Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate H281DRAFT_02375 H281DRAFT_02375 amino acid/amide ABC transporter ATP-binding protein 1, HAAT family
Query= uniprot:A0A165KC86 (260 letters) >FitnessBrowser__Burk376:H281DRAFT_02375 Length = 259 Score = 174 bits (442), Expect = 1e-48 Identities = 96/253 (37%), Positives = 151/253 (59%), Gaps = 10/253 (3%) Query: 7 EVVLKVAGISKRFGGLQALSDVGITIKRGQVYGLIGPNGAGKTTFFNVITGLYTPDAGTF 66 + +L+ G+++ F G A++ V + ++RG ++ LIGPNGAGKTT FN++T P AG Sbjct: 5 DTILETRGLTREFKGFIAVNGVNLRVRRGSIHALIGPNGAGKTTCFNLLTKFLEPTAGQI 64 Query: 67 ELAGKPYEPTAVHEVAKAGIARTFQNIRLFAEMTALENVMVGRHIRTGSGLFGAVFRTKG 126 G+ ++A+ GI R+FQ +F +TAL+NV +G G+ Sbjct: 65 VFNGEDITNERPAQIARRGIIRSFQISAVFPHLTALQNVRIGLQRSLGTAF-------HF 117 Query: 127 FKAEEA--AIAKRAQELLDYVGIGKFADYKARTLSYGDQRRLEIARALATDPQLIALDEP 184 +K+E + RA +LL VG+ FAD LSYG +R LEIA LA +P+L+ LDEP Sbjct: 118 WKSERTLRQLDDRAMDLLTQVGLTDFADVLTVELSYGRKRALEIATTLAMEPELMLLDEP 177 Query: 185 AAGMNATEKVQLRELIDRIRNDNRTILLIEHDVKLVMGLCDRVTVLDYGKQIAEGNPAEV 244 GM + ++ LI ++ + RTIL++EH++ ++ G+ D +TVL G+ +AEG+ AEV Sbjct: 178 TQGMGHEDVDRVTALIKKV-SSGRTILMVEHNMNVIAGISDTITVLQRGEVLAEGSYAEV 236 Query: 245 QKNEKVIEAYLGT 257 KN V++AY+G+ Sbjct: 237 SKNPLVMQAYMGS 249 Lambda K H 0.319 0.137 0.384 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: 190 Number of extensions: 8 Number of successful extensions: 3 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: 260 Length of database: 259 Length adjustment: 24 Effective length of query: 236 Effective length of database: 235 Effective search space: 55460 Effective search space used: 55460 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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