Align D-lactate transporter, substrate binding component (characterized)
to candidate WP_029133926.1 A3GO_RS0114015 branched-chain amino acid ABC transporter substrate-binding protein
Query= reanno::Phaeo:GFF1251 (448 letters) >NCBI__GCF_000428045.1:WP_029133926.1 Length = 451 Score = 631 bits (1628), Expect = 0.0 Identities = 316/445 (71%), Positives = 362/445 (81%), Gaps = 7/445 (1%) Query: 2 SKT-DVSRRGVLKTGAIAGAGVALPTIFTASSAAA--FTNEP-TGSTVTLGFNVPQTGPY 57 SKT ++SRRG +K GA A +P F + AA F N P +V GFNVPQTG Y Sbjct: 6 SKTSELSRRGFIKVGAAALTAANMPMFFVKDAWAAKDFRNNPGNAGSVKFGFNVPQTGAY 65 Query: 58 ADEGADELRAYQLAVEHLNGGGDGGMMNTFSSKALQGNGIMGKEVKFVTGDTQTKSDAAR 117 ADEGADELRAY+LAV+H+NG GDGGM+NT L+GNGI+GK++++VTGDTQTKSDAAR Sbjct: 66 ADEGADELRAYKLAVKHINGEGDGGMLNTMKPLTLKGNGILGKKLEYVTGDTQTKSDAAR 125 Query: 118 ASAKSMIEKDGAVMITGGSSSGVAIAVQGLCQEAGVIFMAGLTHSNDTTGKDKKANGFRH 177 ASAK MIEKDG VMITGGSSSGVA+AVQGLCQE GVIFMAGLTHSNDTTGKDK+ GFRH Sbjct: 126 ASAKRMIEKDGVVMITGGSSSGVAVAVQGLCQEMGVIFMAGLTHSNDTTGKDKRRYGFRH 185 Query: 178 FFNGYMSGAALAPVLKNLYGTDRNAYHLTADYTWGWTQEESIAAATEALGWNTVNKVRTP 237 FFN YMSG AL PVLK GTDR AYHLTADYTWGWTQEESI TEALGW T V+TP Sbjct: 186 FFNAYMSGKALGPVLKEEMGTDRKAYHLTADYTWGWTQEESIKNTTEALGWQTTAAVKTP 245 Query: 238 LAATDFSSYIAPVLNSGADVLVLNHYGGNMVNSLTNAVQFGLREKVVNGKNFEIVVPLYS 297 + A DFS YI PVLNSGADVL+LNHYG +M+NSLT AVQFGLR+K VNGKNFEIVVPL+S Sbjct: 246 VGAGDFSQYITPVLNSGADVLILNHYGKDMINSLTQAVQFGLRDKQVNGKNFEIVVPLFS 305 Query: 298 RLMAKGAGANVKGIHGSTNWHWSLQDEGSQAFVRSFGSKYGFPPSQAAHTVYCQTLLYAD 357 RLMA+GAG N+KGI G+TNW+WSLQDEGS+AFV+SFG +YGFPPS AAHT Y Q LLYA+ Sbjct: 306 RLMAQGAGENIKGILGTTNWNWSLQDEGSKAFVKSFGQEYGFPPSMAAHTCYVQALLYAN 365 Query: 358 AVERAGSFNPCAVVEALEGFEFDGLGNGKTLYRAEDHQCFKDVLVVRGKENPTSEFDLLE 417 AVE+AG+F P V++ LEGF+FDG+GNG T YRAEDHQCFKDVLVVRG +NPTS+FDLL+ Sbjct: 366 AVEQAGTFYPPEVIKTLEGFKFDGMGNGPTEYRAEDHQCFKDVLVVRGNQNPTSQFDLLQ 425 Query: 418 VVEVTPAEQVTYAPDHPMFAGGALG 442 V ++ P +V Y D +F GG LG Sbjct: 426 VQKIVPRSEVEY--DAKIF-GGELG 447 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: 732 Number of extensions: 27 Number of successful extensions: 2 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: 451 Length adjustment: 33 Effective length of query: 415 Effective length of database: 418 Effective search space: 173470 Effective search space used: 173470 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