Align MalK, component of Maltose/Maltotriose/maltodextrin (up to 7 glucose units) transporters MalXFGK (MsmK (3.A.1.1.28) can probably substitute for MalK; Webb et al., 2008) (characterized)
to candidate WP_106712549.1 CU102_RS18395 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_003010955.1:WP_106712549.1 Length = 354 Score = 332 bits (852), Expect = 7e-96 Identities = 182/379 (48%), Positives = 247/379 (65%), Gaps = 29/379 (7%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M +++ N+ K + H ++ +++I D EF++ VGPSGCGKST LRM+AGLE+I+ G Sbjct: 1 MASVEFANVRKSF--GTHPVIKGVDIEIADGEFVILVGPSGCGKSTLLRMLAGLENISAG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I +++N +PK+RDIAMVFQNYALYPHM+V +NMAF L L+ K +I KRV AA Sbjct: 59 EIRIGGQVVNGLAPKERDIAMVFQNYALYPHMTVADNMAFSLTLKGAAKSEIEKRVKPAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 EILGL+ L+R P LSGGQRQRVAMGRAIVRD +VFL DEPLSNLDAKLRVAMRAEI + Sbjct: 119 EILGLSHLLDRFPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVAMRAEIKE 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+ TT+YVTHDQ EAMT+AD+IV+M G +EQIG P ELY++PAN Sbjct: 179 LHQRLKTTTVYVTHDQIEAMTMADKIVVMHD----------GLVEQIGAPLELYDQPANL 228 Query: 241 FVAGFIGSPAMNFFEVTV---EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRP 297 FVA FIGSPAMN + + + ++ V + G+ L + + + G + G+RP Sbjct: 229 FVASFIGSPAMNMIKGRLDPNDTQKFVTEKGIVLPVAKAPDSA------KGLTLIYGLRP 282 Query: 298 EDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQ 357 E H T + A+++V E GSE+ + ++ G + T + R S PGE V Sbjct: 283 E--------HMTIAQGGIPAEVVVIEPTGSETQMIMRVGGDDITGVFHQRISARPGEIVG 334 Query: 358 LTFNIAKGHFFDLETEKRI 376 L+ + + FD ET KR+ Sbjct: 335 LSIHAEATYLFDAETGKRL 353 Lambda K H 0.318 0.135 0.379 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: 385 Number of extensions: 15 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: 354 Length adjustment: 30 Effective length of query: 347 Effective length of database: 324 Effective search space: 112428 Effective search space used: 112428 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