GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaH in Novosphingobium barchaimii LL02

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 WP_059150596.1 V474_RS06310 SDR family oxidoreductase

Query= BRENDA::Q99714
         (261 letters)



>NCBI__GCF_001046635.1:WP_059150596.1
          Length = 264

 Score =  171 bits (434), Expect = 1e-47
 Identities = 101/259 (38%), Positives = 141/259 (54%), Gaps = 10/259 (3%)

Query: 11  LVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADVTSEKD 70
           L A++TGGASGLG A+A+ L   G    + D+    GEA A ++G   VF   ++  E  
Sbjct: 7   LAAIVTGGASGLGRASAQALADAGIKVAIFDISEDAGEAFAAQIGG--VFCNVNIMDEDS 64

Query: 71  VQTALALAKGKFGRVDVAVNCAGIAVASKTYNLKKG----QTHTLEDFQRVLDVNLMGTF 126
           V+   A A+   G+  + V+CA +A   KT +  K     +    E   +  +     ++
Sbjct: 65  VEAGFAKARAAHGQERIIVHCALVAGGGKTVSFDKKSGAYKRTATEQIAKSAEGIFTASY 124

Query: 127 NVIRLVAGEMGQNEP-DQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARD 185
            V  + A  M   +P ++ G+RG II T+S AA +GQVGQ AY   KG +  M LP+ARD
Sbjct: 125 RVASIAALGMANADPLNEDGERGTIILTSSAAAQDGQVGQVAYGGGKGAVNAMVLPMARD 184

Query: 186 LAPIGIRVMTIAPGLFGTPLLTSLPE---KVCNFLASQVPFPSRLGDPAEYAHLVQAIIE 242
           L  +GIRV  I PG F TP +  + E   +V   L   VPFP RLG P E+  LV  ++ 
Sbjct: 185 LMDLGIRVNAIMPGTFATPPMLRVKEHAPEVYENLGKAVPFPRRLGHPEEFGSLVLELVR 244

Query: 243 NPFLNGEVIRLDGAIRMQP 261
           N + NG+ IRLDGAIRM P
Sbjct: 245 NIYFNGQCIRLDGAIRMPP 263


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: 178
Number of extensions: 7
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: 264
Length adjustment: 25
Effective length of query: 236
Effective length of database: 239
Effective search space:    56404
Effective search space used:    56404
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 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