Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate BPHYT_RS05500 BPHYT_RS05500 histidine/lysine/arginine/ornithine ABC transporter permease HisM
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__BFirm:BPHYT_RS05500 Length = 237 Score = 210 bits (534), Expect = 2e-59 Identities = 110/214 (51%), Positives = 142/214 (66%), Gaps = 1/214 (0%) Query: 18 GLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGTPMLVQLFLIYYG 77 G+V TL LL +S+ G ++PL + RVSK+ ++ WLYTYV RGTP+ VQL L Y G Sbjct: 22 GVVITLWLLVVSIGLGFCLSIPLAVARVSKKKWLSRLVWLYTYVFRGTPLYVQLLLCYTG 81 Query: 78 LAQFEAVRESFLW-PWLSSATFCACLAFAINTSAYTAEIIAGSLRATPNGEIEAAKAMGM 136 L E +R L + C LAF +NT AYT EI AG+++ATP GEIEAA+A GM Sbjct: 82 LYSLEIIRNHELTNAFFRDGMHCTLLAFTLNTCAYTTEIFAGAIKATPYGEIEAARAYGM 141 Query: 137 SRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAARTVNAQYYLPFE 196 S F +Y+R++LPSALRRALP YSNEVI+ML T++A T+ DI AR VN+ Y F Sbjct: 142 SSFTLYRRVILPSALRRALPYYSNEVILMLHATTVAFTATVPDILKIARDVNSATYQSFN 201 Query: 197 AYITAGVFYLCMTFILVRLFKMAEHRWLGYLAPR 230 A+ A + YLC++F LV LF+ AE RWL YL P+ Sbjct: 202 AFGIAALLYLCISFALVWLFRRAERRWLAYLRPQ 235 Lambda K H 0.329 0.139 0.427 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: 176 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: 232 Length of database: 237 Length adjustment: 23 Effective length of query: 209 Effective length of database: 214 Effective search space: 44726 Effective search space used: 44726 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