Align ABC transporter for L-Histidine, permease component 1 (characterized)
to candidate 5210737 Shew_3165 polar amino acid ABC transporter, inner membrane subunit (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_2554 (222 letters) >FitnessBrowser__PV4:5210737 Length = 226 Score = 140 bits (353), Expect = 2e-38 Identities = 77/211 (36%), Positives = 128/211 (60%), Gaps = 12/211 (5%) Query: 11 GVPQLLAGALVTVEITAASLLLGCVMGLLVGIGRLNPKRRVVYALCTAYVAAIRGTPLLV 70 G+ +L G VT+ +T +++LG ++G+ + +++ + + + YV IRGTP++V Sbjct: 20 GIYLILNGLKVTLIVTLFAMILGAILGVATTLMKMSSRWYLRWP-ANLYVGVIRGTPVVV 78 Query: 71 QLFILFFGLPQFGILLPAF-----VCGVIGLGIYSGAYVSEVVRGAIQSIDKGQMEAARS 125 QL IL+F I+L + +I G+ SGAY+SE++R IQ++DKGQ EAARS Sbjct: 79 QLVILYF------IVLATWDVDKVSAAIIAFGLNSGAYISEIIRAGIQAVDKGQTEAARS 132 Query: 126 IGMSSGLAMRTVVLPQAVVRMIPPLGNEFIALIKNSALVSLLTIHDLMHEGQKIISVSYR 185 +G+S + M+ V+LPQA+ ++P LGNEFI L+K +A++ + DLM G+ I S ++ Sbjct: 133 LGLSQAVTMKEVILPQAIKNILPALGNEFIVLLKETAVIGFIGGVDLMRSGEIIRSRTFE 192 Query: 186 SLEVYLAIAVVYFILTGATTLVLRRIELRLR 216 A++Y LT + T +L + E RL+ Sbjct: 193 DSVPLFTCALIYLALTYSFTFMLSKFEKRLK 223 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: 148 Number of extensions: 7 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: 222 Length of database: 226 Length adjustment: 22 Effective length of query: 200 Effective length of database: 204 Effective search space: 40800 Effective search space used: 40800 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: 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