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) >FitnessBrowser__BFirm:BPHYT_RS07735 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:
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