Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_051305465.1 G494_RS22295 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000429965.1:WP_051305465.1 Length = 362 Score = 130 bits (328), Expect = 4e-35 Identities = 101/354 (28%), Positives = 167/354 (47%), Gaps = 38/354 (10%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLAL--LYVLLALGLNIVVGYAGLLDLGYVAFYAV 66 I+G L++ +L F + L + Y L+ +GL +++GYAG L +G+ F+A+ Sbjct: 9 ILGLAGLVIAVQLLTQFTGTAFYLTQLTMSAYYGLVIIGLGVLMGYAGQLSIGHAGFFAI 68 Query: 67 GAYLFALMASPHL--------------ADNFAAFAAMFPNGLHTSL-WIVIPVAALLAAF 111 G YL A + + +L AD ++ + L T + W +A AA Sbjct: 69 GGYLSAALTTHNLLSYKDSLCIRLLERADMLVLSEDIYGDALLTVVPWGACLMAVGTAAL 128 Query: 112 FGAMLGAPTLKLRGDYLAIVTLGFGEII-RIFLNNLDHPVNLTNGPKGLGQIDSVKVFGL 170 +L P LKL+G YLA+ TLGFG II RI L G+ + ++ Sbjct: 129 IALLLAVPVLKLKGHYLAMATLGFGTIIYRILL-----ATPYFGEADGISDVPPFQLLPA 183 Query: 171 DLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMG 230 G V ++ + YY+ +++V +++ L +SR+GRA ++ E AA+A+G Sbjct: 184 LGGLPPVVVSGSFDNRVVNYYVAWGILIVGMLLLLNLINSRVGRALRSLHSSEEAAEAVG 243 Query: 231 INTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGV 290 INT K+ F + A + ++G + + P +M+SV VA+V +GG+ ++ G Sbjct: 244 INTSRCKVQVFVLSAVYAALAGVFLAHYNAGIGPSEAGVMKSVRYVALVAVGGMTNLWGT 303 Query: 291 ILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 +L V L+ L LR V G LD A+ +LI +ML P G+ Sbjct: 304 LLMGVSLTFLS--LRGVF--------GSLDDAVFGVILIG-----VMLFAPEGI 342 Lambda K H 0.328 0.144 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: 294 Number of extensions: 16 Number of successful extensions: 3 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: 358 Length of database: 362 Length adjustment: 29 Effective length of query: 329 Effective length of database: 333 Effective search space: 109557 Effective search space used: 109557 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 (21.7 bits) S2: 49 (23.5 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