Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS25635 AZOBR_RS25635 high-affinity branched-chain amino acid ABC transporter (permease protein) (fragment)
Query= uniprot:A0A165KER0 (358 letters) >FitnessBrowser__azobra:AZOBR_RS25635 Length = 328 Score = 190 bits (483), Expect = 4e-53 Identities = 119/336 (35%), Positives = 186/336 (55%), Gaps = 48/336 (14%) Query: 13 VALLV---LPLILQSFGNAWV-RIADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGA 68 +ALLV LP +L F + +IA+LAL+++LL+ +++V G AGLL LG+ AFY VGA Sbjct: 7 LALLVFVGLPAVLAGFDRGYFYQIANLALIFILLSASMHLVTGVAGLLHLGHAAFYGVGA 66 Query: 69 YLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYL 128 Y AL+++ GL + +P++ L+AA ++ PT++L Y Sbjct: 67 YTAALLSTKF--------------GL--GFTVTLPLSGLVAALIAFLVALPTMRLVSIYF 110 Query: 129 AIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDLGKRLEVFGFDINSVTL 188 A+ TL G+++ + + N V T GP G+ + K LE+FGF ++ Sbjct: 111 AVATLAIGQMLYLVMLNW---VEFTKGPNGI-----------IVTKGLELFGFSLSGRLA 156 Query: 189 YYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFG 248 YY +V + V+ RL S G A +IRED+ A AMG++T +K+ AF + A F Sbjct: 157 TYYTVATVVALCVLAIGRLSHSYYGNALRSIREDDQCADAMGVSTARLKMEAFTLSAFFA 216 Query: 249 GVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVA 308 GV+G+++ G++SP F ES++I+AMVV+GG+G +PG ++GA+LL LPE LR Sbjct: 217 GVAGSLWAHMTGYISPGDFKFSESILILAMVVVGGLGSLPGAVIGALLLILLPEGLR--- 273 Query: 309 GPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGL 344 A D R +++ L M + +LL P+GL Sbjct: 274 ----AFGD-------FRNIMVGLVMFLSILLLPKGL 298 Score = 24.3 bits (51), Expect = 0.005 Identities = 17/48 (35%), Positives = 28/48 (58%), Gaps = 7/48 (14%) Query: 9 IIGAVALLVLPLILQSFGNAWVRIADLALLYVLLALGLNIVVGYAGLL 56 +IGA+ L++LP L++FG D + V L + L+I++ GLL Sbjct: 259 VIGALLLILLPEGLRAFG-------DFRNIMVGLVMFLSILLLPKGLL 299 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: 312 Number of extensions: 16 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: 328 Length adjustment: 29 Effective length of query: 329 Effective length of database: 299 Effective search space: 98371 Effective search space used: 98371 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 Apr 09 2024. 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