GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpT in Pseudomonas fluorescens GW456-L13

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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