Align AapM, component of General L-amino acid porter; transports basic and acidic amino acids preferentially, but also transports aliphatic amino acids (catalyzes both uptake and efflux) (characterized)
to candidate WP_073037838.1 BUB04_RS05850 amino acid ABC transporter permease
Query= TCDB::Q52814 (384 letters) >NCBI__GCF_900129305.1:WP_073037838.1 Length = 223 Score = 104 bits (259), Expect = 3e-27 Identities = 71/219 (32%), Positives = 117/219 (53%), Gaps = 17/219 (7%) Query: 166 VVET--PLWGGLMVTLVLSFVGIAVSLPVGILLALGRRSRMPVIRMLCVTFIEVIRGVPL 223 VVET L GL +T+V++ G+ +G + L + SR +R L +IE IRG P+ Sbjct: 10 VVETFPMLLRGLKLTVVITIGGLFFGFILGSVAGLMKISRSLFLRKLAGIYIETIRGTPM 69 Query: 224 ITVLFMASVMLPLFLPTGWNVDKLLRALIGVSIFTSAYMAEVIRGGLQAIPKGQFEGADS 283 + +P+ +G + ++ +I +++ + AY+AE++RG +Q+I GQ E S Sbjct: 70 LVQAMFLYYGVPM--ASGVRIPPIVAGIIVIAVNSGAYIAEIVRGAIQSIDPGQMEAGRS 127 Query: 284 LGLGYWQKTRLIIMPQAIKLVIPSIVNTFIGTFKDTSLVTIIGMFDLL----GIVKLNFS 339 +GL Q R II PQA + +IP + N FI + KDTSL+ +IG+ +LL IV +NF Sbjct: 128 IGLTRSQTMRYIIWPQAFRRMIPPLGNQFIISLKDTSLLMVIGVGELLRTGQEIVAVNFR 187 Query: 340 DANWASAVTPITGLIFAGFIFWLFCFGMSRYSGFMERHL 378 AV G ++ + G+++ +E+HL Sbjct: 188 AFEVYMAV---------GIVYLVMTLGIAKALRALEQHL 217 Lambda K H 0.330 0.145 0.469 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: 210 Number of extensions: 9 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: 384 Length of database: 223 Length adjustment: 26 Effective length of query: 358 Effective length of database: 197 Effective search space: 70526 Effective search space used: 70526 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 24 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