Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate PfGW456L13_2613 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2613 Length = 371 Score = 394 bits (1012), Expect = e-114 Identities = 199/359 (55%), Positives = 256/359 (71%), Gaps = 9/359 (2%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA I L ++ H+Y P +DY+++E+DH W GGAYALLGPSGCGK+TLLNIISGLL Sbjct: 1 MAEIRLQNLAHSYTKTPAGPEDYAIREMDHIWEQGGAYALLGPSGCGKSTLLNIISGLLS 60 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 PS G +LFDGK V NL+ + RNIAQVFQFPV+YDTMTV+DNLAFPLRN+G+AEA V +V Sbjct: 61 PSQGHVLFDGKAVNNLTPEKRNIAQVFQFPVVYDTMTVFDNLAFPLRNQGMAEARVHSKV 120 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 ++I E++DL + +KA+ LTAD+KQK+S+GRGLVR+DV+AILFDEPLTVIDPH+KW LR Sbjct: 121 QEIAEVLDLQNLLSKKARNLTADEKQKVSMGRGLVRDDVSAILFDEPLTVIDPHLKWKLR 180 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +LK++H+QF TMVYVTHDQ EA TFA+K+ VMY GQIVQ GTP ELFERPSHTFVGYF Sbjct: 181 RKLKQIHEQFNITMVYVTHDQLEASTFADKIAVMYGGQIVQFGTPRELFERPSHTFVGYF 240 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPK----TSGTAKTELGIRPEFIRLGRE--- 293 IGSPGMN + + + V L L A + S ++GIRPEF+ + E Sbjct: 241 IGSPGMNLIEVQPQPGGVGFASTHLPLSEAMQQRIAESEWKTLKVGIRPEFVHVWDEAFD 300 Query: 294 -GMPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIP-ADARVTFDPSAISIYADSW 350 + + VED+G KI+ P+ + + ED +P A ++F + +YAD + Sbjct: 301 DALRAQVVHVEDLGTYKIMTLNLDGVPLKVRLAEDKPVPQGTAYISFPAQWLMVYADEF 359 Lambda K H 0.321 0.137 0.405 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: 431 Number of extensions: 12 Number of successful extensions: 1 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: 356 Length of database: 371 Length adjustment: 29 Effective length of query: 327 Effective length of database: 342 Effective search space: 111834 Effective search space used: 111834 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 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