Aligments for a candidate for pad-dh in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for pad-dh in Pseudomonas fluorescens GW456-L13

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate PfGW456L13_1083 Betaine aldehyde dehydrogenase (EC 1.2.1.8)

Query= BRENDA::P05091
         (517 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1083
          Length = 490

 Score =  391 bits (1004), Expect = e-113
 Identities = 207/479 (43%), Positives = 285/479 (59%), Gaps = 7/479 (1%)

Query: 38  QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97
           +++I+  + DA S  TF  +NP+ GEV+ +V    KEDV++AV +A    ++   W  M 
Sbjct: 8   KLYIDGAYSDASSDATFEAINPANGEVLAKVQRATKEDVERAVVSAEKGQKI---WAAMT 64

Query: 98  ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157
           A  R R+L R  +++      LAALETLD GK Y  +  VD+      L YYAG      
Sbjct: 65  AMERSRILRRAVEILRERNDELAALETLDTGKAYSETRYVDIVTGADVLEYYAGLVPAIE 124

Query: 158 GKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLT 217
           G+ IP+    F YTR EP+GV   I  WN+P+ +  WK  PALA GN ++ K +E T LT
Sbjct: 125 GEQIPLRTTSFVYTRREPLGVVAGIGAWNYPIQIALWKSAPALAAGNAMIFKPSEVTSLT 184

Query: 218 ALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSS 277
            L +A +  EAG P GV N++ G G   G  +  H  ++KV+FTG T+ G+ +  +A SS
Sbjct: 185 TLKLAEIYTEAGVPNGVFNVLTGSGREVGTWLTEHPRIEKVSFTGGTDTGKKVMASASSS 244

Query: 278 NLKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVE 337
           +LK VT+ELGGKSP II  DAD+D A + A  A F++ GQ C  G+R FV   +   F  
Sbjct: 245 SLKDVTMELGGKSPLIICDDADLDRAADTAMMANFYSSGQVCTNGTRVFVPAHLKAAFEA 304

Query: 338 RSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD---- 393
           +   R     +GNP D  T  GP V     + +LGYI  GK+EGA+LLCGG    D    
Sbjct: 305 KIAERVARIRIGNPEDENTNFGPLVSFAHMESVLGYIAKGKEEGARLLCGGERLTDGEFA 364

Query: 394 RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDL 453
           +G F+ PTVF D  D MTI +EEIFGPVM IL ++T EEV+ RAN++ +GLAA + TKDL
Sbjct: 365 KGAFVAPTVFTDCTDDMTIVREEIFGPVMAILSYETEEEVIRRANDTDFGLAAGIVTKDL 424

Query: 454 DKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
           ++A+ +   L+AG  W+N +    A+ P GGYK SG GRE G   L  +T +K+V V++
Sbjct: 425 NRAHRVIHQLEAGICWINAWGESDAKMPVGGYKQSGVGRENGISSLNNFTRIKSVQVEL 483


Lambda     K      H
   0.319    0.136    0.409 

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: 570
Number of extensions: 27
Number of successful extensions: 3
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: 517
Length of database: 490
Length adjustment: 34
Effective length of query: 483
Effective length of database: 456
Effective search space:   220248
Effective search space used:   220248
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: 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)
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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, 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

GapMind for catabolism of small carbon sources