GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Echinicola vietnamensis KMM 6221, DSM 17526

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Echvi_2990 Echvi_2990 Acyl-CoA dehydrogenases

Query= BRENDA::B0EVL5
         (395 letters)



>FitnessBrowser__Cola:Echvi_2990
          Length = 402

 Score =  403 bits (1035), Expect = e-117
 Identities = 201/386 (52%), Positives = 266/386 (68%)

Query: 8   FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLG 67
           F+  D   LD   T    ++R S R + ++ + P ++E  +       I  + GE+G  G
Sbjct: 16  FEGVDFYGLDDLFTAEHLLIRQSLRDFVKKEVSPYIEEWAQDAHFPSEIVPKFGEIGAFG 75

Query: 68  ATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLP 127
             IP +YGG G++Y+ YGLI +E+ER DSG RS +SVQ SLVM PI+ FGSEE ++K+LP
Sbjct: 76  PQIPAKYGGGGLDYISYGLIMQEIERGDSGMRSTVSVQGSLVMYPIHAFGSEEQREKFLP 135

Query: 128 KLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKD 187
           KLA+GEW+GCFGLTEP+HGS+PG + T  +     Y L+GAKMWI+N+P AD+ VVWAKD
Sbjct: 136 KLASGEWLGCFGLTEPDHGSNPGGLTTSFKDNGDHYLLNGAKMWISNAPEADIAVVWAKD 195

Query: 188 DAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFT 247
           + G I G ++E+G +G + P  H K  LRAS TGE+V D V  P+EN  P   GL  P  
Sbjct: 196 ENGRIHGLIVERGMEGFTTPTTHHKWSLRASCTGELVFDNVKVPKENLLPGKSGLSAPLM 255

Query: 248 CLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQ 307
           CL++ARYGIAWGA+GAA  CYE+A++Y M+R QF +P+AA QL+QKKLA+MLTEIT    
Sbjct: 256 CLDAARYGIAWGAIGAAMDCYESAKRYAMERIQFDKPIAAFQLVQKKLAEMLTEITKAQL 315

Query: 308 GCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLE 367
              RLG LKD+G A     S+ KRN+   +L+IAR AR + GG GI+ ++ I RH++NLE
Sbjct: 316 LAWRLGTLKDQGKATSAQISMAKRNNVAMALEIAREARQIHGGMGITGDYPIMRHMMNLE 375

Query: 368 VVNTYEGTHDIHALILGRAITGLAAF 393
            V TYEGTHDIH LILG+ ITG+ AF
Sbjct: 376 SVITYEGTHDIHLLILGQEITGIPAF 401


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: 444
Number of extensions: 14
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: 402
Length adjustment: 31
Effective length of query: 364
Effective length of database: 371
Effective search space:   135044
Effective search space used:   135044
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.

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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