GapMind for catabolism of small carbon sources

 

Alignments 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)



>NCBI__GCF_000009985.1:WP_011384980.1
          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 (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