Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= BRENDA::Q8NMV1 (376 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 308 bits (788), Expect = 2e-88 Identities = 173/382 (45%), Positives = 237/382 (62%), Gaps = 24/382 (6%) Query: 1 MATVTFKDASLSYPGAKEPTVKKFNLEIADGEFLVLVGPSGCGKSTTLRMLAGLENVTDG 60 MAT+ ++ + +Y T+K L I +GEFL+LVGPSGCGKST + +AGLE +T G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 61 AIFIGDKDVTHVAPRDRDIAMVFQNYALYPHMTVGENMGFALKIAGKSQDEINKRVDEAA 120 AI IGD+DV+ ++P+DRDIAMVFQ+YALYP M+V EN+ F LKI Q +I+ V A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 121 ATLGLTEFLERKPKALSGGQRQRVAMGRAIVRNPQVFLMDEPLSNLDAKLRVQTRTQIAA 180 L + L RKP LSGGQ+QRVAMGRA+ R P+++L DEPLSNLDAKLRV+ RT++ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 LQRKLGVTTVYVTHDQTEALTMGDRIAVLKDGYLQQVGAPRELYDRPANVFVAGFIGSPA 240 + ++L TTVYVTHDQ EA+T+GD++AV+KDG +QQ G P+E+Y+ PAN FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 241 MNLGTFSV--KDGDAT----SGHARIKLSPETLAAMTPEDNGRITIGFRPEALEIIP-EG 293 MN + KDG SG AR +L+ T A + + + +G RPE + + EG Sbjct: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRD--VILGLRPEQIMLAAGEG 298 Query: 294 ESTDLSIPIKLDFVEELGSDSFLYGKLVGEGDLGSSSEDVPESGQIVVRAAPNAAPAPGS 353 +S SI ++ E G D+ ++ +L ++ R AP+ AP G Sbjct: 299 DSAS-SIRAEVQVTEPTGPDTLVFVQL--------------NDTKVCCRLAPDVAPQVGE 343 Query: 354 VFHARIVEGGQHNFSASTGKRL 375 + F A+TG+RL Sbjct: 344 TLTLQFDPSKVLLFDANTGERL 365 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: 400 Number of extensions: 15 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: 376 Length of database: 386 Length adjustment: 30 Effective length of query: 346 Effective length of database: 356 Effective search space: 123176 Effective search space used: 123176 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