Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate 3608830 Dshi_2222 extracellular solute-binding protein family 3 (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_3431 (257 letters) >FitnessBrowser__Dino:3608830 Length = 242 Score = 102 bits (254), Expect = 7e-27 Identities = 73/250 (29%), Positives = 126/250 (50%), Gaps = 19/250 (7%) Query: 3 KLVLLGALALSVLSLPTFA--DEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCEE 60 K ++ G ++++ FA D +++G E AYPP+ G + GF+ ++G+ LC Sbjct: 2 KTLIFGTALATLMAGAAFAASDGTTVRMGTEGAYPPYNFLNDAGEVDGFERELGDELCAR 61 Query: 61 MKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITEDRKKSVDFTNKYYNTPARLVMKAGT 120 ++ C WV ++D +IP L D I++ MSIT++R + +DFT Y M Sbjct: 62 AELTCEWVTNDWDSIIPNLVSGNYDTIIAGMSITDERDEVIDFTQNYTQPDPSAFM---- 117 Query: 121 AVSENLAELKGKNIGVQRGSIHERFAREVLAPLGAEIKPYGSQNEIYLDVAAGRLDGTVA 180 +SE++ +L+G I Q G+I +A GA + + S +E V G D +A Sbjct: 118 GLSEDV-DLEGGVIAAQTGTIQASH----IASTGATLIEFASPDETVAAVRNGEADAVLA 172 Query: 181 DATLLDDGFLKTDAGKGFAFVGPAFTDVKYFGDGVGIAVRKGD-ALKDKINTAIAAIREN 239 D L+ F+ +A FVG DV G G+G+ +R+ D L+ K + AI +++++ Sbjct: 173 DKAFLEP-FVTENA--DLVFVG---EDV-LLGGGIGMGLRESDPELRAKFDAAIQSMKDD 225 Query: 240 GKYKQIQDKY 249 G + K+ Sbjct: 226 GSLNALIAKW 235 Lambda K H 0.318 0.138 0.394 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: 158 Number of extensions: 11 Number of successful extensions: 2 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: 257 Length of database: 242 Length adjustment: 24 Effective length of query: 233 Effective length of database: 218 Effective search space: 50794 Effective search space used: 50794 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: 46 (22.3 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