Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_011653252.1 RL_RS19665 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000009265.1:WP_011653252.1 Length = 357 Score = 199 bits (505), Expect = 1e-55 Identities = 129/354 (36%), Positives = 196/354 (55%), Gaps = 9/354 (2%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L + +I K G L + ++L SG VLLG++ GK++L+ I+AGL T+G V + Sbjct: 4 LEIQNIRKTYGDVETLKGIDISLDSGEFLVLLGSSGCGKSTLLNIIAGLAEATSGDVRIG 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHI 120 G+ V G+ +DR++AMV+Q + YP++ V NI L++R + D V + A L I Sbjct: 64 GRSVLGVHPKDRDIAMVFQSYALYPNLTVHRNIGFGLEMRKVPAQERDRAVHDAAKLLQI 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 + LDR P++LSGGQ+QRVA+ RAL + + L DEPL NLD KLR E+R E+ +L Sbjct: 124 ENLLDRKPSQLSGGQRQRVAIGRALVRKPEVFLFDEPLSNLDAKLRMEMRTEIKRLHQML 183 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 ++TVVY T + EA+ L AV+ +G++ Q G E+++ P +L VA PPMNL+ Sbjct: 184 KTTVVYVTHDQIEAMTLASRIAVMRDGRIEQLGTPEEIYNHPATLYVATFVGAPPMNLLK 243 Query: 241 ASATAQGVRLQGGAELTLPLP----QGAATAAGLTVGVRASALRVHARPGDVSVAGVVEL 296 A+A G+ L G++ LPLP Q A L +G+R ALR S+ +E+ Sbjct: 244 ATARDGGLAL-SGSDAILPLPARFRQTAGNGRDLILGIRPEALRTDGT--GPSIEASLEV 300 Query: 297 AEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLA 350 AE++G + V A L+A L +TL D ++F + L+ Sbjct: 301 AELTGPELVVTALAGHQRLMACLPPRTPIRDNEKLTLFFDEEAMHLFDPETGLS 354 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: 268 Number of extensions: 11 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: 357 Length adjustment: 29 Effective length of query: 334 Effective length of database: 328 Effective search space: 109552 Effective search space used: 109552 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 24 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