Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF857 Psest_0871 ABC-type sugar transport systems, ATPase components
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__psRCH2:GFF857 Length = 371 Score = 287 bits (734), Expect = 4e-82 Identities = 162/324 (50%), Positives = 212/324 (65%), Gaps = 16/324 (4%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MA+VT +D SY G P + +L+I DGEF+V VGPSGCGKST LR++AGLE++T G Sbjct: 1 MASVTLRDICKSYDGT--PITRHIDLDIEDGEFVVFVGPSGCGKSTLLRLIAGLEDITSG 58 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 + I ++ V + P+DR + MVFQ+YALYPHMTV ENM F LK+A + EI +RV+ A Sbjct: 59 DLLIDNQRVNDLPPKDRSVGMVFQSYALYPHMTVAENMAFGLKLASVDKREIKRRVEAVA 118 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L L + LERKPK LSGGQRQRVA+GR +VR P+VFL DEPLSNLDA LRVQ R +IA Sbjct: 119 EILQLDKLLERKPKDLSGGQRQRVAIGRTMVREPKVFLFDEPLSNLDAFLRVQMRIEIAR 178 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 L +++ T +YVTHDQ EA+T+ D+I VL G + QVG P LY P N FVAGF+GSP Sbjct: 179 LHQRIRSTMIYVTHDQVEAMTLADKIVVLNAGEIAQVGQPLHLYHYPKNRFVAGFLGSPQ 238 Query: 241 MNLGTFSVKDGDATSGHARIKLS---PETL----AAMTPEDNGRITIGFRPEALEIIPEG 293 MN V+ A+ I+L P TL +A++P D +T+G RPE ++P Sbjct: 239 MNF--VEVRAISASPETVTIELPSGYPLTLPVDGSAVSPGD--PLTLGIRPEHF-VMP-- 291 Query: 294 ESTDLSIPIKLDFVEELGSDSFLY 317 + D + ++ E LG + LY Sbjct: 292 DEADFTFHGQITVAERLGQYNLLY 315 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: 393 Number of extensions: 22 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: 371 Length adjustment: 30 Effective length of query: 346 Effective length of database: 341 Effective search space: 117986 Effective search space used: 117986 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