GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Rhizobium etli CFN 42

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011428126.1 RHE_RS25445 acyl-CoA dehydrogenase

Query= BRENDA::B0EVL5
         (395 letters)



>NCBI__GCF_000092045.1:WP_011428126.1
          Length = 395

 Score =  642 bits (1657), Expect = 0.0
 Identities = 313/395 (79%), Positives = 348/395 (88%)

Query: 1   MATNRVTFDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEM 60
           M   R  FDWADP  L  QLT+ ERMV+D+A AY+Q++L PRV +AFR+EKTD AIF EM
Sbjct: 1   MQHTREVFDWADPFRLVEQLTNEERMVQDTAHAYAQQKLAPRVLDAFRNEKTDPAIFREM 60

Query: 61  GELGLLGATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEE 120
           GELGLLG TI  +YGG+G+ Y  YGLIAREVERVDSGYRSMMSVQSSLVMVPI  FGS  
Sbjct: 61  GELGLLGPTISPEYGGAGLGYTAYGLIAREVERVDSGYRSMMSVQSSLVMVPIETFGSAA 120

Query: 121 TKQKYLPKLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADV 180
            KQKYLPKLATGEW+GCFGLTEP+HGSDPGSM TRA+KVDGGYSL+G+K WI+N+PIADV
Sbjct: 121 QKQKYLPKLATGEWIGCFGLTEPDHGSDPGSMATRAKKVDGGYSLTGSKTWISNAPIADV 180

Query: 181 FVVWAKDDAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVR 240
           FVVWAK + G IRGF+LEKGWKGLSAPAIHGKVGLRASITGE+VMD VF PEEN  P V 
Sbjct: 181 FVVWAKTEDGLIRGFILEKGWKGLSAPAIHGKVGLRASITGEVVMDGVFVPEENLLPGVT 240

Query: 241 GLKGPFTCLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLT 300
           GLKGPFTCLNSAR+GIAWGALGAAE CY  ARQY ++RKQFGRPLAANQLIQKKLADM  
Sbjct: 241 GLKGPFTCLNSARFGIAWGALGAAEDCYARARQYVLERKQFGRPLAANQLIQKKLADMAA 300

Query: 301 EITLGLQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIA 360
           EI LGLQGCLRLGR+K+EG+ PVELTSI+KRNSCGK+L++AR ARDMLGGNGISDEF IA
Sbjct: 301 EIALGLQGCLRLGRMKEEGHPPVELTSILKRNSCGKALEMARAARDMLGGNGISDEFGIA 360

Query: 361 RHLVNLEVVNTYEGTHDIHALILGRAITGLAAFSN 395
           RHLVNLEVVNTYEGTHDIHALI+GR+ITG+AAF+N
Sbjct: 361 RHLVNLEVVNTYEGTHDIHALIIGRSITGIAAFAN 395


Lambda     K      H
   0.319    0.136    0.409 

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: 565
Number of extensions: 11
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: 395
Length of database: 395
Length adjustment: 31
Effective length of query: 364
Effective length of database: 364
Effective search space:   132496
Effective search space used:   132496
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: 50 (23.9 bits)

This GapMind analysis is from Apr 09 2024. 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