Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897 (386 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 182 bits (463), Expect = 1e-50 Identities = 110/344 (31%), Positives = 188/344 (54%), Gaps = 13/344 (3%) Query: 1 MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60 M+ LE+R++ G LK I+L+ + G+++ L+GPSG GKS L+ I G G Sbjct: 1 MSFLEVRDIYLDVGSF---ELKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQG 57 Query: 61 AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120 ++ ++ DI+ SP R I++V+Q L+P M + +NIA+ L+ + +I+ EV +++ Sbjct: 58 SVFLEGRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIA 117 Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L I LL RKP LSGG++QR ++ R+L RPK+ L DEP S LDA+ R ++R +K Sbjct: 118 GVLGIRELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKK 177 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240 TT ++VTHD + L ++V V++ G + Q G P+ ++ P+ FVA F+G+ Sbjct: 178 AIADYSTTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT-- 235 Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGMQDAGLEDREVILGIRPEQIILANG--EA 298 N + ++ +G+L + G + + D V + IRPE+IILA G E+ Sbjct: 236 -NVLKGTVKALEGKLTVIDAEG-----MEIYSADPAEPGENVTVSIRPEEIILAGGTVES 289 Query: 299 NGLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVG 342 + T++ V +V V + ++++ + P +G Sbjct: 290 SARNTLKGRVSGIFKKEHLVVVEVKMGNSEIKAVVTPTSCEMLG 333 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: 317 Number of extensions: 11 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: 386 Length of database: 353 Length adjustment: 30 Effective length of query: 356 Effective length of database: 323 Effective search space: 114988 Effective search space used: 114988 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: 49 (23.5 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