GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acdH in Ruegeria conchae TW15

Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase

Query= reanno::MR1:200844
         (385 letters)



>NCBI__GCF_000192475.1:WP_010441027.1
          Length = 385

 Score =  227 bits (579), Expect = 4e-64
 Identities = 131/374 (35%), Positives = 213/374 (56%), Gaps = 7/374 (1%)

Query: 7   EDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEGGMGLSR 66
           ++ R FAE+A +F  D L P   KW E+    +D   +AG+ G  +    E  GG+G   
Sbjct: 13  DEHRMFAEMAGRFMDDALVPNTEKWAEDGVVDRDFWLQAGQTGLMAGSIAEEYGGVGGGM 72

Query: 67  -LDASIIFEELSKGCTATTAMLTIHNMATWMVTTWGTETLRQAWSEPLTTGQMLASYCLT 125
             D+  ++E+ ++G         I ++ T  +TT+G+E  +  W   L +G+M+ +  +T
Sbjct: 73  GFDSVTLYEQTARGDAGWG--YGIQSIVTHYITTYGSEDQKHKWLPKLASGEMIGALAMT 130

Query: 126 EPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTGQA-GPKGISAIAI 184
           EPG GSD  +++T A  DG+ Y + GSK+FI+   S +L++V  +T ++ G KG+S IA+
Sbjct: 131 EPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSLGAKGVSLIAV 190

Query: 185 PAD-SEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLG-EEGQGFTFAMKGLDGGRI 242
             + +EG   G+  +K+G     T  + F++V+VP+ NLLG EEGQGF   MK L   R+
Sbjct: 191 ETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMKQLPWERL 250

Query: 243 NIATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRLAAF 302
            I   ++G    A+    +Y+ ER+ FG+ +  FQ  +FKLA+  T+    R  V     
Sbjct: 251 TIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEVLRSFVNDCIG 310

Query: 303 KLDSGDPEGTAYCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVRVHQILE 362
           KL++G+ +  A  +M K + ++V  ++    LQ+ GGYG++ EYP+ R + D RV  I  
Sbjct: 311 KLEAGELD-AATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLYADARVQMIYG 369

Query: 363 GTNEIMRLIIARRL 376
           GTNE+M+ +IAR L
Sbjct: 370 GTNEVMKELIARSL 383


Lambda     K      H
   0.319    0.134    0.396 

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: 370
Number of extensions: 21
Number of successful extensions: 5
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: 385
Length of database: 385
Length adjustment: 30
Effective length of query: 355
Effective length of database: 355
Effective search space:   126025
Effective search space used:   126025
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 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