Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_051378059.1 H566_RS0104985 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000482785.1:WP_051378059.1 Length = 392 Score = 168 bits (425), Expect = 3e-46 Identities = 107/315 (33%), Positives = 172/315 (54%), Gaps = 44/315 (13%) Query: 37 LLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMAS-----PHLADNFAAFAAMFP 91 LLY + LGLNI +GYAG+++ +AF+ VG+Y A + + PHLA Sbjct: 107 LLYATVCLGLNIQIGYAGVVNFSAMAFFGVGSYAAAWLTTNAPTLPHLA----------- 155 Query: 92 NGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVN 151 V+ +A AA GAML P L+ RG Y ++VT+ F + R F+ VN Sbjct: 156 ---------VLALAGGAAALVGAMLLFPVLRTRGHYASLVTVAFAVLFRSFME-----VN 201 Query: 152 LTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSR 211 T G ++ + +FG D +E+FG Y + + + ++ + +R++ S Sbjct: 202 ETFGGAQGMKLPGLSMFGHDFNDDIELFGLTFTFYAGYAAVAFAIALSALALTWRIERSW 261 Query: 212 IGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLME 271 IG + A+R DEIAA GIN K+ AF +G +F GV+GA+F GFV+P +F+ + Sbjct: 262 IGVNFDAVRSDEIAAACFGINIARWKITAFLIGNAFAGVAGALFALMTGFVAPNNFNFGD 321 Query: 272 SVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIAL 331 S+++++++VLGG+G++ G++ A+++ LPE LQA+ + R LL A Sbjct: 322 SLVMLSILVLGGLGNLWGILPAALIVIILPE-------KLQAIQEYRF-------LLYAA 367 Query: 332 AMIIIMLLRPRGLWP 346 A+I I+L RP+GL+P Sbjct: 368 AVIAILLFRPQGLFP 382 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: 444 Number of extensions: 38 Number of successful extensions: 4 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: 392 Length adjustment: 30 Effective length of query: 328 Effective length of database: 362 Effective search space: 118736 Effective search space used: 118736 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: 50 (23.9 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