GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Salinicoccus carnicancri Crm

Align 3-hydroxybutyryl-CoA dehydrogenase; EC 1.1.1.35 (characterized)
to candidate WP_017549142.1 C792_RS0108990 3-hydroxyacyl-CoA dehydrogenase

Query= SwissProt::Q0AVM2
         (279 letters)



>NCBI__GCF_000330705.1:WP_017549142.1
          Length = 285

 Score =  229 bits (583), Expect = 7e-65
 Identities = 120/279 (43%), Positives = 172/279 (61%), Gaps = 2/279 (0%)

Query: 2   KIMVLGAGTMGAGIVQTAAQAGFEVVVRDIKQEFVDRGIAGIDKLLSKNVDKGRMTAEDK 61
           KI V+GAG MG GI   ++ AGF+ V+ D+ ++ VD+    I +L  K V + +++  D+
Sbjct: 5   KITVIGAGVMGKGIAYASSLAGFDTVIMDVDEKMVDKSYRDIKELFDKGVGRHKISMTDR 64

Query: 62  AAVMGRISGTVDMGAAA-DCDLVIEAALEVMDIKKAIFKELDSICKPECILASNTSALSV 120
              +GR+  +V    A  +CDLVIEA  EV  IK+A+ + +        I ASNTS +S 
Sbjct: 65  ENALGRLEVSVSYEEAIKECDLVIEAVPEVAVIKRAVHEAVSEKAMSHTIFASNTSTMSP 124

Query: 121 TEIAAATGRADKVIGMHFFNPVPAMKLVEVIRGASTSQATYDAIKDLSVKMGKSPVEINE 180
           TEIA+   R +  I MHFFNPV  M LVE++RG  TS AT   ++ ++ KMGK  V INE
Sbjct: 125 TEIASYGNRPENSIAMHFFNPVHRMPLVEIVRGLETSDATVTEVEAVAKKMGKETVVINE 184

Query: 181 APGFVVNRLLIPMLNEGMYCLMEGVANAADIDTSMKFGAGHPMGPLALADMIGLDICLKI 240
            PGFV +R+   + NE  + L EG+   ADID +++FG  HPMGP  L D++GLD  L  
Sbjct: 185 FPGFVTSRMSCLIGNEAFHMLQEGLGTPADIDKAVRFGLNHPMGPFELVDLVGLDARLNN 244

Query: 241 METLYKEFGDPKYRPCPLLAKMVRANKLGRKTGEGFFAY 279
           M+ L+ + G+ ++RP PLL K V A +LG+K+G G + Y
Sbjct: 245 MKELHSKLGE-RFRPAPLLEKYVNAGRLGKKSGRGVYDY 282


Lambda     K      H
   0.321    0.137    0.389 

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: 259
Number of extensions: 13
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: 279
Length of database: 285
Length adjustment: 26
Effective length of query: 253
Effective length of database: 259
Effective search space:    65527
Effective search space used:    65527
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: 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