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_4212 N515DRAFT_4212 multiple sugar transport system ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Dyella79:N515DRAFT_4212 Length = 364 Score = 334 bits (857), Expect = 2e-96 Identities = 187/380 (49%), Positives = 249/380 (65%), Gaps = 28/380 (7%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M ++LD + K YPN H V + +I D E +V VGPSGCGK+T LRMIAGLE I+ G Sbjct: 1 MAKVRLDKLRKVYPNG-HVGVAEASFEIADGELLVLVGPSGCGKTTLLRMIAGLESISGG 59 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 L I ++++ND +PKDRDIAMVFQNYALYPHM+V EN+ FGLKLR K +I +RV EAA Sbjct: 60 TLSIGERVVNDIAPKDRDIAMVFQNYALYPHMTVAENLGFGLKLRGQPKAEIERRVAEAA 119 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 +L L + L+ +PA LSGGQRQRVA+GRA+VRD KVFL+DEPLSNLDAKLR++MR EIA+ Sbjct: 120 RMLELEQRLDSRPAALSGGQRQRVALGRALVRDPKVFLLDEPLSNLDAKLRLSMRVEIAR 179 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 IH+R+ AT +YVTHDQ EAMTL RIV+++ G I+QI TP LY+ PAN Sbjct: 180 IHQRLKATMVYVTHDQIEAMTLGQRIVVLNG----------GVIQQIDTPMNLYDTPANL 229 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEE-------KGYLGKKVTL 293 FVAGF+GSPAMN + L G LA+PQG E +L E + + + + + Sbjct: 230 FVAGFLGSPAMNLL-----RGILYRDGGWKLAMPQG-ELVLGELPQGAALEAWRDRDIVV 283 Query: 294 GIRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPG 353 G+RPED+ ++ A++ A + V E +G+E L ++ G +R+ R+ +PG Sbjct: 284 GLRPEDL----LLCADAAGAALAAQLEVVEPVGNEVFLNLRHGELALVSRMPPRELPAPG 339 Query: 354 EKVQLTFNIAKGHFFDLETE 373 + F + HFFD + E Sbjct: 340 STLHFGFAPERLHFFDAKGE 359 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: 368 Number of extensions: 17 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: 364 Length adjustment: 30 Effective length of query: 347 Effective length of database: 334 Effective search space: 115898 Effective search space used: 115898 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