Align ABC transporter related (characterized, see rationale)
to candidate BWI76_RS02800 BWI76_RS02800 ABC transporter
Query= uniprot:A0KWY5 (499 letters) >FitnessBrowser__Koxy:BWI76_RS02800 Length = 500 Score = 502 bits (1292), Expect = e-146 Identities = 261/494 (52%), Positives = 349/494 (70%), Gaps = 3/494 (0%) Query: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 IL + +SK +PGVKAL++V+ L GE+ ALLGENGAGKSTL+K +TG D G I Sbjct: 9 ILRTEGLSKFFPGVKALDNVNFSLRRGEIMALLGENGAGKSTLIKALTGVYHADRGAIWL 68 Query: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 G AQ+ GI TVYQEVNL+PN++VA NLF+G EPRR GL+ K+M A A Sbjct: 69 EGREISPKNTAHAQQLGIGTVYQEVNLLPNMSVADNLFIGREPRRFGLLQRKEMEKRATA 128 Query: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 ++ + +DV PL+ +S+A+QQ++AI R + +SAKVL+LDEPTASLD +EV++LF ++ Sbjct: 129 LMASYGFSLDVREPLNRFSVAMQQIVAICRAIDLSAKVLILDEPTASLDTQEVEMLFTLM 188 Query: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 QL+ GV+++F+THFLDQVY +SDRITVLRNG F+G T ELPQ +L++ MLGR L+ Sbjct: 189 RQLRDSGVSLIFVTHFLDQVYAVSDRITVLRNGGFVGCRETRELPQIELVKMMLGRELEH 248 Query: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVKGSIQSMNLTVPKGQAVGLAGLLGSGRSEVCNA 303 + Q RT+ ++ + + ED KG+I NL V G+ VGLAGLLGSGR+E Sbjct: 249 NAL--QRAGRTLL-SDKPVAAFEDFGKKGTIAPFNLQVRPGEIVGLAGLLGSGRTETAEV 305 Query: 304 VFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENIILALQA 363 +FG+ DSG + G+ L P A GI CPEDRK DGII S+RENI+LALQA Sbjct: 306 IFGIKPADSGKAWIKGKPQTLRSPHQASCLGIGFCPEDRKTDGIIAAASVRENIVLALQA 365 Query: 364 RIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLAIEPILLV 423 + GW R +S Q EIA+ FI +L I TP A++PIE LSGGNQQKV+L+RWL +P L+ Sbjct: 366 QRGWLRPISRREQNEIAERFIRQLGIRTPSAEQPIEFLSGGNQQKVLLSRWLLTKPQFLI 425 Query: 424 LDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRDRYAVRELS 483 LDEPTRGID+GAHAEI++LI TLC +G++LLV SSEL+ELV ++++V+++RDR V EL+ Sbjct: 426 LDEPTRGIDVGAHAEIIRLIETLCADGLALLVISSELEELVGYADRVIIMRDRQQVAELA 485 Query: 484 GAELTSQHVMQAIA 497 +EL+ +M AIA Sbjct: 486 LSELSVPAIMNAIA 499 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: 619 Number of extensions: 26 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 499 Length of database: 500 Length adjustment: 34 Effective length of query: 465 Effective length of database: 466 Effective search space: 216690 Effective search space used: 216690 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 Sep 17 2021. 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