Align Amino acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine (characterized, see rationale)
to candidate WP_010936196.1 DET_RS02295 amino acid ABC transporter permease
Query= uniprot:Q31RN9 (396 letters) >NCBI__GCF_000011905.1:WP_010936196.1 Length = 273 Score = 125 bits (315), Expect = 1e-33 Identities = 86/252 (34%), Positives = 139/252 (55%), Gaps = 33/252 (13%) Query: 157 RFLPTLWGVLFLVGLWLLQGGLGL-RPVSSND-----WSGLLLTLATALISMVCSLPLGI 210 R P W + G+++L GGL L +P D W G+ +T+ A++S L LG+ Sbjct: 23 RMDPWWW---LVAGVFVLTGGLMLFQPDPFLDIFKYVWVGIGITVLVAVVSYFLMLILGM 79 Query: 211 LLALGRQSSLPAIRWLSVTYIELFRGLPLVTILFFGQVMVPLMLDS-----------EWR 259 ALGR S +R L+ Y+E+ RG+PL+ L + P+++ S ++ Sbjct: 80 FGALGRLSKNTILRGLATFYVEIVRGIPLLVQLIWWYFAFPVIIQSIGQGLNFGPMMNYQ 139 Query: 260 IDRILRAIVGLTIFLSAYLAETVRGGLQAIPQGQFEAAAALGLNLFQTYRFIVLPQALRI 319 + I+ AI G+T AY++E R G+Q+IP+GQ EAA +LG++ Q R+++LPQALR+ Sbjct: 140 ANPIVMAIWGMTFCYGAYMSEIYRAGIQSIPKGQMEAARSLGMSHTQAMRYVILPQALRV 199 Query: 320 SIPAIVGLFLNLLQDTTLLSIVGLLELLGISRSILA---NPAYLGRYAEVYLFLGVLYWL 376 +P + F+ LL+DT+L+S V + +++ + R A NP EV+ +G+LY + Sbjct: 200 VLPPMGNEFIALLKDTSLVSTVAVADMVRLGREFTATNFNP------IEVWTMIGLLYLI 253 Query: 377 CCYGLAQLSRRL 388 L LS RL Sbjct: 254 ----LTLLSSRL 261 Lambda K H 0.329 0.142 0.471 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: 230 Number of extensions: 12 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: 396 Length of database: 273 Length adjustment: 28 Effective length of query: 368 Effective length of database: 245 Effective search space: 90160 Effective search space used: 90160 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: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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