Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_377 Lysine-arginine-ornithine-binding periplasmic protein precursor (TC 3.A.1.3.1)
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_377 Length = 249 Score = 129 bits (325), Expect = 5e-35 Identities = 86/265 (32%), Positives = 133/265 (50%), Gaps = 33/265 (12%) Query: 19 AAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKLQCNLVA 78 AAA+ A + +T+ + +E Y P+N G + GF+ E+ LC ++K++C +V Sbjct: 10 AAAVTLAFSAGAMAETLKMGIEAAYPPFNNKDASGNVVGFDKEIGDALCAKMKVECTVVT 69 Query: 79 QDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLPKAAPGA 138 DWDG+IP L A KFD L+ ++SIT ER++ + F+ PY + F Sbjct: 70 SDWDGIIPALNAKKFDFLISSMSITDERKQAVDFTDPYYSNKLQF--------------- 114 Query: 139 GVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRVYKTSPERD 198 + K D K D + LKGK IG Q T+ F+ D + D TI++Y T Sbjct: 115 -IAKKDIDFKTD-------KAALKGKIIGAQRATLAGTFLEDNYGDDITIKLYDTQENAY 166 Query: 199 LDLANGRIDASFDD--VTYYAANIDKKETASIVMAGPKIGGPIWGPGE-GLAFRKQDADL 255 LDL +GR+D D V Y D + G P+ + G+A RK+D + Sbjct: 167 LDLTSGRLDGILADKYVNYEWLKSDAGRSYEFK------GDPVEESDKIGIAVRKKD-PI 219 Query: 256 KAKFDTAISAALADGTVKKLSNKWF 280 + K +TA+ +ADGT KK+++K+F Sbjct: 220 REKLNTALKEIVADGTYKKINDKYF 244 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: 11 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: 249 Length adjustment: 25 Effective length of query: 261 Effective length of database: 224 Effective search space: 58464 Effective search space used: 58464 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