GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Novosphingobium barchaimii LL02

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_082699858.1 V474_RS17855 3-hydroxybutyryl-CoA dehydrogenase

Query= BRENDA::C4IEM5
         (282 letters)



>NCBI__GCF_001046635.1:WP_082699858.1
          Length = 289

 Score =  295 bits (755), Expect = 8e-85
 Identities = 149/281 (53%), Positives = 191/281 (67%)

Query: 1   MKKVFVLGAGTMGAGIVQAFAAKGCEVIVRDIKEEFVDRGIATITKSLSKLVAKEKITEA 60
           M+ V ++GAG MGAGI Q  A+KG +V++ D+  E  ++G A I KSL+KLV KEKIT+A
Sbjct: 1   MQTVGIIGAGIMGAGIAQTVASKGMDVVLTDVSLENAEKGKAGIAKSLAKLVTKEKITQA 60

Query: 61  DKEEILSRISGTTDMKLAADCDLVVEAAIENMKIKKEIFAELDGICKPETILASNTSSLS 120
           D + +L+RI+   D    +  DL++EAA E   IK +IF     +    +I+ASNTSS+ 
Sbjct: 61  DADALLARITPAADYSAMSGADLIIEAATEREDIKHKIFEAAGKVLGANSIMASNTSSIP 120

Query: 121 ITEVASATKRADKVIGMHFFNPAPVMKLVEVIRGAATSQETFDAVKEMSESIGKTPVEVA 180
           IT +A+++  A +  G+HFFNP PVM LVEVI G ATSQ+T D +K   E +GKT V   
Sbjct: 121 ITRMAASSPDAARFCGLHFFNPVPVMGLVEVIPGLATSQDTIDRMKAFGEKLGKTVVLAG 180

Query: 181 EAPGFVVNRILIPMINEATFILQEGVAKEEDIDAAMKLGANHPMGPLALGDLIGLDVCLA 240
           + PGFVVNRIL PM+NEA F+L  G+   EDIDA  K+G NHPMGPL L D +GLD    
Sbjct: 181 DEPGFVVNRILCPMLNEAIFVLGAGIGSVEDIDAGCKIGLNHPMGPLTLADFVGLDTLYE 240

Query: 241 IMDVLYNETGDTKYRASSLLRKYVRAGWLGRKTGKGFYDYS 281
           IM V    TGD KYR + LL+KYV AGW GRK+GKGFYDYS
Sbjct: 241 IMKVFQATTGDPKYRPAPLLQKYVEAGWYGRKSGKGFYDYS 281


Lambda     K      H
   0.317    0.134    0.369 

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: 270
Number of extensions: 8
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: 289
Length adjustment: 26
Effective length of query: 256
Effective length of database: 263
Effective search space:    67328
Effective search space used:    67328
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: 47 (22.7 bits)

This GapMind analysis is from Sep 24 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