Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate 3607124 Dshi_0546 ABC transporter related (RefSeq)
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Dino:3607124 Length = 338 Score = 187 bits (474), Expect = 5e-52 Identities = 113/349 (32%), Positives = 187/349 (53%), Gaps = 19/349 (5%) Query: 3 LALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTVD 62 + +D I+K G L+D++L ++ G V +G + GK++L+R +AGL+ ++GR+ + Sbjct: 4 IKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIEIG 63 Query: 63 GKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG-EKNI-DARVREIASRLHI 120 G+DVT + DR++AMV+Q + YP M V N+ +K+ G E ++ R+ E A L + Sbjct: 64 GRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVLQL 123 Query: 121 DMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFAAG 180 + +LDR P +LSGGQ+QRVA+ RA+ K + L DEPL NLD KLR ++R EL L Sbjct: 124 EDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHKQL 183 Query: 181 QSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNLMA 240 +T++Y T + EA+ + VL+ G++ Q G +++H PNS VA P MN+ + Sbjct: 184 GATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIGSPAMNVFS 243 Query: 241 ASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGVVELAEIS 300 + Q + L A VG R + + GD +A V + E Sbjct: 244 SDVGLQDISLDASAAF---------------VGCRPEHIEI-VPDGDGHIAATVHVKERL 287 Query: 301 GSDTFVHASTP-WGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGR 348 G ++ ++ G +VA++ G ++G A++L + + F GR Sbjct: 288 GGESLLYLGLKGGGQIVARVGGDDETKVGAAVSLRFSRHRLHQFDEAGR 336 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: 251 Number of extensions: 9 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: 338 Length adjustment: 29 Effective length of query: 334 Effective length of database: 309 Effective search space: 103206 Effective search space used: 103206 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