GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Pseudomonas fluorescens FW300-N1B4

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Pf1N1B4_4789 Butyryl-CoA dehydrogenase (EC 1.3.99.2)

Query= BRENDA::Q3JP94
         (395 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4789
          Length = 383

 Score =  211 bits (537), Expect = 3e-59
 Identities = 122/374 (32%), Positives = 202/374 (54%), Gaps = 2/374 (0%)

Query: 15  DQQLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGG 74
           D +L++++ M+RD A  +A+G++AP      +    D  +  +MGE+GLLG  +PE++GG
Sbjct: 3   DIELSEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVAKMGELGLLGMVVPEEWGG 62

Query: 75  PGLDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIG 134
             +DYV+Y L   E+   D    ++MS+ +S+   P+  +G++ QK+++LP LA+G+ IG
Sbjct: 63  TYVDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGTEEQKQQWLPDLASGQAIG 122

Query: 135 CFGLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEI 193
           CF LTEP  GS+  ++ TRA    G + ++G+K +++N   A + +V+A  D E G+  I
Sbjct: 123 CFCLTEPQAGSEAHNLRTRAELRDGQWVINGAKQFVSNGKRAKLAIVFAVTDPELGKRGI 182

Query: 194 RGFILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNS 252
             F++     G        K+G+RAS T  + L+   VPE N+L    KGL    + L  
Sbjct: 183 SAFLVPTETAGFIVDRSEHKMGIRASDTCAVTLNNCTVPEANLLGERGKGLAIALSNLEG 242

Query: 253 ARYGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLR 312
            R GIA  ALG A + +  A  Y  DR QF +P+  +Q I   LADM T +      +L 
Sbjct: 243 GRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSIANMLADMHTRLNAARLLILH 302

Query: 313 LGRMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNT 372
             R++  G   +   S  K  +   A  +   A  + GG G  +++ V R+  +  +   
Sbjct: 303 AARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQI 362

Query: 373 YEGTHDIHALILGR 386
           YEG+ +I  +++ R
Sbjct: 363 YEGSSEIQRMVIAR 376


Lambda     K      H
   0.320    0.138    0.414 

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: 372
Number of extensions: 18
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: 395
Length of database: 383
Length adjustment: 30
Effective length of query: 365
Effective length of database: 353
Effective search space:   128845
Effective search space used:   128845
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: 50 (23.9 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:

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