Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 259 bits (662), Expect = 8e-74 Identities = 146/321 (45%), Positives = 199/321 (61%), Gaps = 28/321 (8%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + + K+Y G + + L I GEF+V +GPSGCGKST+LRMIAGLE I+GG Sbjct: 1 MAFLELKNVDKYY-GKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQ 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L + G + ++P +R++AMVFQ+YALYPHM+V +N++F LR K A I +V+ A Sbjct: 60 LILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAAD 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 LNL A L+R P+A+SGGQ+QR AI R+I+++P VFLFDEPLSNLDA LR R +I L Sbjct: 120 KLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+ L TTVYVTHDQ+EAMTLADRV++++DG I Q G+P ELY P N F A FIG P M Sbjct: 180 HRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQM 239 Query: 241 NFLSGTVQRQDGQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAASL 300 N ++ Q A ++ +RP+H+++ + + Sbjct: 240 NVAPASLFGQ-----------------------FPAQVAEVGIRPEHLQMVSPEDGLLA- 275 Query: 301 TCPVSVELVEILGADALLTTR 321 V LVE LG + L+ R Sbjct: 276 ---GKVVLVEALGNETLVHVR 293 Lambda K H 0.321 0.137 0.403 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: 364 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: 406 Length of database: 348 Length adjustment: 30 Effective length of query: 376 Effective length of database: 318 Effective search space: 119568 Effective search space used: 119568 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 Apr 09 2024. 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