Align D-lactate transporter, permease component 1 (characterized)
to candidate WP_011385249.1 AMB_RS14460 branched-chain amino acid ABC transporter permease
Query= reanno::Phaeo:GFF1249 (400 letters) >NCBI__GCF_000009985.1:WP_011385249.1 Length = 329 Score = 137 bits (345), Expect = 5e-37 Identities = 119/368 (32%), Positives = 170/368 (46%), Gaps = 71/368 (19%) Query: 13 LVVAILTLFAPFILNPFPTGSALAQFNAGYPDLMQRF---VIFGIFAIGFNILFGLTGYL 69 L + +L L A L FP LA F+A Y L+Q+ +I I A+ ++L G+ G + Sbjct: 8 LSLLLLVLLAALAL--FPAWGPLA-FSAKYAFLLQKLTGIMILAILAMSLDLLVGVAGLV 64 Query: 70 SFGHAAFLGVGSYSAVWMFKLLSMNVVPAIVLSVIVAGLFAL-----VIGYVSLRRSGIY 124 S GHAAF G+G Y M LLS A V+ A + A+ V+G++++R +GIY Sbjct: 65 SLGHAAFFGLGGY----MLALLSPQYEAANAWVVLPAAMGAVAAVSAVVGFLAIRTAGIY 120 Query: 125 FSILTLAFAQMSFNLAYSVLTPITNGETGLQLTLDDPRVLGVSATADGSIPVTSLFGLEM 184 F ++TLAF QM + + + G G + + P V T L LE Sbjct: 121 FIMVTLAFGQMGYYFFND--SKLAGGSDGAYIYVK-PNVEAFGIT---------LVNLES 168 Query: 185 RSTFEMVVGPWAFQFNAGYYLCALILLAAFYLSIRI-FRSPFGLMLKAVKSNQQRMNYTG 243 + F VV L L A YL +R+ SPFG +L A+ N+ R+ G Sbjct: 169 KQAFFFVV---------------LGCLVAVYLWLRVVLASPFGRVLAAIGVNEGRVRGLG 213 Query: 244 LNTRPYTLAAFVISGMYAGLAGGLMASMDPLAGAERMQWTASGEVVLMTILGGAGTLIGP 303 N Y L AF ++G AGLAG L A+ + W SG V++M ILGG GTL GP Sbjct: 214 FNPMVYKLVAFALAGALAGLAGFLAATQYGFVSPAMLGWHQSGHVLVMVILGGMGTLFGP 273 Query: 304 VLGAGFIKYFENIFSKINDNVLHSWFSFMPDGIEDAMVFIVHPFIGKGWHLTLGILFMLV 363 VLGA FI + G+E + + W L +G+L + + Sbjct: 274 VLGA-FILELAHF------------------GLE---------AVTEHWLLPMGVLVITI 305 Query: 364 VIFLPGGL 371 V+ LP G+ Sbjct: 306 VLALPKGV 313 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: 386 Number of extensions: 24 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 400 Length of database: 329 Length adjustment: 29 Effective length of query: 371 Effective length of database: 300 Effective search space: 111300 Effective search space used: 111300 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