Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 350388 BT0860 putative ABC transporter ATP-binding protein (NCBI ptt file)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Btheta:350388 Length = 224 Score = 127 bits (318), Expect = 4e-34 Identities = 76/194 (39%), Positives = 109/194 (56%), Gaps = 8/194 (4%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRD------ 78 ++E+ GEF+ ++GPSGCGKST L +L L+N T G ++ +V+ R Sbjct: 25 SIEVKQGEFVAIMGPSGCGKSTLLNILGLLDNPTGGEYYLNGTEVSKYTESQRTSLRKGV 84 Query: 79 IAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSG 138 I VFQ++ L + V EN+ L G S E KRV+ A + +T + P+ LSG Sbjct: 85 IGFVFQSFNLIDELNVYENIELPLLYMGISASERKKRVETAMERMAITHRSKHFPQQLSG 144 Query: 139 GQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTE 198 GQ+QRVA+ RA+V NP++ L DEP NLD+K + ++ L ++ G T V VTH Q + Sbjct: 145 GQQQRVAIARAVVANPKLILADEPTGNLDSKNGKEVMGLLSELNKE-GTTIVMVTHSQHD 203 Query: 199 ALTMGDRIAVLKDG 212 A DRI L DG Sbjct: 204 A-GYADRIINLFDG 216 Lambda K H 0.316 0.135 0.380 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: 186 Number of extensions: 10 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: 376 Length of database: 224 Length adjustment: 26 Effective length of query: 350 Effective length of database: 198 Effective search space: 69300 Effective search space used: 69300 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 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