GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Dechlorosoma suillum PS

Align 3-hydroxy-2-methylbutyryl-CoA dehydrogenase subunit (EC 1.1.1.178) (characterized)
to candidate Dsui_0676 Dsui_0676 short-chain dehydrogenase of unknown substrate specificity

Query= metacyc::MONOMER-11802
         (255 letters)



>FitnessBrowser__PS:Dsui_0676
          Length = 257

 Score = 82.0 bits (201), Expect = 1e-20
 Identities = 68/201 (33%), Positives = 100/201 (49%), Gaps = 14/201 (6%)

Query: 3   IANKHFIVSGAASGLGAATAQMLVEAGAKVMLVDLNAQAVEAKAREL-GDNARFAVADIS 61
           +A+    ++GA+SG+GAA A+   E GA + L     QA+     +L G +A +A+ D+S
Sbjct: 1   MASLKVFITGASSGIGAALARHYAEQGATLGLAARRQQALTDLLADLPGHHAAYAL-DVS 59

Query: 62  DEQAAQSAVDAAVSAFGSLHGLVNCAGIVGAEKVLG--KQGPHGLASFAKVINVNLIGSF 119
           D  A    + AA + F + HG  +   I  A   +G   + P  LA+F KV++ N+ G  
Sbjct: 60  DAPA----LAAAAADFTARHGAPDIV-IANAGVSVGTLSECPEDLAAFRKVMDTNVYGMA 114

Query: 120 NLLRLAAAAMAEGAADESGERGVIINTASIAAYDGQIGQAAYAASKGAIASLTLPAAREL 179
                    MA    D       ++  AS+A   G  G  AY+ASK A  +       E+
Sbjct: 115 ATFVPFIGPMAAAGGDRR-----LVGIASVAGIRGLPGAEAYSASKAAAIAYLESLRLEM 169

Query: 180 ARFGIRVMTIAPGIFETPMMA 200
           A  GI+V+TIAPG  ETPM A
Sbjct: 170 APKGIKVVTIAPGYIETPMTA 190


Lambda     K      H
   0.318    0.131    0.358 

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: 139
Number of extensions: 9
Number of successful extensions: 2
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: 255
Length of database: 257
Length adjustment: 24
Effective length of query: 231
Effective length of database: 233
Effective search space:    53823
Effective search space used:    53823
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 47 (22.7 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