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.
AVX54734.1
JCVISYN3A_0352
Uncharacterized protein.
M. mycoides homolog: Q6MTJ3.
TIGRfam Classification: 2=Generic.
Category: Essential.
Statistics
Total GO Annotation: 8
Unique PROST Go: 6
Unique BLAST Go: 0
Unique Foldseek Go: 0
Total Homologs: 14
Unique PROST Homologs: 13
Unique BLAST Homologs: 0
Unique Foldseek Homologs: 0
Literature
Danchin and Fang [1]: DNA remodelling primosomal protein|in B. subtilis co-evolves with endonuclease III
Yang and Tsui [2]: Regulatory protein RecX (Protein OraA)
Antczak et al. [3]: DnaD family protein
Zhang et al. [4]: GO:0006269|DNA replication, synthesis of RNA primer
Bianchi et al. [5]: DNA Replication Protein (DnaD-like)
Structures and Sequence Alignment
The best structural homolog that predicted by 2. PF was
P39787
(DNA replication protein DnaD) with a FATCAT P-Value: 7.39e-09 and RMSD of 2.09 angstrom. The sequence alignment identity is 25.5%.
Structural alignment shown in left. Query protein AVX54734.1 colored as red in alignment, homolog P39787 colored as blue.
Query protein AVX54734.1 is also shown in right top, homolog P39787 showed in right bottom. They are colored based on secondary structures.
AVX54734.1 ----MILKMLEKGIISKKKLLLEYYKKLNLTDNQALIILMI-MYLNDQTRKMTTPNLLANYLNLSSVEIE--KELELLAEKDLIEIKSDFI----DFSNL 89 P39787 MKKQQFIDMQEQGTSTIPNLLLTHYKQLGLNETELILLLKIKMHL-EKGSYFPTPNQLQEGMSI-SVE-ECTNRLRMFIQKGFL-----FIEECEDQNGI 92 AVX54734.1 -FQKIGL--L---VNDSFLIEQNITFFNDL-----EKNL--LF------SLT--EHQKLKL-LD-------LLKTSIKKEQVL--QLS---INKKLFSFE 155 P39787 KFEKYSLQPLWGKLYEYIQLAQNQT--QERKAEGEQKSLYTIFEEEFARPLSPLECETLAIWQDQDQHDAQLIKHAL-KEAVLSGKLSFRYIDRILFEWK 189 AVX54734.1 E-LLKEVEIFLK-STNKF-----KQ-------------FDWLDDQNV 182 P39787 KNGLKTVE-QAKIHSQKFRRVQAKQNEPQKEYKRQVPFYNWLEQ--- 232
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 |
|---|---|---|
| 2. PF | GO:0006269 | DNA replication, synthesis of RNA primer |
| 2. PF | GO:1990077 | primosome complex |
| 5. P | GO:0003677 | DNA binding |
| 5. P | GO:0045892 | negative regulation of transcription, DNA-templated |
| 5. P | GO:0003700 | DNA-binding transcription factor activity |
| 5. P | GO:0006367 | transcription initiation from RNA polymerase II promoter |
| 5. P | GO:0030435 | sporulation resulting in formation of a cellular spore |
| 5. P | GO:0006355 | regulation of transcription, DNA-templated |
Uniprot GO Annotations
| GO | Description |
|---|
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 |
|---|---|---|---|---|---|---|
| 2. PF | P39787 | DNA replication protein DnaD | 7.39e-09 | 2.16e-07 | NA | 0.472 |
| 5. P | Q9KDM7 | HTH-type transcriptional regulator Hpr | 4.55e-04 | 5.91e-03 | NA | NA |
| 5. P | A6UW55 | Transcription factor E | 1.09e-04 | 2.06e-02 | NA | NA |
| 5. P | Q2FT22 | Transcription factor E | 1.18e-03 | 2.68e-02 | NA | NA |
| 5. P | P03687 | DNA replication protein gp18 | NA | 2.93e-04 | NA | NA |
| 5. P | Q47839 | Transcriptional repressor CopY | 2.20e-04 | 3.81e-04 | NA | NA |
| 5. P | P71015 | HTH-type transcriptional repressor GbsR | 1.00e-04 | 8.48e-07 | NA | NA |
| 5. P | A7I7T6 | Transcription factor E | 1.62e-03 | 1.26e-02 | NA | NA |
| 5. P | P42546 | Uncharacterized 25.6 kDa protein | NA | 2.21e-11 | NA | NA |
| 5. P | P45909 | Uncharacterized protein YqaL | 8.04e-04 | 8.24e-05 | NA | NA |
| 5. P | C0SPB8 | Putative HTH-type transcriptional regulator YvaV | 1.33e-05 | 2.38e-05 | NA | NA |
| 5. P | O34709 | HTH-type transcriptional repressor OpcR | 6.75e-05 | 1.05e-05 | NA | NA |
| 5. P | Q58183 | Uncharacterized protein MJ0773 | 4.41e-03 | 4.18e-02 | NA | NA |
| 5. P | Q58958 | Putative HTH-type transcriptional regulator MJ1563 | 2.57e-05 | 1.29e-04 | NA | NA |