Align Trehalose/maltose import ATP-binding protein MalK; EC 7.5.2.1 (characterized)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= SwissProt::Q9YGA6 (372 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 155 bits (391), Expect = 2e-42 Identities = 79/224 (35%), Positives = 136/224 (60%), Gaps = 4/224 (1%) Query: 19 VREMSLEVKDGEFMILLGPSGCGKTTTLRMIAGLEEPSRGQIYIGDKLVADPEKGIFVPP 78 ++ +S E+K G+ + ++G SG GK+T L+ I GL + G+I+ DK V P++ + P Sbjct: 23 IKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIFFEDKRVKGPDEQLI--P 80 Query: 79 KDRDIAMVFQSYALYPHMTVYDNIAFPLKLRKVPRQEIDQRVREVAELLGLTELLNRKPR 138 + + MV Q ++L + VYDNIA L + + ++ ++ E L + L N+K Sbjct: 81 GHKQMKMVTQDFSLNIYAKVYDNIASQLSNTDLKTKA--EKTLQIMEHLRILPLQNKKII 138 Query: 139 ELSGGQRQRVALGRAIVRKPQVFLMDEPLSNLDAKLRVRMRAELKKLQRQLGVTTIYVTH 198 ELSGG++QRVA+ +A+V QV L+DEP S +DA L+ ++RA++K++ + GVT I V+H Sbjct: 139 ELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADIKRVASETGVTVILVSH 198 Query: 199 DQVEAMTMGDRIAVMNRGVLQQVGSPDEVYDKPANTFVAGFIGS 242 D + + + D++ ++ G L Q G P E+Y P + + A +G+ Sbjct: 199 DPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGN 242 Lambda K H 0.323 0.142 0.406 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: 268 Number of extensions: 13 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: 372 Length of database: 330 Length adjustment: 29 Effective length of query: 343 Effective length of database: 301 Effective search space: 103243 Effective search space used: 103243 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.5 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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