Align ABC transporter (characterized, see rationale)
to candidate WP_024851725.1 N745_RS0108650 ABC transporter ATP-binding protein
Query= uniprot:A0A166QFW2 (381 letters) >NCBI__GCF_000526715.1:WP_024851725.1 Length = 282 Score = 152 bits (385), Expect = 8e-42 Identities = 90/226 (39%), Positives = 131/226 (57%), Gaps = 16/226 (7%) Query: 3 KLKLDNVNKQL----GGMRILRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGG 58 K+ + +NK G + +L + L + EFV VG SGCGKSTLLR+I GL+ + G Sbjct: 4 KIIISGLNKTFITKKGAVEVLESIDLTVKENEFVALVGASGCGKSTLLRIIGGLEKLTKG 63 Query: 59 DLLIDGRRVNDLEPRERGVGMVFQSYALYPHMSVYDNISFGLKLAKT-------DKTSLR 111 +L+D VN ++R MVFQ Y+LYP ++V +NI F L D S+ Sbjct: 64 QVLVDEEIVNK-PGKDRA--MVFQDYSLYPWLTVKENIQFSRNLKINGQGNGLGDIGSMV 120 Query: 112 ERVLKTAQILQLDKLLQRKPKELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQ 171 +R ++ L+K+ P +LSGG RQRVA+ RA+ +PD+LL DEP LDA R Sbjct: 121 DRSYALLDLMGLEKVQDSHPNQLSGGMRQRVAIARALMSKPDVLLMDEPFGALDAQTREV 180 Query: 172 MRNEIARLHDRLGSTMIYVTHDQVEAMTLADKIVVL--NGGRVEQV 215 M + I L + ST+++VTHD EA+ LAD++VV+ N GR++ + Sbjct: 181 MHDLILHLFEIEKSTIVFVTHDVEEAIYLADRVVVMAPNPGRIDSI 226 Lambda K H 0.320 0.137 0.394 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: 244 Number of extensions: 11 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: 381 Length of database: 282 Length adjustment: 28 Effective length of query: 353 Effective length of database: 254 Effective search space: 89662 Effective search space used: 89662 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 (21.8 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