GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gcdH in Algoriphagus aquaeductus T4

Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_111395068.1 CLV31_RS21080 acyl-CoA dehydrogenase

Query= BRENDA::Q60759
         (438 letters)



>NCBI__GCF_003253485.1:WP_111395068.1
          Length = 452

 Score =  228 bits (581), Expect = 3e-64
 Identities = 132/350 (37%), Positives = 195/350 (55%), Gaps = 5/350 (1%)

Query: 87  NRNEVFHRDIVYEMGELGVLGPTIKGYGCAGVSSVAYGLLTRELERVDSGYRSMMSVQSS 146
           NR E F   I+ +M EL + G T +GYGC G S++  G +  E+ RVD+   +   VQS 
Sbjct: 105 NRAE-FPMHIIPKMAELNIAGLTYQGYGCPGHSALLEGFIAMEMARVDTSISTFFGVQSG 163

Query: 147 LVMHPIYTYGSEEQRQKYLPGLAKGELLGCFGLTEPNHGSDP-GGMETRARHNPSNQSYT 205
           L M  +Y  GSE Q+Q++LP + K E +G FGLTEP  GS   GG+ T  +       + 
Sbjct: 164 LAMGSVYLCGSEAQKQEWLPAMQKLEKIGAFGLTEPEVGSGAAGGLTTTCKRE--GDVWI 221

Query: 206 LSGTKTWITNSPVADLFIVWAR-CEDNCIRGFILEKGMRGLSAPRIEGKFSLRASATGMI 264
           L+G K WI N+  +D+ ++WAR  +DN ++GFI+ KG  G  A +++ K +LR     +I
Sbjct: 222 LNGQKKWIGNATFSDMTVIWARDLDDNQVKGFIVRKGNPGFQAEKLKDKMALRTVQNALI 281

Query: 265 IMDSVEVPEENVLPNVSSLAGPFGCLNTARYGITWGVLGAAEFCLHTARQYALDRIQFGV 324
            + + EVPE + L + +S       L   R G+ W  +G A      A  Y  +R QFG 
Sbjct: 282 TLTNCEVPESDRLQSANSFKDTAKVLRMTRAGVAWQAVGCARGAYELALAYTNERQQFGR 341

Query: 325 PLARNQLVQKKLADMLTEITLGLHACLQLGRLKDQDKATPEMVSMLKRNNCGKALDIARQ 384
           P+A  QLVQ  L  ML ++T       +L +++DQ +   E  S+ K     +   I   
Sbjct: 342 PIASFQLVQDLLVTMLGDLTAMQTMVFRLSQMQDQGELLDEHASLAKVFCTLRMRSIVDH 401

Query: 385 ARDILGGNGISDEYHVIRHAMNLEAVNTYEGTHDIHALILGRAITGIQAF 434
           AR++ GGNGI  ++ + R   + EAV +YEGT +I++LI+GRAITG  AF
Sbjct: 402 ARELFGGNGILLQHDIARFVADAEAVYSYEGTKEINSLIVGRAITGHSAF 451


Lambda     K      H
   0.320    0.136    0.408 

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: 373
Number of extensions: 10
Number of successful extensions: 3
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 24 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