Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS10140 BPHYT_RS10140 ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__BFirm:BPHYT_RS10140 Length = 260 Score = 116 bits (290), Expect = 6e-31 Identities = 84/279 (30%), Positives = 127/279 (45%), Gaps = 27/279 (9%) Query: 10 KTLIGAV-LGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCE 68 K+L+ ++ + AI + A AK+W TV ++ Y P+ GKL GF+ +L +C Sbjct: 2 KSLLASLSIALLAISSGNAIAKEWSTVRFGVDASYPPFESKSADGKLVGFDIDLGNEICR 61 Query: 69 RIKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADA 128 R+ +C V +DGMIP L+ KFD ++ +S+TP R+ IAFS P Sbjct: 62 RLNAKCVWVENAFDGMIPALKGRKFDGVLSTMSMTPARQAQIAFSSKVFRIPTRLVAKKG 121 Query: 129 KVLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDI-AT 187 + PT +A LKGK IG++ G++ + ++ A Sbjct: 122 STI-------------------TPTPEA----LKGKRIGVEQGSIQETYAKTYWEPAGAV 158 Query: 188 IRVYKTSPERDLDLANGRIDASFDD-VTYYAANIDKKETASIVMAGPKI-GGPIWGPGEG 245 I Y+ DL GRIDAS + V + AG + G G Sbjct: 159 IVAYQDQDLVYSDLLAGRIDASLQNAVQADVGFLRTPRGKDFAFAGNALYDAKTLGSGTA 218 Query: 246 LAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 + RK+D DLKA+ D AI+ ADGT +++ K+F DV Sbjct: 219 IGLRKEDTDLKAQIDKAIADTRADGTYDRIAKKYFDFDV 257 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: 7 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: 260 Length adjustment: 25 Effective length of query: 261 Effective length of database: 235 Effective search space: 61335 Effective search space used: 61335 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