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 CCNA_01670 CCNA_01670 sulfate transport ATP-binding protein cysA
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__Caulo:CCNA_01670 Length = 339 Score = 191 bits (485), Expect = 3e-53 Identities = 113/292 (38%), Positives = 163/292 (55%), Gaps = 31/292 (10%) Query: 10 YKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELKIDGEVV 69 + +YP ++ DL+I + E + +GPSG GK+T LR +AGLE G++ DG+ V Sbjct: 12 FGRYP-----ALNKVDLEIADGELLALLGPSGSGKTTLLRTIAGLEFPDAGQVLFDGQDV 66 Query: 70 NDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHY----SKEAIDKRVKEAAQILGL 125 + R + VFQ YAL+ HM+V N+AFGL +R SK I +RV+E +++ L Sbjct: 67 TYASAAARRVGFVFQQYALFKHMTVAKNIAFGLDVRKGKDKPSKAEIARRVEELLKLVEL 126 Query: 126 TEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHRRI 185 R P+ LSGGQRQRVA+ RA+ V L+DEP LDA +R S+R E+ ++H Sbjct: 127 EGLGGRYPSQLSGGQRQRVALSRALAVQPSVLLLDEPFGALDATVRKSLRRELRRVHDAT 186 Query: 186 GATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVAGF 245 G TTI+VTHDQ EA+ LADR+ I+++ GR+EQ+GTP ++++ P FV GF Sbjct: 187 GVTTIFVTHDQEEALELADRVAILNN----------GRIEQIGTPDQVHDAPETAFVCGF 236 Query: 246 IGSPAMNFFDVTIKDGHLVS----------KDGLTIAVTEGQLKMLESKGFK 287 +G N FD + G + KDG A L+ GF+ Sbjct: 237 VGE--ANRFDGQVSGGRFKAGALTVPASALKDGAATAYVRPHDFALDEAGFE 286 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: 328 Number of extensions: 14 Number of successful extensions: 4 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: 339 Length adjustment: 29 Effective length of query: 348 Effective length of database: 310 Effective search space: 107880 Effective search space used: 107880 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