Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ac3H11_2941 Various polyols ABC transporter, ATP-binding component
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2941 Length = 350 Score = 295 bits (756), Expect = 1e-84 Identities = 163/359 (45%), Positives = 225/359 (62%), Gaps = 21/359 (5%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 MA L+LR + K +G +K I+L+I++GEF++ VGPSGCGKSTL+ IAGLE I GG Sbjct: 1 MAYLQLRGIEKFFGEHR--AIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 ++M+ +D++ RD+AMVFQSYALYP MSV EN+ F LK+ K+ + ID +V A Sbjct: 59 SLMLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAA 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 ++L + L R P +LSGGQ+QRVA+GRA+ R PK++LFDEPLSNLDA LR + R E+ Sbjct: 119 RILNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAK 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 +H+ L TT+YVTHDQ+EAMTL D+V V++DGII+Q GTP E+Y+ PANQFVA FIG+P Sbjct: 179 LHRDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQ 238 Query: 241 MNFVPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDS 300 MN VP+ L Q + A G +GLRPE I + Sbjct: 239 MNVVPVD---------KLPQPVQQQAPAAPAGAAVG------AIGLRPENITVRT---TG 280 Query: 301 ASSIRAEVQVTEPTGPDTLVFVQL-NDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFD 358 A+ + +V + E G +TL++V + R +VG+ ++L D S+ FD Sbjct: 281 ATPVGGQVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDIDASQAHWFD 339 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: 339 Number of extensions: 9 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: 350 Length adjustment: 30 Effective length of query: 356 Effective length of database: 320 Effective search space: 113920 Effective search space used: 113920 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 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