Align ABC transporter permease; SubName: Full=Amino acid ABC transporter permease; SubName: Full=Histidine ABC transporter permease HisM; SubName: Full=Histidine transport system permease protein; SubName: Full=Histidine/lysine/arginine/ornithine ABC transporter permease HisM (characterized, see rationale)
to candidate 8500827 DvMF_1568 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= uniprot:A0A1N7U128 (237 letters) >FitnessBrowser__Miya:8500827 Length = 224 Score = 102 bits (255), Expect = 5e-27 Identities = 62/208 (29%), Positives = 103/208 (49%), Gaps = 10/208 (4%) Query: 21 SGVAMTLWLFIISVVLGFFLSIPLALARVSEHVWLRWPVEVYTYLFRGTPLYIQLLICYT 80 +G+ M++ L + S V G + + + RV W++ YT LFRG PL +QL I Y Sbjct: 17 AGLWMSVKLIVPSAVFGLLFGVIIGIVRVFGKPWMQRIANAYTALFRGVPLLVQLFILYF 76 Query: 81 GLYSLEIVQDNALLNQFFRNALNCTLLAFVLNTCAYTVEIFAGAIRNIPHGEIEAARAYG 140 GL ++ I + ++L F+L + AY E GA+ +I G++ AA+A G Sbjct: 77 GLPNIGI----------YLEPYAASVLGFILCSAAYNSEYVRGALLSIRQGQLRAAQALG 126 Query: 141 LHGWRLNLFVVVPAALRRALPAYSNEMILMLHATSLAFTATVADILKVARDANAETFLTF 200 + + +VVP A+RRALP NE++ ++ +SLA+ T ++ A+ + TF Sbjct: 127 FSTMQTLVSIVVPQAVRRALPGCGNEIVYLIKYSSLAYVITCIELTGEAKVLASRTFRFT 186 Query: 201 QAFGIAALLYMLLSFALVGLFRLAERRW 228 + F + Y+ L L E R+ Sbjct: 187 EVFLVVGAYYLFLVTVASWLLHKLEERF 214 Lambda K H 0.332 0.143 0.443 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: 173 Number of extensions: 9 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: 237 Length of database: 224 Length adjustment: 23 Effective length of query: 214 Effective length of database: 201 Effective search space: 43014 Effective search space used: 43014 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (22.0 bits) S2: 46 (22.3 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