Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_037572389.1 BS73_RS14235 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_000744815.1:WP_037572389.1 Length = 386 Score = 172 bits (435), Expect = 2e-47 Identities = 118/357 (33%), Positives = 186/357 (52%), Gaps = 16/357 (4%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L L ++KK G+ T + + L + G+ LLGA+ GKT+ +R+++GL+APTAGR+ + Sbjct: 19 LRLTGLTKKFGSFTAVDGVDLTIAQGSFFALLGASGCGKTTTLRMISGLEAPTAGRIHLG 78 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNIDARVREIASRLHIDM 122 +DVT R V V+Q + +P + + N+A L+ RG +++ V ++ + + Sbjct: 79 DQDVTDRKPYRRPVNTVFQNYALFPHLDIFENVAFGLRRRGIRSVKKPVEDMLDLVELGH 138 Query: 123 FLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAGQS 182 R P +LSGGQQQR+ALARAL ++LLDEPL LD KLR +++ EL ++ Sbjct: 139 LARRKPTQLSGGQQQRIALARALINQPQVLLLDEPLGALDLKLRRQMQIELKRIQLEVGL 198 Query: 183 TVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMAA- 241 T V+ T + EA+ + AV++ G++ Q G AE++ PN+ VA NL+A Sbjct: 199 TFVHVTHDQEEAMTMADTIAVMNHGRIEQLGSPAELYENPNTTFVANFLGQ--SNLIAGT 256 Query: 242 --SATAQGVRLQG-GAELTLPLPQGAATAAGLTVGVRASALRVHARPGDV-----SVAGV 293 S + V++ G L LP + T+ + +GVR +R+ +V + G Sbjct: 257 VESVSGDVVQVAAHGRSLALPAARCRTTSGPVILGVRPEKVRIAKTEAEVPSGANHLTGK 316 Query: 294 VELAEISGSDTFVHASTPWGDLVA---QLTGVHYFELGTAITLHLDPAQAYVFGADG 347 V A G T P G+ +A Q TG G + +H DP+Q FG DG Sbjct: 317 VTDASFIGVSTQYLVELPSGEELAVFEQNTGQEIQRPGAEVVVHWDPSQG--FGLDG 371 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: 301 Number of extensions: 13 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: 386 Length adjustment: 30 Effective length of query: 333 Effective length of database: 356 Effective search space: 118548 Effective search space used: 118548 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: 50 (23.9 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