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 PP_0411 PP_0411 Polyamine ABC transporter, ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Putida:PP_0411 Length = 374 Score = 229 bits (585), Expect = 7e-65 Identities = 130/303 (42%), Positives = 180/303 (59%), Gaps = 22/303 (7%) Query: 2 TTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61 T + + K Y + + V++ NLDI EF+ +GPSG GK+T+L M+AG E T G Sbjct: 13 TLVSFRGVQKSY-DGESLIVKDLNLDIRKGEFLTLLGPSGSGKTTSLMMLAGFETPTAGE 71 Query: 62 LYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAE 121 + + + +N+ P RDI MVFQNYAL+PHM+V EN+AF L +R K DI++RV Sbjct: 72 IQLGGRSINNVPPHKRDIGMVFQNYALFPHMTVAENLAFPLTVRNLSKTDISERVKRVLN 131 Query: 122 ILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKI 181 ++ L F +R P LSGGQ+QRVA+ RA+V + ++ LMDEPL LD +LR M+ EI I Sbjct: 132 MVQLDAFAKRYPGQLSGGQQQRVALARALVFEPQLVLMDEPLGALDKQLREHMQMEIKHI 191 Query: 182 HRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKF 241 H+R+G T +YVTHDQ EA+T++DR+ + G I+QI P+ LY EP N F Sbjct: 192 HQRLGVTVVYVTHDQGEALTMSDRVAVFHQ----------GEIQQIADPRTLYEEPCNTF 241 Query: 242 VAGFIGSPAMNFFEVTVEKERLVNQDG--LSLALPQGQ--EKILEEKGYLGKKVTLGIRP 297 VA FIG E L+ DG + LP+G+ E + G G+ VTL IRP Sbjct: 242 VANFIG-------ENNRISGTLLASDGKRCQVQLPRGERVEALAVNVGQAGEPVTLSIRP 294 Query: 298 EDI 300 E + Sbjct: 295 ERV 297 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: 305 Number of extensions: 11 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: 374 Length adjustment: 30 Effective length of query: 347 Effective length of database: 344 Effective search space: 119368 Effective search space used: 119368 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