Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 152 bits (384), Expect = 1e-41 Identities = 90/216 (41%), Positives = 122/216 (56%), Gaps = 14/216 (6%) Query: 3 KIQFSNIKKSF----GSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSG 58 KI S + K+F G+ +VL+ IDL + EF+ LVG SGCGKSTLLR + GLE G Sbjct: 4 KIIISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKG 63 Query: 59 TISIDGKKINDIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAE-------IT 111 + +D + +N +D AMVFQ Y+LYP +TV EN+ F LK + Sbjct: 64 QVLVDEEIVNK---PGKDRAMVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMV 120 Query: 112 KRVNEISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQ 171 R + +L+ ++ + D P +LSGG RQRVA+ RAL + V+L DEP LDA R Sbjct: 121 DRSYALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREV 180 Query: 172 MRLEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVL 207 M I L KST+++VTHD EA L DR+ V+ Sbjct: 181 MHDLILHLFEIEKSTIVFVTHDVEEAIYLADRVVVM 216 Lambda K H 0.318 0.136 0.383 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: 253 Number of extensions: 10 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: 347 Length of database: 282 Length adjustment: 27 Effective length of query: 320 Effective length of database: 255 Effective search space: 81600 Effective search space used: 81600 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 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 09 2024. 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