Align D-lactate transporter, substrate binding component (characterized)
to candidate 3607996 Dshi_1404 branched-chain amino acid ABC transporter, periplasmic binding protein, putative (RefSeq)
Query= reanno::Phaeo:GFF1251 (448 letters) >FitnessBrowser__Dino:3607996 Length = 451 Score = 772 bits (1994), Expect = 0.0 Identities = 378/451 (83%), Positives = 409/451 (90%), Gaps = 3/451 (0%) Query: 1 MSKTDVSRRGVLKTGAIAGAGVALPTIFTASS-AAAFTNEPTGSTVTLGFNVPQTGPYAD 59 MS +++SRR VLKTGA GAG+ALPTIFT ++ +A FTNEPTGSTVTLGFNVPQ+GPYAD Sbjct: 1 MSNSEISRRRVLKTGAATGAGLALPTIFTGAAWSAGFTNEPTGSTVTLGFNVPQSGPYAD 60 Query: 60 EGADELRAYQLAVEHLNGGGDGGMMNTFSSKALQGNGIMGKEVKFVTGDTQTKSDAARAS 119 EGADELRAY+LAVEHLNGGGDGGMM+TFSSKALQGNGI+GK+V++VTGDTQTKSDAARAS Sbjct: 61 EGADELRAYELAVEHLNGGGDGGMMSTFSSKALQGNGILGKKVEYVTGDTQTKSDAARAS 120 Query: 120 AKSMIEKDGAVMITGGSSSGVAIAVQGLCQEAGVIFMAGLTHSNDTTGKDKKANGFRHFF 179 A+SMIEKDGAVMITGGSSSGVA+AVQ LCQEAG+IFMAGLTHSNDTTGKD+KANGFRHFF Sbjct: 121 ARSMIEKDGAVMITGGSSSGVAVAVQALCQEAGIIFMAGLTHSNDTTGKDRKANGFRHFF 180 Query: 180 NGYMSGAALAPVLKNLYGTDRNAYHLTADYTWGWTQEESIAAATEALGWNTVNKVRTPLA 239 N YMSGAALAP+L YGTDR AYHLTADY WG+T EE++ ++TEA+GW TVN V TPL Sbjct: 181 NSYMSGAALAPILAKNYGTDRKAYHLTADYNWGYTTEEAVRSSTEAMGWETVNTVLTPLT 240 Query: 240 ATDFSSYIAPVLNSGADVLVLNHYGGNMVNSLTNAVQFGLREKVVNGKNFEIVVPLYSRL 299 TDFS+YI PVL S ADVLVLNHYGGNMVNSLTNAVQFGLR++VVNGKNFEIVVPLYSRL Sbjct: 241 QTDFSAYITPVLQSDADVLVLNHYGGNMVNSLTNAVQFGLRDRVVNGKNFEIVVPLYSRL 300 Query: 300 MAKGAGANVKGIHGSTNWHWSLQDEGSQAFVRSFGSKYGFPPSQAAHTVYCQTLLYADAV 359 MAKGAGANVKGI GSTNWHWSLQD GSQAFVRSFG+KYGFPPSQAAHT Y Q LLYADAV Sbjct: 301 MAKGAGANVKGIFGSTNWHWSLQDAGSQAFVRSFGTKYGFPPSQAAHTCYVQALLYADAV 360 Query: 360 ERAGSFNPCAVVEALEGFEFDGLGNGKTLYRAEDHQCFKDVLVVRGKENPTSEFDLLEVV 419 ERAGSFNPCAV EAL FEFDG+GNG TLYRA DHQCFKDVLVVRGKENPTSEFDLLE+V Sbjct: 361 ERAGSFNPCAVDEALSDFEFDGMGNGPTLYRAADHQCFKDVLVVRGKENPTSEFDLLEIV 420 Query: 420 EVTPAEQVTYAPDHPMFAG--GALGTCNSGA 448 EVTP EQVTYAPDHP F G LGTCN GA Sbjct: 421 EVTPVEQVTYAPDHPQFGGAEATLGTCNPGA 451 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: 835 Number of extensions: 27 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: 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 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