Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate 7026050 Shewana3_3192 sulfate ABC transporter, ATPase subunit (RefSeq)
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__ANA3:7026050 Length = 376 Score = 215 bits (548), Expect = 1e-60 Identities = 112/239 (46%), Positives = 159/239 (66%), Gaps = 6/239 (2%) Query: 4 VLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEGNLY 63 + L +I K + GQ + + NLDIQ+ E +GPSG GKTT LR+IAGLE G ++ Sbjct: 3 IRLTNISKKF-GQFQ-ALSPLNLDIQEGEMIGLLGPSGSGKTTLLRIIAGLEGADSGQIH 60 Query: 64 IGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGL----KLRKVPKAEIDRRVQEA 119 G+R V V +DR + VFQNYAL+ HMTV N+AFGL K ++ KAEI +RV Sbjct: 61 FGNRDVTQVHVRDRRVGFVFQNYALFRHMTVADNVAFGLEVIPKKQRPSKAEIQKRVSHL 120 Query: 120 AKILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIR 179 +++ + HL R P+ LSGGQ+QR+AL RA+ +P+V L+DEP LDAK+R ++R +R Sbjct: 121 LEMVQLGHLAQRYPEQLSGGQKQRIALARALATQPEVLLLDEPFGALDAKVRKELRRWLR 180 Query: 180 KLHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGS 238 LH L+ T ++VTHDQ EA+ + DR+VVM +G I+Q +TP +Y+QP + FV F+G+ Sbjct: 181 SLHDELKFTSVFVTHDQDEALELSDRVVVMSNGNIEQVNTPIELYAQPNSRFVFDFLGN 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: 358 Number of extensions: 6 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