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_0738 Echvi_0738 Acyl-CoA dehydrogenases

Query= BRENDA::Q92947
         (438 letters)



>FitnessBrowser__Cola:Echvi_0738
          Length = 452

 Score =  229 bits (585), Expect = 1e-64
 Identities = 138/380 (36%), Positives = 203/380 (53%), Gaps = 2/380 (0%)

Query: 56  LEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTIKGYGC 115
           LE+ L   E  I    R + ++ + P          F   II +M ELG+ G T KGYGC
Sbjct: 73  LEKTLPPHEQEIVAKVRDFMEKEVRPIANEYWNKGHFPMHIIPKMAELGIAGLTYKGYGC 132

Query: 116 AGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGELLG 175
            G S++  G LA E+ RVD+   +   VQS L M  IY  GSEEQ+Q++LP++ K +++G
Sbjct: 133 PGHSALLEGFLAMEMARVDTSISTFFGVQSGLAMGSIYVCGSEEQKQEWLPKMQKMDVIG 192

Query: 176 CFGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWAR-CEDGCIR 234
            FGLTEP  GS  +   T       ++ + +NG K WI N+  +D+ V+WAR  +D  ++
Sbjct: 193 AFGLTEPKVGSGVAGGLTTTCKREGDE-WVINGQKKWIGNATFSDITVIWARDLDDQQVK 251

Query: 235 GFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLGGPFGCLNNAR 294
           GF++ K   G    +I+ K +LR     +I M    VPE + L  A+S       L   R
Sbjct: 252 GFIVRKDNPGFHPEKIENKMALRTVQNALITMKDCRVPESDRLQNANSFKDTSEILRLTR 311

Query: 295 YGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLGLHACLQLG 354
            G+AW  +G        A +Y  +R QFG P+A  QL+Q  L  ML ++T       +L 
Sbjct: 312 AGVAWQAVGCGRGAYEAALRYTNERKQFGRPIAGFQLVQDLLVTMLGDLTAMQTMVYRLS 371

Query: 355 RLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMNLEAVNTYE 414
           +++D  +   E  SL K     +   I   +R++ GGNGI  EY + R   + EA+ +YE
Sbjct: 372 KMQDAGELKDEHASLAKVFCTLRMRTIVDHSRELFGGNGILLEYDIARFVADAEAIYSYE 431

Query: 415 GTHDIHALILGRAITGIQAF 434
           GT +I++LI+GRAITG  AF
Sbjct: 432 GTKEINSLIVGRAITGHSAF 451


Lambda     K      H
   0.319    0.135    0.400 

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: 407
Number of extensions: 15
Number of successful extensions: 4
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: 438
Length of database: 452
Length adjustment: 32
Effective length of query: 406
Effective length of database: 420
Effective search space:   170520
Effective search space used:   170520
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: 51 (24.3 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