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_106711245.1 CU102_RS11585 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_003010955.1:WP_106711245.1 Length = 355 Score = 336 bits (861), Expect = 7e-97 Identities = 187/376 (49%), Positives = 235/376 (62%), Gaps = 28/376 (7%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M ++ + ++ K Y N + ++DI D EF++ VGPSGCGKST LRMIAGLE+IT G Sbjct: 1 MASVSIRDVTKTYGNVN--VMHGVSVDIEDGEFVILVGPSGCGKSTLLRMIAGLEEITGG 58 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I +++ND K+RDIAMVFQNYALYPHM+V +NM F L L+ K + RV AA Sbjct: 59 EIAIGSRVVNDLPAKERDIAMVFQNYALYPHMTVADNMGFALMLKNAPKQEKESRVGRAA 118 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 EILGL + L+R P LSGGQRQRVAMGRAIVRD +VFL DEPLSNLDAKLRV MR+EI Sbjct: 119 EILGLEKLLDRFPRQLSGGQRQRVAMGRAIVRDPQVFLFDEPLSNLDAKLRVQMRSEIKG 178 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +H+R+G T +YVTHDQ EAMT+AD+IV+M G +EQIGTP +LY+ PAN Sbjct: 179 LHQRLGTTIVYVTHDQIEAMTMADKIVVMKD----------GLVEQIGTPLDLYDYPANL 228 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300 FVAGFIGSPAMNF + VE V DG+ L LP G E T GIRPE Sbjct: 229 FVAGFIGSPAMNFIKGKVENGAFVTPDGVKLPLPSGLGSTAE--------ATYGIRPE-- 278 Query: 301 SSDQIVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARDSHSPGEKVQLTF 360 H + + + V E GSE M+ K G+ E + R S PG+ + + Sbjct: 279 ------HIRMAESGIPVKVDVVEPTGSEIMVVGKIGAQEISCLFRDRLSIKPGDTIHVAI 332 Query: 361 NIAKGHFFDLETEKRI 376 + A H FD+ + RI Sbjct: 333 DPATSHLFDMASGARI 348 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: 389 Number of extensions: 16 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: 355 Length adjustment: 30 Effective length of query: 347 Effective length of database: 325 Effective search space: 112775 Effective search space used: 112775 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