Align MsiK protein, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate WP_043527041.1 JH15_RS03500 sn-glycerol-3-phosphate import ATP-binding protein UgpC
Query= TCDB::P96483 (377 letters) >NCBI__GCF_000759345.1:WP_043527041.1 Length = 354 Score = 305 bits (781), Expect = 1e-87 Identities = 174/376 (46%), Positives = 239/376 (63%), Gaps = 30/376 (7%) Query: 1 MATVTFDKATRIYPGSDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGG 60 MA++ + Y G+ + AV +D+ I DGEF+VLVGPSGCGKST LRM+AGLE + G Sbjct: 1 MASIQLTGLKKTYAGNVE-AVKGIDLEIADGEFVVLVGPSGCGKSTLLRMVAGLETITDG 59 Query: 61 AIRIGDRDVTHLPPKDRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAA 120 ++I DR V L P +RDIAMVFQNYALYPHMTV N+ + LK GV + EI ++V +AA Sbjct: 60 TLKIDDRVVNDLEPAERDIAMVFQNYALYPHMTVFGNLAYGLKNRGVKREEIERRVHDAA 119 Query: 121 KILDLTQYLDRKPKALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIAS 180 +L++ +L+RKP+ LSGGQRQRVAMGRA+VREP FL DEPLSNLDAKLRV R +I Sbjct: 120 AMLEIEPFLERKPRKLSGGQRQRVAMGRALVREPSAFLFDEPLSNLDAKLRVQMRVEIKQ 179 Query: 181 LQRRLGITTVYVTHDQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPA 240 LQRRL T++YVTHDQ+EA+T+GDR+ VL G ++QV +P +Y+KPA++FVA FIGSPA Sbjct: 180 LQRRLKTTSLYVTHDQLEALTLGDRLVVLNGGSIEQVGTPMEVYEKPASMFVATFIGSPA 239 Query: 241 MNLVEVPITDGGVKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLS 300 MN+ +P+ + N ++ AAD T +G+RP+ + Sbjct: 240 MNM--LPVAYLRERGANGLLD-----HLAAD----TDVIGIRPDDLRI------------ 276 Query: 301 KDSADAPAGLAV--SVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVV 358 A L V +V + E GA+ ++Y + E G + V+R + R +G T+ Sbjct: 277 --EAPDEDHLVVTGTVELFEAAGAESHLYVSLE--GSDQPTVIRTSARPPVAEGETMRFH 332 Query: 359 PRPGETHVFSTSTGER 374 P H F+ ++G+R Sbjct: 333 VLPSALHPFNQASGKR 348 Lambda K H 0.317 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: 352 Number of extensions: 20 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: 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 (21.6 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