Align MsmK aka SMU.882, component of The raffinose/stachyose transporter, MsmEFGK (MalK (3.A.1.1.27) can probably substitute for MsmK; Webb et al., 2008). This system may also transport melibiose, isomaltotriose and sucrose as well as isomaltosaccharides (characterized)
to candidate RR42_RS27800 RR42_RS27800 ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Cup4G11:RR42_RS27800 Length = 357 Score = 219 bits (557), Expect = 1e-61 Identities = 146/371 (39%), Positives = 208/371 (56%), Gaps = 38/371 (10%) Query: 4 LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63 + L H K + + + +++ DLDI E +V +GPSGCGK+TTLR++AGLE G + Sbjct: 7 ITLRHCGKTFADGT-LALQPLDLDIGAGETVVLLGPSGCGKTTTLRIIAGLEFPDAGGVV 65 Query: 64 IDGEVVNDKAP---KDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 + G+ ND P + R + MVFQ+YAL+P+M+V +N+A+GL++R A +RV E Sbjct: 66 MFGD--NDVTPLPIEQRGVGMVFQSYALFPNMTVAENIAYGLRVRRIDAAARRRRVDEML 123 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 ++ L F ER+ LSGGQRQRVA+ RAI +V L+DEPL+ LDAKLR ++RA+I + Sbjct: 124 AMMHLGPFAERRIDQLSGGQRQRVALARAIAVQPRVLLLDEPLTALDAKLRDALRADINQ 183 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240 + R + T +YVTHDQ EAM L DRI++M GR+ Q GTPQ++Y PAN Sbjct: 184 LLRSLHITAVYVTHDQAEAMALGDRIIVMDR----------GRIAQTGTPQQIYRAPANA 233 Query: 241 FVAGFIGS----PAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNLIFGIR 296 FVA FIG+ PA+ D G LV + G ++ E L+F R Sbjct: 234 FVADFIGTMNRLPAVLEADAWRVPGGLVPRHGTAASLAAAPSPRAE--------LLF--R 283 Query: 297 PEDISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLG-QTEFAARVDARDFHEPGEK 355 PED++ L Q DA + VV + LG+ T L + +G RD G++ Sbjct: 284 PEDVA---LAQA--EDAHLGGSVVTALFLGNYTRLLVDVGAPAPLVVDTTRRDGWLAGDR 338 Query: 356 VSLTFNVAKGH 366 V L + GH Sbjct: 339 VGLRLDT--GH 347 Lambda K H 0.318 0.135 0.375 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: 297 Number of extensions: 10 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