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 AZOBR_RS00060 AZOBR_RS00060 sn-glycerol-3-phosphate ABC transporter ATP-binding protein
Query= TCDB::Q00752 (377 letters) >FitnessBrowser__azobra:AZOBR_RS00060 Length = 357 Score = 315 bits (808), Expect = 9e-91 Identities = 187/375 (49%), Positives = 234/375 (62%), Gaps = 27/375 (7%) Query: 1 MVELNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKG 60 M ++LN + K Y + +++ D+ + + EF+V +GPSGCGKST LRMVAGLE IT G Sbjct: 1 MATVDLNQVRKSY--GAVEAIKGIDISVADGEFLVLLGPSGCGKSTLLRMVAGLESITGG 58 Query: 61 ELKIDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAA 120 E+ I G VVN PKDRDIAMVFQNYALYPHMSV+DNMA+GLK+R K I RV +AA Sbjct: 59 EIAIGGRVVNGLEPKDRDIAMVFQNYALYPHMSVFDNMAYGLKIRGLPKAEIQARVAKAA 118 Query: 121 QILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAK 180 +IL L FL+R+P+ LSGGQRQRVAMGRAIVR+ FL DEPLSNLDAKLR MR EI + Sbjct: 119 EILELNRFLDRRPSQLSGGQRQRVAMGRAIVREPAAFLFDEPLSNLDAKLRTQMRVEIKR 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANK 240 + R+G T++YVTHDQ EAMTLADRI++M+ G EQVGTP E+Y RPA+ Sbjct: 179 LQDRLGITSLYVTHDQVEAMTLADRILVMNH----------GVAEQVGTPLEVYQRPASL 228 Query: 241 FVAGFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKML--ESKGFKNKNLIFGIRPE 298 FVAGFIGSP MN D DG G +A+ G +L + + G+RPE Sbjct: 229 FVAGFIGSPPMNVLDARF-DG-----AGQAVALPGGTAFLLPRPRPDMAGRPVKLGVRPE 282 Query: 299 DISSSLLVQETYPDATVDAEVVVSELLGSETMLYLKLGQTE-FAARVDARDFHEPGEKVS 357 L V + V + V E LG++T++Y +L E RV F GE + Sbjct: 283 ----HLAVTPGHGPLIVTVDXV--EALGADTVVYGRLPDGEGMVVRVAGLPFCREGETLR 336 Query: 358 LTFNVAKGHFFDAET 372 + H FDAET Sbjct: 337 VGAPPDALHLFDAET 351 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: 397 Number of extensions: 17 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: 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