Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_043917831.1 jaqu_RS04945 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000877395.1:WP_043917831.1 Length = 429 Score = 105 bits (261), Expect = 3e-27 Identities = 114/418 (27%), Positives = 176/418 (42%), Gaps = 85/418 (20%) Query: 13 VALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFA 72 VALL L N + I ++A++ ++ALG+N+ GYAGL ++G + F A+G Sbjct: 11 VALLFLGTGFVQSWNVALTILNMAMVSAIMALGVNMQWGYAGLFNVGVMGFVALGGLGAV 70 Query: 73 LMASPHLAD--------------------------------------------NFAAFAA 88 L+ P + + F AF A Sbjct: 71 LVGMPPVNEAWAAGGLRVVGGLLIGAATIAAAVMAWDRMRRFRGLAVAALLLIGFFAFRA 130 Query: 89 MFPNGLHT---------------SLWIVI--PVAALLAAFFGAMLGAPTLKLRGDYLAIV 131 +F G+ L I+I PV LLAA +G L LR DYLAI Sbjct: 131 VFDGGVQMVEAVNPASTGYLGGLGLPIIIGWPVGGLLAAGAAWFIGKTALGLRSDYLAIA 190 Query: 132 TLGFGEIIRIFLNNLDHPVNLTNGPKGLG-----QID-----SVKVFGLDLGKRLEVFGF 181 TLG EI+ L N D GL ++D + F +LG V Sbjct: 191 TLGIAEIVIAVLKNEDWLARGVKNVIGLPRPVPYEVDLQNSAGFREFAAELGTD-PVTAS 249 Query: 182 DINSVTLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAF 241 I Y LF V++ + + + S GR AIR++E+AA+AMG + L F Sbjct: 250 TIAVKLAYLGLFGVVLGLLLWLAQAALASPWGRMMRAIRDNEVAAEAMGKDVTARHLQIF 309 Query: 242 GMGASFGGVSGAMFGAFQGFVSPESFS-LMESVMIVAMVVLGGIGHIPGVILGAVLLSAL 300 +G++ G++GAM G ++P ++ L + +I MV++GG G+ G +LG L+ L Sbjct: 310 ILGSAVCGLAGAMMTTLDGQLTPGTYQPLRYTFLIWVMVIVGGSGNNWGAVLGGFLIWWL 369 Query: 301 -PEVLRYVAGPLQAMTDGRLD-----------SAILRQLLIALAMIIIMLLRPRGLWP 346 +V A + +T G D +A +R L + L +++++ PRGL P Sbjct: 370 WVQVEPLGALLMDTITAGMADGTWLKGHLQDAAAHMRLLTMGLVLLLVLRFSPRGLIP 427 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: 427 Number of extensions: 23 Number of successful extensions: 4 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: 429 Length adjustment: 31 Effective length of query: 327 Effective length of database: 398 Effective search space: 130146 Effective search space used: 130146 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