Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_019388681.1 P735_RS0114015 ATP-binding cassette domain-containing protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000283015.1:WP_019388681.1 Length = 227 Score = 83.6 bits (205), Expect = 5e-21 Identities = 66/217 (30%), Positives = 104/217 (47%), Gaps = 9/217 (4%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L L S G L ++++ + G L+G T GK+S M+ + G T G + Sbjct: 6 LQLKDASIFQGDSLVLSNVNVEINKGEFVYLIGKTGTGKSSFMKTLYGDLPLTEGEGHIV 65 Query: 63 GKDVTGMPVRD-----RNVAMVYQQFINYPSMKVAANIASPLKLRGEKNID---ARVREI 114 D+ + +D R + +V+Q F + N+ LK G K+ D RV E+ Sbjct: 66 DFDLKNLKEKDIPYLRRKLGVVFQDFKLLTDRTINDNLLFVLKATGWKDKDKMKTRVEEV 125 Query: 115 ASRLHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELT 174 +++ + ++P ELSGG+QQRVA+ARAL L+L DEP NLD + E+ E L Sbjct: 126 LTKVDMKTKGFKFPHELSGGEQQRVAIARALLNNPELILADEPTGNLDPQTSVEVMEVLQ 185 Query: 175 QLFAAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQ 211 + G +T++ AT + L T DE Q+ + Sbjct: 186 DINKNG-NTILMATHDYALLLKYPSKTLKCDENQVYE 221 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: 119 Number of extensions: 3 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: 227 Length adjustment: 26 Effective length of query: 337 Effective length of database: 201 Effective search space: 67737 Effective search space used: 67737 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: 47 (22.7 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