Align ABC transporter for Glycerol, ATPase component 2 (characterized)
to candidate 3607949 Dshi_1357 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_792 (358 letters) >FitnessBrowser__Dino:3607949 Length = 349 Score = 207 bits (527), Expect = 3e-58 Identities = 124/331 (37%), Positives = 186/331 (56%), Gaps = 11/331 (3%) Query: 29 MEFEDGGAYALLGPSGCGKTTMLNIMSGLLVPSHGKVLFDGRDVTRASPQERNIAQVFQF 88 +E DG +GPSGCGK+T+L ++ GL S G +L DG DVT P +R + VFQ Sbjct: 24 LEIRDGEFVVFVGPSGCGKSTLLRMIGGLEDTSRGAMLIDGVDVTDHPPAKRGLTMVFQS 83 Query: 89 PVIYDTMTVAENLAFPLRNRKVPEGQIKQRVGVIAEMLEMSGQLNQRAAGLAADAKQKIS 148 +Y M+V EN+ F L+ P +I ++V A +L++ L++R L+ +Q+++ Sbjct: 84 YALYPHMSVRENMGFSLKTAGAPAAEIAEKVEAAAAVLKLEPYLDRRPKDLSGGQRQRVA 143 Query: 149 LGRGLVRADVAAVLFDEPLTVIDPHLKWQLRRKLKQIHHELKLTLIYVTHDQVEALTFAD 208 +GR +VRA A LFDEPL+ +D L+ ++R ++ ++H L T+IYVTHDQVEA+T AD Sbjct: 144 IGRSIVRAPTA-FLFDEPLSNLDAALRVEMRYEIAKLHQSLDTTMIYVTHDQVEAMTLAD 202 Query: 209 QVVVMTRGKAVQVGSADALFERPAHTFVGHFIGSPGMNFLPAHRDGENLSVAGHRLASPV 268 ++VV+ GK QVG+ L+E PA+ FV FIGSP MN +P D +RL++ Sbjct: 203 RIVVLEFGKIAQVGTPRELYETPANLFVAQFIGSPKMNVMPCTTD-----AGRYRLSAGR 257 Query: 269 GRALPAG--ALQVGIRPEYLALAQPQQAGALPGTVVQVQDIGTYQMLTAKVG-EHTVKAR 325 G A+Q+GIRPE++ P GA G V V+ +G +L G E V R Sbjct: 258 GGVFSGDRPAVQLGIRPEHITPGAP-GTGACDGRVDVVEYLGADTLLVLDCGPEGRVTVR 316 Query: 326 FTPETRLPSSGDTAWLQVLGEHTCYYKNEEL 356 +T L + GD L + ++ + L Sbjct: 317 VIGDTDL-TPGDAVGLSFNPDRLSFFDTDGL 346 Lambda K H 0.320 0.136 0.395 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: 273 Number of extensions: 13 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: 358 Length of database: 349 Length adjustment: 29 Effective length of query: 329 Effective length of database: 320 Effective search space: 105280 Effective search space used: 105280 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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