Query 001083
Match_columns 1160
No_of_seqs 417 out of 2315
Neff 6.7
Searched_HMMs 46136
Date Thu Mar 28 15:21:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/001083.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/001083hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0966 ATP-dependent DNA liga 100.0 4E-149 9E-154 1301.3 62.4 851 3-910 1-881 (881)
2 PLN03113 DNA ligase 1; Provisi 100.0 5E-100 1E-104 931.0 55.8 552 5-605 127-731 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 2.3E-97 5E-102 905.6 53.6 545 7-605 1-583 (590)
4 KOG0967 ATP-dependent DNA liga 100.0 4.3E-95 9E-100 832.4 36.8 552 5-604 97-704 (714)
5 TIGR00574 dnl1 DNA ligase I, A 100.0 1.2E-89 2.7E-94 828.9 50.9 495 62-601 1-513 (514)
6 PRK09247 ATP-dependent DNA lig 100.0 3.6E-88 7.7E-93 815.1 51.2 523 9-603 1-537 (539)
7 PRK03180 ligB ATP-dependent DN 100.0 6.4E-88 1.4E-92 806.8 50.7 493 7-601 1-506 (508)
8 PHA02587 30 DNA ligase; Provis 100.0 1.1E-60 2.3E-65 570.5 41.5 447 13-599 3-485 (488)
9 COG1793 CDC9 ATP-dependent DNA 100.0 1.4E-58 3E-63 543.8 32.3 422 100-601 18-443 (444)
10 TIGR02779 NHEJ_ligase_lig DNA 100.0 2.6E-54 5.6E-59 488.4 33.3 288 243-592 10-297 (298)
11 PRK09632 ATP-dependent DNA lig 100.0 9E-54 1.9E-58 523.6 32.8 307 218-592 455-761 (764)
12 PRK08224 ligC ATP-dependent DN 100.0 1.7E-51 3.6E-56 471.5 33.5 315 217-592 2-330 (350)
13 PRK05972 ligD ATP-dependent DN 100.0 1.1E-50 2.4E-55 500.4 32.7 304 222-592 232-536 (860)
14 PRK09633 ligD ATP-dependent DN 100.0 1.7E-49 3.8E-54 480.8 32.2 310 224-601 1-317 (610)
15 PRK07636 ligB ATP-dependent DN 100.0 8.4E-45 1.8E-49 405.3 31.5 272 224-583 3-274 (275)
16 cd07900 Adenylation_DNA_ligase 100.0 7.6E-44 1.6E-48 385.7 23.0 213 216-446 2-219 (219)
17 TIGR02776 NHEJ_ligase_prk DNA 100.0 3E-42 6.4E-47 413.7 26.0 257 271-592 1-258 (552)
18 cd07903 Adenylation_DNA_ligase 100.0 2.9E-41 6.2E-46 368.3 21.9 214 215-447 3-224 (225)
19 cd07902 Adenylation_DNA_ligase 100.0 1.9E-40 4.2E-45 358.2 22.1 206 216-446 6-213 (213)
20 cd07901 Adenylation_DNA_ligase 100.0 3.5E-40 7.5E-45 355.1 22.5 205 220-445 1-207 (207)
21 PRK09125 DNA ligase; Provision 100.0 1.1E-39 2.4E-44 364.8 25.6 253 224-585 28-281 (282)
22 PHA00454 ATP-dependent DNA lig 100.0 5.8E-39 1.2E-43 365.6 29.8 285 225-584 7-314 (315)
23 cd07897 Adenylation_DNA_ligase 100.0 1E-38 2.2E-43 343.4 21.0 202 222-446 3-206 (207)
24 cd08039 Adenylation_DNA_ligase 100.0 2.2E-38 4.8E-43 345.1 22.4 201 234-446 11-235 (235)
25 cd07898 Adenylation_DNA_ligase 100.0 2.9E-38 6.2E-43 338.8 22.5 200 224-445 1-201 (201)
26 PF01068 DNA_ligase_A_M: ATP d 100.0 1.7E-37 3.8E-42 332.7 18.2 200 226-443 1-202 (202)
27 cd07905 Adenylation_DNA_ligase 100.0 1.2E-36 2.6E-41 324.3 19.9 191 224-445 1-193 (194)
28 cd07906 Adenylation_DNA_ligase 100.0 6.7E-36 1.5E-40 317.7 19.1 189 224-444 1-189 (190)
29 cd07967 OBF_DNA_ligase_III The 100.0 6E-32 1.3E-36 270.8 14.8 137 450-596 2-139 (139)
30 cd07896 Adenylation_kDNA_ligas 100.0 3.8E-30 8.2E-35 269.9 15.4 173 224-444 1-174 (174)
31 PF04675 DNA_ligase_A_N: DNA l 100.0 3.5E-29 7.5E-34 263.3 13.1 169 7-187 1-177 (177)
32 cd06846 Adenylation_DNA_ligase 100.0 2.4E-28 5.2E-33 258.1 18.0 178 225-444 1-182 (182)
33 cd07968 OBF_DNA_ligase_IV The 100.0 1.1E-27 2.3E-32 241.8 15.0 139 450-594 1-140 (140)
34 cd07969 OBF_DNA_ligase_I The O 99.9 2.2E-26 4.8E-31 232.8 15.7 134 450-602 1-143 (144)
35 KOG4437 ATP-dependent DNA liga 99.9 1.4E-24 3E-29 233.3 19.1 318 7-346 155-482 (482)
36 cd07972 OBF_DNA_ligase_Arch_Li 99.9 5.6E-25 1.2E-29 217.0 14.2 121 451-598 1-121 (122)
37 cd07895 Adenylation_mRNA_cappi 99.9 8.6E-25 1.9E-29 237.1 14.6 173 239-444 35-215 (215)
38 cd07893 OBF_DNA_ligase The Oli 99.9 7.3E-24 1.6E-28 210.9 14.8 122 451-591 1-129 (129)
39 cd07971 OBF_DNA_ligase_LigD Th 99.8 1.3E-18 2.8E-23 170.2 13.9 114 452-591 2-115 (115)
40 PF04679 DNA_ligase_A_C: ATP d 99.7 1.2E-17 2.7E-22 158.4 11.3 97 467-586 1-97 (97)
41 cd08040 OBF_DNA_ligase_family 99.7 3.1E-17 6.7E-22 158.7 13.0 108 451-583 1-108 (108)
42 cd07894 Adenylation_RNA_ligase 99.6 2.6E-15 5.6E-20 172.1 15.0 162 245-446 48-218 (342)
43 cd07970 OBF_DNA_ligase_LigC Th 99.6 7.1E-15 1.5E-19 144.9 13.4 120 451-592 1-121 (122)
44 PF00533 BRCT: BRCA1 C Terminu 99.1 9.4E-11 2E-15 105.7 7.9 74 654-728 2-78 (78)
45 PF01331 mRNA_cap_enzyme: mRNA 99.0 9.2E-11 2E-15 125.3 1.8 173 242-443 13-192 (192)
46 smart00292 BRCT breast cancer 99.0 1.7E-09 3.7E-14 96.6 8.1 76 656-731 1-80 (80)
47 KOG1929 Nucleotide excision re 99.0 4.6E-09 1E-13 130.3 14.1 185 654-915 6-192 (811)
48 KOG3524 Predicted guanine nucl 98.9 2.7E-09 5.9E-14 126.1 9.1 183 653-914 114-296 (850)
49 cd08041 OBF_kDNA_ligase_like T 98.9 4.8E-09 1E-13 95.3 8.3 76 452-583 2-77 (77)
50 cd00027 BRCT Breast Cancer Sup 98.8 1.4E-08 3.1E-13 88.6 7.6 70 660-729 1-72 (72)
51 COG5226 CEG1 mRNA capping enzy 98.8 1E-08 2.2E-13 111.2 7.9 183 242-459 59-257 (404)
52 PF00533 BRCT: BRCA1 C Terminu 98.7 2.3E-08 5E-13 90.1 7.5 75 801-898 3-78 (78)
53 KOG3226 DNA repair protein [Re 98.6 2.5E-08 5.3E-13 110.4 4.5 94 650-745 310-404 (508)
54 COG1423 ATP-dependent DNA liga 98.6 7.9E-07 1.7E-11 99.1 14.8 152 241-432 84-240 (382)
55 smart00292 BRCT breast cancer 98.5 2.1E-07 4.5E-12 83.1 7.7 76 803-901 2-80 (80)
56 TIGR01209 RNA ligase, Pab1020 98.5 8.9E-07 1.9E-11 101.8 14.5 151 242-429 76-229 (374)
57 PF12738 PTCB-BRCT: twin BRCT 98.5 1.1E-07 2.3E-12 82.9 4.8 62 661-723 1-63 (63)
58 PRK07956 ligA NAD-dependent DN 98.3 4.6E-05 9.9E-10 95.6 23.8 74 657-730 590-664 (665)
59 cd00027 BRCT Breast Cancer Sup 98.3 1.9E-06 4E-11 75.1 7.5 71 806-899 1-72 (72)
60 KOG3548 DNA damage checkpoint 98.2 1.9E-06 4.1E-11 105.2 8.0 88 655-745 923-1038(1176)
61 TIGR00575 dnlj DNA ligase, NAD 98.2 9.7E-05 2.1E-09 92.6 22.1 68 655-722 582-650 (652)
62 KOG1929 Nucleotide excision re 98.1 5E-06 1.1E-10 103.9 9.1 178 654-859 100-285 (811)
63 cd09232 Snurportin-1_C C-termi 98.0 6.6E-05 1.4E-09 79.7 12.6 176 225-445 5-186 (186)
64 PF11411 DNA_ligase_IV: DNA li 98.0 4.6E-06 1E-10 63.0 2.6 35 747-781 1-35 (36)
65 KOG2481 Protein required for n 97.8 1E-05 2.2E-10 94.0 4.0 79 655-739 325-413 (570)
66 PF14743 DNA_ligase_OB_2: DNA 97.8 1.5E-05 3.2E-10 70.2 4.0 37 463-510 2-38 (66)
67 COG0272 Lig NAD-dependent DNA 97.8 0.0028 6.2E-08 77.7 24.7 73 656-728 593-666 (667)
68 PLN03122 Poly [ADP-ribose] pol 97.7 9E-05 2E-09 93.6 8.7 87 654-742 186-278 (815)
69 KOG2481 Protein required for n 97.6 5.6E-05 1.2E-09 88.1 4.9 82 801-913 325-417 (570)
70 smart00532 LIGANc Ligase N fam 97.5 0.0011 2.3E-08 79.5 14.6 196 246-472 104-332 (441)
71 COG5163 NOP7 Protein required 97.5 7.2E-05 1.6E-09 84.2 3.9 79 655-739 348-437 (591)
72 PF12738 PTCB-BRCT: twin BRCT 97.5 0.00012 2.6E-09 63.7 4.2 62 807-893 1-63 (63)
73 cd00114 LIGANc NAD+ dependent 97.3 0.0023 4.9E-08 73.4 13.1 168 246-439 102-299 (307)
74 KOG3226 DNA repair protein [Re 97.3 0.00047 1E-08 77.3 6.7 90 801-915 315-405 (508)
75 PRK08097 ligB NAD-dependent DN 97.2 0.0048 1E-07 75.7 14.9 209 224-472 95-329 (562)
76 COG5163 NOP7 Protein required 97.1 0.00046 1E-08 77.9 4.5 83 801-914 348-442 (591)
77 PRK14351 ligA NAD-dependent DN 97.0 0.0077 1.7E-07 76.0 15.1 194 245-472 132-359 (689)
78 PF01653 DNA_ligase_aden: NAD- 97.0 0.00033 7.2E-09 80.5 2.7 160 246-430 108-293 (315)
79 PLN03123 poly [ADP-ribose] pol 97.0 0.0014 3E-08 84.9 7.7 86 653-739 389-478 (981)
80 PRK14350 ligA NAD-dependent DN 96.6 0.023 5E-07 71.5 14.8 226 246-510 111-364 (669)
81 KOG4362 Transcriptional regula 96.6 0.0075 1.6E-07 74.2 9.8 193 657-903 474-680 (684)
82 PRK01109 ATP-dependent DNA lig 96.6 0.0087 1.9E-07 74.9 10.5 97 4-114 112-211 (590)
83 TIGR02307 RNA_lig_RNL2 RNA lig 96.5 0.029 6.2E-07 64.3 12.9 106 242-367 22-145 (325)
84 PLN03122 Poly [ADP-ribose] pol 96.4 0.0067 1.4E-07 77.2 8.3 95 800-914 186-280 (815)
85 PRK14350 ligA NAD-dependent DN 95.9 0.016 3.4E-07 73.0 7.9 74 655-728 591-665 (669)
86 PLN03123 poly [ADP-ribose] pol 95.8 0.015 3.2E-07 75.7 7.1 90 801-912 391-481 (981)
87 PF09414 RNA_ligase: RNA ligas 95.8 0.016 3.4E-07 61.7 6.2 106 246-367 2-129 (186)
88 PRK14351 ligA NAD-dependent DN 95.6 0.029 6.3E-07 70.9 8.2 76 655-730 607-684 (689)
89 COG5275 BRCT domain type II [G 95.4 0.049 1.1E-06 57.6 7.7 81 649-729 148-230 (276)
90 KOG2093 Translesion DNA polyme 95.3 0.019 4.1E-07 71.4 5.3 200 651-912 41-245 (1016)
91 PRK06063 DNA polymerase III su 95.3 0.036 7.7E-07 64.1 7.2 74 654-728 229-305 (313)
92 PRK06195 DNA polymerase III su 95.3 0.036 7.8E-07 64.0 7.1 75 654-728 217-306 (309)
93 PHA02142 putative RNA ligase 93.8 0.69 1.5E-05 54.1 13.0 103 242-367 166-298 (366)
94 KOG2043 Signaling protein SWIF 93.4 0.18 4E-06 65.1 8.2 127 675-850 671-799 (896)
95 KOG2043 Signaling protein SWIF 91.9 0.17 3.7E-06 65.4 5.1 72 831-915 671-742 (896)
96 TIGR02306 RNA_lig_DRB0094 RNA 91.0 2 4.3E-05 50.2 12.0 153 244-444 158-335 (341)
97 KOG3132 m3G-cap-specific nucle 87.1 3 6.4E-05 45.4 8.9 172 226-441 101-277 (325)
98 PRK09247 ATP-dependent DNA lig 87.1 0.96 2.1E-05 56.3 6.2 82 127-208 2-91 (539)
99 KOG3548 DNA damage checkpoint 84.6 1.3 2.8E-05 56.1 5.4 32 884-915 1008-1039(1176)
100 PRK03180 ligB ATP-dependent DN 83.1 6.1 0.00013 48.9 10.5 93 6-114 72-167 (508)
101 KOG0966 ATP-dependent DNA liga 82.6 2.2 4.7E-05 53.7 6.1 89 800-909 630-719 (881)
102 PF04675 DNA_ligase_A_N: DNA l 82.2 1.7 3.7E-05 45.8 4.6 84 126-209 3-100 (177)
103 KOG4362 Transcriptional regula 79.3 2.4 5.2E-05 53.0 5.1 82 654-735 584-682 (684)
104 PLN03113 DNA ligase 1; Provisi 74.5 6.4 0.00014 50.7 7.1 86 122-207 127-229 (744)
105 KOG2386 mRNA capping enzyme, g 70.0 2.6 5.7E-05 49.7 2.1 93 245-367 285-384 (393)
106 TIGR00574 dnl1 DNA ligase I, A 66.8 17 0.00037 45.2 8.3 93 5-113 53-148 (514)
107 PRK06195 DNA polymerase III su 64.0 22 0.00048 41.2 8.1 48 802-859 219-267 (309)
108 KOG0323 TFIIF-interacting CTD 63.4 3.7 8.1E-05 51.4 1.7 84 655-738 439-527 (635)
109 KOG3524 Predicted guanine nucl 61.0 5.1 0.00011 49.7 2.2 75 655-731 208-283 (850)
110 COG4566 TtrR Response regulato 56.4 39 0.00085 36.2 7.5 81 101-181 84-174 (202)
111 PRK07956 ligA NAD-dependent DN 55.2 30 0.00066 44.3 7.8 225 246-509 109-366 (665)
112 PF02178 AT_hook: AT hook moti 52.9 5.9 0.00013 23.9 0.5 12 971-982 1-12 (13)
113 PRK06063 DNA polymerase III su 50.2 45 0.00097 38.8 7.6 75 801-898 230-305 (313)
114 KOG0323 TFIIF-interacting CTD 49.6 15 0.00033 46.1 3.8 95 801-915 439-534 (635)
115 TIGR00575 dnlj DNA ligase, NAD 43.6 44 0.00096 42.8 6.7 225 246-510 97-355 (652)
116 COG0272 Lig NAD-dependent DNA 40.2 66 0.0014 40.8 7.2 195 245-471 109-336 (667)
117 COG5275 BRCT domain type II [G 39.1 86 0.0019 34.0 6.8 54 799-862 152-206 (276)
118 PF09511 RNA_lig_T4_1: RNA lig 38.0 2.4E+02 0.0053 30.9 10.6 32 246-277 46-78 (221)
119 KOG2093 Translesion DNA polyme 32.2 46 0.00099 42.9 4.1 89 800-915 44-134 (1016)
120 PF14909 SPATA6: Spermatogenes 26.2 1.5E+02 0.0033 30.3 5.9 58 540-602 11-70 (140)
121 PF15101 DUF4557: Domain of un 25.8 1.6E+02 0.0035 31.8 6.2 70 675-747 14-92 (212)
122 smart00384 AT_hook DNA binding 24.4 42 0.0009 24.2 1.1 13 971-983 1-13 (26)
123 cd00950 DHDPS Dihydrodipicolin 23.0 1.7E+02 0.0037 33.2 6.4 67 343-426 36-104 (284)
No 1
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=4.2e-149 Score=1301.34 Aligned_cols=851 Identities=41% Similarity=0.694 Sum_probs=701.7
Q ss_pred CCCCCcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCC----chHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHh
Q 001083 3 KTEETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS----VDYFSALRLILPSLDRERGSYGLKESVLANCLIDAL 78 (1160)
Q Consensus 3 ~~~~~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~----~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~ 78 (1160)
||+++.|+.+|++|+.|+.+.....|++++++++++|+.+ +|+||++||++|++||+|+.||||+..|+++|+++|
T Consensus 1 ~~~~~~F~~~~~~f~~i~~t~~~~~k~~~~~k~~~s~~~~~e~~sd~y~~lRL~lp~lDReR~~Yglket~La~l~i~~l 80 (881)
T KOG0966|consen 1 MASPQNFSEVVDFFNKIRRTSNVKSKQAKFRKNFESWCRPCEVGSDMYVALRLILPDLDRERGSYGLKETVLARLYIRAL 80 (881)
T ss_pred CCCccccchHHHHHHHHHHhhhhHhHHHHHhhccccccccccCCcchhhhhhhcccchhhcccccCchHHHHHHHHHHHh
Confidence 6899999999999999999999999999999999999876 999999999999999999999999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcCCC-CCCCcHHHHHHHHHHHHhhhhHHHHH-HHHHHHHHhC
Q 001083 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI-SGGLTIKELNDLLDRLASSENRAEKI-SVLSTLIKKT 156 (1160)
Q Consensus 79 gl~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~-~~~LTi~eVn~~Ld~LA~~~~~~~k~-~il~~ll~~~ 156 (1160)
++|++|.||++|.||+.++.+. |||+.++++++++|+... ++.|||.|||++||.||+......+. ..|..|+++|
T Consensus 81 ~lprds~Da~rL~nwr~~~~~~--Gdfs~i~~~vl~~R~~~~~s~alTi~evN~lLD~LA~~~~~~~~~~~~l~~lv~~~ 158 (881)
T KOG0966|consen 81 HLPRDSADAVRLKNWRASTGAR--GDFSLILYEVLQRRCENPSSGALTIKEVNDLLDSLASGPSEDGKKFKKLSQLVEQC 158 (881)
T ss_pred cCCCCcHHHHHHHhhccCCCcC--ccHHHHHHHHHHHHhcCCCCCceeHHHHHHHHHHHcCCchhhhhhhHHHHHHHHhC
Confidence 9999999999999999987755 999999999999999654 44599999999999999887655443 7899999999
Q ss_pred CHHHHHHHHHHHhhhhccCCcccccccccCccHHHHHhhhCCHHHHHHHHhhhhccccccc--cccCCccccccccccCC
Q 001083 157 NAQEMKWIIMIILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQD--IEVGKAVRPQLAMRIGD 234 (1160)
Q Consensus 157 t~~E~k~l~RiIlkdLriGi~e~til~~~hpda~~~~~~~~DL~~V~~~L~~~~~~~~~~~--i~~g~p~~PmLA~~~~~ 234 (1160)
||.|+|||+|||||++++|++|++||.+|||||.++|++|+||+.||+.|+||+.+++..+ |++|..|+||||++...
T Consensus 159 S~~ElkWliriiLK~lklG~se~~Il~vfHPdA~dl~~vtsDLk~Vc~~L~Dp~~~l~~~~~~i~lfsa~~PqLa~~~~~ 238 (881)
T KOG0966|consen 159 SPLELKWLIRIILKNLKLGASEKKILSVFHPDAQDLYNVTSDLKAVCKKLYDPSVGLKELDEDIELFSAFRPQLAQKQKL 238 (881)
T ss_pred CHHHHHHHHHHHHHhhhcCCccchhhhhcCccHHHHHHHhhhHHHHHHHhcCCccCccccccceeehhhcCHHHHhhhcc
Confidence 9999999999999999999999999999999999999999999999999999999998887 99999999999999877
Q ss_pred hH-HHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCc-----chhh-HHHHHHHhc--ccCceeeceeEEE
Q 001083 235 AH-AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-----YGHA-MSKIIEQNV--LVDRCILDGEMLV 305 (1160)
Q Consensus 235 ~~-~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~-----~~~~-l~~~l~~~~--~~~~~ILDGElv~ 305 (1160)
.. +++++|++.+||+|+|+||||+|+|++|+.++||||||.|||. +..+ +...+...+ ....||||||||+
T Consensus 239 ~~~~~~e~m~~~~f~lEtK~DGERiQlHk~g~~~~yfSRNg~dyT~~yg~s~~~g~lt~~i~~~f~~~v~~cILDGEMm~ 318 (881)
T KOG0966|consen 239 GDWAIIEKMGGQDFYLETKFDGERIQLHKDGGEYKYFSRNGNDYTYEYGASYAHGTLTQRIHGAFNKEVESCILDGEMMT 318 (881)
T ss_pred chHHHHHHhcCCceEEEeeccCceEEEEecCCEEEEEecCCcchhhhcCcccccccccHHHHhhhhhcchheEecceEEE
Confidence 66 6789999999999999999999999999999999999999993 2222 223332222 2789999999999
Q ss_pred EeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001083 306 WDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 385 (1160)
Q Consensus 306 ~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 385 (1160)
||+.+.+|+|||+++++...... +.+.+ +||+|||+||+||++|.+.||.+|+++|..++.+.+++++|+
T Consensus 319 wD~~~~~f~~~G~~~dik~~~~~--~~~~q-p~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~------- 388 (881)
T KOG0966|consen 319 WDTKTKRFCPFGSNSDIKELSSR--DGSQQ-PCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIV------- 388 (881)
T ss_pred eecchhhhccCCchhhHHHhhcc--ccCCC-ceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEe-------
Confidence 99999999999999988766542 23344 999999999999999999999999999999999999998764
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccccc-CCCcccEEEEEEEeCC
Q 001083 386 SHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGS 464 (1160)
Q Consensus 386 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~-~g~~lDlvIIG~~~G~ 464 (1160)
++..+++.++|+++|++||++|.||||+|.++|.|.||.|+++|+|+||+|+. +|+++|++|||||||.
T Consensus 389 ----------~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y~pg~R~~gW~K~KPeYlkg~g~dLD~lIiGgy~G~ 458 (881)
T KOG0966|consen 389 ----------RSEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSYVPGQRSNGWIKLKPEYLKGFGEDLDLLIIGGYYGR 458 (881)
T ss_pred ----------ehhhcccHHHHHHHHHHHHhcCCCceEEeccCcccCccccCCCcEeecHHHHhhcCccccEEEEecccCC
Confidence 24567899999999999999999999999999999999999999999999999 5899999999999999
Q ss_pred CCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCC-cccccCCCCCCCcE
Q 001083 465 GRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS-FYQVTNNSKERPDV 543 (1160)
Q Consensus 465 Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~-~~~~~~~~~~~Pdv 543 (1160)
|+++|.+.+|+||+.+...++.+|.+|.++|+||+|+|++|+..+.++|++||.. ..+. +||. ++..+ ...||+
T Consensus 459 g~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v~~klr~~w~~-~~~~-apP~s~l~~t---k~~Pd~ 533 (881)
T KOG0966|consen 459 GDRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTVREKLRGHWKP-TSLE-APPESFLFGT---KKIPDV 533 (881)
T ss_pred CCCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHHHHhhhhhccc-cccc-CCCHHHHhcc---cCCCce
Confidence 9999999999999998777777899999999999999999999999999999987 2444 4554 44433 347999
Q ss_pred EEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHHHccCCCcccccccCCCCCCCCc
Q 001083 544 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPK 623 (1160)
Q Consensus 544 wi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~el~~~~~~~~~~~~~~~~~~~~~~~ 623 (1160)
||+ |..|+|++|++ ++++.+..|.++|||||||+.++|+||+|+||+|+++|.++...+. ++.+.+. +++
T Consensus 534 wI~-P~~SiIlqika-a~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~~-------~d~~~~~-kk~ 603 (881)
T KOG0966|consen 534 WID-PDNSIILQIKA-AEIVPSSNFVTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVSK-------SDVEDKE-KKK 603 (881)
T ss_pred eEC-CCCceEEEeeh-heeeecccccccceeecceeeeeecCCcHHHHhhHHHHHHHhcccc-------CCcchhh-hhc
Confidence 999 99999999995 3456899999999999999999999999999999999999985311 1111111 111
Q ss_pred ccccccccccccccccCCccccCccccccCCCCcccCeEEEEEcCC-CCCChHHHHHHHHHcCCEEEecCCCCceEEEE-
Q 001083 624 QFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVP-PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA- 701 (1160)
Q Consensus 624 ~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~s~lF~G~~F~vv~~~-~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia- 701 (1160)
+ .+.+++++.+. .-+...+..+.+.+.+++|.|+.|||+++. ...++.+|+++|++|||++++|++++.|+||+
T Consensus 604 ~-~t~~~~k~~~~---~i~~~~~~~~~~~~~s~if~gl~f~Vlsgt~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~ 679 (881)
T KOG0966|consen 604 R-DTLKVRKRTRK---AIHDSAPNRSKVAKISNIFDGLEFCVLSGTSETHTKAKLEEIIVENGGKIVQNVGPSDTLCIAT 679 (881)
T ss_pred c-cchhhhhhhhh---hhcccccchhcccchhhhhcCeeEEEecCCcccccHHHHHHHHHHcCCEEEEcCCCCCcceEEe
Confidence 1 11111111111 123334556677788999999999999876 45679999999999999999999988999996
Q ss_pred ecC--CChhhHhhhcCCCeeecchHHHHHhcCccCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhcc
Q 001083 702 ADN--KGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNV 779 (1160)
Q Consensus 702 ~~~--~~~K~~~a~~~~~VV~p~WV~dCi~~~~lLp~~p~~~l~~s~~t~~~~~~~~D~~gDSy~~~~~~~~L~~ll~~i 779 (1160)
+.. .+.++.++.+..+||+|+||+||+...+++||.|+++++.++..++.++..+|+|||||++|++.+.|+.+++.+
T Consensus 680 a~~et~~vk~~~~~~~cdVl~p~Wlldcc~~~~l~p~~P~~~fh~~e~~~~~~a~~~D~~gdSy~~di~l~~l~~~ls~~ 759 (881)
T KOG0966|consen 680 AGKETTRVKAQAIKRSCDVLKPAWLLDCCKKQRLLPWLPRDLFHATEKGREKLAKEVDCLGDSYENDIDLEQLKKVLSGI 759 (881)
T ss_pred ccccchHHHHHHHhccCceeeHHHHHHHHhhhhccccccHHHHhhCchHHHHHHHHHhhhcchhhhhccHHHHHHHHhhh
Confidence 333 334566666655999999999999999999999999999999999999999999999999999999999999988
Q ss_pred CCCCCcchhhHHhhhcCCCCCCccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-------Cce
Q 001083 780 DRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-------NAT 852 (1160)
Q Consensus 780 ~~~~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-------~vT 852 (1160)
..+.+...+.......++...+.+|.-|..+|+..+...+.+ .......+..+||.+.+.-. .+|
T Consensus 760 k~S~ds~~~~~~~~~~~~e~r~~~~~~~~~~f~~~~~~~~se--------~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t 831 (881)
T KOG0966|consen 760 KKSQDSLPPMGASEKDSLERRFSLFLSSLRMFYVLRRKLSSE--------EVIIELKLKNFGGRITDAQSECNNIGAKYT 831 (881)
T ss_pred hhcccccCchhhhhhhcHHHhhccccccceeeecccccccHH--------HHHHHHHHHHhcceeeeccchhhhccccee
Confidence 876544322211111111112222222222333322212222 23445567788998887653 269
Q ss_pred EEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEeccchHHHHHHcCCccCCCCCC
Q 001083 853 HVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYS 910 (1160)
Q Consensus 853 HVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~ 910 (1160)
|+|+..-. ......+. +.......++ +||.+.||.+|+.++.++||++|+
T Consensus 832 ~~v~~~i~-----~~h~~~~~--~~~~~lt~~r-kv~~~~wv~~s~~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 832 HCVLRCID-----EDHEKIKE--QKKASLTIKR-KVVAPSWVDHSINENCLLPEEDFP 881 (881)
T ss_pred eeeeeecc-----hHHHHHHH--HHHHHhcccc-cccCHHHHHHhhcccccCccccCC
Confidence 99986221 11111111 1111122234 999999999999999999999995
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=5.2e-100 Score=930.95 Aligned_cols=552 Identities=24% Similarity=0.415 Sum_probs=472.3
Q ss_pred CCCcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhc--CCCchHhhhHhhc----CCCCCcCcccCCCCHHHHHHHHHHHh
Q 001083 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTY--CDSVDYFSALRLI----LPSLDRERGSYGLKESVLANCLIDAL 78 (1160)
Q Consensus 5 ~~~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~--~~~~d~~p~lrLl----lP~~d~er~~ygike~~L~k~~~~~~ 78 (1160)
.+|+|+.||++|++|+.++++++|+.+|.+||... .+++|++|+++|+ +|.. ++.+|||+++.|+++|++++
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~--e~~elgige~~L~kai~e~~ 204 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETGRIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAH--EGVELGIGEATIIKALAEAF 204 (744)
T ss_pred CCccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccc--cCcccCcCHHHHHHHHHHHH
Confidence 56999999999999999999999999999999986 3578999999995 5554 46799999999999999999
Q ss_pred CCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcC-CCCCCCcHHHHHHHHHHHHhhhh---HHHHHHHHHHHHH
Q 001083 79 GMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIK 154 (1160)
Q Consensus 79 gl~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~-~~~~~LTi~eVn~~Ld~LA~~~~---~~~k~~il~~ll~ 154 (1160)
|++..... . .| ...||||+||+.+.+.+.. ..+.+|||.+|++.|.+||..+| +.+|..+|..||.
T Consensus 205 g~~~~~ik---~-~y------~~~GDlG~vA~~~~~~q~~~~~~~~LTi~~V~~~L~~IA~~~G~~sq~~K~~~i~~Ll~ 274 (744)
T PLN03113 205 GRTEKQVK---K-QY------KELGDLGLVAKASRSSQSMMRKPEPLTVVKVFNTFQQIAKESGKDSQEKKKNRIKALLV 274 (744)
T ss_pred CcCHHHHH---H-HH------HHhCCHHHHHHhhhcccccccCCCCCCHHHHHHHHHHHHhhhCccCHHHHHHHHHHHHH
Confidence 99865432 1 34 4579999999977655443 23578999999999999998876 5678899999999
Q ss_pred hCCHHHHHHHHHHHhhhhccCCcccccccccCccH------------------------HHHHhhhCCHHHHHHHHhhhh
Q 001083 155 KTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA------------------------EDLFNVTCDLKLVCEKLKDRN 210 (1160)
Q Consensus 155 ~~t~~E~k~l~RiIlkdLriGi~e~til~~~hpda------------------------~~~~~~~~DL~~V~~~L~~~~ 210 (1160)
.+++.|++||+|+|+++||||+++++|+.++|+.+ .++|+.++|++.|+..|....
T Consensus 275 ~~~~~E~k~liR~l~g~LRIGv~e~tVl~ALa~a~~~~~~~~~~~~~~~~~l~~~~~~v~~a~~~~p~~~~i~~~ll~~g 354 (744)
T PLN03113 275 AATDCEPLYLIRLLQTKLRIGLAGQTLLAALGQAAVYNEEHSTPPPNIQSPLEEAAKIVKQVYSVLPVYDKIVPALLSGG 354 (744)
T ss_pred hCCHHHHHHHHHHHhccccccccHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHhccCCCHHHHHHHHHhCC
Confidence 99999999999999999999999999999887653 257888999998888776543
Q ss_pred -ccc-cccccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEE-eCCEEEEEeCCCCCCCcchhhHHHH
Q 001083 211 -QRH-KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMSKI 287 (1160)
Q Consensus 211 -~~~-~~~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~-~g~~v~~fSR~g~d~t~~~~~l~~~ 287 (1160)
..+ ..+.|++|.||+||||++.+.+.+++++|.+.+|++|+||||+|||||+ .++.|++|||||+++|..+|++...
T Consensus 355 ~~~l~~~~~i~~g~Pi~PMLA~~~~~~~eil~~~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~ 434 (744)
T PLN03113 355 VWNLPKTCSFTPGVPVGPMLAKPTKGVSEIVNKFQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVA 434 (744)
T ss_pred cccccccccccCCCCCCCccCCCCCChHHHhhccCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHH
Confidence 233 5677999999999999999999899999988899999999999999998 4789999999999999999999887
Q ss_pred HHHhc--ccCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCC--CCCccEEEEEEeeeecCCcccccCCHHHHHHH
Q 001083 288 IEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLS--SDRQVLCYFAFDVLYVGDTSVIHQSLKERHEL 363 (1160)
Q Consensus 288 l~~~~--~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~--~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~ 363 (1160)
+.... .+.+||||||||+||..+++++||+.+|.. .+.... ....++||+||||||+||++|++.||.+||++
T Consensus 435 ~~~~~~~~~~~~ILDGEiVa~d~~~~~~lpFq~Lq~R---~rk~~~~~~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~ 511 (744)
T PLN03113 435 ISRLKKPSVKSFILDCELVAYDREKKKILPFQILSTR---ARKNVVMSDIKVDVCIFAFDMLYLNGQPLIQEQLKIRREH 511 (744)
T ss_pred HHHhccccCCCEEEEeEEEEEECCCCCcCCHHHHHhh---hccccchhccccceEEEEEeccccCccChhcCCHHHHHHH
Confidence 65432 157899999999999888889999877753 222211 11235999999999999999999999999999
Q ss_pred HHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCeEE
Q 001083 364 LQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLK 441 (1160)
Q Consensus 364 L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~--ds~Y~pGkRs~~WlK 441 (1160)
|++++.+.++++++.. ...+.+.+++.++|++++++|+||||+|++ +|+|.||+|+.+|+|
T Consensus 512 L~~~~~~~~~~i~~~~-----------------~~~~~~~ee~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlK 574 (744)
T PLN03113 512 LYESFEEDPGFFQFAT-----------------AITSNDLEEIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLK 574 (744)
T ss_pred HHHHhccCCCcEEEee-----------------eeccCCHHHHHHHHHHHHHcCCceEEEeccCCCCCccCCCCCCCeEE
Confidence 9999988777765431 234578999999999999999999999986 899999999999999
Q ss_pred EccccccC-CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhccccccc
Q 001083 442 LKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKY 520 (1160)
Q Consensus 442 lKpeY~~~-g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~ 520 (1160)
+|++|+++ ++++||||||||||+|+|+|.+|+||||||++++ +.|++|||||||||++++++|.+.|++++..
T Consensus 575 lK~dy~~~~~dtlDlVvIGa~~G~GkR~g~~g~fLla~yd~~~-----~~~~~v~KvgTGfsd~~l~~l~~~L~~~~~~- 648 (744)
T PLN03113 575 LKKDYMESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDSNK-----EEFQSICKIGTGFSEAVLEERSASLRSQVIP- 648 (744)
T ss_pred EechhhccccccccEEEEEEEeCCCCcCCccceEEEEEEcCCC-----CEEEEeeEECCCCCHHHHHHHHHHHHHhccc-
Confidence 99999984 7999999999999999999999999999998653 3899999999999999999999999988764
Q ss_pred CCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeeccccc---------CCceeeCceeeeeecCCCccCc
Q 001083 521 EYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDC 591 (1160)
Q Consensus 521 ~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~---------~g~tLRFPR~~riR~DK~~~d~ 591 (1160)
.||.|+.+. ...+||+||+ |. +|+||++... ..|+.|+ .|++||||||+|||+||+|+||
T Consensus 649 -----~~~~~~~~~--~~~~pdvwve-P~--~V~EV~~aei-t~Sp~h~a~~g~~~~~~G~sLRFPRf~riR~DK~~~da 717 (744)
T PLN03113 649 -----TPKSYYRYG--DSIKPDVWFE-PT--EVWEVKAADL-TISPVHRAAVGIVDPDKGISLRFPRLVRVREDKSPEQA 717 (744)
T ss_pred -----CCCcccccC--CCCCCcEEEC-Cc--eEEEEEeeee-ccCcccccccccccCCCCeEEECCEEEEEECCCChHHC
Confidence 245565442 2458999999 75 7999996432 3688887 4899999999999999999999
Q ss_pred CCHHHHHHHHHccC
Q 001083 592 LDVQSFVELVHSSN 605 (1160)
Q Consensus 592 ~t~~el~el~~~~~ 605 (1160)
+|++++.+||+++.
T Consensus 718 tt~~~l~~ly~~Q~ 731 (744)
T PLN03113 718 TSSEQVADMYNAQK 731 (744)
T ss_pred CCHHHHHHHHHHHH
Confidence 99999999997554
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=2.3e-97 Score=905.62 Aligned_cols=545 Identities=27% Similarity=0.472 Sum_probs=472.4
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCc----hHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCc
Q 001083 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSV----DYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (1160)
Q Consensus 7 ~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~~----d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~ 82 (1160)
|+|+.||++|++|+.++++++|+.+|.+||.... ++ .+|+++++++|..+. ++|||+++.|+++|++++|++.
T Consensus 1 m~f~~l~~~~~~i~~t~~r~~k~~~l~~~~~~~~-~~~~~~~~~l~~~~~~p~~~~--~~~gi~~~~l~k~i~~~~g~~~ 77 (590)
T PRK01109 1 MEFSELAEYFERLEKTTSRTQLTKLLADLLKKTP-PEIIDKVVYLIQGKLWPDWLG--LELGVGEKLLIKAISMATGISE 77 (590)
T ss_pred CcHHHHHHHHHHHHhhhchHHHHHHHHHHHHhCC-HHhhhhhHHHHhCCcCccccC--cccCcCHHHHHHHHHHHHCcCH
Confidence 7899999999999999999999999999999874 33 457777778898874 6999999999999999999998
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcCC------CCCCCcHHHHHHHHHHHHhhh---hHHHHHHHHHHHH
Q 001083 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM------ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLI 153 (1160)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~------~~~~LTi~eVn~~Ld~LA~~~---~~~~k~~il~~ll 153 (1160)
+..+. .| ...||||.+|+.++++++.. .+++||+.+|++.|++||..+ ++.+|..+|..||
T Consensus 78 ~~~~~----~~------~~~GDlg~~a~~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll 147 (590)
T PRK01109 78 KEVEN----LY------KKTGDLGEVARRLKSKKKQKSLLAFFSKEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLL 147 (590)
T ss_pred HHHHH----HH------HhcCCHHHHHHHHHhhcccccccccCCCCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHH
Confidence 76543 13 45799999999999876532 357899999999999999887 3678899999999
Q ss_pred HhCCHHHHHHHHHHHhhhhccCCccccccc----ccC-----ccHHHHHhhhCCHHHHHHHHhhhh-ccccccccccCCc
Q 001083 154 KKTNAQEMKWIIMIILKDLKLGISEKSIFH----EFH-----PDAEDLFNVTCDLKLVCEKLKDRN-QRHKRQDIEVGKA 223 (1160)
Q Consensus 154 ~~~t~~E~k~l~RiIlkdLriGi~e~til~----~~h-----pda~~~~~~~~DL~~V~~~L~~~~-~~~~~~~i~~g~p 223 (1160)
.++++.|++||+|+|+++||||+++++|++ +|| ++++++|+.|+||+.||+.|..+. ..+....|++|.|
T Consensus 148 ~~~~~~E~k~iirli~g~lriGv~e~~il~ALa~A~~~~~~~~~ve~~y~~~~Dlg~va~~l~~~g~~~~~~~~i~~~~P 227 (590)
T PRK01109 148 KDASPLEAKYIARFVEGRLRLGVGDATILDALAIAFGGAVARELVERAYNLRADLGYIAKILAEGGIEALKKVKPQVGIP 227 (590)
T ss_pred HhCCHHHHHHHHHHHhhhhhcCccHHHHHHHHHHHHhcccchHHHHHHHHhCCCHHHHHHHHHhcchhhhccCcccCCCC
Confidence 999999999999999999999999999997 344 788999999999999999998764 3556778999999
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
|+||||++++.+++++++++ ..|++|+||||+|||+|++++.|++|||||+++|..+|++.+.+...+...+|||||||
T Consensus 228 v~PmLA~~~~~~~~~~~~~~-~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~~~~~~~ILDGEl 306 (590)
T PRK01109 228 IRPMLAERLSSPKEILKKMG-GEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEAIKAEEAIVEGEI 306 (590)
T ss_pred CCcccCCccCCHHHHHHHcC-CCeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHhcCccceEEeeeE
Confidence 99999999998888888885 46999999999999999999999999999999999999999887665656899999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccC-CC--CCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeecc
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDG-LS--SDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP 380 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~-~~--~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p 380 (1160)
|+||+.+++++||+.++.. .+.. .. ....++||+||||||+||++|++.||.+||++|++++.+.+ ++.+.
T Consensus 307 v~~d~~~g~~~~F~~l~~R---~r~~~~~~~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~-- 380 (590)
T PRK01109 307 VAVDPETGEMRPFQELMHR---KRKYDIEEAIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-KVKLA-- 380 (590)
T ss_pred EEEECCCCcccChHHHhhc---ccccchhhhcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCC-ceEEe--
Confidence 9999777888999877643 1111 10 11235999999999999999999999999999999998754 34332
Q ss_pred CCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCeEEEccccccC-CCcccEEE
Q 001083 381 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIRA-GSDLDVLI 457 (1160)
Q Consensus 381 ~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~--ds~Y~pGkRs~~WlKlKpeY~~~-g~~lDlvI 457 (1160)
....+++.+++.++|+.++++|+||||+|++ +|+|.||+|+.+|+|+|++|++. ++++||||
T Consensus 381 ---------------~~~~~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~Dlvv 445 (590)
T PRK01109 381 ---------------ERIITDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVV 445 (590)
T ss_pred ---------------eeEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEE
Confidence 1345678999999999999999999999999 99999999999999999999984 78999999
Q ss_pred EEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCC
Q 001083 458 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 537 (1160)
Q Consensus 458 IG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~ 537 (1160)
||++||+|+|+|.+|+|+||+||+++ +.|+++|+||||||++++++|.+.|++++... .|| ++ ..
T Consensus 446 iG~~~g~Gkr~~~~g~~ll~~~d~~~-----~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~~-----~~~-~~----~~ 510 (590)
T PRK01109 446 VGAFYGRGRRGGKYGSLLMAAYDPKT-----DTFETVCKVGSGFTDEDLDELPKMLKPYKIDH-----KHP-RV----VS 510 (590)
T ss_pred EEeEeCCCccCCccccEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHHhhhhcccC-----CCc-cc----cc
Confidence 99999999999999999999998653 38999999999999999999999999988641 133 32 13
Q ss_pred CCCCcEEEeCCcceEEEEEEeeeeeeeccccc---------CCceeeCceeeeeecCCCccCcCCHHHHHHHHHccC
Q 001083 538 KERPDVWIESPEKSIILSITSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSSN 605 (1160)
Q Consensus 538 ~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~---------~g~tLRFPR~~riR~DK~~~d~~t~~el~el~~~~~ 605 (1160)
..+||+||+ | ++|+||+++.. ..|+.|+ .|++||||||++||+||+|+||+|++++.+||+++.
T Consensus 511 ~~~pdvwv~-P--~~V~eV~~~~i-t~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q~ 583 (590)
T PRK01109 511 KMEPDVWVE-P--KLVAEIIGAEI-TLSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQK 583 (590)
T ss_pred ccCCcEEEe-c--cEEEEEEeeec-ccCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHhh
Confidence 568999999 7 59999996543 3578888 689999999999999999999999999999997544
No 4
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=4.3e-95 Score=832.38 Aligned_cols=552 Identities=27% Similarity=0.508 Sum_probs=477.6
Q ss_pred CCCcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcC--CCchHhhhHhhcCCCC--CcCcccCCCCHHHHHHHHHHHhCC
Q 001083 5 EETEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYC--DSVDYFSALRLILPSL--DRERGSYGLKESVLANCLIDALGM 80 (1160)
Q Consensus 5 ~~~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~--~~~d~~p~lrLllP~~--d~er~~ygike~~L~k~~~~~~gl 80 (1160)
+.+||.+||.+|+.|+.+++|.+.+.++.+||.+.. +|+|+.|+++|.+..+ |.++.++||+|..|.|+|++++|.
T Consensus 97 ~~~py~~~a~tF~kIe~~s~Rl~i~~il~n~f~~v~~~sP~dLlp~vYLsiN~l~P~yeGlELGvGes~l~KAi~EatGr 176 (714)
T KOG0967|consen 97 SKVPYLELARTFEKIEETSGRLEIIDILSNFLRSVLATSPDDLLPTVYLSINKLAPDYEGLELGVGESLLMKAIAEATGR 176 (714)
T ss_pred CcCcHHHHHHHHHHHHhhccceeHHHHHHHHHHHHHhcCchhhhhHHHHhhhccCccccCccccccHHHHHHHHHHHhCc
Confidence 469999999999999999999999999999999874 5899999999998887 677889999999999999999999
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcC-CCCCCCcHHHHHHHHHHHHhhhh---HHHHHHHHHHHHHhC
Q 001083 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQG-MISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKT 156 (1160)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~-~~~~~LTi~eVn~~Ld~LA~~~~---~~~k~~il~~ll~~~ 156 (1160)
+... .|+ .| ...||+|+||+...+.... ..+.+|||.+|+..|.+||..+| +.+|..++..||..|
T Consensus 177 t~~~---vk~-~~------~~~GDLG~VA~~sR~sQ~~m~~P~pLtV~~VF~~Lr~IAk~sG~~S~~kK~~lik~Llvac 246 (714)
T KOG0967|consen 177 TLSH---VKN-QY------NKLGDLGLVAQGSRSSQRMMFKPKPLTVRDVFSTLRKIAKESGKGSQNKKKDLIKALLVAC 246 (714)
T ss_pred cHHH---HHH-HH------HhcCcHHHHHhhcccccccccCCCCccHHHHHHHHHHHHHhhCcchhHHHHHHHHHHHHhc
Confidence 8653 333 23 5689999999886544332 35679999999999999999887 678899999999999
Q ss_pred CHHHHHHHHHHHhhhhccCCccccccccc------C----------cc------------HHHHHhhhCCHHHHHHHHhh
Q 001083 157 NAQEMKWIIMIILKDLKLGISEKSIFHEF------H----------PD------------AEDLFNVTCDLKLVCEKLKD 208 (1160)
Q Consensus 157 t~~E~k~l~RiIlkdLriGi~e~til~~~------h----------pd------------a~~~~~~~~DL~~V~~~L~~ 208 (1160)
++.|+|||+|.|.++||||++++|||.++ + ++ +.++|..++|+..|+..|..
T Consensus 247 ~~~E~kyLiRsL~gkLRiGlaeqTvL~AL~~A~~~~~~~~~~~~~~~d~~kd~le~~~~ivk~afcq~P~ydiivp~lL~ 326 (714)
T KOG0967|consen 247 RGIEAKYLIRSLEGKLRIGLAEQTVLAALGQAFVLNDNNDEEKSKKPDSLKDPLEEAAQIVKQAFCQLPDYDIIVPALLE 326 (714)
T ss_pred ccccHHHHHHHHHhhhhhhhhHHHHHHHHHHHHhccCchhhhccCCcchhhhhhHHHHHHHHHHHhcCCchhhhHHHHHH
Confidence 99999999999999999999999998643 1 22 24579999999999988865
Q ss_pred hh--ccccccccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEE-eCCEEEEEeCCCCCCCcchhhHH
Q 001083 209 RN--QRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHK-NGSEIHYFSRSFLDHSEYGHAMS 285 (1160)
Q Consensus 209 ~~--~~~~~~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~-~g~~v~~fSR~g~d~t~~~~~l~ 285 (1160)
.+ ...+.+.+.||.|++||||++.+.+.+++++|++..|.+|+||||+|+|||+ .+|.|.+||||+++.|..+|++.
T Consensus 327 ~Gie~L~e~c~l~PGIPlKPMLAkpTK~i~evl~rf~~~~FTCEyKYDGeRAQIH~~edG~v~IfSRN~E~~T~kYPDi~ 406 (714)
T KOG0967|consen 327 HGIENLPETCKLTPGIPLKPMLAKPTKGIQEVLERFQDKAFTCEYKYDGERAQIHKLEDGTVEIFSRNSENNTGKYPDII 406 (714)
T ss_pred hhhhhccccCccCCCCCCcchhcCcchhHHHHHHHhhCceeEEEeecCceeeeeEEccCCcEEEEecccccccccCccHH
Confidence 43 2245688999999999999999999999999999999999999999999997 57899999999999999999998
Q ss_pred HHHHHhc--ccCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCC--CccEEEEEEeeeecCCcccccCCHHHHH
Q 001083 286 KIIEQNV--LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSD--RQVLCYFAFDVLYVGDTSVIHQSLKERH 361 (1160)
Q Consensus 286 ~~l~~~~--~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~--~~~~~~~vFDiL~lng~sl~~~pl~eRr 361 (1160)
..+.... .+.++|||||+|+||...++++||+ .+..+.|+..+.. ...+|+++|||||+||++|++.||.+||
T Consensus 407 ~~~~~~~kp~v~sFIlD~EvVA~Dr~~~~IlpFQ---vLSTRkRk~v~v~dikV~Vcvf~FDily~ng~~Li~~pL~eRR 483 (714)
T KOG0967|consen 407 EVISKLKKPSVKSFILDCEVVAWDREKGKILPFQ---VLSTRKRKNVDVNDIKVKVCVFVFDILYLNGESLIQEPLRERR 483 (714)
T ss_pred HHHHHhhCCccceeEEeeeEEEEeccCCccCchh---hhhhhhccccchhhceEEEEEEEEeeeeeCChhhhhhhHHHHH
Confidence 8765433 3579999999999999989999994 4445555543322 1249999999999999999999999999
Q ss_pred HHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecC--CCCCcCCCCCCCe
Q 001083 362 ELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKW 439 (1160)
Q Consensus 362 ~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~--ds~Y~pGkRs~~W 439 (1160)
++|.+.+..++|.++++. ...+.+.++|++||++++..++||+|+|.+ ++.|+|.+|+.+|
T Consensus 484 ~~l~e~f~e~~g~f~fat-----------------~~~tn~~~eiq~Fl~~sv~~~cEGlMvKtLd~~atYep~kRs~~W 546 (714)
T KOG0967|consen 484 ELLHESFKEIPGEFQFAT-----------------SLDTNDIDEIQEFLEESVQNSCEGLMVKTLDTNATYEPSKRSNNW 546 (714)
T ss_pred HHHHhhcccCCCceeEee-----------------eeccCCHHHHHHHHHHhhccCcceeEEEeeccccccCchhhccch
Confidence 999999999999887642 344689999999999999999999999976 5889999999999
Q ss_pred EEEccccccC-CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhccccc
Q 001083 440 LKLKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFR 518 (1160)
Q Consensus 440 lKlKpeY~~~-g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~ 518 (1160)
+|+|++|+++ |+++|||+||||||.|||.|++|+||+|||+++.. +|+++||+||||||+++.++...|.....
T Consensus 547 lKlKkDYldgvgdslDLv~iga~~G~GrrtG~yg~fLlacyn~dte-----efqsiCKigtGFsD~~l~e~~~~l~~~~~ 621 (714)
T KOG0967|consen 547 LKLKKDYLDGVGDSLDLVVIGAYYGRGRRTGWYGGFLLACYNPDTE-----EFQSICKIGTGFSDEFLQELHESLSSTVI 621 (714)
T ss_pred hhhhhhhhcccccceeeeeeeeeeccccccccccceeEEeecCchH-----HHHHHHhhcCCCCHHHHHHHHHHhhhccc
Confidence 9999999995 89999999999999999999999999999998753 89999999999999999999998875543
Q ss_pred ccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEE-eeeeeeecccccC---------CceeeCceeeeeecCCCc
Q 001083 519 KYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSIT-SDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPW 588 (1160)
Q Consensus 519 ~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~-~~i~~~~s~~~~~---------g~tLRFPR~~riR~DK~~ 588 (1160)
. .|+.+|.+. ...+||+|++ |. .||||+ |++. -|+.|.+ |.|||||||.|||+||.+
T Consensus 622 ~------~~~~~y~~d--~s~kPd~wf~-p~--~VwEvk~Adlt--~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~p 688 (714)
T KOG0967|consen 622 D------SPKPYYRFD--ESLKPDVWFE-PT--EVWEVKAADLT--LSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNP 688 (714)
T ss_pred c------CcHhhcccC--ccCCCccccC-HH--HHHHHhhcccc--ccchhHhhhcCcCCCCceeEecceeeEeeccCCh
Confidence 2 355677664 3567999999 76 789998 5553 3666653 789999999999999999
Q ss_pred cCcCCHHHHHHHHHcc
Q 001083 589 HDCLDVQSFVELVHSS 604 (1160)
Q Consensus 589 ~d~~t~~el~el~~~~ 604 (1160)
+||+|-+++.+||+.+
T Consensus 689 eeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 689 EEATTSSQIAEMYQAQ 704 (714)
T ss_pred hhcccHHHHHHHHHHH
Confidence 9999999999999866
No 5
>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=1.2e-89 Score=828.86 Aligned_cols=495 Identities=34% Similarity=0.598 Sum_probs=426.6
Q ss_pred cCCCCHHHHHHHHHHHhCCCcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhhc--CCCCCCCcHHHHHHHHHHHHhh
Q 001083 62 SYGLKESVLANCLIDALGMSKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQ--GMISGGLTIKELNDLLDRLASS 139 (1160)
Q Consensus 62 ~ygike~~L~k~~~~~~gl~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~--~~~~~~LTi~eVn~~Ld~LA~~ 139 (1160)
+||||++.|+++|++++|+++++.++..+ ..||+|.+++.++.... ...+.+|||.+||+.|++||..
T Consensus 1 ~~gi~~~~l~k~~~~~~~~~~~~~~~~~~----------~~gd~g~~~~~~~~~~~~~~~~~~~lti~eV~~~L~~ia~~ 70 (514)
T TIGR00574 1 EYGIGEKLLIKAISKALGIPKDEIEEKVK----------EDGDLGEVIEGLFSKQKQTSFFSAPLTVKEVYETLKNIAET 70 (514)
T ss_pred CCCCcHHHHHHHHHHHHCcCHHHHHHHHH----------hcCCHHHHHHHHhccccccccCCCCcCHHHHHHHHHHHHHh
Confidence 49999999999999999999988877443 35899999999887553 3346789999999999999988
Q ss_pred hh---HHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhccCCcccccccccCccH-------HHHHhhhCCHHHHHHHHhhh
Q 001083 140 EN---RAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEKSIFHEFHPDA-------EDLFNVTCDLKLVCEKLKDR 209 (1160)
Q Consensus 140 ~~---~~~k~~il~~ll~~~t~~E~k~l~RiIlkdLriGi~e~til~~~hpda-------~~~~~~~~DL~~V~~~L~~~ 209 (1160)
++ +.+|..+|..|+.+|+|.|++||+|||+++||||+++++|+.++|+++ +++|++|+||+.||+.|.++
T Consensus 71 ~g~~s~~~k~~~l~~ll~~~~~~e~k~l~r~i~~~lriG~~~~~il~al~~~~~~~~~~~~~~~~~~~dl~~v~~~l~~~ 150 (514)
T TIGR00574 71 SGEGSQDKKIKLLKSLLKRASPLEAKYLIRTILGDLRIGIAEKTILDALAKAFLLSHPDVERAFNLTNDLGKVAKILLEP 150 (514)
T ss_pred hCCCcHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhcccCccHHHHHHHHHHHhccchHHHHHHHHhCCCHHHHHHHHHhc
Confidence 75 578889999999999999999999999999999999999999998877 99999999999999999876
Q ss_pred hccc--cccccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhH-HH
Q 001083 210 NQRH--KRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAM-SK 286 (1160)
Q Consensus 210 ~~~~--~~~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l-~~ 286 (1160)
.... ....+++|.||+||||+++..+.+++.++.+ +|++|+||||+|||+|+++++|++|||||+++|..+|++ .+
T Consensus 151 ~~~~~~~~~~i~~~~p~~PMLA~~~~~~~~~~~~~~~-~~~~E~K~DG~R~qih~~~~~v~l~SR~g~~~t~~~pei~~~ 229 (514)
T TIGR00574 151 GLRGLDKDLSIQLGIPFKPMLAERAKSIEEALKKKGN-KFYVEYKYDGERVQIHKDGDKFKIFSRRLENYTYAYPEIFTE 229 (514)
T ss_pred ChhhhcccceeecCCcCccccCCccCCHHHHHHHhCC-ceEEEEeecceEEEEEEcCCEEEEEcCCCcccccccchhHHH
Confidence 5432 3467999999999999999998888888754 899999999999999999999999999999999989998 76
Q ss_pred HHHHhcc-cCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHH
Q 001083 287 IIEQNVL-VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQ 365 (1160)
Q Consensus 287 ~l~~~~~-~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~ 365 (1160)
.+...+. ..+||||||||+||..+++++||+.++...++..........+++|+||||||+||++++++||.+|+++|+
T Consensus 230 ~~~~~~~~~~~~ILDGElv~~d~~~g~~~~F~~l~~r~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~ 309 (514)
T TIGR00574 230 FIKEAFPGIKSCILDGEMVAIDPETGKILPFQTLLRRKRRYDIDSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILE 309 (514)
T ss_pred HHHHhcCccceeeecceEEEEEcCCCCCcCcHhHHhhhhhccccccccccceEEEEEEEEEECCcchhcCcHHHHHHHHH
Confidence 6554443 368999999999998778889998877643221000011123499999999999999999999999999999
Q ss_pred HhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001083 366 KVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 445 (1160)
Q Consensus 366 ~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpe 445 (1160)
+++.+.++++.++. ...+++.+++.++|++++++|+||||+|+++|+|.||+|+..|+|+|++
T Consensus 310 ~~~~~~~~~i~~~~-----------------~~~~~~~e~~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~ 372 (514)
T TIGR00574 310 SILKPIPNRIEIAE-----------------MKITSNVEELEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKPE 372 (514)
T ss_pred HhccCCCCcEEEEE-----------------EEecCCHHHHHHHHHHHHHcCCceEEEecCCCcccCCCCCCcceeCchh
Confidence 99988877665431 3456789999999999999999999999999999999999999999999
Q ss_pred cccC-CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCC
Q 001083 446 YIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPK 524 (1160)
Q Consensus 446 Y~~~-g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~ 524 (1160)
|+++ ++++|++|||+++|+|+++|.+|+|+||++++.. ++|+++|+||||||++++++|.+++.++|.... +.
T Consensus 373 y~~~~~~~~D~vvig~~~g~gk~~g~~~~~l~g~~d~~~-----~~~~~v~kvgsG~sd~~l~~l~~~l~~~~~~~~-~~ 446 (514)
T TIGR00574 373 YLEGMGDTLDLVVIGAYYGKGKRTGMYGSFLLACYDPES-----EEFKTITKVGTGFTDADLQELGKKLPPLWIDPP-GS 446 (514)
T ss_pred hcccccCceeEEEEeeEecCCccCCceeEEEEEEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHhccCcEecCC-CC
Confidence 9984 6899999999999999999999999999997653 389999999999999999999999999987521 11
Q ss_pred CCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC-CceeeCceeeeeecCCCccCcCCHHHHHHHH
Q 001083 525 RAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 601 (1160)
Q Consensus 525 ~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~-g~tLRFPR~~riR~DK~~~d~~t~~el~el~ 601 (1160)
.+|.+ ....|++|++ | ++|+||+++.. ..|+.|++ |++||||||++||+||+|+||+|++++.+||
T Consensus 447 -~~~~~------~~~~~~~w~~-p--~~V~eV~~~e~-t~s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly 513 (514)
T TIGR00574 447 -RVPSI------LSDEPDIWFD-P--AIVWEVTGAEI-TRSPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELY 513 (514)
T ss_pred -CCccc------ccCCCeEEec-C--CeEEEEEhhhe-eecCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHh
Confidence 12222 1357999998 7 48999996543 46899999 9999999999999999999999999999998
No 6
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=3.6e-88 Score=815.15 Aligned_cols=523 Identities=20% Similarity=0.248 Sum_probs=439.0
Q ss_pred HHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCcChHHHH
Q 001083 9 VIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAV 88 (1160)
Q Consensus 9 F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~~s~~~~ 88 (1160)
+++||++|++|+.++++++|+.+|.+||.++ +++++.++++|+++... .|||+++.|+++|++++|++....+.
T Consensus 1 ~~~fa~~~~~i~~t~~~~ek~~~l~~~~~~~-~~~d~~~~~~ll~g~~~----~~~i~~~~l~k~~~~~~g~~~~~~~~- 74 (539)
T PRK09247 1 MKAFAELLDRLDLTTSTNAKLALLADYFRSA-PDPDRAWALALLTGGLP----RRLVKTRLLRELAAERADLPPWLFEE- 74 (539)
T ss_pred ChHHHHHHHHHHhccCHHHHHHHHHHHHHhC-CHHHHHHHHHHhcCCcc----cCCCCHHHHHHHHHHHHCcCHHHHHH-
Confidence 4789999999999999999999999999998 46789999999999886 48999999999999999999765442
Q ss_pred HHhhhhcCCCCCCCCCHHHHHHHHhhhhcCCC---CCCCcHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHH
Q 001083 89 RLINWRKGGAAPNAGNFPMVAAEVLQRRQGMI---SGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWII 165 (1160)
Q Consensus 89 ~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~---~~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~t~~E~k~l~ 165 (1160)
. +..+||+|++|+.+++.++... +.++||.+|...|..++.. +|...|..|+.+|+|.|++||+
T Consensus 75 ---~------~~~~GDlg~~~~~~~~~~~~~~~~~~~~~tv~~v~~~l~~~~~~----~k~~~l~~ll~~~~~~e~~~i~ 141 (539)
T PRK09247 75 ---S------YDYVGDLAETIALLLPAPSDEASDLPLAPWLEEVLLPLRGLGRE----ELRAALADLWDRLDEDGRFALN 141 (539)
T ss_pred ---H------HHhcCCHHHHHHHhcccccccccCCCccccHHHHHHHHHhhhHH----HHHHHHHHHHHhCCHHHHHHHH
Confidence 1 2468999999999987765321 2568999998888888643 4778899999999999999999
Q ss_pred HHHhhhhccCCcccccccccC----cc---HHHHHhh--hCCHHHHHHHHhhhhccccccccccCCccccccccccCChH
Q 001083 166 MIILKDLKLGISEKSIFHEFH----PD---AEDLFNV--TCDLKLVCEKLKDRNQRHKRQDIEVGKAVRPQLAMRIGDAH 236 (1160)
Q Consensus 166 RiIlkdLriGi~e~til~~~h----pd---a~~~~~~--~~DL~~V~~~L~~~~~~~~~~~i~~g~p~~PmLA~~~~~~~ 236 (1160)
|+|+++||||+++++|+.+++ .+ ..++|+. ++|++.+++.+..+ .....+++|.|++||||+++.+..
T Consensus 142 rli~g~lRiG~~~~~v~~ala~a~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~P~~pMLA~~~~~~~ 218 (539)
T PRK09247 142 KLITGGFRVGVSARLVTRALAELGGVDEARIAQRLMGLWPPYADLFAWLIGPE---EDPLPADPGQPYPFFLAHPLEDED 218 (539)
T ss_pred HHhhCccccchhHHHHHHHHHHHhCCCHHHHHHHHhCCCCCcHHHHHHHhhCC---ccccCCCCCCcCCCeeCCcCCCch
Confidence 999999999999999998653 22 3455666 78888888777652 256678999999999999998765
Q ss_pred HHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeEEEEeCCCCccccc
Q 001083 237 AAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (1160)
Q Consensus 237 ~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF 316 (1160)
+.. +...+|++|+||||+|||+|++++.+++|||||+++|..+|++.+.+. .+ +.+||||||||+||+.++.+.||
T Consensus 219 ~~~--~~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~-~l-~~~~ILDGElv~~~~~~~~~~~F 294 (539)
T PRK09247 219 LTL--GDPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAE-AL-PDGTVLDGELLVWRPEDGRPQPF 294 (539)
T ss_pred hhh--cCCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHH-hC-CCCEEEEeEEEEEECCCCCcCCH
Confidence 433 334589999999999999999999999999999999999999988653 33 46799999999999766788999
Q ss_pred ccHHHHHHHhccC-CCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCC-cceeeccCCCCCccccCCCCC
Q 001083 317 GSNQEIAKAARDG-LSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVPDHGLNSHVRPQGEP 394 (1160)
Q Consensus 317 ~~lq~i~~~~r~~-~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~-~~~i~~p~~~~~~~v~~~~~~ 394 (1160)
+.+|....+.... ......++||+||||||+||+++++.||.+||++|++++.+.++ ++.+.
T Consensus 295 ~~l~~R~~rk~~~~~~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~~~~i~~~---------------- 358 (539)
T PRK09247 295 ADLQQRIGRKTVGKKLLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPRLDLS---------------- 358 (539)
T ss_pred HHHHHHhcccccchhhhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccCCCeEEec----------------
Confidence 8877643321110 00112359999999999999999999999999999999987643 44432
Q ss_pred ccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCccceE
Q 001083 395 CWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQF 474 (1160)
Q Consensus 395 ~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~G~Grr~g~~gsf 474 (1160)
....+.+.+++.++|++++++|+||||+|+++|+|.||+|+..|+|+|++| .++|+|||||++|+|+|+|.+|+|
T Consensus 359 -~~~~~~~~~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~~WlK~K~~~----~t~DlVvig~~~G~Gkr~g~~~~~ 433 (539)
T PRK09247 359 -PLVPFSDWDELAALRAAARERGVEGLMLKRRDSPYLVGRKKGPWWKWKRDP----LTIDAVLMYAQRGHGRRASLYTDY 433 (539)
T ss_pred -CceecCCHHHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcchhhcccCCC----CcEEEEEEEeecCCCCcCCccccE
Confidence 134467899999999999999999999999999999999999999999998 489999999999999999999999
Q ss_pred EEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEE
Q 001083 475 LVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIIL 554 (1160)
Q Consensus 475 llg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vl 554 (1160)
+|||++++.+ ...|++|||||||||++++++|.+.++++... ...|++||+ |. +|+
T Consensus 434 lla~~~~~~~---~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~~------------------~~~~~~~v~-P~--~V~ 489 (539)
T PRK09247 434 TFGVWDGPEG---GRQLVPFAKAYSGLTDEEIKQLDRWVRKNTVE------------------RFGPVRSVR-PE--LVF 489 (539)
T ss_pred EEEEEcCCCC---ceeEEEEEEECCCCCHHHHHHHHHHHhhcccc------------------cCCCceEec-Cc--eEE
Confidence 9999976531 13699999999999999999999877653211 235899998 75 999
Q ss_pred EEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHHHc
Q 001083 555 SITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHS 603 (1160)
Q Consensus 555 ev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~el~~~ 603 (1160)
||+++.. ..|+.|++|++||||||+++|+||+|+||+|++++.+||+.
T Consensus 490 EV~~~ei-t~S~~~~~G~~LRfPr~~~~R~DK~~~ea~t~~~l~~l~~~ 537 (539)
T PRK09247 490 EIAFEGI-QRSKRHKSGIAVRFPRILRWRWDKPAREADTLETLQALLDA 537 (539)
T ss_pred EEEecee-eecCCcCCCcEEEcceEEEEeCCCChHHCcCHHHHHHHHhc
Confidence 9996532 47899999999999999999999999999999999999953
No 7
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=6.4e-88 Score=806.78 Aligned_cols=493 Identities=21% Similarity=0.344 Sum_probs=423.9
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCcChHH
Q 001083 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (1160)
Q Consensus 7 ~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~~s~~ 86 (1160)
|+|++||++|++|+.|+++++|+++|++||... +++++.++++|+...+. .++.|++++.+.++++.
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 789999999999999999999999999999988 46899999999999986 35899998666655221
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcCCCCCCCcHHHHHHHHHHHHhhhh---HHHHHHHHHHHHHhCCHHHHHH
Q 001083 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSEN---RAEKISVLSTLIKKTNAQEMKW 163 (1160)
Q Consensus 87 ~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~LA~~~~---~~~k~~il~~ll~~~t~~E~k~ 163 (1160)
...++|||.+||+.|++||..+| +..|..+|..|+.+|++.|++|
T Consensus 68 --------------------------------~~~~~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~~~~E~~~ 115 (508)
T PRK03180 68 --------------------------------AAEPTLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAATEDEQRF 115 (508)
T ss_pred --------------------------------cCCCCCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhCCHHHHHH
Confidence 01256999999999999998765 5788999999999999999999
Q ss_pred HHHHHhhhhccCCccccccccc-------CccHHHHHhhhCCHHHHHHHHh-hhhccccccccccCCccccccccccCCh
Q 001083 164 IIMIILKDLKLGISEKSIFHEF-------HPDAEDLFNVTCDLKLVCEKLK-DRNQRHKRQDIEVGKAVRPQLAMRIGDA 235 (1160)
Q Consensus 164 l~RiIlkdLriGi~e~til~~~-------hpda~~~~~~~~DL~~V~~~L~-~~~~~~~~~~i~~g~p~~PmLA~~~~~~ 235 (1160)
|+|||+++||||+++++|+.++ +++++++|++|+||+.||+.+. ++..++....|++|.||+||||++...+
T Consensus 116 l~r~i~~~lRiGv~~~~v~~Ala~a~~~~~~~v~~a~~~~~dl~~v~~~~l~~~~~~~~~~~i~~~~P~~PMLA~~~~~~ 195 (508)
T PRK03180 116 LRRLLTGELRQGALDGVMADAVARAAGVPAAAVRRAAMLAGDLPAVAAAALTGGAAALARFRLEVGRPVRPMLAQTATSV 195 (508)
T ss_pred HHHHHhCCCcccccHHHHHHHHHHHhCCCHHHHHHHHHHcCCHHHHHHHHHhcCccccccCCCCCCCCCCCccCCcCCCh
Confidence 9999999999999999999877 3567889999999999999665 4455567778999999999999999888
Q ss_pred HHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeEEEEeCCCCcccc
Q 001083 236 HAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAE 315 (1160)
Q Consensus 236 ~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~p 315 (1160)
++++++++ .+|++|+||||+|||+|++++++++|||||+++|..+|++.+.+. .+..++||||||||+||+ .++++|
T Consensus 196 ~~~~~~~~-~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~fPei~~~~~-~~~~~~~ILDGElv~~d~-~g~~~~ 272 (508)
T PRK03180 196 AEALARLG-GPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAVR-ALPVRSLVLDGEAIALRP-DGRPRP 272 (508)
T ss_pred HHHHHHhC-CCeEEEEEEceeEEEEEEECCEEEEEeCCCCcchhhhHHHHHHHH-hCCCcceeecceEEEECC-CCCcCC
Confidence 88888884 579999999999999999999999999999999999999988653 355678999999999997 467889
Q ss_pred cccHHHHHHHhccCCC--CCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCC
Q 001083 316 FGSNQEIAKAARDGLS--SDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGE 393 (1160)
Q Consensus 316 F~~lq~i~~~~r~~~~--~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~ 393 (1160)
|+.++....+. .... ....+++|++|||||+||++++++||.+||++|++++.+. .. .+
T Consensus 273 F~~l~~R~~~k-~~~~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~-~~----~~------------- 333 (508)
T PRK03180 273 FQVTASRFGRR-VDVAAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAA-HR----VP------------- 333 (508)
T ss_pred HHHHHHHhccc-cchhhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhccc-cc----cc-------------
Confidence 97665433221 1111 1123599999999999999999999999999999998642 11 01
Q ss_pred CccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCccce
Q 001083 394 PCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQ 473 (1160)
Q Consensus 394 ~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~G~Grr~g~~gs 473 (1160)
.....+.++++++|++++++|+||||+|+++|+|.||+|+.+|+|+|+. +++|+||||+++|+|+|+|.+|+
T Consensus 334 ---~~~~~~~~~~~~~~~~a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K~~-----~t~D~VviG~~~G~Gkr~g~~~~ 405 (508)
T PRK03180 334 ---RLVTADPAAAAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKPV-----HTLDLVVLAAEWGSGRRTGKLSN 405 (508)
T ss_pred ---ceecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCcEEEcCC-----CceEEEEEeeecCCCCCCCCccc
Confidence 2235678999999999999999999999999999999999999999996 49999999999999999999999
Q ss_pred EEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEE
Q 001083 474 FLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSII 553 (1160)
Q Consensus 474 fllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~V 553 (1160)
|+||+||+++ +.|++||+||||||++++++|.+.+.++... ...|++||+ |. +|
T Consensus 406 ~llg~~d~~~-----~~l~~vgkv~sG~td~~l~~l~~~l~~~~~~------------------~~~~~vwv~-P~--~V 459 (508)
T PRK03180 406 LHLGARDPAT-----GGFVMLGKTFKGMTDAMLAWQTERFLELAVG------------------RDGWTVYVR-PE--LV 459 (508)
T ss_pred eEEEEEeCCC-----CeEEEecCccCCCCHHHHHHHHHHHHhhccC------------------CCCCCEEee-CC--EE
Confidence 9999997653 3899999999999999999999888765321 236899999 76 89
Q ss_pred EEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHH
Q 001083 554 LSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 601 (1160)
Q Consensus 554 lev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~el~ 601 (1160)
+||+++.. ..|+.|++|++||||||++||+||+|+||+|++++.+||
T Consensus 460 ~EV~~~~i-t~S~~~~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~ 506 (508)
T PRK03180 460 VEIAFDGV-QRSTRYPGGVALRFARVLRYRPDKTPAEADTIDTVRALL 506 (508)
T ss_pred EEEEeeEe-eeCCcccCCeEEECCeeeEeeCCCChHHCcCHHHHHHHh
Confidence 99996543 468899999999999999999999999999999999998
No 8
>PHA02587 30 DNA ligase; Provisional
Probab=100.00 E-value=1.1e-60 Score=570.50 Aligned_cols=447 Identities=21% Similarity=0.284 Sum_probs=333.0
Q ss_pred HHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCcChHHHHHHhh
Q 001083 13 VSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSADAVRLIN 92 (1160)
Q Consensus 13 ~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~~s~~~~~L~~ 92 (1160)
-+++++|+++.++++|.+||.+... .+.+--+++|.+...- .|||+.
T Consensus 3 ~~il~~~~~~~~~~~k~~il~~~~~----n~~l~~~~~~~~~~~~----~~~~~~------------------------- 49 (488)
T PHA02587 3 LDILNELASTDSTKEKEAILKENKD----NELLKEVFRLTYNKQI----NFGIKK------------------------- 49 (488)
T ss_pred HHHHHHHHhccCcchHHHHHHhccc----ChHHHHHHHHHhCcce----eEeeeE-------------------------
Confidence 4789999999999999998887633 3445667788876552 566442
Q ss_pred hhcCCCCCCCCCHHHHHHHHhhhhcCCCCCCCcHHH-HHHHHHHHHhhhh-HHHHHHHHHHHHHhCCHHHHHHHHHHHhh
Q 001083 93 WRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKE-LNDLLDRLASSEN-RAEKISVLSTLIKKTNAQEMKWIIMIILK 170 (1160)
Q Consensus 93 wk~~~~~~~~GD~~~~a~~vl~~r~~~~~~~LTi~e-Vn~~Ld~LA~~~~-~~~k~~il~~ll~~~t~~E~k~l~RiIlk 170 (1160)
|.+++.. ....+.+++.+ +..++.+||+..- ...++..|..++.+|+|.|++||+|||++
T Consensus 50 ~~~~~~~------------------~~~~~~~~~~~~~~~~~~~l~~r~~~~~~~~~~l~~ll~~~~~~e~~~l~rli~~ 111 (488)
T PHA02587 50 WPKPGHV------------------EGSDGMLSLEDLLDFLEFDLATRKLTGNAAIEELAQILSSMNEDDAEVLRRVLMR 111 (488)
T ss_pred cCCCccc------------------cCCCCceeHHHHHHHHHHHHHHhhcchhHHHHHHHHHHHhCCHHHHHHHHHHHhc
Confidence 2111110 00123456666 4455667886643 56678899999999999999999999999
Q ss_pred hhccCCcccccccccCccHHHHHhhhCCHHHHHHHHhhhhccccccccccCCcccc-ccccccCChHHHHHhcCCCcEEE
Q 001083 171 DLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRNQRHKRQDIEVGKAVRP-QLAMRIGDAHAAWRKLHGKEVVI 249 (1160)
Q Consensus 171 dLriGi~e~til~~~hpda~~~~~~~~DL~~V~~~L~~~~~~~~~~~i~~g~p~~P-mLA~~~~~~~~~~~~~~~~~~~~ 249 (1160)
+||||+++++|+++||+ +.|++| |||++... ++++++-+.+|++
T Consensus 112 ~lriGvs~~~i~~~~~~---------------------------------~~P~~p~mLA~~~~~--~~~~~~~~~~~~~ 156 (488)
T PHA02587 112 DLECGASEKIANKVWKG---------------------------------LIPEQPQMLASSFSE--KLIKKNIKFPAYA 156 (488)
T ss_pred ccCCCccHHHHHHHhcC---------------------------------CccCCCCccCCCCCH--HHHHhhccCcEEE
Confidence 99999999999988864 578887 99998543 4566632448999
Q ss_pred EEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcc-----cCceeeceeEEEEeCCCCccccccc------
Q 001083 250 ECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL-----VDRCILDGEMLVWDTSLNRFAEFGS------ 318 (1160)
Q Consensus 250 E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~-----~~~~ILDGElv~~d~~~~~~~pF~~------ 318 (1160)
|+||||+|||+|++++.+++|||+|++++. +|++.+.+..... +.++|||||+|+|+..++ .||+.
T Consensus 157 E~K~DG~R~q~h~~~~~v~l~SR~g~~~~~-~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~~~~~~--~~~~~~f~~~~ 233 (488)
T PHA02587 157 QLKADGARCFADIDADGIEIRSRNGNEYLG-LDLLKEELKKMTAEARQRPGGVVIDGELVYVEVETK--KPNGLSFLFDD 233 (488)
T ss_pred EEccCceEEEEEEeCCEEEEEecCCccccC-ChhHHHHHHHHhhhhcccCCcEEEEeEEEEEecccC--CCccchhhccc
Confidence 999999999999999999999999999986 5887776543221 478999999999987655 34431
Q ss_pred -----H-HHHHHHhc-cCC----------CCCCccEEEEEEeeeecC---CcccccCCHHHHHHHHHHhhcc-CCCccee
Q 001083 319 -----N-QEIAKAAR-DGL----------SSDRQVLCYFAFDVLYVG---DTSVIHQSLKERHELLQKVVKP-SKGRLET 377 (1160)
Q Consensus 319 -----l-q~i~~~~r-~~~----------~~~~~~~~~~vFDiL~ln---g~sl~~~pl~eRr~~L~~~v~~-~~~~~~i 377 (1160)
. |.+..+.+ .+. .....+++|+|||||+++ |..+++.||.+||++|++++.. ..+++.+
T Consensus 234 ~~~~~f~q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~~~~i~l 313 (488)
T PHA02587 234 SKAKEFVGVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCGYDRVEL 313 (488)
T ss_pred ccccchhhhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcCCCcEEE
Confidence 0 22222221 110 012245999999999653 4447789999999999999963 2334433
Q ss_pred eccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEE
Q 001083 378 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLI 457 (1160)
Q Consensus 378 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvI 457 (1160)
+ ....+++.+++.++|+++++.|+||||+|+++|+|.+| |+.+|+|+|+.+ ++|++|
T Consensus 314 ~-----------------~~~~~~~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~G-Rs~~WlKiK~~~-----~~dlvV 370 (488)
T PHA02587 314 I-----------------ENQVVNNLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIKFKEVI-----DIDLEI 370 (488)
T ss_pred E-----------------eeEEcCCHHHHHHHHHHHHhCCCCeEEEECCCCCCCCC-CCCCcEEecCCC-----ceEEEE
Confidence 2 12346789999999999999999999999999999999 888999999974 899999
Q ss_pred EEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCC
Q 001083 458 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 537 (1160)
Q Consensus 458 IG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~ 537 (1160)
||+|+|. +++|.+|+|+|++++ + . .+|+||||||++++++|...+. . +| +... ..
T Consensus 371 vG~~~~~-k~~~~~gs~ll~~~~--g------~--~~~~vgsGftd~~~~~l~~~~~--~---------~p-~~~~--~~ 425 (488)
T PHA02587 371 VGVYEHK-KDPNKVGGFTLESAC--G------K--ITVNTGSGLTDTTHRKKDGKKV--V---------IP-LSER--HE 425 (488)
T ss_pred EeEEeCC-CCCCceeEEEEEecC--C------c--EEEEECCCCChHHhhhhccccc--e---------ec-cccc--ch
Confidence 9999965 578889999997653 1 2 4799999999999999876543 0 11 1111 12
Q ss_pred CCCCcEEEeCCc-ceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHH
Q 001083 538 KERPDVWIESPE-KSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVE 599 (1160)
Q Consensus 538 ~~~Pdvwi~~P~-~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~e 599 (1160)
..++.+|.+++. ...|+||+++.. ..|+.|++|++||||||+|+|+||+ +|+|++++..
T Consensus 426 ~~r~~~~~~~~~~~~~V~EV~~~~i-t~S~~~~~g~sLRfPrf~r~R~DK~--~Adt~~~v~~ 485 (488)
T PHA02587 426 LDREELMANKGKYIGKIAECECNGL-QRSKGRKDKVSLFLPIIKRIRIDKT--EANTLEDVFA 485 (488)
T ss_pred hcchhhhhCcccccceEEEEEeceE-EeCCCCCCCeeEEccceeEEeCCCC--cccCHHHHhh
Confidence 346677876221 137999997543 4788999999999999999999999 9999999863
No 9
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.4e-58 Score=543.75 Aligned_cols=422 Identities=26% Similarity=0.397 Sum_probs=345.6
Q ss_pred CCCCCHHHHHHHHhhhhcCCCCCCCcHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhccCCccc
Q 001083 100 PNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLKLGISEK 179 (1160)
Q Consensus 100 ~~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~t~~E~k~l~RiIlkdLriGi~e~ 179 (1160)
...||+|..+..+.. +.+|+..|..++...| . . .++..|+..++ +|++++
T Consensus 18 ~~~Gdlg~~~~~~~~-----------v~~v~~~~~~~~~~~g-~-~-~~~~~L~~~~~----------------~gv~~~ 67 (444)
T COG1793 18 IPQGDLGEGAVLLWD-----------VEGVYLTLSKVAERTG-Q-E-RLLWLLLDEAD----------------IGVSEG 67 (444)
T ss_pred cccCccchhheeeee-----------cccchhhHHHHHhhcC-c-h-hHHHHHHHhcc----------------cchhhH
Confidence 568999998766543 8899999999998888 2 2 78888888888 999999
Q ss_pred ccccccCccHHHHHhhhCCHHHHHHHHhhh-hccccccccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEE
Q 001083 180 SIFHEFHPDAEDLFNVTCDLKLVCEKLKDR-NQRHKRQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRI 258 (1160)
Q Consensus 180 til~~~hpda~~~~~~~~DL~~V~~~L~~~-~~~~~~~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~ 258 (1160)
+++.++....+..|+.++|++.++..+... ..++....+.+|.|+.||||.......+...+..+ .|++|+||||+|+
T Consensus 68 ~~~~ala~~~~~~~~~~~d~g~~a~~~~~~~~~~~~~~~~~~~~p~~~~la~~~~~~~~~~~~~~~-~w~~E~K~DG~R~ 146 (444)
T COG1793 68 TVLDALAEAVERAYLWHNDLGALAKILLTLGAEALDKATLLPGRPLPPMLAPMLASLEEALPRDGG-DWAYEEKFDGYRV 146 (444)
T ss_pred HHHHHHHHHhhhhhccCCCchhhhhhhhhcccccccccccccCCccchhhccccccccccCCCCCC-CEEEEEeeceEEE
Confidence 999877665888899999999988877543 34445566789999999999998877665555433 5999999999999
Q ss_pred EEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeEEEEeCCCCcccccccHHHHHHHhccC-CCCCCccE
Q 001083 259 QIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDG-LSSDRQVL 337 (1160)
Q Consensus 259 qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~-~~~~~~~~ 337 (1160)
|+|+.++.|++|||+|.|+|..+|++...+...+..+++|||||+|++|+. ...||+.+|...++..+. ......++
T Consensus 147 q~h~~~~~vrl~SR~g~d~T~~fP~~~~~~~~~l~~~~~iiDGE~V~~~~~--~~~~F~~Lq~r~~~k~~v~~~~~~~~~ 224 (444)
T COG1793 147 QIHIDGGKVRLYSRNGEDWTGRFPDILEAAAEALPADDFILDGEIVVLDEE--GRLDFQALQQRLRRKYDVAKLRRETPL 224 (444)
T ss_pred EEEEcCCEEEEEeCCCccchhhChHHHHHHHhcCCCCceEEeeeEEEECCC--CCCCHHHHHHHhhhccchhhhccCCce
Confidence 999999999999999999999999766666566777899999999999975 458998887655332110 01122359
Q ss_pred EEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcC
Q 001083 338 CYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENR 417 (1160)
Q Consensus 338 ~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g 417 (1160)
+|++|||||+||.+|.++||.+||++|++++... +.+.+. .....++.++++.+|+.+++.|
T Consensus 225 ~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~-~~~~~~-----------------~~i~~~~~~~~~~~~~~a~~~g 286 (444)
T COG1793 225 VLFAFDLLYLDGEDLRGLPLEERRALLEELVKSS-DKIEIA-----------------ERIPFSDAEEGEAFLEAAIELG 286 (444)
T ss_pred EEEEEEEEeECCcccccCchHHHHHHHHHHhccc-cccccc-----------------cceeccChhhHHHHHHHHHhcC
Confidence 9999999999999999999999999999999874 222111 0122378899999999999999
Q ss_pred CceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeee
Q 001083 418 DEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRV 497 (1160)
Q Consensus 418 ~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kV 497 (1160)
+||||+|+++|+|++|+|+..|+|+|+. +++|++|+|+++|.|+|+ .+|+|+||+|++.+ +.|.++|+|
T Consensus 287 ~EGvv~K~~ds~Y~~g~R~~~W~K~K~~-----~~~d~vv~G~~~g~Gkr~-~~~slll~~~~~~~-----~~~~~v~kV 355 (444)
T COG1793 287 LEGVVAKRPDSPYRAGGRSNKWLKVKRD-----ETLDLVVVGAEYGKGKRS-LYGSLLLGVYDGDG-----GGLLYVGKV 355 (444)
T ss_pred ceEEEEeCCCCCcCCCCCCCcceEeccC-----CcccEEEEEEEecCCccc-ccceEEEEEEcCCC-----ceEEEEecc
Confidence 9999999999999999999999999997 489999999999999999 89999999998764 379999999
Q ss_pred cCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC--Cceee
Q 001083 498 GTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA--PYSLR 575 (1160)
Q Consensus 498 gtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~--g~tLR 575 (1160)
||||+++++++|.++|++++... . .| ..+..|..+|. +|+||++... ..+..|.. |++||
T Consensus 356 gtGf~~~~l~~l~~~l~~~~~~~----~-~~----------~~~~~~~~~p~--~V~EV~~~~~-t~~~~~r~~~~~~lR 417 (444)
T COG1793 356 GTGFSDAELEELTERLEPLIVSR----F-NG----------KVPGKVVPPPG--LVAEVRFAEI-TKSGRLRHASGLGLR 417 (444)
T ss_pred cCCCCHHHHHHHHHHHHHhccCc----C-CC----------ccCceeecCCc--EEEEEEEeec-ccCCceecccCcccC
Confidence 99999999999999999987641 1 11 01121554454 8999986543 25677776 89999
Q ss_pred CceeeeeecCCCccCcCCHHHHHHHH
Q 001083 576 FPRIDRVRYDKPWHDCLDVQSFVELV 601 (1160)
Q Consensus 576 FPR~~riR~DK~~~d~~t~~el~el~ 601 (1160)
|||+.++|+||.+.+++|++++.+|+
T Consensus 418 fpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 418 FPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred cCcccccccccCcccccccccchhhc
Confidence 99999999999999999999998875
No 10
>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=2.6e-54 Score=488.36 Aligned_cols=288 Identities=28% Similarity=0.422 Sum_probs=239.9
Q ss_pred CCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeEEEEeCCCCcccccccHHHH
Q 001083 243 HGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEI 322 (1160)
Q Consensus 243 ~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF~~lq~i 322 (1160)
.+.+|++|+||||+|||+|++++.|++|||||+++|..+|.+...+ ..+...+||||||||+||.. ++ .+|+.+|..
T Consensus 10 ~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~-~~~~~~~~iLDGElv~~d~~-g~-~~F~~l~~r 86 (298)
T TIGR02779 10 TGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAAL-AALPILPAVLDGEIVVLDES-GR-SDFSALQNR 86 (298)
T ss_pred CCCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHHHHH-HhCCCCcEEEEeEEEEECCC-CC-CCHHHHHhh
Confidence 4678999999999999999999999999999999999889887764 34456799999999999974 33 589777654
Q ss_pred HHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCC
Q 001083 323 AKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHN 402 (1160)
Q Consensus 323 ~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~ 402 (1160)
... . .. .+++|+||||||+||++++++||.+|+++|++++.+.++++.+.. . ..++
T Consensus 87 ~~~---~--~~-~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~-----------------~-~~~~ 142 (298)
T TIGR02779 87 LRA---G--RD-RPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDR-----------------Y-SVHF 142 (298)
T ss_pred hhc---C--CC-CceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCCCceeEe-----------------c-ccCc
Confidence 322 1 11 349999999999999999999999999999999987654432210 0 2356
Q ss_pred HHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCccceEEEEEecCC
Q 001083 403 VDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERP 482 (1160)
Q Consensus 403 ~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~ 482 (1160)
.+++.++|++++++|+||||+|+++|+|.||+ +..|+|+|+.+ +.|++|+|+++|.|++ |.+|+|+||++++.
T Consensus 143 ~~~~~~~~~~~~~~g~EGiv~K~~ds~Y~~Gr-s~~WlK~K~~~-----~~d~vV~G~~~g~g~~-~~~gslll~~~~~~ 215 (298)
T TIGR02779 143 EGDGQALLEAACRLGLEGVVAKRRDSPYRSGR-SADWLKLKCRR-----RQEFVIGGYTPPNGSR-SGFGALLLGVYEGG 215 (298)
T ss_pred hhHHHHHHHHHHHcCCceEEEeCCCCCCCCCC-CCCcEEEccCC-----CCEEEEEEEECCCCCC-CccceEEEEEECCC
Confidence 78999999999999999999999999999995 99999999986 8999999988999988 77999999999642
Q ss_pred CCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeee
Q 001083 483 APDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRT 562 (1160)
Q Consensus 483 ~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~ 562 (1160)
.|.++|+||||||++++++|.+.|.+++... . +|. .....|++||+ |. +|+||++.
T Consensus 216 -------~l~~vg~vgsG~s~~~~~~l~~~l~~~~~~~----~-~~~------~~~~~~~~wv~-P~--lV~eV~~~--- 271 (298)
T TIGR02779 216 -------GLRYVGRVGTGFSEAELATIKERLKPLESKP----D-KPG------AREKRGVHWVK-PE--LVAEVEFA--- 271 (298)
T ss_pred -------eEEEEeEecCCCCHHHHHHHHHHHHhhccCc----C-CCC------cccCCCCEEeC-Ce--EEEEEEec---
Confidence 6899999999999999999999999987652 1 221 12346899998 74 89999763
Q ss_pred eecccccCCceeeCceeeeeecCCCccCcC
Q 001083 563 IRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 592 (1160)
Q Consensus 563 ~~s~~~~~g~tLRFPR~~riR~DK~~~d~~ 592 (1160)
.++.|++||||||+++|+||+|+||+
T Consensus 272 ----~~t~~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 272 ----GWTRDGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred ----ccCCCCeEeccEEEeeeCCCCHHHcc
Confidence 23458899999999999999999996
No 11
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=9e-54 Score=523.56 Aligned_cols=307 Identities=26% Similarity=0.395 Sum_probs=253.1
Q ss_pred cccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCce
Q 001083 218 IEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRC 297 (1160)
Q Consensus 218 i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ 297 (1160)
..++.+|+||||...... .+.+..|++|+||||+|||+|++++.|++|||||+++|..+|++... ...+...+|
T Consensus 455 ~~~~~~v~PMLA~~~~~~-----~~~~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~~-~~~l~~~~~ 528 (764)
T PRK09632 455 AEEADDLAPMLATAGTVA-----GLKASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAAL-AEDLADHHV 528 (764)
T ss_pred CCCCCCCcCccCCcCCCC-----CCCCCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHHH-HhhCCCcce
Confidence 568899999999976431 24567899999999999999999999999999999999999998874 345556799
Q ss_pred eeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCccee
Q 001083 298 ILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET 377 (1160)
Q Consensus 298 ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i 377 (1160)
|||||||+||.. ++ .+|+.+|... + ..+++|+||||||+||++|+++||.+||++|++++.+ .+.+.+
T Consensus 529 ILDGEiVvld~~-G~-~~F~~Lq~r~---~------~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~-~~~i~~ 596 (764)
T PRK09632 529 VLDGEIVALDDS-GV-PSFGLLQNRG---R------DTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPS-GGSLTV 596 (764)
T ss_pred eeeeEEEEeCCC-CC-CCHHHHhhhh---h------cCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCC-CCcEEe
Confidence 999999999975 33 5898777531 1 1349999999999999999999999999999999863 223321
Q ss_pred eccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEE
Q 001083 378 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLI 457 (1160)
Q Consensus 378 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvI 457 (1160)
+ .....++.++|+.++++|.||||+|+++|+|.+|+|+.+|+|+|+.| +.|++|
T Consensus 597 --s-------------------~~~~~~~~~~l~~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~-----~~e~VI 650 (764)
T PRK09632 597 --P-------------------PLLPGDGAEALAYSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWR-----TQEVVI 650 (764)
T ss_pred --c-------------------ceecccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCC-----ceEEEE
Confidence 1 01123478899999999999999999999999999999999999986 899999
Q ss_pred EEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCC
Q 001083 458 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNS 537 (1160)
Q Consensus 458 IG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~ 537 (1160)
+|+++|.|+++|.+|+||||+++++ .|.++|+||||||++++++|.++|.++.+. .|| |.......
T Consensus 651 ~G~~~g~G~r~g~~gsLLlGv~d~~-------~L~yvGkVGTGftd~~l~~L~~~L~~l~~~------~~P-f~~~~~~~ 716 (764)
T PRK09632 651 GGWRPGEGGRSSGIGSLLLGIPDPG-------GLRYVGRVGTGFTERELASLKETLAPLHRD------TSP-FDADLPAA 716 (764)
T ss_pred EEEEcCCCCcCCceeeEEEEEEcCC-------eeEEEEEEeCCCCHHHHHHHHHHHHhhccC------CCC-cccccccc
Confidence 9999999999999999999999643 589999999999999999999999987653 123 32111122
Q ss_pred CCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcC
Q 001083 538 KERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 592 (1160)
Q Consensus 538 ~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~ 592 (1160)
..+|++||+ |. +|+||++. .++.+++||||||+++|.||+++||.
T Consensus 717 ~~~~~~WV~-P~--LV~EV~f~-------e~T~~g~LR~P~f~glR~DK~p~dv~ 761 (764)
T PRK09632 717 DAKGATWVR-PE--LVGEVRYS-------EWTPDGRLRQPSWRGLRPDKKPGDVV 761 (764)
T ss_pred cCCCcEEEe-cc--EEEEEEEe-------eccCCCceecceEEEeeCCCCHHHcc
Confidence 457899999 76 89999753 24567899999999999999999985
No 12
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.7e-51 Score=471.53 Aligned_cols=315 Identities=22% Similarity=0.353 Sum_probs=247.6
Q ss_pred ccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCc
Q 001083 217 DIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDR 296 (1160)
Q Consensus 217 ~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~ 296 (1160)
++.+|.|++||||..+..++ .+.+|++|+||||+|||+|+++++|++|||||+++|..||+|.+.+.. +.+.+
T Consensus 2 ~~~~~~~i~PMLA~~~~~~~------~~~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~~-~~~~~ 74 (350)
T PRK08224 2 DLPVMPPVEPMLAKSVDAIP------PGDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRA-ELPER 74 (350)
T ss_pred CCCCCCCcCCccCCccCCCC------CCCcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHHh-hCCCC
Confidence 46789999999999876432 345799999999999999999999999999999999999999887643 45679
Q ss_pred eeeceeEEEEeCCCCcccccccHHHHHHHhccCC--CCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCc
Q 001083 297 CILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGL--SSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 374 (1160)
Q Consensus 297 ~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~--~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~ 374 (1160)
||||||||+++.. + .+|+.+|.......... .....+++|++|||||+||.+|+++||.+|+++|++++... +.
T Consensus 75 ~vLDGEiVv~~~~-~--~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~-~~ 150 (350)
T PRK08224 75 CVLDGEIVVARDG-G--LDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGS-GP 150 (350)
T ss_pred EEEeeEEEEeCCC-C--CCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCC-Cc
Confidence 9999999999843 2 78988876432110000 01123499999999999999999999999999999998543 23
Q ss_pred ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCccc
Q 001083 375 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLD 454 (1160)
Q Consensus 375 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lD 454 (1160)
+.+. ....+.++++++|++++++|.||||+|+.+|+|.+|+|+ |+|+|+.+ ++|
T Consensus 151 i~~~-------------------~~~~~~~~~~~~~~~a~~~G~EGIV~Kr~dS~Y~~Grr~--WlKiK~~~-----~~d 204 (350)
T PRK08224 151 VHLT-------------------PATTDPATARRWFEEFEGAGLDGVIAKPLDGPYQPGKRA--MFKVKHER-----TAD 204 (350)
T ss_pred EEEe-------------------cccCCHHHHHHHHHHHHhCCCcEEEEeCCCCCcCCCCcC--EEEEccCC-----cEE
Confidence 3221 012457899999999999999999999999999999987 99999974 899
Q ss_pred EEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCC----Cc
Q 001083 455 VLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP----SF 530 (1160)
Q Consensus 455 lvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP----~~ 530 (1160)
++|+|+++|.|+ |.+|+|+||+|++++ ++.++|+|| |||++++++|.+.|++++.... .+| +|
T Consensus 205 ~vI~G~~~g~~~--~~~gslllg~~d~~g------~l~~vG~v~-Gf~~~~~~~L~~~l~~l~~~~~----~~p~~~~pf 271 (350)
T PRK08224 205 CVVAGYRYHKSG--PVVGSLLLGLYDDDG------QLHHVGVTS-AFPMARRRELTAELEPLRTPFG----DHPWNWAAF 271 (350)
T ss_pred EEEEEEEcCCCC--CccccEEEEEECCCC------cEEEEEEEC-CCCHHHHHHHHHHHHhhhcCCC----CCccccCcc
Confidence 999999998875 789999999997543 688999986 9999999999999998875411 012 22
Q ss_pred ccccC-----CCCCCCcEE--EeCCcceEEEEEEeeeeeeecccccCCceeeCc-eeeeeecCCCccCcC
Q 001083 531 YQVTN-----NSKERPDVW--IESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 592 (1160)
Q Consensus 531 ~~~~~-----~~~~~Pdvw--i~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFP-R~~riR~DK~~~d~~ 592 (1160)
..... ....+..+| ++ |. +|+||++ ..++ +..||+| +|+++|.||+++||+
T Consensus 272 ~~~~~~~~~~~~~~~~~~w~~v~-P~--lv~eV~~-------~~~t-~~~lR~p~~f~g~r~Dk~p~~v~ 330 (350)
T PRK08224 272 TGRAPGGPSRWSAGKDLSWVPLR-PE--RVVEVRY-------DHME-GGRFRHTAQFLRWRPDRDPRSCT 330 (350)
T ss_pred cccCCCccccccccCCcEEEeee-EE--EEEEEec-------Cccc-CCeecCCCeeEEEcCCCChHHCC
Confidence 11100 011235789 98 75 7888865 2344 4599998 999999999999996
No 13
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.1e-50 Score=500.38 Aligned_cols=304 Identities=26% Similarity=0.404 Sum_probs=244.6
Q ss_pred CccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeece
Q 001083 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (1160)
Q Consensus 222 ~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDG 301 (1160)
..++||||..+..+. .+.+|++|.||||+|||+|++++.+++|||||+++|..||+|.+.+. .+...+|||||
T Consensus 232 ~~i~PMLAt~~~~~p------~g~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~-~l~~~~~ILDG 304 (860)
T PRK05972 232 DFLAPQLATLVDRPP------SGDGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAA-ALGLPDAWLDG 304 (860)
T ss_pred cccCcccCccCCCCC------CcCceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHH-hcCCCceeEeE
Confidence 458999999877653 35689999999999999999999999999999999999999988764 45568999999
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCC-cceeecc
Q 001083 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG-RLETLVP 380 (1160)
Q Consensus 302 Elv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~-~~~i~~p 380 (1160)
|||+||.. ++ .+|+.+|..... + . ..+++|++|||||+||.+|+++||.+|+++|++++.+..+ ++.+.
T Consensus 305 EIVvld~~-G~-~~F~~Lq~r~~~---~--~-~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s-- 374 (860)
T PRK05972 305 EIVVLDED-GV-PDFQALQNAFDE---G--R-TEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFS-- 374 (860)
T ss_pred EEEEECCC-CC-CCHHHHHHHhhc---c--C-CCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEe--
Confidence 99999975 33 489877754322 1 1 1349999999999999999999999999999999976532 33221
Q ss_pred CCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEE
Q 001083 381 DHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGG 460 (1160)
Q Consensus 381 ~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~ 460 (1160)
.....+..++|+.+++.|+||||+|+.+|+|.+| |+.+|+|+|+.+ +.|+||+|+
T Consensus 375 -------------------~~~~~~g~~ll~~a~~~GlEGIVaKr~dS~Y~~G-Rs~~WlKiK~~~-----~~E~VIgGy 429 (860)
T PRK05972 375 -------------------EHFDAGGDAVLASACRLGLEGVIGKRADSPYVSG-RSEDWIKLKCRA-----RQEFVIGGY 429 (860)
T ss_pred -------------------ceecchHHHHHHHHHHcCCceEEEeCCCCCCCCC-CCCCcEEEecCC-----CceEEEEEE
Confidence 1122457889999999999999999999999988 899999999975 567766666
Q ss_pred EeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCC
Q 001083 461 YYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKER 540 (1160)
Q Consensus 461 ~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~ 540 (1160)
+.|.|+|+| +|+||||++++. .|+++|+||||||++++++|.++|.++.+. .+| |..........
T Consensus 430 ~~~~Gkr~g-~gSLLlGvyd~~-------~L~yvGkVGTGfsd~~l~~L~~~L~~l~~~------~~P-f~~~~~~~~~~ 494 (860)
T PRK05972 430 TDPKGSRSG-FGSLLLGVHDDD-------HLRYAGRVGTGFGAATLKTLLPRLKALATD------KSP-FAGKPAPRKAR 494 (860)
T ss_pred eCCCCcccc-ceeEEEEEecCC-------EEEEEEEECCCCCHHHHHHHHHHHHhhccC------CCC-ccccCccccCC
Confidence 667888887 999999999742 799999999999999999999999987653 133 32211112234
Q ss_pred CcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcC
Q 001083 541 PDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCL 592 (1160)
Q Consensus 541 Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~ 592 (1160)
+++||+ |. +|+||++.. ++.+..||||+|+++|.||+++||.
T Consensus 495 ~~~WV~-P~--LV~EV~f~e-------~T~~g~LR~P~F~glR~DK~p~ev~ 536 (860)
T PRK05972 495 GVHWVK-PE--LVAEVEFAG-------WTRDGIVRQAVFKGLREDKPAREVV 536 (860)
T ss_pred CCEEEc-cC--EEEEEEEee-------ccCCCCCccceEEEeecCCChHHhC
Confidence 579998 86 899998632 3445689999999999999999986
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.7e-49 Score=480.83 Aligned_cols=310 Identities=22% Similarity=0.274 Sum_probs=240.5
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcc----cCceee
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVL----VDRCIL 299 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~----~~~~IL 299 (1160)
++||||.....++ .+.+|++|+||||+|||+|++++.|++|||||+++|..||++.+.+..... ..+|||
T Consensus 1 ~~PMLa~~~~~~p------~g~~w~~E~K~DG~R~~~h~~~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~~~~~~IL 74 (610)
T PRK09633 1 MKPMQPTLTTSIP------IGDEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEFCESNFEHLKEELPLTL 74 (610)
T ss_pred CCCCcCCcCCCCC------CCCcEEEEEeEcceEEEEEEECCEEEEEeCCCCcchhhhhHHHHHHHhhhhccccCCceee
Confidence 4799998876543 467899999999999999999999999999999999999999876533111 137999
Q ss_pred ceeEEEEeCCCCcccccccHHHHHHHhccC-C--CCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcce
Q 001083 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDG-L--SSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE 376 (1160)
Q Consensus 300 DGElv~~d~~~~~~~pF~~lq~i~~~~r~~-~--~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~ 376 (1160)
|||||+||..+. .+|+.+|......+.. . .....+++|+||||||+||.+|++.||.+||++|++++.+......
T Consensus 75 DGEiVvld~~g~--~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~ 152 (610)
T PRK09633 75 DGELVCLVNPYR--SDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPAS 152 (610)
T ss_pred eeEEEEecCCCC--CCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhcccccc
Confidence 999999986432 5887777543211110 0 0112348999999999999999999999999999999975431000
Q ss_pred eeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEE
Q 001083 377 TLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVL 456 (1160)
Q Consensus 377 i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlv 456 (1160)
+ . +.+.+ ....+.+.++++++|+.+++.|.||||+|+.+|+|.+|+|+.+|+|+|+.+ +.|++
T Consensus 153 ---~-~-------~~~~~-~i~~~~~~~~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~-----~~d~v 215 (610)
T PRK09633 153 ---P-D-------PYAKA-RIQYIPSTTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWR-----YVHVI 215 (610)
T ss_pred ---c-c-------ccccc-ceEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccC-----CceeE
Confidence 0 0 00000 012334677999999999999999999999999999999999999999963 78998
Q ss_pred EEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCC
Q 001083 457 IIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNN 536 (1160)
Q Consensus 457 IIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~ 536 (1160)
|+|+..|. |.|++|+++. ++|.++|+||||||++++++|.+.|+++.+.
T Consensus 216 I~G~~~~~-------g~~llgv~~~-------g~l~~vGkvgtGft~~~~~~L~~~l~~l~~~----------------- 264 (610)
T PRK09633 216 VTGYDPSN-------GYFTGSVYKD-------GQLTEVGSVKHGMEDEERQTLRAIFKQNGTK----------------- 264 (610)
T ss_pred EEEEecCC-------ceEEEEEecC-------CeEEEEEEecCCCCHHHHHHHHHHHHHhccC-----------------
Confidence 88865543 3688898842 2799999999999999999999999876432
Q ss_pred CCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHHHHH
Q 001083 537 SKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 601 (1160)
Q Consensus 537 ~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~el~ 601 (1160)
...+.+|++ |. +|+||++.. + +|+.||||+|+++|.||+++||++.++..+++
T Consensus 265 -~~~~~~wV~-P~--LV~EV~~~e-------~-t~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~ 317 (610)
T PRK09633 265 -TKSGEYTLE-PS--ICVTVACIT-------F-DGGTLREPSFVSFLFDMDPTECTYQQLQRQLA 317 (610)
T ss_pred -CCCCcEEEe-ee--EEEEEEEee-------c-CCCeEEeeEEeEEEcCCChHHcchhhhhhhhc
Confidence 123589999 75 899998632 2 27899999999999999999999887776554
No 15
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=8.4e-45 Score=405.29 Aligned_cols=272 Identities=24% Similarity=0.344 Sum_probs=213.3
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
++||||...... +.+.+|++|+||||+|||+|+.++.+++|||+|+++|..+|++.... ...+|||||||
T Consensus 3 ~~PmLa~~~~~~------~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~~----~~~~~vLDGEl 72 (275)
T PRK07636 3 ISPMLLESAKEP------FNSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNLD----IPDGTVLDGEL 72 (275)
T ss_pred cCCccCCcCCCC------CCCCcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhhh----cCCCEEEEeEE
Confidence 789999887643 34668999999999999999999999999999999999899887642 24679999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 383 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 383 (1160)
|+||.. ++ .+|+.+|......+ .....+++|+||||||+||++++++||.+|+++|++++.+.+ ++.++
T Consensus 73 v~~d~~-g~-~~F~~l~~r~~~~~---~~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~----- 141 (275)
T PRK07636 73 IVLGST-GA-PDFEAVMERFQSKK---STKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPHP-NVKII----- 141 (275)
T ss_pred EEECCC-CC-CCHHHHHHHhcccc---ccccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCCC-CEEEc-----
Confidence 999964 33 47977765432211 111245899999999999999999999999999999987543 22211
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeC
Q 001083 384 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYG 463 (1160)
Q Consensus 384 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~G 463 (1160)
....+++.++|+.++++|.||||+|+++|+|.+|+|+.+|+|+|+. ++.|++|+|+..|
T Consensus 142 ----------------~~~~~~~~~~~~~~~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK~~-----~~~e~vV~G~~~~ 200 (275)
T PRK07636 142 ----------------EGIEGHGTAYFELVEERELEGIVIKKANSPYEINKRSDNWLKVINY-----QYTDVLITGYRKE 200 (275)
T ss_pred ----------------ccccccHHHHHHHHHHcCCcEEEEeCCCCCCCCCCCCCCeEEEecC-----CeEEEEEEEEecC
Confidence 1123467889999999999999999999999999999999999974 5899988776432
Q ss_pred CCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcE
Q 001083 464 SGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDV 543 (1160)
Q Consensus 464 ~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdv 543 (1160)
.+|.+ ||+++ + . ++|+||| |+++++++|.+.|.+.... ..++.+
T Consensus 201 ------~~g~l-lg~~~--g------~--~~G~vgt-~~~~~~~~l~~~l~~~~~~------------------~~~~~~ 244 (275)
T PRK07636 201 ------EFGLL-LSYLD--G------R--SAGIMEF-MPYDARKKFYKRAKRLVVG------------------EDKKFV 244 (275)
T ss_pred ------CCcEE-EEecC--C------e--EEEEECC-CCHHHHHHHHHHhhhhccC------------------ccCCCE
Confidence 25655 78764 1 3 5799999 9999999999888654321 235789
Q ss_pred EEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeee
Q 001083 544 WIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 583 (1160)
Q Consensus 544 wi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR 583 (1160)
|++ |. +|.||++. .++.+..||||+|+++|
T Consensus 245 wv~-P~--lv~eV~~~-------e~t~~g~lR~p~f~g~r 274 (275)
T PRK07636 245 YIE-PI--IGCRVKHR-------FKTKNGMLRIPSFVEWR 274 (275)
T ss_pred EeC-Cc--EEEEEEEE-------EecCCCCEEccEEEEEe
Confidence 998 75 88888752 23444559999999998
No 16
>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=7.6e-44 Score=385.73 Aligned_cols=213 Identities=29% Similarity=0.536 Sum_probs=183.0
Q ss_pred cccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeC-CEEEEEeCCCCCCCcchhhHHHHHHHhc--
Q 001083 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNV-- 292 (1160)
Q Consensus 216 ~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g-~~v~~fSR~g~d~t~~~~~l~~~l~~~~-- 292 (1160)
..|++|.||+||||++..+++++++.+.+.+|++|+||||+|||+|+.+ +.|++|||||+++|..+|++.+.+...+
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 4588999999999999888888888898889999999999999999986 8999999999999999999988775543
Q ss_pred ccCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCC
Q 001083 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK 372 (1160)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~ 372 (1160)
...+||||||||+||..++++.||+.++...+.. ........+++|++|||||+||++|+++||.+|+++|++++.+.+
T Consensus 82 ~~~~~iLDGElv~~~~~~g~~~~F~~l~~r~~~~-~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~ 160 (219)
T cd07900 82 SVKSFILDSEIVAYDRETGKILPFQVLSTRKRKD-VDANDIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVP 160 (219)
T ss_pred cCccEEEeeEEEEEEcCCCCCcChHHHhhhcccc-cccccCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcCCCC
Confidence 3678999999999998777788998877543211 111112245999999999999999999999999999999998777
Q ss_pred CcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCC--CCCcCCCCCCCeEEEcccc
Q 001083 373 GRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEY 446 (1160)
Q Consensus 373 ~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~d--s~Y~pGkRs~~WlKlKpeY 446 (1160)
+++.++. ...+++.+++.++|++++++|.||||+|+++ |+|.||+|+.+|+|+|++|
T Consensus 161 ~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~~~s~Y~~g~Rs~~W~K~K~dY 219 (219)
T cd07900 161 GRFQFAT-----------------SKDSEDTEEIQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKDY 219 (219)
T ss_pred CeEEEEE-----------------EEecCCHHHHHHHHHHHHHcCCceEEEecCCCCCccCCCCcCCCceEeCCCC
Confidence 6665431 3456789999999999999999999999999 9999999999999999998
No 17
>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=100.00 E-value=3e-42 Score=413.71 Aligned_cols=257 Identities=25% Similarity=0.371 Sum_probs=203.5
Q ss_pred eCCCCCCCcchhhHHHHHHHhcccCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCc
Q 001083 271 SRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDT 350 (1160)
Q Consensus 271 SR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~ 350 (1160)
||||+++|..||+|.+.+. .+...+||||||||+||.. ++ .+|+.+|.+.+.. ...+++|++|||||+||+
T Consensus 1 SRng~d~T~~fPel~~~~~-~l~~~~~ILDGElVvld~~-G~-~~F~~Lq~~~~~~------~~~pv~~~vFDlL~l~G~ 71 (552)
T TIGR02776 1 TRNGHDWTKRFPEIVKALA-LLKLLPAWIDGEIVVLDER-GR-ADFAALQNALSAG------ASRPLTYYAFDLLFLSGE 71 (552)
T ss_pred CCCcCcchhhhHHHHHHHh-hCCCCCEEEEEEEEEECCC-CC-CCHHHHHHHHHhc------ccCceEEEEEeccccCCc
Confidence 8999999999999998764 4556899999999999974 43 4698887754321 123499999999999999
Q ss_pred ccccCCHHHHHHHHHHhhccCCCc-ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCC
Q 001083 351 SVIHQSLKERHELLQKVVKPSKGR-LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSK 429 (1160)
Q Consensus 351 sl~~~pl~eRr~~L~~~v~~~~~~-~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~ 429 (1160)
+|+++||.+|+++|++++.+..+. +.+. .. ..++..++|+.++++|+||||+|+++|+
T Consensus 72 dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~-----------------~~----~~~~~~~~~~~a~~~G~EGIV~K~~dS~ 130 (552)
T TIGR02776 72 DLRDLPLEERKKRLKQLLKAQDEPAIRYS-----------------DH----FESDGDALLESACRLGLEGVVSKRLDSP 130 (552)
T ss_pred ccccCCHHHHHHHHHHHhhhcCCCcEEEe-----------------ee----ecccHHHHHHHHHHCCCceEEEeCCCCC
Confidence 999999999999999999765332 2211 01 1234458999999999999999999999
Q ss_pred CcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHH
Q 001083 430 WEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 509 (1160)
Q Consensus 430 Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l 509 (1160)
|.+| |+.+|+|+|+.| +.|++|+|++.|. |.+|+|+||+++. ++|+++|+||||||++++++|
T Consensus 131 Y~~G-Rs~~WlKlK~~~-----~~e~vI~Gy~~~~----r~~gslLlg~~d~-------g~l~~vgkVgsGfsd~~~~~L 193 (552)
T TIGR02776 131 YRSG-RSKDWLKLKCRR-----RQEFVITGYTPPN----RRFGALLVGVYEG-------GQLVYAGKVGTGFGADTLKTL 193 (552)
T ss_pred CCCC-CCcchhcccccc-----cceEEEEEEecCC----CceeeEEEEEecC-------CeEEEEEEEcCCCCHHHHHHH
Confidence 9999 999999999986 6777665544443 2399999999962 279999999999999999999
Q ss_pred HHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCcc
Q 001083 510 VTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWH 589 (1160)
Q Consensus 510 ~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~ 589 (1160)
.+.|+++++.. +| |.. .......|++||+ |. +|+||++. .++.|++||||||+++|.||+|+
T Consensus 194 ~~~l~~~~~~~------~P-f~~-~~~~~~~~~~Wv~-P~--lV~EV~~~-------e~T~~g~LR~Prf~~~R~DK~~~ 255 (552)
T TIGR02776 194 LARLKALGAKA------SP-FSG-PAGAKTRGVHWVR-PS--LVAEVEYA-------GITRDGILREASFKGLREDKPAE 255 (552)
T ss_pred HHHHHhhcccC------CC-ccC-CccccCCCcEEEc-cC--EEEEEEee-------eccCCCeeEccEEEEEeCCCCHH
Confidence 99999887641 12 211 1112346899999 75 89999863 24458899999999999999999
Q ss_pred CcC
Q 001083 590 DCL 592 (1160)
Q Consensus 590 d~~ 592 (1160)
||+
T Consensus 256 e~t 258 (552)
T TIGR02776 256 EVT 258 (552)
T ss_pred Hcc
Confidence 995
No 18
>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=2.9e-41 Score=368.29 Aligned_cols=214 Identities=42% Similarity=0.698 Sum_probs=180.3
Q ss_pred ccccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHH------
Q 001083 215 RQDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKII------ 288 (1160)
Q Consensus 215 ~~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l------ 288 (1160)
..++++|.||+||||+++......+..+.+.+|++|+||||+|||+|++++.+++|||+|+++|..+|.+....
T Consensus 3 ~~~~~~~~p~~PmLa~~~~~~~~~~~~~~~~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~l 82 (225)
T cd07903 3 DLSIELFSPFRPMLAERLNIGYVEIKLLKGKPFYIETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYGASLTPGSLTPYI 82 (225)
T ss_pred CceeecCCcCccccCCCCCCHHHHHHhhcCCeEEEEEeeCceEEEEEecCCEEEEEeCCCccccccccccccccccchhh
Confidence 35689999999999999987766556777889999999999999999999999999999999999888776532
Q ss_pred HH--hcccCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHH
Q 001083 289 EQ--NVLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQK 366 (1160)
Q Consensus 289 ~~--~~~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~ 366 (1160)
.. .....+||||||||+||..++.+.+|+.++.+...... .....+++|+|||||++||.+++++||.+|+++|.+
T Consensus 83 ~~~~~~~~~~~iLDGElv~~~~~~~~~~~f~~l~~~~~~~~~--~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~ 160 (225)
T cd07903 83 HLAFNPKVKSCILDGEMVVWDKETKRFLPFGTLKDVAKLREV--EDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEK 160 (225)
T ss_pred hhhccccCcEEEeceEEEEEEcCcCeeccchHHHHHHhhccc--ccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHH
Confidence 11 12357899999999999877788999988765432110 112234999999999999999999999999999999
Q ss_pred hhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccc
Q 001083 367 VVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 446 (1160)
Q Consensus 367 ~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY 446 (1160)
++.+..+++.++. ...+++.+++.++|+.++++|+||||+|+++|+|++|+|+.+|+|+||+|
T Consensus 161 ~~~~~~~~i~~~~-----------------~~~~~~~~~~~~~~~~~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~~Y 223 (225)
T cd07903 161 IITPIPGRLEVVK-----------------RTEASTKEEIEEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIKPEY 223 (225)
T ss_pred hcCCCCCeEEEEE-----------------EEeCCCHHHHHHHHHHHHHcCCceEEEecCCCCCccCCcCCCcEEechhh
Confidence 9988766665431 34567889999999999999999999999999999999999999999999
Q ss_pred c
Q 001083 447 I 447 (1160)
Q Consensus 447 ~ 447 (1160)
+
T Consensus 224 ~ 224 (225)
T cd07903 224 L 224 (225)
T ss_pred c
Confidence 6
No 19
>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=1.9e-40 Score=358.22 Aligned_cols=206 Identities=30% Similarity=0.477 Sum_probs=172.9
Q ss_pred cccccCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCc-chhhHHHHHHHhcc-
Q 001083 216 QDIEVGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE-YGHAMSKIIEQNVL- 293 (1160)
Q Consensus 216 ~~i~~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~-~~~~l~~~l~~~~~- 293 (1160)
..|++|.||+||||++....+++++++. ..|++|+||||+|||+|++++.+++|||||+++|. .+|++.+.+.+.+.
T Consensus 6 ~~~~~~~p~~PmLA~~~~~~~~~i~~~~-~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~~~~~~~~~~~~~~~ 84 (213)
T cd07902 6 VRASLMTPVKPMLAEACKSVEDAMKKCP-NGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPKAFPH 84 (213)
T ss_pred EEeEcCCcccCccCCcCCCHHHHHHhcC-CceEEEeccCCEEEEEEEcCCEEEEEcCCCcccccchhHHHHHHHHHhccc
Confidence 4588999999999999888776666652 46999999999999999999999999999999995 56777776655544
Q ss_pred cCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCC
Q 001083 294 VDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG 373 (1160)
Q Consensus 294 ~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~ 373 (1160)
..+||||||||+||..++++++|+.++...+ .. ... .+++|+|||||++||.+++++||.+|+++|+.++.+.++
T Consensus 85 ~~~~iLDGEiv~~d~~~g~~~~F~~l~~~~~---~~-~~~-~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~ 159 (213)
T cd07902 85 GHSMILDSEVLLVDTKTGKPLPFGTLGIHKK---SA-FKD-ANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPN 159 (213)
T ss_pred ccceeeeeEEEEEECCCCcccccchhhhhhc---cc-ccc-CceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCC
Confidence 6789999999999987788889988764321 11 112 249999999999999999999999999999999987665
Q ss_pred cceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccc
Q 001083 374 RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 446 (1160)
Q Consensus 374 ~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY 446 (1160)
++.+. ....+.+.+++.++|++++++|.||||+|+++|+|.+|+| +|+|+|+||
T Consensus 160 ~~~~~-----------------~~~~~~~~~~l~~~~~~~~~~g~EGvV~K~~~s~Y~~G~r--~W~K~K~dY 213 (213)
T cd07902 160 RIMLS-----------------EMKFVKKADDLSAMIARVIKEGLEGLVLKDLKSVYEPGKR--HWLKVKKDY 213 (213)
T ss_pred eEEEE-----------------EEEEcCCHHHHHHHHHHHHHCCCCeEEEeCCCCCccCCCC--CceEeCCCC
Confidence 54332 1234578899999999999999999999999999999988 699999998
No 20
>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=3.5e-40 Score=355.08 Aligned_cols=205 Identities=32% Similarity=0.560 Sum_probs=171.6
Q ss_pred cCCccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceee
Q 001083 220 VGKAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCIL 299 (1160)
Q Consensus 220 ~g~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~IL 299 (1160)
||.||+||||++...+++++++. +.+|++|+||||+|||+|++++.+++|||+|+++|..+|++...+...+...+|||
T Consensus 1 ~~~p~~PmLA~~~~~~~~~~~~~-~~~~~~E~K~DG~R~~~~~~~~~v~~~SR~~~~~t~~~pel~~~~~~~~~~~~~iL 79 (207)
T cd07901 1 VGRPVRPMLAQRAPSVEEALIKE-GGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEAVRELVKAEDAIL 79 (207)
T ss_pred CCCCCccccCCCCCCHHHHHHhc-CCcEEEEEeEcceeEEEEEeCCEEEEEeCCCccccchhhHHHHHHHhcCCCCCEEE
Confidence 58999999999998877766655 56899999999999999999999999999999999999999887654332378999
Q ss_pred ceeEEEEeCCCCcccccccHHHHHHHhccCCC--CCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCccee
Q 001083 300 DGEMLVWDTSLNRFAEFGSNQEIAKAARDGLS--SDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET 377 (1160)
Q Consensus 300 DGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~--~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i 377 (1160)
|||||+||+ .+++.+|+.++....+.. ... ....+++|+||||||+||++++++||.+|+++|.+++.+. +++.+
T Consensus 80 DGElv~~~~-~g~~~~F~~l~~r~~~~~-~~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~ 156 (207)
T cd07901 80 DGEAVAYDP-DGRPLPFQETLRRFRRKY-DVEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILL 156 (207)
T ss_pred eCEEEEECC-CCCccCHHHHHHHhcccc-chhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEE
Confidence 999999997 577789987776533211 111 1123499999999999999999999999999999999875 34433
Q ss_pred eccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001083 378 LVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 445 (1160)
Q Consensus 378 ~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpe 445 (1160)
+ ....+++.+++.++|++++++|.||||+|+++|+|.+|+|+.+|+|+||+
T Consensus 157 ~-----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K~~ 207 (207)
T cd07901 157 A-----------------PRIVTDDPEEAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVKPD 207 (207)
T ss_pred E-----------------EEEecCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEecCC
Confidence 2 13345788999999999999999999999999999999999999999996
No 21
>PRK09125 DNA ligase; Provisional
Probab=100.00 E-value=1.1e-39 Score=364.85 Aligned_cols=253 Identities=23% Similarity=0.353 Sum_probs=193.6
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
+.||||...... +.+.+|++|+||||+|||+ + .+++|||+|++++. |.. +...+ .++|||||+
T Consensus 28 ~~~~LA~~~~~~------~~~~~~~~E~K~DG~R~~~--~--~v~l~SR~g~~it~--p~~---~~~~~--~~~vLDGEl 90 (282)
T PRK09125 28 PDLQLATVYDKG------QDISGYLVSEKLDGVRAYW--D--GKQLLTRQGNPIAA--PAW---FTAGF--PPFPLDGEL 90 (282)
T ss_pred CCceechhcccC------CChhhEEEEeeeeeEeEEE--C--CeEEEcCCCCcCCC--chh---HHhcC--CCccEeEEE
Confidence 689999887531 2346899999999999975 2 48999999999987 432 22222 489999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCC-CcceeeccCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDH 382 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~-~~~~i~~p~~ 382 (1160)
|+++ .+|+.++...++. ........+++|+|||||++|| ||.+|+++|++++.+.+ +.+.++
T Consensus 91 v~~~------~~F~~l~~r~~~k-~~~~~~~~~v~~~vFDll~~~g------pl~eRr~~L~~li~~~~~~~i~~~---- 153 (282)
T PRK09125 91 WAGR------GQFEAISSIVRDK-TPDDAAWRKVRFMVFDLPDAPG------DFEERLAVLKKLLAKLPSPYIKII---- 153 (282)
T ss_pred EeCC------CCHHHHHHHHccC-CcchhhhcccEEEEEEcCCCCC------CHHHHHHHHHHHHhhCCCCcEEEE----
Confidence 9864 3686666544322 1111222459999999999986 99999999999997652 233221
Q ss_pred CCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEe
Q 001083 383 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYY 462 (1160)
Q Consensus 383 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG~~~ 462 (1160)
....+++.++++++|+.++++|+||||+|+++|+|++| |+.+|+|+|++| +.|++|||+++
T Consensus 154 -------------~~~~~~~~~~~~~~~~~~~~~G~EGiV~K~~ds~Y~~G-Rs~~wlKiK~~~-----~~d~vIvG~~~ 214 (282)
T PRK09125 154 -------------EQIRVRSEAALQQFLDQIVAAGGEGLMLHRPDAPYEAG-RSDDLLKLKPYY-----DAEATVIGHLP 214 (282)
T ss_pred -------------eEEEcCCHHHHHHHHHHHHHcCCCEEEEeCCCCCCcCC-CCCCcEEEEecC-----CCcEEEEEEEc
Confidence 13456789999999999999999999999999999999 899999999986 78999999999
Q ss_pred CCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCc
Q 001083 463 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPD 542 (1160)
Q Consensus 463 G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pd 542 (1160)
|.|+++|.+|+|+|+..+ +. .| +||||||+++++. +|.+
T Consensus 215 g~Gk~~g~~gsllv~~~~--g~-----~~----~VgsG~t~~~r~~------------------~~~~------------ 253 (282)
T PRK09125 215 GKGKFAGMLGALLVETPD--GR-----EF----KIGSGFSDAEREN------------------PPKI------------ 253 (282)
T ss_pred CCCcccCceeeEEEEeCC--CC-----EE----EeCCCCCHHHhcC------------------CCCC------------
Confidence 999999999999999643 21 23 7899999998641 1211
Q ss_pred EEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecC
Q 001083 543 VWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYD 585 (1160)
Q Consensus 543 vwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~D 585 (1160)
..+++|++ ..++....||||+|++||+|
T Consensus 254 --------g~~~~V~y-------~e~t~~g~lR~P~f~g~R~D 281 (282)
T PRK09125 254 --------GSIITYKY-------RGLTKNGLPRFASFLRVRED 281 (282)
T ss_pred --------CCEEEEEe-------cccCCCCcccCCEEEEEecC
Confidence 02556654 23456788999999999998
No 22
>PHA00454 ATP-dependent DNA ligase
Probab=100.00 E-value=5.8e-39 Score=365.57 Aligned_cols=285 Identities=21% Similarity=0.315 Sum_probs=209.5
Q ss_pred ccccccccCC--hHHHHHhcCCCcEEEEEecceEEEEEEEeCC-EEEEEeCCCCCCCcchhhHH-------HHHHH--hc
Q 001083 225 RPQLAMRIGD--AHAAWRKLHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHSEYGHAMS-------KIIEQ--NV 292 (1160)
Q Consensus 225 ~PmLA~~~~~--~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~-~v~~fSR~g~d~t~~~~~l~-------~~l~~--~~ 292 (1160)
+|++|..++. +.+++.+++ .|++|+||||+|||+|++++ .+++|||||+++++. .++. +.+.. ..
T Consensus 7 ~~~~~~~~~~~~i~~~~~~~g--~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g~~~p~l-~~~~~~~~~~~~~~~~~~~~ 83 (315)
T PHA00454 7 NPFRAVDFNESAIEKALEKAG--YLIADVKYDGVRGNIVVDNTADHGWLSREGKTIPAL-EHLNGFDRRWAKLLNDDRCI 83 (315)
T ss_pred CccccccCCHHHHHHHHHhCC--cEEEEEccceEEEEEEEcCCCeEEEEeCCCCcccch-hhhhhhhhhhhhhhhhhhhc
Confidence 6899998876 778888873 89999999999999999876 499999999987652 1121 11110 12
Q ss_pred ccCceeeceeEEEEeCCCCcccccccHHHHHHHhcc-CCCCCCccEEEEEEeeeecC----Cccc---ccCCHHHHHHHH
Q 001083 293 LVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARD-GLSSDRQVLCYFAFDVLYVG----DTSV---IHQSLKERHELL 364 (1160)
Q Consensus 293 ~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~-~~~~~~~~~~~~vFDiL~ln----g~sl---~~~pl~eRr~~L 364 (1160)
.++++|||||+|+.+ .+|+.++...++... .......++.|+|||||++| |.++ ..+||.+|+++|
T Consensus 84 l~~~~vLDGElv~~~------~~f~~~~~~l~~k~~~~~~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L 157 (315)
T PHA00454 84 FPDGFMLDGELMVKG------VDFNTGSGLLRRKWKVLFELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMV 157 (315)
T ss_pred CCCCeEEEEEEEecC------CCHHHHHHHhccCccchhhhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHH
Confidence 246899999999965 467665554432210 01122345999999999999 5565 789999999999
Q ss_pred HHhhccCCC-cceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 001083 365 QKVVKPSKG-RLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 443 (1160)
Q Consensus 365 ~~~v~~~~~-~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlK 443 (1160)
+.++.+.+. .+.+. ....+.+.+++.++|+.++++|.||||+|+++|+|.+|+|+. |+|+|
T Consensus 158 ~~l~~~~~~~~~~~~-----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~ds~Y~~Grr~~-~~K~K 219 (315)
T PHA00454 158 PLLMEYFPEIDWFLS-----------------ESYEVYDMESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSG-WWKMK 219 (315)
T ss_pred HHHHhhCCCcceEee-----------------ceEEcCCHHHHHHHHHHHHhCCCceEEEeCCCCCCCCCCccC-cEEEc
Confidence 999865442 12211 134567899999999999999999999999999999998875 88999
Q ss_pred cccccCCCcccEEEEEEEeCCCC--CCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccC
Q 001083 444 PEYIRAGSDLDVLIIGGYYGSGR--RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYE 521 (1160)
Q Consensus 444 peY~~~g~~lDlvIIG~~~G~Gr--r~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~ 521 (1160)
+.+ ++|++|||+++|.|. ..|.+++|+|.+ .++ .+.. |||||++++++|.+.+.++-..
T Consensus 220 ~~~-----~~d~vIvG~~~g~g~~~~~g~~~~~~~~~--~~g------~l~~----gtGfs~~~~~~l~~~l~~~~~~-- 280 (315)
T PHA00454 220 PEC-----EADGTIVGVVWGTPGLANEGKVIGFRVLL--EDG------RVVN----ATGISRALMEEFTANVKEHGED-- 280 (315)
T ss_pred ccC-----ceeEEEEEEEECCCCccCCceEEEEEEEe--CCC------cEEE----ccCCCHHHHHHHHHHHHhhccC--
Confidence 985 899999999999864 346777777765 222 3432 8999999999999998775221
Q ss_pred CCCCCCCCcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeec
Q 001083 522 YPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRY 584 (1160)
Q Consensus 522 ~~~~~pP~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~ 584 (1160)
...+ |....|+||++. .++.+..||||+|+++|+
T Consensus 281 --~~~~--------------------p~~~~v~eV~y~-------e~T~~g~lR~P~F~g~Rd 314 (315)
T PHA00454 281 --YEAM--------------------PYNGRACQVSYM-------ERTPDGSLRHPSFDRFRD 314 (315)
T ss_pred --cccc--------------------CCCCeEEEEEEE-------EcCCCCcccCceeeeeec
Confidence 0001 221247788652 356778999999999995
No 23
>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=1e-38 Score=343.37 Aligned_cols=202 Identities=23% Similarity=0.283 Sum_probs=166.1
Q ss_pred CccccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeece
Q 001083 222 KAVRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDG 301 (1160)
Q Consensus 222 ~p~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDG 301 (1160)
.|+.||||+++....+.+ .....|++|+||||+|||+|++++.+++|||+|+++|..+|++...+. .+ +.+|||||
T Consensus 3 ~~~~pmLA~~~~~~~~~~--~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~-~l-~~~~iLDG 78 (207)
T cd07897 3 RPYPFMLAHPLEDDPEDL--GDPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAE-AL-PDGTVLDG 78 (207)
T ss_pred CCCCceeCCcCCCchhhh--cCcccEEEEEeEceEEEEEEEcCCEEEEEeCCCCcccccchHHHHHHH-hC-CCCeEEEe
Confidence 689999999998776543 345689999999999999999999999999999999999999887653 33 46899999
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhccC-CCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCC-Ccceeec
Q 001083 302 EMLVWDTSLNRFAEFGSNQEIAKAARDG-LSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLV 379 (1160)
Q Consensus 302 Elv~~d~~~~~~~pF~~lq~i~~~~r~~-~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~-~~~~i~~ 379 (1160)
|||+||. +...+|+.++....+.... ......+++|+||||||+||.++++.||.+|+++|++++.+.+ +++.+.
T Consensus 79 Elv~~~~--~~~~~F~~l~~r~~~~~~~~~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~i~~~- 155 (207)
T cd07897 79 ELLVWRD--GRPLPFNDLQQRLGRKTVGKKLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPRLDLS- 155 (207)
T ss_pred EEEEecC--CCccCHHHHHHHhcccccchhhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCCceeec-
Confidence 9999986 4568998877654321110 0011234899999999999999999999999999999997763 333321
Q ss_pred cCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcccc
Q 001083 380 PDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 446 (1160)
Q Consensus 380 p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY 446 (1160)
....+++.+++.++|++++++|+||||+|+++|+|.+|+|++.|+|+|++-
T Consensus 156 ----------------~~~~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d~ 206 (207)
T cd07897 156 ----------------PLIAFADWEELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWKIDP 206 (207)
T ss_pred ----------------ceEecCCHHHHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCCC
Confidence 134567899999999999999999999999999999999999999999973
No 24
>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=2.2e-38 Score=345.14 Aligned_cols=201 Identities=26% Similarity=0.413 Sum_probs=162.1
Q ss_pred ChHHHHHhcCCCcEEEEEecceEEEEEEEe----CCEEEEEeCCCCCCCcchhhHHHHHHHhc--------ccCceeece
Q 001083 234 DAHAAWRKLHGKEVVIECKFDGDRIQIHKN----GSEIHYFSRSFLDHSEYGHAMSKIIEQNV--------LVDRCILDG 301 (1160)
Q Consensus 234 ~~~~~~~~~~~~~~~~E~K~DGeR~qih~~----g~~v~~fSR~g~d~t~~~~~l~~~l~~~~--------~~~~~ILDG 301 (1160)
++..+++.+.+..|++|+||||+|||+|+. ++.|++|||||+++|..+|++.+.+...+ .+++|||||
T Consensus 11 ~~~~~~~~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDG 90 (235)
T cd08039 11 SIKHCCKMIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEG 90 (235)
T ss_pred CHHHHHHHhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEEe
Confidence 456677888889999999999999999997 88999999999999999999887654432 257899999
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhcc-------CCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCc
Q 001083 302 EMLVWDTSLNRFAEFGSNQEIAKAARD-------GLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGR 374 (1160)
Q Consensus 302 Elv~~d~~~~~~~pF~~lq~i~~~~r~-------~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~ 374 (1160)
|||+||..++++.||+.+|....+... .......++||+||||||+||.+|++.||.+|+++|++++.+.+++
T Consensus 91 EiVv~d~~~g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~~ 170 (235)
T cd08039 91 EMVVWSDRQGKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPGY 170 (235)
T ss_pred EEEEEECCCCccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCCc
Confidence 999999877888999988764321110 0111223599999999999999999999999999999999888776
Q ss_pred ceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCC-----CCCeEEEcccc
Q 001083 375 LETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-----SGKWLKLKPEY 446 (1160)
Q Consensus 375 ~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkR-----s~~WlKlKpeY 446 (1160)
++++... .+. .....+.++++++|++++++|+||||+|+++|+|.||++ +..|+|+||||
T Consensus 171 ~~~~~~~-----~i~-------~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 171 AGLSERF-----PID-------FSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred EEEEEEE-----eec-------ccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcccccccCCCeEEeCCCC
Confidence 6543210 000 011346789999999999999999999999999999753 58999999998
No 25
>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=2.9e-38 Score=338.83 Aligned_cols=200 Identities=32% Similarity=0.498 Sum_probs=166.4
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
|+||||++++.+.++ .++.+.+|++|+||||+|||+|++++.|++|||+|+++|..+|.+...+.. .+.+|||||||
T Consensus 1 i~pmLa~~~~~~~~~-~~~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~i~~~~~~--~~~~~vLDGEl 77 (201)
T cd07898 1 IKPMLAHPEESAEAA-KAKKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAKA--LPHEFILDGEI 77 (201)
T ss_pred CCCeecCcCCChHHH-HhhCCCeEEEEEeeceEEEEEEEeCCEEEEEcCCChhchhhhhhHHHHHHh--CCCCEEEEEEE
Confidence 689999999887654 556778999999999999999999999999999999999988988876542 35899999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCC-CCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGL-SSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDH 382 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~-~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~ 382 (1160)
|+||.... .||..++....+..... .....+++|+|||||++||++++++||.||+++|++++.+.++++.++
T Consensus 78 v~~~~~~~--~~f~~~~~~~~~~~~~~~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~---- 151 (201)
T cd07898 78 LAWDDNRG--LPFSELFKRLGRKFRDKFLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIA---- 151 (201)
T ss_pred EEEeCCCC--CcHHHHHHHhcccccchhhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEe----
Confidence 99986432 58887765443221110 012234999999999999999999999999999999998876665442
Q ss_pred CCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001083 383 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 445 (1160)
Q Consensus 383 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpe 445 (1160)
....+++.+++.++|++++++|+||||+|+++|+|.+|+|+.+|+|+|||
T Consensus 152 -------------~~~~~~~~~~~~~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~~ 201 (201)
T cd07898 152 -------------PALPVESAEELEAAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKKE 201 (201)
T ss_pred -------------eeEEcCCHHHHHHHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCCC
Confidence 13346788999999999999999999999999999999999999999996
No 26
>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=1.7e-37 Score=332.72 Aligned_cols=200 Identities=31% Similarity=0.522 Sum_probs=166.5
Q ss_pred cccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhccc--CceeeceeE
Q 001083 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEM 303 (1160)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~--~~~ILDGEl 303 (1160)
||||+++..++.+++++ +.+|++|+||||+|||+|+.++.+++|||+|++++..+|.+...+...+.. .+|||||||
T Consensus 1 PmLA~~~~~~~~~~~~~-~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~~~vLDGEl 79 (202)
T PF01068_consen 1 PMLAQPFDSIEKALKKF-GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGKDITSQFPELAEALRELLFPDGPDFVLDGEL 79 (202)
T ss_dssp -EEEEEESSHHHHHHHT-TSCEEEEEEESSEEEEEEEETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCTEEEEEEEE
T ss_pred CcCCccccCHHHHHHhc-CCCeEEEEeEeeEEeeeeeccccceeecccccchhhHHHHHHHHHHHHhcCCCCceEEEEEE
Confidence 99999999888889888 678999999999999999999999999999999999889888877665443 479999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 383 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 383 (1160)
|+||+.++.+.||+.++....+..........+++|+|||||++||.++++.||.+|+++|++++.+..+.+.++
T Consensus 80 v~~d~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~~~----- 154 (202)
T PF01068_consen 80 VVLDPNTGSPLPFQELSGRLNRRSKKIPEQSEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIRIV----- 154 (202)
T ss_dssp EEBETTTSSBCCHHHHHHHHBHSSSCHHHHHSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEEEE-----
T ss_pred EEEecCCCcchhHHHHhhhhhhhcccchhccCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCceeEe-----
Confidence 999998888999977665442211100001235999999999999999999999999999999996666555442
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 001083 384 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 443 (1160)
Q Consensus 384 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlK 443 (1160)
....+++.++++++|++++++|+||+|+|+++|+|++|+|+.+|+|+|
T Consensus 155 ------------~~~~~~~~~~~~~~~~~~~~~g~EG~v~K~~~~~Y~~Gkrs~~w~K~K 202 (202)
T PF01068_consen 155 ------------ESYVVNSKEELEELFEEAIDQGFEGLVLKDPDSPYEPGKRSSGWLKVK 202 (202)
T ss_dssp ------------EEEEESSHHHHHHHHHHHHHTTSSEEEEEETTSSC-TTEEEEEEEEEE
T ss_pred ------------eeecCCCHHHHHHHHHHHHHcCCceEEEECCCCccCCCCcCCCcEEEC
Confidence 145678999999999999999999999999999999999999999998
No 27
>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=1.2e-36 Score=324.25 Aligned_cols=191 Identities=27% Similarity=0.406 Sum_probs=156.2
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
|+||||..+..+.+ +.+|++|+||||+|||+|++++.+++|||||+++|..+|.+.+.+.. ..+.+|||||||
T Consensus 1 i~PmLa~~~~~~~~------~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~-~~~~~~iLDGEl 73 (194)
T cd07905 1 VEPMLARAVDALPE------PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARA-LLPPGCVLDGEL 73 (194)
T ss_pred CCceeCCccCCCCC------CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHHHh-hCCCCEEEEeEE
Confidence 58999998876432 56899999999999999999999999999999999999999887644 346789999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCC--CCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGL--SSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 381 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~--~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~ 381 (1160)
|+||.. . .+|+.+|.......... .....+++|+||||||+||.++++.||.+|+++|++++.+..+++.++
T Consensus 74 v~~~~~--~-~~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~--- 147 (194)
T cd07905 74 VVWRGG--R-LDFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLS--- 147 (194)
T ss_pred EEEcCC--C-CCHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEEC---
Confidence 999863 2 49988776542211110 112345999999999999999999999999999999998765554432
Q ss_pred CCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001083 382 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 445 (1160)
Q Consensus 382 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpe 445 (1160)
+ ...+.+++.++|++++++|+||||+|+++|+|.+|+| +|+|+|+.
T Consensus 148 --------~--------~~~~~~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Gr~--~WlK~K~~ 193 (194)
T cd07905 148 --------P--------ATTDRAEAREWLEEFEGAGLEGVVAKRLDGPYRPGER--AMLKVKHR 193 (194)
T ss_pred --------C--------ccCCHHHHHHHHHHHHHCCCceEEEeCCCCCcCCCCC--cEEEEecc
Confidence 0 1346789999999999999999999999999999974 89999984
No 28
>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=6.7e-36 Score=317.72 Aligned_cols=189 Identities=28% Similarity=0.440 Sum_probs=154.6
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
++||||+++.... .+.+|++|+||||+|||+|++++.+++|||+|+++|..+|++...+.. +...+|||||||
T Consensus 1 i~pmLa~~~~~~~------~~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~t~~~p~l~~~~~~-~~~~~~iLDGEl 73 (190)
T cd07906 1 IEPMLATLVDEPP------DGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAA-LPVRDAVLDGEI 73 (190)
T ss_pred CCCeECCcCCCCC------CCCCeEEEEeEceEEEEEEEECCEEEEEcCCCCcchhhhHHHHHHHHh-cCCCCEEEEeEE
Confidence 5899999988652 356899999999999999999999999999999999988988876643 346899999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 383 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 383 (1160)
|+||.... .+|+.++....+.. ......+++|+|||||++||.+++++||.||+++|++++.+..+++.++.
T Consensus 74 v~~~~~~~--~~F~~l~~~~~~~~--~~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~---- 145 (190)
T cd07906 74 VVLDEGGR--PDFQALQNRLRLRR--RLARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSE---- 145 (190)
T ss_pred EEECCCCC--CCHHHHHHhhcccc--hhcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECc----
Confidence 99997532 58876665433211 11223459999999999999999999999999999999988755554321
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001083 384 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 444 (1160)
Q Consensus 384 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKp 444 (1160)
+.. .+.+++|++++++|.||||+|+++|+|++|+|+.+|+|+|+
T Consensus 146 -------------~~~----~~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~K~ 189 (190)
T cd07906 146 -------------HFE----GGGAALFAAACELGLEGIVAKRADSPYRSGRRSRDWLKIKC 189 (190)
T ss_pred -------------eEc----CCHHHHHHHHHHcCCcEEEEecCCCCcCCCCCCCccEEEec
Confidence 111 12378999999999999999999999999999999999996
No 29
>cd07967 OBF_DNA_ligase_III The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase III is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, 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 proph
Probab=99.97 E-value=6e-32 Score=270.82 Aligned_cols=137 Identities=26% Similarity=0.530 Sum_probs=118.3
Q ss_pred CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCC
Q 001083 450 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 529 (1160)
Q Consensus 450 g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~ 529 (1160)
++++||||||||+|.|+++|.+|+||||++++++ +.|+++|+||||||++++++|.++|+++++.. +...||.
T Consensus 2 ~dtlDlVViG~~~g~G~r~~~~gslLlg~~d~~~-----~~l~~vgkVGTGfs~~~l~~l~~~L~~l~~~~--~~~~~p~ 74 (139)
T cd07967 2 ADTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNS-----KKWCTVTKCGNGHDDATLARLQKELKMVKISK--DPSKVPS 74 (139)
T ss_pred CceEeEEEEEEEECCCCCCCccceEEEEEEeCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhhhcccc--CCcCCCc
Confidence 4789999999999999999999999999998653 38999999999999999999999999998763 3334677
Q ss_pred cccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeeccccc-CCceeeCceeeeeecCCCccCcCCHHH
Q 001083 530 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQS 596 (1160)
Q Consensus 530 ~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~-~g~tLRFPR~~riR~DK~~~d~~t~~e 596 (1160)
|+.+. ...+||+||.+|++|+|+||+++..+ .|+.|. +|+|||||||++||+||+|+||+|++|
T Consensus 75 ~~~~~--~~~~Pdv~~~~P~~s~V~EV~~aeit-~S~~~~a~G~tLRFPr~~~iR~DK~~~d~~t~~~ 139 (139)
T cd07967 75 WLKCN--KSLVPDFIVKDPKKAPVWEITGAEFS-KSEAHTADGISIRFPRVTRIRDDKDWKTATSLPE 139 (139)
T ss_pred eEeec--CCCCCCEEEeCCCccEEEEEEeeeEE-ecCcccccCEEEEccEEEEEeCCCCHHHCccccC
Confidence 77653 35799999977999999999964433 577777 699999999999999999999999875
No 30
>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=99.97 E-value=3.8e-30 Score=269.91 Aligned_cols=173 Identities=20% Similarity=0.309 Sum_probs=135.1
Q ss_pred cccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeE
Q 001083 224 VRPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEM 303 (1160)
Q Consensus 224 ~~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGEl 303 (1160)
|+||||.++....+ +.+|++|+||||+|||+|. + ++|||+|+++|.. +. +...+ ..+||||||
T Consensus 1 ~~pmla~~~~~~~~------~~~~~~e~K~DG~R~~~~~--~--~~~SR~g~~~t~~-~~----~~~~l--~~~ilDGEl 63 (174)
T cd07896 1 PELLLAKTYDEGED------ISGYLVSEKLDGVRAYWDG--K--QLLSRSGKPIAAP-AW----FTAGL--PPFPLDGEL 63 (174)
T ss_pred CccccccccccCCC------hHHeeechhhceEEEEEec--c--EEEecCCcCCCCC-HH----HHhhC--CCCccCceE
Confidence 58999998875432 4589999999999999973 2 9999999999974 22 22323 349999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCC-CcceeeccCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSK-GRLETLVPDH 382 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~-~~~~i~~p~~ 382 (1160)
|+|++ ||+.++...++... ......+++|++||||+ ++.||.+|+++|+.++.+.. +.+.++
T Consensus 64 v~~~~------~f~~l~~~~~~~~~-~~~~~~~~~f~vFDil~------~~~p~~eR~~~L~~~i~~~~~~~~~~~---- 126 (174)
T cd07896 64 WIGRG------QFEQTSSIVRSKKP-DDEDWRKVKFMVFDLPS------AKGPFEERLERLKNLLEKIPNPHIKIV---- 126 (174)
T ss_pred EcCCC------CHHHHHHHHhcCCC-ChhhcccceEEEEeCCC------CCCCHHHHHHHHHHHHHhCCCCcEEEE----
Confidence 99863 88777665443211 11123459999999999 67899999999999998652 333332
Q ss_pred CCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001083 383 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 444 (1160)
Q Consensus 383 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKp 444 (1160)
....+.+.+++.+++++++++|+||||+|+++|+|.+| |+.+|+|+||
T Consensus 127 -------------~~~~~~~~~~i~~~~~~~~~~g~EGlv~K~~ds~Y~~g-R~~~wlK~Kp 174 (174)
T cd07896 127 -------------PQIPVKSNEALDQYLDEVVAAGGEGLMLRRPDAPYETG-RSDNLLKLKP 174 (174)
T ss_pred -------------eeeeeCCHHHHHHHHHHHHhcCCCeEEEecCCCcccCC-cCCCceeeCC
Confidence 13456788999999999999999999999999999988 7899999997
No 31
>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=99.96 E-value=3.5e-29 Score=263.33 Aligned_cols=169 Identities=36% Similarity=0.656 Sum_probs=136.7
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCC---chHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCcC
Q 001083 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDS---VDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKD 83 (1160)
Q Consensus 7 ~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~---~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~~ 83 (1160)
|+|++||++|++|++++++.+|+++|.+||..+... .++|+++++++|++| +| +|||+++.|++++++++|++++
T Consensus 1 m~F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d-~r-~~~i~~~~L~k~~~~~~~~~~~ 78 (177)
T PF04675_consen 1 MPFSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYD-GR-EYGIGEKLLAKAIAEALGLPEK 78 (177)
T ss_dssp GBHHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTC-S----S--HHHHHHHHHHHHTS-HH
T ss_pred CcHHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchh-hh-HhccchhHHHHHHHHHHcCCHH
Confidence 799999999999999999999999999999999653 689999999999999 55 9999999999999999999988
Q ss_pred hHHHHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcCC--CCCCCcHHHHHHHHHHHHhhh---hHHHHHHHHHHHHHhCCH
Q 001083 84 SADAVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGM--ISGGLTIKELNDLLDRLASSE---NRAEKISVLSTLIKKTNA 158 (1160)
Q Consensus 84 s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~--~~~~LTi~eVn~~Ld~LA~~~---~~~~k~~il~~ll~~~t~ 158 (1160)
+.++ .|+ ..||||.+++++++++... .+.+|||.+||+.|++||..+ ++..|..+|..|+.+|+|
T Consensus 79 ~~~~----~~~------~~GD~g~~~~~~~~~~~~~~~~~~~lTi~~V~~~L~~la~~~g~~s~~~k~~~l~~ll~~~s~ 148 (177)
T PF04675_consen 79 SIDE----SYK------KVGDLGEVAEEVLQKRKSETSKPSPLTISEVNETLDELAAASGKGSQDEKIDILKELLRRCSP 148 (177)
T ss_dssp HHHH----HHH------HHS-HHHHHHHHHHHHTTTS--SS--BHHHHHHHHHHHHH--STTHHHHHHHHHHHHHTTS-H
T ss_pred HHHH----HHH------hcCcHHHHHHHHHhhccccccCCCCCCHHHHHHHHHHHHHhhCccchHHHHHHHHHHHHhCCH
Confidence 7665 443 3799999999999888743 358999999999999999887 478889999999999999
Q ss_pred HHHHHHHHHHhhhhccCCcccccccccCc
Q 001083 159 QEMKWIIMIILKDLKLGISEKSIFHEFHP 187 (1160)
Q Consensus 159 ~E~k~l~RiIlkdLriGi~e~til~~~hp 187 (1160)
.|++||+|||+|+||||+++++|+++|||
T Consensus 149 ~E~k~i~Riil~~lriG~~~~~il~ala~ 177 (177)
T PF04675_consen 149 EEAKWIVRIILKDLRIGVSEKTILDALAP 177 (177)
T ss_dssp HHHHHHHHHHTT--SSS--HHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCeeCccHHHHHHHhCc
Confidence 99999999999999999999999999997
No 32
>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=99.96 E-value=2.4e-28 Score=258.13 Aligned_cols=178 Identities=22% Similarity=0.310 Sum_probs=138.8
Q ss_pred ccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeEE
Q 001083 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEML 304 (1160)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv 304 (1160)
.||||........ ..+.+.+|++|+||||+|||+|+.++.+++|||+|+++|..++.+..... .....++|||||||
T Consensus 1 ~~~~~~~~~~~~~--~~~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~~~~~~~~~~~~~~~-~~~~~~~ilDGElv 77 (182)
T cd06846 1 PQLLNPILEEALS--EYDEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPGREL-LTLKPGFILDGELV 77 (182)
T ss_pred CCccchhhhHHHh--hccccCcEEEEEccCceEEEEEEcCCeEEEEeCCCCEEecccccccchHH-hccCCCeeEEEEEE
Confidence 3788887765432 23557789999999999999999999999999999999987776543111 11357899999999
Q ss_pred EEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCC--cceeeccCC
Q 001083 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKG--RLETLVPDH 382 (1160)
Q Consensus 305 ~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~--~~~i~~p~~ 382 (1160)
+++... ...+++|++||||++||.+++++||.+|+++|++++.+..+ ++.+...
T Consensus 78 ~~~~~~----------------------~~~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~-- 133 (182)
T cd06846 78 VENREV----------------------ANPKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPL-- 133 (182)
T ss_pred eccCCC----------------------ccceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEe--
Confidence 987421 01238999999999999999999999999999999987642 2222110
Q ss_pred CCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCC--cCCCCCCCeEEEcc
Q 001083 383 GLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW--EPGDRSGKWLKLKP 444 (1160)
Q Consensus 383 ~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y--~pGkRs~~WlKlKp 444 (1160)
.......+++.+++++++.+|.||||+|+++|+| .+| |+..|+|+||
T Consensus 134 --------------~~~~~~~~~~~~~~~~~~~~g~EGvi~K~~~s~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 134 --------------ENAPSYDETLDDLLEKLKKKGKEGLVFKHPDAPYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred --------------ecccccchHHHHHHHHhhhcCCceEEEEcCCCCccccCC-CCCceEeecC
Confidence 0011123348999999999999999999999999 888 7999999998
No 33
>cd07968 OBF_DNA_ligase_IV The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase IV is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases 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 pro
Probab=99.95 E-value=1.1e-27 Score=241.85 Aligned_cols=139 Identities=53% Similarity=1.053 Sum_probs=114.8
Q ss_pred CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCC-CCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCC
Q 001083 450 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP-DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 528 (1160)
Q Consensus 450 g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~-~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP 528 (1160)
++++||||||||+|.|+++|.+|+||||+++.++. ...+.+|++||+||||||++++++|.++|+++|.. ++...||
T Consensus 1 ~~~lDlvViG~~~g~g~~~~~~~slllG~~~~~~~~~~~~~~l~~vgkVgtGfs~~~~~~L~~~l~~~~~~--~~~~~~P 78 (140)
T cd07968 1 GEDLDLLIIGGYYGEGRRGGKVSSFLCGVAEDDDPESDKPSVFYSFCKVGSGFSDEELDEIRRKLKPHWKP--FDKKAPP 78 (140)
T ss_pred CCcEeEEEEccEeCCCCcCCccccEEEEEEcCCCCCCCCCCEEEEEEEEccCCCHHHHHHHHHHhcCcEEE--cCcCCCC
Confidence 47999999999999999999999999999975431 12234899999999999999999999999999876 3333455
Q ss_pred CcccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCH
Q 001083 529 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDV 594 (1160)
Q Consensus 529 ~~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~ 594 (1160)
.+ .......+|++||+ |.+|+|+||++... ..+..|++|++||||||+++|+||+|+||+|+
T Consensus 79 ~~--~~~~~~~~~~~Wv~-P~~slV~EV~~~e~-t~s~~~~~g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 79 SS--LLKFGKEKPDVWIE-PKDSVVLEVKAAEI-VPSDSYKTGYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cc--cccccccCCcEEEe-cCCCEEEEEEeeeE-eecCcccCCcEEEcceEeEEECCCCHHHccCC
Confidence 43 11234568999998 88999999996433 36788999999999999999999999999984
No 34
>cd07969 OBF_DNA_ligase_I The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase I is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, eukarya, archaea and bacteria. There are three classes of ATP-dependent DNA ligases in eukaryotic cells (I, III and IV). This group is composed of eukaryotic DNA ligase I, Sulfolobus solfataricus DNA ligase and similar proteins. DNA ligase I is required for the ligation of Okazaki fragments during lagging-strand DNA synthesis and for base excision repair (BER). ATP dependent DNA ligases have a highly modular architecture consist
Probab=99.94 E-value=2.2e-26 Score=232.83 Aligned_cols=134 Identities=37% Similarity=0.585 Sum_probs=114.3
Q ss_pred CCcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCC
Q 001083 450 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 529 (1160)
Q Consensus 450 g~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~ 529 (1160)
++++||||||+++|+|++.|.+|+||||++++++ ++|+++|+||||||++++++|.++|.+++... ||.
T Consensus 1 ~~t~D~vViG~~~g~g~~~~~~~slllG~~~~~~-----~~l~~vgkvgtGft~~~~~~L~~~l~~~~~~~------~p~ 69 (144)
T cd07969 1 GDTLDLVPIGAYYGKGKRTGVYGAFLLACYDPET-----EEFQTVCKIGTGFSDEFLEELYESLKEHVIPK------KPY 69 (144)
T ss_pred CCceeEEEEEEEECCCCCCCCcceEEEEEEeCCC-----CEEEEEeEEccCCCHHHHHHHHHHhhhhcccc------CCc
Confidence 4789999999999999998999999999997653 38999999999999999999999999998651 232
Q ss_pred cccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC---------CceeeCceeeeeecCCCccCcCCHHHHHHH
Q 001083 530 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 600 (1160)
Q Consensus 530 ~~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~---------g~tLRFPR~~riR~DK~~~d~~t~~el~el 600 (1160)
+.. ...+|++||+ |. +|+||+++.. ..|+.|++ |++||||||+++|+||+|+||+++++|.+|
T Consensus 70 ~~~----~~~~~~vWv~-P~--lV~EV~~~e~-t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~~~l~~l 141 (144)
T cd07969 70 RVD----SSLEPDVWFE-PK--EVWEVKAADL-TLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTSEQIAEM 141 (144)
T ss_pred ccc----ccCCCcEEEe-ee--EEEEEEEeEe-ecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCHHHHHHH
Confidence 211 1258999999 74 9999997533 35778876 899999999999999999999999999999
Q ss_pred HH
Q 001083 601 VH 602 (1160)
Q Consensus 601 ~~ 602 (1160)
++
T Consensus 142 ~~ 143 (144)
T cd07969 142 YK 143 (144)
T ss_pred Hh
Confidence 85
No 35
>KOG4437 consensus ATP-dependent DNA ligase III [Replication, recombination and repair]
Probab=99.92 E-value=1.4e-24 Score=233.30 Aligned_cols=318 Identities=24% Similarity=0.339 Sum_probs=248.2
Q ss_pred CcHHHHHHHHHHHHhhCChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCcChHH
Q 001083 7 TEVIVLVSLFNWIQKTKPAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSKDSAD 86 (1160)
Q Consensus 7 ~~F~~l~~l~e~i~~~~~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~~s~~ 86 (1160)
-+|.+|..+|.-|+..+....|.++|..+|.+---+.|+|.+|++|+-+.|. |.|||.++.|+++++++|.+...+.
T Consensus 155 N~F~ef~kiCS~L~~~p~~~~Kt~VI~~LL~kdNFDGDL~LWL~FLIRESD~--R~YNl~DkKLI~lfsKiLn~~~~~~- 231 (482)
T KOG4437|consen 155 NLFREFRKLCSMLADNPSYNTKTQVIQDLLRKDNFDGDLYLWLKFLIRESDK--RVYNLNDKKLIKLFSKILNCNPDDM- 231 (482)
T ss_pred hHHHHHHHHHHHHHhCcCccchhHHHHHHHhccCCCcchhhhhhhhhccccc--ccccccHHHHHHHHHHHHccChHHH-
Confidence 3588888888888888888999999999997543368999999999999986 5999999999999999999986532
Q ss_pred HHHHhhhhcCCCCCCCCCHHHHHHHHhhhhcCCCCCCCcHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHH
Q 001083 87 AVRLINWRKGGAAPNAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIM 166 (1160)
Q Consensus 87 ~~~L~~wk~~~~~~~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~t~~E~k~l~R 166 (1160)
+..|-. ...+.+..++..-.+.....++-+||++|+++|.+|+..+..++....|+.+..+|++.|++.|+|
T Consensus 232 ---~~~Y~~-----~S~~~~i~i~~~~~K~~~~~K~~~siQ~~D~~L~rLSKi~~~D~~~~~L~~~A~R~~~~~L~~iIR 303 (482)
T KOG4437|consen 232 ---ARDYEQ-----GSVSETIRVFFEQSKSFPPAKSLLTIQEVDEFLLRLSKLTKEDEQQQALQDIASRCTANDLKCIIR 303 (482)
T ss_pred ---HHHHHh-----ccchhhhhhhHhhccCCCCcccceeHHHHHHHHHHHhcccchHHHHHHHHHHHHhcccchHHHHHH
Confidence 233432 234555555544444445677899999999999999999998899999999999999999999999
Q ss_pred HHhhhhccCCcccccccccCccHHHHHhhhCCHHHHHHHHhhhh--------cc-ccccccccCCccccccccccCChHH
Q 001083 167 IILKDLKLGISEKSIFHEFHPDAEDLFNVTCDLKLVCEKLKDRN--------QR-HKRQDIEVGKAVRPQLAMRIGDAHA 237 (1160)
Q Consensus 167 iIlkdLriGi~e~til~~~hpda~~~~~~~~DL~~V~~~L~~~~--------~~-~~~~~i~~g~p~~PmLA~~~~~~~~ 237 (1160)
+|-++|.+..+.+.||+++||.|+++|.. +.|..|.+...... .+ -....-....|++|||+...++++-
T Consensus 304 LIr~~L~~~s~A~~iL~~~~P~A~E~F~S-~~L~~ViEr~~~N~~~~~~~~~~~~~~s~~s~~~s~~Q~~~~~~~~~VE~ 382 (482)
T KOG4437|consen 304 LIKHDLKMNSGAKHVLDALDPNAYEAFKS-RNLQDVVERVLHNAQEVEKEPGQRRALSVQASLMTPVQPMLAEACKSVEY 382 (482)
T ss_pred HHHHHhccCCChhHHHhccCCCcHHHHHh-cCHHHHHHHHHHhHHHHhhCccccccccchhhhcCCcChhhhhhhhhHHH
Confidence 99999999999999999999999999964 45777777654321 11 0001123467899999998888776
Q ss_pred HHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhc-ccCceeeceeEEEEeCCCCccccc
Q 001083 238 AWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNV-LVDRCILDGEMLVWDTSLNRFAEF 316 (1160)
Q Consensus 238 ~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~-~~~~~ILDGElv~~d~~~~~~~pF 316 (1160)
+.++..| +..-|.||||+|.|+|.+|+.|.+|||--....+.. +.+.+.+ ...+.++|||....+..+++++||
T Consensus 383 s~~~~~~-~~~S~~~~D~E~~~~~~~~D~~S~~S~~~~~~s~FK----~~~P~~~~~G~~~~~~~~~~~I~~K~~~P~~~ 457 (482)
T KOG4437|consen 383 AMKKCPN-GMFSEIKYDGERVQVHKNGDHFSYFSRLPHKVAHFK----DYIPQAFPGGHSMILDSEVLLIDNKTGKPLPF 457 (482)
T ss_pred HhccCCC-CccccccCCCceeeccCCCcchhhhccChHhhhhhh----hcCchhcCCCccccccccccceecccCCCCCc
Confidence 6666554 578999999999999999999999999765544321 1111122 357899999999999999999999
Q ss_pred ccHHHHHHHhccCCCCCCccEEEEEEeeee
Q 001083 317 GSNQEIAKAARDGLSSDRQVLCYFAFDVLY 346 (1160)
Q Consensus 317 ~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~ 346 (1160)
+++..-.+..+. +.. +|.++||++|
T Consensus 458 ~~~~~~~K~~~~----~~~-~~~~~~~~~~ 482 (482)
T KOG4437|consen 458 GTLGVHKKAAFQ----DAN-VCLFVFDCIY 482 (482)
T ss_pred hhcchhhHHHhc----Ccc-hheeecccCC
Confidence 987655554432 223 7899999875
No 36
>cd07972 OBF_DNA_ligase_Arch_LigB The Oligonucleotide/oligosaccharide binding (OB)-fold domain of archaeal and bacterial ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, 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 Pyrococcus furiosus DN
Probab=99.92 E-value=5.6e-25 Score=217.02 Aligned_cols=121 Identities=31% Similarity=0.575 Sum_probs=106.4
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001083 451 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 530 (1160)
Q Consensus 451 ~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 530 (1160)
+++|+||+|+++|.|+++|.+|+||||++++++ +.|+++|+||||||++++++|.++|+++++.
T Consensus 1 ~t~d~vi~G~~~~~g~~~~~~~slllg~~d~~~-----g~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~----------- 64 (122)
T cd07972 1 ETLDLVVIGAEWGEGRRAGLLGSYTLAVRDEET-----GELVPVGKVATGLTDEELEELTERLRELIIE----------- 64 (122)
T ss_pred CceeEEEEeeEeCCCCcCCCcccEEEEEEcCCC-----CeEEEEEEEccCCCHHHHHHHHHHhhhhhcc-----------
Confidence 479999999999999999999999999997652 2799999999999999999999999887643
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCcCCHHHHH
Q 001083 531 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 598 (1160)
Q Consensus 531 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~~t~~el~ 598 (1160)
..+|++||+ |. +|+||++.. ...|+.|++|++||||||+++|+||+|+||+|+++|.
T Consensus 65 -------~~~~~~wv~-P~--lV~eV~~~e-~t~s~~~~~g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 65 -------KFGPVVSVK-PE--LVFEVAFEE-IQRSPRYKSGYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred -------ccCCcEEEe-ce--EEEEEEeeE-EEecCccccCceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 125799998 75 899999643 2468889999999999999999999999999999985
No 37
>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=99.92 E-value=8.6e-25 Score=237.12 Aligned_cols=173 Identities=21% Similarity=0.280 Sum_probs=129.0
Q ss_pred HHhcCCCcEEEEEecceEEEEEEEeC-CEEEEEeCCCCCCCcchhhHHHHHHHhcccCceeeceeEEEEeCCCCcccccc
Q 001083 239 WRKLHGKEVVIECKFDGDRIQIHKNG-SEIHYFSRSFLDHSEYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (1160)
Q Consensus 239 ~~~~~~~~~~~E~K~DGeR~qih~~g-~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF~ 317 (1160)
+..+...+|++|+|+||+|+|+|+.+ +.+.+|||+++.++..+|.+.+.........++|||||||+++...
T Consensus 35 ~~~~~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~~~~~~~~~~~~~ilDGElv~~~~~~------- 107 (215)
T cd07895 35 LELLKQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFPRRKNLEPHHQGTLLDGELVIDKVPG------- 107 (215)
T ss_pred HHHHhhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCCCcccccccccCeeeEEEEEEEcCCC-------
Confidence 33455678999999999999999998 9999999999998876665532111112357899999999987421
Q ss_pred cHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcce----eeccCCCCCccccCCCC
Q 001083 318 SNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLE----TLVPDHGLNSHVRPQGE 393 (1160)
Q Consensus 318 ~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~----i~~p~~~~~~~v~~~~~ 393 (1160)
..+++|+|||||++||+++.+.||.+|+++|++++........ ...+. ..+.|+
T Consensus 108 ----------------~~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~--~~~~i~---- 165 (215)
T cd07895 108 ----------------KKRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAK--EPFSVR---- 165 (215)
T ss_pred ----------------ceEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCC--CCeEEE----
Confidence 1238999999999999999999999999999999854321100 00000 000110
Q ss_pred CccceecCCHHHHHHHHHHH---HHcCCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001083 394 PCWSLVAHNVDEVEKFFKET---IENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 444 (1160)
Q Consensus 394 ~~~~~~~~~~~ei~~~~~~a---i~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKp 444 (1160)
.......+++..+++.+ +.+|.||||+|+.+++|.+| |+..|+|+||
T Consensus 166 ---~k~~~~~~~~~~~~~~~~~~~~~~~EGlIfk~~~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 166 ---LKDFFPLYKIEKLFEKIIPKLPHENDGLIFTPNDEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred ---ecceEeHHhHHHHHHhccccCCCCCCCEEEccCCCCccCc-cCCcceeeCC
Confidence 01122356888888888 59999999999999999999 9999999997
No 38
>cd07893 OBF_DNA_ligase The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit 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 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 and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV, V and V
Probab=99.91 E-value=7.3e-24 Score=210.92 Aligned_cols=122 Identities=42% Similarity=0.787 Sum_probs=103.5
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001083 451 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 530 (1160)
Q Consensus 451 ~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 530 (1160)
+++||||+|+++|.|+++|.+|+||||++++++ +.|+++|+||||||++++++|.++|.+++... .|| +
T Consensus 1 d~~D~VI~G~~~~~g~~~~~~~slLlg~~d~~~-----~~l~~vgkvgtGfs~~~~~~l~~~l~~~~~~~-----~p~-~ 69 (129)
T cd07893 1 DTLDLVIVGAYYGKGRRGGGIGAFLCAVYDPER-----DEFQTICKVGSGFTDEELEELRELLKELKTPE-----KPP-R 69 (129)
T ss_pred CcEEEEEEeeEcCCCCcCCCcceEEEEEEcCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhcccccC-----CCC-c
Confidence 479999999999999999999999999997543 38999999999999999999999999988641 133 2
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccC-------CceeeCceeeeeecCCCccCc
Q 001083 531 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-------PYSLRFPRIDRVRYDKPWHDC 591 (1160)
Q Consensus 531 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~-------g~tLRFPR~~riR~DK~~~d~ 591 (1160)
. ....+|++||+ | ++|+||+++.. ..|+.|++ |++||||||+++|+||+|+||
T Consensus 70 ~----~~~~~~~~wv~-P--~lV~EV~~~e~-t~s~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~e~ 129 (129)
T cd07893 70 V----NSIEKPDFWVE-P--KVVVEVLADEI-TRSPMHTAGRGEEEEGYALRFPRFVRIRDDKGPEDA 129 (129)
T ss_pred c----cccCCCcEEEe-e--eEEEEEEeeee-eeCcccccccccCCCceEEECCEEEEEeCCCChhhC
Confidence 1 23468999999 7 59999996433 35788888 899999999999999999997
No 39
>cd07971 OBF_DNA_ligase_LigD The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigD is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, 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 Mycobacterium tuberculosis LigD and similar ba
Probab=99.78 E-value=1.3e-18 Score=170.17 Aligned_cols=114 Identities=27% Similarity=0.458 Sum_probs=90.8
Q ss_pred cccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcc
Q 001083 452 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 531 (1160)
Q Consensus 452 ~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~ 531 (1160)
+.|++|+|++.+.| +.|.+|+||||++++. .|+++|+||||||++++++|.+.|++++.. .|| |.
T Consensus 2 ~~~~vI~G~~~~~g-~~~~~gslllg~~~~~-------~l~~vG~vgtG~s~~~~~~l~~~l~~~~~~------~~p-~~ 66 (115)
T cd07971 2 RQEFVIGGYTPPKG-SRGGFGSLLLGVYDGG-------RLVYVGRVGTGFSAATLRELRERLAPLERK------TSP-FA 66 (115)
T ss_pred CceEEEEEEECCCC-CCCcccEEEEEEEcCC-------EEEEeeeEcCCCCHHHHHHHHHHhhcccCC------CCC-Cc
Confidence 46888887777777 7788999999999753 799999999999999999999999987653 133 21
Q ss_pred cccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCCCccCc
Q 001083 532 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 591 (1160)
Q Consensus 532 ~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK~~~d~ 591 (1160)
.. ......|++||+ |. +|+||++.. ++.+++||||+|+++|+||+|++|
T Consensus 67 ~~-~~~~~~~~~wv~-P~--lv~eV~~~~-------~t~~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 67 DP-PPADARGAVWVK-PE--LVAEVEFAE-------WTPDGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred cc-ccccCCCCEEec-CC--EEEEEEEEE-------ecCCCcEECCeeeEeeCCCCcccC
Confidence 11 112457899999 75 899998632 345679999999999999999987
No 40
>PF04679 DNA_ligase_A_C: ATP dependent DNA ligase C terminal region ; InterPro: IPR012309 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 constitute part of the catalytic core of ATP dependent DNA ligase []. ; GO: 0003910 DNA ligase (ATP) activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3RR5_A 2CFM_A 1X9N_A 1VS0_B 3GDE_A 2HIX_A 2HIV_A 3L2P_A 4EQ5_A.
Probab=99.73 E-value=1.2e-17 Score=158.38 Aligned_cols=97 Identities=42% Similarity=0.746 Sum_probs=73.1
Q ss_pred CCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcccccCCCCCCCcEEEe
Q 001083 467 RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIE 546 (1160)
Q Consensus 467 r~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~~~~~~~~~~Pdvwi~ 546 (1160)
|+|.+|+||||+++++. +.|.++|+||||||++++++|.++|.++|... ||...... ...+|++||+
T Consensus 1 R~g~~~slllg~~d~~~-----~~l~~vg~vgtG~~~~~~~~l~~~l~~~~~~~------~p~~~~~~--~~~~~~~wv~ 67 (97)
T PF04679_consen 1 RGGGIGSLLLGVYDPDS-----GRLVYVGKVGTGFSDEELRELRERLEPLWIKK------PPFDVKPP--SRERPDVWVE 67 (97)
T ss_dssp GTTSEEEEEEEEEETTT-----TEEEEEEEE-SS--HHHHHHHHHHHGGGEEEE------ETTTCCEC--CSCTTEEEE-
T ss_pred CCCccceEEEEEEcCCC-----CcEEEEEEECCCCCHHHHHHHHHHhhCccccC------CCCccccc--cCccCcEEeC
Confidence 56789999999999762 38999999999999999999999999998652 33222221 1268999998
Q ss_pred CCcceEEEEEEeeeeeeecccccCCceeeCceeeeeecCC
Q 001083 547 SPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 586 (1160)
Q Consensus 547 ~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR~DK 586 (1160)
|. +|+||++...+ .+ | +||||||++||+||
T Consensus 68 -P~--~V~eV~~~e~t-~~-----G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 68 -PE--LVVEVKFAEIT-PS-----G-SLRFPRFKRIREDK 97 (97)
T ss_dssp -ST---EEEEEESEEE-EE-----S-EEESEEEEEEETTS
T ss_pred -CC--EEEEEEEEEEc-CC-----C-eEECCEEeEEeCCC
Confidence 87 59999975432 22 6 99999999999998
No 41
>cd08040 OBF_DNA_ligase_family The Oligonucleotide/oligosaccharide binding (OB)-fold domain is a DNA-binding module that is part of the catalytic core unit 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 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 and C-terminal OB-fold domains comprise a catalytic core unit that is common to most members of the ATP-dependent DNA ligase family. The catalytic core unit contains six conserved sequence motifs (I, III, IIIa, IV,
Probab=99.73 E-value=3.1e-17 Score=158.74 Aligned_cols=108 Identities=22% Similarity=0.306 Sum_probs=87.1
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001083 451 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 530 (1160)
Q Consensus 451 ~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 530 (1160)
+++|++|+|+++|.|++.|.+|+||||+++++ .+.++|+||||||++++++|.+.|++++.. .. |+.+
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~-------~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~----~~-~~~~ 68 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED-------GLQAVFSVGTGFSADERRDLWQNLEPLVTS----FD-DHPV 68 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC-------ceEEEEEEcCCCCHHHHHHHHHhcchhccC----CC-CCcc
Confidence 47899999999999999999999999998754 377999999999999999999999988754 11 2211
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeee
Q 001083 531 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 583 (1160)
Q Consensus 531 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR 583 (1160)
. .....+|++|++ |. +|+||++.. ++.+.+||||||+++|
T Consensus 69 ~---~~~~~~~~vwv~-P~--lv~eV~~~~-------~t~~~~lR~P~f~~~R 108 (108)
T cd08040 69 W---NVGKDLSFVPLY-PG--KVVEVKYFE-------MGSKDCLRFPVFIGIR 108 (108)
T ss_pred c---ccccCCCCEEee-ce--EEEEEEeEE-------eeCCCeEECCeEEEeC
Confidence 1 123457999999 74 899998632 3458999999999997
No 42
>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=99.63 E-value=2.6e-15 Score=172.05 Aligned_cols=162 Identities=20% Similarity=0.271 Sum_probs=117.0
Q ss_pred CcEEEEEecceEEEEEEEeCCEEEEEeCCCCCC---CcchhhHHHHHHHhc-ccCceeeceeEEEEeCCCCcccccccHH
Q 001083 245 KEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDH---SEYGHAMSKIIEQNV-LVDRCILDGEMLVWDTSLNRFAEFGSNQ 320 (1160)
Q Consensus 245 ~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~---t~~~~~l~~~l~~~~-~~~~~ILDGElv~~d~~~~~~~pF~~lq 320 (1160)
.+|++|+||||.|+++|+.+|++..|||+|... |+.+|.+... ..+ ..++++||||+++.+. ||. +
T Consensus 48 ~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~i~e~~T~~~~eiv~~--~~~~~~p~~iLdGElvg~~~------p~v--~ 117 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRIGGKVLAFTRGGFICPFTTDRLRDLIDP--EFFDDHPDLVLCGEVVGPEN------PYV--P 117 (342)
T ss_pred CCEEEEEeECCcEEEEEEECCEEEEEeCCCccCccchhhHhhhchH--HhhccCCCEEEEEEEEecCC------ccc--c
Confidence 589999999999999999999999999998644 6666766321 111 1367999999998752 331 0
Q ss_pred HHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceec
Q 001083 321 EIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVA 400 (1160)
Q Consensus 321 ~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~ 400 (1160)
... ....++.|++|||++.|+ ...+|+.+|+++|+++.-+....+ .....
T Consensus 118 -------~~~-~~~~~v~F~vFDI~~~~~--~~~lp~~eR~~lLe~lg~~~v~~~--------------------~~~~~ 167 (342)
T cd07894 118 -------GSY-PEVEDVGFFVFDIRKKNT--GRPLPVEERRELLEKYGLPTVRLF--------------------GEFTA 167 (342)
T ss_pred -------ccC-ccccccEEEEEeeEEcCC--CCCCCHHHHHHHHHhcCCCCcceE--------------------EEEec
Confidence 000 111248999999999885 567899999999998733221110 02234
Q ss_pred CCHHHHHHHHHHHHHcCCceEEEecCCC-----CCcCCCCCCCeEEEcccc
Q 001083 401 HNVDEVEKFFKETIENRDEGIVLKDLGS-----KWEPGDRSGKWLKLKPEY 446 (1160)
Q Consensus 401 ~~~~ei~~~~~~ai~~g~EGlVlK~~ds-----~Y~pGkRs~~WlKlKpeY 446 (1160)
.+.+++.++++.+.++|.||||+|++++ .|.-...+-++|++--.|
T Consensus 168 ~d~~~l~~~l~~~~~~G~EGVVlK~~~~~~~~~Ky~t~~~~~~di~~~~~~ 218 (342)
T cd07894 168 DEIEELKEIIRELDKEGREGVVLKDPDMRVPPLKYTTSYSNCSDIRYAFRY 218 (342)
T ss_pred CCHHHHHHHHHHHHHCCCceEEEeccccccCcceeecCCCCcHHHHHHhhh
Confidence 5689999999999999999999999998 676655555666665554
No 43
>cd07970 OBF_DNA_ligase_LigC The Oligonucleotide/oligosaccharide binding (OB)-fold domain of ATP-dependent DNA ligase LigC is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, 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 Mycobacterium tuberculosis LigC and similar ba
Probab=99.60 E-value=7.1e-15 Score=144.91 Aligned_cols=120 Identities=22% Similarity=0.261 Sum_probs=86.9
Q ss_pred CcccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCc
Q 001083 451 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 530 (1160)
Q Consensus 451 ~~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~ 530 (1160)
++.|++|+|+.++. +.+|++|||++++++ .|.++|+| ||||++++++|.+.|+++.....++ ..+|.|
T Consensus 1 ~~~e~vI~G~~~~~----~~~gsLlLg~~~~~g------~l~yvG~v-tGf~~~~~~~L~~~l~~l~~~~p~~-~~~~~~ 68 (122)
T cd07970 1 RTADCVVGGVRGHK----DRPGSLLLGLYDDGG------RLRHVGRT-SPLAAAERRELAELLEPARAGHPWT-GRAPGF 68 (122)
T ss_pred CcEeEEEEEEECCC----CCccEEEEEEECCCC------CEEEEEEE-CCCCHHHHHHHHHHHHHhhcCCCCc-cccccc
Confidence 36788888877665 459999999996532 69999999 9999999999999998875431111 111213
Q ss_pred ccccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCc-eeeeeecCCCccCcC
Q 001083 531 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCL 592 (1160)
Q Consensus 531 ~~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFP-R~~riR~DK~~~d~~ 592 (1160)
..........+.+|++ |. +|+||++.. ++.+..|||| +|+++|+||+++||.
T Consensus 69 ~~~~~~~~~~~~~wv~-P~--lV~eV~~~e-------~t~~G~LRhP~~f~glR~Dk~~~~v~ 121 (122)
T cd07970 69 PSRWGTRKSLEWVPVR-PE--LVVEVSADT-------AEGGGRFRHPLRFLRWRPDKSPEDCT 121 (122)
T ss_pred ccccCcccCCCeEEee-cc--EEEEEEeeE-------EecCCceeCCceeEEEcCCCCHHHCc
Confidence 1111112345789999 75 899997632 3445599999 899999999999986
No 44
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=99.15 E-value=9.4e-11 Score=105.73 Aligned_cols=74 Identities=24% Similarity=0.501 Sum_probs=66.5
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC--CChhhHhhhcCC-CeeecchHHHHH
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN--KGLKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~--~~~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
.+.+|+|+.||+ ++.....+++|+++|..|||++....+..+||+|+... .+.++..+...+ +||+++||.||+
T Consensus 2 ~~~~F~g~~f~i-~~~~~~~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~~k~~~~~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 2 KPKIFEGCTFCI-SGFDSDEREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRTKKYKAAIANGIPIVSPDWIEDCI 78 (78)
T ss_dssp STTTTTTEEEEE-SSTSSSHHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCCHHHHHHHHTTSEEEETHHHHHHH
T ss_pred CCCCCCCEEEEE-ccCCCCCHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCccHHHHHHHHCCCeEecHHHHHHhC
Confidence 357999999999 66667889999999999999999999889999998776 777899888888 999999999997
No 45
>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=99.01 E-value=9.2e-11 Score=125.33 Aligned_cols=173 Identities=17% Similarity=0.254 Sum_probs=103.9
Q ss_pred cCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCc---chhhHHHHHHHhcccCceeeceeEEEEeCCCCccccccc
Q 001083 242 LHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFGS 318 (1160)
Q Consensus 242 ~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~---~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF~~ 318 (1160)
+...+|+|.+|-||.|+++...++.+-++.|+..-+.- .+|.-.... ..-...+.+||||||. |...+
T Consensus 13 l~~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~~v~~~~~p~~~~~~-~~~~~~~TLLDGElV~-d~~~~------- 83 (192)
T PF01331_consen 13 LQQKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVFKVDNLHFPSKKDSS-DGRHHQDTLLDGELVL-DKDPG------- 83 (192)
T ss_dssp HHHS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EEEESSST-ECTTC---TTCEGCSEEEEEEEEE-EECTT-------
T ss_pred HhhCCcEEEECCCCcEEEEEEecceEEEEeCCCcEEEecCcccccccccc-cccccCCEEEEEEEEc-ccCCC-------
Confidence 34468999999999999999988899999999765431 122111000 0112468999999987 21100
Q ss_pred HHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCccee---eccCCCCCccccCCCCCc
Q 001083 319 NQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLET---LVPDHGLNSHVRPQGEPC 395 (1160)
Q Consensus 319 lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i---~~p~~~~~~~v~~~~~~~ 395 (1160)
...+.|++||+|++||.++++.|+.+|...|.+.+........+ .......++.++.-
T Consensus 84 ---------------~~~~~flifD~l~~~G~~v~~~~~~~Rl~~l~~~i~~p~~~~~~~~~~~~~~~~pf~i~~K---- 144 (192)
T PF01331_consen 84 ---------------EKKPRFLIFDILAINGQNVTDKPLDERLAYLQEEIIEPRKNAELKSGIIKKKKEPFSIRIK---- 144 (192)
T ss_dssp ---------------CEEEEEEEEEEEEETTEEGCCSBHHHHHHHHHHHTHHHHHHHHCHTTSCTCTTSSSEEEE-----
T ss_pred ---------------CCceEEEEEeeehhCCcEeccCCHHHHHHHHHHHHHHHHHhhccccccccccccceeeecc----
Confidence 12389999999999999999999999999997655321111000 00000001111100
Q ss_pred cceecCCHHH-HHHHHHHHHHcCCceEEEecCCCCCcCCCCCCCeEEEc
Q 001083 396 WSLVAHNVDE-VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 443 (1160)
Q Consensus 396 ~~~~~~~~~e-i~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs~~WlKlK 443 (1160)
........+. +...+..-+.+...|||+-..+.+|.+| +...++|||
T Consensus 145 ~~~~~~~~~~~~~~~~~~~l~h~~DGLIFtp~~~pY~~G-t~~~llKWK 192 (192)
T PF01331_consen 145 DFFPIYQIEKLLFEEFIPKLPHETDGLIFTPVNTPYVPG-TCPNLLKWK 192 (192)
T ss_dssp --EEGGGHHHHCHHCCCCCTTSTEEEEEEEESSSB--SE-EEEEEEEE-
T ss_pred ccHHHHhhHHHHHHHhhccCCCCCCEEEEecCCCCccCC-CCCccEeeC
Confidence 0111222333 2222233456788999999999999999 678999998
No 46
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.97 E-value=1.7e-09 Score=96.63 Aligned_cols=76 Identities=24% Similarity=0.430 Sum_probs=63.7
Q ss_pred CcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCC-CceEEEEecCCChh--hHhhhcCC-CeeecchHHHHHhcC
Q 001083 656 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN-SVTHCVAADNKGLK--YEAAKRRG-DVIHYSWVLDCCSQK 731 (1160)
Q Consensus 656 ~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~-~~Th~Ia~~~~~~K--~~~a~~~~-~VV~p~WV~dCi~~~ 731 (1160)
.+|+|+.||+.+......+++|.++|..+||+++..+.. .+||+|+.+....+ +..+...+ +||+++||.||++.+
T Consensus 1 ~~f~g~~~~~~g~~~~~~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~~~ 80 (80)
T smart00292 1 KLFKGKVFVITGKFDKNERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGKLELLLAIALGIPIVTEDWLLDCLKAG 80 (80)
T ss_pred CccCCeEEEEeCCCCCccHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCccHHHHHHHHcCCCCccHHHHHHHHHCc
Confidence 489999999986455678999999999999999999886 79999998765554 45565556 999999999999864
No 47
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=98.95 E-value=4.6e-09 Score=130.32 Aligned_cols=185 Identities=21% Similarity=0.290 Sum_probs=140.5
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHHhcCc
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQKK 732 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi~~~~ 732 (1160)
-+..|+|+.||-.... ...+++|.+.+..+||.++..++.++||+|+..-...+|.++.+.+ +|++++||...+..+.
T Consensus 6 ~~~~~~~v~~~~t~i~-p~~~~~l~~~~~~~Gg~~~~~~t~~~thli~~~~~s~~~~~a~~~~~~~~~~~wi~~~~d~~~ 84 (811)
T KOG1929|consen 6 YSKPMSGVTFSPTGIN-PIKREELSKKFIKLGGIDFKDFTPSVTHLIVGSVTSSKYAAAHRFDIKVLDSSWIDYIYDLWL 84 (811)
T ss_pred cCcccCCceeccCcCC-HHHHHHHHHHHHhcCceeeeccCCcCceeecccccccchhhhhcCCCceecchHHHHHHHHhh
Confidence 3568899999965443 5678999999999999999999999999998877777886666666 9999999999887665
Q ss_pred cCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhhHHhhhcCCCCCCccCCCeEEEEc
Q 001083 733 LLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFY 812 (1160)
Q Consensus 733 lLp~~p~~~l~~s~~t~~~~~~~~D~~gDSy~~~~~~~~L~~ll~~i~~~~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~ 812 (1160)
+ . .. .+. .|... ......+|.||.||+.
T Consensus 85 ~-~-~e--~~~------------~~~l~------------------------------------~~~~~p~~~~~~Vc~t 112 (811)
T KOG1929|consen 85 L-N-KE--IRL------------LDPLR------------------------------------DTMKCPGFFGLKVCLT 112 (811)
T ss_pred h-h-cc--Ccc------------Cccch------------------------------------hhhcCCcccceEEEec
Confidence 4 1 10 000 01000 0123457999999999
Q ss_pred cCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEecc
Q 001083 813 HSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRS 891 (1160)
Q Consensus 813 ~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVt~ 891 (1160)
|+.. .++..+..+|..+||+....|+ +++||++...... .+|+ ..+ .+..+||+.
T Consensus 113 gl~~-----------~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~-~kYe---~al---------~wn~~v~~~ 168 (811)
T KOG1929|consen 113 GLSG-----------DEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKT-EKYE---QAL---------KWNIPVVSD 168 (811)
T ss_pred ccch-----------HHHHHHHHHhhhcccEEehhhhhhhheeeeccccch-HHHH---HHH---------hhCCccccH
Confidence 9863 3577899999999999999998 4777777654321 2333 222 467899999
Q ss_pred chHHHHHHcCCccCCCCCCCCCCC
Q 001083 892 QWLEDCLAKEQKSEEYEYSLKPTG 915 (1160)
Q Consensus 892 ~Wl~eci~~~~~v~Ee~Y~v~~~~ 915 (1160)
+|+++|+..+..++...|.+.+..
T Consensus 169 ~w~~~s~~~~~~~~~~~~e~~~~~ 192 (811)
T KOG1929|consen 169 DWLFDSIEKTAVLETKPYEGAPVA 192 (811)
T ss_pred HHHhhhhccccccccccccccccc
Confidence 999999999999999999999963
No 48
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=98.91 E-value=2.7e-09 Score=126.12 Aligned_cols=183 Identities=19% Similarity=0.216 Sum_probs=135.2
Q ss_pred CCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCCCeeecchHHHHHhcCc
Q 001083 653 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKK 732 (1160)
Q Consensus 653 ~~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~~VV~p~WV~dCi~~~~ 732 (1160)
.-...|.|+..|+.+.- ...++|-.+|+.+||.+..+.+..+||.|+....+-++..+.-.-++++|.||+.||+..-
T Consensus 114 ly~~~m~~vvlcfTg~r--kk~e~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t~~~~~rp~wv~~aw~~rn 191 (850)
T KOG3524|consen 114 LYCELMKDVVMCFTGER--KKKEELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALVGVPTMRPDWVTEAWKHRN 191 (850)
T ss_pred ccchhhcCceeeeeccc--hhhHHHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEeeccceechHhhhhhhcCcc
Confidence 44668999999987543 2345899999999999999998889999998888888887765569999999999997553
Q ss_pred cCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhhHHhhhcCCCCCCccCCCeEEEEc
Q 001083 733 LLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFY 812 (1160)
Q Consensus 733 lLp~~p~~~l~~s~~t~~~~~~~~D~~gDSy~~~~~~~~L~~ll~~i~~~~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~ 812 (1160)
-+- +....+.|-|-| ...-|.||.|+|+
T Consensus 192 ~~y----------------fda~~~~f~d~h------------------------------------rl~~feg~~~~f~ 219 (850)
T KOG3524|consen 192 DSY----------------FDAMEPCFVDKH------------------------------------RLGVFEGLSLFFH 219 (850)
T ss_pred hhh----------------hhhhccchhhhh------------------------------------ccccccCCeEeec
Confidence 111 000111111111 3346999999999
Q ss_pred cCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCCCceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEeccc
Q 001083 813 HSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQ 892 (1160)
Q Consensus 813 ~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVt~~ 892 (1160)
||.. .+.+.|-+.++..||++......||||||++.......+. .+..-++|..+
T Consensus 220 gF~~-----------ee~~~m~~sle~~gg~~a~~d~~cthvvv~e~~~~~~p~~--------------~s~~~~~vk~e 274 (850)
T KOG3524|consen 220 GFKQ-----------EEIDDMLRSLENTGGKLAPSDTLCTHVVVNEDNDEVEPLA--------------VSSNQVHVKKE 274 (850)
T ss_pred CCcH-----------HHHHHHHHHHHhcCCcccCCCCCceeEeecCCcccccccc--------------ccccceeeccc
Confidence 9963 2356788889999999999666799999986431111111 13455899999
Q ss_pred hHHHHHHcCCccCCCCCCCCCC
Q 001083 893 WLEDCLAKEQKSEEYEYSLKPT 914 (1160)
Q Consensus 893 Wl~eci~~~~~v~Ee~Y~v~~~ 914 (1160)
|.+-+|..|...-|.+|..+.-
T Consensus 275 wfw~siq~g~~a~e~~yl~~~~ 296 (850)
T KOG3524|consen 275 WFWVSIQRGCCAIEDNYLLPTG 296 (850)
T ss_pred ceEEEEecchhccccceecccc
Confidence 9999999999999999987654
No 49
>cd08041 OBF_kDNA_ligase_like The Oligonucleotide/oligosaccharide binding (OB)-fold domain of kDNA ligase-like ATP-dependent DNA ligases is a DNA-binding module that is part of the catalytic core unit. 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, bacteriohages, eukarya, archaea and bacteria. The mitochondrial DNA of parasitic protozoan 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-de
Probab=98.89 E-value=4.8e-09 Score=95.35 Aligned_cols=76 Identities=26% Similarity=0.395 Sum_probs=60.2
Q ss_pred cccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHHHhhcccccccCCCCCCCCCcc
Q 001083 452 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 531 (1160)
Q Consensus 452 ~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~~~l~~~~~~~~~~~~~pP~~~ 531 (1160)
+.|++|+|+++|.|++.|.+|+|+|+.++.. .++||||||+++++++. |
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g~-----------~~~vgtG~t~~~r~~~~-----------------~--- 50 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDGI-----------RFKIGSGFSDEQRRNPP-----------------P--- 50 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCCC-----------EEEEcCCCCHHHHhcCC-----------------C---
Confidence 6899999999999999999999999987521 45899999999988542 1
Q ss_pred cccCCCCCCCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceeeeee
Q 001083 532 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 583 (1160)
Q Consensus 532 ~~~~~~~~~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~riR 583 (1160)
| . .|+||++ ..++++..||||+|+++|
T Consensus 51 -------------~--g---~v~~V~y-------~e~t~~g~lR~P~f~g~R 77 (77)
T cd08041 51 -------------I--G---SIITYKY-------QGLTKNGLPRFPVFLRVR 77 (77)
T ss_pred -------------C--C---CEEEEEE-------EecCCCCcccCCEEEecC
Confidence 0 0 2667765 234568899999999997
No 50
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.79 E-value=1.4e-08 Score=88.60 Aligned_cols=70 Identities=23% Similarity=0.492 Sum_probs=59.3
Q ss_pred CeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChh-hHhhhcCC-CeeecchHHHHHh
Q 001083 660 DMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLK-YEAAKRRG-DVIHYSWVLDCCS 729 (1160)
Q Consensus 660 G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K-~~~a~~~~-~VV~p~WV~dCi~ 729 (1160)
|+.||+.+......+++|+++|..+||+++..+...+||+|+......+ +..+...+ +||+++||.||++
T Consensus 1 ~~~~~i~g~~~~~~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~~~~~~~~~~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 1 GLTFVITGDLPSEERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPKKLLKAIKLGIPIVTPEWLLDCLK 72 (72)
T ss_pred CCEEEEEecCCCcCHHHHHHHHHHcCCEEeccccCCceEEEECCCCCchHHHHHHHcCCeEecHHHHHHHhC
Confidence 6789988765467899999999999999999888789999998766554 66666666 9999999999984
No 51
>COG5226 CEG1 mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=98.79 E-value=1e-08 Score=111.20 Aligned_cols=183 Identities=20% Similarity=0.319 Sum_probs=117.6
Q ss_pred cCCCcEEEEEecceEEEEEEEe-----C-CEEEEEeCCCCCCC---cchhhHHHHHHHhcccCceeeceeEEEEeCCCCc
Q 001083 242 LHGKEVVIECKFDGDRIQIHKN-----G-SEIHYFSRSFLDHS---EYGHAMSKIIEQNVLVDRCILDGEMLVWDTSLNR 312 (1160)
Q Consensus 242 ~~~~~~~~E~K~DGeR~qih~~-----g-~~v~~fSR~g~d~t---~~~~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~ 312 (1160)
+...+|++.+|-||.||++.+. | -...+|.|..+-|. ..+|.+...........+..||||+|. |
T Consensus 59 Ll~~dy~VCEKsDGvR~Ll~vte~p~tg~~~~y~~DR~nnfY~v~~~f~p~~~~~k~ge~l~~dtlldgelV~-d----- 132 (404)
T COG5226 59 LLNNDYLVCEKSDGVRALLLVTEEPVTGAFRGYFYDRRNNFYEVHTSFPPCSTVLKDGEVLLEDTLLDGELVF-D----- 132 (404)
T ss_pred HHhCCeEEEEccCCeEEEEEEEecccCCCcceEEEeccCceEEeccccCCcccccccCcEEeccceecceEEE-E-----
Confidence 3456899999999999999874 2 25778999887653 223322211111123467789999986 2
Q ss_pred ccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeecc--CCCCCccccC
Q 001083 313 FAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVP--DHGLNSHVRP 390 (1160)
Q Consensus 313 ~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p--~~~~~~~v~~ 390 (1160)
.+|.+.++. +.|.+||+|-++|.-+..++.++|.+.|.+-+...-.+.....+ .+..++|
T Consensus 133 ~~p~~k~~q---------------lryl~fdcLa~~g~~~~~~~~s~Rl~~l~Ke~~kp~~~~r~s~~~~~~~fpf~--- 194 (404)
T COG5226 133 CLPYEKVPQ---------------LRYLLFDCLAYAGMFVERMEKSERLKTLQKEDEKPRERKRVSIEIDSGSFPFH--- 194 (404)
T ss_pred eccccchHH---------------HHHHHHHHhhhcceeEeecchhhHHHHhhhhhcccHhhhhheeecccccccee---
Confidence 356654432 55889999999999999999999999998765422111111111 1111111
Q ss_pred CCCCccceecCCH---HHHHHHHHHH--HHcCCceEEEecCCCCCcCCCCCCCeEEEccccccCCCcccEEEEE
Q 001083 391 QGEPCWSLVAHNV---DEVEKFFKET--IENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIG 459 (1160)
Q Consensus 391 ~~~~~~~~~~~~~---~ei~~~~~~a--i~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpeY~~~g~~lDlvIIG 459 (1160)
+...-. -.+-++|+.. +.+|..|||+-..+.+|..|++ +..+|+||.-+ .++|+..|=
T Consensus 195 -------~s~K~M~~syg~~ki~k~ip~L~HgnDGLIFTp~~~PY~~Gkd-~~lLKWKP~~~---NTiDF~lvl 257 (404)
T COG5226 195 -------FSVKQMLKSYGFWKIYKKIPELKHGNDGLIFTPADEPYSVGKD-GALLKWKPASL---NTIDFRLVL 257 (404)
T ss_pred -------eeHHHHHhhhhHHHHHhhcccccCCCCceEeccCCCCcccCcc-ceeeecCcccc---Cceeeeeee
Confidence 111111 1233444222 4689999999999999999965 68999999743 478876653
No 52
>PF00533 BRCT: BRCA1 C Terminus (BRCT) domain; InterPro: IPR001357 The BRCT domain (after the C_terminal domain of a breast cancer susceptibility protein) is found predominantly in proteins involved in cell cycle checkpoint functions responsive to DNA damage [], for example as found in the breast cancer DNA-repair protein BRCA1. The domain is an approximately 100 amino acid tandem repeat, which appears to act as a phospho-protein binding domain []. A chitin biosynthesis protein from yeast also seems to belong to this group. ; GO: 0005622 intracellular; PDB: 3L46_A 3AL3_A 3AL2_A 1WF6_A 3II6_X 2NTE_B 3FA2_A 2R1Z_A 2COK_A 2K7F_A ....
Probab=98.74 E-value=2.3e-08 Score=90.07 Aligned_cols=75 Identities=25% Similarity=0.439 Sum_probs=55.7
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
..+|+||.|||.++.. . .++.+..+|+.+||++++.++ .+||||+....... .+ ...+
T Consensus 3 ~~~F~g~~f~i~~~~~---~--------~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~--~k-~~~~------- 61 (78)
T PF00533_consen 3 PKIFEGCTFCISGFDS---D--------EREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRT--KK-YKAA------- 61 (78)
T ss_dssp TTTTTTEEEEESSTSS---S--------HHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCC--HH-HHHH-------
T ss_pred CCCCCCEEEEEccCCC---C--------CHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCcc--HH-HHHH-------
Confidence 4689999999966542 1 356889999999999999998 59999998651111 11 1111
Q ss_pred hccCCccEEeccchHHHHH
Q 001083 880 LLWNKKLHVVRSQWLEDCL 898 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci 898 (1160)
....+.||+++||.+||
T Consensus 62 --~~~~i~iV~~~Wi~~ci 78 (78)
T PF00533_consen 62 --IANGIPIVSPDWIEDCI 78 (78)
T ss_dssp --HHTTSEEEETHHHHHHH
T ss_pred --HHCCCeEecHHHHHHhC
Confidence 13578999999999997
No 53
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=98.62 E-value=2.5e-08 Score=110.44 Aligned_cols=94 Identities=21% Similarity=0.423 Sum_probs=83.8
Q ss_pred cccCCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHH
Q 001083 650 DIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 650 ~~~~~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
+-..-+.|++|++|++ +|.....+.+|+......|++|-.+++..+||+||+.++|+||+.....| .||+-+||.+|.
T Consensus 310 ~t~el~klL~GVV~Vl-SGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~Cy 388 (508)
T KOG3226|consen 310 NTTELSKLLEGVVFVL-SGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITECY 388 (508)
T ss_pred CchhHHHhhhceEEEE-ecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhcccCCceEeeHHHHHHHH
Confidence 4446688999999886 56668889999999999999999999989999999999999999998887 999999999999
Q ss_pred hcCccCCCCcccccccC
Q 001083 729 SQKKLLQLQPKYYLHLS 745 (1160)
Q Consensus 729 ~~~~lLp~~p~~~l~~s 745 (1160)
+.+++||++- |++++.
T Consensus 389 ~~kk~lp~rr-Ylm~~~ 404 (508)
T KOG3226|consen 389 AQKKLLPIRR-YLMHAG 404 (508)
T ss_pred HHHhhccHHH-HHhcCC
Confidence 9999999984 566654
No 54
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=98.58 E-value=7.9e-07 Score=99.06 Aligned_cols=152 Identities=23% Similarity=0.343 Sum_probs=103.8
Q ss_pred hcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCC---cchhhHHHH-HHHhcccCceeeceeEEEEeCCCCccccc
Q 001083 241 KLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHS---EYGHAMSKI-IEQNVLVDRCILDGEMLVWDTSLNRFAEF 316 (1160)
Q Consensus 241 ~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t---~~~~~l~~~-l~~~~~~~~~ILDGElv~~d~~~~~~~pF 316 (1160)
.|+...+++|+|+||..+-|.+-+|.+--.||.|--++ ...+.+.+. +... -++.+|.|||+..+. -+.|
T Consensus 84 ~F~~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG~ICPfTT~r~~~l~~~eff~d--~p~lvlcgEmvG~en---PYv~- 157 (382)
T COG1423 84 HFGRGKVVVEEKMNGYNVRVVKLGGEVYAITRGGLICPFTTERLRDLIDLEFFDD--YPDLVLCGEMVGPEN---PYVP- 157 (382)
T ss_pred hcCCCcEEEEEeccCceEEEEEECCEEEEEecCceecCchhHHHHhhcchhhHhh--CCCcEEEEEeccCCC---CCCC-
Confidence 45567899999999999999999999999999997543 223333221 1121 378999999998653 1222
Q ss_pred ccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCcc
Q 001083 317 GSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCW 396 (1160)
Q Consensus 317 ~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~ 396 (1160)
+ . ......+.|++|||--.|.. ..+|..||++++++.--+ +++++ +
T Consensus 158 ~----------~--~y~~e~v~fFvFDire~~tg--r~Lp~eer~~l~ekYgl~---~V~~f-------------g---- 203 (382)
T COG1423 158 G----------P--YYEKEDVGFFVFDIREKNTG--RPLPVEERLELAEKYGLP---HVEIF-------------G---- 203 (382)
T ss_pred C----------C--CCccCCceEEEEEEEecCCC--CCCCHHHHHHHHHHcCCC---ceEEe-------------e----
Confidence 0 0 11122388999999987643 346999999999886322 12221 1
Q ss_pred ceecCCH-HHHHHHHHHHHHcCCceEEEecCCCCCcC
Q 001083 397 SLVAHNV-DEVEKFFKETIENRDEGIVLKDLGSKWEP 432 (1160)
Q Consensus 397 ~~~~~~~-~ei~~~~~~ai~~g~EGlVlK~~ds~Y~p 432 (1160)
.+..++. ++|.++.++.-.+|.||+|+|+++..-.|
T Consensus 204 ~~~~~e~~eei~eIve~L~keGREGVV~Kdpdm~~~p 240 (382)
T COG1423 204 EFPADEAGEEIYEIVERLNKEGREGVVMKDPDMRVPP 240 (382)
T ss_pred eechhHhHHHHHHHHHHHhhcCCcceEecCcccccCc
Confidence 1122334 78899999999999999999998755433
No 55
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.54 E-value=2.1e-07 Score=83.07 Aligned_cols=76 Identities=30% Similarity=0.389 Sum_probs=57.4
Q ss_pred cCCCeEEEEcc-CCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC--CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 803 CFHGCCIYFYH-STEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA--NATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 803 lF~gc~~yl~~-~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls--~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
+|+||+||+.+ +.. . ..+.+.+.|..+||++...++ ++||||+.+.... ... ++..
T Consensus 2 ~f~g~~~~~~g~~~~---~--------~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~--~~~-~~~~------- 60 (80)
T smart00292 2 LFKGKVFVITGKFDK---N--------ERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGG--KLE-LLLA------- 60 (80)
T ss_pred ccCCeEEEEeCCCCC---c--------cHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCc--cHH-HHHH-------
Confidence 79999999998 321 1 356899999999999999998 7999999865422 111 1211
Q ss_pred hccCCccEEeccchHHHHHHcC
Q 001083 880 LLWNKKLHVVRSQWLEDCLAKE 901 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci~~~ 901 (1160)
....++||+++||.+|++.+
T Consensus 61 --~~~~~~iV~~~Wi~~~~~~~ 80 (80)
T smart00292 61 --IALGIPIVTEDWLLDCLKAG 80 (80)
T ss_pred --HHcCCCCccHHHHHHHHHCc
Confidence 13568999999999999864
No 56
>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=98.54 E-value=8.9e-07 Score=101.76 Aligned_cols=151 Identities=23% Similarity=0.300 Sum_probs=96.0
Q ss_pred cCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHHHHHhccc--CceeeceeEEEEeCCCCcccccccH
Q 001083 242 LHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKIIEQNVLV--DRCILDGEMLVWDTSLNRFAEFGSN 319 (1160)
Q Consensus 242 ~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~l~~~~~~--~~~ILDGElv~~d~~~~~~~pF~~l 319 (1160)
|.++.+++|+|+||..+-|..-+|++..+||.|--.+-...-+.+.+...++. ++.+|.|||+.-+. |+.
T Consensus 76 f~~~~v~vEEKlDG~Nvri~~~~g~l~a~tRGgyicp~tt~r~~~~~~~~~~~d~p~l~LcGE~iGpen------pY~-- 147 (374)
T TIGR01209 76 FKDPEVVVEEKMNGYNVRIVKYGGNVYALTRGGFICPFTTERLPDLIDLEFFDDNPDLVLCGEMAGPEN------PYT-- 147 (374)
T ss_pred cCCCcEEEEEeecCceEEEEeECCEEEEEccCcccCCCcHHHHHHHhhHHhhccCCCeEEEEEEcCCCC------CCc--
Confidence 45656999999999999998888999999999987632111122222222333 78999999997432 220
Q ss_pred HHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCcccee
Q 001083 320 QEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLV 399 (1160)
Q Consensus 320 q~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~ 399 (1160)
+..+.-...+..|++|||.- ...-.-+|+.+|+++++..--+....+ . ...
T Consensus 148 -------~hs~~y~~l~~~FfvFDI~d--~~t~~~L~~~er~~l~e~yglp~Vpvl-----------g---------~~~ 198 (374)
T TIGR01209 148 -------PEYYPEVKEDLGFFLFDIRE--GKTNRSLPVEERLELAEKYGLPHVEIL-----------G---------VYT 198 (374)
T ss_pred -------ccCccccCCCceEEEEEEEE--CCCCccCCHHHHHHHHHHCCCCcccee-----------e---------EEc
Confidence 11111111136799999974 333456799999999987632211000 0 011
Q ss_pred cCC-HHHHHHHHHHHHHcCCceEEEecCCCC
Q 001083 400 AHN-VDEVEKFFKETIENRDEGIVLKDLGSK 429 (1160)
Q Consensus 400 ~~~-~~ei~~~~~~ai~~g~EGlVlK~~ds~ 429 (1160)
..+ .+++.++++..=++|.||||+|+++..
T Consensus 199 ~~~~~~~~~eii~~L~~~gREGVVlK~~~~~ 229 (374)
T TIGR01209 199 ADEAVEEIYEIIERLNKEGREGVVMKDPEMR 229 (374)
T ss_pred HHHHHHHHHHHHHHhhhcCcceEEEcCcccc
Confidence 122 236667777777899999999998654
No 57
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=98.51 E-value=1.1e-07 Score=82.90 Aligned_cols=62 Identities=29% Similarity=0.545 Sum_probs=50.5
Q ss_pred eEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-Ceeecch
Q 001083 661 MVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSW 723 (1160)
Q Consensus 661 ~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~W 723 (1160)
+.||+.+.. ...++.|.++|..+||++..+++..+||+|+....+.||+.|.+++ +||+|+|
T Consensus 1 ~~i~~sg~~-~~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 1 VVICFSGFS-GKERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp -EEEEEEB--TTTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred CEEEECCCC-HHHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence 467876544 4458999999999999999999989999999888999999999998 9999999
No 58
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=98.34 E-value=4.6e-05 Score=95.56 Aligned_cols=74 Identities=16% Similarity=0.163 Sum_probs=65.9
Q ss_pred cccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHHhc
Q 001083 657 IFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQ 730 (1160)
Q Consensus 657 lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi~~ 730 (1160)
.|.|+.|||++.....+|++++++|.++||+++...+..++++|+++..+-|...|...+ +|++-+-+++.+++
T Consensus 590 ~~~g~~~v~TG~l~~~~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK~~kA~~lgI~ii~E~~f~~~l~~ 664 (665)
T PRK07956 590 DLAGKTVVLTGTLEQLSRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSKLAKAQELGIEVLDEEEFLRLLGE 664 (665)
T ss_pred CccccEEEEeCCCCCCCHHHHHHHHHHcCCEEeCcccCCCCEEEECCCCChHHHHHHHcCCeEEcHHHHHHHHhc
Confidence 499999999877667799999999999999999999888888998877778999998888 99999988888764
No 59
>cd00027 BRCT Breast Cancer Suppressor Protein (BRCA1), carboxy-terminal domain. The BRCT domain is found within many DNA damage repair and cell cycle checkpoint proteins. The unique diversity of this domain superfamily allows BRCT modules to interact forming homo/hetero BRCT multimers, BRCT-non-BRCT interactions, and interactions within DNA strand breaks.
Probab=98.30 E-value=1.9e-06 Score=75.06 Aligned_cols=71 Identities=31% Similarity=0.418 Sum_probs=53.2
Q ss_pred CeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhccCC
Q 001083 806 GCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNK 884 (1160)
Q Consensus 806 gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~ 884 (1160)
||.||++++.. .. ....+.++|..+||++...++ .+||||+....... .+... ...
T Consensus 1 ~~~~~i~g~~~--~~--------~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~----~~~~~---------~~~ 57 (72)
T cd00027 1 GLTFVITGDLP--SE--------ERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPK----KLLKA---------IKL 57 (72)
T ss_pred CCEEEEEecCC--Cc--------CHHHHHHHHHHcCCEEeccccCCceEEEECCCCCch----HHHHH---------HHc
Confidence 68999999752 11 256899999999999999998 69999998654221 01111 135
Q ss_pred ccEEeccchHHHHHH
Q 001083 885 KLHVVRSQWLEDCLA 899 (1160)
Q Consensus 885 ~~~IVt~~Wl~eci~ 899 (1160)
.++||+++||.+|++
T Consensus 58 ~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 58 GIPIVTPEWLLDCLK 72 (72)
T ss_pred CCeEecHHHHHHHhC
Confidence 689999999999984
No 60
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=98.24 E-value=1.9e-06 Score=105.24 Aligned_cols=88 Identities=23% Similarity=0.348 Sum_probs=61.8
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEe----c-CC-------------------CCc-eEEEEecC--CCh
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSM----N-LN-------------------NSV-THCVAADN--KGL 707 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~----n-~~-------------------~~~-Th~Ia~~~--~~~ 707 (1160)
.+||.||.|.+.+.. .+.+....-+..|||.+.. + ++ .++ --|++++. .+.
T Consensus 923 kniFd~cvF~lTsa~--~sd~~~r~s~e~~gg~vle~gl~~~Fn~p~~g~~~~lr~Ln~~q~~ks~~qalLIsdth~Rt~ 1000 (1176)
T KOG3548|consen 923 KNIFDGCVFMLTSAN--RSDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred cchhcceeEEEeccc--cchhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 489999999987643 2344555555668888742 1 11 012 12455665 566
Q ss_pred hhHhhhcCC-CeeecchHHHHHhcCccCCCCcccccccC
Q 001083 708 KYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLS 745 (1160)
Q Consensus 708 K~~~a~~~~-~VV~p~WV~dCi~~~~lLp~~p~~~l~~s 745 (1160)
||-.+...| ||||+.||.+|+++++++++.+| +|.+.
T Consensus 1001 KYLeaLA~giPcVh~~fI~aC~e~nr~Vdy~~Y-LLpsG 1038 (1176)
T KOG3548|consen 1001 KYLEALARGIPCVHNTFIQACGEQNRCVDYTDY-LLPSG 1038 (1176)
T ss_pred HHHHHHHcCCCcccHHHHHHHHhccccccchhh-cccCc
Confidence 888777777 99999999999999999999876 66543
No 61
>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=98.19 E-value=9.7e-05 Score=92.56 Aligned_cols=68 Identities=18% Similarity=0.286 Sum_probs=59.3
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-Ceeecc
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYS 722 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~ 722 (1160)
...|.|.+|||++.....+|++++++|.++||+++.+.+..++++|+++..+.|++.|...+ +|++-+
T Consensus 582 ~~~l~gk~~v~TG~l~~~~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsKl~kA~~lgi~ii~E~ 650 (652)
T TIGR00575 582 GSPLAGKTFVLTGTLSQMSRDEAKELLENLGGKVASSVSKKTDYVIAGEKAGSKLAKAQELGIPIINEE 650 (652)
T ss_pred CCCccCcEEEEeccCCCCCHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCChHHHHHHHcCCcEechh
Confidence 45799999999877667899999999999999999999888889998887778999998887 888654
No 62
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=98.14 E-value=5e-06 Score=103.86 Aligned_cols=178 Identities=14% Similarity=0.150 Sum_probs=119.1
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC-CChhhHhhhcCC-CeeecchHHHHHhcC
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN-KGLKYEAAKRRG-DVIHYSWVLDCCSQK 731 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~-~~~K~~~a~~~~-~VV~p~WV~dCi~~~ 731 (1160)
....|.||.+|+.+. ....|.++..+|..|||++...+...+.|+++... .+-||+.|++|. +||+.+|+++|++++
T Consensus 100 ~~p~~~~~~Vc~tgl-~~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~ 178 (811)
T KOG1929|consen 100 KCPGFFGLKVCLTGL-SGDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKT 178 (811)
T ss_pred cCCcccceEEEeccc-chHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhccc
Confidence 356899999997654 45679999999999999999999877777776544 348999999997 999999999999999
Q ss_pred ccCCCCcccccccChhhhhhhhhccc-----ccCCCcccCCChhHHHHHhhccCCCCCcchhhHHhhhcCCCCCCccCCC
Q 001083 732 KLLQLQPKYYLHLSDSSKKKLQEEVD-----EFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHG 806 (1160)
Q Consensus 732 ~lLp~~p~~~l~~s~~t~~~~~~~~D-----~~gDSy~~~~~~~~L~~ll~~i~~~~~~~~i~~l~~~~~~~~~~~lF~g 806 (1160)
.+++..++.+-.... .... ....+ --||+|+...+...- .+..++. +..+ ..+..+..+
T Consensus 179 ~~~~~~~~e~~~~~~-~is~-~~~~~~~~~~~~~~s~t~~~~~~~~-~~~~n~~-------~~p~------~a~~~~~~~ 242 (811)
T KOG1929|consen 179 AVLETKPYEGAPVAE-AISG-PIGSTLPKEILDGDSRTANDTWSTS-KVVTNIK-------VLPF------QAKIGNLDD 242 (811)
T ss_pred ccccccccccccccc-eecc-CCccccccccccccchhhhccccch-hcccccc-------cchh------hhhcccccc
Confidence 999998865433100 0000 00000 122333211110000 0000000 0000 012237889
Q ss_pred eEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecC
Q 001083 807 CCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSV 859 (1160)
Q Consensus 807 c~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~ 859 (1160)
|.+|++++... .++.+++.++.+||...++.. .++|++++..
T Consensus 243 c~v~~s~~~~~-----------~~s~l~r~~~~g~~~~~~e~~e~~st~l~~~~ 285 (811)
T KOG1929|consen 243 CLVETSGTTSR-----------NRSALSRLSNNGGSLRFLERLEETSTSLLGDF 285 (811)
T ss_pred ceeeecCCccc-----------chhHhHHhhhcccceeecccCccccchhhccc
Confidence 99999998741 356899999999999999877 6999999753
No 63
>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=97.98 E-value=6.6e-05 Score=79.68 Aligned_cols=176 Identities=13% Similarity=0.086 Sum_probs=116.8
Q ss_pred ccccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCc---chhhHHHHHHHhcccCceeece
Q 001083 225 RPQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSE---YGHAMSKIIEQNVLVDRCILDG 301 (1160)
Q Consensus 225 ~PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~---~~~~l~~~l~~~~~~~~~ILDG 301 (1160)
..||+.-...+++-+ ..+|++=+===|-||+|....|.+.+++|+|.-+.. .+|+=.. .+ -+||
T Consensus 5 ~lml~Ewm~~~p~~l----~~~w~~~~~P~G~R~lvv~~~g~t~~~~r~g~~~~~f~s~lP~g~~--------~~-~~~g 71 (186)
T cd09232 5 QLMLSEWMVEVPDDL----SEEWLVVPCPVGKRCLVVASKGKTVARSKNGRTLHRFSSALPGGSR--------KT-SNSG 71 (186)
T ss_pred ceechhhcccCCCcc----CcceEEEECcCceEEEEEEeCCEEEEEeCCCCEEEecccCCCCCCc--------CC-CCCC
Confidence 356666544433311 356888888889999999999999999999987532 2232100 00 3555
Q ss_pred eEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccC
Q 001083 302 EMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPD 381 (1160)
Q Consensus 302 Elv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~ 381 (1160)
|+|. |- +.. +.. ..|+|+|||..||.++.+.+...|...|++-+.+....-. ....
T Consensus 72 ~tIL-Dc----i~~-----------------~~~-~~yyVlDii~w~g~~l~d~~~~~Rf~wl~skl~E~~~~~~-~~~~ 127 (186)
T cd09232 72 YTIL-DC----IYN-----------------EDD-RTYYVLDVLCWNGHPLYDCETEFRFFWLRSKLEELPELDE-PSEK 127 (186)
T ss_pred CEEE-EE----ecC-----------------CCC-CEEEEEEEeeeCCcccccCCcchhHHHHHhhCCCcccccc-cccc
Confidence 5553 21 100 001 5799999999999999999999999999988876542110 0000
Q ss_pred CCCCccccCCCCCccceecCCHHHHHHHHHHHH---HcCCceEEEecCCCCCcCCCCCCCeEEEccc
Q 001083 382 HGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETI---ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 445 (1160)
Q Consensus 382 ~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai---~~g~EGlVlK~~ds~Y~pGkRs~~WlKlKpe 445 (1160)
. .+.+++. ....+ +.+.+.+.|...+ ..-..||++-..++.|.+| +++.|+|+||.
T Consensus 128 ~--~~~f~~~----p~~~~-~~~~l~~~~~~~~~~~~~e~DGLlFyhk~~~Y~~G-~tPlvl~wKp~ 186 (186)
T cd09232 128 N--PFRFVPL----PYFPC-TKESLQSAYSGPLNDDPYELDGLLFYHKESHYTPG-STPLVLWLKDY 186 (186)
T ss_pred C--CceEEec----CcccC-cHHHHHHHHhcccccCCCCCceEEEEeCCCcccCc-CCCcEEEecCC
Confidence 1 1111110 12222 2367888888888 7888999999999999999 68999999983
No 64
>PF11411 DNA_ligase_IV: DNA ligase IV; InterPro: IPR021536 DNA ligase IV along with Xrcc4 functions in DNA non-homologous end joining. This process is required to mend double-strand breaks. Upon ligase binding to an Xrcc4 dimer, the helical tails unwind leading to a flat interaction surface []. ; GO: 0003910 DNA ligase (ATP) activity; PDB: 3II6_Y 2E2W_A 1IK9_C.
Probab=97.97 E-value=4.6e-06 Score=62.95 Aligned_cols=35 Identities=26% Similarity=0.495 Sum_probs=26.3
Q ss_pred hhhhhhhhcccccCCCcccCCChhHHHHHhhccCC
Q 001083 747 SSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDR 781 (1160)
Q Consensus 747 ~t~~~~~~~~D~~gDSy~~~~~~~~L~~ll~~i~~ 781 (1160)
+|+++++++||+|||||+.++++.+|+.+|++|..
T Consensus 1 sTk~~fa~eyD~yGDSY~~Dtd~~~Lk~vF~~i~~ 35 (36)
T PF11411_consen 1 STKEHFAKEYDCYGDSYTVDTDEDQLKEVFNRIKK 35 (36)
T ss_dssp HHHHHHHHHB-TTS-BSSS---HHHHHHHHHCS--
T ss_pred CHHHHHHHHhccccccccccCCHHHHHHHHHHhcc
Confidence 47889999999999999999999999999999864
No 65
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=97.85 E-value=1e-05 Score=94.02 Aligned_cols=79 Identities=23% Similarity=0.383 Sum_probs=58.7
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCC----------CCceEEEEecCCChhhHhhhcCCCeeecchH
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN----------NSVTHCVAADNKGLKYEAAKRRGDVIHYSWV 724 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~----------~~~Th~Ia~~~~~~K~~~a~~~~~VV~p~WV 724 (1160)
-.+|+|+.||+-.. ..++.|+-+|..+||.++.++. ..+||-|+ +..+..-.. -....|.|+||
T Consensus 325 kslF~glkFfl~re---VPresL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~Iv-DrP~~~~~v--~gR~YvQPQWv 398 (570)
T KOG2481|consen 325 KSLFSGLKFFLNRE---VPRESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIV-DRPGQQTSV--IGRTYVQPQWV 398 (570)
T ss_pred HHHhhcceeeeecc---CchHHHHHHHHHcCCceecCccCCCCcccccccceeeeee-cccCcccee--eeeeeecchhh
Confidence 46999999998543 4579999999999999998751 23588775 332322111 11278999999
Q ss_pred HHHHhcCccCCCCcc
Q 001083 725 LDCCSQKKLLQLQPK 739 (1160)
Q Consensus 725 ~dCi~~~~lLp~~p~ 739 (1160)
+|||+++.++|.+.|
T Consensus 399 fDsvNar~llpt~~Y 413 (570)
T KOG2481|consen 399 FDSVNARLLLPTEKY 413 (570)
T ss_pred hhhccchhhccHhhh
Confidence 999999999998854
No 66
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=97.85 E-value=1.5e-05 Score=70.17 Aligned_cols=37 Identities=22% Similarity=0.462 Sum_probs=24.4
Q ss_pred CCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHH
Q 001083 463 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 510 (1160)
Q Consensus 463 G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~ 510 (1160)
|.|+..|++|+|+|-..+ + ..++|||||||++++++.
T Consensus 2 G~Gk~~g~~Galv~~~~~--G---------~~f~iGsG~td~~R~~~~ 38 (66)
T PF14743_consen 2 GKGKFKGMLGALVCETED--G---------VEFKIGSGFTDEEREEPP 38 (66)
T ss_dssp ---EEEEEEEEEEEEE-T--T---------EEEEE-SS--HHHHHHHH
T ss_pred CccccCCCEEEEEEEeCC--C---------CEEEECCCCCHHHHhcCC
Confidence 788999999999998743 1 356899999999998764
No 67
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=97.84 E-value=0.0028 Score=77.71 Aligned_cols=73 Identities=21% Similarity=0.228 Sum_probs=65.5
Q ss_pred CcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHH
Q 001083 656 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 656 ~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
..|.|.+|++++.-+..+|++...++...||++....+..++++|+++.-|-|+..|...| +|+.-+++..-+
T Consensus 593 ~~l~gkt~V~TGtL~~~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl~kA~eLgv~i~~E~~~~~ll 666 (667)
T COG0272 593 SPLAGKTFVLTGTLEGMSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKLAKAQELGVKIIDEEEFLALL 666 (667)
T ss_pred cccCCCEEEEeccCCCCCHHHHHHHHHHcCCEEeceecccccEEEEcCCCChHHHHHHHcCCeEecHHHHHHhh
Confidence 7899999999988788999999999999999999998877788888888888999999998 999988877643
No 68
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.67 E-value=9e-05 Score=93.62 Aligned_cols=87 Identities=21% Similarity=0.323 Sum_probs=74.0
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCC----C-hhhHhhhcCC-CeeecchHHHH
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNK----G-LKYEAAKRRG-DVIHYSWVLDC 727 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~----~-~K~~~a~~~~-~VV~p~WV~dC 727 (1160)
....|.|+.|+|++.... +++++.++|..+||+++...+ .+||||++... + -|++.|...+ +||+.+||.+|
T Consensus 186 ~~kpL~G~~fviTGtl~~-sr~elK~~Ie~~GGkvsssVs-~~T~lIvt~~ev~k~gsSKlkkAk~lgIpIVsEd~L~d~ 263 (815)
T PLN03122 186 PGKPFSGMMISLSGRLSR-THQYWKKDIEKHGGKVANSVE-GVTCLVVSPAERERGGSSKIAEAMERGIPVVREAWLIDS 263 (815)
T ss_pred cCCCcCCcEEEEeCCCCC-CHHHHHHHHHHcCCEEccccc-cceEEEEcCccccccCccHHHHHHHcCCcCccHHHHHHH
Confidence 445799999999876544 899999999999999998884 58899987643 3 6899998888 99999999999
Q ss_pred HhcCccCCCCccccc
Q 001083 728 CSQKKLLQLQPKYYL 742 (1160)
Q Consensus 728 i~~~~lLp~~p~~~l 742 (1160)
++.+..+++.+|++.
T Consensus 264 i~~~k~~~~~~y~l~ 278 (815)
T PLN03122 264 IEKQEAQPLEAYDVV 278 (815)
T ss_pred HhcCCcccchhhhhc
Confidence 999999999987654
No 69
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=97.60 E-value=5.6e-05 Score=88.10 Aligned_cols=82 Identities=21% Similarity=0.211 Sum_probs=63.9
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccC---------CC--ceEEEEecCCCcccchhhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNL---------AN--ATHVVVLSVLGYDVNFNSL 869 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~l---------s~--vTHVVV~~~~~~~~~~~~l 869 (1160)
..||+||+|||....+ ++-|..+|+.+||.|+.+. ++ +||=||+.+. ....+
T Consensus 325 kslF~glkFfl~reVP-------------resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~-~~~~v--- 387 (570)
T KOG2481|consen 325 KSLFSGLKFFLNREVP-------------RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPG-QQTSV--- 387 (570)
T ss_pred HHHhhcceeeeeccCc-------------hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccC-cccee---
Confidence 4699999999998654 4578899999999999883 12 6999997653 11111
Q ss_pred HHHHHHHhhhhccCCccEEeccchHHHHHHcCCccCCCCCCCCC
Q 001083 870 TESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKP 913 (1160)
Q Consensus 870 ~~~l~~~~~~~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~ 913 (1160)
-.-..|.|.||.+|+.++.++|-+.|.+..
T Consensus 388 --------------~gR~YvQPQWvfDsvNar~llpt~~Y~~G~ 417 (570)
T KOG2481|consen 388 --------------IGRTYVQPQWVFDSVNARLLLPTEKYFPGK 417 (570)
T ss_pred --------------eeeeeecchhhhhhccchhhccHhhhCCCc
Confidence 123679999999999999999999997653
No 70
>smart00532 LIGANc Ligase N family.
Probab=97.53 E-value=0.0011 Score=79.51 Aligned_cols=196 Identities=17% Similarity=0.252 Sum_probs=116.2
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhh---HHHHHHHhcccCceeeceeEEEEeCCCCc-----
Q 001083 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHA---MSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~~~---l~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1160)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+.... +-..|. ...+..+.+-||++.-...-.+
T Consensus 104 ~~~~epKiDGlsisL~Ye~G~l~~a~TRGDG~~GeDVT~nv~~i~~iP~~i~-~~~p~~leiRGEv~~~~~~F~~ln~~~ 182 (441)
T smart00532 104 AYVVEPKIDGLSVSLLYENGKLVQAATRGDGTVGEDVTQNVKTIRSIPLRLS-GDVPERLEVRGEVFMPKEDFLALNEEL 182 (441)
T ss_pred eEEEEEecccEEEEEEEECCEEEEEEecCCCCcceehhhhhhhhcCcChhhc-ccCCCeEEEEceEEEEHHHHHHHHHHH
Confidence 589999999999999998776 889999 68899863222 211121 0013458899999874321000
Q ss_pred ----ccccccHHHHH-HHhcc--CCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001083 313 ----FAEFGSNQEIA-KAARD--GLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 385 (1160)
Q Consensus 313 ----~~pF~~lq~i~-~~~r~--~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 385 (1160)
-.+|..-+..+ ...|. .-......+.|++|++...++... .....++.+.|..+-=+...
T Consensus 183 ~~~g~~~faNpRN~aAG~lr~ld~~~~~~r~L~~~~y~~~~~~~~~~-~~t~~e~l~~L~~~GF~v~~------------ 249 (441)
T smart00532 183 EEEGEKPFANPRNAAAGSLRQLDPRITAKRKLRAFFYGLGTGEELFL-PKTQSEALKWLKELGFPVSP------------ 249 (441)
T ss_pred HhcCCCcccChHHHHHHHHHhcCchhhhhccceEEEEEcccCCCCCC-ccCHHHHHHHHHHCCCCCCC------------
Confidence 01333222211 11111 101112249999999864443211 24678888888876211110
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcC--C--CCCCCe---EEEccccccCCCc
Q 001083 386 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSD 452 (1160)
Q Consensus 386 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~p--G--kRs~~W---lKlKpeY~~~g~~ 452 (1160)
....+.+.+++..+++...+. .-.|||+|--+-.+.. | .+.+.| +|+.++ .
T Consensus 250 ----------~~~~~~~~~ei~~~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~lG~ts~~PrwaiA~Kf~~~------~ 313 (441)
T smart00532 250 ----------HTRLCKNADEVIEYYEEWEEKRAELPYEIDGVVVKVDDLALQRELGFTSKAPRWAIAYKFPAE------E 313 (441)
T ss_pred ----------CeEeeCCHHHHHHHHHHHHHhcccCCCCcCcEEEEecCHHHHHHhCccCCCCCeeEEECCCCc------e
Confidence 123456789999999877653 5679999987666554 3 245667 566664 4
Q ss_pred ccEEEEEEEeCCCCCCCccc
Q 001083 453 LDVLIIGGYYGSGRRGGEVA 472 (1160)
Q Consensus 453 lDlvIIG~~~G~Grr~g~~g 472 (1160)
..-.|.+..|-.|| .|.+.
T Consensus 314 ~~T~l~~I~~qVGR-TG~iT 332 (441)
T smart00532 314 AETKLLDIIVQVGR-TGKIT 332 (441)
T ss_pred eEEEEEEEEEecCC-Cceee
Confidence 55677777887775 44443
No 71
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=97.50 E-value=7.2e-05 Score=84.17 Aligned_cols=79 Identities=25% Similarity=0.381 Sum_probs=57.5
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCC-----------CCceEEEEecCCChhhHhhhcCCCeeecch
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN-----------NSVTHCVAADNKGLKYEAAKRRGDVIHYSW 723 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~-----------~~~Th~Ia~~~~~~K~~~a~~~~~VV~p~W 723 (1160)
..||+|+.|||.... ....|+-+|..+||.++..+. ..+||-|+ +...++-+. .....|.|+|
T Consensus 348 ~slFS~f~FyisreV---p~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~-drp~~~~kv--egrtYiQPQw 421 (591)
T COG5163 348 KSLFSGFKFYISREV---PGDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIV-DRPVMKNKV--EGRTYIQPQW 421 (591)
T ss_pred hhhhhceEEEEeccc---cchHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhc-cchhhhhhh--cceeeechHH
Confidence 469999999987543 357899999999999987652 23677775 332222111 1127899999
Q ss_pred HHHHHhcCccCCCCcc
Q 001083 724 VLDCCSQKKLLQLQPK 739 (1160)
Q Consensus 724 V~dCi~~~~lLp~~p~ 739 (1160)
|+|||++|.+.+.+.|
T Consensus 422 ~fDsiNkG~l~~~~~Y 437 (591)
T COG5163 422 LFDSINKGKLACVENY 437 (591)
T ss_pred HHhhhccccchhhhhc
Confidence 9999999999987754
No 72
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.47 E-value=0.00012 Score=63.70 Aligned_cols=62 Identities=24% Similarity=0.384 Sum_probs=42.1
Q ss_pred eEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhccCCc
Q 001083 807 CCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKK 885 (1160)
Q Consensus 807 c~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ 885 (1160)
|+|+++||.+. + +..+..++..+||++..+++ ++||+|+....+. .++ .+. ...
T Consensus 1 ~~i~~sg~~~~---~--------~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~--K~~---~A~---------~~g 55 (63)
T PF12738_consen 1 VVICFSGFSGK---E--------RSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGK--KYR---KAK---------EWG 55 (63)
T ss_dssp -EEEEEEB-TT---T--------CCHHHHHHHCTT-EEESSSSTT-SEEEEES--HH--HHH---HHH---------HCT
T ss_pred CEEEECCCCHH---H--------HHHHHHHHHHCCCEEeccccCCceEEEEeCCCcH--HHH---HHH---------HCC
Confidence 57999999752 2 35889999999999999998 5999999764422 232 111 245
Q ss_pred cEEeccch
Q 001083 886 LHVVRSQW 893 (1160)
Q Consensus 886 ~~IVt~~W 893 (1160)
++||+++|
T Consensus 56 i~vV~~~W 63 (63)
T PF12738_consen 56 IPVVSPDW 63 (63)
T ss_dssp SEEEEHHH
T ss_pred CcEECCCC
Confidence 89999999
No 73
>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=97.30 E-value=0.0023 Score=73.41 Aligned_cols=168 Identities=17% Similarity=0.233 Sum_probs=98.6
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhh---HHHHHHHhcccCceeeceeEEEEeCCCCc-----
Q 001083 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHA---MSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~~~---l~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1160)
.|++|+|+||.-+.+.+.+|+ ++..|| .|+|+|+.... +-..|. . .+..+.+-||++.-...-.+
T Consensus 102 ~~~vepKiDGlsisL~Y~~G~L~~a~TRGdG~~GeDVT~nv~~I~~IP~~i~-~-~~~~levRGEv~m~~~~F~~~n~~~ 179 (307)
T cd00114 102 AYVVEPKIDGLSISLRYENGVLVQAATRGDGTTGEDVTENVRTIRSIPLTLA-G-APETLEVRGEVFMPKADFEALNKER 179 (307)
T ss_pred cEEEEEeccceEEEEEEECCEEEEEEecCCCcchhhHHhhHhhhcccChhhc-C-CCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 699999999999999887665 788999 58888863222 111221 1 14568899999874211000
Q ss_pred ----ccccccHHHHH-HHhcc--CCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001083 313 ----FAEFGSNQEIA-KAARD--GLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 385 (1160)
Q Consensus 313 ----~~pF~~lq~i~-~~~r~--~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 385 (1160)
-.+|..-+..+ ...|. ........+.|++|++...++.. .....++.+.|..+-=++..
T Consensus 180 ~~~~~~~faNpRNaaAGsLr~ld~~~~~~r~L~f~~y~~~~~~~~~--~~t~~e~l~~L~~~GF~v~~------------ 245 (307)
T cd00114 180 EERGEKPFANPRNAAAGSLRQLDPKITAKRPLRFFIYGLGEAEGLG--PKTQSEALAFLKEWGFPVSP------------ 245 (307)
T ss_pred HHcCCCCccChHHHHHHHHHhcCcchhhcCcceEEEEecccccCCC--CCCHHHHHHHHHHCCCCCCC------------
Confidence 01332222211 11111 10111234999999997544311 24778888888875322111
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe
Q 001083 386 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW 439 (1160)
Q Consensus 386 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~----pGkRs~~W 439 (1160)
....+.+.+++.++++.+... .-.|||+|--+-.+. ...+.+.|
T Consensus 246 ----------~~~~~~~~~ev~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~tsk~PrW 299 (307)
T cd00114 246 ----------ETRLCKNIEEVLAFYDEIEAKRDSLPYEIDGVVVKVDDLALQRELGFTSKAPRW 299 (307)
T ss_pred ----------CeEEeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEEeCHHHHHHhCccCCCCCc
Confidence 123456889999998887443 567999997655443 23344566
No 74
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.27 E-value=0.00047 Score=77.34 Aligned_cols=90 Identities=13% Similarity=0.248 Sum_probs=71.0
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
..|+.|.+|-|+||.. ++ +..|+.....+|+++..+-+ +|||+|+.-++ ...|..+.
T Consensus 315 ~klL~GVV~VlSGfqN---P~--------Rs~LRskAl~LGAkY~pDW~~gsThLICAF~N--TPKy~QV~--------- 372 (508)
T KOG3226|consen 315 SKLLEGVVFVLSGFQN---PE--------RSTLRSKALTLGAKYQPDWNAGSTHLICAFPN--TPKYRQVE--------- 372 (508)
T ss_pred HHhhhceEEEEecccC---ch--------HHHHHHHHHhhcccccCCcCCCceeEEEecCC--Ccchhhcc---------
Confidence 4589999999999963 33 45777888899999999987 69999998654 22343211
Q ss_pred hccCCccEEeccchHHHHHHcCCccCCCCCCCCCCC
Q 001083 880 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 915 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~~~ 915 (1160)
...=+||+-+||++|-...++||-+.|++..+.
T Consensus 373 ---g~Gg~IV~keWI~~Cy~~kk~lp~rrYlm~~~~ 405 (508)
T KOG3226|consen 373 ---GNGGTIVSKEWITECYAQKKLLPIRRYLMHAGK 405 (508)
T ss_pred ---cCCceEeeHHHHHHHHHHHhhccHHHHHhcCCC
Confidence 223389999999999999999999999987664
No 75
>PRK08097 ligB NAD-dependent DNA ligase LigB; Reviewed
Probab=97.19 E-value=0.0048 Score=75.72 Aligned_cols=209 Identities=15% Similarity=0.203 Sum_probs=119.2
Q ss_pred cccccccc-cCChHHH---HHhcCCCcEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcch---hhHHHHHHHh
Q 001083 224 VRPQLAMR-IGDAHAA---WRKLHGKEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQN 291 (1160)
Q Consensus 224 ~~PmLA~~-~~~~~~~---~~~~~~~~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~---~~l~~~l~~~ 291 (1160)
-.|||.-. +.+.++. +++. ..|++|+|+||.-+.+.+.+|. ++..|| -|+|+|+.. +++-..+. .
T Consensus 95 ~~PMlSL~k~~s~eel~~w~~~~--~~~~vepKiDGlsisL~Ye~G~Lv~a~TRGDG~~GEDVT~nv~~I~~IP~~l~-~ 171 (562)
T PRK08097 95 PVAHTGVKKLADKQALARWMAGR--SDLWVQPKVDGVAVTLVYRDGKLVQAISRGNGLKGEDWTAKARLIPAIPQQLP-G 171 (562)
T ss_pred CCCcccccccCCHHHHHHHHhhc--cceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHHhhHhhhcccchhhc-C
Confidence 35898653 2233332 2222 2699999999999999887665 688999 578888632 12222221 1
Q ss_pred cccCceeeceeEEEEeCCCCc-----ccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHH
Q 001083 292 VLVDRCILDGEMLVWDTSLNR-----FAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQK 366 (1160)
Q Consensus 292 ~~~~~~ILDGElv~~d~~~~~-----~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~ 366 (1160)
.+..+.+-||++.-...-.+ --|.......+++. +..... .++.|++|++. +| .....++.+.|..
T Consensus 172 -~~~~levRGEv~m~~~~F~~~~~g~aNPRN~AAGsLr~~-d~~~~~-r~L~~f~y~~~--~~----~~t~~e~l~~L~~ 242 (562)
T PRK08097 172 -ALANLVLQGELFLRREGHIQQQMGGINARAKVAGLMMRK-DPSPTL-NQIGVFVWAWP--DG----PASMPERLAQLAT 242 (562)
T ss_pred -CCCeEEEEEEEEEeHHHHHHHhcCcCCchHHHhHHHhhc-CcHhhh-ccceEEEEECC--CC----CCCHHHHHHHHHH
Confidence 13358899999874321000 01111111111111 110112 24899999983 44 2467888888877
Q ss_pred hhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHH----cCCceEEEecCCCCCcCC--CCCCCe-
Q 001083 367 VVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIE----NRDEGIVLKDLGSKWEPG--DRSGKW- 439 (1160)
Q Consensus 367 ~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~----~g~EGlVlK~~ds~Y~pG--kRs~~W- 439 (1160)
+-=++.. .....+.+.+++.++++.... -.-.|+|+|--+..|..| .+.+.|
T Consensus 243 ~GF~v~~---------------------~~~~~~~~~~~i~~~~~~~~r~~l~y~iDGiViKvn~~~~~~~~ts~~PrWA 301 (562)
T PRK08097 243 AGFPLTQ---------------------RYTHPVKNAEEVARWRERWYRAPLPFVTDGVVVRQAKEPPGRYWQPGQGEWA 301 (562)
T ss_pred CCCCcCc---------------------cceEeeCCHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHhhccCCCCCce
Confidence 6322110 012235678888888876543 266899999766665543 356677
Q ss_pred --EEEccccccCCCcccEEEEEEEeCCCCCCCccc
Q 001083 440 --LKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVA 472 (1160)
Q Consensus 440 --lKlKpeY~~~g~~lDlvIIG~~~G~Grr~g~~g 472 (1160)
+|+-++ ...-.|.+..|..|| .|.+.
T Consensus 302 iAyKf~~~------~~~T~l~~I~~qVGR-TG~iT 329 (562)
T PRK08097 302 VAWKYPPV------QQVAEVRAVQFAVGR-TGKIT 329 (562)
T ss_pred EEEcCCCc------EEEEEEEEEEEecCC-Cceee
Confidence 555554 456677888887775 44443
No 76
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=97.09 E-value=0.00046 Score=77.88 Aligned_cols=83 Identities=22% Similarity=0.285 Sum_probs=62.5
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccC-----C-----C--ceEEEEecCCCcccchhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNL-----A-----N--ATHVVVLSVLGYDVNFNS 868 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~l-----s-----~--vTHVVV~~~~~~~~~~~~ 868 (1160)
.+||+|++||++..-+ .+.|..+|..+||.|..+. . + +||-||+.+.
T Consensus 348 ~slFS~f~FyisreVp-------------~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~-------- 406 (591)
T COG5163 348 KSLFSGFKFYISREVP-------------GDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPV-------- 406 (591)
T ss_pred hhhhhceEEEEecccc-------------chHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchh--------
Confidence 4699999999998654 2478889999999987653 1 1 7888886532
Q ss_pred hHHHHHHHhhhhccCCccEEeccchHHHHHHcCCccCCCCCCCCCC
Q 001083 869 LTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPT 914 (1160)
Q Consensus 869 l~~~l~~~~~~~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~~ 914 (1160)
+.+. ......|.|.||.+||..|.+++.+.|.+...
T Consensus 407 ~~~k----------vegrtYiQPQw~fDsiNkG~l~~~~~Y~~G~~ 442 (591)
T COG5163 407 MKNK----------VEGRTYIQPQWLFDSINKGKLACVENYCVGKR 442 (591)
T ss_pred hhhh----------hcceeeechHHHHhhhccccchhhhhcccccc
Confidence 1111 12346799999999999999999999987643
No 77
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=97.04 E-value=0.0077 Score=76.01 Aligned_cols=194 Identities=19% Similarity=0.213 Sum_probs=114.0
Q ss_pred CcEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhH---HHHHHHhcccCceeeceeEEEEeCCCCc----
Q 001083 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAM---SKIIEQNVLVDRCILDGEMLVWDTSLNR---- 312 (1160)
Q Consensus 245 ~~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~~~l---~~~l~~~~~~~~~ILDGElv~~d~~~~~---- 312 (1160)
..|++|+|+||.-+-+.+.+|+ ++..|| .|+|+|+....+ -..+. ...+..+.+=||++.-...-.+
T Consensus 132 ~~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDVT~nv~~I~~IP~~l~-~~~p~~levRGEv~m~~~~F~~lN~~ 210 (689)
T PRK14351 132 VEYVCEPKFDGLSVEVVYEDGEYQRAATRGDGREGDDVTANVRTIRSVPQKLR-GDYPDFLAVRGEVYMPKDAFQAYNRE 210 (689)
T ss_pred ceEEEEEecccEEEEEEEECCEEEEEEecCCCCcceeHhhhhhhhcccchhhc-ccCCCeEEEEEEEEEEHHHHHHHHHH
Confidence 4699999999999999887664 788999 688988632222 11221 1113457888999874321000
Q ss_pred -----ccccccHHHHH-HHhccCCCC---CCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCC
Q 001083 313 -----FAEFGSNQEIA-KAARDGLSS---DRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 383 (1160)
Q Consensus 313 -----~~pF~~lq~i~-~~~r~~~~~---~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 383 (1160)
-.+|..-+..+ ...|. .++ ....+.|++|++...++. .....++.+.|..+-=++..
T Consensus 211 ~~~~g~~~faNpRN~aAGslR~-ldp~~~~~r~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~---------- 276 (689)
T PRK14351 211 RIERGEEPFANPRNAAAGTLRQ-LDPSVVAERPLDIFFFDVLDASEL---FDSHWEELERFPEWGLRVTD---------- 276 (689)
T ss_pred HHHcCCCCcCCHHHHHhhHhhc-cChHHHhcCCceEEEEecccCCCC---CCCHHHHHHHHHHCCCCcCC----------
Confidence 01232222111 11111 111 112499999999655441 24677888888876322211
Q ss_pred CCccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe---EEEccccccCC
Q 001083 384 LNSHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAG 450 (1160)
Q Consensus 384 ~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~----pGkRs~~W---lKlKpeY~~~g 450 (1160)
....+.+.+++.++++.+.+. .-.|||+|--+-.+. ...+.+.| +|+.++
T Consensus 277 ------------~~~~~~~~~~~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~----- 339 (689)
T PRK14351 277 ------------RTERVDDIDDAIAYRDRLLAARDDLNYEIDGVVIKVDDRDAREELGATARAPRWAFAYKFPAR----- 339 (689)
T ss_pred ------------ceEeeCCHHHHHHHHHHHHHhhhcCCCCCceEEEEeCCHHHHHHhCccCCCCCceEEEcCCCc-----
Confidence 123456788988888766533 457999997665442 13356677 566664
Q ss_pred CcccEEEEEEEeCCCCCCCccc
Q 001083 451 SDLDVLIIGGYYGSGRRGGEVA 472 (1160)
Q Consensus 451 ~~lDlvIIG~~~G~Grr~g~~g 472 (1160)
...-.|.+..|-.|| .|.+.
T Consensus 340 -~~~T~l~~I~~qVGR-TG~iT 359 (689)
T PRK14351 340 -AEETTIRDIVVQVGR-TGRLT 359 (689)
T ss_pred -eeEEEEEEEEEecCC-Cceee
Confidence 455677788887775 44443
No 78
>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=97.03 E-value=0.00033 Score=80.49 Aligned_cols=160 Identities=20% Similarity=0.268 Sum_probs=89.2
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEeCC----CCCCCcchhhHHHHHHHhcc--cCceeeceeEEEEeCCCCc------
Q 001083 246 EVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNVL--VDRCILDGEMLVWDTSLNR------ 312 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~g~~-v~~fSR~----g~d~t~~~~~l~~~l~~~~~--~~~~ILDGElv~~d~~~~~------ 312 (1160)
.|++|+|+||.-|.+++.+|. ++..||. |+|+|.....+.. +-..+. +..+.+=||++.-...-.+
T Consensus 108 ~~~~e~KiDGlsi~L~Y~~G~L~~a~TRGdG~~GeDvT~n~~~i~~-iP~~i~~~p~~~eVRGEv~m~~~~F~~ln~~~~ 186 (315)
T PF01653_consen 108 EFVVEPKIDGLSISLIYENGKLVRAATRGDGEVGEDVTHNVRTIKS-IPLRIPEKPGRLEVRGEVYMSKSDFEKLNEERE 186 (315)
T ss_dssp EEEEEEEESSEEEEEEEETTEEEEEEEETTSSEEEB-HHHHCTSTT-S-SB-SSSSSEEEEEEEEE--HHHHHHHHHHHH
T ss_pred ceeEeeccceeEEEEEEeCCEEEEEEEcCCCccchhHHHHHHHHhc-CchhhccCCcceEEEEEEEEehhhHHHHHHHHH
Confidence 499999999999999998776 6889994 6777752211110 001111 3677888998863110000
Q ss_pred ---ccccccHHHHHH-HhccCCCC---CCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001083 313 ---FAEFGSNQEIAK-AARDGLSS---DRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 385 (1160)
Q Consensus 313 ---~~pF~~lq~i~~-~~r~~~~~---~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 385 (1160)
--+|..-+..+. ..+. .++ ....+.|++|++.+.+| ...-....++.+.|..+-=++..
T Consensus 187 ~~~~~~faNpRN~aAGsLr~-~d~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~------------ 252 (315)
T PF01653_consen 187 EEGEKPFANPRNAAAGSLRQ-KDPSITAERKLSFFAYGIGEPEG-DLGFNTQSERLQFLKEWGFPVNP------------ 252 (315)
T ss_dssp HTTS---SSHHHHHHHHHTS-SSHHHHHTS--EEEEEEEEEETT-STT-SBHHHHHHHHHHTT--B-T------------
T ss_pred HhccchhhhhhHHHHHhhhh-ccchhhhcCeeEEEEEEeccccc-ccChHHHHHHHHHHHHcCCCCCc------------
Confidence 012221111111 1111 111 11249999999999887 33345788888888875322111
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCC
Q 001083 386 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKW 430 (1160)
Q Consensus 386 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y 430 (1160)
....+.+.+++..+++.+.+. .-.|||+|--+-.+
T Consensus 253 ----------~~~~~~~~~~v~~~~~~~~~~R~~l~y~iDGiVikvn~~~~ 293 (315)
T PF01653_consen 253 ----------YIRFCKSIEEVEEYIEEWEERREELPYPIDGIVIKVNDLAL 293 (315)
T ss_dssp ----------TEEEESSHHHHHHHHHHHHHHGCCSSS-EEEEEEEESBHHH
T ss_pred ----------ceEecCCHHHHHHHHHHHHhhhhccccccCcEEEEecCHHH
Confidence 123457899999999887764 45699999655443
No 79
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=96.96 E-value=0.0014 Score=84.89 Aligned_cols=86 Identities=17% Similarity=0.361 Sum_probs=71.4
Q ss_pred CCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEec---CCChhhHhhhcCC-CeeecchHHHHH
Q 001083 653 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD---NKGLKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 653 ~~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~---~~~~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
.....|.|+.|++++.. ...+.++.++|..|||+++......+||+|+.. +.+.+++.|...+ +||+.+||.||+
T Consensus 389 ~~~~~l~~~~i~i~G~~-~~~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k~~~kv~qAk~~~ipIVsedwL~ds~ 467 (981)
T PLN03123 389 SESEFLGDLKVSIVGAS-KEKVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDDEDAEMRKARRMKIPIVREDYLVDCF 467 (981)
T ss_pred ccCCCcCCeEEEEecCC-CCcHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhhcchHHHHHHhcCCCcccHHHHHHHH
Confidence 56689999999998654 345689999999999999998887789888653 3456788888887 999999999999
Q ss_pred hcCccCCCCcc
Q 001083 729 SQKKLLQLQPK 739 (1160)
Q Consensus 729 ~~~~lLp~~p~ 739 (1160)
..+..+|...+
T Consensus 468 ~~~~~~p~~~y 478 (981)
T PLN03123 468 KKKKKLPFDKY 478 (981)
T ss_pred hccccCcchhh
Confidence 99988887654
No 80
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.64 E-value=0.023 Score=71.54 Aligned_cols=226 Identities=16% Similarity=0.154 Sum_probs=121.2
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchhhHHHHHHHhcc-cCceeeceeEEEEeCCCC-----ccc
Q 001083 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGHAMSKIIEQNVL-VDRCILDGEMLVWDTSLN-----RFA 314 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~~~l~~~l~~~~~-~~~~ILDGElv~~d~~~~-----~~~ 314 (1160)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+....+.. +-..+. ...+.+-||++.-...-. .-.
T Consensus 111 ~~~~epKiDGlaisL~YenG~L~~a~TRGDG~~GEDVT~n~~~I~~-IP~~l~~~~~levRGEv~m~~~~F~~lN~~~~~ 189 (669)
T PRK14350 111 GISVEPKIDGCSIVLYYKDGILEKALTRGDGRFGNDVTENVRTIRN-VPLFIDEKVELVLRGEIYITKENFLKINKTLEK 189 (669)
T ss_pred eEEEEEecccEEEEEEEECCEEEEEEecCCCCcchhHhhhhhhhcc-cchhcCCCceEEEEEEEEeeHHHHHHHHHhhhc
Confidence 599999999999999887665 688999 58888863211111 111111 245888999987421100 012
Q ss_pred ccccHHHHH-HHhcc--C-CCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccC
Q 001083 315 EFGSNQEIA-KAARD--G-LSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRP 390 (1160)
Q Consensus 315 pF~~lq~i~-~~~r~--~-~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~ 390 (1160)
+|..-+..+ ...|. . ....+ .+.|++|++...++. ..+..++.+.|..+-=++.....+
T Consensus 190 ~faNpRNaaAGsLr~~d~~~~a~r-~L~f~~y~~~~~~~~---~~t~~e~l~~L~~~GF~v~~~~~~------------- 252 (669)
T PRK14350 190 PYTNARNLASGILRRIDSREVANF-PLDIFVYDILYSSLE---LKTNHDAFDKLKKFGFKVNPFCRF------------- 252 (669)
T ss_pred cCCChhHHHHHHHHccCchhhhcC-ceEEEEEEcccCCCC---CCCHHHHHHHHHHCCCCCCcceEE-------------
Confidence 333222211 11111 1 01122 499999998532221 236778888888763222111000
Q ss_pred CCCCccceecCCHHHHHHHHHHHHH------cCCceEEEecCCCCCcC--C--CCCCCe---EEEccccccCCCcccEEE
Q 001083 391 QGEPCWSLVAHNVDEVEKFFKETIE------NRDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGSDLDVLI 457 (1160)
Q Consensus 391 ~~~~~~~~~~~~~~ei~~~~~~ai~------~g~EGlVlK~~ds~Y~p--G--kRs~~W---lKlKpeY~~~g~~lDlvI 457 (1160)
.....+.+++..+++++.. -.-.|||+|--+-.+.. | .+.+.| +|+.++ ...-.|
T Consensus 253 ------~~~~~~~~e~~~~~~~~~~~R~~l~y~iDGiViKvn~~~~q~~lG~ts~~PrWaiA~Kf~~~------~~~T~l 320 (669)
T PRK14350 253 ------FDGKNSIEEILNYVKDIEKKRNSFEYEIDGVVLKVSDFALREILGYTSHHPKWSMAYKFESL------SGFSKV 320 (669)
T ss_pred ------EcCCCcHHHHHHHHHHHHHHHhcCCCCCCcEEEEecCHHHHHhcCCcCCCCCceEEEcCCCc------eeEEEE
Confidence 0011347788887776533 35579999965543321 2 245677 676664 455677
Q ss_pred EEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHH
Q 001083 458 IGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 510 (1160)
Q Consensus 458 IG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~ 510 (1160)
.+..|-.|| .|.+.-. |..++-.- .+ .+|.+ .|..+.++++++.
T Consensus 321 ~~I~~qVGR-TG~iTPV--A~l~PV~l---~G--~tVsr-ATLhN~~~I~~~d 364 (669)
T PRK14350 321 NDIVVQVGR-SGKITPV--ANIEKVFV---AG--AFITN-ASLHNQDYIDSIG 364 (669)
T ss_pred EEEEEecCC-ceeeeEE--EEEEeEEE---CC--EEEEE-eccCCHHHHHHcC
Confidence 788887775 4444322 22222100 01 13344 3677777776543
No 81
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.60 E-value=0.0075 Score=74.23 Aligned_cols=193 Identities=21% Similarity=0.240 Sum_probs=115.7
Q ss_pred cccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEec------CCChhhHhhhcCC-CeeecchHHHHHh
Q 001083 657 IFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD------NKGLKYEAAKRRG-DVIHYSWVLDCCS 729 (1160)
Q Consensus 657 lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~------~~~~K~~~a~~~~-~VV~p~WV~dCi~ 729 (1160)
=|.--.-.++++.....++-|++..+. ++..+....+||+|+.- ..|.+|.-.+-.| =|+++.|+..|++
T Consensus 474 ~~~kk~~~~~s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~k 550 (684)
T KOG4362|consen 474 RFKKKLVLLVSGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASLK 550 (684)
T ss_pred CcccceeeeeccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHHH
Confidence 333333344555555567788888777 77777877899999843 2456676666667 8999999999999
Q ss_pred cCccCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhhHHhhhcCCCCCCccCCCeEE
Q 001083 730 QKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCI 809 (1160)
Q Consensus 730 ~~~lLp~~p~~~l~~s~~t~~~~~~~~D~~gDSy~~~~~~~~L~~ll~~i~~~~~~~~i~~l~~~~~~~~~~~lF~gc~~ 809 (1160)
.+.+++.+|+.+-.-+...++.. + ...+ --......||.|.-|
T Consensus 551 ~~~~~~eepfEl~~d~~~~~~~~----------~-----~~~~----------------------~a~s~~~kLf~gl~~ 593 (684)
T KOG4362|consen 551 LRKWVSEEPFELQIDVPGAREGP----------K-----EKRL----------------------RAESYKPKLFEGLKF 593 (684)
T ss_pred hcCCCCCCCeeEeecccCcccCc----------c-----cccc----------------------cccccCcchhcCCcc
Confidence 99999999976533222111100 0 0000 001124569999999
Q ss_pred EEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC------CceEEEEecC-CCcccchhhhHHHHHHHhhhhcc
Q 001083 810 YFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA------NATHVVVLSV-LGYDVNFNSLTESFTAREKHLLW 882 (1160)
Q Consensus 810 yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls------~vTHVVV~~~-~~~~~~~~~l~~~l~~~~~~~~~ 882 (1160)
||.|-- .+.. .+.|..++..-||++..--+ .++-|++.+. +........-...+ . .+..
T Consensus 594 ~~~g~f--s~~p--------~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~-e---a~~~ 659 (684)
T KOG4362|consen 594 YFVGDF--SNPP--------KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDA-E---ALAL 659 (684)
T ss_pred eeeccc--ccCc--------HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccH-H---HHHH
Confidence 999843 2222 35788899999999865432 3555554432 21111110000000 0 0111
Q ss_pred CCccEEeccchHHHHHHcCCc
Q 001083 883 NKKLHVVRSQWLEDCLAKEQK 903 (1160)
Q Consensus 883 ~~~~~IVt~~Wl~eci~~~~~ 903 (1160)
.-+.+.|+..||.+++.-.++
T Consensus 660 s~~a~~~~~~wvl~s~a~~~~ 680 (684)
T KOG4362|consen 660 SQRARAVSSSWVLDSIAGYQI 680 (684)
T ss_pred hcCCCccchhhhhcchhceee
Confidence 245688999999999875443
No 82
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=96.58 E-value=0.0087 Score=74.89 Aligned_cols=97 Identities=14% Similarity=0.112 Sum_probs=79.5
Q ss_pred CCCCcHHHHHHHHHHHHhhC---ChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCC
Q 001083 4 TEETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGM 80 (1160)
Q Consensus 4 ~~~~~F~~l~~l~e~i~~~~---~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl 80 (1160)
.++++|.+++++|++|++++ ++.+|..+|.++|.+. .+.+...++||++..+. .|++++++.++|+.++|.
T Consensus 112 ~~~lti~eV~~~L~~Ia~~sg~~s~~~k~~iL~~Ll~~~-~~~E~k~iirli~g~lr-----iGv~e~~il~ALa~A~~~ 185 (590)
T PRK01109 112 KEPLTVKEVYDTLVKIALATGEGSQDLKIKLLAGLLKDA-SPLEAKYIARFVEGRLR-----LGVGDATILDALAIAFGG 185 (590)
T ss_pred CCCcCHHHHHHHHHHHHhhhCCCcHHHHHHHHHHHHHhC-CHHHHHHHHHHHhhhhh-----cCccHHHHHHHHHHHHhc
Confidence 46799999999999999997 7789999999999987 56889999999999883 699999999999999982
Q ss_pred CcChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 001083 81 SKDSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (1160)
Q Consensus 81 ~~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~ 114 (1160)
.....+..++.+ .+||++.+|..+..
T Consensus 186 ~~~~~~ve~~y~--------~~~Dlg~va~~l~~ 211 (590)
T PRK01109 186 AVARELVERAYN--------LRADLGYIAKILAE 211 (590)
T ss_pred ccchHHHHHHHH--------hCCCHHHHHHHHHh
Confidence 222334444433 47999999887653
No 83
>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=96.48 E-value=0.029 Score=64.32 Aligned_cols=106 Identities=17% Similarity=0.110 Sum_probs=63.6
Q ss_pred cCCCcEEEEEecceEEEEEEEeCC-EEEEEeCCCCCCC-----cc---hhhHHHHHH---Hhc------ccCceeeceeE
Q 001083 242 LHGKEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHS-----EY---GHAMSKIIE---QNV------LVDRCILDGEM 303 (1160)
Q Consensus 242 ~~~~~~~~E~K~DGeR~qih~~g~-~v~~fSR~g~d~t-----~~---~~~l~~~l~---~~~------~~~~~ILDGEl 303 (1160)
+.+.+|.+.+|+||.-.-+.++++ .+++.||++.-.. .+ .+.+...+. ..+ ...++++=||+
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 445689999999999988888877 8999999965332 11 111211111 111 24678999999
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHh
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 367 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~ 367 (1160)
+.|.-..+.. +. ...|++|||.+.......-+++.+-.+.....
T Consensus 102 ~G~~~q~~~~----------------Y~----~~~fyaFdI~~~~~~~~~~L~~d~~~e~~~~~ 145 (325)
T TIGR02307 102 AGPGYQKPVV----------------YS----DKDFYAFDIKYTETSDDVTLVDDYMMESFCNV 145 (325)
T ss_pred ecCcccCccc----------------cc----cccEEEEEEEEeccCcceEecHHHHHHHHHHc
Confidence 9864211100 11 25799999955312123345666666655543
No 84
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=96.44 E-value=0.0067 Score=77.20 Aligned_cols=95 Identities=24% Similarity=0.327 Sum_probs=69.8
Q ss_pred CCccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCCCceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 800 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 800 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
+...|.|++|.|.|... . .+..++.+|..+||+++..++.+||+|+....-....-..++++.
T Consensus 186 ~~kpL~G~~fviTGtl~---~--------sr~elK~~Ie~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkkAk------ 248 (815)
T PLN03122 186 PGKPFSGMMISLSGRLS---R--------THQYWKKDIEKHGGKVANSVEGVTCLVVSPAERERGGSSKIAEAM------ 248 (815)
T ss_pred cCCCcCCcEEEEeCCCC---C--------CHHHHHHHHHHcCCEEccccccceEEEEcCccccccCccHHHHHH------
Confidence 34469999999999642 1 145889999999999999998899999875320000001122211
Q ss_pred hccCCccEEeccchHHHHHHcCCccCCCCCCCCCC
Q 001083 880 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPT 914 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~~ 914 (1160)
...++||+.+||.+|++.+..+++..|.+..+
T Consensus 249 ---~lgIpIVsEd~L~d~i~~~k~~~~~~y~l~~~ 280 (815)
T PLN03122 249 ---ERGIPVVREAWLIDSIEKQEAQPLEAYDVVSD 280 (815)
T ss_pred ---HcCCcCccHHHHHHHHhcCCcccchhhhhccc
Confidence 24689999999999999999999999988533
No 85
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.94 E-value=0.016 Score=73.03 Aligned_cols=74 Identities=16% Similarity=0.249 Sum_probs=65.2
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHH
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
...|.|.+|||++.....+|++++++|.++||++....+..++++|++...|-|...|...| +|++.+.+.+-+
T Consensus 591 ~~~l~gktfV~TG~l~~~~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aGsKl~KA~~LGI~Ii~e~~f~~~l 665 (669)
T PRK14350 591 NSFLFGKKFCITGSFNGYSRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLKLKKANNLGIKIMSLFDIKSYV 665 (669)
T ss_pred CCccCCcEEEEecccCCCCHHHHHHHHHHcCCEEeccccCCCcEEEECCCCCchHHHHHHcCCEEecHHHHHHHh
Confidence 35799999999887777899999999999999999999888889999887788999999998 999988887643
No 86
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=95.82 E-value=0.015 Score=75.73 Aligned_cols=90 Identities=19% Similarity=0.286 Sum_probs=65.9
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
...|.|++|.+.|-.. . ....++..|..+||+++..++ ++||||+...... .-..++++
T Consensus 391 ~~~l~~~~i~i~G~~~----~-------~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e~~k--~~~kv~qA------- 450 (981)
T PLN03123 391 SEFLGDLKVSIVGASK----E-------KVTEWKAKIEEAGGVFHATVKKDTNCLVVCGELDD--EDAEMRKA------- 450 (981)
T ss_pred CCCcCCeEEEEecCCC----C-------cHHHHHHHHHhcCCEEeeeccCCceEEEccHHhhh--cchHHHHH-------
Confidence 4579999999999532 1 124778899999999999998 5999888642110 00112221
Q ss_pred hccCCccEEeccchHHHHHHcCCccCCCCCCCC
Q 001083 880 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLK 912 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~ 912 (1160)
....++||+.+||++|+..+.++|+..|.+.
T Consensus 451 --k~~~ipIVsedwL~ds~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 451 --RRMKIPIVREDYLVDCFKKKKKLPFDKYKLE 481 (981)
T ss_pred --HhcCCCcccHHHHHHHHhccccCcchhhhhc
Confidence 1235899999999999999999999999664
No 87
>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=95.80 E-value=0.016 Score=61.67 Aligned_cols=106 Identities=21% Similarity=0.315 Sum_probs=60.6
Q ss_pred cEEEEEecceEEEEEEEe-CCEEEEEeCCCCC-----CCcc-------hhh---HHHHHHHh-----cccCceeeceeEE
Q 001083 246 EVVIECKFDGDRIQIHKN-GSEIHYFSRSFLD-----HSEY-------GHA---MSKIIEQN-----VLVDRCILDGEML 304 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~-g~~v~~fSR~g~d-----~t~~-------~~~---l~~~l~~~-----~~~~~~ILDGElv 304 (1160)
+|++.+|+||.-+.+.+. ++.+++.+|++.- +... ... +....... ....++++=||++
T Consensus 2 e~vvtEKldGtn~~i~~~~~~~~~~~~R~~~l~~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~GE~~ 81 (186)
T PF09414_consen 2 EVVVTEKLDGTNFSIYFDNDGRVRFQSRSHILDPNEDFFGYQSGDNRYWAQARWLFELLKLAELASELLPENIIIYGELV 81 (186)
T ss_dssp EEEEEEE-SSEEEEEEEEECTCEEEEETTEE--TT---TTCHHHHHHCHHHHHHHHHHHHHHCCEC----SEEEEEEEEE
T ss_pred eEEEEEEeCCccEEEEEeCCCceeEeccccccCccccccccccchHHHHHHHHHHHhhhhhhhhcccccceEEEEEEEee
Confidence 699999999999998885 4459999999822 1111 011 11111111 1356889999999
Q ss_pred EEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCc-ccccCCHHHHHHHHHHh
Q 001083 305 VWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDT-SVIHQSLKERHELLQKV 367 (1160)
Q Consensus 305 ~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~-sl~~~pl~eRr~~L~~~ 367 (1160)
.|-+. +..- . .+. .....|++|||...+.. ...=+++.+.+.+++.+
T Consensus 82 G~~~~---Iq~~-~---------~~~---~~~~~F~~Fdi~~~~~~~~~~~l~~~~~~~~~~~~ 129 (186)
T PF09414_consen 82 GAKPS---IQKN-R---------YQL---DPPKDFYVFDIYDIDEQGEIRYLSWDEVREFAEEL 129 (186)
T ss_dssp CEECT---TCSS-----------------ECCCEEEEEEEEEEETCCGEEE-HHHHHHHHHCCC
T ss_pred eeccc---cccc-c---------ccc---CCCceEEEEEEEEcCCCCeeEECCHHHHHHHHHHC
Confidence 86532 1100 0 000 11378999999988532 12345777888777664
No 88
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=95.55 E-value=0.029 Score=70.94 Aligned_cols=76 Identities=14% Similarity=0.252 Sum_probs=67.1
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCC-hhhHhhhcCC-CeeecchHHHHHhc
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG-LKYEAAKRRG-DVIHYSWVLDCCSQ 730 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~-~K~~~a~~~~-~VV~p~WV~dCi~~ 730 (1160)
...|.|.+|||++.....+|++++++|.++||++..+.+..++++|+++..+ -|.+.|...+ +|++-+-+.+-++.
T Consensus 607 ~~~l~g~~~v~TG~l~~~~R~~~~~~i~~~Gg~v~~sVs~kt~~Lv~G~~~g~sKl~kA~~lgi~ii~E~~f~~ll~~ 684 (689)
T PRK14351 607 GDALDGLTFVFTGSLSGYTRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQSKRDDAEANDVPTLDEEEFEELLAE 684 (689)
T ss_pred CCCCCCcEEEEccCCCCCCHHHHHHHHHHcCCEEcCCcCCCccEEEEcCCCChhHHHHHHHCCCeEecHHHHHHHHHh
Confidence 4579999999988777789999999999999999999988889999887777 5999998888 99999988887764
No 89
>COG5275 BRCT domain type II [General function prediction only]
Probab=95.39 E-value=0.049 Score=57.65 Aligned_cols=81 Identities=25% Similarity=0.215 Sum_probs=68.8
Q ss_pred ccccCCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCCh-hhHhhhcCC-CeeecchHHH
Q 001083 649 SDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGL-KYEAAKRRG-DVIHYSWVLD 726 (1160)
Q Consensus 649 s~~~~~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~-K~~~a~~~~-~VV~p~WV~d 726 (1160)
|-.++..+++.|+.|.|.+.-...+|++-+.+|..+||++...+...++++|+++..|+ |.+.+++.+ ++|.-+=++.
T Consensus 148 S~peg~~~cL~G~~fVfTG~l~TlsR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP~K~ekiKqlkIkaidEegf~~ 227 (276)
T COG5275 148 SVPEGERECLKGKVFVFTGDLKTLSRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGPSKMEKIKQLKIKAIDEEGFDS 227 (276)
T ss_pred CCCCCCcccccccEEEEecccccccchhHHHHHHHhCCeeecccccceeEEEecCCCChHHHHHHHHhCCccccHHHHHH
Confidence 44557889999999999887777899999999999999999999888899999888776 788888877 8888877766
Q ss_pred HHh
Q 001083 727 CCS 729 (1160)
Q Consensus 727 Ci~ 729 (1160)
.|.
T Consensus 228 LI~ 230 (276)
T COG5275 228 LIK 230 (276)
T ss_pred HHh
Confidence 664
No 90
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=95.34 E-value=0.019 Score=71.40 Aligned_cols=200 Identities=15% Similarity=0.161 Sum_probs=120.2
Q ss_pred ccCCCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEE-ecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHH
Q 001083 651 IKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFS-MNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 651 ~~~~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v-~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
-...+..|+|..||+ ++....+..++.+.-.-|||.+. ......++|+|+.+-...+++.+ .. ..++++|+.+|+
T Consensus 41 ~~t~~s~fs~is~~~-ngs~~e~~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~a~~vk~~--~~~~~~~~e~iie~~ 117 (1016)
T KOG2093|consen 41 AATGSSSFSGISISV-NGSTDESANELKLQNMFHTGASAASYERSGTENIIAQGLPADLVKGF--TIPKHISIEWIIECC 117 (1016)
T ss_pred CcCCcceeeeeeecc-CCccccchHHHhhhhhhcccccccccccccceeeecccchHHHhccc--cchhhhcHHHHHHHH
Confidence 346778999999995 66667788899999999999987 55555678898865443333322 12 789999999999
Q ss_pred hcCccCCCCcccccccChhhhhhhhhcccccCCCcccCCChhHHHHHhhccCCCCCcchhhHHhhhcCCCCCCccCCCeE
Q 001083 729 SQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCC 808 (1160)
Q Consensus 729 ~~~~lLp~~p~~~l~~s~~t~~~~~~~~D~~gDSy~~~~~~~~L~~ll~~i~~~~~~~~i~~l~~~~~~~~~~~lF~gc~ 808 (1160)
+.+.++.+.|++........+..+.-..+. +. .+. +. ...+.-+|.+|+
T Consensus 118 ~~~~~~~~~~~~~~t~~~h~q~~~~~~~~~----~~------------------~D~--------q~-~~~~~ki~~~n~ 166 (1016)
T KOG2093|consen 118 ENGMDVGYYPYQLYTGQSHEQAQLAFPVTS----FP------------------KDQ--------QI-SSQSSKIFKNNV 166 (1016)
T ss_pred hccCccccccceeeccchhcccccCCCccc----CC------------------ccc--------cc-cccchhccccce
Confidence 999999999876654332222222111110 00 000 00 012456899999
Q ss_pred EEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC--C-ceEEEEecCCCcccchhhhHHHHHHHhhhhccCCc
Q 001083 809 IYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA--N-ATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKK 885 (1160)
Q Consensus 809 ~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls--~-vTHVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~ 885 (1160)
||+-|++...+-| + + --....|++...+..+ + ++|.+-..-. ++ .+--.
T Consensus 167 ikinG~~E~~~~d------l--e--pp~gv~~d~~~~~~~~~rd~v~~~l~~~~l---------~n---------~~f~n 218 (1016)
T KOG2093|consen 167 IKINGYNEPESLD------L--E--PPSGVLHDKAEDDSTSARDHVDHELAGNLL---------LN---------KRFVN 218 (1016)
T ss_pred eeecCCCCccccc------c--C--CCcccccchhhhhhhhHHHHHHHHhccccc---------cc---------cccce
Confidence 9999987421101 0 0 0011112333333222 2 4555543210 00 01134
Q ss_pred cEEeccchHHHHHHcCCccCCCCCCCC
Q 001083 886 LHVVRSQWLEDCLAKEQKSEEYEYSLK 912 (1160)
Q Consensus 886 ~~IVt~~Wl~eci~~~~~v~Ee~Y~v~ 912 (1160)
...++|.|+.+.+..-...+-.+|.-.
T Consensus 219 ~~~~sP~~~~~k~~~a~~~~~~~~Ss~ 245 (1016)
T KOG2093|consen 219 IENTSPDWIVDKELTAHTGTGQNYSSE 245 (1016)
T ss_pred eeecCchhhhhhhhhhccCCccccccc
Confidence 577999999999998888888888733
No 91
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=95.31 E-value=0.036 Score=64.09 Aligned_cols=74 Identities=15% Similarity=0.146 Sum_probs=62.9
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCC--hhhHhhhcCC-CeeecchHHHHH
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG--LKYEAAKRRG-DVIHYSWVLDCC 728 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~--~K~~~a~~~~-~VV~p~WV~dCi 728 (1160)
...+|.|.+|+|++.-. .+|++++++|.++||++..+.+..++++|+++..+ -|.+.|.+.+ +||+..=+++-+
T Consensus 229 ~~~l~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll 305 (313)
T PRK06063 229 GRPLVQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELL 305 (313)
T ss_pred CCcccCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHH
Confidence 35789999999987654 69999999999999999999988889999987766 5888888888 999887666655
No 92
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=95.27 E-value=0.036 Score=63.97 Aligned_cols=75 Identities=19% Similarity=0.197 Sum_probs=58.0
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecC---------CChhhHhhhcC-----C-Ce
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN---------KGLKYEAAKRR-----G-DV 718 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~---------~~~K~~~a~~~-----~-~V 718 (1160)
....|+|..|||++.....+|.+++++|.++||++..+.+..++++|+++. .+-|++.|... + +|
T Consensus 217 ~~~~l~g~~~vfTG~l~~~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~~~~~~~~~~~~~K~~kA~~l~~~g~~i~i 296 (309)
T PRK06195 217 GFTAFKEEVVVFTGGLASMTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTKDIEDLNREEMSNKLKKAIDLKKKGQNIKF 296 (309)
T ss_pred CCccccCCEEEEccccCCCCHHHHHHHHHHhCCEecCCcccCceEEEECCCcchhhcccCcChHHHHHHHHHhCCCCcEE
Confidence 346799999999877777899999999999999999999887888888742 34577776543 4 78
Q ss_pred eecchHHHHH
Q 001083 719 IHYSWVLDCC 728 (1160)
Q Consensus 719 V~p~WV~dCi 728 (1160)
++-+=+++-+
T Consensus 297 i~E~~f~~l~ 306 (309)
T PRK06195 297 LNEEEFLQKC 306 (309)
T ss_pred ecHHHHHHHH
Confidence 8765444443
No 93
>PHA02142 putative RNA ligase
Probab=93.82 E-value=0.69 Score=54.08 Aligned_cols=103 Identities=16% Similarity=0.202 Sum_probs=64.5
Q ss_pred cCCCcEEEEEecceEEEEEEEe---------------------CCEEEEEeCCCCC-CC--c-chh-----hHHHHHHHh
Q 001083 242 LHGKEVVIECKFDGDRIQIHKN---------------------GSEIHYFSRSFLD-HS--E-YGH-----AMSKIIEQN 291 (1160)
Q Consensus 242 ~~~~~~~~E~K~DGeR~qih~~---------------------g~~v~~fSR~g~d-~t--~-~~~-----~l~~~l~~~ 291 (1160)
..+..|.+-+|+||.-|.+.+. .+.+...|||..- +. . ++. .+.+.+.+
T Consensus 166 ~~~~~f~~TeKLDGsS~tvy~~~~~~~~~~~~~~~~~~~~~~~~~~~gv~srn~~l~~~~~~~~W~~a~~~~i~~~l~~- 244 (366)
T PHA02142 166 YADVKFAKSLKLDGSSITMAWVTDPDLFLDLGTEDEPYAHDYDDAQFIVASRNQVLRYNADSKWWKGVENYQIVDRLKE- 244 (366)
T ss_pred hcCceEEEEEEecceeEEEEEecCCcccccccccccccccccCCCceeEeeccccccccCCchHHHHHHHcCcHHHHHh-
Confidence 4467789999999999988732 4677888998752 21 1 111 12222221
Q ss_pred cccCceeeceeEEEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHh
Q 001083 292 VLVDRCILDGEMLVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 367 (1160)
Q Consensus 292 ~~~~~~ILDGElv~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~ 367 (1160)
...++.+=||++.-.-.++.. +. . ...|++|||-.+++.. =+++.++.++++++
T Consensus 245 -~~~~iaIqGEl~Gp~IQ~N~~---------------~~-~---~~~F~vF~v~~i~~~~--yl~~~e~~~~~~~~ 298 (366)
T PHA02142 245 -LGMSVAIQGELMGPGIQKNRE---------------NF-D---KYRIFAFRAWFIDEQR--FATDEEFQDLCRTL 298 (366)
T ss_pred -hCCcEEEEEEEecccccCccc---------------cC-C---CCceEEEEEEEeccce--eCCHHHHHHHHHHc
Confidence 135788999999732111110 00 1 1469999997777664 45889999988876
No 94
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=93.42 E-value=0.18 Score=65.13 Aligned_cols=127 Identities=20% Similarity=0.309 Sum_probs=85.1
Q ss_pred HHHHHHHHHcCCEEEecCCCCceEEEEec-CCChhhHhhhcCC-CeeecchHHHHHhcCccCCCCcccccccChhhhhhh
Q 001083 675 DSLHKMVVENGGTFSMNLNNSVTHCVAAD-NKGLKYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKL 752 (1160)
Q Consensus 675 ~eL~klI~~~GG~~v~n~~~~~Th~Ia~~-~~~~K~~~a~~~~-~VV~p~WV~dCi~~~~lLp~~p~~~l~~s~~t~~~~ 752 (1160)
.-+...++..||.+..+.. ..||+|+.. ..|.++-.++..| +||+++||.+|+..|..++..|| +++-... ..+
T Consensus 671 ~~~k~~~k~lg~s~~ss~~-e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g~~~dek~y-il~D~ek-Ek~- 746 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSDS-EATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSGEKLDEKPY-ILHDEEK-EKE- 746 (896)
T ss_pred hhhhhHHhhccceeecccc-cceeeeehhhhccHHHHhhhccCCcccchHHHHHHhhccccccCccc-cccCHHH-Hhc-
Confidence 4577888889988887776 479999742 3567777777778 99999999999999999999986 4432211 000
Q ss_pred hhcccccCCCcccCCChhHHHHHhhccCCCCCcchhhHHhhhcCCCCCCccCCCeEEEEccCCCCCCChhHHHHHHHHHH
Q 001083 753 QEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRR 832 (1160)
Q Consensus 753 ~~~~D~~gDSy~~~~~~~~L~~ll~~i~~~~~~~~i~~l~~~~~~~~~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~ 832 (1160)
|| | .+...+.+. ....+|.|..||+.-+... ....
T Consensus 747 ------~g--f-------~l~ssl~RA-------------------r~~plL~g~~v~vtp~v~p-----------~~~~ 781 (896)
T KOG2043|consen 747 ------FG--F-------RLKSSLLRA-------------------RADPLLEGINVHVTPSVTP-----------SPKT 781 (896)
T ss_pred ------cC--c-------chhhHHHHh-------------------hcchhhcCceEEecccccc-----------Ccch
Confidence 00 0 000011100 1124789999999875421 1346
Q ss_pred HHHHHHhcCCEEEccCCC
Q 001083 833 LKLEISFHGGKVCNNLAN 850 (1160)
Q Consensus 833 l~~~I~~~GG~v~~~ls~ 850 (1160)
+-.+|...||.+...+..
T Consensus 782 v~eiie~~ggnvv~~~p~ 799 (896)
T KOG2043|consen 782 VVEIIEISGGNVVSDSPK 799 (896)
T ss_pred hHHHHhhcCcceecccCc
Confidence 777999999999998863
No 95
>KOG2043 consensus Signaling protein SWIFT and related BRCT domain proteins [Transcription; Signal transduction mechanisms; Cell cycle control, cell division, chromosome partitioning; Replication, recombination and repair]
Probab=91.94 E-value=0.17 Score=65.40 Aligned_cols=72 Identities=28% Similarity=0.434 Sum_probs=55.2
Q ss_pred HHHHHHHHhcCCEEEccCCCceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEeccchHHHHHHcCCccCCCCCC
Q 001083 831 RRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYS 910 (1160)
Q Consensus 831 ~~l~~~I~~~GG~v~~~ls~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~ 910 (1160)
..+.+.+.+.||.+.....++||+|+..-- +...+ -.++ ....-||++.||.+|.+.|..++|..|.
T Consensus 671 ~~~k~~~k~lg~s~~ss~~e~Th~i~~rir-RT~k~---Leai---------~~G~~ivT~~wL~s~~k~g~~~dek~yi 737 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSDSEATHFIADRIR-RTLKF---LEAI---------SSGKPLVTPQWLVSSLKSGEKLDEKPYI 737 (896)
T ss_pred hhhhhHHhhccceeecccccceeeeehhhh-ccHHH---Hhhh---------ccCCcccchHHHHHHhhccccccCcccc
Confidence 368889999999999999999999997321 11111 1111 2345899999999999999999999998
Q ss_pred CCCCC
Q 001083 911 LKPTG 915 (1160)
Q Consensus 911 v~~~~ 915 (1160)
+...-
T Consensus 738 l~D~e 742 (896)
T KOG2043|consen 738 LHDEE 742 (896)
T ss_pred ccCHH
Confidence 87664
No 96
>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=91.04 E-value=2 Score=50.20 Aligned_cols=153 Identities=18% Similarity=0.197 Sum_probs=82.1
Q ss_pred CCcEEEEEecceEEEEEEEeCC--EEE-----EEeCCCCCC---Cc-ch-----hhHHHHHHHhcccCceeeceeEEEEe
Q 001083 244 GKEVVIECKFDGDRIQIHKNGS--EIH-----YFSRSFLDH---SE-YG-----HAMSKIIEQNVLVDRCILDGEMLVWD 307 (1160)
Q Consensus 244 ~~~~~~E~K~DGeR~qih~~g~--~v~-----~fSR~g~d~---t~-~~-----~~l~~~l~~~~~~~~~ILDGElv~~d 307 (1160)
+..|.+-+|+||--|.+.+..+ .+. +-|||..-. .. |+ .+|.+.+.+.....++.+=||++.-.
T Consensus 158 ~~~~~~TeKldGss~tv~~~~~~~~~~~~~~Gvcsr~~~l~~~~~~~~W~~a~~~~i~~~l~~~~~~~~vaiqGEl~G~g 237 (341)
T TIGR02306 158 GEKVAKTEKLHGTSITVAWVTDEERFLVLSKGVASRNLVLRENADNKYWKAVENYQIVDRAKAAELRMSVAIFGEVMGPG 237 (341)
T ss_pred CceEEEEEEecceeEEEEEecCCcccccccceeecCCcccccCCCchhHHHHHhcChHHHHhhcccCceEEEEEEEeCcc
Confidence 5689999999999998876322 222 346876521 11 21 22334443223345788899998732
Q ss_pred CCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCcc
Q 001083 308 TSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSH 387 (1160)
Q Consensus 308 ~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~ 387 (1160)
-.++ . +..+.. -.|++|+| +.+|.. .=+++.++.+++..+..|. +.
T Consensus 238 IQ~n---~--------------Yg~~~~-~~~f~F~v-~~~~~~-ryld~~~~~~~~~~~~VPv------L~-------- 283 (341)
T TIGR02306 238 IQKN---R--------------YGFDKY-RTVFAFRA-FFDGEQ-RFLTDEDFQDLCLTLIVPQ------LY-------- 283 (341)
T ss_pred ccCC---c--------------CCCCCC-ceEEEEEE-EEcCcc-eecCHHHHHHHHHhcccce------EE--------
Confidence 1111 0 111111 12777777 544442 2358899998887752221 10
Q ss_pred ccCCCCCccceecCCHHHHHHHHHHHHHc---------CCceEEEecCCCCCcCCCCCCCeEEEcc
Q 001083 388 VRPQGEPCWSLVAHNVDEVEKFFKETIEN---------RDEGIVLKDLGSKWEPGDRSGKWLKLKP 444 (1160)
Q Consensus 388 v~~~~~~~~~~~~~~~~ei~~~~~~ai~~---------g~EGlVlK~~ds~Y~pGkRs~~WlKlKp 444 (1160)
..+.++ ...++.++.. =.||+|+|.....+.... +.-|+|.|.
T Consensus 284 ------------~g~~de-~~~~~~~ig~a~~~~~~~~irEGvViKp~~~~~~~~G-~r~~fK~is 335 (341)
T TIGR02306 284 ------------EGPFDE-FTVVKDMLGAETVSGIGLHIREGVVYKSVELRFAVDG-RMVHFKAIS 335 (341)
T ss_pred ------------EechhH-hhhhhhhhcccccCccccceeceEEEeeccccccCCC-ceEEEEEcC
Confidence 011111 1222222221 289999999877664332 235999986
No 97
>KOG3132 consensus m3G-cap-specific nuclear import receptor (Snurportin1) [RNA processing and modification]
Probab=87.14 E-value=3 Score=45.42 Aligned_cols=172 Identities=14% Similarity=0.142 Sum_probs=110.1
Q ss_pred cccccccCChHHHHHhcCCCcEEEEEecceEEEEEEEeCCEEEEEeCCCCCCCcchhhHHHH-HHHhcc-cCceeeceeE
Q 001083 226 PQLAMRIGDAHAAWRKLHGKEVVIECKFDGDRIQIHKNGSEIHYFSRSFLDHSEYGHAMSKI-IEQNVL-VDRCILDGEM 303 (1160)
Q Consensus 226 PmLA~~~~~~~~~~~~~~~~~~~~E~K~DGeR~qih~~g~~v~~fSR~g~d~t~~~~~l~~~-l~~~~~-~~~~ILDGEl 303 (1160)
-||..-+-++++. + +.+|++=.-==|-||.|.-..|-..-|.|+|..+.. ||..... -.++.. ..=.|||+
T Consensus 101 lMLsEWliDvP~~---L-sqdW~vv~~PvGKR~lvVaSrG~Tvay~k~G~~v~r-F~S~LPGGnrr~~~a~~ytILDC-- 173 (325)
T KOG3132|consen 101 LMLSEWLIDVPDN---L-SQDWYVVARPVGKRCLVVASRGTTVAYVKNGSTVHR-FPSALPGGNRRKGPANSYTILDC-- 173 (325)
T ss_pred hhhHHHhccCccc---c-CcceEEEEeecCceEEEEecCCceEEEecCCeeEee-ccccCCCCCcCCCCcccceeeee--
Confidence 4665554444332 2 467998888899999998888888899999987643 2221100 000000 12246665
Q ss_pred EEEeCCCCcccccccHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCC
Q 001083 304 LVWDTSLNRFAEFGSNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHG 383 (1160)
Q Consensus 304 v~~d~~~~~~~pF~~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~ 383 (1160)
+|+. ++ -.|+|.|++..+|.++.+-|+.-|.-.|.+-+.+.++- ..|..+
T Consensus 174 -Iy~e-----------------------sn---QTYYVlD~~cWrgh~~yec~~dFRffwl~SKL~E~~~l---~~~t~~ 223 (325)
T KOG3132|consen 174 -IYHE-----------------------SN---QTYYVLDMVCWRGHSLYECTSDFRFFWLQSKLAETGAL---DPPTVY 223 (325)
T ss_pred -eecc-----------------------cC---ceEEEEEEEeecCcccccCchHHHHHHHhhhccccccC---CCCCcC
Confidence 1221 11 35999999999999999999999999999877654421 001000
Q ss_pred C--CccccCCCCCccceecCCHHHHHHHHHHHHHcCCceEEEecCCCCCcCCCCC-CCeEE
Q 001083 384 L--NSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRS-GKWLK 441 (1160)
Q Consensus 384 ~--~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EGlVlK~~ds~Y~pGkRs-~~WlK 441 (1160)
- .+.+.| .+ .-+.+.+.+++...+.-...||.+-.-.-.|.||... -+|+|
T Consensus 224 ~~f~Fs~vp------~~-pC~q~~l~~~~~~~~pf~~DGLLFYhks~~yqpgqsplvgwlk 277 (325)
T KOG3132|consen 224 HKFRFSVVP------FY-PCDQSGLHSAYTGSLPFVRDGLLFYHKSVVYQPGQSPLVGWLK 277 (325)
T ss_pred ccceecccC------CC-CCCHHHHHHHHcCCCceeeeeEEEeecceeeCCCCCccccccc
Confidence 0 011111 11 2367888888888888888999999999999999642 47764
No 98
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=87.13 E-value=0.96 Score=56.28 Aligned_cols=82 Identities=17% Similarity=0.261 Sum_probs=69.2
Q ss_pred HHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhc-cCCccccccccc----Cc---cHHHHHhhhCC
Q 001083 127 KELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK-LGISEKSIFHEF----HP---DAEDLFNVTCD 198 (1160)
Q Consensus 127 ~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~t~~E~k~l~RiIlkdLr-iGi~e~til~~~----hp---da~~~~~~~~D 198 (1160)
.+.-+++++|+..+++.+|..+|..+|..+++.+.-|.++++++.+. .|++++.+.+++ .. ...+.|....|
T Consensus 2 ~~fa~~~~~i~~t~~~~ek~~~l~~~~~~~~~~d~~~~~~ll~g~~~~~~i~~~~l~k~~~~~~g~~~~~~~~~~~~~GD 81 (539)
T PRK09247 2 KAFAELLDRLDLTTSTNAKLALLADYFRSAPDPDRAWALALLTGGLPRRLVKTRLLRELAAERADLPPWLFEESYDYVGD 81 (539)
T ss_pred hHHHHHHHHHHhccCHHHHHHHHHHHHHhCCHHHHHHHHHHhcCCcccCCCCHHHHHHHHHHHHCcCHHHHHHHHHhcCC
Confidence 34567788999999999999999999999999999999999999885 999999988765 21 23556888899
Q ss_pred HHHHHHHHhh
Q 001083 199 LKLVCEKLKD 208 (1160)
Q Consensus 199 L~~V~~~L~~ 208 (1160)
|+.||..+..
T Consensus 82 lg~~~~~~~~ 91 (539)
T PRK09247 82 LAETIALLLP 91 (539)
T ss_pred HHHHHHHhcc
Confidence 9999988764
No 99
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=84.56 E-value=1.3 Score=56.11 Aligned_cols=32 Identities=13% Similarity=0.297 Sum_probs=28.5
Q ss_pred CccEEeccchHHHHHHcCCccCCCCCCCCCCC
Q 001083 884 KKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 915 (1160)
Q Consensus 884 ~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~~~ 915 (1160)
..+.+|...||-+|++.+++|+-.+|+++--.
T Consensus 1008 ~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsGy 1039 (1176)
T KOG3548|consen 1008 RGIPCVHNTFIQACGEQNRCVDYTDYLLPSGY 1039 (1176)
T ss_pred cCCCcccHHHHHHHHhccccccchhhcccCcc
Confidence 56789999999999999999999999887554
No 100
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=83.14 E-value=6.1 Score=48.91 Aligned_cols=93 Identities=22% Similarity=0.245 Sum_probs=72.9
Q ss_pred CCcHHHHHHHHHHHHhhC---ChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCCc
Q 001083 6 ETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMSK 82 (1160)
Q Consensus 6 ~~~F~~l~~l~e~i~~~~---~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~~ 82 (1160)
+.+..++-++|++|...+ +..+|..+|..++.+. ++.+...++|+|+..+. .|+++.++..+++.+++++.
T Consensus 72 ~ltl~~V~~~l~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~E~~~l~r~i~~~lR-----iGv~~~~v~~Ala~a~~~~~ 145 (508)
T PRK03180 72 TLTVADVDAALSEIAAVAGAGSQARRAALLAALFAAA-TEDEQRFLRRLLTGELR-----QGALDGVMADAVARAAGVPA 145 (508)
T ss_pred CCcHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHhC-CHHHHHHHHHHHhCCCc-----ccccHHHHHHHHHHHhCCCH
Confidence 456777777889888875 4478899999999987 57889999999999883 69999999999999998864
Q ss_pred ChHHHHHHhhhhcCCCCCCCCCHHHHHHHHhh
Q 001083 83 DSADAVRLINWRKGGAAPNAGNFPMVAAEVLQ 114 (1160)
Q Consensus 83 ~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl~ 114 (1160)
.+..+..+| +||++.++...+.
T Consensus 146 --~~v~~a~~~--------~~dl~~v~~~~l~ 167 (508)
T PRK03180 146 --AAVRRAAML--------AGDLPAVAAAALT 167 (508)
T ss_pred --HHHHHHHHH--------cCCHHHHHHHHHh
Confidence 333344333 6899988875553
No 101
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=82.55 E-value=2.2 Score=53.67 Aligned_cols=89 Identities=18% Similarity=0.278 Sum_probs=61.1
Q ss_pred CCccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhh
Q 001083 800 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREK 878 (1160)
Q Consensus 800 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~ 878 (1160)
-..+|.|..||+..-... .+ .+..|..+|.-+||+++..+. ..||.|...+.. ...... +.+
T Consensus 630 ~s~if~gl~f~Vlsgt~~--~~-------tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~e-t~~vk~--~~~----- 692 (881)
T KOG0966|consen 630 ISNIFDGLEFCVLSGTSE--TH-------TKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKE-TTRVKA--QAI----- 692 (881)
T ss_pred hhhhhcCeeEEEecCCcc--cc-------cHHHHHHHHHHcCCEEEEcCCCCCcceEEecccc-chHHHH--HHH-----
Confidence 346899999999865431 11 256889999999999999887 488888643211 111111 111
Q ss_pred hhccCCccEEeccchHHHHHHcCCccCCCCC
Q 001083 879 HLLWNKKLHVVRSQWLEDCLAKEQKSEEYEY 909 (1160)
Q Consensus 879 ~~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y 909 (1160)
.....||.+.||.+|....++++-..+
T Consensus 693 ----~~~cdVl~p~Wlldcc~~~~l~p~~P~ 719 (881)
T KOG0966|consen 693 ----KRSCDVLKPAWLLDCCKKQRLLPWLPR 719 (881)
T ss_pred ----hccCceeeHHHHHHHHhhhhccccccH
Confidence 136789999999999999997765544
No 102
>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=82.19 E-value=1.7 Score=45.81 Aligned_cols=84 Identities=24% Similarity=0.423 Sum_probs=60.4
Q ss_pred HHHHHHHHHHHHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhh-------ccCCccccccccc----Cc---cHHH
Q 001083 126 IKELNDLLDRLASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDL-------KLGISEKSIFHEF----HP---DAED 191 (1160)
Q Consensus 126 i~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~t~~E~k~l~RiIlkdL-------riGi~e~til~~~----hp---da~~ 191 (1160)
..++-++|++|+..+++.+|..+|+.+|....+.+.-|.+..+++-+ ..|++++++.+++ +- ...+
T Consensus 3 F~~l~~l~~~l~~~~~~~~k~~~l~~~~~~~~~~~~~~~~~~~~~~l~P~~d~r~~~i~~~~L~k~~~~~~~~~~~~~~~ 82 (177)
T PF04675_consen 3 FSDLCELFEKLESTSSRLEKIAILSNFFRSWREEDLGPDLYLLLRLLFPEYDGREYGIGEKLLAKAIAEALGLPEKSIDE 82 (177)
T ss_dssp HHHHHHHHHHHHT---HHHHHHHHHHHHHTSHCCGHHCHHHHHHTHSSTTTCS---S--HHHHHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHHhccCHHHHHHHHHHHHHHcccchhhhHHHHHhcccccchhhhHhccchhHHHHHHHHHHcCCHHHHHH
Confidence 45677889999998889999999999999988777888888888844 6899999988654 42 2345
Q ss_pred HHhhhCCHHHHHHHHhhh
Q 001083 192 LFNVTCDLKLVCEKLKDR 209 (1160)
Q Consensus 192 ~~~~~~DL~~V~~~L~~~ 209 (1160)
.|....|++.++..+...
T Consensus 83 ~~~~~GD~g~~~~~~~~~ 100 (177)
T PF04675_consen 83 SYKKVGDLGEVAEEVLQK 100 (177)
T ss_dssp HHHHHS-HHHHHHHHHHH
T ss_pred HHHhcCcHHHHHHHHHhh
Confidence 678899999999988753
No 103
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=79.32 E-value=2.4 Score=53.04 Aligned_cols=82 Identities=24% Similarity=0.335 Sum_probs=55.1
Q ss_pred CCCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCC-----CCceEEE-EecC---------CChhhHhhhcC-C-
Q 001083 654 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN-----NSVTHCV-AADN---------KGLKYEAAKRR-G- 716 (1160)
Q Consensus 654 ~s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~-----~~~Th~I-a~~~---------~~~K~~~a~~~-~- 716 (1160)
.-.||.|+.||+++......+++|.++|...||++.+-.+ ..++-++ .... ..-+..++... +
T Consensus 584 ~~kLf~gl~~~~~g~fs~~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~~s~~a 663 (684)
T KOG4362|consen 584 KPKLFEGLKFYFVGDFSNPPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALALSQRA 663 (684)
T ss_pred CcchhcCCcceeecccccCcHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccHHHHHHhcCC
Confidence 4579999999999877778899999999999999976432 1122122 1111 01123333333 4
Q ss_pred CeeecchHHHHHhcCccCC
Q 001083 717 DVIHYSWVLDCCSQKKLLQ 735 (1160)
Q Consensus 717 ~VV~p~WV~dCi~~~~lLp 735 (1160)
+.|+-.||+|+++--.+++
T Consensus 664 ~~~~~~wvl~s~a~~~~~~ 682 (684)
T KOG4362|consen 664 RAVSSSWVLDSIAGYQILV 682 (684)
T ss_pred Cccchhhhhcchhceeeee
Confidence 9999999999997555443
No 104
>PLN03113 DNA ligase 1; Provisional
Probab=74.53 E-value=6.4 Score=50.68 Aligned_cols=86 Identities=13% Similarity=0.293 Sum_probs=72.0
Q ss_pred CCCcHHHHHHHHHHHHhhhhHHHHHHHHHHHHHhC---CHHHHHHHHHHHhhhhc-------cCCcccccccccC----c
Q 001083 122 GGLTIKELNDLLDRLASSENRAEKISVLSTLIKKT---NAQEMKWIIMIILKDLK-------LGISEKSIFHEFH----P 187 (1160)
Q Consensus 122 ~~LTi~eVn~~Ld~LA~~~~~~~k~~il~~ll~~~---t~~E~k~l~RiIlkdLr-------iGi~e~til~~~h----p 187 (1160)
.++.-.++-+.++.|...+++.++..+|..+|... +|.+.-|.+.++.+.+- +||+++.|.+++. .
T Consensus 127 ~~~~f~~l~~~~~~Ie~tt~rlek~~~L~~~~r~~~~~~p~dl~~~vyL~~~~l~P~~e~~elgige~~L~kai~e~~g~ 206 (744)
T PLN03113 127 ERVPFLFVALAFDLISNETGRIVITDIVCNMLRTVMATTPEDLVAVVYLLANRIAPAHEGVELGIGEATIIKALAEAFGR 206 (744)
T ss_pred CCccHHHHHHHHHHHHhccCHHHHHHHHHHHHHHhccCChHHHHHHHHHHhCCCCccccCcccCcCHHHHHHHHHHHHCc
Confidence 45778888999999999999999999999999984 99999999999888764 6999999987662 1
Q ss_pred ---cHHHHHhhhCCHHHHHHHHh
Q 001083 188 ---DAEDLFNVTCDLKLVCEKLK 207 (1160)
Q Consensus 188 ---da~~~~~~~~DL~~V~~~L~ 207 (1160)
.....|....||+.|+..+.
T Consensus 207 ~~~~ik~~y~~~GDlG~vA~~~~ 229 (744)
T PLN03113 207 TEKQVKKQYKELGDLGLVAKASR 229 (744)
T ss_pred CHHHHHHHHHHhCCHHHHHHhhh
Confidence 23556888899999998664
No 105
>KOG2386 consensus mRNA capping enzyme, guanylyltransferase (alpha) subunit [RNA processing and modification]
Probab=70.01 E-value=2.6 Score=49.72 Aligned_cols=93 Identities=20% Similarity=0.344 Sum_probs=61.6
Q ss_pred CcEEEEEecceEEEEEEEeCC-EEEEEeCCCCCCCc---ch---hhHHHHHHHhcccCceeeceeEEEEeCCCCcccccc
Q 001083 245 KEVVIECKFDGDRIQIHKNGS-EIHYFSRSFLDHSE---YG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLNRFAEFG 317 (1160)
Q Consensus 245 ~~~~~E~K~DGeR~qih~~g~-~v~~fSR~g~d~t~---~~---~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~~~pF~ 317 (1160)
..|.+.+|.||.|...-.+++ .+..|-|.-..+-. ++ ....+ .....++||||+. |..+..
T Consensus 285 ~~y~~~We~dg~~~~~L~~~~~~~~~~dR~~~~~~~~~~~~~~~~~~~~------~~~~tl~dge~~l-D~l~~~----- 352 (393)
T KOG2386|consen 285 EYYEASWEADGTRYMMLIDGDGEYYDFDRWRFVKGRENLRKIREDSDTK------VLHQTLLDGEMIL-DRLKEE----- 352 (393)
T ss_pred hhhhhhhcccCcEEEEEecCCceeEechhhhHHHhhhhhhcccccccch------hhhhhhcccceec-cccccc-----
Confidence 346789999999998888765 45555554322110 00 01111 1246789999988 643210
Q ss_pred cHHHHHHHhccCCCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHh
Q 001083 318 SNQEIAKAARDGLSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKV 367 (1160)
Q Consensus 318 ~lq~i~~~~r~~~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~ 367 (1160)
. .+.|.+||++-+|++.+...|+. |.+.+.+-
T Consensus 353 ----------------~-~~r~l~Yd~~r~n~~~v~~~~f~-r~~~~~~e 384 (393)
T KOG2386|consen 353 ----------------A-IPRYLIYDMVRFNSQKVEKRPFS-RWQIIEKE 384 (393)
T ss_pred ----------------c-chhheeeeeeeccCcccccCcch-HHHHHHHH
Confidence 1 15689999999999999999999 88877653
No 106
>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=66.81 E-value=17 Score=45.22 Aligned_cols=93 Identities=22% Similarity=0.253 Sum_probs=72.1
Q ss_pred CCCcHHHHHHHHHHHHhhC---ChHHHHHHHHHHHhhcCCCchHhhhHhhcCCCCCcCcccCCCCHHHHHHHHHHHhCCC
Q 001083 5 EETEVIVLVSLFNWIQKTK---PAAKKRSKFRKFLDTYCDSVDYFSALRLILPSLDRERGSYGLKESVLANCLIDALGMS 81 (1160)
Q Consensus 5 ~~~~F~~l~~l~e~i~~~~---~~~~K~~~l~~~l~~~~~~~d~~p~lrLllP~~d~er~~ygike~~L~k~~~~~~gl~ 81 (1160)
.+++-.++-++|++|.+.+ +..+|..+|..++.+. ++.+...++|+|+-.+. .|++++++..+|+.+++++
T Consensus 53 ~~lti~eV~~~L~~ia~~~g~~s~~~k~~~l~~ll~~~-~~~e~k~l~r~i~~~lr-----iG~~~~~il~al~~~~~~~ 126 (514)
T TIGR00574 53 APLTVKEVYETLKNIAETSGEGSQDKKIKLLKSLLKRA-SPLEAKYLIRTILGDLR-----IGIAEKTILDALAKAFLLS 126 (514)
T ss_pred CCcCHHHHHHHHHHHHHhhCCCcHHHHHHHHHHHHHhC-CHHHHHHHHHHHhhhcc-----cCccHHHHHHHHHHHhccc
Confidence 3466778888888888776 4568889999999876 57888999999999883 5999999999999999876
Q ss_pred cChHHHHHHhhhhcCCCCCCCCCHHHHHHHHh
Q 001083 82 KDSADAVRLINWRKGGAAPNAGNFPMVAAEVL 113 (1160)
Q Consensus 82 ~~s~~~~~L~~wk~~~~~~~~GD~~~~a~~vl 113 (1160)
.. +..++ | ..+.|++.++..++
T Consensus 127 ~~--~~~~~--~------~~~~dl~~v~~~l~ 148 (514)
T TIGR00574 127 HP--DVERA--F------NLTNDLGKVAKILL 148 (514)
T ss_pred hH--HHHHH--H------HhCCCHHHHHHHHH
Confidence 43 22232 2 34678998887765
No 107
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=63.97 E-value=22 Score=41.16 Aligned_cols=48 Identities=15% Similarity=0.211 Sum_probs=38.7
Q ss_pred ccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCCC-ceEEEEecC
Q 001083 802 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLAN-ATHVVVLSV 859 (1160)
Q Consensus 802 ~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~-vTHVVV~~~ 859 (1160)
..|.|.+|+|.|.-.. ..+..+..+|..+||++.+..+. ++++|++..
T Consensus 219 ~~l~g~~~vfTG~l~~----------~~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~ 267 (309)
T PRK06195 219 TAFKEEVVVFTGGLAS----------MTRDEAMILVRRLGGTVGSSVTKKTTYLVTNTK 267 (309)
T ss_pred ccccCCEEEEccccCC----------CCHHHHHHHHHHhCCEecCCcccCceEEEECCC
Confidence 4699999999996421 12568889999999999999995 889998853
No 108
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=63.42 E-value=3.7 Score=51.35 Aligned_cols=84 Identities=14% Similarity=0.199 Sum_probs=58.1
Q ss_pred CCcccCeEEEEEcCC---CCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC--CeeecchHHHHHh
Q 001083 655 TSIFSDMVFYFVNVP---PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG--DVIHYSWVLDCCS 729 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~---~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~--~VV~p~WV~dCi~ 729 (1160)
+..+.|+.+.+.+.. ......++-.+....|...+.+....+||+|+....+.+...+...+ .||.+.|++.|++
T Consensus 439 ~~v~~~~~~vfSg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~e 518 (635)
T KOG0323|consen 439 TKVLKGSQIVFSGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKAVVSGSAKVVNAAWLWRSLE 518 (635)
T ss_pred hHHhhccceeecccccCcCCcchhhhhhhhhcccceecccccchhhhHHhhccCcceeeccccccceeEechhHHHHHHH
Confidence 345555555544321 12223555566677887777787777899999888777776666655 8999999999999
Q ss_pred cCccCCCCc
Q 001083 730 QKKLLQLQP 738 (1160)
Q Consensus 730 ~~~lLp~~p 738 (1160)
+...+.-.+
T Consensus 519 ~w~~v~ek~ 527 (635)
T KOG0323|consen 519 KWGKVEEKL 527 (635)
T ss_pred Hhcchhccc
Confidence 876665444
No 109
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=61.00 E-value=5.1 Score=49.68 Aligned_cols=75 Identities=13% Similarity=0.286 Sum_probs=53.4
Q ss_pred CCcccCeEEEEEcCCCCCChHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhhHhhhcCC-CeeecchHHHHHhcC
Q 001083 655 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQK 731 (1160)
Q Consensus 655 s~lF~G~~F~vv~~~~~~~k~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~~~~K~~~a~~~~-~VV~p~WV~dCi~~~ 731 (1160)
-..|.|+.||+.+. .....+.+.....+.||+.-.. ...+||+|+.+....---.+.... .+|.-.|..-+|.+|
T Consensus 208 l~~feg~~~~f~gF-~~ee~~~m~~sle~~gg~~a~~-d~~cthvvv~e~~~~~~p~~~s~~~~~vk~ewfw~siq~g 283 (850)
T KOG3524|consen 208 LGVFEGLSLFFHGF-KQEEIDDMLRSLENTGGKLAPS-DTLCTHVVVNEDNDEVEPLAVSSNQVHVKKEWFWVSIQRG 283 (850)
T ss_pred cccccCCeEeecCC-cHHHHHHHHHHHHhcCCcccCC-CCCceeEeecCCccccccccccccceeecccceEEEEecc
Confidence 35899999998654 4566788888889999999883 346999998654332111223333 899999988777766
No 110
>COG4566 TtrR Response regulator [Signal transduction mechanisms]
Probab=56.38 E-value=39 Score=36.24 Aligned_cols=81 Identities=19% Similarity=0.345 Sum_probs=54.0
Q ss_pred CCCCHHHHHHHHhhhhcCCCCCCCcHHHHHHHHHH----HHhhhhHHHHHHHHHHHHHhCCHHHHHHHHHHHhhhhc---
Q 001083 101 NAGNFPMVAAEVLQRRQGMISGGLTIKELNDLLDR----LASSENRAEKISVLSTLIKKTNAQEMKWIIMIILKDLK--- 173 (1160)
Q Consensus 101 ~~GD~~~~a~~vl~~r~~~~~~~LTi~eVn~~Ld~----LA~~~~~~~k~~il~~ll~~~t~~E~k~l~RiIlkdLr--- 173 (1160)
-.||.+.+++.+...--.+-..|..-+++.+.+.+ .+..........-+..+|..+||.|...|-+++.+-+-
T Consensus 84 GhgDIpmaV~AmK~GAvDFLeKP~~~q~Lldav~~Al~~~~~~~~~~~~~~~~~~~l~tLT~RERqVl~~vV~G~~NKqI 163 (202)
T COG4566 84 GHGDIPMAVQAMKAGAVDFLEKPFSEQDLLDAVERALARDASRRAEADRQAAIRARLATLTPRERQVLDLVVRGLMNKQI 163 (202)
T ss_pred CCCChHHHHHHHHcchhhHHhCCCchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcCHHHHHHHHHHHcCcccHHH
Confidence 35899988776543222223455555555444433 33333334445678899999999999999999987653
Q ss_pred ---cCCccccc
Q 001083 174 ---LGISEKSI 181 (1160)
Q Consensus 174 ---iGi~e~ti 181 (1160)
+|+|+.||
T Consensus 164 A~dLgiS~rTV 174 (202)
T COG4566 164 AFDLGISERTV 174 (202)
T ss_pred HHHcCCchhhH
Confidence 79999987
No 111
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=55.23 E-value=30 Score=44.31 Aligned_cols=225 Identities=19% Similarity=0.231 Sum_probs=126.7
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcch---hhHHHHHHHhcccCceeeceeEEEEeCCCCc-----
Q 001083 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYG---HAMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~---~~l~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1160)
.|++|+|+||.-+.+.+.+|. ++..|| .|+|+|+.. +++-..|.. ..+..+.+-||++.-...-.+
T Consensus 109 ~~~~epKiDGlsisL~Y~~G~L~~a~TRGDG~~GeDvT~n~~~I~~IP~~l~~-~~p~~levRGEv~m~~~~F~~lN~~~ 187 (665)
T PRK07956 109 TYLCELKIDGLAVSLLYENGVLVRAATRGDGTTGEDITANVRTIRSIPLRLHG-NEPERLEVRGEVFMPKADFEALNEER 187 (665)
T ss_pred ceEEEEecccEEEEEEEECCEEEEEEecCCCccchhHhhhhhhhccCChhhcc-cCCCeEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999999887665 688999 588888632 222222210 113458899999874321000
Q ss_pred ----ccccccHHHHH-HHhccC--CCCCCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCCC
Q 001083 313 ----FAEFGSNQEIA-KAARDG--LSSDRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLN 385 (1160)
Q Consensus 313 ----~~pF~~lq~i~-~~~r~~--~~~~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~ 385 (1160)
-.+|..-+..+ ...|.. ......++.|++|++...++ ........++.+.|..+-=++..
T Consensus 188 ~~~g~~~faNpRNaaAGslr~ld~~~~~~r~L~f~~y~~~~~~~-~~~~~t~~e~l~~L~~~GF~v~~------------ 254 (665)
T PRK07956 188 REEGEKPFANPRNAAAGSLRQLDPKITAKRPLSFFAYGVGEVEG-GELPDSQSEALEFLKAWGFPVNP------------ 254 (665)
T ss_pred HhcCCCcccChHHHHhhhhhccChHHHhcCCCEEEEEecccccC-CCCCCCHHHHHHHHHHCCCCcCC------------
Confidence 01332222211 111110 00112249999999964431 11134778888888876322110
Q ss_pred ccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe---EEEccccccCCCc
Q 001083 386 SHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAGSD 452 (1160)
Q Consensus 386 ~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~----pGkRs~~W---lKlKpeY~~~g~~ 452 (1160)
....+.+.+++.++++.+.+. .-.|||+|--+-.|. ...+.+.| +|+.++ .
T Consensus 255 ----------~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrWaiA~Kf~~~------~ 318 (665)
T PRK07956 255 ----------YRKLCTSIEEVLAFYEEIEEERHDLPYDIDGVVIKVDDLALQEELGFTAKAPRWAIAYKFPAE------E 318 (665)
T ss_pred ----------ceEeeCCHHHHHHHHHHHHHhhccCCCCCCcEEEEecCHHHHHhcCccCCCCCceeEecCCCc------e
Confidence 123456889999998877643 567999997664442 12345667 676664 4
Q ss_pred ccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHH
Q 001083 453 LDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 509 (1160)
Q Consensus 453 lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l 509 (1160)
..-.|.+..|..|| .|.+.-. |..++-.- .+. +|.+ .|..+.++++.+
T Consensus 319 ~~T~l~~I~~qVGR-TG~iTPV--A~l~PV~l---~G~--tVsr-AtLhN~~~i~~~ 366 (665)
T PRK07956 319 ATTKLLDIEVQVGR-TGAVTPV--ARLEPVEV---AGV--TVSR-ATLHNADEIERK 366 (665)
T ss_pred eEEEEEEEEEecCC-CceeeeE--EEEEeEEE---CCE--EEEE-eecCCHHHHHHc
Confidence 55677888887775 4444332 22222100 011 2333 367777777654
No 112
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=52.95 E-value=5.9 Score=23.94 Aligned_cols=12 Identities=58% Similarity=0.947 Sum_probs=3.8
Q ss_pred ccccCCCCCCCc
Q 001083 971 KRKRGRPAGGSA 982 (1160)
Q Consensus 971 ~~~~~~~~~~~~ 982 (1160)
+++||||+....
T Consensus 1 ~r~RGRP~k~~~ 12 (13)
T PF02178_consen 1 KRKRGRPRKNAK 12 (13)
T ss_dssp S--SS--TT---
T ss_pred CCcCCCCccccC
Confidence 478899987543
No 113
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=50.24 E-value=45 Score=38.77 Aligned_cols=75 Identities=11% Similarity=0.006 Sum_probs=51.5
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCCC-ceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLAN-ATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~-vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
..||.|-+|.|.|.-. . .++.++.+|..+||++.+..+. +++||+++..+.....+ ++
T Consensus 230 ~~l~~g~~~v~TG~l~---~--------~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~---kA------- 288 (313)
T PRK06063 230 RPLVQGMRVALSAEVS---R--------THEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGY---HA------- 288 (313)
T ss_pred CcccCCCEEEEecCCC---C--------CHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHH---HH-------
Confidence 3578999999999532 1 2568899999999999999985 89999987554212222 11
Q ss_pred hccCCccEEeccchHHHHH
Q 001083 880 LLWNKKLHVVRSQWLEDCL 898 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci 898 (1160)
....+.|++.+=+.+=+
T Consensus 289 --~~~gi~ii~e~~f~~ll 305 (313)
T PRK06063 289 --RQLGVPVLDEAAFLELL 305 (313)
T ss_pred --HHcCCccccHHHHHHHH
Confidence 12456777776555433
No 114
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=49.58 E-value=15 Score=46.10 Aligned_cols=95 Identities=19% Similarity=0.145 Sum_probs=63.4
Q ss_pred CccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 001083 801 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 879 (1160)
Q Consensus 801 ~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~~~ 879 (1160)
..-+.||.+-|+|.-+....+.. ..+-.....+|...+.+.+ .+||+|....... ..+++
T Consensus 439 ~~v~~~~~~vfSg~~P~~~~~~~-------s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~-k~~~a----------- 499 (635)
T KOG0323|consen 439 TKVLKGSQIVFSGLHPTGSTDES-------ADILGVAQQLGAVSAPDVSDKTTHLIAANAGTK-KVYKA----------- 499 (635)
T ss_pred hHHhhccceeecccccCcCCcch-------hhhhhhhhcccceecccccchhhhHHhhccCcc-eeecc-----------
Confidence 34688899999986542211111 1222345677888888887 5999998754311 11111
Q ss_pred hccCCccEEeccchHHHHHHcCCccCCCCCCCCCCC
Q 001083 880 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 915 (1160)
Q Consensus 880 ~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~~~ 915 (1160)
......+||.+.||+.|+..=..+.|-.|......
T Consensus 500 -~~~~~~~Vv~~~wl~~~~e~w~~v~ek~~~l~~~~ 534 (635)
T KOG0323|consen 500 -VVSGSAKVVNAAWLWRSLEKWGKVEEKLEPLDDDQ 534 (635)
T ss_pred -ccccceeEechhHHHHHHHHhcchhcccccccccc
Confidence 11234899999999999999999999999877766
No 115
>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=43.64 E-value=44 Score=42.80 Aligned_cols=225 Identities=18% Similarity=0.244 Sum_probs=126.8
Q ss_pred cEEEEEecceEEEEEEEeCCE-EEEEeC----CCCCCCcchh---hHHHHHHHhcccCceeeceeEEEEeCCCCc-----
Q 001083 246 EVVIECKFDGDRIQIHKNGSE-IHYFSR----SFLDHSEYGH---AMSKIIEQNVLVDRCILDGEMLVWDTSLNR----- 312 (1160)
Q Consensus 246 ~~~~E~K~DGeR~qih~~g~~-v~~fSR----~g~d~t~~~~---~l~~~l~~~~~~~~~ILDGElv~~d~~~~~----- 312 (1160)
.|++|+|+||.-+.+.+.+|+ ++..|| .|+|+|+... .+-..+.....+..+.+-||++.-...-.+
T Consensus 97 ~~~~epKiDGlaisL~Ye~G~L~~a~TRGDG~~GeDvT~nv~~I~~iP~~i~~~~~p~~levRGEv~m~~~~F~~~N~~~ 176 (652)
T TIGR00575 97 EYVVEPKIDGLSVSLTYENGVLVRALTRGDGTVGEDVTANVRTIRSIPLRLAGDNPPERLEVRGEVFMPKEDFEALNEER 176 (652)
T ss_pred eEEEEEeccceEEEEEEECCEEEEEEecCCCccchhHhhhhhhhcccchhhcCCCCCceEEEEEEEEEEHHHHHHHHHHH
Confidence 599999999999999997665 788999 5888886322 111122100013458899999874211000
Q ss_pred ----ccccccHHHHH-HHhccCCCC---CCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCC
Q 001083 313 ----FAEFGSNQEIA-KAARDGLSS---DRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 384 (1160)
Q Consensus 313 ----~~pF~~lq~i~-~~~r~~~~~---~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~ 384 (1160)
-.+|..-+..+ ...|. .++ ...++.|++|++...++ .......++.+.|..+-=++..
T Consensus 177 ~~~g~~~faNpRN~aAGslr~-ld~~~~~~r~L~~~~y~~~~~~~--~~~~t~~e~l~~L~~~GF~v~~----------- 242 (652)
T TIGR00575 177 REQGEKPFANPRNAAAGSLRQ-LDPRITAKRKLRFFAYGLGEGLE--LPDATQYEALAWLKKWGFPVSP----------- 242 (652)
T ss_pred HHcCCCCCCCcHHHHHHHHHc-CCchhhhcCccEEEEEeccccCC--CCCCCHHHHHHHHHHCCCCCCC-----------
Confidence 01333222211 11111 111 12249999999853222 1124778888888876322111
Q ss_pred CccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCc----CCCCCCCe---EEEccccccCCC
Q 001083 385 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWE----PGDRSGKW---LKLKPEYIRAGS 451 (1160)
Q Consensus 385 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~----pGkRs~~W---lKlKpeY~~~g~ 451 (1160)
....+.+.+++.++++++.+. .-.|+|+|--+-.+. ...+.+.| +|+.++
T Consensus 243 -----------~~~~~~~~~ei~~~~~~~~~~R~~l~y~iDGiViKvn~~~~~~~lG~t~~~PrwaiA~Kf~~~------ 305 (652)
T TIGR00575 243 -----------HIRLCDSIEEVLEYYREIEEKRDSLPYEIDGVVVKVDDLALQDELGFTSKAPRWAIAYKFPAE------ 305 (652)
T ss_pred -----------CeEeeCCHHHHHHHHHHHHHhhhcCCCCCCcEEEEecCHHHHHHhCccCCCCCceEEEcCCCc------
Confidence 123456889999998877433 567999997655543 12346677 666664
Q ss_pred cccEEEEEEEeCCCCCCCccceEEEEEecCCCCCCCCceEEEEeeecCCCCHHHHHHHH
Q 001083 452 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVV 510 (1160)
Q Consensus 452 ~lDlvIIG~~~G~Grr~g~~gsfllg~~d~~~~~~~~~~~~s~~kVgtG~sdeel~~l~ 510 (1160)
...-.|.+..|-.|| .|.+.-. |..++-.- .+. +|.+ .|..+.++++.+.
T Consensus 306 ~~~T~l~~I~~qVGR-TG~iTPv--A~lePV~l---~G~--~Vsr-AtLhN~~~i~~~~ 355 (652)
T TIGR00575 306 EAQTKLLDVVVQVGR-TGAITPV--AKLEPVFV---AGT--TVSR-ATLHNEDEIEELD 355 (652)
T ss_pred eeeEEEEEEEEecCC-CceeeeE--EEEeeEEE---CCE--EEEE-eecCCHHHHHHcC
Confidence 456678888887775 4545432 22222100 011 2333 3677777776543
No 116
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=40.22 E-value=66 Score=40.78 Aligned_cols=195 Identities=20% Similarity=0.275 Sum_probs=115.0
Q ss_pred CcEEEEEecceEEEEEEEeCCE-EEEEeCC----CCCCCcchhhHHHHHHHhc--ccCceeeceeEEEEeCCCCc-----
Q 001083 245 KEVVIECKFDGDRIQIHKNGSE-IHYFSRS----FLDHSEYGHAMSKIIEQNV--LVDRCILDGEMLVWDTSLNR----- 312 (1160)
Q Consensus 245 ~~~~~E~K~DGeR~qih~~g~~-v~~fSR~----g~d~t~~~~~l~~~l~~~~--~~~~~ILDGElv~~d~~~~~----- 312 (1160)
..|++|+|+||.-+-+.+.+|. ++--||. |+|+|.-...|... -..+ .+..+-+=||++.--..-..
T Consensus 109 ~~y~~EpKiDGlsisL~YenG~Lv~aaTRGdG~~GEDiT~NvrtI~~I-P~~l~~~p~~lEVRGEvfm~k~~F~~lN~~~ 187 (667)
T COG0272 109 VEYVVEPKIDGLAISLVYENGKLVRAATRGDGTTGEDITANVRTIRSI-PLKLPGAPAVLEVRGEVFMPKEDFEALNEER 187 (667)
T ss_pred cceEEEeecceEEEEEEEECCEEEEeeccCCCccccchhhhhhhHhhh-hhhccCCCceEEEEeEEEEeHHHHHHHHHHH
Confidence 4799999999999988887664 7788885 78888644333322 1112 25667888998763110000
Q ss_pred ----ccccccHHHHH-HHhccCCCC---CCccEEEEEEeeeecCCcccccCCHHHHHHHHHHhhccCCCcceeeccCCCC
Q 001083 313 ----FAEFGSNQEIA-KAARDGLSS---DRQVLCYFAFDVLYVGDTSVIHQSLKERHELLQKVVKPSKGRLETLVPDHGL 384 (1160)
Q Consensus 313 ----~~pF~~lq~i~-~~~r~~~~~---~~~~~~~~vFDiL~lng~sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~ 384 (1160)
-.+|..-+..+ ...| .+++ ...++.+++|.+-...+. ..-....++.+.|..+-=++..
T Consensus 188 ~~~g~~~faNpRNaAAGsLR-qlD~~ita~R~L~~f~y~~~~~~~~-~~~~t~~e~l~~L~~~GF~v~~----------- 254 (667)
T COG0272 188 EEEGEKPFANPRNAAAGSLR-QLDPKITAKRKLGFFIYAVGDGEEG-LLADTQSERLAFLKAWGFPVNP----------- 254 (667)
T ss_pred HHhCCCCcCChhhhhhhhhh-ccCHHHHhcCCceEEEEeCCccCCC-CCccCHHHHHHHHHHcCCCCCc-----------
Confidence 01221111110 0011 0111 112389999999876654 5566888999999887322211
Q ss_pred CccccCCCCCccceecCCHHHHHHHHHHHHHc------CCceEEEecCCCCCcC--C--CCCCCe---EEEccccccCCC
Q 001083 385 NSHVRPQGEPCWSLVAHNVDEVEKFFKETIEN------RDEGIVLKDLGSKWEP--G--DRSGKW---LKLKPEYIRAGS 451 (1160)
Q Consensus 385 ~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~------g~EGlVlK~~ds~Y~p--G--kRs~~W---lKlKpeY~~~g~ 451 (1160)
....+.+.+++.++++.+... --.|+|+|--+-.... | .|.+.| +|+.++-
T Consensus 255 -----------~~~~~~~~~ev~~~~~~~~~~R~~L~y~IDGvViKvn~l~~q~~lG~tsk~PrWAiAyKFpa~e----- 318 (667)
T COG0272 255 -----------YTRLCKNADEVLAFYEEWEKKRASLPYDIDGVVIKVNDLALQRELGFTSKAPRWAIAYKFPAEE----- 318 (667)
T ss_pred -----------HhhhcCCHHHHHHHHHHHHhhcccCCCccceEEEEeccHHHHHHhCCccCCCceeeeecCCchh-----
Confidence 133578999999999998764 3569999965422211 2 356788 7888762
Q ss_pred cccEEEEEEEeCCCCCCCcc
Q 001083 452 DLDVLIIGGYYGSGRRGGEV 471 (1160)
Q Consensus 452 ~lDlvIIG~~~G~Grr~g~~ 471 (1160)
.--.+.+..+.-|| .|.+
T Consensus 319 -~~T~l~dI~~qVGR-TG~i 336 (667)
T COG0272 319 -AVTKLLDIEVQVGR-TGAI 336 (667)
T ss_pred -eeeEEEEEEEecCC-ceee
Confidence 22234444554554 4444
No 117
>COG5275 BRCT domain type II [General function prediction only]
Probab=39.10 E-value=86 Score=34.05 Aligned_cols=54 Identities=20% Similarity=0.282 Sum_probs=41.4
Q ss_pred CCCccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEEccCCC-ceEEEEecCCCc
Q 001083 799 DKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLAN-ATHVVVLSVLGY 862 (1160)
Q Consensus 799 ~~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~~~ls~-vTHVVV~~~~~~ 862 (1160)
-....+.|.+|-|.|....+ .++--..++..|||.|+-.++. .|+||.++..++
T Consensus 152 g~~~cL~G~~fVfTG~l~Tl----------sR~~a~~lvk~yGgrvT~~pSskTtflvlGdnaGP 206 (276)
T COG5275 152 GERECLKGKVFVFTGDLKTL----------SRDDAKTLVKVYGGRVTAVPSSKTTFLVLGDNAGP 206 (276)
T ss_pred CCcccccccEEEEecccccc----------cchhHHHHHHHhCCeeecccccceeEEEecCCCCh
Confidence 34557899999999975422 3455667899999999999985 888888876655
No 118
>PF09511 RNA_lig_T4_1: RNA ligase; InterPro: IPR019039 Members of this family include T4 phage proteins with ATP-dependent RNA ligase activity. Host defence to phage may include cleavage and inactivation of specific tRNA molecules; members of this family act to reverse this RNA damage. The enzyme is adenylated, transiently, on a Lys residue in a motif KXDGSL. This family also includes fungal tRNA ligases that have adenylyltransferase activity []. tRNA ligases are enzymes required for the splicing of precursor tRNA molecules containing introns. Please see the following relevant references: [, ]. ; PDB: 2C5U_B.
Probab=37.96 E-value=2.4e+02 Score=30.86 Aligned_cols=32 Identities=25% Similarity=0.158 Sum_probs=23.2
Q ss_pred cEEEEEecceEEE-EEEEeCCEEEEEeCCCCCC
Q 001083 246 EVVIECKFDGDRI-QIHKNGSEIHYFSRSFLDH 277 (1160)
Q Consensus 246 ~~~~E~K~DGeR~-qih~~g~~v~~fSR~g~d~ 277 (1160)
++.+-.|+||.=+ .....+|.+.+-|+.+..-
T Consensus 46 p~~v~~K~dGsli~~~~~~~g~~~~~SK~s~~s 78 (221)
T PF09511_consen 46 PVEVYEKEDGSLIFIPYLDDGELIVASKGSFDS 78 (221)
T ss_dssp EEEEEEE--SEEE-EEEEETTEEEEEETTBSSS
T ss_pred cEEEEEecCcEEEEEeeecCCeEEEEecCcccc
Confidence 7999999999444 3345788999999998653
No 119
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=32.24 E-value=46 Score=42.90 Aligned_cols=89 Identities=20% Similarity=0.295 Sum_probs=64.4
Q ss_pred CCccCCCeEEEEccCCCCCCChhHHHHHHHHHHHHHHHHhcCCEEE-ccCC-CceEEEEecCCCcccchhhhHHHHHHHh
Q 001083 800 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVC-NNLA-NATHVVVLSVLGYDVNFNSLTESFTARE 877 (1160)
Q Consensus 800 ~~~lF~gc~~yl~~~~~~~~~d~~~i~~~~~~~l~~~I~~~GG~v~-~~ls-~vTHVVV~~~~~~~~~~~~l~~~l~~~~ 877 (1160)
....|++.-+|..|... +. ...+++.-.++||... .... ..||||....+ .++-.
T Consensus 44 ~~s~fs~is~~~ngs~~---e~--------~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~------a~~vk------ 100 (1016)
T KOG2093|consen 44 GSSSFSGISISVNGSTD---ES--------ANELKLQNMFHTGASAASYERSGTENIIAQGLP------ADLVK------ 100 (1016)
T ss_pred CcceeeeeeeccCCccc---cc--------hHHHhhhhhhcccccccccccccceeeecccch------HHHhc------
Confidence 56789999999999763 22 3467778889999987 4443 48999986532 11111
Q ss_pred hhhccCCccEEeccchHHHHHHcCCccCCCCCCCCCCC
Q 001083 878 KHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTG 915 (1160)
Q Consensus 878 ~~~~~~~~~~IVt~~Wl~eci~~~~~v~Ee~Y~v~~~~ 915 (1160)
....+...+.+|+.+|++.+..+.--.|......
T Consensus 101 ----~~~~~~~~~~e~iie~~~~~~~~~~~~~~~~t~~ 134 (1016)
T KOG2093|consen 101 ----GFTIPKHISIEWIIECCENGMDVGYYPYQLYTGQ 134 (1016)
T ss_pred ----cccchhhhcHHHHHHHHhccCccccccceeeccc
Confidence 1245677899999999999999988888765554
No 120
>PF14909 SPATA6: Spermatogenesis-assoc protein 6
Probab=26.18 E-value=1.5e+02 Score=30.34 Aligned_cols=58 Identities=21% Similarity=0.398 Sum_probs=42.2
Q ss_pred CCcEEEeCCcceEEEEEEeeeeeeecccccCCceeeCceee--eeecCCCccCcCCHHHHHHHHH
Q 001083 540 RPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRID--RVRYDKPWHDCLDVQSFVELVH 602 (1160)
Q Consensus 540 ~Pdvwi~~P~~s~Vlev~~~i~~~~s~~~~~g~tLRFPR~~--riR~DK~~~d~~t~~el~el~~ 602 (1160)
=|.+|.. +...+-+.|..-.+..++. -..-.||-+- ++|.+|....|.+..++.++..
T Consensus 11 CPGv~L~-~~~~vyL~v~~lg~~~~T~----~~ppvFPllfhek~~FeK~F~~~~dp~~l~~~Le 70 (140)
T PF14909_consen 11 CPGVWLC-DKGDVYLSVCILGQYKRTR----CLPPVFPLLFHEKFRFEKVFPNAVDPAQLADLLE 70 (140)
T ss_pred cCCeEeC-CCCCEEEEEEEcccEeecc----cCCCcCCeeEeeEEEeEEEecCCCCHHHHHHHhh
Confidence 4789997 6767777775322222332 3445899664 7999999999999999999885
No 121
>PF15101 DUF4557: Domain of unknown function (DUF4557)
Probab=25.83 E-value=1.6e+02 Score=31.81 Aligned_cols=70 Identities=20% Similarity=0.335 Sum_probs=45.4
Q ss_pred HHHHHHHHHcCCEEEecCCCCceEEEEecC---CChh-hH--hhhcCC-CeeecchHHHHHhcCc--cCCCCcccccccC
Q 001083 675 DSLHKMVVENGGTFSMNLNNSVTHCVAADN---KGLK-YE--AAKRRG-DVIHYSWVLDCCSQKK--LLQLQPKYYLHLS 745 (1160)
Q Consensus 675 ~eL~klI~~~GG~~v~n~~~~~Th~Ia~~~---~~~K-~~--~a~~~~-~VV~p~WV~dCi~~~~--lLp~~p~~~l~~s 745 (1160)
.++..+=+++||+++. +. ...++-..+. .|.. |. .++... .|.++.||..|.++.. -+++. .|+|++.
T Consensus 14 ~~~~~~Wv~~GG~isd-~~-~AdFLFS~DAshpDT~~iy~S~dY~~d~aTVFha~yl~a~~na~s~~sV~LG-hyVL~~P 90 (212)
T PF15101_consen 14 QDLRQFWVKEGGTISD-WD-AADFLFSCDASHPDTARIYQSLDYIEDRATVFHASYLSAVANAESKNSVALG-HYVLNTP 90 (212)
T ss_pred hHHHHHHHhcCCccCC-hh-hcceeeecCCCCcchHhhhhhhhhhhcCeeeeeHHHHHHHhhhhhcCCcccc-ceEecCC
Confidence 5788999999999987 33 2456665544 3332 22 233444 8999999999998653 34443 4566666
Q ss_pred hh
Q 001083 746 DS 747 (1160)
Q Consensus 746 ~~ 747 (1160)
|+
T Consensus 91 P~ 92 (212)
T PF15101_consen 91 PE 92 (212)
T ss_pred HH
Confidence 65
No 122
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=24.45 E-value=42 Score=24.25 Aligned_cols=13 Identities=54% Similarity=0.871 Sum_probs=8.9
Q ss_pred ccccCCCCCCCcc
Q 001083 971 KRKRGRPAGGSAK 983 (1160)
Q Consensus 971 ~~~~~~~~~~~~~ 983 (1160)
+|+||||+.....
T Consensus 1 kRkRGRPrK~~~~ 13 (26)
T smart00384 1 KRKRGRPRKAPKD 13 (26)
T ss_pred CCCCCCCCCCCCc
Confidence 4788888765543
No 123
>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=23.02 E-value=1.7e+02 Score=33.19 Aligned_cols=67 Identities=19% Similarity=0.217 Sum_probs=49.7
Q ss_pred eeeecCCc--ccccCCHHHHHHHHHHhhccCCCcceeeccCCCCCccccCCCCCccceecCCHHHHHHHHHHHHHcCCce
Q 001083 343 DVLYVGDT--SVIHQSLKERHELLQKVVKPSKGRLETLVPDHGLNSHVRPQGEPCWSLVAHNVDEVEKFFKETIENRDEG 420 (1160)
Q Consensus 343 DiL~lng~--sl~~~pl~eRr~~L~~~v~~~~~~~~i~~p~~~~~~~v~~~~~~~~~~~~~~~~ei~~~~~~ai~~g~EG 420 (1160)
|-++++|. -...++..||+++++.+.....+++.++. .....+.++..++.+.+.+.|..|
T Consensus 36 ~gl~v~GstGE~~~lt~~Er~~l~~~~~~~~~~~~~vi~-----------------gv~~~~~~~~~~~a~~a~~~G~d~ 98 (284)
T cd00950 36 DGLVVCGTTGESPTLSDEEHEAVIEAVVEAVNGRVPVIA-----------------GTGSNNTAEAIELTKRAEKAGADA 98 (284)
T ss_pred CEEEECCCCcchhhCCHHHHHHHHHHHHHHhCCCCcEEe-----------------ccCCccHHHHHHHHHHHHHcCCCE
Confidence 33455553 23578999999999999887776654432 122457789999999999999999
Q ss_pred EEEecC
Q 001083 421 IVLKDL 426 (1160)
Q Consensus 421 lVlK~~ 426 (1160)
+|+=.+
T Consensus 99 v~~~~P 104 (284)
T cd00950 99 ALVVTP 104 (284)
T ss_pred EEEccc
Confidence 999875
Done!