Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate BPHYT_RS07735 BPHYT_RS07735 ABC transporter substrate-binding protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >lcl|FitnessBrowser__BFirm:BPHYT_RS07735 BPHYT_RS07735 ABC transporter substrate-binding protein Length = 264 Score = 236 bits (602), Expect = 4e-67 Identities = 115/249 (46%), Positives = 158/249 (63%) Query: 7 LGALALSVLSLPTFADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEEMKVKCV 66 L A A + AD K + G+EA+Y PF SK+P G + GFD D+GNA+C ++K KCV Sbjct: 13 LFAAASATAGTAAAADIKEVHFGVEASYAPFESKSPSGELQGFDIDVGNAVCAKLKAKCV 72 Query: 67 WVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGTQVSDNL 126 WVE FDGLIPAL+ RK +AI S M+ITD R+++VDFT+ Y P +++ K G+ + Sbjct: 73 WVENSFDGLIPALQARKFNAINSDMTITDQRRQAVDFTDPIYTIPNQMIAKKGSGLLPTP 132 Query: 127 AELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTVADATLLD 186 A LKGK +GV +G+I +A+ P G ++ PY +Q++IY D+A+GRLD DA Sbjct: 133 ASLKGKHVGVLQGTIQETYAKARWAPAGVDVVPYQTQDQIYADLASGRLDAAFQDAEAAS 192 Query: 187 DGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRANGKYKQI 246 GFLK G GF F GPA TDEK G G+G VRKGDKA D +N A+ ++A+G + Sbjct: 193 KGFLKKPQGAGFEFAGPAVTDEKLLGAGVGFGVRKGDKALKDALNQALKELKADGTIDRF 252 Query: 247 QDKYFNFDI 255 KYF+ + Sbjct: 253 AAKYFDVKV 261 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: 230 Number of extensions: 16 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: 258 Length of database: 264 Length adjustment: 25 Effective length of query: 233 Effective length of database: 239 Effective search space: 55687 Effective search space used: 55687 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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