Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_015887278.1 NGR_RS05625 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000018545.1:WP_015887278.1 Length = 360 Score = 206 bits (524), Expect = 8e-58 Identities = 133/358 (37%), Positives = 201/358 (56%), Gaps = 15/358 (4%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L + +I K+ G L + +AL+SG VLLG++ GK++L+ I+AGL P+ G + + Sbjct: 4 LEIRNIRKRYGDVETLKSIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILIG 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDAR--VREIASRLHI 120 + + G +DR++AMV+Q + YP+M VA NI L++R + VR+ A L I Sbjct: 64 ERSILGAHPKDRDIAMVFQSYALYPNMSVARNIGFGLEMRKVPAAEREKAVRDTARLLQI 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 + LDR P++LSGGQ+QRVA+ RAL + + L DEPL NLD KLR E+R EL +L Sbjct: 124 ENLLDRKPSQLSGGQRQRVAIGRALVREPQVFLFDEPLSNLDAKLRMEMRTELKRLHQML 183 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 ++TVVY T + EA+ L AV+ +G++ Q G AE++ P +L VA PPMN++ Sbjct: 184 KTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLGTPAEIYDRPATLYVAGFVGSPPMNILD 243 Query: 241 ASATAQGVRLQGGAELTLPL----PQGAATAAGLTVGVRASALRVHARPGDVSVAG---- 292 A T G+R+ G+E TLPL P G T + VG+R ALR+ GD + G Sbjct: 244 AEGTGSGLRIL-GSENTLPLGGAFPNG-TTGRRVKVGIRPEALRL---AGDDATGGRLTA 298 Query: 293 VVELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLA 350 +VE+ E++G + + A + A L E G+ D A ++F + L+ Sbjct: 299 IVEVMELTGPELVITARIGEQRITACLPPRTSLEPGSTQAFSFDEAALHLFDPESGLS 356 Lambda K H 0.318 0.133 0.375 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: 303 Number of extensions: 13 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: 363 Length of database: 360 Length adjustment: 29 Effective length of query: 334 Effective length of database: 331 Effective search space: 110554 Effective search space used: 110554 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