Align Inositol transport system ATP-binding protein (characterized)
to candidate WP_086509449.1 BZY95_RS08165 ABC transporter ATP-binding protein
Query= reanno::Phaeo:GFF717 (261 letters) >NCBI__GCF_002151265.1:WP_086509449.1 Length = 250 Score = 107 bits (266), Expect = 3e-28 Identities = 74/240 (30%), Positives = 124/240 (51%), Gaps = 12/240 (5%) Query: 3 MSQPLIRMQGIEKHFGSVIALAGVSVDVFPGECHCLLGDNGAGKSTFIKTMSGVHKPTKG 62 MS+ ++ + + K FG++ A VS+D++PGE H L+G NGAGKST I ++G KP G Sbjct: 1 MSEAVLELIDLNKRFGALQATRDVSLDLYPGEIHALIGPNGAGKSTLIGQIAGSLKPDSG 60 Query: 63 DILFEGQPLHFADPRDAIAAGIATVHQHLAMIPLMSVSRNFFMGNEPI-----RKIGPLK 117 I+ GQ + G+ Q ++ +SV RN + + + R P++ Sbjct: 61 RIVLAGQEITSLSVAQRARLGLGRSFQVSSLAEPLSVKRNVMIAVQALQGHSFRFWKPVQ 120 Query: 118 LFDHDYANRITMEEMRKMGINLRGPDQAVGTLSGGERQTVAIARAVHFGAKVLILDEPTS 177 + A +E + +M + R D V LS GER+ V +A A+ +VL+LDEP + Sbjct: 121 RDESLLAP--ALEALERMALTHRA-DTQVAELSHGERRQVEVACALALKPRVLLLDEPMA 177 Query: 178 ALGVRQTANVLATIDKVRKQGVAVVFITHNVRHALAVGDRFTVLNRGKTLGTAQRGDISA 237 LG TA++ ++ ++ + V ++ I H++ + DR +VL G G +GD +A Sbjct: 178 GLGPEGTAHLTELLEALKLE-VPILLIEHDMDAVFRLADRISVLVAG---GVIAQGDSAA 233 Lambda K H 0.321 0.137 0.395 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: 138 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 261 Length of database: 250 Length adjustment: 24 Effective length of query: 237 Effective length of database: 226 Effective search space: 53562 Effective search space used: 53562 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
This GapMind analysis is from Sep 24 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