GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Desulfacinum infernum DSM 9756

Align Glutaryl-CoA dehydrogenase, mitochondrial; GCD; EC 1.3.8.6 (characterized)
to candidate WP_073035809.1 BUB04_RS00225 acyl-CoA dehydrogenase family protein

Query= SwissProt::P81140
         (408 letters)



>NCBI__GCF_900129305.1:WP_073035809.1
          Length = 382

 Score =  176 bits (447), Expect = 8e-49
 Identities = 127/383 (33%), Positives = 194/383 (50%), Gaps = 18/383 (4%)

Query: 28  QLTADEILIRDTFRTYCQEHLMPRIVLANRNEVFHREIIS----EMGELGVLGPTIKG-Y 82
           +LT ++ +I+DT   + +  L P  V A  +   +REI+     ++ ELG +G  +   Y
Sbjct: 4   ELTEEQKIIQDTAAKFAKNELEP--VAAELDRTKNREILKRNLKKLAELGFMGLNVDPEY 61

Query: 83  GCAGVSSVAYGLLARELERVDSGYRSAMSVQSSLVMHPIYAYGSEEQQQQKYLPRLAKGE 142
           G  G   VA+ L   EL R  +      SV +++V   I A G+EEQ++ KY+P L  GE
Sbjct: 62  GGTGAGVVAFSLAMTELGRACASTTVTTSV-TNMVAEVIQAVGTEEQKR-KYIPPLCSGE 119

Query: 143 LL-GCFGLTEPNHGSDPGSMETRALHNPSNRSYTLNGAKTWITNSPVADLFVVWARCEDN 201
              G FGL+E   GSDP SM T A+ +     + LNG+K WIT++  A +FVVWA  +  
Sbjct: 120 FAAGSFGLSEAGAGSDPASMRTSAVQDGDY--WVLNGSKMWITSAEYAGVFVVWAVTDKE 177

Query: 202 CIRG-----FLLEKGMRGLSAPKIEGKFSLRASATGMIIMDDVEVPEENVLPKASS-LAV 255
             +G     FL+E G  G +  K E K     S+T  ++ +D  V ++NVL K +    +
Sbjct: 178 APKGKGITCFLVEPGTPGFTIGKDEKKLGQHGSSTNELLFEDCRVHKDNVLGKVNDGFRI 237

Query: 256 PFGCLNNARYGISWGVLGAAEFCLHTARQYTLDRIQFGVPLAKNQLIQRKLADMLTEITL 315
               L   R GI    LG     +  A  Y+ +RIQFGVP+AK+Q IQ  +AD  T +  
Sbjct: 238 AVSELAGGRIGIGSMALGIGLAAMDFATNYSKERIQFGVPIAKHQAIQWMIADNYTRLEA 297

Query: 316 GLHACLQLGRLKDQDKVTPEMVSLLKRNNCGKALDIARQARDMLGGNGISDEYHVIRHAM 375
                L+   LK+Q +   +  S+ K      A      A  +LGG G + ++ + R+  
Sbjct: 298 ARLLLLRAAYLKEQGRPYSKEASMGKVYATEAANKACYDALQILGGYGYTQDFPIERYYR 357

Query: 376 NLEAVNTYEGTHDIHALILGRAI 398
           ++   + YEGT +I  LI+ R +
Sbjct: 358 DVRVTSIYEGTSEIQRLIIAREL 380


Lambda     K      H
   0.319    0.136    0.404 

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: 378
Number of extensions: 22
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: 408
Length of database: 382
Length adjustment: 31
Effective length of query: 377
Effective length of database: 351
Effective search space:   132327
Effective search space used:   132327
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 Apr 09 2024. 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