GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bkdB in Azospirillum brasilense Sp245

Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate AZOBR_RS26490 AZOBR_RS26490 pyruvate dehydrogenase

Query= BRENDA::Q9HIA4
         (319 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS26490 AZOBR_RS26490 pyruvate
           dehydrogenase
          Length = 324

 Score =  258 bits (659), Expect = 1e-73
 Identities = 145/325 (44%), Positives = 200/325 (61%), Gaps = 13/325 (4%)

Query: 1   MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60
           +  V A+  A++  M+ D +V+++GEDV   GG F+ T GL   +GP+RV DTP+SE  +
Sbjct: 5   LRYVNAVAQALNDAMAADPAVMLMGEDVAAAGGPFKATRGLLDAHGPERVRDTPISEASL 64

Query: 61  VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120
           VG A+G A+ G+KP+ EI F DF+  +MD ++NQ AK R+  GG  +VP+VLRTP GGG+
Sbjct: 65  VGAAVGAALTGMKPVVEIMFMDFVTLAMDAVVNQAAKARFMFGGQCSVPMVLRTPHGGGL 124

Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQ--- 177
             G  HSQ  EA+FAH  GL VV P+   DA  LL +AIE+PDPV+ +E K LY  Q   
Sbjct: 125 NAGPQHSQCLEAWFAHIPGLRVVCPATVADAYSLLRAAIEAPDPVVVVENKALYALQGDI 184

Query: 178 KVEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASK---SKYDVEVIDLRTIA 234
            V  P E     + KA + + G D TIVTYG+ +    + A +      + E++DLR I 
Sbjct: 185 DVNAPRE-----VGKARIDRAGRDATIVTYGATLYAARAAADRLATEGIEAEIVDLRWIQ 239

Query: 235 PMDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTP-- 292
           P D + + +SV KT RVVI HEA +  GVGAEI+A I+  A + L AP++RV  P  P  
Sbjct: 240 PWDEEAVFASVAKTHRVVIAHEAVQAFGVGAEIAARIAADAFDDLDAPVLRVGAPFMPIA 299

Query: 293 FPYRLEEYYLPNEGRINAALDRVMS 317
           F   LE  YLP+  RI AA+   ++
Sbjct: 300 FAKTLEAAYLPDADRIVAAVKSTLA 324


Lambda     K      H
   0.318    0.137    0.388 

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: 256
Number of extensions: 13
Number of successful extensions: 3
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: 319
Length of database: 324
Length adjustment: 28
Effective length of query: 291
Effective length of database: 296
Effective search space:    86136
Effective search space used:    86136
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: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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