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_037573817.1 BS73_RS18100 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000744815.1:WP_037573817.1 Length = 369 Score = 317 bits (812), Expect = 3e-91 Identities = 178/389 (45%), Positives = 239/389 (61%), Gaps = 33/389 (8%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M T+ D + YP +V+ +L+I D EF+V VGPSGCGKST+LRM+AGLED+ G Sbjct: 1 MATVTYDKATRIYPGGDKPAVDALDLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNNG 60 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I ++ + PKDRDIAMVFQNYALYPHM+V +NM F LK+ K +I +V EAA Sbjct: 61 AIRIGERDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVNKAEIRSKVEEAA 120 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 +IL LTEFL+RKP LSGGQRQRVAMGRAIVR+ +VFLMDEPLSNLDAKLRV+ R +IA Sbjct: 121 KILDLTEFLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAG 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 + RR+G TT+YVTHDQ EAMT+ DR+ ++ G ++Q+ TP+ +Y+ PAN Sbjct: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKD----------GLLQQVDTPRNMYDRPANL 230 Query: 241 FVAGFIGSPAMNFFEVTV--------EKERLVNQDGLSLALPQGQEKILEEKGYLGKKVT 292 FVAGFIGSPAMN EV + E V++D + A G K VT Sbjct: 231 FVAGFIGSPAMNLVEVPITDGGVKFGESVVQVSRDAVGEAANAGD-----------KTVT 279 Query: 293 LGIRPEDISSDQIVHETFPNASVTADILVSELLGSESMLY--VKFG--STEFTARVNARD 348 +G+RPE + + + + V E LG++ +Y K G + + RV RD Sbjct: 280 VGVRPEHLDIVGGTEGGGEDKGLAVTVNVVEELGADGYVYGSAKVGTETIDLVVRVGGRD 339 Query: 349 SHSPGEKVQLTFNIAKGHFFDLETEKRIN 377 G+++++ + H F T KR++ Sbjct: 340 IPMKGDQLRVVPRAGETHVFSTSTGKRLS 368 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: 382 Number of extensions: 20 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: 369 Length adjustment: 30 Effective length of query: 347 Effective length of database: 339 Effective search space: 117633 Effective search space used: 117633 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