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

GapMind for catabolism of small carbon sources

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

Align 4-(gamma-glutamylamino)butanal dehydrogenase (EC 1.2.1.99) (characterized)
to candidate PfGW456L13_2360 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::P23883
         (495 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2360
          Length = 496

 Score =  385 bits (989), Expect = e-111
 Identities = 219/480 (45%), Positives = 297/480 (61%), Gaps = 9/480 (1%)

Query: 21  RLFINGEYTAAAENETFETVDPVTQAPLAKIARGKSVDIDRAMSAARGVFERGDWSLSSP 80
           R+ I G++  AA+ +T    +P T   L  + R    D+DRA+ AAR  F+   W+ + P
Sbjct: 19  RMLIGGDWVEAADGQTMPLHNPATGEVLCVVPRATPEDVDRAVLAARQAFDDSAWTRTRP 78

Query: 81  AKRKAVLNKLADLMEAHAEELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYG 140
            +R+ +L KLADLM+  AE LA LE L+ GK    +   D+  A   +R+ A    K+ G
Sbjct: 79  RERQNLLWKLADLMQRDAELLAQLECLNNGKSAAVAQVMDVQLAIDFLRYMAGWATKIEG 138

Query: 141 EVATTSSHEL------AMIVREPVGVIAAIVPWNFPLLLTCWKLGPALAAGNSVILKPSE 194
                S+  +      + I RE VGV+ AIV WNFPLLL CWKLGPALA G +V+LKP++
Sbjct: 139 STVDVSAPLMPNDQFHSFIRREAVGVVGAIVAWNFPLLLACWKLGPALATGCTVVLKPAD 198

Query: 195 KSPLSAIRLAGLAKEAGLPDGVLNVVTGFGHEAGQALSRHNDIDAIAFTGSTRTGKQLLK 254
           ++PL+A++LA L  EAG P+GV NVVTG G  AG AL+ +  +D + FTGST  GKQ+ K
Sbjct: 199 ETPLTALKLAELVLEAGYPEGVFNVVTGTGITAGSALTHNPLVDKLTFTGSTAVGKQIGK 258

Query: 255 DAGDSNMKRVWLEAGGKSANIVFADCPDLQQAASATAAGIFYNQGQVCIAGTRLLLEESI 314
            A DS M RV LE GGKS  IV AD  DL+ AA+  A+ IF+NQGQVC AG+RL ++   
Sbjct: 259 IAMDS-MTRVTLELGGKSPTIVMADA-DLKTAAAGAASAIFFNQGQVCCAGSRLYVQRKH 316

Query: 315 ADEFLALLKQQAQNWQPGHPLDPATTMGTLIDCAHADSVHSFIREG-ESKGQLLLDGRNA 373
            D  +A +   A   + G+ LDP+  MG LI     + V+ +I +G ES   +   G   
Sbjct: 317 FDNVVADISDIANAMKLGNGLDPSVDMGPLISARQQERVYGYIEKGRESGATIACGGEQF 376

Query: 374 GLAAAIGPTIFVDVDPNASLSREEIFGPVLVVTRFTSEEQALQLANDSQYGLGAAVWTRD 433
           G    + PT+ VDVD   SL +EEIFGPVLV   F  E  AL++ANDS YGLGA++W+ D
Sbjct: 377 GPGFFVKPTVIVDVDQKHSLVQEEIFGPVLVAIPFDDEADALRMANDSPYGLGASIWSND 436

Query: 434 LSRAHRMSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWISL 493
           L+  HRM  R+K+GSV+VN ++  D  +PFGGYK SG GR+    A+E +TELK++ I L
Sbjct: 437 LAAVHRMIPRIKSGSVWVNCHSALDPALPFGGYKMSGVGREMGYAAIEHYTELKSVLIKL 496


Lambda     K      H
   0.317    0.133    0.389 

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: 574
Number of extensions: 22
Number of successful extensions: 4
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: 495
Length of database: 496
Length adjustment: 34
Effective length of query: 461
Effective length of database: 462
Effective search space:   212982
Effective search space used:   212982
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: 52 (24.6 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

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:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources