GapMind for catabolism of small carbon sources

 

Aligments for a candidate for fadB in Caulobacter crescentus NA1000

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate CCNA_00752 CCNA_00752 3-hydroxybutyryl-CoA dehydrogenase

Query= CharProtDB::CH_091789
         (282 letters)



>lcl|FitnessBrowser__Caulo:CCNA_00752 CCNA_00752
           3-hydroxybutyryl-CoA dehydrogenase
          Length = 292

 Score =  300 bits (768), Expect = 2e-86
 Identities = 153/280 (54%), Positives = 194/280 (69%)

Query: 1   MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60
           +K V VIGAG MGSGIA   A  G++V L D+  E +D G+  I KN+++ V +G I++A
Sbjct: 4   IKTVGVIGAGQMGSGIAHVVALGGYDVRLHDVSRERIDAGIAVIEKNMARQVGRGIIDDA 63

Query: 61  TKVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120
                L RI     L      DL IEAA E  ++KK IF  L    KPET+LASNTSS+S
Sbjct: 64  AMKAALARIQPAEGLEAIGATDLAIEAATENEEVKKSIFRSLQPYLKPETLLASNTSSIS 123

Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVA 180
           IT +ASAT RP++ IG+HF NP P+MKLVE+IRGIAT   T++     + ++GK      
Sbjct: 124 ITRLASATDRPERFIGLHFMNPVPLMKLVEIIRGIATDVPTYERAVTFAQSLGKITSNAE 183

Query: 181 EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLA 240
           + P F+VNR+L+PMINEA+  L EG+ +V+ ID AMKLGANHPMGPLELGDFIGLD  L+
Sbjct: 184 DFPAFIVNRVLVPMINEAIYTLYEGVGTVDAIDTAMKLGANHPMGPLELGDFIGLDTVLS 243

Query: 241 IMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280
           IM+VL+    DSKYRP  LL KYV AGWLG+K+G+GFYDY
Sbjct: 244 IMNVLHEGLADSKYRPCPLLVKYVEAGWLGKKTGRGFYDY 283


Lambda     K      H
   0.319    0.137    0.386 

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: 246
Number of extensions: 2
Number of successful extensions: 1
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: 282
Length of database: 292
Length adjustment: 26
Effective length of query: 256
Effective length of database: 266
Effective search space:    68096
Effective search space used:    68096
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 (21.7 bits)
S2: 47 (22.7 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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, 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