Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_050465262.1 AKL27_RS23270 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_001189915.1:WP_050465262.1 Length = 293 Score = 144 bits (363), Expect = 3e-39 Identities = 95/307 (30%), Positives = 160/307 (52%), Gaps = 61/307 (19%) Query: 41 LLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWI 100 +LAL + + + GLL L AF +GAY +L+ + T L Sbjct: 26 MLALSIYVTLS-CGLLSLANAAFMGIGAYTASLIT------------------MQTGLPF 66 Query: 101 VIPVAA--LLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKG 158 + +AA +L A ++G PTL+L G YLA+ TLGFGE++R+ + N+D +T GP G Sbjct: 67 PVALAAGGVLPALVALVIGIPTLRLSGVYLAMATLGFGEVVRVIVLNMD----ITGGPMG 122 Query: 159 LGQIDSVKVFGLDLGKRLEVFGFDINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMA 218 L + + T ++++ L+L +V R++ S++GRA+ A Sbjct: 123 LNGVPPI---------------------TEWWHIVLLLGA-TVYFLARVRRSKVGRAFEA 160 Query: 219 IREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAM 278 I+EDE+AA+ MG+N KLLAF +GA+ GV+G + + + P +++ +V I+ M Sbjct: 161 IKEDEVAARLMGVNVAGYKLLAFVIGAAIAGVAGGLNAHYTFTIGPNNYAFENAVDILTM 220 Query: 279 VVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIML 338 V GG ++ G ++G+ +L+ LPEVLR+ D RL + L +++++L Sbjct: 221 AVFGGTSNLIGPVIGSTILTLLPEVLRH-------FKDFRLAAN-------GLILVLVVL 266 Query: 339 LRPRGLW 345 P+G+W Sbjct: 267 YLPKGIW 273 Score = 23.1 bits (48), Expect = 0.010 Identities = 14/38 (36%), Positives = 23/38 (60%), Gaps = 2/38 (5%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGL 46 +IG+ L +LP +L+ F + R+A L+ VL+ L L Sbjct: 233 VIGSTILTLLPEVLRHFKD--FRLAANGLILVLVVLYL 268 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: 227 Number of extensions: 9 Number of successful extensions: 5 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: 358 Length of database: 293 Length adjustment: 28 Effective length of query: 330 Effective length of database: 265 Effective search space: 87450 Effective search space used: 87450 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: 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