Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 3608244 Dshi_1648 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Dino:3608244 Length = 373 Score = 183 bits (464), Expect = 7e-51 Identities = 118/351 (33%), Positives = 179/351 (50%), Gaps = 10/351 (2%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 L L + K G L +++L +Q G + V +G + GK++L+R++AGL+ T G + +D Sbjct: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKL--RGEKNIDARVREIASRLHI 120 G V +P R +AMV+Q + YP M V N++ LK+ + + IDA V A +L + Sbjct: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEAAAEKLQL 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQL-FAA 179 +LDR P LSGGQ+QRVA+ R++ + + L DEPL NLD LR R E+ QL A Sbjct: 124 GQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQLKEAM 183 Query: 180 GQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLM 239 +ST+VY T + EA+ L VL G + Q G E++ P + VA+ P MNL+ Sbjct: 184 PESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPKMNLL 243 Query: 240 AASATAQGVR-----LQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVV 294 G + GG ++ + A + VGVR + A GD G V Sbjct: 244 PGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGGDYVFEGKV 303 Query: 295 ELAEISGSDTFVHASTPWGD--LVAQLTGVHYFELGTAITLHLDPAQAYVF 343 + E G T ++ P G+ + +L G+H G L +PA+ +VF Sbjct: 304 AITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 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: 340 Number of extensions: 18 Number of successful extensions: 5 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: 373 Length adjustment: 30 Effective length of query: 333 Effective length of database: 343 Effective search space: 114219 Effective search space used: 114219 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 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