Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate 8502259 DvMF_2969 ABC transporter related (RefSeq)
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Miya:8502259 Length = 418 Score = 206 bits (523), Expect = 1e-57 Identities = 105/255 (41%), Positives = 151/255 (59%), Gaps = 6/255 (2%) Query: 3 APASRSSFNPRGRHVGS------LQLKTIRKAFGSHEVLKGIDLDVKDGEFVIFVGPSGC 56 +P + S P V S L + + K F + + +V+ G F +GPSGC Sbjct: 6 SPVASSDAFPNASPVASPSASADLSVTRLVKRFEKFTAVNDVSFEVEQGRFFSILGPSGC 65 Query: 57 GKSTLLRTIAGLEDATSGSVQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGL 116 GK+TLLR IAG E SG + I G ++ +AP +R + ++FQ AL+P ++V +N+ GL Sbjct: 66 GKTTLLRMIAGFESPDSGVIAIRGRDMAGIAPNRRPVNLIFQHLALFPMMSVAENVAFGL 125 Query: 117 KQAGVPKAEIEEKVAKAAGMLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEP 176 K+ G+ EI +V + L Y + PA+LSGGQ+QRVAI R +V EP + L DEP Sbjct: 126 KRRGMAGGEISRRVQDVLERVGLPGYGVKMPAQLSGGQKQRVAIARCLVLEPAVLLLDEP 185 Query: 177 LSNLDAALRVNTRLEIARLHRSLKATMIYVTHDQVEAMTLADKIVVLNAGRIEQVGSPME 236 L LD LR ++E+ L + T +Y+THDQ EA+ ++D + V+NAGR EQV +P Sbjct: 186 LGALDLKLREQMKVELKTLQAEVGTTFVYITHDQSEALVMSDHVAVMNAGRFEQVDTPRN 245 Query: 237 LYNRPANLFVAGFIG 251 LY RPA+ FVAGF+G Sbjct: 246 LYRRPASAFVAGFVG 260 Lambda K H 0.320 0.137 0.393 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: 353 Number of extensions: 13 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: 352 Length of database: 418 Length adjustment: 30 Effective length of query: 322 Effective length of database: 388 Effective search space: 124936 Effective search space used: 124936 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