Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_011020381.1 MA_RS01715 ATP-binding cassette domain-containing protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_000007345.1:WP_011020381.1 Length = 353 Score = 184 bits (468), Expect = 3e-51 Identities = 105/324 (32%), Positives = 186/324 (57%), Gaps = 11/324 (3%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+ LE+R++ G+ LK I+L ++G+++ L+GPSG GKS L+ I G G Sbjct: 1 MSFLEVRDIYLDVGSF---ELKGIDLRAEKGDYVALIGPSGSGKSLLLETIIGFYGPRQG 57 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 ++ + +D++ SP R I++V+Q L+P M + ENI + L+ + + I+ EV ++A Sbjct: 58 SVFLEGRDITFFSPDKRQISIVYQDNMLFPHMDIFENIAYALRKKLKDKKQIELEVTQIA 117 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 +L I LL+RKP LSGG++QR ++ R+L RPK+ L DEP S LDA+ R ++R +K Sbjct: 118 GVLGIRELLHRKPDTLSGGEKQRASLARSLVARPKLLLLDEPFSALDARTREKLREMLKK 177 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 TT ++VTHD + L ++V V++ G + Q G P+ ++ P+ FVA F+G+ Sbjct: 178 AIADYSTTVLHVTHDFEDVWALANRVVVIRKGEVMQVGDPESVFRRPSPDFVAEFLGT-- 235 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 N + ++ +G+L + G + + + + +V + +RPE+I+LA G +S Sbjct: 236 -NVLKGTVKALEGKLTVIDAEG-----MEIYSADPAEPGENVTVSIRPEEIILAGGTVES 289 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQL 324 ++ + +V+ + LV V++ Sbjct: 290 SARNTLKGRVSGIFKKEHLVVVEV 313 Lambda K H 0.318 0.135 0.382 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: 302 Number of extensions: 10 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 ( 7.3 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