Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate WP_139134956.1 BEN30_RS09695 transporter substrate-binding domain-containing protein
Query= uniprot:B2TBJ6 (286 letters) >NCBI__GCF_001746755.1:WP_139134956.1 Length = 244 Score = 128 bits (322), Expect = 1e-34 Identities = 92/267 (34%), Positives = 128/267 (47%), Gaps = 33/267 (12%) Query: 17 LGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQCNL 76 + ++ A A A + I EG Y P+NL G+L GF+ ++ LC +K +C Sbjct: 3 IATLSVIALTATAYAADKLRIGTEGAYPPFNLVDSNGELQGFDVDIAKALCASMKAECTF 62 Query: 77 VAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKAAP 136 V QDWDGMIP L KFD ++ ++SIT ER+K + FS+ Y F Sbjct: 63 VKQDWDGMIPALNKRKFDAIVASMSITEERQKAVDFSERYYTNKLQF------------- 109 Query: 137 GAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRVYKTSPE 196 V K D VD LKGK IG Q T+ +++ D A I++Y T Sbjct: 110 ---VGKKGMD-------VDISAAGLKGKVIGAQRATISGQWLEQNRAD-ADIKLYDTQEN 158 Query: 197 RDLDLANGRIDASFDD--VTYYAANIDKKETASIVMAGPKIGGPIW-GPGEGLAFRKQDA 253 LDLA+GR+DA D V Y N D A G P++ G G+A RK + Sbjct: 159 AYLDLASGRLDAILADAFVNYEWLNSDAGN------AFEAKGDPVFDGDLIGIAIRKGED 212 Query: 254 DLKAKFDTAISAALADGTVKKLSNKWF 280 DL+ K + AI +ADGT K++ K+F Sbjct: 213 DLRIKLNKAIKDIVADGTYGKINAKYF 239 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: 161 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: 286 Length of database: 244 Length adjustment: 25 Effective length of query: 261 Effective length of database: 219 Effective search space: 57159 Effective search space used: 57159 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 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