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 RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= TCDB::Q8DT25 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 211 bits (538), Expect = 2e-59 Identities = 143/379 (37%), Positives = 207/379 (54%), Gaps = 42/379 (11%) Query: 2 TTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEGN 61 TT+ L + K + + +++ +LDI E +V +GPSGCGK+TTLR+IAGLE G Sbjct: 5 TTITLRHCGKTFADGT-LALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGG 63 Query: 62 LYIDDKLMNDASP---KDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHE 118 + + ND +P + R + MVFQ+YAL+P+M+V EN+A+GL++R+ +RV E Sbjct: 64 VVMFGD--NDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDE 121 Query: 119 AAEILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEI 178 ++ L F ER+ LSGGQRQRVA+ RAI +V L+DEPL+ LDAKLR A+RA+I Sbjct: 122 MLAMMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADI 181 Query: 179 AKIHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPA 238 ++ R + T +YVTHDQ EAM L DRI++M GRI Q GTPQ++Y PA Sbjct: 182 NQLLRSLHITAVYVTHDQAEAMALGDRIIVMDR----------GRIAQTGTPQQIYRAPA 231 Query: 239 NKFVAGFIGSPAMNFFEVTVEKER------LVNQDGLSLALPQGQEKILEEKGYLGKKVT 292 N FVA FIG+ MN +E + LV + G + +L + Sbjct: 232 NAFVADFIGT--MNRLPAVLEADAWRVPGGLVPRHGTAASLAAAP----------SPRAE 279 Query: 293 LGIRPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGS-TEFTARVNARDSHS 351 L RPED++ Q +A + ++ + LG+ + L V G+ RD Sbjct: 280 LLFRPEDVALAQA-----EDAHLGGSVVTALFLGNYTRLLVDVGAPAPLVVDTTRRDGWL 334 Query: 352 PGEKVQLTFNIAKGHFFDL 370 G++V L + GH L Sbjct: 335 AGDRVGL--RLDTGHLITL 351 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: 325 Number of extensions: 14 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: 357 Length adjustment: 30 Effective length of query: 347 Effective length of database: 327 Effective search space: 113469 Effective search space used: 113469 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