Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate PfGW456L13_379 Amino acid ABC transporter, permease protein
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_379 Length = 229 Score = 216 bits (550), Expect = 3e-61 Identities = 111/221 (50%), Positives = 157/221 (71%), Gaps = 1/221 (0%) Query: 4 DYNVIWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIR 63 ++ VI + LP G TL+L+A++++ GLL A+PLG+ R S+ V + Y + R Sbjct: 2 NWEVIIKWLPKLAQGATLTLELVAIAVIAGLLLAIPLGIARSSRLWWVRAFPYGYIFFFR 61 Query: 64 GTPMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRAT 123 GTP+LVQLFL+YYGLAQF+A+R S +WP+L +CA ++T+AY AEI+ G+++A Sbjct: 62 GTPLLVQLFLVYYGLAQFDAIRNSSMWPYLRDPFWCATATMTLHTAAYIAEILRGAIQAI 121 Query: 124 PNGEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGA 183 P GEIEAA+A+GMS+ K I+LP A R LP YSNEVI+ML+ ++LAS VTL+++TG Sbjct: 122 PPGEIEAARALGMSKPKALFYIMLPRAARIGLPAYSNEVILMLKASALASTVTLLELTGM 181 Query: 184 ARTVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHRWL 224 ART+ A+ YLP E + AG+FYL M ++LVR FK+ E RWL Sbjct: 182 ARTIIARTYLPVEIFFAAGMFYLVMAYVLVRGFKLLE-RWL 221 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: 174 Number of extensions: 4 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: 232 Length of database: 229 Length adjustment: 23 Effective length of query: 209 Effective length of database: 206 Effective search space: 43054 Effective search space used: 43054 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