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.
AVX54626.1
JCVISYN3A_0128
DNA-directed RNA polymerase subunit delta.
M. mycoides homolog: Q6MUA4.
TIGRfam Classification: 4=Probable.
Category: Quasiessential.
Statistics
Total GO Annotation: 30
Unique PROST Go: 27
Unique BLAST Go: 0
Unique Foldseek Go: 0
Total Homologs: 119
Unique PROST Homologs: 104
Unique BLAST Homologs: 0
Unique Foldseek Homologs: 0
Structures and Sequence Alignment
The best structural homolog that predicted by 2. PF was
A7Z9T5
(Probable DNA-directed RNA polymerase subunit delta) with a FATCAT P-Value: 6.12e-06 and RMSD of 3.12 angstrom. The sequence alignment identity is 28.3%.
Structural alignment shown in left. Query protein AVX54626.1 colored as red in alignment, homolog A7Z9T5 colored as blue.
Query protein AVX54626.1 is also shown in right top, homolog A7Z9T5 showed in right bottom. They are colored based on secondary structures.
AVX54626.1 MS-K------VRNLDLV---YSYLQSTKTPSS----LNEIWKSISKDIISQKKDEI-SVIADLYGDMVLDNRF-ALTTDNLWALSSNSSVENIKKQYDDF 84 A7Z9T5 MSIKQYSQEQLKQMALVEIAHEIFSEHKKPVPFQELLNEM---IS--LLGVTKEELGDRIAQFYTDLNIDGRFIAL-SDQTWGLRSWYPYDQL----DEE 90 AVX54626.1 IN-T-DHKHRYSDS--DEELTID-------DEMLLDE-DYDSDFTQELDDF-DEDFD--DTDQTYIDD-----DE--YNR------- 142 A7Z9T5 TQPTVKAKKKKAKKVVEEDLDLDEFEEVDEDDIDLDEIEEDIDL--EADSFDDEDIDEEDDDELEIEDEMIEEDEEDYDDEEEDRKD 175
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:0003899 | DNA-directed 5'-3' RNA polymerase activity |
| 1. PBF | GO:0006351 | transcription, DNA-templated |
| 1. PBF | GO:0006355 | regulation of transcription, DNA-templated |
| 5. P | GO:0040011 | locomotion |
| 5. P | GO:0031492 | nucleosomal DNA binding |
| 5. P | GO:0016251 | RNA polymerase II general transcription initiation factor activity |
| 5. P | GO:0003677 | DNA binding |
| 5. P | GO:0006334 | nucleosome assembly |
| 5. P | GO:0045910 | negative regulation of DNA recombination |
| 5. P | GO:0006366 | transcription by RNA polymerase II |
| 5. P | GO:0000786 | nucleosome |
| 5. P | GO:0005737 | cytoplasm |
| 5. P | GO:0030261 | chromosome condensation |
| 5. P | GO:0016584 | nucleosome positioning |
| 5. P | GO:0000122 | negative regulation of transcription by RNA polymerase II |
| 5. P | GO:0001046 | core promoter sequence-specific DNA binding |
| 5. P | GO:0060698 | endoribonuclease inhibitor activity |
| 5. P | GO:0046982 | protein heterodimerization activity |
| 5. P | GO:0090575 | RNA polymerase II transcription regulator complex |
| 5. P | GO:0018991 | oviposition |
| 5. P | GO:0060465 | pharynx development |
| 5. P | GO:0003713 | transcription coactivator activity |
| 5. P | GO:0045944 | positive regulation of transcription by RNA polymerase II |
| 5. P | GO:0031936 | obsolete negative regulation of chromatin silencing |
| 5. P | GO:0010171 | body morphogenesis |
| 5. P | GO:0045111 | intermediate filament cytoskeleton |
| 5. P | GO:0017054 | negative cofactor 2 complex |
| 5. P | GO:0017025 | TBP-class protein binding |
| 5. P | GO:0003714 | transcription corepressor activity |
| 5. P | GO:0001091 | RNA polymerase II general transcription initiation factor binding |
Uniprot GO Annotations
| GO | Description |
|---|---|
| GO:0016740 | transferase activity |
| GO:0016779 | nucleotidyltransferase activity |
| GO:0006351 | transcription, DNA-templated |
| GO:0000428 | DNA-directed RNA polymerase complex |
| GO:0006355 | regulation of transcription, DNA-templated |
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 | B9IRX2 | Probable DNA-directed RNA polymerase subunit delta | 1.50e-04 | 4.17e-23 | 0.044 | 0.4411 |
| 1. PBF | B7HY99 | Probable DNA-directed RNA polymerase subunit delta | 1.34e-04 | 4.17e-23 | 0.044 | 0.4425 |
| 2. PF | Q5WB42 | Probable DNA-directed RNA polymerase subunit delta | 1.88e-04 | 8.44e-28 | NA | 0.4393 |
| 2. PF | Q81JW0 | Probable DNA-directed RNA polymerase subunit delta | 1.01e-05 | 7.00e-26 | NA | 0.441 |
| 2. PF | Q04D45 | Probable DNA-directed RNA polymerase subunit delta | 2.95e-05 | 2.28e-07 | NA | 0.4969 |
| 2. PF | Q6HAU4 | Probable DNA-directed RNA polymerase subunit delta | 8.78e-06 | 2.48e-25 | NA | 0.4538 |
| 2. PF | A0RLC4 | Probable DNA-directed RNA polymerase subunit delta | 9.27e-05 | 3.00e-25 | NA | 0.4481 |
| 2. PF | A7Z9T5 | Probable DNA-directed RNA polymerase subunit delta | 6.12e-06 | 3.53e-23 | NA | 0.4044 |
| 2. PF | Q9K6D6 | Probable DNA-directed RNA polymerase subunit delta | 2.50e-05 | 1.03e-24 | NA | 0.449 |
| 2. PF | Q814T1 | Probable DNA-directed RNA polymerase subunit delta | 3.96e-05 | 9.53e-24 | NA | 0.4468 |
| 2. PF | Q65DT6 | Probable DNA-directed RNA polymerase subunit delta | 8.43e-05 | 5.69e-22 | NA | 0.4452 |
| 2. PF | B7HFN7 | Probable DNA-directed RNA polymerase subunit delta | 1.35e-05 | 9.53e-24 | NA | 0.4466 |
| 2. PF | Q630Q9 | Probable DNA-directed RNA polymerase subunit delta | 6.96e-05 | 3.00e-25 | NA | 0.4454 |
| 4. PB | Q72XA8 | Probable DNA-directed RNA polymerase subunit delta | 2.37e-04 | 1.28e-23 | 0.048 | NA |
| 4. PB | P47268 | Probable DNA-directed RNA polymerase subunit delta | 7.45e-05 | 1.27e-17 | 0.011 | NA |
| 5. P | A4YWD3 | DNA-directed RNA polymerase subunit omega | 6.07e-02 | 9.74e-03 | NA | NA |
| 5. P | B9DTJ7 | Probable DNA-directed RNA polymerase subunit delta | 7.25e-04 | 9.84e-23 | NA | NA |
| 5. P | Q88Z77 | Probable DNA-directed RNA polymerase subunit delta | 3.51e-05 | 1.49e-15 | NA | NA |
| 5. P | P66715 | Probable DNA-directed RNA polymerase subunit delta | 3.42e-05 | 4.45e-24 | NA | NA |
| 5. P | Q2FWD0 | Probable DNA-directed RNA polymerase subunit delta | 3.80e-05 | 4.45e-24 | NA | NA |
| 5. P | Q6GEU7 | Probable DNA-directed RNA polymerase subunit delta | 3.68e-05 | 4.45e-24 | NA | NA |
| 5. P | P75090 | Probable DNA-directed RNA polymerase subunit delta | 7.80e-06 | 2.54e-19 | NA | NA |
| 5. P | Q92H89 | DNA-directed RNA polymerase subunit omega | 7.16e-02 | 1.04e-02 | NA | NA |
| 5. P | A6U3L3 | Probable DNA-directed RNA polymerase subunit delta | 2.55e-05 | 4.45e-24 | NA | NA |
| 5. P | A7X4Y0 | Probable DNA-directed RNA polymerase subunit delta | 2.81e-05 | 4.45e-24 | NA | NA |
| 5. P | C1C5L8 | Probable DNA-directed RNA polymerase subunit delta | 1.20e-03 | 4.49e-23 | NA | NA |
| 5. P | Q1WV31 | Probable DNA-directed RNA polymerase subunit delta | 4.57e-04 | 6.69e-20 | NA | NA |
| 5. P | B5E1U3 | Probable DNA-directed RNA polymerase subunit delta | 1.68e-03 | 4.49e-23 | NA | NA |
| 5. P | Q5FME7 | Probable DNA-directed RNA polymerase subunit delta | 3.90e-04 | 8.59e-22 | NA | NA |
| 5. P | Q99281 | Histone H1.1, embryonic (Fragments) | 7.53e-04 | 7.65e-05 | NA | NA |
| 5. P | B1MXM6 | Probable DNA-directed RNA polymerase subunit delta | 1.42e-05 | 1.55e-14 | NA | NA |
| 5. P | C0MFQ8 | Probable DNA-directed RNA polymerase subunit delta | 1.00e-03 | 1.64e-26 | NA | NA |
| 5. P | Q71WL9 | Probable DNA-directed RNA polymerase subunit delta | 1.40e-04 | 3.98e-20 | NA | NA |
| 5. P | Q8NZF7 | Probable DNA-directed RNA polymerase subunit delta | 1.14e-03 | 3.73e-28 | NA | NA |
| 5. P | A2RIW1 | Probable DNA-directed RNA polymerase subunit delta | 2.25e-04 | 8.32e-19 | NA | NA |
| 5. P | P66717 | Probable DNA-directed RNA polymerase subunit delta | 2.57e-03 | 2.33e-21 | NA | NA |
| 5. P | Q5M1S8 | Probable DNA-directed RNA polymerase subunit delta | 1.82e-03 | 1.84e-26 | NA | NA |
| 5. P | Q49Z74 | Probable DNA-directed RNA polymerase subunit delta | 3.61e-05 | 3.07e-19 | NA | NA |
| 5. P | Q1GBQ3 | Probable DNA-directed RNA polymerase subunit delta | 9.34e-05 | 9.52e-19 | NA | NA |
| 5. P | Q5M6C1 | Probable DNA-directed RNA polymerase subunit delta | 9.03e-04 | 1.84e-26 | NA | NA |
| 5. P | B6IN07 | DNA-directed RNA polymerase subunit omega | 3.71e-02 | 1.16e-02 | NA | NA |
| 5. P | Q8EM52 | Probable DNA-directed RNA polymerase subunit delta | 6.59e-05 | 1.97e-19 | NA | NA |
| 5. P | Q9CHT4 | Probable DNA-directed RNA polymerase subunit delta | 8.38e-04 | 2.21e-20 | NA | NA |
| 5. P | Q8Y494 | Probable DNA-directed RNA polymerase subunit delta | 2.75e-04 | 3.50e-21 | NA | NA |
| 5. P | Q2W519 | DNA-directed RNA polymerase subunit omega | 3.11e-02 | 1.97e-03 | NA | NA |
| 5. P | Q9PPP2 | Probable DNA-directed RNA polymerase subunit delta | 8.68e-06 | 7.82e-27 | NA | NA |
| 5. P | Q8E291 | Probable DNA-directed RNA polymerase subunit delta | 1.49e-03 | 4.83e-23 | NA | NA |
| 5. P | P66719 | Probable DNA-directed RNA polymerase subunit delta | 1.10e-03 | 4.21e-28 | NA | NA |
| 5. P | P66718 | Probable DNA-directed RNA polymerase subunit delta | 4.16e-04 | 2.33e-21 | NA | NA |
| 5. P | A2RCL2 | Probable DNA-directed RNA polymerase subunit delta | 1.69e-03 | 4.21e-28 | NA | NA |
| 5. P | Q8DWG2 | Probable DNA-directed RNA polymerase subunit delta | 7.82e-04 | 4.02e-27 | NA | NA |
| 5. P | P44831 | Regulator of ribonuclease activity B | 4.70e-02 | 1.05e-02 | NA | NA |
| 5. P | Q9D6N5 | Dr1-associated corepressor | 6.92e-02 | 5.38e-03 | NA | NA |
| 5. P | C1CQ00 | Probable DNA-directed RNA polymerase subunit delta | 1.39e-03 | 4.49e-23 | NA | NA |
| 5. P | A8GW64 | DNA-directed RNA polymerase subunit omega | 7.79e-02 | 1.39e-03 | NA | NA |
| 5. P | P27464 | 60S acidic ribosomal protein P1 | 2.84e-02 | 1.58e-02 | NA | NA |
| 5. P | C3PP13 | DNA-directed RNA polymerase subunit omega | 1.51e-01 | 1.04e-02 | NA | NA |
| 5. P | B2IM97 | Probable DNA-directed RNA polymerase subunit delta | 1.61e-03 | 2.33e-21 | NA | NA |
| 5. P | Q8E7P9 | Probable DNA-directed RNA polymerase subunit delta | 1.45e-03 | 4.83e-23 | NA | NA |
| 5. P | C0M8K7 | Probable DNA-directed RNA polymerase subunit delta | 9.27e-04 | 1.67e-26 | NA | NA |
| 5. P | Q18336 | Histone H1.X | 1.06e-02 | 1.70e-03 | NA | NA |
| 5. P | Q5XA09 | Probable DNA-directed RNA polymerase subunit delta | 9.81e-04 | 1.28e-27 | NA | NA |
| 5. P | Q3K3S3 | Probable DNA-directed RNA polymerase subunit delta | 2.77e-03 | 4.83e-23 | NA | NA |
| 5. P | B2G5K4 | Probable DNA-directed RNA polymerase subunit delta | 6.05e-05 | 1.97e-19 | NA | NA |
| 5. P | A4VZE7 | Probable DNA-directed RNA polymerase subunit delta | 1.01e-03 | 3.50e-08 | NA | NA |
| 5. P | A8AVB9 | Probable DNA-directed RNA polymerase subunit delta | 6.76e-04 | 2.89e-24 | NA | NA |
| 5. P | B1IA31 | Probable DNA-directed RNA polymerase subunit delta | 1.16e-03 | 4.49e-23 | NA | NA |
| 5. P | B8ZLX1 | Probable DNA-directed RNA polymerase subunit delta | 1.54e-03 | 4.49e-23 | NA | NA |
| 5. P | Q5HE72 | Probable DNA-directed RNA polymerase subunit delta | 2.34e-05 | 4.45e-24 | NA | NA |
| 5. P | Q6G7I2 | Probable DNA-directed RNA polymerase subunit delta | 2.08e-05 | 4.45e-24 | NA | NA |
| 5. P | B9E8H2 | Probable DNA-directed RNA polymerase subunit delta | 1.27e-04 | 2.99e-26 | NA | NA |
| 5. P | P66714 | Probable DNA-directed RNA polymerase subunit delta | 6.88e-06 | 4.45e-24 | NA | NA |
| 5. P | Q04C52 | Probable DNA-directed RNA polymerase subunit delta | 4.52e-04 | 9.60e-18 | NA | NA |
| 5. P | B9DMC7 | Probable DNA-directed RNA polymerase subunit delta | 7.76e-06 | 5.43e-30 | NA | NA |
| 5. P | A5IUS3 | Probable DNA-directed RNA polymerase subunit delta | 2.80e-05 | 4.45e-24 | NA | NA |
| 5. P | A6QIX2 | Probable DNA-directed RNA polymerase subunit delta | 2.25e-05 | 4.45e-24 | NA | NA |
| 5. P | Q14919 | Dr1-associated corepressor | 7.19e-02 | 2.80e-02 | NA | NA |
| 5. P | B6JGF6 | DNA-directed RNA polymerase subunit omega | 5.46e-02 | 4.19e-02 | NA | NA |
| 5. P | O31949 | SPbeta prophage-derived uncharacterized protein YonI | 1.58e-03 | 3.83e-02 | NA | NA |
| 5. P | Q1D6D8 | Integration host factor subunit alpha | 1.64e-01 | 1.67e-02 | NA | NA |
| 5. P | B7IQZ2 | Probable DNA-directed RNA polymerase subunit delta | 1.04e-04 | 1.82e-23 | NA | NA |
| 5. P | B0BYC5 | DNA-directed RNA polymerase subunit omega | 9.24e-02 | 2.98e-02 | NA | NA |
| 5. P | A4VT63 | Probable DNA-directed RNA polymerase subunit delta | 3.45e-03 | 8.96e-28 | NA | NA |
| 5. P | A8YY93 | Probable DNA-directed RNA polymerase subunit delta | 4.87e-05 | 4.45e-24 | NA | NA |
| 5. P | A8GSU9 | DNA-directed RNA polymerase subunit omega | 2.38e-01 | 2.98e-02 | NA | NA |
| 5. P | O29842 | Uncharacterized protein AF_0405 | 2.93e-01 | 3.80e-02 | NA | NA |
| 5. P | B2GA55 | Probable DNA-directed RNA polymerase subunit delta | 5.89e-04 | 6.57e-20 | NA | NA |
| 5. P | Q927T3 | Probable DNA-directed RNA polymerase subunit delta | 2.66e-04 | 3.98e-20 | NA | NA |
| 5. P | A5EKM2 | DNA-directed RNA polymerase subunit omega | 5.78e-02 | 9.74e-03 | NA | NA |
| 5. P | Q1RHU0 | DNA-directed RNA polymerase subunit omega | 9.44e-02 | 1.39e-03 | NA | NA |
| 5. P | Q2FF00 | Probable DNA-directed RNA polymerase subunit delta | 3.19e-05 | 4.45e-24 | NA | NA |
| 5. P | Q8CRM5 | Probable DNA-directed RNA polymerase subunit delta | 1.38e-04 | 5.44e-20 | NA | NA |
| 5. P | Q5HM94 | Probable DNA-directed RNA polymerase subunit delta | 5.05e-05 | 5.44e-20 | NA | NA |
| 5. P | P12464 | DNA-directed RNA polymerase subunit delta | 5.63e-05 | 3.55e-24 | NA | NA |
| 5. P | Q9K4Q3 | Integration host factor subunit alpha | 1.57e-01 | 1.67e-02 | NA | NA |
| 5. P | A5VI25 | Probable DNA-directed RNA polymerase subunit delta | 2.96e-05 | 1.97e-19 | NA | NA |
| 5. P | Q030Z9 | Probable DNA-directed RNA polymerase subunit delta | 1.75e-03 | 9.12e-20 | NA | NA |
| 5. P | Q23646 | Probable RNA-binding protein EIF1AD | 1.16e-01 | 4.35e-02 | NA | NA |
| 5. P | C1CIY6 | Probable DNA-directed RNA polymerase subunit delta | 9.33e-04 | 4.49e-23 | NA | NA |
| 5. P | A0ALP6 | Probable DNA-directed RNA polymerase subunit delta | 2.17e-04 | 4.70e-24 | NA | NA |
| 5. P | P47363 | Uncharacterized protein MG117 | 1.55e-01 | 2.68e-02 | NA | NA |
| 5. P | Q03YU3 | Probable DNA-directed RNA polymerase subunit delta | 6.95e-05 | 7.02e-18 | NA | NA |
| 5. P | Q2YDP3 | Dr1-associated corepressor | 4.75e-02 | 2.00e-02 | NA | NA |
| 5. P | C1CCN9 | Probable DNA-directed RNA polymerase subunit delta | 2.76e-04 | 4.49e-23 | NA | NA |
| 5. P | A8FIE6 | Probable DNA-directed RNA polymerase subunit delta | 9.01e-05 | 3.40e-15 | NA | NA |
| 5. P | P0DF34 | Probable DNA-directed RNA polymerase subunit delta | 1.89e-03 | 4.21e-28 | NA | NA |
| 5. P | P0DF35 | Probable DNA-directed RNA polymerase subunit delta | 1.71e-03 | 4.21e-28 | NA | NA |
| 5. P | Q04LZ9 | Probable DNA-directed RNA polymerase subunit delta | 2.64e-04 | 4.49e-23 | NA | NA |
| 5. P | C4K1J3 | DNA-directed RNA polymerase subunit omega | 1.20e-01 | 1.10e-02 | NA | NA |
| 5. P | P54671 | Histone H1 | 2.19e-03 | 4.16e-03 | NA | NA |
| 5. P | Q03MQ8 | Probable DNA-directed RNA polymerase subunit delta | 8.53e-04 | 4.56e-25 | NA | NA |
| 5. P | Q74LG3 | Probable DNA-directed RNA polymerase subunit delta | 6.36e-04 | 1.47e-18 | NA | NA |
| 5. P | Q03DX9 | Probable DNA-directed RNA polymerase subunit delta | 2.47e-05 | 6.60e-21 | NA | NA |
| 5. P | A8GP45 | DNA-directed RNA polymerase subunit omega | 1.21e-01 | 5.59e-04 | NA | NA |
| 5. P | P0C659 | Probable RNA-binding protein EIF1AD | 1.42e-01 | 2.75e-03 | NA | NA |
| 5. P | Q4UKX8 | DNA-directed RNA polymerase subunit omega | 9.18e-02 | 3.60e-03 | NA | NA |
| 5. P | A0JPP1 | Dr1-associated corepressor | 5.45e-02 | 1.93e-02 | NA | NA |
| 5. P | P66716 | Probable DNA-directed RNA polymerase subunit delta | 8.97e-05 | 4.45e-24 | NA | NA |
| 5. P | Q2YUM5 | Probable DNA-directed RNA polymerase subunit delta | 3.97e-05 | 2.14e-24 | NA | NA |