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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 APIS192
Inhibited defense system
CLAN ID CLAN045
Seed protein property
Accession ID Gene name Protein length Molecular weight Isoelectric point Charge
KM677185_00114
gene_page: 280 32712.20 7.2682 1.5
Phage property
Phage Assembly id
KM677185
PMID/References
PDB structures ;
Pfam domains PF02086.20,PF02086.20
Phrog
Host taxa d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Streptococcaceae;g__Lactococcus;s__unclassified Lactococcus species
Gene Location Start: 59057;  End: 59899;  Strand: +
Description
Note This family does not have seed protein, but we infer its function is defending restriction-modification (RM) because it belongs to the same clan as family APIS107,APIS136,APIS152 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
KM677185 52511 53026 + KM677185_00109 171 19917.67 -3.5 5.3284 hypothetical protein phrog_6282
KM677185 53691 53798 + KM677185_00110 35 3588.62 2.0 9.5126 hypothetical protein phrog_9039
KM677185 53813 54469 + KM677185_00111 218 24242.51 -6.5 4.7391 tail fiber protein phrog_1491
KM677185 54968 56923 + KM677185_00112 651 73130.41 -16.0 4.9997 DNA topoisomerase 4 subunit B phrog_12023 ; phrog_543 ; phrog_7229 PF00986.26 ;PF00204.30 ;PF01751.27 ;PF02518.31
KM677185 56925 59039 + KM677185_00113 704 79093.02 5.5 8.4084 DNA gyrase subunit A phrog_551 ; phrog_20354 PF00521.25 ;PF03989.18
KM677185 59057 59899 + KM677185_00114 280 32712.20 1.5 7.2682 IS1595 family transposase ISCco4 PF02086.20 ;PF02086.20
KM677185 59925 60221 + KM677185_00115 98 11541.09 -3.0 4.3699 hypothetical protein phrog_8616
KM677185 60310 60570 + KM677185_00116 86 9915.33 3.5 8.6297 hypothetical protein phrog_8518
KM677185 60570 61088 + KM677185_00117 172 19047.26 -17.0 3.9082 nucleoside 2-deoxyribosyltransferase phrog_7995 PF05014.20 ;PF15891.10
KM677185 61081 61740 + KM677185_00118 219 24998.94 12.0 10.4268 PnuC-like nicotinamide mononucleotide transport phrog_1880 PF04973.17
KM677185 61819 64320 + KM677185_00119 833 95751.58 -14.5 5.4099 Anaerobic ribonucleoside-triphosphate reductase phrog_4218 ; phrog_487 ; phrog_26446 ; phrog_29160 PF13597.11 ;PF01228.26

Seed genomic context- JBrowse     

Predicted 3D structure by alphafold2 with pTM = 0.87 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

Structure homologs against by afdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
AF-A0A0H3GWR3-F1-model_v4 1 280 1 270 0.8448 0.8243
AF-Q32AJ9-F1-model_v4 1 280 1 269 0.838 0.822
AF-P0DMP3-F1-model_v4 1 280 1 269 0.8381 0.8218
AF-P0AEE8-F1-model_v4 1 280 1 269 0.8379 0.8215
AF-Q8ZMS3-F1-model_v4 4 280 1 261 0.8256 0.806
AF-Q58015-F1-model_v4 2 280 1 289 0.8296 0.8007
AF-Q5F5M8-F1-model_v4 1 280 1 333 0.7165 0.6399
AF-Q0PBT1-F1-model_v4 1 280 2 361 0.7052 0.61

Structure homologs against by esmdb (html) ; download full result table

Hit Query start Query end Hit start Hit end TMscore(ali) TMscore(avg)
MGYP000271406668.pdb 1 280 1 280 0.9279 0.9203
MGYP000852631647.pdb 2 280 1 280 0.9262 0.9195
MGYP003289805481.pdb 1 280 1 282 0.9259 0.9165
MGYP000860657186.pdb 1 280 1 283 0.9259 0.9154
MGYP001271616406.pdb 1 280 2 283 0.9268 0.9152
MGYP000259042174.pdb 1 280 2 280 0.9213 0.9151
MGYP000998795295.pdb 1 280 3 284 0.9273 0.9141
MGYP000137025303.pdb 1 280 3 286 0.9297 0.9132
MGYP000042165803.pdb 2 272 1 260 0.951 0.9117
MGYP001773599837.pdb 1 280 1 283 0.9334 0.9115

Family information      Download help

Fam ID Seed protein Member count Model Alignment
APIS192 KM677185_00114 118 HMM model Member alignment

Host Taxa distribution

Length distribution

Homology to other families       help

Clan ID: CLAN045

APIS192 has no similar APIS family.

Family members, sources, and their hosts        help

Results of representative protein blast against members.
Member pident evalue bitscore qcovs phage host SourceDB Pfam Phrog
uvig_63133_43 54.100 1.240E-90 295 1.000% GPD PF02086 phrog_
IMGVR_UViG_3300050336_000170|3300050336|Ga0528475_000182_39440_40246 57.600 1.129E-86 284 0.907% IMGVR PF02086 phrog_
uvig_227030_83 53.800 5.974E-90 293 1.000% GPD PF02086 phrog_
uvig_72932_53 54.500 1.881E-91 297 1.000% GPD PF02086 phrog_
IMGVR_UViG_3300000114_000710|3300000114|IMNBL3_1000015266 52.000 1.555E-83 274 1.000% IMGVR PF02086 phrog_
IMGVR_UViG_3300031578_000004|3300031578|Ga0307376_10000096154 55.500 4.871E-88 287 0.961% IMGVR PF02086 phrog_
OM654377_00123 47.900 2.633E-73 245 0.989% Pseudaeromonas phage vB_PpeM_ KLEP7 Pseudaeromonas INPHARED PF02086 phrog_
IMGVR_UViG_3300007641_000052|3300007641|Ga0105527_10090531 57.200 1.503E-95 309 1.000% Lachnospiraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300029870_000004|3300029870|Ga0245312_10019833 54.300 8.338E-75 249 0.857% Lachnospiraceae IMGVR PF02086 phrog_
uvig_287002_35 56.200 3.155E-93 302 1.000% Agathobacter rectalis GPD PF02086 phrog_
MGV-GENOME-0347840_25 56.200 3.155E-93 302 1.000% Agathobacter MGV PF02086 phrog_
uvig_82291_23 55.500 1.003E-91 298 1.000% Roseburia intestinalis GPD PF02086 phrog_
IMGVR_UViG_3300045988_068959|3300045988|Ga0495776_036263_58804_59685 56.500 4.781E-94 305 1.000% Lachnospiraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_079149|3300045988|Ga0495776_020132_48221_49102 57.200 1.503E-95 309 1.000% Lachnospiraceae IMGVR PF02086 phrog_
uvig_199453_38 57.200 1.503E-95 309 1.000% Roseburia intestinalis GPD PF02086 phrog_
MGV-GENOME-0238785_35 57.200 1.503E-95 309 1.000% Agathobacter MGV PF02086 phrog_
IMGVR_UViG_3300045988_087999|3300045988|Ga0495776_159774_13197_14078 57.200 1.503E-95 309 1.000% Lachnospiraceae IMGVR PF02086 phrog_
uvig_325396_85 56.200 3.155E-93 302 1.000% Agathobacter rectalis GPD PF02086 phrog_
MGV-GENOME-0335420_24 56.300 1.682E-93 303 1.000% Lachnospiraceae MGV PF02086 phrog_
IMGVR_UViG_3300045988_090604|3300045988|Ga0495776_090540_48190_49071 56.200 3.155E-93 302 1.000% Lachnospiraceae IMGVR PF02086 phrog_
uvig_466879_63 57.100 2.059E-95 309 1.000% Roseburia intestinalis GPD PF02086 phrog_
MGV-GENOME-0297977_63 57.100 2.059E-95 309 1.000% Lachnospiraceae MGV PF02086 phrog_
uvig_257041_10 55.900 1.520E-92 301 1.000% Coprococcus GPD PF02086 phrog_
IMGVR_UViG_3300045988_075102|3300045988|Ga0495776_159199_6070_6789 53.800 1.027E-73 246 0.857% Lachnospiraceae IMGVR PF02086 phrog_
uvig_49953_31 56.700 1.861E-94 306 1.000% Coprococcus GPD PF02086 phrog_
IMGVR_UViG_3300014948_000069|3300014948|Ga0134487_10093717 53.500 3.604E-73 244 0.857% Lachnospiraceae IMGVR PF02086 phrog_
uvig_53229_85 56.400 1.228E-93 304 1.000% Coprococcus GPD PF02086 phrog_
IMGVR_UViG_3300045988_088352|3300045988|Ga0495776_111601_14310_15191 56.300 1.682E-93 303 1.000% Lachnospiraceae IMGVR PF02086 phrog_
MGV-GENOME-0330722_25 56.700 1.861E-94 306 1.000% Lachnospiraceae MGV PF02086 phrog_
IMGVR_UViG_3300045988_098899|3300045988|Ga0495776_078790_18853_19734 56.400 1.228E-93 304 1.000% Lachnospiraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_094201|3300045988|Ga0495776_036059_14554_15435 56.700 1.861E-94 306 1.000% Lachnospiraceae IMGVR PF02086 phrog_
MGV-GENOME-0331271_97 56.500 4.781E-94 305 1.000% Lachnospiraceae MGV PF02086 phrog_
MGV-GENOME-0322456_70 56.200 3.155E-93 302 1.000% Lachnospiraceae MGV PF02086 phrog_
IMGVR_UViG_3300029095_000148|3300029095|Ga0169229_10049427 56.200 3.155E-93 302 1.000% Lachnospiraceae IMGVR PF02086 phrog_
MGV-GENOME-0308427_78 56.400 1.228E-93 304 1.000% Lachnospiraceae MGV PF02086 phrog_
uvig_11600_35 57.200 1.503E-95 309 1.000% Roseburia intestinalis GPD PF02086 phrog_
MGV-GENOME-0270393_30 56.700 1.861E-94 306 1.000% Lachnospiraceae MGV PF02086 phrog_
MGV-GENOME-0334703_70 57.200 1.503E-95 309 1.000% Lachnospiraceae MGV PF02086 phrog_
IMGVR_UViG_3300014548_000137|3300014548|Ga0134459_10011591 53.600 2.633E-73 245 0.857% Lachnospiraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_081344|3300045988|Ga0495776_028794_11998_12879 56.700 1.861E-94 306 1.000% Lachnospiraceae IMGVR PF02086 phrog_
uvig_145906_26 56.500 4.781E-94 305 1.000% Roseburia intestinalis GPD PF02086 phrog_
IMGVR_UViG_3300045988_079302|3300045988|Ga0495776_098430_31020_31901 57.100 2.059E-95 309 1.000% Lachnospiraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_109447|3300045988|Ga0495776_166772_16694_17575 56.200 3.155E-93 302 1.000% Lachnospiraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_170342|3300045988|Ga0495776_150975_63798_64691 50.800 9.238E-82 269 1.000% Pseudoruminococcus IMGVR PF02086 phrog_
MGV-GENOME-0373011_88 50.800 9.238E-82 269 1.000% Lachnospiraceae MGV PF02086 phrog_
MGV-GENOME-0376885_54 42.000 1.209E-60 208 0.993% Dialister MGV PF02086 phrog_
IMGVR_UViG_3300045988_165826|3300045988|Ga0495776_167000_50928_51773 42.000 1.209E-60 208 0.993% Anaeroglobus IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_161461|3300045988|Ga0495776_034372_41150_41995 42.000 1.209E-60 208 0.993% Anaeroglobus IMGVR PF02086 phrog_
MGV-GENOME-0372858_44 42.000 1.209E-60 208 0.993% Dialister MGV PF02086 phrog_
IMGVR_UViG_3300007728_000003|3300007728|Ga0105754_1000002215 47.700 9.239E-73 243 0.989% Haemophilus IMGVR PF02086 phrog_
IMGVR_UViG_3300008643_000002|3300008643|Ga0111423_100005153 46.500 4.906E-70 235 0.989% Pasteurellaceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_162752|3300045988|Ga0495776_057247_31201_32034 47.200 8.309E-72 241 0.989% Haemophilus IMGVR PF02086 phrog_
IMGVR_UViG_7000000305_000024|7000000305|SRS062761_LANL_scaffold_38752__gene_45083 47.700 9.239E-73 243 0.989% Haemophilus IMGVR PF02086 phrog_
MGV-GENOME-0363407_54 47.200 8.309E-72 241 0.989% Haemophilus MGV PF02086 phrog_
IMGVR_UViG_3300010351_001363|3300010351|Ga0116248_100525793 51.100 3.600E-82 271 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300007312_000183|3300007312|Ga0104941_1020548 50.600 4.942E-79 261 0.975% Acutalibacteraceae IMGVR PF02086 phrog_
IMGVR_UViG_3300026522_000462|3300026522|Ga0256406_100094341 53.300 2.345E-87 286 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300029460_000109|3300029460|Ga0244138_10028370 50.700 1.265E-81 269 1.000% IMGVR PF02086 phrog_
IMGVR_UViG_3300035198_000134|3300035198|Ga0315269_0001980_2879_3751 48.500 2.138E-74 248 0.975% IMGVR PF02086 phrog_
IMGVR_UViG_3300029607_000289|3300029607|Ga0244907_10002380 51.500 3.992E-83 273 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300029739_000087|3300029739|Ga0245187_10055454 51.000 4.929E-82 270 0.996% Clostridia IMGVR PF02086 phrog_
IMGVR_UViG_3300029114_000172|3300029114|Ga0168819_1014939 51.000 4.929E-82 270 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_7000000295_000084|7000000295|SRS019219_WUGC_scaffold_57095__gene_85291 50.800 1.265E-81 269 0.989% IMGVR PF02086 phrog_
IMGVR_UViG_3300028591_000083|3300028591|Ga0247611_10000054234 46.400 3.989E-71 239 1.000% IMGVR PF02086 phrog_
MGV-GENOME-0373880_137 56.600 2.304E-93 303 0.993% Clostridia MGV PF02086 phrog_
IMGVR_UViG_3300045988_139973|3300045988|Ga0495776_019974_102176_103027 57.300 5.290E-95 308 0.993% IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_126140|3300045988|Ga0495776_019952_114322_115173 56.600 2.304E-93 303 0.993% Clostridia IMGVR PF02086 phrog_
MGV-GENOME-0374123_138 57.300 5.290E-95 308 0.993% MGV PF02086 phrog_
MGV-GENOME-0374378_168 52.400 6.059E-84 276 0.993% Intestinibacter MGV PF02086 phrog_
IMGVR_UViG_3300029245_000005|3300029245|Ga0168762_1001183 52.700 1.724E-84 277 0.993% IMGVR PF02086 phrog_
MGV-GENOME-0374453_132 52.700 1.259E-84 278 0.993% Bacteria MGV PF02086 phrog_
MGV-GENOME-0373849_54 52.700 1.724E-84 277 0.993% Intestinibacter MGV PF02086 phrog_
IMGVR_UViG_3300045988_129603|3300045988|Ga0495776_019801_127332_128171 52.400 6.059E-84 276 0.993% Peptostreptococcaceae IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_125645|3300045988|Ga0495776_019988_132362_133198 52.700 1.259E-84 278 0.993% IMGVR PF02086 phrog_
IMGVR_UViG_3300028805_000066|3300028805|Ga0247608_1000014887 53.000 2.616E-85 280 0.993% IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_138620|3300045988|Ga0495776_019991_99570_100412 53.700 6.022E-87 284 0.993% IMGVR PF02086 phrog_
MGV-GENOME-0374277_110 53.700 6.022E-87 284 0.993% MGV PF02086 phrog_
IMGVR_UViG_3300033696_000004|3300033696|Ga0373164_00001_94944_95780 39.400 3.578E-53 186 0.975% IMGVR PF02086 phrog_
IMGVR_UViG_3300028888_000045|3300028888|Ga0247609_1000000739 59.500 8.631E-103 330 1.000% IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_136492|3300045988|Ga0495776_019989_130286_131128 52.700 1.259E-84 278 0.993% IMGVR PF02086 phrog_
MGV-GENOME-0374248_171 52.700 1.259E-84 278 0.993% Intestinibacter MGV PF02086 phrog_
IMGVR_UViG_3300021426_000068|3300021426|Ga0224482_1000009853 50.500 4.006E-80 265 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300028833_000195|3300028833|Ga0247610_1000052548 55.700 4.830E-91 296 0.989% IMGVR PF02086 phrog_
IMGVR_UViG_3300028591_000072|3300028591|Ga0247611_10000016119 53.900 1.012E-88 289 0.996% Gammaproteobacteria IMGVR PF02086 phrog_
IMGVR_UViG_3300013383_000001|3300013383|Ga0116616_1000016226 47.900 4.932E-73 244 0.986% IMGVR PF02086 phrog_
IMGVR_UViG_3300020112_002004|3300020112|Ga0207380_119552912 45.100 1.899E-67 228 0.996% IMGVR PF02086 PF03602 phrog_
IMGVR_UViG_3300045988_127377|3300045988|Ga0495776_140719_12540_13364 50.100 6.095E-78 258 0.986% IMGVR PF02086 phrog_
MGV-GENOME-0372689_20 50.100 6.095E-78 258 0.986% MGV PF02086 phrog_
IMGVR_UViG_3300028048_000238|3300028048|Ga0256405_1000257341 50.400 4.942E-79 261 0.989% IMGVR PF02086 phrog_
MGV-GENOME-0356065_33 46.900 1.027E-73 246 1.000% Ruminococcus MGV PF02086 phrog_
IMGVR_UViG_3300023496_000014|3300023496|Ga0257043_10057844 46.500 1.264E-72 243 1.000% Ruminococcus IMGVR PF02086 phrog_
uvig_82868_31 46.500 1.264E-72 243 1.000% Ruminococcus bromii GPD PF02086 phrog_
uvig_538702_32 47.100 4.005E-74 247 1.000% Ruminococcus bromii GPD PF02086 phrog_
uvig_217229_67 47.500 4.450E-75 250 1.000% Ruminococcus bromii GPD PF02086 phrog_
uvig_262883_23 47.000 5.482E-74 247 1.000% Ruminococcus bromii GPD PF02086 phrog_
uvig_103331_32 46.100 8.309E-72 241 1.000% Ruminococcus bromii GPD PF02086 phrog_
uvig_8022_69 46.900 1.027E-73 246 1.000% Ruminococcus bromii GPD PF02086 phrog_
uvig_49238_13 49.000 6.095E-78 258 0.996% GPD PF02086 phrog_
IMGVR_UViG_3300023493_000002|3300023493|Ga0257031_100060154 49.000 6.095E-78 258 0.996% Clostridia IMGVR PF02086 phrog_
IMGVR_UViG_2806310702_000001|2806310702|2807288466 50.500 2.616E-85 280 0.996% Clostridium haemolyticum IMGVR PF02086 phrog_1996
MGV-GENOME-0373177_102 56.100 4.321E-93 302 0.996% MGV PF02086 phrog_
IMGVR_UViG_2744054576_000007|2744054576|2744833060 57.000 1.534E-89 292 0.943% Paenibacillus ottowii IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_165075|3300045988|Ga0495776_151031_58514_59374 56.100 4.321E-93 302 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300020112_001004|3300020112|Ga0207380_1071906133 56.500 6.548E-94 304 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300038317_000237|3300038317|Ga0134849_000707_17514_18425 44.400 4.436E-72 241 0.989% Anaerotignaceae IMGVR PF02086 phrog_
uvig_162736_29 46.100 4.011E-77 256 0.989% GPD PF02086 phrog_
IMGVR_UViG_3300045988_181639|3300045988|Ga0495776_156002_8489_9316 42.700 1.653E-60 208 0.961% IMGVR PF02086 phrog_
MGV-GENOME-0345030_14 43.500 5.358E-65 221 0.996% MGV PF02086 phrog_
IMGVR_UViG_3300045988_180795|3300045988|Ga0495776_158903_45774_46658 50.000 5.484E-80 264 0.996% IMGVR PF02086 phrog_
MGV-GENOME-0318104_59 50.000 5.484E-80 264 0.996% MGV PF02086 phrog_
IMGVR_UViG_3300010163_000003|3300010163|Ga0136175_1000004822 43.700 1.102E-62 214 0.975% IMGVR PF02086 phrog_
MGV-GENOME-0376238_55 49.800 1.926E-79 263 0.996% MGV PF02086 phrog_
IMGVR_UViG_3300045988_157508|3300045988|Ga0495776_138167_29544_30404 49.800 1.926E-79 263 0.996% IMGVR PF02086 phrog_
IMGVR_UViG_3300045988_155053|3300045988|Ga0495776_003981_75594_76454 50.500 3.246E-81 268 0.996% IMGVR PF02086 phrog_
MGV-GENOME-0379728_104 50.500 3.246E-81 268 0.996% MGV PF02086 phrog_
KM677185_00114 100.000 2.412E-187 574 1.000% Lactococcus phage WRP3 Lactococcus INPHARED PF02086 PF02086 phrog_
HM029250_00094 94.600 7.220E-182 558 1.000% Lactococcus phage 949 Lactococcus INPHARED PF02086 phrog_
KY554777_00111 96.200 1.453E-185 569 1.000% Lactococcus phage LW81 Lactococcus INPHARED PF02086 phrog_