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_3817 PP_3817 Polyamine ABC transporter, ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Putida:PP_3817 Length = 382 Score = 220 bits (561), Expect = 4e-62 Identities = 136/359 (37%), Positives = 203/359 (56%), Gaps = 30/359 (8%) Query: 17 KHY----SVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGNLYIDDKLMNDA 72 KHY +V+N +L+I D EF+ F+G SG GKSTTL M+AG E + G + +D + + + Sbjct: 22 KHYGDFTAVDNLDLEIQDGEFLTFLGSSGSGKSTTLSMLAGFETPSSGEILVDGQSLVNV 81 Query: 73 SPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAAEILGLTEFLERK 132 P RDI MVFQ Y+L+PH++V +N+AF L +RK + KRV +++ L +F RK Sbjct: 82 PPHKRDIGMVFQRYSLFPHLNVRDNIAFPLAIRKLGAAETAKRVDAMLKLVQLEQFAHRK 141 Query: 133 PADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAKIHRRIGATTIYV 192 P+ +SGGQ+QRVA+ RA+V + ++ LMDEPL LD KLR ++ E+ ++HRR+G T +YV Sbjct: 142 PSQMSGGQQQRVAIARALVYEPRILLMDEPLGALDKKLREDLQDELRQLHRRLGITIVYV 201 Query: 193 THDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANKFVAGFIGSPAMN 252 THDQ EAM L+ RI I S G+I +GT +LY P N FVA F+G+ N Sbjct: 202 THDQEEAMRLSQRIAIFSH----------GKIVGLGTGYDLYQNPPNAFVASFLGN--SN 249 Query: 253 FFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPED---ISSDQIVHET 309 F + + +G +A+ L + + +RPE +S++Q + E Sbjct: 250 FLRIKASSNGAGSFEGQPVAIR------LTPGLAASQDALIMVRPEKAVAMSAEQAMREP 303 Query: 310 FPNA--SVTADILVSELLG-SESMLYVKFGSTEFTARV--NARDSHSPGEKVQLTFNIA 363 P VTA + LG S++ V G TE T + A PG+ V++ + +A Sbjct: 304 LPAGWNEVTAKVGEVLFLGESQTCHVVTAGGTELTVKALSAAGMPMQPGDSVKVRWAVA 362 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: 306 Number of extensions: 8 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: 382 Length adjustment: 30 Effective length of query: 347 Effective length of database: 352 Effective search space: 122144 Effective search space used: 122144 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