Align MtlK, component of The polyol (mannitol, glucitol (sorbitol), arabitol (arabinitol; lyxitol)) uptake porter, MtlEFGK (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::O30494 (367 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 208 bits (529), Expect = 2e-58 Identities = 118/300 (39%), Positives = 176/300 (58%), Gaps = 22/300 (7%) Query: 3 NLKIKNLQKGFEGFSIIKGIDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIEL 62 +L I+ L + + F+ + L++ + EFV +GPSG GKS+LLR++AGL++ G + Sbjct: 2 SLSIRQLTRRYGAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDVLR 61 Query: 63 DGRDITEVTPAKRDLAMVFQTYALYPHMSVRKNMSFALDLAG----VDKQLVESKVNEAA 118 DG D+ + +RD+ +VFQ YAL+PHM+V N++F L + ++ + ++V + Sbjct: 62 DGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVEDLL 121 Query: 119 RILELGPLLERKPKQLSGGQRQRVAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELAR 178 R ++L L R P QLSGGQRQRVA+ RA+ P + L DEP LDA +R +R+ L Sbjct: 122 RRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWLRD 181 Query: 179 LHKELQATMIYVTHDQVEAMTLADKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPK 238 L + L T + VTHDQ EA+ LAD+VVV+N GRIEQVG+P E+Y +PA FV GF+G + Sbjct: 182 LQRSLGLTTVLVTHDQDEALELADRVVVMNRGRIEQVGAPSEIYREPATPFVHGFVG--R 239 Query: 239 MGFLKGKVTR----VDGQGCEVQLDAGTLISLPLSGASLSVGSAVTLGIRPEHLEIASPG 294 ++G V R + G + +L G + +RPEHL +AS G Sbjct: 240 ANRIRGHVERDRLHLGGHSFQGELPGDL------------AGREIEAWLRPEHLALASRG 287 Lambda K H 0.319 0.137 0.387 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: 344 Number of extensions: 21 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: 367 Length of database: 384 Length adjustment: 30 Effective length of query: 337 Effective length of database: 354 Effective search space: 119298 Effective search space used: 119298 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: 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