Align ABC transporter for D-Sorbitol, ATPase component (characterized)
to candidate 200449 SO1271 polyamine ABC transporter, ATP-binding protein (NCBI ptt file)
Query= reanno::Phaeo:GFF1302 (334 letters) >FitnessBrowser__MR1:200449 Length = 378 Score = 224 bits (572), Expect = 2e-63 Identities = 114/241 (47%), Positives = 161/241 (66%), Gaps = 2/241 (0%) Query: 4 IKLESVTKNFGPVEVIPPLDLTIEDGEFTVFVGPSGCGKSTLLRLIAGLEDITSGTIRID 63 +K+E V+K F V + + LTI GE +G SG GKSTLLR++AG E TSG I +D Sbjct: 21 LKIERVSKLFDDVRAVDDVSLTINKGEIFALLGGSGSGKSTLLRMLAGFERPTSGRIYLD 80 Query: 64 GEDATNIPPAKRGLAMVFQSYALYPHMSVRKNIAFPMKMAGIPADEQKRRIDNAAAALNL 123 GED T++PP +R + M+FQSYAL+PHM+V +NIAF +K +P E ++R+ +++ Sbjct: 81 GEDITDLPPYERPINMMFQSYALFPHMTVAQNIAFGLKQDKLPKAEIEQRVQEMLKLVHM 140 Query: 124 TDYLDRRPGQLSGGQRQRVAIGRAIVREPAAFLFDEPLSNLDAALRVGMRLEISELHKRL 183 Y R+P QLSGGQRQRVA+ R++ + P L DEP+ LD LR M+LE+ E+ +R+ Sbjct: 141 EQYGKRKPHQLSGGQRQRVALARSLAKRPKLLLLDEPMGALDKKLRTQMQLEVVEILERV 200 Query: 184 ATTMIYVTHDQVEAMTMADKIVVLQAGVIEQVGSPMELYRAPRNVFVAGFIGSPKMNLLT 243 T + VTHDQ EAMTMA +I ++ G I Q GSPM++Y +P + +A FIGS +NL + Sbjct: 201 GVTCVMVTHDQEEAMTMAGRISIMSDGWIAQTGSPMDIYESPNSRMIAEFIGS--VNLFS 258 Query: 244 G 244 G Sbjct: 259 G 259 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: 287 Number of extensions: 8 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: 378 Length adjustment: 29 Effective length of query: 305 Effective length of database: 349 Effective search space: 106445 Effective search space used: 106445 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