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 BPHYT_RS05040 BPHYT_RS05040 sugar ABC transporter ATPase
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__BFirm:BPHYT_RS05040 Length = 371 Score = 313 bits (803), Expect = 4e-90 Identities = 171/386 (44%), Positives = 241/386 (62%), Gaps = 26/386 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M +L + ++YK YPN ++ N+DI D +F++ VG SGCGKST L MIAGLE +T+G Sbjct: 1 MASLSIRDVYKTYPNGVPV-LKGVNIDIEDGQFLILVGGSGCGKSTLLNMIAGLETVTKG 59 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + ID K +N+ SPKDRDIAMVFQ+YALYP M+V EN++FGL +RK K++ + V + Sbjct: 60 EIQIDGKTVNNLSPKDRDIAMVFQSYALYPSMTVRENISFGLNIRKVPKNEQTQIVDRVS 119 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 L +T L+RKP LSGGQRQRVAMGRA+ RD +FL DEPLSNLDAKLR+ MR+EI Sbjct: 120 NTLQITHLLDRKPGQLSGGQRQRVAMGRALARDPVMFLFDEPLSNLDAKLRIEMRSEIKL 179 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+G T +YVTHDQ EAMTL DRI +M G ++Q G PQE+Y+ P+N Sbjct: 180 LHQRLGTTIVYVTHDQIEAMTLGDRIAVMKD----------GIVQQFGAPQEIYDSPSNL 229 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQD-GLSLALPQGQEKI--------LEEKGYLGKKV 291 FVAGFIG+P MNF + +LV Q G++L L G + + + ++G++V Sbjct: 230 FVAGFIGAPPMNFIQ-----GKLVEQGAGVALELDTGVARTALNLPFDSAKVRSHVGREV 284 Query: 292 TLGIRPEDISSDQIVH-ETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSH 350 LG+RPE I+ + H + + + V E G +++++ + +RV+ + Sbjct: 285 ILGLRPERITDARGAHGDNAKLQPIEVKVDVIEPTGPDTLVFAQVNGKRIVSRVHPASNP 344 Query: 351 SPGEKVQLTFNIAKGHFFDLETEKRI 376 P L F+ +K FD E+RI Sbjct: 345 QPLANTTLLFDTSKAVLFDPSNEERI 370 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: 363 Number of extensions: 13 Number of successful extensions: 5 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: 371 Length adjustment: 30 Effective length of query: 347 Effective length of database: 341 Effective search space: 118327 Effective search space used: 118327 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