Align D-lactate transporter, permease component 1 (characterized)
to candidate WP_011384722.1 AMB_RS11750 branched-chain amino acid ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >NCBI__GCF_000009985.1:WP_011384722.1 Length = 316 Score = 178 bits (452), Expect = 2e-49 Identities = 111/304 (36%), Positives = 165/304 (54%), Gaps = 34/304 (11%) Query: 23 PFILNPFPTGSALAQFNAGYPDLMQRFVIFGIFAIGFNILFGLTGYLSFGHAAFLGVGSY 82 PF+L G L A YP + + + FG+FA FN+L G G LSFGHA F G +Y Sbjct: 13 PFVLALLGLGLVLPL--AVYPVFLMKGLCFGLFAAAFNLLLGYVGLLSFGHAMFFGWSAY 70 Query: 83 SAVWMFKLLSMNVVPAIVLSVIVAGLFALVIGYVSLRRSGIYFSILTLAFAQMSFNLAYS 142 + K + AI+L V +A V+G++++RR GIYF+++TLA AQ+ F +A Sbjct: 71 VTAYAAKEWGLTPELAILLGVALATALGAVVGWLAIRRQGIYFAMITLALAQLGFFVA-- 128 Query: 143 VLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGL-EMRSTFEMVVGPWAFQFNA 201 V P+T+GE G+Q +P LFGL ++ +T M Sbjct: 129 VQAPMTHGEDGIQ-----------------GVPRGMLFGLIDLSNTMAMY---------- 161 Query: 202 GYYLCALILLAAFYLSIRIFRSPFGLMLKAVKSNQQRMNYTGLNTRPYTLAAFVISGMYA 261 Y++ A+ +L+ +L R+ SPFG +LKA++ N+ R G Y L AFV+S +A Sbjct: 162 -YFVLAVFVLSLLFLH-RVVNSPFGQVLKAIRDNEPRAISLGYEVTRYKLIAFVLSSAFA 219 Query: 262 GLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGPVLGAGFIKYFENIFSKIN 321 GLAG L + + LA + W SGEVVLMT+LGG GT++GP++GA + ++ F+ I Sbjct: 220 GLAGSLKSLVFQLASLADVSWHMSGEVVLMTLLGGVGTVLGPMVGAFLVVAIQDFFAGIG 279 Query: 322 DNVL 325 V+ Sbjct: 280 SWVI 283 Lambda K H 0.327 0.143 0.435 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: 437 Number of extensions: 28 Number of successful extensions: 3 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: 400 Length of database: 316 Length adjustment: 29 Effective length of query: 371 Effective length of database: 287 Effective search space: 106477 Effective search space used: 106477 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 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