Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Ac3H11_1610 Putrescine transport ATP-binding protein PotA (TC 3.A.1.11.1)
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1610 Length = 362 Score = 248 bits (633), Expect = 2e-70 Identities = 141/342 (41%), Positives = 211/342 (61%), Gaps = 16/342 (4%) Query: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 M++LQL + KF+G A++ ++L++++GEF+ +GPSGCGK+T L+++AG EA+ G + Sbjct: 1 MSFLQLTDVTKFYGSTCAVQSMNLSVEKGEFVSLLGPSGCGKTTTLQMVAGFEAVTSGRI 60 Query: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 L GRDIT ++ R L +VFQSYAL+PHM+V +N+SF L++ KV K ++V A + Sbjct: 61 ELAGRDITHAKANTRGLGIVFQSYALFPHMTVADNVSFGLEMRKVPKAERKDRVAQALGL 120 Query: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 ++L ++ R P+ELSGGQRQRVA+ RA+V P V L DEPLSNLDA LR + + E+ ++ Sbjct: 121 VHLEKHAGRYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDAKLREEMQFELRQIQ 180 Query: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 R +G TT+ VTHDQ EAM+++DRVVV+ G Q+ P +Y+ P +F++ F+G + N Sbjct: 181 RKVGTTTVMVTHDQSEAMSISDRVVVMEAGRATQIDHPHRVYEHPRTRFISTFVG--KAN 238 Query: 241 VVP------------VDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQV 288 +VP V P V+ + GAAV + +RPE + + T + G+V Sbjct: 239 LVPGQVTTASATHTHVGAGPIEVRVEGAQFRPGAAV-LLSVRPEKLQLVPTVQGRIDGEV 297 Query: 289 DLIEALGAETLIYVTTPGGAQFVSRQND-RTDLRVGDAVSLD 329 LG++ L V T G V ND R L G+ LD Sbjct: 298 CERFFLGSQWLYRVGTGMGDLMVLAPNDGRGALEEGERTGLD 339 Lambda K H 0.320 0.137 0.388 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: 313 Number of extensions: 12 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: 350 Length of database: 362 Length adjustment: 29 Effective length of query: 321 Effective length of database: 333 Effective search space: 106893 Effective search space used: 106893 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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