Align ABC-type maltose transporter (EC 7.5.2.1) (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= BRENDA::Q70HW1 (384 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 334 bits (856), Expect = 3e-96 Identities = 174/385 (45%), Positives = 243/385 (63%), Gaps = 28/385 (7%) Query: 1 MARVLLEHIYKTYPGQTEPTVKDFNLDIQDKEFTVFVGPSGCGKTTTLRMIAGLEDITEG 60 MA + L ++ KTY T+K+ L I++ EF + VGPSGCGK+T + IAGLE IT G Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 61 NLYIGDRRVNDVPPKDRDIAMVFQNYALYPHMTVYQNMAFGLKLRKVPKAEIDRRVQEAA 120 + IGD+ V+ + PKDRDIAMVFQ+YALYP M+V +N+ FGLK+RK+P+A+ID V A Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 Query: 121 KILDIAHLLDRKPKALSGGQRQRVALGRAIVREPQVFLMDEPLSNLDAKLRVQMRAEIRK 180 K+L I HLL+RKP LSGGQ+QRVA+GRA+ R P+++L DEPLSNLDAKLRV+MR E++ Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 LHQRLQTTVIYVTHDQTEAMTMGDRIVVMRDGVIQQADTPQVVYSQPKNMFVAGFIGSPA 240 +HQRL+TT +YVTHDQ EAMT+GD++ VM+DG+IQQ TP+ +Y+ P N FVA FIGSP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 Query: 241 MNFIRGEIVQDGDAFYFRAPSISLRLPEGRYGVLKASGAIGKPVVLGVRPEDLHDEEVFM 300 MNF+ + L+ +GR L SG + L L D +V + Sbjct: 241 MNFV----------------PLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVIL 284 Query: 301 TTYPDSV------------LQMQVEVVEHMGSEVYLHTSIGPNTIVARVNPRHVYHVGSS 348 P+ + ++ +V+V E G + + + + R+ P VG + Sbjct: 285 GLRPEQIMLAAGEGDSASSIRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGET 344 Query: 349 VKLAIDLNKIHIFDAETEESIGFAA 373 + L D +K+ +FDA T E +G A+ Sbjct: 345 LTLQFDPSKVLLFDANTGERLGTAS 369 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: 410 Number of extensions: 18 Number of successful extensions: 1 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: 386 Length adjustment: 30 Effective length of query: 354 Effective length of database: 356 Effective search space: 126024 Effective search space used: 126024 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