Align ABC-type maltose transport, ATP binding protein (characterized, see rationale)
to candidate CA265_RS15880 CA265_RS15880 sugar ABC transporter ATP-binding protein
Query= uniprot:Q6MNM2 (347 letters) >FitnessBrowser__Pedo557:CA265_RS15880 Length = 330 Score = 147 bits (370), Expect = 5e-40 Identities = 88/253 (34%), Positives = 146/253 (57%), Gaps = 10/253 (3%) Query: 4 IQFSNIKKSFGS--ADVLKGIDLDIAPGEFLVLVGPSGCGKSTLLRTLAGLESADSGTIS 61 I N+ K + + A +K + +I G+ + ++G SG GKSTLL+++ GL D G I Sbjct: 6 ISVKNLTKQYQAEQAGGIKNVSFEIKQGDVVAIIGESGSGKSTLLKSIYGLLKTDEGEIF 65 Query: 62 IDGKKIN----DIEPQNRDIAMVFQSYALYPHMTVAENMGFGLKLKNLAAAEITKRVNEI 117 + K++ + P ++ + MV Q ++L + V +N+ +L N ++ +I Sbjct: 66 FEDKRVKGPDEQLIPGHKQMKMVTQDFSLNIYAKVYDNIAS--QLSNTDLKTKAEKTLQI 123 Query: 118 SELLQIKHLLDRKPKELSGGQRQRVALGRALSRQTPVILFDEPLSNLDAHLRSQMRLEIK 177 E L+I L ++K ELSGG++QRVA+ +A+ T V+L DEP S +DA L++Q+R +IK Sbjct: 124 MEHLRILPLQNKKIIELSGGEQQRVAIAKAMVADTQVLLLDEPFSQVDALLKNQLRADIK 183 Query: 178 RLHHNSKSTMIYVTHDQMEATTLGDRIAVLKDGVIEQIGTPSEIYHRPKNTFIATFIGSP 237 R+ + T+I V+HD + L D++ +LK+G + Q G PSEIY PK+ + A +G+ Sbjct: 184 RVASETGVTVILVSHDPADGLFLADQLLILKNGELLQTGKPSEIYQHPKHIYTAQILGNA 243 Query: 238 EMNFLEGAVLEKI 250 + L A EKI Sbjct: 244 VV--LSQADAEKI 254 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: 250 Number of extensions: 6 Number of successful extensions: 2 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: 330 Length adjustment: 28 Effective length of query: 319 Effective length of database: 302 Effective search space: 96338 Effective search space used: 96338 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: 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