GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Rhodococcus qingshengii djl-6-2

Align 3-hydroxyacyl-CoA dehydrogenase (EC 1.1.1.35) (characterized)
to candidate WP_003940434.1 C1M55_RS25285 3-hydroxybutyryl-CoA dehydrogenase

Query= BRENDA::P9WNP7
         (286 letters)



>NCBI__GCF_002893965.1:WP_003940434.1
          Length = 282

 Score =  307 bits (787), Expect = 2e-88
 Identities = 151/282 (53%), Positives = 200/282 (70%), Gaps = 1/282 (0%)

Query: 5   IQRVGVVGAGQMGSGIAEVSARAGVEVTVFEPAEALITAGRNRIVKSLERAVSAGKVTER 64
           ++ VGV+G G MG+GIAEV A+AG  V V E  E    A R RI KS+ R V+ GK+T+ 
Sbjct: 1   MELVGVIGGGTMGAGIAEVCAKAGSSVLVLETKEEFAAAARERIAKSINRGVAKGKITQE 60

Query: 65  ERDRALGLLTFTTDLNDLSDRQLVIEAVVEDEAVKSEIFAELDRVVTDPDAVLASNTSSI 124
           E D A+  +  T D+ + +DR LVIEA  E EA+K EIF +LD++V  P  +LA+NTSSI
Sbjct: 61  EADAAIARVRVTLDMEEFADRDLVIEAAPEIEALKYEIFGKLDKIVK-PAGILATNTSSI 119

Query: 125 PIMKVAAATKQPQRVLGLHFFNPVPVLPLVELVRTLVTDEAAAARTEEFASTVLGKQVVR 184
           P++K+A AT +P +V+G+HFFNPVPV+PLVE+V +L T E       ++A   L K+ VR
Sbjct: 120 PVIKIAKATSRPGQVVGVHFFNPVPVMPLVEIVVSLTTSEETVLAVTDYAKNTLRKKTVR 179

Query: 185 CSDRSGFVVNALLVPYLLSAIRMVEAGFATVEDVDKAVVAGLSHPMGPLRLSDLVGLDTL 244
             DRSGF+VNALL+PYL  A+RM+E+G+AT ED+D+A+  G  +PMGPL L D VGLD  
Sbjct: 180 AGDRSGFIVNALLIPYLCQAVRMLESGYATAEDIDEAMKGGCGYPMGPLTLLDTVGLDIA 239

Query: 245 KLIADKMFEEFKEPHYGPPPLLLRMVEAGQLGKKSGRGFYTY 286
              A+ ++ EF EPHY PP LL RMV+AG+LGKK+GRGFY Y
Sbjct: 240 LAAAESLYAEFAEPHYAPPALLRRMVDAGRLGKKTGRGFYEY 281


Lambda     K      H
   0.318    0.135    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: 249
Number of extensions: 7
Number of successful extensions: 2
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: 286
Length of database: 282
Length adjustment: 26
Effective length of query: 260
Effective length of database: 256
Effective search space:    66560
Effective search space used:    66560
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 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