Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate 5208351 Shew_0863 ABC transporter-related protein (RefSeq)
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__PV4:5208351 Length = 342 Score = 176 bits (447), Expect = 6e-49 Identities = 122/359 (33%), Positives = 191/359 (53%), Gaps = 22/359 (6%) Query: 1 MADLKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTL 60 M+ L + V Y +L ++L + QGE+ +GPSGCGK+TLL+ IAGL+ I+ G + Sbjct: 1 MSTLTIEQVHSDYQGQTILRGLDLVLHQGEIAALLGPSGCGKTTLLKAIAGLQPISQGRI 60 Query: 61 EIDGTVVND----VPPAQRGIAMVFQSYALYPHMTVRENMSFALKIAKKSQAEIDAAVEA 116 I+G +++ VP +R + M+FQ YAL+PH+TV EN+ F +K K+ + Sbjct: 61 SINGRLLSGPETFVPSERREVGMIFQDYALFPHLTVAENILFGVKGLDKAARQARLGEML 120 Query: 117 AAEKLQ-LGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLE 175 A KL+ LG R P LSGGQ+QRV+I R++ +P++ L DEP SN+DA +R +E Sbjct: 121 ALVKLEGLG---GRYPHELSGGQQQRVSIARALAYEPELLLLDEPFSNIDAKVRGEMMVE 177 Query: 176 IAQLKEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFI 235 I ++ + S V+VTH + EA A ++ + GGIAQ GS LY +P +++VA+F+ Sbjct: 178 IREILKQRGVSA-VFVTHSKDEAFVFADKLALFKDGGIAQYGSAESLYAEPTDKYVAEFL 236 Query: 236 GSPKMNLLPGKIIGTGAQTTVEMTDGGRAVSDYPSDDSLMGAAVNVGVRPEDMVEAAPGG 295 G ++N L ++ T + ++ SD P G + +RPE + A G Sbjct: 237 G--QVNYLSCEVKDRARLQT--LLGEVQSSSDLPKAAGYRGELL---LRPEQLQMA---G 286 Query: 296 DYVFEGKVAITEALGEVTLLYFEAPSGEDPTIGKLQGIHKDLKGQVTRLTAEPAKVHVF 354 D EG + LG L ++ GE+ + +H GQ L+ P +F Sbjct: 287 DEQGEGTIIARRFLG--NLCHYSILIGEE-ILAVRSPLHHFSPGQKVGLSVTPHPAVLF 342 Lambda K H 0.316 0.135 0.379 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: 339 Number of extensions: 15 Number of successful extensions: 4 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: 373 Length of database: 342 Length adjustment: 29 Effective length of query: 344 Effective length of database: 313 Effective search space: 107672 Effective search space used: 107672 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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