GapMind for catabolism of small carbon sources

 

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

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate PfGW456L13_3314 3-carboxymuconate cyclase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3314
          Length = 389

 Score =  378 bits (970), Expect = e-109
 Identities = 206/382 (53%), Positives = 265/382 (69%), Gaps = 7/382 (1%)

Query: 9   LLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKG-PLRVAHTSNP 67
           LL    +  +  Q  +A  Y LLVG+YT G S+GI    FD   G +   PL+V  ++NP
Sbjct: 7   LLMAGSIGAMGVQVASAEDYQLLVGSYTAGQSQGIYRLAFDSRTGQIDASPLQVIKSANP 66

Query: 68  SYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSL 127
           S+LT + DQR LFVVNENG G + D VGR +S+  DP +  L  ISQVQ+L + PT+SSL
Sbjct: 67  SWLTLSKDQRHLFVVNENGPG-QTDPVGRVSSFAIDPKTHALSLISQVQSLGNEPTHSSL 125

Query: 128 SHDGRYLFVANYSV--QPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSV 184
           S DG +LFV+NYSV   P G++AVLPV ADG L  VVQ+ SH AS+V+P RQ S HVHS 
Sbjct: 126 SIDGSHLFVSNYSVAEDPGGTLAVLPVAADGKLKAVVQMSSHPASRVNPERQASAHVHST 185

Query: 185 VSSPDGQYLFAPDLGADKVFVYRYAPE-QAERPLQAADPAFVPTPPGSGPRHLIFSADGR 243
           + SPDG+Y+FA DLGADKVF YR+ P+   E PL  A PAFV  PPGSGPRHL+FSADG+
Sbjct: 186 IPSPDGRYVFANDLGADKVFAYRFDPKANPELPLTPATPAFVQLPPGSGPRHLLFSADGK 245

Query: 244 FAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRG 303
            A+LT+E+S QV VF +  +G+L Q Q  DLA         A ALH SADG+FL V NRG
Sbjct: 246 HAWLTMEMSAQVAVFDYH-DGQLEQTQMVDLAAGQPVSDKAAAALHASADGKFLYVSNRG 304

Query: 304 DDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQ 363
             NQL+ FA+DPA+G L  ++RR+VEG  PREF+  P G+F+L+ANQ S+Q+ V  RD +
Sbjct: 305 TANQLLVFAIDPATGHLSELQRRAVEGDHPREFSLDPSGKFLLIANQKSNQIVVVERDAR 364

Query: 364 SGQVGKTLQSVEVGSPSDLRFV 385
           +G +GKT+Q + + +PSDLRF+
Sbjct: 365 TGLLGKTVQKLPMDAPSDLRFL 386


Lambda     K      H
   0.318    0.135    0.395 

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: 589
Number of extensions: 37
Number of successful extensions: 14
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: 388
Length of database: 389
Length adjustment: 30
Effective length of query: 358
Effective length of database: 359
Effective search space:   128522
Effective search space used:   128522
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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