Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate GFF4321 PS417_22130 sugar ABC transporter ATPase
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__WCS417:GFF4321 Length = 386 Score = 199 bits (506), Expect = 1e-55 Identities = 127/372 (34%), Positives = 199/372 (53%), Gaps = 13/372 (3%) Query: 3 LALDSISKKVGA--QTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 L L +++K GA L ++ L+++ G +L+G + GK++LM +AGL+ T G + Sbjct: 4 LELRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIM 63 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLRG--EKNIDARVREIASRL 118 + +DV+GM +DR++AMV+Q + YP+M V NI LK+R + +IDA V +A L Sbjct: 64 IGDQDVSGMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVAKLL 123 Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178 I+ L+R P +LSGGQQQRVA+ RALA+ + L DEPL NLD KLR E+R E+ + Sbjct: 124 QIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQ 183 Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238 ++T VY T + EA+ LG AV+ +G + Q+G E+++ P + VA PPMN Sbjct: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPPMNF 243 Query: 239 MAASATAQGVRL-------QGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGD--VS 289 + + RL Q EL L + + +G+R + + A GD S Sbjct: 244 VPLRLQRKDGRLVALLDSGQARCELALNTTEAGLEDRDVILGLRPEQIMLAAGEGDSASS 303 Query: 290 VAGVVELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGRL 349 + V++ E +G DT V + +L ++G +TL DP++ +F A+ Sbjct: 304 IRAEVQVTEPTGPDTLVFVQLNDTKVCCRLAPDVAPQVGETLTLQFDPSKVLLFDANTGE 363 Query: 350 AQAPARPVTAQG 361 A + AQG Sbjct: 364 RLGTASSLPAQG 375 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: 287 Number of extensions: 15 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: 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 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