Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate GFF5028 PS417_25760 spermidine/putrescine ABC transporter ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__WCS417:GFF5028 Length = 370 Score = 218 bits (555), Expect = 2e-61 Identities = 121/296 (40%), Positives = 181/296 (61%), Gaps = 11/296 (3%) Query: 4 LEIRNIRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62 + R ++K Y GE +K +++ + GEFL LLG SG GK+T L ++AG P+ G+I + Sbjct: 11 VSFRGVQKSYDGENLIVKDLNLEIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQL 70 Query: 63 GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQ 122 RS+ V P RDI MVFQ+YAL+P+++VA N+ F L +R + + + + V+ ++Q Sbjct: 71 AGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLSVRALSKTDISERVKRVLSMVQ 130 Query: 123 IENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQM 182 ++ R P+QLSGGQ+QRVA+ RALV PQ+ L DEPL LD +LR M+ E+K LHQ Sbjct: 131 LDAFAQRYPAQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHLHQR 190 Query: 183 LRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNIL 242 L TVVYVTHDQ EA+T++ R+AV G I+Q+AAP +Y+ P +VA F+G N L Sbjct: 191 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIAAPRTLYEEPKNTFVANFIGE--NNRL 248 Query: 243 DAEMTANG-----LKIEGCEEVLPLPAAFNGAAWAGRRVKVGIRPEALRLAAGSEA 293 + + ++ +++ E+V L G V + +RPE + L SE+ Sbjct: 249 NGRLHSHSGERCVVELARGEKVEALAV---NVGQVGGPVTLSVRPERVSLNGSSES 301 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: 309 Number of extensions: 9 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: 360 Length of database: 370 Length adjustment: 30 Effective length of query: 330 Effective length of database: 340 Effective search space: 112200 Effective search space used: 112200 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