Query psy14581
Match_columns 124
No_of_seqs 130 out of 824
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 23:29:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14581.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14581hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0967|consensus 99.9 3.2E-23 6.8E-28 179.9 6.1 70 27-96 627-704 (714)
2 KOG0966|consensus 99.7 2.1E-18 4.5E-23 152.7 6.9 61 35-96 530-592 (881)
3 cd07967 OBF_DNA_ligase_III The 99.7 1.9E-17 4.2E-22 121.2 2.6 59 30-88 78-139 (139)
4 PLN03113 DNA ligase 1; Provisi 99.6 1.9E-16 4.2E-21 141.0 5.5 73 30-102 656-736 (744)
5 PRK01109 ATP-dependent DNA lig 99.6 1.4E-16 3.1E-21 138.7 4.5 68 32-99 510-585 (590)
6 cd07969 OBF_DNA_ligase_I The O 99.6 5.1E-16 1.1E-20 114.0 3.7 61 34-94 75-143 (144)
7 PRK09247 ATP-dependent DNA lig 99.5 5.8E-15 1.3E-19 127.6 4.5 61 35-96 478-538 (539)
8 PRK03180 ligB ATP-dependent DN 99.5 1.6E-14 3.5E-19 124.1 4.4 59 34-93 448-506 (508)
9 TIGR00574 dnl1 DNA ligase I, A 99.5 2.9E-14 6.3E-19 122.3 4.1 61 34-94 454-514 (514)
10 cd07972 OBF_DNA_ligase_Arch_Li 99.5 3.9E-14 8.5E-19 101.0 3.5 55 35-90 67-121 (122)
11 cd07893 OBF_DNA_ligase The Oli 99.3 5.1E-13 1.1E-17 96.2 2.5 51 33-83 73-129 (129)
12 cd07968 OBF_DNA_ligase_IV The 99.3 8.3E-13 1.8E-17 96.3 2.8 54 32-86 85-140 (140)
13 cd08039 Adenylation_DNA_ligase 99.1 3.7E-11 8E-16 94.5 4.6 69 1-69 18-96 (235)
14 PLN03113 DNA ligase 1; Provisi 99.0 1.7E-10 3.6E-15 103.3 4.7 69 2-70 388-457 (744)
15 cd07900 Adenylation_DNA_ligase 98.9 1E-09 2.2E-14 85.1 4.2 67 2-69 28-96 (219)
16 PHA02587 30 DNA ligase; Provis 98.9 1.3E-09 2.8E-14 93.6 3.4 53 35-90 428-484 (488)
17 PF04679 DNA_ligase_A_C: ATP d 98.8 1.7E-09 3.7E-14 73.9 2.7 38 34-78 60-97 (97)
18 PRK03180 ligB ATP-dependent DN 98.8 3E-09 6.5E-14 91.7 4.5 62 5-69 204-265 (508)
19 cd07898 Adenylation_DNA_ligase 98.8 5.7E-09 1.2E-13 79.3 4.3 63 2-68 18-80 (201)
20 cd07905 Adenylation_DNA_ligase 98.8 5.9E-09 1.3E-13 79.1 3.8 62 4-68 15-76 (194)
21 cd07903 Adenylation_DNA_ligase 98.8 1.4E-08 3.1E-13 78.2 5.9 66 3-68 31-102 (225)
22 PRK01109 ATP-dependent DNA lig 98.8 5.8E-09 1.3E-13 91.3 4.0 64 4-69 247-310 (590)
23 cd07901 Adenylation_DNA_ligase 98.8 9.1E-09 2E-13 78.7 4.4 63 4-68 24-86 (207)
24 cd07902 Adenylation_DNA_ligase 98.7 9.7E-09 2.1E-13 79.1 3.8 64 5-69 34-98 (213)
25 cd07897 Adenylation_DNA_ligase 98.7 1.4E-08 3E-13 78.0 4.5 63 3-69 22-84 (207)
26 TIGR00574 dnl1 DNA ligase I, A 98.7 1.1E-08 2.5E-13 87.9 4.5 63 5-68 187-250 (514)
27 PRK09247 ATP-dependent DNA lig 98.7 1.4E-08 3.1E-13 88.1 4.1 63 3-69 223-285 (539)
28 cd07906 Adenylation_DNA_ligase 98.7 1.8E-08 4E-13 75.9 3.9 63 3-68 14-76 (190)
29 TIGR02779 NHEJ_ligase_lig DNA 98.7 1.9E-08 4.2E-13 81.1 4.2 64 3-69 10-73 (298)
30 PF01068 DNA_ligase_A_M: ATP d 98.6 3.2E-08 7E-13 74.1 4.2 65 4-68 18-82 (202)
31 COG1793 CDC9 ATP-dependent DNA 98.6 3.5E-08 7.6E-13 84.1 4.1 76 6-93 134-209 (444)
32 PRK09633 ligD ATP-dependent DN 98.6 6.2E-08 1.3E-12 85.4 4.7 67 3-69 14-82 (610)
33 cd07971 OBF_DNA_ligase_LigD Th 98.5 9.2E-08 2E-12 67.3 3.1 44 33-83 72-115 (115)
34 PRK07636 ligB ATP-dependent DN 98.5 2.4E-07 5.1E-12 74.3 5.3 61 3-69 16-76 (275)
35 PHA02587 30 DNA ligase; Provis 98.4 2.1E-07 4.6E-12 80.0 4.3 62 6-68 153-217 (488)
36 cd06846 Adenylation_DNA_ligase 98.4 4.5E-07 9.8E-12 67.6 5.5 64 2-68 16-79 (182)
37 PRK08224 ligC ATP-dependent DN 98.4 2.4E-07 5.1E-12 76.8 4.3 62 4-68 23-84 (350)
38 PRK05972 ligD ATP-dependent DN 98.4 2.9E-07 6.3E-12 83.8 4.7 64 3-69 247-310 (860)
39 PRK09632 ATP-dependent DNA lig 98.4 3.8E-07 8.3E-12 82.2 5.3 65 2-69 474-538 (764)
40 TIGR02779 NHEJ_ligase_lig DNA 98.4 2E-07 4.4E-12 75.2 2.3 46 32-84 252-297 (298)
41 COG1793 CDC9 ATP-dependent DNA 98.3 2.1E-07 4.6E-12 79.3 1.6 56 38-93 387-443 (444)
42 cd07895 Adenylation_mRNA_cappi 98.1 7.7E-06 1.7E-10 62.7 5.9 64 3-68 39-103 (215)
43 TIGR02776 NHEJ_ligase_prk DNA 98.1 1.7E-06 3.6E-11 75.7 2.3 46 34-86 215-260 (552)
44 cd07970 OBF_DNA_ligase_LigC Th 98.0 3.2E-06 7E-11 60.5 2.7 45 34-85 77-122 (122)
45 PRK09633 ligD ATP-dependent DN 97.9 5.7E-06 1.2E-10 73.1 2.5 53 35-95 267-319 (610)
46 cd08040 OBF_DNA_ligase_family 97.5 5.7E-05 1.2E-09 52.4 2.0 34 35-75 75-108 (108)
47 PHA00454 ATP-dependent DNA lig 97.4 0.00013 2.8E-09 59.5 3.8 34 5-38 27-61 (315)
48 PRK09632 ATP-dependent DNA lig 97.4 6.1E-05 1.3E-09 68.2 2.0 44 34-84 718-761 (764)
49 cd07896 Adenylation_kDNA_ligas 97.4 8.7E-05 1.9E-09 54.9 2.4 51 4-67 15-65 (174)
50 PRK05972 ligD ATP-dependent DN 97.3 0.00012 2.6E-09 67.0 2.0 45 35-86 494-538 (860)
51 cd07894 Adenylation_RNA_ligase 96.9 0.0013 2.8E-08 54.7 4.7 31 5-35 48-78 (342)
52 PRK09125 DNA ligase; Provision 96.2 0.0036 7.9E-08 50.5 2.9 33 3-39 41-73 (282)
53 PRK07636 ligB ATP-dependent DN 93.5 0.049 1.1E-06 43.7 2.0 35 34-75 240-274 (275)
54 PRK08224 ligC ATP-dependent DN 93.1 0.059 1.3E-06 44.9 2.0 43 35-85 286-331 (350)
55 KOG4437|consensus 84.8 0.36 7.8E-06 40.9 0.6 34 4-38 389-422 (482)
56 PF14743 DNA_ligase_OB_2: DNA 68.3 2.1 4.6E-05 27.5 0.5 28 41-75 39-66 (66)
57 TIGR01209 RNA ligase, Pab1020 53.8 23 0.00049 30.2 4.3 34 2-35 76-109 (374)
58 COG1423 ATP-dependent DNA liga 53.7 24 0.00052 30.1 4.4 33 2-34 85-117 (382)
59 PF09414 RNA_ligase: RNA ligas 51.9 24 0.00053 25.8 3.8 29 6-34 2-31 (186)
60 PHA00454 ATP-dependent DNA lig 49.6 9.7 0.00021 31.0 1.4 30 40-76 285-314 (315)
61 cd08041 OBF_kDNA_ligase_like T 46.8 9.2 0.0002 24.6 0.8 26 43-75 52-77 (77)
62 PF14275 DUF4362: Domain of un 33.7 67 0.0015 22.2 3.5 32 2-33 40-71 (98)
63 TIGR02307 RNA_lig_RNL2 RNA lig 33.1 79 0.0017 26.4 4.4 33 2-34 22-55 (325)
64 PRK10737 FKBP-type peptidyl-pr 32.7 26 0.00056 27.1 1.4 36 41-76 105-141 (196)
65 PF01653 DNA_ligase_aden: NAD- 30.4 94 0.002 25.5 4.4 27 6-32 108-135 (315)
66 PF01331 mRNA_cap_enzyme: mRNA 26.8 54 0.0012 24.3 2.2 34 4-37 15-48 (192)
67 PRK15095 FKBP-type peptidyl-pr 23.2 49 0.0011 24.3 1.4 34 42-75 110-144 (156)
68 TIGR03738 PRTRC_C PRTRC system 22.0 1.1E+02 0.0024 19.9 2.6 42 56-108 6-47 (66)
No 1
>KOG0967|consensus
Probab=99.88 E-value=3.2e-23 Score=179.90 Aligned_cols=70 Identities=36% Similarity=0.641 Sum_probs=63.4
Q ss_pred eEEeecCccceeeccccccceeccceeccccceecc--------ceEeecccceeeecCCCccccCCHHHHHHHHHHc
Q psy14581 27 FKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTAD--------GISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96 (124)
Q Consensus 27 ~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~--------G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~ 96 (124)
+.-|...++|++|+.|..||||++|+++.||.|.+. |++||||||+|||+||.++||||.+++.+||++|
T Consensus 627 ~y~~d~s~kPd~wf~p~~VwEvk~Adlt~SPiy~Aa~Glv~~dkGISlRFPRfiRiR~DK~peeAtts~qiaemY~~Q 704 (714)
T KOG0967|consen 627 YYRFDESLKPDVWFEPTEVWEVKAADLTLSPIYKAALGLVDPDKGISLRFPRFIRIRDDKNPEEATTSSQIAEMYQAQ 704 (714)
T ss_pred hcccCccCCCccccCHHHHHHHhhccccccchhHhhhcCcCCCCceeEecceeeEeeccCChhhcccHHHHHHHHHHH
Confidence 333444448999999999999999999999999863 8999999999999999999999999999999998
No 2
>KOG0966|consensus
Probab=99.74 E-value=2.1e-18 Score=152.74 Aligned_cols=61 Identities=30% Similarity=0.444 Sum_probs=57.4
Q ss_pred cceeeccc--cccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHHHHHHHc
Q psy14581 35 KPVLEHKA--QPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96 (124)
Q Consensus 35 ep~t~~~P--s~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~ 96 (124)
.|++|+.| ++|++|+++++++|..| .++++|||||+.++|.||+|.||+|+.+|.+|....
T Consensus 530 ~Pd~wI~P~~SiIlqikaa~i~~s~~f-~tn~tLrfPr~ekvR~DK~W~ec~tl~~l~~l~~~~ 592 (881)
T KOG0966|consen 530 IPDVWIDPDNSIILQIKAAEIVPSSNF-VTNYTLRFPRIEKVRLDKPWHECLTLNELGDLVNVS 592 (881)
T ss_pred CCceeECCCCceEEEeehheeeecccc-cccceeecceeeeeecCCcHHHHhhHHHHHHHhccc
Confidence 39999888 69999999999999999 899999999999999999999999999999999864
No 3
>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=99.67 E-value=1.9e-17 Score=121.16 Aligned_cols=59 Identities=71% Similarity=1.147 Sum_probs=52.7
Q ss_pred eecCccceeec-cc--cccceeccceeccccceeccceEeecccceeeecCCCccccCCHHH
Q psy14581 30 FSRSLKPVLEH-KA--QPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPE 88 (124)
Q Consensus 30 fSRn~ep~t~~-~P--s~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~ 88 (124)
+.....|++|+ .| ++||||++++++.|+.|.++|++||||||.++|+||+|+||+|++|
T Consensus 78 ~~~~~~Pdv~~~~P~~s~V~EV~~aeit~S~~~~a~G~tLRFPr~~~iR~DK~~~d~~t~~~ 139 (139)
T cd07967 78 CNKSLVPDFIVKDPKKAPVWEITGAEFSKSEAHTADGISIRFPRVTRIRDDKDWKTATSLPE 139 (139)
T ss_pred ecCCCCCCEEEeCCCccEEEEEEeeeEEecCcccccCEEEEccEEEEEeCCCCHHHCccccC
Confidence 44456899995 36 8999999999999999977899999999999999999999999874
No 4
>PLN03113 DNA ligase 1; Provisional
Probab=99.64 E-value=1.9e-16 Score=141.04 Aligned_cols=73 Identities=30% Similarity=0.603 Sum_probs=65.7
Q ss_pred eecCccceeeccccccceeccceeccccceec--------cceEeecccceeeecCCCccccCCHHHHHHHHHHcccCCC
Q psy14581 30 FSRSLKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSD 101 (124)
Q Consensus 30 fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~--------~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~~~~~~ 101 (124)
|+....|++|+.|..||||++++++.||.|++ .|++||||||.++|.||+|+||+|+++|.+||++|.....
T Consensus 656 ~~~~~~pdvwveP~~V~EV~~aeit~Sp~h~a~~g~~~~~~G~sLRFPRf~riR~DK~~~datt~~~l~~ly~~Q~~~~~ 735 (744)
T PLN03113 656 YGDSIKPDVWFEPTEVWEVKAADLTISPVHRAAVGIVDPDKGISLRFPRLVRVREDKSPEQATSSEQVADMYNAQKHNHP 735 (744)
T ss_pred cCCCCCCcEEECCceEEEEEeeeeccCcccccccccccCCCCeEEECCEEEEEECCCChHHCCCHHHHHHHHHHHHHhhc
Confidence 45456799999999999999999999999975 5999999999999999999999999999999998865554
Q ss_pred c
Q psy14581 102 F 102 (124)
Q Consensus 102 ~ 102 (124)
.
T Consensus 736 ~ 736 (744)
T PLN03113 736 S 736 (744)
T ss_pred c
Confidence 4
No 5
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=99.63 E-value=1.4e-16 Score=138.68 Aligned_cols=68 Identities=35% Similarity=0.557 Sum_probs=63.4
Q ss_pred cCccceeeccccccceeccceeccccceec--------cceEeecccceeeecCCCccccCCHHHHHHHHHHcccC
Q psy14581 32 RSLKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKET 99 (124)
Q Consensus 32 Rn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~--------~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~~~~ 99 (124)
....|++|..|+.||||++++++.|+.|++ .|++|||||+.++|.||+|+||+|+++|.+||++|+.+
T Consensus 510 ~~~~pdvwv~P~~V~eV~~~~it~S~~~~~~~~~~~~~~g~~LRfPr~~~~R~DK~~~d~~t~~~~~~ly~~q~~~ 585 (590)
T PRK01109 510 SKMEPDVWVEPKLVAEIIGAEITLSPLHTCCLGVVEKGAGLAIRFPRFIRWRDDKSPEDATTTEEILEMYKRQKKK 585 (590)
T ss_pred cccCCcEEEeccEEEEEEeeecccCcceecccccccCCCceeEEcCeeeEeeCCCChhhCcCHHHHHHHHHHhhhc
Confidence 346899999999999999999999999985 79999999999999999999999999999999988765
No 6
>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=99.60 E-value=5.1e-16 Score=114.00 Aligned_cols=61 Identities=38% Similarity=0.720 Sum_probs=57.3
Q ss_pred ccceeeccccccceeccceeccccceec--------cceEeecccceeeecCCCccccCCHHHHHHHHH
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTA--------DGISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~--------~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~ 94 (124)
..|++|..|.+|+||++++++.|+.|++ +|.+|||||+.++|.||+|.+|+++++|.+||+
T Consensus 75 ~~~~vWv~P~lV~EV~~~e~t~s~~~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~~~~~~~~l~~l~~ 143 (144)
T cd07969 75 LEPDVWFEPKEVWEVKAADLTLSPVHTAAIGLVDEEKGISLRFPRFIRVRDDKKPEDATTSEQIAEMYK 143 (144)
T ss_pred CCCcEEEeeeEEEEEEEeEeecCcceeccccccccCCceEEEeeEEEEeeCCCChHHCCCHHHHHHHHh
Confidence 4799999999999999999999999975 478999999999999999999999999999996
No 7
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=99.53 E-value=5.8e-15 Score=127.58 Aligned_cols=61 Identities=31% Similarity=0.504 Sum_probs=58.2
Q ss_pred cceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHHHHHHHc
Q psy14581 35 KPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKS 96 (124)
Q Consensus 35 ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~ 96 (124)
.|.+|..|..||||++++++.|+.| .+|++||||||.++|+||+|+||+|+++|.+||+.+
T Consensus 478 ~~~~~v~P~~V~EV~~~eit~S~~~-~~G~~LRfPr~~~~R~DK~~~ea~t~~~l~~l~~~~ 538 (539)
T PRK09247 478 GPVRSVRPELVFEIAFEGIQRSKRH-KSGIAVRFPRILRWRWDKPAREADTLETLQALLDAE 538 (539)
T ss_pred CCceEecCceEEEEEeceeeecCCc-CCCcEEEcceEEEEeCCCChHHCcCHHHHHHHHhcC
Confidence 5899999999999999999999999 579999999999999999999999999999999865
No 8
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=99.49 E-value=1.6e-14 Score=124.15 Aligned_cols=59 Identities=22% Similarity=0.270 Sum_probs=56.5
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHHHHH
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLF 93 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~ 93 (124)
..|++|..|..||||++++++.|+.| .+|++|||||+.++|.||+|+||+|++++.+||
T Consensus 448 ~~~~vwv~P~~V~EV~~~~it~S~~~-~~G~~LRfPr~~r~R~DK~~~ea~tl~~~~~l~ 506 (508)
T PRK03180 448 DGWTVYVRPELVVEIAFDGVQRSTRY-PGGVALRFARVLRYRPDKTPAEADTIDTVRALL 506 (508)
T ss_pred CCCCEEeeCCEEEEEEeeEeeeCCcc-cCCeEEECCeeeEeeCCCChHHCcCHHHHHHHh
Confidence 36899999999999999999999999 679999999999999999999999999999999
No 9
>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=99.47 E-value=2.9e-14 Score=122.31 Aligned_cols=61 Identities=41% Similarity=0.713 Sum_probs=57.3
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHHHHHH
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFK 94 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~ 94 (124)
..|++|+.|+.||||++++++.|+.|.++|++||||||.++|.||+|+||+|+++|.+||+
T Consensus 454 ~~~~~w~~p~~V~eV~~~e~t~s~~~~~~g~~LRfPr~~~~R~DK~~~d~~~~~~~~~ly~ 514 (514)
T TIGR00574 454 DEPDIWFDPAIVWEVTGAEITRSPTYKANGISLRFPRFSRIRDDKGPEDATTIEEIKELYE 514 (514)
T ss_pred CCCeEEecCCeEEEEEhhheeecCcccccceEEEcceEEEEcCCCChHHCCCHHHHHHHhC
Confidence 3689999999999999999999999955499999999999999999999999999999984
No 10
>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=99.46 E-value=3.9e-14 Score=101.03 Aligned_cols=55 Identities=35% Similarity=0.580 Sum_probs=52.3
Q ss_pred cceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHH
Q psy14581 35 KPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELK 90 (124)
Q Consensus 35 ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~ 90 (124)
.|.+|..|.+|+||++++++.|+.| .+|.+|||||+.++|.||+|.+|+|+++|.
T Consensus 67 ~~~~wv~P~lV~eV~~~e~t~s~~~-~~g~~LR~Prf~~~R~Dk~~~~~~t~~~~~ 121 (122)
T cd07972 67 GPVVSVKPELVFEVAFEEIQRSPRY-KSGYALRFPRIVRIRDDKDPDEADTLERVE 121 (122)
T ss_pred CCcEEEeceEEEEEEeeEEEecCcc-ccCceEEccEEeEEeCCCChHHCcCHHHHh
Confidence 6889999999999999999999999 579999999999999999999999999985
No 11
>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=99.33 E-value=5.1e-13 Score=96.24 Aligned_cols=51 Identities=37% Similarity=0.550 Sum_probs=47.0
Q ss_pred Cccceeeccccccceeccceeccccceecc------ceEeecccceeeecCCCcccc
Q psy14581 33 SLKPVLEHKAQPVWEISGAEFSQAEIHTAD------GISIRFPRVTKIRDDKDWKTA 83 (124)
Q Consensus 33 n~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~------G~~lrFPR~~~iR~DK~~~~a 83 (124)
...|++|..|++||||++++++.|+.|..+ |.+|||||+.++|+||+|+||
T Consensus 73 ~~~~~~wv~P~lV~EV~~~e~t~s~~~~~~~~~~~~g~~LRfPr~~~~R~Dk~~~e~ 129 (129)
T cd07893 73 IEKPDFWVEPKVVVEVLADEITRSPMHTAGRGEEEEGYALRFPRFVRIRDDKGPEDA 129 (129)
T ss_pred cCCCcEEEeeeEEEEEEeeeeeeCcccccccccCCCceEEECCEEEEEeCCCChhhC
Confidence 447999999999999999999999999654 999999999999999999987
No 12
>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=99.31 E-value=8.3e-13 Score=96.27 Aligned_cols=54 Identities=35% Similarity=0.558 Sum_probs=49.4
Q ss_pred cCccceeecccc--ccceeccceeccccceeccceEeecccceeeecCCCccccCCH
Q psy14581 32 RSLKPVLEHKAQ--PVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNL 86 (124)
Q Consensus 32 Rn~ep~t~~~Ps--~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~ 86 (124)
....|++|..|. +|+||++++++.|+.| .+|.+|||||+.++|.||+|.||+|+
T Consensus 85 ~~~~~~~Wv~P~~slV~EV~~~e~t~s~~~-~~g~~LR~Pr~~~~R~DK~~~e~~t~ 140 (140)
T cd07968 85 GKEKPDVWIEPKDSVVLEVKAAEIVPSDSY-KTGYTLRFPRCEKIRYDKDWHDCLTL 140 (140)
T ss_pred cccCCcEEEecCCCEEEEEEeeeEeecCcc-cCCcEEEcceEeEEECCCCHHHccCC
Confidence 345689999998 9999999999999999 47999999999999999999999984
No 13
>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=99.15 E-value=3.7e-11 Score=94.49 Aligned_cols=69 Identities=26% Similarity=0.311 Sum_probs=54.1
Q ss_pred CCCCceeEEEeeeccceeeEeee----CCeeEEeecCccceeeccccccceeccce-ec-----cccceeccceEeecc
Q psy14581 1 MAKNERCYSEIKYDGERVQVHKK----GNEFKYFSRSLKPVLEHKAQPVWEISGAE-FS-----QAEIHTADGISIRFP 69 (124)
Q Consensus 1 ~~~~~~f~~E~K~DGER~QiH~~----~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~-~~-----~s~~~~~~G~~lrFP 69 (124)
|++++.|++|+||||+|+|+|+. ++.+++||||++++|..+|.++.-+..+- +. ....+++||+.|.+.
T Consensus 18 ~~~~~~~~~E~K~DG~R~qih~~~~~~~~~v~lfSR~~~d~T~~~pel~~~~~~~~~~~~~~~~~~~~~ILDGEiVv~d 96 (235)
T cd08039 18 MIGSRRMWVETKYDGEYCQIHIDLSKDSSPIRIFSKSGKDSTADRAGVHSIIRKALRIGKPGCKFSKNCILEGEMVVWS 96 (235)
T ss_pred HhCCCcEEEEEeecceEEEEEEecccCCCEEEEEeCCCCcccccchhHHHHHHHHhhccccccCCCccEEEEeEEEEEE
Confidence 57788999999999999999987 78999999999999988887654333221 11 134677999998764
No 14
>PLN03113 DNA ligase 1; Provisional
Probab=99.04 E-value=1.7e-10 Score=103.34 Aligned_cols=69 Identities=23% Similarity=0.265 Sum_probs=54.0
Q ss_pred CCCceeEEEeeeccceeeEeee-CCeeEEeecCccceeeccccccceeccceeccccceeccceEeeccc
Q psy14581 2 AKNERCYSEIKYDGERVQVHKK-GNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPR 70 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~-~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR 70 (124)
|.++.|++|+||||||+|+|+. ++.+++||||++++|..+|+++-.+..........+++||+.|.+.+
T Consensus 388 ~~g~~~~~E~KyDGeR~QiH~~~~g~v~lfSRn~ed~T~~fPel~~~~~~~~~~~~~~~ILDGEiVa~d~ 457 (744)
T PLN03113 388 FQDMEFTCEYKYDGERAQIHFLEDGSVEIYSRNAERNTGKYPDVVVAISRLKKPSVKSFILDCELVAYDR 457 (744)
T ss_pred cCCCCEEEEEeeccceEEEEEecCCEEEEEeCCCCcccccchhHHHHHHHhccccCCCEEEEeEEEEEEC
Confidence 4567899999999999999985 67899999999999999998864443221112346789999988753
No 15
>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=98.92 E-value=1e-09 Score=85.11 Aligned_cols=67 Identities=25% Similarity=0.347 Sum_probs=52.1
Q ss_pred CCCceeEEEeeeccceeeEeeeC-CeeEEeecCccceeeccccccceeccceec-cccceeccceEeecc
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKG-NEFKYFSRSLKPVLEHKAQPVWEISGAEFS-QAEIHTADGISIRFP 69 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~-~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~-~s~~~~~~G~~lrFP 69 (124)
+.+..|++|+||||+|+|+|+.+ +.+.+||||++++|..+|.++-.+... +. ..+.+++||+.+.+.
T Consensus 28 ~~~~~~~~E~K~DG~R~~~h~~~~~~v~l~SR~g~~~t~~~pel~~~~~~~-~~~~~~~~iLDGElv~~~ 96 (219)
T cd07900 28 FEDKEFTCEYKYDGERAQIHLLEDGKVKIFSRNLENNTEKYPDIVAVLPKS-LKPSVKSFILDSEIVAYD 96 (219)
T ss_pred hCCCeEEEEEeecceEEEEEEcCCCeEEEECCCCccccchhhHHHHHHHHH-hcccCccEEEeeEEEEEE
Confidence 34568999999999999999976 899999999999998888765443322 21 235567899988763
No 16
>PHA02587 30 DNA ligase; Provisional
Probab=98.87 E-value=1.3e-09 Score=93.58 Aligned_cols=53 Identities=21% Similarity=0.275 Sum_probs=46.6
Q ss_pred cceeeccc----cccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHH
Q psy14581 35 KPVLEHKA----QPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELK 90 (124)
Q Consensus 35 ep~t~~~P----s~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~ 90 (124)
.+.+|..+ ..||||.+++++.|+.| .+|++||||||.++|.||+ +|+|++++.
T Consensus 428 r~~~~~~~~~~~~~V~EV~~~~it~S~~~-~~g~sLRfPrf~r~R~DK~--~Adt~~~v~ 484 (488)
T PHA02587 428 REELMANKGKYIGKIAECECNGLQRSKGR-KDKVSLFLPIIKRIRIDKT--EANTLEDVF 484 (488)
T ss_pred chhhhhCcccccceEEEEEeceEEeCCCC-CCCeeEEccceeEEeCCCC--cccCHHHHh
Confidence 56677443 47999999999999999 4699999999999999999 999999984
No 17
>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=98.84 E-value=1.7e-09 Score=73.90 Aligned_cols=38 Identities=39% Similarity=0.620 Sum_probs=33.6
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecccceeeecCC
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDK 78 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK 78 (124)
..|++|..|..|+||++++++.+ | +|||||+.++|+||
T Consensus 60 ~~~~~wv~P~~V~eV~~~e~t~~------G-~lR~P~~~~~R~DK 97 (97)
T PF04679_consen 60 ERPDVWVEPELVVEVKFAEITPS------G-SLRFPRFKRIREDK 97 (97)
T ss_dssp CTTEEEE-ST-EEEEEESEEEEE------S-EEESEEEEEEETTS
T ss_pred ccCcEEeCCCEEEEEEEEEEcCC------C-eEECCEEeEEeCCC
Confidence 57999999999999999998865 8 99999999999998
No 18
>PRK03180 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.83 E-value=3e-09 Score=91.73 Aligned_cols=62 Identities=26% Similarity=0.435 Sum_probs=50.4
Q ss_pred ceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 5 ERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 5 ~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
+.|++|+||||+|+|+|+.++.+.+||||+++.|..+|+++-.+.. + +...+++||+.+.+.
T Consensus 204 ~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~fPei~~~~~~--~-~~~~~ILDGElv~~d 265 (508)
T PRK03180 204 GPAAVEAKLDGARVQVHRDGDDVRVYTRTLDDITARLPEVVEAVRA--L-PVRSLVLDGEAIALR 265 (508)
T ss_pred CCeEEEEEEceeEEEEEEECCEEEEEeCCCCcchhhhHHHHHHHHh--C-CCcceeecceEEEEC
Confidence 5799999999999999999999999999999999888876632222 2 234567899998764
No 19
>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=98.79 E-value=5.7e-09 Score=79.27 Aligned_cols=63 Identities=30% Similarity=0.422 Sum_probs=49.3
Q ss_pred CCCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
+.+..|++|.||||+|+|+|+.++++.+|||++.+++..+|.++-.+. ......++||+.+.+
T Consensus 18 ~~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~i~~~~~----~~~~~~vLDGElv~~ 80 (201)
T cd07898 18 KKPAAAWVEDKYDGIRAQVHKDGGRVEIFSRSLEDITDQFPELAAAAK----ALPHEFILDGEILAW 80 (201)
T ss_pred hCCCeEEEEEeeceEEEEEEEeCCEEEEEcCCChhchhhhhhHHHHHH----hCCCCEEEEEEEEEE
Confidence 456789999999999999999999999999999999987775432221 112455688988864
No 20
>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=98.77 E-value=5.9e-09 Score=79.11 Aligned_cols=62 Identities=24% Similarity=0.208 Sum_probs=49.2
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
++.|++|.||||+|+|+|+.++.+.+||||+++++..+|.++-.+... ....+++||+.+..
T Consensus 15 ~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~---~~~~~iLDGElv~~ 76 (194)
T cd07905 15 PGGWQYEPKWDGFRCLAFRDGDEVRLQSRSGKPLTRYFPELVAAARAL---LPPGCVLDGELVVW 76 (194)
T ss_pred CCceEEEeeeceEEEEEEEeCCEEEEEeCCCCchhhhhHHHHHHHHhh---CCCCEEEEeEEEEE
Confidence 567999999999999999999999999999999998778654222211 12356789998875
No 21
>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=98.77 E-value=1.4e-08 Score=78.24 Aligned_cols=66 Identities=36% Similarity=0.420 Sum_probs=51.1
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceec------cceeccccceeccceEeec
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEIS------GAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~------~a~~~~s~~~~~~G~~lrF 68 (124)
.+..|++|+||||+|+|+|+.++.+.+|||++.+++..+|.++-.+. .+.....+.+++||+.+.+
T Consensus 31 ~~~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~p~~~~~~~~~~~l~~~~~~~~~~~iLDGElv~~ 102 (225)
T cd07903 31 KGKPFYIETKLDGERIQLHKDGNEFKYFSRNGNDYTYLYGASLTPGSLTPYIHLAFNPKVKSCILDGEMVVW 102 (225)
T ss_pred cCCeEEEEEeeCceEEEEEecCCEEEEEeCCCccccccccccccccccchhhhhhccccCcEEEeceEEEEE
Confidence 46789999999999999999999999999999999988887654331 1111223556689988864
No 22
>PRK01109 ATP-dependent DNA ligase; Provisional
Probab=98.76 E-value=5.8e-09 Score=91.28 Aligned_cols=64 Identities=34% Similarity=0.475 Sum_probs=51.3
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
++.|++|+||||+|+|+|+.++.+++||||++++|..+|+++-.+..+ + ....+++||+.+.+.
T Consensus 247 ~~~~~~E~K~DG~R~qih~~~~~v~l~SR~~~d~T~~~pel~~~~~~~-~-~~~~~ILDGElv~~d 310 (590)
T PRK01109 247 GGEALVEYKYDGERAQIHKKGDKVKIFSRRLENITHQYPDVVEYAKEA-I-KAEEAIVEGEIVAVD 310 (590)
T ss_pred CCCeEEEecCCceEEEEEEcCCEEEEEeCCchhhccccchHHHHHHHh-c-CccceEEeeeEEEEE
Confidence 356899999999999999999999999999999999899865433321 2 234567899988874
No 23
>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=98.75 E-value=9.1e-09 Score=78.69 Aligned_cols=63 Identities=33% Similarity=0.496 Sum_probs=49.9
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
++.|++|.||||+|+|+|+.++.+.+|||++++.|..+|.++-.+... ...+.+++||+.+..
T Consensus 24 ~~~~~~E~K~DG~R~~~~~~~~~v~~~SR~~~~~t~~~pel~~~~~~~--~~~~~~iLDGElv~~ 86 (207)
T cd07901 24 GGEAAVEYKYDGIRVQIHKDGDEVRIFSRRLEDITNALPEVVEAVREL--VKAEDAILDGEAVAY 86 (207)
T ss_pred CCcEEEEEeEcceeEEEEEeCCEEEEEeCCCccccchhhHHHHHHHhc--CCCCCEEEeCEEEEE
Confidence 578999999999999999999999999999999998888754322221 112456789988765
No 24
>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=98.72 E-value=9.7e-09 Score=79.13 Aligned_cols=64 Identities=48% Similarity=0.692 Sum_probs=45.2
Q ss_pred ceeEEEeeeccceeeEeeeCCeeEEeecCccceeec-cccccceeccceeccccceeccceEeecc
Q psy14581 5 ERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEH-KAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 5 ~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~-~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
+.|++|.||||+|+|+|+.++++.+||||+++++.. .|...-.+.. .+.....+++||+.+.+.
T Consensus 34 ~~~~~E~K~DG~R~~i~~~~~~v~l~SR~g~~~t~~~~~~~~~~~~~-~~~~~~~~iLDGEiv~~d 98 (213)
T cd07902 34 NGMYAEIKYDGERVQVHKQGDNFKFFSRSLKPVLPHKVAHFKDYIPK-AFPHGHSMILDSEVLLVD 98 (213)
T ss_pred CceEEEeccCCEEEEEEEcCCEEEEEcCCCcccccchhHHHHHHHHH-hcccccceeeeeEEEEEE
Confidence 469999999999999999999999999999998842 3322111221 122234566888887643
No 25
>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=98.72 E-value=1.4e-08 Score=77.98 Aligned_cols=63 Identities=19% Similarity=0.229 Sum_probs=49.2
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
....|++|.||||+|+|+|+.++.+.+||||+++.+..+|.++--+. .+ ...+++||+.+...
T Consensus 22 ~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~--~l--~~~~iLDGElv~~~ 84 (207)
T cd07897 22 DPSDWQAEWKWDGIRGQLIRRGGEVFLWSRGEELITGSFPELLAAAE--AL--PDGTVLDGELLVWR 84 (207)
T ss_pred CcccEEEEEeEceEEEEEEEcCCEEEEEeCCCCcccccchHHHHHHH--hC--CCCeEEEeEEEEec
Confidence 35689999999999999999999999999999999987886542111 11 13567899988654
No 26
>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=98.72 E-value=1.1e-08 Score=87.92 Aligned_cols=63 Identities=40% Similarity=0.579 Sum_probs=48.8
Q ss_pred ceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccce-eccceeccccceeccceEeec
Q psy14581 5 ERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWE-ISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 5 ~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~E-I~~a~~~~s~~~~~~G~~lrF 68 (124)
+.|++|+||||+|+|+|+.++++.+||||+++++..+|.++.+ +..+ +......++||+.+.+
T Consensus 187 ~~~~~E~K~DG~R~qih~~~~~v~l~SR~g~~~t~~~pei~~~~~~~~-~~~~~~~ILDGElv~~ 250 (514)
T TIGR00574 187 NKFYVEYKYDGERVQIHKDGDKFKIFSRRLENYTYAYPEIFTEFIKEA-FPGIKSCILDGEMVAI 250 (514)
T ss_pred CceEEEEeecceEEEEEEcCCEEEEEcCCCcccccccchhHHHHHHHh-cCccceeeecceEEEE
Confidence 4899999999999999999999999999999999888877322 2222 3222344678888765
No 27
>PRK09247 ATP-dependent DNA ligase; Validated
Probab=98.69 E-value=1.4e-08 Score=88.07 Aligned_cols=63 Identities=22% Similarity=0.311 Sum_probs=50.9
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
+...|++|+||||+|+|+|+.++++.+||||+++.+..+|.++-.+. .+. ..+++||+.+.+.
T Consensus 223 ~~~~~~~E~K~DG~R~qih~~~~~v~lfSR~g~d~t~~fPei~~~~~--~l~--~~~ILDGElv~~~ 285 (539)
T PRK09247 223 DPADWQAEWKWDGIRVQLVRRGGEVRLWSRGEELITERFPELAEAAE--ALP--DGTVLDGELLVWR 285 (539)
T ss_pred CCCcEEEEEeEcceEEEEEEeCCEEEEEeCCCccchhhhHHHHHHHH--hCC--CCEEEEeEEEEEE
Confidence 34579999999999999999999999999999999988887653222 122 3467899998765
No 28
>cd07906 Adenylation_DNA_ligase_LigD_LigC Adenylation domain of Mycobacterium tuberculosis LigD and LigC-like ATP-dependent DNA ligases. Bacterial DNA ligases are divided into two broad classes: NAD-dependent and ATP-dependent. All bacterial species have a NAD-dependent DNA ligase (LigA). Some bacterial genomes contain multiple genes for DNA ligases that are predicted to use ATP as their cofactor, including Mycobacterium tuberculosis LigB, LigC, and LigD. This group is composed of ATP-dependent DNA ligases similar to Mycobacterium tuberculosis LigC. ATP-dependent polynucleotide ligases catalyze phosphodiester bond formation using nicked nucleic acid substrates with the high energy nucleotide of ATP as a cofactor in a three step reaction mechanism. DNA ligases play a vital role in the diverse processes of DNA replication, recombination and repair. Members of this group contain adenylation and C-terminal oligonucleotide/oligosaccharide binding (OB)-fold domains, comprising a catalytic cor
Probab=98.67 E-value=1.8e-08 Score=75.89 Aligned_cols=63 Identities=19% Similarity=0.230 Sum_probs=49.0
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
.+..|++|.||||+|+|+|+.++.+.+|||++++.+...|.+...... + ..+..++||+.+-.
T Consensus 14 ~~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~t~~~p~l~~~~~~--~-~~~~~iLDGElv~~ 76 (190)
T cd07906 14 DGEDWLYEIKWDGYRALARVDGGRVRLYSRNGLDWTARFPELAEALAA--L-PVRDAVLDGEIVVL 76 (190)
T ss_pred CCCCeEEEEeEceEEEEEEEECCEEEEEcCCCCcchhhhHHHHHHHHh--c-CCCCEEEEeEEEEE
Confidence 356899999999999999999999999999999999777765432221 1 23455688988864
No 29
>TIGR02779 NHEJ_ligase_lig DNA polymerase LigD, ligase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the ligase domain.
Probab=98.67 E-value=1.9e-08 Score=81.14 Aligned_cols=64 Identities=19% Similarity=0.172 Sum_probs=50.0
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
.++.|++|+||||+|+|+|+.++.+.+||||+++++..+|.+..-.. ..+....++||+.+.+.
T Consensus 10 ~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~~p~l~~~~~---~~~~~~~iLDGElv~~d 73 (298)
T TIGR02779 10 TGDDWRYEVKYDGYRCLARIEGGKVRLISRNGHDWTEKFPILAAALA---ALPILPAVLDGEIVVLD 73 (298)
T ss_pred CCCCEEEEEEEceEEEEEEEeCCEEEEEeCCCCchHhHhHHHHHHHH---hCCCCcEEEEeEEEEEC
Confidence 57889999999999999999999999999999999987775443211 11223566899988753
No 30
>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=98.63 E-value=3.2e-08 Score=74.11 Aligned_cols=65 Identities=28% Similarity=0.381 Sum_probs=50.2
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
+..|++|.||||+|+|+|+.++.+.+|||++++++...|.++-.+...-....+.++++|+.+-+
T Consensus 18 ~~~~~~e~K~DG~R~~i~~~~~~v~~~SR~g~~~~~~~~~l~~~l~~~~~~~~~~~vLDGElv~~ 82 (202)
T PF01068_consen 18 GGPWYVEPKYDGVRCQIHKDGGGVRLFSRNGKDITSQFPELAEALRELLFPDGPDFVLDGELVVL 82 (202)
T ss_dssp TSCEEEEEEESSEEEEEEEETTEEEEEETTSSB-GGGHHHHHHHHHHHBCTSCTEEEEEEEEEEB
T ss_pred CCCeEEEEeEeeEEeeeeeccccceeecccccchhhHHHHHHHHHHHHhcCCCCceEEEEEEEEE
Confidence 57899999999999999999999999999999999867766544443322223457789988874
No 31
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=98.61 E-value=3.5e-08 Score=84.06 Aligned_cols=76 Identities=20% Similarity=0.221 Sum_probs=58.0
Q ss_pred eeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCC
Q psy14581 6 RCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATN 85 (124)
Q Consensus 6 ~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t 85 (124)
.|.+|+||||+|+|+|+.++.++.|||+++|+|..+|+.+..+..+ +... .++++|+.+.+..- ...+
T Consensus 134 ~w~~E~K~DG~R~q~h~~~~~vrl~SR~g~d~T~~fP~~~~~~~~~-l~~~-~~iiDGE~V~~~~~----------~~~~ 201 (444)
T COG1793 134 DWAYEEKFDGYRVQIHIDGGKVRLYSRNGEDWTGRFPDILEAAAEA-LPAD-DFILDGEIVVLDEE----------GRLD 201 (444)
T ss_pred CEEEEEeeceEEEEEEEcCCEEEEEeCCCccchhhChHHHHHHHhc-CCCC-ceEEeeeEEEECCC----------CCCC
Confidence 5999999999999999999999999999999999999754444332 3322 56789998887511 4556
Q ss_pred HHHHHHHH
Q psy14581 86 LPELKVLF 93 (124)
Q Consensus 86 ~~~l~~l~ 93 (124)
+++|+.-.
T Consensus 202 F~~Lq~r~ 209 (444)
T COG1793 202 FQALQQRL 209 (444)
T ss_pred HHHHHHHh
Confidence 66666544
No 32
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=98.57 E-value=6.2e-08 Score=85.40 Aligned_cols=67 Identities=16% Similarity=0.134 Sum_probs=51.6
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccc--eeccccceeccceEeecc
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGA--EFSQAEIHTADGISIRFP 69 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a--~~~~s~~~~~~G~~lrFP 69 (124)
.++.|++|+||||+|+|+|+.++++.+||||+++++..+|.++-.+... .+.....+++||+.+.+.
T Consensus 14 ~g~~w~~E~K~DG~R~~~h~~~~~V~L~SRng~d~T~~fPel~~~~~~~~~~~~~~~~~ILDGEiVvld 82 (610)
T PRK09633 14 IGDEWRYEVKYDGFRCLLIIDETGITLISRNGRELTNTFPEIIEFCESNFEHLKEELPLTLDGELVCLV 82 (610)
T ss_pred CCCcEEEEEeEcceEEEEEEECCEEEEEeCCCCcchhhhhHHHHHHHhhhhccccCCceeeeeEEEEec
Confidence 4678999999999999999999999999999999999899765322211 111112357899998864
No 33
>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=98.49 E-value=9.2e-08 Score=67.26 Aligned_cols=44 Identities=23% Similarity=0.246 Sum_probs=38.8
Q ss_pred CccceeeccccccceeccceeccccceeccceEeecccceeeecCCCcccc
Q psy14581 33 SLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTA 83 (124)
Q Consensus 33 n~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a 83 (124)
...+.+|.+|.+|+||+.++++. +.+||||||.++|.||+|++|
T Consensus 72 ~~~~~~wv~P~lv~eV~~~~~t~-------~~~LR~P~f~~~R~Dk~~~~~ 115 (115)
T cd07971 72 DARGAVWVKPELVAEVEFAEWTP-------DGRLRHPVFKGLREDKPAAEV 115 (115)
T ss_pred cCCCCEEecCCEEEEEEEEEecC-------CCcEECCeeeEeeCCCCcccC
Confidence 34688999999999999998774 349999999999999999986
No 34
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=98.47 E-value=2.4e-07 Score=74.30 Aligned_cols=61 Identities=20% Similarity=0.256 Sum_probs=49.1
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
.++.|++|.||||+|+|+|+.++.+.+||||+++++..+|.++-. .+. ..+++||+.+.+.
T Consensus 16 ~~~~~~~E~K~DG~R~~~~~~~~~v~l~SR~g~~~t~~fPe~~~~----~~~--~~~vLDGElv~~d 76 (275)
T PRK07636 16 NSENYITEPKFDGIRLIASKNNGLIRLYTRHNNEVTAKFPELLNL----DIP--DGTVLDGELIVLG 76 (275)
T ss_pred CCCcEEEEEEEceeEEEEEEeCCEEEEEeCCCCCchhhhhhHHhh----hcC--CCEEEEeEEEEEC
Confidence 467899999999999999999999999999999999888865421 121 2356899988753
No 35
>PHA02587 30 DNA ligase; Provisional
Probab=98.43 E-value=2.1e-07 Score=80.01 Aligned_cols=62 Identities=19% Similarity=0.133 Sum_probs=47.3
Q ss_pred eeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccce--ecc-ccceeccceEeec
Q psy14581 6 RCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAE--FSQ-AEIHTADGISIRF 68 (124)
Q Consensus 6 ~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~--~~~-s~~~~~~G~~lrF 68 (124)
.|++|+||||+|+|+|+.++.+.+|||++++++ ..|.++-.+.... +.. .+.+++||+.+.+
T Consensus 153 ~~~~E~K~DG~R~q~h~~~~~v~l~SR~g~~~~-~~p~i~~~l~~~~~~~~~~~~~~VLDGElv~~ 217 (488)
T PHA02587 153 PAYAQLKADGARCFADIDADGIEIRSRNGNEYL-GLDLLKEELKKMTAEARQRPGGVVIDGELVYV 217 (488)
T ss_pred cEEEEEccCceEEEEEEeCCEEEEEecCCcccc-CChhHHHHHHHHhhhhcccCCcEEEEeEEEEE
Confidence 899999999999999999999999999999997 3565544433211 111 2456789999887
No 36
>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=98.42 E-value=4.5e-07 Score=67.59 Aligned_cols=64 Identities=17% Similarity=0.072 Sum_probs=47.1
Q ss_pred CCCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
+.++.|++|.|+||+|+|+|+.++.+.+|||++++++...|..+- .+.....+..++||+.+..
T Consensus 16 ~~~~~~~~e~K~DG~R~~~~~~~~~v~~~sR~g~~~~~~~~~~~~---~~~~~~~~~~ilDGElv~~ 79 (182)
T cd06846 16 DEQDEYYVQEKYDGKRALIVALNGGVFAISRTGLEVPLPSILIPG---RELLTLKPGFILDGELVVE 79 (182)
T ss_pred cccCcEEEEEccCceEEEEEEcCCeEEEEeCCCCEEecccccccc---hHHhccCCCeeEEEEEEec
Confidence 567889999999999999999999999999999999987775431 0001112334567776653
No 37
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=98.42 E-value=2.4e-07 Score=76.82 Aligned_cols=62 Identities=26% Similarity=0.227 Sum_probs=48.7
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
++.|.+|.||||+|+|+|+.++++.+||||+++++..+|.++-.+.. +. ...+++||+.+.+
T Consensus 23 ~~~w~~E~K~DG~R~~~~~~~~~v~l~SRng~d~t~~fPel~~~~~~--~~-~~~~vLDGEiVv~ 84 (350)
T PRK08224 23 GDGWSYEPKWDGFRCLVFRDGDEVELGSRNGKPLTRYFPELVAALRA--EL-PERCVLDGEIVVA 84 (350)
T ss_pred CCcEEEEEeECeeEEEEEEECCEEEEEeCCCCCchhhhHHHHHHHHh--hC-CCCEEEeeEEEEe
Confidence 45799999999999999999999999999999999878865422221 11 2356689998875
No 38
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=98.40 E-value=2.9e-07 Score=83.83 Aligned_cols=64 Identities=19% Similarity=0.202 Sum_probs=52.5
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
.++.|++|+||||+|+|+|+.++.+++||||+++++..+|.++..+.. + ..+.+++||+.+.+.
T Consensus 247 ~g~~W~~E~K~DG~R~~a~~~gg~vrL~SRnG~d~T~~fPel~~~~~~--l-~~~~~ILDGEIVvld 310 (860)
T PRK05972 247 SGDGWIYEIKFDGYRILARIEGGEVRLFTRNGLDWTAKLPALAKAAAA--L-GLPDAWLDGEIVVLD 310 (860)
T ss_pred CcCceEEEeeeCcEEEEEEEECCEEEEEeCCCCccccccHHHHHHHHh--c-CCCceeEeEEEEEEC
Confidence 357899999999999999999999999999999999888877654432 2 224567899998875
No 39
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=98.40 E-value=3.8e-07 Score=82.22 Aligned_cols=65 Identities=18% Similarity=0.190 Sum_probs=51.1
Q ss_pred CCCceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEeecc
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP 69 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP 69 (124)
+.++.|++|+||||+|+|+|+.++.+.+||||+++++..+|.++. +. ..+. ....++||+.+.+.
T Consensus 474 ~~~~~w~~E~K~DG~R~~~~~~~g~vrL~SRnG~d~T~~fPel~~-~~-~~l~-~~~~ILDGEiVvld 538 (764)
T PRK09632 474 LKASQWAFEGKWDGYRLLAEADHGALRLRSRSGRDVTAEYPELAA-LA-EDLA-DHHVVLDGEIVALD 538 (764)
T ss_pred CCCCCEEEEEEECceeEEEEEeCCEEEEEeCCCCCccccchhHHH-HH-hhCC-CcceeeeeEEEEeC
Confidence 356789999999999999999999999999999999988886543 21 1122 23456899998764
No 40
>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=98.35 E-value=2e-07 Score=75.20 Aligned_cols=46 Identities=24% Similarity=0.201 Sum_probs=40.7
Q ss_pred cCccceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccC
Q psy14581 32 RSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTAT 84 (124)
Q Consensus 32 Rn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~ 84 (124)
....+.+|..|.+|+||+.++++. |.+|||||+.++|.||+|+||+
T Consensus 252 ~~~~~~~wv~P~lV~eV~~~~~t~-------~~~lR~P~~~~~R~Dk~~~~~~ 297 (298)
T TIGR02779 252 REKRGVHWVKPELVAEVEFAGWTR-------DGRLRQASFVGLREDKPASEVT 297 (298)
T ss_pred ccCCCCEEeCCeEEEEEEecccCC-------CCeEeccEEEeeeCCCCHHHcc
Confidence 445688999999999999998774 5689999999999999999986
No 41
>COG1793 CDC9 ATP-dependent DNA ligase [DNA replication, recombination, and repair]
Probab=98.31 E-value=2.1e-07 Score=79.31 Aligned_cols=56 Identities=29% Similarity=0.452 Sum_probs=51.4
Q ss_pred eeccccccceeccceeccccceec-cceEeecccceeeecCCCccccCCHHHHHHHH
Q psy14581 38 LEHKAQPVWEISGAEFSQAEIHTA-DGISIRFPRVTKIRDDKDWKTATNLPELKVLF 93 (124)
Q Consensus 38 t~~~Ps~V~EI~~a~~~~s~~~~~-~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~ 93 (124)
.|+.|..|+||+.++++.++.|.+ .|.+|||||+.++|.||.+.+++|++++..||
T Consensus 387 ~~~~p~~V~EV~~~~~t~~~~~r~~~~~~lRfpr~~rvr~dk~~~~a~t~~~~~~~~ 443 (444)
T COG1793 387 VVPPPGLVAEVRFAEITKSGRLRHASGLGLRFPRFVRVRDDKLPEDADTIEEIEALY 443 (444)
T ss_pred eecCCcEEEEEEEeecccCCceecccCcccCcCcccccccccCcccccccccchhhc
Confidence 557779999999999999999965 49999999999999999999999999998886
No 42
>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=98.09 E-value=7.7e-06 Score=62.68 Aligned_cols=64 Identities=17% Similarity=0.038 Sum_probs=44.6
Q ss_pred CCceeEEEeeeccceeeEeeeC-CeeEEeecCccceeeccccccceeccceeccccceeccceEeec
Q psy14581 3 KNERCYSEIKYDGERVQVHKKG-NEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRF 68 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~-~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrF 68 (124)
..+.|++|+|+||+|+|+|..+ +.+.+++|+++..+-..|..+ +..... ...+..++||+.+..
T Consensus 39 ~~~~y~ve~K~DG~R~~l~~~~~~~v~l~sR~~~~~~~~~~~~~-~~~~~~-~~~~~~ilDGElv~~ 103 (215)
T cd07895 39 KQNDYFVCEKSDGVRYLLLITGRGEVYLIDRKNDVFKVPGLFFP-RRKNLE-PHHQGTLLDGELVID 103 (215)
T ss_pred hhCCeEEEEeEcCeEEEEEEecCCcEEEEeCCCCeEEeccccCC-Cccccc-ccccCeeeEEEEEEE
Confidence 4678999999999999999998 899999999887776555432 111111 112334467776654
No 43
>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=98.08 E-value=1.7e-06 Score=75.68 Aligned_cols=46 Identities=20% Similarity=0.093 Sum_probs=40.7
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCH
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNL 86 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~ 86 (124)
..+.+|..|.+|+||+.++++. |.+||||||.++|.||+|+||+..
T Consensus 215 ~~~~~Wv~P~lV~EV~~~e~T~-------~g~LR~Prf~~~R~DK~~~e~t~e 260 (552)
T TIGR02776 215 TRGVHWVRPSLVAEVEYAGITR-------DGILREASFKGLREDKPAEEVTLE 260 (552)
T ss_pred CCCcEEEccCEEEEEEeeeccC-------CCeeEccEEEEEeCCCCHHHcchh
Confidence 3578999999999999998874 569999999999999999999754
No 44
>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=98.04 E-value=3.2e-06 Score=60.50 Aligned_cols=45 Identities=24% Similarity=0.252 Sum_probs=39.6
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecc-cceeeecCCCccccCC
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFP-RVTKIRDDKDWKTATN 85 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP-R~~~iR~DK~~~~a~t 85 (124)
..+.+|.+|.+|.||+..+++. +| .||+| |+..+|.||++++|+.
T Consensus 77 ~~~~~wv~P~lV~eV~~~e~t~------~G-~LRhP~~f~glR~Dk~~~~v~~ 122 (122)
T cd07970 77 SLEWVPVRPELVVEVSADTAEG------GG-RFRHPLRFLRWRPDKSPEDCTL 122 (122)
T ss_pred CCCeEEeeccEEEEEEeeEEec------CC-ceeCCceeEEEcCCCCHHHCcC
Confidence 4578999999999999998774 56 99999 8999999999999863
No 45
>PRK09633 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.91 E-value=5.7e-06 Score=73.14 Aligned_cols=53 Identities=15% Similarity=0.050 Sum_probs=46.9
Q ss_pred cceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCHHHHHHHHHH
Q psy14581 35 KPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKK 95 (124)
Q Consensus 35 ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~ 95 (124)
.+.+|.+|.+|+||..++++ |..||||||.++|.||+++||++.+++.++|..
T Consensus 267 ~~~~wV~P~LV~EV~~~e~t--------~g~LR~P~f~glR~DK~~~ev~~~~~~~~~~~~ 319 (610)
T PRK09633 267 SGEYTLEPSICVTVACITFD--------GGTLREPSFVSFLFDMDPTECTYQQLQRQLAPL 319 (610)
T ss_pred CCcEEEeeeEEEEEEEeecC--------CCeEEeeEEeEEEcCCChHHcchhhhhhhhccC
Confidence 45789999999999998763 668999999999999999999999988887765
No 46
>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=97.50 E-value=5.7e-05 Score=52.39 Aligned_cols=34 Identities=24% Similarity=0.236 Sum_probs=30.4
Q ss_pred cceeeccccccceeccceeccccceeccceEeecccceeee
Q psy14581 35 KPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIR 75 (124)
Q Consensus 35 ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR 75 (124)
.+++|..|+.|+||+.++++. +.+||||||.++|
T Consensus 75 ~~~vwv~P~lv~eV~~~~~t~-------~~~lR~P~f~~~R 108 (108)
T cd08040 75 LSFVPLYPGKVVEVKYFEMGS-------KDCLRFPVFIGIR 108 (108)
T ss_pred CCCEEeeceEEEEEEeEEeeC-------CCeEECCeEEEeC
Confidence 588999999999999998763 7899999999987
No 47
>PHA00454 ATP-dependent DNA ligase
Probab=97.45 E-value=0.00013 Score=59.49 Aligned_cols=34 Identities=24% Similarity=0.365 Sum_probs=30.0
Q ss_pred ceeEEEeeeccceeeEeeeCCe-eEEeecCcccee
Q psy14581 5 ERCYSEIKYDGERVQVHKKGNE-FKYFSRSLKPVL 38 (124)
Q Consensus 5 ~~f~~E~K~DGER~QiH~~~~~-~k~fSRn~ep~t 38 (124)
..|+.|+||||.|+|+|+.++. +..||||++++.
T Consensus 27 g~~~~E~K~DG~R~~~~~~~~~~v~l~SR~g~~~p 61 (315)
T PHA00454 27 GYLIADVKYDGVRGNIVVDNTADHGWLSREGKTIP 61 (315)
T ss_pred CcEEEEEccceEEEEEEEcCCCeEEEEeCCCCccc
Confidence 4799999999999999998764 999999998643
No 48
>PRK09632 ATP-dependent DNA ligase; Reviewed
Probab=97.44 E-value=6.1e-05 Score=68.22 Aligned_cols=44 Identities=20% Similarity=0.152 Sum_probs=38.9
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccC
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTAT 84 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~ 84 (124)
..+.+|..|.+|+||+.++++. +..||||||.++|.||+++||+
T Consensus 718 ~~~~~WV~P~LV~EV~f~e~T~-------~g~LR~P~f~glR~DK~p~dv~ 761 (764)
T PRK09632 718 AKGATWVRPELVGEVRYSEWTP-------DGRLRQPSWRGLRPDKKPGDVV 761 (764)
T ss_pred CCCcEEEeccEEEEEEEeeccC-------CCceecceEEEeeCCCCHHHcc
Confidence 4578999999999999998773 3379999999999999999986
No 49
>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=97.43 E-value=8.7e-05 Score=54.94 Aligned_cols=51 Identities=24% Similarity=0.163 Sum_probs=36.3
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccceeeccccccceeccceeccccceeccceEee
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLEHKAQPVWEISGAEFSQAEIHTADGISIR 67 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lr 67 (124)
++.|++|.||||+|+|+|. . .+|||++++++.. .. +. +.+ +..++||+.+.
T Consensus 15 ~~~~~~e~K~DG~R~~~~~---~-~~~SR~g~~~t~~--~~---~~-~~l---~~~ilDGElv~ 65 (174)
T cd07896 15 ISGYLVSEKLDGVRAYWDG---K-QLLSRSGKPIAAP--AW---FT-AGL---PPFPLDGELWI 65 (174)
T ss_pred hHHeeechhhceEEEEEec---c-EEEecCCcCCCCC--HH---HH-hhC---CCCccCceEEc
Confidence 4579999999999999983 2 9999999999853 11 11 111 22567888774
No 50
>PRK05972 ligD ATP-dependent DNA ligase; Reviewed
Probab=97.28 E-value=0.00012 Score=67.04 Aligned_cols=45 Identities=22% Similarity=0.220 Sum_probs=38.8
Q ss_pred cceeeccccccceeccceeccccceeccceEeecccceeeecCCCccccCCH
Q psy14581 35 KPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRDDKDWKTATNL 86 (124)
Q Consensus 35 ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~ 86 (124)
.+.+|.+|.+|+||+.++++.+ | .||||||.++|.||++++|+--
T Consensus 494 ~~~~WV~P~LV~EV~f~e~T~~------g-~LR~P~F~glR~DK~p~ev~~e 538 (860)
T PRK05972 494 RGVHWVKPELVAEVEFAGWTRD------G-IVRQAVFKGLREDKPAREVVAE 538 (860)
T ss_pred CCCEEEccCEEEEEEEeeccCC------C-CCccceEEEeecCCChHHhChh
Confidence 3468999999999999988753 4 6999999999999999998743
No 51
>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=96.93 E-value=0.0013 Score=54.68 Aligned_cols=31 Identities=23% Similarity=0.237 Sum_probs=28.7
Q ss_pred ceeEEEeeeccceeeEeeeCCeeEEeecCcc
Q psy14581 5 ERCYSEIKYDGERVQVHKKGNEFKYFSRSLK 35 (124)
Q Consensus 5 ~~f~~E~K~DGER~QiH~~~~~~k~fSRn~e 35 (124)
+.|++|.|+||.|+|+|+.++.+..|||++.
T Consensus 48 ~~~~vEEKlDG~nvri~~~~G~v~a~TR~G~ 78 (342)
T cd07894 48 GPVAVEEKMNGYNVRIVRIGGKVLAFTRGGF 78 (342)
T ss_pred CCEEEEEeECCcEEEEEEECCEEEEEeCCCc
Confidence 5899999999999999999999999999964
No 52
>PRK09125 DNA ligase; Provisional
Probab=96.25 E-value=0.0036 Score=50.46 Aligned_cols=33 Identities=18% Similarity=0.185 Sum_probs=28.4
Q ss_pred CCceeEEEeeeccceeeEeeeCCeeEEeecCccceee
Q psy14581 3 KNERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVLE 39 (124)
Q Consensus 3 ~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t~ 39 (124)
..+.|++|.||||.|+|++ .+..|||++++.+.
T Consensus 41 ~~~~~~~E~K~DG~R~~~~----~v~l~SR~g~~it~ 73 (282)
T PRK09125 41 DISGYLVSEKLDGVRAYWD----GKQLLTRQGNPIAA 73 (282)
T ss_pred ChhhEEEEeeeeeEeEEEC----CeEEEcCCCCcCCC
Confidence 3468999999999999863 58999999999875
No 53
>PRK07636 ligB ATP-dependent DNA ligase; Reviewed
Probab=93.46 E-value=0.049 Score=43.72 Aligned_cols=35 Identities=14% Similarity=0.165 Sum_probs=29.6
Q ss_pred ccceeeccccccceeccceeccccceeccceEeecccceeee
Q psy14581 34 LKPVLEHKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIR 75 (124)
Q Consensus 34 ~ep~t~~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR 75 (124)
..+.+|..|.+|.||+.++++. +|. ||||+|.++|
T Consensus 240 ~~~~~wv~P~lv~eV~~~e~t~------~g~-lR~p~f~g~r 274 (275)
T PRK07636 240 DKKFVYIEPIIGCRVKHRFKTK------NGM-LRIPSFVEWR 274 (275)
T ss_pred cCCCEEeCCcEEEEEEEEEecC------CCC-EEccEEEEEe
Confidence 3578999999999999888773 466 9999999887
No 54
>PRK08224 ligC ATP-dependent DNA ligase; Reviewed
Probab=93.08 E-value=0.059 Score=44.86 Aligned_cols=43 Identities=21% Similarity=0.275 Sum_probs=35.7
Q ss_pred cceee--ccccccceeccceeccccceeccceEeecc-cceeeecCCCccccCC
Q psy14581 35 KPVLE--HKAQPVWEISGAEFSQAEIHTADGISIRFP-RVTKIRDDKDWKTATN 85 (124)
Q Consensus 35 ep~t~--~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP-R~~~iR~DK~~~~a~t 85 (124)
.+.+| .+|.+|.||...+.+ +| .||-| +|..+|.||++.||+-
T Consensus 286 ~~~~w~~v~P~lv~eV~~~~~t-------~~-~lR~p~~f~g~r~Dk~p~~v~~ 331 (350)
T PRK08224 286 KDLSWVPLRPERVVEVRYDHME-------GG-RFRHTAQFLRWRPDRDPRSCTY 331 (350)
T ss_pred CCcEEEeeeEEEEEEEecCccc-------CC-eecCCCeeEEEcCCCChHHCCH
Confidence 35677 899999999987654 23 78998 9999999999999984
No 55
>KOG4437|consensus
Probab=84.81 E-value=0.36 Score=40.91 Aligned_cols=34 Identities=65% Similarity=0.942 Sum_probs=28.1
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCcccee
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPVL 38 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~t 38 (124)
|+.| .|.+|||||.|+|..++.+.||||.-+...
T Consensus 389 ~~~~-S~~~~D~E~~~~~~~~D~~S~~S~~~~~~s 422 (482)
T KOG4437|consen 389 NGMF-SEIKYDGERVQVHKNGDHFSYFSRLPHKVA 422 (482)
T ss_pred CCcc-ccccCCCceeeccCCCcchhhhccChHhhh
Confidence 4444 899999999999999999999999755443
No 56
>PF14743 DNA_ligase_OB_2: DNA ligase OB-like domain; PDB: 2Q2U_D 2Q2T_A 1FVI_A 1P8L_A.
Probab=68.32 E-value=2.1 Score=27.45 Aligned_cols=28 Identities=25% Similarity=0.462 Sum_probs=16.8
Q ss_pred cccccceeccceeccccceeccceEeecccceeee
Q psy14581 41 KAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIR 75 (124)
Q Consensus 41 ~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR 75 (124)
...-+++++.-+++. +| .+|||++.++|
T Consensus 39 ~iG~iit~ky~~~t~------~g-~pRfP~f~~~R 66 (66)
T PF14743_consen 39 YIGKIITVKYQGLTK------DG-SPRFPVFVRVR 66 (66)
T ss_dssp HTT-EEEEEEE-TTS------SS-S-EEEEEEEE-
T ss_pred CCCCEEEEEEEccCC------CC-ccccCEEEEeC
Confidence 345666777665553 23 78999999997
No 57
>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=53.77 E-value=23 Score=30.20 Aligned_cols=34 Identities=24% Similarity=0.226 Sum_probs=28.3
Q ss_pred CCCceeEEEeeeccceeeEeeeCCeeEEeecCcc
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGNEFKYFSRSLK 35 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~e 35 (124)
|.+..+++|.|.||-++-|...++++.-.||.+.
T Consensus 76 f~~~~v~vEEKlDG~Nvri~~~~g~l~a~tRGgy 109 (374)
T TIGR01209 76 FKDPEVVVEEKMNGYNVRIVKYGGNVYALTRGGF 109 (374)
T ss_pred cCCCcEEEEEeecCceEEEEeECCEEEEEccCcc
Confidence 3455599999999999999888888988888764
No 58
>COG1423 ATP-dependent DNA ligase, homolog of eukaryotic ligase III [DNA replication, recombination, and repair]
Probab=53.67 E-value=24 Score=30.07 Aligned_cols=33 Identities=27% Similarity=0.244 Sum_probs=28.6
Q ss_pred CCCceeEEEeeeccceeeEeeeCCeeEEeecCc
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGNEFKYFSRSL 34 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ 34 (124)
++.+.+++|.|+||.++-|.+.++++.--+|.+
T Consensus 85 F~~~~v~VEEKmnGYNVRV~k~~g~vyAiTRgG 117 (382)
T COG1423 85 FGRGKVVVEEKMNGYNVRVVKLGGEVYAITRGG 117 (382)
T ss_pred cCCCcEEEEEeccCceEEEEEECCEEEEEecCc
Confidence 346789999999999999999988888878876
No 59
>PF09414 RNA_ligase: RNA ligase; InterPro: IPR021122 This entry represents the RNA ligase domain. RNA ligase enzyme repairs RNA strand breaks in nicked DNA:RNA and RNA:RNA but not in DNA:DNA duplexes []. Members of this RNA ligase family include: RNA editing ligase 1 (REL1) , which is essential for RNA editing and may be active in U-deletion editing [, , ]. RNA editing ligase 2 (REL2), which may be active in U-insertion editing []. RnlB RNA ligase 2 (or Rnl2), second RNA ligase of Enterobacteria phage T4 (Bacteriophage T4); unlike RNA ligase 1, RnlB prefers doule stranded substrates [, ]. ; PDB: 2HVS_B 2HVR_A 1S68_A 2HVQ_A 1XDN_A.
Probab=51.94 E-value=24 Score=25.78 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=23.8
Q ss_pred eeEEEeeeccceeeEeeeCC-eeEEeecCc
Q psy14581 6 RCYSEIKYDGERVQVHKKGN-EFKYFSRSL 34 (124)
Q Consensus 6 ~f~~E~K~DGER~QiH~~~~-~~k~fSRn~ 34 (124)
+++++.|+||..+.+...++ .+.+.+|+.
T Consensus 2 e~vvtEKldGtn~~i~~~~~~~~~~~~R~~ 31 (186)
T PF09414_consen 2 EVVVTEKLDGTNFSIYFDNDGRVRFQSRSH 31 (186)
T ss_dssp EEEEEEE-SSEEEEEEEEECTCEEEEETTE
T ss_pred eEEEEEEeCCccEEEEEeCCCceeEecccc
Confidence 68999999999999998665 478888876
No 60
>PHA00454 ATP-dependent DNA ligase
Probab=49.61 E-value=9.7 Score=31.02 Aligned_cols=30 Identities=23% Similarity=0.263 Sum_probs=21.5
Q ss_pred ccccccceeccceeccccceeccceEeecccceeeec
Q psy14581 40 HKAQPVWEISGAEFSQAEIHTADGISIRFPRVTKIRD 76 (124)
Q Consensus 40 ~~Ps~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR~ 76 (124)
+.|..|.||+..+.|. +-.||||+|.++|+
T Consensus 285 p~~~~v~eV~y~e~T~-------~g~lR~P~F~g~Rd 314 (315)
T PHA00454 285 PYNGRACQVSYMERTP-------DGSLRHPSFDRFRD 314 (315)
T ss_pred CCCCeEEEEEEEEcCC-------CCcccCceeeeeec
Confidence 4455677887766552 23899999999985
No 61
>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=46.82 E-value=9.2 Score=24.65 Aligned_cols=26 Identities=15% Similarity=0.230 Sum_probs=18.9
Q ss_pred cccceeccceeccccceeccceEeecccceeee
Q psy14581 43 QPVWEISGAEFSQAEIHTADGISIRFPRVTKIR 75 (124)
Q Consensus 43 s~V~EI~~a~~~~s~~~~~~G~~lrFPR~~~iR 75 (124)
..|.+|+..+.+. .-.||||++..+|
T Consensus 52 g~v~~V~y~e~t~-------~g~lR~P~f~g~R 77 (77)
T cd08041 52 GSIITYKYQGLTK-------NGLPRFPVFLRVR 77 (77)
T ss_pred CCEEEEEEEecCC-------CCcccCCEEEecC
Confidence 4577777765553 4589999999876
No 62
>PF14275 DUF4362: Domain of unknown function (DUF4362)
Probab=33.73 E-value=67 Score=22.23 Aligned_cols=32 Identities=16% Similarity=0.534 Sum_probs=25.2
Q ss_pred CCCceeEEEeeeccceeeEeeeCCeeEEeecC
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGNEFKYFSRS 33 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~~~k~fSRn 33 (124)
.+|++.+..+.|||.+++...+...-++|+..
T Consensus 40 ~EGdPI~~~L~~~G~~I~y~~Dnt~d~~~~g~ 71 (98)
T PF14275_consen 40 IEGDPIFQDLEYDGNQIKYTSDNTRDKFFAGQ 71 (98)
T ss_pred CCCCCEEEEEEECCCEEEEEECCCcccccCcc
Confidence 47899999999999998887776666666553
No 63
>TIGR02307 RNA_lig_RNL2 RNA ligase, Rnl2 family. Members of this family ligate (seal breaks in) RNA. Members so far include phage proteins that can counteract a host defense of cleavage of specific tRNA molecules, trypanosome ligases involved in RNA editing, but no prokaryotic host proteins.
Probab=33.12 E-value=79 Score=26.43 Aligned_cols=33 Identities=9% Similarity=0.037 Sum_probs=29.0
Q ss_pred CCCceeEEEeeeccceeeEeeeCC-eeEEeecCc
Q psy14581 2 AKNERCYSEIKYDGERVQVHKKGN-EFKYFSRSL 34 (124)
Q Consensus 2 ~~~~~f~~E~K~DGER~QiH~~~~-~~k~fSRn~ 34 (124)
|.+.+|.+..|.+|-++.+-..++ .+.+.+|+.
T Consensus 22 l~~~ewvatEKlhGaNfsi~~~~~~~i~~akR~~ 55 (325)
T TIGR02307 22 LGLTEWVAREKIHGTNFSIIIERDFKVTCAKRTG 55 (325)
T ss_pred cCCceEEEEEEecCcceEEEEeCCceEEEeeccc
Confidence 456799999999999999999877 899999983
No 64
>PRK10737 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=32.74 E-value=26 Score=27.11 Aligned_cols=36 Identities=17% Similarity=0.273 Sum_probs=29.9
Q ss_pred cccccceeccceeccccceeccceEeecc-cceeeec
Q psy14581 41 KAQPVWEISGAEFSQAEIHTADGISIRFP-RVTKIRD 76 (124)
Q Consensus 41 ~Ps~V~EI~~a~~~~s~~~~~~G~~lrFP-R~~~iR~ 76 (124)
.|..|.+|....++..-+|++.|.+|.|. +++.+|.
T Consensus 105 ~~~~V~ev~~d~V~vD~NHPLAG~~L~F~veV~~vr~ 141 (196)
T PRK10737 105 VPVEITAVEDDHVVVDGNHMLAGQNLKFNVEVVAIRE 141 (196)
T ss_pred EEEEEEEEcCCEEEEECCCcCCCCEEEEEEEEEEecc
Confidence 35568888888888888999999999999 7778883
No 65
>PF01653 DNA_ligase_aden: NAD-dependent DNA ligase adenylation domain; InterPro: IPR013839 DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC). This entry represents the N-terminal adenylation domain of NAD-dependent DNA ligases. These are proteins of about 75 to 85 Kd whose sequence is well conserved [, ]. They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd. Despite a complete lack of detectable sequence similarity, the fold of the central core of this adenyaltion domain shares homology with the equivalent region of ATP-dependent DNA ligases [, ].; GO: 0003911 DNA ligase (NAD+) activity; PDB: 1ZAU_A 3SGI_A 1B04_A 3JSL_A 3JSN_A 1DGS_A 1V9P_A 3PN1_A 3BAC_A 3UQ8_A ....
Probab=30.38 E-value=94 Score=25.52 Aligned_cols=27 Identities=19% Similarity=0.245 Sum_probs=22.8
Q ss_pred eeEEEeeeccceeeEeeeCCee-EEeec
Q psy14581 6 RCYSEIKYDGERVQVHKKGNEF-KYFSR 32 (124)
Q Consensus 6 ~f~~E~K~DGER~QiH~~~~~~-k~fSR 32 (124)
.|.+|.|+||-.+.+++.++.. +-.+|
T Consensus 108 ~~~~e~KiDGlsi~L~Y~~G~L~~a~TR 135 (315)
T PF01653_consen 108 EFVVEPKIDGLSISLIYENGKLVRAATR 135 (315)
T ss_dssp EEEEEEEESSEEEEEEEETTEEEEEEEE
T ss_pred ceeEeeccceeEEEEEEeCCEEEEEEEc
Confidence 5999999999999999988764 55666
No 66
>PF01331 mRNA_cap_enzyme: mRNA capping enzyme, catalytic domain; InterPro: IPR001339 The mRNA capping enzyme in yeasts is composed of two separate chains, alpha a mRNA guanyltransferase and beta an RNA 5'-triphosphate. X-ray crystallography reveals a large conformational change during guanyl transfer by mRNA capping enzymes []. Binding of the enzyme to nucleotides is specific to the GMP moiety of GTP. The viral mRNA capping enzyme is a monomer that transfers a GMP cap onto the end of mRNA that terminates with a 5'-diphosphate tail.; GO: 0004484 mRNA guanylyltransferase activity, 0006370 mRNA capping, 0006397 mRNA processing; PDB: 3RTX_A 3KYH_D 3S24_G 1CKN_B 1CKO_A 1CKM_B 1P16_B.
Probab=26.80 E-value=54 Score=24.28 Aligned_cols=34 Identities=18% Similarity=0.150 Sum_probs=26.1
Q ss_pred CceeEEEeeeccceeeEeeeCCeeEEeecCccce
Q psy14581 4 NERCYSEIKYDGERVQVHKKGNEFKYFSRSLKPV 37 (124)
Q Consensus 4 ~~~f~~E~K~DGER~QiH~~~~~~k~fSRn~ep~ 37 (124)
...|++-+|-||.|.-+....+.+..++|+.+..
T Consensus 15 ~~~Y~V~eKaDG~Ryll~i~~~~~ylidr~~~~~ 48 (192)
T PF01331_consen 15 QKDYFVCEKADGTRYLLLITDNGVYLIDRKNNVF 48 (192)
T ss_dssp HS-EEEEEEESSEEEEEEEEEEEEEEEETTS-EE
T ss_pred hCCcEEEECCCCcEEEEEEecceEEEEeCCCcEE
Confidence 3467788899999999998888888889986544
No 67
>PRK15095 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=23.22 E-value=49 Score=24.30 Aligned_cols=34 Identities=24% Similarity=0.356 Sum_probs=27.6
Q ss_pred ccccceeccceeccccceeccceEeecc-cceeee
Q psy14581 42 AQPVWEISGAEFSQAEIHTADGISIRFP-RVTKIR 75 (124)
Q Consensus 42 Ps~V~EI~~a~~~~s~~~~~~G~~lrFP-R~~~iR 75 (124)
+..|.+|....++..-+|++.|.+|.|- ++..+|
T Consensus 110 ~~~V~~i~~~~v~vD~NHPLAGk~L~f~v~i~~v~ 144 (156)
T PRK15095 110 PGVIREINGDSITVDFNHPLAGQTVHFDIEVLEID 144 (156)
T ss_pred EEEEEEEcCCEEEEECCCcCCCCEEEEEEEEEEec
Confidence 3457777777788888899999999998 777887
No 68
>TIGR03738 PRTRC_C PRTRC system protein C. A novel genetic system characterized by six major proteins, included a ParB homolog and a ThiF homolog, is designated PRTRC, or ParB-Related,ThiF-Related Cassette. It is often found on plasmids. This protein family is designated PRTRC system protein C.
Probab=22.04 E-value=1.1e+02 Score=19.88 Aligned_cols=42 Identities=12% Similarity=0.108 Sum_probs=28.3
Q ss_pred ccceeccceEeecccceeeecCCCccccCCHHHHHHHHHHcccCCCccccCcc
Q psy14581 56 AEIHTADGISIRFPRVTKIRDDKDWKTATNLPELKVLFKKSKETSDFTLKPKY 108 (124)
Q Consensus 56 s~~~~~~G~~lrFPR~~~iR~DK~~~~a~t~~~l~~l~~~~~~~~~~~~~~~~ 108 (124)
...|+..| ++++ +++-.++++++.++|..+=-.--...+.++
T Consensus 6 ~RvF~~~g--i~L~---------DP~p~~spe~V~dfYs~~YPeLttA~v~gP 47 (66)
T TIGR03738 6 SRVFTYNG--VRLA---------DPSPAMSPEQVRDFYSAQYPELLNAEVEGP 47 (66)
T ss_pred EEEEEECC--eEcC---------CCCCCCCHHHHHHHHhccCchheeeeeeCC
Confidence 34566666 5555 678899999999999886544444444444
Done!