Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate PP_4486 PP_4486 lysine / arginine / ornithine ABC transporter - periplasmic binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__Putida:PP_4486 Length = 261 Score = 130 bits (326), Expect = 4e-35 Identities = 88/276 (31%), Positives = 137/276 (49%), Gaps = 31/276 (11%) Query: 15 AVLGAAA--IFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIKL 72 A+LGA A +F+ +QA + K + I +E Y P+ P G + GF+ ++ LCE +K Sbjct: 5 ALLGALALSVFSLVSQAAE-KPLKIGIEAAYPPFAFKQPDGSIAGFDYDIGNALCEEMKT 63 Query: 73 QCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVLP 132 +C V Q++DG+IP L+ K D ++ ++SIT +R+K + F+K Y TPA + D Sbjct: 64 KCTWVEQEFDGLIPALKVRKIDAILSSMSITDDRKKSVDFTKRYYLTPARLVMKDG---- 119 Query: 133 KAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFIND--GFKDIATIRV 190 TV +LKGK IG+Q G+++ +F + G K AT+ Sbjct: 120 -------------------TTVSDSLDELKGKKIGVQRGSIHDRFAKEVLGAKG-ATVVP 159 Query: 191 YKTSPERDLDLANGRIDASFDDVTYYAANIDKKETA-SIVMAGPKI-GGPIWGPGEGLAF 248 Y T E LD+A GR+D + D T K + GP +G G G+A Sbjct: 160 YGTQNEIYLDVAAGRLDGTVADATLLEDGFLKTDAGKGFAFVGPAFTDAKYFGDGIGIAV 219 Query: 249 RKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 RK D + + AI A A+G K++ +K+F D+ Sbjct: 220 RKGDKANVDRINAAIDAIRANGKYKEIESKYFNFDI 255 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: 187 Number of extensions: 11 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: 261 Length adjustment: 25 Effective length of query: 261 Effective length of database: 236 Effective search space: 61596 Effective search space used: 61596 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