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.
AVX54798.1
JCVISYN3A_0437
Putative 3'-5' exoribonuclease.
M. mycoides homolog: Q6MTB1.
TIGRfam Classification: 2=Generic.
Category: Essential.
Statistics
Total GO Annotation: 32
Unique PROST Go: 12
Unique BLAST Go: 1
Unique Foldseek Go: 15
Total Homologs: 107
Unique PROST Homologs: 57
Unique BLAST Homologs: 1
Unique Foldseek Homologs: 19
Literature
Danchin and Fang [1]: 3'-5' exonuclease, small oligoribonucleotide nuclease|moonlighting, may replace RNase R in Mollicutes
Yang and Tsui [2]: CMP binding factor cbF
Antczak et al. [3]: yhaM; 3'-5' exoribonuclease
Zhang et al. [4]: GO:0042578|phosphoric ester hydrolase activity
Bianchi et al. [5]: yham-like 5'-3' exoribonuclease
Structures and Sequence Alignment
The best structural homolog that predicted by 1. PBF was
A9VI37
(3'-5' exoribonuclease YhaM) with a FATCAT P-Value: 0 and RMSD of 2.11 angstrom. The sequence alignment identity is 37.2%.
Structural alignment shown in left. Query protein AVX54798.1 colored as red in alignment, homolog A9VI37 colored as blue.
Query protein AVX54798.1 is also shown in right top, homolog A9VI37 showed in right bottom. They are colored based on secondary structures.
AVX54798.1 MKKVKDINIE-DHLIDTILRIERVIVST-G--SSGNNYLILHLADSTGRIEARKWVVS-EKDKQLLKPNTIV-LLKDTIVHEYRNILQLKVEDYQVIDEK 94 A9VI37 MKK-KIVEYEVGEQVDVFLLIK---TATKGLASNGKPFLTVILQDPSGDIEAKLWDVSPEVEKQYV-AETIVKVAGD-ILN-YKGRIQLRVKQIRVANEN 93 AVX54798.1 DLLKYNLNKTDL--YI-TAPL---DI--K-TSYL-ELISLLNSINNQTYKTITLNLIEKYKKEFLTFPAAMSIHHNVTSGLFWHSYTLVKNVLNL-KE-N 182 A9VI37 EV-------TDISDFVEKAPIKKEDMVEKITQYIFEM-------RNPNIQRLTRHLLNKHQNEFLEYPAAMKNHHEFVSGLAYH---VV-SMLDLAKAIS 175 AVX54798.1 YFYANIDWDLLICGAILHDIGKVIEISDVNG---SDYSLEGKLLGHISI-GNAEINKLADKLNLYKDQNNKINKEITLLQHMILASHGKKEFGSPIEPVL 278 A9VI37 ALYPSLDKDLLYAGVILHDLGKVFELS---GPISTTYTLEGNLLGHISIMVN-EIGKAAEELQI--DA-----EEVLILQHIVLSHHGKAEWGSPKPPLV 264 AVX54798.1 IEAVILSALDDLDAKVYKIND-ELSKIEIDNWTQKITSIDNKMFYK---HKK 326 A9VI37 KEAEILHYIDNLDAKM-NMMDRALGRTKPGEYTERVFALDNRSFYKPTFHN- 314
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:0031125 | rRNA 3'-end processing |
| 1. PBF | GO:0000175 | 3'-5'-exoribonuclease activity |
| 1. PBF | GO:0003676 | nucleic acid binding |
| 3. BF | GO:0003677 | DNA binding |
| 5. P | GO:0052927 | CTP:tRNA cytidylyltransferase activity |
| 5. P | GO:0001680 | tRNA 3'-terminal CCA addition |
| 5. P | GO:0052928 | CTP:3'-cytidine-tRNA cytidylyltransferase activity |
| 5. P | GO:0052929 | ATP:3'-cytidine-cytidine-tRNA adenylyltransferase activity |
| 5. P | GO:0016021 | integral component of membrane |
| 5. P | GO:0016437 | tRNA cytidylyltransferase activity |
| 5. P | GO:0004112 | cyclic-nucleotide phosphodiesterase activity |
| 5. P | GO:0000049 | tRNA binding |
| 5. P | GO:0005524 | ATP binding |
| 5. P | GO:0016791 | phosphatase activity |
| 5. P | GO:0042245 | RNA repair |
| 5. P | GO:0000287 | magnesium ion binding |
| 6. F | GO:0006261 | DNA-dependent DNA replication |
| 6. F | GO:0006260 | DNA replication |
| 6. F | GO:0003697 | single-stranded DNA binding |
| 6. F | GO:0043047 | single-stranded telomeric DNA binding |
| 6. F | GO:0005697 | telomerase holoenzyme complex |
| 6. F | GO:0000724 | double-strand break repair via homologous recombination |
| 6. F | GO:0006281 | DNA repair |
| 6. F | GO:0003678 | DNA helicase activity |
| 6. F | GO:0006974 | cellular response to DNA damage stimulus |
| 6. F | GO:0008408 | 3'-5' exonuclease activity |
| 6. F | GO:0003887 | DNA-directed DNA polymerase activity |
| 6. F | GO:0007004 | telomere maintenance via telomerase |
| 6. F | GO:0010212 | response to ionizing radiation |
| 6. F | GO:0044818 | mitotic G2/M transition checkpoint |
| 6. F | GO:0070876 | SOSS complex |
| 7. B | GO:0044682 | archaeal-specific GTP cyclohydrolase activity |
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 |
|---|---|---|---|---|---|---|
| 1. PBF | Q5WHU5 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.92e-69 | 1.34e-53 | 0.8249 |
| 1. PBF | Q6HME9 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.95e-66 | 1.42e-52 | 0.9036 |
| 1. PBF | Q929F3 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 8.39e-64 | 1.45e-47 | 0.8957 |
| 1. PBF | C1EKC8 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 4.75e-67 | 8.48e-53 | 0.9069 |
| 1. PBF | A0AKX3 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.83e-66 | 2.72e-49 | 0.8943 |
| 1. PBF | B7IK95 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 3.56e-66 | 1.41e-53 | 0.9078 |
| 1. PBF | B7JCU0 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.75e-66 | 1.36e-52 | 0.8986 |
| 1. PBF | Q65LT6 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 4.80e-69 | 3.37e-56 | 0.9157 |
| 1. PBF | A0RAN0 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.95e-66 | 1.42e-52 | 0.9067 |
| 1. PBF | Q81H06 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.95e-66 | 1.42e-52 | 0.905 |
| 1. PBF | B7HFZ0 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.95e-66 | 1.42e-52 | 0.9003 |
| 1. PBF | Q8Y556 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.37e-64 | 1.56e-49 | 0.8932 |
| 1. PBF | C1KXH5 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.22e-65 | 1.27e-49 | 0.8975 |
| 1. PBF | A7GLX6 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.11e-67 | 8.58e-51 | 0.9012 |
| 1. PBF | Q8CUG1 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 5.63e-66 | 1.05e-52 | 0.8786 |
| 1. PBF | Q9KDN6 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 4.48e-66 | 3.93e-51 | 0.8426 |
| 1. PBF | Q5L299 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.45e-64 | 1.01e-58 | 0.8846 |
| 1. PBF | A7Z305 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.32e-70 | 2.42e-52 | 0.9092 |
| 1. PBF | A8FBK3 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.13e-66 | 4.90e-52 | 0.9091 |
| 1. PBF | C5D6L2 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 7.79e-70 | 1.67e-61 | 0.8749 |
| 1. PBF | A9VI37 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.42e-66 | 4.09e-52 | 0.9036 |
| 1. PBF | B7HYS8 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 7.75e-67 | 1.59e-52 | 0.9047 |
| 1. PBF | Q71XE5 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.22e-65 | 1.27e-49 | 0.8954 |
| 1. PBF | B9ISF7 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.55e-66 | 1.03e-52 | 0.9029 |
| 1. PBF | Q73CF4 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.95e-66 | 1.42e-52 | 0.8941 |
| 1. PBF | O07521 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 2.18e-67 | 7.29e-56 | 0.9195 |
| 1. PBF | C3LCZ8 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.55e-66 | 1.03e-52 | 0.9033 |
| 1. PBF | Q63EZ0 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.95e-66 | 1.42e-52 | 0.9026 |
| 1. PBF | Q81U72 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.55e-66 | 1.03e-52 | 0.8997 |
| 1. PBF | C3P2S0 | 3'-5' exoribonuclease YhaM | 0.00e+00 | 1.55e-66 | 1.03e-52 | 0.8995 |
| 5. P | B2HV23 | Multifunctional CCA protein | 8.77e-03 | 2.34e-02 | NA | NA |
| 5. P | A5F5I2 | Multifunctional CCA protein | 9.93e-03 | 1.91e-02 | NA | NA |
| 5. P | Q5ZRX9 | Multifunctional CCA protein | 1.04e-02 | 2.09e-02 | NA | NA |
| 5. P | A6WKL1 | Multifunctional CCA protein | 6.67e-03 | 2.15e-02 | NA | NA |
| 5. P | Q9L7A3 | Multifunctional CCA protein | 2.32e-02 | 3.49e-03 | NA | NA |
| 5. P | Q0ACP8 | Multifunctional CCA protein | 8.82e-03 | 1.32e-02 | NA | NA |
| 5. P | Q9KPC6 | Multifunctional CCA protein | 9.59e-03 | 2.45e-02 | NA | NA |
| 5. P | Q5F8K9 | Multifunctional CCA protein | 9.72e-03 | 3.45e-02 | NA | NA |
| 5. P | A8H161 | Multifunctional CCA protein | 1.29e-02 | 4.72e-02 | NA | NA |
| 5. P | P47376 | Ribonuclease Y | 2.84e-02 | 1.02e-02 | NA | NA |
| 5. P | Q0HG49 | Multifunctional CCA protein | 1.02e-02 | 1.01e-02 | NA | NA |
| 5. P | B6EM10 | Multifunctional CCA protein | 1.00e-02 | 2.47e-02 | NA | NA |
| 5. P | Q8Y395 | Multifunctional CCA protein | 1.63e-02 | 3.67e-02 | NA | NA |
| 5. P | Q4UYN8 | Multifunctional CCA protein | 9.83e-03 | 1.50e-02 | NA | NA |
| 5. P | A3N0S5 | Multifunctional CCA protein | 1.72e-02 | 7.97e-03 | NA | NA |
| 5. P | A5UCK0 | Multifunctional CCA protein | 6.12e-03 | 1.40e-02 | NA | NA |
| 5. P | Q8PPG9 | Multifunctional CCA protein | 1.18e-02 | 1.23e-02 | NA | NA |
| 5. P | P45269 | Multifunctional CCA protein | 6.67e-03 | 2.43e-02 | NA | NA |
| 5. P | Q3BXK9 | Multifunctional CCA protein | 1.00e-02 | 1.04e-02 | NA | NA |
| 5. P | B3GXR2 | Multifunctional CCA protein | 1.69e-02 | 7.97e-03 | NA | NA |
| 5. P | Q87DS9 | Multifunctional CCA protein | 1.19e-02 | 2.85e-02 | NA | NA |
| 5. P | Q5X1E5 | Multifunctional CCA protein | 9.89e-03 | 1.70e-02 | NA | NA |
| 5. P | A9L5J0 | Multifunctional CCA protein | 6.75e-03 | 1.69e-02 | NA | NA |
| 5. P | B0VUU0 | Multifunctional CCA protein | 1.01e-02 | 1.02e-02 | NA | NA |
| 5. P | A9LZC1 | Multifunctional CCA protein | 9.83e-03 | 3.51e-02 | NA | NA |
| 5. P | B7GZN3 | Multifunctional CCA protein | 1.03e-02 | 2.34e-02 | NA | NA |
| 5. P | Q8P5D4 | Multifunctional CCA protein | 1.18e-02 | 1.50e-02 | NA | NA |
| 5. P | B8EBU8 | Multifunctional CCA protein | 6.78e-03 | 1.18e-02 | NA | NA |
| 5. P | B4SIY9 | Multifunctional CCA protein | 9.16e-03 | 1.22e-02 | NA | NA |
| 5. P | A0KZT1 | Multifunctional CCA protein | 1.14e-02 | 1.54e-02 | NA | NA |
| 5. P | C3LQY9 | Multifunctional CCA protein | 1.03e-02 | 2.45e-02 | NA | NA |
| 5. P | A3D1R1 | Multifunctional CCA protein | 8.55e-03 | 1.48e-02 | NA | NA |
| 5. P | Q12KC4 | Multifunctional CCA protein | 1.00e-02 | 3.25e-02 | NA | NA |
| 5. P | Q5WT58 | Multifunctional CCA protein | 9.50e-03 | 2.30e-02 | NA | NA |
| 5. P | Q9CP21 | Multifunctional CCA protein | 8.90e-03 | 6.16e-03 | NA | NA |
| 5. P | A3M767 | Multifunctional CCA protein | 1.01e-02 | 2.61e-02 | NA | NA |
| 5. P | P75506 | Ribonuclease Y | 2.43e-02 | 1.42e-02 | NA | NA |
| 5. P | Q2NZ41 | Multifunctional CCA protein | 1.24e-02 | 1.07e-02 | NA | NA |
| 5. P | A1KU50 | Multifunctional CCA protein | 9.23e-03 | 4.37e-02 | NA | NA |
| 5. P | B0RNU6 | Multifunctional CCA protein | 1.15e-02 | 1.50e-02 | NA | NA |
| 5. P | Q07YU1 | Multifunctional CCA protein | 1.47e-02 | 4.11e-02 | NA | NA |
| 5. P | Q0HSE2 | Multifunctional CCA protein | 1.08e-02 | 1.56e-02 | NA | NA |
| 5. P | Q9PDL7 | Multifunctional CCA protein | 1.16e-02 | 2.87e-02 | NA | NA |
| 5. P | A4G969 | Multifunctional CCA protein | 1.07e-02 | 1.88e-02 | NA | NA |
| 5. P | B0VBE4 | Multifunctional CCA protein | 9.93e-03 | 2.34e-02 | NA | NA |
| 5. P | C1DAG2 | Multifunctional CCA protein | 7.72e-03 | 2.34e-02 | NA | NA |
| 5. P | A1SRC9 | Multifunctional CCA protein | 1.14e-02 | 1.39e-02 | NA | NA |
| 5. P | B4RLV5 | Multifunctional CCA protein | 1.08e-02 | 4.04e-02 | NA | NA |
| 5. P | B8CJF9 | Multifunctional CCA protein | 1.11e-02 | 3.51e-02 | NA | NA |
| 5. P | A5UJ23 | Multifunctional CCA protein | 6.66e-03 | 1.75e-02 | NA | NA |
| 5. P | B7I3L8 | Multifunctional CCA protein | 9.25e-03 | 2.34e-02 | NA | NA |
| 5. P | Q87SK9 | Multifunctional CCA protein | 1.13e-02 | 2.82e-02 | NA | NA |
| 5. P | B0U6J4 | Multifunctional CCA protein | 1.15e-02 | 2.24e-02 | NA | NA |
| 5. P | B2I9I0 | Multifunctional CCA protein | 1.17e-02 | 2.85e-02 | NA | NA |
| 5. P | A7MWN9 | Multifunctional CCA protein | 1.07e-02 | 2.80e-02 | NA | NA |
| 5. P | B2FUP5 | Multifunctional CCA protein | 9.19e-03 | 1.80e-02 | NA | NA |
| 5. P | C5BHG5 | Multifunctional CCA protein | 1.15e-02 | 1.58e-02 | NA | NA |
| 6. F | A6QLK2 | SOSS complex subunit B1 | 7.83e-04 | NA | NA | 0.5861 |
| 6. F | P14567 | DNA polymerase III subunit alpha | 7.04e-01 | NA | NA | 0.5549 |
| 6. F | Q9PQB4 | DNA polymerase III PolC-type | 3.19e-01 | NA | NA | 0.3057 |
| 6. F | Q8FL05 | DNA polymerase III subunit alpha | 7.09e-01 | NA | NA | 0.5541 |
| 6. F | Q6DE02 | SOSS complex subunit B1-A | 7.51e-04 | NA | NA | 0.5832 |
| 6. F | Q8XJR3 | DNA polymerase III PolC-type | 1.94e-01 | NA | NA | 0.799 |
| 6. F | D2CVN6 | Telomeric repeat-binding subunit 1 | 1.20e-01 | NA | NA | 0.6683 |
| 6. F | P47277 | DNA polymerase III PolC-type | 3.00e-01 | NA | NA | 0.2599 |
| 6. F | P43809 | ATP-dependent DNA helicase RecG | 1.08e-02 | NA | NA | 0.2872 |
| 6. F | Q04MH6 | DNA polymerase III PolC-type | 3.28e-01 | NA | NA | 0.8037 |
| 6. F | Q9CMB4 | ATP-dependent DNA helicase RecG | 9.91e-03 | NA | NA | 0.3966 |
| 6. F | Q66K94 | SOSS complex subunit B1 | 7.05e-04 | NA | NA | 0.5698 |
| 6. F | O67125 | DNA polymerase III subunit alpha | 2.60e-01 | NA | NA | 0.5419 |
| 6. F | Q6NRF9 | SOSS complex subunit B1-B | 4.70e-04 | NA | NA | 0.5703 |
| 6. F | Q03FS8 | DNA polymerase III PolC-type | 2.62e-01 | NA | NA | 0.2879 |
| 6. F | Q8X8X5 | DNA polymerase III subunit alpha | 3.13e-01 | NA | NA | 0.5698 |
| 6. F | Q9X289 | Exodeoxyribonuclease 7 large subunit | 1.71e-03 | NA | NA | 0.2356 |
| 6. F | Q9XDH6 | DNA polymerase III subunit alpha | 6.99e-01 | NA | NA | 0.5609 |
| 6. F | A5D7P8 | SOSS complex subunit B2 | 1.00e-04 | NA | NA | 0.7983 |
| 7. B | Q58247 | Dihydroneopterin 2',3'-cyclic phosphate phosphodiesterase | 3.01e-11 | NA | 1.99e-04 | NA |