Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate N515DRAFT_1562 N515DRAFT_1562 sulfate transport system ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Dyella79:N515DRAFT_1562 Length = 384 Score = 200 bits (509), Expect = 5e-56 Identities = 111/265 (41%), Positives = 164/265 (61%), Gaps = 18/265 (6%) Query: 3 TLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNL 62 +L + + +RY ++++F+LDI + EF+ +GPSG GKS+ LR++AGL+D G++ Sbjct: 2 SLSIRQLTRRY--GAFAALDDFSLDIAEGEFVALLGPSGSGKSSLLRILAGLDDPDRGDV 59 Query: 63 YIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLR----KYKKDDINKRVHE 118 D + + RDI +VFQ+YAL+PHM+V +N+AFGL++R + + DI RV + Sbjct: 60 LRDGTDLLALPAQRRDIGLVFQHYALFPHMTVADNIAFGLRVRPRARRPSRRDIAARVED 119 Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178 + L E R P LSGGQRQRVA+ RA+ + + L+DEP LDA++R +R + Sbjct: 120 LLRRVQLEELGRRYPTQLSGGQRQRVALARALAVEPSLLLLDEPFGALDAQVRGTLRVWL 179 Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPA 238 + R +G TT+ VTHDQ EA+ LADR+V+M+ GRIEQ+G P E+Y EPA Sbjct: 180 RDLQRSLGLTTVLVTHDQDEALELADRVVVMNR----------GRIEQVGAPSEIYREPA 229 Query: 239 NKFVAGFIGSPAMNFFEVTVEKERL 263 FV GF+G N VE++RL Sbjct: 230 TPFVHGFVG--RANRIRGHVERDRL 252 Lambda K H 0.318 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: 328 Number of extensions: 12 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: 377 Length of database: 384 Length adjustment: 30 Effective length of query: 347 Effective length of database: 354 Effective search space: 122838 Effective search space used: 122838 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 (21.7 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