Align ABC transporter for Glycerol, ATPase component 1 (characterized)
to candidate H281DRAFT_05887 H281DRAFT_05887 carbohydrate ABC transporter ATP-binding protein, CUT1 family
Query= reanno::acidovorax_3H11:Ac3H11_791 (363 letters) >FitnessBrowser__Burk376:H281DRAFT_05887 Length = 345 Score = 184 bits (467), Expect = 3e-51 Identities = 123/356 (34%), Positives = 182/356 (51%), Gaps = 26/356 (7%) Query: 2 QLALDSISKKVGAQTWLYDMSLALQSGAVTVLLGATQAGKTSLMRIMAGLDAPTAGRVTV 61 ++ L ++SK+ G + D+S+ + G VLLG + AGKT+ +R++AGL+ P AG V + Sbjct: 3 EIQLRNVSKRFGDIAAVDDISIDVADGEFVVLLGPSGAGKTTTLRLIAGLERPDAGDVLI 62 Query: 62 DGKDVTGMPVRDRNVAMVYQQFINYPSMKVAANIASPLKL----RGEKNIDARVREIASR 117 DG TG+ DR+VA ++QQ+ YP + V N+A PL+ E ++ ARV +A Sbjct: 63 DGTIATGVHPSDRDVAFIFQQYSLYPHLTVFGNLAFPLRSPRRRSSEADVRARVHAVAEM 122 Query: 118 LHIDMFLDRYPAELSGGQQQRVALARALAKGAPLMLLDEPLVNLDYKLREELREELTQLF 177 LH++ LD LSGG+ QRVA+ RAL + L+DEPL +LD KLREELR EL +L Sbjct: 123 LHMEAKLDNMATHLSGGEMQRVAIGRALVRQPKAFLMDEPLSSLDAKLREELRIELKRLH 182 Query: 178 AAGQSTVVYATTEPGEALLLGGYTAVLDEGQLLQYGPTAEVFHAPNSLRVARAFSDPPMN 237 +T+VY T + EA L +LD G+L+Q G EV+ P SL A+ PP+N Sbjct: 183 RTIGATIVYVTHDQVEATTLADRIGILDHGRLVQLGTPREVYGNPVSLSAAQRLGSPPIN 242 Query: 238 LMAASATAQGVRLQGGAELTLPLPQGAATAAGLTVGVRASALRVHARPGDVSVAGV---- 293 L+ + + +P G A TVG+R + +H P + +G Sbjct: 243 LLPPTLFD-----------SAHMPAGTA-----TVGIRPEDIVLH-DPAEGHASGAQDAL 285 Query: 294 -VELAEISGSDTFVHASTPWGDLVAQLTGVHYFELGTAITLHLDPAQAYVFGADGR 348 + + E S + +VA F G + + L P F ADGR Sbjct: 286 DLTVLEYSPLRHLLILDRAGTAVVATTVTERSFSPGQRVGVSLPPRSLLYFHADGR 341 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: 283 Number of extensions: 14 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: 345 Length adjustment: 29 Effective length of query: 334 Effective length of database: 316 Effective search space: 105544 Effective search space used: 105544 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