Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 224 bits (572), Expect = 2e-63 Identities = 138/345 (40%), Positives = 193/345 (55%), Gaps = 24/345 (6%) Query: 4 LQLRGIEKFFGEHR-AIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAID-GGSLM 61 + LR K F + A++ +DL I GE +V +GPSGCGK+T LR+IAGLE D GG +M Sbjct: 7 ITLRHCGKTFADGTLALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVVM 66 Query: 62 LDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARIL 121 D+T P +R + MVFQSYAL+P+M+V EN+++ L++ ++D +V ++ Sbjct: 67 FGDNDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEMLAMM 126 Query: 122 NLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLHR 181 +L + +R +LSGGQRQRVA+ RAI P+V L DEPL+ LDA LR R +I +L R Sbjct: 127 HLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQLLR 186 Query: 182 DLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMNV 241 L T +YVTHDQ EAM L DR++V+ G I Q GTP ++Y PAN FVA FIGT Sbjct: 187 SLHITAVYVTHDQAEAMALGDRIIVMDRGRIAQTGTPQQIYRAPANAFVADFIGT----- 241 Query: 242 VPVDKLPQPVQQQAPAAPAG--------AAVGA-------IGLRPENITVRTTGATPVGG 286 +++LP ++ A P G A++ A + RPE++ + +GG Sbjct: 242 --MNRLPAVLEADAWRVPGGLVPRHGTAASLAAAPSPRAELLFRPEDVALAQAEDAHLGG 299 Query: 287 QVDLIEALGAETLIYVTTPGGAQFVSRQNDRTDLRVGDAVSLDID 331 V LG T + V A V R GD V L +D Sbjct: 300 SVVTALFLGNYTRLLVDVGAPAPLVVDTTRRDGWLAGDRVGLRLD 344 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: 310 Number of extensions: 13 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: 350 Length of database: 357 Length adjustment: 29 Effective length of query: 321 Effective length of database: 328 Effective search space: 105288 Effective search space used: 105288 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