Align ABC transporter for D-Alanine, permease component 2 (characterized)
to candidate Ac3H11_1956 Glutamate Aspartate transport system permease protein GltJ (TC 3.A.1.3.4)
Query= reanno::pseudo6_N2E2:Pf6N2E2_5403 (375 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1956 Length = 252 Score = 92.8 bits (229), Expect = 9e-24 Identities = 50/133 (37%), Positives = 81/133 (60%), Gaps = 1/133 (0%) Query: 240 IPELLALTLALTVYTAAFIAEIVRSGIKSVSHGQTEAARSLGLRNGPTLRKVIIPQALRV 299 +P + LAL +T+A IAE VRSGI+++ GQ A ++G T R V++P A R+ Sbjct: 108 VPGFALVVLALGFFTSARIAEQVRSGIQALPRGQRYAGMAVGFTTFQTYRYVLLPMAFRI 167 Query: 300 IIPPLTSQYLNLAKNSSLAAGIGYPEMVSLFAGTVLNQTGQAIEVIAITMSVYLAISISI 359 IIPPLTS+ +N+ KNSS+A + E+ ++FA +T + IEV S+Y+ + +I Sbjct: 168 IIPPLTSETMNIFKNSSVAFAVSVAEL-TMFAMQAQEETSRGIEVYLAVTSLYIISAFAI 226 Query: 360 SLLMNWYNKRIAL 372 + +M + KR+ + Sbjct: 227 NRIMAFIEKRVRI 239 Score = 50.4 bits (119), Expect = 5e-11 Identities = 28/70 (40%), Positives = 42/70 (60%), Gaps = 7/70 (10%) Query: 73 TLLVTFIGVILATILGFIIGVARLSQNW-IISKLATVYVEVFRNIPPLLQILFWY----- 126 T+ V+ + ++LA +LG +IG R Q+ +I +L +VE+FRNIP L+QI WY Sbjct: 41 TVSVSLLALVLALVLGSLIGTLRTLQDRPMIVRLGNAWVELFRNIPLLVQIFLWYHVIPS 100 Query: 127 -FAVFLSMPG 135 F V +PG Sbjct: 101 LFPVMKGVPG 110 Lambda K H 0.328 0.141 0.430 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: 242 Number of extensions: 14 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 375 Length of database: 252 Length adjustment: 27 Effective length of query: 348 Effective length of database: 225 Effective search space: 78300 Effective search space used: 78300 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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