Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate SM_b20706 SM_b20706 amino acid uptake ABC transporter substrate-binding protein precursor
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__Smeli:SM_b20706 Length = 258 Score = 161 bits (408), Expect = 1e-44 Identities = 100/286 (34%), Positives = 151/286 (52%), Gaps = 36/286 (12%) Query: 3 VKRTTAAKTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPEL 62 +++ A L G L ++A+ A + + I EG Y P+N GK+GGF+ E+ Sbjct: 1 MRKLILALALAGTALSSSAVAA--------EKLKIGTEGAYPPFNFVDSSGKIGGFDVEI 52 Query: 63 VANLCERIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPAT 122 LCER+K++C +VAQDWDG+IPGL A K+D+++ ++ IT ER+K +AF+ PY T Sbjct: 53 GLALCERMKVECEVVAQDWDGIIPGLLAKKYDMIIASMFITEERKKQVAFTNPYYLAAMT 112 Query: 123 FAVADAKVLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGF 182 A A GAG+ S + L+GK IG QSGT +I + Sbjct: 113 HA---------APKGAGISAFSNE-------------ALQGKVIGAQSGTTQADYIAAVY 150 Query: 183 KDIATIRVYKTSPERDLDLANGRIDASFDD----VTYYAANIDKKETASIVMAGPKIGGP 238 D A I++Y T E +LD+ NGR+D D + + N D K +V P Sbjct: 151 PD-AEIKLYPTQDEANLDMVNGRLDLQVGDMLPLLDWVTKNDDGKGCCELV-GEPITDKK 208 Query: 239 IWGPGEGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 G G G+A R++D +++ K + A+ ADGT KK+++K+F DV Sbjct: 209 FVGDGVGIAVRQEDNEMREKLNKALDEIRADGTYKKINDKYFTIDV 254 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: 183 Number of extensions: 10 Number of successful extensions: 4 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: 258 Length adjustment: 25 Effective length of query: 261 Effective length of database: 233 Effective search space: 60813 Effective search space used: 60813 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