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 WP_086510784.1 BZY95_RS15425 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_002151265.1:WP_086510784.1 Length = 373 Score = 308 bits (789), Expect = 2e-88 Identities = 173/384 (45%), Positives = 244/384 (63%), Gaps = 20/384 (5%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M L+++N+ K + + + +++ +L I EF++ VGPSGCGKST + IAGLE +T G Sbjct: 1 MAALEINNVCKDFGSEQ--VLKDVSLAIDSGEFLILVGPSGCGKSTLMNAIAGLEPVTSG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I + + +P +RDIAMVFQ+YALYP M+V +N++FGL++RK K + V A Sbjct: 59 EIRIAGESVTWQTPAERDIAMVFQSYALYPSMTVRQNISFGLEMRKVPKAEREAAVERVA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 ++L + LERKP+ LSGGQRQRVAMGRA+ R+ KV+L DEPLSNLDAKLRV MR EI K Sbjct: 119 DLLQIGHLLERKPSQLSGGQRQRVAMGRALAREPKVYLFDEPLSNLDAKLRVDMRTEIKK 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+G T +YVTHDQ EAMTLAD I +M GRI Q+G+P E+YN+P + Sbjct: 179 LHQRLGTTIVYVTHDQIEAMTLADCIAVMRD----------GRILQLGSPDEVYNDPVDL 228 Query: 241 FVAGFIGSPAMNFFEVTV------EKERLVNQDGLSLALPQGQEKILEEKG-YLGKKVTL 293 FVAGF+GSP+MNF T+ + R+ +L LP QE+ G +G++V L Sbjct: 229 FVAGFMGSPSMNFISATLVGGSGAYRLRVETPGEETLELPWPQERETPALGEKVGERVIL 288 Query: 294 GIRPEDISSDQI-VHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSP 352 G+RPE + D + E ++T I V E G++ +L +K G E TARV + Sbjct: 289 GLRPEHFTEDDARLGEYAEGVALTPRITVVEPTGADILLQLKLGDGEATARVGPKCRVKA 348 Query: 353 GEKVQLTFNIAKGHFFDLETEKRI 376 GE++ L ++ + FD ETEKR+ Sbjct: 349 GERLTLRIDMGRAVMFDRETEKRL 372 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: 373 Number of extensions: 22 Number of successful extensions: 4 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: 373 Length adjustment: 30 Effective length of query: 347 Effective length of database: 343 Effective search space: 119021 Effective search space used: 119021 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 24 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