GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gcdH in Magnetospirillum magneticum AMB-1

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase

Query= BRENDA::Q92947
         (438 letters)



>lcl|NCBI__GCF_000009985.1:WP_011384980.1 AMB_RS13080 acyl-CoA
           dehydrogenase
          Length = 383

 Score =  181 bits (459), Expect = 4e-50
 Identities = 124/380 (32%), Positives = 190/380 (50%), Gaps = 12/380 (3%)

Query: 55  VLEEQLTTDEILIRDTFRTYCQERLMPRILLANRNEVFHREIISEMGELGVLGPTI-KGY 113
           ++ +Q   +++L  DT   + +ERL+P       ++    EII+EM +LG+ G +I + Y
Sbjct: 1   MIRDQEILNQLL--DTLSRFVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEY 58

Query: 114 GCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQRQKYLPQLAKGEL 173
           G  G++     L A E+ +    +RS     + +    I   G+EEQ+QKYLP+LA GEL
Sbjct: 59  GGLGLTMEEEVLCAFEIGQTSPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLATGEL 118

Query: 174 LGCFGLTEPNSGSDPSSMETRAHYNSSNKSYTLNGTKTWITNSPMADLFVVWARCED--- 230
           +  F LTEPN+GSD +S+ T A  +  +  Y +NGTK +ITN+P A +F + AR +    
Sbjct: 119 IASFALTEPNAGSDAASLRTTARKDGDH--YIVNGTKRFITNAPEASIFTLMARTDPNNK 176

Query: 231 --GCIRGFLLEKGMRGLSAPRIQGKFSLRASATGMIIMDGVEVPEENVLPGASSLG--GP 286
             G I  F++E    GLS  +I  K   + + T  +I + V VP  N++ G    G    
Sbjct: 177 GAGGISAFIVEADSPGLSLGKIDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTA 236

Query: 287 FGCLNNARYGIAWGVLGASEFCLHTARQYALDRMQFGVPLARNQLIQKKLADMLTEITLG 346
              L+  R  I+   +G SE  +  + +YA +R+QFG P+   QL+Q  LAD  TE    
Sbjct: 237 MKVLDRGRLHISATCVGVSERLIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAA 296

Query: 347 LHACLQLGRLKDQDKAAPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAMN 406
               L   R KDQ        +  K         IA +A  + GG G   +Y + R   +
Sbjct: 297 RCMVLDAARKKDQGINVSTEAACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRD 356

Query: 407 LEAVNTYEGTHDIHALILGR 426
           +     YEGT  I  L++ R
Sbjct: 357 VRLFRIYEGTTQIQQLVIAR 376


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: 376
Number of extensions: 26
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: 438
Length of database: 383
Length adjustment: 31
Effective length of query: 407
Effective length of database: 352
Effective search space:   143264
Effective search space used:   143264
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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

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