Alignments for a candidate for adh in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for adh in Pseudomonas fluorescens FW300-N2C3

Align Putative aldehyde dehydrogenase DhaS; EC 1.2.1.3 (characterized)
to candidate AO356_28685 AO356_28685 betaine-aldehyde dehydrogenase

Query= SwissProt::O34660
         (495 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_28685
          Length = 496

 Score =  503 bits (1294), Expect = e-147
 Identities = 252/494 (51%), Positives = 339/494 (68%), Gaps = 8/494 (1%)

Query: 6   MQVTKRLETFLQGTKKLYIDGKFVPSASGATFDTPNPATGETLMTLYEAQAADVDKAVKA 65
           +Q+   +E FL    +L+I G +  +A+G  F   NPAT  TL  + E    DVD AV A
Sbjct: 4   IQLLPAVEKFLSQPGRLFIGGTWQDAANGRRFAVENPATEHTLAEVAEGGERDVDAAVAA 63

Query: 66  ARKAFDQGEWRTMSPASRSRLMYKLADLMEEHKTELAQLETLDNGKPINETTNGDIPLAI 125
           AR AF  G W   SPA R  L+++LA+L+++H+ ELAQL TL+NGKPI     G+   A 
Sbjct: 64  ARAAFT-GTWAQQSPAQRGLLLFRLAELLDQHREELAQLITLENGKPIG-AARGEAASAA 121

Query: 126 EHMRYYAGWCTKITGQTIPVSGA----YFNYTRHEPVGVVGQIIPWNFPLLMAMWKMGAA 181
             +RY+AGW TKI G T+PVS +      NYT  EPVGV   I+PWNFPL M +WK+G  
Sbjct: 122 NIIRYFAGWPTKIEGSTLPVSPSSGAPMLNYTLREPVGVCALIVPWNFPLTMCVWKLGPV 181

Query: 182 LATGCTIVLKPAEQTPLSALYLAELIDQAGFPAGVINIIPGFGEDAGEALTNHEAVDKIA 241
           LATGC  VLKPAEQTPL A+ L +LI+ AGFPAGV+N++ G G   G  L  H  VDKIA
Sbjct: 182 LATGCVAVLKPAEQTPLVAIRLVQLIEAAGFPAGVVNLLTGLGAQTGAPLAQHPDVDKIA 241

Query: 242 FTGSTEIGKKIMSTAAKSIKRVTLELGGKSPNILLPDANLKKAIPGALNGVMFNQGQVCC 301
           FTGST++G+ I   A  ++K+V+LELGGKSPNI+LPDA++ +A  GA +G+ +NQGQVC 
Sbjct: 242 FTGSTQVGRLIAQAATGNMKKVSLELGGKSPNIILPDADIVRAAKGAADGIFYNQGQVCT 301

Query: 302 AGSRVFIHKDQYDEVVDEMASYAESLRQGAGLHKDTQIGPLVSKEQHERVLSYIQKGKDE 361
           AGSR+++H    D+V++E+  +A +   G GL   + +GPLVS  Q   V  Y+Q+G++E
Sbjct: 302 AGSRLYVHASVLDQVLEELQRHAAAHVLGPGLDPASSMGPLVSARQLGTVRGYLQRGQEE 361

Query: 362 GAKAVTGGSCP--FEAGYFVAPTVFANVEDEMTIAKEEIFGPVLTAIPYETVDEVIERAN 419
           GA+ + GG  P   E G+F+ P+VF +  +   +A+EEIFGPVLT + +  +DE++ RAN
Sbjct: 362 GAELICGGDRPAHLERGHFIRPSVFLDRAERACVAREEIFGPVLTVMSWTEIDELVLRAN 421

Query: 420 HSEYGLAAGLWTENVKQAHYIADRLQAGTVWVNCYNVFDAASPFGGYKQSGLGREMGSYA 479
            S YGLAAGLWT +++ AH +A +L+AG+VW+NC+NV D ASPFGGYKQSG GREMG   
Sbjct: 422 DSPYGLAAGLWTRDLRSAHRVAAQLKAGSVWINCWNVVDPASPFGGYKQSGWGREMGKNV 481

Query: 480 LDNYTEVKSVWVNL 493
           +D YTE KSV+V+L
Sbjct: 482 IDAYTETKSVYVDL 495


Lambda     K      H
   0.316    0.133    0.391 

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: 686
Number of extensions: 21
Number of successful extensions: 5
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 (21.6 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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Protein sequences (fasta format)
Organisms (tab-delimited)
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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