Align ABC transporter for Xylitol, ATPase component (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= reanno::Dino:3607124 (338 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 216 bits (549), Expect = 1e-60 Identities = 120/292 (41%), Positives = 168/292 (57%), Gaps = 22/292 (7%) Query: 2 AGIKIDKINKFYGTTQALFDINLDIEDGEFVVFVGPSGCGKSTLLRTLAGLEGVSSGRIE 61 A + + ++ K + A+ D++ ++E G F +GPSGCGK+TLLR +AG E SG I Sbjct: 27 ADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGCGKTTLLRMIAGFESPDSGVIA 86 Query: 62 IGGRDVTTVEPADRDLAMVFQSYALYPHMTVRENMEFGMKVNGFEPDLRKERIAEAARVL 121 I GRD+ + P R + ++FQ AL+P M+V EN+ FG+K G R+ + + Sbjct: 87 IRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGLKRRGMAGGEISRRVQDVLERV 146 Query: 122 QLEDYLDRKPGQLSGGQRQRVAIGRAIVKNPSVFLFDEPLSNLDAKLRVQMRVELEGLHK 181 L Y + P QLSGGQ+QRVAI R +V P+V L DEPL LD KLR QM+VEL+ L Sbjct: 147 GLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEPLGALDLKLREQMKVELKTLQA 206 Query: 182 QLGATMIYVTHDQVEAMTMADKIVVLNRGRIEQVGSPMDLYHKPNSRFVAEFIG-----S 236 ++G T +Y+THDQ EA+ M+D + V+N GR EQV +P +LY +P S FVA F+G S Sbjct: 207 EVGTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRNLYRRPASAFVAGFVGETNVWS 266 Query: 237 PAMNVFSSDVGLQDISLDASAAF---------------VGCRPEHIEIVPDG 273 + + D GL + D A F + RPE + I PDG Sbjct: 267 GTLEEATGDAGL--VRTDEGAVFRARVAAGLAKGTRVDMFIRPEAVLIDPDG 316 Lambda K H 0.320 0.139 0.396 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: 376 Number of extensions: 18 Number of successful extensions: 1 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: 338 Length of database: 418 Length adjustment: 30 Effective length of query: 308 Effective length of database: 388 Effective search space: 119504 Effective search space used: 119504 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: 50 (23.9 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