Align N-Acetyl-D-glucosamine ABC transport system, ATPase component (characterized)
to candidate H281DRAFT_02629 H281DRAFT_02629 carbohydrate ABC transporter ATP-binding protein, CUT1 family (TC 3.A.1.1.-)
Query= reanno::Smeli:SMc02869 (352 letters) >FitnessBrowser__Burk376:H281DRAFT_02629 Length = 381 Score = 313 bits (802), Expect = 5e-90 Identities = 177/363 (48%), Positives = 234/363 (64%), Gaps = 35/363 (9%) Query: 17 VGSLQLKTIRKAF-GSHEVLKGIDLDVKDGEFVIFVGPSGCGKSTLLRTIAGLEDATSGS 75 + ++ L+ I+K F G+ VL+ ++L++ + EF +F+GPSGCGKSTLLR +AGLED T G Sbjct: 1 MAAISLRGIQKTFDGNAPVLRDLNLEIGEHEFCVFLGPSGCGKSTLLRIVAGLEDQTDGD 60 Query: 76 VQIDGVEVGHVAPAKRGIAMVFQSYALYPHLTVKDNMGLGLKQAGVPKAEIEEKVAKAAG 135 V I G + V A+RG+AMVFQSYAL+PH+TV +NM GLK A PKAEI+ KV +AA Sbjct: 61 VSIGGRTMNSVPAAERGVAMVFQSYALFPHMTVYENMAFGLKLARTPKAEIDRKVREAAH 120 Query: 136 MLSLEPYLARRPAELSGGQRQRVAIGRAIVREPKLFLFDEPLSNLDAALRVNTRLEIARL 195 +L L+ LAR+P ELSGGQRQRVAIGRAIVREP +FLFDEPLSNLDAALR TR+EIARL Sbjct: 121 VLQLDALLARKPRELSGGQRQRVAIGRAIVREPGVFLFDEPLSNLDAALRGQTRIEIARL 180 Query: 196 H-RSLKATMIYVTHDQVEAMTLADKIVVLNA-------GRIEQVGSPMELYNRPANLFVA 247 H R +A+++YVTHDQ+EAMTLADKIV+L+A G I Q+G+P+ELY+RP + FVA Sbjct: 181 HQRYAQASVVYVTHDQIEAMTLADKIVLLHAGAETQRLGSIAQIGAPLELYHRPRSKFVA 240 Query: 248 GFIGSPQMNFIEAA-------------------------KLGDGEAKTIGIRPEHIGLSR 282 GFIGSP+MNFI+ +L G+ T+GIRPEH+ Sbjct: 241 GFIGSPRMNFIDGVVERIADDSVEVSMPGTALRVLVDGRRLKPGQRVTLGIRPEHVRFDG 300 Query: 283 ESGDWKGKVIHVEHLGADTIIYIESETVGLLTVRLFGEHRYATDDIVHATPVIGSMHRFD 342 + + E LG + ++ + G L + G+ + + + H FD Sbjct: 301 GTQTLAVNALLTEQLGEHSYLHAD-HAGGTLIAKAPGDLHVRNGERLALHLPADACHLFD 359 Query: 343 ADG 345 DG Sbjct: 360 EDG 362 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: 420 Number of extensions: 19 Number of successful extensions: 4 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: 381 Length adjustment: 30 Effective length of query: 322 Effective length of database: 351 Effective search space: 113022 Effective search space used: 113022 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