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 14400 b0262 putative ATP-binding component of a transport system (VIMSS)
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Keio:14400 Length = 348 Score = 214 bits (544), Expect = 4e-60 Identities = 127/329 (38%), Positives = 195/329 (59%), Gaps = 26/329 (7%) Query: 4 LKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLY 63 ++L N+ KR+ + ++N NL I + + +GPSGCGK+T LR++AGLE +EG ++ Sbjct: 7 VELRNVTKRF--GSNTVIDNINLTIPQGQMVTLLGPSGCGKTTILRLVAGLEKPSEGQIF 64 Query: 64 IDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEIL 123 ID + + S + RDI MVFQ+YAL+PHMS+ EN+ +GLK+ + ++ RV EA ++ Sbjct: 65 IDGEDVTHRSIQQRDICMVFQSYALFPHMSLGENVGYGLKMLGVPRAELKARVKEALAMV 124 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHR 183 L F +R +SGGQ+QRVA+ RA++ KV L DEPLSNLDA LR +MR +I ++ + Sbjct: 125 DLEGFEDRFVDQISGGQQQRVALARALILKPKVLLFDEPLSNLDANLRRSMRDKIRELQK 184 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVA 243 + T++YVTHDQ+EA ++D +++M+ G I QIG+PQ+LY +PA++F+A Sbjct: 185 QFDITSLYVTHDQSEAFAVSDTVLVMNK----------GHIMQIGSPQDLYRQPASRFMA 234 Query: 244 GFIGSPAMNFFEVTVEKERLVNQDGLSLALP-----QGQEKILEEKGYLGKKVTLGIRPE 298 F+G N F T + V+ G L P QG+ + G + +TL R E Sbjct: 235 SFMGD--ANLFPATF-SDGYVDIYGYHLPRPLHFGTQGEGMV----GVRPEAITLSDRGE 287 Query: 299 DISSDQIVHETF--PNASVTADILVSELL 325 + I H + P VT + E+L Sbjct: 288 ESQRCVIRHVAYMGPQYEVTVEWHGQEIL 316 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: 330 Number of extensions: 10 Number of successful extensions: 2 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: 348 Length adjustment: 29 Effective length of query: 348 Effective length of database: 319 Effective search space: 111012 Effective search space used: 111012 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: 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