Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >FitnessBrowser__psRCH2:GFF1860 Length = 390 Score = 557 bits (1436), Expect = e-163 Identities = 287/368 (77%), Positives = 317/368 (86%), Gaps = 2/368 (0%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 MA+LELRNV K+YG TLK+I LKID GEFLILVGPSGCGKSTLMNCIAGLE I+GG Sbjct: 1 MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 ILVD DIS SPKDRDIAMVFQSYALYPTMSVRDNIAFGLK+RK+P A+I+EEVARV+ Sbjct: 61 EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 KLLQIE LL RKP QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE+KL Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDG+IQQFGTP +IYNNPANLFVASFIGSPP Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGM-QDAGLEDREVILGIRPEQIILANGEAN 299 MNF+PLR++++DGR + +L+S Q CELPL + D GL DRE+ILGIRPEQI LA + Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGSA 300 Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359 ++ +++V EPTGPDTLV LN K CCRLAPD AP VGETL LQFDP + LLFDA Sbjct: 301 DF-SLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFDPRRALLFDA 359 Query: 360 KTGERLGV 367 +TGERLGV Sbjct: 360 QTGERLGV 367 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: 519 Number of extensions: 11 Number of successful extensions: 3 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: 390 Length adjustment: 30 Effective length of query: 356 Effective length of database: 360 Effective search space: 128160 Effective search space used: 128160 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