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NC_055055.1__YP_010084014.1__KMD55_gp11__00011
Bact-VirNC_055055.1__YP_010084014.1__KMD55_gp11__00011
Identity
- Accession:
- NC_055055 ↗
- Kingdom:
- phage
Quality
73.6
mean pLDDT
Taxonomy
Loebvirae›
Hofneiviricota›
Faserviricetes›
Tubulavirales›
Inoviridae›
Xylivirus›
Xanthomonas_phage_Xf409
TaxID: 1979540
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
medium
residues 125-284
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF23343.3 best | REP_ORF2-G2P | 110.6 | 5.30e-32 | 66.9% | 97.0% |
CATH (26)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 6h8oA00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.74 | 43.0 | 5.47e-01 | 80.6% | 96.8% |
| 3luyA03 | 3.30.70.260 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT domain | 0.69 | 39.0 | 5.15e-01 | 81.2% | 100.0% |
| 2hw0A00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.68 | 41.0 | 4.75e-01 | 80.0% | 83.5% |
| 1l2mA00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.67 | 44.0 | 5.06e-01 | 80.6% | 89.8% |
| 4ushA00 | 3.30.70.120 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.67 | 38.0 | 4.62e-01 | 81.2% | 85.4% |
| 1f08B00 | 3.40.1310.10 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.66 | 43.0 | 4.54e-01 | 80.6% | 71.7% |
| 1r9wA00 | 3.40.1310.10 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.64 | 42.0 | 4.48e-01 | 80.6% | 75.4% |
| 1m55A00 | 3.40.1310.20 | Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › | 0.63 | 52.0 | 4.89e-01 | 86.9% | 88.6% |
| 1r89A03 | 3.30.70.590 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain | 0.62 | 49.0 | 5.30e-01 | 93.8% | 98.5% |
| 1pbuA00 | 3.30.70.1010 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Translation elongation factor EF1B, gamma chain, conserved domain | 0.61 | 51.0 | 5.10e-01 | 91.9% | 87.0% |
| 3hvwA00 | 3.30.70.270 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain | 0.60 | 45.0 | 4.57e-01 | 77.5% | 83.6% |
| 4i6yA02 | 3.30.70.420 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding domain | 0.60 | 41.0 | 4.75e-01 | 84.4% | 100.0% |
| 3mcsA00 | 3.30.70.100 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.59 | 47.0 | 4.25e-01 | 83.1% | 97.2% |
| 2bvfA03 | 3.40.462.20 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › | 0.59 | 47.0 | 4.30e-01 | 83.1% | 76.7% |
| 2ipiA02 | 3.40.462.20 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › | 0.58 | 45.0 | 3.93e-01 | 81.9% | 63.7% |
| 1unnC00 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.58 | 31.0 | 3.68e-01 | 96.2% | 73.9% |
| 6julA02 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.57 | 32.0 | 3.96e-01 | 98.1% | 88.5% |
| 1ywhC03 | 2.10.60.10 | Mainly Beta › Ribbon › CD59 › CD59 | 0.57 | 28.0 | 3.68e-01 | 81.2% | 84.1% |
| 3popA02 | 3.40.462.20 | Alpha Beta › 3-Layer(aba) Sandwich › Vanillyl-alcohol Oxidase; Chain A, domain 3 › | 0.57 | 45.0 | 3.94e-01 | 85.0% | 64.3% |
| 4ndhB00 | 3.30.428.10 | Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like | 0.56 | 32.0 | 3.16e-01 | 86.9% | 49.4% |
| 4u7cB04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.56 | 32.0 | 3.79e-01 | 97.5% | 81.7% |
| 1q2lA02 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.56 | 39.0 | 3.50e-01 | 71.9% | 82.3% |
| 1f3vA00 | 3.30.70.680 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › TRADD, N-terminal domain | 0.55 | 44.0 | 4.46e-01 | 82.5% | 92.4% |
| 3mfiA04 | 3.30.1490.100 | Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain | 0.55 | 34.0 | 3.83e-01 | 97.5% | 81.5% |
| 2fgeA02 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.51 | 39.0 | 3.45e-01 | 81.2% | 67.8% |
| 4fprB00 | 3.30.70.2910 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › | 0.50 | 38.0 | 4.11e-01 | 83.7% | 98.4% |
ECOD (67)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4007464 | 304.55.1.19 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Inovirus_Gp2 | 0.79 | 68.0 | 6.41e-01 | 90.6% | 100.0% |
| 3947798 | 304.8.1.70 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Phage_GPA | 0.79 | 74.0 | 6.05e-01 | 100.0% | 86.8% |
| 4511949 | 304.48.1.74 ↗ | a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Phage_GPA | 0.78 | 73.0 | 6.29e-01 | 100.0% | 89.6% |
| 4173640 | 304.55.1.27 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Phage_GPA | 0.77 | 73.0 | 5.98e-01 | 100.0% | 94.5% |
| 4170426 | 304.8.1.70 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Phage_GPA | 0.77 | 73.0 | 5.91e-01 | 100.0% | 91.2% |
| 4959045 | 304.8.1.81 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P | 0.76 | 67.0 | 6.93e-01 | 99.4% | 99.3% |
| 4319983 | 304.55.1.25 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Rep_1 | 0.75 | 70.0 | 6.07e-01 | 100.0% | 86.8% |
| 4081561 | 304.8.1.50 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Rep_1 | 0.74 | 69.0 | 6.27e-01 | 100.0% | 94.3% |
| 4315665 | 304.8.1.91 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › DUF1424 | 0.73 | 68.0 | 6.16e-01 | 99.4% | 95.7% |
| 4965189 | 304.8.1.126 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › PF26475 | 0.73 | 69.0 | 6.53e-01 | 100.0% | 93.0% |
| 3375241 | 304.8.1.23 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N | 0.73 | 68.0 | 5.42e-01 | 100.0% | 84.9% |
| 4304749 | 304.8.1.81 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › REP_ORF2-G2P | 0.73 | 68.0 | 5.70e-01 | 100.0% | 63.5% |
| 3372454 | 304.55.1.20 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N, REP_ORF2-G2P | 0.73 | 67.0 | 5.89e-01 | 97.5% | 99.6% |
| 3381094 | 304.8.1.64 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N, REP_ORF2-G2P | 0.73 | 68.0 | 5.48e-01 | 100.0% | 82.6% |
| None | — | 0.72 | 68.0 | 5.75e-01 | 100.0% | 100.0% | |
| 3682672 | 304.8.1.64 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N, REP_ORF2-G2P | 0.72 | 67.0 | 5.40e-01 | 100.0% | 74.2% |
| 3680906 | 304.8.1.23 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N | 0.72 | 64.0 | 5.29e-01 | 94.4% | 92.7% |
| 3678501 | 304.55.1.20 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N, REP_ORF2-G2P | 0.72 | 68.0 | 5.45e-01 | 100.0% | 73.3% |
| 5035799 | 304.57.1.1 ↗ | a+b two layers › Alpha-beta plaits › Rpp14/Pop5-like › Rpp14/Pop5-like › RNase_P_Rpp14 | 0.72 | 50.0 | 5.59e-01 | 70.6% | 95.2% |
| 3344616 | 304.8.1.64 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N, REP_ORF2-G2P | 0.71 | 66.0 | 6.05e-01 | 98.8% | 99.5% |
| 3682007 | 304.8.1.64 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N, REP_ORF2-G2P | 0.71 | 67.0 | 6.19e-01 | 100.0% | 94.0% |
| 3377701 | 304.8.1.23 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N | 0.71 | 66.0 | 5.93e-01 | 97.5% | 100.0% |
| 3986356 | 304.55.1.14 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Y2_Tnp | 0.71 | 67.0 | 5.45e-01 | 100.0% | 89.6% |
| 3373540 | 304.55.1.15 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N | 0.71 | 67.0 | 5.66e-01 | 100.0% | 96.0% |
| None | — | 0.71 | 66.0 | 5.68e-01 | 100.0% | 95.9% | |
| 3678732 | 304.55.1.20 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N, REP_ORF2-G2P | 0.71 | 64.0 | 5.71e-01 | 96.2% | 100.0% |
| 3926520 | 304.8.1.23 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N | 0.71 | 65.0 | 6.10e-01 | 97.5% | 100.0% |
| 3683205 | 304.55.1.20 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N, REP_ORF2-G2P | 0.71 | 66.0 | 6.40e-01 | 98.8% | 100.0% |
| 3680071 | 304.28.1.25 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Helitron_like_N, REP_ORF2-G2P | 0.71 | 65.0 | 5.52e-01 | 98.1% | 92.0% |
| 3369213 | 304.28.1.25 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Helitron_like_N, REP_ORF2-G2P | 0.70 | 65.0 | 6.04e-01 | 98.8% | 100.0% |
| 3301841 | 304.55.1.20 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N, REP_ORF2-G2P | 0.70 | 65.0 | 5.72e-01 | 98.8% | 94.2% |
| None | — | 0.70 | 66.0 | 5.43e-01 | 100.0% | 78.7% | |
| 3656761 | 304.55.1.15 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N | 0.68 | 63.0 | 5.34e-01 | 98.8% | 85.4% |
| 3813645 | 304.9.1.9 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_2 | 0.66 | 52.0 | 4.74e-01 | 81.9% | 65.2% |
| 3370071 | 304.9.1.9 ↗ | a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › RRM_2 | 0.66 | 51.0 | 5.03e-01 | 81.2% | 79.4% |
| 4105022 | 304.5.1.7 ↗ | a+b two layers › Alpha-beta plaits › GlnB-like › GlnB-like › DUF2179 | 0.65 | 35.0 | 4.50e-01 | 80.6% | 91.1% |
| 3735140 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.65 | 49.0 | 4.08e-01 | 77.5% | 73.7% |
| 2834623 | 304.55.1.7 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Rep_N | 0.65 | 50.0 | 4.90e-01 | 80.6% | 92.0% |
| 3596967 | 304.46.1.0 ↗ | a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain | 0.64 | 50.0 | 5.11e-01 | 91.9% | 83.5% |
| 4030594 | 304.46.1.1 ↗ | a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G | 0.64 | 52.0 | 5.23e-01 | 90.6% | 85.0% |
| 3735269 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.63 | 48.0 | 4.09e-01 | 79.4% | 74.6% |
| 3497180 | 304.46.1.1 ↗ | a+b two layers › Alpha-beta plaits › eEF1-gamma domain › eEF1-gamma domain › EF1G | 0.63 | 50.0 | 5.13e-01 | 90.0% | 85.8% |
| 4016693 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.62 | 47.0 | 3.79e-01 | 78.1% | 63.3% |
| 3680601 | 304.8.1.23 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N | 0.62 | 58.0 | 5.24e-01 | 100.0% | 83.2% |
| 3706456 | 304.55.2.8 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Transposase IS200-like › FAZ1_cons | 0.62 | 34.0 | 4.52e-01 | 74.4% | 96.7% |
| 3185512 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.62 | 48.0 | 4.16e-01 | 82.5% | 60.5% |
| 3665778 | 878.1.1.2 ↗ | a+b two layers › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Hypothetical protein MTH677 › Helitron_like_N | 0.62 | 52.0 | 5.09e-01 | 98.8% | 81.1% |
| 3372782 | 304.8.1.64 ↗ | a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Helitron_like_N, REP_ORF2-G2P | 0.61 | 55.0 | 5.03e-01 | 95.0% | 87.8% |
| 3653135 | 101.1.2.594 ↗ | alpha arrays › HTH › HTH › winged helix domain › Helitron_like_N | 0.61 | 52.0 | 5.45e-01 | 100.0% | 98.6% |
| 3342333 | 304.28.1.10 ↗ | a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Helitron_like_N | 0.61 | 54.0 | 5.23e-01 | 98.1% | 85.4% |
| 4942796 | 302.1.1.1 ↗ | a+b two layers › Reverse ferredoxin › Lesion bypass DNA polymerase (Y-family), little finger domain › Lesion bypass DNA polymerase (Y-family), little finger domain › IMS_C | 0.60 | 33.0 | 3.92e-01 | 98.1% | 77.3% |
| 4043242 | 304.6.1.5 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › Cytokin-bind | 0.60 | 44.0 | 3.90e-01 | 77.5% | 75.0% |
| 4035986 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.59 | 46.0 | 4.02e-01 | 81.2% | 62.5% |
| 4309132 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.58 | 45.0 | 3.95e-01 | 80.6% | 62.5% |
| 4183108 | 304.47.1.1 ↗ | a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA | 0.58 | 43.0 | 4.18e-01 | 76.9% | 85.6% |
| 4015784 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.58 | 45.0 | 3.88e-01 | 82.5% | 60.0% |
| 3277124 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.58 | 46.0 | 3.95e-01 | 85.0% | 63.4% |
| 4263302 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.58 | 47.0 | 4.00e-01 | 85.6% | 60.0% |
| 4018691 | 304.6.1.3 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain › BBE | 0.57 | 46.0 | 3.92e-01 | 85.0% | 61.5% |
| 4011130 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.57 | 46.0 | 3.93e-01 | 85.6% | 61.6% |
| 4622719 | 304.6.1.0 ↗ | a+b two layers › Alpha-beta plaits › FAD-linked oxidases, C-terminal domain › FAD-linked oxidases, C-terminal domain | 0.57 | 45.0 | 3.93e-01 | 83.1% | 71.0% |
| 3651182 | 304.55.1.15 ↗ | a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › Helitron_like_N | 0.56 | 52.0 | 4.87e-01 | 98.8% | 87.3% |
| 3280334 | 304.11.1.0 ↗ | a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase | 0.56 | 42.0 | 4.04e-01 | 80.0% | 79.5% |
| 3528002 | 11.1.1.789 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › KIAA1549 | 0.54 | 37.0 | 4.27e-01 | 71.2% | 100.0% |
| 3601534 | 309.1.1.0 ↗ | a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase | 0.54 | 40.0 | 3.68e-01 | 76.2% | 92.7% |
| 4443054 | 3115.1.1.9 ↗ | a+b two layers › GP2-like › RplX-like › RplX-like › YjeJ | 0.50 | 31.0 | 3.56e-01 | 79.4% | 81.7% |
| 3508713 | 382.1.1.25 ↗ | few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like › YjeJ | 0.50 | 31.0 | 3.54e-01 | 79.4% | 81.7% |
D2
medium
residues 295-345
Domain cluster:
rep: U38235.1__AAC54631.1__X__00002__D115-161