Align ABC transporter for D-Sorbitol, permease component 1 (characterized)
to candidate WP_007665545.1 BN137_RS16135 carbohydrate ABC transporter permease
Query= reanno::BFirm:BPHYT_RS16105 (291 letters) >NCBI__GCF_000319285.1:WP_007665545.1 Length = 281 Score = 137 bits (345), Expect = 3e-37 Identities = 83/263 (31%), Positives = 137/263 (52%), Gaps = 8/263 (3%) Query: 35 AWLVALLLFFPIFWMTITAFKTEQQAYASSLFFIPT---LDSFREVFARSNYFSFAWNSI 91 A + L FP ++ I++ + Q+ + + F PT D++ + NS+ Sbjct: 20 ALMACLFCVFPFYYAIISSLREGQELFTPAYF--PTGWHWDNYVVALVDNGIARSLLNSV 77 Query: 92 LISAGVTILCLILAVPAAYAMAFFPTRRTQKVLLWMLSTKMMPSVGVLVPIYLLWKNSGL 151 L++A LCL ++V AA+A+A P R + +L +L M P V VL ++ L + GL Sbjct: 78 LVAAVTVGLCLFVSVTAAFALARVPFRGRRVLLFTILCVSMFPQVAVLTGMFELVRFLGL 137 Query: 152 LDSVSGLVIVYTLINLPIAVWMSFTYFAEIPRDILEAGRIDGAATWQEIVYLLMPMSLPG 211 DS+ LVI YT +LP VW+ T+ IP ++ EA +DGA T I + P+ P Sbjct: 138 YDSLGALVISYTTFSLPFTVWVLTTFMKSIPVELEEAAIVDGAKTGTIIRRIFAPVLAPA 197 Query: 212 LASTALLLVILSWNEAFWSINL---SSSNAAPLTVFIASYSSPEGLFWAKLSAASLLAVA 268 + +T LL I +WNE +++ P+ + + S +S L W + AAS++ Sbjct: 198 MVTTGLLAFIGAWNEFMFALTFIISGDKRTVPVAISLFSGASSYELPWGSIMAASVVVTL 257 Query: 269 PILIVGWLSQKQLVRGLTFGAVK 291 PI+++ + QK++V GLT GA+K Sbjct: 258 PIIVLVLIFQKRIVSGLTSGAIK 280 Lambda K H 0.326 0.136 0.421 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: 232 Number of extensions: 12 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: 291 Length of database: 281 Length adjustment: 26 Effective length of query: 265 Effective length of database: 255 Effective search space: 67575 Effective search space used: 67575 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: 47 (22.7 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