Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Putida:PP_1484 Length = 343 Score = 219 bits (558), Expect = 9e-62 Identities = 112/246 (45%), Positives = 161/246 (65%), Gaps = 2/246 (0%) Query: 4 VTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIF 63 V F S ++ K V + +++I DGEF ++GPSG GK+T LR++AG E + G+I Sbjct: 5 VQFTQVSRTFGEVK--AVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGSIR 62 Query: 64 IGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATL 123 I + + P RD+ VFQ+YAL+PHM V EN+ + LK+ G + E + R +EA A + Sbjct: 63 IQGVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVKGVGKAERHSRAEEALAMV 122 Query: 124 GLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQR 183 L + RKP LSGGQRQRVA+ RA+V P+V L+DEPL LD KLR Q + ++ LQR Sbjct: 123 ALAGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQR 182 Query: 184 KLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNL 243 +LG+T ++VTHDQTEAL+M DR+AV G ++QV PR LY +P+ FVA F+G+ + Sbjct: 183 QLGITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVGTSNVVR 242 Query: 244 GTFSVK 249 G +++ Sbjct: 243 GELAMQ 248 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: 321 Number of extensions: 16 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: 343 Length adjustment: 29 Effective length of query: 347 Effective length of database: 314 Effective search space: 108958 Effective search space used: 108958 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: 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