Summary

The literature section presents previous knowledge about this protein. There have been five different efforts to annotate minimal organism genome. The annotations from those efforts are given in the Literature section for completeness.

AVX55005.1
JCVISYN3A_0859

DNA topoisomerase I.
M. mycoides homolog: Q6MS50.
TIGRfam Classification: 4=Probable.
Category: Essential.

Statistics

Total GO Annotation: 35
Unique PROST Go: 1
Unique BLAST Go: 1
Unique Foldseek Go: 0

Total Homologs: 127
Unique PROST Homologs: 0
Unique BLAST Homologs: 2
Unique Foldseek Homologs: 0

Literature

Danchin and Fang [1]: NA
Yang and Tsui [2]: NA
Antczak et al. [3]: topA; DNA topoisomerase 1
Zhang et al. [4]: GO:0003917|DNA topoisomerase type I activity
Bianchi et al. [5]: NA

Structures and Sequence Alignment

The best structural homolog that predicted by 1. PBF was Q92IH1 (DNA topoisomerase 1) with a FATCAT P-Value: 0 and RMSD of 2.46 angstrom. The sequence alignment identity is 30.2%.
Structural alignment shown in left. Query protein AVX55005.1 colored as red in alignment, homolog Q92IH1 colored as blue. Query protein AVX55005.1 is also shown in right top, homolog Q92IH1 showed in right bottom. They are colored based on secondary structures. 

  AVX55005.1 MKVLVLLESPSKIEKIKHYLEESFPENQFVVLASGGHINSI-ADKGAWGLGIDLETMQPD--FVI--DSSRK--KIISQIKKEGKTADLIILASDPDREG 93
      Q92IH1 MK-LVIVESPAKAKTINKYLGD-----EFKVIASFGHIRDLPSKKGS--V---L----PDENFAMKYDISDKAGKYVDAIVKDAKKADAVYLATDPDREG 85

  AVX55005.1 EAIAYHLANLFKDHTNI------KRITFNEITSEAITNAFNNLKDIDMNLVNAQISRQILDKIIGYLVSKSL-QKSTGLMSAGRVQTPALNILTTRDTLI 186
      Q92IH1 ESISWHVAEVIKEKNQVKSDDFFKRVAFNEITKKAIIHAVENPRKLDTNLVNAQQARRALDYLVGFTLSPLLWRKLPGCKSAGRVQSVALRLICEREDEI 185

  AVX55005.1 KNFKEVLYKKIFVIESKRAINLSL-VKDKNNVLVNTEK-TYYIDEKQAK-AIVDE--LGEVYRCT-DYKSTAY-----ETRSFK-----PYSTAGLLQDG 270
      Q92IH1 ERFKSEEY-----------WDISLKMQNSNNELF-TAKLTHVNDQKLEKFSIINEKNAKDL---TKKLKSHKFHVDKIEKKQQKRQPQPPFITSSLQQEA 270

  AVX55005.1 FTKLKLS---TSQITLAAQKLYE--------LGYITYIRTDSVKYSSQFISEVKDYISKNYSSD--LFKAPVVGK-KDQNSQEAHESIRPTNIWLTPE-- 354
      Q92IH1 ARKLGFSAKKTMQI---AQKLYEGVDIGKETIGLITYMRTDGVTLSNDAIADIRKLIDKSY-GDKYLPTSPRIYKSKVKNAQEAHEAIRPTNITYTPDSL 366

  AVX55005.1 KASLEIEDNLLKRVYNLIWWNSIKSLMKGPSGFN---HRWTFN----NNGYEFKQSWQEVK-DLG-YQAIKHSSSD----EN--I-ELTDDGEEVVKTKD 438
      Q92IH1 KEKLD-KD-YYK-LYELIWKRTIACQME-----NVIMDLVVANLASENKEYLAKANGSTIAFD-GFYKVYRESMDDEAEEENKMLPPLKE--QEPLKTKA 455

  AVX55005.1 PKPEYQFNDDFEINISKKYIKIEDAKTNPPKMFNQASLIKELKNLGIGRPSTYNPILTKLKDREYVEFPKSK--P--I--VVTN--KGYSANQYLYDHYL 530
      Q92IH1 VIP----NQHF---------------TEPPPRYSEASLVKKLEELGIGRPSTYASILSVLQDRKYVALEKKRFIPEELGRLVTVFLVGF-FKKYV--EY- 532

  AVX55005.1 DFFNLNYTAEMEEKLDEITKGSFDY---VN--WLKEIYN----ALN-------IK-VKKEI-----GEAKTEA-ICPRCGANLVYIK-SRFNRG--RGCS 604
      Q92IH1 DF-----TAGLENELDAIAAGKLEWKAALNNFW--SGFNHNIESVNEQKITEIISYVQKALDYHLFGENK-ESKICPSCNTGELSLKLGKF--GAFLACS 622

  AVX55005.1 NFTKTKCGYR----------EYE-----QPD-----GTWKE----YVKEEK-PQ----EESSTETK-STKKSKTKKD-NK-------------------- 653
      Q92IH1 NY--PECTFRKSIVSGNDNNENEGEPAAMPNENKVLGTDKDGVEIYLK--KGPYGPYIQLGKQEGKVKPKRSPVPASLNQNDITLDIALKLLSLPLKIGI 718

  AVX55005.1 ---------------------------------------------------------- 653
      Q92IH1 HKDSDEEIMIGYGKFGPYIKYMGQFISVQKKYDFLNLSLDDAMKLIEENKAKLEKKQA 776

Go Annotations

1. PBF indicates the go terms that are found by both PROST and BLAST and Foldseek.
2. PF indicates the go terms that are found by only PROST and Foldseek.
3. BF indicates the go terms that are found by only BLAST and Foldseek.
4. PB indicates the go terms that are found by both PROST and BLAST.
5. P indicates the go terms that are found by only PROST.
6. F indicates the go terms that are found by only Foldseek.
7. B indicates the go terms that are found by only BLAST.

Source GO Description
1. PBF GO:0006301 postreplication repair
1. PBF GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity
1. PBF GO:0003677 DNA binding
1. PBF GO:0043007 maintenance of rDNA
1. PBF GO:0000287 magnesium ion binding
1. PBF GO:0005694 chromosome
1. PBF GO:0031422 RecQ family helicase-topoisomerase III complex
1. PBF GO:0006265 DNA topological change
1. PBF GO:0046872 metal ion binding
1. PBF GO:0003916 DNA topoisomerase activity
1. PBF GO:1902969 mitotic DNA replication
1. PBF GO:0000018 regulation of DNA recombination
2. PF GO:0006314 intron homing
3. BF GO:0140603 obsolete ATP hydrolysis activity
3. BF GO:0003918 DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
3. BF GO:0006268 DNA unwinding involved in DNA replication
3. BF GO:0008270 zinc ion binding
3. BF GO:0016539 intein-mediated protein splicing
3. BF GO:0003678 DNA helicase activity
3. BF GO:0004519 endonuclease activity
4. PB GO:0051304 chromosome separation
4. PB GO:0007064 mitotic sister chromatid cohesion
4. PB GO:0035861 site of double-strand break
4. PB GO:0098847 sequence-specific single stranded DNA binding
4. PB GO:0000712 resolution of meiotic recombination intermediates
4. PB GO:0007131 reciprocal meiotic recombination
4. PB GO:0000793 condensed chromosome
4. PB GO:0060701 negative regulation of ribonuclease activity
4. PB GO:0016605 PML body
4. PB GO:0032042 mitochondrial DNA metabolic process
4. PB GO:0007004 telomere maintenance via telomerase
4. PB GO:0043597 cytoplasmic replication fork
4. PB GO:0007059 chromosome segregation
5. P GO:0051321 meiotic cell cycle
7. B GO:0005886 plasma membrane

Uniprot GO Annotations

GO Description
GO:0003917 DNA topoisomerase type I (single strand cut, ATP-independent) activity
GO:0003677 DNA binding
GO:0016853 isomerase activity
GO:0006265 DNA topological change
GO:0046872 metal ion binding
GO:0003916 DNA topoisomerase activity

Homologs

1. PBF indicates the homologs that are found by both PROST and BLAST and Foldseek.
2. PF indicates the homologs that are found by only PROST and Foldseek.
3. BF indicates the homologs that are found by only BLAST and Foldseek.
4. PB indicates the homologs that are found by both PROST and BLAST.
5. P indicates the homologs that are found by only PROST.
6. F indicates the homologs that are found by only Foldseek.
7. B indicates the homologs that are found by only BLAST.

Source Homolog Description Fatcat Pvalue PROST Evalue BLAST Evalue Foldseek TMScore
1. PBF Q4UM42 DNA topoisomerase 1 0.00e+00 7.23e-30 2.67e-75 0.7879
1. PBF Q73E74 DNA topoisomerase 3 0.00e+00 4.30e-43 5.12e-21 0.7179
1. PBF Q49X35 DNA topoisomerase 1 0.00e+00 1.00e-47 3.20e-74 0.7665
1. PBF Q6G767 DNA topoisomerase 3 0.00e+00 5.86e-44 5.13e-26 0.7083
1. PBF Q5HGI2 DNA topoisomerase 1 0.00e+00 6.57e-47 2.02e-73 0.769
1. PBF Q9ZDK2 DNA topoisomerase 1 0.00e+00 1.11e-30 2.99e-73 0.7931
1. PBF Q9CG80 DNA topoisomerase 1 0.00e+00 2.87e-44 2.46e-73 0.7562
1. PBF Q99S17 DNA topoisomerase 3 0.00e+00 5.86e-44 5.13e-26 0.7132
1. PBF O83409 DNA topoisomerase 1 0.00e+00 8.67e-49 2.89e-74 0.7665
1. PBF Q1RIM1 DNA topoisomerase 1 0.00e+00 3.89e-26 5.96e-76 0.7909
1. PBF P78032 DNA topoisomerase 1 0.00e+00 1.13e-61 2.83e-77 0.7553
1. PBF A0A0L0P6P7 DNA topoisomerase 3 0.00e+00 1.79e-15 1.87e-17 0.7282
1. PBF Q9ZMV7 DNA topoisomerase 1 0.00e+00 4.79e-32 4.98e-85 0.8262
1. PBF P57371 DNA topoisomerase 1 0.00e+00 7.41e-24 7.51e-66 0.7603
1. PBF P0A621 DNA topoisomerase 1 1.11e-15 1.34e-21 1.22e-71 0.7568
1. PBF P40114 DNA topoisomerase 1 2.85e-13 4.61e-11 2.12e-13 0.6519
1. PBF Q63GK5 DNA topoisomerase 3 0.00e+00 4.42e-43 1.90e-20 0.7024
1. PBF Q7A075 DNA topoisomerase 3 0.00e+00 5.86e-44 5.13e-26 0.7109
1. PBF P55991 DNA topoisomerase 1 0.00e+00 1.56e-31 2.63e-87 0.8072
1. PBF O34204 DNA topoisomerase 1 0.00e+00 9.66e-40 1.13e-73 0.7604
1. PBF Q9X909 DNA topoisomerase 1 3.66e-15 3.39e-16 2.33e-69 0.7615
1. PBF P40687 DNA topoisomerase 3 0.00e+00 2.84e-27 4.59e-11 0.6842
1. PBF A0R5D9 DNA topoisomerase 1 1.33e-15 6.96e-21 1.05e-72 0.7619
1. PBF P0C2W6 Putative DNA topoisomerase 3 0.00e+00 2.04e-44 4.30e-26 0.7106
1. PBF Q2YXL8 DNA topoisomerase 1 0.00e+00 3.52e-47 1.70e-73 0.7669
1. PBF Q8CRF7 DNA topoisomerase 3 0.00e+00 1.15e-40 2.71e-21 0.6994
1. PBF Q9PHK2 DNA topoisomerase I, plasmid 0.00e+00 2.22e-55 1.07e-61 0.8174
1. PBF Q4L8B8 DNA topoisomerase 3 0.00e+00 2.33e-42 6.57e-25 0.7107
1. PBF Q81IH1 DNA topoisomerase 3 0.00e+00 9.16e-43 1.87e-21 0.7042
1. PBF Q92IH1 DNA topoisomerase 1 0.00e+00 2.44e-29 2.18e-73 0.7877
1. PBF Q65N90 DNA topoisomerase 3 0.00e+00 5.76e-42 8.42e-25 0.7193
1. PBF Q9CP53 DNA topoisomerase 3 0.00e+00 9.94e-26 5.68e-16 0.6469
1. PBF P46799 DNA topoisomerase 1 0.00e+00 2.47e-67 9.74e-70 0.7547
1. PBF O73954 DNA topoisomerase 1 1.04e-07 3.92e-11 2.07e-14 0.6336
1. PBF Q99UM1 DNA topoisomerase 1 0.00e+00 7.95e-47 7.68e-74 0.7688
1. PBF Q5HDV4 DNA topoisomerase 3 0.00e+00 5.86e-44 5.13e-26 0.7114
1. PBF Q81Z97 DNA topoisomerase 3 0.00e+00 3.06e-43 4.82e-21 0.719
1. PBF A0R979 DNA topoisomerase 3 0.00e+00 3.06e-43 4.82e-21 0.7173
1. PBF Q9HZJ5 DNA topoisomerase 1 0.00e+00 2.17e-21 1.17e-72 0.7481
1. PBF O27661 DNA topoisomerase 1 0.00e+00 5.99e-40 2.57e-31 0.6723
1. PBF Q9KRB2 DNA topoisomerase 1 0.00e+00 1.06e-23 1.62e-69 0.7466
1. PBF Q2FEN5 DNA topoisomerase 3 0.00e+00 5.86e-44 5.13e-26 0.711
1. PBF P34185 DNA topoisomerase 1 0.00e+00 1.66e-20 3.68e-78 0.7374
1. PBF Q9JN65 DNA topoisomerase 1 0.00e+00 1.22e-57 9.69e-69 0.7761
1. PBF Q49ZH2 DNA topoisomerase 3 0.00e+00 1.85e-42 2.43e-23 0.7222
1. PBF P9WG48 DNA topoisomerase 1 2.56e-13 1.34e-21 1.22e-71 0.761
1. PBF Q9PLZ2 DNA topoisomerase 1 0.00e+00 1.94e-49 1.64e-85 0.7966
1. PBF P47368 DNA topoisomerase 1 0.00e+00 3.84e-59 2.02e-78 0.751
1. PBF O58356 DNA topoisomerase 1 0.00e+00 1.43e-34 6.95e-34 0.7065
1. PBF Q9KA23 DNA topoisomerase 1 0.00e+00 1.58e-45 4.15e-78 0.7714
1. PBF Q9YB01 DNA topoisomerase 1 0.00e+00 6.81e-37 2.30e-11 0.6708
1. PBF Q7A455 DNA topoisomerase 3 0.00e+00 5.86e-44 5.13e-26 0.7086
1. PBF Q5HPU2 DNA topoisomerase 1 0.00e+00 2.11e-46 4.55e-73 0.761
1. PBF Q9PEV8 DNA topoisomerase 1 0.00e+00 8.13e-25 2.02e-70 0.7666
1. PBF Q87AQ6 DNA topoisomerase 1 0.00e+00 6.36e-25 5.88e-70 0.7659
1. PBF O28469 DNA topoisomerase 1 0.00e+00 1.17e-37 2.01e-36 0.7089
1. PBF Q8K9P7 DNA topoisomerase 1 0.00e+00 2.17e-21 4.93e-63 0.7633
1. PBF Q8NWZ9 DNA topoisomerase 1 0.00e+00 7.95e-47 7.68e-74 0.7685
1. PBF Q4L5V2 DNA topoisomerase 1 0.00e+00 1.05e-48 4.16e-75 0.766
1. PBF P96583 DNA topoisomerase 3 0.00e+00 1.29e-43 5.87e-23 0.7184
1. PBF Q68X45 DNA topoisomerase 1 0.00e+00 5.36e-29 3.83e-70 0.7797
1. PBF Q9KQF5 DNA topoisomerase 3 0.00e+00 5.94e-24 4.62e-14 0.7247
1. PBF Q06AK7 DNA topoisomerase 1 0.00e+00 4.87e-47 3.38e-73 0.7684
1. PBF Q6G9W3 DNA topoisomerase 1 0.00e+00 7.95e-47 7.68e-74 0.7691
1. PBF Q9HM08 DNA topoisomerase 1 9.33e-15 1.13e-33 6.87e-27 0.6941
1. PBF P39814 DNA topoisomerase 1 0.00e+00 4.18e-50 8.82e-75 0.769
1. PBF O69548 DNA topoisomerase 1 2.05e-13 1.73e-20 2.18e-68 0.7587
1. PBF Q9CN30 DNA topoisomerase 1 0.00e+00 1.64e-22 7.05e-73 0.7537
1. PBF Q6GEH9 DNA topoisomerase 3 0.00e+00 1.29e-43 5.18e-26 0.7088
1. PBF P0A2I2 DNA topoisomerase 1 1.11e-16 2.42e-25 2.77e-66 0.7329
1. PBF Q5HLZ4 DNA topoisomerase 3 0.00e+00 6.42e-41 2.78e-21 0.7049
1. PBF Q6HP19 DNA topoisomerase 3 0.00e+00 3.06e-43 4.82e-21 0.718
1. PBF Q6GHI5 DNA topoisomerase 1 0.00e+00 7.95e-47 7.68e-74 0.7678
1. PBF O51768 DNA topoisomerase 1 0.00e+00 2.57e-28 1.64e-72 0.77
1. PBF Q2FHI8 DNA topoisomerase 1 0.00e+00 6.57e-47 2.02e-73 0.7667
1. PBF P73810 DNA topoisomerase 1 0.00e+00 2.22e-19 6.03e-78 0.7488
1. PBF Q7A5Y5 DNA topoisomerase 1 0.00e+00 7.95e-47 7.68e-74 0.7716
1. PBF Q9UYS8 DNA topoisomerase 1 0.00e+00 5.23e-34 4.61e-36 0.7149
1. PBF P43012 DNA topoisomerase 1 0.00e+00 1.08e-24 1.88e-73 0.7377
1. PBF Q8Z6F5 DNA topoisomerase 3 0.00e+00 2.50e-27 4.40e-11 0.6865
1. PBF P43704 DNA topoisomerase 3 1.11e-12 4.31e-28 2.57e-10 0.6763
1. PBF Q8CSU3 DNA topoisomerase 1 0.00e+00 2.11e-46 4.55e-73 0.7602
1. PBF P0A2I1 DNA topoisomerase 1 1.11e-16 2.42e-25 2.77e-66 0.7318
1. PBF O66893 DNA topoisomerase 1 0.00e+00 1.79e-20 4.79e-77 0.8578
1. PBF Q5WAX6 DNA topoisomerase 3 0.00e+00 5.87e-39 3.32e-22 0.7263
3. BF P95479 Reverse gyrase 1.44e-10 NA 4.71e-41 0.6728
3. BF Q08582 Reverse gyrase 5.70e-11 NA 1.69e-36 0.622
3. BF Q9UZ86 Reverse gyrase 0.00e+00 NA 1.02e-43 0.6853
3. BF O58530 Reverse gyrase 7.46e-05 NA 1.73e-19 0.5814
3. BF O67037 Reverse gyrase 1 1.18e-10 NA 1.06e-45 0.7251
3. BF Q6F598 Reverse gyrase 6.28e-04 NA 2.51e-25 0.6344
3. BF P74759 Reverse gyrase 1.80e-08 NA 2.50e-36 0.6486
3. BF Q9YC75 Reverse gyrase 2 2.96e-09 NA 3.05e-29 0.6249
3. BF O51934 Reverse gyrase 0.00e+00 NA 6.71e-37 0.6917
3. BF Q9X3X7 DNA topoisomerase 1 1.67e-13 NA 3.17e-62 0.7598
3. BF Q8ZXT5 Reverse gyrase 3.12e-08 NA 1.12e-37 0.6542
3. BF Q975P6 Reverse gyrase 2 1.58e-09 NA 1.31e-36 0.6353
3. BF Q8R979 Reverse gyrase 0.00e+00 NA 2.93e-39 0.7044
3. BF O67226 Reverse gyrase 2 3.88e-11 NA 2.11e-47 0.6868
3. BF O29238 Reverse gyrase 0.00e+00 NA 8.79e-44 0.6715
3. BF Q97ZZ8 Reverse gyrase 1 5.53e-07 NA 8.25e-41 0.6276
3. BF Q9YCB6 Reverse gyrase 1 2.53e-09 NA 1.53e-27 0.6601
3. BF Q971T7 Reverse gyrase 1 3.70e-11 NA 1.02e-37 0.6536
3. BF Q97ZF5 Reverse gyrase 2 6.58e-08 NA 1.24e-36 0.6479
4. PB F4ISQ7 DNA topoisomerase 3-beta 0.00e+00 6.76e-14 7.86e-12 NA
4. PB O70157 DNA topoisomerase 3-alpha 7.64e-13 2.65e-08 1.17e-14 NA
4. PB Q59046 DNA topoisomerase 1 2.44e-15 2.25e-32 6.82e-42 NA
4. PB C7J0A2 DNA topoisomerase 3-alpha 7.77e-16 2.58e-11 1.25e-09 NA
4. PB Q9LVP1 DNA topoisomerase 3-alpha 1.60e-13 6.92e-13 2.76e-13 NA
4. PB Q5UQB5 DNA topoisomerase 1 type prokaryotic NA 2.38e-20 1.60e-68 NA
4. PB Q2FZ32 DNA topoisomerase 1 0.00e+00 6.57e-47 2.02e-73 NA
4. PB Q2FW03 DNA topoisomerase 3 0.00e+00 2.80e-44 7.25e-26 NA
4. PB Q13472 DNA topoisomerase 3-alpha 8.10e-15 8.51e-07 1.25e-11 NA
4. PB O60126 DNA topoisomerase 3 0.00e+00 7.05e-20 5.42e-14 NA
4. PB P06612 DNA topoisomerase 1 1.11e-16 7.05e-25 3.55e-66 NA
4. PB P9WG49 DNA topoisomerase 1 1.11e-15 1.34e-21 1.22e-71 NA
4. PB P13099 DNA topoisomerase 3 0.00e+00 4.18e-20 9.51e-16 NA
4. PB O95985 DNA topoisomerase 3-beta-1 0.00e+00 3.19e-13 2.68e-17 NA
4. PB P34184 DNA topoisomerase 1 NA 8.93e-42 3.31e-16 NA
4. PB Q8T2T7 DNA topoisomerase 3 0.00e+00 1.69e-23 5.98e-12 NA
4. PB Q9Z321 DNA topoisomerase 3-beta-1 0.00e+00 2.60e-13 2.01e-15 NA
4. PB Q0J0S6 DNA topoisomerase 3-beta 1.11e-16 9.26e-12 3.05e-12 NA
4. PB O96651 DNA topoisomerase 3-beta 0.00e+00 2.29e-11 5.76e-10 NA
4. PB O61660 DNA topoisomerase 3 3.33e-16 9.13e-27 7.06e-28 NA
4. PB P14294 DNA topoisomerase 3 0.00e+00 6.22e-28 2.47e-11 NA
7. B Q9NG98 DNA topoisomerase 3-alpha 6.97e-13 NA 8.67e-17 NA
7. B Q58907 Reverse gyrase 2.56e-04 NA 2.03e-16 NA