Query psy8717
Match_columns 69
No_of_seqs 111 out of 1111
Neff 5.4
Searched_HMMs 46136
Date Fri Aug 16 17:27:21 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8717.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8717hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00436 TOP1Bc Bacterial DN 99.9 7.8E-26 1.7E-30 139.9 4.9 52 2-56 38-89 (89)
2 PRK07220 DNA topoisomerase I; 99.9 8.4E-24 1.8E-28 166.6 5.6 65 1-65 167-231 (740)
3 TIGR01056 topB DNA topoisomera 99.9 1.8E-23 4E-28 163.2 7.2 65 1-65 166-231 (660)
4 COG0550 TopA Topoisomerase IA 99.9 1.3E-23 2.7E-28 162.7 5.7 62 1-65 145-206 (570)
5 PRK08173 DNA topoisomerase III 99.9 3.9E-23 8.5E-28 165.2 7.3 64 1-64 165-229 (862)
6 cd00186 TOP1Ac DNA Topoisomera 99.9 2.6E-23 5.6E-28 153.1 5.4 56 1-58 12-67 (381)
7 PRK14973 DNA topoisomerase I; 99.9 5.3E-23 1.2E-27 165.7 7.5 65 1-65 166-230 (936)
8 TIGR01057 topA_arch DNA topois 99.9 5.3E-23 1.1E-27 159.1 7.0 65 1-65 160-226 (618)
9 PRK05776 DNA topoisomerase I; 99.9 4.7E-23 1E-27 161.2 6.3 65 1-65 163-229 (670)
10 PRK14724 DNA topoisomerase III 99.9 6E-23 1.3E-27 165.9 7.0 64 1-64 173-237 (987)
11 PRK07219 DNA topoisomerase I; 99.9 4.9E-23 1.1E-27 163.5 6.0 64 1-64 166-230 (822)
12 TIGR01051 topA_bact DNA topois 99.9 9.4E-23 2E-27 157.8 6.6 61 1-65 137-197 (610)
13 PRK07726 DNA topoisomerase III 99.9 1.1E-22 2.4E-27 158.5 6.7 61 1-61 161-222 (658)
14 PRK08780 DNA topoisomerase I; 99.9 1.7E-22 3.6E-27 160.2 5.1 61 1-65 145-205 (780)
15 PRK05582 DNA topoisomerase I; 99.9 2.6E-22 5.7E-27 155.9 5.8 61 1-65 141-201 (650)
16 PF01131 Topoisom_bac: DNA top 99.9 2E-22 4.3E-27 149.0 4.6 59 1-65 15-73 (403)
17 PRK06599 DNA topoisomerase I; 99.9 3.7E-22 8E-27 155.8 6.2 59 1-63 144-202 (675)
18 PRK06319 DNA topoisomerase I/S 99.9 7.4E-22 1.6E-26 157.6 6.0 61 1-63 140-200 (860)
19 PRK07561 DNA topoisomerase I s 99.8 9.6E-22 2.1E-26 156.8 5.7 59 1-63 154-212 (859)
20 PTZ00407 DNA topoisomerase IA; 99.8 3.5E-20 7.7E-25 148.0 6.9 58 1-62 198-257 (805)
21 PRK14701 reverse gyrase; Provi 99.7 1.7E-17 3.7E-22 139.5 5.0 56 1-60 768-823 (1638)
22 TIGR01054 rgy reverse gyrase. 99.7 3.3E-17 7.2E-22 134.5 5.3 55 1-60 787-841 (1171)
23 PRK09401 reverse gyrase; Revie 99.7 5E-17 1.1E-21 133.5 5.5 52 1-57 787-838 (1176)
24 KOG1956|consensus 99.6 1.1E-16 2.5E-21 126.1 3.7 65 2-66 177-245 (758)
25 KOG1957|consensus 99.0 5.3E-11 1.1E-15 91.8 0.2 44 22-65 183-226 (555)
26 COG1110 Reverse gyrase [DNA re 99.0 1.8E-10 4E-15 94.9 1.4 48 1-51 803-850 (1187)
27 PF13061 DUF3923: Protein of u 70.7 2.5 5.3E-05 24.9 1.1 16 25-40 27-42 (66)
28 TIGR02923 AhaC ATP synthase A1 44.9 56 0.0012 23.2 4.6 22 24-49 301-322 (343)
29 COG0055 AtpD F0F1-type ATP syn 40.3 21 0.00044 28.2 1.8 33 34-66 390-422 (468)
30 PRK14745 RepA leader peptide T 36.4 14 0.00031 18.1 0.3 9 24-32 17-25 (26)
31 PF11279 DUF3080: Protein of u 35.7 24 0.00051 25.9 1.5 21 24-44 64-84 (316)
32 PRK14746 RepA leader peptide T 27.7 25 0.00055 17.2 0.4 9 24-32 16-24 (26)
33 PF08483 IstB_IS21_ATP: IstB-l 26.3 59 0.0013 16.3 1.6 12 36-47 18-29 (30)
34 PF15343 DEPP: Decidual protei 25.4 28 0.00062 24.5 0.4 11 2-12 81-91 (188)
35 TIGR03475 tap_IncFII_lead RepA 25.1 29 0.00063 17.0 0.3 9 24-32 17-25 (26)
36 PF08259 Periviscerokin: Periv 24.0 41 0.00088 13.5 0.6 8 24-31 4-11 (11)
37 PF11469 Ribonucleas_3_2: Ribo 23.1 2.1E+02 0.0045 18.7 4.1 42 3-49 8-49 (120)
38 PF08048 RepA1_leader: Tap Rep 21.9 36 0.00077 16.6 0.3 7 25-31 18-24 (25)
No 1
>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain. Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Probab=99.92 E-value=7.8e-26 Score=139.93 Aligned_cols=52 Identities=40% Similarity=0.588 Sum_probs=49.2
Q ss_pred hHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEE
Q psy8717 2 LDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWL 56 (69)
Q Consensus 2 lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~ 56 (69)
+||++|+|+||++|.+++. +.+|+||||||||++||+||+||+||+|++||+
T Consensus 38 ~D~l~G~n~Sr~~t~~~~~---~~ls~GRVQtptL~lIv~R~~ei~~F~~~~y~~ 89 (89)
T smart00436 38 LDRLIGFNLSRLLTKKLRK---GVLSAGRVQTPTLGLIVEREREIKNFVPKPYWE 89 (89)
T ss_pred HHHHHhHhhhHHHHHHhCC---CCcceecchHHHHHHHHHHHHHHHcCCCCCCCC
Confidence 7999999999999998874 479999999999999999999999999999994
No 2
>PRK07220 DNA topoisomerase I; Validated
Probab=99.89 E-value=8.4e-24 Score=166.58 Aligned_cols=65 Identities=32% Similarity=0.498 Sum_probs=58.1
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||+++.+++..+.+.+|+||||||||+|||+||+||+||+|++||.|.+.+..++
T Consensus 167 ~~D~lvG~nlSr~~t~~~~~~~~~~lS~GRVQtptL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~ 231 (740)
T PRK07220 167 VIDLVWGAALTRYISLAAGRLGKMFLSVGRVQSPTLALIVDREKEREAFVPTPYWEIYATLENNG 231 (740)
T ss_pred HHHHHhchhcCHHHHHHHHhhCCccccccccchhhhHHHHhhHHHHHhCCCCccEEEEEEEEcCC
Confidence 48999999999999998864333579999999999999999999999999999999999887654
No 3
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=99.89 E-value=1.8e-23 Score=163.16 Aligned_cols=65 Identities=25% Similarity=0.361 Sum_probs=57.7
Q ss_pred ChHHHHHHHHHHHHHhhhCCCC-CCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLD-ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~-~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||++|.+.+..+ .+.+|+||||||||+|||+||+||+||+|++||.|.+.+..++
T Consensus 166 ~~D~lvG~nlSr~lt~~~~~~g~~~~lS~GRVQtptL~lIveRe~eI~~F~p~~y~~i~~~~~~~~ 231 (660)
T TIGR01056 166 RADWLVGINLTRAFTKLGREAGNDGVLSVGRVQTPTLAMVVKRENEIKNFVGKPFYEVSATINKDE 231 (660)
T ss_pred HHHHHHHHhHhHHHHHhhhhcCCCCceecccchhhhhHHHHHHHHHHHcCCCCccEEEEEEEEcCC
Confidence 5899999999999999865432 3489999999999999999999999999999999999886543
No 4
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=99.89 E-value=1.3e-23 Score=162.66 Aligned_cols=62 Identities=31% Similarity=0.456 Sum_probs=57.9
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
+|||++|+++||+|+.+.++ +.||+||||||||++||+||+||++|+|++||.|.+.+..++
T Consensus 145 ~lD~lvG~~lSr~l~~~~~~---~~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~~~ 206 (570)
T COG0550 145 ILDRLVGYNLSRLLWKKLKR---GVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGG 206 (570)
T ss_pred HHHHHhhhhhhHHHHHhhcc---CCCCCccccchhhhhhHhhHHHHHhCCCCcceEEEEEEecCC
Confidence 48999999999999999986 269999999999999999999999999999999999988765
No 5
>PRK08173 DNA topoisomerase III; Validated
Probab=99.88 E-value=3.9e-23 Score=165.21 Aligned_cols=64 Identities=30% Similarity=0.339 Sum_probs=55.6
Q ss_pred ChHHHHHHHHHHHHHhhhCCCC-CCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLD-ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN 64 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~-~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~ 64 (69)
.+||++|+|+||++|...+..+ .+++|+||||||||+|||+||+||+||+|++||+|.+.+..+
T Consensus 165 ~aDwlvG~N~TR~~T~~~~~~g~~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~y~~i~~~~~~~ 229 (862)
T PRK08173 165 EADWLVGINGTRAMTAFNSKGGGFFLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFVAA 229 (862)
T ss_pred HHHHHhhHHHhHHHHHhHhhcCCccccccccchhhHHHHHHHHHHHHHcCCCCccEEEEEEEecC
Confidence 3799999999999997543322 347999999999999999999999999999999999988643
No 6
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=99.88 E-value=2.6e-23 Score=153.08 Aligned_cols=56 Identities=36% Similarity=0.535 Sum_probs=51.8
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEE
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLD 58 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~ 58 (69)
++||++|+|+||++|.+++. .+.+|+||||||||++||+||+||+||+|++||.|.
T Consensus 12 ~~D~liG~n~sr~~t~~~~~--~~~lS~GRVQtPtL~liv~Re~ei~~F~p~~y~~i~ 67 (381)
T cd00186 12 ILDRLVGFNLSRLLTKKLRR--KGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEIK 67 (381)
T ss_pred HHHHHhhhhhhHHHHHHhCC--CCCCccccchhhHhHHHHHHHHHHHhCCCcceEEee
Confidence 48999999999999998873 347999999999999999999999999999999984
No 7
>PRK14973 DNA topoisomerase I; Provisional
Probab=99.88 E-value=5.3e-23 Score=165.72 Aligned_cols=65 Identities=29% Similarity=0.473 Sum_probs=58.5
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||++|.+++....+++|+||||||||+|||+||+||+||+|++||.|.+.+..++
T Consensus 166 ~~D~lvG~nlSr~lt~~~~~g~~~~lS~GRVQTPtL~lIveRe~EI~~Fvp~~Yw~I~~~~~~~~ 230 (936)
T PRK14973 166 IIDLIWGASLTRFISLAAHRGGDNILSVGRVQSPTLAMIVDREKEIEAFVPEKYWMLSLATEKDG 230 (936)
T ss_pred HHHHHHHHHHhHHHHHHhhcCCCcceeeccccchHHHHHHhHHHHHHcCCCCceEEEEEEEecCC
Confidence 48999999999999998875334579999999999999999999999999999999999887654
No 8
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=99.88 E-value=5.3e-23 Score=159.08 Aligned_cols=65 Identities=32% Similarity=0.476 Sum_probs=57.7
Q ss_pred ChHHHHHHHHHHHHHhhhCCC--CCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDL--DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~--~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||++|.+++.. .+.++|+||||||||++||+||+||+||+|++||.|.+.+..++
T Consensus 160 ~~D~liG~n~Sr~~t~~~~~~~~~~~~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~ 226 (618)
T TIGR01057 160 ILDWYWGINLSRALMEAIRAAAGRWVILSAGRVQGPTLAFLVEREREINLFVPKPYWVIKATLEKGG 226 (618)
T ss_pred HHHHHHhhhhhHHHHHHhhccCCCcccccccccchhHHHHHHHhHHHHHcCcCCccEEEEEEEecCC
Confidence 479999999999999877632 23479999999999999999999999999999999999887655
No 9
>PRK05776 DNA topoisomerase I; Provisional
Probab=99.88 E-value=4.7e-23 Score=161.22 Aligned_cols=65 Identities=29% Similarity=0.396 Sum_probs=57.8
Q ss_pred ChHHHHHHHHHHHHHhhhCCC--CCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDL--DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~--~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||++|.+++.. ....+|+||||||||++||+||+||++|+|++||.|.+.+..++
T Consensus 163 ~lD~lvG~nlSr~lt~~~~~~~g~~~~lS~GRVQsptL~lVveRe~eI~~Fvp~~yw~i~~~~~~~~ 229 (670)
T PRK05776 163 ELDWLWGINVSRALMSSVRDASGKRVILSAGRVQSPTLKYVVEREIERNLFVPLPYFSVSIIIEKNG 229 (670)
T ss_pred HHHHHHhHHHhHHHHHHhhhhcCCccceecceecCchhhHhHhhHHHHHcCCCCcceEEEEEEecCC
Confidence 589999999999999987642 22479999999999999999999999999999999999987654
No 10
>PRK14724 DNA topoisomerase III; Provisional
Probab=99.88 E-value=6e-23 Score=165.92 Aligned_cols=64 Identities=28% Similarity=0.332 Sum_probs=54.9
Q ss_pred ChHHHHHHHHHHHHHhhhCC-CCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeC
Q psy8717 1 MLDLLKLNLKEADYQGKYGD-LDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN 64 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~-~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~ 64 (69)
++|||+|+|+||++|..... .+..++|+||||||||+|||+||+||+||+|++||.|.+.+..+
T Consensus 173 ~aDwLvG~N~SR~~T~~~~~~~~~~~lSvGRVQTPtL~lVv~Re~eI~~F~p~~Y~~i~a~~~~~ 237 (987)
T PRK14724 173 EADWLVGINGTRAMTAFNSRDGGFFLTTVGRVQTPTLSLVVEREEKIRKFVSRDYWEIHAGFHAE 237 (987)
T ss_pred HHHHHhHHHHhHHHHHHHHhcCCcceeccccchhHHHHHHHHHHHHHHhCCCCccEEEEEEEecC
Confidence 47999999999999984432 12236899999999999999999999999999999999988643
No 11
>PRK07219 DNA topoisomerase I; Validated
Probab=99.88 E-value=4.9e-23 Score=163.47 Aligned_cols=64 Identities=33% Similarity=0.509 Sum_probs=57.1
Q ss_pred ChHHHHHHHHHHHHHhhhCCCC-CCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLD-ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLN 64 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~-~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~ 64 (69)
++||++|+|+||++|.+++..+ ...+|+||||||||++||+||+||+||+|++||.|.+.+..+
T Consensus 166 ~~D~lvG~nlSr~lt~~~~~~g~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~yw~i~~~~~~~ 230 (822)
T PRK07219 166 IIDLYWGAALTRFLSLSVRQLGRWDFLSVGRVQTPTLAFIVDREREIRAFDPEDYWKIEALLDKE 230 (822)
T ss_pred HHHHHhhhhhCHHHHHHHHhccccCccccccccchhhHHHHHHHHHHHcCCCcccEEEEEEEEec
Confidence 4899999999999999876432 258999999999999999999999999999999999988653
No 12
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=99.87 E-value=9.4e-23 Score=157.77 Aligned_cols=61 Identities=30% Similarity=0.401 Sum_probs=55.6
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||+++.+++. .+|+||||||||+|||+||++|+||+|++||.|.+.+..++
T Consensus 137 ~~D~liG~n~Tr~~t~~~~~----~lSvGRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~ 197 (610)
T TIGR01051 137 ILDRLVGYTLSPLLWKKVAK----GLSAGRVQSVALRLIVDREREIKRFVPEEYWTIDATFQKGE 197 (610)
T ss_pred HHHHHHhHhhhHHHHHhhcC----CCCcceehHHHHHHHHHHHHHHHhcCCCceEEEEEEEecCC
Confidence 37999999999999997654 59999999999999999999999999999999999886544
No 13
>PRK07726 DNA topoisomerase III; Provisional
Probab=99.87 E-value=1.1e-22 Score=158.45 Aligned_cols=61 Identities=31% Similarity=0.468 Sum_probs=55.1
Q ss_pred ChHHHHHHHHHHHHHhhhCCCC-CCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEE
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLD-ASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTL 61 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~-~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~ 61 (69)
++||++|+|+||++|.+++..+ .+.+|+||||||||+|||+||++|+||+|++||.|.+.+
T Consensus 161 ~~D~liG~nlSr~~t~~~~~~g~~~~lS~GRVQTPtL~lVv~Re~eI~~F~p~~y~~i~~~~ 222 (658)
T PRK07726 161 RADWLVGINMTRAYTLLGRKAGYNGVLSVGRVQTPTLALVVRRDEEIENFVPKPYWEVEAHL 222 (658)
T ss_pred HHHHHhhhhHhHHHHHHHhhcCCCcceeecccccchhHHHHHHHHHHHcCCCcccEEEEEEE
Confidence 4899999999999999854332 358999999999999999999999999999999999888
No 14
>PRK08780 DNA topoisomerase I; Provisional
Probab=99.86 E-value=1.7e-22 Score=160.17 Aligned_cols=61 Identities=26% Similarity=0.317 Sum_probs=56.2
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
+|||++|+++||+++.+.+. .+|+||||||||+|||+||+||++|+|++||.|.+.+..++
T Consensus 145 ~lD~lvG~~lSr~l~~~~~~----~lSaGRVQspaL~lIveRE~eI~~F~p~~yw~i~~~~~~~~ 205 (780)
T PRK08780 145 ALDYLVGFNLSPLLWRKIQR----GLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAHPS 205 (780)
T ss_pred HHHHhcCeeecHHHHHhhCC----CCcccccHHHHHHHHHHHHHHHHhCCCcceEEEEEEEecCC
Confidence 58999999999999998864 69999999999999999999999999999999999986543
No 15
>PRK05582 DNA topoisomerase I; Validated
Probab=99.86 E-value=2.6e-22 Score=155.92 Aligned_cols=61 Identities=28% Similarity=0.390 Sum_probs=55.6
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||++|.++++ .+|+||||||||+|||+||++|+||+|++||.|.+.+..++
T Consensus 141 ~~D~liG~n~tr~~t~~~~~----~ls~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~~~ 201 (650)
T PRK05582 141 ILDRLVGYKLSPLLWKKVKK----GLSAGRVQSVALKLIIDREKEIRAFVPEEYWTIDAEFKKGK 201 (650)
T ss_pred HHHHHhhhhcCHHHHHhhcC----CCccccchHhHHHHHHhHHHHHHhCCCCccEEEEEEEecCC
Confidence 47999999999999997764 59999999999999999999999999999999999886443
No 16
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=99.86 E-value=2e-22 Score=148.96 Aligned_cols=59 Identities=36% Similarity=0.532 Sum_probs=52.7
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
++||++|+|+||+++ . + +.+|+||||||||++||+||++|+||+|++||.|.+.+..++
T Consensus 15 ~~D~liG~n~Sr~~t-~-~----~~ls~GRVQtp~L~li~~Re~ei~~f~~~~y~~i~~~~~~~~ 73 (403)
T PF01131_consen 15 EADWLIGMNLSRALT-G-N----GVLSVGRVQTPTLGLIVEREREIENFKPEPYYEIKAQFKKGG 73 (403)
T ss_dssp HHHHHHHHHHHHHHH-H-S----TT-TTHTTHHHHHHHHHHHHHHHHCEEEEEEEEEEEEEETCC
T ss_pred HHHHhcChhcCHhhc-C-C----CccccCcccchHHHHHHHHHhhhhccCCCceEEEEEEecccc
Confidence 379999999999998 1 2 599999999999999999999999999999999999986543
No 17
>PRK06599 DNA topoisomerase I; Validated
Probab=99.86 E-value=3.7e-22 Score=155.75 Aligned_cols=59 Identities=29% Similarity=0.362 Sum_probs=55.1
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEee
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 63 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~ 63 (69)
++||++|+|+||++|.+++. .+|+||||||||++||+||++|+||+|++||.|.+.+..
T Consensus 144 ~~D~liG~n~tr~~t~~~~~----~lS~GRVQtPtL~lvv~Re~eI~~F~p~~y~~i~~~~~~ 202 (675)
T PRK06599 144 ALDYLVGFKLSPLLWKKVRR----GLSAGRVQSVALRLICEREDEIEAFIPQEYWTIEADLAT 202 (675)
T ss_pred HHHHHhhhhhCHHHHHhccC----CCccceeHHHHhHHHHHhHHHHHhcCCCceEEEEEEEEc
Confidence 48999999999999998864 699999999999999999999999999999999988865
No 18
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.85 E-value=7.4e-22 Score=157.65 Aligned_cols=61 Identities=26% Similarity=0.344 Sum_probs=55.7
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEee
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 63 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~ 63 (69)
+|||++|+|+||++|.+++. ...+|+||||||||+||||||+||+||+|++||.|.+.+..
T Consensus 140 ~lD~lvG~nlSr~l~~~~~~--~~~lSaGRVQsp~L~lIveRe~eI~~F~p~~yw~i~~~~~~ 200 (860)
T PRK06319 140 LLDRIVGYKISPILSRKLQR--RSGVSAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVHLKD 200 (860)
T ss_pred HHHHHhhhhcCHHHHHhhcc--CCCCcCCccchhhhHHHHHHHHHHHcCCCCceEEEEEEEec
Confidence 48999999999999998863 13699999999999999999999999999999999998864
No 19
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=99.85 E-value=9.6e-22 Score=156.80 Aligned_cols=59 Identities=29% Similarity=0.380 Sum_probs=55.3
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEee
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNL 63 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~ 63 (69)
+|||++|+++||+++.+.+. .+|+||||||||+|||+||+||++|+|++||.|.+.+..
T Consensus 154 ~lD~lvG~~lS~~l~~~~~~----~lSaGRVQsp~L~lIv~Re~eI~~F~p~~yw~i~~~~~~ 212 (859)
T PRK07561 154 FLDRLVGYMVSPLLWKKIAR----GLSAGRVQSVAVRLIVEREREIEAFVPEEYWDIHADLTT 212 (859)
T ss_pred HHHHHhhhhcCHHHHHhhcc----CCCcccchhhhhHHHHHHHHHHHhcCCCccEEEEEEEEe
Confidence 48999999999999998764 699999999999999999999999999999999998864
No 20
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=99.81 E-value=3.5e-20 Score=147.96 Aligned_cols=58 Identities=24% Similarity=0.259 Sum_probs=52.4
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCc--ceEEEEEEEe
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPE--PYWLLDLTLN 62 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~--~y~~i~~~~~ 62 (69)
.|||++|+|+|++++.+.+ +.+|+||||||||+|||+||+||++|+|+ +||.|.+.+.
T Consensus 198 ~lD~LVG~nlS~~l~~~~~----~~lSaGRVQTPtL~LIVeRE~EIe~Fkpee~~Yw~I~a~~~ 257 (805)
T PTZ00407 198 AMDRIFGFLGSSVVRAANS----QMRSIGRVQTPALILINEREDKIKAFLESNKSTFEVQAMCQ 257 (805)
T ss_pred HHHHHhhhhhhHHHHhhcc----CceeecccchHHHHHHHHHHHHHHhcCCccCceEEEEEEEe
Confidence 3899999999999987543 48999999999999999999999999999 6999988764
No 21
>PRK14701 reverse gyrase; Provisional
Probab=99.69 E-value=1.7e-17 Score=139.47 Aligned_cols=56 Identities=21% Similarity=0.242 Sum_probs=50.7
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEE
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLT 60 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~ 60 (69)
++||++|+|+||+++.++++ ..+|+||||||||+|||+||+||+| +|++||.+.+.
T Consensus 768 ~~D~~iG~nlSr~l~~~~~~---~~lS~GRVQTPtL~~Iv~Re~ei~~-~~~~~~~i~~~ 823 (1638)
T PRK14701 768 IEDRWIGFELSQKLWEVFED---RNLSAGRVQTPVLGWIIQRYKEFTE-SKVPFLGIILE 823 (1638)
T ss_pred HHHHHHHHHHHHHHHHhccC---CceeecccccchhhhhHhhHHHHhc-CCCceEEEEEc
Confidence 47999999999999998864 4699999999999999999999999 59999998654
No 22
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=99.68 E-value=3.3e-17 Score=134.46 Aligned_cols=55 Identities=22% Similarity=0.238 Sum_probs=48.4
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEE
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLT 60 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~ 60 (69)
++||++|+++||++|.++++ +.+|+||||||||+|||+||+||++| .+||.+.+.
T Consensus 787 ~~D~liG~~lSr~lt~~~~~---~~lSaGRVQTPtL~lIVeRe~ei~~~--~~~~~i~~~ 841 (1171)
T TIGR01054 787 IEDRWIGFTLSQKLWEAFNK---RWLSAGRVQTPVLGWIIDRYRESREK--RGYLLIFAL 841 (1171)
T ss_pred HHHHHHhhhhCHHHHHhhcC---CCcccceecchhhHHHHHHHHHHhCC--CceEEEEEe
Confidence 37999999999999998764 46999999999999999999999996 458988653
No 23
>PRK09401 reverse gyrase; Reviewed
Probab=99.67 E-value=5e-17 Score=133.53 Aligned_cols=52 Identities=33% Similarity=0.378 Sum_probs=46.1
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEE
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLL 57 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i 57 (69)
++||++|+++||++|.++++ ..+|+||||||||+|||+||+||++|++ ||.+
T Consensus 787 ~~D~~iG~~lSr~l~~~~~~---~~lSaGRVQTPtL~~IVeRe~ei~~f~~--~~~~ 838 (1176)
T PRK09401 787 IEDRWIGFELSQKLQKKFGK---RNLSAGRVQTPVLGWIVERYKEYKKSKG--YVLV 838 (1176)
T ss_pred HHHHHHHHHHHHHHHHHhcc---cCccccccccchhhhhhhhHHHhcccCC--EEEE
Confidence 47999999999999998864 4799999999999999999999999965 4443
No 24
>KOG1956|consensus
Probab=99.64 E-value=1.1e-16 Score=126.07 Aligned_cols=65 Identities=42% Similarity=0.723 Sum_probs=54.7
Q ss_pred hHHHHH----HHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCCe
Q psy8717 2 LDLLKL----NLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66 (69)
Q Consensus 2 lD~i~g----~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~~ 66 (69)
||..+| |++|..|+.++.-.+.+++|+|+||+|||++||||+.+|++|+|+.||.|.+...+++.
T Consensus 177 LDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefWtl~~~~~~~~~ 245 (758)
T KOG1956|consen 177 LDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFWTLKFKHTHKGG 245 (758)
T ss_pred HHHHhhhhHHHHHhHHHHhhhhhhhccccccccccCcceeeeeehHHHHhccCCcceEEEEEEEeccCc
Confidence 677766 66777777776633558999999999999999999999999999999999998877663
No 25
>KOG1957|consensus
Probab=99.01 E-value=5.3e-11 Score=91.80 Aligned_cols=44 Identities=68% Similarity=1.338 Sum_probs=40.6
Q ss_pred CCCceeccccchHHHHHHHHHHHHHHcCCCcceEEEEEEEeeCC
Q psy8717 22 DASLISYGPCQTPTLGFCVERHDKIRTFKPEPYWLLDLTLNLNG 65 (69)
Q Consensus 22 ~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~ 65 (69)
+...+|+|.||||||++.|+|..+|..|+||.||.++..+..++
T Consensus 183 ds~~isygpcqtptlgfcv~rhd~i~tfkpe~~w~l~~~~~~~~ 226 (555)
T KOG1957|consen 183 DSSLISYGPCQTPTLGFCVTRHDQIQTFKPEQYWVLQTNFTTDD 226 (555)
T ss_pred hhcceeecCCCCCcceeeeeehhhhhccCccceEEEeeecCCCC
Confidence 34689999999999999999999999999999999999887665
No 26
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=98.96 E-value=1.8e-10 Score=94.86 Aligned_cols=48 Identities=21% Similarity=0.230 Sum_probs=43.7
Q ss_pred ChHHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcCCC
Q psy8717 1 MLDLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTFKP 51 (69)
Q Consensus 1 ~lD~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F~~ 51 (69)
+.||-+|.-+|+.+|..+++ ..||+||||||+|+||++|++|-+.=.+
T Consensus 803 IeDRWIGF~LS~~Lw~~F~~---~nLsAGRVQTPVLGWIV~Ry~e~~~~~~ 850 (1187)
T COG1110 803 IEDRWIGFELSQKLWDVFNN---KNLSAGRVQTPVLGWIVNRYEEYKEKRG 850 (1187)
T ss_pred hhhcccceeecHHHHHHhCc---cCccccccccccceeehhhHHHHhhccc
Confidence 46999999999999999976 7999999999999999999999886554
No 27
>PF13061 DUF3923: Protein of unknown function (DUF3923)
Probab=70.69 E-value=2.5 Score=24.87 Aligned_cols=16 Identities=31% Similarity=0.366 Sum_probs=13.2
Q ss_pred ceeccccchHHHHHHH
Q psy8717 25 LISYGPCQTPTLGFCV 40 (69)
Q Consensus 25 ~lS~GRVQtPtL~~vv 40 (69)
+=.+|.+|||.++++.
T Consensus 27 vDgaGv~qT~~~k~it 42 (66)
T PF13061_consen 27 VDGAGVVQTPELKLIT 42 (66)
T ss_pred ccccccccCHHHHHHH
Confidence 4468999999998873
No 28
>TIGR02923 AhaC ATP synthase A1, C subunit. The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 "stalk" complex (AhaABCDEFG) which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex.
Probab=44.95 E-value=56 Score=23.17 Aligned_cols=22 Identities=27% Similarity=0.694 Sum_probs=18.3
Q ss_pred CceeccccchHHHHHHHHHHHHHHcC
Q psy8717 24 SLISYGPCQTPTLGFCVERHDKIRTF 49 (69)
Q Consensus 24 ~~lS~GRVQtPtL~~vv~Re~~i~~F 49 (69)
..+|+| |+++++..+|.||+|-
T Consensus 301 ~~~~~~----~~~~yl~~ke~Ei~nl 322 (343)
T TIGR02923 301 YPLSVG----PVLGYILKKEREVRNL 322 (343)
T ss_pred CCCchH----HHHHHHHHHHHHHHHH
Confidence 356666 9999999999999973
No 29
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=40.32 E-value=21 Score=28.22 Aligned_cols=33 Identities=21% Similarity=0.419 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHcCCCcceEEEEEEEeeCCe
Q psy8717 34 PTLGFCVERHDKIRTFKPEPYWLLDLTLNLNGE 66 (69)
Q Consensus 34 PtL~~vv~Re~~i~~F~~~~y~~i~~~~~~~~~ 66 (69)
+-=+++|.|-++|++|-++|||.-+.-....|+
T Consensus 390 eedk~~V~rArki~~FlSQpF~vAE~FTg~pG~ 422 (468)
T COG0055 390 EEDKLTVARARKIQRFLSQPFFVAEVFTGSPGK 422 (468)
T ss_pred hhHHHHHHHHHHHHHHhcCcchhhheecCCCce
Confidence 344689999999999999999987644334443
No 30
>PRK14745 RepA leader peptide Tap; Provisional
Probab=36.42 E-value=14 Score=18.11 Aligned_cols=9 Identities=22% Similarity=0.471 Sum_probs=7.2
Q ss_pred Cceeccccc
Q psy8717 24 SLISYGPCQ 32 (69)
Q Consensus 24 ~~lS~GRVQ 32 (69)
-.+|+|||-
T Consensus 17 cnisagr~d 25 (26)
T PRK14745 17 CIVSAGRSD 25 (26)
T ss_pred ccccccccC
Confidence 379999984
No 31
>PF11279 DUF3080: Protein of unknown function (DUF3080); InterPro: IPR021431 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently this family has no known function.
Probab=35.66 E-value=24 Score=25.95 Aligned_cols=21 Identities=24% Similarity=0.143 Sum_probs=18.3
Q ss_pred CceeccccchHHHHHHHHHHH
Q psy8717 24 SLISYGPCQTPTLGFCVERHD 44 (69)
Q Consensus 24 ~~lS~GRVQtPtL~~vv~Re~ 44 (69)
++=+.||||.|.-.+.+|++.
T Consensus 64 RNS~LGKV~~~s~rl~Ye~~f 84 (316)
T PF11279_consen 64 RNSSLGKVQDPSQRLLYEIEF 84 (316)
T ss_pred hccccccccCHHHhhhHHHHH
Confidence 466899999999999999874
No 32
>PRK14746 RepA leader peptide Tap; Provisional
Probab=27.73 E-value=25 Score=17.22 Aligned_cols=9 Identities=44% Similarity=0.711 Sum_probs=7.2
Q ss_pred Cceeccccc
Q psy8717 24 SLISYGPCQ 32 (69)
Q Consensus 24 ~~lS~GRVQ 32 (69)
-.+|+|||-
T Consensus 16 CniSAg~~d 24 (26)
T PRK14746 16 CNISAGRCD 24 (26)
T ss_pred ceecccccC
Confidence 389999984
No 33
>PF08483 IstB_IS21_ATP: IstB-like ATP binding N-terminal; InterPro: IPR013690 This bacterial domain is found to the N terminus of the IPR002611 from INTERPRO-like ATP binding domain in proteins which are putative transposase subunits [].
Probab=26.35 E-value=59 Score=16.28 Aligned_cols=12 Identities=42% Similarity=0.559 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHH
Q psy8717 36 LGFCVERHDKIR 47 (69)
Q Consensus 36 L~~vv~Re~~i~ 47 (69)
|++.|+||..-+
T Consensus 18 l~LLvdrE~~~R 29 (30)
T PF08483_consen 18 LGLLVDREWTWR 29 (30)
T ss_pred HHHHHHHHHHhc
Confidence 788999987654
No 34
>PF15343 DEPP: Decidual protein induced by progesterone family
Probab=25.37 E-value=28 Score=24.47 Aligned_cols=11 Identities=36% Similarity=0.232 Sum_probs=8.7
Q ss_pred hHHHHHHHHHH
Q psy8717 2 LDLLKLNLKEA 12 (69)
Q Consensus 2 lD~i~g~~~T~ 12 (69)
||||||-++..
T Consensus 81 LDWLFGqsQek 91 (188)
T PF15343_consen 81 LDWLFGQSQEK 91 (188)
T ss_pred HHHhhcccccc
Confidence 79999977654
No 35
>TIGR03475 tap_IncFII_lead RepA leader peptide Tap. This protein is a translated leader peptide that actis in the regulation of the expression of the plasmid replication protein RepA in incF2 group plasmids.
Probab=25.12 E-value=29 Score=17.05 Aligned_cols=9 Identities=44% Similarity=0.711 Sum_probs=7.0
Q ss_pred Cceeccccc
Q psy8717 24 SLISYGPCQ 32 (69)
Q Consensus 24 ~~lS~GRVQ 32 (69)
-.+|+|||-
T Consensus 17 cniSAg~cD 25 (26)
T TIGR03475 17 CNISAGRCD 25 (26)
T ss_pred hcccccccC
Confidence 379999983
No 36
>PF08259 Periviscerokin: Periviscerokinin family; InterPro: IPR013231 Perviscerokinin neuropeptides are found in the abdominal perisympathetic organs of insects. They mediate visceral muscle contractile activity (myotropic activity). CAPA, which are in the periviscerokinin and pyrokinin peptide families, has potential medical importance. This is due to its myotropic effects on, for example, heart muscles and due to its occurrence in the Ixodoidea (ticks), which are important vectors in the transmission of many animal diseases []. These peptides also have a strong diuretic or anti-diuretic effect, suggesting they have significant medical implications [].
Probab=24.00 E-value=41 Score=13.46 Aligned_cols=8 Identities=25% Similarity=0.476 Sum_probs=6.1
Q ss_pred Cceecccc
Q psy8717 24 SLISYGPC 31 (69)
Q Consensus 24 ~~lS~GRV 31 (69)
+.+|.+||
T Consensus 4 GlI~fpR~ 11 (11)
T PF08259_consen 4 GLIPFPRV 11 (11)
T ss_pred cccccCCC
Confidence 57888886
No 37
>PF11469 Ribonucleas_3_2: Ribonuclease III; InterPro: IPR021568 This archaeal family of proteins has no known function. ; PDB: 1ZTD_A.
Probab=23.07 E-value=2.1e+02 Score=18.73 Aligned_cols=42 Identities=14% Similarity=0.018 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHhhhCCCCCCceeccccchHHHHHHHHHHHHHHcC
Q psy8717 3 DLLKLNLKEADYQGKYGDLDASLISYGPCQTPTLGFCVERHDKIRTF 49 (69)
Q Consensus 3 D~i~g~~~T~~~t~~~~~~~~~~lS~GRVQtPtL~~vv~Re~~i~~F 49 (69)
|-++-...|.+++.-.| .-+.|||-...|++-.++-.-.+.-
T Consensus 8 DSLvNfl~SlALse~lG-----~Ptg~rVPnaSLaiAl~~a~L~~~~ 49 (120)
T PF11469_consen 8 DSLVNFLFSLALSEYLG-----RPTGDRVPNASLAIALELAGLSHLL 49 (120)
T ss_dssp HHHHHHHHHHHHHHHHT-----S-------HHHHHHHHHHTTGGGCS
T ss_pred HHHHHHHHHHHHHHHhC-----CCCCCCCCChHHHHHHHHHhhhhhC
Confidence 66777888888887776 5688999999999988875544433
No 38
>PF08048 RepA1_leader: Tap RepA1 leader peptide; InterPro: IPR012605 This entry represents of the RepA1 leader peptide known as Tap found in IncFII plasmids. The frequency of replication of IncFII plasmid NR1 during the cell division cycle is regulated by the control of the synthesis of the plasmid-specific replication initiation protein (RepA1). When RepA1 is synthesised, it binds to the plasmid replication origin (ori) and effects the assembly of a replication complex composed of host proteins that mediate the replication of the plasmid [, ]. The tap gene encodes a 24-amino acid peptide whose translation is required for the translation of repA.
Probab=21.91 E-value=36 Score=16.59 Aligned_cols=7 Identities=57% Similarity=0.866 Sum_probs=6.0
Q ss_pred ceecccc
Q psy8717 25 LISYGPC 31 (69)
Q Consensus 25 ~lS~GRV 31 (69)
.+|+|||
T Consensus 18 niSAg~~ 24 (25)
T PF08048_consen 18 NISAGRC 24 (25)
T ss_pred hcccccC
Confidence 7899987
Done!