Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate Pf1N1B4_5844 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5844 Length = 259 Score = 129 bits (324), Expect = 7e-35 Identities = 89/283 (31%), Positives = 147/283 (51%), Gaps = 38/283 (13%) Query: 10 KTLIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCER 69 + + GA+ A ++ + A A D K + + +E GY P+++ P GKL GF+ ++ LCE+ Sbjct: 4 RVMFGAL--ALSMLSLTAMADDAKPIRLGIEAGYPPFSMKNPDGKLTGFDVDIGDALCEQ 61 Query: 70 IKLQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAK 129 +K++C V Q++DG+IP L+ K D ++ +++IT +R+K + F+ Y TPA F Sbjct: 62 MKVKCTWVEQEFDGLIPALKVKKIDAILSSMTITDDRKKNVDFTIKYYHTPARF------ 115 Query: 130 VLPKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGF--KDIAT 187 V+K D K D L +LKGK +G+ + + +F + I Sbjct: 116 ----------VMKEGTDVK------DPL-TELKGKKVGVLRASTHDRFATEVLVPAGINL 158 Query: 188 IRVYKTSPERDLDLANGRIDASFDDVTYYAANIDKKETASIVMAGPKIGGPIW------G 241 +R Y + E +LD+ GR+DA D + N+D + G GP + G Sbjct: 159 VR-YGSQQEANLDMVAGRLDAMLAD----SVNLDDGFLKTDAGKGFAFVGPTYEDAKYFG 213 Query: 242 PGEGLAFRKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 G G+A RK D +L KF+TAI+ A+G K++ +K+F DV Sbjct: 214 GGAGIAVRKGDKELADKFNTAITEIRANGKYKQVQDKYFNFDV 256 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: 179 Number of extensions: 8 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: 259 Length adjustment: 25 Effective length of query: 261 Effective length of database: 234 Effective search space: 61074 Effective search space used: 61074 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