GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__azobra:AZOBR_RS26490
          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:

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