Align ABC transporter for D-Glucosamine, ATPase component (characterized)
to candidate PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= reanno::Smeli:SM_b21216 (360 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 225 bits (573), Expect = 2e-63 Identities = 125/295 (42%), Positives = 181/295 (61%), Gaps = 9/295 (3%) Query: 4 LEIRNIRKRY-GEVETLKGIDIALESGEFLVLLGSSGCGKSTLLNIIAGLAEPSGGDILI 62 + R ++K Y GE +K +++ + GEFL LLG SG GK+T L ++AG P+ G+I + Sbjct: 15 VSFRGVQKSYDGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGEIQL 74 Query: 63 GERSVLGVHPKDRDIAMVFQSYALYPNLSVARNIGFGLEMRRVPQAEHDKAVRDTARLLQ 122 G RS+ V P RDI MVFQ+YAL+P+++VA N+ F L +R + + + + V+ ++Q Sbjct: 75 GGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLNMVQ 134 Query: 123 IENLLDRKPSQLSGGQRQRVAIGRALVRNPQVFLFDEPLSNLDAKLRMEMRTELKRLHQM 182 ++ R P QLSGGQ+QRVA+ RALV PQ+ L DEPL LD +LR M+ E+K +HQ Sbjct: 135 LDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHIHQR 194 Query: 183 LRTTVVYVTHDQIEAMTLATRIAVMRDGRIEQLAAPDEVYDRPATLYVAGFVGSPPMNIL 242 L TVVYVTHDQ EA+T++ R+AV G I+Q+A P +Y+ P +VA F+G N + Sbjct: 195 LGVTVVYVTHDQGEALTMSDRVAVFHQGEIQQIADPRTLYEEPCNTFVANFIGE--NNRI 252 Query: 243 DAEMTANGLKIEGCEEVLP----LPAAFNGAAWAGRRVKVGIRPEALRLAAGSEA 293 + A+ K C+ LP + A AG V + IRPE +RL SE+ Sbjct: 253 SGTLLASDGK--RCQVQLPRGERVEALAVNVGQAGEPVTLSIRPERVRLNGHSES 305 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: 308 Number of extensions: 11 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: 374 Length adjustment: 30 Effective length of query: 330 Effective length of database: 344 Effective search space: 113520 Effective search space used: 113520 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