GapMind for catabolism of small carbon sources

 

Aligments for a candidate for patD in Pseudomonas fluorescens GW456-L13

Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate PfGW456L13_3737 Aldehyde dehydrogenase (EC 1.2.1.3)

Query= BRENDA::P77674
         (474 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3737 Aldehyde
           dehydrogenase (EC 1.2.1.3)
          Length = 496

 Score =  352 bits (904), Expect = e-101
 Identities = 196/481 (40%), Positives = 284/481 (59%), Gaps = 9/481 (1%)

Query: 2   QHKLLINGELVSGEGEKQPVYNPATGDVLLEIAEASAEQVDAAVRAADAAFAE--WGQTT 59
           +H   I+G+ V  EG+   V NPATG  L E  +A  E V+ AV+++  AF    W    
Sbjct: 17  RHGCFIDGQWVLAEGDSIAVVNPATGQTLCETLDAPLELVERAVQSSHKAFKSGVWSSLR 76

Query: 60  PKVRAECLLKLADVIEENGQVFAELESRNCGKPLHSAFNDEIPAIVDVFRFFAGAARCLN 119
           P  R   LL    ++EE+ +  A+LE+ + GK ++ A   ++ A V+  R+ +G A  + 
Sbjct: 77  PADRERILLNFTRLVEEHAEELAQLETLSQGKSINMARALDLNATVEFMRYMSGWATKIE 136

Query: 120 GLAAGEYLE-----GHTSMIRRDPLGVVASIAPWNYPLMMAAWKLAPALAAGNCVVLKPS 174
           G      +        T+  +R+P+GVV  I PWN+PL++AAWKL PALA G  V++KP+
Sbjct: 137 GQTFDVSIPLPPGAKFTAFTKREPVGVVVGIVPWNFPLLIAAWKLMPALATGCTVIIKPA 196

Query: 175 EITPLTALKLAELAKDI-FPAGVINILFGRGKTVGDPLTGHPKVRMVSLTGSIATGEHII 233
             TPLTA++LAELA +   PAGV N++ G G +VG  LT HP V  VS TGS A G+ + 
Sbjct: 197 METPLTAMRLAELALEAGIPAGVFNVVTGGGASVGGVLTQHPLVSKVSFTGSTAVGKSVG 256

Query: 234 SHTASSIKRTHMELGGKAPVIVFDDADIEAVVEGVRTFGYYNAGQDCTAACRIYAQKGIY 293
                ++ R  +ELGGK P+IV  DADIE  V+G    G  N GQ C AA R Y  + I+
Sbjct: 257 VACMENMTRFSLELGGKNPMIVLADADIEKAVQGAILGGLLNNGQVCAAASRFYVHRSIH 316

Query: 294 DTLVEKLGAAVATLKSGAPDDESTELGPLSSLAHLERVGKAVEEAKATGHIKVITGGEKR 353
           D  VE L AAV+++  GA  +    + PL S    + V K +E A+  G  +V+TGGE  
Sbjct: 317 DQFVEALAAAVSSMPIGAGMNCDAAINPLVSRKQQQSVLKHIELARQQG-ARVVTGGELL 375

Query: 354 KGNGYYYAPTLLAGALQDDAIVQKEVFGPVVSVTPFDNEEQVVNWANDSQYGLASSVWTK 413
           +G+G++  PT+LA      A+ ++EVFGPV+ V PFD+E+ V+  AND++YGLA+S+WT 
Sbjct: 376 EGDGFFVQPTILADIDHSMAVAREEVFGPVLGVMPFDDEDAVIELANDNRYGLAASLWTN 435

Query: 414 DVGRAHRVSARLQYGCTWVNTHFMLVSEMPHGGQKLSGYGKDMSLYGLEDYTVVRHVMVK 473
           D+G+A  +  R++ G  WVN H +L   MP GG K SG G++     +E YT ++ V + 
Sbjct: 436 DLGKAMNLVPRIEAGTVWVNAHVLLDPAMPFGGVKQSGMGREFGRAVIEAYTELKSVCIA 495

Query: 474 H 474
           H
Sbjct: 496 H 496


Lambda     K      H
   0.317    0.134    0.397 

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: 551
Number of extensions: 25
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: 474
Length of database: 496
Length adjustment: 34
Effective length of query: 440
Effective length of database: 462
Effective search space:   203280
Effective search space used:   203280
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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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 preprint 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