Align D-lactate transporter, substrate binding component (characterized)
to candidate GFF3050 Psest_3108 ABC-type branched-chain amino acid transport systems, periplasmic component
Query= reanno::Phaeo:GFF1251 (448 letters) >FitnessBrowser__psRCH2:GFF3050 Length = 414 Score = 190 bits (483), Expect = 6e-53 Identities = 134/398 (33%), Positives = 205/398 (51%), Gaps = 44/398 (11%) Query: 45 VTLGFNVPQTGPYADEGADELRAYQLAVEHLNGGGDGGMMNTFSSKALQGNGIMGKEVKF 104 +TLG N P+TG Y +EG ++R +A++ +N Q G++G+ ++ Sbjct: 23 ITLGLNYPRTGSYKEEGLAQMRGALMAIDEIN----------------QAGGVLGRPLQL 66 Query: 105 VTGDTQTKSDAARASAKSMIEKDGAVMITGGSSSGVAIAVQGLCQEAGVIFMAGLTHSND 164 ++ +T ++ D A A+ M + +G M+ GG SS VAIA +E G+++ LT+SND Sbjct: 67 ISRNTASRPDKAIANVDKMAD-EGVAMLFGGVSSAVAIAASKRAKERGLLYFGTLTYSND 125 Query: 165 TTGKDKKANGFRHFFNGYMSGAALAPVL-KNLYGTDRNAYHLTADYTWGWTQEESIAAAT 223 TTGKD FR N +MS L L +N+ G + +++T+DYTWG T E S+ AT Sbjct: 126 TTGKDGHRYMFRECNNAWMSARVLGQYLNENMPG--KTYFYITSDYTWGHTSESSLRQAT 183 Query: 224 EALGWNTVNKVRTPLAATDFSSYIAPV---LNSGADVLVLNHYGGNMVNSLTNAVQFGLR 280 + N V+T S Y A + NSGA+VLVL +G +MV ++ A + GL Sbjct: 184 GTVDQNRHQGVKTAFPGARLSDYRAALEKASNSGAEVLVLVLFGEDMVRAMRIADELGLN 243 Query: 281 EKVVNGKNFEIVVPLYSRLMAKGAGANV-KGIHGSTNWHWSLQD-EGSQ---AFVRSFGS 335 +K+ +I +P + M + AG ++ +G+ G+ W W + + EGS+ AFVR+FG Sbjct: 244 KKM------QIAIPNLTLSMVELAGPDIMRGVLGTEPWTWRVPELEGSERGKAFVRNFGD 297 Query: 336 KYGFPPSQAAHTVYCQTLLYADAVERAGSFNPCAVVEALEGFEFDGLGNGKTLYRAEDHQ 395 +Y PS +A + Y +ADA RA S V+ ALE + L G+ +R DHQ Sbjct: 298 RYQTHPSSSAASAYSIVYQWADAATRAKSIGSEQVISALENHSY-SLLKGQQQWRGFDHQ 356 Query: 396 CFKDVLVVRGKENPTSEF-------DLLEVVEVTPAEQ 426 + V VR K P E D E+V EQ Sbjct: 357 NVQTVYAVRVK--PREEVLKDRFKQDYFEIVHRLSGEQ 392 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: 401 Number of extensions: 23 Number of successful extensions: 5 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: 414 Length adjustment: 32 Effective length of query: 416 Effective length of database: 382 Effective search space: 158912 Effective search space used: 158912 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