GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Shewanella oneidensis MR-1

Align glutaryl-CoA dehydrogenase (EC 1.3.8.6) (characterized)
to candidate 200844 SO1679 acyl-CoA dehydrogenase family protein (NCBI ptt file)

Query= metacyc::G1G01-166-MONOMER
         (393 letters)



>FitnessBrowser__MR1:200844
          Length = 385

 Score =  155 bits (393), Expect = 1e-42
 Identities = 110/378 (29%), Positives = 182/378 (48%), Gaps = 12/378 (3%)

Query: 15  LDQQLTEEERMVRDSAYQFAQDKLAPRVLEAFRHEQTDPAIFREMGEVGLLGATIPEQYG 74
           +D    E++R   + A QFA D+LAP   +          + ++ GE+G      PE  G
Sbjct: 1   MDFNFNEDQRQFAELARQFATDELAPFAAKWDEEHHFPKDVIQKAGELGFCSLYSPESEG 60

Query: 75  GSGLNYVCYGLIAREVERIDSGYRSMMSVQSSLVMVPINEFGTEAQKQKYLPKLASGEWI 134
           G GL+ +   +I  E+ +  +   +M+++ +    + +  +GTE  +Q +   L +G+ +
Sbjct: 61  GMGLSRLDASIIFEELSKGCTATTAMLTIHNMATWM-VTTWGTETLRQAWSEPLTTGQML 119

Query: 135 GCFGLTEPNHGSDPGSMITRARKVDGGYRLTGSKMWITNSPIADVFVVWAKDDAGDIRGF 194
             + LTEP  GSD  S+ T+A      Y ++GSKM+I+ +   ++ VV  +      +G 
Sbjct: 120 ASYCLTEPGAGSDAASLQTKAVPDGDEYVVSGSKMFISGAGSTELLVVMCRTGQAGPKGI 179

Query: 195 ---VLEKGWQGLSAPAIHGKVGLRASITGEIVMDNVFVPEENIFPDV-RGLKGPFTCLNS 250
               +    +G+       K+G  A  T  +  DNV VP  N+  +  +G       L+ 
Sbjct: 180 SAIAIPADSEGIIYGKAEDKMGWNAQPTRLVTFDNVRVPVANLLGEEGQGFTFAMKGLDG 239

Query: 251 ARYGISWGALGAAEACWHTARQYTLDRQQFGRPLAANQLIQKKLADMQTEITLALQ---- 306
            R  I+  ++G A+A    A QY  +RQQFG+PLAA Q +Q KLADM TE+  A Q    
Sbjct: 240 GRINIATCSVGTAQAALERASQYMNERQQFGKPLAAFQALQFKLADMATELVAARQMVRL 299

Query: 307 GCLRLGRMKDEGTAAVEITSIMKRNSCGKALDIARMARDMLGGNGISDEFGVARHLVNLE 366
              +L     EGTA     ++ KR +      +   A  + GG G   E+ + RH  ++ 
Sbjct: 300 AAFKLDSGDPEGTA---YCAMAKRFATDVGFQVCDAALQIHGGYGYIREYPLERHFRDVR 356

Query: 367 VVNTYEGTHDVHALILGR 384
           V    EGT+++  LI+ R
Sbjct: 357 VHQILEGTNEIMRLIIAR 374


Lambda     K      H
   0.320    0.137    0.413 

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: 354
Number of extensions: 18
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: 393
Length of database: 385
Length adjustment: 30
Effective length of query: 363
Effective length of database: 355
Effective search space:   128865
Effective search space used:   128865
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 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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