Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate WP_200806763.1 B5D49_RS03200 ABC transporter ATP-binding protein
Query= reanno::WCS417:GFF4321 (386 letters) >NCBI__GCF_900167125.1:WP_200806763.1 Length = 406 Score = 210 bits (534), Expect = 7e-59 Identities = 111/266 (41%), Positives = 173/266 (65%), Gaps = 11/266 (4%) Query: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 + L+ + K +G + ++ +L+I+ GE + L+GPSGCGK+T++ IAGLET T G I Sbjct: 45 VRLQGLMKRFGKTV--AVQETDLTIETGELVTLLGPSGCGKTTILRMIAGLETPTKGDIY 102 Query: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 I + ++ R++ M+FQ+YAL+P ++ EN+ FGLK R + + ++ +VA+ +++ Sbjct: 103 IKGRRINDTPIHKRNLGMIFQNYALFPHKTIFENVAFGLKYRNVSREEMREKVAQALEMV 162 Query: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 ++ + R QLSGGQQQR+A+ RA+ P + L DEPLS LD KLR EMR E+ + Q Sbjct: 163 RLPGVEKRYASQLSGGQQQRIALARAIVIEPDVLLMDEPLSALDEKLREEMRMEIDNIQQ 222 Query: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 +L TT++VTHDQ EA+++ +K+ VMKDG QQ GTP+++Y+ P N FVA F+G NF Sbjct: 223 QLNLTTLFVTHDQREALSMSNKIVVMKDGRKQQEGTPEDVYDYPDNYFVADFLGH--ANF 280 Query: 244 VPLRLQRKDGRLVALLDSGQARCELA 269 D R++ +LD+ Q R +A Sbjct: 281 F-------DARVLEVLDNDQVRVRIA 299 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: 362 Number of extensions: 15 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: 406 Length adjustment: 31 Effective length of query: 355 Effective length of database: 375 Effective search space: 133125 Effective search space used: 133125 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: 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