Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_092484009.1 BM299_RS11075 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_900115975.1:WP_092484009.1 Length = 344 Score = 134 bits (337), Expect = 4e-36 Identities = 77/228 (33%), Positives = 131/228 (57%), Gaps = 3/228 (1%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L L+ ++ K+G + L D++L +Q G ++LG T GKT ++ +AG+ P G + Sbjct: 2 LRLEHVTVKLG-EFQLLDINLEVQEGEYFIILGPTGTGKTVILETIAGMYRPDKGTIRFK 60 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRLHI 120 +++ + R V VYQ + +P + V NI ++R +K I +++ E+ + L I Sbjct: 61 ERNLATLAPEQRKVGFVYQDYALFPHLTVKENIIFGAQIRKLPKKIIKSKLDELVAMLGI 120 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 L+R+P+ LSGG+QQR ALARAL ++LLDEPL LD + +E +EEL ++ Sbjct: 121 GHLLNRHPSTLSGGEQQRTALARALIISPEILLLDEPLSALDPRSKENFQEELKKIHQTL 180 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVA 228 ++T ++ T + EA+ L V+ +GQ++Q G E+F+ P + VA Sbjct: 181 KTTTLHVTHDFNEAMYLADKIGVMHQGQIIQVGTPQEIFYKPQNDFVA 228 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: 201 Number of extensions: 6 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: 344 Length adjustment: 29 Effective length of query: 334 Effective length of database: 315 Effective search space: 105210 Effective search space used: 105210 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