Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate Dsui_0258 Dsui_0258 sulfate ABC transporter, ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__PS:Dsui_0258 Length = 360 Score = 193 bits (491), Expect = 6e-54 Identities = 95/220 (43%), Positives = 141/220 (64%), Gaps = 4/220 (1%) Query: 23 DFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMV 82 D +L I E +GPSGCGKTT LR+IAG+E EG + + ++R + V Sbjct: 20 DVSLSIPTGELVALLGPSGCGKTTLLRIIAGMETADEGQVMFEGSEATHLHARERQVGFV 79 Query: 83 FQNYALYPHMTVYQNMAFGLKLR----KVPKAEIDRRVQEAAKILDIAHLLDRKPKALSG 138 FQ+YAL+ HM V++N+AFGL+++ + ++EI +RV + ++ + L DR P LSG Sbjct: 80 FQHYALFRHMNVFENVAFGLRVKPRKERPCESEIRKRVMDLLSLVQLDWLADRYPTQLSG 139 Query: 139 GQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTE 198 GQRQR+AL RA+ EP+V L+DEP LD K+R ++R +R+LH + + ++VTHDQ E Sbjct: 140 GQRQRIALARALAVEPKVLLLDEPFGALDTKVRKELRRWLRRLHDEMHISSVFVTHDQEE 199 Query: 199 AMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGS 238 A+ + DR+VVM G I+Q +P VYS P + FV F+G+ Sbjct: 200 ALEVADRVVVMNKGRIEQVGSPDEVYSNPASPFVYQFLGN 239 Lambda K H 0.321 0.138 0.395 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: 374 Number of extensions: 14 Number of successful extensions: 2 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: 384 Length of database: 360 Length adjustment: 30 Effective length of query: 354 Effective length of database: 330 Effective search space: 116820 Effective search space used: 116820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Apr 09 2024. 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