Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate 3608624 Dshi_2017 ABC transporter related (RefSeq)
Query= TCDB::G3LHY9 (356 letters) >FitnessBrowser__Dino:3608624 Length = 333 Score = 203 bits (516), Expect = 6e-57 Identities = 120/357 (33%), Positives = 199/357 (55%), Gaps = 32/357 (8%) Query: 1 MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60 MA +TLD+++ ++G K + V + +G ++GPSGCGK+TLL +++GL Sbjct: 1 MATLTLDNVKKSFG------KTDVIHGVSIDVTEGEFIVIVGPSGCGKSTLLRMVAGLET 54 Query: 61 PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120 S G + DG+ V L R+IA VFQ +Y M+V+DN+A+ L+ V +A++ RV Sbjct: 55 VSSGEVRIDGRVVNTLEPMDRDIAMVFQNYALYPHMSVFDNMAYGLKIAKVPKAEIADRV 114 Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180 +++ L + RK + L+ Q+Q++++GR +VR LFDEPL+ +D ++ +R Sbjct: 115 AVAAKLLQLEPYLGRKPKELSGGQRQRVAMGRAIVRKPA-VFLFDEPLSNLDAKLRVQMR 173 Query: 181 SQLKRLHKQFGFTMVYVTHDQTEALTFAEKVVVMYDGQIVQIGTPAELFERPSHTFVGYF 240 ++K L ++ G T +YVTHDQ EA+T A++++VM G QIG P E++ P FV F Sbjct: 174 LEIKALQRELGVTSLYVTHDQVEAMTLADRMIVMNGGVADQIGAPLEVYANPQTAFVAGF 233 Query: 241 IGSPGMNFMPARIEGSTVKVGDETLTLEYAPKTSGTAKTELGIRPEFIRLGREG-MPITI 299 IGSP NF+PA + +G A ++GIRPE +R+ +G + + Sbjct: 234 IGSPPTNFLPADM------------------VRAGPAGQQVGIRPEHLRVAPQGRLEAHV 275 Query: 300 SKVEDIGRQKIVRARFADQPIAIVVPEDADIP-----ADARVTFDPSAISIYADSWR 351 + E +G + ++ R A Q + V +DA P A ++ +D S ++AD+ R Sbjct: 276 AYAEALGAETLLHLR-ASQGTTLTVRQDAAAPMPAEGATVQLDWDDSDTMLFADNGR 331 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: 297 Number of extensions: 11 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: 333 Length adjustment: 29 Effective length of query: 327 Effective length of database: 304 Effective search space: 99408 Effective search space used: 99408 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