sublogo

Seed proteins  | Seed genomic context  | Seed protein 3D structures  |  Structural homologs  |  Family infomation  | Homology to other families  | Family members, sources, and their hosts  

Seed protein information help

APIS family ID APIS083
Inhibited defense system
CLAN ID CLAN001
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
CP067347_00056
gene_page: 322 38316 6.4978 0
Phage property
Phage Assembly id
Clostridioides phage ES-S-0107-01 CP067347
PMID/References
PDB structures ;
Pfam domains
Phrog phrog_20113
Host taxa d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Peptostreptococcaceae;g__Clostridioides;
Gene Location Start: 35664;  End: 36632;  Strand: -
Description
Note This family does not have seed protein, but we infer its function is defending Gabija because it belongs to the same clan as family APIS005 which has seed protein.

Seed genomic context      Download table help

Genome accession Start End Strand Protein ID Length Molecular weight Charge Isoelectric point Function Phrog PFAM
CP067347 34332 34475 - CP067347_00051 47 5787.53 5787.53 4.1079 hypothetical protein phrog_12737
CP067347 34502 34942 - CP067347_00052 146 17017.54 17017.54 5.2592 hypothetical protein
CP067347 34951 35064 - CP067347_00053 37 4623.26 4623.26 4.8180 hypothetical protein
CP067347 35096 35368 - CP067347_00054 90 10742.49 10742.49 7.9955 hypothetical protein phrog_1810 ; phrog_4502 ; phrog_419
CP067347 35459 35629 - CP067347_00055 56 6464.32 6464.32 4.7740 hypothetical protein
CP067347 35664 36632 - CP067347_00056 322 38315.99 38315.99 6.4978 hypothetical protein phrog_20113 ; phrog_8027
CP067347 36660 37061 - CP067347_00057 133 16301.40 16301.40 4.5071 hypothetical protein phrog_4334
CP067347 37101 37715 - CP067347_00058 204 23371.78 23371.78 4.9879 RNA-splicing ligase RtcB phrog_1075 ; phrog_32430 PF01139.20
CP067347 37712 38353 - CP067347_00059 213 24170.04 24170.04 9.5013 tRNA splicing ligase phrog_1075 PF01139.20
CP067347 38382 38849 - CP067347_00060 155 19109.70 19109.70 4.3658 hypothetical protein phrog_9459
CP067347 38887 39330 - CP067347_00061 147 17443.43 17443.43 9.6657 hypothetical protein phrog_9643

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.69 Download help

pTM is for the estimate of the TM-score, which is obtained from a pairwise error prediction. The higher pTM score indicates better model quality.

pLDDT is for per-residue accuracy of the structure, which representes the quality of the residue. A higher value indicates better prediction accuracy. More detail please see AlphaFold .

Residues were colored according to plddt ( blue-> high quality; red-> low quality ).

Full Sequence
90 < plddt <=100 ;
70 < plddt <= 90 ;
50 < plddt <= 70 ;
0 <= plddt <= 50 ;      Download help

Structural homologs

No homologs found in AlphaFold database

No homologs found in esmfold database

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS083 CP067347_00056 47 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       download full data without filtering help

Clan ID: CLAN001

Hit APIS family E-Value Query Start Query End Hit Start Hit End Immune system Seed protein
APIS046 1.24E-87 21 346 1 328 IMGVR_UViG_3300009034_000088|3300009034|Ga0115863_100105265
APIS068 1.67E-74 21 345 1 332 IMGVR_UViG_3300035698_004593|3300035698|Ga0374944_618332_7825_8844
APIS005 7.52E-64 22 346 7 305 Gabija APD21271.1
APIS065 1.87E-62 19 345 2 342 KJ018209_00009
APIS071 4.36E-62 22 343 4 336 IMGVR_UViG_3300037628_000643|3300037628|Ga0310922_0000037_90720_91751
APIS088 3.70E-48 22 345 5 304 uvig_218805_40
APIS057 1.98E-43 25 346 2 322 IMGVR_UViG_3300021167_000128|3300021167|Ga0216365_13592277
APIS053 3.04E-38 29 344 86 375 IMGVR_UViG_3300014203_000236|3300014203|Ga0172378_100030802

Family members, sources, and their hosts        help

Results of representative protein blast against members.

Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
CP067347_00056 100.000 0.0 654 100% Clostridioides phage ES-S-0107-01 Clostridioides INPHARED phrog_20113
IMGVR_UViG_2035918000_000024|2035918000|AECFG_236830 45.342 3.79e-94 290 98% Enterobacteriaceae IMGVR phrog_20113
IMGVR_UViG_2518285522_000006|2518285522|2518345193 39.564 5.41e-83 262 98% Photorhabdus khanii IMGVR phrog_20113
IMGVR_UViG_2630968879_000003|2630968879|2633606445 43.925 9.92e-91 282 98% Xenorhabdus griffiniae_A IMGVR phrog_20113
IMGVR_UViG_2836746200_000002|2836746200|2836748367 43.827 1.99e-91 283 99% Cedecea lapagei IMGVR phrog_20113
IMGVR_UViG_2836746200_000004|2836746200|2836749800 43.519 6.18e-91 282 99% Cedecea lapagei IMGVR phrog_20113
IMGVR_UViG_2848576382_000023|2848576382|2848579059 43.077 7.84e-89 277 98% Xenorhabdus stockiae IMGVR phrog_20113
IMGVR_UViG_2902088857_000011|2902088857|2902090275 43.574 7.23e-81 257 97% Proteus penneri IMGVR phrog_20113
IMGVR_UViG_2926546190_000002|2926546190|2926548021 44.025 7.89e-88 274 98% Pectinatus IMGVR phrog_20113
IMGVR_UViG_3300006147_000078|3300006147|Ga0080710_100057247 49.844 8.02e-102 310 95% IMGVR phrog_20113
IMGVR_UViG_3300010266_000361|3300010266|Ga0129314_1000001391 45.652 2.29e-83 263 93% IMGVR phrog_20113
IMGVR_UViG_3300011187_000419|3300011187|Ga0136596_10035924 36.395 8.83e-40 149 100% IMGVR phrog_20113
IMGVR_UViG_3300011189_000046|3300011189|Ga0136558_100044210 37.383 1.27e-50 179 96% IMGVR phrog_20113
IMGVR_UViG_3300011820_000003|3300011820|Ga0120787_10010614 45.511 2.13e-94 292 94% Enterobacter IMGVR phrog_20113
IMGVR_UViG_3300012170_000008|3300012170|Ga0136598_10002407 36.646 8.11e-51 179 96% Firmicutes IMGVR phrog_20113
IMGVR_UViG_3300012178_000029|3300012178|Ga0136557_10010824 36.646 9.84e-51 179 96% IMGVR phrog_20113
IMGVR_UViG_3300012983_000036|3300012983|Ga0123349_1000005482 51.703 1.94e-111 335 91% IMGVR phrog_20113
IMGVR_UViG_3300024308_000125|3300024308|Ga0247725_10031319 45.679 1.68e-93 289 99% Enterobacteriaceae IMGVR phrog_20113
IMGVR_UViG_3300024999_000164|3300024999|Ga0209728_100027959 51.703 2.89e-115 344 98% IMGVR phrog_20113
IMGVR_UViG_3300025813_000004|3300025813|Ga0210064_1000034105 45.846 1.28e-91 285 95% IMGVR phrog_20113
IMGVR_UViG_3300028374_000203|3300028374|Ga0306906_10009517 37.267 4.71e-52 182 97% IMGVR phrog_20113
IMGVR_UViG_3300028377_000057|3300028377|Ga0306869_100034021 36.646 9.54e-51 179 97% IMGVR phrog_20113
IMGVR_UViG_3300029704_000002|3300029704|Ga0245212_100099129 51.258 1.93e-105 320 90% CAG-353 IMGVR phrog_20113
IMGVR_UViG_3300035208_006181|3300035208|Ga0376279_0001262_6692_7732 46.894 5.70e-96 296 92% IMGVR phrog_20113
IMGVR_UViG_3300035700_000373|3300035700|Ga0399893_000586_10755_11702 36.957 1.86e-51 181 97% IMGVR phrog_20113
IMGVR_UViG_3300035702_000341|3300035702|Ga0399894_000623_11141_12088 36.646 7.87e-51 179 97% IMGVR phrog_20113
IMGVR_UViG_3300037067_014547|3300037067|Ga0378408_0009517_394_1380 47.335 1.89e-91 284 96% IMGVR phrog_20113
IMGVR_UViG_3300038566_000181|3300038566|Ga0135254_00012_14651_15610 45.283 6.15e-87 272 98% IMGVR phrog_20113
IMGVR_UViG_3300042923_000231|3300042923|Ga0456365_0002801_17661_18683 46.440 3.06e-96 296 94% IMGVR phrog_20113
IMGVR_UViG_3300045988_127283|3300045988|Ga0495776_186729_5835_6905 43.653 4.26e-87 274 90% Salmonella IMGVR phrog_20113
IMGVR_UViG_3300045988_134731|3300045988|Ga0495776_019811_33299_34267 48.750 7.02e-90 280 98% Intestinibacter IMGVR phrog_20113
IMGVR_UViG_3300045988_136492|3300045988|Ga0495776_019989_55134_56102 48.287 1.30e-91 284 98% IMGVR phrog_20113
IMGVR_UViG_3300045988_136853|3300045988|Ga0495776_048793_8205_9185 48.308 4.42e-92 285 98% Clostridia IMGVR phrog_20113
IMGVR_UViG_3300045988_175669|3300045988|Ga0495776_183410_23130_24146 49.057 1.72e-97 300 94% CAG-353 IMGVR phrog_20113
ivig_2608_15 43.963 7.07e-89 277 99% Escherichia coli GPD phrog_20113
MGV-GENOME-0294891_13 43.653 1.42e-87 274 98% Escherichia MGV phrog_20113
MGV-GENOME-0351898_15 48.308 4.58e-92 285 98% Clostridia MGV phrog_20113
MGV-GENOME-0372528_117 51.258 2.00e-105 320 90% CAG-353 MGV phrog_20113
MGV-GENOME-0374248_85 48.308 1.19e-93 289 98% Intestinibacter MGV phrog_20113
MGV-GENOME-0374453_34 48.765 8.42e-92 285 98% Bacteria MGV phrog_20113
MGV-GENOME-4431062_40 49.057 1.78e-97 300 94% CAG-353 MGV phrog_20113
MGV-GENOME-4432118_39 51.258 1.10e-105 320 94% CAG-353 MGV phrog_20113
uvig_156729_49 51.258 1.06e-105 320 94% GPD phrog_20113
uvig_250944_44 49.686 8.76e-101 308 94% GPD phrog_20113
uvig_317459_17 46.605 5.38e-96 295 99% GPD phrog_20113
uvig_420121_45 49.538 5.09e-95 293 98% GPD phrog_20113
uvig_596313_104 49.371 5.85e-98 301 94% GPD phrog_20113