Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 219 bits (557), Expect = 1e-61 Identities = 109/245 (44%), Positives = 166/245 (67%), Gaps = 4/245 (1%) Query: 1 MATLELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGG 60 M+ L+L +V K YG+ ++++ LS+++GEF+ L+GPSGCGK+T + +AG E +T G Sbjct: 1 MSFLQLTDVTKFYGSTC--AVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSG 58 Query: 61 AIMIGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA 120 I + +D++ R + +VFQSYAL+P M+V +N+ FGL++RK+P+A+ VA+ Sbjct: 59 RIELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQAL 118 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 L+ +E R P +LSGGQ+QRVA+ RAL P + L DEPLSNLDAKLR EM+ E++ Sbjct: 119 GLVHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQ 178 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 + +++ TTTV VTHDQ EAM++ D+V VM+ G Q P +Y +P +F+++F+G Sbjct: 179 IQRKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVGK-- 236 Query: 241 MNFVP 245 N VP Sbjct: 237 ANLVP 241 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: 331 Number of extensions: 13 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: 362 Length adjustment: 30 Effective length of query: 356 Effective length of database: 332 Effective search space: 118192 Effective search space used: 118192 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 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