Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate SMc03133 SMc03133 amino-acid transport system permease ABC transporter protein
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__Smeli:SMc03133 Length = 323 Score = 145 bits (365), Expect = 1e-39 Identities = 71/197 (36%), Positives = 126/197 (63%), Gaps = 1/197 (0%) Query: 18 GALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLVQLFILFF 77 G + T+ I+ S+ + V+ L+ I +L+ K V+Y L T Y + RG PLL+Q++I++ Sbjct: 121 GVVTTLYISVISIAVATVIALVGAIAKLS-KNGVIYGLATFYTSLFRGLPLLMQIYIIYL 179 Query: 78 GLPQFGILLPAFVCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARSIGMSSGLAMRTV 137 GLPQ G ++ A G++ L + GAY++E+ R I+SI +GQ E A ++G+S M V Sbjct: 180 GLPQVGYVISAVPAGILALSLCYGAYMTEIFRAGIESIPRGQTEGATALGLSPSQTMGLV 239 Query: 138 VLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYRSLEVYLAIAVVY 197 +LPQA+ +IPP GN+FIA++K+S+L+S++ + +LM+ + +R +E+ + +++Y Sbjct: 240 ILPQAMRVIIPPTGNQFIAMLKDSSLISVVGVWELMYLARTQGQTEFRHIEMLITASMIY 299 Query: 198 FILTGATTLVLRRIELR 214 +IL+ + R+E R Sbjct: 300 WILSIGLEYMQSRVEAR 316 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: 204 Number of extensions: 8 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: 222 Length of database: 323 Length adjustment: 25 Effective length of query: 197 Effective length of database: 298 Effective search space: 58706 Effective search space used: 58706 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: 47 (22.7 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