Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate SMc00140 SMc00140 amino-acid binding periplasmic protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__Smeli:SMc00140 Length = 260 Score = 224 bits (571), Expect = 1e-63 Identities = 119/258 (46%), Positives = 169/258 (65%), Gaps = 5/258 (1%) Query: 2 KKLVLLGALALSVLSLPT-FADEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 ++L + A+ VL A+ + + IG E AYPPF + DG++ GFD DI ALCEE Sbjct: 5 RRLAATASAAVFVLMAGVAMAEGEKVVIGTEGAYPPFNNLESDGTLTGFDIDIAKALCEE 64 Query: 61 MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAGT 120 MK +C +V Q++DG+IPAL +K DAI++SMSIT++RK+ VDFTNKYYNTP +V+ + Sbjct: 65 MKAECTFVTQDWDGIIPALIAKKFDAIVASMSITEERKQQVDFTNKYYNTPPAIVVPKDS 124 Query: 121 QVSD-NLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTV 179 +++ A L GK +G Q + H+ +AE +K +E+K Y + +E LD+A GR+D + Sbjct: 125 PITEATAAALSGKALGAQGSTTHSNYAEAHMKE--SEVKLYPTADEYKLDLANGRIDAAI 182 Query: 180 ADATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRA 239 D +L + +LKT+ G +G D G+G GIA+RKGD A +K+N AI AIRA Sbjct: 183 DDVVVLSE-WLKTEDGACCKLLGTLPIDPVINGEGAGIAIRKGDDALREKLNKAIEAIRA 241 Query: 240 NGKYKQIQDKYFNFDIYG 257 NGKYKQI +KYF FD+YG Sbjct: 242 NGKYKQINEKYFPFDVYG 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: 214 Number of extensions: 11 Number of successful extensions: 4 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: 260 Length adjustment: 24 Effective length of query: 234 Effective length of database: 236 Effective search space: 55224 Effective search space used: 55224 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