Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 194 bits (493), Expect = 4e-54 Identities = 103/233 (44%), Positives = 148/233 (63%), Gaps = 6/233 (2%) Query: 23 DFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLYIGDRRVNDVPPKDRDIAMV 82 DF+LDI + EF +GPSG GK++ LR++AGL+D G++ + +P + RDI +V Sbjct: 20 DFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRDGTDLLALPAQRRDIGLV 79 Query: 83 FQNYALYPHMTVYQNMAFGLKLR----KVPKAEIDRRVQEAAKILDIAHLLDRKPKALSG 138 FQ+YAL+PHMTV N+AFGL++R + + +I RV++ + + + L R P LSG Sbjct: 80 FQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLRRVQLEELGRRYPTQLSG 139 Query: 139 GQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRKLHQRLQTTVIYVTHDQTE 198 GQRQRVAL RA+ EP + L+DEP LDA++R +R +R L + L T + VTHDQ E Sbjct: 140 GQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDLQRSLGLTTVLVTHDQDE 199 Query: 199 AMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPAMNFIRGEIVQD 251 A+ + DR+VVM G I+Q P +Y +P FV GF+G N IRG + +D Sbjct: 200 ALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVG--RANRIRGHVERD 250 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: 378 Number of extensions: 10 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: 384 Length adjustment: 30 Effective length of query: 354 Effective length of database: 354 Effective search space: 125316 Effective search space used: 125316 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: 50 (23.9 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