Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate AO356_05180 AO356_05180 sugar ABC transporter ATP-binding protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_05180 Length = 386 Score = 693 bits (1789), Expect = 0.0 Identities = 349/386 (90%), Positives = 366/386 (94%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MATLELRNVNKTYG GLPDTLKNIEL I DGEFLILVGPSGCGKSTLMNCIAGLETI+GG Sbjct: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKDGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 AI++ D D+SGMSPKDRDIAMVFQSYALYPTMSVR+NI FGLKIRKM + IDEEV RV+ Sbjct: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMNQSAIDEEVNRVA 120 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 KLLQIEHLL+RKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL Sbjct: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIY NPANLFVASFIGSPP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYTNPANLFVASFIGSPP 240 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANGEANG 300 MNFIPLRLQRKDGRLLALLDSGQARCELP+GMQDAGLEDREVILG+RPEQI+LA E NG Sbjct: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPMGMQDAGLEDREVILGMRPEQIMLAGSEPNG 300 Query: 301 LPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDAK 360 LPTIRAEVQVTEPTGPDTLVFV+LNDTKVCCRLAPDVAP VGETLTLQFDP+KVLLFDA+ Sbjct: 301 LPTIRAEVQVTEPTGPDTLVFVSLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDAQ 360 Query: 361 TGERLGVAGVPKAEAHADNVAQFKGR 386 +GERLGVAG P+ +A NVAQFKGR Sbjct: 361 SGERLGVAGQPQTDARTANVAQFKGR 386 Lambda K H 0.319 0.138 0.393 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: 634 Number of extensions: 11 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: 386 Length of database: 386 Length adjustment: 30 Effective length of query: 356 Effective length of database: 356 Effective search space: 126736 Effective search space used: 126736 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 (21.7 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