GapMind for catabolism of small carbon sources

 

Aligments for a candidate for pad-dh in Pseudomonas fluorescens FW300-N1B4

Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf1N1B4_2132 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::P05091
         (517 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2132 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 497

 Score =  403 bits (1036), Expect = e-117
 Identities = 210/476 (44%), Positives = 298/476 (62%), Gaps = 4/476 (0%)

Query: 40  FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99
           +IN E+ DAVS +TF  ++P  G ++ ++A  D  D  +AV  ARA F  G+ W R+  +
Sbjct: 23  YINGEYTDAVSGETFECISPVDGRLLGKIASCDAADAQRAVDNARATFNSGA-WSRLAPT 81

Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159
            R   + R A L+++    LA LETLD GKP   S  +D+    + L +     DK + +
Sbjct: 82  KRKATMIRFAGLLKQHAEELALLETLDMGKPISDSLYIDVPGAAQALSWSGEAIDKIYDE 141

Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219
                 D       EPVGV G I+PWNFPL+M  WKLGPAL+TGN V++K +E++PLTA+
Sbjct: 142 VAATPHDQLGLVTREPVGVVGAIVPWNFPLMMACWKLGPALSTGNSVILKPSEKSPLTAI 201

Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279
            +A L  EAG P GV+N++PG+G T G A+A H DVD + FTGST+I + + + +G SN+
Sbjct: 202 RIAALAVEAGIPKGVLNVLPGYGHTVGKALALHNDVDTLVFTGSTKIAKQLLIYSGESNM 261

Query: 280 KRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338
           KRV LE GGKSPNI+ +DA D+  A E A  A+ FNQG+ C AGSR  V+  I D+F+  
Sbjct: 262 KRVWLEAGGKSPNIVFADAPDLQAAAEAAAGAIAFNQGEVCTAGSRLLVERSIKDKFLPL 321

Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--IAADRGY 396
            +   K+   GNP D  T  G  VD  Q   +L YI +G  +GAKL+ GG   +    G 
Sbjct: 322 VIEALKTWKPGNPLDPATNVGALVDTQQMNTVLSYIESGHTDGAKLVAGGKRILQETGGT 381

Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456
           +++PT+F  V + M IA+EEIFGPV+ ++ F + EE +  AN++ YGLAAAV+T D+ KA
Sbjct: 382 YVEPTIFDGVSNAMKIAQEEIFGPVLSVITFDSAEEAIQIANDTPYGLAAAVWTADISKA 441

Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKV 512
           +  ++AL+AG+VWVN YD     +PFGG+K SG+GR+   +    YTE+K   +K+
Sbjct: 442 HLTAKALRAGSVWVNQYDGGDMTAPFGGFKQSGNGRDKSLHAFDKYTELKATWIKL 497


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: 627
Number of extensions: 21
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: 517
Length of database: 497
Length adjustment: 34
Effective length of query: 483
Effective length of database: 463
Effective search space:   223629
Effective search space used:   223629
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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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 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