Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate GFF2658 PS417_13550 amino acid ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__WCS417:GFF2658 Length = 284 Score = 129 bits (324), Expect = 7e-35 Identities = 96/287 (33%), Positives = 134/287 (46%), Gaps = 30/287 (10%) Query: 1 MKVKRTTAAKTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGG-YAPWNLTLPGGKLGGFE 59 MK KR A L AVL AA F+ A+ K + A+ Y P+ + G+ GFE Sbjct: 1 MKSKRM--ATWLGSAVLMLAAGFSWAAE----KPIVFAVAAEPYPPFTVKGGNGQWSGFE 54 Query: 60 PELVANLCERIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAAT 119 +L+ LCE +K +C + WDG+IP L A K DV+ ++S+T EREK IAFS+ Y + Sbjct: 55 VDLIHKLCEGMKAECQIKEVAWDGIIPSLLAKKIDVIFSSMSVTDEREKQIAFSRAYYDS 114 Query: 120 PATFAVADAKVLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFIN 179 +L A P V++S LKGK IG+Q TV ++ Sbjct: 115 ----------LLGVAGPKGSEVEISP-------------AGLKGKLIGVQISTVSANYLK 151 Query: 180 DGFKDIATIRVYKTSPERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAGPKIGGPI 239 +++IA ++ Y T + DL GRID D T A + E + + PI Sbjct: 152 KYYENIADLKYYDTQESANADLIAGRIDYMMADDTAIAMMVKTPEASGLAHIASVPYDPI 211 Query: 240 WGPGEGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDVTP 286 G G G RK+D LKA+ D AI L LS +F V+P Sbjct: 212 IGRGVGAGLRKEDTALKARLDKAIGELLVSKDYDDLSQHYFGLSVSP 258 Lambda K H 0.316 0.134 0.396 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: 177 Number of extensions: 9 Number of successful extensions: 2 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: 286 Length of database: 284 Length adjustment: 26 Effective length of query: 260 Effective length of database: 258 Effective search space: 67080 Effective search space used: 67080 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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