Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate AO353_11995 AO353_11995 amino acid ABC transporter
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__pseudo3_N2E3:AO353_11995 Length = 251 Score = 127 bits (318), Expect = 3e-34 Identities = 84/271 (30%), Positives = 135/271 (49%), Gaps = 38/271 (14%) Query: 16 VLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQCN 75 +L AAA A A + + + +E Y P+N G++ GF+ ++ LC +++++C Sbjct: 8 LLAAAATLVFSANAMAAEKLKMGIEAAYPPFNNKDASGQVVGFDKDIGDALCAKMRVECE 67 Query: 76 LVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKAA 135 +V DWDG+IP L A KFD L+ ++SIT ER++ + F+ PY + F + PK Sbjct: 68 VVTSDWDGIIPALNAKKFDFLVSSLSITEERKQAVDFTDPYYSNKLQF------IAPK-- 119 Query: 136 PGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRVYKTSP 195 + D K D + LKGK IG Q T+ ++ D + + TI++Y T Sbjct: 120 --------NVDLKTD-------KDSLKGKIIGTQRATLAGTWLEDNYGNDVTIKLYDTQE 164 Query: 196 ERDLDLANGRIDASFDD--VTYYAANIDKKETASI----VMAGPKIGGPIWGPGEGLAFR 249 LDL +GR+DA D Y D + V+A KI G+A R Sbjct: 165 NAYLDLTSGRVDAILADKYANYDWLKSDAGKNYEFKGEPVVASDKI---------GIAVR 215 Query: 250 KQDADLKAKFDTAISAALADGTVKKLSNKWF 280 K +L+ K + A+ ++DGT KK+++K+F Sbjct: 216 KGQDELRNKLNAALKEIVSDGTYKKINDKYF 246 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: 159 Number of extensions: 9 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: 251 Length adjustment: 25 Effective length of query: 261 Effective length of database: 226 Effective search space: 58986 Effective search space used: 58986 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