Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate Pf1N1B4_3974 ABC transporter, ATP-binding protein
Query= reanno::acidovorax_3H11:Ac3H11_2941 (350 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3974 Length = 341 Score = 259 bits (661), Expect = 9e-74 Identities = 140/334 (41%), Positives = 212/334 (63%), Gaps = 6/334 (1%) Query: 1 MAYLQLRGIEKFFGEHRAIKGIDLTIQQGEFIVFVGPSGCGKSTLLRLIAGLEAIDGGSL 60 MA++QL + K +GE A+ +L++++GEF+ +GPSGCGK+T L++IAG + G + Sbjct: 1 MAFVQLENLGKRYGEIDAVVATNLSVEKGEFVSLLGPSGCGKTTTLQMIAGFVEVSSGRI 60 Query: 61 MLDGRDITDQPSSKRDLAMVFQSYALYPHMSVYENMSFALKLAKVDKQVIDEKVQNAARI 120 +LDGRDIT + R L +VFQSYAL+PHM+V +N++F L++ KV + ++V ++ Sbjct: 61 VLDGRDITHAKPASRGLGVVFQSYALFPHMTVRDNVAFGLRMRKVPNDELQQRVDRVLKL 120 Query: 121 LNLTQYLQRTPKELSGGQRQRVAIGRAIVRAPKVFLFDEPLSNLDAALRGQTRVEIAKLH 180 + L Q+ +R P+ELSGGQRQRVA+ RA+V P V L DEPLSNLDA LR + + EI ++ Sbjct: 121 VRLNQHAERYPRELSGGQRQRVALARALVIEPPVLLLDEPLSNLDANLREEMQFEIRRIQ 180 Query: 181 RDLGATTIYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDKPANQFVAQFIGTPQMN 240 R++G TT+ VTHDQ EA++++DRVVV++ G I Q+ P LY+ P +F++ F+G + N Sbjct: 181 REVGITTLMVTHDQSEALSISDRVVVMQAGRITQIDAPYTLYEHPRTEFISGFVG--KAN 238 Query: 241 VVPVDKLPQPVQQQAPAAPAGAAVGAIGLRPENITVRTTGATPVGGQVDLIEALGAETLI 300 ++P ++ V Q + LRPE I +R G + G++ LG++ L Sbjct: 239 LLPGERDSAGVVQ---VCNRDNGELTLSLRPEKIDLRDVGLGRLQGKIVSRFFLGSQWLY 295 Query: 301 YVTTPGGAQFVSRQND-RTDLRVGDAVSLDIDAS 333 V+T G V R+ND L G AV LD D + Sbjct: 296 GVSTSLGELSVVRRNDGSAPLIEGTAVGLDWDTA 329 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: 309 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: 341 Length adjustment: 29 Effective length of query: 321 Effective length of database: 312 Effective search space: 100152 Effective search space used: 100152 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