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_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 279 bits (714), Expect = 7e-80 Identities = 169/374 (45%), Positives = 228/374 (60%), Gaps = 46/374 (12%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M L+L N+ K Y K ++++ +L+I EFIVFVGPSGCGKST LRMIAGLE I G Sbjct: 1 MAFLELKNVDKYY--GKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 L +D + + + P RD+AMVFQ+YALYPHM+V ENM+F L+L K I ++V AA Sbjct: 59 QLILDGRDITEVPPSQRDLAMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 + L LT +L+R P LSGGQRQRVA+GR+IVR KVFL DEPLSNLDA LR R EIA Sbjct: 119 DKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIAS 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +HR +GATT+YVTHDQ EAMTLADR+V++ G IEQ+GTP ELY++P N+ Sbjct: 179 LHRELGATTVYVTHDQVEAMTLADRVVVLRD----------GIIEQVGTPLELYDQPINR 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300 FVA FIG P MN V L Q + + +GIRPE + Sbjct: 229 FVARFIGMPQMN-----VAPASLFGQ-------------------FPAQVAEVGIRPEHL 264 Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTE----FTARVNARDSHSPGEKV 356 Q+V + + +++ E LG+E++++V+ + R+ R + G++V Sbjct: 265 ---QMVSP--EDGLLAGKVVLVEALGNETLVHVRPDKVQLEEPLIVRLYGRTTVHVGDRV 319 Query: 357 QLTFNIAKG-HFFD 369 L ++ +K H+FD Sbjct: 320 GLKWDDSKHIHYFD 333 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: 327 Number of extensions: 13 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 Apr 09 2024. 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