Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate GFF3454 PS417_17680 ABC transporter
Query= uniprot:A0A159ZWL6 (233 letters) >FitnessBrowser__WCS417:GFF3454 Length = 231 Score = 207 bits (526), Expect = 2e-58 Identities = 110/231 (47%), Positives = 150/231 (64%), Gaps = 4/231 (1%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 ML EN+ ++Y K L V++ V GE+VTL+G NGAGK+T L ++ G G I + Sbjct: 1 MLIVENIHSYYDKSHVLEGVSLTVNPGELVTLLGRNGAGKTTTLRSILGIICPRKGQIHF 60 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQEQMDKVLHLF 120 G+ LVGQ I R+ +A+VPE R +F LTVEENL + T + Q++ V +F Sbjct: 61 NGQALVGQKIFEIARQGLALVPENRGIFRLLTVEENLRIATRKTSRW----QLEDVYGMF 116 Query: 121 PRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQLR 180 PRLKER G +SGGEQQMLAI RAL++ PKLL+LDEP+ GLAP+I+ ++ I+ +++ Sbjct: 117 PRLKERRKNAGHALSGGEQQMLAIARALLNDPKLLILDEPTEGLAPVIVDELVKILRKVK 176 Query: 181 KDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYL 231 DG+ V LVEQN K+ADR YVLE GRVV +G+ EA DP ++ YL Sbjct: 177 DDGLPVLLVEQNLMVCDKLADRHYVLEQGRVVYEGSAEAFRADPTIKNRYL 227 Lambda K H 0.320 0.137 0.381 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: 163 Number of extensions: 4 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: 233 Length of database: 231 Length adjustment: 23 Effective length of query: 210 Effective length of database: 208 Effective search space: 43680 Effective search space used: 43680 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 (21.8 bits) S2: 46 (22.3 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