GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaH 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)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3783 N515DRAFT_3783
           NAD(P)-dependent dehydrogenase, short-chain alcohol
           dehydrogenase family
          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.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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