Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 202699 SO3602 sulfate ABC transporter, ATP-binding protein (NCBI ptt file)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__MR1:202699 Length = 376 Score = 213 bits (543), Expect = 5e-60 Identities = 112/241 (46%), Positives = 161/241 (66%), Gaps = 10/241 (4%) Query: 4 VLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLY 63 + L +I K + GQ + + NLDIQ+ E +GPSG GKTT LR+IAGLE G+++ Sbjct: 3 IRLTNISKKF-GQFQ-ALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGHIH 60 Query: 64 IGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPK------AEIDRRVQ 117 G+R V V +DR + VFQNYAL+ HMTV N+AFGL++ +PK AEI +RV Sbjct: 61 FGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEV--IPKKQRPSAAEIQKRVS 118 Query: 118 EAAKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAE 177 +++ + HL R P+ LSGGQ+QR+AL RA+ +P+V L+DEP LDAK+R ++R Sbjct: 119 HLLEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRW 178 Query: 178 IRKLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIG 237 +R LH L+ T ++VTHDQ EA+ + DR+VVM +G I+Q +TP +Y+QP + FV F+G Sbjct: 179 LRSLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLG 238 Query: 238 S 238 + Sbjct: 239 N 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: 354 Number of extensions: 8 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: 376 Length adjustment: 30 Effective length of query: 354 Effective length of database: 346 Effective search space: 122484 Effective search space used: 122484 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 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