Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000016765.1:WP_012048833.1 Length = 241 Score = 104 bits (260), Expect = 2e-27 Identities = 78/232 (33%), Positives = 123/232 (53%), Gaps = 11/232 (4%) Query: 8 ISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVDGKDVT 67 + K G L ++SL + G V+ G + +GK++L+R + GL+ G + + +V Sbjct: 7 VGKWYGGYHALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVR 66 Query: 68 G-----MPVRDRNVAMVYQQFINYPSMKVAANIA-SPLKLRG--EKNIDARVREIASRLH 119 +R R V MV+Q F +P + + N A +P+K+RG +A RE+ R+ Sbjct: 67 PDRRVLQRIRAR-VGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVR 125 Query: 120 IDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAA 179 I D+YPA+LSGGQQQR A+ARALA ++L DEP LD ++ +E+ + + L Sbjct: 126 IADQADKYPAQLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEMVKEVLDIMKALATE 185 Query: 180 GQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAF 231 G T++ T E G A + +D GQ+++ G + F AP R RAF Sbjct: 186 G-ITMLCVTHEMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHER-TRAF 235 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: 160 Number of extensions: 8 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: 241 Length adjustment: 26 Effective length of query: 337 Effective length of database: 215 Effective search space: 72455 Effective search space used: 72455 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