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_017178050.1 A1QA_RS0106175 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::Q8DT25 (377 letters) >NCBI__GCF_000295095.1:WP_017178050.1 Length = 375 Score = 338 bits (866), Expect = 2e-97 Identities = 188/388 (48%), Positives = 250/388 (64%), Gaps = 27/388 (6%) Query: 1 MTTLKLDNIYKRYPNAKHYSVENFNLDIHDKEFIVFVGPSGCGKSTTLRMIAGLEDITEG 60 M T+ D+ + YP SV+ NL+I D EF+V VGPSGCGKST+LRM+AGLED+ G Sbjct: 1 MATVTFDHATRIYPGNDRPSVDQLNLEIADGEFLVLVGPSGCGKSTSLRMLAGLEDVNSG 60 Query: 61 NLYIDDKLMNDASPKDRDIAMVFQNYALYPHMSVYENMAFGLKLRKYKKDDINKRVHEAA 120 + I D+ + D PKDRDIAMVFQNYALYPHMSV++NM F LK+ K++I+KRV EAA Sbjct: 61 RILIGDRDVTDVQPKDRDIAMVFQNYALYPHMSVHDNMGFALKIAGTPKEEIDKRVREAA 120 Query: 121 EILGLTEFLERKPADLSGGQRQRVAMGRAIVRDAKVFLMDEPLSNLDAKLRVAMRAEIAK 180 +ILGLTE+L+RKP LSGGQRQRVAMGRAIVR KVFLMDEPLSNLDAKLRV R +IA Sbjct: 121 KILGLTEYLDRKPKALSGGQRQRVAMGRAIVRKPKVFLMDEPLSNLDAKLRVQTRTQIAS 180 Query: 181 IHRRIGATTIYVTHDQTEAMTLADRIVIMSATPNPDKTGSIGRIEQIGTPQELYNEPANK 240 + R +G TT+YVTHDQTEA+T+ DRI ++ G ++Q+GTP+E+Y++PAN+ Sbjct: 181 LQRSLGVTTVYVTHDQTEALTMGDRIAVLKD----------GLLQQVGTPREMYDKPANE 230 Query: 241 FVAGFIGSPAMNFFEVTVEKERLVNQDGLSLALPQGQEKILEEKGYLGKKVTLGIRPEDI 300 FVAGFIGSPAMN TV + + + + L + ++ + G KV +G RPE + Sbjct: 231 FVAGFIGSPAMNLGHFTVSGD-VASIGSAKIQLSRATLDAIKPED--GGKVAIGFRPESL 287 Query: 301 ----SSDQ--------IVHETFPNASVTADILVSELLGSESMLYVKFGSTEFTARVNARD 348 +SD+ V E +A + +++ +E GSE L S++ RV R Sbjct: 288 EVVSASDEHSIPVRVSFVEELGSDAYIYGELVGAE--GSEDKLGSGEDSSQIIVRVPPRT 345 Query: 349 SHSPGEKVQLTFNIAKGHFFDLETEKRI 376 + GE V + + H F T +R+ Sbjct: 346 APGAGETVYVRIKPGQEHIFSAATGERL 373 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: 407 Number of extensions: 13 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: 375 Length adjustment: 30 Effective length of query: 347 Effective length of database: 345 Effective search space: 119715 Effective search space used: 119715 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