Align ABC transporter for L-Arginine and L-Citrulline, periplasmic substrate-binding component (characterized)
to candidate AO356_01470 AO356_01470 ABC transporter substrate-binding protein
Query= reanno::pseudo3_N2E3:AO353_03055 (258 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01470 Length = 259 Score = 368 bits (944), Expect = e-107 Identities = 181/258 (70%), Positives = 209/258 (81%), Gaps = 1/258 (0%) Query: 1 MKKLVLLGALALSVLSLPTFA-DEKPLKIGIEAAYPPFASKAPDGSIVGFDYDIGNALCE 59 MKKL + GALALSVLSL A D KP+++GIEA YPPF+ K PDG + GFD DIG+ALCE Sbjct: 1 MKKLAMFGALALSVLSLSAVAEDAKPIRLGIEAGYPPFSMKTPDGKLAGFDVDIGDALCE 60 Query: 60 EMKVKCVWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTNKYYNTPARLVMKAG 119 +MKVKCVWVEQEFDGLIPALKV+KIDAILSSM+ITDDRKK+VDFT KYY+TPAR VMK G Sbjct: 61 QMKVKCVWVEQEFDGLIPALKVKKIDAILSSMTITDDRKKNVDFTIKYYHTPARFVMKEG 120 Query: 120 TQVSDNLAELKGKKIGVQRGSIHNRFAEEVLKPLGAEIKPYGSQNEIYLDVAAGRLDGTV 179 + + D L ELKGKK+GV R S H+RFA EVL P G ++ YGSQ E LD+ AGRLD + Sbjct: 121 SNIKDPLTELKGKKVGVLRASTHDRFATEVLVPAGIDLVRYGSQQEANLDMVAGRLDAML 180 Query: 180 ADATLLDDGFLKTDSGKGFAFVGPAFTDEKYFGDGIGIAVRKGDKAELDKINAAIVAIRA 239 AD+ LD+GFLKTD+GKGFAFVGP + D KYFG G GIAVRKGDKA D+ NAAI IRA Sbjct: 181 ADSVNLDEGFLKTDAGKGFAFVGPTYEDAKYFGGGAGIAVRKGDKALADQFNAAITEIRA 240 Query: 240 NGKYKQIQDKYFNFDIYG 257 NG YK++QDKYF FD+YG Sbjct: 241 NGTYKKVQDKYFAFDVYG 258 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: 273 Number of extensions: 8 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: 259 Length adjustment: 24 Effective length of query: 234 Effective length of database: 235 Effective search space: 54990 Effective search space used: 54990 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