Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate BPHYT_RS08555 BPHYT_RS08555 ABC transporter permease
Query= reanno::pseudo3_N2E3:AO353_03045 (232 letters) >FitnessBrowser__BFirm:BPHYT_RS08555 Length = 219 Score = 133 bits (335), Expect = 2e-36 Identities = 74/217 (34%), Positives = 124/217 (57%), Gaps = 9/217 (4%) Query: 6 NVIWEALPLYFGGLVTTLKLLALSLLFGLLAALPLGLMRVSKQPIVNMSAWLYTYVIRGT 65 +++ E+LP+ G V T+K LS++FGL+A L LM VS ++N A +Y V+RGT Sbjct: 5 SLLVESLPVLAQGAVLTVKFAVLSMIFGLIAGAVLALMGVSHNRVLNWIARIYVSVMRGT 64 Query: 66 PMLVQLFLIYYGLAQFEAVRESFLWPWLSSATFCACLAFAINTSAYTAEIIAGSLRATPN 125 P+LVQ+F+IYYGL F + T +A + N +AY +E + G++ N Sbjct: 65 PLLVQIFVIYYGLPSFGISLDP---------TPAGVIALSANVAAYLSESMRGAILGIHN 115 Query: 126 GEIEAAKAMGMSRFKMYKRILLPSALRRALPQYSNEVIMMLQTTSLASIVTLIDITGAAR 185 G+ AA ++G+SR + + ++ P ALR A+P SN +I +++ TSL S++T+ ++ +A+ Sbjct: 116 GQWLAAYSLGLSRRQTLRYVIAPQALRIAVPSMSNSLISLIKDTSLVSVITVTELLRSAQ 175 Query: 186 TVNAQYYLPFEAYITAGVFYLCMTFILVRLFKMAEHR 222 + A Y P Y+ A Y + +L + + E R Sbjct: 176 EIIASTYQPLPLYLAAAAVYWVLCQVLESVQRWYERR 212 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: 118 Number of extensions: 3 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: 219 Length adjustment: 22 Effective length of query: 210 Effective length of database: 197 Effective search space: 41370 Effective search space used: 41370 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