Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate GFF3832 PGA1_262p02360 putative histidine-binding periplasmic protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__Phaeo:GFF3832 Length = 259 Score = 177 bits (449), Expect = 2e-49 Identities = 97/249 (38%), Positives = 147/249 (59%), Gaps = 4/249 (1%) Query: 11 ALSVLSLPTFADEKPLKIGIEAA-YPPFASKAPDGSIVGFDYDIGNALCEEMKVKCVWVE 69 A +V + A +P+KIG+ A YPPFAS G VG++ D+ NA+C ++ CV Sbjct: 14 AATVAATCAVAQAEPVKIGVAAEPYPPFASLDSSGQWVGWEIDVINAVCAAAELDCVITP 73 Query: 70 QEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNLAEL 129 +DG+IP+L +++DAI++SMSIT++R K++DF++ YYNTPA +V + L Sbjct: 74 VAWDGIIPSLTGQQVDAIMASMSITEERLKTIDFSDPYYNTPAVIVADKSMDIEATPESL 133 Query: 130 KGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLDDGF 189 GK +G+Q +IH +A+E K +E++ Y +Q+E D+ AGR+D T AD+ + D F Sbjct: 134 AGKVVGIQASTIHQAYAQEHFK--DSELRVYQTQDEANQDLFAGRIDATQADSIAMAD-F 190 Query: 190 LKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQIQDK 249 + +D+G G DE G G+G VRKGD L +N I AI A+G + +I K Sbjct: 191 VGSDAGGCCEIKGAVANDEAILGKGVGAGVRKGDSDVLAALNKGIAAILADGTHAEITSK 250 Query: 250 YFNFDIYGK 258 YF IY + Sbjct: 251 YFTTSIYSE 259 Lambda K H 0.318 0.138 0.395 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: 182 Number of extensions: 11 Number of successful extensions: 3 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: 258 Length of database: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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