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_038857748.1 AFK65_RS05695 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_001277175.1:WP_038857748.1 Length = 371 Score = 319 bits (818), Expect = 7e-92 Identities = 181/367 (49%), Positives = 235/367 (64%), Gaps = 32/367 (8%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M L+L+ + KRY ++ +L I+ EF+V VGPSGCGKST LR++AGLE+IT+G Sbjct: 1 MAQLRLEKVQKRYGTHAEV-IKPLDLQINSGEFVVVVGPSGCGKSTLLRLVAGLEEITDG 59 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 ++YIDD+ +ND SP +R I MVFQ+YALYPHM+VY+NMAF L++ K + +I++RV E+A Sbjct: 60 DMYIDDQRVNDDSPSERGIGMVFQSYALYPHMTVYQNMAFALEMAKVPEKEIDERVRESA 119 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 IL L L+R+P DLSGGQRQRVA+GRAIVR+ +FL DEPLSNLDA LRV MR EIA Sbjct: 120 RILQLEHLLDRRPKDLSGGQRQRVAIGRAIVREPSLFLFDEPLSNLDASLRVQMRMEIAA 179 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 +HRRI AT +YVTHDQ EAMTLADRIV+++ G+IEQ+GTP LY+ PAN Sbjct: 180 LHRRIHATILYVTHDQVEAMTLADRIVVLNQ----------GQIEQVGTPLALYDTPANV 229 Query: 241 FVAGFIGSPAMN-----FFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGI 295 FVA FIGSP MN V + ++GL L LP + G G V LGI Sbjct: 230 FVAQFIGSPKMNLIPGKMLRVMEHACEVELENGLRLTLP-----VQAVAGQEGDAVQLGI 284 Query: 296 RPEDISSDQIVHETFPNASVTADILVSELLGSESMLYVKFG------STEFTARVNARDS 349 RPE + T A V ++L E +G+E+++YV G T R+ R Sbjct: 285 RPEHVEI-----MTLAKADVEGEVLFVEHMGNETLVYVNGGYGAEPLVMRHTERLEVRPE 339 Query: 350 HSPGEKV 356 H G K+ Sbjct: 340 HHLGLKL 346 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: 352 Number of extensions: 17 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: 371 Length adjustment: 30 Effective length of query: 347 Effective length of database: 341 Effective search space: 118327 Effective search space used: 118327 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 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