Align ABC transporter related (characterized, see rationale)
to candidate WP_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= uniprot:A0KWY5 (499 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 208 bits (529), Expect = 4e-58 Identities = 142/471 (30%), Positives = 251/471 (53%), Gaps = 11/471 (2%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 ++ +K ++K + V A +D+SL ++ G V ALLGENGAGKSTL+ ++ G D G I Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 G+P F++ DA +AGI VYQ LV ++TVA+N+ LG E ++ K+M + Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQEGS--FFLNPKEMRNRVQE 141 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 + ++ LDID +A +SD S+ +Q + I + + ++VL+ DEPTA L +E LF L Sbjct: 142 LSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEAL 201 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAEL-PQPKLIEAMLGRSLQ 242 ++ +G +IVFI+H L++V ++D I +LR G+ GE+ +E+ + L M+G+ + Sbjct: 202 WKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEVL 261 Query: 243 EQLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCN 302 + VD++ + +AVL + ++ + + +G+ V + G+ G+G+ + Sbjct: 262 LE-VDRE----AMPHGDAVLQVRNLTGI--GLEDITFDLHQGEVVAVVGVAGNGQKALVE 314 Query: 303 AVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQ 362 A+ GL ++ + G++ + +A PEDR L++ +N++L + Sbjct: 315 AICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTTR 374 Query: 363 ARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILL 422 +L + I K I QLSGGN QK +LAR L P L+ Sbjct: 375 QGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRLI 434 Query: 423 VLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVL 473 V ++PT+G+DI A ++ + E +L+ + +L+E + +++V V+ Sbjct: 435 VAEQPTQGLDIAATEQVWNHL-LAAREMAGILLVTGDLNEALQLADRVAVI 484 Score = 70.1 bits (170), Expect = 2e-16 Identities = 53/214 (24%), Positives = 108/214 (50%), Gaps = 8/214 (3%) Query: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336 ++L + G+ L G G+G+S + + + G D+G+I L G+ + S DAI AGI Sbjct: 43 ISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIALDGKPVRFSSARDAIEAGIG 102 Query: 337 LCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADK 396 + + + + +++ EN++L + R QE++ + L I D Sbjct: 103 MVYQHFML---VESMTVAENVLLGQEGSFFLNPKEMRNRVQELSVRY--GLDI---DPAA 154 Query: 397 PIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVA 456 + LS G +Q+V + + L + +L+ DEPT + + + + + ++G S++ Sbjct: 155 RVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEALWKIAEQGKSIVFI 214 Query: 457 SSELDELVAFSNKVVVLRDRYAVRELSGAELTSQ 490 S +L+E++A ++++ +LR E S +E+TS+ Sbjct: 215 SHKLEEVLAVADEIAILRQGRIEGEFSESEVTSK 248 Score = 55.5 bits (132), Expect = 5e-12 Identities = 55/230 (23%), Positives = 108/230 (46%), Gaps = 19/230 (8%) Query: 20 LEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGE--------PQHFN 71 LED++ L GEV A++G G G+ LV+ + G + + + +G+ P N Sbjct: 286 LEDITFDLHQGEVVAVVGVAGNGQKALVEAICGLRKPPVDTMFIMGKRWRDFYAKPSWKN 345 Query: 72 TP--MDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARAVLTQFK 129 + + + G++T + +NLV NL + P + KK D ++ +F Sbjct: 346 SLAYIPEDRLGLATC-RNLNLVDNLLLTTRQGFARGP----WLDKKKAARDTTELIKKFD 400 Query: 130 LDIDVSAPLS-DYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLKA 188 + A L+ S Q +AR + +++V ++PT LD + ++ L L A Sbjct: 401 IRPGRIAALAWQLSGGNLQKSVLARELYRCPRLIVAEQPTQGLDIAATEQVWNHL--LAA 458 Query: 189 KGVA-IVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAML 237 + +A I+ +T L++ Q++DR+ V+ G+F+ + ++ + I M+ Sbjct: 459 REMAGILLVTGDLNEALQLADRVAVIYRGRFMDVFSVSDKQKVNRIGLMM 508 Lambda K H 0.319 0.136 0.377 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 533 Number of extensions: 28 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 3 Length of query: 499 Length of database: 514 Length adjustment: 34 Effective length of query: 465 Effective length of database: 480 Effective search space: 223200 Effective search space used: 223200 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory