Align Maltose/maltodextrin import ATP-binding protein; EC 3.6.3.19 (characterized, see rationale)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= uniprot:A8LLL2 (373 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 187 bits (475), Expect = 4e-52 Identities = 114/296 (38%), Positives = 172/296 (58%), Gaps = 16/296 (5%) Query: 4 LKLTGVEKAYGDVKVLSNINLDIQQGELIVFVGPSGCGKSTLLRMIAGLEKITGGTLEID 63 L + + + YG L + +LDI +GE + +GPSG GKS+LLR++AGL+ G + D Sbjct: 3 LSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLRD 62 Query: 64 GTVVNDVPPAQRGIAMVFQSYALYPHMTVRENMSFALKI----AKKSQAEIDAAVEAAAE 119 GT + +P +R I +VFQ YAL+PHMTV +N++F L++ + S+ +I A VE Sbjct: 63 GTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLLR 122 Query: 120 KLQLGQYLDRLPKALSGGQRQRVAIGRSIVRDPKVYLFDEPLSNLDAALRVATRLEIAQL 179 ++QL + R P LSGGQRQRVA+ R++ +P + L DEP LDA +R R+ + L Sbjct: 123 RVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRDL 182 Query: 180 KEAMPESTMVYVTHDQVEAMTLATRIVVLAGGGIAQVGSPLELYEKPENEFVAQFIGSPK 239 + ++ +T V VTHDQ EA+ LA R+VV+ G I QVG+P E+Y +P FV F+G + Sbjct: 183 QRSLGLTT-VLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVG--R 239 Query: 240 MNLLPGKIIGTGAQTTVEMTDGGRAV-SDYPSDDSLMGAAVNVGVRPEDMVEAAPG 294 N + G + + GG + + P D L G + +RPE + A+ G Sbjct: 240 ANRIRGHV------ERDRLHLGGHSFQGELPGD--LAGREIEAWLRPEHLALASRG 287 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: 350 Number of extensions: 15 Number of successful extensions: 3 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: 384 Length adjustment: 30 Effective length of query: 343 Effective length of database: 354 Effective search space: 121422 Effective search space used: 121422 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: 50 (23.9 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