GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Dinoroseobacter shibae DFL-12

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.157 (characterized)
to candidate 3606783 Dshi_0214 3-hydroxybutyryl-CoA dehydrogenase (RefSeq)

Query= CharProtDB::CH_091789
         (282 letters)



>FitnessBrowser__Dino:3606783
          Length = 291

 Score =  299 bits (765), Expect = 5e-86
 Identities = 153/280 (54%), Positives = 191/280 (68%)

Query: 1   MKKVCVIGAGTMGSGIAQAFAAKGFEVVLRDIKDEFVDRGLDFINKNLSKLVKKGKIEEA 60
           +K V VIGAG MG+GIA  FA  GF+V++ DI  + +D+ +  I +NL + V + KI   
Sbjct: 3   IKSVGVIGAGQMGNGIAHVFAVAGFDVMMTDISQDALDQAMALIRRNLERQVSREKISRE 62

Query: 61  TKVEILTRISGTVDLNMAADCDLVIEAAVERMDIKKQIFADLDNICKPETILASNTSSLS 120
                + RI+ T+ L      DLVIEAA ER  +K  IF DL    KPETIL SNTSS+S
Sbjct: 63  DMETAMARITTTLKLPELGQTDLVIEAATERETVKSAIFEDLQPHLKPETILTSNTSSIS 122

Query: 121 ITEVASATKRPDKVIGMHFFNPAPVMKLVEVIRGIATSQETFDAVKETSIAIGKDPVEVA 180
           IT +AS T RP++ +G HF NP PVM+LVE+IRGIAT + T+  +      +GK      
Sbjct: 123 ITRLASRTDRPERFMGFHFMNPVPVMQLVELIRGIATDEATYKTLLGVVEKLGKTAASAE 182

Query: 181 EAPGFVVNRILIPMINEAVGILAEGIASVEDIDKAMKLGANHPMGPLELGDFIGLDICLA 240
           + P F+VNRIL+PMINEAV  L EG+ SV  ID++MKLGANHPMGPLEL DFIGLD CLA
Sbjct: 183 DFPAFIVNRILMPMINEAVYTLYEGVGSVRSIDESMKLGANHPMGPLELADFIGLDTCLA 242

Query: 241 IMDVLYSETGDSKYRPHTLLKKYVRAGWLGRKSGKGFYDY 280
           IM+VL+    D+KYRP  LL KYV AGWLGRK+ +GFYDY
Sbjct: 243 IMNVLHDGLADTKYRPCPLLTKYVEAGWLGRKTQRGFYDY 282


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: 223
Number of extensions: 7
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: 291
Length adjustment: 26
Effective length of query: 256
Effective length of database: 265
Effective search space:    67840
Effective search space used:    67840
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 (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