GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fadB in Dyella japonica UNC79MFTsu3.2

Align GDP-6-deoxy-D-talose 4-dehydrogenase (EC 1.1.1.135); 3-hydroxy-2-methylbutyryl-CoA dehydrogenase (EC 1.1.1.178) (characterized)
to candidate N515DRAFT_3783 N515DRAFT_3783 NAD(P)-dependent dehydrogenase, short-chain alcohol dehydrogenase family

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3783
          Length = 255

 Score =  244 bits (623), Expect = 1e-69
 Identities = 129/249 (51%), Positives = 168/249 (67%), Gaps = 2/249 (0%)

Query: 13  AVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKDVQ 72
           A+ITGGASGLG A A+ LV  G    L D+    G+  A+ LG +  F   DVTSE  V 
Sbjct: 8   AIITGGASGLGYAVAQHLVAAGGQVALFDVNEDKGQEAARALGASAHFFRTDVTSEDGVS 67

Query: 73  TALALAKGKFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNLMGTFNVIRLV 132
             +A A+   G ++V +NCAGI  A +   L K     L  F   + VNL+G+FNV +  
Sbjct: 68  ANVAAAREAMGGLNVVMNCAGILGAGRV--LGKEGPMPLGTFASTVMVNLVGSFNVAKAA 125

Query: 133 AGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIR 192
           A  M  NE  + G+RGVI+NTASVAA+EGQ+GQAAYSASKGG+VGMTLP+AR+L+  GIR
Sbjct: 126 AALMQSNEAGEDGERGVIVNTASVAAYEGQIGQAAYSASKGGVVGMTLPMARELSRFGIR 185

Query: 193 VMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQAIIENPFLNGEVIR 252
           V TIAPG+F TP++  +P +V   L++ +PFPSRLG P E+A LV  I+ N ++NGE IR
Sbjct: 186 VATIAPGIFWTPMVDGMPPQVQESLSASIPFPSRLGRPEEFASLVAFILTNRYINGETIR 245

Query: 253 LDGAIRMQP 261
           LDGA+R+QP
Sbjct: 246 LDGAVRLQP 254


Lambda     K      H
   0.318    0.135    0.385 

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: 214
Number of extensions: 6
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: 261
Length of database: 255
Length adjustment: 24
Effective length of query: 237
Effective length of database: 231
Effective search space:    54747
Effective search space used:    54747
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