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.

AVX54570.1
JCVISYN3A_0002

DNA polymerase III subunit beta.
M. mycoides homolog: Q6MUM6.
TIGRfam Classification: 5=Equivalog.
Category: Essential.

Statistics

Total GO Annotation: 58
Unique PROST Go: 13
Unique BLAST Go: 1
Unique Foldseek Go: 27

Total Homologs: 152
Unique PROST Homologs: 13
Unique BLAST Homologs: 0
Unique Foldseek Homologs: 49

Literature

Danchin and Fang [1]: NA
Yang and Tsui [2]: NA
Antczak et al. [3]: dnaN; DNA polymerase III subunit beta
Zhang et al. [4]: GO:0003887|DNA-directed DNA polymerase activity
Bianchi et al. [5]: NA

Structures and Sequence Alignment

The best structural homolog that predicted by 1. PBF was O84078 (Beta sliding clamp) with a FATCAT P-Value: 0 and RMSD of 1.94 angstrom. The sequence alignment identity is 21.2%.
Structural alignment shown in left. Query protein AVX54570.1 colored as red in alignment, homolog O84078 colored as blue. Query protein AVX54570.1 is also shown in right top, homolog O84078 showed in right bottom. They are colored based on secondary structures.

  AVX54570.1 --------------------------------------------------MNFSINRMVLLDNLSKAAKV--IDPKNVN-PSLAGIYLNVLSDQVNIIAT 47
      O84078 MNFRLHGAFSNPSFVKIFFTKASPERRLTCFHVTKHGYSFQTDLHDYRKIMKFVISRNE-LGNLIK--KVQNVVPQSTPIPVLTHVLIESCNDELVFTAT 97

  AVX54570.1 SGILSFKSILNNQNSDLEVKQEGKVLLKP--KFVLEMLRRLDDEFVVFSMVEDNELIIKTDNSD-F---SIGVLNSEDYPLIGFREKGIEFNLNPKEVK- 140
      O84078 DLTVSTRCVVK-----AKVYESGSVTI-PSRRF-FQLIRELTEANIEVA-AHSGEMATITSGSSCFRLLSMG---KEDFPMLPDMQNALRFTLDSERLKD 186

  AVX54570.1 ---KTIYQVFVSMNENNKKLILTGLNLKLNNNKAIFSTTDSFRISQKI-LEIQSDNNEDIDITIPFKTALELPKLLD-NAENLK-IIIVEGYITFI-ID- 232
      O84078 MFQRTSF--AVSREES--RYVLTGVLLSIANGTMTVVGTDGKRLA-KIDTEISLDPSFSGDYIIPIK-AVE--EIIRMSSEDVQSTIFLDQ--TKIAVEC 276

  AVX54570.1 -NVIFQSNLIDGRFPNVQIAFPTKFETIITVKQKSILKVLSRFDLVADD---GL-----PAIVNIKVNEDKIEFKSFISEVGKYEEDFDDFVIE--GNKS 321
      O84078 GNTLLVTKLLSGEFPDFSPVISTHSSVQLDLHREELISLLKQVALFTNESSHSVKFSFSPGELTLTANCTK------VGE-GKV-----SMAVNYTG-ET 363

  AVX54570.1 LSISFNTRFLIDAIK-TLDEDRIELKLINSTKPIVINNVYD--EHLKQVILPTFLSN- 375
      O84078 LEIAFNPFFFLDILKHSRDE-LVQLGISDSYNPGIIT---DSTRSL-FVIMPMRLHDD 416

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:0003677 DNA binding
1. PBF GO:0006260 DNA replication
1. PBF GO:0008408 3'-5' exonuclease activity
1. PBF GO:0003887 DNA-directed DNA polymerase activity
1. PBF GO:0006271 DNA strand elongation involved in DNA replication
1. PBF GO:0009360 DNA polymerase III complex
2. PF GO:0019985 translesion synthesis
2. PF GO:0006272 leading strand elongation
2. PF GO:0070182 DNA polymerase binding
2. PF GO:0030337 DNA polymerase processivity factor activity
2. PF GO:0030896 checkpoint clamp complex
2. PF GO:0006275 regulation of DNA replication
2. PF GO:0043626 PCNA complex
2. PF GO:0051598 meiotic recombination checkpoint signaling
4. PB GO:0042276 error-prone translesion synthesis
4. PB GO:0005737 cytoplasm
4. PB GO:0044787 bacterial-type DNA replication
5. P GO:0039695 DNA-templated viral transcription
5. P GO:0031573 mitotic intra-S DNA damage checkpoint signaling
5. P GO:0035861 site of double-strand break
5. P GO:0000077 DNA damage checkpoint signaling
5. P GO:0044778 meiotic DNA integrity checkpoint signaling
5. P GO:0000724 double-strand break repair via homologous recombination
5. P GO:0140445 chromosome, telomeric repeat region
5. P GO:0005694 chromosome
5. P GO:0033314 mitotic DNA replication checkpoint signaling
5. P GO:0071479 cellular response to ionizing radiation
5. P GO:0021762 substantia nigra development
5. P GO:0000723 telomere maintenance
5. P GO:0008853 exodeoxyribonuclease III activity
6. F GO:0005652 nuclear lamina
6. F GO:0003682 chromatin binding
6. F GO:1900264 positive regulation of DNA-directed DNA polymerase activity
6. F GO:0043596 nuclear replication fork
6. F GO:0032139 dinucleotide insertion or deletion binding
6. F GO:0006298 mismatch repair
6. F GO:0031297 replication fork processing
6. F GO:0070557 PCNA-p21 complex
6. F GO:0035035 histone acetyltransferase binding
6. F GO:0032077 positive regulation of deoxyribonuclease activity
6. F GO:0016604 nuclear body
6. F GO:1902990 mitotic telomere maintenance via semi-conservative replication
6. F GO:0000701 purine-specific mismatch base pair DNA N-glycosylase activity
6. F GO:0000307 cyclin-dependent protein kinase holoenzyme complex
6. F GO:0032405 MutLalpha complex binding
6. F GO:0045739 positive regulation of DNA repair
6. F GO:0071466 cellular response to xenobiotic stimulus
6. F GO:0045740 positive regulation of DNA replication
6. F GO:0005813 centrosome
6. F GO:0008022 protein C-terminus binding
6. F GO:0006287 base-excision repair, gap-filling
6. F GO:0030855 epithelial cell differentiation
6. F GO:0030971 receptor tyrosine kinase binding
6. F GO:0034644 cellular response to UV
6. F GO:0003684 damaged DNA binding
6. F GO:0031571 mitotic G1 DNA damage checkpoint signaling
6. F GO:0000785 chromatin
7. B GO:0046677 response to antibiotic

Uniprot GO Annotations

GO Description
GO:0016740 transferase activity
GO:0016779 nucleotidyltransferase activity
GO:0003677 DNA binding
GO:0006260 DNA replication
GO:0090305 nucleic acid phosphodiester bond hydrolysis
GO:0005737 cytoplasm
GO:0008408 3'-5' exonuclease activity
GO:0003887 DNA-directed DNA polymerase activity
GO:0009360 DNA polymerase III complex
GO:0071897 DNA biosynthetic process

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 Q4ULS3 Beta sliding clamp 0.00e+00 6.65e-38 2.29e-15 0.9132
1. PBF P52851 Beta sliding clamp 0.00e+00 1.46e-23 2.71e-21 0.9023
1. PBF Q5HK00 Beta sliding clamp 0.00e+00 6.17e-35 8.11e-43 0.9092
1. PBF Q8CQK6 Beta sliding clamp 0.00e+00 6.17e-35 8.11e-43 0.9084
1. PBF P43744 Beta sliding clamp 0.00e+00 9.83e-29 5.11e-21 0.913
1. PBF P34029 Beta sliding clamp 0.00e+00 7.36e-47 5.62e-61 0.9107
1. PBF Q9EVE4 Beta sliding clamp 0.00e+00 1.68e-33 2.51e-12 0.9107
1. PBF Q6GKU3 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9064
1. PBF O25242 Beta sliding clamp 0.00e+00 8.39e-38 7.31e-10 0.874
1. PBF P46387 Beta sliding clamp 0.00e+00 1.01e-25 5.65e-19 0.9003
1. PBF O84078 Beta sliding clamp 0.00e+00 2.26e-07 8.71e-13 0.9156
1. PBF Q5HJZ4 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9247
1. PBF Q9KVX5 Beta sliding clamp 0.00e+00 3.43e-31 2.63e-23 0.928
1. PBF A0QND6 Beta sliding clamp 0.00e+00 1.46e-23 2.71e-21 0.9015
1. PBF P05649 Beta sliding clamp 0.00e+00 3.73e-36 2.90e-39 0.9426
1. PBF Q9ZDB3 Beta sliding clamp 0.00e+00 4.31e-37 1.11e-15 0.9251
1. PBF P0A023 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9104
1. PBF P27903 Beta sliding clamp 0.00e+00 1.13e-35 5.53e-23 0.9175
1. PBF Q9L7L6 Beta sliding clamp 0.00e+00 9.18e-24 3.72e-21 0.9068
1. PBF B8GXP6 Beta sliding clamp 0.00e+00 1.09e-30 1.93e-14 0.9247
1. PBF P0CAU5 Beta sliding clamp 0.00e+00 1.09e-30 1.93e-14 0.9259
1. PBF P72856 Beta sliding clamp 0.00e+00 5.40e-36 1.73e-19 0.9043
1. PBF Q9CJJ1 Beta sliding clamp 0.00e+00 7.26e-41 6.76e-24 0.9334
1. PBF Q68WW0 Beta sliding clamp 0.00e+00 2.62e-36 6.93e-14 0.9256
1. PBF P9WNU0 Beta sliding clamp 0.00e+00 2.16e-21 1.07e-21 0.9065
1. PBF Q9PKW4 Beta sliding clamp 0.00e+00 3.79e-40 1.01e-12 0.9397
1. PBF Q89B36 Beta sliding clamp 0.00e+00 3.38e-29 2.72e-10 0.9174
1. PBF O83048 Beta sliding clamp 0.00e+00 8.89e-35 1.43e-07 0.9115
1. PBF P29439 Beta sliding clamp 0.00e+00 4.81e-33 8.78e-11 0.9051
1. PBF O54376 Beta sliding clamp 0.00e+00 5.24e-40 8.48e-24 0.9349
1. PBF Q50313 Beta sliding clamp 0.00e+00 1.62e-44 3.09e-12 0.8876
1. PBF Q1RIS7 Beta sliding clamp 0.00e+00 2.26e-38 2.64e-16 0.9224
1. PBF A0A0E3URH8 Beta sliding clamp homolog GriR 0.00e+00 1.54e-30 4.76e-12 0.8926
1. PBF P0A022 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9118
1. PBF P26464 Beta sliding clamp 0.00e+00 3.63e-30 3.51e-20 0.9281
1. PBF P22838 Beta sliding clamp 0.00e+00 8.01e-31 1.02e-15 0.9237
1. PBF P57127 Beta sliding clamp 0.00e+00 7.41e-35 2.46e-05 0.8975
1. PBF Q9Z8K0 Beta sliding clamp 0.00e+00 4.30e-41 6.87e-13 0.9335
1. PBF P24117 Beta sliding clamp 0.00e+00 2.80e-75 0.0 0.9981
1. PBF P99103 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9083
1. PBF Q98RK6 Beta sliding clamp 0.00e+00 6.80e-41 3.85e-06 0.9155
1. PBF P0A989 Beta sliding clamp 0.00e+00 1.18e-29 1.21e-18 0.9293
1. PBF P0A990 Beta sliding clamp 0.00e+00 1.18e-29 1.21e-18 0.9304
1. PBF Q9ZLX4 Beta sliding clamp 0.00e+00 5.52e-36 1.16e-11 0.8673
1. PBF Q6GD88 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9102
1. PBF O67725 Beta sliding clamp 0.00e+00 4.91e-40 3.09e-07 0.9189
1. PBF P21174 Beta sliding clamp (Fragment) 0.00e+00 4.58e-09 8.01e-16 0.9275
1. PBF P0A121 Beta sliding clamp 0.00e+00 1.69e-30 5.46e-23 0.9504
1. PBF P0A120 Beta sliding clamp 0.00e+00 1.69e-30 5.46e-23 0.9502
1. PBF P59651 Beta sliding clamp 0.00e+00 5.45e-42 5.24e-39 0.9327
1. PBF O33914 Beta sliding clamp 0.00e+00 5.41e-21 6.29e-22 0.9037
1. PBF O06672 Beta sliding clamp 0.00e+00 3.54e-43 2.64e-39 0.9318
1. PBF Q9I7C4 Beta sliding clamp 0.00e+00 4.32e-29 3.03e-21 0.9516
1. PBF P47247 Beta sliding clamp 0.00e+00 6.95e-42 1.39e-16 0.8818
1. PBF P0A024 Beta sliding clamp 0.00e+00 5.08e-36 7.95e-45 0.9085
1. PBF P52023 Beta sliding clamp 0.00e+00 2.28e-29 2.27e-16 0.9281
1. PBF Q9RCA1 Beta sliding clamp 0.00e+00 1.08e-37 2.07e-38 0.935
1. PBF Q92I37 Beta sliding clamp 0.00e+00 4.75e-38 4.83e-15 0.9267
2. PF O29912 DNA polymerase sliding clamp 1.80e-13 2.13e-03 NA 0.717
2. PF Q9UWR9 DNA polymerase sliding clamp 2.53e-12 5.43e-03 NA 0.4358
2. PF O58398 DNA polymerase sliding clamp 1.62e-12 1.85e-02 NA 0.4362
2. PF P31008 Proliferating cell nuclear antigen 1.54e-12 1.73e-02 NA 0.6482
2. PF Q975M2 DNA polymerase sliding clamp 2 2.60e-12 2.89e-02 NA 0.4065
2. PF Q9UYX8 DNA polymerase sliding clamp 2.23e-12 3.53e-02 NA 0.4338
2. PF C6A1Y5 DNA polymerase sliding clamp 2.91e-12 1.15e-02 NA 0.4419
2. PF P33761 Beta sliding clamp 0.00e+00 3.20e-29 NA 0.8931
2. PF A0RXH7 DNA polymerase sliding clamp 1.79e-13 2.53e-02 NA 0.7426
2. PF Q74MV1 DNA polymerase sliding clamp 8.83e-13 9.28e-04 NA 0.7215
2. PF A1RXU8 DNA polymerase sliding clamp 5.00e-13 1.06e-03 NA 0.7203
2. PF A2SSW6 DNA polymerase sliding clamp 1.15e-13 1.83e-02 NA 0.7112
2. PF Q8ZYL6 DNA polymerase sliding clamp 2 5.04e-12 5.52e-03 NA 0.6762
2. PF B6YVZ1 DNA polymerase sliding clamp 3.20e-12 2.79e-02 NA 0.4317
2. PF P57763 DNA polymerase sliding clamp 2 1.98e-11 6.03e-03 NA 0.4008
2. PF Q5JFD3 DNA polymerase sliding clamp 2 5.19e-12 4.59e-03 NA 0.4319
2. PF Q97Z84 DNA polymerase sliding clamp 2 3.71e-12 1.91e-03 NA 0.653
2. PF P57766 DNA polymerase sliding clamp 1 3.37e-12 1.26e-03 NA 0.4002
2. PF Q8ZTY0 DNA polymerase sliding clamp 1 4.27e-13 2.75e-02 NA 0.7058
2. PF Q2NE55 DNA polymerase sliding clamp 4.46e-13 7.63e-03 NA 0.751
2. PF O16852 Proliferating cell nuclear antigen 2.55e-13 1.67e-02 NA 0.6782
2. PF Q975N2 DNA polymerase sliding clamp 1 1.83e-11 3.86e-02 NA 0.6732
2. PF Q9YEZ5 DNA polymerase sliding clamp 3 2.05e-12 1.01e-03 NA 0.6875
2. PF P57762 DNA polymerase sliding clamp 1 1.77e-11 1.83e-02 NA 0.6773
2. PF Q973F5 DNA polymerase sliding clamp 3 1.53e-12 3.39e-03 NA 0.6728
2. PF C5A5N6 DNA polymerase sliding clamp 2.36e-12 7.18e-03 NA 0.4393
2. PF Q8TWK3 DNA polymerase sliding clamp 1.49e-12 3.31e-03 NA 0.6652
2. PF Q5JF32 DNA polymerase sliding clamp 1 2.17e-12 1.47e-02 NA 0.4341
2. PF Q9Y9V7 DNA polymerase sliding clamp 2 1.80e-13 6.04e-05 NA 0.4236
3. BF P52620 Beta sliding clamp (Fragment) 3.27e-11 NA 0.012 0.8705
4. PB P0A988 Beta sliding clamp 0.00e+00 1.18e-29 1.21e-18 NA
4. PB P9WNU1 Beta sliding clamp 0.00e+00 2.16e-21 1.07e-21 NA
5. P P61074 Proliferating cell nuclear antigen 2.05e-12 1.73e-02 NA NA
5. P P78955 Checkpoint protein hus1 1.21e-10 1.14e-02 NA NA
5. P Q8NHY5 Checkpoint protein HUS1B 1.28e-10 7.77e-03 NA NA
5. P P32990 Late transcription factor 1 NA 1.16e-03 NA NA
5. P O02115 Proliferating cell nuclear antigen 8.42e-13 2.15e-02 NA NA
5. P O57198 Late transcription factor 1 NA 1.17e-02 NA NA
5. P Q5R7X9 Cell cycle checkpoint protein RAD1 6.05e-13 1.88e-02 NA NA
5. P Q57697 DNA polymerase sliding clamp 1.87e-12 3.09e-02 NA NA
5. P P68613 Late transcription factor 1 NA 1.76e-02 NA NA
5. P P68612 Late transcription factor 1 NA 1.76e-02 NA NA
5. P Q9QWZ1 Cell cycle checkpoint protein RAD1 2.30e-12 5.67e-04 NA NA
5. P Q84513 Probable DNA polymerase sliding clamp 1 NA 5.87e-03 NA NA
5. P O60671 Cell cycle checkpoint protein RAD1 3.21e-12 1.88e-02 NA NA
6. F Q4JAI6 DNA polymerase sliding clamp 1 1.24e-11 NA NA 0.6787
6. F Q9HJQ0 DNA polymerase sliding clamp 2.80e-14 NA NA 0.7116
6. F Q6KZF1 DNA polymerase sliding clamp 1.59e-14 NA NA 0.7122
6. F Q4J9A8 DNA polymerase sliding clamp 2 2.79e-12 NA NA 0.6969
6. F Q6LWJ8 DNA polymerase sliding clamp 1.45e-12 NA NA 0.7054
6. F Q9YFT8 DNA polymerase sliding clamp 1 2.92e-12 NA NA 0.6832
6. F A6VHX7 DNA polymerase sliding clamp 1.46e-12 NA NA 0.706
6. F Q18E60 DNA polymerase sliding clamp 1.45e-13 NA NA 0.7437
6. F Q9MAY3 Proliferating cell nuclear antigen 1.91e-13 NA NA 0.6832
6. F Q0W2J4 DNA polymerase sliding clamp 2.90e-14 NA NA 0.7793
6. F Q6B6N4 Proliferating cell nuclear antigen 7.38e-13 NA NA 0.6815
6. F Q9P9H8 DNA polymerase sliding clamp 1.56e-13 NA NA 0.742
6. F Q9HN45 DNA polymerase sliding clamp 1.54e-13 NA NA 0.7392
6. F P57761 Proliferating cell nuclear antigen 8.72e-13 NA NA 0.6915
6. F A7I849 DNA polymerase sliding clamp 6.03e-13 NA NA 0.4024
6. F Q3ZBW4 Proliferating cell nuclear antigen 1.58e-12 NA NA 0.6898
6. F P61258 Proliferating cell nuclear antigen 1.39e-12 NA NA 0.6939
6. F Q8PX25 DNA polymerase sliding clamp 5.20e-14 NA NA 0.7109
6. F Q12U18 DNA polymerase sliding clamp 1.61e-13 NA NA 0.4079
6. F O82134 Proliferating cell nuclear antigen 1.93e-13 NA NA 0.6981
6. F Q755A0 DNA damage checkpoint protein 1 1.05e-03 NA NA 0.2709
6. F Q46E39 DNA polymerase sliding clamp 1.42e-13 NA NA 0.7093
6. F O73947 DNA polymerase sliding clamp 3.05e-12 NA NA 0.4385
6. F Q9DEA3 Proliferating cell nuclear antigen 1.21e-12 NA NA 0.6747
6. F Q43124 Proliferating cell nuclear antigen 1.74e-13 NA NA 0.7073
6. F Q979S2 DNA polymerase sliding clamp 1.62e-14 NA NA 0.7121
6. F A6UQZ4 DNA polymerase sliding clamp 1.31e-12 NA NA 0.706
6. F B0R7F7 DNA polymerase sliding clamp 1.61e-13 NA NA 0.7393
6. F A0B7Y8 DNA polymerase sliding clamp 9.27e-14 NA NA 0.7077
6. F Q9W644 Proliferating cell nuclear antigen 7.24e-13 NA NA 0.6763
6. F Q2FNX1 DNA polymerase sliding clamp 2.25e-12 NA NA 0.7418
6. F P18248 Proliferating cell nuclear antigen 4.79e-12 NA NA 0.6721
6. F O01377 Proliferating cell nuclear antigen 2.31e-13 NA NA 0.6874
6. F Q3IU15 DNA polymerase sliding clamp 1.58e-13 NA NA 0.4032
6. F A4G0K8 DNA polymerase sliding clamp 1.50e-12 NA NA 0.6967
6. F A5UMB4 DNA polymerase sliding clamp 5.34e-13 NA NA 0.745
6. F O27367 DNA polymerase sliding clamp 6.22e-13 NA NA 0.7455
6. F A9A8V2 DNA polymerase sliding clamp 1.42e-12 NA NA 0.7057
6. F Q758W7 DNA damage checkpoint control protein RAD17 5.33e-07 NA NA 0.4759
6. F A6UUW0 DNA polymerase sliding clamp 1.95e-12 NA NA 0.7324
6. F Q00265 Proliferating cell nuclear antigen large form 1.89e-08 NA NA 0.6743
6. F B9LU30 DNA polymerase sliding clamp 1.61e-13 NA NA 0.4076
6. F P53358 Proliferating cell nuclear antigen 3.47e-12 NA NA 0.6678
6. F Q8TUF7 DNA polymerase sliding clamp 7.06e-14 NA NA 0.4081
6. F A9A2X4 DNA polymerase sliding clamp 2.07e-13 NA NA 0.7342
6. F P57765 DNA polymerase sliding clamp 3 6.76e-12 NA NA 0.4148
6. F B8GG80 DNA polymerase sliding clamp 9.45e-14 NA NA 0.3984
6. F A3CVJ2 DNA polymerase sliding clamp 3.96e-13 NA NA 0.745
6. F Q00268 Proliferating cell nuclear antigen 2.10e-13 NA NA 0.7023