Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate WP_090447186.1 BLS63_RS18125 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >NCBI__GCF_900100495.1:WP_090447186.1 Length = 386 Score = 192 bits (487), Expect = 2e-53 Identities = 120/357 (33%), Positives = 197/357 (55%), Gaps = 15/357 (4%) Query: 3 LALDSISKKVGA--QTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVT 60 L L +++K G+ L ++ +A+ SG +L+G + GK++LM +AGL+ + G + Sbjct: 4 LELRNVNKTYGSGLPDTLKNIEIAIDSGEFLILVGPSGCGKSTLMNCIAGLEDISGGAIL 63 Query: 61 VDGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKLR--GEKNIDARVREIASRL 118 V+G+D++GM +DR++AMV+Q + YP+M V NIA LK+R +ID V +A L Sbjct: 64 VEGQDISGMSPKDRDIAMVFQSYALYPTMTVRDNIAFGLKIRKMAPADIDTEVARVAKLL 123 Query: 119 HIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLFA 178 I+ L R P +LSGGQQQRVA+ RALA+ + L DEPL NLD KLR E+R E+ + Sbjct: 124 QIEHLLARKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKLMHQ 183 Query: 179 AGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMNL 238 ++T VY T + EA+ LG AV+ +G + Q+G ++++ P +L VA PPMN Sbjct: 184 RLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPQQIYNDPANLFVASFIGSPPMNF 243 Query: 239 MAASATAQGVRL-------QGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVA 291 + + +L Q EL L + + + +G+R + + A+ GD S+ Sbjct: 244 IPLRLQRRDGQLWALLDSGQARCELPLGAMEEGLESREVILGIRPEQIGI-AQGGDGSLP 302 Query: 292 GV---VELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGA 345 + V++ E +G DT V + +L ++G ++ L +P++ +F A Sbjct: 303 SIRAEVQVTEPTGPDTLVFVELNQTKVCCRLAPDAAPQVGASLELQFEPSKVLLFDA 359 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: 289 Number of extensions: 13 Number of successful extensions: 2 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 24 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