Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate WP_086510097.1 BZY95_RS11680 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= TCDB::G3LHY9 (356 letters) >NCBI__GCF_002151265.1:WP_086510097.1 Length = 368 Score = 215 bits (548), Expect = 1e-60 Identities = 127/322 (39%), Positives = 189/322 (58%), Gaps = 20/322 (6%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA +TLD I +G+ + +K+VD +G +GPSGCGK+TLL +I+GL Sbjct: 1 MASVTLDKINKVFGST------HIIKDVDLAIGEGEFVVFVGPSGCGKSTLLRLIAGLES 54 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 + G + + V L + R + VFQ +Y MTVY+N+AF L+ A+ V RV Sbjct: 55 ITDGELSIGDQVVNELPPRERGVGMVFQSYALYPHMTVYENMAFGLKLAKTAKETVHERV 114 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 ++ L RK + L+ Q+Q++++GR + R + +LFDEPL+ +D ++ +R Sbjct: 115 MATARILQLEELLERKPKALSGGQRQRVAMGRAMAR-EPRILLFDEPLSNLDASLRVQMR 173 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 +++ RLHK+ G TMVYVTHDQ EA+T A+K+VV+ G++ Q+G+P EL++RP+ FV F Sbjct: 174 NEIARLHKRLGSTMVYVTHDQVEAMTLADKIVVLDGGRVEQVGSPQELYQRPATKFVAGF 233 Query: 241 IGSPGMNFMPARIEGSTV---KVGDETLT-LEYAPKTSGTAK---TELGIRPEFIRL--- 290 IGSP MNF+PAR+ G+ ++G LT L SG A+ LGIRPE +RL Sbjct: 234 IGSPTMNFLPARLLGADATGCRIGATGLTELALPQDASGHAQGAALTLGIRPEHLRLSEA 293 Query: 291 -GREGMPITISKVEDIGRQKIV 311 G EG I VE +G + V Sbjct: 294 QGSEGFEIV--NVEYLGNEVYV 313 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: 323 Number of extensions: 13 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: 356 Length of database: 368 Length adjustment: 29 Effective length of query: 327 Effective length of database: 339 Effective search space: 110853 Effective search space used: 110853 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 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