Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate GFF1645 PGA1_c16680 sugar ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Phaeo:GFF1645 Length = 355 Score = 190 bits (482), Expect = 6e-53 Identities = 123/356 (34%), Positives = 192/356 (53%), Gaps = 7/356 (1%) Query: 2 QLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61 ++ L ++K+ GA L D++L +Q G VL+G + GK++L+R++AGL+ T+G + Sbjct: 3 RIELRDVAKRYGAVEVLRDINLDIQDGEFIVLVGPSGCGKSTLLRMIAGLEPITSGDFEI 62 Query: 62 DGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRGEKNID--ARVREIASRLH 119 DG+ + + RDR++AMV+Q + YP M VA N+ +++R + + +RV A L Sbjct: 63 DGQRMNDVRPRDRDIAMVFQSYALYPHMDVARNMGFSMEIRKDPAEERRSRVARAAETLG 122 Query: 120 IDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAA 179 + +DR P LSGGQ+QRVA+ RA+ + L DEPL NLD LR E+R E+ +L Sbjct: 123 LSSLVDRLPKALSGGQRQRVAMGRAIIRDPRAFLFDEPLSNLDAALRVEMRLEIARLHKQ 182 Query: 180 GQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLM 239 +T++Y T + EAL L VL+ G + Q G E++ P + VA+ P MN++ Sbjct: 183 LGATMIYVTHDQVEALTLADRIVVLNGGDIQQVGSPLELYERPANKFVAQFIGSPTMNIL 242 Query: 240 AASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEI 299 S A GV G LTL TAA + +G+R L V PG+ + V ++ E Sbjct: 243 PVSGAASGVMATNGMMLTLDHMHD--TAAAVELGIRPEHLDV-VEPGEGHLIAVADVVER 299 Query: 300 SGSDTFVHASTP-WGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRLAQAPA 354 GSDT ++A G L+ + G G + L + A++F D +A PA Sbjct: 300 LGSDTNIYAKVDGLGPLMVRKHGNVPVRSGERLGLRVQAQNAHIFD-DRGIALRPA 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: 277 Number of extensions: 17 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: 355 Length adjustment: 29 Effective length of query: 334 Effective length of database: 326 Effective search space: 108884 Effective search space used: 108884 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