Align Extracellular solute-binding protein family 3; Flags: Precursor (characterized, see rationale)
to candidate PfGW456L13_3699 Arginine/ornithine ABC transporter, periplasmic arginine/ornithine binding protein
Query= uniprot:B2TBJ6 (286 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3699 Length = 258 Score = 135 bits (341), Expect = 7e-37 Identities = 88/276 (31%), Positives = 138/276 (50%), Gaps = 29/276 (10%) Query: 12 LIGAVLGAAAIFAAPAQAKDWKTVTIALEGGYAPWNLTLPGGKLGGFEPELVANLCERIK 71 L+GA+ A F A A D ++ I +E Y P++ P G + GF+ ++ LCE +K Sbjct: 6 LLGALALCAFSFLAHA---DEDSLRIGIEAAYPPFSFKTPEGNVSGFDYDIGNALCEEMK 62 Query: 72 LQCNLVAQDWDGMIPGLQAGKFDVLMDAISITPEREKIIAFSKPYAATPATFAVADAKVL 131 ++C V Q++DGMIP L+ K D ++ ++SIT +R K + FSK Y TP FA+ V+ Sbjct: 63 VKCEWVIQEFDGMIPSLKVRKIDAVLSSMSITEDRMKSVDFSKKYYHTPGKFAMKAGNVI 122 Query: 132 PKAAPGAGVVKLSGDPKADQPTVDALRKQLKGKTIGIQSGTVYTKFINDGFKDIATIRV- 190 DP D LKGK +G+Q + Y +F + + + V Sbjct: 123 -------------NDPLVD----------LKGKKVGVQRSSTYDRFATEQLEKAGVVVVR 159 Query: 191 YKTSPERDLDLANGRIDASFDDVTYYAANIDKKETA-SIVMAGPKIGGP-IWGPGEGLAF 248 Y + E LDLA+GR+DA+ D+ + K + GP I P +G G G+A Sbjct: 160 YSSQNEAFLDLASGRLDATLADIVNTDESFIKTAAGQGFALTGPDINDPKYFGRGAGIAV 219 Query: 249 RKQDADLKAKFDTAISAALADGTVKKLSNKWFKTDV 284 RK D+ A+ AI A A+G +++ ++F D+ Sbjct: 220 RKGDSANVARLSAAIDAIRANGKYQQVMARYFAFDI 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: 172 Number of extensions: 6 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: 258 Length adjustment: 25 Effective length of query: 261 Effective length of database: 233 Effective search space: 60813 Effective search space used: 60813 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