Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate WP_017178740.1 A1QA_RS0109835 amino acid ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >NCBI__GCF_000295095.1:WP_017178740.1 Length = 270 Score = 159 bits (401), Expect = 1e-43 Identities = 95/254 (37%), Positives = 138/254 (54%), Gaps = 21/254 (8%) Query: 3 KIQFSNIKKSFGSADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTISI 62 K++ + + K F VL+G+DL + G VLVGPSG GKSTLLR + LES D+G + + Sbjct: 16 KVRIAGLHKFFDELHVLRGVDLTVPAGTVTVLVGPSGSGKSTLLRCINELESIDAGRVWV 75 Query: 63 DGKKINDIEPQNRD-------------------IAMVFQSYALYPHMTVAEN-MGFGLKL 102 DG+ I E RD I MVFQ + L+PHMT +N M + + Sbjct: 76 DGELIGMREVPGRDGTPVLHALSDKDRAAQRAKIGMVFQRFNLFPHMTALQNVMEAPVHV 135 Query: 103 KNLAAAEITKRVNEISELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLS 162 K + + KR E+ E + + +D P +LSGGQ+QRVA+ RAL+ ++LFDEP S Sbjct: 136 KRMPKEQARKRAAELLERVGLADRMDHYPSQLSGGQQQRVAIARALAMDPELMLFDEPTS 195 Query: 163 NLDAHLRSQMRLEIKRLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIY 222 LD L ++ +K L + TM+ VTH+ A +GD++ + GV+ + G PSE+ Sbjct: 196 ALDPELVGEVLSVMKDLARDG-MTMVVVTHEMGFAREVGDQLLFMDGGVVVERGVPSEVL 254 Query: 223 HRPKNTFIATFIGS 236 RP N F+ S Sbjct: 255 DRPANERTRAFLSS 268 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: 229 Number of extensions: 9 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: 347 Length of database: 270 Length adjustment: 27 Effective length of query: 320 Effective length of database: 243 Effective search space: 77760 Effective search space used: 77760 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 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