Align D-lactate transporter, substrate binding component (characterized)
to candidate WP_037375469.1 A3GO_RS0113945 branched-chain amino acid ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF1251 (448 letters) >NCBI__GCF_000428045.1:WP_037375469.1 Length = 438 Score = 499 bits (1285), Expect = e-146 Identities = 256/434 (58%), Positives = 313/434 (72%), Gaps = 11/434 (2%) Query: 12 LKTGAIAGAGVALPTIFTASSAAA---FTNEPT-GSTVTLGFNVPQTGPYADEGADELRA 67 +K GA + A A +F A A N P G TV GFN PQ+G YADEGADE RA Sbjct: 1 MKLGAASIAAAANTPMFFVKDAWAEQSIGNYPVRGKTVKFGFNYPQSGAYADEGADEGRA 60 Query: 68 YQLAVEHLNGGGDGGMMNTFSSKALQGNGIMGKEVKFVTGDTQTKSDAARASAKSMIEKD 127 Y+LAV+H+N GG GM+NT AL+GNGI+GK+V++V GDTQ+ AR SA+ MIE+D Sbjct: 61 YKLAVQHINNGG--GMLNTLQPLALKGNGILGKKVEYVIGDTQSSPGPARTSARRMIEQD 118 Query: 128 GAVMITGGSSSGVAIAVQGLCQEAGVIFMAGLTHSNDTTGKDKKANGFRHFFNGYMSGAA 187 G +M +GGSSS VAIA Q L QE GVIFM GLTHSNDTTGKD++ GFRHFFN YMSG A Sbjct: 119 GIIMFSGGSSSSVAIAQQYLAQEKGVIFMCGLTHSNDTTGKDRRRYGFRHFFNAYMSGKA 178 Query: 188 LAPVLKNLYGTDRNAYHLTADYTWGWTQEESIAAATEALGWNTVNKVRTPLAATDFSSYI 247 LAPVL YG DR A+HLTADY+WG TQ S+ TE GW TVN + TPL + DFS +I Sbjct: 179 LAPVLARNYGKDRRAFHLTADYSWGHTQYASMKEFTEKEGWTTVNNIMTPLGSNDFSMFI 238 Query: 248 APVLNSGADVLVLNHYGGNMVNSLTNAVQFGLREKVVNGKNFEIVVPLYSRLMAKGAG-A 306 +LNS ADVL+LNHYG +MVNSLT AV+FGLR+ NGK E+VVPL+SR+MAKGAG A Sbjct: 239 TAILNSDADVLILNHYGKDMVNSLTQAVEFGLRDLQKNGKTIEVVVPLFSRVMAKGAGAA 298 Query: 307 NVKGIHGSTNWHWSLQDEGSQAFVRSFGSKYGFPPSQAAHTVYCQTLLYADAVERAGSFN 366 N+ G+ G+T W+W+LQD GSQAFV SF +YGFPPSQAAHT Y QTLLYA+A E+AG+F Sbjct: 299 NIDGVFGTTGWNWTLQDPGSQAFVNSFTKEYGFPPSQAAHTCYVQTLLYANACEKAGTFY 358 Query: 367 PCAVVEALEGFEFDGLGNGKTLYRAEDHQCFKDVLVVRGK--ENPTSEFDLLEVVEVTPA 424 P V++ LE + G+G G+T YR EDHQCFKD+LV++G + T ++DLL++VE Sbjct: 359 PPEVIKTLENSRYAGIGPGETFYRGEDHQCFKDMLVMKGNGPDKMTGQYDLLKIVEQVKG 418 Query: 425 EQVTYAPDHPMFAG 438 E Y DH F+G Sbjct: 419 EDTVY--DHNTFSG 430 Lambda K H 0.315 0.131 0.387 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: 666 Number of extensions: 28 Number of successful extensions: 4 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: 448 Length of database: 438 Length adjustment: 32 Effective length of query: 416 Effective length of database: 406 Effective search space: 168896 Effective search space used: 168896 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 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