Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate BPHYT_RS29525 BPHYT_RS29525 ABC transporter substrate-binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__BFirm:BPHYT_RS29525 Length = 260 Score = 148 bits (373), Expect = 1e-40 Identities = 96/278 (34%), Positives = 138/278 (49%), Gaps = 26/278 (9%) Query: 10 KTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCER 69 K L + A + A AKDW TV ++ Y P+ GKL GF+ +L +C R Sbjct: 3 KLLAALTVALLATVSIGAHAKDWSTVRFGVDASYPPFESKGSDGKLVGFDIDLGNEICAR 62 Query: 70 IKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAK 129 +K +C V D+DGMIP L+A KFD ++ ++S+TP+R + IAFS TP Sbjct: 63 MKAKCVWVENDFDGMIPALKAKKFDGVLSSMSMTPQRAEQIAFSNKLFNTPTRLV----- 117 Query: 130 VLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIAT-I 188 A G+G++ PT D+ LKGKT+G++ GT+ + ++ T + Sbjct: 118 ----AKKGSGIL----------PTADS----LKGKTVGVEQGTIQETYAKTYWEPKGTKV 159 Query: 189 RVYKTSPERDLDLANGRIDASFDDVTYYAANIDK-KETASIVMAGPKIGGP-IWGPGEGL 246 Y+ + DL +GR+DA+ D K A G + P I G G G+ Sbjct: 160 VPYQNQDQVYADLLSGRLDAALQDAVQAEIGFLKTPRGAGFDFVGKNLDDPKILGNGAGI 219 Query: 247 AFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 RK+D DLKAK D AI+ + DGT KKL K+F DV Sbjct: 220 GMRKEDTDLKAKVDKAIADIIKDGTYKKLEKKYFDFDV 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: 219 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: 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