Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 8501226 DvMF_1960 putrescine/spermidine ABC transporter ATPase protein (RefSeq)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Miya:8501226 Length = 399 Score = 233 bits (595), Expect = 5e-66 Identities = 111/213 (52%), Positives = 153/213 (71%) Query: 25 NLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAMVFQ 84 +L I +GEFL L+GPSGCGK+T LR+++G E T G + I + V V P R + VFQ Sbjct: 27 DLTIRNGEFLTLLGPSGCGKTTILRLVSGFEQPTSGEVRINGQVVNRVPPEQRQVNTVFQ 86 Query: 85 NYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQRQRV 144 NYAL+PHMTV +N+ F LK+ G + DE +RV +A + L F +RKP+ LSGGQ+QRV Sbjct: 87 NYALFPHMTVRDNVAFGLKMQGVAADETARRVLDALRMVHLENFADRKPRQLSGGQQQRV 146 Query: 145 AMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALTMGD 204 A+ RA++ NP V L+DEP S LD KLR Q + +I LQR+LG+T V+VTHDQ EA M D Sbjct: 147 AIARAVINNPLVLLLDEPFSALDFKLRKQMQLEIKHLQRQLGITFVFVTHDQEEAFAMSD 206 Query: 205 RIAVLKDGYLQQVGAPRELYDRPANVFVAGFIG 237 R+ V+ +G ++Q+GAP+E+Y+ PAN++VA F+G Sbjct: 207 RVVVMNEGRIEQIGAPKEIYEEPANMYVARFVG 239 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: 382 Number of extensions: 13 Number of successful extensions: 1 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: 399 Length adjustment: 30 Effective length of query: 346 Effective length of database: 369 Effective search space: 127674 Effective search space used: 127674 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