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 350819 BT1291 spermidine/putrescine transport ATP-binding protein (NCBI ptt file)
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Btheta:350819 Length = 463 Score = 235 bits (599), Expect = 2e-66 Identities = 122/298 (40%), Positives = 193/298 (64%), Gaps = 23/298 (7%) Query: 4 LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63 + ++H+ K + + + +++D L++K EF+ +GPSGCGK+T LR++AG + ++GE++ Sbjct: 10 IEVSHVSKFFGDKT--ALDDVTLNVKKGEFVTILGPSGCGKTTLLRLIAGFQTASEGEIR 67 Query: 64 IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123 I G+ + P R + VFQ YAL+PH++VYDN+AFGLKL+ K+ I K+VK A +++ Sbjct: 68 ISGKEITQTPPHKRPVNTVFQKYALFPHLNVYDNIAFGLKLKKTPKQTIGKKVKAALKMV 127 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183 G+T++ R LSGGQ+QRVA+ RAIV + +V L+DEPL+ LD K+R M+ E+ ++H+ Sbjct: 128 GMTDYEYRDVDSLSGGQQQRVAIARAIVNEPEVLLLDEPLAALDLKMRKDMQMELKEMHK 187 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243 +G T +YVTHDQ EA+TL+D IV+MS G+++Q+GTP ++YN P N FVA Sbjct: 188 SLGITFVYVTHDQEEALTLSDTIVVMSE----------GKIQQIGTPIDIYNEPINSFVA 237 Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGF-KNKNLIFGIRPEDI 300 FIG + I +G ++ + TE + +GF +N + IRPED+ Sbjct: 238 DFIG-------ESNILNGTMIHDKLVRFCGTEFE---CVDEGFGENTPVDVVIRPEDL 285 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: 454 Number of extensions: 20 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: 463 Length adjustment: 32 Effective length of query: 345 Effective length of database: 431 Effective search space: 148695 Effective search space used: 148695 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 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