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 WP_085637757.1 MGEO_RS11955 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q00752 (377 letters) >NCBI__GCF_002115805.1:WP_085637757.1 Length = 365 Score = 296 bits (759), Expect = 5e-85 Identities = 167/375 (44%), Positives = 233/375 (62%), Gaps = 25/375 (6%) Query: 4 LNLNHIYKKYPNSSHYSVEDFDLDIKNKEFIVFVGPSGCGKSTTLRMVAGLEDITKGELK 63 L++ ++YK Y + ++D ++ I+ +F+V VGPSGCGKST L +AGLE IT G + Sbjct: 5 LDIKNLYKSYGTTE--ILKDINVSIEPGDFLVLVGPSGCGKSTLLNCIAGLEPITGGSIN 62 Query: 64 IDGEVVNDKAPKDRDIAMVFQNYALYPHMSVYDNMAFGLKLRHYSKEAIDKRVKEAAQIL 123 I G+ + +PKDRDIAMVFQ+YALYP M+V N+ FG+K+R + D+++ + AQ L Sbjct: 63 IGGKDMTHVSPKDRDIAMVFQSYALYPTMTVAKNITFGMKVRGVDQATQDRKLAQVAQQL 122 Query: 124 GLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVSMRAEIAKIHR 183 + L R+P LSGGQRQRVAMGRA+VRD K+FL DEPLSNLDAKLRV MR EI +H Sbjct: 123 QIEPLLNRRPGQLSGGQRQRVAMGRALVRDPKLFLFDEPLSNLDAKLRVEMRTEIKSLHH 182 Query: 184 RIGATTIYVTHDQTEAMTLADRIVIMSSTKNEDGSGTIGRVEQVGTPQELYNRPANKFVA 243 +GA+ +YVTHDQ EAMTLA +IV+M G ++Q+G+P E+YNRPAN FVA Sbjct: 183 NLGASMVYVTHDQIEAMTLATKIVVMKG----------GVIQQIGSPAEIYNRPANLFVA 232 Query: 244 GFIGSPAMNFFDVTIKDGHLVSKDGLTIAVTEGQLKMLESKGFKNKNL----IFGIRPED 299 F+GSPAMN + +G I +T + + KN++L I G+RPED Sbjct: 233 DFMGSPAMNLIPAKAHR----ADEGTRIEITRKSGEPIVLTDTKNRDLPEDVILGVRPED 288 Query: 300 ISSSLLVQETYPDATVDAEVVVS--ELLGSETMLYLKLGQTEFAARVDARDFHEPGEKVS 357 I+ L +A AE ++ E G++T ++LG AR+ A +PG+ Sbjct: 289 IADPDL---RGAEAAQAAECLIDMVEPAGADTFAVMQLGGKHVTARLHAETTAKPGQPKR 345 Query: 358 LTFNVAKGHFFDAET 372 L+F++ K +F ET Sbjct: 346 LSFDLGKVSYFAPET 360 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: 360 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: 365 Length adjustment: 30 Effective length of query: 347 Effective length of database: 335 Effective search space: 116245 Effective search space used: 116245 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 24 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