Align Monosaccharide-transporting ATPase; EC 3.6.3.17 (characterized, see rationale)
to candidate BPHYT_RS16925 BPHYT_RS16925 arabinose ABC transporter permease
Query= uniprot:B2SYR4 (338 letters) >FitnessBrowser__BFirm:BPHYT_RS16925 Length = 338 Score = 645 bits (1664), Expect = 0.0 Identities = 338/338 (100%), Positives = 338/338 (100%) Query: 1 MQARENLAQQAAKGAAEALIPQSNDKAKWWQQITEYSLIVIFVVMFATMSLTVDHFFSIE 60 MQARENLAQQAAKGAAEALIPQSNDKAKWWQQITEYSLIVIFVVMFATMSLTVDHFFSIE Sbjct: 1 MQARENLAQQAAKGAAEALIPQSNDKAKWWQQITEYSLIVIFVVMFATMSLTVDHFFSIE 60 Query: 61 NMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVAFAGVLCAMVLNATGNTFIAIVAA 120 NMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVAFAGVLCAMVLNATGNTFIAIVAA Sbjct: 61 NMLGLALSISQIGMVSCTMMFCLASRDFDLSVGSTVAFAGVLCAMVLNATGNTFIAIVAA 120 Query: 121 VAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLS 180 VAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLS Sbjct: 121 VAAGGVIGFVNGAVIAYLRINALITTLATMEIVRGLGFIVSHGQAVGVSSDTFIALGGLS 180 Query: 181 FFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQG 240 FFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQG Sbjct: 181 FFGVSLPIWVTLLCFIVFGVMLNQTVYGRNTLAIGGNPEASRLAGINVERTRVYIFLIQG 240 Query: 241 AVTALAGVILASRITSGQPNAAQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTV 300 AVTALAGVILASRITSGQPNAAQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTV Sbjct: 241 AVTALAGVILASRITSGQPNAAQGFELNVISACVLGGVSLLGGRATISGVVIGVLIMGTV 300 Query: 301 ENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKNRGSRD 338 ENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKNRGSRD Sbjct: 301 ENVMNLMNIDAFYQYLVRGAILLAAVLLDQLKNRGSRD 338 Lambda K H 0.326 0.139 0.396 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: 547 Number of extensions: 14 Number of successful extensions: 1 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: 338 Length of database: 338 Length adjustment: 28 Effective length of query: 310 Effective length of database: 310 Effective search space: 96100 Effective search space used: 96100 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