Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_041378948.1 SWIT_RS04010 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000016765.1:WP_041378948.1 Length = 252 Score = 124 bits (311), Expect = 3e-33 Identities = 86/253 (33%), Positives = 127/253 (50%), Gaps = 14/253 (5%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 ++ D + K + L D+SL ++ G+ L+GA+ AGKT+L++ + L G + ++ Sbjct: 2 ISFDHVGKHYAGRHVLDDVSLTIERGSFVALVGASGAGKTTLLKAINRLVEIDTGTIAIE 61 Query: 63 GKDVTGMPVRD--RNVAMVYQQFINYPSMKVAANIASPLKLRGEKNID--ARVREIASRL 118 G+DV PV + R + V+Q +P M VA N+A +L+G + ARV E+ + Sbjct: 62 GRDVAAQPVAELRRRIGYVFQGIGLFPHMSVAENVALVPRLQGVPREERAARVAELLDLV 121 Query: 119 HIDM-FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLF 177 + F +R PA+LSGGQ QRV ARALA +ML+DEP LD R+EL L Sbjct: 122 ALPADFAERRPAQLSGGQAQRVGFARALAARPAIMLMDEPFGALDPVTRDELGAAYRALH 181 Query: 178 AAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMN 237 A T + T + EALLL V+ EG++L P + H DP + Sbjct: 182 EAMGLTSLIVTHDMAEALLLADRVIVIGEGRILADQPPRALIHGA---------GDPRIE 232 Query: 238 LMAASATAQGVRL 250 M A A RL Sbjct: 233 AMIAVARRSAARL 245 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: 185 Number of extensions: 6 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: 252 Length adjustment: 27 Effective length of query: 336 Effective length of database: 225 Effective search space: 75600 Effective search space used: 75600 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: 48 (23.1 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