Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate PP_1484 PP_1484 predicted polyamine ABC transporter, ATP-binding protein
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__Putida:PP_1484 Length = 343 Score = 231 bits (590), Expect = 2e-65 Identities = 127/296 (42%), Positives = 181/296 (61%), Gaps = 9/296 (3%) Query: 4 IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63 ++ V++ FG V+ + + + I DGEF +GPSG GK+T LRLIAG E +SG+IRI Sbjct: 5 VQFTQVSRTFGEVKAVDQVSIDIIDGEFFSMLGPSGSGKTTCLRLIAGFEQPSSGSIRIQ 64 Query: 64 GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123 G +A +PP +R + VFQ YAL+PHM+V +NIA+ +K+ G+ E+ R + A A + L Sbjct: 65 GVEAAGLPPYQRDVNTVFQDYALFPHMNVLENIAYGLKVKGVGKAERHSRAEEALAMVAL 124 Query: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183 Y R+P QLSGGQRQRVA+ RA+V P L DEPL LD LR M+ E+ +L ++L Sbjct: 125 AGYGARKPAQLSGGQRQRVALARALVNRPRVLLLDEPLGALDLKLREQMQGELKKLQRQL 184 Query: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243 T I+VTHDQ EA++M+D++ V G IEQV +P LY P FVA F+G+ N++ Sbjct: 185 GITFIFVTHDQTEALSMSDRVAVFNRGRIEQVDTPRNLYMKPSTTFVAEFVGT--SNVVR 242 Query: 244 GPQAAQHNA--ATIGIRPEHLSISET-----EGMWAGTIGVSEHLGSDTFFHVQCD 292 G A Q N A IRPE + + + E +G + ++ GS T + +Q D Sbjct: 243 GELAMQINGSPAPFSIRPELIRLGDPVVTSHEVQVSGVLHDVQYQGSATRYELQLD 298 Lambda K H 0.320 0.138 0.400 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: 279 Number of extensions: 14 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: 334 Length of database: 343 Length adjustment: 28 Effective length of query: 306 Effective length of database: 315 Effective search space: 96390 Effective search space used: 96390 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