Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate GFF3026 PS417_15485 amino acid ABC transporter permease
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__WCS417:GFF3026 Length = 222 Score = 160 bits (405), Expect = 2e-44 Identities = 86/213 (40%), Positives = 135/213 (63%), Gaps = 7/213 (3%) Query: 3 LDFSPVWAGVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAA 62 LDF P+ LL GA VT++IT S LL +GL++ + +L+P R + + T + Sbjct: 11 LDFLPI------LLQGAWVTIQITVLSFLLSSALGLVLALIKLSPIRALSWTASTI-INV 63 Query: 63 IRGTPLLVQLFILFFGLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEA 122 IRG P++VQLF ++F LP G+ L AF GVIG+GI AY +E R I ++++GQ EA Sbjct: 64 IRGLPIIVQLFYIYFVLPDMGVHLTAFYAGVIGMGIAYSAYQAENFRTGIIAVEQGQREA 123 Query: 123 ARSIGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISV 182 A ++GM S L MR V+LPQA +PP GN + ++K+S+LVS +T+ ++ +GQ I S Sbjct: 124 AEALGMRSALMMRRVILPQAFRIALPPYGNTLVMMLKDSSLVSTITVAEMTRQGQLIASS 183 Query: 183 SYRSLEVYLAIAVVYFILTGATTLVLRRIELRL 215 +++++ VY +A++Y +++ LRR+E L Sbjct: 184 TFQNMTVYTLVALLYLLMSLPLVYGLRRMEQHL 216 Lambda K H 0.328 0.143 0.412 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: 135 Number of extensions: 5 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: 222 Length of database: 222 Length adjustment: 22 Effective length of query: 200 Effective length of database: 200 Effective search space: 40000 Effective search space used: 40000 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 (21.8 bits) S2: 45 (21.9 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