Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 221 bits (563), Expect = 3e-62 Identities = 118/279 (42%), Positives = 163/279 (58%) Query: 17 KEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRD 76 K V + E+ G F ++GPSGCGK+T LRM+AG E+ G I I +D+ +AP Sbjct: 40 KFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIAIRGRDMAGIAPNR 99 Query: 77 RDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKAL 136 R + ++FQ+ AL+P M+V EN+ F LK G + EI++RV + +GL + + P L Sbjct: 100 RPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERVGLPGYGVKMPAQL 159 Query: 137 SGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQ 196 SGGQ+QRVA+ R +V P V L+DEPL LD KLR Q + ++ LQ ++G T VY+THDQ Sbjct: 160 SGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQAEVGTTFVYITHDQ 219 Query: 197 TEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSG 256 +EAL M D +AV+ G +QV PR LY RPA+ FVAGF+G + GT GDA Sbjct: 220 SEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVGETNVWSGTLEEATGDAGLV 279 Query: 257 HARIKLSPETLAAMTPEDNGRITIGFRPEALEIIPEGES 295 A R+ + RPEA+ I P+G S Sbjct: 280 RTDEGAVFRARVAAGLAKGTRVDMFIRPEAVLIDPDGAS 318 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: 402 Number of extensions: 24 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: 376 Length of database: 418 Length adjustment: 31 Effective length of query: 345 Effective length of database: 387 Effective search space: 133515 Effective search space used: 133515 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: 50 (23.9 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