Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate WP_022529984.1 L248_RS09480 transporter substrate-binding domain-containing protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >NCBI__GCF_000469325.1:WP_022529984.1 Length = 274 Score = 97.4 bits (241), Expect = 3e-25 Identities = 69/214 (32%), Positives = 108/214 (50%), Gaps = 17/214 (7%) Query: 43 DGSIVGFDYDIGNALCEEM---KVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKK 99 DG I GFD DI + + V+ +V IP LK +DAI+++M+ T DR+K Sbjct: 61 DGQIKGFDIDIAKEVSHRIIGQNVQINFVPVTSQTRIPLLKNGNVDAIIATMTNTPDRRK 120 Query: 100 SVDFTNKYYNTPARLVMKAGTQVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKP 159 VDF++ Y+N L++K G+ + KG K+ +GS + ++V A++ Sbjct: 121 VVDFSDTYFNAGQALLVKKGSPIKSVKDLKKGTKVIGVQGSNSVQNIKKVAP--DAQVLQ 178 Query: 160 YGSQNEIYLDVAAGRLDGTVADATLLDDGFL--KTDSGKGFAFVGPAFTDEKYFGDGIGI 217 + + + +G+ DA D+G L + + VG FT E Y I Sbjct: 179 LSDYAQAFTALQSGQ-----GDALTTDNGILYGMSADNPNYVVVGGTFTKEPY-----AI 228 Query: 218 AVRKGDKAELDKINAAIVAIRANGKYKQIQDKYF 251 AV KG KA LD +N A+ ++R +G YKQI+DK+F Sbjct: 229 AVNKGQKAFLDDVNLALTSMRQDGTYKQIEDKWF 262 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: 193 Number of extensions: 8 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: 274 Length adjustment: 25 Effective length of query: 233 Effective length of database: 249 Effective search space: 58017 Effective search space used: 58017 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 24 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