Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 217 bits (553), Expect = 4e-61 Identities = 132/310 (42%), Positives = 180/310 (58%), Gaps = 12/310 (3%) Query: 3 ALEIRNIRKRYGEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62 +L IR + +RYG L + + GEF+ LLG SG GKS+LL I+AGL +P GD+L Sbjct: 2 SLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLR 61 Query: 63 GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMR----RVPQAEHDKAVRDTA 118 +L + + RDI +VFQ YAL+P+++VA NI FGL +R R + + V D Sbjct: 62 DGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLL 121 Query: 119 RLLQIENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKR 178 R +Q+E L R P+QLSGGQRQRVA+ RAL P + L DEP LDA++R +R L+ Sbjct: 122 RRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRD 181 Query: 179 LHQMLRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPP 238 L + L T V VTHDQ EA+ LA R+ VM GRIEQ+ AP E+Y PAT +V GFVG Sbjct: 182 LQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVGR-- 239 Query: 239 MNILDAEMTANGLKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEAQRLTA 298 N + + + L + G LP AGR ++ +RPE L LA+ T Sbjct: 240 ANRIRGHVERDRLHLGGHSFQGELPGDL-----AGREIEAWLRPEHLALASRG-LGGWTG 293 Query: 299 SVEVVELTGP 308 ++ ++L GP Sbjct: 294 RLQHLDLAGP 303 Lambda K H 0.320 0.136 0.385 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: 342 Number of extensions: 12 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: 360 Length of database: 384 Length adjustment: 30 Effective length of query: 330 Effective length of database: 354 Effective search space: 116820 Effective search space used: 116820 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