GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ivdG in Azospirillum brasilense Sp245

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 AZOBR_RS24695 AZOBR_RS24695 3-oxoacyl-ACP reductase

Query= BRENDA::Q99714
         (261 letters)



>FitnessBrowser__azobra:AZOBR_RS24695
          Length = 256

 Score =  105 bits (263), Expect = 7e-28
 Identities = 91/259 (35%), Positives = 127/259 (49%), Gaps = 27/259 (10%)

Query: 6   RSVKGLVAVITGGASGLGLATAERLVGQGASAVLLDLPNSGGEAQAKKLGNNCVFAPADV 65
           R + G VA +TGG  G+G A  ERL  +GA+ V+ D+     E  A  L      A A  
Sbjct: 9   RRLAGRVAFVTGGGGGIGRAVCERLAAEGAAVVVADIGAEVAETVAAALRAEGAQAHATA 68

Query: 66  TSEKDVQTALALAKG---KFGRVDVAVNCAGIAVASKTYNLKKGQTHTLEDFQRVLDVNL 122
            +  D ++  A   G    F  VD+ VN AGI    +  +L K    T  ++  V+DVNL
Sbjct: 69  LNVADRESWGAAVTGLPEAFRGVDIMVNVAGIV---RDRSLPK---MTDAEWSAVIDVNL 122

Query: 123 MGTF----NVIRLVAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGM 178
            GT+       RLV         D+G  R  I+N AS A   G  GQA YSASK G+VG+
Sbjct: 123 RGTWLGCQTAFRLVG--------DRGWGR--IVNIASTAIL-GTFGQANYSASKAGVVGL 171

Query: 179 TLPIARDLAPIGIRVMTIAPGLFGTPLLTSLPEKVCNFLASQVPFPSRLGDPAEYAHLVQ 238
           T   A + A  GI V  +APG+  T ++  +P+ V +    + P   RLG PAE A +V 
Sbjct: 172 TRTAALEGARRGILVNAVAPGVVETAIVEGVPDAVRSQWLEKTPI-GRLGKPAEIAAVVA 230

Query: 239 AIIEN--PFLNGEVIRLDG 255
            +  +   ++ G+ I  DG
Sbjct: 231 FLASDDAAYVTGQTIVADG 249


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: 193
Number of extensions: 15
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: 256
Length adjustment: 24
Effective length of query: 237
Effective length of database: 232
Effective search space:    54984
Effective search space used:    54984
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