Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate WP_008538734.1 HMPREF9454_RS06810 amino acid ABC transporter ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >NCBI__GCF_000245775.1:WP_008538734.1 Length = 239 Score = 148 bits (373), Expect = 2e-40 Identities = 86/236 (36%), Positives = 136/236 (57%), Gaps = 6/236 (2%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 +++ + K++G V+VL +++ I++ E++V +GPSG GKSTLLR + LE+ T G + +D Sbjct: 2 IEIKNLHKSFGHVEVLKGVDVSIEEKEVVVIIGPSGSGKSTLLRCMNYLEEPTSGDITVD 61 Query: 64 GTVVN---DVPPAQRGIAMVFQSYALYPHMTVRENMSFA-LKIAKKSQAEIDAAVEAAAE 119 ++ D+ + I MVFQ + L+PHMTV EN+ A K+ K S+ E + + Sbjct: 62 NMKLDKHADINKIRENIGMVFQRFNLFPHMTVLENIVLAPTKVLKISRDEAISTAMDLLQ 121 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 ++ L + + P LSGGQ+QRVAI R++ PKV LFDEP S LD + T + Sbjct: 122 RVGLKEKANSYPSQLSGGQQQRVAIARALAMKPKVMLFDEPTSALDP--EMVTEVLDVMK 179 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235 A TMV VTH+ A + R++ + G I + G+P E++E P+ E F+ Sbjct: 180 SLANQGMTMVVVTHEMGFAREVGDRVLFVDEGRIIEEGTPKEIFENPKQERTKLFL 235 Lambda K H 0.316 0.135 0.379 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: 203 Number of extensions: 11 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: 373 Length of database: 239 Length adjustment: 26 Effective length of query: 347 Effective length of database: 213 Effective search space: 73911 Effective search space used: 73911 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: 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