||||+|||+|+ .++.|++|||||+++|..||++...+... ...+||||||||+||.. ...+|+.
T Consensus 10 ~~~~~~~E~K~DG~R~~~~~-~~~~v~l~SR~g~~~t~~~p~l~~~~~~~---~~~~~iLDGElv~~d~~---g~~~F~~ 82 (298)
T TIGR02779 10 TGDDWRYEVKYDGYRCLARI-EGGKVRLISRNGHDWTEKFPILAAALAAL---PILPAVLDGEIVVLDES---GRSDFSA 82 (298)
T ss_pred CCCCEEEEEEEceEEEEEEE-eCCEEEEEeCCCCchHhHhHHHHHHHHhC---CCCcEEEEeEEEEECCC---CCCCHHH
Confidence 46789999999999999999 48899999999999999999998876543 45799999999999973 2469999
Q ss_pred HhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCcccc
Q 001045 1057 LSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDV 1136 (1176)
Q Consensus 1057 L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~ 1136 (1176)
|++|.+... ..+++|++||||++||++++++||.+||++|++++ ...++.+.+... . ..
T Consensus 83 l~~r~~~~~---------~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~-~~~~~~~~~~~~-~----------~~ 141 (298)
T TIGR02779 83 LQNRLRAGR---------DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELL-KAIKGPLAPDRY-S----------VH 141 (298)
T ss_pred HHhhhhcCC---------CCceEEEEEeeeeECceehhcCCHHHHHHHHHHHh-cccCCCceeEec-c----------cC
Confidence 999976432 26799999999999999999999999999999999 443344333221 1 23
Q ss_pred CHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1137 SLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1137 ~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
+.+++.++|++++++|+||||+|+++ |+|+||+ |.+|
T Consensus 142 ~~~~~~~~~~~~~~~g~EGiv~K~~d--s~Y~~Gr-s~~W 178 (298)
T TIGR02779 142 FEGDGQALLEAACRLGLEGVVAKRRD--SPYRSGR-SADW 178 (298)
T ss_pred chhHHHHHHHHHHHcCCceEEEeCCC--CCCCCCC-CCCc
Confidence 56789999999999999999999998 9999995 8888
No 30
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.4e-32 Score=340.94 Aligned_cols=182 Identities=29% Similarity=0.487 Sum_probs=156.1
Q ss_pred CCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeE
Q 001045 956 VPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFI 1035 (1176)
Q Consensus 956 ~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~I 1035 (1176)
.+++||||.....+++ +.+|++|+||||+|||+|+ .++.|++|||||+++|.+||+|...+..+ ...+||
T Consensus 232 ~~i~PMLAt~~~~~p~------g~~W~~E~K~DG~R~~a~~-~gg~vrL~SRnG~d~T~~fPel~~~~~~l---~~~~~I 301 (860)
T PRK05972 232 DFLAPQLATLVDRPPS------GDGWIYEIKFDGYRILARI-EGGEVRLFTRNGLDWTAKLPALAKAAAAL---GLPDAW 301 (860)
T ss_pred cccCcccCccCCCCCC------cCceEEEeeeCcEEEEEEE-ECCEEEEEeCCCCccccccHHHHHHHHhc---CCCcee
Confidence 3589999998776653 5789999999999999999 58899999999999999999999988764 457999
Q ss_pred EEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCC
Q 001045 1036 LDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMG 1115 (1176)
Q Consensus 1036 LDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~ 1115 (1176)
||||||+||.. ...+|+.|++|.+... ..+++|++|||||+||++|+++||.+||++|++++.....+
T Consensus 302 LDGEIVvld~~---G~~~F~~Lq~r~~~~~---------~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~ 369 (860)
T PRK05972 302 LDGEIVVLDED---GVPDFQALQNAFDEGR---------TEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSD 369 (860)
T ss_pred EeEEEEEECCC---CCCCHHHHHHHhhccC---------CCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCC
Confidence 99999999964 3469999999865421 34799999999999999999999999999999999322235
Q ss_pred cEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1116 YFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1116 ~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.+++++++. .+.+++|+.+++.|+||||+|+++ |+|++| ||.+|
T Consensus 370 ~i~~s~~~~--------------~~g~~ll~~a~~~GlEGIVaKr~d--S~Y~~G-Rs~~W 413 (860)
T PRK05972 370 RIRFSEHFD--------------AGGDAVLASACRLGLEGVIGKRAD--SPYVSG-RSEDW 413 (860)
T ss_pred cEEEeceec--------------chHHHHHHHHHHcCCceEEEeCCC--CCCCCC-CCCCc
Confidence 788877653 246789999999999999999998 999987 89898
No 31
>TIGR00649 MG423 conserved hypothetical protein. Contains an ATP-binding domain at the N-terminal end of the protein. Possibly part of a superfamily of beta-lactmases
Probab=100.00 E-value=3e-31 Score=315.51 Aligned_cols=314 Identities=21% Similarity=0.274 Sum_probs=218.9
Q ss_pred CCCCCCeeE-eCCccEEEecCCcC---------------------CCCccEEEeccCChhhhCCcccCCC---CceEEeC
Q 001045 35 PRTFPPSKH-VPNTRFLIDAFRYA---------------------ADFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCS 89 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~~~~---------------------~~~i~avfITHaH~DHiggL~~l~~---~~pIY~s 89 (1176)
+.+.+|+.+ ..+..++|||+... ..++++|||||+|.||++||+.++. ..|||++
T Consensus 11 eiG~n~~ll~~~~~~iliD~G~~~~~~~~~g~~~~iPd~~~l~~~~~~i~~I~iTH~H~DHiggl~~l~~~~~~~~Vy~~ 90 (422)
T TIGR00649 11 EIGKNMYVVEIDDDVFIFDAGILFPEDAMLGVDGVIPDFSYLQENQDKVKGIFITHGHEDHIGAVPYLFHTVGFPPIYGT 90 (422)
T ss_pred ccCCeEEEEEECCeEEEEeCCCCCCcccccCCccccCCHHHHHhccccCCEEEECCCChHHhCcHHHHHHhCCCCeEEeC
Confidence 456778888 68889999998421 2478999999999999999998653 3689999
Q ss_pred HHHHHHHHHhhc---cC-CCceEEeCCCceEEEC-CEEEEEEecCC-CcCceEEEEEEcCCCCcccEEEEECCCCCcccc
Q 001045 90 EITSRLLSQILN---IN-PKFIYPLPIKIPVLID-GCEVVLVGANH-CPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTM 163 (1176)
Q Consensus 90 ~~T~~ll~~~l~---~~-~~~i~~l~~~~~~~i~-~~~Vt~~~a~H-~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~ 163 (1176)
+.|..++...+. +. ...+++++++++++++ +++|++++++| +|||++|+|++++ ++++|||||++....
T Consensus 91 ~~t~~~l~~~~~~~~~~~~~~~~~~~~~~~~~ig~~~~v~~~~~~H~~p~s~g~~i~~~~-----~~ivytGD~~~~~~~ 165 (422)
T TIGR00649 91 PLTIALIKSKIKENKLNVRTDLLEIHEGEPIETGENHTIEFIRITHSIPDSVGFALHTPL-----GYIVYTGDFKFDNTP 165 (422)
T ss_pred HHHHHHHHHHHHhcCCCCCCceEEeCCCCEEEeCCceEEEEEECCCCCcceEEEEEEeCC-----cEEEECCCcCCCCCc
Confidence 999999987653 11 2247789999999996 59999999999 8999999999864 589999999987655
Q ss_pred cch-h----hhhcc--CCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccc--cchHHH
Q 001045 164 LLQ-P----VMNEF--AGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYV--IGKEKI 234 (1176)
Q Consensus 164 ~~~-~----~l~~~--~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~s--lGR~q~ 234 (1176)
... + .+... .++|+||+||||+.+....++++...+.+.+.+++. +++ +++++|+ ++|.|+
T Consensus 166 ~~~~~~d~~~l~~~~~~g~d~Li~EsT~~~~~~~~~~e~~~~~~i~~~~~~~--------~~~--viv~~fa~~~~R~~~ 235 (422)
T TIGR00649 166 VIGEPPDLNRIAEYGKKGVLLLISDSTNVENPGFTPSEAKVLEQLNDIFKNA--------KGR--VIVATFASNIHRVQQ 235 (422)
T ss_pred cCCcccCHHHHHhhcccCeEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHhC--------CCE--EEEEEccccHHHHHH
Confidence 431 1 12221 579999999999975555567777766666655432 556 6888998 999999
Q ss_pred HHHHHHHcCCcEEEccchHH----HHHHhCCCC-CC--cc-----ccCCCCCe-EEEecChH----HH--HhcCC-----
Q 001045 235 LIEIFKKCGRKVCVDSRKME----VLRVLGYGD-SG--VF-----TEDESETD-VHVVGWNE----IM--VERGY----- 290 (1176)
Q Consensus 235 ll~ia~~~g~~I~vdg~~~~----il~~lg~~~-~~--~~-----t~d~~~~~-I~v~~~~~----~~--~~~g~----- 290 (1176)
++++|++++++|+++|+.+. ++..+|+.. +. .+ ...+.+.. +.+++.+. .+ ...+.
T Consensus 236 i~~~a~~~~r~v~v~g~~~~~~~~~~~~~g~~~~~~~~~~~~~~i~~~~~~~~vii~tg~~g~~~~~l~~~~~~~~~~i~ 315 (422)
T TIGR00649 236 LIQIARKQGRKFAVYGRSMEHLFGIARRLGLIKNPHNNFISLKEVNNSPDENYLIITTGSQGEPYAALTRIANNEHEQIR 315 (422)
T ss_pred HHHHHHHhCCEEEEECccHHHHHHHHHHcCCccCCccceeCHHHHhcCCcccEEEEEeCCCCcHHHHHHHHhCCCCCcEE
Confidence 99999999999999986553 334455431 11 11 11111223 44455551 11 11111
Q ss_pred ---CceEEEEeccceeec-ccCc--ee-eeccCCeeEE-EEeecCCCCHHHHHHHHHHcCCCEEEEEecCCCCcCchHHH
Q 001045 291 ---DKVVGFVPTGWTYEV-KRNK--FA-VRSKDAFEIH-LVPYSEHSNYDELREYVKFLKPKRVIPTVGMDIEKLDSKHA 362 (1176)
Q Consensus 291 ---~~~v~i~ptGw~~~~-~~~~--~~-v~~~~~~~v~-~i~~SgHAs~~EL~~~V~~lrPk~VIPvHG~~~e~~~~~E~ 362 (1176)
...+.+..++|.... .... .. ...+.+++++ .+|+||||+.+||+.|++.++|+++||||| |+
T Consensus 316 l~~~d~vi~s~~~~~G~~~~~~~~~~~~~~~~~~~~~~~~~h~SgHa~~~dl~~~i~~~~Pk~~ipvHg---------e~ 386 (422)
T TIGR00649 316 IRKGDTVVFSAPPIPGNENIAVSILLDIRLNEVGARVIKRIHVSGHASQEDHKLLLRLLKPKYIIPVHG---------EY 386 (422)
T ss_pred eCCCCEEEEECCCCCcHHHHHHHHHHHHHHHhcCCEEEeceEecCCCCHHHHHHHHHHhCCCEEEecCC---------cH
Confidence 123444434444322 1000 00 0122344443 489999999999999999999999999999 88
Q ss_pred HHHHHHHHHH
Q 001045 363 NKMRKYFAGL 372 (1176)
Q Consensus 363 ~~m~k~f~~l 372 (1176)
+++.+|.+-+
T Consensus 387 ~~~~~~~~~a 396 (422)
T TIGR00649 387 RMLINHTKLA 396 (422)
T ss_pred HHHHHHHHHH
Confidence 8888777644
No 32
>COG1236 YSH1 Predicted exonuclease of the beta-lactamase fold involved in RNA processing [Translation, ribosomal structure and biogenesis]
Probab=99.98 E-value=3.2e-31 Score=313.53 Aligned_cols=318 Identities=23% Similarity=0.309 Sum_probs=232.6
Q ss_pred CCCCCCeeE-eCCccEEEecCCcCC------------CCccEEEeccCChhhhCCcccCCC---CceEEeCHHHHHHHHH
Q 001045 35 PRTFPPSKH-VPNTRFLIDAFRYAA------------DFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCSEITSRLLSQ 98 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~~~~~------------~~i~avfITHaH~DHiggL~~l~~---~~pIY~s~~T~~ll~~ 98 (1176)
+.+.+|..+ ..+..+++||+-... +.+|++||||+|.||+|+||.+.. .++||||+.|+++++.
T Consensus 11 evg~s~~~l~~~~~~il~D~G~~~~~~~~~~p~~~~~~~vDavllTHaHlDH~g~lp~l~~~~~~~~v~aT~~T~~l~~~ 90 (427)
T COG1236 11 EVGRSCVLLETGGTRILLDCGLFPGDPSPERPLLPPFPKVDAVLLTHAHLDHIGALPYLVRNGFEGPVYATPPTAALLKV 90 (427)
T ss_pred CcCcEEEEEEECCceEEEECCCCcCcCCccCCCCCCCCCcCEEEeccCchhhhcccHHHHHhccCCceeeccCHHHHHHH
Confidence 456778888 677899999984332 137999999999999999998544 4799999999999997
Q ss_pred hhc----cC----------------CCceEEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCC
Q 001045 99 ILN----IN----------------PKFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFR 158 (1176)
Q Consensus 99 ~l~----~~----------------~~~i~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr 158 (1176)
.+. .. ...++++++++++++++++|++++|||++||++|.++..+ .+|+||||++
T Consensus 91 ~l~d~~~~~~~~~~~~~~~~d~~~~~~~~~~~~yg~~~~v~~~~v~~~~AGHilGsa~~~le~~~-----~~ilytGD~~ 165 (427)
T COG1236 91 LLGDSLKLAEGPDKPPYSEEDVERVPDLIRPLPYGEPVEVGGVKVTFYNAGHILGSAAILLEVDG-----GRILYTGDVK 165 (427)
T ss_pred HHHHHHhhhcCCCCCCCchhHHHhhHhhEEEecCCCceEeeeEEEEEecCCCccceeEEEEEeCC-----ceEEEEeccC
Confidence 762 11 1246789999999999999999999999999999999865 5899999999
Q ss_pred CcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccchHHHHHHH
Q 001045 159 FCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIGKEKILIEI 238 (1176)
Q Consensus 159 ~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slGR~q~ll~i 238 (1176)
...+.+..++-.. ..+|+||+|+||++ ..+|++.+..+.+++.+++.+.+ ||. +++|+|++||.|+++.+
T Consensus 166 ~~~~~l~~~a~~~-~~~DvLI~EsTYg~--~~~~~r~~~e~~f~~~v~~~l~~-----GG~--vlipafa~graQEll~~ 235 (427)
T COG1236 166 RRKDRLLNGAELP-PCIDVLIVESTYGD--RLHPNRDEVERRFIESVKAALER-----GGT--VLIPAFALGRAQELLLI 235 (427)
T ss_pred CCcCCCCCccccC-CCCcEEEEecccCC--ccCCCHHHHHHHHHHHHHHHHhC-----CCE--EEEecccccHHHHHHHH
Confidence 8877766655111 22699999999999 46899999999999999999876 677 79999999999999999
Q ss_pred HHHcC----CcEEEccchHHHHHHh-----CCCCCCc-------c----------ccCC-CCCeEEEecCh--------H
Q 001045 239 FKKCG----RKVCVDSRKMEVLRVL-----GYGDSGV-------F----------TEDE-SETDVHVVGWN--------E 283 (1176)
Q Consensus 239 a~~~g----~~I~vdg~~~~il~~l-----g~~~~~~-------~----------t~d~-~~~~I~v~~~~--------~ 283 (1176)
++.++ .||++|+...+++..+ ++..... + .... ....+++...+ .
T Consensus 236 L~~~~~~~~~pi~~d~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~vi~a~~gm~~~g~~~~ 315 (427)
T COG1236 236 LRELGFAGDYPIYVDGPIARVALAYAKYPIGLDLPDLLKVAESRFRFVESRRNSMREGIDKGPAVVLAAPGMLKGGRSRY 315 (427)
T ss_pred HHHHhccCCCCeEeccHHHHHHHHHHHhchhccChHHHHHHHhhcccccchhhhhhhhccCCceEEEEecccccCCcHHH
Confidence 99988 8999999887665432 1111100 0 0000 11123333222 1
Q ss_pred HHHhcCCCceEEEEeccceeecccCc--------ee---eeccCCeeEEEEeecCCCCHHHHHHHHHHcCCCEEEEEecC
Q 001045 284 IMVERGYDKVVGFVPTGWTYEVKRNK--------FA---VRSKDAFEIHLVPYSEHSNYDELREYVKFLKPKRVIPTVGM 352 (1176)
Q Consensus 284 ~~~~~g~~~~v~i~ptGw~~~~~~~~--------~~---v~~~~~~~v~~i~~SgHAs~~EL~~~V~~lrPk~VIPvHG~ 352 (1176)
........+...+..+|++...+.++ +. ...+.+.+++.+-+|+||+..||.+||+.+.|++|+.+||.
T Consensus 316 ~~~~~~~~~~n~~~l~~~~~~~t~gr~~~~~~~~~~~~~~~i~~~~~ve~~~~s~Had~~~l~~~i~~~~~~~v~~~Hg~ 395 (427)
T COG1236 316 YLKHLLSDEKNWVLLPGYQAEGTLGRVLLEGGTSVHIKGIEIKVKARVEELDFSAHADGDELLEFIKDISPPKVVLVHGE 395 (427)
T ss_pred HHHHHhcCCcceEEEcccccCCcchhHHhcCCcEEeecceeecccceEEEeccccccCcHHHHHHHhcCCCceEEEEeCC
Confidence 11111122223344577776654322 11 12345567888999999999999999999999999999994
Q ss_pred CCCcCchHHHHHHHHHHHHHHHHh
Q 001045 353 DIEKLDSKHANKMRKYFAGLVDEM 376 (1176)
Q Consensus 353 ~~e~~~~~E~~~m~k~f~~l~~~~ 376 (1176)
. ..+...++.++.+.
T Consensus 396 ~---------~~~~~~~~~~~~e~ 410 (427)
T COG1236 396 P---------EYGAALRARLLEEL 410 (427)
T ss_pred c---------hhhhHHHHHHHHhh
Confidence 3 33344555555553
No 33
>KOG1136 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=99.97 E-value=1.5e-29 Score=273.24 Aligned_cols=304 Identities=15% Similarity=0.198 Sum_probs=221.2
Q ss_pred CCCCCCeeE-eCCccEEEecC---------CcC-----------CCCccEEEeccCChhhhCCcccC----CCCceEEeC
Q 001045 35 PRTFPPSKH-VPNTRFLIDAF---------RYA-----------ADFSVSYFLSHFHSDHYTGLSPS----WSKGIIFCS 89 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~---------~~~-----------~~~i~avfITHaH~DHiggL~~l----~~~~pIY~s 89 (1176)
..+.+|+++ |.|.++.+||+ |++ .+-++.|+|||+|.||+|+||+. .+++|||++
T Consensus 14 dvGrSCilvsi~Gk~iM~DCGMHMG~nD~rRfPdFSyI~~~g~~~~~idCvIIsHFHlDHcGaLPyfsEv~GY~GPIYMt 93 (501)
T KOG1136|consen 14 DVGRSCILVSIGGKNIMFDCGMHMGFNDDRRFPDFSYISKSGRFTDAIDCVIISHFHLDHCGALPYFSEVVGYDGPIYMT 93 (501)
T ss_pred ccCceEEEEEECCcEEEEecccccccCccccCCCceeecCCCCcccceeEEEEeeecccccccccchHhhhCCCCceEEe
Confidence 457789999 99999999997 111 15689999999999999999985 348999999
Q ss_pred HHHHHHHHHhhc------cC----------------CCceEEeCCCceEEEC-CEEEEEEecCCCcCceEEEEEEcCCCC
Q 001045 90 EITSRLLSQILN------IN----------------PKFIYPLPIKIPVLID-GCEVVLVGANHCPGAVQFLFKVPGRNG 146 (1176)
Q Consensus 90 ~~T~~ll~~~l~------~~----------------~~~i~~l~~~~~~~i~-~~~Vt~~~a~H~pGS~~flie~~~~~G 146 (1176)
.+|+++....+. ++ .+.+.++...+++.++ ++.|+++-|||+.|++||.+...+
T Consensus 94 ~PTkaicPvlLeDyRkv~vd~kGe~n~FT~q~I~nCMKKVv~i~l~qt~~vD~dl~IrayYAGHVLGAaMf~ikvGd--- 170 (501)
T KOG1136|consen 94 YPTKAICPVLLEDYRKVAVDRKGESNFFTTQDIKNCMKKVVAIDLHQTIQVDEDLQIRAYYAGHVLGAAMFYIKVGD--- 170 (501)
T ss_pred cchhhhchHHHHHHHHHhccccCcccceeHHHHHHHHhheeEeeehheEEecccceeeeeecccccceeEEEEEecc---
Confidence 999998776541 11 1236788889999985 799999999999999999999865
Q ss_pred cccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEec
Q 001045 147 GFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVAT 226 (1176)
Q Consensus 147 ~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~ 226 (1176)
.+|+||||+...++....+++..-.++|+||.|+||+... ..++...++++.+.+.+...+ ||+ ++||.
T Consensus 171 --~svvYTGDYnmTpDrHLGaA~id~~rpdlLIsESTYatti--Rdskr~rERdFLk~VhecVa~-----GGk--vlIPv 239 (501)
T KOG1136|consen 171 --QSVVYTGDYNMTPDRHLGAAWIDKCRPDLLISESTYATTI--RDSKRCRERDFLKKVHECVAR-----GGK--VLIPV 239 (501)
T ss_pred --eeEEEecCccCCcccccchhhhccccCceEEeeccceeee--ccccchhHHHHHHHHHHHHhc-----CCe--EEEEe
Confidence 6999999999999988888766668999999999999742 344455566788888887666 788 78999
Q ss_pred cccchHHHHHHHHHHc------CCcEEEc-cchH---HHHHHhC-CCC----CCccccCC----------------CCCe
Q 001045 227 YVIGKEKILIEIFKKC------GRKVCVD-SRKM---EVLRVLG-YGD----SGVFTEDE----------------SETD 275 (1176)
Q Consensus 227 ~slGR~q~ll~ia~~~------g~~I~vd-g~~~---~il~~lg-~~~----~~~~t~d~----------------~~~~ 275 (1176)
|++||+|++.-++..+ ..||++. |..- ..|..+. +.. ..++..+. ....
T Consensus 240 FALGRAQElCiLLd~YWERm~lk~Piyfs~Glte~an~yyk~fiswtn~~v~k~~~~rNmfdfkhiKpfd~~~~~~pGp~ 319 (501)
T KOG1136|consen 240 FALGRAQELCILLDDYWERMNLKVPIYFSSGLTEKANMYYKMFISWTNENVKKKFVERNMFDFKHIKPFDRSYIEAPGPM 319 (501)
T ss_pred eecchHHHHHHHHHHHHHhhccCCCccccccccchhchHhhhhhhhcccchhhhhccCCccccccCChhhhhhhcCCCCE
Confidence 9999999998888654 5788885 3322 1222221 110 01111111 1112
Q ss_pred EEEecCh--------HHHHhcCCCceEEEEeccceeecccCc--------eee---eccCCeeEEEEeecCCCCHHHHHH
Q 001045 276 VHVVGWN--------EIMVERGYDKVVGFVPTGWTYEVKRNK--------FAV---RSKDAFEIHLVPYSEHSNYDELRE 336 (1176)
Q Consensus 276 I~v~~~~--------~~~~~~g~~~~v~i~ptGw~~~~~~~~--------~~v---~~~~~~~v~~i~~SgHAs~~EL~~ 336 (1176)
+.....+ .++.++.+++...++.+||....+-|. ..+ .....+.++.+.||.||+...+.+
T Consensus 320 VlFatPGMLhaG~SLkvFK~W~~~~~NlvimPGYcV~GTvG~kvl~G~~kvei~~~~~eirl~V~~maFSaHaDAkGIm~ 399 (501)
T KOG1136|consen 320 VLFATPGMLHAGFSLKVFKKWCPDPLNLVIMPGYCVAGTVGHKVLNGATKVEIYGTKVEIRLKVEYMAFSAHADAKGIMQ 399 (501)
T ss_pred EEEcCCcccccccchHHHHhhCCCccceEeecCceeccchhhhhhCCccEEEEeeeEEEEEEEEEEeeeccccCchhHHH
Confidence 2222111 345555555544455688887654221 111 123446778899999999999999
Q ss_pred HHHHcCCCEEEEEecC
Q 001045 337 YVKFLKPKRVIPTVGM 352 (1176)
Q Consensus 337 ~V~~lrPk~VIPvHG~ 352 (1176)
+++...|++|+.|||.
T Consensus 400 li~~csPknVmlVHGE 415 (501)
T KOG1136|consen 400 LIKQCSPKNVMLVHGE 415 (501)
T ss_pred HHHhcCcceEEEEecc
Confidence 9999999999999993
No 34
>cd07896 Adenylation_kDNA_ligase_like Adenylation domain of kDNA ligases and similar proteins. The mitochondrial DNA of parasitic protozoans is highly unusual. It is termed the kinetoplast DNA (kDNA) and consists of circular DNA molecules (maxicircles) and several thousand smaller circular molecules (minicircles). This group is composed of kDNA ligase, Chlorella virus DNA ligase, and similar proteins. kDNA ligase and Chlorella virus DNA ligase are the smallest known ATP-dependent ligases. They are involved in DNA replication or repair. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. They have a highly modular architecture consisting of a unique arrangement of two or more discrete domains. The adenylation and the C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains comprise a catalytic core unit that is common to most me
Probab=99.96 E-value=3.5e-29 Score=262.95 Aligned_cols=169 Identities=23% Similarity=0.270 Sum_probs=136.6
Q ss_pred ccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEE
Q 001045 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILD 1037 (1176)
Q Consensus 958 i~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILD 1037 (1176)
++||||++.....+ +..|++|+||||+|||+|. + ++|||+|+++|.. +. +... ..++|||
T Consensus 1 ~~pmla~~~~~~~~------~~~~~~e~K~DG~R~~~~~--~---~~~SR~g~~~t~~-~~----~~~~----l~~~ilD 60 (174)
T cd07896 1 PELLLAKTYDEGED------ISGYLVSEKLDGVRAYWDG--K---QLLSRSGKPIAAP-AW----FTAG----LPPFPLD 60 (174)
T ss_pred CccccccccccCCC------hHHeeechhhceEEEEEec--c---EEEecCCcCCCCC-HH----HHhh----CCCCccC
Confidence 57999998875543 4689999999999999973 2 9999999999976 22 2221 2349999
Q ss_pred EEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcE
Q 001045 1038 AEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYF 1117 (1176)
Q Consensus 1038 GElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i 1117 (1176)
||+|+|+ .||+.+++|.++.... .....+++|++||||+ .+.||.+|+++|++++....++.+
T Consensus 61 GElv~~~-------~~f~~l~~~~~~~~~~----~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~~~~~ 123 (174)
T cd07896 61 GELWIGR-------GQFEQTSSIVRSKKPD----DEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNPHI 123 (174)
T ss_pred ceEEcCC-------CCHHHHHHHHhcCCCC----hhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCCCCcE
Confidence 9999975 2999999997654321 1235689999999999 678999999999999932225678
Q ss_pred EEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1118 QYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1118 ~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
.+++...+ .+.+++.++++++++.|+||||+|+++ ++|++| |+.+|
T Consensus 124 ~~~~~~~~----------~~~~~i~~~~~~~~~~g~EGlv~K~~d--s~Y~~g-R~~~w 169 (174)
T cd07896 124 KIVPQIPV----------KSNEALDQYLDEVVAAGGEGLMLRRPD--APYETG-RSDNL 169 (174)
T ss_pred EEEeeeee----------CCHHHHHHHHHHHHhcCCCeEEEecCC--CcccCC-cCCCc
Confidence 88888765 467899999999999999999999987 999988 78888
No 35
>PHA00454 ATP-dependent DNA ligase
Probab=99.96 E-value=1.5e-28 Score=280.69 Aligned_cols=190 Identities=21% Similarity=0.265 Sum_probs=150.0
Q ss_pred cCCCCcccCC--hhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHH------HhhcC--
Q 001045 959 KPMLAKITNG--VPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISII------NEFCK-- 1028 (1176)
Q Consensus 959 ~PMLA~~~~~--~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l------~~~~~-- 1028 (1176)
+||+|...+. +.+++++++ .|++|+||||+|||+|+.+++.|++|||||++ ||++.... .+.+.
T Consensus 7 ~~~~~~~~~~~~i~~~~~~~g--~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g~~----~p~l~~~~~~~~~~~~~~~~~ 80 (315)
T PHA00454 7 NPFRAVDFNESAIEKALEKAG--YLIADVKYDGVRGNIVVDNTADHGWLSREGKT----IPALEHLNGFDRRWAKLLNDD 80 (315)
T ss_pred CccccccCCHHHHHHHHHhCC--cEEEEEccceEEEEEEEcCCCeEEEEeCCCCc----ccchhhhhhhhhhhhhhhhhh
Confidence 5889887765 888888874 89999999999999999533359999999985 57665443 22211
Q ss_pred --CCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeC----Cccc---ccCCHH
Q 001045 1029 --PAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFAN----GEQL---LGYTLR 1099 (1176)
Q Consensus 1029 --~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~ln----G~~L---l~~Pl~ 1099 (1176)
..+.++|||||+|+.+ .+|+.+++|.++... +.......++.|++||||++| |+++ ..+||.
T Consensus 81 ~~~l~~~~vLDGElv~~~-------~~f~~~~~~l~~k~~--~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~ 151 (315)
T PHA00454 81 RCIFPDGFMLDGELMVKG-------VDFNTGSGLLRRKWK--VLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYE 151 (315)
T ss_pred hhcCCCCeEEEEEEEecC-------CCHHHHHHHhccCcc--chhhhccCceEEEEEEeeEeccccCCccccccccccHH
Confidence 1246899999999963 489999999764332 112234678999999999999 6665 789999
Q ss_pred HHHHHHHHhhcccCCC-cEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1100 QRRKYLKDLFYDEKMG-YFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1100 eRr~lL~~~~~~~~~~-~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
+||++|++++ ...+. .+++++++.+ .+.++++++|+++++.|+||||+|+++ |+|+||+|+.+|
T Consensus 152 ~Rr~~L~~l~-~~~~~~~~~~~~~~~~----------~~~~~~~~~~~~~~~~g~EGiv~K~~d--s~Y~~Grr~~~~ 216 (315)
T PHA00454 152 HVRAMVPLLM-EYFPEIDWFLSESYEV----------YDMESLQELYEKKRAEGHEGLVVKDPS--LIYRRGKKSGWW 216 (315)
T ss_pred HHHHHHHHHH-hhCCCcceEeeceEEc----------CCHHHHHHHHHHHHhCCCceEEEeCCC--CCCCCCCccCcE
Confidence 9999999998 33332 4788888764 468999999999999999999999998 999999998765
No 36
>KOG1137 consensus mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification]
Probab=99.96 E-value=2.9e-28 Score=277.98 Aligned_cols=335 Identities=18% Similarity=0.199 Sum_probs=246.4
Q ss_pred CCCCCCCeeE-eCCccEEEecCCcC---------------CCCccEEEeccCChhhhCCcccCCC----CceEEeCHHHH
Q 001045 34 IPRTFPPSKH-VPNTRFLIDAFRYA---------------ADFSVSYFLSHFHSDHYTGLSPSWS----KGIIFCSEITS 93 (1176)
Q Consensus 34 ~~r~~p~~~~-ipg~~~liD~~~~~---------------~~~i~avfITHaH~DHiggL~~l~~----~~pIY~s~~T~ 93 (1176)
.+.+++|..+ ..|..+++||+-++ .+.++.++|||+|.||++.||+... .+.+|++..|+
T Consensus 23 ~EVGRSC~ile~kGk~iMld~gvhpaysg~aslpf~d~vd~s~id~llIthFhldh~aslp~~~qkTsf~grvfmth~Tk 102 (668)
T KOG1137|consen 23 NEVGRSCHILEYKGKTIMLDCGVHPAYSGMASLPFYDEVDLSAIDPLLITHFHLDHAASLPFTLQKTSFIGRVFMTHPTK 102 (668)
T ss_pred cccCceEEEEEecCeEEEeccccCccccccccccchhhcccccccHHHHhhhhhhhcccccceeeeccccceeEEecchH
Confidence 3567888888 89999999998322 1578999999999999999999764 68999999999
Q ss_pred HHHHHhhc-------cC--------------CCceEEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEE
Q 001045 94 RLLSQILN-------IN--------------PKFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYV 152 (1176)
Q Consensus 94 ~ll~~~l~-------~~--------------~~~i~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~Il 152 (1176)
++.+..+. +. ...+.++++.+.+++.++++.++.|||+.|+|||.++..+ -+|+
T Consensus 103 Ai~kwllsdyvrvs~~s~~~~Ly~e~dl~~s~dKie~idfhe~~ev~gIkf~p~~aGhVlgacMf~veiag-----v~lL 177 (668)
T KOG1137|consen 103 AIYKWLLSDYVRVSNRSGDDRLYTEGDLMESMDKIETIDFHETVEVNGIKFWPYHAGHVLGACMFMVEIAG-----VRLL 177 (668)
T ss_pred HHHHhhhhcceEeeeccCccccccchhHHHhhhhheeeeeccccccCCeEEEeeccchhhhheeeeeeece-----EEEE
Confidence 99997762 00 1247788999999999999999999999999999999965 7999
Q ss_pred EECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccchH
Q 001045 153 HTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIGKE 232 (1176)
Q Consensus 153 YTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slGR~ 232 (1176)
|||||....++....+..+-.++|+||.|+||+. ..|.++++.+..+..+|..+..+ ||| +++|+|++||+
T Consensus 178 yTGd~sreeDrhl~aae~P~~~~dvli~estygv--~~h~~r~~re~rlt~vIh~~v~r-----GGR--~L~PvFAlgrA 248 (668)
T KOG1137|consen 178 YTGDYSREEDRHLIAAEMPPTGPDVLITESTYGV--QIHEPREEREGRLTWVIHSTVPR-----GGR--VLIPVFALGRA 248 (668)
T ss_pred eccccchhhcccccchhCCCCCccEEEEEeeeeE--EecCchHHhhhhhhhhHHhhccC-----CCc--eEeeeeecchH
Confidence 9999988777655444223368999999999997 45788999999999999999877 799 79999999999
Q ss_pred HHHHHHHHHc--------CCcEEEccchH----HHHHHhC------CC----CCCc--c-------cc----CCCCCeEE
Q 001045 233 KILIEIFKKC--------GRKVCVDSRKM----EVLRVLG------YG----DSGV--F-------TE----DESETDVH 277 (1176)
Q Consensus 233 q~ll~ia~~~--------g~~I~vdg~~~----~il~~lg------~~----~~~~--~-------t~----d~~~~~I~ 277 (1176)
||++.++.++ ++||++..... .+++.+- ++ ..+. | +- |.....+.
T Consensus 249 qELllildeyw~~h~~l~~iPiyyaSslakkcm~vfQtyv~~mnd~Irk~~~~~Npfifk~vs~L~~~D~f~D~gP~vv~ 328 (668)
T KOG1137|consen 249 QELLLILDEYWGNHVDLRDIPIYYASSLAKKCMGVFQTYVNMMNDRIRKQSALRNPFIFKHVSILRTGDWFDDEGPSVVM 328 (668)
T ss_pred HHHHHHHHHHhhcchhhhcCceeehhhHHHhhhhhHheehhhhhhhhHHhhccCCceEeeccccccccccccccCCceeE
Confidence 9999999775 47899864322 2332210 00 0000 0 00 11111223
Q ss_pred EecCh-------HHHHhcCCCceEEEEeccceeecccCcee------e------eccCCeeEEEEeecCCCCHHHHHHHH
Q 001045 278 VVGWN-------EIMVERGYDKVVGFVPTGWTYEVKRNKFA------V------RSKDAFEIHLVPYSEHSNYDELREYV 338 (1176)
Q Consensus 278 v~~~~-------~~~~~~g~~~~v~i~ptGw~~~~~~~~~~------v------~~~~~~~v~~i~~SgHAs~~EL~~~V 338 (1176)
+++.. +.+..+-.+...++..+||+.+.+..+.. + ....++.|..+.||.|.+|-+-.+|+
T Consensus 329 aspgmlqsglSRelfe~wcsD~kN~vlipGy~Vegtlak~il~eP~eI~a~~G~klp~~m~V~~isFaAhvdy~q~s~fi 408 (668)
T KOG1137|consen 329 ASPGMLQSGLSRELFERWCSDSKNAVLIPGYCVEGTLAKDILSEPKEIMAMNGRKLPLRMQVEYISFAAHVDYLQNSEFI 408 (668)
T ss_pred eCchHhhhhhhHHHHHHhCCCCCCcEEeccceechhHHHHHhcCchhhhcccCCcccccceEEEEEeeechhhhhhHHHH
Confidence 33221 12222334555555669999876432110 0 13346789999999999999999999
Q ss_pred HHcCCCEEEEEecCCCCcCchHHHHHHHHHHHHHHHHhhhhHHhhhhccccCc
Q 001045 339 KFLKPKRVIPTVGMDIEKLDSKHANKMRKYFAGLVDEMASKKEFLMGFHRGTS 391 (1176)
Q Consensus 339 ~~lrPk~VIPvHG~~~e~~~~~E~~~m~k~f~~l~~~~~~k~~fl~~~~~~~~ 391 (1176)
+.+.|+++|.||| |+..|......+...-.+.+--+.+|.+++|
T Consensus 409 ~~i~~~~lilVHG---------E~neM~rLKs~L~~~f~d~kv~i~v~tprn~ 452 (668)
T KOG1137|consen 409 ADITPPHLILVHG---------EANEMMRLKSALEAAFRDGKVPIDVSTPRNC 452 (668)
T ss_pred HHhCCCeEEEEec---------ccchhHHHHHHHHHHhccCCCcceecCCccc
Confidence 9999999999999 6777777666666554444445666667766
No 37
>cd06846 Adenylation_DNA_ligase_like Adenylation domain of proteins similar to ATP-dependent polynucleotide ligases. ATP-dependent polynucleotide ligases catalyze the phosphodiester bond formation of nicked nucleic acid substrates using ATP as a cofactor in a three step reaction mechanism. This family includes ATP-dependent DNA and RNA ligases. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. ATP-dependent DNA ligases have a highly modular architecture, consisting of a unique arrangement of two or more discrete domains, including a DNA-binding domain, an adenylation or nucleotidyltransferase (NTase) domain, and an oligonucleotide/oligosaccharide binding (OB)-fold domain. The adenylation domain binds ATP and contains many active site residues. Together with the C-terminal OB-fold domain, it comprises a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core contains six conserved seq
Probab=99.95 E-value=1.3e-27 Score=252.78 Aligned_cols=173 Identities=25% Similarity=0.297 Sum_probs=136.4
Q ss_pred cCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEE
Q 001045 959 KPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDA 1038 (1176)
Q Consensus 959 ~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDG 1038 (1176)
.|||+.+.....+ ..+.+.+|++|+||||+|||+|+. ++.+++|||+|+++|..||++.... +.....++||||
T Consensus 1 ~~~~~~~~~~~~~--~~~~~~~~~~e~K~DG~R~~~~~~-~~~v~~~sR~g~~~~~~~~~~~~~~---~~~~~~~~ilDG 74 (182)
T cd06846 1 PQLLNPILEEALS--EYDEQDEYYVQEKYDGKRALIVAL-NGGVFAISRTGLEVPLPSILIPGRE---LLTLKPGFILDG 74 (182)
T ss_pred CCccchhhhHHHh--hccccCcEEEEEccCceEEEEEEc-CCeEEEEeCCCCEEecccccccchH---HhccCCCeeEEE
Confidence 3788887665433 256678999999999999999994 7899999999999999999886411 112457899999
Q ss_pred EEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCC--Cc
Q 001045 1039 EVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKM--GY 1116 (1176)
Q Consensus 1039 ElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~--~~ 1116 (1176)
|||+|+.. + ...+++|++||||++||.+++++||.+|+++|++++ ...+ ..
T Consensus 75 Elv~~~~~-------~-------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v-~~~~~~~~ 127 (182)
T cd06846 75 ELVVENRE-------V-------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLL-KEFEGLDP 127 (182)
T ss_pred EEEeccCC-------C-------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHh-hhhccCCc
Confidence 99998642 1 123699999999999999999999999999999999 3332 23
Q ss_pred EEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCc--ccCCCCCCC
Q 001045 1117 FQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGY--SPSKRSDSW 1176 (1176)
Q Consensus 1117 i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y--~pGkRs~~W 1176 (1176)
+.+.....+. ...++++++|+++++.|+||||+|.++ ++| .+| |+.+|
T Consensus 128 ~~i~~~~~~~---------~~~~~~~~~~~~~~~~g~EGvi~K~~~--s~Y~~~~g-r~~~w 177 (182)
T cd06846 128 VKLVPLENAP---------SYDETLDDLLEKLKKKGKEGLVFKHPD--APYKGRPG-SSGNQ 177 (182)
T ss_pred eeEEEeeccc---------ccchHHHHHHHHhhhcCCceEEEEcCC--CCccccCC-CCCce
Confidence 4444333221 122348999999999999999999998 999 888 88888
No 38
>PRK09125 DNA ligase; Provisional
Probab=99.95 E-value=2.6e-27 Score=265.82 Aligned_cols=169 Identities=25% Similarity=0.343 Sum_probs=135.5
Q ss_pred ccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEE
Q 001045 958 IKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILD 1037 (1176)
Q Consensus 958 i~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILD 1037 (1176)
.+||||..... .+.+.+|++|+||||+|||+ + .+++|||+|+++|. |+.. .. ...++|||
T Consensus 28 ~~~~LA~~~~~------~~~~~~~~~E~K~DG~R~~~----~-~v~l~SR~g~~it~--p~~~---~~----~~~~~vLD 87 (282)
T PRK09125 28 PDLQLATVYDK------GQDISGYLVSEKLDGVRAYW----D-GKQLLTRQGNPIAA--PAWF---TA----GFPPFPLD 87 (282)
T ss_pred CCceechhccc------CCChhhEEEEeeeeeEeEEE----C-CeEEEcCCCCcCCC--chhH---Hh----cCCCccEe
Confidence 57999987642 22456899999999999974 2 38999999999998 4432 12 12389999
Q ss_pred EEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcE
Q 001045 1038 AEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYF 1117 (1176)
Q Consensus 1038 GElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i 1117 (1176)
||+|+++ .+|+.+++|.+..... .....+++|++||||++|| ||.+||++|++++.....+.+
T Consensus 88 GElv~~~-------~~F~~l~~r~~~k~~~----~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~~~~i 150 (282)
T PRK09125 88 GELWAGR-------GQFEAISSIVRDKTPD----DAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLPSPYI 150 (282)
T ss_pred EEEEeCC-------CCHHHHHHHHccCCcc----hhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCCCCcE
Confidence 9999853 3799999997654322 1223589999999999987 999999999999943235678
Q ss_pred EEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1118 QYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1118 ~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
++++.+.+ .+.++++++|+++++.|+||||+|+++ |+|++| |+.+|
T Consensus 151 ~~~~~~~~----------~~~~~~~~~~~~~~~~G~EGiV~K~~d--s~Y~~G-Rs~~w 196 (282)
T PRK09125 151 KIIEQIRV----------RSEAALQQFLDQIVAAGGEGLMLHRPD--APYEAG-RSDDL 196 (282)
T ss_pred EEEeEEEc----------CCHHHHHHHHHHHHHcCCCEEEEeCCC--CCCcCC-CCCCc
Confidence 88888764 468999999999999999999999987 999999 88888
No 39
>cd07895 Adenylation_mRNA_capping Adenylation domain of GTP-dependent mRNA capping enzymes. RNA capping enzymes transfer GMP from GTP to the 5'-diphosphate end of nascent mRNAs to form a G(5')ppp(5')RNA cap structure. The RNA cap is found only in eukarya. RNA capping is chemically analogous to the first two steps of polynucleotide ligation. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. Structural studies reveal a shared structure for DNA ligases and capping enzymes, with a common catalytic core composed of an adenylation or nucleotidyltransferase domain and a C-terminal OB-fold domain containing conserved sequence motifs. The adenylation domain binds ATP and contains many active site residues.
Probab=99.91 E-value=5.6e-24 Score=231.00 Aligned_cols=157 Identities=23% Similarity=0.280 Sum_probs=124.7
Q ss_pred HhccCceEEEEEecceeEEEEEEeeC-CeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCccc
Q 001045 974 KLFQNKAFTCEYKYDGQRAQIHKLVD-GTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIM 1052 (1176)
Q Consensus 974 ~~~~~~~f~~E~KyDGeR~QiH~~~~-g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~ 1052 (1176)
..+...+|++|+||||+|+|+|+. + +.|.+|||+++.++..+|++.+... ......++|||||+|+++.. +
T Consensus 36 ~~~~~~~y~ve~K~DG~R~~l~~~-~~~~v~l~sR~~~~~~~~~~~~~~~~~--~~~~~~~~ilDGElv~~~~~--~--- 107 (215)
T cd07895 36 ELLKQNDYFVCEKSDGVRYLLLIT-GRGEVYLIDRKNDVFKVPGLFFPRRKN--LEPHHQGTLLDGELVIDKVP--G--- 107 (215)
T ss_pred HHHhhCCeEEEEeEcCeEEEEEEe-cCCcEEEEeCCCCeEEeccccCCCccc--ccccccCeeeEEEEEEEcCC--C---
Confidence 335678899999999999999994 6 8999999999999999988754211 12246799999999998642 1
Q ss_pred ChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCC--------------cEE
Q 001045 1053 SFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMG--------------YFQ 1118 (1176)
Q Consensus 1053 pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~--------------~i~ 1118 (1176)
..+++|++||||++||+++++.||.+|+++|++++...... .+.
T Consensus 108 ----------------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~ 165 (215)
T cd07895 108 ----------------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVR 165 (215)
T ss_pred ----------------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEE
Confidence 12699999999999999999999999999999998322111 111
Q ss_pred EeEEEEEcCCCCCCccccCHHHHHHHHHHH---HhCCCceEEEecCCCCCCcccCCCCCCC
Q 001045 1119 YAKEMTVEGDDNCLTSDVSLSKINNFLEEA---LHSSCEGIIVKSLDVDAGYSPSKRSDSW 1176 (1176)
Q Consensus 1119 ~~~~~~v~~~~~~~~~~~~~eei~~~~~~a---i~~g~EGlmvK~ld~~s~Y~pGkRs~~W 1176 (1176)
..+. ...+++.++|+.+ +.+|.||||+|..+ ++|.+| |+..|
T Consensus 166 ~k~~-------------~~~~~~~~~~~~~~~~~~~~~EGlIfk~~~--~~Y~~G-r~~~~ 210 (215)
T cd07895 166 LKDF-------------FPLYKIEKLFEKIIPKLPHENDGLIFTPND--EPYVPG-TDKNL 210 (215)
T ss_pred ecce-------------EeHHhHHHHHHhccccCCCCCCCEEEccCC--CCccCc-cCCcc
Confidence 1111 2346888898888 59999999999998 999999 99988
No 40
>TIGR02776 NHEJ_ligase_prk DNA ligase D. Members of this protein family are DNA ligases involved in the repair of DNA double-stranded breaks by non-homologous end joining (NHEJ). The system of the bacterial Ku protein (TIGR02772) plus this DNA ligase is seen in about 20 % of bacterial genomes to date and at least one archaeon (Archeoglobus fulgidus). This model describes a central and a C-terminal domain. These two domains may be permuted, as in genus Mycobacterium, or divided into tandem ORFs, and therefore not be identified by this model. An additional N-terminal 3'-phosphoesterase (PE) domain present in some but not all examples of this ligase is not included in the seed alignment for this model; This alignment models only the central ATP-dependent ligase domain and the C-terminal polymerase domain. Most examples of genes for this ligase are adjacent to the gene for Ku.
Probab=99.89 E-value=4e-23 Score=249.39 Aligned_cols=139 Identities=29% Similarity=0.531 Sum_probs=117.3
Q ss_pred cCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEe
Q 001045 1006 SRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDI 1085 (1176)
Q Consensus 1006 SR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDi 1085 (1176)
||||+|+|.+||+|++++... ...+||||||||+||.+ ...+||.|+++.+.. ...++||++|||
T Consensus 1 SRng~d~T~~fPel~~~~~~l---~~~~~ILDGElVvld~~---G~~~F~~Lq~~~~~~---------~~~pv~~~vFDl 65 (552)
T TIGR02776 1 TRNGHDWTKRFPEIVKALALL---KLLPAWIDGEIVVLDER---GRADFAALQNALSAG---------ASRPLTYYAFDL 65 (552)
T ss_pred CCCcCcchhhhHHHHHHHhhC---CCCCEEEEEEEEEECCC---CCCCHHHHHHHHHhc---------ccCceEEEEEec
Confidence 899999999999999988753 46799999999999963 346899999986532 245899999999
Q ss_pred eeeCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCC
Q 001045 1086 MFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDA 1165 (1176)
Q Consensus 1086 L~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s 1165 (1176)
||+||++|+++||.+||++|++++.....+.+.+++++. ++.+++|++++++|+||||+|+++ |
T Consensus 66 L~l~G~dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~~~~~--------------~~~~~~~~~a~~~G~EGIV~K~~d--S 129 (552)
T TIGR02776 66 LFLSGEDLRDLPLEERKKRLKQLLKAQDEPAIRYSDHFE--------------SDGDALLESACRLGLEGVVSKRLD--S 129 (552)
T ss_pred cccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEeeeec--------------ccHHHHHHHHHHCCCceEEEeCCC--C
Confidence 999999999999999999999999432234577776632 233489999999999999999998 9
Q ss_pred CcccCCCCCCC
Q 001045 1166 GYSPSKRSDSW 1176 (1176)
Q Consensus 1166 ~Y~pGkRs~~W 1176 (1176)
+|+|| ||.+|
T Consensus 130 ~Y~~G-Rs~~W 139 (552)
T TIGR02776 130 PYRSG-RSKDW 139 (552)
T ss_pred CCCCC-CCcch
Confidence 99999 99999
No 41
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.81 E-value=3.6e-19 Score=192.74 Aligned_cols=333 Identities=21% Similarity=0.347 Sum_probs=235.9
Q ss_pred ccccCCCCCCCcccccccCCCCCcchHHHHHHHHHHHhhhchHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCc
Q 001045 690 TLVSLPPEKYDPIEHACWSSGQPAPYIHLARTFDLVEAERGKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHE 769 (1176)
Q Consensus 690 ~~~~~~~~~~~~~~~~~~~~g~~~~F~~l~~~~~~i~~t~~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~ 769 (1176)
++.++-+..+.|.- .--.|..+.+++..++.......|+++++.+++.- ..+.+ +||.+.-|.-..+
T Consensus 139 ~~rS~R~~~~~~~S-------kFN~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kd-NFDGD-----L~LWL~FLIRESD 205 (482)
T KOG4437|consen 139 PKRSLRSSKCDPRS-------KFNLFREFRKLCSMLADNPSYNTKTQVIQDLLRKD-NFDGD-----LYLWLKFLIRESD 205 (482)
T ss_pred chhccccccCCccc-------cchHHHHHHHHHHHHHhCcCccchhHHHHHHHhcc-CCCcc-----hhhhhhhhhcccc
Confidence 34555555555422 24578999999999999999999999999998872 12223 4444555556778
Q ss_pred ccccccchhhHHHHHHHHhCCChHHHHHHHHhc-CChHHHHHHHHhhccc--cCCCCCCcHHHHHHHHHHhhhhcCCCch
Q 001045 770 NIELNIGGSLVTSAIEEACGTNRSKIRDMYNRL-GDLGDVAQECRQTQAL--LAPPPPLLIKDVYSMLCKISVQTGSGST 846 (1176)
Q Consensus 770 ~~elgige~~L~kal~~~~g~~~~~i~~~~~~~-GDlG~va~~~~~~q~~--l~~~~~LTi~eV~~~L~~IA~~~g~~s~ 846 (1176)
.|.|+|....|++.+++++.+.+......|-.. -|. |-.+.-.|.. .....-+||.+|++.|.+|+..+..
T Consensus 206 ~R~YNl~DkKLI~lfsKiLn~~~~~~~~~Y~~~S~~~---~i~i~~~~~K~~~~~K~~~siQ~~D~~L~rLSKi~~~--- 279 (482)
T KOG4437|consen 206 KRVYNLNDKKLIKLFSKILNCNPDDMARDYEQGSVSE---TIRVFFEQSKSFPPAKSLLTIQEVDEFLLRLSKLTKE--- 279 (482)
T ss_pred cccccccHHHHHHHHHHHHccChHHHHHHHHhccchh---hhhhhHhhccCCCCcccceeHHHHHHHHHHHhcccch---
Confidence 899999999999999999999876655555432 222 2222222221 2234569999999999999988764
Q ss_pred HHHHHHHHHHHhhcchhhHHHHHHHHhhccccCcchhhHHHHHHHhhccCcccccccccchhHHHHHHHHHHHHHHHHHh
Q 001045 847 ARKKSLIVNLMCSCREKEMKFLVRTLVRNLRIGAMMRTILPALAQAVVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYN 926 (1176)
Q Consensus 847 ~~K~~il~~Ll~~~~~~E~k~LvRiIlk~LRiG~~~~tvl~aLa~A~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~ 926 (1176)
...++.|+....+|+..|.+.|+|+|-++|......+.||++++ +.+.++|.
T Consensus 280 D~~~~~L~~~A~R~~~~~L~~iIRLIr~~L~~~s~A~~iL~~~~----------------------------P~A~E~F~ 331 (482)
T KOG4437|consen 280 DEQQQALQDIASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALD----------------------------PNAYEAFK 331 (482)
T ss_pred HHHHHHHHHHHHhcccchHHHHHHHHHHHhccCCChhHHHhccC----------------------------CCcHHHHH
Confidence 34577899999999999999999999999999999999999863 12222222
Q ss_pred hCCChHHHHHHHh--------ccccCCCccccCcCCCCCccCCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEee
Q 001045 927 ILPSLDLLIPSLM--------NKGIGFSASTLSMVPGVPIKPMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLV 998 (1176)
Q Consensus 927 ~~pdl~~v~~~L~--------~~g~~~~~~~~~l~~g~Pi~PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~ 998 (1176)
..+|+.|++..+ ++|.+...+ ..-....|.+|||+..+++++-..++..+.. .-|.||||+|.|+|. +
T Consensus 332 -S~~L~~ViEr~~~N~~~~~~~~~~~~~~s-~~s~~~s~~Q~~~~~~~~~VE~s~~~~~~~~-~S~~~~D~E~~~~~~-~ 407 (482)
T KOG4437|consen 332 -SRNLQDVVERVLHNAQEVEKEPGQRRALS-VQASLMTPVQPMLAEACKSVEYAMKKCPNGM-FSEIKYDGERVQVHK-N 407 (482)
T ss_pred -hcCHHHHHHHHHHhHHHHhhCcccccccc-chhhhcCCcChhhhhhhhhHHHHhccCCCCc-cccccCCCceeeccC-C
Confidence 123333333222 223221111 1123447899999999999988888776655 479999999999999 5
Q ss_pred CCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccce
Q 001045 999 DGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDI 1078 (1176)
Q Consensus 999 ~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v 1078 (1176)
++.|.+|||--+.. ..+.+.+++.+ ++..+.|+|||....+.++| .++||+.+.-..+... ....+
T Consensus 408 ~D~~S~~S~~~~~~----s~FK~~~P~~~-~~G~~~~~~~~~~~I~~K~~-~P~~~~~~~~~~K~~~--------~~~~~ 473 (482)
T KOG4437|consen 408 GDHFSYFSRLPHKV----AHFKDYIPQAF-PGGHSMILDSEVLLIDNKTG-KPLPFGTLGVHKKAAF--------QDANV 473 (482)
T ss_pred CcchhhhccChHhh----hhhhhcCchhc-CCCccccccccccceecccC-CCCCchhcchhhHHHh--------cCcch
Confidence 88999999976554 33444555554 46789999999999999986 8999999975532110 12358
Q ss_pred EEEEEEeee
Q 001045 1079 CVFVFDIMF 1087 (1176)
Q Consensus 1079 ~~~vFDiL~ 1087 (1176)
|.++||..|
T Consensus 474 ~~~~~~~~~ 482 (482)
T KOG4437|consen 474 CLFVFDCIY 482 (482)
T ss_pred heeecccCC
Confidence 999999765
No 42
>TIGR02651 RNase_Z ribonuclease Z. Processing of the 3-prime end of tRNA precursors may be the result of endonuclease or exonuclease activity, and differs in different species. Member of this family are ribonuclease Z, a tRNA 3-prime endonuclease that processes tRNAs to prepare for addition of CCA. In species where all tRNA sequences already have the CCA tail, such as E. coli, the need for such an enzyme is unclear. Protein similar to the E. coli enzyme, matched by TIGR02649, are designated ribonuclease BN.
Probab=99.78 E-value=1.8e-18 Score=196.97 Aligned_cols=179 Identities=17% Similarity=0.209 Sum_probs=134.3
Q ss_pred cCCCCCCCCCCCCCCCCCeeE-eCCccEEEecCC--------c--CCCCccEEEeccCChhhhCCcccCC---------C
Q 001045 23 SSPPDSLIFPPIPRTFPPSKH-VPNTRFLIDAFR--------Y--AADFSVSYFLSHFHSDHYTGLSPSW---------S 82 (1176)
Q Consensus 23 ~~l~s~~~~p~~~r~~p~~~~-ipg~~~liD~~~--------~--~~~~i~avfITHaH~DHiggL~~l~---------~ 82 (1176)
-.||||+++|...|..+|+.+ .++..++|||+. . ...++++|||||+|.||++||+.+. .
T Consensus 3 ~~lGtg~~~p~~~r~~~~~~v~~~~~~iLiD~G~g~~~~l~~~~~~~~~i~~IfiTH~H~DH~~Gl~~l~~~~~~~~~~~ 82 (299)
T TIGR02651 3 TFLGTGGGVPTKERNLPSIALKLNGELWLFDCGEGTQRQMLRSGISPMKIDRIFITHLHGDHILGLPGLLSTMSFQGRKE 82 (299)
T ss_pred EEEeCCCCCCCCCCCCceEEEEECCeEEEEECCHHHHHHHHHcCCCHHHCcEEEEECCchhhhcChHHHHHhhccCCCCc
Confidence 458999999999999999999 788999999982 1 1246899999999999999998542 1
Q ss_pred CceEEeCHHHHHHHHHhhccC------CCceEEeCCCc-eEEECCEEEEEEecCCCcCceEEEEEEcCC-----------
Q 001045 83 KGIIFCSEITSRLLSQILNIN------PKFIYPLPIKI-PVLIDGCEVVLVGANHCPGAVQFLFKVPGR----------- 144 (1176)
Q Consensus 83 ~~pIY~s~~T~~ll~~~l~~~------~~~i~~l~~~~-~~~i~~~~Vt~~~a~H~pGS~~flie~~~~----------- 144 (1176)
+++||+++.+.+.+...+... .-.+.++..++ .+.+++++|+++++.|...+++|.|+.++.
T Consensus 83 ~i~Iy~p~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~H~~~~~gy~i~~~~~~~~~~~~k~~~ 162 (299)
T TIGR02651 83 PLTIYGPPGIKEFIETSLRVSYTYLNYPIKIHEIEEGGLVFEDDGFKVEAFPLDHSIPSLGYRFEEKDRPGKFDREKAKE 162 (299)
T ss_pred eEEEECCccHHHHHHHHHHHcccCCCceEEEEEccCCCceEecCCEEEEEEEcCCCCceEEEEEEECCCCCCcCHHHHHH
Confidence 568999999999887654321 11256677777 588999999999999987899999997521
Q ss_pred ------------------------------------CCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCC
Q 001045 145 ------------------------------------NGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPK 188 (1176)
Q Consensus 145 ------------------------------------~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~ 188 (1176)
.| ++++|+||+++.+. ....+.++|+||+||||....
T Consensus 163 ~~l~~g~~~~~L~~g~~v~~~~G~~~~~~~~~~~~~~g--~~i~y~gDt~~~~~-----~~~~~~~~dlLi~E~~~~~~~ 235 (299)
T TIGR02651 163 LGIPPGPLYGKLKRGETVTLIDGRIIDPEDVLGPPRKG--RKIAYTGDTRPCEE-----VIEFAKNADLLIHEATFLDED 235 (299)
T ss_pred CCCCcchhHHHhhCCCeEEeCCCeEEeHHHcccCCcCC--cEEEEecCCCChHH-----HHHHHcCCCEEEEECCCCchh
Confidence 13 58999999987543 122236899999999998743
Q ss_pred CC--CCChHHHHHHHHHHHHHH
Q 001045 189 FL--FPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 189 ~~--~p~~~e~~~~l~~~i~~~ 208 (1176)
.. ....|.+.+++.+++++.
T Consensus 236 ~~~~~~~~H~t~~~a~~~~~~~ 257 (299)
T TIGR02651 236 KKLAKEYGHSTAAQAAEIAKEA 257 (299)
T ss_pred HHHHhhcCCCCHHHHHHHHHHc
Confidence 21 123445555666666654
No 43
>TIGR02649 true_RNase_BN ribonuclease BN. Members of this protein family are ribonuclease BN of Escherichia coli K-12 and closely related proteins believed to be equivalent in function. Note that E. coli appears to lack RNase Z per se, and this protein of E. coli appears orthologous to (but not functionally equivalent to) RNase Z of Bacillus subtilis and various other species. Meanwhile, the yihY gene product of E. coli previously was incorrectly identified as RNase BN.
Probab=99.77 E-value=3.2e-18 Score=195.51 Aligned_cols=179 Identities=16% Similarity=0.100 Sum_probs=133.8
Q ss_pred cCCCCCCCCCCCCCCCCCeeE-eC----CccEEEecCCc----------CCCCccEEEeccCChhhhCCcccCC------
Q 001045 23 SSPPDSLIFPPIPRTFPPSKH-VP----NTRFLIDAFRY----------AADFSVSYFLSHFHSDHYTGLSPSW------ 81 (1176)
Q Consensus 23 ~~l~s~~~~p~~~r~~p~~~~-ip----g~~~liD~~~~----------~~~~i~avfITHaH~DHiggL~~l~------ 81 (1176)
-.||||+++|...|.++|+.+ +. +..+++||+.. ...++++|||||.|.||++||+.+.
T Consensus 2 ~~LGt~~~~p~~~r~~s~~lv~~~~~~~~~~iLiD~G~g~~~~l~~~~i~~~~id~IfiTH~H~DHi~Gl~~ll~~~~~~ 81 (303)
T TIGR02649 2 IFLGTSAGVPTRTRNVTAILLNLQHPTQSGLWLFDCGEGTQHQLLHTAFNPGKLDKIFISHLHGDHLFGLPGLLCSRSMS 81 (303)
T ss_pred EEEecCCCCCCCCCCccEEEEEccCCCCCCEEEEECCccHHHHHHHhCCCHHHCcEEEEeCCChhhcCCHHHHHHHHHhc
Confidence 358999999999999999999 53 36799999821 1257999999999999999998632
Q ss_pred ---CCceEEeCHHHHHHHHHhhccC------CCceEEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCC--------
Q 001045 82 ---SKGIIFCSEITSRLLSQILNIN------PKFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGR-------- 144 (1176)
Q Consensus 82 ---~~~pIY~s~~T~~ll~~~l~~~------~~~i~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~-------- 144 (1176)
.+++||+++.+.+.+...+.+. ...++.+..++.+..++++|+++++.|...+++|.|+..+.
T Consensus 82 ~~~~~l~Iygp~~~~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~v~~~~~~H~~~~~gy~i~~~~~~g~~~~~k 161 (303)
T TIGR02649 82 GIIQPLTIYGPQGIREFVETALRISGSWTDYPLEIVEIGAGEILDDGLRKVTAYPLEHPLECYGYRIEEHDKPGALNAQA 161 (303)
T ss_pred CCCCCeEEEechhHHHHHHHHHHhcccccCCceEEEEcCCCceEecCCeEEEEEEccCccceEEEEEeccCCcCCCCHHH
Confidence 2478999999999887654321 12356777788888889999999999977899999987321
Q ss_pred ---------------------------------------CCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCC
Q 001045 145 ---------------------------------------NGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYC 185 (1176)
Q Consensus 145 ---------------------------------------~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~ 185 (1176)
.| .+|+|+||+++... .+....++|+||+||||.
T Consensus 162 l~~lgi~~g~~~~~L~~g~~v~~~dg~~~~~~~~~~~~~~g--~~i~y~gDt~~~~~-----~~~~~~~adlLi~Eat~~ 234 (303)
T TIGR02649 162 LKAAGVPPGPLFQELKAGKTITLEDGRQINGADYLAAPVPG--KALAIFGDTGPCDA-----ALDLAKGVDVMVHEATLD 234 (303)
T ss_pred HHHCCCCCChHHHHhcCCCeEEeCCCcEEcHHHeeCCCCCC--cEEEEecCCCChHH-----HHHHhcCCCEEEEeccCC
Confidence 23 68999999987433 122237999999999997
Q ss_pred CCCC--CCCChHHHHHHHHHHHHHH
Q 001045 186 NPKF--LFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 186 ~~~~--~~p~~~e~~~~l~~~i~~~ 208 (1176)
+... .....|.+..++.+++++.
T Consensus 235 ~~~~~~a~~~~H~t~~~a~~~a~~~ 259 (303)
T TIGR02649 235 ITMEAKANSRGHSSTRQAATLAREA 259 (303)
T ss_pred hhhHHHHhhcCCCCHHHHHHHHHHc
Confidence 5321 1123455566666666654
No 44
>PRK11244 phnP carbon-phosphorus lyase complex accessory protein; Provisional
Probab=99.75 E-value=1.7e-17 Score=184.41 Aligned_cols=177 Identities=18% Similarity=0.152 Sum_probs=126.4
Q ss_pred cCCCCCCC------------------CCCCCCCCCCeeE-eCCccEEEecCC------cCCCCccEEEeccCChhhhCCc
Q 001045 23 SSPPDSLI------------------FPPIPRTFPPSKH-VPNTRFLIDAFR------YAADFSVSYFLSHFHSDHYTGL 77 (1176)
Q Consensus 23 ~~l~s~~~------------------~p~~~r~~p~~~~-ipg~~~liD~~~------~~~~~i~avfITHaH~DHiggL 77 (1176)
--||||++ .|...|..+++.+ ..+..++||++- ....++++|||||.|.||++||
T Consensus 4 ~~lGs~~~~~~p~~~c~c~~c~~~~~~p~~~r~~~s~li~~~~~~iLiD~G~~~~~~~~~~~~i~~i~iTH~H~DHi~gl 83 (250)
T PRK11244 4 TLLGTGGAQGVPVFGCECAACARARRDPAYRRRPCSALIEFNGARTLIDAGLPDLAERFPPGSLQQILLTHYHMDHVQGL 83 (250)
T ss_pred EEEeccCCCCccCCCccchhhhhhhcCCCCCcceeEEEEEECCCEEEEECCChHHhhcCCcccCCEEEEccCchhhhccH
Confidence 35788887 8888888888877 788899999982 2236799999999999999999
Q ss_pred ccC-C---CCceEEeCHHHHHHHHHhhccCC-Cce-EEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEE
Q 001045 78 SPS-W---SKGIIFCSEITSRLLSQILNINP-KFI-YPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERY 151 (1176)
Q Consensus 78 ~~l-~---~~~pIY~s~~T~~ll~~~l~~~~-~~i-~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~I 151 (1176)
..+ + .+++||+++.+..+.. .+.... ..+ ..+..++++.+++++|+++++.|..++++|+|+.++ +++
T Consensus 84 ~~l~~~~~~~i~i~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~I~~~~~~H~~~s~g~~i~~~~-----~~i 157 (250)
T PRK11244 84 FPLRWGVGDPIPVYGPPDPEGCDD-LFKHPGILDFSHPLEPFEPFDLGGLQVTPLPLNHSKLTFGYLLETAH-----SRV 157 (250)
T ss_pred HHHHhhcCCceeEEeCCchhhHHH-HhcCccccccccccCCCCCeeECCEEEEEEeeCCCcceeEEEEecCC-----eEE
Confidence 754 2 3578999988754332 222211 112 357788899999999999999998889999999754 699
Q ss_pred EEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHH
Q 001045 152 VHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 152 lYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~ 208 (1176)
+|+||+......... .+ ...++|+||+|+||..... ....+....++++++++.
T Consensus 158 ~ysgDt~~~~~~~~~-~~-~~~~~Dlli~e~~~~~~~~-~~~~H~~~~~a~~~a~~~ 211 (250)
T PRK11244 158 AYLTDTVGLPEDTLK-FL-RNNQPDLLVLDCSHPPQED-APRNHNDLTTALAIIEVL 211 (250)
T ss_pred EEEcCCCCCCHHHHH-HH-hcCCCCEEEEeCcCCCCCC-CCCCCCCHHHHHHHHHhc
Confidence 999998754332111 11 1158999999999975421 122344445566666544
No 45
>cd07894 Adenylation_RNA_ligase Adenylation domain of RNA circularization proteins. RNA circularization proteins are capable of circularizing RNA molecules in an ATP-dependent reaction. RNA circularization may protect RNA from exonuclease activity. This model comprises the adenylation domain, the minimal catalytic unit that is common to all members of the ATP-dependent DNA ligase family, and the carboxy-terminal extension of RNA circularization protein that serves as a dimerization module. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation of nicked nucleic acid substrates using the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. The adenylation domain binds ATP and contains many active site residues.
Probab=99.71 E-value=1e-16 Score=183.96 Aligned_cols=144 Identities=27% Similarity=0.378 Sum_probs=107.8
Q ss_pred ceEEEEEecceeEEEEEEeeCCeEEEEcCCCc---cCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChH
Q 001045 979 KAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGD---ETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQ 1055 (1176)
Q Consensus 979 ~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~---d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq 1055 (1176)
..|++|+||||.|+|+|+ .+|++.+|||+|. +.|+.+|++.. ..++ ...+++|||||+++.+. ||.
T Consensus 48 ~~~~vEEKlDG~nvri~~-~~G~v~a~TR~G~i~e~~T~~~~eiv~--~~~~-~~~p~~iLdGElvg~~~-------p~v 116 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVR-IGGKVLAFTRGGFICPFTTDRLRDLID--PEFF-DDHPDLVLCGEVVGPEN-------PYV 116 (342)
T ss_pred CCEEEEEeECCcEEEEEE-ECCEEEEEeCCCccCccchhhHhhhch--HHhh-ccCCCEEEEEEEEecCC-------ccc
Confidence 689999999999999999 4889999999975 45899999842 2322 23467999999998651 331
Q ss_pred HHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccc
Q 001045 1056 ELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSD 1135 (1176)
Q Consensus 1056 ~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~ 1135 (1176)
. .... ...++.|++|||++.|+ ...+|+.+|+++|+++.-.. .....+..+
T Consensus 117 ~------~~~~-------~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~----v~~~~~~~~---------- 167 (342)
T cd07894 117 P------GSYP-------EVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPT----VRLFGEFTA---------- 167 (342)
T ss_pred c------ccCc-------cccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCC----cceEEEEec----------
Confidence 0 1000 01368999999999885 66789999999999983121 122223332
Q ss_pred cCHHHHHHHHHHHHhCCCceEEEecCC
Q 001045 1136 VSLSKINNFLEEALHSSCEGIIVKSLD 1162 (1176)
Q Consensus 1136 ~~~eei~~~~~~ai~~g~EGlmvK~ld 1162 (1176)
++.+++.++|+++.+.|+||||+|+++
T Consensus 168 ~d~~~l~~~l~~~~~~G~EGVVlK~~~ 194 (342)
T cd07894 168 DEIEELKEIIRELDKEGREGVVLKDPD 194 (342)
T ss_pred CCHHHHHHHHHHHHHCCCceEEEeccc
Confidence 357899999999999999999999987
No 46
>PRK02113 putative hydrolase; Provisional
Probab=99.68 E-value=7e-16 Score=171.51 Aligned_cols=158 Identities=16% Similarity=0.189 Sum_probs=117.5
Q ss_pred CCCCCCCeeE-eCCccEEEecCC--------cCCCCccEEEeccCChhhhCCcccCC-----CCceEEeCHHHHHHHHHh
Q 001045 34 IPRTFPPSKH-VPNTRFLIDAFR--------YAADFSVSYFLSHFHSDHYTGLSPSW-----SKGIIFCSEITSRLLSQI 99 (1176)
Q Consensus 34 ~~r~~p~~~~-ipg~~~liD~~~--------~~~~~i~avfITHaH~DHiggL~~l~-----~~~pIY~s~~T~~ll~~~ 99 (1176)
..|..+++.+ ..|..++||++. ....++++|||||.|.||++||+.+. .+.+||+++.+.+.+...
T Consensus 31 ~~R~~~s~li~~~~~~iLiD~G~g~~~~l~~~~~~~id~I~lTH~H~DH~~gl~~l~~~~~~~~~~i~~~~~~~~~l~~~ 110 (252)
T PRK02113 31 DNRLRTSALVETEGARILIDCGPDFREQMLRLPFGKIDAVLITHEHYDHVGGLDDLRPFCRFGEVPIYAEQYVAERLRSR 110 (252)
T ss_pred CcceeeEEEEEECCeEEEEECCchHHHHHHhcCccccCEEEECCCChhhhCCHHHHHHhccCCCceEEECHHHHHHHHhh
Confidence 3677788888 788899999983 12257999999999999999998542 368999999999988765
Q ss_pred hcc----------CCCceEEeCCCceEEECCEEEEEEecCCC-cCceEEEEEEcCCCCcccEEEEECCCCCcccccchhh
Q 001045 100 LNI----------NPKFIYPLPIKIPVLIDGCEVVLVGANHC-PGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPV 168 (1176)
Q Consensus 100 l~~----------~~~~i~~l~~~~~~~i~~~~Vt~~~a~H~-pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~ 168 (1176)
+.. ....++.++.++++++++++|+++++.|. ..+++|.+ + +++|+||+...+.. .
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~i~~~~~~H~~~~~~gy~i---~------~i~y~~Dt~~~~~~----~ 177 (252)
T PRK02113 111 MPYCFVEHSYPGVPNIPLREIEPDRPFLVNHTEVTPLRVMHGKLPILGYRI---G------KMAYITDMLTMPEE----E 177 (252)
T ss_pred CCeeeccCCCCCCcceeeEEcCCCCCEEECCeEEEEEEecCCCccEEEEEe---C------CEEEccCCCCCCHH----H
Confidence 421 11236778889999999999999999995 45788888 1 69999999754432 1
Q ss_pred hhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHH
Q 001045 169 MNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 169 l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~ 208 (1176)
+..+.++|+||+|+++..+.. .+...+++.+.++++
T Consensus 178 ~~~~~~~DlLi~e~~~~~~~~----~H~t~~~a~~~~~~~ 213 (252)
T PRK02113 178 YEQLQGIDVLVMNALRIAPHP----THQSLEEALENIKRI 213 (252)
T ss_pred HHHhcCCCEEEEhhhcCCCCC----CcCCHHHHHHHHHHh
Confidence 222379999999998743322 244445566666655
No 47
>TIGR03307 PhnP phosphonate metabolism protein PhnP. This family of proteins found in operons encoding phosphonate C-P lyase systems as is observed in E. coli and is a member of the metallo-beta-lactamase superfamily (pfam00753). As defined by this model, all instances of this protein are associated with the C-P lyase, but not all genomes containing the C-P lyase system contain phnP.
Probab=99.67 E-value=1.5e-15 Score=167.61 Aligned_cols=168 Identities=18% Similarity=0.196 Sum_probs=116.5
Q ss_pred CCCCCCCCCeeE-eCCccEEEecCC------cCCCCccEEEeccCChhhhCCcccC-C---CCceEEeCHHHHHHHHHhh
Q 001045 32 PPIPRTFPPSKH-VPNTRFLIDAFR------YAADFSVSYFLSHFHSDHYTGLSPS-W---SKGIIFCSEITSRLLSQIL 100 (1176)
Q Consensus 32 p~~~r~~p~~~~-ipg~~~liD~~~------~~~~~i~avfITHaH~DHiggL~~l-~---~~~pIY~s~~T~~ll~~~l 100 (1176)
|...|..+++.+ ..+..++||++- ....++++|||||.|.||++||+.+ + .+++||+++.+..+.. .+
T Consensus 21 ~~~~r~~~s~~i~~~~~~iliD~G~~~~~~~~~~~~id~i~iTH~H~DHi~gl~~l~~~~~~~~~v~~~~~~~~~~~-~~ 99 (238)
T TIGR03307 21 PDYRRQPCSAVIEFNGARTLIDAGLTDLAERFPPGSLQAILLTHYHMDHVQGLFPLRWGVGEPIPVYGPPDEEGCDD-LF 99 (238)
T ss_pred ccccCcceEEEEEECCcEEEEECCChhHhhccCccCCCEEEEecCchhhhcchHHHHHhcCCceeEEeCchHhhHHH-Hh
Confidence 445566777766 678899999982 2235799999999999999999643 2 3578999998864432 22
Q ss_pred ccC--CCceEEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEE
Q 001045 101 NIN--PKFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAV 178 (1176)
Q Consensus 101 ~~~--~~~i~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvL 178 (1176)
... ......+..++++.+++++|+++++.|..++++|.|+.++ ++++|+||+.......... +. ..++|+|
T Consensus 100 ~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~H~~~~~g~~i~~~~-----~~i~y~gDt~~~~~~~~~~-~~-~~~~D~l 172 (238)
T TIGR03307 100 KHPGILDFSKPLEAFEPFDLGGLRVTPLPLVHSKLTFGYLLETDG-----QRVAYLTDTAGLPPDTEAF-LK-NHPLDVL 172 (238)
T ss_pred cCcccccccccccCCceEEECCEEEEEEecCCCCcceEEEEecCC-----cEEEEEecCCCCCHHHHHH-Hh-cCCCCEE
Confidence 211 1112347788999999999999999998889999999754 6999999996543321111 11 1379999
Q ss_pred EEeCCCCCCCCCCCChHHHHHHHHHHHHHH
Q 001045 179 FLDTTYCNPKFLFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 179 I~EsTy~~~~~~~p~~~e~~~~l~~~i~~~ 208 (1176)
|+||||...... ...+....++.+.+++.
T Consensus 173 i~e~~~~~~~~~-~~~H~~~~~~~~~~~~~ 201 (238)
T TIGR03307 173 ILDCSHPPQSDA-PRNHNDLTRALAINEQL 201 (238)
T ss_pred EEeCCcCccccC-CCCcCCHHHHHHHHHHc
Confidence 999999743211 12344455666666544
No 48
>PRK05184 pyrroloquinoline quinone biosynthesis protein PqqB; Provisional
Probab=99.65 E-value=1e-15 Score=174.67 Aligned_cols=144 Identities=17% Similarity=0.154 Sum_probs=105.2
Q ss_pred CCCCCCCeeEe-CCc-cEEEecC--------Cc---------CCCCccEEEeccCChhhhCCcccCCC--CceEEeCHHH
Q 001045 34 IPRTFPPSKHV-PNT-RFLIDAF--------RY---------AADFSVSYFLSHFHSDHYTGLSPSWS--KGIIFCSEIT 92 (1176)
Q Consensus 34 ~~r~~p~~~~i-pg~-~~liD~~--------~~---------~~~~i~avfITHaH~DHiggL~~l~~--~~pIY~s~~T 92 (1176)
+.|..+++.+. .|. .+|||++ +. ...++++|||||.|.||++||+.+.. +++||+++.|
T Consensus 35 ~~R~~ss~li~~~g~~~iLiD~G~g~~~ql~~~~~~~~~~g~~~~~ldav~lTH~H~DHi~Gl~~l~~~~~l~Vyg~~~~ 114 (302)
T PRK05184 35 KPRTQSSIAVSADGEDWVLLNASPDIRQQIQATPALQPARGLRDTPIAAVVLTDGQIDHTTGLLTLREGQPFPVYATPAV 114 (302)
T ss_pred CcccccEEEEEcCCCEEEEEECChhHHHHHHhchhcCccccCCcccccEEEEeCCchhhhhChHhhccCCCeEEEeCHHH
Confidence 67888888884 454 5899998 21 11369999999999999999987643 6899999999
Q ss_pred HHHHHHhhc---c----CCCceEEeCCCceEEEC---CEEEEEEecCC-------------CcCceEEEEEEcCCCCccc
Q 001045 93 SRLLSQILN---I----NPKFIYPLPIKIPVLID---GCEVVLVGANH-------------CPGAVQFLFKVPGRNGGFE 149 (1176)
Q Consensus 93 ~~ll~~~l~---~----~~~~i~~l~~~~~~~i~---~~~Vt~~~a~H-------------~pGS~~flie~~~~~G~~~ 149 (1176)
.+.+...+. + ..-.++.+..+++++++ +++|+++++.| ...+++|+|+... +| +
T Consensus 115 ~~~l~~~~~~f~~~~~~~~~~~~~i~~~~~~~i~~~~~~~Vt~~~v~H~~~~~~~~~~~~h~~~~~gyri~~~~-~g--~ 191 (302)
T PRK05184 115 LEDLSTGFPIFNVLDHYGGVQRRPIALDGPFAVPGLPGLRFTAFPVPSKAPPYSPHRSDPEPGDNIGLRIEDRA-TG--K 191 (302)
T ss_pred HHHHHhcCCcccccccccceeeEEecCCCceEecCCCCcEEEEEEcCCCCCcccccccCCCCCCeEEEEEEecC-CC--c
Confidence 998876421 1 11135677888888886 89999999976 2459999996211 23 6
Q ss_pred EEEEECCCCCcccccchhhhhccCCCcEEEEeCCC
Q 001045 150 RYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTY 184 (1176)
Q Consensus 150 ~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy 184 (1176)
+++|++|...... ..+..+.++|+||+|||+
T Consensus 192 ~~~y~tD~~~~~~----~~~~~~~gaDlli~da~~ 222 (302)
T PRK05184 192 RLFYAPGLAEVTD----ALRARLAGADCVLFDGTL 222 (302)
T ss_pred EEEEECCCCCCCH----HHHHHHhcCCEEEEeCCC
Confidence 8999988632221 122233789999999995
No 49
>COG1234 ElaC Metal-dependent hydrolases of the beta-lactamase superfamily III [General function prediction only]
Probab=99.63 E-value=1.7e-15 Score=171.66 Aligned_cols=210 Identities=16% Similarity=0.132 Sum_probs=135.4
Q ss_pred cCCCCCCCCCCCCCCCCCeeE-eCCccEEEecCC----------cCCCCccEEEeccCChhhhCCcccCC---------C
Q 001045 23 SSPPDSLIFPPIPRTFPPSKH-VPNTRFLIDAFR----------YAADFSVSYFLSHFHSDHYTGLSPSW---------S 82 (1176)
Q Consensus 23 ~~l~s~~~~p~~~r~~p~~~~-ipg~~~liD~~~----------~~~~~i~avfITHaH~DHiggL~~l~---------~ 82 (1176)
--||||+++|...|..+++.+ .+|..+++|||. ....++++|||||.|.||+.||+.+. .
T Consensus 5 ~fLGtg~~~Pt~~r~~~s~ll~~~~~~~L~DcGeGt~~~l~~~~~~~~~i~~IfITH~H~DHi~gL~~ll~~~~~~~~~~ 84 (292)
T COG1234 5 TFLGTGGAVPTKDRNVSSILLRLEGEKFLFDCGEGTQHQLLRAGLPPRKIDAIFITHLHGDHIAGLPGLLVSRSFRGRRE 84 (292)
T ss_pred EEEecCCCCCcCccccceeEEEeCCeeEEEECCHhHHHHHHHhcCChhhccEEEeeccccchhcCcHHHHHHhhccCCCC
Confidence 458999999999999999999 799999999982 22247999999999999999998521 1
Q ss_pred CceEEeCHHHHHHHHHhhccCCC------ceEEeCC---------------------CceEEEC------------CEEE
Q 001045 83 KGIIFCSEITSRLLSQILNINPK------FIYPLPI---------------------KIPVLID------------GCEV 123 (1176)
Q Consensus 83 ~~pIY~s~~T~~ll~~~l~~~~~------~i~~l~~---------------------~~~~~i~------------~~~V 123 (1176)
+..||+++..++.+...+..... ..+.+.. .++...+ ++.+
T Consensus 85 ~l~iygP~g~~~~~~~~~~~~~~~~~~~i~~~e~~~~~~~v~~~~~~h~~~~~~y~~~e~~~~~~~~~~~~~~~~~g~~~ 164 (292)
T COG1234 85 PLKIYGPPGIKEFVETSLRLSYSKLTYEIIGHEIEEDAFEVEALELDHGVPALGYRIEEPDRPGRFDAEKLKGLPPGPLI 164 (292)
T ss_pred ceeEECCcchhhhhhhhhhhcccccceEEEEEEeccCceEEEEEecCCCccccceeeecCCCcCcCCHHHhcCCCCchHH
Confidence 46899999988887765422110 0111110 0000111 4566
Q ss_pred EEEecCCC----cCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCC-CCCh-HHH
Q 001045 124 VLVGANHC----PGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFL-FPLQ-EES 197 (1176)
Q Consensus 124 t~~~a~H~----pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~-~p~~-~e~ 197 (1176)
+.++++|. .-..++++.... .| ++|+||||++++..... ..+++|+||+||||.+.... -... |.+
T Consensus 165 ~~l~~~h~~~~~~~~~~~~~~~~~-~G--~~v~ysGDT~p~~~~~~-----~a~~aDlLiHEat~~~~~~~~a~~~~HsT 236 (292)
T COG1234 165 TALKAGHPVEERVITPADRIGEPR-KG--KSVVYSGDTRPCDELID-----LAKGADLLIHEATFEDDLEDLANEGGHST 236 (292)
T ss_pred HHHhCCCceeeeecCHHHhccccC-CC--cEEEEECCCCCCHHHHH-----HhcCCCEEEEeccCCchhhhHHhhcCCCC
Confidence 66667775 344444444332 24 69999999998876322 12799999999999874322 1222 677
Q ss_pred HHHHHHHHHHHhhhccccCCCeEEEEEeccccc--hHHHHHHHHH-HcCCcEEE
Q 001045 198 VEYVVNVVNRVGGELNEGLQKRVLFLVATYVIG--KEKILIEIFK-KCGRKVCV 248 (1176)
Q Consensus 198 ~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slG--R~q~ll~ia~-~~g~~I~v 248 (1176)
..+++++++++ +.+.|++.+..+-. ....++..++ .+..++.+
T Consensus 237 ~~eAa~iA~~A--------~vk~LiLtH~s~ry~~~~~~~~~ea~~~f~~~~~~ 282 (292)
T COG1234 237 AEEAAEIAKEA--------GVKKLILTHFSPRYPKDDEELLKEARAIFPGETIV 282 (292)
T ss_pred HHHHHHHHHHc--------CCCeEEEEeecccccchHHHHHHHHHHhCCCceEE
Confidence 77788887766 44555665444422 3444444444 45444554
No 50
>PRK00055 ribonuclease Z; Reviewed
Probab=99.60 E-value=2e-15 Score=168.79 Aligned_cols=175 Identities=15% Similarity=0.143 Sum_probs=114.8
Q ss_pred ccCCCCCCCCCCCCCCCCCeeE-eCCccEEEecCCc----------CCCCccEEEeccCChhhhCCcccCC---------
Q 001045 22 QSSPPDSLIFPPIPRTFPPSKH-VPNTRFLIDAFRY----------AADFSVSYFLSHFHSDHYTGLSPSW--------- 81 (1176)
Q Consensus 22 ~~~l~s~~~~p~~~r~~p~~~~-ipg~~~liD~~~~----------~~~~i~avfITHaH~DHiggL~~l~--------- 81 (1176)
+-.||||+++|.+.|..+|+.+ .++..++|||+.. ...++++|||||.|.||++||+.+.
T Consensus 4 i~~LGsg~~~~~~~r~~~~~li~~~~~~iLiD~G~g~~~~l~~~~~~~~~i~~i~lTH~H~DHi~Gl~~l~~~~~~~~~~ 83 (270)
T PRK00055 4 LTFLGTGSGVPTPTRNVSSILLRLGGELFLFDCGEGTQRQLLKTGIKPRKIDKIFITHLHGDHIFGLPGLLSTRSLSGRT 83 (270)
T ss_pred EEEEecCCCCCcCCCCCCEEEEEECCcEEEEECCHHHHHHHHHcCCCHHHCCEEEEeCCCchhhCcHHHHHHHhhhcCCC
Confidence 4568999999999999999999 7888999999821 1256999999999999999998642
Q ss_pred CCceEEeCHHHHHHHHHhhccCCC---ceE------E----------eCCCceE-EE-CCEEEEEEecCC--CcCceEEE
Q 001045 82 SKGIIFCSEITSRLLSQILNINPK---FIY------P----------LPIKIPV-LI-DGCEVVLVGANH--CPGAVQFL 138 (1176)
Q Consensus 82 ~~~pIY~s~~T~~ll~~~l~~~~~---~i~------~----------l~~~~~~-~i-~~~~Vt~~~a~H--~pGS~~fl 138 (1176)
.+++||+++.+...+...+..... .+. . +..+..+ .+ .+.++. ..+| +.++.+|.
T Consensus 84 ~~l~iy~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~--~~~~~~i~~~~~~~ 161 (270)
T PRK00055 84 EPLTIYGPKGIKEFVETLLRASGSLGYRIAEKDKPGKLDAEKLKALGVPPGPLFGKLKRGEDVT--LEDGRIINPADVLG 161 (270)
T ss_pred ceEEEECCccHHHHHHHHHHHhhceeEEEEEcCCCCCCCHHHHHHCCCCCCchHHHhhCCCeEE--eCCCcEEeHHHeec
Confidence 256899999999888765422110 000 0 0011100 01 122222 2344 44788888
Q ss_pred EEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCC--CCChHHHHHHHHHHHHHH
Q 001045 139 FKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFL--FPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 139 ie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~--~p~~~e~~~~l~~~i~~~ 208 (1176)
++.++ ++++|+||+++.+. .+..+.++|+||+||||...... ....|...+++.+++++.
T Consensus 162 ~~~~g-----~~~~y~~Dt~~~~~-----~~~~~~~~d~li~E~~~~~~~~~~~~~~~H~~~~~a~~~~~~~ 223 (270)
T PRK00055 162 PPRKG-----RKVAYCGDTRPCEA-----LVELAKGADLLVHEATFGDEDEELAKEYGHSTARQAAEIAKEA 223 (270)
T ss_pred cCCCC-----cEEEEeCCCCCcHH-----HHHHhCCCCEEEEeccCCcchhhHHhhcCCCCHHHHHHHHHHc
Confidence 88653 69999999987643 12223689999999999865321 122344444555555544
No 51
>TIGR02108 PQQ_syn_pqqB coenzyme PQQ biosynthesis protein B. This model describes coenzyme PQQ biosynthesis protein B, a gene required for the biosynthesis of pyrrolo-quinoline-quinone (coenzyme PQQ). PQQ is required for some glucose dehydrogenases and alcohol dehydrogenases. Note that this gene appears to be required for PQQ in biosynthesis in Methylobacterium extorquens (under the name pqqG) and in Klebiella pneumoniae but that the equivalent pqqV in Acinetobacter calcoaceticus is not necessary for heterologous expression of PQQ biosynthesis in E. coli. Based on this latter finding, it is suggested (Goosen, et al. 1989) that PqqB might be a transporter or a PQQ-dependent enzyme rather than a PQQ biosynthesis enzyme.
Probab=99.58 E-value=2.7e-14 Score=162.68 Aligned_cols=145 Identities=19% Similarity=0.165 Sum_probs=105.3
Q ss_pred CCCCCCCCeeE-e-CCccEEEecC--------CcC---------CCCccEEEeccCChhhhCCcccCC--CCceEEeCHH
Q 001045 33 PIPRTFPPSKH-V-PNTRFLIDAF--------RYA---------ADFSVSYFLSHFHSDHYTGLSPSW--SKGIIFCSEI 91 (1176)
Q Consensus 33 ~~~r~~p~~~~-i-pg~~~liD~~--------~~~---------~~~i~avfITHaH~DHiggL~~l~--~~~pIY~s~~ 91 (1176)
.+.|..+++.+ - .+..+|||++ +.. ...|++|||||.|.||++||+.+. .++|||+++.
T Consensus 33 ~~~R~rss~ll~~~g~~~iLID~Gpd~r~ql~~~~~~~~~~gl~~~~IdaI~lTH~H~DHi~GL~~L~~~~~lpVya~~~ 112 (302)
T TIGR02108 33 AKARTQSSIAVSADGERWVLLNASPDIRQQIQATPALHPQRGLRHTPIAGVVLTDGEIDHTTGLLTLREGQPFTLYATEM 112 (302)
T ss_pred CccccccEEEEEeCCCEEEEEECCHHHHHHHHhCcccccccCCCcccCCEEEEeCCCcchhhCHHHHcCCCCceEEECHH
Confidence 33567777777 3 4457999997 121 367999999999999999998764 3789999999
Q ss_pred HHHHHHHh--hcc-CCC--ceEEeCCCceEEEC-----CEEEEEEecC--------C------CcCceEEEEEEcCCCCc
Q 001045 92 TSRLLSQI--LNI-NPK--FIYPLPIKIPVLID-----GCEVVLVGAN--------H------CPGAVQFLFKVPGRNGG 147 (1176)
Q Consensus 92 T~~ll~~~--l~~-~~~--~i~~l~~~~~~~i~-----~~~Vt~~~a~--------H------~pGS~~flie~~~~~G~ 147 (1176)
|.+.+... ++. ... ..+.++.++++.++ +++|++|++. | ...+++|.|+.++ .|
T Consensus 113 t~~~L~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~g~~I~~f~v~h~~~~~~~H~~~d~~~~~~~Gy~i~~~~-~g- 190 (302)
T TIGR02108 113 VLQDLSDNPIFNVLDHWNVRRQPIALNEKFEFRIVARPGLEFTPFAVPGKAPLYSEHRAGDPHPGDTLGLKIEDGT-TG- 190 (302)
T ss_pred HHHHHHhCCCccccchhhccceEecCCCcEEecccccCCEEEEEEEcCCCCCccccccccCCCCCCcEEEEEEeCC-CC-
Confidence 99998742 111 111 13567788888764 5999999999 5 1368999999741 02
Q ss_pred ccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCC
Q 001045 148 FERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTY 184 (1176)
Q Consensus 148 ~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy 184 (1176)
++++|++|+..-.. ..+..+.++|+||+||||
T Consensus 191 -~~~~y~tD~g~~~~----~~~~~l~~~d~liida~~ 222 (302)
T TIGR02108 191 -KRLFYIPGCAEITD----DLKARMAGADLVFFDGTL 222 (302)
T ss_pred -cEEEEECCCCCCCH----HHHHHHhCCCEEEEeCCC
Confidence 79999999864332 223334789999999994
No 52
>PRK02126 ribonuclease Z; Provisional
Probab=99.53 E-value=1.2e-13 Score=159.33 Aligned_cols=174 Identities=13% Similarity=0.082 Sum_probs=119.2
Q ss_pred CCCCCCCCCeeEe---CCccEEEecCC------cCCCCccEEEeccCChhhhCCcccCC-------CCceEEeCHHHHHH
Q 001045 32 PPIPRTFPPSKHV---PNTRFLIDAFR------YAADFSVSYFLSHFHSDHYTGLSPSW-------SKGIIFCSEITSRL 95 (1176)
Q Consensus 32 p~~~r~~p~~~~i---pg~~~liD~~~------~~~~~i~avfITHaH~DHiggL~~l~-------~~~pIY~s~~T~~l 95 (1176)
+..+-..+++.+. .+..++|||+. ....++++|||||.|.||++|++.+. .+++||+++.|.+.
T Consensus 10 ~~g~~~dn~~~l~~~~~~~~iLiD~G~~~~l~~~~~~~i~~I~iTH~H~DHi~Gl~~l~~~~~~r~~~l~iygp~~~~~~ 89 (334)
T PRK02126 10 VNGPFDDPGLYVDFLFERRALLFDLGDLHHLPPRELLRISHIFVSHTHMDHFIGFDRLLRHCLGRPRRLRLFGPPGFADQ 89 (334)
T ss_pred ecCCCCCcEEEEEECCCCeEEEEcCCCHHHHhhcCCCccCEEEEcCCChhHhCcHHHHHHHhccCCCCeEEEECHHHHHH
Confidence 3445567777773 36789999983 12268999999999999999998752 24699999999999
Q ss_pred HHHhhc-c--------CCC-ceEEeC----------------------------CCceEEECCEEEEEEecCCCcCceEE
Q 001045 96 LSQILN-I--------NPK-FIYPLP----------------------------IKIPVLIDGCEVVLVGANHCPGAVQF 137 (1176)
Q Consensus 96 l~~~l~-~--------~~~-~i~~l~----------------------------~~~~~~i~~~~Vt~~~a~H~pGS~~f 137 (1176)
+...+. + ++. .+..++ .+..+..++++|+++++.|...|++|
T Consensus 90 l~~~~~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~a~~~~H~vp~~gy 169 (334)
T PRK02126 90 VEHKLAGYTWNLVENYPTTFRVHEVELHDGRIRRALFSCRRAFAREAEEELSLPDGVLLDEPWFRVRAAFLDHGIPCLAF 169 (334)
T ss_pred HHHHhccccccCcccCCCceEEEEEEccCccceeeeecccccccccccccccCCCCeEEeCCCEEEEEEEccCCCceeEE
Confidence 998774 1 111 122221 22335668999999999997779999
Q ss_pred EEEEc-------------------------------------------CC---------------------CCcccEEEE
Q 001045 138 LFKVP-------------------------------------------GR---------------------NGGFERYVH 153 (1176)
Q Consensus 138 lie~~-------------------------------------------~~---------------------~G~~~~IlY 153 (1176)
.|+.+ +| .| ++|+|
T Consensus 170 ~~~e~~~~~~~~ek~~~~gi~~g~~~~~Lk~~~~~~~~~~~~v~~~~~~g~~~~~~~~~~~~~~~~~~~~~~g--~~v~y 247 (334)
T PRK02126 170 ALEEKAHINIDKNRLAELGLPPGPWLRELKHAVLRGEPDDTPIRVLWRDGGGEHERVRPLGELKERVLRIEPG--QKIGY 247 (334)
T ss_pred EEEecCCcCcCHHHHHHcCCCCChHHHHHHhhhhccCCCCceEEeeccCCCccceeEecHHHHHHHhccCCCC--CEEEE
Confidence 99852 10 13 58999
Q ss_pred ECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCC--CCChHHHHHHHHHHHHHH
Q 001045 154 TGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFL--FPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 154 TGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~--~p~~~e~~~~l~~~i~~~ 208 (1176)
+||+++.+... .....-..++|+||+||||...... ....|.+..++.++++++
T Consensus 248 ~gDT~~~~~~~-~~l~~~a~~aDlLI~Eat~~~~~~~~a~~~gH~t~~~a~~lA~~a 303 (334)
T PRK02126 248 VTDIGYTEENL-ARIVELAAGVDLLFIEAVFLDEDAEKARRKNHLTARQAGRLAREA 303 (334)
T ss_pred ECCCCCCcccH-HHHHHHHcCCCEEEEEcccChHHhhhcccCCCCCHHHHHHHHHHc
Confidence 99998876421 1111223799999999999864321 223455555666666654
No 53
>PF12706 Lactamase_B_2: Beta-lactamase superfamily domain; PDB: 3BV6_F 1WW1_A 2E7Y_A 3RPC_D 3ZWF_A 3JXP_A 1XTO_A 2CBN_A 3G1P_B 3P2U_A ....
Probab=99.53 E-value=3.5e-14 Score=150.48 Aligned_cols=136 Identities=19% Similarity=0.270 Sum_probs=102.3
Q ss_pred CccEEEeccCChhhhCCcccCCC-----CceEEeCHHHHHHHHH-hhcc-------CCCceEEeCCCceEEECCEEEEEE
Q 001045 60 FSVSYFLSHFHSDHYTGLSPSWS-----KGIIFCSEITSRLLSQ-ILNI-------NPKFIYPLPIKIPVLIDGCEVVLV 126 (1176)
Q Consensus 60 ~i~avfITHaH~DHiggL~~l~~-----~~pIY~s~~T~~ll~~-~l~~-------~~~~i~~l~~~~~~~i~~~~Vt~~ 126 (1176)
.+++|||||.|.||+.||+.+.. ..+|||++.+.+.+.. .++. ....+..+..++.+++++++|+++
T Consensus 29 ~id~v~iTH~H~DH~~gl~~l~~~~~~~~~~i~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~ 108 (194)
T PF12706_consen 29 DIDAVFITHSHPDHIAGLPSLIPAWAKHPKPIYGPPETKEFLREYKFGILDLYPEEDNFDIIEISPGDEFEIGDFRITPF 108 (194)
T ss_dssp CEEEEE-SBSSHHHHTTHHHHHHHHHHCTTEEEECHHHHHHHHHHHHTHHTTCCTTSGEEEEEECTTEEEEETTEEEEEE
T ss_pred CCCEEEECCCCccccCChHHHHHHhhcccceEEecHHHHHHHHhhhcccccccccccceeEEEeccCceEEeceEEEEEE
Confidence 78999999999999999765322 2399999999999994 2321 123467888889999999999999
Q ss_pred ecCCCcCceE----EEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCC---CCCChHHHHH
Q 001045 127 GANHCPGAVQ----FLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKF---LFPLQEESVE 199 (1176)
Q Consensus 127 ~a~H~pGS~~----flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~---~~p~~~e~~~ 199 (1176)
++.|..++++ |+|+.++ ++|+|+||+.+ . +..+.++|+||+||++..... ...+.+....
T Consensus 109 ~~~H~~~~~~~~~g~~i~~~~-----~~i~~~gD~~~--~------~~~~~~~D~li~~~~~~~~~~~~~~~~~~h~~~~ 175 (194)
T PF12706_consen 109 PANHGPPSYGGNKGFVIEPDG-----KKIFYSGDTNY--D------FEELKNIDLLILECGYIDEEEEPPARGPGHMTLE 175 (194)
T ss_dssp EEESSSCCEEECCEEEEEETT-----EEEEEETSSSS--C------HHHHTTBSEEEEEBCBSSGGHHCHHCCTTSBBHH
T ss_pred eccccccccccCceEEEecCC-----cceEEeeccch--h------hhhhccCCEEEEeCCCcchhhcccccCCCCCCHH
Confidence 9999888887 9999754 79999999988 1 233378999999999984221 1223444455
Q ss_pred HHHHHHHHH
Q 001045 200 YVVNVVNRV 208 (1176)
Q Consensus 200 ~l~~~i~~~ 208 (1176)
++.+.+++.
T Consensus 176 ~~~~~~~~~ 184 (194)
T PF12706_consen 176 EALELAKEL 184 (194)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHc
Confidence 666666665
No 54
>KOG1135 consensus mRNA cleavage and polyadenylation factor II complex, subunit CFT2 (CPSF subunit) [RNA processing and modification]
Probab=99.51 E-value=2.2e-13 Score=160.86 Aligned_cols=194 Identities=16% Similarity=0.130 Sum_probs=158.8
Q ss_pred CCCCCCeeE-eCCccEEEecCC-------------cCCCCccEEEeccCChhhhCCcccCCC----CceEEeCHHHHHHH
Q 001045 35 PRTFPPSKH-VPNTRFLIDAFR-------------YAADFSVSYFLSHFHSDHYTGLSPSWS----KGIIFCSEITSRLL 96 (1176)
Q Consensus 35 ~r~~p~~~~-ipg~~~liD~~~-------------~~~~~i~avfITHaH~DHiggL~~l~~----~~pIY~s~~T~~ll 96 (1176)
.....||.+ +.|+.|+||||. ...+.|++|+|||...-|+||||+... +.|||+|-++..+=
T Consensus 12 de~~~cyllqiD~~~iLiDcGwd~~f~~~~i~~l~~~i~~iDaILLShpd~~hlGaLpY~~~k~gl~~~VYAT~PV~~mG 91 (764)
T KOG1135|consen 12 DEGPLCYLLQIDGVRILIDCGWDESFDMSMIKELKPVIPTIDAILLSHPDILHLGALPYAVGKLGLNAPVYATLPVIKMG 91 (764)
T ss_pred CCCcceEEEEEcCeEEEEeCCCcchhccchhhhhhcccccccEEEecCCChHHhccchhhHhhCCccceEEEecchhhhh
Confidence 345668888 999999999982 122689999999999999999998543 68999999998875
Q ss_pred HHhh-----c------c----------CCCceEEeCCCceEEEC----CEEEEEEecCCCcCceEEEEEEcCCCCcccEE
Q 001045 97 SQIL-----N------I----------NPKFIYPLPIKIPVLID----GCEVVLVGANHCPGAVQFLFKVPGRNGGFERY 151 (1176)
Q Consensus 97 ~~~l-----~------~----------~~~~i~~l~~~~~~~i~----~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~I 151 (1176)
+..+ . + .-..+.++.|.+++.+. |++|++++|||++|.+.+.|...+ .+|
T Consensus 92 ~m~myD~~~S~~~~~df~l~sldDvd~aFd~I~~LKYsQ~v~L~gk~~Gl~itaynAGhmiGGsIWkI~k~~-----E~i 166 (764)
T KOG1135|consen 92 QMFMYDLYRSHGNVGDFDLFSLDDVDAAFDKIIQLKYSQPVALKGKGSGLTITAYNAGHMIGGSIWKISKVG-----EDI 166 (764)
T ss_pred hhhHHHHHhcccccccccccchhhhHHHHhheeeeeccceEEeccccCceEEeeecCCCccCceEEEEEecC-----ceE
Confidence 5322 1 0 12357899999999884 579999999999999999998754 699
Q ss_pred EEECCCCCcccccchhh-hhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccc
Q 001045 152 VHTGDFRFCKTMLLQPV-MNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIG 230 (1176)
Q Consensus 152 lYTGDfr~~~~~~~~~~-l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slG 230 (1176)
+|.-||+.....+.++. +..+.++.+||+++.... +..+++...-+++.+.+.+.+.. +|+ |++|+-..|
T Consensus 167 vYavd~NHkKe~HLNG~~l~~l~RPsllITda~~~~--~~~~~rkkRDe~f~d~v~~~L~~-----~G~--VlipVDtAg 237 (764)
T KOG1135|consen 167 VYAVDFNHKKERHLNGCSLSGLNRPSLLITDANHAL--YSQPRRKKRDEQFLDTVLKTLRS-----GGN--VLIPVDTAG 237 (764)
T ss_pred EEEEecccchhcccCCccccccCCcceEEecccccc--ccccchhHHHHHHHHHHHHHhcC-----CCc--EEEEecccH
Confidence 99999999887777666 666789999999998876 55688888888999999998776 788 788999999
Q ss_pred hHHHHHHHHHHc
Q 001045 231 KEKILIEIFKKC 242 (1176)
Q Consensus 231 R~q~ll~ia~~~ 242 (1176)
|.-++..++.++
T Consensus 238 RvLELa~iLdql 249 (764)
T KOG1135|consen 238 RVLELALILDQL 249 (764)
T ss_pred HHHHHHHHHHHH
Confidence 999998888764
No 55
>TIGR02650 RNase_Z_T_toga ribonuclease Z, Thermotoga type. Members of this protein family are ribonuclease Z as found in the genus Thermotoga, where the enzyme cleaves after the CCA, in contrast to the activities characterized for other enzymes also designated ribonuclease Z. In other systems, cleavage occurs 5-prime to the location of the CCA sequence, and CCA is added subsequently. A species may lack ribonuclease Z if all tRNA genes encode the CCA sequence, or if the CCA is exposed by exonuclease activity rather than endonuclease activity. Note that members of this sequence family differ considerably from the majority of RNase Z sequences.
Probab=99.40 E-value=2.1e-12 Score=143.27 Aligned_cols=161 Identities=12% Similarity=0.020 Sum_probs=108.2
Q ss_pred eeEeCCccEEEe-cCCcCC-------CCccEEEeccCChhhhCCcccC-----C-----CCceEEeCHHHHHHHHHhh--
Q 001045 41 SKHVPNTRFLID-AFRYAA-------DFSVSYFLSHFHSDHYTGLSPS-----W-----SKGIIFCSEITSRLLSQIL-- 100 (1176)
Q Consensus 41 ~~~ipg~~~liD-~~~~~~-------~~i~avfITHaH~DHiggL~~l-----~-----~~~pIY~s~~T~~ll~~~l-- 100 (1176)
..+.+..++++| ++.... ..++.+||||+|.||++||+.+ | .+..||+++.+.+.++..+
T Consensus 13 ~~~~~~~~ilfD~ag~g~~~~l~~k~~~l~~vFlTH~H~DHi~gL~~~~~~~~~~~~~~~p~~Vy~P~g~~~~ve~~~~~ 92 (277)
T TIGR02650 13 TIIYSPEEIIFDAAEEGSSTLGGKKVAAFKVFFLHGGHDDHAAGLGGVNIINNGGGDDEEKLDDFFPKEGNAAEEETSEF 92 (277)
T ss_pred EEEECchhheehhhcccchhHHhhhHhhcCEEEeecCchhhhcchHHHHhhhhhcccCCCCCeEECCcchhHHHHHHHHH
Confidence 344678889999 664332 5689999999999999999531 1 1456999999988888433
Q ss_pred -ccC------CCceEEeCCCceEEEC-C---EEEEEEecCCCc---CceEEEEEEcCC--------------------CC
Q 001045 101 -NIN------PKFIYPLPIKIPVLID-G---CEVVLVGANHCP---GAVQFLFKVPGR--------------------NG 146 (1176)
Q Consensus 101 -~~~------~~~i~~l~~~~~~~i~-~---~~Vt~~~a~H~p---GS~~flie~~~~--------------------~G 146 (1176)
... .-.+.+++.++.+... + ..|.++++.|.. -|.+|.|..... +|
T Consensus 93 ~~~~~~~~~~~~~~~~~~~~e~~~~r~~~~~~~V~~f~t~H~v~~~~s~GY~~~~~r~KLK~E~~~l~~~eI~~l~~~gg 172 (277)
T TIGR02650 93 IKAANEDLFFFFNHHLEEEDERFFLDAAGFFKRVQPFFRKHHASEESFFGHHFEERRKKKEEEFGGDDKKEARLLKEEGG 172 (277)
T ss_pred HHHhhhhhccCcccCCCCCCcEEEeecCCccEEEecCccccccCccCccCeEEEEEeecchHhHcCCCHHHHHHHHHhCC
Confidence 211 1123445566666666 3 899999999963 488887763100 00
Q ss_pred -------cccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHH
Q 001045 147 -------GFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 147 -------~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~ 208 (1176)
.-++|+||||+++... + ...++|+||+||||.+........|....++++.++++
T Consensus 173 ~~~t~e~~~~~vvysGDT~~~~~----~---~a~~adlLIhEaTf~d~~~~~~~gH~t~~eaa~~A~~a 234 (277)
T TIGR02650 173 DDFTREEHHKILLIIGDDLAADD----E---EEEGGEELIHECCFFDDADDRRKKHAAADDEMEESKKA 234 (277)
T ss_pred ccccccccCcEEEEeCCCCCCCh----H---HhcCCCEEEEecccccccccccCCCCCHHHHHHHHHHc
Confidence 1158999999987742 1 22699999999999886432223355566666666654
No 56
>PRK00685 metal-dependent hydrolase; Provisional
Probab=99.39 E-value=8.8e-12 Score=136.34 Aligned_cols=184 Identities=18% Similarity=0.203 Sum_probs=124.9
Q ss_pred CCCeeE-eCCccEEEecCCc---------CCCCccEEEeccCChhhhCCcccCC--CCceEEeCHHHHHHHHHhhccCCC
Q 001045 38 FPPSKH-VPNTRFLIDAFRY---------AADFSVSYFLSHFHSDHYTGLSPSW--SKGIIFCSEITSRLLSQILNINPK 105 (1176)
Q Consensus 38 ~p~~~~-ipg~~~liD~~~~---------~~~~i~avfITHaH~DHiggL~~l~--~~~pIY~s~~T~~ll~~~l~~~~~ 105 (1176)
.+|+.+ ..+..+++|++.. ...++++|||||.|.||++++..+. ...+||+++.+...+... ++.
T Consensus 8 ~s~~li~~~~~~iLiDP~~~~~~~~~~~~~~~~id~vliTH~H~DH~~~~~~~~~~~~~~v~~~~~~~~~~~~~-~~~-- 84 (228)
T PRK00685 8 HSAFLIETGGKKILIDPFITGNPLADLKPEDVKVDYILLTHGHGDHLGDTVEIAKRTGATVIANAELANYLSEK-GVE-- 84 (228)
T ss_pred ceEEEEEECCEEEEECCCCCCCCCCCCChhcCcccEEEeCCCCccccccHHHHHHhCCCEEEEeHHHHHHHHhc-CCC--
Confidence 457777 7889999997421 1237999999999999999887643 367899999988877643 322
Q ss_pred ceEEeCCCceEEECCEEEEEEecCCCcC------------ceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccC
Q 001045 106 FIYPLPIKIPVLIDGCEVVLVGANHCPG------------AVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFA 173 (1176)
Q Consensus 106 ~i~~l~~~~~~~i~~~~Vt~~~a~H~pG------------S~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~ 173 (1176)
.+..++.++.+.+++++|+++++.|... .++|.|+.++ ++++|+||+.+.+... .+....
T Consensus 85 ~~~~~~~~~~~~~~~~~i~~~p~~H~~~~~~~~~~~~~~~~~g~~i~~~~-----~~i~~~GDt~~~~~~~---~~~~~~ 156 (228)
T PRK00685 85 KTHPMNIGGTVEFDGGKVKLTPALHSSSFIDEDGITYLGNPTGFVITFEG-----KTIYHAGDTGLFSDMK---LIGELH 156 (228)
T ss_pred ceeeccCCCcEEECCEEEEEEEEEcCCCCcCCCCcccCCCceEEEEEECC-----eEEEEecCccchhHHH---HHHHhh
Confidence 4678889999999999999999999432 5899999854 6999999998765421 122224
Q ss_pred CCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEecc--cc--chHHHHHHHHHHcCCcEEE
Q 001045 174 GCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATY--VI--GKEKILIEIFKKCGRKVCV 248 (1176)
Q Consensus 174 ~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~--sl--GR~q~ll~ia~~~g~~I~v 248 (1176)
++|++++.... ..+.+. +++.+.++.. +.+.+|.++.. .. +..+++...+++.+.++.+
T Consensus 157 ~~D~~~~~~~~----~~h~~~----~ea~~~~~~~--------~~k~~v~~H~~~~~~~~~~~~~~~~~~~~~~~~~~~ 219 (228)
T PRK00685 157 KPDVALLPIGD----NFTMGP----EDAALAVELI--------KPKIVIPMHYNTFPLIEQDPEKFKALVEGLGTKVVI 219 (228)
T ss_pred CCCEEEEecCC----ccccCH----HHHHHHHHhh--------CCCEEEEeccCCCcCCcCCHHHHHHHHHhcCCcEEE
Confidence 78999986531 123333 3445555544 34444444432 22 3356666666666666554
No 57
>PRK04286 hypothetical protein; Provisional
Probab=99.29 E-value=4.2e-11 Score=136.64 Aligned_cols=208 Identities=16% Similarity=0.108 Sum_probs=124.4
Q ss_pred ccCCCCCCCCCCCCCCCCCeeE-eCCccEEEecCCcC---------------------------CCCccEEEeccCChhh
Q 001045 22 QSSPPDSLIFPPIPRTFPPSKH-VPNTRFLIDAFRYA---------------------------ADFSVSYFLSHFHSDH 73 (1176)
Q Consensus 22 ~~~l~s~~~~p~~~r~~p~~~~-ipg~~~liD~~~~~---------------------------~~~i~avfITHaH~DH 73 (1176)
+.+||+++ .+....|+.+ ..+..+|||+|... ..++++|||||.|.||
T Consensus 3 ~~~l~s~s----~g~~~~~~~I~~~~~~iLID~G~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~id~IliTH~H~DH 78 (298)
T PRK04286 3 IIPLASES----LGVRSMATFVETKDVRILIDPGVSLAPRRYGLPPHPIELERLEEVREKILEYAKKADVITISHYHYDH 78 (298)
T ss_pred EEEEEeCC----CCceeeEEEEEECCeEEEEcCCCCcCccccCCCCcchhHHHHHHHHHHhhcccccCCEEEecCCcccc
Confidence 34566655 3445566777 78999999998321 2479999999999999
Q ss_pred hCCcccCC-------CCceEEeCHHHHHH-HHH------hh---cc----C-CCceEEeCCCceEEECCEEEEEE-ecCC
Q 001045 74 YTGLSPSW-------SKGIIFCSEITSRL-LSQ------IL---NI----N-PKFIYPLPIKIPVLIDGCEVVLV-GANH 130 (1176)
Q Consensus 74 iggL~~l~-------~~~pIY~s~~T~~l-l~~------~l---~~----~-~~~i~~l~~~~~~~i~~~~Vt~~-~a~H 130 (1176)
++++.... .+.+||+++.+... ... .+ .+ . ......+..++++.+++++|+++ +++|
T Consensus 79 i~g~~~~~y~~~~~~~~i~iy~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~g~~~~ig~~~V~~~~~v~H 158 (298)
T PRK04286 79 HTPFYEDPYELSDEEIPKEIYKGKIVLIKDPTENINWSQRRRAPRFLKAVKDIAKKIEYADGKTFRFGGTTIEFSPPVPH 158 (298)
T ss_pred CCCccccccccccccchHHHhcCceecccCHHHHcCHHHHhhHHhHHHHHHhcCCceEECCCCEEEECCEEEEEeccCCC
Confidence 98886531 13567776555421 000 00 00 0 01134567788999999999966 8899
Q ss_pred -Cc-CceEEEE----EEcCCCCcccEEEEECCCC-CcccccchhhhhccCCCcEEEEeC--CCCC-CCCCCCChHHHHHH
Q 001045 131 -CP-GAVQFLF----KVPGRNGGFERYVHTGDFR-FCKTMLLQPVMNEFAGCDAVFLDT--TYCN-PKFLFPLQEESVEY 200 (1176)
Q Consensus 131 -~p-GS~~fli----e~~~~~G~~~~IlYTGDfr-~~~~~~~~~~l~~~~~vDvLI~Es--Ty~~-~~~~~p~~~e~~~~ 200 (1176)
.+ ++++|.+ +.+ | ++++|+||+. ........ .+.. .++|+|++++ +|.. ........+.+.+.
T Consensus 159 ~~~~~~~Gy~i~~ri~~g---g--~~~~~~gDt~~~~~~~~~~-~l~~-~d~dlLi~~~~p~~lk~~ri~~~~~h~s~~~ 231 (298)
T PRK04286 159 GADGSKLGYVIMVRISDG---D--ESFVFASDVQGPLNDEAVE-FILE-KKPDVVIIGGPPTYLLGRRLSEEDLEKGIEN 231 (298)
T ss_pred CCCCCccceEEEEEEEeC---C--EEEEEECCCCCCCCHHHHH-HHhc-CCCCEEEeCCcchhhhhhhhccccHHHHHHH
Confidence 44 4555544 443 3 7999999997 22221111 1111 4899999998 3443 11123344555555
Q ss_pred HHHHHHHHhhhccccCCCeEEEEEeccc--cc---hHHHHHHHHHHcCCcEEEc
Q 001045 201 VVNVVNRVGGELNEGLQKRVLFLVATYV--IG---KEKILIEIFKKCGRKVCVD 249 (1176)
Q Consensus 201 l~~~i~~~~~~~~~~~~g~vlvli~~~s--lG---R~q~ll~ia~~~g~~I~vd 249 (1176)
+.+++.. +.+.+++.++-+ .. ..+.+.+.++..++.++..
T Consensus 232 ~~~l~~~---------~~k~liLtHHls~~~n~~~~~~~l~~~~~~~~~~~~~~ 276 (298)
T PRK04286 232 LEEIVKN---------TPETLILDHHLLRDKNYREKLKELYERAEDRGVRVLTA 276 (298)
T ss_pred HHHHHhc---------CCCEEEEeccccccCCcHHHHHHHHHHHhhcCceEEeH
Confidence 5444432 234445553433 22 3346666688888888874
No 58
>KOG2121 consensus Predicted metal-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]
Probab=99.21 E-value=2.9e-12 Score=153.67 Aligned_cols=179 Identities=15% Similarity=0.161 Sum_probs=121.9
Q ss_pred cccCCCCCCCCCCCCCCCCCeeE-eCCcc-EEEecC---------CcC-------CCCccEEEeccCChhhhCCcccCCC
Q 001045 21 TQSSPPDSLIFPPIPRTFPPSKH-VPNTR-FLIDAF---------RYA-------ADFSVSYFLSHFHSDHYTGLSPSWS 82 (1176)
Q Consensus 21 ~~~~l~s~~~~p~~~r~~p~~~~-ipg~~-~liD~~---------~~~-------~~~i~avfITHaH~DHiggL~~l~~ 82 (1176)
.|-.||||++.|...|..+.+.+ ++... |++||| .|+ ..++.+|||||.|.||..||+....
T Consensus 444 eIi~LGTGSaiPskyRNVSS~lv~i~~~~~IlLDCGEgTlgql~R~YG~~~~~~~lr~LraI~ISHlHADHh~Gl~~vL~ 523 (746)
T KOG2121|consen 444 EIIFLGTGSAIPSKYRNVSSILVRIDSDDSILLDCGEGTLGQLVRHYGVENVDTALRKLRAIFISHLHADHHLGLISVLQ 523 (746)
T ss_pred EEEEecCCccCCCcccceEEEEEeccCCccEEeecCCchHHHHHHHhhhcchHHHHHhHHHHHHHhhcccccccHHHHHH
Confidence 34579999999999999999999 75555 999998 233 1578899999999999999975211
Q ss_pred ------------CceEEeCHHHHHHHHHhhcc---CCC-------ceEEeCCCce------------EEECCEEEEEEec
Q 001045 83 ------------KGIIFCSEITSRLLSQILNI---NPK-------FIYPLPIKIP------------VLIDGCEVVLVGA 128 (1176)
Q Consensus 83 ------------~~pIY~s~~T~~ll~~~l~~---~~~-------~i~~l~~~~~------------~~i~~~~Vt~~~a 128 (1176)
+.-|.++..-...++..... ... ....+..+.+ -+.+...|...++
T Consensus 524 ~r~k~~k~~~~~pl~vv~P~ql~~wl~~y~~~~~~~~~~~~~i~~~g~lf~~~s~~s~~~~~~~~~l~~~~l~~i~tc~v 603 (746)
T KOG2121|consen 524 ARTKLLKGVENSPLLVVAPRQLKKWLQEYHRCPSFPASSVAKIGAPGALFAQKSPDSVPERLLSYLLRELGLESIQTCPV 603 (746)
T ss_pred HHHHhccccccCceEEeChHHHHHHHHHHhcCcccchhhhhhhcCchhhhhccCccccchhhhhHHHHhcCceeEEecCc
Confidence 23455777777777654311 000 0000110111 1246789999999
Q ss_pred CCCcCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCC--CCCChHHHHHHHHHHHH
Q 001045 129 NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKF--LFPLQEESVEYVVNVVN 206 (1176)
Q Consensus 129 ~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~--~~p~~~e~~~~l~~~i~ 206 (1176)
-|||.|++..+.... | .+|+|+||+|.++....-. .+.|+||+|+|+.+.-. .....|.+..+++++.+
T Consensus 604 iHCp~syg~~i~~~~--~--~Ki~YSGDTrP~~~~v~~g-----~datlLIHEAT~ED~l~EeAv~k~HST~sEAi~V~~ 674 (746)
T KOG2121|consen 604 IHCPQSYGCSITHGS--G--WKIVYSGDTRPCEDLVKAG-----KDATLLIHEATLEDDLEEEAVEKGHSTTSEAISVAK 674 (746)
T ss_pred EecChhhceeEeccc--c--eEEEEcCCCCCchhHhhhc-----cCCceEEeehhhchhHHHHHHHhCCCCHHHHHHHHH
Confidence 999999999998754 3 6999999999866532211 68999999999987421 12233444555555555
Q ss_pred HH
Q 001045 207 RV 208 (1176)
Q Consensus 207 ~~ 208 (1176)
..
T Consensus 675 ~m 676 (746)
T KOG2121|consen 675 KM 676 (746)
T ss_pred hc
Confidence 43
No 59
>smart00849 Lactamase_B Metallo-beta-lactamase superfamily. Apart from the beta-lactamases a number of other proteins contain this domain PUBMED:7588620. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.
Probab=99.17 E-value=9.1e-11 Score=122.31 Aligned_cols=120 Identities=22% Similarity=0.246 Sum_probs=93.1
Q ss_pred CCCCCeeE-eCCccEEEecC-Cc-----------CCCCccEEEeccCChhhhCCcccCC--CCceEEeCHHHHHHHHHhh
Q 001045 36 RTFPPSKH-VPNTRFLIDAF-RY-----------AADFSVSYFLSHFHSDHYTGLSPSW--SKGIIFCSEITSRLLSQIL 100 (1176)
Q Consensus 36 r~~p~~~~-ipg~~~liD~~-~~-----------~~~~i~avfITHaH~DHiggL~~l~--~~~pIY~s~~T~~ll~~~l 100 (1176)
+..+++.+ .++..+++|++ .. ...++++|||||.|.||++|++.+. .+.+||+++.+.+.+....
T Consensus 4 ~~~~~~li~~~~~~iliD~g~~~~~~~~~~l~~~~~~~i~~i~iTH~H~DH~~g~~~~~~~~~~~i~~~~~~~~~~~~~~ 83 (183)
T smart00849 4 VGVNSYLVEGDGGAILIDTGPGEAEDLLAELKKLGPKDIDAIILTHGHPDHIGGLPELLEAPGAPVYAPEGTAELLKDLL 83 (183)
T ss_pred cceeEEEEEeCCceEEEeCCCChhHHHHHHHHHcCchhhcEEEecccCcchhccHHHHHhCCCCcEEEchhhhHHHhccc
Confidence 45566677 68889999998 21 1358999999999999999998654 3678999999998887432
Q ss_pred c---------cCCCceEEeCCCceEEECCEEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCCccc
Q 001045 101 N---------INPKFIYPLPIKIPVLIDGCEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKT 162 (1176)
Q Consensus 101 ~---------~~~~~i~~l~~~~~~~i~~~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~ 162 (1176)
. .....+..+..++++.+++.+++++++ +|.+|+++++++. .+++|+||+.....
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~~~~~~~~~-------~~vl~~gD~~~~~~ 148 (183)
T smart00849 84 KLGGALGAEAPPPPPDRTLKDGEELDLGGLELEVIHTPGHTPGSIVLYLPE-------GKILFTGDLLFSGG 148 (183)
T ss_pred hhccccCcCCCCCccceecCCCCEEEeCCceEEEEECCCCCCCcEEEEECC-------CCEEEECCeeeccC
Confidence 1 112345678889999999888888887 8899999988763 48999999876654
No 60
>PF07522 DRMBL: DNA repair metallo-beta-lactamase; InterPro: IPR011084 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in DNA repair [].
Probab=99.10 E-value=2.7e-10 Score=111.09 Aligned_cols=90 Identities=47% Similarity=0.858 Sum_probs=70.8
Q ss_pred CCccccCCCCCeEEEecChHH--------HH--hcCCCceEEEEeccceeecccCceee------eccCCeeEEEEeecC
Q 001045 264 SGVFTEDESETDVHVVGWNEI--------MV--ERGYDKVVGFVPTGWTYEVKRNKFAV------RSKDAFEIHLVPYSE 327 (1176)
Q Consensus 264 ~~~~t~d~~~~~I~v~~~~~~--------~~--~~g~~~~v~i~ptGw~~~~~~~~~~v------~~~~~~~v~~i~~Sg 327 (1176)
.++||.++.+++||+++++.+ +. ...++++++|.||||.+....+.... ....+..++.+|||.
T Consensus 4 ~~~~T~d~~~t~iHvv~~~~~~~~~l~~~~~~~~~~~~~vi~i~PTgW~~~~~~~~~~~~~~~~~~~~~~~~~~~VPYSe 83 (110)
T PF07522_consen 4 SSLFTTDPSETRIHVVPMGQLSKETLEKYLKSLKPRFDPVIGIRPTGWSFSNKKKKSSVSISPSLQSRGNVRIYRVPYSE 83 (110)
T ss_pred hceeecCCCCCeEEEEECCcCCHHHHHHHHHhhcccCCCeEEEEeCccccccCCCccccccccccccCCCceEEEEeccc
Confidence 457899999999999988721 11 12377999999999988765433221 134567889999999
Q ss_pred CCCHHHHHHHHHHcCCCEEEEEecCC
Q 001045 328 HSNYDELREYVKFLKPKRVIPTVGMD 353 (1176)
Q Consensus 328 HAs~~EL~~~V~~lrPk~VIPvHG~~ 353 (1176)
||++.||++||+.++|++|||++..+
T Consensus 84 HSSf~EL~~Fv~~l~P~~IiPtV~~~ 109 (110)
T PF07522_consen 84 HSSFSELKEFVSFLKPKKIIPTVNVS 109 (110)
T ss_pred CCCHHHHHHHHHhcCCcEEEccccCC
Confidence 99999999999999999999998743
No 61
>PRK11709 putative L-ascorbate 6-phosphate lactonase; Provisional
Probab=99.04 E-value=3e-09 Score=123.78 Aligned_cols=138 Identities=15% Similarity=0.137 Sum_probs=95.4
Q ss_pred CCccEEEeccCChhhhC--CcccCC----CCceEEeCHHHHHHHHHhhccCCCceEEeCCCceEEECCEEEEEEecCCC-
Q 001045 59 DFSVSYFLSHFHSDHYT--GLSPSW----SKGIIFCSEITSRLLSQILNINPKFIYPLPIKIPVLIDGCEVVLVGANHC- 131 (1176)
Q Consensus 59 ~~i~avfITHaH~DHig--gL~~l~----~~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a~H~- 131 (1176)
+++|+|||||.|.||+. .+..+. .+.+++++..+.+++.. ++++...++.++.|+++.+++++|+++++.|.
T Consensus 108 ~~IDaVLiTH~H~DHlD~~tl~~l~~~~~~~~~~v~p~~~~~~~~~-~Gvp~~rv~~v~~Ge~i~ig~v~It~lpa~h~~ 186 (355)
T PRK11709 108 REIDAVLATHDHSDHIDVNVAAAVLQNCADHVKFIGPQACVDLWIG-WGVPKERCIVVKPGDVVKVKDIKIHALDSFDRT 186 (355)
T ss_pred CCCCEEEECCCcccccChHHHHHHHhhcCCCcEEEEcHHHHHHHHh-cCCCcceEEEecCCCcEEECCEEEEEEeccccc
Confidence 57999999999999984 222221 24678999998887664 57766678999999999999999999999541
Q ss_pred ---------------------cCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCC
Q 001045 132 ---------------------PGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFL 190 (1176)
Q Consensus 132 ---------------------pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~ 190 (1176)
..+++|+|+.++ ++|+|+||..+.+... ..... .++|++++...- .+..
T Consensus 187 ~~i~~p~~h~~~~~~~~~d~~~~~~gyvie~~~-----~tvy~sGDT~~~~~~~--~i~~~-~~iDvall~iG~-~p~~- 256 (355)
T PRK11709 187 ALVTLPADGKAAGGVLPDDMDRRAVNYLFKTPG-----GNIYHSGDSHYSNYFA--KHGND-HQIDVALGSYGE-NPRG- 256 (355)
T ss_pred cccccccccccccccccccCCcceEEEEEEeCC-----eEEEEeCCCCccHHHH--HHHhc-CCCCEEEecCCC-CCCC-
Confidence 125899999864 6999999998864321 11222 369999985432 2221
Q ss_pred CCChHHHHHHHHHHHHHH
Q 001045 191 FPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 191 ~p~~~e~~~~l~~~i~~~ 208 (1176)
...+...+++.+.++.+
T Consensus 257 -~~~hm~p~ea~~~a~~l 273 (355)
T PRK11709 257 -ITDKMTSIDILRMAESL 273 (355)
T ss_pred -CcCCCCHHHHHHHHHHc
Confidence 12234444566666554
No 62
>PRK11921 metallo-beta-lactamase/flavodoxin domain-containing protein; Provisional
Probab=98.96 E-value=2e-09 Score=127.78 Aligned_cols=113 Identities=15% Similarity=0.141 Sum_probs=88.5
Q ss_pred CCCCeeEeCCccEEEecCCc--------------CCCCccEEEeccCChhhhCCcccCC---CCceEEeCHHHHHHHHHh
Q 001045 37 TFPPSKHVPNTRFLIDAFRY--------------AADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSEITSRLLSQI 99 (1176)
Q Consensus 37 ~~p~~~~ipg~~~liD~~~~--------------~~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~~T~~ll~~~ 99 (1176)
...+|++..+..+|||++.. ...++++|++||.|.||+||++.+. ++.+|||++.+...+...
T Consensus 32 ~~NsyLI~~~~~vLIDtg~~~~~~~~~~~l~~~~~~~~Id~IilTH~H~DHiggl~~l~~~~p~a~V~~~~~~~~~l~~~ 111 (394)
T PRK11921 32 SYNSYLIKDEKTVLIDTVWQPFAKEFVENLKKEIDLDKIDYIVANHGEIDHSGALPELMKEIPDTPIYCTKNGAKSLKGH 111 (394)
T ss_pred EEEEEEEeCCCEEEEeCCCCCcHHHHHHHHHhhcCcccCCEEEeCCCCCchhhHHHHHHHHCCCCEEEECHHHHHHHHHH
Confidence 34455555566899999731 1247999999999999999998643 468999999999888755
Q ss_pred hccCCCceEEeCCCceEEECCEEEEEEecC--CCcCceEEEEEEcCCCCcccEEEEECCC
Q 001045 100 LNINPKFIYPLPIKIPVLIDGCEVVLVGAN--HCPGAVQFLFKVPGRNGGFERYVHTGDF 157 (1176)
Q Consensus 100 l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a~--H~pGS~~flie~~~~~G~~~~IlYTGDf 157 (1176)
+.. ...+..+..|+.+.+++.+++++++. |.||+++++++. .++|||||+
T Consensus 112 ~~~-~~~~~~v~~g~~l~lG~~~l~~i~tP~~H~p~~~~~y~~~-------~~vLFsgD~ 163 (394)
T PRK11921 112 YHQ-DWNFVVVKTGDRLEIGSNELIFIEAPMLHWPDSMFTYLTG-------DNILFSNDA 163 (394)
T ss_pred hCC-CCceEEeCCCCEEeeCCeEEEEEeCCCCCCCCceEEEEcC-------CCEEEecCc
Confidence 432 12366788899999999999999763 999999999864 469999996
No 63
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=98.90 E-value=4.5e-09 Score=127.28 Aligned_cols=114 Identities=13% Similarity=0.127 Sum_probs=90.0
Q ss_pred CCCCeeEeCCccEEEecCCc--------------CCCCccEEEeccCChhhhCCcccCC---CCceEEeCHHHHHHHHHh
Q 001045 37 TFPPSKHVPNTRFLIDAFRY--------------AADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSEITSRLLSQI 99 (1176)
Q Consensus 37 ~~p~~~~ipg~~~liD~~~~--------------~~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~~T~~ll~~~ 99 (1176)
...+|++..+..++||++.. ...+|++|++||.|.||+|+++.+. .+.+||+++.+...+...
T Consensus 34 t~NsYLI~~~~~vLIDtg~~~~~~~~l~~l~~~~~~~~Id~IilTH~H~DH~Ggl~~Ll~~~p~a~V~~s~~~~~~l~~~ 113 (479)
T PRK05452 34 SYNSYLIREEKNVLIDTVDHKFSREFVQNLRNEIDLADIDYIVINHAEEDHAGALTELMAQIPDTPIYCTANAIDSINGH 113 (479)
T ss_pred EEEEEEEECCCEEEEeCCCcccHHHHHHHHHhcCCHhhCCEEEeCCCCcchhchHHHHHHHCCCCEEEECHHHHHHHHHh
Confidence 44566666677899998631 1147999999999999999998754 468999999999888765
Q ss_pred hccCCCceEEeCCCceEEEC-CEEEEEEec--CCCcCceEEEEEEcCCCCcccEEEEECCC
Q 001045 100 LNINPKFIYPLPIKIPVLID-GCEVVLVGA--NHCPGAVQFLFKVPGRNGGFERYVHTGDF 157 (1176)
Q Consensus 100 l~~~~~~i~~l~~~~~~~i~-~~~Vt~~~a--~H~pGS~~flie~~~~~G~~~~IlYTGDf 157 (1176)
.......++.+..|+.+.++ +.+++++++ .|.||+++++++. .++|||||+
T Consensus 114 ~~~~~~~~~~v~~G~~l~lG~~~~l~~i~tP~~H~pgs~~~y~~~-------~~vLFsgD~ 167 (479)
T PRK05452 114 HHHPEWNFNVVKTGDTLDIGNGKQLIFVETPMLHWPDSMMTYLTG-------DAVLFSNDA 167 (479)
T ss_pred hcCCcCeEEEeCCCCEEecCCCcEEEEEECCCCCCCCceEEEEcC-------CCEEEeccc
Confidence 44333346788999999998 478888888 4999999999864 469999995
No 64
>PF02112 PDEase_II: cAMP phosphodiesterases class-II; InterPro: IPR000396 Cyclic-AMP phosphodiesterase (3.1.4.17 from EC) (PDE) catalyses the hydrolysis of cAMP to the corresponding nucleoside 5' monophosphate. On the basis of sequence similarity, most PDEs can be grouped together [], but some enzymes lie apart from the main family and represent a second distinct class [] that includes PDEs from Dictyostelium and yeast. This entry contains class-II cyclic-AMP phosphodiesterases.; GO: 0004115 3',5'-cyclic-AMP phosphodiesterase activity, 0006198 cAMP catabolic process
Probab=98.86 E-value=2.9e-08 Score=113.98 Aligned_cols=147 Identities=19% Similarity=0.249 Sum_probs=99.5
Q ss_pred CCccEEEeccCChhhhCCcc----cCC----CCceEEeCHHHHHHHHHhh---ccCCC-------------ceEEeCCCc
Q 001045 59 DFSVSYFLSHFHSDHYTGLS----PSW----SKGIIFCSEITSRLLSQIL---NINPK-------------FIYPLPIKI 114 (1176)
Q Consensus 59 ~~i~avfITHaH~DHiggL~----~l~----~~~pIY~s~~T~~ll~~~l---~~~~~-------------~i~~l~~~~ 114 (1176)
..|.++||||+|.||++||- ... .+.+||+.+.|.+.++..+ .++++ .+..+.++.
T Consensus 78 ~~I~~ylItH~HLDHi~gLvinsp~~~~~~~~~K~i~gl~~ti~alk~hiFN~~iWPNl~~~~~~~~~~~~~~~~l~~~~ 157 (335)
T PF02112_consen 78 NHIKGYLITHPHLDHIAGLVINSPEDYLPNSSPKTIYGLPSTIEALKNHIFNDIIWPNLSDEGEGDYLYKYRYFDLSPGE 157 (335)
T ss_pred HhhheEEecCCchhhHHHHHhcCcccccccCCCCcEEECHHHHHHHHHcccCCccCCCCCCcCcccceeeeeeeeccccc
Confidence 36889999999999999994 221 4678999999999999753 12221 123344443
Q ss_pred eEEEC-------------CEEEEEEecCC-CcC-----ceEEEEEEcCCCCcccEEEEECCCCCcccccc---hhhhh--
Q 001045 115 PVLID-------------GCEVVLVGANH-CPG-----AVQFLFKVPGRNGGFERYVHTGDFRFCKTMLL---QPVMN-- 170 (1176)
Q Consensus 115 ~~~i~-------------~~~Vt~~~a~H-~pG-----S~~flie~~~~~G~~~~IlYTGDfr~~~~~~~---~~~l~-- 170 (1176)
...+. ++.|++++.+| ..- |.+|+|+.... | +.|+|.||+..+..-.. ...|.
T Consensus 158 ~~~~~~~~~s~~~~~~~~~~~v~~~~l~H~~~~~~~~~SsAfli~~~~t-~--~~il~fGD~e~Ds~s~~~~~~~iW~~~ 234 (335)
T PF02112_consen 158 LIPLNNTTLSVIPNEFPNSSSVTPFPLSHGNSVSSPVYSSAFLIRDNIT-G--DEILFFGDTEPDSVSKSPRNQKIWRYA 234 (335)
T ss_pred eeeccccccccccccccccccceeeecCCCCcccCCCcceEEEEEeCCC-C--CEEEEEeCCCCCccccCchHHHHHHHH
Confidence 32221 35678899999 444 89999998653 3 68999999987653221 11121
Q ss_pred ----ccCCCcEEEEeCCCCCCC-----CCCCChHHHHHHHHHHHHHH
Q 001045 171 ----EFAGCDAVFLDTTYCNPK-----FLFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 171 ----~~~~vDvLI~EsTy~~~~-----~~~p~~~e~~~~l~~~i~~~ 208 (1176)
...+...+|+||.|.+.. +-|.+....++++..+.+..
T Consensus 235 ap~I~~~~LkaI~IEcS~~~~~~d~~LyGHLtP~~Li~EL~~L~~~~ 281 (335)
T PF02112_consen 235 APKIASGKLKAIFIECSYPNSQPDSQLYGHLTPKHLIEELKVLASKV 281 (335)
T ss_pred HhhccccccCEEEEEeCCCCCCCchHhhccCCHHHHHHHHHHHHhcc
Confidence 126889999999999653 34666677777776666544
No 65
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.85 E-value=3.4e-08 Score=110.11 Aligned_cols=168 Identities=26% Similarity=0.340 Sum_probs=116.6
Q ss_pred cCcCCCCC-cc-CCCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCC---CCchhHHHHHH
Q 001045 950 LSMVPGVP-IK-PMLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETT---SRFPDLISIIN 1024 (1176)
Q Consensus 950 ~~l~~g~P-i~-PMLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T---~~ypdl~~~l~ 1024 (1176)
.-+-.|-| |+ -+|..+ .+-+.|+...+++|+|+||..+.|.+- +|.+.-.||+|-.+. .+.+++.+.
T Consensus 62 ~~vi~GfPkI~R~llL~p-----~ik~~F~~~~v~VEEKmnGYNVRV~k~-~g~vyAiTRgG~ICPfTT~r~~~l~~~-- 133 (382)
T COG1423 62 LFVIRGFPKIRRALLLEP-----TIKKHFGRGKVVVEEKMNGYNVRVVKL-GGEVYAITRGGLICPFTTERLRDLIDL-- 133 (382)
T ss_pred ceEEecCchhheeeccch-----hhHhhcCCCcEEEEEeccCceEEEEEE-CCEEEEEecCceecCchhHHHHhhcch--
Confidence 33455665 33 344432 234567778999999999999999994 899999999998763 444554433
Q ss_pred hhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeC-CcccccCCHHHHHH
Q 001045 1025 EFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFAN-GEQLLGYTLRQRRK 1103 (1176)
Q Consensus 1025 ~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~ln-G~~Ll~~Pl~eRr~ 1103 (1176)
.+...-++.||-||||..+ +...| . .. -..-++.|++|||...| |++| |..||++
T Consensus 134 -eff~d~p~lvlcgEmvG~e----nPYv~---------~-~~------y~~e~v~fFvFDire~~tgr~L---p~eer~~ 189 (382)
T COG1423 134 -EFFDDYPDLVLCGEMVGPE----NPYVP---------G-PY------YEKEDVGFFVFDIREKNTGRPL---PVEERLE 189 (382)
T ss_pred -hhHhhCCCcEEEEEeccCC----CCCCC---------C-CC------CccCCceEEEEEEEecCCCCCC---CHHHHHH
Confidence 2223457899999999865 23444 0 00 01235899999999877 4555 9999999
Q ss_pred HHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCC
Q 001045 1104 YLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLD 1162 (1176)
Q Consensus 1104 lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld 1162 (1176)
+.++.-- .++.+-..+.. .+..++|.++.++.-++|.||||+|+++
T Consensus 190 l~ekYgl----~~V~~fg~~~~---------~e~~eei~eIve~L~keGREGVV~Kdpd 235 (382)
T COG1423 190 LAEKYGL----PHVEIFGEFPA---------DEAGEEIYEIVERLNKEGREGVVMKDPD 235 (382)
T ss_pred HHHHcCC----CceEEeeeech---------hHhHHHHHHHHHHHhhcCCcceEecCcc
Confidence 9998751 22333222221 1223899999999999999999999987
No 66
>TIGR03413 GSH_gloB hydroxyacylglutathione hydrolase. Members of this protein family are hydroxyacylglutathione hydrolase, a detoxification enzyme known as glyoxalase II. It follows lactoylglutathione lyase, or glyoxalase I, and acts to remove the toxic metabolite methylglyoxal and related compounds. This protein belongs to the broader metallo-beta-lactamase family (pfam00753).
Probab=98.79 E-value=1.3e-08 Score=113.48 Aligned_cols=98 Identities=17% Similarity=0.235 Sum_probs=76.7
Q ss_pred ccEEEecCCc---------CCCCccEEEeccCChhhhCCcccCC--CCceEEeCHHHHHHHHHhhccCCCceEEeCCCce
Q 001045 47 TRFLIDAFRY---------AADFSVSYFLSHFHSDHYTGLSPSW--SKGIIFCSEITSRLLSQILNINPKFIYPLPIKIP 115 (1176)
Q Consensus 47 ~~~liD~~~~---------~~~~i~avfITHaH~DHiggL~~l~--~~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~~~ 115 (1176)
..++||++.. ...++++||+||.|.||+||+..+. .+.+||+++.+. +. ...+.+..++.
T Consensus 21 ~~ilID~g~~~~i~~~l~~~g~~l~~Il~TH~H~DHigG~~~l~~~~~~~V~~~~~~~--------~~-~~~~~v~~g~~ 91 (248)
T TIGR03413 21 QAAVVDPGEAEPVLDALEARGLTLTAILLTHHHHDHVGGVAELLEAFPAPVYGPAEER--------IP-GITHPVKDGDT 91 (248)
T ss_pred CEEEEcCCChHHHHHHHHHcCCeeeEEEeCCCCccccCCHHHHHHHCCCeEEeccccc--------CC-CCcEEeCCCCE
Confidence 6899999832 1236899999999999999998753 247899988651 11 12457788999
Q ss_pred EEECCEEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCCc
Q 001045 116 VLIDGCEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFC 160 (1176)
Q Consensus 116 ~~i~~~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~ 160 (1176)
+.+++..|+++.+ ||.+|+++|++.. .+++||||+-+.
T Consensus 92 ~~~g~~~i~v~~tpGHT~g~i~~~~~~-------~~~lftGDtl~~ 130 (248)
T TIGR03413 92 VTLGGLEFEVLAVPGHTLGHIAYYLPD-------SPALFCGDTLFS 130 (248)
T ss_pred EEECCEEEEEEECCCCCcccEEEEECC-------CCEEEEcCcccc
Confidence 9999999999987 6999999998863 369999998543
No 67
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=98.74 E-value=1.3e-08 Score=108.97 Aligned_cols=155 Identities=23% Similarity=0.333 Sum_probs=96.8
Q ss_pred hccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCC---CCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcc
Q 001045 975 LFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETT---SRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKI 1051 (1176)
Q Consensus 975 ~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T---~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~ 1051 (1176)
.+...+|++.+|-||.|+.+.+. ++.+.++.|+.+-+- -.+|--.+-. ......+.+||||||. |...+
T Consensus 12 ~l~~~~Y~V~eKaDG~Ryll~i~-~~~~ylidr~~~~~~v~~~~~p~~~~~~---~~~~~~~TLLDGElV~-d~~~~--- 83 (192)
T PF01331_consen 12 LLQQKDYFVCEKADGTRYLLLIT-DNGVYLIDRKNNVFKVDNLHFPSKKDSS---DGRHHQDTLLDGELVL-DKDPG--- 83 (192)
T ss_dssp HHHHS-EEEEEEESSEEEEEEEE-EEEEEEEETTS-EEEESSST-ECTTC-----TTCEGCSEEEEEEEEE-EECTT---
T ss_pred HHhhCCcEEEECCCCcEEEEEEe-cceEEEEeCCCcEEEecCcccccccccc---cccccCCEEEEEEEEc-ccCCC---
Confidence 34456899999999999999995 558999999987553 2233211100 0123468999999987 22110
Q ss_pred cChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccC------C-------CcEE
Q 001045 1052 MSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEK------M-------GYFQ 1118 (1176)
Q Consensus 1052 ~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~------~-------~~i~ 1118 (1176)
+..+.|++||+|++||+++.+.||.+|...|++.+..+. + ..|.
T Consensus 84 -----------------------~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~~~~~~~pf~ 140 (192)
T PF01331_consen 84 -----------------------EKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGIIKKKKEPFS 140 (192)
T ss_dssp -----------------------CEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTSCTCTTSSSE
T ss_pred -----------------------CCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhcccccccccccccee
Confidence 234899999999999999999999999999987652210 0 1122
Q ss_pred E-eEEEEEcCCCCCCccccCHHH-HHHHHHHHHhCCCceEEEecCCCCCCcccCC
Q 001045 1119 Y-AKEMTVEGDDNCLTSDVSLSK-INNFLEEALHSSCEGIIVKSLDVDAGYSPSK 1171 (1176)
Q Consensus 1119 ~-~~~~~v~~~~~~~~~~~~~ee-i~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGk 1171 (1176)
+ .+...- ....+. +...+..-+..+..|||.=..+ .+|.||.
T Consensus 141 i~~K~~~~---------~~~~~~~~~~~~~~~l~h~~DGLIFtp~~--~pY~~Gt 184 (192)
T PF01331_consen 141 IRIKDFFP---------IYQIEKLLFEEFIPKLPHETDGLIFTPVN--TPYVPGT 184 (192)
T ss_dssp EEE---EE---------GGGHHHHCHHCCCCCTTSTEEEEEEEESS--SB--SEE
T ss_pred eeccccHH---------HHhhHHHHHHHhhccCCCCCCEEEEecCC--CCccCCC
Confidence 2 111110 112222 2222333456788999999876 8999983
No 68
>COG1235 PhnP Metal-dependent hydrolases of the beta-lactamase superfamily I [General function prediction only]
Probab=98.73 E-value=2.8e-08 Score=112.07 Aligned_cols=157 Identities=19% Similarity=0.086 Sum_probs=102.5
Q ss_pred eCCccEEEecCC---cC-----CCCccEEEeccCChhhhCCcccCC--CCceEEeCHHHHHHHHHh--hc-cCCCceEEe
Q 001045 44 VPNTRFLIDAFR---YA-----ADFSVSYFLSHFHSDHYTGLSPSW--SKGIIFCSEITSRLLSQI--LN-INPKFIYPL 110 (1176)
Q Consensus 44 ipg~~~liD~~~---~~-----~~~i~avfITHaH~DHiggL~~l~--~~~pIY~s~~T~~ll~~~--l~-~~~~~i~~l 110 (1176)
+....+++|.+- .. ...+++||+||.|.||+.|++.+. ...++|+.+.|....... .+ ++.....++
T Consensus 38 ~~~~~~lid~g~~~~~~~~~~~~~~idai~~TH~H~DHi~Gl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 117 (269)
T COG1235 38 VGVKTLLIDAGPDLRDQGLRLGVSDLDAILLTHEHSDHIQGLDDLRRAYTLPIYVNPGTLRASTSDRLLGGFPYLFRHPF 117 (269)
T ss_pred ecceeEEEecChhHHhhhhcccccccCeEEEecccHHhhcChHHHHHHhcCCcccccceecccchhhhhccchhhhcCCC
Confidence 344467889861 11 137999999999999999999754 366778777776655532 11 111123344
Q ss_pred CCCceEEECCEEEEEEecCC-CcC-----------------ceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhcc
Q 001045 111 PIKIPVLIDGCEVVLVGANH-CPG-----------------AVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEF 172 (1176)
Q Consensus 111 ~~~~~~~i~~~~Vt~~~a~H-~pG-----------------S~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~ 172 (1176)
..+....++++.+++++..| ... ..+|..+... +.+.|++|+...+.... ..+...
T Consensus 118 ~~~~~~~~~~~~~~~~~~~hd~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~-----~~vay~~Dt~~~~~~~d-~~l~~~ 191 (269)
T COG1235 118 PPFSLPAIGGLEVTPFPVPHDAIEPVGFVIIRTGRKLHGGTDIGYGLEWRI-----GDVAYLTDTELFPSNHD-VELLDN 191 (269)
T ss_pred CccccccccceeeecCCCCCccccCCCcccccCcccccccccceeeeeeee-----ccEEEccccccCcchhH-HHHhcC
Confidence 45666777888888888888 222 2333333221 47889999987766544 233344
Q ss_pred CCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHH
Q 001045 173 AGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRV 208 (1176)
Q Consensus 173 ~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~ 208 (1176)
...++++.+.++..+ .+.+.+...+++.+++...
T Consensus 192 ~~~~~~~~~~~~~~~--gh~~~h~~~~~a~~~~~~~ 225 (269)
T COG1235 192 GLYPLDIKDRILPDP--GHLSNHLSAEEALELIEKL 225 (269)
T ss_pred Cccceeeeecccccc--CCCCCchhHHHHHHHHHhC
Confidence 778999999999875 4566677777777777655
No 69
>PF13483 Lactamase_B_3: Beta-lactamase superfamily domain; PDB: 1VJN_B 3KL7_A.
Probab=98.67 E-value=1.7e-07 Score=97.49 Aligned_cols=118 Identities=21% Similarity=0.227 Sum_probs=75.6
Q ss_pred CCCeeE-eCCccEEEecCCcC------CCCccEEEeccCChhhhCCcccCCCCceEEeCHHHHHHHHHhhccCCCceEEe
Q 001045 38 FPPSKH-VPNTRFLIDAFRYA------ADFSVSYFLSHFHSDHYTGLSPSWSKGIIFCSEITSRLLSQILNINPKFIYPL 110 (1176)
Q Consensus 38 ~p~~~~-ipg~~~liD~~~~~------~~~i~avfITHaH~DHiggL~~l~~~~pIY~s~~T~~ll~~~l~~~~~~i~~l 110 (1176)
..|..+ ..|..+++|++... ..++++|||||.|.||+.. ..+. .. ...+..+
T Consensus 7 ha~~~ie~~g~~iliDP~~~~~~~~~~~~~~D~IlisH~H~DH~~~-~~l~-~~-------------------~~~~~vv 65 (163)
T PF13483_consen 7 HASFLIETGGKRILIDPWFSSVGYAPPPPKADAILISHSHPDHFDP-ETLK-RL-------------------DRDIHVV 65 (163)
T ss_dssp TTEEEEEETTEEEEES--TTT--T-TSS-B-SEEEESSSSTTT-CC-CCCC-CH-------------------HTSSEEE
T ss_pred eeEEEEEECCEEEEECCCCCccCcccccCCCCEEEECCCccccCCh-hHhh-hc-------------------ccccEEE
Confidence 356666 78999999998632 4689999999999999975 1111 11 2246677
Q ss_pred CCCceEEECCEEEEEEecCCC-------cCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCC
Q 001045 111 PIKIPVLIDGCEVVLVGANHC-------PGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTT 183 (1176)
Q Consensus 111 ~~~~~~~i~~~~Vt~~~a~H~-------pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsT 183 (1176)
..++.+++++++|+.+++.|. .+.++|+|+.++ .+|+|.||....... ..+..+.++|++++-..
T Consensus 66 ~~~~~~~~~~~~i~~v~~~~~~~~~~~~~~~~~~~i~~~g-----~~i~~~Gd~~~~~~~---~~~~~~~~vDvl~~p~~ 137 (163)
T PF13483_consen 66 APGGEYRFGGFKITAVPAYHDGPGGHPRGENVGYLIEVGG-----VTIYHAGDTGFPPDD---EQLKQLGKVDVLFLPVG 137 (163)
T ss_dssp -TTEEEECTTEEEEEEEEEE-STGTS-TTCCEEEEEEETT-----EEEEE-TT--S---H---HHHHHH-S-SEEEEE--
T ss_pred ccceEEEEeeeEEEEEeeeccccCCCCcCCeEEEEEEeCC-----CEEEEECCCccCCCH---HHHhcccCCCEEEecCC
Confidence 778899999999999999883 337999999953 799999999764321 22334468999999865
Q ss_pred C
Q 001045 184 Y 184 (1176)
Q Consensus 184 y 184 (1176)
-
T Consensus 138 g 138 (163)
T PF13483_consen 138 G 138 (163)
T ss_dssp T
T ss_pred C
Confidence 4
No 70
>PLN02398 hydroxyacylglutathione hydrolase
Probab=98.64 E-value=6.8e-08 Score=111.07 Aligned_cols=100 Identities=20% Similarity=0.202 Sum_probs=77.2
Q ss_pred ccEEEecCCc---------CCCCccEEEeccCChhhhCCcccCCC--CceEEeCHHHHHHHHHhhccCCCceEEeCCCce
Q 001045 47 TRFLIDAFRY---------AADFSVSYFLSHFHSDHYTGLSPSWS--KGIIFCSEITSRLLSQILNINPKFIYPLPIKIP 115 (1176)
Q Consensus 47 ~~~liD~~~~---------~~~~i~avfITHaH~DHiggL~~l~~--~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~~~ 115 (1176)
..++||.+.. ...++++||+||.|.||+||+..+.. +.+||+++...+.+. + .-..+..|+.
T Consensus 99 ~~~vVDP~~a~~vl~~l~~~g~~L~~ILlTH~H~DH~GG~~~L~~~~ga~V~g~~~~~~~i~---~----~d~~v~dGd~ 171 (329)
T PLN02398 99 TVGVVDPSEAVPVIDALSRKNRNLTYILNTHHHYDHTGGNLELKARYGAKVIGSAVDKDRIP---G----IDIVLKDGDK 171 (329)
T ss_pred EEEEEcCCCHHHHHHHHHhcCCCceEEEECCCCchhhCCHHHHHHhcCCEEEEehHHhhhcc---C----CcEEeCCCCE
Confidence 3578998732 12568999999999999999987542 579999987654321 1 2356788899
Q ss_pred EEECCEEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCCc
Q 001045 116 VLIDGCEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFC 160 (1176)
Q Consensus 116 ~~i~~~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~ 160 (1176)
+.+++.+++.+.+ ||.+|+++|++.. ..++||||+-+.
T Consensus 172 i~lgg~~l~vi~tPGHT~GhI~~~~~~-------~~vLFtGDtLf~ 210 (329)
T PLN02398 172 WMFAGHEVLVMETPGHTRGHISFYFPG-------SGAIFTGDTLFS 210 (329)
T ss_pred EEECCeEEEEEeCCCcCCCCEEEEECC-------CCEEEECCCcCC
Confidence 9999999999888 9999999998752 359999998554
No 71
>TIGR01209 RNA ligase, Pab1020 family. Members of this family are found, so far, in a single copy per genome and largely in thermophiles, of which only Aquifex aeolicus is bacterial rather than archaeal. PSI-BLAST converges after a single iteration to the whole of this family and reveals no convincing similarity to any other protein. The member protein Pab1020 has been characterized as an RNA ligase with circularization activity.
Probab=98.63 E-value=3.5e-07 Score=105.41 Aligned_cols=170 Identities=24% Similarity=0.354 Sum_probs=107.5
Q ss_pred cCcCCCCCc-cC-CCCcccCChhHHHHhccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCC---CCchhHHHHHH
Q 001045 950 LSMVPGVPI-KP-MLAKITNGVPQVLKLFQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETT---SRFPDLISIIN 1024 (1176)
Q Consensus 950 ~~l~~g~Pi-~P-MLA~~~~~~~~~~~~~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T---~~ypdl~~~l~ 1024 (1176)
..+-+|-|= +- |+..+ ++. +.|.++.+++|+|+||..+-|.. -+|++..+||+|-.+. .+++++.+ .
T Consensus 53 ~~vv~GyP~I~R~~~L~~--gi~---~~f~~~~v~vEEKlDG~Nvri~~-~~g~l~a~tRGgyicp~tt~r~~~~~~--~ 124 (374)
T TIGR01209 53 LFVIRGFPHIKRILLLRP--GIK---RHFKDPEVVVEEKMNGYNVRIVK-YGGNVYALTRGGFICPFTTERLPDLID--L 124 (374)
T ss_pred ccEEcCCCCcceeeccch--hhH---HhcCCCcEEEEEeecCceEEEEe-ECCEEEEEccCcccCCCcHHHHHHHhh--H
Confidence 346667763 32 32221 233 44566669999999999999976 5899999999998872 22344433 1
Q ss_pred hhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHH
Q 001045 1025 EFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKY 1104 (1176)
Q Consensus 1025 ~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~l 1104 (1176)
. +...-++++|-||++.-+. |. .+. .......+..|++|||.. ...-.-+|+.+|+++
T Consensus 125 ~-~~~d~p~l~LcGE~iGpen-------pY------~~h------s~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l 182 (374)
T TIGR01209 125 E-FFDDNPDLVLCGEMAGPEN-------PY------TPE------YYPEVKEDLGFFLFDIRE--GKTNRSLPVEERLEL 182 (374)
T ss_pred H-hhccCCCeEEEEEEcCCCC-------CC------ccc------CccccCCCceEEEEEEEE--CCCCccCCHHHHHHH
Confidence 2 3334578999999997431 10 000 011123367899999973 334455799999999
Q ss_pred HHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecCC
Q 001045 1105 LKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLD 1162 (1176)
Q Consensus 1105 L~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld 1162 (1176)
++++--..+| .+. .... ....+++.++.+..-++|.||||+|+++
T Consensus 183 ~e~yglp~Vp-vlg---~~~~---------~~~~~~~~eii~~L~~~gREGVVlK~~~ 227 (374)
T TIGR01209 183 AEKYGLPHVE-ILG---VYTA---------DEAVEEIYEIIERLNKEGREGVVMKDPE 227 (374)
T ss_pred HHHCCCCccc-eee---EEcH---------HHHHHHHHHHHHHhhhcCcceEEEcCcc
Confidence 9987311111 111 1111 1223477888888889999999999885
No 72
>PLN02469 hydroxyacylglutathione hydrolase
Probab=98.59 E-value=1.9e-07 Score=104.68 Aligned_cols=101 Identities=14% Similarity=0.161 Sum_probs=74.0
Q ss_pred ccEEEecCCc---------CCCCccEEEeccCChhhhCCcccCC---CCceEEeCHHHHHHHHHhhccCCCceEEeCCCc
Q 001045 47 TRFLIDAFRY---------AADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSEITSRLLSQILNINPKFIYPLPIKI 114 (1176)
Q Consensus 47 ~~~liD~~~~---------~~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~~ 114 (1176)
..++||++.. ...++++||+||.|.||+||+..+. .+.+||++.... . ....+.+..|+
T Consensus 24 ~~vlIDp~~~~~il~~l~~~g~~l~~Il~TH~H~DH~gG~~~l~~~~~~~~V~~~~~~~--------~-~~~~~~v~~gd 94 (258)
T PLN02469 24 DAAVVDPVDPEKVLQAAHEHGAKIKLVLTTHHHWDHAGGNEKIKKLVPGIKVYGGSLDN--------V-KGCTHPVENGD 94 (258)
T ss_pred eEEEECCCChHHHHHHHHHcCCcccEEEecCCCCccccCHHHHHHHCCCCEEEEechhc--------C-CCCCeEeCCCC
Confidence 5799999732 1247999999999999999998643 357999976421 1 11135677889
Q ss_pred eEEECC-EEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCC
Q 001045 115 PVLIDG-CEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRF 159 (1176)
Q Consensus 115 ~~~i~~-~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~ 159 (1176)
.+.+++ +.++.+.+ ||.+|+++|++....+ . ..++||||+-+
T Consensus 95 ~i~lg~~~~~~vi~tPGHT~ghi~~~~~~~~~-~--~~~lFtGDtLf 138 (258)
T PLN02469 95 KLSLGKDVNILALHTPCHTKGHISYYVTGKEG-E--DPAVFTGDTLF 138 (258)
T ss_pred EEEECCceEEEEEECCCCCCCCEEEEeccCCC-C--CCEEEecCccc
Confidence 999985 67888876 9999999999864211 1 36999999644
No 73
>PLN02962 hydroxyacylglutathione hydrolase
Probab=98.55 E-value=1.6e-07 Score=104.71 Aligned_cols=120 Identities=14% Similarity=0.047 Sum_probs=82.8
Q ss_pred CCCCCCCCCCCeeEeC-----CccEEEecCCcC-----------CCCccEEEeccCChhhhCCcccCC---CCceEEeCH
Q 001045 30 IFPPIPRTFPPSKHVP-----NTRFLIDAFRYA-----------ADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSE 90 (1176)
Q Consensus 30 ~~p~~~r~~p~~~~ip-----g~~~liD~~~~~-----------~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~ 90 (1176)
.+..+...+.+|.++. +..++||++... ..++.+||+||.|.||++|+..+. ...++|+++
T Consensus 15 ~~~~~~~~~~~Yll~d~~~~~~~avlIDP~~~~~~~~l~~l~~~g~~i~~Il~TH~H~DHigg~~~l~~~~~~a~v~~~~ 94 (251)
T PLN02962 15 QLFEKESSTYTYLLADVSHPDKPALLIDPVDKTVDRDLSLVKELGLKLIYAMNTHVHADHVTGTGLLKTKLPGVKSIISK 94 (251)
T ss_pred EeecCCceeEEEEEEeCCCCCCEEEEECCCCCcHHHHHHHHHHCCCeeEEEEcCCCCchhHHHHHHHHHHCCCCeEEecc
Confidence 3444445566777742 346899997311 146889999999999999998753 367898865
Q ss_pred HHHHHHHHhhccCCCceEEeCCCceEEECCEEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCCc
Q 001045 91 ITSRLLSQILNINPKFIYPLPIKIPVLIDGCEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFC 160 (1176)
Q Consensus 91 ~T~~ll~~~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~ 160 (1176)
.. +... -..+..++.+.++++.++.+.+ ||.+|+++|++....+ ....+++||||+-+.
T Consensus 95 ~~--------~~~~--d~~l~~g~~i~~g~~~l~vi~tPGHT~g~v~~~~~d~~~-~~~~~~lftGD~Lf~ 154 (251)
T PLN02962 95 AS--------GSKA--DLFVEPGDKIYFGDLYLEVRATPGHTAGCVTYVTGEGPD-QPQPRMAFTGDALLI 154 (251)
T ss_pred cc--------CCCC--CEEeCCCCEEEECCEEEEEEECCCCCcCcEEEEeccCCC-CCccceEEECCeecc
Confidence 32 1111 2357788899999998888887 9999999998853110 001369999997443
No 74
>PRK10241 hydroxyacylglutathione hydrolase; Provisional
Probab=98.49 E-value=2.4e-07 Score=103.51 Aligned_cols=97 Identities=19% Similarity=0.266 Sum_probs=73.4
Q ss_pred CccEEEecCCcC---------CCCccEEEeccCChhhhCCcccCC---CCceEEeCHHHHHHHHHhhccCCCceEEeCCC
Q 001045 46 NTRFLIDAFRYA---------ADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSEITSRLLSQILNINPKFIYPLPIK 113 (1176)
Q Consensus 46 g~~~liD~~~~~---------~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~ 113 (1176)
+..++||++... ...+++||+||.|.||+||+..+. ...+||++..+.. ....+.+..|
T Consensus 22 ~~~ilIDpg~~~~vl~~l~~~g~~l~~IllTH~H~DHigG~~~l~~~~~~~~V~~~~~~~~---------~~~~~~v~~g 92 (251)
T PRK10241 22 GRCLIVDPGEAEPVLNAIAENNWQPEAIFLTHHHHDHVGGVKELVEKFPQIVVYGPQETQD---------KGTTQVVKDG 92 (251)
T ss_pred CcEEEECCCChHHHHHHHHHcCCccCEEEeCCCCchhhccHHHHHHHCCCCEEEecccccc---------cCCceEeCCC
Confidence 457999998321 235789999999999999998743 3579999876421 1123567788
Q ss_pred ceEEECCEEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCCc
Q 001045 114 IPVLIDGCEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFC 160 (1176)
Q Consensus 114 ~~~~i~~~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~ 160 (1176)
+.+.+++..++++.+ ||.+|+++|+.. .++||||+-+.
T Consensus 93 ~~i~ig~~~~~vi~tPGHT~ghi~~~~~---------~~lFtGDtlf~ 131 (251)
T PRK10241 93 ETAFVLGHEFSVFATPGHTLGHICYFSK---------PYLFCGDTLFS 131 (251)
T ss_pred CEEEeCCcEEEEEEcCCCCccceeeecC---------CcEEEcCeecc
Confidence 999999989999886 899999999641 37999997543
No 75
>PF07521 RMMBL: RNA-metabolising metallo-beta-lactamase; InterPro: IPR011108 The metallo-beta-lactamase fold contains five sequence motifs. The first four motifs are found in IPR001279 from INTERPRO and are common to all metallo-beta-lactamases. The fifth motif appears to be specific to function. This entry represents the fifth motif from metallo-beta-lactamases involved in RNA metabolism [].; PDB: 3ZQ4_D 2I7T_A 2I7V_A 2YCB_B 3BK1_A 3T3N_A 3BK2_A 3T3O_A 3AF5_A 3AF6_A ....
Probab=98.39 E-value=2.7e-07 Score=74.59 Aligned_cols=37 Identities=27% Similarity=0.526 Sum_probs=32.6
Q ss_pred cCCeeEEEEeecCCCCHHHHHHHHHHcCCCEEEEEec
Q 001045 315 KDAFEIHLVPYSEHSNYDELREYVKFLKPKRVIPTVG 351 (1176)
Q Consensus 315 ~~~~~v~~i~~SgHAs~~EL~~~V~~lrPk~VIPvHG 351 (1176)
..+|+++.++|||||+++||.+|++.++|++||||||
T Consensus 4 ~v~a~v~~~~fSgHad~~~L~~~i~~~~p~~vilVHG 40 (43)
T PF07521_consen 4 PVRARVEQIDFSGHADREELLEFIEQLNPRKVILVHG 40 (43)
T ss_dssp E--SEEEESGCSSS-BHHHHHHHHHHHCSSEEEEESS
T ss_pred EeEEEEEEEeecCCCCHHHHHHHHHhcCCCEEEEecC
Confidence 3467889999999999999999999999999999999
No 76
>PF00753 Lactamase_B: Metallo-beta-lactamase superfamily; InterPro: IPR001279 Apart from the beta-lactamases and metallo-beta-lactamases, a number of other proteins contain this domain []. These proteins include thiolesterases, members of the glyoxalase II family, that catalyse the hydrolysis of S-D-lactoyl-glutathione to form glutathione and D-lactic acid and a competence protein that is essential for natural transformation in Neisseria gonorrhoeae and could be a transporter involved in DNA uptake. Except for the competence protein these proteins bind two zinc ions per molecule as cofactor.; GO: 0016787 hydrolase activity; PDB: 3H3E_A 3Q6V_B 3SD9_B 3IOF_A 2GKL_A 1X8I_A 3FAI_A 2QDS_A 3IOG_A 3F9O_A ....
Probab=98.36 E-value=4.5e-07 Score=94.22 Aligned_cols=119 Identities=19% Similarity=0.183 Sum_probs=73.7
Q ss_pred CCeeE-eCCccEEEecCCc--------------CCCCccEEEeccCChhhhCCcccCCC---CceEEeCHHHHHHHHHhh
Q 001045 39 PPSKH-VPNTRFLIDAFRY--------------AADFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCSEITSRLLSQIL 100 (1176)
Q Consensus 39 p~~~~-ipg~~~liD~~~~--------------~~~~i~avfITHaH~DHiggL~~l~~---~~pIY~s~~T~~ll~~~l 100 (1176)
.++.+ .++..++||++.. ...+|++||+||+|.||+||++.+.. ...+++............
T Consensus 7 n~~li~~~~~~iliD~G~~~~~~~~~~~~~~~~~~~~i~~vi~TH~H~DH~ggl~~~~~~~~~~~~~~~~~~~~~~~~~~ 86 (194)
T PF00753_consen 7 NSYLIEGGDGAILIDTGLDPDFAKELELALLGISGEDIDAVILTHAHPDHIGGLPELLEAGPVVIIYSSADAAKAIRPPD 86 (194)
T ss_dssp EEEEEEETTEEEEESEBSSHHHHHHHHHHHHHHTGGGEEEEEESSSSHHHHTTHHHHHHHTTEEEEEEHHHHHHHHHHHH
T ss_pred EEEEEEECCEEEEEeCCCCchhhHHhhhhHhhccCCCeEEEEECcccccccccccccccccceeeeeccccccccccccc
Confidence 45566 6888999999821 22689999999999999999987543 344555555554444322
Q ss_pred cc--------CCCceEEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCCCccc
Q 001045 101 NI--------NPKFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKT 162 (1176)
Q Consensus 101 ~~--------~~~~i~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~ 162 (1176)
.. .................+.....+...|.+++..+.+..++ ++++||||+-+...
T Consensus 87 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~vlftGD~~~~~~ 151 (194)
T PF00753_consen 87 RDSASRRGPAVPPPPIIDEDEDDLEIGGDRILFIIPGPGHGSDSLIIYLPG-----GKVLFTGDLLFSNE 151 (194)
T ss_dssp HHHHHHHHHHHESEEEEEETTTEEEEETTEEEEEEESSSSSTTEEEEEETT-----TTEEEEETTSCTTT
T ss_pred cccccccccccccccceeeecccccccccccccceeccccCCcceEEEeCC-----CcEEEeeeEeccCC
Confidence 10 01112233333444444444555555566666666666554 58999999977654
No 77
>COG5212 PDE1 Low-affinity cAMP phosphodiesterase [Signal transduction mechanisms]
Probab=98.36 E-value=1.5e-06 Score=94.20 Aligned_cols=126 Identities=20% Similarity=0.235 Sum_probs=87.6
Q ss_pred CCccEEEeccCChhhhCCcccCC------CCceEEeCHHHHHHHHHhh---ccCCC---------ceEEeCCCceE--EE
Q 001045 59 DFSVSYFLSHFHSDHYTGLSPSW------SKGIIFCSEITSRLLSQIL---NINPK---------FIYPLPIKIPV--LI 118 (1176)
Q Consensus 59 ~~i~avfITHaH~DHiggL~~l~------~~~pIY~s~~T~~ll~~~l---~~~~~---------~i~~l~~~~~~--~i 118 (1176)
..|..+||||+|.||+.||--.. .+..||+.+.|++.++... -+++. +++.+.+.+.. .+
T Consensus 111 Q~I~~y~ITH~HLDHIsGlVinSp~~~~qkkkTI~gl~~tIDvL~khvFN~lvWP~lt~~gs~~~~~qvv~P~~~~slt~ 190 (356)
T COG5212 111 QSINSYFITHAHLDHISGLVINSPDDSKQKKKTIYGLADTIDVLRKHVFNWLVWPNLTDSGSGTYRMQVVRPAQSLSLTL 190 (356)
T ss_pred hhhhheEeccccccchhceeecCccccccCCceEEechhHHHHHHHHhhcccccCCcccccCceEEEEEeChhHeeeeee
Confidence 36888999999999999984311 2458999999999999764 12221 35566666543 34
Q ss_pred CCEEEEEEecCC-C-cC----ceEEEEEEcCCCCcccEEEEECCCCCcccccc---hhhhhcc------CCCcEEEEeCC
Q 001045 119 DGCEVVLVGANH-C-PG----AVQFLFKVPGRNGGFERYVHTGDFRFCKTMLL---QPVMNEF------AGCDAVFLDTT 183 (1176)
Q Consensus 119 ~~~~Vt~~~a~H-~-pG----S~~flie~~~~~G~~~~IlYTGDfr~~~~~~~---~~~l~~~------~~vDvLI~EsT 183 (1176)
-.+++.+||++| . .| |.||+|.....+ .-++|.||...+..... ...|... .+..-+++||+
T Consensus 191 t~l~~~pfpv~Hg~ktG~p~ySs~~lfr~nkS~---~~f~~fGDvepD~vese~ll~~~Wr~~ae~I~q~~LkgiliEcS 267 (356)
T COG5212 191 TRLTGEPFPVSHGKKTGSPSYSSMLLFRSNKSN---EFFAYFGDVEPDDVESEKLLDTVWRKLAEKITQQQLKGILIECS 267 (356)
T ss_pred eeecceeeeccCCcccCCcccceEEEEecCCCc---ceEEEecCCCcchhhhhHHHHHHHHHHHHhhhHHhhCceEEEec
Confidence 467899999999 3 23 589999976432 57999999976543221 2222221 56788999999
Q ss_pred CCCC
Q 001045 184 YCNP 187 (1176)
Q Consensus 184 y~~~ 187 (1176)
|.+.
T Consensus 268 ~P~~ 271 (356)
T COG5212 268 YPND 271 (356)
T ss_pred CCCC
Confidence 9875
No 78
>KOG1138 consensus Predicted cleavage and polyadenylation specificity factor (CPSF subunit) [RNA processing and modification]
Probab=98.24 E-value=9e-05 Score=86.35 Aligned_cols=173 Identities=15% Similarity=0.110 Sum_probs=116.9
Q ss_pred CCccEEEeccCChhhhCCcccC----CCCceEEeCHHHHHHHHHhhc--------c--------C---------------
Q 001045 59 DFSVSYFLSHFHSDHYTGLSPS----WSKGIIFCSEITSRLLSQILN--------I--------N--------------- 103 (1176)
Q Consensus 59 ~~i~avfITHaH~DHiggL~~l----~~~~pIY~s~~T~~ll~~~l~--------~--------~--------------- 103 (1176)
+.||+|+||..|. +-|||++ .+.+.||+|+.|+.+=+-++. + +
T Consensus 95 stiDvILISNy~~--mlgLPfiTentGF~gkiY~TE~t~qiGrllMEelv~fier~p~~~S~~~Wk~k~~~~~lpsplk~ 172 (653)
T KOG1138|consen 95 STIDVILISNYMG--MLGLPFITENTGFFGKIYATEPTAQIGRLLMEELVSFIERFPKASSAPLWKKKLDSELLPSPLKK 172 (653)
T ss_pred cceeEEEEcchhh--hcccceeecCCCceeEEEEechHHHHHHHHHHHHHHHHHhccccccchhhhhhhhhhhcCCCchh
Confidence 5799999999985 7788874 346899999999987543320 0 0
Q ss_pred -------------------CCceEEeCCCceEEE-CCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCCCcccc
Q 001045 104 -------------------PKFIYPLPIKIPVLI-DGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTM 163 (1176)
Q Consensus 104 -------------------~~~i~~l~~~~~~~i-~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~ 163 (1176)
...++.+.+.+.+.+ |.+.||++..||+.||+-++|.++. +++.|..+-.+-.+.
T Consensus 173 ~~~~~~Wr~~ysl~Dv~sclsKVq~v~f~ekidlfga~~vtplsSG~~lGSsnW~I~t~n-----ek~sYvS~Ss~ltth 247 (653)
T KOG1138|consen 173 AVFLGSWRRLYSLDDVESCLSKVQGVGFAEKIDLFGALIVTPLSSGYDLGSSNWLINTPN-----EKLSYVSGSSFLTTH 247 (653)
T ss_pred hccccceeeeeehhHHHHHHHhheecccceeeeccceEEEEeccccccccccceEEecCC-----cceEEEecCcccccC
Confidence 012456677887776 6799999999999999999999976 589999887654432
Q ss_pred cchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccccchHHHHHHHHHHc-
Q 001045 164 LLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYVIGKEKILIEIFKKC- 242 (1176)
Q Consensus 164 ~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~slGR~q~ll~ia~~~- 242 (1176)
...-....++.+|+||+-+----+. ..|. +-.-++..-+....++ +|. +++|+|..|-+-++++...+.
T Consensus 248 ~r~md~a~Lk~~Dvli~T~lsql~t-anpd--~m~gelc~nvt~~~rn-----~Gs--vL~PcyPsGviydl~Ecls~~i 317 (653)
T KOG1138|consen 248 PRPMDQAGLKETDVLIYTGLSQLPT-ANPD--EMGGELCKNVTLTGRN-----HGS--VLLPCYPSGVIYDLIECLSQDI 317 (653)
T ss_pred CccccccccccccEEEEeccccccc-CCcc--chhhhHHHHHHHHhhc-----CCc--eeeeccCCchhhHHHHHhhhcc
Confidence 2211122347899999876433321 1111 1122233333333333 567 789999999999999887543
Q ss_pred ------CCcEEE
Q 001045 243 ------GRKVCV 248 (1176)
Q Consensus 243 ------g~~I~v 248 (1176)
+.|+|+
T Consensus 318 dna~ls~~P~yf 329 (653)
T KOG1138|consen 318 DNAGLSDTPIYF 329 (653)
T ss_pred cccCCcCCcceE
Confidence 368887
No 79
>COG2220 Predicted Zn-dependent hydrolases of the beta-lactamase fold [General function prediction only]
Probab=98.17 E-value=1.4e-05 Score=89.57 Aligned_cols=140 Identities=19% Similarity=0.182 Sum_probs=100.2
Q ss_pred CCCCeeE-eCCccEEEecCCcC---------------CCCccEEEeccCChhhhCCcc--cCC-CCceEEeCHHHHHHHH
Q 001045 37 TFPPSKH-VPNTRFLIDAFRYA---------------ADFSVSYFLSHFHSDHYTGLS--PSW-SKGIIFCSEITSRLLS 97 (1176)
Q Consensus 37 ~~p~~~~-ipg~~~liD~~~~~---------------~~~i~avfITHaH~DHiggL~--~l~-~~~pIY~s~~T~~ll~ 97 (1176)
...+..+ ..+.++++|.+-.. .+.+++|+|||.|.||+..=. .+. ...+++..+.....+.
T Consensus 13 Gha~~lie~~~~~iliDP~~~~~~~~~~~~~~~~~~~~~~~D~ilitH~H~DHl~~~~~~~~~~~~~~~~~~p~~~~~~~ 92 (258)
T COG2220 13 GHAAFLIETGGKRILIDPVLSGAPSPSNFPGGLFEDLLPPIDYILITHDHYDHLDDETLIALRTNKAPVVVVPLGAGDLL 92 (258)
T ss_pred cceEEEEEECCEEEEECcccCCCCCcccccCcCChhhcCCCCEEEEeCCCccccCHHHHHHHhcCCCcEEEeHHHHHHHH
Confidence 3455666 78889999997321 145899999999999997432 222 2367777777765555
Q ss_pred HhhccCCCceEEeCCCceEEECCEEEEEEecCCC-----cC--------ceEEEEEEcCCCCcccEEEEECCCCCccccc
Q 001045 98 QILNINPKFIYPLPIKIPVLIDGCEVVLVGANHC-----PG--------AVQFLFKVPGRNGGFERYVHTGDFRFCKTML 164 (1176)
Q Consensus 98 ~~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a~H~-----pG--------S~~flie~~~~~G~~~~IlYTGDfr~~~~~~ 164 (1176)
...++....+..+.++..+++++++|++.++.|. ++ .++|+|+.++ .+++|.||..+ .
T Consensus 93 ~~~g~~~~~~~~~~~~~~~~~~~~~i~~~~a~h~~~~~~~~~~~~~~~~~~~~vi~~~g-----~~iyh~GDt~~---~- 163 (258)
T COG2220 93 IRDGVEAERVHELGWGDVIELGDLEITAVPAYHVSARHLPGRGIRPTGLWVGYVIETPG-----GRVYHAGDTGY---L- 163 (258)
T ss_pred HhcCCCcceEEeecCCceEEecCcEEEEEEeecccccccCCCCccccCCceEEEEEeCC-----ceEEeccCccH---H-
Confidence 5567777778999999999999999999999882 22 5779999865 69999999987 1
Q ss_pred chhhhhccCCCcEEEEeCCCC
Q 001045 165 LQPVMNEFAGCDAVFLDTTYC 185 (1176)
Q Consensus 165 ~~~~l~~~~~vDvLI~EsTy~ 185 (1176)
..........+|++++..--.
T Consensus 164 ~~~~~~~~~~~DvallPig~~ 184 (258)
T COG2220 164 FLIIEELDGPVDVALLPIGGY 184 (258)
T ss_pred HHhhhhhcCCccEEEeccCCC
Confidence 111111223489999987643
No 80
>COG0426 FpaA Uncharacterized flavoproteins [Energy production and conversion]
Probab=98.11 E-value=8.3e-06 Score=94.66 Aligned_cols=115 Identities=17% Similarity=0.162 Sum_probs=95.0
Q ss_pred CCCCCeeEeCCccEEEecCCc--------------CCCCccEEEeccCChhhhCCcccCC---CCceEEeCHHHHHHHHH
Q 001045 36 RTFPPSKHVPNTRFLIDAFRY--------------AADFSVSYFLSHFHSDHYTGLSPSW---SKGIIFCSEITSRLLSQ 98 (1176)
Q Consensus 36 r~~p~~~~ipg~~~liD~~~~--------------~~~~i~avfITHaH~DHiggL~~l~---~~~pIY~s~~T~~ll~~ 98 (1176)
.+...|++..+...|||.... ...+|++|+++|.-.||.|+|+.+. ++.+|+||...++.|+.
T Consensus 34 ttyNSYLI~~~k~aLID~~~~~~~~~~l~~l~~~id~k~iDYIi~~H~ePDhsg~l~~ll~~~p~a~ii~s~~~~~~L~~ 113 (388)
T COG0426 34 TTYNSYLIVGDKTALIDTVGEKFFDEYLENLSKYIDPKEIDYIIVNHTEPDHSGSLPELLELAPNAKIICSKLAARFLKG 113 (388)
T ss_pred ceeeeEEEeCCcEEEECCCCcchHHHHHHHHHhhcChhcCeEEEECCCCcchhhhHHHHHHhCCCCEEEeeHHHHHHHHH
Confidence 345567778888999999732 2257999999999999999998754 47899999999999998
Q ss_pred hhccCCCceEEeCCCceEEECCEEEEEEec--CCCcCceEEEEEEcCCCCcccEEEEECCCC
Q 001045 99 ILNINPKFIYPLPIKIPVLIDGCEVVLVGA--NHCPGAVQFLFKVPGRNGGFERYVHTGDFR 158 (1176)
Q Consensus 99 ~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a--~H~pGS~~flie~~~~~G~~~~IlYTGDfr 158 (1176)
.+..+.. +..+..|+.+.+|+-++++++| -|-||+...+... .+||||+|+.
T Consensus 114 ~~~~~~~-~~ivk~Gd~ldlGg~tL~Fi~ap~LHWPd~m~TYd~~-------~kILFS~D~f 167 (388)
T COG0426 114 FYHDPEW-FKIVKTGDTLDLGGHTLKFIPAPFLHWPDTMFTYDPE-------DKILFSCDAF 167 (388)
T ss_pred hcCCccc-eeecCCCCEeccCCcEEEEEeCCCCCCCCceeEeecC-------CcEEEccccc
Confidence 7765544 8899999999999988888888 7899998777654 3699999963
No 81
>COG0491 GloB Zn-dependent hydrolases, including glyoxylases [General function prediction only]
Probab=98.11 E-value=4.3e-06 Score=91.37 Aligned_cols=108 Identities=21% Similarity=0.194 Sum_probs=74.2
Q ss_pred ccEEEecCCcC-------------CCCccEEEeccCChhhhCCcccCCC---CceEEeCHHHHHHHHHhhc---------
Q 001045 47 TRFLIDAFRYA-------------ADFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCSEITSRLLSQILN--------- 101 (1176)
Q Consensus 47 ~~~liD~~~~~-------------~~~i~avfITHaH~DHiggL~~l~~---~~pIY~s~~T~~ll~~~l~--------- 101 (1176)
..++||++-.. ..+|++|++||.|.||+||+..+.. ..++|..+...........
T Consensus 36 ~~~liD~G~~~~~~~~~~~~l~~~~~~i~~vilTH~H~DH~gg~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 115 (252)
T COG0491 36 GAVLIDTGLGDADAEALLEALAALGLDVDAILLTHGHFDHIGGAAVLKEAFGAAPVIAPAEVPLLLREEILRKAGVTAEA 115 (252)
T ss_pred ceEEEeCCCCchHHHHHHHHHHHcCCChheeeecCCchhhhccHHHHHhhcCCceEEccchhhhhhhccccccccccccc
Confidence 68999997322 1268999999999999999976532 3677766666555443321
Q ss_pred --cC-CCceEEeCCCceEEECCEEEEEEec-CCCcCceEEEEEEcCCCCcccEEEEECCCCCcc
Q 001045 102 --IN-PKFIYPLPIKIPVLIDGCEVVLVGA-NHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCK 161 (1176)
Q Consensus 102 --~~-~~~i~~l~~~~~~~i~~~~Vt~~~a-~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~ 161 (1176)
.+ ......+..++.+.+++..++.+++ ||.||+.+|+++. .+++|+||.-+..
T Consensus 116 ~~~~~~~~~~~~~~~~~~~~~~~~~~~i~tpGHT~g~~~~~~~~-------~~~l~~gD~~~~~ 172 (252)
T COG0491 116 YAAPGASPLRALEDGDELDLGGLELEVLHTPGHTPGHIVFLLED-------GGVLFTGDTLFAG 172 (252)
T ss_pred CCCCccccceecCCCCEEEecCeEEEEEECCCCCCCeEEEEECC-------ccEEEecceeccC
Confidence 01 1123445567788888855555554 9999999999985 2499999975543
No 82
>TIGR00361 ComEC_Rec2 DNA internalization-related competence protein ComEC/Rec2. The role for this protein in species that are not naturally transformable is unknown.
Probab=97.93 E-value=8.8e-05 Score=94.04 Aligned_cols=125 Identities=14% Similarity=0.000 Sum_probs=83.5
Q ss_pred CeeE-eCCccEEEecCCc-C----------------CCCccEEEeccCChhhhCCcccCCC---CceEEeCHHHHHHHHH
Q 001045 40 PSKH-VPNTRFLIDAFRY-A----------------ADFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCSEITSRLLSQ 98 (1176)
Q Consensus 40 ~~~~-ipg~~~liD~~~~-~----------------~~~i~avfITHaH~DHiggL~~l~~---~~pIY~s~~T~~ll~~ 98 (1176)
++.+ .++..++||++.. . .-++|+++|||.|.||+||++.+.. ...||.+....
T Consensus 452 aili~~~~~~iLIDtG~~~~~~~~~~~~l~p~L~~~Gi~ID~lilTH~d~DHiGGl~~ll~~~~v~~i~~~~~~~----- 526 (662)
T TIGR00361 452 AMFIGANGKGILYDTGEPWREGSLGEKVIIPFLTAKGIKLEALILSHADQDHIGGAEIILKHHPVKRLVIPKGFV----- 526 (662)
T ss_pred EEEEEECCeEEEEeCCCCCCCCCccHHHHHHHHHHcCCCcCEEEECCCchhhhCcHHHHHHhCCccEEEeccchh-----
Confidence 3444 5778899999732 0 0139999999999999999987543 34677765421
Q ss_pred hhccCCCceEEeCCCceEEECCEEEEEEecCC------CcCceEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhc-
Q 001045 99 ILNINPKFIYPLPIKIPVLIDGCEVVLVGANH------CPGAVQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNE- 171 (1176)
Q Consensus 99 ~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a~H------~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~- 171 (1176)
........+..|+.+++++++++++..+. --.|+.+.++..+ .++++|||........ .+..
T Consensus 527 ---~~~~~~~~~~~G~~~~~~~~~~~vL~P~~~~~~~~N~~S~vl~i~~~~-----~~~L~tGD~~~~~E~~---l~~~~ 595 (662)
T TIGR00361 527 ---EEGVAIEECKRGDVWQWQGLQFHVLSPEAPDPASKNNHSCVLWVDDGG-----NSWLLTGDLEAEGEQE---VMRVF 595 (662)
T ss_pred ---hCCCceEecCCCCEEeECCEEEEEECCCCccCCCCCCCceEEEEEECC-----eeEEEecCCCHHHHHH---HHhcc
Confidence 11123556778899999999999886432 2357888888743 7999999986643321 1111
Q ss_pred -cCCCcEEEE
Q 001045 172 -FAGCDAVFL 180 (1176)
Q Consensus 172 -~~~vDvLI~ 180 (1176)
..++|+|..
T Consensus 596 ~~l~~dvLk~ 605 (662)
T TIGR00361 596 PNIKADVLQV 605 (662)
T ss_pred cCcCccEEEe
Confidence 135677765
No 83
>KOG0813 consensus Glyoxylase [General function prediction only]
Probab=97.86 E-value=2.6e-05 Score=86.38 Aligned_cols=89 Identities=22% Similarity=0.271 Sum_probs=68.0
Q ss_pred CCccEEEeccCChhhhCCcccCCC----CceEEeCHHHHHHHHHhhccCCCceEEeCCCceEEECCEEEEEEec-CCCcC
Q 001045 59 DFSVSYFLSHFHSDHYTGLSPSWS----KGIIFCSEITSRLLSQILNINPKFIYPLPIKIPVLIDGCEVVLVGA-NHCPG 133 (1176)
Q Consensus 59 ~~i~avfITHaH~DHiggL~~l~~----~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a-~H~pG 133 (1176)
..+.+||.||-|.||+||+..+.. ++.+|+.. .... +..-+.+..++.+.+++.+|+.+.+ +|.-|
T Consensus 50 ~~l~~Il~THhH~DHsGGn~~i~~~~~~~~~v~g~~------~~r~---~~i~~~~~~~e~~~~~g~~v~~l~TPgHT~~ 120 (265)
T KOG0813|consen 50 RRLTAILTTHHHYDHSGGNEDIKREIPYDIKVIGGA------DDRI---PGITRGLKDGETVTVGGLEVRCLHTPGHTAG 120 (265)
T ss_pred CceeEEEeccccccccCcHHHHHhhccCCcEEecCC------hhcC---ccccccCCCCcEEEECCEEEEEEeCCCccCC
Confidence 578999999999999999986432 56677764 1111 1123347788999999999999998 99999
Q ss_pred ceEEEEEEcCCCCcccEEEEECCCCCc
Q 001045 134 AVQFLFKVPGRNGGFERYVHTGDFRFC 160 (1176)
Q Consensus 134 S~~flie~~~~~G~~~~IlYTGDfr~~ 160 (1176)
+..|++... .| .+.++|||.-+.
T Consensus 121 hi~~~~~~~--~~--e~~iFtGDtlf~ 143 (265)
T KOG0813|consen 121 HICYYVTES--TG--ERAIFTGDTLFG 143 (265)
T ss_pred cEEEEeecC--CC--CCeEEeCCceee
Confidence 999999851 13 579999997443
No 84
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=97.84 E-value=4.4e-05 Score=95.21 Aligned_cols=94 Identities=18% Similarity=0.295 Sum_probs=88.0
Q ss_pred CCcchHHHHHHHHHHHhhh---chHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHH
Q 001045 711 QPAPYIHLARTFDLVEAER---GKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEA 787 (1176)
Q Consensus 711 ~~~~F~~l~~~~~~i~~t~---~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~ 787 (1176)
.+++|.+++++|++|++++ ++.+|+++|+++|+.+ +|+++.+.++++++.+. +|+++.++.+||+++
T Consensus 113 ~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~---~~~E~k~iirli~g~lr-------iGv~e~~il~ALa~A 182 (590)
T PRK01109 113 EPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDA---SPLEAKYIARFVEGRLR-------LGVGDATILDALAIA 182 (590)
T ss_pred CCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhhh-------cCccHHHHHHHHHHH
Confidence 4689999999999999998 8899999999999996 78999999999999986 899999999999999
Q ss_pred hC--CChHHHHHHHHhcCChHHHHHHHHh
Q 001045 788 CG--TNRSKIRDMYNRLGDLGDVAQECRQ 814 (1176)
Q Consensus 788 ~g--~~~~~i~~~~~~~GDlG~va~~~~~ 814 (1176)
+| .+...+++.|+..||+|.+|..+..
T Consensus 183 ~~~~~~~~~ve~~y~~~~Dlg~va~~l~~ 211 (590)
T PRK01109 183 FGGAVARELVERAYNLRADLGYIAKILAE 211 (590)
T ss_pred HhcccchHHHHHHHHhCCCHHHHHHHHHh
Confidence 99 9999999999999999999998864
No 85
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=97.76 E-value=1.7e-05 Score=87.04 Aligned_cols=166 Identities=17% Similarity=0.169 Sum_probs=103.3
Q ss_pred cCceEEEEEecceeEEEEEEeeC-----CeEEEEcCCCccC---CCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCC
Q 001045 977 QNKAFTCEYKYDGQRAQIHKLVD-----GTVRIFSRNGDET---TSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNG 1048 (1176)
Q Consensus 977 ~~~~f~~E~KyDGeR~QiH~~~~-----g~V~ifSR~g~d~---T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g 1048 (1176)
-..+|++.+|-||.||.+.+... -.+.+|.|..+=| |..||-+...... ...-.+-.||||+|. |
T Consensus 60 l~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~g--e~l~~dtlldgelV~-d---- 132 (404)
T COG5226 60 LNNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDG--EVLLEDTLLDGELVF-D---- 132 (404)
T ss_pred HhCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccC--cEEeccceecceEEE-E----
Confidence 35789999999999999988522 3688999988754 2334433221111 112356789999987 2
Q ss_pred CcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCC
Q 001045 1049 CKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGD 1128 (1176)
Q Consensus 1049 ~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~ 1128 (1176)
..|...+. ++.|.+||+|.+||..+..++..+|.+.|.+-+..+ +.........+..
T Consensus 133 --~~p~~k~~------------------qlryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp---~~~~r~s~~~~~~ 189 (404)
T COG5226 133 --CLPYEKVP------------------QLRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKP---RERKRVSIEIDSG 189 (404)
T ss_pred --eccccchH------------------HHHHHHHHHhhhcceeEeecchhhHHHHhhhhhccc---Hhhhhheeecccc
Confidence 23443333 356789999999999999999999999999877322 1111111111000
Q ss_pred ----CCCCccccCHHHHHHHHHHH--HhCCCceEEEecCCCCCCcccCCCCC
Q 001045 1129 ----DNCLTSDVSLSKINNFLEEA--LHSSCEGIIVKSLDVDAGYSPSKRSD 1174 (1176)
Q Consensus 1129 ----~~~~~~~~~~eei~~~~~~a--i~~g~EGlmvK~ld~~s~Y~pGkRs~ 1174 (1176)
..+++...---.+-.+|+.. +.+|..|||.-..+ .||..|+++.
T Consensus 190 ~fpf~~s~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~~--~PY~~Gkd~~ 239 (404)
T COG5226 190 SFPFHFSVKQMLKSYGFWKIYKKIPELKHGNDGLIFTPAD--EPYSVGKDGA 239 (404)
T ss_pred ccceeeeHHHHHhhhhHHHHHhhcccccCCCCceEeccCC--CCcccCccce
Confidence 00111111112334444322 46899999999987 8999998863
No 86
>cd00114 LIGANc NAD+ dependent DNA ligase adenylation domain. DNA ligases catalyze the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor, but using the same basic reaction mechanism. The enzyme reacts with the cofactor to form a phosphoamide-linked AMP with the amino group of a conserved Lysine in the KXDG motif, and subsequently transfers it to the DNA substrate to yield adenylated DNA. This alignment contains members of the NAD+ dependent subfamily only.
Probab=97.68 E-value=0.00043 Score=79.45 Aligned_cols=177 Identities=19% Similarity=0.205 Sum_probs=105.6
Q ss_pred cCCCCcc-cCChhHH---HHhcc-----CceEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHHHHH
Q 001045 959 KPMLAKI-TNGVPQV---LKLFQ-----NKAFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLISIIN 1024 (1176)
Q Consensus 959 ~PMLA~~-~~~~~~~---~~~~~-----~~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~~l~ 1024 (1176)
.|||.-. +.+.+++ ++++. ...|+||+|+||.-+.+.+. +|. ++..|| .|+|+|....-| ..|+
T Consensus 72 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~vepKiDGlsisL~Y~-~G~L~~a~TRGdG~~GeDVT~nv~~I-~~IP 149 (307)
T cd00114 72 VPMLSLDNAFDEEELRAFDERIKRFLGEEPAYVVEPKIDGLSISLRYE-NGVLVQAATRGDGTTGEDVTENVRTI-RSIP 149 (307)
T ss_pred CcCccccccCCHHHHHHHHHHHHHhcCCCCcEEEEEeccceEEEEEEE-CCEEEEEEecCCCcchhhHHhhHhhh-cccC
Confidence 5898642 3344443 23332 13699999999999999995 555 899999 788999765433 2233
Q ss_pred hhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcC----C--CCch-----hh----hcccccceEEEEEEeeeeC
Q 001045 1025 EFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERG----G--KDSV-----IT----IKSVKVDICVFVFDIMFAN 1089 (1176)
Q Consensus 1025 ~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~----~--~~~~-----i~----~~~~~~~v~~~vFDiL~ln 1089 (1176)
..+...+..+.+=||++.-. ..|+.+...... . ...+ +. ......++.||+|++...+
T Consensus 150 ~~i~~~~~~levRGEv~m~~-------~~F~~~n~~~~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~ 222 (307)
T cd00114 150 LTLAGAPETLEVRGEVFMPK-------ADFEALNKEREERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAE 222 (307)
T ss_pred hhhcCCCCeEEEEEEEEEEH-------HHHHHHHHHHHHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEeccccc
Confidence 32211255789999999832 345555321000 0 0000 00 0112457999999986544
Q ss_pred CcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHh------CCCceEEEecCC
Q 001045 1090 GEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALH------SSCEGIIVKSLD 1162 (1176)
Q Consensus 1090 G~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmvK~ld 1162 (1176)
+.. -....++.+.|+++- -..+....+ ..+.+++.++++...+ -..-|||||--+
T Consensus 223 ~~~--~~t~~e~l~~L~~~G-F~v~~~~~~---------------~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~ 283 (307)
T cd00114 223 GLG--PKTQSEALAFLKEWG-FPVSPETRL---------------CKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDD 283 (307)
T ss_pred CCC--CCCHHHHHHHHHHCC-CCCCCCeEE---------------eCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeC
Confidence 212 247788999998864 222222211 2457888888877643 366899999754
No 87
>PRK11539 ComEC family competence protein; Provisional
Probab=97.67 E-value=0.0003 Score=90.43 Aligned_cols=101 Identities=16% Similarity=0.022 Sum_probs=71.7
Q ss_pred eCCccEEEecCCc-C----------------CCCccEEEeccCChhhhCCcccCCC---CceEEeCHHHHHHHHHhhccC
Q 001045 44 VPNTRFLIDAFRY-A----------------ADFSVSYFLSHFHSDHYTGLSPSWS---KGIIFCSEITSRLLSQILNIN 103 (1176)
Q Consensus 44 ipg~~~liD~~~~-~----------------~~~i~avfITHaH~DHiggL~~l~~---~~pIY~s~~T~~ll~~~l~~~ 103 (1176)
-.+..+++|++.. . .-++|+++|||.|.||+||++.+.. ...||.+....
T Consensus 518 ~~~~~lLiDtG~~~~~~~~~~~~i~P~L~~~Gi~lD~lilSH~d~DH~GGl~~Ll~~~~~~~i~~~~~~~---------- 587 (755)
T PRK11539 518 RNGKAILYDTGNAWPTGDSAQQVIIPWLRWHGLTPEGIILSHEHLDHRGGLASLLHAWPMAWIRSPLNWA---------- 587 (755)
T ss_pred ECCEEEEEeCCCCCCCCcchHHHHHHHHHHcCCCcCEEEeCCCCcccCCCHHHHHHhCCcceeeccCccc----------
Confidence 4677899999731 0 0158999999999999999987543 45677654210
Q ss_pred CCceEEeCCCceEEECCEEEEEEec-CCC-----cCceEEEEEEcCCCCcccEEEEECCCCCcc
Q 001045 104 PKFIYPLPIKIPVLIDGCEVVLVGA-NHC-----PGAVQFLFKVPGRNGGFERYVHTGDFRFCK 161 (1176)
Q Consensus 104 ~~~i~~l~~~~~~~i~~~~Vt~~~a-~H~-----pGS~~flie~~~~~G~~~~IlYTGDfr~~~ 161 (1176)
...++..|+.+..++++++.+.. .|. .+||.+.++..+ .++++|||.....
T Consensus 588 --~~~~~~~g~~~~~~~~~~~vL~P~~~~~~~~N~~S~Vl~i~~~~-----~~~LltGDi~~~~ 644 (755)
T PRK11539 588 --NHLPCVRGEQWQWQGLTFSVHWPLEQSNDAGNNDSCVIRVDDGK-----HSILLTGDLEAQA 644 (755)
T ss_pred --CcccccCCCeEeECCEEEEEEecCcccCCCCCCccEEEEEEECC-----EEEEEEeCCChHH
Confidence 12335567888899998888843 342 468999998743 7999999985543
No 88
>COG1237 Metal-dependent hydrolases of the beta-lactamase superfamily II [General function prediction only]
Probab=97.62 E-value=0.00024 Score=78.07 Aligned_cols=63 Identities=22% Similarity=0.059 Sum_probs=48.0
Q ss_pred CCCCCCCCCeeE---eCCccEEEecCCc-------------CCCCccEEEeccCChhhhCCcccCC----CCceEEeCHH
Q 001045 32 PPIPRTFPPSKH---VPNTRFLIDAFRY-------------AADFSVSYFLSHFHSDHYTGLSPSW----SKGIIFCSEI 91 (1176)
Q Consensus 32 p~~~r~~p~~~~---ipg~~~liD~~~~-------------~~~~i~avfITHaH~DHiggL~~l~----~~~pIY~s~~ 91 (1176)
.++-+..+|..+ ..+.++|+|.+.+ ...++++++|||.|.||+|||+++. ..++||++|.
T Consensus 14 ~~~f~a~hGfS~LVE~~~~riLFDtG~~~~~ll~Na~~lgvd~~did~vvlSHgH~DH~GGL~~~~~~~~~~i~v~ahp~ 93 (259)
T COG1237 14 RPGFRAEHGFSALVEDEGTRILFDTGTDSDVLLHNARLLGVDLRDIDAVVLSHGHYDHTGGLPYLLEENNPGIPVYAHPD 93 (259)
T ss_pred CCcccccCceEEEEEcCCeEEEEeCCCCcHHHHHHHHHcCCCcccCcEEEEeCCCccccCchHhHHhccCCCceEEeChH
Confidence 334456666544 4667899999822 2258999999999999999999753 3679999999
Q ss_pred HHH
Q 001045 92 TSR 94 (1176)
Q Consensus 92 T~~ 94 (1176)
...
T Consensus 94 af~ 96 (259)
T COG1237 94 AFK 96 (259)
T ss_pred HHh
Confidence 876
No 89
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=97.62 E-value=6.6e-05 Score=86.42 Aligned_cols=178 Identities=22% Similarity=0.311 Sum_probs=100.0
Q ss_pred cCCCCc-ccCChhHH---HHh----ccCc--eEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHHHH
Q 001045 959 KPMLAK-ITNGVPQV---LKL----FQNK--AFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLISII 1023 (1176)
Q Consensus 959 ~PMLA~-~~~~~~~~---~~~----~~~~--~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~~l 1023 (1176)
.|||.- .+.+.+++ +++ ++.. .|+||+|+||.-+.+++. +|. ++..|| -|+|+|....-|. .|
T Consensus 77 ~pMlSL~k~~s~eel~~w~~r~~~~~~~~~~~~~~e~KiDGlsi~L~Y~-~G~L~~a~TRGdG~~GeDvT~n~~~i~-~i 154 (315)
T PF01653_consen 77 VPMLSLDKAYSEEELRKWLKRVEKALGEEEEEFVVEPKIDGLSISLIYE-NGKLVRAATRGDGEVGEDVTHNVRTIK-SI 154 (315)
T ss_dssp S-----EEESSHHHHHHHHHHHHHHCSS-SSEEEEEEEESSEEEEEEEE-TTEEEEEEEETTSSEEEB-HHHHCTST-TS
T ss_pred ccccCccccCCHHHHHHHHHHHHHHhcccccceeEeeccceeEEEEEEe-CCEEEEEEEcCCCccchhHHHHHHHHh-cC
Confidence 589853 33444443 233 2232 599999999999999994 666 799999 6788886433321 12
Q ss_pred HhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhh-hcCCCCc-----h-----h----hhcccccceEEEEEEeeee
Q 001045 1024 NEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSR-ERGGKDS-----V-----I----TIKSVKVDICVFVFDIMFA 1088 (1176)
Q Consensus 1024 ~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R-~r~~~~~-----~-----i----~~~~~~~~v~~~vFDiL~l 1088 (1176)
+..+...+..+.+=||++.- ...|..+..+ ....... + + .......++.|++|++.+.
T Consensus 155 P~~i~~~p~~~eVRGEv~m~-------~~~F~~ln~~~~~~~~~~faNpRN~aAGsLr~~d~~~~~~r~L~f~~y~~~~~ 227 (315)
T PF01653_consen 155 PLRIPEKPGRLEVRGEVYMS-------KSDFEKLNEEREEEGEKPFANPRNAAAGSLRQKDPSITAERKLSFFAYGIGEP 227 (315)
T ss_dssp -SB-SSSSSEEEEEEEEE---------HHHHHHHHHHHHHTTS---SSHHHHHHHHHTSSSHHHHHTS--EEEEEEEEEE
T ss_pred chhhccCCcceEEEEEEEEe-------hhhHHHHHHHHHHhccchhhhhhHHHHHhhhhccchhhhcCeeEEEEEEeccc
Confidence 32222225788999999972 3467776521 1100000 0 0 0011245799999999998
Q ss_pred CCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhC------CCceEEEecCC
Q 001045 1089 NGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHS------SCEGIIVKSLD 1162 (1176)
Q Consensus 1089 nG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~------g~EGlmvK~ld 1162 (1176)
+| .+--....++.+.|+++- -+....+.+ ..+.+++.++++...+. ..-|||||--+
T Consensus 228 ~~-~~~~~t~~e~l~~L~~~G-F~v~~~~~~---------------~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~ 290 (315)
T PF01653_consen 228 EG-DLGFNTQSERLQFLKEWG-FPVNPYIRF---------------CKSIEEVEEYIEEWEERREELPYPIDGIVIKVND 290 (315)
T ss_dssp TT-STT-SBHHHHHHHHHHTT---B-TTEEE---------------ESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESB
T ss_pred cc-ccChHHHHHHHHHHHHcC-CCCCcceEe---------------cCCHHHHHHHHHHHHhhhhccccccCcEEEEecC
Confidence 87 343456788888888764 222222221 24678888888877653 45799999754
No 90
>COG2333 ComEC Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=97.60 E-value=0.00055 Score=77.86 Aligned_cols=112 Identities=13% Similarity=0.088 Sum_probs=73.8
Q ss_pred eCCccEEEecCC-------------cCCCCccEEEeccCChhhhCCcccCCC-----CceEEeCHHHHHHHHHhhccCCC
Q 001045 44 VPNTRFLIDAFR-------------YAADFSVSYFLSHFHSDHYTGLSPSWS-----KGIIFCSEITSRLLSQILNINPK 105 (1176)
Q Consensus 44 ipg~~~liD~~~-------------~~~~~i~avfITHaH~DHiggL~~l~~-----~~pIY~s~~T~~ll~~~l~~~~~ 105 (1176)
.++...++|.+. .+..+||.+++||+|.||+||+..+.. .+-||.+..+..... +.-...
T Consensus 61 ~~~~~~l~dtg~~~~~~~iip~Lk~~GV~~iD~lIlTH~d~DHiGg~~~vl~~~~v~~~~i~~~~~~~~~~~--~~~~~~ 138 (293)
T COG2333 61 SEGKTILYDTGNSMGQDVIIPYLKSLGVRKLDQLILTHPDADHIGGLDEVLKTIKVPELWIYAGSDSTSTFV--LRDAGI 138 (293)
T ss_pred eCCceEEeecCcccCceeehhhHhHcCCccccEEEeccCCccccCCHHHHHhhCCCCcEEEeCCCCccchhh--hhhcCC
Confidence 455567777764 112579999999999999999987543 222333333222222 111122
Q ss_pred ceEEeCCCceEEECCEEEEEEecC-C-----CcCceEEEEEEcCCCCcccEEEEECCCCCccc
Q 001045 106 FIYPLPIKIPVLIDGCEVVLVGAN-H-----CPGAVQFLFKVPGRNGGFERYVHTGDFRFCKT 162 (1176)
Q Consensus 106 ~i~~l~~~~~~~i~~~~Vt~~~a~-H-----~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~ 162 (1176)
.+.....|+.+.++++.++++.-. + .-.||++.++..+ .+++.|||......
T Consensus 139 ~~~~~~~G~~~~~~~~~f~vl~P~~~~~~~~N~~S~Vl~v~~g~-----~s~LlTGD~e~~~E 196 (293)
T COG2333 139 PVRSCKAGDSWQWGGVVFQVLSPVGGVSDDLNNDSCVLRVTFGG-----NSFLLTGDLEEKGE 196 (293)
T ss_pred ceeccccCceEEECCeEEEEEcCCccccccccCcceEEEEEeCC-----eeEEEecCCCchhH
Confidence 356677788999999888877543 4 2358999999854 69999999865443
No 91
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.51 E-value=0.0025 Score=78.36 Aligned_cols=180 Identities=15% Similarity=0.141 Sum_probs=106.0
Q ss_pred cCCCCc-ccCChhHHHHhcc-CceEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHHHHHhhcCCCC
Q 001045 959 KPMLAK-ITNGVPQVLKLFQ-NKAFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLISIINEFCKPAA 1031 (1176)
Q Consensus 959 ~PMLA~-~~~~~~~~~~~~~-~~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~~l~~~~~~~~ 1031 (1176)
.|||.- .+.+.+++.+=.. ...|+||+|+||.=+-+.+. +|. ++..|| -|+|+|...--| ..++..+...+
T Consensus 96 ~PMlSL~k~~s~eel~~w~~~~~~~~vepKiDGlsisL~Ye-~G~Lv~a~TRGDG~~GEDVT~nv~~I-~~IP~~l~~~~ 173 (562)
T PRK08097 96 VAHTGVKKLADKQALARWMAGRSDLWVQPKVDGVAVTLVYR-DGKLVQAISRGNGLKGEDWTAKARLI-PAIPQQLPGAL 173 (562)
T ss_pred CCcccccccCCHHHHHHHHhhccceEEEEecccEEEEEEEE-CCEEEEEEecCCCccchhHHhhHhhh-cccchhhcCCC
Confidence 499863 3445555432111 12699999999999999995 554 789999 788888754322 22333332224
Q ss_pred CCeEEEEEEEEEecCCCCcccChHHHhh-----h------hcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHH
Q 001045 1032 GTFILDAEVVAIDRKNGCKIMSFQELSS-----R------ERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQ 1100 (1176)
Q Consensus 1032 ~~~ILDGElVa~d~~~g~~~~pFq~L~~-----R------~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~e 1100 (1176)
..+.+-||++.-. ..|+.... | .|.. +..+ ...++.||+|++. +| .....+
T Consensus 174 ~~levRGEv~m~~-------~~F~~~~~g~aNPRN~AAGsLr~~-d~~~----~~r~L~~f~y~~~--~~----~~t~~e 235 (562)
T PRK08097 174 ANLVLQGELFLRR-------EGHIQQQMGGINARAKVAGLMMRK-DPSP----TLNQIGVFVWAWP--DG----PASMPE 235 (562)
T ss_pred CeEEEEEEEEEeH-------HHHHHHhcCcCCchHHHhHHHhhc-CcHh----hhccceEEEEECC--CC----CCCHHH
Confidence 4689999999832 35654321 1 0111 1111 1457999999973 44 246788
Q ss_pred HHHHHHHhhcccCCCcEEEeE-EEEEcCCCCCCccccCHHHHHHHHHHHH----hCCCceEEEecCCCCCCcccC--CCC
Q 001045 1101 RRKYLKDLFYDEKMGYFQYAK-EMTVEGDDNCLTSDVSLSKINNFLEEAL----HSSCEGIIVKSLDVDAGYSPS--KRS 1173 (1176)
Q Consensus 1101 Rr~lL~~~~~~~~~~~i~~~~-~~~v~~~~~~~~~~~~~eei~~~~~~ai----~~g~EGlmvK~ld~~s~Y~pG--kRs 1173 (1176)
+.+.|+++- -+ ..+ .... ..+.+++.++++... .-.--|||+|--+ -.|..| .|.
T Consensus 236 ~l~~L~~~G-F~------v~~~~~~~---------~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn~--~~~~~~~ts~~ 297 (562)
T PRK08097 236 RLAQLATAG-FP------LTQRYTHP---------VKNAEEVARWRERWYRAPLPFVTDGVVVRQAK--EPPGRYWQPGQ 297 (562)
T ss_pred HHHHHHHCC-CC------cCccceEe---------eCCHHHHHHHHHHHhhccCCCCCCcEEEEecC--HHHHhhccCCC
Confidence 888888764 12 221 1110 235677777776543 2367899999755 344332 345
Q ss_pred CCC
Q 001045 1174 DSW 1176 (1176)
Q Consensus 1174 ~~W 1176 (1176)
..|
T Consensus 298 PrW 300 (562)
T PRK08097 298 GEW 300 (562)
T ss_pred CCc
Confidence 555
No 92
>smart00532 LIGANc Ligase N family.
Probab=97.50 E-value=0.00072 Score=81.17 Aligned_cols=178 Identities=19% Similarity=0.189 Sum_probs=105.2
Q ss_pred cCCCCc-ccCChhHH---HHhccC-----ceEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHHHHH
Q 001045 959 KPMLAK-ITNGVPQV---LKLFQN-----KAFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLISIIN 1024 (1176)
Q Consensus 959 ~PMLA~-~~~~~~~~---~~~~~~-----~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~~l~ 1024 (1176)
.|||.- .+.+.+++ ++++.. -.|+||+|+||.-+-+.+. +|. ++..|| .|+|+|....-|.. ++
T Consensus 74 ~pMlSL~k~~~~~el~~f~~~~~~~~~~~~~~~~epKiDGlsisL~Ye-~G~l~~a~TRGDG~~GeDVT~nv~~i~~-iP 151 (441)
T smart00532 74 VPMLSLDNAFDEDELRAFDERIEKALGSPFAYVVEPKIDGLSVSLLYE-NGKLVQAATRGDGTVGEDVTQNVKTIRS-IP 151 (441)
T ss_pred CcccCccccCCHHHHHHHHHHHHHhcCCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcceehhhhhhhhcC-cC
Confidence 499864 33445543 223211 2699999999999999995 666 899999 88999976543321 22
Q ss_pred hhcC-CCCCCeEEEEEEEEEecCCCCcccChHHHhhhhc--C----CCCch-----hh----hcccccceEEEEEEeeee
Q 001045 1025 EFCK-PAAGTFILDAEVVAIDRKNGCKIMSFQELSSRER--G----GKDSV-----IT----IKSVKVDICVFVFDIMFA 1088 (1176)
Q Consensus 1025 ~~~~-~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r--~----~~~~~-----i~----~~~~~~~v~~~vFDiL~l 1088 (1176)
..+. ..+..+.+-||++.- ...|+.|-.... . ....+ +. ......++.||+|++...
T Consensus 152 ~~i~~~~p~~leiRGEv~~~-------~~~F~~ln~~~~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~ 224 (441)
T smart00532 152 LRLSGDVPERLEVRGEVFMP-------KEDFLALNEELEEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTG 224 (441)
T ss_pred hhhcccCCCeEEEEceEEEE-------HHHHHHHHHHHHhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccC
Confidence 2111 123568999999983 235666532100 0 00000 00 011234799999998644
Q ss_pred CCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHh------CCCceEEEecCC
Q 001045 1089 NGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALH------SSCEGIIVKSLD 1162 (1176)
Q Consensus 1089 nG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmvK~ld 1162 (1176)
++... .....++.+.|+++- -... +.... ..+.+++.++++...+ -.--|||+|--+
T Consensus 225 ~~~~~-~~t~~e~l~~L~~~G-F~v~------~~~~~---------~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn~ 287 (441)
T smart00532 225 EELFL-PKTQSEALKWLKELG-FPVS------PHTRL---------CKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDD 287 (441)
T ss_pred CCCCC-ccCHHHHHHHHHHCC-CCCC------CCeEe---------eCCHHHHHHHHHHHHHhcccCCCCcCcEEEEecC
Confidence 43211 246788888888763 1122 21111 2457888888887655 366899999755
No 93
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=97.40 E-value=0.0042 Score=67.66 Aligned_cols=124 Identities=11% Similarity=0.064 Sum_probs=70.8
Q ss_pred EEeCCCceEEECCEEEEEEec-CCCcC-c-----eEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhcc--CCCcEE
Q 001045 108 YPLPIKIPVLIDGCEVVLVGA-NHCPG-A-----VQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEF--AGCDAV 178 (1176)
Q Consensus 108 ~~l~~~~~~~i~~~~Vt~~~a-~H~pG-S-----~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~--~~vDvL 178 (1176)
.....|++|++|+..|.+-+. -|-+. + +|+.+...+ .+|+|+.|.-- ...+..+..+ .++|++
T Consensus 134 ie~ADgk~f~fG~t~IefS~pvpHG~eGskLGyVl~v~V~dg~-----~~i~faSDvqG---p~~~~~l~~i~e~~P~v~ 205 (304)
T COG2248 134 IEYADGKTFEFGGTVIEFSPPVPHGREGSKLGYVLMVAVTDGK-----SSIVFASDVQG---PINDEALEFILEKRPDVL 205 (304)
T ss_pred eEecCCceEEeCCEEEEecCCCCCCCcccccceEEEEEEecCC-----eEEEEcccccC---CCccHHHHHHHhcCCCEE
Confidence 355678899999999998775 88553 3 455554432 69999999841 1222221111 689999
Q ss_pred EEeC--CCCCC-CCCCCChHHHHHHHHHHHHHHhhhccccCCCeEEEEEeccc--c---chHHHHHHHHHHcCCcEEE
Q 001045 179 FLDT--TYCNP-KFLFPLQEESVEYVVNVVNRVGGELNEGLQKRVLFLVATYV--I---GKEKILIEIFKKCGRKVCV 248 (1176)
Q Consensus 179 I~Es--Ty~~~-~~~~p~~~e~~~~l~~~i~~~~~~~~~~~~g~vlvli~~~s--l---GR~q~ll~ia~~~g~~I~v 248 (1176)
|+++ ||... .+.....+..++.+..++.+. + .+||+=++-- . .+.+++...++..|..|..
T Consensus 206 ii~GPpty~lg~r~~~~~~E~~irNl~~ii~~~--------~-~~lViDHHllRD~~y~e~l~~l~~~~~~~GV~v~T 274 (304)
T COG2248 206 IIGGPPTYLLGYRVGPKSLEKGIRNLERIIEET--------N-ATLVIDHHLLRDKNYREFLEELFERAEKAGVEVAT 274 (304)
T ss_pred EecCCchhHhhhhcChHHHHHHHHHHHHHHHhC--------c-ceEEEeehhhcCCCHHHHHHHHHhhHhhcCceeee
Confidence 9997 43321 111123344455554444433 2 3434333322 2 2345666677777877765
No 94
>cd09232 Snurportin-1_C C-terminal m3G cap-binding domain of nuclear import adaptor snurportin-1. Snurportin-1 (SPN1 or SNUPN) is a nuclear import adaptor for m3G-capped spliceosomal U small nucleoproteins (snRNPs), which are assembled in the cytoplasm. After capping and assembly, the U snRNPs are transported into the nucleus by SPN1 and importin beta; SPN1 is then returned to the cytoplasm by exportin 1 (CRM1), which also transports the non-capped U snRNPs. The U snRNPs are essential elements of the spliceosome, which catalyzes the excision of introns and the ligation of exons to form a mature mRNA. SPN1 contains two domains, an N-terminal importin beta-binding (IBB) domain and a C-terminal m3G cap-binding domain.
Probab=97.19 E-value=0.0023 Score=68.39 Aligned_cols=145 Identities=17% Similarity=0.220 Sum_probs=100.4
Q ss_pred CceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcC--CCCCCeEEEEEEEEEecCCCCcccChH
Q 001045 978 NKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCK--PAAGTFILDAEVVAIDRKNGCKIMSFQ 1055 (1176)
Q Consensus 978 ~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~--~~~~~~ILDGElVa~d~~~g~~~~pFq 1055 (1176)
...|++=+-==|.||.|... +|.+.+++|+|.-+. .|+.. ++.--. .....+|||+-. +.
T Consensus 20 ~~~w~~~~~P~G~R~lvv~~-~g~t~~~~r~g~~~~-~f~s~---lP~g~~~~~~~g~tILDci~---~~---------- 81 (186)
T cd09232 20 SEEWLVVPCPVGKRCLVVAS-KGKTVARSKNGRTLH-RFSSA---LPGGSRKTSNSGYTILDCIY---NE---------- 81 (186)
T ss_pred CcceEEEECcCceEEEEEEe-CCEEEEEeCCCCEEE-ecccC---CCCCCcCCCCCCCEEEEEec---CC----------
Confidence 35788888888999999995 999999999998752 22111 111000 012345555542 11
Q ss_pred HHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCC---------CcEEEeEEEEEc
Q 001045 1056 ELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKM---------GYFQYAKEMTVE 1126 (1176)
Q Consensus 1056 ~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~---------~~i~~~~~~~v~ 1126 (1176)
....|+|+|||.+||.++.+.++..|...|++-+.+... -.|...+...+
T Consensus 82 --------------------~~~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~~~~~~~~~f~~~p~~~~- 140 (186)
T cd09232 82 --------------------DDRTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDEPSEKNPFRFVPLPYFPC- 140 (186)
T ss_pred --------------------CCCEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCccccccccccCCceEEecCcccC-
Confidence 124799999999999999999999999999998832211 13444444432
Q ss_pred CCCCCCccccCHHHHHHHHHHHH---hCCCceEEEecCCCCCCcccCCCCC
Q 001045 1127 GDDNCLTSDVSLSKINNFLEEAL---HSSCEGIIVKSLDVDAGYSPSKRSD 1174 (1176)
Q Consensus 1127 ~~~~~~~~~~~~eei~~~~~~ai---~~g~EGlmvK~ld~~s~Y~pGkRs~ 1174 (1176)
+.+.+++.|...+ ..--.||..=..+ +.|++| ++.
T Consensus 141 ----------~~~~l~~~~~~~~~~~~~e~DGLlFyhk~--~~Y~~G-~tP 178 (186)
T cd09232 141 ----------TKESLQSAYSGPLNDDPYELDGLLFYHKE--SHYTPG-STP 178 (186)
T ss_pred ----------cHHHHHHHHhcccccCCCCCceEEEEeCC--CcccCc-CCC
Confidence 2367888888888 8888999998877 789999 443
No 95
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.08 E-value=0.0044 Score=78.35 Aligned_cols=177 Identities=15% Similarity=0.192 Sum_probs=104.0
Q ss_pred cCCCCc-ccCChhHH---HHh----ccCceEEEEEecceeEEEEEEeeCCeEEEEcC----CCccCCCCchhHHHHHHhh
Q 001045 959 KPMLAK-ITNGVPQV---LKL----FQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSR----NGDETTSRFPDLISIINEF 1026 (1176)
Q Consensus 959 ~PMLA~-~~~~~~~~---~~~----~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR----~g~d~T~~ypdl~~~l~~~ 1026 (1176)
.|||.- .+.+.+++ .++ ++...|+||+|+||.=+-+.+.+|.=++..|| .|+|+|.....| ..|+..
T Consensus 104 ~pMlSL~k~~~~~el~~f~~r~~~~~~~~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDVT~nv~~I-~~IP~~ 182 (689)
T PRK14351 104 APMLSIDQSGEADDVREFDERVRREVGAVEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTI-RSVPQK 182 (689)
T ss_pred CcccccCccCCHHHHHHHHHHHHHhcCCceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceeHhhhhhhh-cccchh
Confidence 489864 23344544 222 23346999999999999999953334889999 789999764432 222222
Q ss_pred cC-CCCCCeEEEEEEEEEecCCCCcccChHHHhhh-h----------cCCCCchhhh----cccccceEEEEEEeeeeCC
Q 001045 1027 CK-PAAGTFILDAEVVAIDRKNGCKIMSFQELSSR-E----------RGGKDSVITI----KSVKVDICVFVFDIMFANG 1090 (1176)
Q Consensus 1027 ~~-~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R-~----------r~~~~~~i~~----~~~~~~v~~~vFDiL~lnG 1090 (1176)
+. ..+..+++=||++.-. ..|+.+... . |......+.. .....++.||+|++...++
T Consensus 183 l~~~~p~~levRGEv~m~~-------~~F~~lN~~~~~~g~~~faNpRN~aAGslR~ldp~~~~~r~L~f~~y~~~~~~~ 255 (689)
T PRK14351 183 LRGDYPDFLAVRGEVYMPK-------DAFQAYNRERIERGEEPFANPRNAAAGTLRQLDPSVVAERPLDIFFFDVLDASE 255 (689)
T ss_pred hcccCCCeEEEEEEEEEEH-------HHHHHHHHHHHHcCCCCcCCHHHHHhhHhhccChHHHhcCCceEEEEecccCCC
Confidence 21 1244688999999832 356665421 0 0000000000 1123579999999865554
Q ss_pred cccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHH------hCCCceEEEecCC
Q 001045 1091 EQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEAL------HSSCEGIIVKSLD 1162 (1176)
Q Consensus 1091 ~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai------~~g~EGlmvK~ld 1162 (1176)
. .....++.+.|.++- -+ +++.... ..+.+++.++++... .-..-|||+|--+
T Consensus 256 ~---~~t~~e~l~~L~~~G-F~------v~~~~~~---------~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~ 314 (689)
T PRK14351 256 L---FDSHWEELERFPEWG-LR------VTDRTER---------VDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDD 314 (689)
T ss_pred C---CCCHHHHHHHHHHCC-CC------cCCceEe---------eCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeCC
Confidence 1 246778888888764 12 2222111 245677777776553 3466799999754
No 96
>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=97.04 E-value=0.0026 Score=80.24 Aligned_cols=177 Identities=18% Similarity=0.218 Sum_probs=104.2
Q ss_pred cCCCCcc-cCChhHH---HHhccC-----ceEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHHHHH
Q 001045 959 KPMLAKI-TNGVPQV---LKLFQN-----KAFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLISIIN 1024 (1176)
Q Consensus 959 ~PMLA~~-~~~~~~~---~~~~~~-----~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~~l~ 1024 (1176)
.|||.-. +.+.+++ ++++.. -.|+||+|+||.=+.+.+. +|. ++..|| -|+|+|.....| ..++
T Consensus 67 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~~epKiDGlaisL~Ye-~G~L~~a~TRGDG~~GeDvT~nv~~I-~~iP 144 (652)
T TIGR00575 67 TPMLSLDNAFDEDELAAFIKRIRRQLGLKVEYVVEPKIDGLSVSLTYE-NGVLVRALTRGDGTVGEDVTANVRTI-RSIP 144 (652)
T ss_pred CcCcCccccCCHHHHHHHHHHHHHhcCCCceEEEEEeccceEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhh-cccc
Confidence 4898642 3344443 233321 2599999999999999995 665 889999 789999764333 2233
Q ss_pred hhcC--CCCCCeEEEEEEEEEecCCCCcccChHHHhhh-hc-C----CCCch-----hh----hcccccceEEEEEEeee
Q 001045 1025 EFCK--PAAGTFILDAEVVAIDRKNGCKIMSFQELSSR-ER-G----GKDSV-----IT----IKSVKVDICVFVFDIMF 1087 (1176)
Q Consensus 1025 ~~~~--~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R-~r-~----~~~~~-----i~----~~~~~~~v~~~vFDiL~ 1087 (1176)
..+. +.+..+.+-||++.-. ..|+.+-.. .. . ....+ +. ......++.||+|++..
T Consensus 145 ~~i~~~~~p~~levRGEv~m~~-------~~F~~~N~~~~~~g~~~faNpRN~aAGslr~ld~~~~~~r~L~~~~y~~~~ 217 (652)
T TIGR00575 145 LRLAGDNPPERLEVRGEVFMPK-------EDFEALNEERREQGEKPFANPRNAAAGSLRQLDPRITAKRKLRFFAYGLGE 217 (652)
T ss_pred hhhcCCCCCceEEEEEEEEEEH-------HHHHHHHHHHHHcCCCCCCCcHHHHHHHHHcCCchhhhcCccEEEEEeccc
Confidence 3221 1245689999999832 356655321 00 0 00000 00 01124579999999853
Q ss_pred eCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHh------CCCceEEEecC
Q 001045 1088 ANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALH------SSCEGIIVKSL 1161 (1176)
Q Consensus 1088 lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmvK~l 1161 (1176)
.. ........++.+.|+++- -+......+ ..+.+++.+++++..+ -.--|||+|--
T Consensus 218 ~~--~~~~~t~~e~l~~L~~~G-F~v~~~~~~---------------~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn 279 (652)
T TIGR00575 218 GL--ELPDATQYEALAWLKKWG-FPVSPHIRL---------------CDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVD 279 (652)
T ss_pred cC--CCCCCCHHHHHHHHHHCC-CCCCCCeEe---------------eCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEec
Confidence 22 211247788888888763 122222111 2467888888876643 36689999975
Q ss_pred C
Q 001045 1162 D 1162 (1176)
Q Consensus 1162 d 1162 (1176)
+
T Consensus 280 ~ 280 (652)
T TIGR00575 280 D 280 (652)
T ss_pred C
Confidence 4
No 97
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.95 E-value=0.0078 Score=76.04 Aligned_cols=178 Identities=20% Similarity=0.263 Sum_probs=104.8
Q ss_pred cCCCCc-ccCChhHH---HHhccC------ceEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHHHH
Q 001045 959 KPMLAK-ITNGVPQV---LKLFQN------KAFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLISII 1023 (1176)
Q Consensus 959 ~PMLA~-~~~~~~~~---~~~~~~------~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~~l 1023 (1176)
.|||.- .+.+.+++ ++++.. ..|+||+|+||.=+.+.+. +|. ++..|| -|+|+|...--| ..|
T Consensus 78 ~pMlSL~k~~~~~el~~w~~r~~~~~~~~~~~~~~epKiDGlsisL~Y~-~G~L~~a~TRGDG~~GeDvT~n~~~I-~~I 155 (665)
T PRK07956 78 VPMLSLDNAFSEEELRAFDKRVRKRLPDPPLTYLCELKIDGLAVSLLYE-NGVLVRAATRGDGTTGEDITANVRTI-RSI 155 (665)
T ss_pred CcCcCccccCCHHHHHHHHHHHHHhcCCCCcceEEEEecccEEEEEEEE-CCEEEEEEecCCCccchhHhhhhhhh-ccC
Confidence 489864 23344443 233321 2599999999999999995 554 789999 789999754322 122
Q ss_pred HhhcC-CCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcC-C-----CCch-----hh----hcccccceEEEEEEeee
Q 001045 1024 NEFCK-PAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERG-G-----KDSV-----IT----IKSVKVDICVFVFDIMF 1087 (1176)
Q Consensus 1024 ~~~~~-~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~-~-----~~~~-----i~----~~~~~~~v~~~vFDiL~ 1087 (1176)
+..+. ..+..+++-||++.- ...|+.+..+... + ...+ .. ......++.||+|++..
T Consensus 156 P~~l~~~~p~~levRGEv~m~-------~~~F~~lN~~~~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~ 228 (665)
T PRK07956 156 PLRLHGNEPERLEVRGEVFMP-------KADFEALNEERREEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGE 228 (665)
T ss_pred ChhhcccCCCeEEEEEEEEEE-------HHHHHHHHHHHHhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEeccc
Confidence 22221 224568999999983 2356665432100 0 0000 00 01124579999999864
Q ss_pred eCCcccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHh------CCCceEEEecC
Q 001045 1088 ANGEQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALH------SSCEGIIVKSL 1161 (1176)
Q Consensus 1088 lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~------~g~EGlmvK~l 1161 (1176)
.++ ........++.+.|+++- -+......+ ..+.+++.++++...+ -..-|||+|--
T Consensus 229 ~~~-~~~~~t~~e~l~~L~~~G-F~v~~~~~~---------------~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn 291 (665)
T PRK07956 229 VEG-GELPDSQSEALEFLKAWG-FPVNPYRKL---------------CTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVD 291 (665)
T ss_pred ccC-CCCCCCHHHHHHHHHHCC-CCcCCceEe---------------eCCHHHHHHHHHHHHHhhccCCCCCCcEEEEec
Confidence 431 111246788888888864 122211111 2457888888876653 46689999975
Q ss_pred C
Q 001045 1162 D 1162 (1176)
Q Consensus 1162 d 1162 (1176)
+
T Consensus 292 ~ 292 (665)
T PRK07956 292 D 292 (665)
T ss_pred C
Confidence 4
No 98
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.85 E-value=0.0098 Score=74.94 Aligned_cols=178 Identities=16% Similarity=0.246 Sum_probs=102.7
Q ss_pred cCCCCc-ccCChhHH---HHhcc------C--ceEEEEEecceeEEEEEEeeCCe-EEEEcC----CCccCCCCchhHHH
Q 001045 959 KPMLAK-ITNGVPQV---LKLFQ------N--KAFTCEYKYDGQRAQIHKLVDGT-VRIFSR----NGDETTSRFPDLIS 1021 (1176)
Q Consensus 959 ~PMLA~-~~~~~~~~---~~~~~------~--~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR----~g~d~T~~ypdl~~ 1021 (1176)
.|||.- .+.+.+++ .+++. + ..|+||+|+||.-+-+.+. +|. ++..|| .|+|+|...--| .
T Consensus 78 ~pMlSL~k~~~~~el~~~~~r~~~~~~~~~~~~~~~~epKiDGlaisL~Ye-nG~L~~a~TRGDG~~GEDVT~n~~~I-~ 155 (669)
T PRK14350 78 FPILSLDKVYDLKLLKLWIEKMDLENSNLGFDFGISVEPKIDGCSIVLYYK-DGILEKALTRGDGRFGNDVTENVRTI-R 155 (669)
T ss_pred CccccccccCCHHHHHHHHHHHHHhhccCCCCceEEEEEecccEEEEEEEE-CCEEEEEEecCCCCcchhHhhhhhhh-c
Confidence 499863 33344443 23332 1 2599999999999999995 555 789999 789998764322 2
Q ss_pred HHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCC--CCch-----hh----hcccccceEEEEEEeeeeCC
Q 001045 1022 IINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGG--KDSV-----IT----IKSVKVDICVFVFDIMFANG 1090 (1176)
Q Consensus 1022 ~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~--~~~~-----i~----~~~~~~~v~~~vFDiL~lnG 1090 (1176)
.++..+. ....+.+-||++.- ...|+.|.....+. .+.+ +. ......++.||+|++...++
T Consensus 156 ~IP~~l~-~~~~levRGEv~m~-------~~~F~~lN~~~~~~faNpRNaaAGsLr~~d~~~~a~r~L~f~~y~~~~~~~ 227 (669)
T PRK14350 156 NVPLFID-EKVELVLRGEIYIT-------KENFLKINKTLEKPYTNARNLASGILRRIDSREVANFPLDIFVYDILYSSL 227 (669)
T ss_pred ccchhcC-CCceEEEEEEEEee-------HHHHHHHHHhhhccCCChhHHHHHHHHccCchhhhcCceEEEEEEcccCCC
Confidence 2333221 23568999999983 23566653221100 0000 00 01124479999999853222
Q ss_pred cccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHH------hCCCceEEEecCC
Q 001045 1091 EQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEAL------HSSCEGIIVKSLD 1162 (1176)
Q Consensus 1091 ~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai------~~g~EGlmvK~ld 1162 (1176)
. ..+..++.+.|+++- -+..+...+.. ..++.+++.+++++.. .-..-|||+|--+
T Consensus 228 ~---~~t~~e~l~~L~~~G-F~v~~~~~~~~------------~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~ 289 (669)
T PRK14350 228 E---LKTNHDAFDKLKKFG-FKVNPFCRFFD------------GKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSD 289 (669)
T ss_pred C---CCCHHHHHHHHHHCC-CCCCcceEEEc------------CCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecC
Confidence 1 236778888888764 22222222211 1134677777776543 2456899999754
No 99
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.
Probab=96.44 E-value=0.0061 Score=64.93 Aligned_cols=110 Identities=18% Similarity=0.180 Sum_probs=64.9
Q ss_pred ceEEEEEecceeEEEEEEeeCCeEEEEcCCCcc-----C------CCCchhHHHHH---Hhhc----CCCCCCeEEEEEE
Q 001045 979 KAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDE-----T------TSRFPDLISII---NEFC----KPAAGTFILDAEV 1040 (1176)
Q Consensus 979 ~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d-----~------T~~ypdl~~~l---~~~~----~~~~~~~ILDGEl 1040 (1176)
++|.+.+|+||--+.+.+..++.+++.+|++.. + ...|......+ .... .....+++|=||+
T Consensus 1 ~e~vvtEKldGtn~~i~~~~~~~~~~~~R~~~l~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~GE~ 80 (186)
T PF09414_consen 1 REVVVTEKLDGTNFSIYFDNDGRVRFQSRSHILDPNEDFFGYQSGDNRYWAQARWLFELLKLAELASELLPENIIIYGEL 80 (186)
T ss_dssp SEEEEEEE-SSEEEEEEEEECTCEEEEETTEE--TT---TTCHHHHHHCHHHHHHHHHHHHHHCCEC----SEEEEEEEE
T ss_pred CeEEEEEEeCCccEEEEEeCCCceeEeccccccCccccccccccchHHHHHHHHHHHhhhhhhhhcccccceEEEEEEEe
Confidence 369999999999999999767779999999932 1 12222222111 1111 1256789999999
Q ss_pred EEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCc-ccccCCHHHHHHHHHHh
Q 001045 1041 VAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGE-QLLGYTLRQRRKYLKDL 1108 (1176)
Q Consensus 1041 Va~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~-~Ll~~Pl~eRr~lL~~~ 1108 (1176)
++|-+.- + + +.. ...-+..|++|||...+.. ...=+++.+++.+++.+
T Consensus 81 ~G~~~~I----------q----~----~~~--~~~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~ 129 (186)
T PF09414_consen 81 VGAKPSI----------Q----K----NRY--QLDPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEEL 129 (186)
T ss_dssp ECEECTT----------C----S----S------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCC
T ss_pred eeecccc----------c----c----ccc--ccCCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHC
Confidence 9864211 0 0 000 0012578999999888643 22445777777777654
No 100
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.
Probab=96.07 E-value=0.036 Score=63.79 Aligned_cols=109 Identities=12% Similarity=0.106 Sum_probs=65.6
Q ss_pred ccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCC-CCc-------hhHHHHHH---hhcC----CCCCCeEEEEEE
Q 001045 976 FQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETT-SRF-------PDLISIIN---EFCK----PAAGTFILDAEV 1040 (1176)
Q Consensus 976 ~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T-~~y-------pdl~~~l~---~~~~----~~~~~~ILDGEl 1040 (1176)
+.+..|.+.+|.||-..-|.++.++.+++.||++.--- +.| +++...++ +.+. ....++++=||+
T Consensus 22 l~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~~l~~~e~f~G~~~i~~~l~~~~~~l~~~l~~~~~~~~~~v~IyGEl 101 (325)
T TIGR02307 22 LGLTEWVAREKIHGTNFSIIIERDFKVTCAKRTGIILPNEDFFGYHILIKNYTASVKAIQDILETKAIIVVVSVQVFGEL 101 (325)
T ss_pred cCCceEEEEEEecCcceEEEEeCCceEEEeecccccCcccccccHHHHHHHHHHHHHHHHHHHhhhcccccceEEEEEEe
Confidence 34679999999999999999853338999999954321 111 22322222 2221 245789999999
Q ss_pred EEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHh
Q 001045 1041 VAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDL 1108 (1176)
Q Consensus 1041 Va~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~ 1108 (1176)
++|.-.+. .. .. +..|++|||.+....+-.=+++.+-.+....+
T Consensus 102 ~G~~~q~~--~~---------------------Y~-~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~ 145 (325)
T TIGR02307 102 AGPGYQKP--VV---------------------YS-DKDFYAFDIKYTETSDDVTLVDDYMMESFCNV 145 (325)
T ss_pred ecCcccCc--cc---------------------cc-cccEEEEEEEEeccCcceEecHHHHHHHHHHc
Confidence 99743211 00 11 36799999955422123345666555555443
No 101
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=95.99 E-value=0.0059 Score=49.46 Aligned_cols=42 Identities=29% Similarity=0.472 Sum_probs=34.7
Q ss_pred hHhHHHHHhhhcCCcchhhHHHHHHHHhcccchhhhhccccccCC
Q 001045 590 GEEIDQFLKIINGNESLKGYAATLLEKTKGNVSMALDLYYDNQEG 634 (1176)
Q Consensus 590 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 634 (1176)
++.|.||+.|..- ..+.|+.+|+...+|++.|++.||+++++
T Consensus 1 ~e~i~~F~~iTg~---~~~~A~~~L~~~~wdle~Av~~y~~~~~~ 42 (43)
T PF14555_consen 1 DEKIAQFMSITGA---DEDVAIQYLEANNWDLEAAVNAYFDDGEA 42 (43)
T ss_dssp HHHHHHHHHHH-S---SHHHHHHHHHHTTT-HHHHHHHHHHSS-S
T ss_pred CHHHHHHHHHHCc---CHHHHHHHHHHcCCCHHHHHHHHHhCCCC
Confidence 3679999999953 56999999999999999999999997664
No 102
>KOG0814 consensus Glyoxylase [General function prediction only]
Probab=95.89 E-value=0.016 Score=59.89 Aligned_cols=84 Identities=20% Similarity=0.156 Sum_probs=59.0
Q ss_pred CccEEEeccCChhhhCCcccCCCCceEEeCHHHHHHHHHhhccCCCceEEeCCCceEEECCEEEEEEec-CCCcCceEEE
Q 001045 60 FSVSYFLSHFHSDHYTGLSPSWSKGIIFCSEITSRLLSQILNINPKFIYPLPIKIPVLIDGCEVVLVGA-NHCPGAVQFL 138 (1176)
Q Consensus 60 ~i~avfITHaH~DHiggL~~l~~~~pIY~s~~T~~ll~~~l~~~~~~i~~l~~~~~~~i~~~~Vt~~~a-~H~pGS~~fl 138 (1176)
++.+-+-||.|.||+-|-..+..-. |..+.++...-|-.. -.-++.|+.++||++.+....+ ||.+|++-|.
T Consensus 57 ~LiYa~NTH~HADHiTGtg~Lkt~~-----pg~kSVis~~SGakA--D~~l~~Gd~i~~G~~~le~ratPGHT~GC~TyV 129 (237)
T KOG0814|consen 57 DLIYALNTHVHADHITGTGLLKTLL-----PGCKSVISSASGAKA--DLHLEDGDIIEIGGLKLEVRATPGHTNGCVTYV 129 (237)
T ss_pred eeeeeecceeecccccccchHHHhc-----ccHHHHhhhcccccc--ccccCCCCEEEEccEEEEEecCCCCCCceEEEE
Confidence 4556688999999999876543211 123333333333222 2347889999999999988887 9999999988
Q ss_pred EEEcCCCCcccEEEEECCC
Q 001045 139 FKVPGRNGGFERYVHTGDF 157 (1176)
Q Consensus 139 ie~~~~~G~~~~IlYTGDf 157 (1176)
... .+.+||||.
T Consensus 130 ~~d-------~~~aFTGDa 141 (237)
T KOG0814|consen 130 EHD-------LRMAFTGDA 141 (237)
T ss_pred ecC-------cceeeecce
Confidence 764 479999994
No 103
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.73 E-value=0.08 Score=65.67 Aligned_cols=155 Identities=22% Similarity=0.259 Sum_probs=104.9
Q ss_pred ceEEEEEecceeEEEEEEeeCCe-EEEEcCC----CccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccC
Q 001045 979 KAFTCEYKYDGQRAQIHKLVDGT-VRIFSRN----GDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMS 1053 (1176)
Q Consensus 979 ~~f~~E~KyDGeR~QiH~~~~g~-V~ifSR~----g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~p 1053 (1176)
..|+||+|.||.=+-+.+. +|. ++--||. |+|+|....-|. .|+.-+...+..+-+=||++.- ...
T Consensus 109 ~~y~~EpKiDGlsisL~Ye-nG~Lv~aaTRGdG~~GEDiT~NvrtI~-~IP~~l~~~p~~lEVRGEvfm~-------k~~ 179 (667)
T COG0272 109 VEYVVEPKIDGLAISLVYE-NGKLVRAATRGDGTTGEDITANVRTIR-SIPLKLPGAPAVLEVRGEVFMP-------KED 179 (667)
T ss_pred cceEEEeecceEEEEEEEE-CCEEEEeeccCCCccccchhhhhhhHh-hhhhhccCCCceEEEEeEEEEe-------HHH
Confidence 4799999999999999994 554 7888885 789998765554 4554443346788999999983 246
Q ss_pred hHHHhhhhc--C----------------CCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCCC
Q 001045 1054 FQELSSRER--G----------------GKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKMG 1115 (1176)
Q Consensus 1054 Fq~L~~R~r--~----------------~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~~ 1115 (1176)
|+.+..... + ..+..+ ..+.++.+|++.+-+..+. ..-.+..++.+.|+++- -+...
T Consensus 180 F~~lN~~~~~~g~~~faNpRNaAAGsLRqlD~~i---ta~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~G-F~v~~ 254 (667)
T COG0272 180 FEALNEEREEEGEKPFANPRNAAAGSLRQLDPKI---TAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWG-FPVNP 254 (667)
T ss_pred HHHHHHHHHHhCCCCcCChhhhhhhhhhccCHHH---HhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcC-CCCCc
Confidence 777753311 0 001111 1245789999998766554 66677889999998874 12111
Q ss_pred cEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhC------CCceEEEecCC
Q 001045 1116 YFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHS------SCEGIIVKSLD 1162 (1176)
Q Consensus 1116 ~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~------g~EGlmvK~ld 1162 (1176)
... ...+.+++.++++...+. --.|+|+|--+
T Consensus 255 ~~~---------------~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~ 292 (667)
T COG0272 255 YTR---------------LCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVND 292 (667)
T ss_pred Hhh---------------hcCCHHHHHHHHHHHHhhcccCCCccceEEEEecc
Confidence 111 145789999999887764 45699999754
No 104
>PF14597 Lactamase_B_5: Metallo-beta-lactamase superfamily; PDB: 2P97_B.
Probab=94.36 E-value=0.037 Score=58.09 Aligned_cols=107 Identities=19% Similarity=0.183 Sum_probs=61.5
Q ss_pred CCCCeeE-eCCccEEEecCCcCC---------CCccEEEeccCChhhhCCcccCC--CCceEEeCHHHHHHHHHhhccCC
Q 001045 37 TFPPSKH-VPNTRFLIDAFRYAA---------DFSVSYFLSHFHSDHYTGLSPSW--SKGIIFCSEITSRLLSQILNINP 104 (1176)
Q Consensus 37 ~~p~~~~-ipg~~~liD~~~~~~---------~~i~avfITHaH~DHiggL~~l~--~~~pIY~s~~T~~ll~~~l~~~~ 104 (1176)
...|+.+ .|+.+++||.-.... ..+.+|+||| .||+..-.... ...+||++..-++. +.+..
T Consensus 22 dfng~~~~~p~GnilIDP~~ls~~~~~~l~a~ggv~~IvLTn--~dHvR~A~~ya~~~~a~i~~p~~d~~~----~p~~~ 95 (199)
T PF14597_consen 22 DFNGHAWRRPEGNILIDPPPLSAHDWKHLDALGGVAWIVLTN--RDHVRAAEDYAEQTGAKIYGPAADAAQ----FPLAC 95 (199)
T ss_dssp EEEEEEE--TT--EEES-----HHHHHHHHHTT--SEEE-SS--GGG-TTHHHHHHHS--EEEEEGGGCCC-----SS--
T ss_pred CceeEEEEcCCCCEEecCccccHHHHHHHHhcCCceEEEEeC--ChhHhHHHHHHHHhCCeeeccHHHHhh----CCCCC
Confidence 3445556 799999999964332 4789999996 68987644321 25688888776522 22222
Q ss_pred CceEEeCCCceEEECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCCCc
Q 001045 105 KFIYPLPIKIPVLIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFC 160 (1176)
Q Consensus 105 ~~i~~l~~~~~~~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~ 160 (1176)
-+.+..|+ ..+++++|..++-.|.||.++++++. ++++|||.-..
T Consensus 96 --D~~l~dge-~i~~g~~vi~l~G~ktpGE~ALlled--------~vLi~GDl~~~ 140 (199)
T PF14597_consen 96 --DRWLADGE-EIVPGLWVIHLPGSKTPGELALLLED--------RVLITGDLLRS 140 (199)
T ss_dssp --SEEE-TT--BSSTTEEEEEE-SSSSTTEEEEEETT--------TEEEESSSEEB
T ss_pred --ccccccCC-CccCceEEEEcCCCCCCceeEEEecc--------ceEEecceeee
Confidence 13444554 33588999999999999999999973 59999996433
No 105
>PHA02142 putative RNA ligase
Probab=94.31 E-value=0.51 Score=55.31 Aligned_cols=152 Identities=14% Similarity=0.174 Sum_probs=89.6
Q ss_pred ChhHHH-HhccCceEEEEEecceeEEEEEEe--------------------eCCeEEEEcCCCc---cCCCCchhHH---
Q 001045 968 GVPQVL-KLFQNKAFTCEYKYDGQRAQIHKL--------------------VDGTVRIFSRNGD---ETTSRFPDLI--- 1020 (1176)
Q Consensus 968 ~~~~~~-~~~~~~~f~~E~KyDGeR~QiH~~--------------------~~g~V~ifSR~g~---d~T~~ypdl~--- 1020 (1176)
++.+.+ .+..+..|++-.|+||-=|-+.+. ..+.+..-|||.. .-+..|.+++
T Consensus 157 n~~~~~~~~~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~~ 236 (366)
T PHA02142 157 NIFNRYKEKYADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVENY 236 (366)
T ss_pred hhhhhhhhhhcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHHc
Confidence 444443 235578899999999999888742 2567788999986 3233444432
Q ss_pred ---HHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCC
Q 001045 1021 ---SIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYT 1097 (1176)
Q Consensus 1021 ---~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~P 1097 (1176)
+.+.+ ...++.+=||+++-.-+.+ +. . -....|++|||-.++++. =++
T Consensus 237 ~i~~~l~~----~~~~iaIqGEl~Gp~IQ~N--------------------~~--~-~~~~~F~vF~v~~i~~~~--yl~ 287 (366)
T PHA02142 237 QIVDRLKE----LGMSVAIQGELMGPGIQKN--------------------RE--N-FDKYRIFAFRAWFIDEQR--FAT 287 (366)
T ss_pred CcHHHHHh----hCCcEEEEEEEecccccCc--------------------cc--c-CCCCceEEEEEEEeccce--eCC
Confidence 23333 3568999999998422110 00 0 002479999987777665 468
Q ss_pred HHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHh-----CCCceEEEecC
Q 001045 1098 LRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALH-----SSCEGIIVKSL 1161 (1176)
Q Consensus 1098 l~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~-----~g~EGlmvK~l 1161 (1176)
.++++++++++= +..++.+... ....... .++++++.|-- .-+||+|+|..
T Consensus 288 ~~e~~~~~~~~g-------l~~VPvL~~~---~~~~~~~---s~eE~L~~A~~p~~~~~~~EGiViKp~ 343 (366)
T PHA02142 288 DEEFQDLCRTLG-------MEIVPQLGYS---YPFQEFT---NVKEMLAAADIPSINHKIAEGVVYKSV 343 (366)
T ss_pred HHHHHHHHHHcC-------Cceeeeeccc---ccccccC---CHHHHHhhcCCCcccccccceEEEeec
Confidence 889999888764 1233332210 0000011 34555555421 33899999985
No 106
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=93.95 E-value=0.2 Score=62.27 Aligned_cols=89 Identities=19% Similarity=0.195 Sum_probs=73.9
Q ss_pred HHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHHHhhccc-cCcchhhHHHHHHHhhccCcccccccccc
Q 001045 828 KDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNLR-IGAMMRTILPALAQAVVMNSSLEFSHEGK 906 (1176)
Q Consensus 828 ~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiIlk~LR-iG~~~~tvl~aLa~A~~~~~~~~~~~~~~ 906 (1176)
.++-+.+++|++++ +...|.++|.++|+.+++.+.-|.++++++.+. .|++++.+.++++.+++.+.
T Consensus 2 ~~fa~~~~~i~~t~---~~~ek~~~l~~~~~~~~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~~g~~~--------- 69 (539)
T PRK09247 2 KAFAELLDRLDLTT---STNAKLALLADYFRSAPDPDRAWALALLTGGLPRRLVKTRLLRELAAERADLPP--------- 69 (539)
T ss_pred hHHHHHHHHHHhcc---CHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHHHCcCH---------
Confidence 35566777787655 467899999999999999999999999998875 89999999999999988764
Q ss_pred hhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhc
Q 001045 907 MENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMN 940 (1176)
Q Consensus 907 ~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~ 940 (1176)
..+.+.|....|++.++..+..
T Consensus 70 ------------~~~~~~~~~~GDlg~~~~~~~~ 91 (539)
T PRK09247 70 ------------WLFEESYDYVGDLAETIALLLP 91 (539)
T ss_pred ------------HHHHHHHHhcCCHHHHHHHhcc
Confidence 4556788888999998877754
No 107
>PF04675 DNA_ligase_A_N: DNA ligase N terminus; InterPro: IPR012308 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalysing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase, one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC), the latter being restricted to eubacteria. Eukaryotic, archaebacterial, viral and some eubacterial DNA ligases are ATP-dependent. The first step in the ligation reaction is the formation of a covalent enzyme-AMP complex. The co-factor ATP is cleaved to pyrophosphate and AMP, with the AMP being covalently joined to a highly conserved lysine residue in the active site of the ligase. The activated AMP residue is then transferred to the 5'phosphate of the nick, before the nick is sealed by phosphodiester-bond formation and AMP elimination [,]. Vertebrate cells encode three well-characterised DNA ligases (DNA ligases I, III and IV), all of which are related in structure and sequence. With the exception of the atypically small PBCV-1 viral enzyme, two regions of primary sequence are common to all members of the family. The catalytic region comprises six conserved sequence motifs (I, III, IIIa, IV, V-VI), motif I includes the lysine residue that is adenylated in the first step of the ligation reaction. The function of the second, less well-conserved region is unknown. When folded, each protein comprises of two distinct sub-domains: a large amino-terminal sub-domain ('domain 1') and a smaller carboxy-terminal sub-domain ('domain 2'). The ATP-binding site of the enzyme lies in the cleft between the two sub-domains. Domain 1 consists of two antiparallel beta sheets flanked by alpha helices, whereas domain 2 consists of a five-stranded beta barrel and a single alpha helix, which form the oligonucleotide-binding fold [, ]. This region is found in many but not all ATP-dependent DNA ligase enzymes (6.5.1.1 from EC). It is thought to be involved in DNA binding and in catalysis. In human DNA ligase I (P18858 from SWISSPROT), and in Saccharomyces cerevisiae (Baker's yeast) (P04819 from SWISSPROT), this region was necessary for catalysis, and separated from the amino terminus by targeting elements. In Vaccinia virus (P16272 from SWISSPROT) this region was not essential for catalysis, but deletion decreases the affinity for nicked DNA and decreased the rate of strand joining at a step subsequent to enzyme-adenylate formation []. ; GO: 0003677 DNA binding, 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 2CFM_A 3RR5_A 2HIX_A 2HIV_A 3L2P_A 1X9N_A 4EQ5_A 3GDE_A.
Probab=93.60 E-value=0.22 Score=52.62 Aligned_cols=91 Identities=21% Similarity=0.293 Sum_probs=66.8
Q ss_pred HHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhcchhhHHHHHHHHhhcc-------ccCcchhhHHHHHHHhhccCccc
Q 001045 827 IKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNL-------RIGAMMRTILPALAQAVVMNSSL 899 (1176)
Q Consensus 827 i~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiIlk~L-------RiG~~~~tvl~aLa~A~~~~~~~ 899 (1176)
..++-+.+++|++. .+...|.++|.+++..+.+.+..|.+..+++-+ ..|++++++.++++++++++.
T Consensus 3 F~~l~~l~~~l~~~---~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~-- 77 (177)
T PF04675_consen 3 FSDLCELFEKLEST---SSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPE-- 77 (177)
T ss_dssp HHHHHHHHHHHHT------HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-H--
T ss_pred HHHHHHHHHHHHhc---cCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCH--
Confidence 45667788888764 356789999999999999887777777777643 689999999999999998765
Q ss_pred ccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHhcc
Q 001045 900 EFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLMNK 941 (1176)
Q Consensus 900 ~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~~~ 941 (1176)
..+.+.|....|++.++..++..
T Consensus 78 -------------------~~~~~~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 78 -------------------KSIDESYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp -------------------HHHHHHHHHHS-HHHHHHHHHHH
T ss_pred -------------------HHHHHHHHhcCcHHHHHHHHHhh
Confidence 45566888899999999888754
No 108
>COG2015 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=93.59 E-value=0.2 Score=59.22 Aligned_cols=59 Identities=24% Similarity=0.240 Sum_probs=41.0
Q ss_pred CCCCeeEe-CCcc-EEEecC---------------CcCCCCccEEEeccCChhhhCCcccCCC-------CceEEeCHHH
Q 001045 37 TFPPSKHV-PNTR-FLIDAF---------------RYAADFSVSYFLSHFHSDHYTGLSPSWS-------KGIIFCSEIT 92 (1176)
Q Consensus 37 ~~p~~~~i-pg~~-~liD~~---------------~~~~~~i~avfITHaH~DHiggL~~l~~-------~~pIY~s~~T 92 (1176)
..+++-++ .++. |+||.. ..+..+|.+|+.||.|.||+||+-.+.. .++|.++..-
T Consensus 124 DisNITfveGdtg~IViDpL~t~~tA~aAldl~~~~~g~rPV~aVIYtHsH~DHfGGVkGiv~eadV~sGkV~iiAP~GF 203 (655)
T COG2015 124 DISNITFVEGDTGWIVIDPLVTPETAKAALDLYNQHRGQRPVVAVIYTHSHSDHFGGVKGIVSEADVKSGKVQIIAPAGF 203 (655)
T ss_pred cccceEEEcCCcceEEEcccCCcHHHHHHHHHHHHhcCCCCeEEEEeecccccccCCeeeccCHHHcccCceeEecchhH
Confidence 44555554 3443 678885 1234689999999999999999976432 5789988775
Q ss_pred HHH
Q 001045 93 SRL 95 (1176)
Q Consensus 93 ~~l 95 (1176)
.+-
T Consensus 204 me~ 206 (655)
T COG2015 204 MEE 206 (655)
T ss_pred HHH
Confidence 443
No 109
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=93.07 E-value=0.39 Score=59.30 Aligned_cols=92 Identities=16% Similarity=0.203 Sum_probs=80.8
Q ss_pred CcchHHHHHHHHHHHhhh---chHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHh
Q 001045 712 PAPYIHLARTFDLVEAER---GKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEAC 788 (1176)
Q Consensus 712 ~~~F~~l~~~~~~i~~t~---~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~ 788 (1176)
+.+-.++-..|++|...+ ++.+|.++|..++.+. +|.+.-+.+.++++.+. +|+++.++..|+++++
T Consensus 72 ~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~---~~~E~~~l~r~i~~~lR-------iGv~~~~v~~Ala~a~ 141 (508)
T PRK03180 72 TLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA---TEDEQRFLRRLLTGELR-------QGALDGVMADAVARAA 141 (508)
T ss_pred CCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC---CHHHHHHHHHHHhCCCc-------ccccHHHHHHHHHHHh
Confidence 566777777888888765 5588999999999986 89999999999988874 7999999999999999
Q ss_pred CCChHHHHHHHHhcCChHHHHHHHH
Q 001045 789 GTNRSKIRDMYNRLGDLGDVAQECR 813 (1176)
Q Consensus 789 g~~~~~i~~~~~~~GDlG~va~~~~ 813 (1176)
+++...+++.|.-.||++.++....
T Consensus 142 ~~~~~~v~~a~~~~~dl~~v~~~~l 166 (508)
T PRK03180 142 GVPAAAVRRAAMLAGDLPAVAAAAL 166 (508)
T ss_pred CCCHHHHHHHHHHcCCHHHHHHHHH
Confidence 9999999999999999999998665
No 110
>KOG3798 consensus Predicted Zn-dependent hydrolase (beta-lactamase superfamily) [General function prediction only]
Probab=92.41 E-value=0.7 Score=50.82 Aligned_cols=159 Identities=15% Similarity=0.165 Sum_probs=84.4
Q ss_pred CCccEEEeccCChhhhCCcccC-C--CCceE-EeCHHHHHHHHHhhccCCCceEEeCCCceEEE----CCEEEEEEecCC
Q 001045 59 DFSVSYFLSHFHSDHYTGLSPS-W--SKGII-FCSEITSRLLSQILNINPKFIYPLPIKIPVLI----DGCEVVLVGANH 130 (1176)
Q Consensus 59 ~~i~avfITHaH~DHiggL~~l-~--~~~pI-Y~s~~T~~ll~~~l~~~~~~i~~l~~~~~~~i----~~~~Vt~~~a~H 130 (1176)
+.++-+++||.|.||.-.-... + .+.++ |.+..-+..+. +-....+..+..+....+ +-++|-+.|+.|
T Consensus 131 p~~d~~~vsh~h~dhld~~~~~~~~~~~~~~wfvp~g~k~~m~---~~gc~~v~el~wwe~~~~vkn~~~~ti~~tPaqH 207 (343)
T KOG3798|consen 131 PDLDFAVVSHDHYDHLDADAVKKITDRNPQIWFVPLGMKKWME---GDGSSTVTELNWGESSEFVKNGKTYTIWCLPAQH 207 (343)
T ss_pred CCCceeccccccccccchHHHHhhhccCccceeehhhhhheec---CCCCCceeEeeccchhceecCCcEEEEEEcchhh
Confidence 5789999999999997543211 1 12233 23332222222 111222344444444333 237888899999
Q ss_pred -CcCc---------eEEEEEEcCCCCcccEEEEECCCCCcccccchhhhhccCCCcEEEEeCCCCCCCCCCCChHHHHHH
Q 001045 131 -CPGA---------VQFLFKVPGRNGGFERYVHTGDFRFCKTMLLQPVMNEFAGCDAVFLDTTYCNPKFLFPLQEESVEY 200 (1176)
Q Consensus 131 -~pGS---------~~flie~~~~~G~~~~IlYTGDfr~~~~~~~~~~l~~~~~vDvLI~EsTy~~~~~~~p~~~e~~~~ 200 (1176)
+--+ +++.+..+. .+++|.||+++++..... .-..|..+|+-.+=+.-..|.....+++-.-++
T Consensus 208 w~~R~L~D~Nk~LW~sw~v~g~~-----nrfffaGDTGyc~~~F~~-IgerfGpfdLAaiPiGaYePrWfmK~~HInPeE 281 (343)
T KOG3798|consen 208 WGQRGLFDRNKRLWSSWAVIGEN-----NRFFFAGDTGYCDGEFKK-IGERFGPFDLAAIPIGAYEPRWFMKSQHINPEE 281 (343)
T ss_pred hcccccccCCcceeeeeEEecCC-----ceEEecCCCCcccHHHHH-HHHhcCCcceeeccccccCchhhcccccCCHHH
Confidence 4332 345554432 589999999999853221 112345688866665533444333334333334
Q ss_pred HHHHHHHHhhhccccCCCeEEEEEeccccchH
Q 001045 201 VVNVVNRVGGELNEGLQKRVLFLVATYVIGKE 232 (1176)
Q Consensus 201 l~~~i~~~~~~~~~~~~g~vlvli~~~slGR~ 232 (1176)
++++-+..-.+ ...-|..++|.+|.+
T Consensus 282 av~Ihkdv~ar------ns~gIHWGTf~l~~E 307 (343)
T KOG3798|consen 282 AVEIHKDVRAK------NSIGIHWGTFHLGSE 307 (343)
T ss_pred HHHHHHHHhhh------cceeEeeeeeecccc
Confidence 44444443222 123367888887764
No 111
>PLN03113 DNA ligase 1; Provisional
Probab=90.34 E-value=1.4 Score=56.74 Aligned_cols=93 Identities=20% Similarity=0.205 Sum_probs=75.2
Q ss_pred CCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhc---chhhHHHHHHHHhhccc-------cCcchhhHHHHHHHh
Q 001045 823 PPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSC---REKEMKFLVRTLVRNLR-------IGAMMRTILPALAQA 892 (1176)
Q Consensus 823 ~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~---~~~E~k~LvRiIlk~LR-------iG~~~~tvl~aLa~A 892 (1176)
.++...++-+.|++|...++ ...|.++|.++|+.+ ++.+.-|.++++.+.+. +|++++.+.+|++.+
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~---rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~ 203 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETG---RIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEA 203 (744)
T ss_pred CCccHHHHHHHHHHHHhccC---HHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHH
Confidence 34667888888888887665 467899999999985 89999999999887764 599999999999999
Q ss_pred hccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHHh
Q 001045 893 VVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSLM 939 (1176)
Q Consensus 893 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L~ 939 (1176)
++.+. ..++..|....|++.|+..+.
T Consensus 204 ~g~~~---------------------~~ik~~y~~~GDlG~vA~~~~ 229 (744)
T PLN03113 204 FGRTE---------------------KQVKKQYKELGDLGLVAKASR 229 (744)
T ss_pred HCcCH---------------------HHHHHHHHHhCCHHHHHHhhh
Confidence 98764 346667777888888877554
No 112
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=87.96 E-value=2.1 Score=53.23 Aligned_cols=92 Identities=16% Similarity=0.232 Sum_probs=79.5
Q ss_pred CcchHHHHHHHHHHHhhh---chHHHHHHHHHHHHhhhcCCCCChhhHHHHhcccCCCCCcccccccchhhHHHHHHHHh
Q 001045 712 PAPYIHLARTFDLVEAER---GKIKAMSMLCNMFRSLLALSPDDVLPAVYLCTNKIASNHENIELNIGGSLVTSAIEEAC 788 (1176)
Q Consensus 712 ~~~F~~l~~~~~~i~~t~---~r~~k~~~L~~~~r~~~~~~p~dl~~~v~l~~~~l~P~~~~~elgige~~L~kal~~~~ 788 (1176)
+..-.++-.+|+.|.+.+ ++.+|.++|.++++.. +|.+.-+.+.++++.+. .|+++.++..++..++
T Consensus 54 ~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~---~~~e~k~l~r~i~~~lr-------iG~~~~~il~al~~~~ 123 (514)
T TIGR00574 54 PLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA---SPLEAKYLIRTILGDLR-------IGIAEKTILDALAKAF 123 (514)
T ss_pred CcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhcc-------cCccHHHHHHHHHHHh
Confidence 456677777888887765 5678999999999985 88999999998887763 6999999999999999
Q ss_pred CCChHHHHHHHHhcCChHHHHHHHH
Q 001045 789 GTNRSKIRDMYNRLGDLGDVAQECR 813 (1176)
Q Consensus 789 g~~~~~i~~~~~~~GDlG~va~~~~ 813 (1176)
+++...+.+.|+...|++.|+..+.
T Consensus 124 ~~~~~~~~~~~~~~~dl~~v~~~l~ 148 (514)
T TIGR00574 124 LLSHPDVERAFNLTNDLGKVAKILL 148 (514)
T ss_pred ccchHHHHHHHHhCCCHHHHHHHHH
Confidence 9999999999999999999999986
No 113
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=84.98 E-value=2.9 Score=45.70 Aligned_cols=145 Identities=20% Similarity=0.266 Sum_probs=98.8
Q ss_pred CceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHhhcCCCCCCeEEEEEEEEEecCCCCcccChHHH
Q 001045 978 NKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINEFCKPAAGTFILDAEVVAIDRKNGCKIMSFQEL 1057 (1176)
Q Consensus 978 ~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~~~~~~~~~~ILDGElVa~d~~~g~~~~pFq~L 1057 (1176)
+.+|++-.-==|-||.|.- ..|...-|.|+|..+ .+||...+--..--.+...=-||||= |++
T Consensus 115 sqdW~vv~~PvGKR~lvVa-SrG~Tvay~k~G~~v-~rF~S~LPGGnrr~~~a~~ytILDCI---y~e------------ 177 (325)
T KOG3132|consen 115 SQDWYVVARPVGKRCLVVA-SRGTTVAYVKNGSTV-HRFPSALPGGNRRKGPANSYTILDCI---YHE------------ 177 (325)
T ss_pred CcceEEEEeecCceEEEEe-cCCceEEEecCCeeE-eeccccCCCCCcCCCCcccceeeeee---ecc------------
Confidence 4689998888999999987 588888899999876 34554311000000111222566652 221
Q ss_pred hhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhhcccCC--------CcEEE--eEEEEEcC
Q 001045 1058 SSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLFYDEKM--------GYFQY--AKEMTVEG 1127 (1176)
Q Consensus 1058 ~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~~~~~~--------~~i~~--~~~~~v~~ 1127 (1176)
..-.|+|.|+|.++|.++.+.|..-|.=.|++-+. +.+ .++.+ ++...+
T Consensus 178 ------------------snQTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~-E~~~l~~~t~~~~f~Fs~vp~~pC-- 236 (325)
T KOG3132|consen 178 ------------------SNQTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLA-ETGALDPPTVYHKFRFSVVPFYPC-- 236 (325)
T ss_pred ------------------cCceEEEEEEEeecCcccccCchHHHHHHHhhhcc-ccccCCCCCcCccceecccCCCCC--
Confidence 12468999999999999999999999999998873 322 12333 333222
Q ss_pred CCCCCccccCHHHHHHHHHHHHhCCCceEEEecCCCCCCcccCC
Q 001045 1128 DDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSLDVDAGYSPSK 1171 (1176)
Q Consensus 1128 ~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~ld~~s~Y~pGk 1171 (1176)
+.+.+-+.+...+--...||.+=... -.|.||.
T Consensus 237 ---------~q~~l~~~~~~~~pf~~DGLLFYhks--~~yqpgq 269 (325)
T KOG3132|consen 237 ---------DQSGLHSAYTGSLPFVRDGLLFYHKS--VVYQPGQ 269 (325)
T ss_pred ---------CHHHHHHHHcCCCceeeeeEEEeecc--eeeCCCC
Confidence 46778888887777788999987765 6899995
No 114
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=83.20 E-value=0.77 Score=54.21 Aligned_cols=103 Identities=17% Similarity=0.158 Sum_probs=67.8
Q ss_pred ccCceEEEEEecceeEEEEEEeeCCeEEEEcCCCccCCCCchhHHHHHHh-hcCCCCCCeEEEEEEEEEecCCCCcccCh
Q 001045 976 FQNKAFTCEYKYDGQRAQIHKLVDGTVRIFSRNGDETTSRFPDLISIINE-FCKPAAGTFILDAEVVAIDRKNGCKIMSF 1054 (1176)
Q Consensus 976 ~~~~~f~~E~KyDGeR~QiH~~~~g~V~ifSR~g~d~T~~ypdl~~~l~~-~~~~~~~~~ILDGElVa~d~~~g~~~~pF 1054 (1176)
+.-..|.+++|.||.|...-++.++.+..|-|.....- -+-...++. .........++|||++. |.-++.
T Consensus 282 ~~~~~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~---~~~~~~~~~~~~~~~~~~tl~dge~~l-D~l~~~----- 352 (393)
T KOG2386|consen 282 LVFEYYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKG---RENLRKIREDSDTKVLHQTLLDGEMIL-DRLKEE----- 352 (393)
T ss_pred hhhhhhhhhhcccCcEEEEEecCCceeEechhhhHHHh---hhhhhcccccccchhhhhhhcccceec-cccccc-----
Confidence 33345678999999999888866666777776543321 100000000 00112345799999998 654320
Q ss_pred HHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHhh
Q 001045 1055 QELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDLF 1109 (1176)
Q Consensus 1055 q~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~~ 1109 (1176)
....+.++|++-.|++.+...|+. |.+.+++-+
T Consensus 353 ---------------------~~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~ev 385 (393)
T KOG2386|consen 353 ---------------------AIPRYLIYDMVRFNSQKVEKRPFS-RWQIIEKEV 385 (393)
T ss_pred ---------------------cchhheeeeeeeccCcccccCcch-HHHHHHHHh
Confidence 124578999999999999999999 998877655
No 115
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=82.72 E-value=1.4 Score=34.42 Aligned_cols=36 Identities=28% Similarity=0.400 Sum_probs=29.9
Q ss_pred hHhHHHHHhhhcCCcchhhHHHHHHHHhcccchhhhhccc
Q 001045 590 GEEIDQFLKIINGNESLKGYAATLLEKTKGNVSMALDLYY 629 (1176)
Q Consensus 590 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 629 (1176)
++.|+|++.+ | -++..+...|++++||+++|++..+
T Consensus 2 ~~~v~~L~~m--G--f~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 2 EEKLEQLLEM--G--FSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHc--C--CCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 4567778777 3 4599999999999999999998765
No 116
>KOG4736 consensus Uncharacterized conserved protein [Function unknown]
Probab=82.10 E-value=4.5 Score=45.86 Aligned_cols=106 Identities=14% Similarity=-0.008 Sum_probs=62.6
Q ss_pred CCccEEEecCCc-------CCCCccEEEeccCChhhhCCcccCCCCceEEeCHHHHHHHHHhhccCC-CceEEeCCCceE
Q 001045 45 PNTRFLIDAFRY-------AADFSVSYFLSHFHSDHYTGLSPSWSKGIIFCSEITSRLLSQILNINP-KFIYPLPIKIPV 116 (1176)
Q Consensus 45 pg~~~liD~~~~-------~~~~i~avfITHaH~DHiggL~~l~~~~pIY~s~~T~~ll~~~l~~~~-~~i~~l~~~~~~ 116 (1176)
.+..+++|.+-. ..+.|+.+.+||.|.+|++.+...... |+ +...+..... ..-..++.+...
T Consensus 103 ~~~v~v~~~gls~lak~~vt~d~i~~vv~t~~~~~hlgn~~~f~~s-p~--------l~~s~e~~gr~~~pt~l~e~~~~ 173 (302)
T KOG4736|consen 103 GGDVVVVDTGLSVLAKEGVTLDQIDSVVITHKSPGHLGNNNLFPQS-PI--------LYHSMEYIGRHVTPTELDERPYL 173 (302)
T ss_pred CCceEEEecCCchhhhcCcChhhcceeEEeccCcccccccccccCC-HH--------HhhhhhhcCCccChhhhccCCcc
Confidence 344567777622 127899999999999999987543221 11 1122211111 112234444555
Q ss_pred EECCEEEEEEecCCCcCceEEEEEEcCCCCcccEEEEECCCCCccc
Q 001045 117 LIDGCEVVLVGANHCPGAVQFLFKVPGRNGGFERYVHTGDFRFCKT 162 (1176)
Q Consensus 117 ~i~~~~Vt~~~a~H~pGS~~flie~~~~~G~~~~IlYTGDfr~~~~ 162 (1176)
++++.-+-.--.||.+-+...+++..+.- ++++||||+-....
T Consensus 174 ~l~~~~~V~~TpGht~~~isvlv~n~~~~---GTv~itGDLf~~~~ 216 (302)
T KOG4736|consen 174 KLSPNVEVWKTPGHTQHDISVLVHNVDLY---GTVAITGDLFPREE 216 (302)
T ss_pred ccCCceeEeeCCCCCCcceEEEEEeeccc---ceEEEEeecccCCc
Confidence 66543333345688888888888875533 59999999855443
No 117
>TIGR02306 RNA_lig_DRB0094 RNA ligase, DRB0094 family. The member of this family from Deinococcus radiodurans, a species that withstands and recovers from extensive radiation or dessication damage, is an apparent RNA ligase. It repairs RNA stand breaks in nicked DNA:RNA and RNA:RNA but not DNA:DNA duplexes. It has adenylyltransferase activity associated with the C-terminal domain. Related proteins also in this family are found in Streptomyces avermitilis MA-4680 and in bacteriophage 44RR2.8t. The phage example is unsurprising since one mechanism of host cell defense against phage is cleavage and inactivation of certain tRNA molecules. A fungal sequence from Neurospora crassa scores between trusted and noise cutofffs and may be similar in function.
Probab=81.86 E-value=19 Score=42.28 Aligned_cols=105 Identities=16% Similarity=0.110 Sum_probs=61.4
Q ss_pred CceEEEEEecceeEEEEEEee-CCeEE-----EEcCCCc---cCCCCchhH------HHHHHhhcCCCCCCeEEEEEEEE
Q 001045 978 NKAFTCEYKYDGQRAQIHKLV-DGTVR-----IFSRNGD---ETTSRFPDL------ISIINEFCKPAAGTFILDAEVVA 1042 (1176)
Q Consensus 978 ~~~f~~E~KyDGeR~QiH~~~-~g~V~-----ifSR~g~---d~T~~ypdl------~~~l~~~~~~~~~~~ILDGElVa 1042 (1176)
+..|++-.|+||-=|-+.+.. .+.+. +-|||.+ +-+..|... .+.+.+. ....++.+=||+++
T Consensus 158 ~~~~~~TeKldGss~tv~~~~~~~~~~~~~~Gvcsr~~~l~~~~~~~~W~~a~~~~i~~~l~~~--~~~~~vaiqGEl~G 235 (341)
T TIGR02306 158 GEKVAKTEKLHGTSITVAWVTDEERFLVLSKGVASRNLVLRENADNKYWKAVENYQIVDRAKAA--ELRMSVAIFGEVMG 235 (341)
T ss_pred CceEEEEEEecceeEEEEEecCCcccccccceeecCCcccccCCCchhHHHHHhcChHHHHhhc--ccCceEEEEEEEeC
Confidence 578999999999998777632 22222 3478876 333445443 3333321 24567889999997
Q ss_pred EecCCCCcccChHHHhhhhcCCCCchhhhcccccceEEEEEEeeeeCCcccccCCHHHHHHHHHHh
Q 001045 1043 IDRKNGCKIMSFQELSSRERGGKDSVITIKSVKVDICVFVFDIMFANGEQLLGYTLRQRRKYLKDL 1108 (1176)
Q Consensus 1043 ~d~~~g~~~~pFq~L~~R~r~~~~~~i~~~~~~~~v~~~vFDiL~lnG~~Ll~~Pl~eRr~lL~~~ 1108 (1176)
..- |.. .- ....+-.+++|++ +..|+. .=++.+++.++++++
T Consensus 236 ~gI------------Q~n-~Y---------g~~~~~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~ 277 (341)
T TIGR02306 236 PGI------------QKN-RY---------GFDKYRTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTL 277 (341)
T ss_pred ccc------------cCC-cC---------CCCCCceEEEEEE-EEcCcc-eecCHHHHHHHHHhc
Confidence 321 111 00 0011122788887 555443 235889999888874
No 118
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=79.96 E-value=2.6 Score=33.85 Aligned_cols=39 Identities=21% Similarity=0.450 Sum_probs=33.9
Q ss_pred HHHHHHHhhhccccccHHHHHHhHhhcCCchHHhhhhhhh
Q 001045 455 EKMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVSNFYE 494 (1176)
Q Consensus 455 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 (1176)
+.+++.|.++.|.| +.+.+...|..++||+..|+..+.+
T Consensus 2 ~~~v~~L~~mFP~~-~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 2 EEMVQQLQEMFPDL-DREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHHHHHHHHHSSSS--HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHHHHHHHHHCCCC-CHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 57889999999987 5667999999999999999998876
No 119
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=78.42 E-value=2.2 Score=33.05 Aligned_cols=35 Identities=31% Similarity=0.396 Sum_probs=29.5
Q ss_pred hHhHHHHHhhhcCCcchhhHHHHHHHHhcccchhhhhcc
Q 001045 590 GEEIDQFLKIINGNESLKGYAATLLEKTKGNVSMALDLY 628 (1176)
Q Consensus 590 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 628 (1176)
++.|+|++.+ | -.+..|...|++++||+++|++..
T Consensus 2 ~~~v~~L~~m---G-f~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEM---G-FSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHc---C-CCHHHHHHHHHHhCCCHHHHHHHH
Confidence 5677888887 3 678899999999999999998764
No 120
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=73.26 E-value=4.5 Score=31.55 Aligned_cols=35 Identities=29% Similarity=0.416 Sum_probs=29.2
Q ss_pred hhHhHHHHHhhhcCCcchhhHHHHHHHHhcccchhhhhc
Q 001045 589 YGEEIDQFLKIINGNESLKGYAATLLEKTKGNVSMALDL 627 (1176)
Q Consensus 589 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 627 (1176)
+++.|.|++.+ | =++..|...|..+.||+++|++.
T Consensus 2 ~~~~v~~L~~m--G--f~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 2 DEEKVQQLMEM--G--FSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HHHHHHHHHHH--T--S-HHHHHHHHHHTTTSHHHHHHH
T ss_pred CHHHHHHHHHc--C--CCHHHHHHHHHHcCCCHHHHHHh
Confidence 35778899998 4 57789999999999999999974
No 121
>PF13691 Lactamase_B_4: tRNase Z endonuclease
Probab=71.29 E-value=7 Score=34.59 Aligned_cols=39 Identities=15% Similarity=0.157 Sum_probs=31.4
Q ss_pred CCCeeE-eCCccEEE-ecCC----------cCCCCccEEEeccCC-hhhhCC
Q 001045 38 FPPSKH-VPNTRFLI-DAFR----------YAADFSVSYFLSHFH-SDHYTG 76 (1176)
Q Consensus 38 ~p~~~~-ipg~~~li-D~~~----------~~~~~i~avfITHaH-~DHigg 76 (1176)
.|+..+ .+..++++ +++. ....++.+||||+.+ .|++||
T Consensus 12 ~p~l~l~~d~~rYlFGn~gEGtQR~~~e~~ikl~kl~~IFlT~~~~w~~~GG 63 (63)
T PF13691_consen 12 GPSLLLFFDSRRYLFGNCGEGTQRACNEHKIKLSKLNDIFLTGLSSWENIGG 63 (63)
T ss_pred CCEEEEEeCCceEEeccCCcHHHHHHHHcCCCccccceEEECCCCcccccCC
Confidence 378877 78889999 8862 222789999999999 999986
No 122
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=70.27 E-value=6.2 Score=30.79 Aligned_cols=34 Identities=21% Similarity=0.273 Sum_probs=29.1
Q ss_pred HHHHHHHHhhhccccccHHHHHHhHhhcCCchHHhhh
Q 001045 454 TEKMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVS 490 (1176)
Q Consensus 454 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 490 (1176)
.++.+++|.++ .+++++....|..++||+..|+.
T Consensus 2 ~~~~v~~L~~m---Gf~~~~~~~AL~~~~~nve~A~~ 35 (37)
T PF00627_consen 2 DEEKVQQLMEM---GFSREQAREALRACNGNVERAVD 35 (37)
T ss_dssp HHHHHHHHHHH---TS-HHHHHHHHHHTTTSHHHHHH
T ss_pred CHHHHHHHHHc---CCCHHHHHHHHHHcCCCHHHHHH
Confidence 46778888777 89999999999999999999985
No 123
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=67.50 E-value=35 Score=42.71 Aligned_cols=92 Identities=18% Similarity=0.263 Sum_probs=67.9
Q ss_pred CCCcHHHHHHHHHHhhhhcCCCchHHHHHHHHHHHhhc---chhhH---HHHH-HHHh---hccccCcchhhHHHHHHHh
Q 001045 823 PPLLIKDVYSMLCKISVQTGSGSTARKKSLIVNLMCSC---REKEM---KFLV-RTLV---RNLRIGAMMRTILPALAQA 892 (1176)
Q Consensus 823 ~~LTi~eV~~~L~~IA~~~g~~s~~~K~~il~~Ll~~~---~~~E~---k~Lv-RiIl---k~LRiG~~~~tvl~aLa~A 892 (1176)
...+-.+|-.+|.+|...+|. .+-..++.++|+.. +|.+. =||. .-|- ..+.+|+++.++++|++.|
T Consensus 97 ~~~py~~~a~tF~kIe~~s~R---l~i~~il~n~f~~v~~~sP~dLlp~vYLsiN~l~P~yeGlELGvGes~l~KAi~Ea 173 (714)
T KOG0967|consen 97 SKVPYLELARTFEKIEETSGR---LEIIDILSNFLRSVLATSPDDLLPTVYLSINKLAPDYEGLELGVGESLLMKAIAEA 173 (714)
T ss_pred CcCcHHHHHHHHHHHHhhccc---eeHHHHHHHHHHHHHhcCchhhhhHHHHhhhccCccccCccccccHHHHHHHHHHH
Confidence 456778899999999888764 33456776776653 45443 2443 2333 3588999999999999999
Q ss_pred hccCcccccccccchhHHHHHHHHHHHHHHHHHhhCCChHHHHHHH
Q 001045 893 VVMNSSLEFSHEGKMENLKEKLQSLSAAAVEAYNILPSLDLLIPSL 938 (1176)
Q Consensus 893 ~~~~~~~~~~~~~~~~~~~~~l~~~~~~v~~ay~~~pdl~~v~~~L 938 (1176)
++.+. ..++.-|+...||+.|+...
T Consensus 174 tGrt~---------------------~~vk~~~~~~GDLG~VA~~s 198 (714)
T KOG0967|consen 174 TGRTL---------------------SHVKNQYNKLGDLGLVAQGS 198 (714)
T ss_pred hCccH---------------------HHHHHHHHhcCcHHHHHhhc
Confidence 98765 57889999999999998544
No 124
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=66.87 E-value=8 Score=31.30 Aligned_cols=37 Identities=5% Similarity=0.289 Sum_probs=28.2
Q ss_pred HHHHHHhhhccccccHHHHHHhHhhcCCchHHhhhhhhh
Q 001045 456 KMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVSNFYE 494 (1176)
Q Consensus 456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 (1176)
+++.+...+-. ++.+....+|..+++|+..||+.||+
T Consensus 2 e~i~~F~~iTg--~~~~~A~~~L~~~~wdle~Av~~y~~ 38 (43)
T PF14555_consen 2 EKIAQFMSITG--ADEDVAIQYLEANNWDLEAAVNAYFD 38 (43)
T ss_dssp HHHHHHHHHH---SSHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHC--cCHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 34444444443 48899999999999999999999998
No 125
>PF13483 Lactamase_B_3: Beta-lactamase superfamily domain; PDB: 1VJN_B 3KL7_A.
Probab=60.80 E-value=11 Score=39.15 Aligned_cols=34 Identities=29% Similarity=0.420 Sum_probs=25.2
Q ss_pred CeeEEEEeecCC--CCHHHHHHHHHHcCCCEEEEEe
Q 001045 317 AFEIHLVPYSEH--SNYDELREYVKFLKPKRVIPTV 350 (1176)
Q Consensus 317 ~~~v~~i~~SgH--As~~EL~~~V~~lrPk~VIPvH 350 (1176)
.+.+..++.+|. .+.++..++++.++|+.|||+|
T Consensus 128 ~vDvl~~p~~g~~~~~~~~a~~~~~~l~pk~viP~H 163 (163)
T PF13483_consen 128 KVDVLFLPVGGPFTMGPEEAAELAERLKPKLVIPMH 163 (163)
T ss_dssp S-SEEEEE--TTTS--HHHHHHHHHHCT-SEEEEES
T ss_pred CCCEEEecCCCCcccCHHHHHHHHHHcCCCEEEeCC
Confidence 466777888884 6899999999999999999999
No 126
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=56.27 E-value=16 Score=29.39 Aligned_cols=40 Identities=13% Similarity=0.465 Sum_probs=34.2
Q ss_pred HHHHHHHHhhhccccccHHHHHHhHhhcCCchHHhhhhhhh
Q 001045 454 TEKMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVSNFYE 494 (1176)
Q Consensus 454 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 494 (1176)
.++++..|.++.|. ++..++...|..++||+..|+..+.+
T Consensus 2 ~~~~v~~L~~mFP~-l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 2 NDEALHDLKDMFPN-LDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred hHHHHHHHHHHCCC-CCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 45788899999986 56778999999999999999998865
No 127
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=53.04 E-value=20 Score=27.79 Aligned_cols=35 Identities=9% Similarity=0.182 Sum_probs=28.0
Q ss_pred HHHHHHhhhccccccHHHHHHhHhhcCCchHHhhhhhh
Q 001045 456 KMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVSNFY 493 (1176)
Q Consensus 456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 493 (1176)
+.+++|.+ +.+++++....|..++||+..|+.-++
T Consensus 3 ~~v~~L~~---mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 3 EKLEQLLE---MGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHH---cCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 34555544 489999999999999999999987654
No 128
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=51.86 E-value=21 Score=27.49 Aligned_cols=34 Identities=9% Similarity=0.222 Sum_probs=26.8
Q ss_pred HHHHHHhhhccccccHHHHHHhHhhcCCchHHhhhhh
Q 001045 456 KMVQEIRNCLPTWVTQNQILDLISSSGRNIVDAVSNF 492 (1176)
Q Consensus 456 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 492 (1176)
+.+++|.++ .+++++....|...+||+.+|+.-+
T Consensus 3 ~~v~~L~~m---Gf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 3 EKIDQLLEM---GFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHc---CCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 445555444 8999999999999999999887644
No 129
>KOG1135 consensus mRNA cleavage and polyadenylation factor II complex, subunit CFT2 (CPSF subunit) [RNA processing and modification]
Probab=47.98 E-value=26 Score=44.09 Aligned_cols=65 Identities=12% Similarity=0.182 Sum_probs=49.6
Q ss_pred cCCeeEEEEeecCCCCHHHHHHHHHHcCCCEEEEEecCCCCcCchHHHHHHHHHHHHHHHHhhhhHHhhhhccccCc
Q 001045 315 KDAFEIHLVPYSEHSNYDELREYVKFLKPKRVIPTVGMDIEKLDSKHANKMRKYFAGLVDEMASKKEFLMGFHRGTS 391 (1176)
Q Consensus 315 ~~~~~v~~i~~SgHAs~~EL~~~V~~lrPk~VIPvHG~~~e~~~~~E~~~m~k~f~~l~~~~~~k~~fl~~~~~~~~ 391 (1176)
...|++..+-|=|-++.+-++.++..++|+++|.|||... +.+.|.++++.+.-. ..++|.|+.-
T Consensus 534 ~vs~~v~~iDyeGisDgrSik~ii~ql~Pr~lIlvh~s~e------~~r~~~~~c~~l~~~------~~~vyaP~~~ 598 (764)
T KOG1135|consen 534 EVSCRVEKIDYEGISDGRSIKKIIAQLSPRKLILVHGSAE------DTRDLKHTCASLGCF------TIDVYAPKSG 598 (764)
T ss_pred EEEEEEEEeeeeccccchhHHHHHhccCccEEEEecCCch------hhHHHHHHHHhcCCC------cceeeccccc
Confidence 3467888999999999999999999999999999999653 346666666644321 2567776654
No 130
>PF12706 Lactamase_B_2: Beta-lactamase superfamily domain; PDB: 3BV6_F 1WW1_A 2E7Y_A 3RPC_D 3ZWF_A 3JXP_A 1XTO_A 2CBN_A 3G1P_B 3P2U_A ....
Probab=42.23 E-value=21 Score=37.53 Aligned_cols=25 Identities=36% Similarity=0.355 Sum_probs=24.5
Q ss_pred cCCCCHHHHHHHHHHcCCCEEEEEe
Q 001045 326 SEHSNYDELREYVKFLKPKRVIPTV 350 (1176)
Q Consensus 326 SgHAs~~EL~~~V~~lrPk~VIPvH 350 (1176)
++|++.+++.++++.++|+++||+|
T Consensus 169 ~~h~~~~~~~~~~~~~~~~~~il~H 193 (194)
T PF12706_consen 169 PGHMTLEEALELAKELKAKKVILIH 193 (194)
T ss_dssp TTSBBHHHHHHHHHHHTTSEEEEES
T ss_pred CCCCCHHHHHHHHHHcCCCEEEEEC
Confidence 8899999999999999999999999
No 131
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=38.73 E-value=84 Score=34.00 Aligned_cols=85 Identities=14% Similarity=0.173 Sum_probs=56.0
Q ss_pred hcCChHHHHHHHHhhccccCCCCCCcHHHHHHHHHHhhhh-cCCCchHHHHHHHHHHHhhcchhhHHHHHHHHhhcc---
Q 001045 801 RLGDLGDVAQECRQTQALLAPPPPLLIKDVYSMLCKISVQ-TGSGSTARKKSLIVNLMCSCREKEMKFLVRTLVRNL--- 876 (1176)
Q Consensus 801 ~~GDlG~va~~~~~~q~~l~~~~~LTi~eV~~~L~~IA~~-~g~~s~~~K~~il~~Ll~~~~~~E~k~LvRiIlk~L--- 876 (1176)
-+||...+++.++..-..+. .+|..-.++.+.+.+--.. .........+.-+..+|..+|+.|...|-+++.|-+
T Consensus 84 GhgDIpmaV~AmK~GAvDFL-eKP~~~q~Lldav~~Al~~~~~~~~~~~~~~~~~~~l~tLT~RERqVl~~vV~G~~NKq 162 (202)
T COG4566 84 GHGDIPMAVQAMKAGAVDFL-EKPFSEQDLLDAVERALARDASRRAEADRQAAIRARLATLTPRERQVLDLVVRGLMNKQ 162 (202)
T ss_pred CCCChHHHHHHHHcchhhHH-hCCCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCHHHHHHHHHHHcCcccHH
Confidence 36899999988886533222 4566666665555543211 111122334567889999999999888888887654
Q ss_pred ---ccCcchhhHH
Q 001045 877 ---RIGAMMRTIL 886 (1176)
Q Consensus 877 ---RiG~~~~tvl 886 (1176)
-+|++++||-
T Consensus 163 IA~dLgiS~rTVe 175 (202)
T COG4566 163 IAFDLGISERTVE 175 (202)
T ss_pred HHHHcCCchhhHH
Confidence 2688888886
No 132
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=31.90 E-value=41 Score=26.94 Aligned_cols=40 Identities=18% Similarity=0.302 Sum_probs=32.4
Q ss_pred hhHhHHHHHhhhcCCcchhhHHHHHHHHhcccchhhhhcccc
Q 001045 589 YGEEIDQFLKIINGNESLKGYAATLLEKTKGNVSMALDLYYD 630 (1176)
Q Consensus 589 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 630 (1176)
|.+.|+++..|.+. -.++.....|++..|||+.|++....
T Consensus 1 ~~~~v~~L~~mFP~--~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 1 REEMVQQLQEMFPD--LDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp CHHHHHHHHHHSSS--S-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred CHHHHHHHHHHCCC--CCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 35678888888875 47889999999999999999987654
No 133
>KOG1137 consensus mRNA cleavage and polyadenylation factor II complex, BRR5 (CPSF subunit) [RNA processing and modification]
Probab=28.86 E-value=23 Score=43.48 Aligned_cols=97 Identities=12% Similarity=0.057 Sum_probs=63.7
Q ss_pred CCccEEEeccCChhhhCCcccCCC----C-----ceEEeCHHHHHHHHHhhccCCCc--eEEeC--CCc---eEEECCEE
Q 001045 59 DFSVSYFLSHFHSDHYTGLSPSWS----K-----GIIFCSEITSRLLSQILNINPKF--IYPLP--IKI---PVLIDGCE 122 (1176)
Q Consensus 59 ~~i~avfITHaH~DHiggL~~l~~----~-----~pIY~s~~T~~ll~~~l~~~~~~--i~~l~--~~~---~~~i~~~~ 122 (1176)
....++-++|.|.||.+.|++... + .|||+...+.+|+..+..++... .+.++ +-. ..-.+-++
T Consensus 206 estygv~~h~~r~~re~rlt~vIh~~v~rGGR~L~PvFAlgrAqELllildeyw~~h~~l~~iPiyyaSslakkcm~vfQ 285 (668)
T KOG1137|consen 206 ESTYGVQIHEPREEREGRLTWVIHSTVPRGGRVLIPVFALGRAQELLLILDEYWGNHVDLRDIPIYYASSLAKKCMGVFQ 285 (668)
T ss_pred EeeeeEEecCchHHhhhhhhhhHHhhccCCCceEeeeeecchHHHHHHHHHHHhhcchhhhcCceeehhhHHHhhhhhHh
Confidence 356789999999999999987432 3 69999999999998776544321 12111 111 11134567
Q ss_pred EEEEecCC-CcCceE----EEEEEcCCCCcccEEEEECCCCCccc
Q 001045 123 VVLVGANH-CPGAVQ----FLFKVPGRNGGFERYVHTGDFRFCKT 162 (1176)
Q Consensus 123 Vt~~~a~H-~pGS~~----flie~~~~~G~~~~IlYTGDfr~~~~ 162 (1176)
..+.-.+| ++...+ |.|.. .++|.+||...+..
T Consensus 286 tyv~~mnd~Irk~~~~~Npfifk~-------vs~L~~~D~f~D~g 323 (668)
T KOG1137|consen 286 TYVNMMNDRIRKQSALRNPFIFKH-------VSILRTGDWFDDEG 323 (668)
T ss_pred eehhhhhhhhHHhhccCCceEeec-------cccccccccccccC
Confidence 77777888 665444 34443 48999999865543
No 134
>PRK00685 metal-dependent hydrolase; Provisional
Probab=27.22 E-value=75 Score=34.56 Aligned_cols=34 Identities=26% Similarity=0.355 Sum_probs=27.5
Q ss_pred eEEEEee--cCCCCHHHHHHHHHHcCCCEEEEEecC
Q 001045 319 EIHLVPY--SEHSNYDELREYVKFLKPKRVIPTVGM 352 (1176)
Q Consensus 319 ~v~~i~~--SgHAs~~EL~~~V~~lrPk~VIPvHG~ 352 (1176)
.+..++. ..|.+.+|..++++.++|+.+||+|-.
T Consensus 159 D~~~~~~~~~~h~~~~ea~~~~~~~~~k~~v~~H~~ 194 (228)
T PRK00685 159 DVALLPIGDNFTMGPEDAALAVELIKPKIVIPMHYN 194 (228)
T ss_pred CEEEEecCCccccCHHHHHHHHHhhCCCEEEEeccC
Confidence 3333444 349999999999999999999999974
No 135
>KOG3592 consensus Microtubule-associated proteins [Cytoskeleton]
Probab=23.99 E-value=36 Score=42.94 Aligned_cols=37 Identities=19% Similarity=0.212 Sum_probs=29.4
Q ss_pred eCCccEEEecCCc----------CCCCccEEEeccCChhhhCCcccC
Q 001045 44 VPNTRFLIDAFRY----------AADFSVSYFLSHFHSDHYTGLSPS 80 (1176)
Q Consensus 44 ipg~~~liD~~~~----------~~~~i~avfITHaH~DHiggL~~l 80 (1176)
+.|+++|++.|.- +.++|++|||||.-.|..+||..+
T Consensus 55 vnGf~iLv~GgserKS~fwklVrHldrVdaVLLthpg~dNLpginsl 101 (934)
T KOG3592|consen 55 VNGFNILVNGGSERKSCFWKLVRHLDRVDAVLLTHPGADNLPGINSL 101 (934)
T ss_pred ecceEEeecCCcccccchHHHHHHHhhhhhhhhcccccCccccchHH
Confidence 6777788887732 126899999999999999998764
No 136
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=23.73 E-value=99 Score=24.81 Aligned_cols=39 Identities=15% Similarity=0.281 Sum_probs=31.5
Q ss_pred hHhHHHHHhhhcCCcchhhHHHHHHHHhcccchhhhhcccc
Q 001045 590 GEEIDQFLKIINGNESLKGYAATLLEKTKGNVSMALDLYYD 630 (1176)
Q Consensus 590 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 630 (1176)
.+.++++.+|.+. -.+..+...|+..+||++.|++....
T Consensus 3 ~~~v~~L~~mFP~--l~~~~I~~~L~~~~g~ve~~i~~LL~ 41 (43)
T smart00546 3 DEALHDLKDMFPN--LDEEVIKAVLEANNGNVEATINNLLE 41 (43)
T ss_pred HHHHHHHHHHCCC--CCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 3567888888664 47888899999999999999987654
No 137
>PRK11709 putative L-ascorbate 6-phosphate lactonase; Provisional
Probab=23.19 E-value=97 Score=36.85 Aligned_cols=25 Identities=20% Similarity=0.223 Sum_probs=23.9
Q ss_pred CCCCHHHHHHHHHHcCCCEEEEEec
Q 001045 327 EHSNYDELREYVKFLKPKRVIPTVG 351 (1176)
Q Consensus 327 gHAs~~EL~~~V~~lrPk~VIPvHG 351 (1176)
.|.+.+|..++++.++|+.+||+|=
T Consensus 259 ~hm~p~ea~~~a~~l~ak~vIpiH~ 283 (355)
T PRK11709 259 DKMTSIDILRMAESLNAKVVIPVHH 283 (355)
T ss_pred CCCCHHHHHHHHHHcCCCEEEEECh
Confidence 4999999999999999999999996
No 138
>PF00701 DHDPS: Dihydrodipicolinate synthetase family; InterPro: IPR002220 Dihydropicolinate synthase (DHDPS) is the key enzyme in lysine biosynthesis via the diaminopimelate pathway of prokaryotes, some phycomycetes and higher plants. The enzyme catalyses the condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a ping-pong mechanism in which pyruvate binds to the enzyme by forming a Schiff-base with a lysine residue []. Three other proteins are structurally related to DHDPS and probably also act via a similar catalytic mechanism. These are Escherichia coli N-acetylneuraminate lyase (4.1.3.3 from EC) (gene nanA), which catalyzes the condensation of N-acetyl-D-mannosamine and pyruvate to form N-acetylneuraminate; Rhizobium meliloti (Sinorhizobium meliloti) protein mosA [], which is involved in the biosynthesis of the rhizopine 3-o-methyl-scyllo-inosamine; and E. coli hypothetical protein yjhH. The sequences of DHDPS from different sources are well-conserved. The structure takes the form of a homotetramer, in which 2 monomers are related by an approximate 2-fold symmetry []. Each monomer comprises 2 domains: an 8-fold alpha-/beta-barrel, and a C-terminal alpha-helical domain. The fold resembles that of N-acetylneuraminate lyase. The active site lysine is located in the barrel domain, and has access via 2 channels on the C-terminal side of the barrel.; GO: 0016829 lyase activity, 0008152 metabolic process; PDB: 3B4U_B 3S8H_A 3QZE_B 1XXX_F 3L21_F 3IRD_A 3A5F_B 3G0S_B 3DAQ_C 3UQN_A ....
Probab=21.83 E-value=2.5e+02 Score=32.11 Aligned_cols=67 Identities=13% Similarity=0.189 Sum_probs=47.5
Q ss_pred EeeeeCCc--ccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecC
Q 001045 1084 DIMFANGE--QLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSL 1161 (1176)
Q Consensus 1084 DiL~lnG~--~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~l 1161 (1176)
|-+++.|. ....++..||+++++.++ ....+++.+.-.+. ..+.++..++.+.+.+.|..|+|+=.+
T Consensus 37 ~gl~~~GstGE~~~Lt~~Er~~l~~~~~-~~~~~~~~vi~gv~----------~~st~~~i~~a~~a~~~Gad~v~v~~P 105 (289)
T PF00701_consen 37 DGLVVLGSTGEFYSLTDEERKELLEIVV-EAAAGRVPVIAGVG----------ANSTEEAIELARHAQDAGADAVLVIPP 105 (289)
T ss_dssp SEEEESSTTTTGGGS-HHHHHHHHHHHH-HHHTTSSEEEEEEE----------SSSHHHHHHHHHHHHHTT-SEEEEEES
T ss_pred CEEEECCCCcccccCCHHHHHHHHHHHH-HHccCceEEEecCc----------chhHHHHHHHHHHHhhcCceEEEEecc
Confidence 33555552 456789999999999998 45556655544443 346788889999999999999999654
No 139
>cd00408 DHDPS-like Dihydrodipicolinate synthase family. A member of the class I aldolases, which use an active-site lysine which stablilzes a reaction intermediate via Schiff base formation, and have TIM beta/alpha barrel fold. The dihydrodipicolinate synthase family comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways and includes such proteins as N-acetylneuraminate lyase, MosA protein, 5-keto-4-deoxy-glucarate dehydratase, trans-o-hydroxybenzylidenepyruvate hydratase-aldolase, trans-2'-carboxybenzalpyruvate hydratase-aldolase, and 2-keto-3-deoxy- gluconate aldolase. The family is also referred to as the N-acetylneuraminate lyase (NAL) family.
Probab=21.68 E-value=2.1e+02 Score=32.37 Aligned_cols=66 Identities=12% Similarity=0.156 Sum_probs=46.3
Q ss_pred eeeeCCc--ccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecC
Q 001045 1085 IMFANGE--QLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSL 1161 (1176)
Q Consensus 1085 iL~lnG~--~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~l 1161 (1176)
-++++|. ....++..||+++++.+. ....+++.+.-.+. ..+.++..++-+.+.+.|..|+|+=.+
T Consensus 34 gi~~~GstGE~~~ls~~Er~~l~~~~~-~~~~~~~~vi~gv~----------~~~~~~~i~~a~~a~~~Gad~v~v~pP 101 (281)
T cd00408 34 GLVVLGTTGEAPTLTDEERKEVIEAVV-EAVAGRVPVIAGVG----------ANSTREAIELARHAEEAGADGVLVVPP 101 (281)
T ss_pred EEEECCCCcccccCCHHHHHHHHHHHH-HHhCCCCeEEEecC----------CccHHHHHHHHHHHHHcCCCEEEECCC
Confidence 3455552 345678999999999998 44445555443321 245677888888999999999999654
No 140
>cd00950 DHDPS Dihydrodipicolinate synthase (DHDPS) is a key enzyme in lysine biosynthesis. It catalyzes the aldol condensation of L-aspartate-beta- semialdehyde and pyruvate to dihydropicolinic acid via a Schiff base formation between pyruvate and a lysine residue. The functional enzyme is a homotetramer consisting of a dimer of dimers. DHDPS is member of dihydrodipicolinate synthase family that comprises several pyruvate-dependent class I aldolases that use the same catalytic step to catalyze different reactions in different pathways.
Probab=21.26 E-value=2e+02 Score=32.67 Aligned_cols=67 Identities=7% Similarity=0.080 Sum_probs=48.3
Q ss_pred EeeeeCCc--ccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecC
Q 001045 1084 DIMFANGE--QLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSL 1161 (1176)
Q Consensus 1084 DiL~lnG~--~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~l 1161 (1176)
|-++++|. ....++..||+++++.+. ....+++.+.-.+. ..+.++..++-+.+.+.|.-|+|+=.+
T Consensus 36 ~gl~v~GstGE~~~lt~~Er~~l~~~~~-~~~~~~~~vi~gv~----------~~~~~~~~~~a~~a~~~G~d~v~~~~P 104 (284)
T cd00950 36 DGLVVCGTTGESPTLSDEEHEAVIEAVV-EAVNGRVPVIAGTG----------SNNTAEAIELTKRAEKAGADAALVVTP 104 (284)
T ss_pred CEEEECCCCcchhhCCHHHHHHHHHHHH-HHhCCCCcEEeccC----------CccHHHHHHHHHHHHHcCCCEEEEccc
Confidence 44556652 346789999999999998 44455554432221 245678888999999999999999876
No 141
>PRK00055 ribonuclease Z; Reviewed
Probab=20.78 E-value=99 Score=34.39 Aligned_cols=29 Identities=28% Similarity=0.043 Sum_probs=26.8
Q ss_pred ecCCCCHHHHHHHHHHcCCCEEEEEecCC
Q 001045 325 YSEHSNYDELREYVKFLKPKRVIPTVGMD 353 (1176)
Q Consensus 325 ~SgHAs~~EL~~~V~~lrPk~VIPvHG~~ 353 (1176)
..+|++.+|..++.+.++|++++++|-..
T Consensus 207 ~~~H~~~~~a~~~~~~~~~~~~vl~H~~~ 235 (270)
T PRK00055 207 EYGHSTARQAAEIAKEAGVKRLILTHFSP 235 (270)
T ss_pred hcCCCCHHHHHHHHHHcCCCEEEEEeecc
Confidence 57899999999999999999999999854
No 142
>PRK03170 dihydrodipicolinate synthase; Provisional
Probab=20.09 E-value=2.2e+02 Score=32.61 Aligned_cols=65 Identities=11% Similarity=0.132 Sum_probs=46.5
Q ss_pred eeeCCc--ccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecC
Q 001045 1086 MFANGE--QLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSL 1161 (1176)
Q Consensus 1086 L~lnG~--~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~l 1161 (1176)
++++|. ....++..||+++++.+. ....+++.+.-.+. ..+.++..++-+.+.+.|..|+|+=.+
T Consensus 39 i~~~Gs~GE~~~ls~~Er~~~~~~~~-~~~~~~~~vi~gv~----------~~~~~~~i~~a~~a~~~G~d~v~~~pP 105 (292)
T PRK03170 39 LVVVGTTGESPTLTHEEHEELIRAVV-EAVNGRVPVIAGTG----------SNSTAEAIELTKFAEKAGADGALVVTP 105 (292)
T ss_pred EEECCcCCccccCCHHHHHHHHHHHH-HHhCCCCcEEeecC----------CchHHHHHHHHHHHHHcCCCEEEECCC
Confidence 444542 346789999999999998 44556555443321 235678888889999999999999765
No 143
>TIGR02313 HpaI-NOT-DapA 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents a subset of the DapA (dihydrodipicolinate synthase) family which has apparently evolved a separate function. The product of DapA, dihydrodipicolinate, results from the non-enzymatic cyclization and dehydration of 6-amino-2,4-dihydroxyhept-2-ene-1,7-dioic acid, which is different from the substrate of this reaction only in the presence of the amino group. In the absence of this amino group, and running the reaction in the opposite direction, the reaction corresponds to the HpaI aldolase component of the 4-hydroxyphenylacetic acid catabolism pathway (see TIGR02311). At present, this variant of DapA is found only in Oceanobacillus iheyensis HTE831 and Thermus thermophilus HB27. In both of these cases, one or more other DapA genes can be found and the one identified by this model is part of an operon for 4-hydroxyphenylacetic acid catabolism.
Probab=20.05 E-value=2.3e+02 Score=32.67 Aligned_cols=65 Identities=14% Similarity=0.200 Sum_probs=46.7
Q ss_pred eeeCC--cccccCCHHHHHHHHHHhhcccCCCcEEEeEEEEEcCCCCCCccccCHHHHHHHHHHHHhCCCceEEEecC
Q 001045 1086 MFANG--EQLLGYTLRQRRKYLKDLFYDEKMGYFQYAKEMTVEGDDNCLTSDVSLSKINNFLEEALHSSCEGIIVKSL 1161 (1176)
Q Consensus 1086 L~lnG--~~Ll~~Pl~eRr~lL~~~~~~~~~~~i~~~~~~~v~~~~~~~~~~~~~eei~~~~~~ai~~g~EGlmvK~l 1161 (1176)
++.+| -....++..||+++++.++ ....+++.+.-.+. ..+.++..++-+.+.+.|..|+|+=.+
T Consensus 38 i~v~GstGE~~~Ls~~Er~~l~~~~~-~~~~g~~pvi~gv~----------~~~t~~ai~~a~~A~~~Gad~v~v~pP 104 (294)
T TIGR02313 38 ISVGGTSGEPGSLTLEERKQAIENAI-DQIAGRIPFAPGTG----------ALNHDETLELTKFAEEAGADAAMVIVP 104 (294)
T ss_pred EEECccCcccccCCHHHHHHHHHHHH-HHhCCCCcEEEECC----------cchHHHHHHHHHHHHHcCCCEEEEcCc
Confidence 44555 2345689999999999998 45566665543322 245667778888899999999999865
Done!