GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpT in Pseudomonas fluorescens FW300-N1B4

Align GlpT, component of Glycerol uptake porter, GlpSTPQV (characterized)
to candidate Pf1N1B4_4009 Glycerol-3-phosphate ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)

Query= TCDB::G3LHY9
         (356 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4009 Glycerol-3-phosphate
           ABC transporter, ATP-binding protein UgpC (TC 3.A.1.1.3)
          Length = 365

 Score =  391 bits (1005), Expect = e-113
 Identities = 197/359 (54%), Positives = 255/359 (71%), Gaps = 9/359 (2%)

Query: 1   MARITLDHIRHAYGANPKSDKDYSLKEVDHEWNDGGAYALLGPSGCGKTTLLNIISGLLQ 60
           MA I L ++ H+Y + P   +DY+++E+DH W  GGAYALLGPSGCGK+TLLNIISGLL 
Sbjct: 1   MAEIRLQNLAHSYTSTPTGPEDYAIREMDHVWEQGGAYALLGPSGCGKSTLLNIISGLLS 60

Query: 61  PSHGRILFDGKDVTNLSTQSRNIAQVFQFPVIYDTMTVYDNLAFPLRNRGVAEADVDRRV 120
           PS G++LFD K V  L+ + RNIAQVFQFPV+YDTMTV+DNLAFPLRN+G+AEA +  +V
Sbjct: 61  PSQGQVLFDSKVVNELTPEKRNIAQVFQFPVVYDTMTVFDNLAFPLRNQGMAEAKIHTKV 120

Query: 121 RDILEMIDLASWARRKAQGLTADQKQKISLGRGLVRNDVNAILFDEPLTVIDPHMKWVLR 180
            +I E++DL +   +KA+ LTAD+KQK+S+GRGLVR+DV+AILFDEPLTVIDPH+KW LR
Sbjct: 121 HEIAEVLDLQALLYKKARNLTADEKQKVSMGRGLVRDDVSAILFDEPLTVIDPHLKWKLR 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 IGSPGMNLIEVQPQAGGVGFTGTHLPLSDAMQKRIAESEWKTLKVGIRPEFVHVWDEPCD 300

Query: 294 -GMPITISKVEDIGRQKIVRARFADQPIAIVVPEDADIP-ADARVTFDPSAISIYADSW 350
             M   +  VED+G  KI+       P+ + + ED  +P   A ++F    + +YAD +
Sbjct: 301 DAMQAQVVHVEDLGTYKIMTLNLDGAPLKVRLAEDKPVPEGTAYISFPAQWLMVYADDY 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: 429
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: 365
Length adjustment: 29
Effective length of query: 327
Effective length of database: 336
Effective search space:   109872
Effective search space used:   109872
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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