Query 003386
Match_columns 824
No_of_seqs 348 out of 2028
Neff 6.2
Searched_HMMs 46136
Date Thu Mar 28 22:28:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/003386.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/003386hhsearch_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 1.7E-77 3.6E-82 680.7 33.2 509 32-574 344-881 (881)
2 PLN03113 DNA ligase 1; Provisi 100.0 3E-46 6.4E-51 441.6 26.7 243 6-268 459-730 (744)
3 PRK01109 ATP-dependent DNA lig 100.0 4.2E-44 9.1E-49 420.1 24.1 245 2-268 308-582 (590)
4 KOG0967 ATP-dependent DNA liga 100.0 2.7E-44 5.8E-49 402.5 10.8 243 6-268 433-704 (714)
5 PRK03180 ligB ATP-dependent DN 100.0 3.2E-42 7E-47 397.0 24.1 230 3-265 264-506 (508)
6 TIGR00574 dnl1 DNA ligase I, A 100.0 5.8E-42 1.3E-46 397.1 24.2 240 7-265 255-513 (514)
7 PRK09247 ATP-dependent DNA lig 100.0 5.4E-41 1.2E-45 389.5 24.0 232 6-267 288-537 (539)
8 TIGR02779 NHEJ_ligase_lig DNA 100.0 4E-36 8.6E-41 326.4 23.6 205 9-256 77-297 (298)
9 PRK09632 ATP-dependent DNA lig 100.0 4.6E-36 1E-40 354.9 21.2 207 9-256 542-761 (764)
10 PRK05972 ligD ATP-dependent DN 100.0 1.3E-34 2.7E-39 345.7 22.1 212 6-258 312-538 (860)
11 TIGR02776 NHEJ_ligase_prk DNA 100.0 1.2E-34 2.5E-39 335.4 20.6 206 9-257 40-259 (552)
12 COG1793 CDC9 ATP-dependent DNA 100.0 1.3E-33 2.8E-38 320.1 19.3 228 8-265 198-443 (444)
13 PRK08224 ligC ATP-dependent DN 100.0 2.8E-33 6.1E-38 309.1 21.1 216 10-257 89-331 (350)
14 PRK09633 ligD ATP-dependent DN 100.0 4.7E-32 1E-36 316.9 21.9 208 9-265 86-317 (610)
15 cd07967 OBF_DNA_ligase_III The 100.0 1.4E-31 3.1E-36 259.0 14.5 137 114-260 2-139 (139)
16 PHA02587 30 DNA ligase; Provis 100.0 2.5E-29 5.4E-34 289.2 20.7 215 13-262 241-484 (488)
17 cd07968 OBF_DNA_ligase_IV The 100.0 6.6E-29 1.4E-33 241.4 14.0 139 114-258 1-140 (140)
18 PRK07636 ligB ATP-dependent DN 100.0 1.4E-27 3.1E-32 256.4 19.9 181 10-247 81-274 (275)
19 cd07969 OBF_DNA_ligase_I The O 99.9 6.1E-27 1.3E-31 228.5 15.5 134 114-266 1-143 (144)
20 PRK09125 DNA ligase; Provision 99.9 1.1E-25 2.3E-30 242.6 18.9 176 9-249 94-281 (282)
21 cd07972 OBF_DNA_ligase_Arch_Li 99.9 2E-25 4.3E-30 212.2 14.3 121 115-262 1-121 (122)
22 cd07893 OBF_DNA_ligase The Oli 99.9 9.5E-25 2.1E-29 209.4 14.7 122 115-255 1-129 (129)
23 PHA00454 ATP-dependent DNA lig 99.9 7.2E-24 1.6E-28 232.1 19.7 189 10-248 99-314 (315)
24 cd07971 OBF_DNA_ligase_LigD Th 99.8 1.6E-20 3.4E-25 176.8 13.7 113 116-255 2-115 (115)
25 PF04679 DNA_ligase_A_C: ATP d 99.8 2.9E-19 6.3E-24 163.2 9.6 97 131-250 1-97 (97)
26 cd08040 OBF_DNA_ligase_family 99.8 1.2E-18 2.5E-23 162.3 13.0 108 115-247 1-108 (108)
27 cd07970 OBF_DNA_ligase_LigC Th 99.8 9.5E-18 2.1E-22 159.5 13.7 121 115-257 1-122 (122)
28 cd07900 Adenylation_DNA_ligase 99.6 3.5E-16 7.5E-21 163.3 9.8 101 7-110 100-219 (219)
29 cd07897 Adenylation_DNA_ligase 99.6 4.2E-15 9.1E-20 153.9 10.6 103 7-110 86-206 (207)
30 cd08039 Adenylation_DNA_ligase 99.6 3.1E-15 6.7E-20 157.6 8.6 104 7-110 100-235 (235)
31 cd07901 Adenylation_DNA_ligase 99.6 8.4E-15 1.8E-19 151.6 10.3 102 6-109 89-207 (207)
32 cd07898 Adenylation_DNA_ligase 99.5 1.8E-14 3.9E-19 148.3 10.5 100 9-109 85-201 (201)
33 cd07902 Adenylation_DNA_ligase 99.5 1.6E-14 3.5E-19 150.2 8.8 96 6-110 101-213 (213)
34 cd07903 Adenylation_DNA_ligase 99.5 2.5E-14 5.5E-19 149.7 8.4 100 8-111 108-224 (225)
35 cd07905 Adenylation_DNA_ligase 99.5 9E-14 2E-18 142.5 8.6 100 7-109 79-193 (194)
36 cd07906 Adenylation_DNA_ligase 99.4 1.7E-13 3.6E-18 140.0 8.9 97 9-109 81-190 (190)
37 cd07896 Adenylation_kDNA_ligas 99.4 7.9E-13 1.7E-17 133.1 9.8 95 10-108 68-174 (174)
38 PF01068 DNA_ligase_A_M: ATP d 99.3 1.8E-12 3.9E-17 132.8 7.6 99 7-107 87-202 (202)
39 PF00533 BRCT: BRCA1 C Terminu 99.3 1.7E-11 3.6E-16 105.8 8.4 74 318-392 2-78 (78)
40 smart00292 BRCT breast cancer 99.1 3.6E-10 7.8E-15 96.2 8.4 76 320-395 1-80 (80)
41 cd08041 OBF_kDNA_ligase_like T 99.0 1.5E-09 3.3E-14 95.1 8.1 76 116-247 2-77 (77)
42 cd06846 Adenylation_DNA_ligase 98.9 1.4E-09 3E-14 110.3 7.2 75 33-108 86-182 (182)
43 cd00027 BRCT Breast Cancer Sup 98.9 3.5E-09 7.6E-14 88.1 7.9 70 324-393 1-72 (72)
44 KOG1929 Nucleotide excision re 98.9 5.1E-09 1.1E-13 125.5 12.1 183 319-578 7-191 (811)
45 PF00533 BRCT: BRCA1 C Terminu 98.8 1.3E-08 2.8E-13 87.8 7.3 75 465-562 3-78 (78)
46 KOG3524 Predicted guanine nucl 98.7 2.2E-08 4.8E-13 115.3 8.7 182 318-578 115-296 (850)
47 smart00292 BRCT breast cancer 98.7 6.2E-08 1.4E-12 82.3 7.1 77 467-565 2-80 (80)
48 KOG3226 DNA repair protein [Re 98.6 2.3E-08 4.9E-13 107.9 4.6 92 316-409 312-404 (508)
49 PF12738 PTCB-BRCT: twin BRCT 98.6 5.9E-08 1.3E-12 81.4 4.9 62 325-387 1-63 (63)
50 cd07895 Adenylation_mRNA_cappi 98.5 1.1E-07 2.4E-12 99.1 6.1 75 33-108 109-215 (215)
51 cd00027 BRCT Breast Cancer Sup 98.4 8.8E-07 1.9E-11 73.5 7.6 71 470-563 1-72 (72)
52 KOG3548 DNA damage checkpoint 98.3 2.1E-06 4.5E-11 101.9 9.0 88 319-409 923-1038(1176)
53 PF11411 DNA_ligase_IV: DNA li 98.2 1.4E-06 2.9E-11 64.5 3.1 35 411-445 1-35 (36)
54 KOG2481 Protein required for n 98.2 1.2E-06 2.7E-11 98.6 4.0 79 319-403 325-413 (570)
55 KOG2481 Protein required for n 98.1 2.9E-06 6.3E-11 95.7 4.9 82 465-577 325-417 (570)
56 KOG1929 Nucleotide excision re 98.0 1.8E-05 3.9E-10 95.6 9.3 176 319-522 101-284 (811)
57 COG5163 NOP7 Protein required 97.9 6.8E-06 1.5E-10 89.8 3.2 79 319-403 348-437 (591)
58 PLN03122 Poly [ADP-ribose] pol 97.8 4.5E-05 9.7E-10 92.8 8.6 87 318-406 186-278 (815)
59 COG5163 NOP7 Protein required 97.7 5.4E-05 1.2E-09 83.0 5.6 105 465-600 348-464 (591)
60 PF14743 DNA_ligase_OB_2: DNA 97.6 6.1E-05 1.3E-09 64.3 3.6 65 127-247 2-66 (66)
61 PF12738 PTCB-BRCT: twin BRCT 97.6 3.4E-05 7.4E-10 64.6 1.9 62 471-557 1-63 (63)
62 cd07894 Adenylation_RNA_ligase 97.3 0.00021 4.5E-09 79.8 4.5 77 34-110 125-218 (342)
63 KOG3226 DNA repair protein [Re 97.2 0.00067 1.5E-08 74.2 7.0 88 466-578 316-404 (508)
64 PLN03123 poly [ADP-ribose] pol 97.1 0.001 2.2E-08 83.0 8.0 86 317-403 389-478 (981)
65 KOG4362 Transcriptional regula 96.9 0.0031 6.8E-08 74.9 9.4 194 320-567 473-680 (684)
66 PRK14350 ligA NAD-dependent DN 96.4 0.0074 1.6E-07 73.0 8.2 74 319-392 591-665 (669)
67 PRK07956 ligA NAD-dependent DN 96.3 0.0092 2E-07 72.3 8.3 74 321-394 590-664 (665)
68 PLN03122 Poly [ADP-ribose] pol 96.3 0.0067 1.5E-07 74.4 6.9 92 465-576 187-278 (815)
69 PRK14351 ligA NAD-dependent DN 96.2 0.013 2.8E-07 71.3 8.5 76 319-394 607-684 (689)
70 PRK06195 DNA polymerase III su 96.0 0.015 3.3E-07 64.2 7.5 75 318-392 217-306 (309)
71 PRK06063 DNA polymerase III su 96.0 0.017 3.6E-07 64.1 7.6 73 319-392 230-305 (313)
72 PLN03123 poly [ADP-ribose] pol 96.0 0.011 2.4E-07 74.0 6.6 90 465-576 391-481 (981)
73 TIGR00575 dnlj DNA ligase, NAD 95.7 0.021 4.6E-07 69.1 7.6 68 319-386 582-650 (652)
74 KOG2093 Translesion DNA polyme 95.6 0.015 3.2E-07 70.2 5.3 89 315-406 41-131 (1016)
75 COG0272 Lig NAD-dependent DNA 95.2 0.045 9.8E-07 65.3 7.7 73 320-392 593-666 (667)
76 COG5275 BRCT domain type II [G 95.0 0.076 1.7E-06 54.8 7.6 80 313-392 148-229 (276)
77 KOG2043 Signaling protein SWIF 93.2 0.19 4.1E-06 62.6 7.6 127 339-514 671-799 (896)
78 KOG2043 Signaling protein SWIF 93.0 0.078 1.7E-06 65.9 3.9 70 496-578 672-741 (896)
79 KOG3548 DNA damage checkpoint 90.9 0.3 6.6E-06 59.6 5.3 36 548-583 1008-1043(1176)
80 KOG0966 ATP-dependent DNA liga 89.2 0.78 1.7E-05 55.6 6.8 89 465-574 631-720 (881)
81 KOG4362 Transcriptional regula 83.3 1.6 3.5E-05 52.7 5.3 83 317-399 583-682 (684)
82 cd09232 Snurportin-1_C C-termi 73.9 2.7 5.9E-05 43.3 3.0 41 68-109 143-186 (186)
83 COG1423 ATP-dependent DNA liga 73.2 4.1 8.9E-05 45.4 4.3 60 34-93 165-237 (382)
84 TIGR01209 RNA ligase, Pab1020 72.2 4.4 9.5E-05 46.0 4.4 61 33-93 156-229 (374)
85 KOG0323 TFIIF-interacting CTD 69.2 2.4 5.3E-05 51.1 1.6 85 318-402 438-527 (635)
86 PRK06195 DNA polymerase III su 67.0 22 0.00048 39.4 8.5 48 466-523 219-267 (309)
87 PRK07956 ligA NAD-dependent DN 54.0 32 0.0007 42.3 7.4 74 467-564 590-664 (665)
88 KOG3524 Predicted guanine nucl 53.7 7.7 0.00017 46.8 2.0 74 320-395 209-283 (850)
89 PRK14350 ligA NAD-dependent DN 53.5 32 0.0007 42.3 7.3 73 466-562 592-665 (669)
90 PF02178 AT_hook: AT hook moti 51.3 6.7 0.00015 23.2 0.5 11 635-645 1-11 (13)
91 KOG0323 TFIIF-interacting CTD 48.5 19 0.00042 43.6 4.3 96 465-580 439-535 (635)
92 PRK14351 ligA NAD-dependent DN 48.3 46 0.00099 41.2 7.5 77 465-564 607-684 (689)
93 TIGR00575 dnlj DNA ligase, NAD 41.2 49 0.0011 40.7 6.3 50 466-525 583-633 (652)
94 PRK06063 DNA polymerase III su 36.5 1E+02 0.0022 34.4 7.4 49 465-524 230-279 (313)
95 PHA02142 putative RNA ligase 32.4 50 0.0011 37.7 4.1 71 35-109 270-358 (366)
96 KOG2093 Translesion DNA polyme 30.5 46 0.001 41.5 3.6 90 464-580 44-135 (1016)
97 COG0272 Lig NAD-dependent DNA 28.9 1.3E+02 0.0029 36.8 7.0 71 466-560 593-664 (667)
98 PF15101 DUF4557: Domain of un 28.2 1.8E+02 0.0038 30.5 6.8 70 339-411 14-92 (212)
99 smart00384 AT_hook DNA binding 26.1 38 0.00083 23.8 1.1 12 635-646 1-12 (26)
No 1
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=100.00 E-value=1.7e-77 Score=680.70 Aligned_cols=509 Identities=35% Similarity=0.594 Sum_probs=389.0
Q ss_pred CccEEEEEccHHHH-------------HHHHHHhhcCCCCc----eEEecCCHHHHHHHHHHHHhCCCceEEEeCCCCCC
Q 003386 32 GICVCVHVYMLSQL-------------RSQIMAADQTGEPC----WSLVAHNVDEVEKFFKETIENRDEGIVLKDLGSKW 94 (824)
Q Consensus 32 ~~~v~~~~FDll~l-------------r~~L~~l~~~~~~~----~~~~~~~~~di~~~~~~ai~~g~EGIV~K~~dS~Y 94 (824)
...+||.+||||++ ++.|..++-+.... ....++..++++++|++||++|.||||+|+++|.|
T Consensus 344 ~~qp~yvvfDLLylNgksL~~~~l~qR~e~L~~v~~p~~~~iei~~~~~~~~~edi~~~f~~ai~~~~EGIVlK~~~S~Y 423 (881)
T KOG0966|consen 344 SQQPCYVVFDLLYLNGKSLFGAPLHQRLEILKKVIVPKSGRIEIVRSEVGSTKEDIEQFFEEAIDNGEEGIVLKKPDSSY 423 (881)
T ss_pred CCCceEEEeeeeeecCcccCCccHHHHHHHHHhcccCCCCeeEEeehhhcccHHHHHHHHHHHHhcCCCceEEeccCccc
Confidence 56899999999975 56677777665433 34467889999999999999999999999999999
Q ss_pred cCCCCCCCeEEEcccccc-CCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHH
Q 003386 95 EPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAV 173 (824)
Q Consensus 95 ~pg~Rs~~WiKiK~~y~~-~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L 173 (824)
.||.|+++|||+||+|+. +|+++|++|||||||+|+++|.+.+|+||+.++..++.+|.+|.+||+||+|+|..++..|
T Consensus 424 ~pg~R~~gW~K~KPeYlkg~g~dLD~lIiGgy~G~g~rgg~~~~fl~a~~ek~~p~~~p~~f~sfcrvg~g~s~~e~~~v 503 (881)
T KOG0966|consen 424 VPGQRSNGWIKLKPEYLKGFGEDLDLLIIGGYYGRGDRGGKVLSFLCALAEKAPPNSRPEKFCSFCRVGNGISQKERDTV 503 (881)
T ss_pred CccccCCCcEeecHHHHhhcCccccEEEEecccCCCCCCCeeeeeeehhcccCCCCCccceeeEeeEecCCccHHHHHHH
Confidence 999999999999999999 6999999999999999999999999999999987777889999999999999999999999
Q ss_pred HHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEecCCCcc
Q 003386 174 VTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWH 253 (824)
Q Consensus 174 ~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR~DK~~~ 253 (824)
+.+|++||.++ ..+.+|++|+..+ +..|++||+ |..|+|++|++ .+++.+..|.++|||||||+.++|.||+|+
T Consensus 504 ~~klr~~w~~~-~~~apP~s~l~~t---k~~Pd~wI~-P~~SiIlqika-a~i~~s~~f~tn~tLrfPr~ekvR~DK~W~ 577 (881)
T KOG0966|consen 504 REKLRGHWKPT-SLEAPPESFLFGT---KKIPDVWID-PDNSIILQIKA-AEIVPSSNFVTNYTLRFPRIEKVRLDKPWH 577 (881)
T ss_pred HHhhhhhcccc-cccCCCHHHHhcc---cCCCceeEC-CCCceEEEeeh-heeeecccccccceeecceeeeeecCCcHH
Confidence 99999999982 4444444455443 347999999 99999999995 456789999999999999999999999999
Q ss_pred CcCCHHHHHHHHHhcCCccccccccCCCCCCCCcccccccccccccccccCCccccCCcccccCCCCCccCeEEEEEcCC
Q 003386 254 DCLDVQSFVELVHSSNGTTQKGKEYGGLQDDKPKQFRSSRKGEKKNVSIVPSHFLQTDVSDIKGETSIFSDMVFYFVNVP 333 (824)
Q Consensus 254 e~~t~~el~el~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~~~k~~~~~~~~~~~~~~~s~~~~~s~lF~Gl~FcV~~~~ 333 (824)
||+|+++|.+|...+. ++.+.+. ++++ ...+++++.+.. -+......+.+.+.+++|.|+.|||+++.
T Consensus 578 ec~tl~~l~~l~~~~~-------~d~~~~~-kk~~-~t~~~~k~~~~~---i~~~~~~~~~~~~~s~if~gl~f~Vlsgt 645 (881)
T KOG0966|consen 578 ECLTLNELGDLVNVSK-------SDVEDKE-KKKR-DTLKVRKRTRKA---IHDSAPNRSKVAKISNIFDGLEFCVLSGT 645 (881)
T ss_pred HHhhHHHHHHHhcccc-------CCcchhh-hhcc-cchhhhhhhhhh---hcccccchhcccchhhhhcCeeEEEecCC
Confidence 9999999999985321 1111111 1111 111111111111 12233445567788999999999999875
Q ss_pred -CCCCHHHHHHHHHHcCCEEEecCCCCceEEEE-ecC--CChhHHhHhcCCCeeecchHHHHHhcCccCCCCccccccCC
Q 003386 334 -PAYSLDSLHKMVVENGGTFSMNLNNSVTHCVA-ADN--KGLKYEAAKRRGDVIHYSWVLDCCSQKKLLQLQPKYYLHLS 409 (824)
Q Consensus 334 -~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia-~~~--~t~K~~~a~~~~dIV~p~WV~DCI~~~~lLp~eP~~ll~~S 409 (824)
...++.+|+++|++|||++++|++++.|+||+ ++. .+++++++.+.++||+|+||+||+...+++||.|+++|+++
T Consensus 646 ~~~~tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et~~vk~~~~~~~cdVl~p~Wlldcc~~~~l~p~~P~~~fh~~ 725 (881)
T KOG0966|consen 646 SETHTKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKETTRVKAQAIKRSCDVLKPAWLLDCCKKQRLLPWLPRDLFHAT 725 (881)
T ss_pred cccccHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccchHHHHHHHhccCceeeHHHHHHHHhhhhccccccHHHHhhC
Confidence 46679999999999999999999998999995 333 34566666665699999999999999999999999999999
Q ss_pred hhhHhhhhhhccccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCeEEEEccCCCCCCCchHHH
Q 003386 410 DSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVL 489 (824)
Q Consensus 410 ~~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc~~YL~g~~~~~~~d~~~i 489 (824)
+..++.++..+|+|||||++|++.+.|+.+++.+..+.+............+...+.+|.-|..+|+......+.+
T Consensus 726 e~~~~~~a~~~D~~gdSy~~di~l~~l~~~ls~~k~S~ds~~~~~~~~~~~~e~r~~~~~~~~~~f~~~~~~~~se---- 801 (881)
T KOG0966|consen 726 EKGREKLAKEVDCLGDSYENDIDLEQLKKVLSGIKKSQDSLPPMGASEKDSLERRFSLFLSSLRMFYVLRRKLSSE---- 801 (881)
T ss_pred chHHHHHHHHHhhhcchhhhhccHHHHHHHHhhhhhcccccCchhhhhhhcHHHhhccccccceeeecccccccHH----
Confidence 9999999999999999999999999999999988876654322211111111112222222223333333233322
Q ss_pred HHHHHHHHHHHHHhcCCEEEccCC-------CceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEecccHHHHHH
Q 003386 490 LGLALRRLKLEISFHGGKVCNNLA-------NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCL 562 (824)
Q Consensus 490 ~~~~l~~L~~~I~~~GG~V~~~ls-------~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~~~~IVt~~WLedCi 562 (824)
.......+..+||.+++.-. .+||+|+.... .. .. +.+. ........++ +||.+.||.+|+
T Consensus 802 ----~~~~~l~~k~~g~~i~~~~~~~~~~~~~~t~~v~~~i~-~~--h~--~~~~--~~~~~lt~~r-kv~~~~wv~~s~ 869 (881)
T KOG0966|consen 802 ----EVIIELKLKNFGGRITDAQSECNNIGAKYTHCVLRCID-ED--HE--KIKE--QKKASLTIKR-KVVAPSWVDHSI 869 (881)
T ss_pred ----HHHHHHHHHHhcceeeeccchhhhcccceeeeeeeecc-hH--HH--HHHH--HHHHHhcccc-cccCHHHHHHhh
Confidence 23445678889999987553 37999986322 11 11 1111 1111122344 999999999999
Q ss_pred HhCCccCCCCCC
Q 003386 563 AKEQKSEEYEYS 574 (824)
Q Consensus 563 ~~g~~l~Ee~Y~ 574 (824)
.++.++||++|.
T Consensus 870 ~~~~~~~e~~~~ 881 (881)
T KOG0966|consen 870 NENCLLPEEDFP 881 (881)
T ss_pred cccccCccccCC
Confidence 999999999995
No 2
>PLN03113 DNA ligase 1; Provisional
Probab=100.00 E-value=3e-46 Score=441.60 Aligned_cols=243 Identities=26% Similarity=0.537 Sum_probs=207.0
Q ss_pred cccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEEe----cCCHH
Q 003386 6 FAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSLV----AHNVD 68 (824)
Q Consensus 6 ~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~~----~~~~~ 68 (824)
.++++|||.|++|.++... .. +.++|+||||||||+ ||++|++++.+..+.+++. .++.+
T Consensus 459 ~~~~lpFq~Lq~R~rk~~~-~~--~~~~pv~~~aFDlLylnG~~L~~~PL~eRR~~L~~~~~~~~~~i~~~~~~~~~~~e 535 (744)
T PLN03113 459 KKKILPFQILSTRARKNVV-MS--DIKVDVCIFAFDMLYLNGQPLIQEQLKIRREHLYESFEEDPGFFQFATAITSNDLE 535 (744)
T ss_pred CCCcCCHHHHHhhhccccc-hh--ccccceEEEEEeccccCccChhcCCHHHHHHHHHHHhccCCCcEEEeeeeccCCHH
Confidence 3668999999999766544 33 236899999999985 4889999997654455553 35688
Q ss_pred HHHHHHHHHHhCCCceEEEeCC--CCCCcCCCCCCCeEEEcccccc-CCCcccEEEEEEEeCCCCCCCCcceEEEEEecC
Q 003386 69 EVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSGRRGGEVAQFLVALAER 145 (824)
Q Consensus 69 di~~~~~~ai~~g~EGIV~K~~--dS~Y~pg~Rs~~WiKiK~~y~~-~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~ 145 (824)
++.++|++++++|+||||+|++ +|+|.||+|+.+|+|+|++|++ .|+++|+||||||+|+|+|.|.+|+||||||++
T Consensus 536 e~~~~~~~ai~~g~EGlmvK~l~~dS~Y~pGkRs~~WlKlK~dy~~~~~dtlDlVvIGa~~G~GkR~g~~g~fLla~yd~ 615 (744)
T PLN03113 536 EIQKFLDAAVDASCEGLIIKTLNKDATYEPSKRSNNWLKLKKDYMESIGDSLDLVPIAAFHGRGKRTGVYGAFLLACYDS 615 (744)
T ss_pred HHHHHHHHHHHcCCceEEEeccCCCCCccCCCCCCCeEEEechhhccccccccEEEEEEEeCCCCcCCccceEEEEEEcC
Confidence 9999999999999999999986 8999999999999999999999 489999999999999999999999999999986
Q ss_pred CCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEeccc
Q 003386 146 PAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIR 225 (824)
Q Consensus 146 ~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~ 225 (824)
++ +.|++||+||||||++++++|...|++++++ .||.|+..+ ...+|++||+ |. .|+||+++..
T Consensus 616 ~~-----~~~~~v~KvgTGfsd~~l~~l~~~L~~~~~~------~~~~~~~~~--~~~~pdvwve-P~--~V~EV~~aei 679 (744)
T PLN03113 616 NK-----EEFQSICKIGTGFSEAVLEERSASLRSQVIP------TPKSYYRYG--DSIKPDVWFE-PT--EVWEVKAADL 679 (744)
T ss_pred CC-----CEEEEeeEECCCCCHHHHHHHHHHHHHhccc------CCCcccccC--CCCCCcEEEC-Cc--eEEEEEeeee
Confidence 43 3899999999999999999999999998875 244465443 2457999999 97 5999997543
Q ss_pred cccccccc---------CCceeeccEEeeEecCCCccCcCCHHHHHHHHHhc
Q 003386 226 TIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 268 (824)
Q Consensus 226 ~~~s~~~~---------~g~tLRfPr~~~iR~DK~~~e~~t~~el~el~~~~ 268 (824)
..|..|+ .|++||||||.++|+||+|+||+|++++.+|++++
T Consensus 680 -t~Sp~h~a~~g~~~~~~G~sLRFPRf~riR~DK~~~datt~~~l~~ly~~Q 730 (744)
T PLN03113 680 -TISPVHRAAVGIVDPDKGISLRFPRLVRVREDKSPEQATSSEQVADMYNAQ 730 (744)
T ss_pred -ccCcccccccccccCCCCeEEECCEEEEEECCCChHHCCCHHHHHHHHHHH
Confidence 3577887 48899999999999999999999999999999754
No 3
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=100.00 E-value=4.2e-44 Score=420.11 Aligned_cols=245 Identities=29% Similarity=0.529 Sum_probs=206.9
Q ss_pred ccc-ccccccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEE----e
Q 003386 2 VFE-LFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSL----V 63 (824)
Q Consensus 2 ~~~-~~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~----~ 63 (824)
++| --|+++|||.|++|.++..+ .. +...+|+||+||||| +||++|++++.+.. .+.+ .
T Consensus 308 ~~d~~~g~~~~F~~l~~R~r~~~~-~~-~~~~~p~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~-~~~~~~~~~ 384 (590)
T PRK01109 308 AVDPETGEMRPFQELMHRKRKYDI-EE-AIKEYPVNVFLFDLLYVDGEDLTDKPLPERRKKLEEIVKEND-KVKLAERII 384 (590)
T ss_pred EEECCCCcccChHHHhhcccccch-hh-hcccCceEEEEEEEEEECCcchhhCcHHHHHHHHHHhcCCCC-ceEEeeeEe
Confidence 344 35788999999999544433 33 334789999999987 45899999997643 3433 4
Q ss_pred cCCHHHHHHHHHHHHhCCCceEEEeCC--CCCCcCCCCCCCeEEEcccccc-CCCcccEEEEEEEeCCCCCCCCcceEEE
Q 003386 64 AHNVDEVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSGRRGGEVAQFLV 140 (824)
Q Consensus 64 ~~~~~di~~~~~~ai~~g~EGIV~K~~--dS~Y~pg~Rs~~WiKiK~~y~~-~ge~lDlvVIGG~~g~Grr~g~~~sfll 140 (824)
.++.+++.++|+.++++|+||||+|++ +|+|.||+|+.+|+|+|++|++ .++++|+||||+|+|+|+|+|.+|+|||
T Consensus 385 ~~~~~~~~~~~~~a~~~g~EGiv~K~~~~ds~Y~~g~Rs~~WlK~K~dy~~~~~~~~DlvviG~~~g~Gkr~~~~g~~ll 464 (590)
T PRK01109 385 TDDVEELEKFFHRAIEEGCEGLMAKSLGKDSIYQAGARGWLWIKYKRDYQSEMADTVDLVVVGAFYGRGRRGGKYGSLLM 464 (590)
T ss_pred cCCHHHHHHHHHHHHHcCCceEEEecCCCCCCcCCCCCCccHHHhhHHhhcccCCceeEEEEEeEeCCCccCCccccEEE
Confidence 567789999999999999999999999 9999999999999999999999 5899999999999999999999999999
Q ss_pred EEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEE
Q 003386 141 ALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSI 220 (824)
Q Consensus 141 Gv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEV 220 (824)
|+|++++ +.|++||+||||||++++++|...|++++.+. .|| +.. ...+|++||+ |. +|+||
T Consensus 465 ~~~d~~~-----~~~~~v~kvgtG~sd~~~~~l~~~l~~~~~~~-----~~~-~~~----~~~~pdvwv~-P~--~V~eV 526 (590)
T PRK01109 465 AAYDPKT-----DTFETVCKVGSGFTDEDLDELPKMLKPYKIDH-----KHP-RVV----SKMEPDVWVE-PK--LVAEI 526 (590)
T ss_pred EEEcCCC-----CeEEEEEEECCCCCHHHHHHHHHHhhhhcccC-----CCc-ccc----cccCCcEEEe-cc--EEEEE
Confidence 9997543 38999999999999999999999999998761 234 321 3468999999 95 79999
Q ss_pred Eeccccccccccc---------CCceeeccEEeeEecCCCccCcCCHHHHHHHHHhc
Q 003386 221 TSDIRTIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 268 (824)
Q Consensus 221 ka~~~~~~s~~~~---------~g~tLRfPr~~~iR~DK~~~e~~t~~el~el~~~~ 268 (824)
+++.. ..|..|+ .|++||||||+++|+||+|+||+|++++.+|+.++
T Consensus 527 ~~~~i-t~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q 582 (590)
T PRK01109 527 IGAEI-TLSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQ 582 (590)
T ss_pred Eeeec-ccCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHh
Confidence 97644 3577787 68899999999999999999999999999999744
No 4
>KOG0967 consensus ATP-dependent DNA ligase I [Replication, recombination and repair]
Probab=100.00 E-value=2.7e-44 Score=402.47 Aligned_cols=243 Identities=30% Similarity=0.580 Sum_probs=209.7
Q ss_pred cccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEE----ecCCHH
Q 003386 6 FAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSL----VAHNVD 68 (824)
Q Consensus 6 ~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~----~~~~~~ 68 (824)
.|+|+|||+|++|++++++ .. +++|.||+|+||+++ ||+.|.+.+....+.+++ ...+.+
T Consensus 433 ~~~IlpFQvLSTRkRk~v~-v~--dikV~Vcvf~FDily~ng~~Li~~pL~eRR~~l~e~f~e~~g~f~fat~~~tn~~~ 509 (714)
T KOG0967|consen 433 KGKILPFQVLSTRKRKNVD-VN--DIKVKVCVFVFDILYLNGESLIQEPLRERRELLHESFKEIPGEFQFATSLDTNDID 509 (714)
T ss_pred CCccCchhhhhhhhccccc-hh--hceEEEEEEEEeeeeeCChhhhhhhHHHHHHHHHhhcccCCCceeEeeeeccCCHH
Confidence 3599999999999999988 33 459999999999764 478888888877655544 456789
Q ss_pred HHHHHHHHHHhCCCceEEEeCC--CCCCcCCCCCCCeEEEccccccC-CCcccEEEEEEEeCCCCCCCCcceEEEEEecC
Q 003386 69 EVEKFFKETIENRDEGIVLKDL--GSKWEPGDRSGKWLKLKPEYIRA-GSDLDVLIIGGYYGSGRRGGEVAQFLVALAER 145 (824)
Q Consensus 69 di~~~~~~ai~~g~EGIV~K~~--dS~Y~pg~Rs~~WiKiK~~y~~~-ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~ 145 (824)
+++.||++++.+++||+|+|-+ ++.|+|.+||.+|+|+|.+|+++ |+++||||||+|||+|+|.|.+|.||+|||++
T Consensus 510 eiq~Fl~~sv~~~cEGlMvKtLd~~atYep~kRs~~WlKlKkDYldgvgdslDLv~iga~~G~GrrtG~yg~fLlacyn~ 589 (714)
T KOG0967|consen 510 EIQEFLEESVQNSCEGLMVKTLDTNATYEPSKRSNNWLKLKKDYLDGVGDSLDLVVIGAYYGRGRRTGWYGGFLLACYNP 589 (714)
T ss_pred HHHHHHHHhhccCcceeEEEeeccccccCchhhccchhhhhhhhhcccccceeeeeeeeeeccccccccccceeEEeecC
Confidence 9999999999999999999977 57999999999999999999996 99999999999999999999999999999998
Q ss_pred CCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEeccc
Q 003386 146 PAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIR 225 (824)
Q Consensus 146 ~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~ 225 (824)
+. +.|.++||+|||||++++.++...|...... .|+.+|.+. ...+||+|++ |.. |+||+|+..
T Consensus 590 dt-----eefqsiCKigtGFsD~~l~e~~~~l~~~~~~------~~~~~y~~d--~s~kPd~wf~-p~~--VwEvk~Adl 653 (714)
T KOG0967|consen 590 DT-----EEFQSICKIGTGFSDEFLQELHESLSSTVID------SPKPYYRFD--ESLKPDVWFE-PTE--VWEVKAADL 653 (714)
T ss_pred ch-----HHHHHHHhhcCCCCHHHHHHHHHHhhhcccc------CcHhhcccC--ccCCCccccC-HHH--HHHHhhccc
Confidence 75 4899999999999999999999988765443 355577775 3467999998 984 799997544
Q ss_pred cccccccc---------CCceeeccEEeeEecCCCccCcCCHHHHHHHHHhc
Q 003386 226 TIRSEVFS---------APYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHSS 268 (824)
Q Consensus 226 ~~~s~~~~---------~g~tLRfPr~~~iR~DK~~~e~~t~~el~el~~~~ 268 (824)
++ |+.|. .|.+||||||.|+|+||.+++|+|-+++.+|++++
T Consensus 654 t~-SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~peeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 654 TL-SPIYKAALGLVDPDKGISLRFPRFIRIRDDKNPEEATTSSQIAEMYQAQ 704 (714)
T ss_pred cc-cchhHhhhcCcCCCCceeEecceeeEeeccCChhhcccHHHHHHHHHHH
Confidence 43 66654 37899999999999999999999999999999765
No 5
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=3.2e-42 Score=396.95 Aligned_cols=230 Identities=20% Similarity=0.299 Sum_probs=196.9
Q ss_pred ccccccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEEecCCHHH
Q 003386 3 FELFAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSLVAHNVDE 69 (824)
Q Consensus 3 ~~~~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~~~~~~~d 69 (824)
+|-.|+++|||.+++|.+++... ..+...+|++|++||||+ ||++|++++.+......+..++.++
T Consensus 264 ~d~~g~~~~F~~l~~R~~~k~~~-~~~~~~~pv~~~~FDlL~l~G~dl~~~pl~eRr~~L~~~~~~~~~~~~~~~~~~~~ 342 (508)
T PRK03180 264 LRPDGRPRPFQVTASRFGRRVDV-AAARATQPLSPFFFDALHLDGRDLLDAPLSERLAALDALVPAAHRVPRLVTADPAA 342 (508)
T ss_pred ECCCCCcCCHHHHHHHhccccch-hhhcccCceEEEEEeehhcCCcchhcCCHHHHHHHHHHhhcccccccceecCCHHH
Confidence 34457889999999998776653 334457899999999985 4888999986422222455677899
Q ss_pred HHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCC
Q 003386 70 VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPD 149 (824)
Q Consensus 70 i~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~ 149 (824)
+.++|+.++++|.||||+|+++|+|.||+|+.+|+|+|+.+ ++|+||||+++|+|+|+|.+|+|+||+|++++
T Consensus 343 ~~~~~~~a~~~g~EGlm~K~~ds~Y~~GrR~~~WlK~K~~~-----t~D~VviG~~~G~Gkr~g~~~~~llg~~d~~~-- 415 (508)
T PRK03180 343 AAAFLAAALAAGHEGVMVKSLDAPYAAGRRGAGWLKVKPVH-----TLDLVVLAAEWGSGRRTGKLSNLHLGARDPAT-- 415 (508)
T ss_pred HHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCcEEEcCCC-----ceEEEEEeeecCCCCCCCCccceEEEEEeCCC--
Confidence 99999999999999999999999999999999999999976 99999999999999999999999999997543
Q ss_pred CCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEeccccccc
Q 003386 150 TYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRS 229 (824)
Q Consensus 150 ~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s 229 (824)
+.|++||+||||||++++++|...+.++... ...|++||+ |. +|+||+++.. ..|
T Consensus 416 ---~~l~~vgkv~sG~td~~l~~l~~~l~~~~~~------------------~~~~~vwv~-P~--~V~EV~~~~i-t~S 470 (508)
T PRK03180 416 ---GGFVMLGKTFKGMTDAMLAWQTERFLELAVG------------------RDGWTVYVR-PE--LVVEIAFDGV-QRS 470 (508)
T ss_pred ---CeEEEecCccCCCCHHHHHHHHHHHHhhccC------------------CCCCCEEee-CC--EEEEEEeeEe-eeC
Confidence 3899999999999999999999888765332 135799999 98 5899997643 468
Q ss_pred ccccCCceeeccEEeeEecCCCccCcCCHHHHHHHH
Q 003386 230 EVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 265 (824)
Q Consensus 230 ~~~~~g~tLRfPr~~~iR~DK~~~e~~t~~el~el~ 265 (824)
+.|++|++||||||.++|+||+|+||+|++++.+|+
T Consensus 471 ~~~~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~ 506 (508)
T PRK03180 471 TRYPGGVALRFARVLRYRPDKTPAEADTIDTVRALL 506 (508)
T ss_pred CcccCCeEEECCeeeEeeCCCChHHCcCHHHHHHHh
Confidence 889999999999999999999999999999999998
No 6
>TIGR00574 dnl1 DNA ligase I, ATP-dependent (dnl1). All proteins in this family with known functions are ATP-dependent DNA ligases. Functions include DNA repair, DNA replication, and DNA recombination (or any process requiring ligation of two single-stranded DNA sections). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=100.00 E-value=5.8e-42 Score=397.14 Aligned_cols=240 Identities=34% Similarity=0.619 Sum_probs=203.7
Q ss_pred ccccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEE----ecCCHHH
Q 003386 7 AQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSL----VAHNVDE 69 (824)
Q Consensus 7 ~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~----~~~~~~d 69 (824)
|+++|||.|++|.++..+ ......+++|||+||+| +||++|.+++.+..+.+.+ .+++.++
T Consensus 255 g~~~~F~~l~~r~~~~~~--~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~~~~~~e~ 332 (514)
T TIGR00574 255 GKILPFQTLLRRKRRYDI--DSMEKKVPVCLFVFDILYLNGESLIDEPLIERREILESILKPIPNRIEIAEMKITSNVEE 332 (514)
T ss_pred CCCcCcHhHHhhhhhccc--cccccccceEEEEEEEEEECCcchhcCcHHHHHHHHHHhccCCCCcEEEEEEEecCCHHH
Confidence 788999999999876322 22334789999999976 4588999999775445433 4567899
Q ss_pred HHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEcccccc-CCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCC
Q 003386 70 VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIR-AGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP 148 (824)
Q Consensus 70 i~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~-~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~ 148 (824)
+.++|++++++|.||||+|+++|+|.||+|+.+|+|+|++|++ +++++|++|||||+|.|+++|.+|+|+||++++..
T Consensus 333 ~~~~~~~~~~~g~EGlv~K~~ds~Y~~G~Rs~~WlK~K~~y~~~~~~~~D~vvig~~~g~gk~~g~~~~~l~g~~d~~~- 411 (514)
T TIGR00574 333 LEKFLNEAISEGCEGLMLKDLKSIYEPGKRGWLWLKFKPEYLEGMGDTLDLVVIGAYYGKGKRTGMYGSFLLACYDPES- 411 (514)
T ss_pred HHHHHHHHHHcCCceEEEecCCCcccCCCCCCcceeCchhhcccccCceeEEEEeeEecCCccCCceeEEEEEEEcCCC-
Confidence 9999999999999999999999999999999999999999999 57999999999999999999999999999997642
Q ss_pred CCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccc
Q 003386 149 DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIR 228 (824)
Q Consensus 149 ~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~ 228 (824)
++|+++|+||+|||++++++|.+++.++|... .+. .+|.+ ....|++|++ |. +|+||+++.. ..
T Consensus 412 ----~~~~~v~kvgsG~sd~~l~~l~~~l~~~~~~~-~~~-~~~~~------~~~~~~~w~~-p~--~V~eV~~~e~-t~ 475 (514)
T TIGR00574 412 ----EEFKTITKVGTGFTDADLQELGKKLPPLWIDP-PGS-RVPSI------LSDEPDIWFD-PA--IVWEVTGAEI-TR 475 (514)
T ss_pred ----CeEEEEEEECCCCCHHHHHHHHHhccCcEecC-CCC-CCccc------ccCCCeEEec-CC--eEEEEEhhhe-ee
Confidence 38999999999999999999999999999862 111 11211 1357899998 96 6899997644 46
Q ss_pred cccccC-CceeeccEEeeEecCCCccCcCCHHHHHHHH
Q 003386 229 SEVFSA-PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 265 (824)
Q Consensus 229 s~~~~~-g~tLRfPr~~~iR~DK~~~e~~t~~el~el~ 265 (824)
|..|++ |++||||||.++|+||+|+||+|++++.+|+
T Consensus 476 s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly 513 (514)
T TIGR00574 476 SPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELY 513 (514)
T ss_pred cCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHh
Confidence 888888 9999999999999999999999999999997
No 7
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=100.00 E-value=5.4e-41 Score=389.55 Aligned_cols=232 Identities=22% Similarity=0.334 Sum_probs=196.0
Q ss_pred cccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCC-CceEE----ecCCH
Q 003386 6 FAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGE-PCWSL----VAHNV 67 (824)
Q Consensus 6 ~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~-~~~~~----~~~~~ 67 (824)
.++++|||.|++|.+++..+.. +...+|+||++||+|+ ||++|++++.... +.+.+ ..++.
T Consensus 288 ~~~~~~F~~l~~R~~rk~~~~~-~~~~~pv~~~vFDiL~l~g~~l~~~Pl~eRr~~L~~~~~~~~~~~i~~~~~~~~~~~ 366 (539)
T PRK09247 288 DGRPQPFADLQQRIGRKTVGKK-LLADYPAFLRAYDLLEDGGEDLRALPLAERRARLEALIARLPDPRLDLSPLVPFSDW 366 (539)
T ss_pred CCCcCCHHHHHHHhcccccchh-hhhcCCeEEEEEEeeeeCCcchhhCCHHHHHHHHHHHhcccCCCeEEecCceecCCH
Confidence 4688999999999766655333 3347899999999874 5889999996642 24433 35678
Q ss_pred HHHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCC
Q 003386 68 DEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPA 147 (824)
Q Consensus 68 ~di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~ 147 (824)
+++.++|++++++|+||||+|+++|+|.||+|+..|+|+|++|. ++|+||||||+|+|+|+|.+|+|+||||++++
T Consensus 367 ~e~~~~~~~a~~~g~EGlm~K~~~s~Y~~Grr~~~WlK~K~~~~----t~DlVvig~~~G~Gkr~g~~~~~lla~~~~~~ 442 (539)
T PRK09247 367 DELAALRAAARERGVEGLMLKRRDSPYLVGRKKGPWWKWKRDPL----TIDAVLMYAQRGHGRRASLYTDYTFGVWDGPE 442 (539)
T ss_pred HHHHHHHHHHHHCCCceEEEecCCCCcCCCCCcchhhcccCCCC----cEEEEEEEeecCCCCcCCccccEEEEEEcCCC
Confidence 89999999999999999999999999999999999999999973 89999999999999999999999999997652
Q ss_pred CCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEeccccc
Q 003386 148 PDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTI 227 (824)
Q Consensus 148 ~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~ 227 (824)
+ ...|++|||||||||++++++|...++++... ...|++||+ |. +|+||+++.. .
T Consensus 443 ~---~~~~~~v~kvgsGftd~~l~~l~~~l~~~~~~------------------~~~~~~~v~-P~--~V~EV~~~ei-t 497 (539)
T PRK09247 443 G---GRQLVPFAKAYSGLTDEEIKQLDRWVRKNTVE------------------RFGPVRSVR-PE--LVFEIAFEGI-Q 497 (539)
T ss_pred C---ceeEEEEEEECCCCCHHHHHHHHHHHhhcccc------------------cCCCceEec-Cc--eEEEEEecee-e
Confidence 1 13699999999999999999999877654321 125789998 97 6899998543 4
Q ss_pred ccccccCCceeeccEEeeEecCCCccCcCCHHHHHHHHHh
Q 003386 228 RSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELVHS 267 (824)
Q Consensus 228 ~s~~~~~g~tLRfPr~~~iR~DK~~~e~~t~~el~el~~~ 267 (824)
.|..|++|++||||||.++|+||+|+||+|++++.+|+..
T Consensus 498 ~S~~~~~G~~LRfPr~~~~R~DK~~~ea~t~~~l~~l~~~ 537 (539)
T PRK09247 498 RSKRHKSGIAVRFPRILRWRWDKPAREADTLETLQALLDA 537 (539)
T ss_pred ecCCcCCCcEEEcceEEEEeCCCChHHCcCHHHHHHHHhc
Confidence 6888999999999999999999999999999999999953
No 8
>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=4e-36 Score=326.40 Aligned_cols=205 Identities=23% Similarity=0.263 Sum_probs=169.2
Q ss_pred ccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCc--eEE-ecCCHHHHHH
Q 003386 9 LMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPC--WSL-VAHNVDEVEK 72 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~--~~~-~~~~~~di~~ 72 (824)
..+||.|++|.+... ..+++|++||||+ ||++|++++...... +.. ..++.+++.+
T Consensus 77 ~~~F~~l~~r~~~~~--------~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~~~~~~~~~~~~ 148 (298)
T TIGR02779 77 RSDFSALQNRLRAGR--------DRPATYYAFDLLYLDGEDLRDLPLSERKKLLEELLKAIKGPLAPDRYSVHFEGDGQA 148 (298)
T ss_pred CCCHHHHHhhhhcCC--------CCceEEEEEeeeeECceehhcCCHHHHHHHHHHHhcccCCCceeEecccCchhHHHH
Confidence 359999999876542 3699999999874 588999998764322 232 4678899999
Q ss_pred HHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCC
Q 003386 73 FFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYP 152 (824)
Q Consensus 73 ~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~ 152 (824)
+|+.++++|+||||+|+++|+|.|| |+.+|+|+|+++ +.|++|+|.+.|.|++ |.+|+|+||+++++
T Consensus 149 ~~~~~~~~g~EGiv~K~~ds~Y~~G-rs~~WlK~K~~~-----~~d~vV~G~~~g~g~~-~~~gslll~~~~~~------ 215 (298)
T TIGR02779 149 LLEAACRLGLEGVVAKRRDSPYRSG-RSADWLKLKCRR-----RQEFVIGGYTPPNGSR-SGFGALLLGVYEGG------ 215 (298)
T ss_pred HHHHHHHcCCceEEEeCCCCCCCCC-CCCCcEEEccCC-----CCEEEEEEEECCCCCC-CccceEEEEEECCC------
Confidence 9999999999999999999999999 599999999998 7886555544588887 77999999999653
Q ss_pred ccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccc
Q 003386 153 RRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVF 232 (824)
Q Consensus 153 ~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~ 232 (824)
.|+++|+||||||++++++|..+|.+++++. .|| +. ....+++||+ |. +|+||+ +.++
T Consensus 216 -~l~~vg~vgsG~s~~~~~~l~~~l~~~~~~~-----~~~-~~-----~~~~~~~wv~-P~--lV~eV~-------~~~~ 273 (298)
T TIGR02779 216 -GLRYVGRVGTGFSEAELATIKERLKPLESKP-----DKP-GA-----REKRGVHWVK-PE--LVAEVE-------FAGW 273 (298)
T ss_pred -eEEEEeEecCCCCHHHHHHHHHHHHhhccCc-----CCC-Cc-----ccCCCCEEeC-Ce--EEEEEE-------eccc
Confidence 6999999999999999999999999998762 123 11 2346789999 97 688998 4556
Q ss_pred cCCceeeccEEeeEecCCCccCcC
Q 003386 233 SAPYSLRFPRIDRVRYDKPWHDCL 256 (824)
Q Consensus 233 ~~g~tLRfPr~~~iR~DK~~~e~~ 256 (824)
+.+++||||+|+++|.||+|+||+
T Consensus 274 t~~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 274 TRDGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred CCCCeEeccEEEeeeCCCCHHHcc
Confidence 778999999999999999999996
No 9
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4.6e-36 Score=354.93 Aligned_cols=207 Identities=23% Similarity=0.343 Sum_probs=174.4
Q ss_pred ccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEEecCCHHHHHHHHH
Q 003386 9 LMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSLVAHNVDEVEKFFK 75 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~~~~~~~di~~~~~ 75 (824)
..+||.||+|. . ..+++|+|||||+ ||++|++++... +.+.++.+...++.++|+
T Consensus 542 ~~~F~~Lq~r~--~---------~~~v~y~vFDLL~lnG~dL~~~Pl~eRR~~L~~l~~~~-~~i~~s~~~~~~~~~~l~ 609 (764)
T PRK09632 542 VPSFGLLQNRG--R---------DTRVEFWAFDLLYLDGRSLLRKPYRDRRKLLEALAPSG-GSLTVPPLLPGDGAEALA 609 (764)
T ss_pred CCCHHHHhhhh--h---------cCCeEEEEEeeeccCCcccccCCHHHHHHHHHHhhCCC-CcEEecceecccHHHHHH
Confidence 35999999982 1 3589999999985 488999998743 467787777778999999
Q ss_pred HHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccE
Q 003386 76 ETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRF 155 (824)
Q Consensus 76 ~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~ 155 (824)
.++++|+||||+|+.+|+|.+|+||.+|+|+|++| +.|+||+|.++|+|++.|.+|+||||+++++ .|
T Consensus 610 ~a~~~GlEGIVaKr~dS~Y~pGrRs~~WlKiK~~~-----~~e~VI~G~~~g~G~r~g~~gsLLlGv~d~~-------~L 677 (764)
T PRK09632 610 YSRELGWEGVVAKRRDSTYQPGRRSSSWIKDKHWR-----TQEVVIGGWRPGEGGRSSGIGSLLLGIPDPG-------GL 677 (764)
T ss_pred HHHHcCCcEEEEeCCCCCCCCCCcCCCeEEEecCC-----ceEEEEEEEEcCCCCcCCceeeEEEEEEcCC-------ee
Confidence 99999999999999999999999999999999998 7896655545699999889999999999753 59
Q ss_pred EEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCC
Q 003386 156 ISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAP 235 (824)
Q Consensus 156 ~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g 235 (824)
+|+|+||||||++++++|.++|+++.++ .|| |.........++++||+ |. +|+||+ +.+|+.+
T Consensus 678 ~yvGkVGTGftd~~l~~L~~~L~~l~~~------~~P-f~~~~~~~~~~~~~WV~-P~--LV~EV~-------f~e~T~~ 740 (764)
T PRK09632 678 RYVGRVGTGFTERELASLKETLAPLHRD------TSP-FDADLPAADAKGATWVR-PE--LVGEVR-------YSEWTPD 740 (764)
T ss_pred EEEEEEeCCCCHHHHHHHHHHHHhhccC------CCC-cccccccccCCCcEEEe-cc--EEEEEE-------EeeccCC
Confidence 9999999999999999999999998765 255 53211123457899999 98 588987 5567889
Q ss_pred ceeeccEEeeEecCCCccCcC
Q 003386 236 YSLRFPRIDRVRYDKPWHDCL 256 (824)
Q Consensus 236 ~tLRfPr~~~iR~DK~~~e~~ 256 (824)
++||||+|+++|.||++.||.
T Consensus 741 g~LR~P~f~glR~DK~p~dv~ 761 (764)
T PRK09632 741 GRLRQPSWRGLRPDKKPGDVV 761 (764)
T ss_pred CceecceEEEeeCCCCHHHcc
Confidence 999999999999999999986
No 10
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=1.3e-34 Score=345.66 Aligned_cols=212 Identities=21% Similarity=0.312 Sum_probs=175.0
Q ss_pred cccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCC-CCceEEecCCHHHHH
Q 003386 6 FAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTG-EPCWSLVAHNVDEVE 71 (824)
Q Consensus 6 ~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~-~~~~~~~~~~~~di~ 71 (824)
.|+ .+||.||+|.+... ..+++|++||||+ ||++|++++... .+.++++.+...++.
T Consensus 312 ~G~-~~F~~Lq~r~~~~~--------~~~v~f~vFDLL~l~G~dL~~~PL~eRr~~L~~ll~~~~~~~i~~s~~~~~~g~ 382 (860)
T PRK05972 312 DGV-PDFQALQNAFDEGR--------TEDLVYFAFDLPFLGGEDLRELPLEERRARLRALLEAARSDRIRFSEHFDAGGD 382 (860)
T ss_pred CCC-CCHHHHHHHhhccC--------CCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEeceecchHH
Confidence 344 49999999875431 3489999999985 488999999764 347888888778899
Q ss_pred HHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEe-CCCCCCCCcceEEEEEecCCCCCC
Q 003386 72 KFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYY-GSGRRGGEVAQFLVALAERPAPDT 150 (824)
Q Consensus 72 ~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~-g~Grr~g~~~sfllGv~~~~~~~~ 150 (824)
++|+.++++|+||||+|+.+|+|.+| |+.+|+|+|+.+ +.+ +|||||+ +.|+++| +|+||||+|+++
T Consensus 383 ~ll~~a~~~GlEGIVaKr~dS~Y~~G-Rs~~WlKiK~~~-----~~E-~VIgGy~~~~Gkr~g-~gSLLlGvyd~~---- 450 (860)
T PRK05972 383 AVLASACRLGLEGVIGKRADSPYVSG-RSEDWIKLKCRA-----RQE-FVIGGYTDPKGSRSG-FGSLLLGVHDDD---- 450 (860)
T ss_pred HHHHHHHHcCCceEEEeCCCCCCCCC-CCCCcEEEecCC-----Cce-EEEEEEeCCCCcccc-ceeEEEEEecCC----
Confidence 99999999999999999999999998 999999999997 344 7788887 5677776 999999999763
Q ss_pred CCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccc
Q 003386 151 YPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSE 230 (824)
Q Consensus 151 ~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~ 230 (824)
+|+|+|+||||||++++++|..+|.++.++ .+| |.........++++||+ |. +|+||+ +.
T Consensus 451 ---~L~yvGkVGTGfsd~~l~~L~~~L~~l~~~------~~P-f~~~~~~~~~~~~~WV~-P~--LV~EV~-------f~ 510 (860)
T PRK05972 451 ---HLRYAGRVGTGFGAATLKTLLPRLKALATD------KSP-FAGKPAPRKARGVHWVK-PE--LVAEVE-------FA 510 (860)
T ss_pred ---EEEEEEEECCCCCHHHHHHHHHHHHhhccC------CCC-ccccCccccCCCCEEEc-cC--EEEEEE-------Ee
Confidence 799999999999999999999999998765 255 53322222345689999 98 588997 45
Q ss_pred cccCCceeeccEEeeEecCCCccCcCCH
Q 003386 231 VFSAPYSLRFPRIDRVRYDKPWHDCLDV 258 (824)
Q Consensus 231 ~~~~g~tLRfPr~~~iR~DK~~~e~~t~ 258 (824)
+||.++.||||+|+++|.||++.+|...
T Consensus 511 e~T~~g~LR~P~F~glR~DK~p~ev~~e 538 (860)
T PRK05972 511 GWTRDGIVRQAVFKGLREDKPAREVVAE 538 (860)
T ss_pred eccCCCCCccceEEEeecCCChHHhChh
Confidence 6788889999999999999999999754
No 11
>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=1.2e-34 Score=335.38 Aligned_cols=206 Identities=23% Similarity=0.345 Sum_probs=168.2
Q ss_pred ccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCC-CCceEEecCCHHHHHHHH
Q 003386 9 LMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTG-EPCWSLVAHNVDEVEKFF 74 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~-~~~~~~~~~~~~di~~~~ 74 (824)
..+||.||++.... ...++||++||||+ ||++|++++... .+.+.++.+..+++.++|
T Consensus 40 ~~~F~~Lq~~~~~~--------~~~pv~~~vFDlL~l~G~dL~~~Pl~eRr~~L~~ll~~~~~~~i~~~~~~~~~~~~~~ 111 (552)
T TIGR02776 40 RADFAALQNALSAG--------ASRPLTYYAFDLLFLSGEDLRDLPLEERKKRLKQLLKAQDEPAIRYSDHFESDGDALL 111 (552)
T ss_pred CCCHHHHHHHHHhc--------ccCceEEEEEeccccCCcccccCCHHHHHHHHHHHhhhcCCCcEEEeeeecccHHHHH
Confidence 45799999965321 25699999999985 488999999764 235666666667788999
Q ss_pred HHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCcc
Q 003386 75 KETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRR 154 (824)
Q Consensus 75 ~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~ 154 (824)
+.++++|+||||+|+.+|+|.+| ||.+|+|+|++| +.| +|||||++.++ .+|+||||++++ ++
T Consensus 112 ~~a~~~G~EGIV~K~~dS~Y~~G-Rs~~WlKlK~~~-----~~e-~vI~Gy~~~~r---~~gslLlg~~d~-------g~ 174 (552)
T TIGR02776 112 ESACRLGLEGVVSKRLDSPYRSG-RSKDWLKLKCRR-----RQE-FVITGYTPPNR---RFGALLVGVYEG-------GQ 174 (552)
T ss_pred HHHHHCCCceEEEeCCCCCCCCC-CCcchhcccccc-----cce-EEEEEEecCCC---ceeeEEEEEecC-------Ce
Confidence 99999999999999999999999 999999999998 455 67888886542 399999999973 27
Q ss_pred EEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccC
Q 003386 155 FISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA 234 (824)
Q Consensus 155 ~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~ 234 (824)
|+|+|+||+|||++++++|.++|++++++ .+| |.. ......++++||+ |. +|+||+ +.+|+.
T Consensus 175 l~~vgkVgsGfsd~~~~~L~~~l~~~~~~------~~P-f~~-~~~~~~~~~~Wv~-P~--lV~EV~-------~~e~T~ 236 (552)
T TIGR02776 175 LVYAGKVGTGFGADTLKTLLARLKALGAK------ASP-FSG-PAGAKTRGVHWVR-PS--LVAEVE-------YAGITR 236 (552)
T ss_pred EEEEEEEcCCCCHHHHHHHHHHHHhhccc------CCC-ccC-CccccCCCcEEEc-cC--EEEEEE-------eeeccC
Confidence 99999999999999999999999998875 234 332 1112346799999 97 588998 445678
Q ss_pred CceeeccEEeeEecCCCccCcCC
Q 003386 235 PYSLRFPRIDRVRYDKPWHDCLD 257 (824)
Q Consensus 235 g~tLRfPr~~~iR~DK~~~e~~t 257 (824)
+++||||+|+++|.||+|+||+.
T Consensus 237 ~g~LR~Prf~~~R~DK~~~e~t~ 259 (552)
T TIGR02776 237 DGILREASFKGLREDKPAEEVTL 259 (552)
T ss_pred CCeeEccEEEEEeCCCCHHHcch
Confidence 99999999999999999999964
No 12
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=100.00 E-value=1.3e-33 Score=320.13 Aligned_cols=228 Identities=24% Similarity=0.359 Sum_probs=190.0
Q ss_pred cccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCC---CCceEEecCCHHHHH
Q 003386 8 QLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTG---EPCWSLVAHNVDEVE 71 (824)
Q Consensus 8 ~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~---~~~~~~~~~~~~di~ 71 (824)
.+.|||.||+|.+++.. ...+....+++|||||||+ ||+.|++++... ...-++..++.+++.
T Consensus 198 ~~~~F~~Lq~r~~~k~~-v~~~~~~~~~~~~aFDlL~~dG~dL~~~pl~eRr~~Le~lv~~~~~~~~~~~i~~~~~~~~~ 276 (444)
T COG1793 198 GRLDFQALQQRLRRKYD-VAKLRRETPLVLFAFDLLYLDGEDLRGLPLEERRALLEELVKSSDKIEIAERIPFSDAEEGE 276 (444)
T ss_pred CCCCHHHHHHHhhhccc-hhhhccCCceEEEEEEEEeECCcccccCchHHHHHHHHHHhccccccccccceeccChhhHH
Confidence 78999999999988866 4455568899999999874 589999999872 111123338899999
Q ss_pred HHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCC
Q 003386 72 KFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTY 151 (824)
Q Consensus 72 ~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~ 151 (824)
.+|+.+++.|+||||+|+.+|+|++|.|+..|+|+||+. ++|+||+|+++|.|+++ .+|+|+||+|++++
T Consensus 277 ~~~~~a~~~g~EGvv~K~~ds~Y~~g~R~~~W~K~K~~~-----~~d~vv~G~~~g~Gkr~-~~~slll~~~~~~~---- 346 (444)
T COG1793 277 AFLEAAIELGLEGVVAKRPDSPYRAGGRSNKWLKVKRDE-----TLDLVVVGAEYGKGKRS-LYGSLLLGVYDGDG---- 346 (444)
T ss_pred HHHHHHHhcCceEEEEeCCCCCcCCCCCCCcceEeccCC-----cccEEEEEEEecCCccc-ccceEEEEEEcCCC----
Confidence 999999999999999999999999999999999999996 89999999999999988 89999999998764
Q ss_pred CccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEeccccccccc
Q 003386 152 PRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEV 231 (824)
Q Consensus 152 ~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~ 231 (824)
+.|+++|+||+||++++++.|..+|++++... ..++ ...+ |+.+|. +|+||+++.. ..+..
T Consensus 347 -~~~~~v~kVgtGf~~~~l~~l~~~l~~~~~~~----~~~~--------~~~~---~~~~p~--~V~EV~~~~~-t~~~~ 407 (444)
T COG1793 347 -GGLLYVGKVGTGFSDAELEELTERLEPLIVSR----FNGK--------VPGK---VVPPPG--LVAEVRFAEI-TKSGR 407 (444)
T ss_pred -ceEEEEecccCCCCHHHHHHHHHHHHHhccCc----CCCc--------cCce---eecCCc--EEEEEEEeec-ccCCc
Confidence 36999999999999999999999999998761 0011 0111 554366 6899997554 34666
Q ss_pred ccC--CceeeccEEeeEecCCCccCcCCHHHHHHHH
Q 003386 232 FSA--PYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 265 (824)
Q Consensus 232 ~~~--g~tLRfPr~~~iR~DK~~~e~~t~~el~el~ 265 (824)
|+. +..||||+|.++|.||.+.+++++.++.+++
T Consensus 408 ~r~~~~~~lRfpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 408 LRHASGLGLRFPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred eecccCcccCcCcccccccccCcccccccccchhhc
Confidence 665 8999999999999999999999999888765
No 13
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=2.8e-33 Score=309.12 Aligned_cols=216 Identities=17% Similarity=0.273 Sum_probs=168.9
Q ss_pred cChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEEecCC--HHHHHHHH
Q 003386 10 MTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSLVAHN--VDEVEKFF 74 (824)
Q Consensus 10 ~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~~~~~--~~di~~~~ 74 (824)
.+||.||+|.++.......+....+++|+|||||+ ||++|++++... +.++++.+. .++++++|
T Consensus 89 ~~F~~Lq~r~~~~~~~~~~~~~~~pv~~~vFDlL~l~G~dl~~~Pl~eRr~~L~~l~~~~-~~i~~~~~~~~~~~~~~~~ 167 (350)
T PRK08224 89 LDFEALQQRIHPAASRVRKLAEETPASFVAFDLLALGDRDLTGRPFAERRAALEAAAAGS-GPVHLTPATTDPATARRWF 167 (350)
T ss_pred CCHHHHHhhhhccccchhhhhhcCCEEEEEEeeeeECCcChhhCCHHHHHHHHHHhcCCC-CcEEEecccCCHHHHHHHH
Confidence 79999999875443222333447899999999985 588999998653 456665443 46999999
Q ss_pred HHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCcc
Q 003386 75 KETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRR 154 (824)
Q Consensus 75 ~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~ 154 (824)
+.++++|+||||+|+.+|+|.+|+|+ |+|+|+.+ +.|++|+|.++|.|+ |.+|+|+||+|++.+ +
T Consensus 168 ~~a~~~G~EGIV~Kr~dS~Y~~Grr~--WlKiK~~~-----~~d~vI~G~~~g~~~--~~~gslllg~~d~~g------~ 232 (350)
T PRK08224 168 EEFEGAGLDGVIAKPLDGPYQPGKRA--MFKVKHER-----TADCVVAGYRYHKSG--PVVGSLLLGLYDDDG------Q 232 (350)
T ss_pred HHHHhCCCcEEEEeCCCCCcCCCCcC--EEEEccCC-----cEEEEEEEEEcCCCC--CccccEEEEEECCCC------c
Confidence 99999999999999999999999887 99999997 899776665567664 679999999997643 7
Q ss_pred EEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCC----cccccCCC-----CCCCCcEE--EeCCcceEEEEEEec
Q 003386 155 FISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP----SFYQVTNN-----SKERPDVW--IESPEKSIILSITSD 223 (824)
Q Consensus 155 ~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP----~~~~~~~~-----~~~~pdvW--i~~P~~svVvEVka~ 223 (824)
++|+|+|| |||++++++|.++|.+++++. + .+| .|...... ...+..+| |+ |.+ |+||+
T Consensus 233 l~~vG~v~-Gf~~~~~~~L~~~l~~l~~~~--~--~~p~~~~pf~~~~~~~~~~~~~~~~~~w~~v~-P~l--v~eV~-- 302 (350)
T PRK08224 233 LHHVGVTS-AFPMARRRELTAELEPLRTPF--G--DHPWNWAAFTGRAPGGPSRWSAGKDLSWVPLR-PER--VVEVR-- 302 (350)
T ss_pred EEEEEEEC-CCCHHHHHHHHHHHHhhhcCC--C--CCccccCcccccCCCccccccccCCcEEEeee-EEE--EEEEe--
Confidence 99999996 999999999999999988752 1 012 14221100 12346789 99 985 77887
Q ss_pred ccccccccccCCceeecc-EEeeEecCCCccCcCC
Q 003386 224 IRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCLD 257 (824)
Q Consensus 224 ~~~~~s~~~~~g~tLRfP-r~~~iR~DK~~~e~~t 257 (824)
+.+|| ++.|||| +|+++|.||++.+|+.
T Consensus 303 -----~~~~t-~~~lR~p~~f~g~r~Dk~p~~v~~ 331 (350)
T PRK08224 303 -----YDHME-GGRFRHTAQFLRWRPDRDPRSCTY 331 (350)
T ss_pred -----cCccc-CCeecCCCeeEEEcCCCChHHCCH
Confidence 56778 5699998 9999999999999974
No 14
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=100.00 E-value=4.7e-32 Score=316.88 Aligned_cols=208 Identities=20% Similarity=0.258 Sum_probs=164.4
Q ss_pred ccChHHHhhccccCCCc-hhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCC----------CceEEec
Q 003386 9 LMTLSVLHDKDNACNIS-TVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGE----------PCWSLVA 64 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~-~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~----------~~~~~~~ 64 (824)
-.+||.||+|.+....+ ...+....+++|||||||+ ||++|++++.... +.++++.
T Consensus 86 ~~~F~~Lq~R~~~~~~~~i~~~~~~~pv~~~vFDlL~lnG~dL~~~PL~eRr~~L~~ll~~~~~~~~~~~~~~~~i~~~~ 165 (610)
T PRK09633 86 RSDFEHVQQRGRLKNTEVIAKSANARPCQLLAFDLLELKGESLTSLPYLERKKQLDKLMKAAKLPASPDPYAKARIQYIP 165 (610)
T ss_pred CCCHHHHHhhhhccccchhhhhhcccceEEEEEeecccCCcccccCCHHHHHHHHHHHhhhcccccccccccccceEEcC
Confidence 35899999985432210 1222336799999999985 4889999986532 2456655
Q ss_pred CCHHHHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEec
Q 003386 65 HNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAE 144 (824)
Q Consensus 65 ~~~~di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~ 144 (824)
+ .++++++|+.++++|+||||+|+.+|+|.+|+||.+|+|+|+.+ +.|+ |||||... -|+|++|+|+
T Consensus 166 ~-~~~~~~l~~~a~~~g~EGIV~Kr~dS~Y~~G~Rs~~WlKiK~~~-----~~d~-vI~G~~~~------~g~~llgv~~ 232 (610)
T PRK09633 166 S-TTDFDALWEAVKRYDGEGIVAKKKTSKWLENKRSKDWLKIKNWR-----YVHV-IVTGYDPS------NGYFTGSVYK 232 (610)
T ss_pred C-HHHHHHHHHHHHHcCCceEEEeCCCCCCCCCCCCCCeEEEeccC-----Ccee-EEEEEecC------CceEEEEEec
Confidence 4 67999999999999999999999999999999999999999976 7885 55666531 1478999995
Q ss_pred CCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecc
Q 003386 145 RPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDI 224 (824)
Q Consensus 145 ~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~ 224 (824)
+ ++|+|+|+||||||++++++|.++|+++.+. ...+.+||+ |. +|+||++
T Consensus 233 ~-------g~l~~vGkvgtGft~~~~~~L~~~l~~l~~~------------------~~~~~~wV~-P~--LV~EV~~-- 282 (610)
T PRK09633 233 D-------GQLTEVGSVKHGMEDEERQTLRAIFKQNGTK------------------TKSGEYTLE-PS--ICVTVAC-- 282 (610)
T ss_pred C-------CeEEEEEEecCCCCHHHHHHHHHHHHHhccC------------------CCCCcEEEe-ee--EEEEEEE--
Confidence 4 2799999999999999999999999887543 123579999 98 4788974
Q ss_pred cccccccccCCceeeccEEeeEecCCCccCcCCHHHHHHHH
Q 003386 225 RTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFVELV 265 (824)
Q Consensus 225 ~~~~s~~~~~g~tLRfPr~~~iR~DK~~~e~~t~~el~el~ 265 (824)
.+|+ ++.||||+|+++|.||+++||++.+...+++
T Consensus 283 -----~e~t-~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~ 317 (610)
T PRK09633 283 -----ITFD-GGTLREPSFVSFLFDMDPTECTYQQLQRQLA 317 (610)
T ss_pred -----eecC-CCeEEeeEEeEEEcCCChHHcchhhhhhhhc
Confidence 3454 7899999999999999999999887766544
No 15
>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=1.4e-31 Score=259.00 Aligned_cols=137 Identities=26% Similarity=0.522 Sum_probs=117.8
Q ss_pred CCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCc
Q 003386 114 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 193 (824)
Q Consensus 114 ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~ 193 (824)
++++||||||||+|+|+++|.+|+||||++++++ ++|+||||||||||++++++|.++|+++++. .+...||.
T Consensus 2 ~dtlDlVViG~~~g~G~r~~~~gslLlg~~d~~~-----~~l~~vgkVGTGfs~~~l~~l~~~L~~l~~~--~~~~~~p~ 74 (139)
T cd07967 2 ADTADLVVLGAYYGTGSKGGMMSVFLMGCYDPNS-----KKWCTVTKCGNGHDDATLARLQKELKMVKIS--KDPSKVPS 74 (139)
T ss_pred CceEeEEEEEEEECCCCCCCccceEEEEEEeCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhhhccc--cCCcCCCc
Confidence 5799999999999999999999999999998543 3899999999999999999999999999987 33334666
Q ss_pred ccccCCCCCCCCcEEEeCCcceEEEEEEeccccccccccc-CCceeeccEEeeEecCCCccCcCCHHH
Q 003386 194 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFS-APYSLRFPRIDRVRYDKPWHDCLDVQS 260 (824)
Q Consensus 194 ~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~-~g~tLRfPr~~~iR~DK~~~e~~t~~e 260 (824)
|+.+. ...+|++||.+|+.|+|+||+++.. +.|..|. +|++||||||++||+||+|+||+|+++
T Consensus 75 ~~~~~--~~~~Pdv~~~~P~~s~V~EV~~aei-t~S~~~~a~G~tLRFPr~~~iR~DK~~~d~~t~~~ 139 (139)
T cd07967 75 WLKCN--KSLVPDFIVKDPKKAPVWEITGAEF-SKSEAHTADGISIRFPRVTRIRDDKDWKTATSLPE 139 (139)
T ss_pred eEeec--CCCCCCEEEeCCCccEEEEEEeeeE-EecCcccccCEEEEccEEEEEeCCCCHHHCccccC
Confidence 76653 3578999996699999999997554 3577777 699999999999999999999999864
No 16
>PHA02587 30 DNA ligase; Provisional
Probab=99.96 E-value=2.5e-29 Score=289.18 Aligned_cols=215 Identities=23% Similarity=0.327 Sum_probs=167.8
Q ss_pred HHHhhccccCCCchhhh------ccCccEEEEEccHHH----------------HHHHHHHhhcC-CCCceEE----ecC
Q 003386 13 SVLHDKDNACNISTVAM------NDGICVCVHVYMLSQ----------------LRSQIMAADQT-GEPCWSL----VAH 65 (824)
Q Consensus 13 q~l~~r~~~~~~~~~~~------~~~~~v~~~~FDll~----------------lr~~L~~l~~~-~~~~~~~----~~~ 65 (824)
|.+++|.+++.+....+ ....|++|+|||+|. ||++|++++.. ..+.+.+ .++
T Consensus 241 q~l~~R~~~~~i~~~~l~~~~~~~~~~pv~~~vFDiL~ld~y~~~~~~~~pl~eRr~~L~~l~~~~~~~~i~l~~~~~~~ 320 (488)
T PHA02587 241 GVVADRATGNGIVNKSLKGTISKEEAQEIVFQVWDIVPLEVYYGKEKSDMPYDDRFSKLAQMFEDCGYDRVELIENQVVN 320 (488)
T ss_pred hhhhhhhhccchhhhhhccccchhhccceEEEEEEeechhhccCCccccCCHHHHHHHHHHHHhhcCCCcEEEEeeEEcC
Confidence 88999987776633321 235799999999872 48889999863 2234433 357
Q ss_pred CHHHHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecC
Q 003386 66 NVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAER 145 (824)
Q Consensus 66 ~~~di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~ 145 (824)
+.+++.++|+++++.|.||||+|+++|+|.+| |+.+|+|+|+.+ ++|++|||+|++. +++|.+|+|+|++++
T Consensus 321 ~~ee~~~~~~~a~~~G~EGimlK~~ds~Y~~G-Rs~~WlKiK~~~-----~~dlvVvG~~~~~-k~~~~~gs~ll~~~~- 392 (488)
T PHA02587 321 NLEEAKEIYKRYVDQGLEGIILKNTDGLWEDG-RSKDQIKFKEVI-----DIDLEIVGVYEHK-KDPNKVGGFTLESAC- 392 (488)
T ss_pred CHHHHHHHHHHHHhCCCCeEEEECCCCCCCCC-CCCCcEEecCCC-----ceEEEEEeEEeCC-CCCCceeEEEEEecC-
Confidence 78999999999999999999999999999999 888999999987 8999988888854 567789999997653
Q ss_pred CCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcc--eEEEEEEec
Q 003386 146 PAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEK--SIILSITSD 223 (824)
Q Consensus 146 ~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~--svVvEVka~ 223 (824)
+ . .+|+||+|||++++++|...++ . +| +...+ ...++.+|.. |.. ..|+||+++
T Consensus 393 -g------~--~~~~vgsGftd~~~~~l~~~~~----~-------~p-~~~~~--~~~r~~~~~~-~~~~~~~V~EV~~~ 448 (488)
T PHA02587 393 -G------K--ITVNTGSGLTDTTHRKKDGKKV----V-------IP-LSERH--ELDREELMAN-KGKYIGKIAECECN 448 (488)
T ss_pred -C------c--EEEEECCCCChHHhhhhccccc----e-------ec-ccccc--hhcchhhhhC-cccccceEEEEEec
Confidence 2 3 3699999999999999866542 1 23 22221 2346778876 432 358999986
Q ss_pred ccccccccccCCceeeccEEeeEecCCCccCcCCHHHHH
Q 003386 224 IRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 262 (824)
Q Consensus 224 ~~~~~s~~~~~g~tLRfPr~~~iR~DK~~~e~~t~~el~ 262 (824)
.. +.|..|++|++||||||++||.||+ +++|++++.
T Consensus 449 ~i-t~S~~~~~g~sLRfPrf~r~R~DK~--~Adt~~~v~ 484 (488)
T PHA02587 449 GL-QRSKGRKDKVSLFLPIIKRIRIDKT--EANTLEDVF 484 (488)
T ss_pred eE-EeCCCCCCCeeEEccceeEEeCCCC--cccCHHHHh
Confidence 54 4688899999999999999999999 899999876
No 17
>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=99.96 E-value=6.6e-29 Score=241.38 Aligned_cols=139 Identities=52% Similarity=1.044 Sum_probs=115.1
Q ss_pred CCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCC-CCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCC
Q 003386 114 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAP-DTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPP 192 (824)
Q Consensus 114 ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~-~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP 192 (824)
||++||||||||+|.|+++|.+++||||+++.++. ...+.+|+|||+||||||++++++|.++|+++|++ ++...||
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 57999999999999999989999999999975431 12234899999999999999999999999999987 4444466
Q ss_pred cccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEecCCCccCcCCH
Q 003386 193 SFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDV 258 (824)
Q Consensus 193 ~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR~DK~~~e~~t~ 258 (824)
|. .......+|++||+ |..|+|+||+++.. ..+..|++|++||||||++||+||+|.||+|+
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 32 22234568999998 99889999997543 35777889999999999999999999999974
No 18
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=99.95 E-value=1.4e-27 Score=256.45 Aligned_cols=181 Identities=19% Similarity=0.218 Sum_probs=146.1
Q ss_pred cChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEEecCCHHHHHHHHHH
Q 003386 10 MTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSLVAHNVDEVEKFFKE 76 (824)
Q Consensus 10 ~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~~~~~~~di~~~~~~ 76 (824)
.+||.|++|.+.+.. ....+++|++|||| +||++|++++.+. +.+.++.+..+++.++|+.
T Consensus 81 ~~F~~l~~r~~~~~~-----~~~~~~~~~vFDlL~~~g~~l~~~pl~eRr~~L~~~~~~~-~~~~~~~~~~~~~~~~~~~ 154 (275)
T PRK07636 81 PDFEAVMERFQSKKS-----TKIHPVVFCVFDVLYINGVSLTALPLSERKEILASLLLPH-PNVKIIEGIEGHGTAYFEL 154 (275)
T ss_pred CCHHHHHHHhccccc-----cccCceEEEEEEeEEECceehhhCCHHHHHHHHHHhcCCC-CCEEEcccccccHHHHHHH
Confidence 489999998765533 12579999999986 4688999998654 5677777777789999999
Q ss_pred HHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEE
Q 003386 77 TIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFI 156 (824)
Q Consensus 77 ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~ 156 (824)
++++|.||||+|+++|+|.+|+||.+|+|+|+.. +.|+ |||||.. +.+|+| ||+++ + +
T Consensus 155 ~~~~g~EGiV~K~~ds~Y~~g~Rs~~WlKiK~~~-----~~e~-vV~G~~~-----~~~g~l-lg~~~--g------~-- 212 (275)
T PRK07636 155 VEERELEGIVIKKANSPYEINKRSDNWLKVINYQ-----YTDV-LITGYRK-----EEFGLL-LSYLD--G------R-- 212 (275)
T ss_pred HHHcCCcEEEEeCCCCCCCCCCCCCCeEEEecCC-----eEEE-EEEEEec-----CCCcEE-EEecC--C------e--
Confidence 9999999999999999999999999999999764 7885 5666743 225655 78774 2 3
Q ss_pred EEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCc
Q 003386 157 SFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPY 236 (824)
Q Consensus 157 ~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~ 236 (824)
|+|+||+ |+++++++|..+|.++.+. ..++++|++ |. +|+||+ +.+||.++
T Consensus 213 ~~G~vgt-~~~~~~~~l~~~l~~~~~~------------------~~~~~~wv~-P~--lv~eV~-------~~e~t~~g 263 (275)
T PRK07636 213 SAGIMEF-MPYDARKKFYKRAKRLVVG------------------EDKKFVYIE-PI--IGCRVK-------HRFKTKNG 263 (275)
T ss_pred EEEEECC-CCHHHHHHHHHHhhhhccC------------------ccCCCEEeC-Cc--EEEEEE-------EEEecCCC
Confidence 7899999 9999999999888765332 245789998 98 477886 55778888
Q ss_pred eeeccEEeeEe
Q 003386 237 SLRFPRIDRVR 247 (824)
Q Consensus 237 tLRfPr~~~iR 247 (824)
.||||+|+++|
T Consensus 264 ~lR~p~f~g~r 274 (275)
T PRK07636 264 MLRIPSFVEWR 274 (275)
T ss_pred CEEccEEEEEe
Confidence 99999999998
No 19
>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=99.95 E-value=6.1e-27 Score=228.45 Aligned_cols=134 Identities=37% Similarity=0.585 Sum_probs=113.8
Q ss_pred CCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCc
Q 003386 114 GSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPS 193 (824)
Q Consensus 114 ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~ 193 (824)
+|++|+||||||+|+|++.|.+++||||++++++ ++|+|||+||+|||++++++|.++|.+++++. ||.
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 4799999999999999888899999999997653 38999999999999999999999999998761 331
Q ss_pred ccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccC---------CceeeccEEeeEecCCCccCcCCHHHHHHH
Q 003386 194 FYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA---------PYSLRFPRIDRVRYDKPWHDCLDVQSFVEL 264 (824)
Q Consensus 194 ~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~---------g~tLRfPr~~~iR~DK~~~e~~t~~el~el 264 (824)
... ...+|++||+ |. +|+||+++.. ..|..|++ |++||||||++||+||+|.+|+++++|.+|
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 111 1258999999 96 6899997543 35777765 889999999999999999999999999999
Q ss_pred HH
Q 003386 265 VH 266 (824)
Q Consensus 265 ~~ 266 (824)
++
T Consensus 142 ~~ 143 (144)
T cd07969 142 YK 143 (144)
T ss_pred Hh
Confidence 85
No 20
>PRK09125 DNA ligase; Provisional
Probab=99.94 E-value=1.1e-25 Score=242.60 Aligned_cols=176 Identities=24% Similarity=0.356 Sum_probs=141.0
Q ss_pred ccChHHHhhccccCCCchhhhccCccEEEEEccHH-------HHHHHHHHhhcCC-CCceEE----ecCCHHHHHHHHHH
Q 003386 9 LMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------QLRSQIMAADQTG-EPCWSL----VAHNVDEVEKFFKE 76 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------~lr~~L~~l~~~~-~~~~~~----~~~~~~di~~~~~~ 76 (824)
-.+||.++.|.+++.... ....|++|++||++ +||+.|++++.+. .+.+.+ .+++.+++.++|+.
T Consensus 94 ~~~F~~l~~r~~~k~~~~---~~~~~v~~~vFDll~~~gpl~eRr~~L~~li~~~~~~~i~~~~~~~~~~~~~~~~~~~~ 170 (282)
T PRK09125 94 RGQFEAISSIVRDKTPDD---AAWRKVRFMVFDLPDAPGDFEERLAVLKKLLAKLPSPYIKIIEQIRVRSEAALQQFLDQ 170 (282)
T ss_pred CCCHHHHHHHHccCCcch---hhhcccEEEEEEcCCCCCCHHHHHHHHHHHHhhCCCCcEEEEeEEEcCCHHHHHHHHHH
Confidence 358999999987664411 12458999999987 5689999998754 233433 45778999999999
Q ss_pred HHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEE
Q 003386 77 TIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFI 156 (824)
Q Consensus 77 ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~ 156 (824)
+++.|.||||+|+.+|+|.+| |+.+|+|+|+++ +.|++|||.++|.|+++|.+|+|+||..+. ..|
T Consensus 171 ~~~~G~EGiV~K~~ds~Y~~G-Rs~~wlKiK~~~-----~~d~vIvG~~~g~Gk~~g~~gsllv~~~~g-------~~~- 236 (282)
T PRK09125 171 IVAAGGEGLMLHRPDAPYEAG-RSDDLLKLKPYY-----DAEATVIGHLPGKGKFAGMLGALLVETPDG-------REF- 236 (282)
T ss_pred HHHcCCCEEEEeCCCCCCcCC-CCCCcEEEEecC-----CCcEEEEEEEcCCCcccCceeeEEEEeCCC-------CEE-
Confidence 999999999999999999999 999999999998 799999998899999999999999996432 133
Q ss_pred EEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCc
Q 003386 157 SFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPY 236 (824)
Q Consensus 157 ~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~ 236 (824)
+||+|||+++++. +| ++ ..+++|+ +.+++..+
T Consensus 237 ---~VgsG~t~~~r~~------------------~~-~~-------------------g~~~~V~-------y~e~t~~g 268 (282)
T PRK09125 237 ---KIGSGFSDAEREN------------------PP-KI-------------------GSIITYK-------YRGLTKNG 268 (282)
T ss_pred ---EeCCCCCHHHhcC------------------CC-CC-------------------CCEEEEE-------ecccCCCC
Confidence 8999999997541 22 10 0256676 56678899
Q ss_pred eeeccEEeeEecC
Q 003386 237 SLRFPRIDRVRYD 249 (824)
Q Consensus 237 tLRfPr~~~iR~D 249 (824)
.||||+|++||+|
T Consensus 269 ~lR~P~f~g~R~D 281 (282)
T PRK09125 269 LPRFASFLRVRED 281 (282)
T ss_pred cccCCEEEEEecC
Confidence 9999999999998
No 21
>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=99.93 E-value=2e-25 Score=212.16 Aligned_cols=121 Identities=31% Similarity=0.570 Sum_probs=105.4
Q ss_pred CcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcc
Q 003386 115 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 194 (824)
Q Consensus 115 e~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~ 194 (824)
|++|+||+|+++|.|+++|.+++||||+|++++ ++|+|||+||+|||++++++|..+|+++++.
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 579999999999999988999999999997652 2899999999999999999999999988654
Q ss_pred cccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEecCCCccCcCCHHHHH
Q 003386 195 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDCLDVQSFV 262 (824)
Q Consensus 195 ~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR~DK~~~e~~t~~el~ 262 (824)
..+|++||+ |. +|+||+++.. ..+..|+.|++||||||++||+||+|.+|+|+++|.
T Consensus 65 -------~~~~~~wv~-P~--lV~eV~~~e~-t~s~~~~~g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 65 -------KFGPVVSVK-PE--LVFEVAFEEI-QRSPRYKSGYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred -------ccCCcEEEe-ce--EEEEEEeeEE-EecCccccCceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 125789999 97 6899997533 457778899999999999999999999999999885
No 22
>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=99.92 E-value=9.5e-25 Score=209.42 Aligned_cols=122 Identities=41% Similarity=0.770 Sum_probs=102.8
Q ss_pred CcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcc
Q 003386 115 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 194 (824)
Q Consensus 115 e~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~ 194 (824)
|++|+||||+++|.|+++|.+++||||++++++ ++|+|+|+||||||++++++|.++|.+++++. +|.+
T Consensus 1 d~~D~VI~G~~~~~g~~~~~~~slLlg~~d~~~-----~~l~~vgkvgtGfs~~~~~~l~~~l~~~~~~~------~p~~ 69 (129)
T cd07893 1 DTLDLVIVGAYYGKGRRGGGIGAFLCAVYDPER-----DEFQTICKVGSGFTDEELEELRELLKELKTPE------KPPR 69 (129)
T ss_pred CcEEEEEEeeEcCCCCcCCCcceEEEEEEcCCC-----CEEEEEeEECCCCCHHHHHHHHHHhhcccccC------CCCc
Confidence 579999999999999988999999999997642 38999999999999999999999999998761 3322
Q ss_pred cccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccC-------CceeeccEEeeEecCCCccCc
Q 003386 195 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSA-------PYSLRFPRIDRVRYDKPWHDC 255 (824)
Q Consensus 195 ~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~-------g~tLRfPr~~~iR~DK~~~e~ 255 (824)
. ....+|++||+ |. +|+||+++.. ..+..|++ |++||||||++||+||+|++|
T Consensus 70 ~----~~~~~~~~wv~-P~--lV~EV~~~e~-t~s~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~e~ 129 (129)
T cd07893 70 V----NSIEKPDFWVE-PK--VVVEVLADEI-TRSPMHTAGRGEEEEGYALRFPRFVRIRDDKGPEDA 129 (129)
T ss_pred c----cccCCCcEEEe-ee--EEEEEEeeee-eeCcccccccccCCCceEEECCEEEEEeCCCChhhC
Confidence 1 13468999999 95 7999997543 34777777 899999999999999999998
No 23
>PHA00454 ATP-dependent DNA ligase
Probab=99.91 E-value=7.2e-24 Score=232.14 Aligned_cols=189 Identities=23% Similarity=0.300 Sum_probs=138.8
Q ss_pred cChHHHhhccccCCCchhhhccCccEEEEEccHHHH--------------------HHHHHHhhcCCCC-ceEE----ec
Q 003386 10 MTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQL--------------------RSQIMAADQTGEP-CWSL----VA 64 (824)
Q Consensus 10 ~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~l--------------------r~~L~~l~~~~~~-~~~~----~~ 64 (824)
.|||.++.|.+++..+.. .....|++|++||||++ |++|.+++..... .+++ .+
T Consensus 99 ~~f~~~~~~l~~k~~~~~-~~~~~~v~~~vFDll~l~~~~~g~~l~~l~~~pl~~Rr~~L~~l~~~~~~~~~~~~~~~~~ 177 (315)
T PHA00454 99 VDFNTGSGLLRRKWKVLF-ELHLKKLHVVVYDVTPLDVLESGEDYDVMSLLMYEHVRAMVPLLMEYFPEIDWFLSESYEV 177 (315)
T ss_pred CCHHHHHHHhccCccchh-hhccCceEEEEEEeeEeccccCCccccccccccHHHHHHHHHHHHhhCCCcceEeeceEEc
Confidence 689999999765542122 22467999999998752 5667777654321 1333 44
Q ss_pred CCHHHHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccccCCCcccEEEEEEEeCCCCC--CCCcceEEEEE
Q 003386 65 HNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYIRAGSDLDVLIIGGYYGSGRR--GGEVAQFLVAL 142 (824)
Q Consensus 65 ~~~~di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~~~ge~lDlvVIGG~~g~Grr--~g~~~sfllGv 142 (824)
.+.+++.++|+.++++|+||||+|+.+|+|.+|+|+. |+|+|+.+ +.|++|+|.++|.|++ .|.+++|+|.+
T Consensus 178 ~~~~~~~~~~~~~~~~g~EGiv~K~~ds~Y~~Grr~~-~~K~K~~~-----~~d~vIvG~~~g~g~~~~~g~~~~~~~~~ 251 (315)
T PHA00454 178 YDMESLQELYEKKRAEGHEGLVVKDPSLIYRRGKKSG-WWKMKPEC-----EADGTIVGVVWGTPGLANEGKVIGFRVLL 251 (315)
T ss_pred CCHHHHHHHHHHHHhCCCceEEEeCCCCCCCCCCccC-cEEEcccC-----ceeEEEEEEEECCCCccCCceEEEEEEEe
Confidence 5678999999999999999999999999999998875 88999998 8998888877887542 24555555544
Q ss_pred ecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEeCCcceEEEEEEe
Q 003386 143 AERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIESPEKSIILSITS 222 (824)
Q Consensus 143 ~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~~P~~svVvEVka 222 (824)
+++ .+++ |||||++++++|..++.++... ...|| ....|+||+
T Consensus 252 --~~g------~l~~----gtGfs~~~~~~l~~~l~~~~~~----~~~~p--------------------~~~~v~eV~- 294 (315)
T PHA00454 252 --EDG------RVVN----ATGISRALMEEFTANVKEHGED----YEAMP--------------------YNGRACQVS- 294 (315)
T ss_pred --CCC------cEEE----ccCCCHHHHHHHHHHHHhhccC----ccccC--------------------CCCeEEEEE-
Confidence 222 5654 8999999999999999876332 10122 111367887
Q ss_pred cccccccccccCCceeeccEEeeEec
Q 003386 223 DIRTIRSEVFSAPYSLRFPRIDRVRY 248 (824)
Q Consensus 223 ~~~~~~s~~~~~g~tLRfPr~~~iR~ 248 (824)
+.+||.++.||||+|+++|.
T Consensus 295 ------y~e~T~~g~lR~P~F~g~Rd 314 (315)
T PHA00454 295 ------YMERTPDGSLRHPSFDRFRD 314 (315)
T ss_pred ------EEEcCCCCcccCceeeeeec
Confidence 55688999999999999985
No 24
>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=99.84 E-value=1.6e-20 Score=176.76 Aligned_cols=113 Identities=29% Similarity=0.551 Sum_probs=90.9
Q ss_pred cccEEEEEEEe-CCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcc
Q 003386 116 DLDVLIIGGYY-GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 194 (824)
Q Consensus 116 ~lDlvVIGG~~-g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~ 194 (824)
+.| +|||||+ +.| ++|.+|+||||+++++ +|+|+|+||+|||++++++|.++|.+++.+ .|| |
T Consensus 2 ~~~-~vI~G~~~~~g-~~~~~gslllg~~~~~-------~l~~vG~vgtG~s~~~~~~l~~~l~~~~~~------~~p-~ 65 (115)
T cd07971 2 RQE-FVIGGYTPPKG-SRGGFGSLLLGVYDGG-------RLVYVGRVGTGFSAATLRELRERLAPLERK------TSP-F 65 (115)
T ss_pred Cce-EEEEEEECCCC-CCCcccEEEEEEEcCC-------EEEEeeeEcCCCCHHHHHHHHHHhhcccCC------CCC-C
Confidence 356 5677776 455 7788999999999764 799999999999999999999999998765 245 3
Q ss_pred cccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEecCCCccCc
Q 003386 195 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDKPWHDC 255 (824)
Q Consensus 195 ~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR~DK~~~e~ 255 (824)
... ......+++||+ |. +|+||++ ..|+.+++||||+|+++|+||+|++|
T Consensus 66 ~~~-~~~~~~~~~wv~-P~--lv~eV~~-------~~~t~~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 66 ADP-PPADARGAVWVK-PE--LVAEVEF-------AEWTPDGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred ccc-ccccCCCCEEec-CC--EEEEEEE-------EEecCCCcEECCeeeEeeCCCCcccC
Confidence 221 112457899999 97 5889984 45577889999999999999999987
No 25
>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=99.79 E-value=2.9e-19 Score=163.17 Aligned_cols=97 Identities=40% Similarity=0.728 Sum_probs=73.5
Q ss_pred CCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCcEEEe
Q 003386 131 RGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPDVWIE 210 (824)
Q Consensus 131 r~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pdvWi~ 210 (824)
|+|.+++||||+++++. ++|+|||+||+|||++++++|.++|.++|++. ||...... ...+|++||+
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 45789999999999862 38999999999999999999999999999762 45212222 1268999998
Q ss_pred CCcceEEEEEEecccccccccccCCceeeccEEeeEecCC
Q 003386 211 SPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVRYDK 250 (824)
Q Consensus 211 ~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR~DK 250 (824)
|.+ |+||+++. |+.+++||||+|++||+||
T Consensus 68 -P~~--V~eV~~~e-------~t~~G~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 68 -PEL--VVEVKFAE-------ITPSGSLRFPRFKRIREDK 97 (97)
T ss_dssp -ST---EEEEEESE-------EEEESEEESEEEEEEETTS
T ss_pred -CCE--EEEEEEEE-------EcCCCeEECCEEeEEeCCC
Confidence 996 89998643 3333599999999999998
No 26
>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=99.78 E-value=1.2e-18 Score=162.28 Aligned_cols=108 Identities=22% Similarity=0.302 Sum_probs=87.4
Q ss_pred CcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcc
Q 003386 115 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 194 (824)
Q Consensus 115 e~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~ 194 (824)
+++|+||+|+++|.|++.|.+++||||+++++ .+.|+|+||+|||++++++|.++|++++.+. +| |
T Consensus 1 ~~~d~vV~G~~~~~g~~~~~~gslllg~~~~~-------~~~~vg~vgtGf~~~~~~~l~~~l~~~~~~~------~~-~ 66 (108)
T cd08040 1 KTAEAVIIGMRAGFGNRSDVMGSLLLGYYGED-------GLQAVFSVGTGFSADERRDLWQNLEPLVTSF------DD-H 66 (108)
T ss_pred CceeEEEEEeEeCCCCCCCceEEEEEEEECCC-------ceEEEEEEcCCCCHHHHHHHHHhcchhccCC------CC-C
Confidence 47898888888899988889999999999764 4789999999999999999999999987651 22 2
Q ss_pred cccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEe
Q 003386 195 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 247 (824)
Q Consensus 195 ~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR 247 (824)
... .....++++|++ |. +|+||++ ..|+.+++||||+|+++|
T Consensus 67 ~~~-~~~~~~~~vwv~-P~--lv~eV~~-------~~~t~~~~lR~P~f~~~R 108 (108)
T cd08040 67 PVW-NVGKDLSFVPLY-PG--KVVEVKY-------FEMGSKDCLRFPVFIGIR 108 (108)
T ss_pred ccc-ccccCCCCEEee-ce--EEEEEEe-------EEeeCCCeEECCeEEEeC
Confidence 111 122457899999 96 5889984 456789999999999997
No 27
>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=99.75 E-value=9.5e-18 Score=159.49 Aligned_cols=121 Identities=22% Similarity=0.295 Sum_probs=88.7
Q ss_pred CcccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcc
Q 003386 115 SDLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSF 194 (824)
Q Consensus 115 e~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~ 194 (824)
++.| +|||||.... +.+++||||+|++++ +|+|+|+| +|||++++++|.++|+++..+..++. .+|.|
T Consensus 1 ~~~e-~vI~G~~~~~---~~~gsLlLg~~~~~g------~l~yvG~v-tGf~~~~~~~L~~~l~~l~~~~p~~~-~~~~~ 68 (122)
T cd07970 1 RTAD-CVVGGVRGHK---DRPGSLLLGLYDDGG------RLRHVGRT-SPLAAAERRELAELLEPARAGHPWTG-RAPGF 68 (122)
T ss_pred CcEe-EEEEEEECCC---CCccEEEEEEECCCC------CEEEEEEE-CCCCHHHHHHHHHHHHHhhcCCCCcc-ccccc
Confidence 3577 5667776432 469999999997643 79999999 89999999999999999866521111 11113
Q ss_pred cccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeecc-EEeeEecCCCccCcCC
Q 003386 195 YQVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFP-RIDRVRYDKPWHDCLD 257 (824)
Q Consensus 195 ~~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfP-r~~~iR~DK~~~e~~t 257 (824)
..........+.+|++ |.+ |+||+ +.+|+.++.|||| +|+++|+||++.+|..
T Consensus 69 ~~~~~~~~~~~~~wv~-P~l--V~eV~-------~~e~t~~G~LRhP~~f~glR~Dk~~~~v~~ 122 (122)
T cd07970 69 PSRWGTRKSLEWVPVR-PEL--VVEVS-------ADTAEGGGRFRHPLRFLRWRPDKSPEDCTL 122 (122)
T ss_pred ccccCcccCCCeEEee-ccE--EEEEE-------eeEEecCCceeCCceeEEEcCCCCHHHCcC
Confidence 2111112245789999 984 78887 5677888899999 8999999999999863
No 28
>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=99.65 E-value=3.5e-16 Score=163.31 Aligned_cols=101 Identities=25% Similarity=0.474 Sum_probs=84.9
Q ss_pred ccccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceE----EecCCHHH
Q 003386 7 AQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWS----LVAHNVDE 69 (824)
Q Consensus 7 ~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~----~~~~~~~d 69 (824)
|++.|||.|++|.++... .. ....+++|++|||| +||++|++++....+.+. +.+++.++
T Consensus 100 g~~~~F~~l~~r~~~~~~-~~--~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~~~~~~~~~~~~~~~ 176 (219)
T cd07900 100 GKILPFQVLSTRKRKDVD-AN--DIKVQVCVFAFDLLYLNGESLLKKPLRERRELLHSLFKEVPGRFQFATSKDSEDTEE 176 (219)
T ss_pred CCCcChHHHhhhcccccc-cc--cCcccEEEEEEEEEEECCchhhcCCHHHHHHHHHHhcCCCCCeEEEEEEEecCCHHH
Confidence 778999999999766544 22 23689999999986 458899999876543443 34577889
Q ss_pred HHHHHHHHHhCCCceEEEeCCC--CCCcCCCCCCCeEEEcccc
Q 003386 70 VEKFFKETIENRDEGIVLKDLG--SKWEPGDRSGKWLKLKPEY 110 (824)
Q Consensus 70 i~~~~~~ai~~g~EGIV~K~~d--S~Y~pg~Rs~~WiKiK~~y 110 (824)
+.++|+.++++|.||||+|+++ |+|.||+||.+|+|+|++|
T Consensus 177 ~~~~~~~~~~~g~EGiv~K~~~~~s~Y~~g~Rs~~W~K~K~dY 219 (219)
T cd07900 177 IQEFLEEAVKNNCEGLMVKTLDSDATYEPSKRSHNWLKLKKDY 219 (219)
T ss_pred HHHHHHHHHHcCCceEEEecCCCCCccCCCCcCCCceEeCCCC
Confidence 9999999999999999999999 9999999999999999998
No 29
>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=99.59 E-value=4.2e-15 Score=153.90 Aligned_cols=103 Identities=17% Similarity=0.253 Sum_probs=83.9
Q ss_pred ccccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCC-CCceE----EecCCHH
Q 003386 7 AQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTG-EPCWS----LVAHNVD 68 (824)
Q Consensus 7 ~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~-~~~~~----~~~~~~~ 68 (824)
+...|||.+++|.+++.... .+....+++|++||+| +||++|.+++... .+.+. +.+++.+
T Consensus 86 ~~~~~F~~l~~r~~~~~~~~-~~~~~~~~~~~vFDil~l~g~~l~~~pl~eRr~~L~~l~~~~~~~~i~~~~~~~~~~~~ 164 (207)
T cd07897 86 GRPLPFNDLQQRLGRKTVGK-KLLAEAPAAFRAYDLLELNGEDLRALPLRERRARLEALLARLPPPRLDLSPLIAFADWE 164 (207)
T ss_pred CCccCHHHHHHHhcccccch-hhHhhCCeEEEEEeeeeECceEhhhCCHHHHHHHHHHhhhhcCCCceeecceEecCCHH
Confidence 56789999999876554423 2334789999999987 4588999998764 23343 3456788
Q ss_pred HHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEcccc
Q 003386 69 EVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 110 (824)
Q Consensus 69 di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y 110 (824)
++.++|++++++|+||||+|+++|+|.+|+|+++|+|+|++-
T Consensus 165 ~~~~~~~~~~~~g~EGiv~K~~~s~Y~~Grr~~~W~K~K~d~ 206 (207)
T cd07897 165 ELAALRAQSRERGAEGLMLKRRDSPYLVGRKKGDWWKWKIDP 206 (207)
T ss_pred HHHHHHHHHHHcCCeEEEEeCCCCCcCCCCcCCCeeEeCCCC
Confidence 999999999999999999999999999999999999999984
No 30
>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=99.58 E-value=3.1e-15 Score=157.58 Aligned_cols=104 Identities=16% Similarity=0.196 Sum_probs=78.6
Q ss_pred ccccChHHHhhccccCCCc-----hhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEE----e-
Q 003386 7 AQLMTLSVLHDKDNACNIS-----TVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSL----V- 63 (824)
Q Consensus 7 ~~~~~fq~l~~r~~~~~~~-----~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~----~- 63 (824)
|++.|||.|+++.++...+ .......++|||++|||| +||++|++++....+.+.+ .
T Consensus 100 g~~~~F~~L~~~~~~~~~~~~~~~~~~~~~~~~v~~~vFDlL~lnG~~l~~~pl~eRr~~L~~l~~~~~~~~~~~~~~~i 179 (235)
T cd08039 100 GKIDPFHKIRKHVERSGSFIGTDNDSPPHEYEHLMIVFFDVLLLDDESLLSKPYSERRDLLESLVHVIPGYAGLSERFPI 179 (235)
T ss_pred CccCCHHHHHhhcccccchhccccccccccccceEEEEEEEEEECChhhhcCCHHHHHHHHHHhcccCCCcEEEEEEEee
Confidence 5588999999886533210 001123578999999987 4588999998764332211 1
Q ss_pred ----cCCHHHHHHHHHHHHhCCCceEEEeCCCCCCcCCCC-----CCCeEEEcccc
Q 003386 64 ----AHNVDEVEKFFKETIENRDEGIVLKDLGSKWEPGDR-----SGKWLKLKPEY 110 (824)
Q Consensus 64 ----~~~~~di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~R-----s~~WiKiK~~y 110 (824)
..+.+++.++|++|+++|+||||+|+++|+|.||++ +++|+|+|++|
T Consensus 180 ~~~~~~~~~~l~~~~~~a~~~g~EGIv~K~~~S~Y~pgr~~~~~r~~~WlKlK~dY 235 (235)
T cd08039 180 DFSRSSGYERLRQIFARAIAERWEGLVLKGDEEPYFDLFLEQGSFSGCWIKLKKDY 235 (235)
T ss_pred cccCCCCHHHHHHHHHHHHHcCCceEEEecCCCCcccCcccccccCCCeEEeCCCC
Confidence 235789999999999999999999999999999743 48999999998
No 31
>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=99.56 E-value=8.4e-15 Score=151.58 Aligned_cols=102 Identities=21% Similarity=0.368 Sum_probs=83.0
Q ss_pred cccccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCce----EEecCCHH
Q 003386 6 FAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCW----SLVAHNVD 68 (824)
Q Consensus 6 ~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~----~~~~~~~~ 68 (824)
.|+++|||.+++|.++... ...+....+++|++||+| +|+++|.+++... +.+ .+..++.+
T Consensus 89 ~g~~~~F~~l~~r~~~~~~-~~~~~~~~~~~~~vFDil~~~g~~l~~~pl~eR~~~L~~~~~~~-~~i~~~~~~~~~~~~ 166 (207)
T cd07901 89 DGRPLPFQETLRRFRRKYD-VEEAAEEIPLTLFLFDILYLDGEDLLDLPLSERRKILEEIVPET-EAILLAPRIVTDDPE 166 (207)
T ss_pred CCCccCHHHHHHHhccccc-hhhhhccCcEEEEEEEEEEECCcchhcCCHHHHHHHHHHhcCcC-CcEEEEEEEecCCHH
Confidence 3677899999999655443 223333679999999986 5688999999764 233 33467789
Q ss_pred HHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccc
Q 003386 69 EVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 109 (824)
Q Consensus 69 di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~ 109 (824)
++.++|+.++++|.||||+|+.+|+|.+|+|+.+|+|+||+
T Consensus 167 ~~~~~~~~~~~~g~EGiv~K~~~s~Y~~g~Rs~~wlK~K~~ 207 (207)
T cd07901 167 EAEEFFEEALEAGHEGVMVKSLDSPYQAGRRGKNWLKVKPD 207 (207)
T ss_pred HHHHHHHHHHHcCCceEEEeCCCCCcCCCCCCCCeEEecCC
Confidence 99999999999999999999999999999999999999986
No 32
>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=99.54 E-value=1.8e-14 Score=148.33 Aligned_cols=100 Identities=24% Similarity=0.310 Sum_probs=82.3
Q ss_pred ccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEE----ecCCHHHHH
Q 003386 9 LMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSL----VAHNVDEVE 71 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~----~~~~~~di~ 71 (824)
.+||+.+++|.++...+. .+....+++|++||+| +|+++|++++....+.+.+ .+++.+++.
T Consensus 85 ~~~f~~~~~~~~~~~~~~-~~~~~~~~~~~vFDil~~~g~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~~~~~~~~~~~~ 163 (201)
T cd07898 85 GLPFSELFKRLGRKFRDK-FLDEDVPVVLMAFDLLYLNGESLLDRPLRERRQLLEELFVEIPGRIRIAPALPVESAEELE 163 (201)
T ss_pred CCcHHHHHHHhcccccch-hhhccCcEEEEEEeEEeECCcchhhCCHHHHHHHHHHhhcCCCCcEEEeeeEEcCCHHHHH
Confidence 358999998876665522 2345779999999986 4688999999775444433 356788999
Q ss_pred HHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccc
Q 003386 72 KFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 109 (824)
Q Consensus 72 ~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~ 109 (824)
++|++++++|.||||+|+++|+|.+|+|+.+|+|+||+
T Consensus 164 ~~~~~~~~~g~EGim~K~~~s~Y~~g~Rs~~wlK~K~~ 201 (201)
T cd07898 164 AAFARARARGNEGLMLKDPDSPYEPGRRGLAWLKLKKE 201 (201)
T ss_pred HHHHHHHHcCCceEEEeCCCCCcCCCCcCCCcEEeCCC
Confidence 99999999999999999999999999999999999986
No 33
>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=99.53 E-value=1.6e-14 Score=150.20 Aligned_cols=96 Identities=26% Similarity=0.404 Sum_probs=78.5
Q ss_pred cccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEE----ecCCHH
Q 003386 6 FAQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSL----VAHNVD 68 (824)
Q Consensus 6 ~~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~----~~~~~~ 68 (824)
.|+.+|||.++.+.+... ...+++|++||+|+ ||++|.+++....+.+.+ ...+.+
T Consensus 101 ~g~~~~F~~l~~~~~~~~-------~~~~v~~~vFDiL~l~g~~l~~~pl~eR~~~L~~~~~~~~~~~~~~~~~~~~~~~ 173 (213)
T cd07902 101 TGKPLPFGTLGIHKKSAF-------KDANVCLFVFDCLYYNGESLMDKPLRERRKILEDNMVEIPNRIMLSEMKFVKKAD 173 (213)
T ss_pred CCcccccchhhhhhcccc-------ccCceEEEEEEEeeeCCcchhcCcHHHHHHHHHHhccCCCCeEEEEEEEEcCCHH
Confidence 477889999988765321 14589999999874 588899988765444433 356788
Q ss_pred HHHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEcccc
Q 003386 69 EVEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEY 110 (824)
Q Consensus 69 di~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y 110 (824)
++.++|+.++++|.||||+|+++|+|.+|+| +|+|+|++|
T Consensus 174 ~l~~~~~~~~~~g~EGvV~K~~~s~Y~~G~r--~W~K~K~dY 213 (213)
T cd07902 174 DLSAMIARVIKEGLEGLVLKDLKSVYEPGKR--HWLKVKKDY 213 (213)
T ss_pred HHHHHHHHHHHCCCCeEEEeCCCCCccCCCC--CceEeCCCC
Confidence 9999999999999999999999999999987 699999998
No 34
>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=99.51 E-value=2.5e-14 Score=149.72 Aligned_cols=100 Identities=30% Similarity=0.578 Sum_probs=79.7
Q ss_pred cccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEE----ecCCHHHH
Q 003386 8 QLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSL----VAHNVDEV 70 (824)
Q Consensus 8 ~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~----~~~~~~di 70 (824)
..+||+.|+++...... .....+++|++||+| +|+++|.+++......+.+ .+++.+++
T Consensus 108 ~~~~f~~l~~~~~~~~~----~~~~~~~~~~vFDiL~~~g~~l~~~pl~eR~~~L~~~~~~~~~~i~~~~~~~~~~~~~~ 183 (225)
T cd07903 108 RFLPFGTLKDVAKLREV----EDSDLQPCFVVFDILYLNGKSLTNLPLHERKKLLEKIITPIPGRLEVVKRTEASTKEEI 183 (225)
T ss_pred eeccchHHHHHHhhccc----ccCCccEEEEEEEEEEECCeecccCcHHHHHHHHHHhcCCCCCeEEEEEEEeCCCHHHH
Confidence 46799999765432110 012568999999985 5689999998765434433 45667899
Q ss_pred HHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccccc
Q 003386 71 EKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPEYI 111 (824)
Q Consensus 71 ~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~y~ 111 (824)
.++|+.++++|.||||+|+++|+|.+|+|+.+|+|+||+|+
T Consensus 184 ~~~~~~~~~~g~EGlv~K~~~s~Y~~g~Rs~~wlK~K~~Y~ 224 (225)
T cd07903 184 EEALNEAIDNREEGIVVKDLDSKYKPGKRGGGWIKIKPEYL 224 (225)
T ss_pred HHHHHHHHHcCCceEEEecCCCCCccCCcCCCcEEechhhc
Confidence 99999999999999999999999999999999999999995
No 35
>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=99.47 E-value=9e-14 Score=142.54 Aligned_cols=100 Identities=19% Similarity=0.245 Sum_probs=78.3
Q ss_pred ccccChHHHhhccccCCCchhhhccCccEEEEEccHHH-------------HHHHHHHhhcCCCCceEEec--CCHHHHH
Q 003386 7 AQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLSQ-------------LRSQIMAADQTGEPCWSLVA--HNVDEVE 71 (824)
Q Consensus 7 ~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll~-------------lr~~L~~l~~~~~~~~~~~~--~~~~di~ 71 (824)
++. |||.|++|.++.......+....+++|++||+|+ ||+.|.+++....+.+.++. .+.+++.
T Consensus 79 ~~~-~F~~l~~r~~~~~~~~~~~~~~~~~~~~vFDiL~l~g~~l~~~pl~eRr~~L~~~~~~~~~~i~~~~~~~~~~~~~ 157 (194)
T cd07905 79 GRL-DFDALQQRIHPAASRVRRLAEETPASFVAFDLLALGGRDLRGRPLRERRAALEALLAGWGPPLHLSPATTDRAEAR 157 (194)
T ss_pred CCC-CHHHHHHHhcccccchhhhhccCCEEEEEEeeeeeCCcccccCCHHHHHHHHHHHhcccCCCeEECCccCCHHHHH
Confidence 344 9999999875543322223347799999999874 58889999876545555543 3456899
Q ss_pred HHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccc
Q 003386 72 KFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 109 (824)
Q Consensus 72 ~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~ 109 (824)
++|+.++++|.||||+|+++|+|.+|+ .+|+|+|+.
T Consensus 158 ~~~~~~~~~g~EGiv~K~~~s~Y~~Gr--~~WlK~K~~ 193 (194)
T cd07905 158 EWLEEFEGAGLEGVVAKRLDGPYRPGE--RAMLKVKHR 193 (194)
T ss_pred HHHHHHHHCCCceEEEeCCCCCcCCCC--CcEEEEecc
Confidence 999999999999999999999999996 489999985
No 36
>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=99.45 E-value=1.7e-13 Score=140.01 Aligned_cols=97 Identities=22% Similarity=0.260 Sum_probs=80.8
Q ss_pred ccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCceEEecCCHHHHHHHHH
Q 003386 9 LMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCWSLVAHNVDEVEKFFK 75 (824)
Q Consensus 9 ~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~~~~~~~~~di~~~~~ 75 (824)
..+||.+++|.++... .....+++|+|||++ +|++.|+.++....+.+.++.+...+.+++|+
T Consensus 81 ~~~F~~l~~~~~~~~~----~~~~~~~~~~vFDil~~~~~~~~~~p~~eR~~~L~~~~~~~~~~i~~~~~~~~~~~~~~~ 156 (190)
T cd07906 81 RPDFQALQNRLRLRRR----LARTVPVVYYAFDLLYLDGEDLRGLPLLERKELLEELLPAGSPRLRVSEHFEGGGAALFA 156 (190)
T ss_pred CCCHHHHHHhhcccch----hcccCceEEEEEeeeeeCCcchhhCCHHHHHHHHHHHhccCCCcEEECceEcCCHHHHHH
Confidence 3699999999877541 123679999999986 45888999998765677776665566689999
Q ss_pred HHHhCCCceEEEeCCCCCCcCCCCCCCeEEEccc
Q 003386 76 ETIENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 109 (824)
Q Consensus 76 ~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~ 109 (824)
.++++|.||||+|+++|+|.+|+|+.+|+|+|+.
T Consensus 157 ~~~~~g~EGiv~K~~~s~Y~~g~rs~~wlK~K~~ 190 (190)
T cd07906 157 AACELGLEGIVAKRADSPYRSGRRSRDWLKIKCR 190 (190)
T ss_pred HHHHcCCcEEEEecCCCCcCCCCCCCccEEEecC
Confidence 9999999999999999999999999999999973
No 37
>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=99.40 E-value=7.9e-13 Score=133.06 Aligned_cols=95 Identities=19% Similarity=0.261 Sum_probs=78.1
Q ss_pred cChHHHhhccccCCCchhhhccCccEEEEEccHH-------HHHHHHHHhhcCC-CCce----EEecCCHHHHHHHHHHH
Q 003386 10 MTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------QLRSQIMAADQTG-EPCW----SLVAHNVDEVEKFFKET 77 (824)
Q Consensus 10 ~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------~lr~~L~~l~~~~-~~~~----~~~~~~~~di~~~~~~a 77 (824)
.|||.++.|.+++... .....+++|++||++ +|+++|++++... .+.+ .+.+++.+++.++|+.+
T Consensus 68 ~~f~~l~~~~~~~~~~---~~~~~~~~f~vFDil~~~~p~~eR~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~~~~~~ 144 (174)
T cd07896 68 GQFEQTSSIVRSKKPD---DEDWRKVKFMVFDLPSAKGPFEERLERLKNLLEKIPNPHIKIVPQIPVKSNEALDQYLDEV 144 (174)
T ss_pred CCHHHHHHHHhcCCCC---hhhcccceEEEEeCCCCCCCHHHHHHHHHHHHHhCCCCcEEEEeeeeeCCHHHHHHHHHHH
Confidence 3899999998776541 123579999999976 6789999999754 2233 33457788999999999
Q ss_pred HhCCCceEEEeCCCCCCcCCCCCCCeEEEcc
Q 003386 78 IENRDEGIVLKDLGSKWEPGDRSGKWLKLKP 108 (824)
Q Consensus 78 i~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~ 108 (824)
+++|.||||+|+.+|+|.+| |+.+|+|+||
T Consensus 145 ~~~g~EGlv~K~~ds~Y~~g-R~~~wlK~Kp 174 (174)
T cd07896 145 VAAGGEGLMLRRPDAPYETG-RSDNLLKLKP 174 (174)
T ss_pred HhcCCCeEEEecCCCcccCC-cCCCceeeCC
Confidence 99999999999999999988 8999999997
No 38
>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=99.33 E-value=1.8e-12 Score=132.83 Aligned_cols=99 Identities=28% Similarity=0.401 Sum_probs=79.0
Q ss_pred ccccChHHHhhccccCCCchhhhccCccEEEEEccHH-------------HHHHHHHHhhcCCCCce----EEecCCHHH
Q 003386 7 AQLMTLSVLHDKDNACNISTVAMNDGICVCVHVYMLS-------------QLRSQIMAADQTGEPCW----SLVAHNVDE 69 (824)
Q Consensus 7 ~~~~~fq~l~~r~~~~~~~~~~~~~~~~v~~~~FDll-------------~lr~~L~~l~~~~~~~~----~~~~~~~~d 69 (824)
+...||+.++.+.++........ ..+++|++||++ +|+++|.+++....+.+ ....++.++
T Consensus 87 ~~~~~f~~~~~~~~~~~~~~~~~--~~~~~~~vFDil~l~~~~l~~~p~~eR~~~L~~~~~~~~~~i~~~~~~~~~~~~~ 164 (202)
T PF01068_consen 87 GSPLPFQELSGRLNRRSKKIPEQ--SEPLQFVVFDILYLDGKDLLDLPYEERRELLEELLEPPPPRIRIVESYVVNSKEE 164 (202)
T ss_dssp SSBCCHHHHHHHHBHSSSCHHHH--HSCEEEEEEEEEEETTEECTTSCHHHHHHHHHHHBG-BTSSEEEEEEEEESSHHH
T ss_pred CcchhHHHHhhhhhhhcccchhc--cCcEEEEEEEEEEeCCeEeeeccHHHHHHHHHHhhccCCCceeEeeeecCCCHHH
Confidence 37899999999985543311112 569999999976 56889999994443333 445678999
Q ss_pred HHHHHHHHHhCCCceEEEeCCCCCCcCCCCCCCeEEEc
Q 003386 70 VEKFFKETIENRDEGIVLKDLGSKWEPGDRSGKWLKLK 107 (824)
Q Consensus 70 i~~~~~~ai~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK 107 (824)
+.++|+.+++.|.||||+|+++|+|.+|+|+.+|+|+|
T Consensus 165 ~~~~~~~~~~~g~EG~v~K~~~~~Y~~Gkrs~~w~K~K 202 (202)
T PF01068_consen 165 LEELFEEAIDQGFEGLVLKDPDSPYEPGKRSSGWLKVK 202 (202)
T ss_dssp HHHHHHHHHHTTSSEEEEEETTSSC-TTEEEEEEEEEE
T ss_pred HHHHHHHHHHcCCceEEEECCCCccCCCCcCCCcEEEC
Confidence 99999999999999999999999999999999999998
No 39
>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=99.26 E-value=1.7e-11 Score=105.81 Aligned_cols=74 Identities=24% Similarity=0.501 Sum_probs=66.3
Q ss_pred CCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecC--CChhHHhHhcCC-CeeecchHHHHH
Q 003386 318 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADN--KGLKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 318 ~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~--~t~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
.+.+|+|+.||+ .+.....+++|+++|+.|||++.....+.+||+|+... .+.++..+...+ +||+++||.|||
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 66667889999999999999999999889999998766 678888888887 999999999997
No 40
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=99.09 E-value=3.6e-10 Score=96.25 Aligned_cols=76 Identities=24% Similarity=0.430 Sum_probs=63.3
Q ss_pred CCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCC-CceEEEEecCCChh--HHhHhcCC-CeeecchHHHHHhcC
Q 003386 320 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN-SVTHCVAADNKGLK--YEAAKRRG-DVIHYSWVLDCCSQK 395 (824)
Q Consensus 320 ~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~-s~Th~Ia~~~~t~K--~~~a~~~~-dIV~p~WV~DCI~~~ 395 (824)
.+|+|+.||+.+......+.+|.++|..+||+++..+.. .+||+|+.+....+ +..+...+ +||+++||.||++.+
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 479999999987456678999999999999999999886 79999987765544 45555555 999999999999864
No 41
>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=98.98 E-value=1.5e-09 Score=95.12 Aligned_cols=76 Identities=25% Similarity=0.383 Sum_probs=59.7
Q ss_pred cccEEEEEEEeCCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCccc
Q 003386 116 DLDVLIIGGYYGSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFY 195 (824)
Q Consensus 116 ~lDlvVIGG~~g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~ 195 (824)
+.|++|+|.++|.|++.|.+|+|+|+.++. . .++||+|||++++++|. | +
T Consensus 2 ~~e~vIvG~~~g~g~~~~~~g~llv~~~~g--------~---~~~vgtG~t~~~r~~~~-----------------~-~- 51 (77)
T cd08041 2 DAEARVVGYEEGKGKYEGMLGALVVETKDG--------I---RFKIGSGFSDEQRRNPP-----------------P-I- 51 (77)
T ss_pred ceeEEEEEEEcCCCccCCcEEEEEEEecCC--------C---EEEEcCCCCHHHHhcCC-----------------C-C-
Confidence 578887777789998888999999998852 2 45999999999887542 1 1
Q ss_pred ccCCCCCCCCcEEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEe
Q 003386 196 QVTNNSKERPDVWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 247 (824)
Q Consensus 196 ~~~~~~~~~pdvWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR 247 (824)
. .|+||+ +.+++.++.||||+|+++|
T Consensus 52 ----------------g---~v~~V~-------y~e~t~~g~lR~P~f~g~R 77 (77)
T cd08041 52 ----------------G---SIITYK-------YQGLTKNGLPRFPVFLRVR 77 (77)
T ss_pred ----------------C---CEEEEE-------EEecCCCCcccCCEEEecC
Confidence 1 267787 5677889999999999997
No 42
>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=98.94 E-value=1.4e-09 Score=110.34 Aligned_cols=75 Identities=20% Similarity=0.253 Sum_probs=59.3
Q ss_pred ccEEEEEccHH-------------HHHHHHHHhhcCCCC--ceEE-----ecCCHHHHHHHHHHHHhCCCceEEEeCCCC
Q 003386 33 ICVCVHVYMLS-------------QLRSQIMAADQTGEP--CWSL-----VAHNVDEVEKFFKETIENRDEGIVLKDLGS 92 (824)
Q Consensus 33 ~~v~~~~FDll-------------~lr~~L~~l~~~~~~--~~~~-----~~~~~~di~~~~~~ai~~g~EGIV~K~~dS 92 (824)
.+++|++||++ +|++.|++++..... ...+ ......++.++|++++.+|.||||+|+++|
T Consensus 86 ~~~~~~~FDil~~~~~~~~~~p~~eR~~~L~~~v~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~g~EGvi~K~~~s 165 (182)
T cd06846 86 PKPTYYAFDVVPLSGVGLRDLPYSDRFAYLKSLLKEFEGLDPVKLVPLENAPSYDETLDDLLEKLKKKGKEGLVFKHPDA 165 (182)
T ss_pred ceeEEEEEEEEEECCCccccCCHHHHHHHHHHHhhhhccCCceeEEEeecccccchHHHHHHHHhhhcCCceEEEEcCCC
Confidence 46899999986 468889999976531 1211 122233489999999999999999999999
Q ss_pred CC--cCCCCCCCeEEEcc
Q 003386 93 KW--EPGDRSGKWLKLKP 108 (824)
Q Consensus 93 ~Y--~pg~Rs~~WiKiK~ 108 (824)
+| .+| |+..|+|+||
T Consensus 166 ~Y~~~~g-r~~~wlK~Kp 182 (182)
T cd06846 166 PYKGRPG-SSGNQLKLKP 182 (182)
T ss_pred CccccCC-CCCceEeecC
Confidence 99 888 8999999997
No 43
>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=98.92 E-value=3.5e-09 Score=88.06 Aligned_cols=70 Identities=23% Similarity=0.492 Sum_probs=59.0
Q ss_pred CeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChh-HHhHhcCC-CeeecchHHHHHh
Q 003386 324 DMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLK-YEAAKRRG-DVIHYSWVLDCCS 393 (824)
Q Consensus 324 Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K-~~~a~~~~-dIV~p~WV~DCI~ 393 (824)
|+.||+.+......+.+|.++|..+||++.......+||+|+......+ +..+...+ +||+++||.||+.
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 6789998765467899999999999999999888789999987766554 66666666 9999999999984
No 44
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=98.92 E-value=5.1e-09 Score=125.50 Aligned_cols=183 Identities=21% Similarity=0.276 Sum_probs=136.9
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHHhcCcc
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQKKL 397 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI~~~~l 397 (824)
+..|+|+.||-+... ...+++|.+.+..+||.++.+.+.++||+|+.....-||.++.+.+ +|++++||......+.+
T Consensus 7 ~~~~~~v~~~~t~i~-p~~~~~l~~~~~~~Gg~~~~~~t~~~thli~~~~~s~~~~~a~~~~~~~~~~~wi~~~~d~~~~ 85 (811)
T KOG1929|consen 7 SKPMSGVTFSPTGIN-PIKREELSKKFIKLGGIDFKDFTPSVTHLIVGSVTSSKYAAAHRFDIKVLDSSWIDYIYDLWLL 85 (811)
T ss_pred CcccCCceeccCcCC-HHHHHHHHHHHHhcCceeeeccCCcCceeecccccccchhhhhcCCCceecchHHHHHHHHhhh
Confidence 457889999976544 5668999999999999999999999999998777777886665555 99999999987766543
Q ss_pred CCCCccccccCChhhHhhhhhhccccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCeEEEEcc
Q 003386 398 LQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYH 477 (824)
Q Consensus 398 Lp~eP~~ll~~S~~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc~~YL~g 477 (824)
. . ..+. .|. .+.......|.||.|++.|
T Consensus 86 -~-~--e~~~------------~~~------------------------------------l~~~~~~p~~~~~~Vc~tg 113 (811)
T KOG1929|consen 86 -N-K--EIRL------------LDP------------------------------------LRDTMKCPGFFGLKVCLTG 113 (811)
T ss_pred -h-c--cCcc------------Ccc------------------------------------chhhhcCCcccceEEEecc
Confidence 1 1 0000 000 0011234579999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEeccc
Q 003386 478 STEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQ 556 (824)
Q Consensus 478 ~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~~~~IVt~~ 556 (824)
+.. .....+..+|.-|||+....|+ +++||++...... ..++. + ..++.+||+.+
T Consensus 114 l~~-----------~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~-~kYe~-------a-----l~wn~~v~~~~ 169 (811)
T KOG1929|consen 114 LSG-----------DEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKT-EKYEQ-------A-----LKWNIPVVSDD 169 (811)
T ss_pred cch-----------HHHHHHHHHhhhcccEEehhhhhhhheeeeccccch-HHHHH-------H-----HhhCCccccHH
Confidence 852 2456789999999999999998 5777777654421 12221 1 14678999999
Q ss_pred HHHHHHHhCCccCCCCCCCCCC
Q 003386 557 WLEDCLAKEQKSEEYEYSLKPT 578 (824)
Q Consensus 557 WLedCi~~g~~l~Ee~Y~v~~~ 578 (824)
|+++|+..+..++...|.+.+.
T Consensus 170 w~~~s~~~~~~~~~~~~e~~~~ 191 (811)
T KOG1929|consen 170 WLFDSIEKTAVLETKPYEGAPV 191 (811)
T ss_pred HHhhhhcccccccccccccccc
Confidence 9999999999999999999885
No 45
>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=98.80 E-value=1.3e-08 Score=87.75 Aligned_cols=75 Identities=27% Similarity=0.448 Sum_probs=54.6
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 543 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~ 543 (824)
..+|.||+|||.++. .. ..+.+..+|+.+||+++..++ .+||||+....... .+ ....
T Consensus 3 ~~~F~g~~f~i~~~~---~~--------~~~~l~~~i~~~GG~v~~~~~~~~thvI~~~~~~~~--~k-~~~~------- 61 (78)
T PF00533_consen 3 PKIFEGCTFCISGFD---SD--------EREELEQLIKKHGGTVSNSFSKKTTHVIVGNPNKRT--KK-YKAA------- 61 (78)
T ss_dssp TTTTTTEEEEESSTS---SS--------HHHHHHHHHHHTTEEEESSSSTTSSEEEESSSHCCC--HH-HHHH-------
T ss_pred CCCCCCEEEEEccCC---CC--------CHHHHHHHHHHcCCEEEeecccCcEEEEeCCCCCcc--HH-HHHH-------
Confidence 468999999995543 22 346789999999999999998 69999998651111 11 1111
Q ss_pred hccCCccEEecccHHHHHH
Q 003386 544 LLWNKKLHVVRSQWLEDCL 562 (824)
Q Consensus 544 ~~~~~~~~IVt~~WLedCi 562 (824)
....+.||+++||.+||
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 13568999999999997
No 46
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=98.73 E-value=2.2e-08 Score=115.26 Aligned_cols=182 Identities=20% Similarity=0.272 Sum_probs=131.1
Q ss_pred CCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCCCeeecchHHHHHhcCcc
Q 003386 318 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRGDVIHYSWVLDCCSQKKL 397 (824)
Q Consensus 318 ~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~dIV~p~WV~DCI~~~~l 397 (824)
....|.|+..|+++.- ...++|-.+|..+||-|..+.+..+||+|+....+-++..+.-.-++++|.||..|+....-
T Consensus 115 y~~~m~~vvlcfTg~r--kk~e~lv~lvh~mgg~irkd~nsktthli~n~s~gek~~~a~t~~~~~rp~wv~~aw~~rn~ 192 (850)
T KOG3524|consen 115 YCELMKDVVMCFTGER--KKKEELVDLVHYMGGSIRKDTNSKTTHLIANKVEGEKQSIALVGVPTMRPDWVTEAWKHRND 192 (850)
T ss_pred cchhhcCceeeeeccc--hhhHHHHHHHHHhcceeEeeeccCceEEEeecccceEEEEEeeccceechHhhhhhhcCcch
Confidence 4567899999987643 23458999999999999999888899999988888777766544699999999999975521
Q ss_pred CCCCccccccCChhhHhhhhhhccccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCeEEEEcc
Q 003386 398 LQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYH 477 (824)
Q Consensus 398 Lp~eP~~ll~~S~~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc~~YL~g 477 (824)
+ | +....+.|-| . -...-|.||.|+|+|
T Consensus 193 ~-----y-----------fda~~~~f~d--------------------------------~----hrl~~feg~~~~f~g 220 (850)
T KOG3524|consen 193 S-----Y-----------FDAMEPCFVD--------------------------------K----HRLGVFEGLSLFFHG 220 (850)
T ss_pred h-----h-----------hhhhccchhh--------------------------------h----hccccccCCeEeecC
Confidence 1 0 0000111111 1 123469999999999
Q ss_pred CCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCCCceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEecccH
Q 003386 478 STEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQW 557 (824)
Q Consensus 478 ~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~~~~IVt~~W 557 (824)
|.+ + ...-|...+...||........||||||.+.. ... .- + ..+..-++|..+|
T Consensus 221 F~~---e--------e~~~m~~sle~~gg~~a~~d~~cthvvv~e~~-~~~-~p-----~-------~~s~~~~~vk~ew 275 (850)
T KOG3524|consen 221 FKQ---E--------EIDDMLRSLENTGGKLAPSDTLCTHVVVNEDN-DEV-EP-----L-------AVSSNQVHVKKEW 275 (850)
T ss_pred CcH---H--------HHHHHHHHHHhcCCcccCCCCCceeEeecCCc-ccc-cc-----c-------cccccceeecccc
Confidence 852 1 23456778899999999966689999997643 111 00 0 0134568999999
Q ss_pred HHHHHHhCCccCCCCCCCCCC
Q 003386 558 LEDCLAKEQKSEEYEYSLKPT 578 (824)
Q Consensus 558 LedCi~~g~~l~Ee~Y~v~~~ 578 (824)
.+-+|..|...-|..|.....
T Consensus 276 fw~siq~g~~a~e~~yl~~~~ 296 (850)
T KOG3524|consen 276 FWVSIQRGCCAIEDNYLLPTG 296 (850)
T ss_pred eEEEEecchhccccceecccc
Confidence 999999999999999987765
No 47
>smart00292 BRCT breast cancer carboxy-terminal domain.
Probab=98.65 E-value=6.2e-08 Score=82.34 Aligned_cols=77 Identities=30% Similarity=0.357 Sum_probs=57.0
Q ss_pred CCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC--CceEEEEecCCCcccchhhhHHHHHHHhhhh
Q 003386 467 CFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA--NATHVVVLSVLGYDVNFNSLTESFTAREKHL 544 (824)
Q Consensus 467 lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls--~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~ 544 (824)
+|+||+|||.+. .... ....+..+|..+||+++..++ ++||||+.+..... .. ++..
T Consensus 2 ~f~g~~~~~~g~--~~~~--------~~~~l~~~i~~~Gg~~~~~~~~~~~thvi~~~~~~~~--~~-~~~~-------- 60 (80)
T smart00292 2 LFKGKVFVITGK--FDKN--------ERDELKELIEALGGKVTSSLSSKTTTHVIVGSPEGGK--LE-LLLA-------- 60 (80)
T ss_pred ccCCeEEEEeCC--CCCc--------cHHHHHHHHHHcCCEEecccCccceeEEEEcCCCCcc--HH-HHHH--------
Confidence 799999999982 1222 246789999999999999998 79999998654221 11 1111
Q ss_pred ccCCccEEecccHHHHHHHhC
Q 003386 545 LWNKKLHVVRSQWLEDCLAKE 565 (824)
Q Consensus 545 ~~~~~~~IVt~~WLedCi~~g 565 (824)
....++||+++||.+|++.+
T Consensus 61 -~~~~~~iV~~~Wi~~~~~~~ 80 (80)
T smart00292 61 -IALGIPIVTEDWLLDCLKAG 80 (80)
T ss_pred -HHcCCCCccHHHHHHHHHCc
Confidence 13568999999999999864
No 48
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=98.63 E-value=2.3e-08 Score=107.90 Aligned_cols=92 Identities=22% Similarity=0.426 Sum_probs=81.5
Q ss_pred cCCCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHHhc
Q 003386 316 KGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQ 394 (824)
Q Consensus 316 ~~~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI~~ 394 (824)
..-+.|++|++|.+ +|.....+.+|.......|++|-.+++..+||+|++..+|+||++....| .||+-+||.+|.++
T Consensus 312 ~el~klL~GVV~Vl-SGfqNP~Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTPKy~QV~g~Gg~IV~keWI~~Cy~~ 390 (508)
T KOG3226|consen 312 TELSKLLEGVVFVL-SGFQNPERSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTPKYRQVEGNGGTIVSKEWITECYAQ 390 (508)
T ss_pred hhHHHhhhceEEEE-ecccCchHHHHHHHHHhhcccccCCcCCCceeEEEecCCCcchhhcccCCceEeeHHHHHHHHHH
Confidence 34578999999965 56667889999999999999999999988999999999999999998887 99999999999999
Q ss_pred CccCCCCccccccCC
Q 003386 395 KKLLQLQPKYYLHLS 409 (824)
Q Consensus 395 ~~lLp~eP~~ll~~S 409 (824)
+++|||+- |++++.
T Consensus 391 kk~lp~rr-Ylm~~~ 404 (508)
T KOG3226|consen 391 KKLLPIRR-YLMHAG 404 (508)
T ss_pred HhhccHHH-HHhcCC
Confidence 99999984 566654
No 49
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=98.58 E-value=5.9e-08 Score=81.41 Aligned_cols=62 Identities=29% Similarity=0.534 Sum_probs=50.4
Q ss_pred eEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-Ceeecch
Q 003386 325 MVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSW 387 (824)
Q Consensus 325 l~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~W 387 (824)
+.||+++... ..+..|.++|..+||++..+++..+||+|+....+.||+.|.+++ +||+|+|
T Consensus 1 ~~i~~sg~~~-~~~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K~~~A~~~gi~vV~~~W 63 (63)
T PF12738_consen 1 VVICFSGFSG-KERSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKKYRKAKEWGIPVVSPDW 63 (63)
T ss_dssp -EEEEEEB-T-TTCCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHHHHHHHHCTSEEEEHHH
T ss_pred CEEEECCCCH-HHHHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHHHHHHHHCCCcEECCCC
Confidence 4678876543 348999999999999999999989999999888999999999998 9999999
No 50
>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=98.52 E-value=1.1e-07 Score=99.13 Aligned_cols=75 Identities=16% Similarity=0.257 Sum_probs=58.8
Q ss_pred ccEEEEEccHH-------------HHHHHHHHhhcCCC-------------C--ceEEec-CCHHHHHHHHHHH---HhC
Q 003386 33 ICVCVHVYMLS-------------QLRSQIMAADQTGE-------------P--CWSLVA-HNVDEVEKFFKET---IEN 80 (824)
Q Consensus 33 ~~v~~~~FDll-------------~lr~~L~~l~~~~~-------------~--~~~~~~-~~~~di~~~~~~a---i~~ 80 (824)
.+++|++||+| +|+++|++++.... . .+.... ....++..+|+.+ +.+
T Consensus 109 ~~~~~~vFDiL~~~g~~l~~~pl~~R~~~L~~~i~~~~~~~~~~~~~~~~~~~~~i~~k~~~~~~~~~~~~~~~~~~~~~ 188 (215)
T cd07895 109 KRPRYLIFDILAFNGQSVTEKPLSERLKYIKKEVIEPRNELLKKGPIDKAKEPFSVRLKDFFPLYKIEKLFEKIIPKLPH 188 (215)
T ss_pred eEEEEEEEEEEEECCcCccCCCHHHHHHHHHHhchhHHHHhhhcChhhcCCCCeEEEecceEeHHhHHHHHHhccccCCC
Confidence 47899999986 46888888884321 1 122222 2246899999999 499
Q ss_pred CCceEEEeCCCCCCcCCCCCCCeEEEcc
Q 003386 81 RDEGIVLKDLGSKWEPGDRSGKWLKLKP 108 (824)
Q Consensus 81 g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~ 108 (824)
+.||||+|+.+|+|.+| |+.+|+|+||
T Consensus 189 ~~EGlIfk~~~~~Y~~G-r~~~~lKwKp 215 (215)
T cd07895 189 ENDGLIFTPNDEPYVPG-TDKNLLKWKP 215 (215)
T ss_pred CCCCEEEccCCCCccCc-cCCcceeeCC
Confidence 99999999999999999 9999999997
No 51
>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=98.41 E-value=8.8e-07 Score=73.47 Aligned_cols=71 Identities=31% Similarity=0.402 Sum_probs=52.6
Q ss_pred CeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhccCC
Q 003386 470 GCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNK 548 (824)
Q Consensus 470 gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~ 548 (824)
||.|||.+... .. ....|..+|..+||+++..++ .+||||+....... . +... ...
T Consensus 1 ~~~~~i~g~~~--~~--------~~~~l~~~i~~~Gg~v~~~~~~~~thvI~~~~~~~~--~--~~~~---------~~~ 57 (72)
T cd00027 1 GLTFVITGDLP--SE--------ERDELKELIEKLGGKVTSSVSKKTTHVIVGSDAGPK--K--LLKA---------IKL 57 (72)
T ss_pred CCEEEEEecCC--Cc--------CHHHHHHHHHHcCCEEeccccCCceEEEECCCCCch--H--HHHH---------HHc
Confidence 68999999741 12 245789999999999999999 79999998654211 0 1111 135
Q ss_pred ccEEecccHHHHHHH
Q 003386 549 KLHVVRSQWLEDCLA 563 (824)
Q Consensus 549 ~~~IVt~~WLedCi~ 563 (824)
.++||+++||.+|++
T Consensus 58 ~~~iV~~~Wi~~~~~ 72 (72)
T cd00027 58 GIPIVTPEWLLDCLK 72 (72)
T ss_pred CCeEecHHHHHHHhC
Confidence 689999999999984
No 52
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=98.27 E-value=2.1e-06 Score=101.86 Aligned_cols=88 Identities=23% Similarity=0.348 Sum_probs=61.3
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEec-C----C-------------------CCc-eEEEEecC--CCh
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMN-L----N-------------------NSV-THCVAADN--KGL 371 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n-~----~-------------------~s~-Th~Ia~~~--~t~ 371 (824)
-+||.||.|.+++... +.+.+..-+..|||.+... + + .++ -.|+++++ .+.
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 KNIFDGCVFMLTSANR--SDSASRPSMEKHGGLVLEKGLMNLFNTPFKGGGIVLRQLNSFQERKSNYQALLISDTHYRTH 1000 (1176)
T ss_pred cchhcceeEEEecccc--chhhhhhhhhccCChhhhccccccccccccCCcchHHhhhHHhhhccccceeEeehhhhHHH
Confidence 3899999999876532 3345555566688887431 1 1 011 23455665 467
Q ss_pred hHHhHhcCC-CeeecchHHHHHhcCccCCCCccccccCC
Q 003386 372 KYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLS 409 (824)
Q Consensus 372 K~~~a~~~~-dIV~p~WV~DCI~~~~lLp~eP~~ll~~S 409 (824)
||-.+...| ||||+.||.+|+++++++++.+| +|.+.
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 887777777 99999999999999999999876 55443
No 53
>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=98.18 E-value=1.4e-06 Score=64.47 Aligned_cols=35 Identities=26% Similarity=0.495 Sum_probs=26.4
Q ss_pred hhHhhhhhhccccCCCccCCCChHHHHHHHhccCC
Q 003386 411 SSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDR 445 (824)
Q Consensus 411 ~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~ 445 (824)
+|+++|+++||+|||||+.++++++|+.+|++|..
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 47899999999999999999999999999999864
No 54
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=98.17 E-value=1.2e-06 Score=98.59 Aligned_cols=79 Identities=23% Similarity=0.390 Sum_probs=59.5
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCC----------CCceEEEEecCCChhHHhHhcCCCeeecchH
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN----------NSVTHCVAADNKGLKYEAAKRRGDVIHYSWV 388 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~----------~s~Th~Ia~~~~t~K~~~a~~~~dIV~p~WV 388 (824)
-.+|+|+.||+... ..++.|+-+|.++||.|+.++. ...||-|+ +..+.+...+ ....|.||||
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-DRPGQQTSVI--GRTYVQPQWV 398 (570)
T ss_pred HHHhhcceeeeecc---CchHHHHHHHHHcCCceecCccCCCCcccccccceeeeee-cccCccceee--eeeeecchhh
Confidence 46999999998653 4578999999999999998851 13588875 4444322111 1278999999
Q ss_pred HHHHhcCccCCCCcc
Q 003386 389 LDCCSQKKLLQLQPK 403 (824)
Q Consensus 389 ~DCI~~~~lLp~eP~ 403 (824)
+|||+++.++|.+-|
T Consensus 399 fDsvNar~llpt~~Y 413 (570)
T KOG2481|consen 399 FDSVNARLLLPTEKY 413 (570)
T ss_pred hhhccchhhccHhhh
Confidence 999999999997744
No 55
>KOG2481 consensus Protein required for normal rRNA processing [RNA processing and modification]
Probab=98.08 E-value=2.9e-06 Score=95.67 Aligned_cols=82 Identities=21% Similarity=0.194 Sum_probs=64.2
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccC---------C--CceEEEEecCCCcccchhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNL---------A--NATHVVVLSVLGYDVNFNSL 533 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~l---------s--~vTHVVV~~~~~~~~~~~~L 533 (824)
..||.||+|||....+ .+-|..+|+.+||.|+.+. + .+||=||+.+. ....
T Consensus 325 kslF~glkFfl~reVP-------------resL~fiI~s~GG~V~wd~~~~g~~~~~~d~~ITH~IvDrP~-~~~~---- 386 (570)
T KOG2481|consen 325 KSLFSGLKFFLNREVP-------------RESLEFIIRSFGGKVSWDPLGIGATYDESDERITHQIVDRPG-QQTS---- 386 (570)
T ss_pred HHHhhcceeeeeccCc-------------hHHHHHHHHHcCCceecCccCCCCcccccccceeeeeecccC-ccce----
Confidence 4699999999988532 4578899999999999883 1 36999998765 1111
Q ss_pred HHHHHHHhhhhccCCccEEecccHHHHHHHhCCccCCCCCCCCC
Q 003386 534 TESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKP 577 (824)
Q Consensus 534 r~~l~~~~~~~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~~ 577 (824)
--....|.|.||.||++++.++|.+.|.++.
T Consensus 387 -------------v~gR~YvQPQWvfDsvNar~llpt~~Y~~G~ 417 (570)
T KOG2481|consen 387 -------------VIGRTYVQPQWVFDSVNARLLLPTEKYFPGK 417 (570)
T ss_pred -------------eeeeeeecchhhhhhccchhhccHhhhCCCc
Confidence 1123669999999999999999999998654
No 56
>KOG1929 consensus Nucleotide excision repair factor NEF2, RAD4/CUT5 component [Replication, recombination and repair]
Probab=97.98 E-value=1.8e-05 Score=95.61 Aligned_cols=176 Identities=13% Similarity=0.127 Sum_probs=115.0
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCC-ChhHHhHhcCC-CeeecchHHHHHhcCc
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNK-GLKYEAAKRRG-DVIHYSWVLDCCSQKK 396 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~-t~K~~~a~~~~-dIV~p~WV~DCI~~~~ 396 (824)
...|.|+.+|+.+.. ...|.++..+|..|||++...+...+.|+++.... +-||+.|++|. +||+.+|+++|++++.
T Consensus 101 ~p~~~~~~Vc~tgl~-~~eK~ei~~~v~k~gg~~~~~L~s~v~~~~~~~~~~~~kYe~al~wn~~v~~~~w~~~s~~~~~ 179 (811)
T KOG1929|consen 101 CPGFFGLKVCLTGLS-GDEKSEIKILVPKHGGTLHRSLSSDVNSLKILPEVKTEKYEQALKWNIPVVSDDWLFDSIEKTA 179 (811)
T ss_pred CCcccceEEEecccc-hHHHHHHHHHhhhcccEEehhhhhhhheeeeccccchHHHHHHHhhCCccccHHHHhhhhcccc
Confidence 457889999997543 45789999999999999998887667777765443 48999999997 9999999999999999
Q ss_pred cCCCCccccccCChhhHhhhhhhcc-----ccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCe
Q 003386 397 LLQLQPKYYLHLSDSSKKKLQEEVD-----EFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGC 471 (824)
Q Consensus 397 lLp~eP~~ll~~S~~t~~~~~~~~D-----~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc 471 (824)
+++..|+..-.. .+.... ..-.+ --||+|+...+...- .+..++ .+..+. .+..+..+|
T Consensus 180 ~~~~~~~e~~~~-~~~is~-~~~~~~~~~~~~~~s~t~~~~~~~~-~~~~n~-------~~~p~~------a~~~~~~~c 243 (811)
T KOG1929|consen 180 VLETKPYEGAPV-AEAISG-PIGSTLPKEILDGDSRTANDTWSTS-KVVTNI-------KVLPFQ------AKIGNLDDC 243 (811)
T ss_pred cccccccccccc-cceecc-CCccccccccccccchhhhccccch-hccccc-------ccchhh------hhccccccc
Confidence 999888644221 000000 00000 122333221111000 000000 000000 122367899
Q ss_pred EEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEec
Q 003386 472 CIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLS 522 (824)
Q Consensus 472 ~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~ 522 (824)
.+|+.++.. ..+..|.+.++.+||.-.+... .++|+++..
T Consensus 244 ~v~~s~~~~-----------~~~s~l~r~~~~g~~~~~~e~~e~~st~l~~~ 284 (811)
T KOG1929|consen 244 LVETSGTTS-----------RNRSALSRLSNNGGSLRFLERLEETSTSLLGD 284 (811)
T ss_pred eeeecCCcc-----------cchhHhHHhhhcccceeecccCccccchhhcc
Confidence 999999863 2345788999999999888776 699999875
No 57
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=97.89 E-value=6.8e-06 Score=89.85 Aligned_cols=79 Identities=25% Similarity=0.381 Sum_probs=58.1
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCC-----------CCceEEEEecCCChhHHhHhcCCCeeecch
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLN-----------NSVTHCVAADNKGLKYEAAKRRGDVIHYSW 387 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~-----------~s~Th~Ia~~~~t~K~~~a~~~~dIV~p~W 387 (824)
..||+|+.|||.... ....|+-+|.++||.++..+. ..+||-|+ ++..++-.. .....|.|||
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 469999999997543 356899999999999988763 24688874 443332111 1227899999
Q ss_pred HHHHHhcCccCCCCcc
Q 003386 388 VLDCCSQKKLLQLQPK 403 (824)
Q Consensus 388 V~DCI~~~~lLp~eP~ 403 (824)
|+|||++|.+.+.+-|
T Consensus 422 ~fDsiNkG~l~~~~~Y 437 (591)
T COG5163 422 LFDSINKGKLACVENY 437 (591)
T ss_pred HHhhhccccchhhhhc
Confidence 9999999998887643
No 58
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=97.81 E-value=4.5e-05 Score=92.82 Aligned_cols=87 Identities=21% Similarity=0.323 Sum_probs=73.5
Q ss_pred CCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCC----C-hhHHhHhcCC-CeeecchHHHH
Q 003386 318 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNK----G-LKYEAAKRRG-DVIHYSWVLDC 391 (824)
Q Consensus 318 ~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~----t-~K~~~a~~~~-dIV~p~WV~DC 391 (824)
....|.|+.|||++.... ++.++.++|..+||++..... .+||||+++.. + -|+..|...+ +||+.+||.+|
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 899999999999999988874 58899987643 3 6888888888 99999999999
Q ss_pred HhcCccCCCCccccc
Q 003386 392 CSQKKLLQLQPKYYL 406 (824)
Q Consensus 392 I~~~~lLp~eP~~ll 406 (824)
+..+..+++.++++.
T Consensus 264 i~~~k~~~~~~y~l~ 278 (815)
T PLN03122 264 IEKQEAQPLEAYDVV 278 (815)
T ss_pred HhcCCcccchhhhhc
Confidence 999999999887654
No 59
>COG5163 NOP7 Protein required for biogenesis of the 60S ribosomal subunit [Translation, ribosomal structure and biogenesis]
Probab=97.66 E-value=5.4e-05 Score=83.03 Aligned_cols=105 Identities=19% Similarity=0.176 Sum_probs=71.3
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccC-----------C-CceEEEEecCCCcccchhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNL-----------A-NATHVVVLSVLGYDVNFNS 532 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~l-----------s-~vTHVVV~~~~~~~~~~~~ 532 (824)
.+||+|++||+...-+ ...|..+|..+||.|..+. + .+||-||+.+. ++
T Consensus 348 ~slFS~f~FyisreVp-------------~dsLefiilscGG~V~~~p~~~~i~~~~~vD~~vth~i~drp~-----~~- 408 (591)
T COG5163 348 KSLFSGFKFYISREVP-------------GDSLEFIILSCGGSVVGSPCEADIHVSEKVDEKVTHQIVDRPV-----MK- 408 (591)
T ss_pred hhhhhceEEEEecccc-------------chHHHHHHHHcCCcccCchhhccCCchhhccchhhhhhccchh-----hh-
Confidence 4699999999988532 2467889999999998643 1 28999998764 21
Q ss_pred hHHHHHHHhhhhccCCccEEecccHHHHHHHhCCccCCCCCCCCCCCCCcccccccccccccCCCCCc
Q 003386 533 LTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQESYLELCEEDLDMEEPSST 600 (824)
Q Consensus 533 Lr~~l~~~~~~~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~~~~~~e~~~~~~~~~~~~~~~~~~ 600 (824)
+. ......|.|.||.+||..|.+++.+.|.++..-..--.--.+....+|.|+-+.
T Consensus 409 --~k----------vegrtYiQPQw~fDsiNkG~l~~~~~Y~~G~~LPpHlSPf~~v~~ydP~a~l~~ 464 (591)
T COG5163 409 --NK----------VEGRTYIQPQWLFDSINKGKLACVENYCVGKRLPPHLSPFASVDSYDPRASLMT 464 (591)
T ss_pred --hh----------hcceeeechHHHHhhhccccchhhhhccccccCCCCcCccccccccCCcchhhh
Confidence 11 123467999999999999999999999876433211111123333556555443
No 60
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=97.58 E-value=6.1e-05 Score=64.29 Aligned_cols=65 Identities=25% Similarity=0.474 Sum_probs=39.3
Q ss_pred CCCCCCCCcceEEEEEecCCCCCCCCccEEEEEEeCCCCCHHHHHHHHHHhccchhccCCCCCCCCcccccCCCCCCCCc
Q 003386 127 GSGRRGGEVAQFLVALAERPAPDTYPRRFISFCRVGTGLSDEELDAVVTKLKPYFRKYEYPKRAPPSFYQVTNNSKERPD 206 (824)
Q Consensus 127 g~Grr~g~~~sfllGv~~~~~~~~~~~~~~~~gkVGtGfs~~e~~~L~~~L~~~~~~~~~~~~~pP~~~~~~~~~~~~pd 206 (824)
|+|+..|.+|+|+|-..+ + ..++||+|||+++++.+. . +
T Consensus 2 G~Gk~~g~~Galv~~~~~--G---------~~f~iGsG~td~~R~~~~------~---------------i--------- 40 (66)
T PF14743_consen 2 GKGKFKGMLGALVCETED--G---------VEFKIGSGFTDEEREEPP------Y---------------I--------- 40 (66)
T ss_dssp ---EEEEEEEEEEEEE-T--T---------EEEEE-SS--HHHHHHHH------H---------------T---------
T ss_pred CccccCCCEEEEEEEeCC--C---------CEEEECCCCCHHHHhcCC------C---------------C---------
Confidence 567777889999996632 1 357899999999987643 0 0
Q ss_pred EEEeCCcceEEEEEEecccccccccccCCceeeccEEeeEe
Q 003386 207 VWIESPEKSIILSITSDIRTIRSEVFSAPYSLRFPRIDRVR 247 (824)
Q Consensus 207 vWi~~P~~svVvEVka~~~~~~s~~~~~g~tLRfPr~~~iR 247 (824)
.-+++|++ ...+..+.+|||+|.++|
T Consensus 41 --------G~iit~ky-------~~~t~~g~pRfP~f~~~R 66 (66)
T PF14743_consen 41 --------GKIITVKY-------QGLTKDGSPRFPVFVRVR 66 (66)
T ss_dssp --------T-EEEEEE-------E-TTSSSS-EEEEEEEE-
T ss_pred --------CCEEEEEE-------EccCCCCccccCEEEEeC
Confidence 02556774 344677899999999998
No 61
>PF12738 PTCB-BRCT: twin BRCT domain; PDB: 3PA6_A 3KTF_C 2WT8_C 3EF1_A 3EF0_A.
Probab=97.56 E-value=3.4e-05 Score=64.63 Aligned_cols=62 Identities=24% Similarity=0.372 Sum_probs=41.3
Q ss_pred eEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhccCCc
Q 003386 471 CCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKK 549 (824)
Q Consensus 471 c~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~~ 549 (824)
|+|++.|+.+ .+ +..+..++..+||++..+++ ++||+|+....+.+ +. . + ....
T Consensus 1 ~~i~~sg~~~---~~--------~~~l~~~i~~~Gg~~~~~lt~~~THLI~~~~~~~K--~~---~----A-----~~~g 55 (63)
T PF12738_consen 1 VVICFSGFSG---KE--------RSQLRKLIEALGGKYSKDLTKKTTHLICSSPEGKK--YR---K----A-----KEWG 55 (63)
T ss_dssp -EEEEEEB-T---TT--------CCHHHHHHHCTT-EEESSSSTT-SEEEEES--HHH--HH---H----H-----HHCT
T ss_pred CEEEECCCCH---HH--------HHHHHHHHHHCCCEEeccccCCceEEEEeCCCcHH--HH---H----H-----HHCC
Confidence 5789999863 12 34788999999999999998 69999997654322 11 1 1 1244
Q ss_pred cEEecccH
Q 003386 550 LHVVRSQW 557 (824)
Q Consensus 550 ~~IVt~~W 557 (824)
++||+++|
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 62
>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=97.30 E-value=0.00021 Score=79.79 Aligned_cols=77 Identities=18% Similarity=0.263 Sum_probs=61.5
Q ss_pred cEEEEEccHHH-----------HHHHHHHhhcCCCCce-EEecCCHHHHHHHHHHHHhCCCceEEEeCCCC-----CCcC
Q 003386 34 CVCVHVYMLSQ-----------LRSQIMAADQTGEPCW-SLVAHNVDEVEKFFKETIENRDEGIVLKDLGS-----KWEP 96 (824)
Q Consensus 34 ~v~~~~FDll~-----------lr~~L~~l~~~~~~~~-~~~~~~~~di~~~~~~ai~~g~EGIV~K~~dS-----~Y~p 96 (824)
++.||+||+++ ++++|+++..+..+.+ ++...+.+++.++|+.+++.|.||||+|++++ .|..
T Consensus 125 ~v~F~vFDI~~~~~~~~lp~~eR~~lLe~lg~~~v~~~~~~~~~d~~~l~~~l~~~~~~G~EGVVlK~~~~~~~~~Ky~t 204 (342)
T cd07894 125 DVGFFVFDIRKKNTGRPLPVEERRELLEKYGLPTVRLFGEFTADEIEELKEIIRELDKEGREGVVLKDPDMRVPPLKYTT 204 (342)
T ss_pred ccEEEEEeeEEcCCCCCCCHHHHHHHHHhcCCCCcceEEEEecCCHHHHHHHHHHHHHCCCceEEEeccccccCcceeec
Confidence 88999999864 3667777733322222 45666789999999999999999999999999 7888
Q ss_pred CCCCCCeEEEcccc
Q 003386 97 GDRSGKWLKLKPEY 110 (824)
Q Consensus 97 g~Rs~~WiKiK~~y 110 (824)
...+-+||++.-.|
T Consensus 205 ~~~~~~di~~~~~~ 218 (342)
T cd07894 205 SYSNCSDIRYAFRY 218 (342)
T ss_pred CCCCcHHHHHHhhh
Confidence 77788899888887
No 63
>KOG3226 consensus DNA repair protein [Replication, recombination and repair]
Probab=97.21 E-value=0.00067 Score=74.16 Aligned_cols=88 Identities=14% Similarity=0.261 Sum_probs=68.1
Q ss_pred CCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhh
Q 003386 466 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHL 544 (824)
Q Consensus 466 ~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~ 544 (824)
.|+.|.+|-|+||. +++ +..|+......|+++..+.. +|||+||.-++-+ .|.++.
T Consensus 316 klL~GVV~VlSGfq---NP~--------Rs~LRskAl~LGAkY~pDW~~gsThLICAF~NTP--Ky~QV~---------- 372 (508)
T KOG3226|consen 316 KLLEGVVFVLSGFQ---NPE--------RSTLRSKALTLGAKYQPDWNAGSTHLICAFPNTP--KYRQVE---------- 372 (508)
T ss_pred HhhhceEEEEeccc---Cch--------HHHHHHHHHhhcccccCCcCCCceeEEEecCCCc--chhhcc----------
Confidence 47899999999974 444 33677788899999999998 7999999876522 233111
Q ss_pred ccCCccEEecccHHHHHHHhCCccCCCCCCCCCC
Q 003386 545 LWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPT 578 (824)
Q Consensus 545 ~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~~~ 578 (824)
...=+||+-+||++|-...++||-+.|.+.-.
T Consensus 373 --g~Gg~IV~keWI~~Cy~~kk~lp~rrYlm~~~ 404 (508)
T KOG3226|consen 373 --GNGGTIVSKEWITECYAQKKLLPIRRYLMHAG 404 (508)
T ss_pred --cCCceEeeHHHHHHHHHHHhhccHHHHHhcCC
Confidence 22338999999999999999999999986544
No 64
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=97.10 E-value=0.001 Score=82.99 Aligned_cols=86 Identities=17% Similarity=0.361 Sum_probs=70.2
Q ss_pred CCCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEec---CCChhHHhHhcCC-CeeecchHHHHH
Q 003386 317 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD---NKGLKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 317 ~~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~---~~t~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
.....|.|+.|++++-. ...+.++.++|..|||++.......+||+|+.. +.+.+++.|...+ +||+.+||.||+
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 45588999999998653 345689999999999999988877789887643 3456788888777 999999999999
Q ss_pred hcCccCCCCcc
Q 003386 393 SQKKLLQLQPK 403 (824)
Q Consensus 393 ~~~~lLp~eP~ 403 (824)
..+..+|...+
T Consensus 468 ~~~~~~p~~~y 478 (981)
T PLN03123 468 KKKKKLPFDKY 478 (981)
T ss_pred hccccCcchhh
Confidence 99887777644
No 65
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=96.91 E-value=0.0031 Score=74.85 Aligned_cols=194 Identities=21% Similarity=0.203 Sum_probs=115.3
Q ss_pred CCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEec------CCChhHHhHhcCC-CeeecchHHHHH
Q 003386 320 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD------NKGLKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 320 ~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~------~~t~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
.=|.-..-.+.++...-.++-|++..+. ++..+....+||+|+.. ..|.|+...+..| =|+++.|+..|+
T Consensus 473 ~~~~kk~~~~~s~l~p~ek~~v~~~a~~---t~~k~~~~~~thvi~~~~~~g~c~rTlk~~~gil~gkwi~~~~w~~~s~ 549 (684)
T KOG4362|consen 473 HRFKKKLVLLVSGLTPSEKQLVEKFAVD---TISKFWIEPVTHVIASTDLEGACLRTLKVLMGILRGKWILSYDWVLASL 549 (684)
T ss_pred cCcccceeeeeccCCcchHHHHHHHHHH---HHhhccCCCceeeeeecccccchhhhHHHHHHhhcCceeeeHHHHHHHH
Confidence 3343333444555444456777777766 77777777899999742 2456676666677 899999999999
Q ss_pred hcCccCCCCccccccCChhhHhhhhhhccccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCeE
Q 003386 393 SQKKLLQLQPKYYLHLSDSSKKKLQEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCC 472 (824)
Q Consensus 393 ~~~~lLp~eP~~ll~~S~~t~~~~~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc~ 472 (824)
..+.+++.+|+.+-.-+ .|-+-... ... + -.......||.|..
T Consensus 550 k~~~~~~eepfEl~~d~-------------~~~~~~~~--~~~-------------------~---~a~s~~~kLf~gl~ 592 (684)
T KOG4362|consen 550 KLRKWVSEEPFELQIDV-------------PGAREGPK--EKR-------------------L---RAESYKPKLFEGLK 592 (684)
T ss_pred HhcCCCCCCCeeEeecc-------------cCcccCcc--ccc-------------------c---cccccCcchhcCCc
Confidence 99999999997653211 11100000 000 0 00112356999999
Q ss_pred EEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccC------CCceEEEEecCC-CcccchhhhHHHHHHHhhhhc
Q 003386 473 IYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNL------ANATHVVVLSVL-GYDVNFNSLTESFTAREKHLL 545 (824)
Q Consensus 473 ~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~l------s~vTHVVV~~~~-~~~~~~~~Lr~~l~~~~~~~~ 545 (824)
|||.+. +.+.. .+.|..++...||++..-- ..++-|++.... ........-...+ -.+.
T Consensus 593 ~~~~g~--fs~~p--------~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~----ea~~ 658 (684)
T KOG4362|consen 593 FYFVGD--FSNPP--------KEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDA----EALA 658 (684)
T ss_pred ceeecc--cccCc--------HHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccH----HHHH
Confidence 999984 44443 3578899999999986532 235555554321 1110010000000 0111
Q ss_pred cCCccEEecccHHHHHHHhCCc
Q 003386 546 WNKKLHVVRSQWLEDCLAKEQK 567 (824)
Q Consensus 546 ~~~~~~IVt~~WLedCi~~g~~ 567 (824)
..-+.+.|+..||.++|.-.+.
T Consensus 659 ~s~~a~~~~~~wvl~s~a~~~~ 680 (684)
T KOG4362|consen 659 LSQRARAVSSSWVLDSIAGYQI 680 (684)
T ss_pred HhcCCCccchhhhhcchhceee
Confidence 2346788999999999875443
No 66
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.42 E-value=0.0074 Score=72.98 Aligned_cols=74 Identities=16% Similarity=0.249 Sum_probs=64.8
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHH
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
...|.|++|||++.....+|++++++|.++||++....+..++++|++...+-|+..|...| +|+.-+.+++-+
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 35799999999987777899999999999999999999888889998877788999998888 999988887643
No 67
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=96.32 E-value=0.0092 Score=72.31 Aligned_cols=74 Identities=16% Similarity=0.163 Sum_probs=65.8
Q ss_pred CccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHHhc
Q 003386 321 IFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQ 394 (824)
Q Consensus 321 lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI~~ 394 (824)
.|.|+.|||++.....+|++++++|.++||++..+.+..++++|+++..+-|+..|...+ +|++-.-+++.+.+
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 499999999987767899999999999999999999888888998877788999998888 99999988887765
No 68
>PLN03122 Poly [ADP-ribose] polymerase; Provisional
Probab=96.30 E-value=0.0067 Score=74.38 Aligned_cols=92 Identities=25% Similarity=0.317 Sum_probs=67.5
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCCCceEEEEecCCCcccchhhhHHHHHHHhhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHL 544 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~ 544 (824)
...|.|++|.|.|.- .. ....++.+|..+||+++..++.+||+|+....-....-..+++ +
T Consensus 187 ~kpL~G~~fviTGtl--~~---------sr~elK~~Ie~~GGkvsssVs~~T~lIvt~~ev~k~gsSKlkk----A---- 247 (815)
T PLN03122 187 GKPFSGMMISLSGRL--SR---------THQYWKKDIEKHGGKVANSVEGVTCLVVSPAERERGGSSKIAE----A---- 247 (815)
T ss_pred CCCcCCcEEEEeCCC--CC---------CHHHHHHHHHHcCCEEccccccceEEEEcCccccccCccHHHH----H----
Confidence 446899999999952 21 1357899999999999999999999998753200000011121 1
Q ss_pred ccCCccEEecccHHHHHHHhCCccCCCCCCCC
Q 003386 545 LWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLK 576 (824)
Q Consensus 545 ~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~ 576 (824)
....++||+.+||.+|+..+..+++..|.+.
T Consensus 248 -k~lgIpIVsEd~L~d~i~~~k~~~~~~y~l~ 278 (815)
T PLN03122 248 -MERGIPVVREAWLIDSIEKQEAQPLEAYDVV 278 (815)
T ss_pred -HHcCCcCccHHHHHHHHhcCCcccchhhhhc
Confidence 1236899999999999999999999999874
No 69
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=96.19 E-value=0.013 Score=71.27 Aligned_cols=76 Identities=14% Similarity=0.252 Sum_probs=66.9
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCC-hhHHhHhcCC-CeeecchHHHHHhc
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG-LKYEAAKRRG-DVIHYSWVLDCCSQ 394 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t-~K~~~a~~~~-dIV~p~WV~DCI~~ 394 (824)
...|.|..|||++.....+|.+++++|.++||++..+.+..++++|+++..+ -|...|...+ +|++-.-+++-++.
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 4579999999998777789999999999999999999988888999887777 5898888888 99999988887765
No 70
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=96.03 E-value=0.015 Score=64.24 Aligned_cols=75 Identities=19% Similarity=0.198 Sum_probs=57.7
Q ss_pred CCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEec---------CCChhHHhHhcC-----C-Ce
Q 003386 318 ETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAAD---------NKGLKYEAAKRR-----G-DV 382 (824)
Q Consensus 318 ~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~---------~~t~K~~~a~~~-----~-dI 382 (824)
....|.|+.|||++.....+|.+++++|+++||++..+.+..++++|+++ ..+-|++.|... + +|
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 34679999999998777789999999999999999999988788888764 235577766543 3 78
Q ss_pred eecchHHHHH
Q 003386 383 IHYSWVLDCC 392 (824)
Q Consensus 383 V~p~WV~DCI 392 (824)
++-+=+++-|
T Consensus 297 i~E~~f~~l~ 306 (309)
T PRK06195 297 LNEEEFLQKC 306 (309)
T ss_pred ecHHHHHHHH
Confidence 7755444433
No 71
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=95.98 E-value=0.017 Score=64.06 Aligned_cols=73 Identities=15% Similarity=0.152 Sum_probs=61.8
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCC--hhHHhHhcCC-CeeecchHHHHH
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKG--LKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t--~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
..+|.|++|+|++... .+|++++++|.++||++..+.+..++++|+++..+ -|.+.|.+.+ +||+-.=+++-+
T Consensus 230 ~~l~~g~~~v~TG~l~-~~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~~~ssK~~kA~~~gi~ii~e~~f~~ll 305 (313)
T PRK06063 230 RPLVQGMRVALSAEVS-RTHEELVERILHAGLAYSDSVDRDTSLVVCNDPAPEQGKGYHARQLGVPVLDEAAFLELL 305 (313)
T ss_pred CcccCCCEEEEecCCC-CCHHHHHHHHHHcCCEecCccccCccEEEECCCCCcccHHHHHHHcCCccccHHHHHHHH
Confidence 4689999999987654 69999999999999999999988889999887666 5888888877 999877666654
No 72
>PLN03123 poly [ADP-ribose] polymerase; Provisional
Probab=95.95 E-value=0.011 Score=73.95 Aligned_cols=90 Identities=18% Similarity=0.261 Sum_probs=65.5
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 543 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~ 543 (824)
...|.|++|.+.|. +.. ....++..|..+||+++..++ .+||||+... +...-..+..+
T Consensus 391 ~~~l~~~~i~i~G~--~~~---------~~~~~k~~Ie~~GG~~s~~v~~~~t~l~tt~e------~~k~~~kv~qA--- 450 (981)
T PLN03123 391 SEFLGDLKVSIVGA--SKE---------KVTEWKAKIEEAGGVFHATVKKDTNCLVVCGE------LDDEDAEMRKA--- 450 (981)
T ss_pred CCCcCCeEEEEecC--CCC---------cHHHHHHHHHhcCCEEeeeccCCceEEEccHH------hhhcchHHHHH---
Confidence 45799999999995 221 124678899999999999998 6999887632 21111112111
Q ss_pred hccCCccEEecccHHHHHHHhCCccCCCCCCCC
Q 003386 544 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLK 576 (824)
Q Consensus 544 ~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~ 576 (824)
....++||+.+||.+|+..+.++|+..|.+.
T Consensus 451 --k~~~ipIVsedwL~ds~~~~~~~p~~~y~~~ 481 (981)
T PLN03123 451 --RRMKIPIVREDYLVDCFKKKKKLPFDKYKLE 481 (981)
T ss_pred --HhcCCCcccHHHHHHHHhccccCcchhhhhc
Confidence 1225899999999999999999999999664
No 73
>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=95.73 E-value=0.021 Score=69.12 Aligned_cols=68 Identities=18% Similarity=0.286 Sum_probs=58.9
Q ss_pred CCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-Ceeecc
Q 003386 319 TSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYS 386 (824)
Q Consensus 319 s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~ 386 (824)
...|.|..|||++.....+|.+++++|.++||++..+.+..++++|+++..+-|+..|...+ +|++-+
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 45799999999987777899999999999999999999888889998877778999888877 887643
No 74
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=95.58 E-value=0.015 Score=70.16 Aligned_cols=89 Identities=15% Similarity=0.165 Sum_probs=66.4
Q ss_pred ccCCCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEE-ecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHH
Q 003386 315 IKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFS-MNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 315 ~~~~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv-~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
-...+..|+|..||+ ++....+.++|.+.-.-|||.+- ......++|+|+.+-...++... .. ..++++|+.+|+
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 346788999999987 44445678899999999999986 44444578888765443333322 12 789999999999
Q ss_pred hcCccCCCCccccc
Q 003386 393 SQKKLLQLQPKYYL 406 (824)
Q Consensus 393 ~~~~lLp~eP~~ll 406 (824)
+.+.++.+.|++..
T Consensus 118 ~~~~~~~~~~~~~~ 131 (1016)
T KOG2093|consen 118 ENGMDVGYYPYQLY 131 (1016)
T ss_pred hccCccccccceee
Confidence 99999999887554
No 75
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=95.21 E-value=0.045 Score=65.28 Aligned_cols=73 Identities=21% Similarity=0.228 Sum_probs=64.8
Q ss_pred CCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHH
Q 003386 320 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCC 392 (824)
Q Consensus 320 ~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI 392 (824)
..|.|++|++++....++|.+...+|.+.||++..+.+..++++|+++..|-|+..|...| +|+.-.++..-+
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 7899999999988888999999999999999999998877788888888888999999988 999988876543
No 76
>COG5275 BRCT domain type II [General function prediction only]
Probab=95.01 E-value=0.076 Score=54.79 Aligned_cols=80 Identities=25% Similarity=0.218 Sum_probs=65.7
Q ss_pred ccccCCCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCCh-hHHhHhcCC-CeeecchHHH
Q 003386 313 SDIKGETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGL-KYEAAKRRG-DVIHYSWVLD 390 (824)
Q Consensus 313 s~~~~~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~-K~~~a~~~~-dIV~p~WV~D 390 (824)
|..+++.+.+.|++|.|++....++|.+-+.+|+.+||++...+...++++|+++..++ |+..++..+ ++|.-+=++.
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 34557789999999999887777899999999999999999998877889999887665 677777766 8877766665
Q ss_pred HH
Q 003386 391 CC 392 (824)
Q Consensus 391 CI 392 (824)
.|
T Consensus 228 LI 229 (276)
T COG5275 228 LI 229 (276)
T ss_pred HH
Confidence 55
No 77
>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=93.21 E-value=0.19 Score=62.63 Aligned_cols=127 Identities=20% Similarity=0.271 Sum_probs=83.6
Q ss_pred HHHHHHHHHcCCEEEecCCCCceEEEEec-CCChhHHhHhcCC-CeeecchHHHHHhcCccCCCCccccccCChhhHhhh
Q 003386 339 DSLHKMVVENGGTFSMNLNNSVTHCVAAD-NKGLKYEAAKRRG-DVIHYSWVLDCCSQKKLLQLQPKYYLHLSDSSKKKL 416 (824)
Q Consensus 339 ~eLeklI~~~GG~vv~n~~~s~Th~Ia~~-~~t~K~~~a~~~~-dIV~p~WV~DCI~~~~lLp~eP~~ll~~S~~t~~~~ 416 (824)
.-+...++..||.+..+.. ..||+|+-. ..|.++-.++..| +||+++||.+|+..|.+++..|| +++-.. +++
T Consensus 671 ~~~k~~~k~lg~s~~ss~~-e~Th~i~~rirRT~k~Leai~~G~~ivT~~wL~s~~k~g~~~dek~y-il~D~e--kEk- 745 (896)
T KOG2043|consen 671 KNYKLAKKFLGGSVASSDS-EATHFIADRIRRTLKFLEAISSGKPLVTPQWLVSSLKSGEKLDEKPY-ILHDEE--KEK- 745 (896)
T ss_pred hhhhhHHhhccceeecccc-cceeeeehhhhccHHHHhhhccCCcccchHHHHHHhhccccccCccc-cccCHH--HHh-
Confidence 3467778888888877766 479998642 3577777788888 99999999999999999999986 443211 110
Q ss_pred hhhccccCCCccCCCChHHHHHHHhccCCCCCcchhHHHhhhcCCCCCCCCCCCeEEEEccCCCCCCCchHHHHHHHHHH
Q 003386 417 QEEVDEFSDLYFWDLDLADIKQLLSNVDRSEDPKTIDYYKKKYCPQDKWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRR 496 (824)
Q Consensus 417 ~~~~D~yGDSy~~dit~~~L~~ll~~~~~se~~~~i~~l~~~~~~~~~~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~ 496 (824)
.||= .|...+.+ - ....+|.|..||+..... .. ...
T Consensus 746 -----~~gf---------~l~ssl~R------------A-------r~~plL~g~~v~vtp~v~--p~---------~~~ 781 (896)
T KOG2043|consen 746 -----EFGF---------RLKSSLLR------------A-------RADPLLEGINVHVTPSVT--PS---------PKT 781 (896)
T ss_pred -----ccCc---------chhhHHHH------------h-------hcchhhcCceEEeccccc--cC---------cch
Confidence 0110 00000100 0 112578899999877531 11 235
Q ss_pred HHHHHHhcCCEEEccCCC
Q 003386 497 LKLEISFHGGKVCNNLAN 514 (824)
Q Consensus 497 L~~~I~~~GG~V~~~ls~ 514 (824)
+-.+|...||.++..+..
T Consensus 782 v~eiie~~ggnvv~~~p~ 799 (896)
T KOG2043|consen 782 VVEIIEISGGNVVSDSPK 799 (896)
T ss_pred hHHHHhhcCcceecccCc
Confidence 677899999999988763
No 78
>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=93.04 E-value=0.078 Score=65.95 Aligned_cols=70 Identities=26% Similarity=0.365 Sum_probs=53.1
Q ss_pred HHHHHHHhcCCEEEccCCCceEEEEecCCCcccchhhhHHHHHHHhhhhccCCccEEecccHHHHHHHhCCccCCCCCCC
Q 003386 496 RLKLEISFHGGKVCNNLANATHVVVLSVLGYDVNFNSLTESFTAREKHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSL 575 (824)
Q Consensus 496 ~L~~~I~~~GG~V~~~ls~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v 575 (824)
.+++.+++.||.+.....++||+|++.-- +. .. .+ .++ ....-||++.||.+|++.|..++|..|.+
T Consensus 672 ~~k~~~k~lg~s~~ss~~e~Th~i~~rir-RT--~k----~L-eai-----~~G~~ivT~~wL~s~~k~g~~~dek~yil 738 (896)
T KOG2043|consen 672 NYKLAKKFLGGSVASSDSEATHFIADRIR-RT--LK----FL-EAI-----SSGKPLVTPQWLVSSLKSGEKLDEKPYIL 738 (896)
T ss_pred hhhhHHhhccceeecccccceeeeehhhh-cc--HH----HH-hhh-----ccCCcccchHHHHHHhhccccccCccccc
Confidence 57889999999999999999999997421 11 11 11 111 23458999999999999999999999976
Q ss_pred CCC
Q 003386 576 KPT 578 (824)
Q Consensus 576 ~~~ 578 (824)
.-.
T Consensus 739 ~D~ 741 (896)
T KOG2043|consen 739 HDE 741 (896)
T ss_pred cCH
Confidence 543
No 79
>KOG3548 consensus DNA damage checkpoint protein RHP9/CRB2/53BP1 [Replication, recombination and repair]
Probab=90.89 E-value=0.3 Score=59.62 Aligned_cols=36 Identities=11% Similarity=0.219 Sum_probs=30.4
Q ss_pred CccEEecccHHHHHHHhCCccCCCCCCCCCCCCCcc
Q 003386 548 KKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGMQES 583 (824)
Q Consensus 548 ~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~~~~~~e~ 583 (824)
..+.+|.+.||-+|++++++|+-.+|+++-......
T Consensus 1008 ~giPcVh~~fI~aC~e~nr~Vdy~~YLLpsGyS~rl 1043 (1176)
T KOG3548|consen 1008 RGIPCVHNTFIQACGEQNRCVDYTDYLLPSGYSIRL 1043 (1176)
T ss_pred cCCCcccHHHHHHHHhccccccchhhcccCcccccc
Confidence 467889999999999999999999998876664333
No 80
>KOG0966 consensus ATP-dependent DNA ligase IV [Replication, recombination and repair]
Probab=89.23 E-value=0.78 Score=55.59 Aligned_cols=89 Identities=18% Similarity=0.243 Sum_probs=62.2
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 543 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~ 543 (824)
..+|.|.-||+..-++.. + ....|+..|.-+||+++..+. ..||.|+.-+... .... ..+
T Consensus 631 s~if~gl~f~Vlsgt~~~--~-------tk~~le~~ivenGG~iv~nv~p~~~~ci~~a~~et-~~vk---~~~------ 691 (881)
T KOG0966|consen 631 SNIFDGLEFCVLSGTSET--H-------TKAKLEEIIVENGGKIVQNVGPSDTLCIATAGKET-TRVK---AQA------ 691 (881)
T ss_pred hhhhcCeeEEEecCCccc--c-------cHHHHHHHHHHcCCEEEEcCCCCCcceEEeccccc-hHHH---HHH------
Confidence 568999999997644211 1 246789999999999999887 5888886432111 1111 111
Q ss_pred hccCCccEEecccHHHHHHHhCCccCCCCCC
Q 003386 544 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYS 574 (824)
Q Consensus 544 ~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~ 574 (824)
......||.+.||.+|+...++++-..+.
T Consensus 692 --~~~~cdVl~p~Wlldcc~~~~l~p~~P~~ 720 (881)
T KOG0966|consen 692 --IKRSCDVLKPAWLLDCCKKQRLLPWLPRD 720 (881)
T ss_pred --HhccCceeeHHHHHHHHhhhhccccccHH
Confidence 12367899999999999999988877654
No 81
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=83.31 E-value=1.6 Score=52.66 Aligned_cols=83 Identities=23% Similarity=0.279 Sum_probs=56.1
Q ss_pred CCCCCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCC-----CceEEE-EecC-----C-C---hhHHhHhcC-C
Q 003386 317 GETSIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNN-----SVTHCV-AADN-----K-G---LKYEAAKRR-G 380 (824)
Q Consensus 317 ~~s~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~-----s~Th~I-a~~~-----~-t---~K~~~a~~~-~ 380 (824)
....||.|+.||+.+......+++|.++|...||++.+-.+. ..+-++ .... . . -+..++... +
T Consensus 583 ~~~kLf~gl~~~~~g~fs~~p~~~l~~l~~~~gg~~l~~~~~~~~~~k~s~~~~~~~~~~~~~~~~~k~~~~ea~~~s~~ 662 (684)
T KOG4362|consen 583 YKPKLFEGLKFYFVGDFSNPPKEQLQELVHLAGGTILQVPRVAYSDKKKSTIVVLSEKPVLDSILWQKVNDAEALALSQR 662 (684)
T ss_pred cCcchhcCCcceeecccccCcHHHHHHHHhhcCcceeeccCcccccccccceeEeecccCCCchhhhhhccHHHHHHhcC
Confidence 456899999999998777788999999999999999764431 111121 1111 0 0 123333333 3
Q ss_pred -CeeecchHHHHHhcCccCC
Q 003386 381 -DVIHYSWVLDCCSQKKLLQ 399 (824)
Q Consensus 381 -dIV~p~WV~DCI~~~~lLp 399 (824)
+.|+..||+|+|+--.+++
T Consensus 663 a~~~~~~wvl~s~a~~~~~~ 682 (684)
T KOG4362|consen 663 ARAVSSSWVLDSIAGYQILV 682 (684)
T ss_pred CCccchhhhhcchhceeeee
Confidence 9999999999998665554
No 82
>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=73.89 E-value=2.7 Score=43.28 Aligned_cols=41 Identities=17% Similarity=0.307 Sum_probs=37.0
Q ss_pred HHHHHHHHHHH---hCCCceEEEeCCCCCCcCCCCCCCeEEEccc
Q 003386 68 DEVEKFFKETI---ENRDEGIVLKDLGSKWEPGDRSGKWLKLKPE 109 (824)
Q Consensus 68 ~di~~~~~~ai---~~g~EGIV~K~~dS~Y~pg~Rs~~WiKiK~~ 109 (824)
+.+...|...+ ..-..||+.=+.++.|.+| +++.|+|+||.
T Consensus 143 ~~l~~~~~~~~~~~~~e~DGLlFyhk~~~Y~~G-~tPlvl~wKp~ 186 (186)
T cd09232 143 ESLQSAYSGPLNDDPYELDGLLFYHKESHYTPG-STPLVLWLKDY 186 (186)
T ss_pred HHHHHHHhcccccCCCCCceEEEEeCCCcccCc-CCCcEEEecCC
Confidence 67778888888 8899999999999999999 89999999984
No 83
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=73.20 E-value=4.1 Score=45.43 Aligned_cols=60 Identities=15% Similarity=0.181 Sum_probs=40.6
Q ss_pred cEEEEEccHHHH-----------HHHHHHhhcCCCCce-EEecCCH-HHHHHHHHHHHhCCCceEEEeCCCCC
Q 003386 34 CVCVHVYMLSQL-----------RSQIMAADQTGEPCW-SLVAHNV-DEVEKFFKETIENRDEGIVLKDLGSK 93 (824)
Q Consensus 34 ~v~~~~FDll~l-----------r~~L~~l~~~~~~~~-~~~~~~~-~di~~~~~~ai~~g~EGIV~K~~dS~ 93 (824)
.+.||+||+.+. +++..+.--+...++ .++.+.. +++..+.+..-.+|.||||+|+++-.
T Consensus 165 ~v~fFvFDire~~tgr~Lp~eer~~l~ekYgl~~V~~fg~~~~~e~~eei~eIve~L~keGREGVV~Kdpdm~ 237 (382)
T COG1423 165 DVGFFVFDIREKNTGRPLPVEERLELAEKYGLPHVEIFGEFPADEAGEEIYEIVERLNKEGREGVVMKDPDMR 237 (382)
T ss_pred CceEEEEEEEecCCCCCCCHHHHHHHHHHcCCCceEEeeeechhHhHHHHHHHHHHHhhcCCcceEecCcccc
Confidence 678999998653 444444433322122 3334444 78888899999999999999998653
No 84
>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=72.25 E-value=4.4 Score=46.04 Aligned_cols=61 Identities=11% Similarity=0.091 Sum_probs=38.9
Q ss_pred ccEEEEEccHH-----------HHHHHHHHhhcCCCCceE-EecCCHH-HHHHHHHHHHhCCCceEEEeCCCCC
Q 003386 33 ICVCVHVYMLS-----------QLRSQIMAADQTGEPCWS-LVAHNVD-EVEKFFKETIENRDEGIVLKDLGSK 93 (824)
Q Consensus 33 ~~v~~~~FDll-----------~lr~~L~~l~~~~~~~~~-~~~~~~~-di~~~~~~ai~~g~EGIV~K~~dS~ 93 (824)
.+..||+||+. +++++++.+--+..+.+- +...... ++.++++..=+.+.||||+|.++..
T Consensus 156 l~~~FfvFDI~d~~t~~~L~~~er~~l~e~yglp~Vpvlg~~~~~~~~~~~~eii~~L~~~gREGVVlK~~~~~ 229 (374)
T TIGR01209 156 EDLGFFLFDIREGKTNRSLPVEERLELAEKYGLPHVEILGVYTADEAVEEIYEIIERLNKEGREGVVMKDPEMR 229 (374)
T ss_pred CCceEEEEEEEECCCCccCCHHHHHHHHHHCCCCccceeeEEcHHHHHHHHHHHHHHhhhcCcceEEEcCcccc
Confidence 36789999973 235556555444333332 2333323 6667777777899999999987654
No 85
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=69.21 E-value=2.4 Score=51.06 Aligned_cols=85 Identities=15% Similarity=0.226 Sum_probs=59.2
Q ss_pred CCCCccCeEEEEEcCCC---CCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC--CeeecchHHHHH
Q 003386 318 ETSIFSDMVFYFVNVPP---AYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG--DVIHYSWVLDCC 392 (824)
Q Consensus 318 ~s~lF~Gl~FcV~~~~~---~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~--dIV~p~WV~DCI 392 (824)
.+..+.|+.+.+.+... .....++-......|...+.+....+||+|+....+.|...+...+ .||.+.|++.|+
T Consensus 438 ~~~v~~~~~~vfSg~~P~~~~~~~s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k~~~a~~~~~~~Vv~~~wl~~~~ 517 (635)
T KOG0323|consen 438 RTKVLKGSQIVFSGLHPTGSTDESADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKKVYKAVVSGSAKVVNAAWLWRSL 517 (635)
T ss_pred hhHHhhccceeecccccCcCCcchhhhhhhhhcccceecccccchhhhHHhhccCcceeeccccccceeEechhHHHHHH
Confidence 34577777776654321 2223455556677887777777777899998887777766665554 899999999999
Q ss_pred hcCccCCCCc
Q 003386 393 SQKKLLQLQP 402 (824)
Q Consensus 393 ~~~~lLp~eP 402 (824)
++...+.-.+
T Consensus 518 e~w~~v~ek~ 527 (635)
T KOG0323|consen 518 EKWGKVEEKL 527 (635)
T ss_pred HHhcchhccc
Confidence 9876665443
No 86
>PRK06195 DNA polymerase III subunit epsilon; Validated
Probab=67.02 E-value=22 Score=39.41 Aligned_cols=48 Identities=17% Similarity=0.172 Sum_probs=37.5
Q ss_pred CCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecC
Q 003386 466 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSV 523 (824)
Q Consensus 466 ~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~ 523 (824)
..|.|.+|.|-|. +..- .+..+..+|..+||+|++..+ .++++|+...
T Consensus 219 ~~l~g~~~vfTG~--l~~~--------~R~~~~~~~~~~Gg~v~~sVs~~t~~lV~G~~ 267 (309)
T PRK06195 219 TAFKEEVVVFTGG--LASM--------TRDEAMILVRRLGGTVGSSVTKKTTYLVTNTK 267 (309)
T ss_pred ccccCCEEEEccc--cCCC--------CHHHHHHHHHHhCCEecCCcccCceEEEECCC
Confidence 4689999999985 2211 245788999999999999999 5888888753
No 87
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=53.95 E-value=32 Score=42.33 Aligned_cols=74 Identities=15% Similarity=0.132 Sum_probs=52.3
Q ss_pred CCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhhc
Q 003386 467 CFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHLL 545 (824)
Q Consensus 467 lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~~ 545 (824)
.|.|.+|.|-|.- ..- .++.++.+|..+||+|++..+ .++++|+....+++ +.+ +
T Consensus 590 ~~~g~~~v~TG~l--~~~--------~R~e~~~~i~~~G~~v~~sVs~kt~~lv~G~~~gsK-----~~k----A----- 645 (665)
T PRK07956 590 DLAGKTVVLTGTL--EQL--------SRDEAKEKLEALGAKVSGSVSKKTDLVVAGEAAGSK-----LAK----A----- 645 (665)
T ss_pred CccccEEEEeCCC--CCC--------CHHHHHHHHHHcCCEEeCcccCCCCEEEECCCCChH-----HHH----H-----
Confidence 4899999999963 211 246788999999999999999 47888887644321 111 1
Q ss_pred cCCccEEecccHHHHHHHh
Q 003386 546 WNKKLHVVRSQWLEDCLAK 564 (824)
Q Consensus 546 ~~~~~~IVt~~WLedCi~~ 564 (824)
....+.|++.+-+.+.+.+
T Consensus 646 ~~lgI~ii~E~~f~~~l~~ 664 (665)
T PRK07956 646 QELGIEVLDEEEFLRLLGE 664 (665)
T ss_pred HHcCCeEEcHHHHHHHHhc
Confidence 1235789998888877654
No 88
>KOG3524 consensus Predicted guanine nucleotide exchange factor (PEBBLE) [Signal transduction mechanisms]
Probab=53.74 E-value=7.7 Score=46.78 Aligned_cols=74 Identities=14% Similarity=0.283 Sum_probs=51.5
Q ss_pred CCccCeEEEEEcCCCCCCHHHHHHHHHHcCCEEEecCCCCceEEEEecCCChhHHhHhcCC-CeeecchHHHHHhcC
Q 003386 320 SIFSDMVFYFVNVPPAYSLDSLHKMVVENGGTFSMNLNNSVTHCVAADNKGLKYEAAKRRG-DVIHYSWVLDCCSQK 395 (824)
Q Consensus 320 ~lF~Gl~FcV~~~~~~~sk~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~~t~K~~~a~~~~-dIV~p~WV~DCI~~~ 395 (824)
..|.|+.||+.+.. ......+.....+.||+.-. ....+||+|+.+-...-.-.+.... .+|.-.|+.=+|..|
T Consensus 209 ~~feg~~~~f~gF~-~ee~~~m~~sle~~gg~~a~-~d~~cthvvv~e~~~~~~p~~~s~~~~~vk~ewfw~siq~g 283 (850)
T KOG3524|consen 209 GVFEGLSLFFHGFK-QEEIDDMLRSLENTGGKLAP-SDTLCTHVVVNEDNDEVEPLAVSSNQVHVKKEWFWVSIQRG 283 (850)
T ss_pred ccccCCeEeecCCc-HHHHHHHHHHHHhcCCcccC-CCCCceeEeecCCccccccccccccceeecccceEEEEecc
Confidence 57999999997654 34567788888999999877 3446999997654322111122233 888888988777666
No 89
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=53.53 E-value=32 Score=42.29 Aligned_cols=73 Identities=11% Similarity=0.048 Sum_probs=51.5
Q ss_pred CCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhhh
Q 003386 466 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKHL 544 (824)
Q Consensus 466 ~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~ 544 (824)
..|.|.+|.|-|. +... .+..++.+|..+||+|++..+ .++++|+....|++ ++ + +.
T Consensus 592 ~~l~gktfV~TG~--l~~~--------~R~e~~~lie~~Ggkv~ssVSkktd~LV~G~~aGsK--l~---K----A~--- 649 (669)
T PRK14350 592 SFLFGKKFCITGS--FNGY--------SRSVLIDKLTKKGAIFNTCVTKYLDFLLVGEKAGLK--LK---K----AN--- 649 (669)
T ss_pred CccCCcEEEEecc--cCCC--------CHHHHHHHHHHcCCEEeccccCCCcEEEECCCCCch--HH---H----HH---
Confidence 4699999999984 2221 256789999999999999999 58899998655433 11 1 11
Q ss_pred ccCCccEEecccHHHHHH
Q 003386 545 LWNKKLHVVRSQWLEDCL 562 (824)
Q Consensus 545 ~~~~~~~IVt~~WLedCi 562 (824)
.-.+.|++.+.+.+-+
T Consensus 650 --~LGI~Ii~e~~f~~~l 665 (669)
T PRK14350 650 --NLGIKIMSLFDIKSYV 665 (669)
T ss_pred --HcCCEEecHHHHHHHh
Confidence 2247888887776643
No 90
>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=51.31 E-value=6.7 Score=23.20 Aligned_cols=11 Identities=64% Similarity=1.045 Sum_probs=3.8
Q ss_pred ccccCCCCCCC
Q 003386 635 KRKRGRPAGGS 645 (824)
Q Consensus 635 ~~~~~~~~~~~ 645 (824)
+|+||||+...
T Consensus 1 ~r~RGRP~k~~ 11 (13)
T PF02178_consen 1 KRKRGRPRKNA 11 (13)
T ss_dssp S--SS--TT--
T ss_pred CCcCCCCcccc
Confidence 47899998754
No 91
>KOG0323 consensus TFIIF-interacting CTD phosphatases, including NLI-interacting factor [Transcription]
Probab=48.53 E-value=19 Score=43.62 Aligned_cols=96 Identities=19% Similarity=0.145 Sum_probs=63.6
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 543 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~ 543 (824)
...+.||.+.|+|..+.-..+.. ..+-.....+|...+.+++ .+||+|........ .+++
T Consensus 439 ~~v~~~~~~vfSg~~P~~~~~~~-------s~~~~~~~~~g~vs~~~~~~~~th~i~~~~gt~k-~~~a----------- 499 (635)
T KOG0323|consen 439 TKVLKGSQIVFSGLHPTGSTDES-------ADILGVAQQLGAVSAPDVSDKTTHLIAANAGTKK-VYKA----------- 499 (635)
T ss_pred hHHhhccceeecccccCcCCcch-------hhhhhhhhcccceecccccchhhhHHhhccCcce-eecc-----------
Confidence 44678898888886432211111 1223355677888887887 69999987643111 1110
Q ss_pred hccCCccEEecccHHHHHHHhCCccCCCCCCCCCCCC
Q 003386 544 LLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGM 580 (824)
Q Consensus 544 ~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~~~~~ 580 (824)
......+||.+.||+.|++.=..+.|-.|.......
T Consensus 500 -~~~~~~~Vv~~~wl~~~~e~w~~v~ek~~~l~~~~~ 535 (635)
T KOG0323|consen 500 -VVSGSAKVVNAAWLWRSLEKWGKVEEKLEPLDDDQR 535 (635)
T ss_pred -ccccceeEechhHHHHHHHHhcchhccccccccccc
Confidence 112348999999999999999999999998776664
No 92
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=48.29 E-value=46 Score=41.17 Aligned_cols=77 Identities=18% Similarity=0.195 Sum_probs=54.1
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCCcccchhhhHHHHHHHhhh
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLGYDVNFNSLTESFTAREKH 543 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~ 543 (824)
...|.|.+|.|-|. +..- .+..++.+|..+||+|.+..+ .++++|+....+. +.+. .+.
T Consensus 607 ~~~l~g~~~v~TG~--l~~~--------~R~~~~~~i~~~Gg~v~~sVs~kt~~Lv~G~~~g~----sKl~----kA~-- 666 (689)
T PRK14351 607 GDALDGLTFVFTGS--LSGY--------TRSEAQELVEAHGGNATGSVSGNTDYLVVGENPGQ----SKRD----DAE-- 666 (689)
T ss_pred CCCCCCcEEEEccC--CCCC--------CHHHHHHHHHHcCCEEcCCcCCCccEEEEcCCCCh----hHHH----HHH--
Confidence 45699999999995 2211 256788999999999999998 5889999865431 1111 111
Q ss_pred hccCCccEEecccHHHHHHHh
Q 003386 544 LLWNKKLHVVRSQWLEDCLAK 564 (824)
Q Consensus 544 ~~~~~~~~IVt~~WLedCi~~ 564 (824)
...++|++.+-+.+=+++
T Consensus 667 ---~lgi~ii~E~~f~~ll~~ 684 (689)
T PRK14351 667 ---ANDVPTLDEEEFEELLAE 684 (689)
T ss_pred ---HCCCeEecHHHHHHHHHh
Confidence 235789998887776654
No 93
>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=41.21 E-value=49 Score=40.67 Aligned_cols=50 Identities=18% Similarity=0.147 Sum_probs=39.1
Q ss_pred CCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCCC
Q 003386 466 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVLG 525 (824)
Q Consensus 466 ~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~~ 525 (824)
..|.|.+|+|-|.- ... .+..++.+|..+||+|++..+ .++++|+.+..+
T Consensus 583 ~~l~gk~~v~TG~l--~~~--------~R~~~~~~i~~~G~~v~~sVs~kt~~lv~G~~~g 633 (652)
T TIGR00575 583 SPLAGKTFVLTGTL--SQM--------SRDEAKELLENLGGKVASSVSKKTDYVIAGEKAG 633 (652)
T ss_pred CCccCcEEEEeccC--CCC--------CHHHHHHHHHHcCCEEeCCcCCCccEEEECCCCC
Confidence 46999999999952 211 245788999999999999999 588888876544
No 94
>PRK06063 DNA polymerase III subunit epsilon; Provisional
Probab=36.51 E-value=1e+02 Score=34.35 Aligned_cols=49 Identities=12% Similarity=0.064 Sum_probs=39.1
Q ss_pred CCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCC-CceEEEEecCC
Q 003386 465 WSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLA-NATHVVVLSVL 524 (824)
Q Consensus 465 ~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls-~vTHVVV~~~~ 524 (824)
..||.|.+|.|.|.- . . .+..++..|..+||+|.+..+ .+++||+.+..
T Consensus 230 ~~l~~g~~~v~TG~l--~-~--------~R~e~~~~~~~~G~~v~~sVs~~t~~lv~g~~~ 279 (313)
T PRK06063 230 RPLVQGMRVALSAEV--S-R--------THEELVERILHAGLAYSDSVDRDTSLVVCNDPA 279 (313)
T ss_pred CcccCCCEEEEecCC--C-C--------CHHHHHHHHHHcCCEecCccccCccEEEECCCC
Confidence 457899999999952 1 1 245788999999999999999 58899987654
No 95
>PHA02142 putative RNA ligase
Probab=32.40 E-value=50 Score=37.69 Aligned_cols=71 Identities=10% Similarity=0.036 Sum_probs=35.9
Q ss_pred EEEEEccH-H-----H-----HHHHHHHhhcCCCCceEEe--cCCHHHHHHHHHHHHh-----CCCceEEEeCCCCCCcC
Q 003386 35 VCVHVYML-S-----Q-----LRSQIMAADQTGEPCWSLV--AHNVDEVEKFFKETIE-----NRDEGIVLKDLGSKWEP 96 (824)
Q Consensus 35 v~~~~FDl-l-----~-----lr~~L~~l~~~~~~~~~~~--~~~~~di~~~~~~ai~-----~g~EGIV~K~~dS~Y~p 96 (824)
..||+||+ . + .++++.++--...|.+.+. ......++++++.|-- +-.||||+|... ..
T Consensus 270 ~~F~vF~v~~i~~~~yl~~~e~~~~~~~~gl~~VPvL~~~~~~~~~~s~eE~L~~A~~p~~~~~~~EGiViKp~~---~~ 346 (366)
T PHA02142 270 YRIFAFRAWFIDEQRFATDEEFQDLCRTLGMEIVPQLGYSYPFQEFTNVKEMLAAADIPSINHKIAEGVVYKSVE---LV 346 (366)
T ss_pred CceEEEEEEEeccceeCCHHHHHHHHHHcCCceeeeecccccccccCCHHHHHhhcCCCcccccccceEEEeecc---cc
Confidence 47888887 1 1 2444555443333333221 1111145555555421 236999999873 22
Q ss_pred CCCCCCeEEEccc
Q 003386 97 GDRSGKWLKLKPE 109 (824)
Q Consensus 97 g~Rs~~WiKiK~~ 109 (824)
+. +.-|+|.|..
T Consensus 347 ~g-~r~~fK~is~ 358 (366)
T PHA02142 347 NG-RMVHFKAINN 358 (366)
T ss_pred CC-ceEEEEEcCH
Confidence 11 2249999864
No 96
>KOG2093 consensus Translesion DNA polymerase - REV1 deoxycytidyl transferase [Replication, recombination and repair]
Probab=30.53 E-value=46 Score=41.55 Aligned_cols=90 Identities=20% Similarity=0.278 Sum_probs=64.5
Q ss_pred CCCCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEcc-CC-CceEEEEecCCCcccchhhhHHHHHHHh
Q 003386 464 KWSCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNN-LA-NATHVVVLSVLGYDVNFNSLTESFTARE 541 (824)
Q Consensus 464 ~~~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~-ls-~vTHVVV~~~~~~~~~~~~Lr~~l~~~~ 541 (824)
....|++..+|..|+.. +. ...+++.-.++||..... .. ..+|||....+ .++-
T Consensus 44 ~~s~fs~is~~~ngs~~---e~--------~nelk~~~~~~t~~~~~~~~rs~T~~ii~~~l~------a~~v------- 99 (1016)
T KOG2093|consen 44 GSSSFSGISISVNGSTD---ES--------ANELKLQNMFHTGASAASYERSGTENIIAQGLP------ADLV------- 99 (1016)
T ss_pred CcceeeeeeeccCCccc---cc--------hHHHhhhhhhcccccccccccccceeeecccch------HHHh-------
Confidence 46789999999999752 22 235777888999998743 33 58999986533 1111
Q ss_pred hhhccCCccEEecccHHHHHHHhCCccCCCCCCCCCCCC
Q 003386 542 KHLLWNKKLHVVRSQWLEDCLAKEQKSEEYEYSLKPTGM 580 (824)
Q Consensus 542 ~~~~~~~~~~IVt~~WLedCi~~g~~l~Ee~Y~v~~~~~ 580 (824)
..-..+...+.+|+.+|++.++.+.--+|.......
T Consensus 100 ---k~~~~~~~~~~e~iie~~~~~~~~~~~~~~~~t~~~ 135 (1016)
T KOG2093|consen 100 ---KGFTIPKHISIEWIIECCENGMDVGYYPYQLYTGQS 135 (1016)
T ss_pred ---ccccchhhhcHHHHHHHHhccCccccccceeeccch
Confidence 123467889999999999999999988886655543
No 97
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=28.90 E-value=1.3e+02 Score=36.85 Aligned_cols=71 Identities=13% Similarity=0.106 Sum_probs=50.7
Q ss_pred CCCCCeEEEEccCCCCCCCchHHHHHHHHHHHHHHHHhcCCEEEccCCC-ceEEEEecCCCcccchhhhHHHHHHHhhhh
Q 003386 466 SCFHGCCIYFYHSTEPLSPDWEVLLGLALRRLKLEISFHGGKVCNNLAN-ATHVVVLSVLGYDVNFNSLTESFTAREKHL 544 (824)
Q Consensus 466 ~lF~gc~~YL~g~~~~~~~d~~~i~~~~l~~L~~~I~~~GG~V~~~ls~-vTHVVV~~~~~~~~~~~~Lr~~l~~~~~~~ 544 (824)
..|.|.+|.|-|.= .. ..+...+.+|+..||+|+.+.+. ..+||+.+..|++. + + +
T Consensus 593 ~~l~gkt~V~TGtL--~~--------~sR~eak~~le~lGakv~~SVSkktD~vvaG~~aGSKl--~---k----A---- 649 (667)
T COG0272 593 SPLAGKTFVLTGTL--EG--------MSRDEAKALLEALGAKVSGSVSKKTDYVVAGENAGSKL--A---K----A---- 649 (667)
T ss_pred cccCCCEEEEeccC--CC--------CCHHHHHHHHHHcCCEEeceecccccEEEEcCCCChHH--H---H----H----
Confidence 67999999999952 21 23567788999999999999994 77888877665532 1 1 1
Q ss_pred ccCCccEEecccHHHH
Q 003386 545 LWNKKLHVVRSQWLED 560 (824)
Q Consensus 545 ~~~~~~~IVt~~WLed 560 (824)
..-.++|.+.+++.+
T Consensus 650 -~eLgv~i~~E~~~~~ 664 (667)
T COG0272 650 -QELGVKIIDEEEFLA 664 (667)
T ss_pred -HHcCCeEecHHHHHH
Confidence 123578888877765
No 98
>PF15101 DUF4557: Domain of unknown function (DUF4557)
Probab=28.21 E-value=1.8e+02 Score=30.54 Aligned_cols=70 Identities=20% Similarity=0.335 Sum_probs=44.7
Q ss_pred HHHHHHHHHcCCEEEecCCCCceEEEEecC---CChh-HH--hHhcCC-CeeecchHHHHHhcCcc--CCCCccccccCC
Q 003386 339 DSLHKMVVENGGTFSMNLNNSVTHCVAADN---KGLK-YE--AAKRRG-DVIHYSWVLDCCSQKKL--LQLQPKYYLHLS 409 (824)
Q Consensus 339 ~eLeklI~~~GG~vv~n~~~s~Th~Ia~~~---~t~K-~~--~a~~~~-dIV~p~WV~DCI~~~~l--Lp~eP~~ll~~S 409 (824)
.+|.++=+++||+++. +. ...++-..+. .|.. |. ..+... .|.++.||..|.+.... +++. .|+|++.
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 5788899999999976 32 2346665443 2332 22 233444 89999999999987543 3333 4566566
Q ss_pred hh
Q 003386 410 DS 411 (824)
Q Consensus 410 ~~ 411 (824)
|+
T Consensus 91 P~ 92 (212)
T PF15101_consen 91 PE 92 (212)
T ss_pred HH
Confidence 65
No 99
>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=26.06 E-value=38 Score=23.85 Aligned_cols=12 Identities=58% Similarity=0.930 Sum_probs=8.7
Q ss_pred ccccCCCCCCCc
Q 003386 635 KRKRGRPAGGSA 646 (824)
Q Consensus 635 ~~~~~~~~~~~~ 646 (824)
+|+||||+....
T Consensus 1 kRkRGRPrK~~~ 12 (26)
T smart00384 1 KRKRGRPRKAPK 12 (26)
T ss_pred CCCCCCCCCCCC
Confidence 478899887644
Done!