GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnl in Pseudomonas fluorescens FW300-N1B4

Align Periplasmic gluconolactonase, PpgL (characterized, see rationale)
to candidate Pf1N1B4_4626 3-carboxymuconate cyclase

Query= uniprot:Q9HWH7
         (388 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4626
          Length = 405

 Score =  369 bits (948), Expect = e-107
 Identities = 201/376 (53%), Positives = 256/376 (68%), Gaps = 7/376 (1%)

Query: 9   LLALAPLTGVAPQAQAASLYNLLVGTYTEGSSEGIQVYRFDGADGSVKG-PLRVAHTSNP 67
           LL    +  +  QA     Y LLVG+YT G S+GI    FD   G +   PL+V  ++NP
Sbjct: 9   LLMAGSVGAMGVQAAPVDSYELLVGSYTAGQSQGIYRLNFDSRTGQIDAKPLQVVKSANP 68

Query: 68  SYLTFAPDQRTLFVVNENGRGGKGDTVGRATSYRFDPISGRLQQISQVQTLADHPTYSSL 127
           S+L  + DQ  LF VNENG G + D VGR +SY  DP +  L  ISQVQTL + PT+SS+
Sbjct: 69  SWLVVSKDQHRLFAVNENGPG-QADPVGRVSSYAIDPKTNELSLISQVQTLGNEPTHSSV 127

Query: 128 SHDGRYLFVANYSV--QPEGSVAVLPVRADGSLAPVVQVESHQASKVHP-RQVSGHVHSV 184
           S D  ++FV+NYSV   P G++AVLPV  DG L PVVQ+ SH +S+V+P RQ S HVHSV
Sbjct: 128 SGDASHVFVSNYSVAEDPGGTLAVLPVGTDGKLKPVVQMSSHPSSRVNPERQKSAHVHSV 187

Query: 185 VSSPDGQYLFAPDLGADKVFVYRYAPE-QAERPLQAADPAFVPTPPGSGPRHLIFSADGR 243
           VSSPDGQY+F+ DLGADK+FVYR+ P+   E PL AA PA V  PPGSGPRHL+FSADG+
Sbjct: 188 VSSPDGQYVFSNDLGADKIFVYRFDPKANPELPLTAAKPASVQLPPGSGPRHLLFSADGK 247

Query: 244 FAYLTLELSGQVMVFAHEGNGRLRQLQTHDLAPAGFQGKVGAGALHLSADGRFLGVLNRG 303
            A+LT+E+S QV VF +  +G+L Q Q  DLA         A ALH SADG+FL V NRG
Sbjct: 248 HAWLTMEMSAQVAVFDYR-DGKLEQTQLVDLAAGLPTSGKAAAALHASADGKFLYVSNRG 306

Query: 304 DDNQLVTFAVDPASGQLRFVERRSVEGTEPREFAFSPGGRFVLVANQNSDQLRVFARDPQ 363
             NQL+ FA+DPA+G L+ ++RRSV+G  PREF+  P G+FVL+ANQ S+Q+ V  RD +
Sbjct: 307 TTNQLLVFAIDPATGNLKELQRRSVDGDHPREFSLDPSGKFVLIANQKSNQIVVVERDAK 366

Query: 364 SGQVGKTLQSVEVGSP 379
           +G +GKT+Q    G P
Sbjct: 367 TGLLGKTVQKTTDGCP 382


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: 582
Number of extensions: 37
Number of successful extensions: 12
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: 405
Length adjustment: 31
Effective length of query: 357
Effective length of database: 374
Effective search space:   133518
Effective search space used:   133518
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