Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000230695.2:WP_015448118.1 Length = 255 Score = 122 bits (305), Expect = 1e-32 Identities = 84/232 (36%), Positives = 125/232 (53%), Gaps = 7/232 (3%) Query: 4 ALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDG 63 AL K+ G L +SLA +G T L+G++ +GK++++R++ GL+ P G V VDG Sbjct: 13 ALVQAGKRYGRLQALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDG 72 Query: 64 KDVTG---MPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRL 118 + + +P+R R V V Q +P + N+A + G + I R ++A+ Sbjct: 73 RPLQRSDVLPLR-RRVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALT 131 Query: 119 HIDM-FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLF 177 H+ L+RYPAELSGGQ+QRVAL RAL +LLDEPL LD +R EL++EL Q+F Sbjct: 132 HLPTGVLERYPAELSGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIF 191 Query: 178 AAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVAR 229 TV+ T + EA +L +G +LQ G ++ P V R Sbjct: 192 DQLGKTVIVVTHDLAEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNR 243 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: 207 Number of extensions: 7 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: 255 Length adjustment: 27 Effective length of query: 336 Effective length of database: 228 Effective search space: 76608 Effective search space used: 76608 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 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