Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate BPHYT_RS17470 BPHYT_RS17470 glycerol-3-phosphate ABC transporter ATP-binding protein
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__BFirm:BPHYT_RS17470 Length = 362 Score = 308 bits (789), Expect = 2e-88 Identities = 180/379 (47%), Positives = 240/379 (63%), Gaps = 24/379 (6%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA +T + +Y G K+ + ++++ADGEF+V+VGPSGCGKST LRM+AGLE +++G Sbjct: 1 MAALTLQGVKKTYDG-KQFVLHGIDVDVADGEFVVMVGPSGCGKSTLLRMVAGLERISEG 59 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 +I I K V + P+DR+IAMVFQNYALYPHM+V ENMG+ALKIAG + +I KRVD AA Sbjct: 60 SISIAGKVVNQLEPKDRNIAMVFQNYALYPHMSVAENMGYALKIAGVDRAQIAKRVDAAA 119 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L L+RKP+ LSGGQRQRVAMGRAIVR P VFL DEPLSNLDA+LRVQ R +I Sbjct: 120 QILELEALLQRKPRELSGGQRQRVAMGRAIVREPAVFLFDEPLSNLDARLRVQMRLEIQR 179 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L +L T++YVTHDQ EA+T+ R+ V+ G+ +Q+GAP E+Y+RPA VFVA FIGSP Sbjct: 180 LHARLATTSLYVTHDQIEAMTLAQRVIVMNKGHAEQIGAPTEVYERPATVFVASFIGSPG 239 Query: 241 MNLGTFSVKDGDA---TSGHARIKLSPETLAAMTPE-DNGR-ITIGFRPEALEIIPEGES 295 MNL V D A +G+ KL +A++ E GR T+G RPE + G++ Sbjct: 240 MNLLEGRVSDDGAFFEVAGNGP-KLPLTDVASIGREVARGREWTLGIRPEHMS---PGQA 295 Query: 296 TDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGSVF 355 + +D E LG+D+ +G+ G+ D + VR PA G Sbjct: 296 DAPHATLTVDSCELLGADNLAHGRW-GKHD-------------VTVRLPHAHRPAAGEAL 341 Query: 356 HARIVEGGQHNFSASTGKR 374 + H F ++G+R Sbjct: 342 QVALPARHLHFFDPASGRR 360 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: 404 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: 362 Length adjustment: 30 Effective length of query: 346 Effective length of database: 332 Effective search space: 114872 Effective search space used: 114872 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