Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 18063 b4035 fused maltose transport subunit, ATP-binding component of ABC superfamily/regulatory protein (NCBI)
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__Keio:18063 Length = 371 Score = 282 bits (722), Expect = 9e-81 Identities = 150/303 (49%), Positives = 204/303 (67%), Gaps = 12/303 (3%) Query: 22 KKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDGAIFIGDKDVTHVAPRDRDIAM 81 K NL+I +GEF+V VGPSGCGKST LRM+AGLE +T G +FIG+K + P +R + M Sbjct: 20 KDINLDIHEGEFVVFVGPSGCGKSTLLRMIAGLETITSGDLFIGEKRMNDTPPAERGVGM 79 Query: 82 VFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAAATLGLTEFLERKPKALSGGQR 141 VFQ+YALYPH++V ENM F LK+AG ++ IN+RV++ A L L L+RKPKALSGGQR Sbjct: 80 VFQSYALYPHLSVAENMSFGLKLAGAKKEVINQRVNQVAEVLQLAHLLDRKPKALSGGQR 139 Query: 142 QRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAALQRKLGVTTVYVTHDQTEALT 201 QRVA+GR +V P VFL+DEPLSNLDA LRVQ R +I+ L ++LG T +YVTHDQ EA+T Sbjct: 140 QRVAIGRTLVAEPSVFLLDEPLSNLDAALRVQMRIEISRLHKRLGRTMIYVTHDQVEAMT 199 Query: 202 MGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPAMNLGTFSVKDGDATSGHARIK 261 + D+I VL G + QVG P ELY PA+ FVAGFIGSP MN VK +++ Sbjct: 200 LADKIVVLDAGRVAQVGKPLELYHYPADRFVAGFIGSPKMNF--LPVKVTATAIDQVQVE 257 Query: 262 L-SPETLAAMTPEDN------GRITIGFRPEALEIIPEGESTDLSIPIKLDFVEELGSDS 314 L P P ++ +++G RPE ++P + D+ + ++ VE+LG+++ Sbjct: 258 LPMPNRQQVWLPVESRDVQVGANMSLGIRPE--HLLP-SDIADVILEGEVQVVEQLGNET 314 Query: 315 FLY 317 ++ Sbjct: 315 QIH 317 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: 358 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: 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