Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_011938227.1 GURA_RS06655 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000016745.1:WP_011938227.1 Length = 353 Score = 134 bits (337), Expect = 4e-36 Identities = 93/282 (32%), Positives = 145/282 (51%), Gaps = 14/282 (4%) Query: 1 MQLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 ++L++ + +G L +SL + G + LLG + +GKT+L+R +AGL+ P+ G + Sbjct: 4 IELSVHDLHVTLGKNHILKGVSLDVNKGEIVALLGPSGSGKTTLLRSIAGLELPSHGSIR 63 Query: 61 VDGKDV------TGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVR 112 + + V + V R + V+Q + +P V N+A LKLR + I RV+ Sbjct: 64 IGEQMVFESAKKIEVSVEKRCLGFVFQSYALWPHRTVYENVAYGLKLRKVPDGEIRQRVQ 123 Query: 113 EIASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREE 172 E+ + L + +R+P +LSGGQQQRVALAR+L ++LLDEPL NLD KLREE R Sbjct: 124 EVLANLGLGDLSERHPHQLSGGQQQRVALARSLVYNPQVILLDEPLSNLDAKLREEARIW 183 Query: 173 LTQLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAF- 231 L QL + V T + EA+ + +L +G + Q G E++ AP SL VA Sbjct: 184 LRQLIIDLNLSAVCVTHDQAEAMAMADKVVLLKDGVIEQAGTPQEMYGAPKSLFVAEFMG 243 Query: 232 SDPPMNLMAASATAQGVRLQGG-----AELTLPLPQGAATAA 268 ++ ++ + R++G L PL G A Sbjct: 244 ANNTISGLVTDVDGDSARIEGNGWALRGRLRTPLKAGDRATA 285 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: 221 Number of extensions: 11 Number of successful extensions: 3 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: 353 Length adjustment: 29 Effective length of query: 334 Effective length of database: 324 Effective search space: 108216 Effective search space used: 108216 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