Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate WP_029133949.1 A3GO_RS0114170 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KER0 (358 letters) >NCBI__GCF_000428045.1:WP_029133949.1 Length = 410 Score = 258 bits (658), Expect = 3e-73 Identities = 149/339 (43%), Positives = 212/339 (62%), Gaps = 48/339 (14%) Query: 9 IIGAVAL--LVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAV 66 + GAV + LV P + ++ I AL+YV+L LGLNIVVG AGLLDLG+VAFYAV Sbjct: 98 LAGAVTVFALVFPYLFDTYQT---NIMTTALMYVVLGLGLNIVVGMAGLLDLGFVAFYAV 154 Query: 67 GAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGD 126 GAY +AL+ + H F W+ +P+ AL AA FG +LG P L+LRGD Sbjct: 155 GAYSYALL-NAHFGIGF---------------WMALPIGALFAASFGIILGFPVLRLRGD 198 Query: 127 YLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSV 186 YLAIVTLGFGEIIR+ L N + + GP G+ I +FG++L + + Sbjct: 199 YLAIVTLGFGEIIRLILENWNE---FSQGPSGISNIPRPGMFGIELS---------LEAA 246 Query: 187 TLY-YYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGA 245 LY YY+ + LV+V++ + RLQDSR+GRAW+A+REDEIA +AMGI+ KL AF +GA Sbjct: 247 ILYIYYIMVALVIVTIFVVNRLQDSRLGRAWIALREDEIACQAMGIDKTKTKLTAFALGA 306 Query: 246 SFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLR 305 ++ G+ G +F A F++P SF+ +ES +I+++VVLGG+G I GVI+GA++L LPE LR Sbjct: 307 TWAGMMGVIFAAKTTFINPASFTFLESAIILSIVVLGGMGSILGVIVGALVLILLPEYLR 366 Query: 306 YVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 A++D R L ++++M+ +P+G+ Sbjct: 367 -------ALSD-------YRMLAFGAILVVMMIFKPQGI 391 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: 400 Number of extensions: 19 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: 410 Length adjustment: 30 Effective length of query: 328 Effective length of database: 380 Effective search space: 124640 Effective search space used: 124640 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