GapMind for catabolism of small carbon sources

 

Alignments for a candidate for kguD in Azospirillum brasilense Sp245

Align 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) (characterized)
to candidate AZOBR_RS10940 AZOBR_RS10940 3-phosphoglycerate dehydrogenase

Query= reanno::BFirm:BPHYT_RS11290
         (321 letters)



>FitnessBrowser__azobra:AZOBR_RS10940
          Length = 415

 Score =  142 bits (359), Expect = 1e-38
 Identities = 101/278 (36%), Positives = 143/278 (51%), Gaps = 16/278 (5%)

Query: 45  GIGSSVKITPAMLEGATRLKALSTISVGFDQFDVADLTRRGIVLANTPDVLTESTADTVF 104
           GI S   +T  +LE A+RL ++    +G +Q D+    R GI + N P   T S A+ V 
Sbjct: 58  GIRSRTHLTAKVLEAASRLFSVGCFCIGTNQVDLKAARRLGIPVFNAPYSNTRSVAELVI 117

Query: 105 SLILASARRVVELAEWVKAGHWQHSIGPALFGVDVQGKTLGIVGLGRIGGAVARRAALGF 164
             I+   R +   +  V  G W  S   A    +++GKTLGIVG G IG  V+  A    
Sbjct: 118 GEIIMLMRGIFSKSNLVHGGGWMKS---AKDSYEIRGKTLGIVGYGHIGTQVSIMAE-SM 173

Query: 165 NMKVLY---TNRSANPQAEEAYGARRVELAELLATADFVCLQVPLTPETKHLIGAAELKS 221
            MKV Y    N+ A   A+  +      L ELLA +D V L VP TP+T+ +IG A++++
Sbjct: 174 GMKVRYYDVVNKLALGNAQPCHS-----LEELLAVSDVVTLHVPDTPQTRDMIGEAQIRA 228

Query: 222 MKKSAILINASRGATVDEKALIEALQNGTIHGAGLDVFETEPLPS----DSPLLKLANVV 277
           MKK A LINA+RG  V  +AL  AL++  + GA +DVF  EP       +S L  L N +
Sbjct: 229 MKKGAHLINAARGKVVVIEALAAALRDKHLLGAAIDVFPKEPGGDKEVFESALRGLDNAI 288

Query: 278 ALPHIGSATHETRHAMARNAAENLVAALDGTLTSNIVN 315
             PHIG +T E +  +    ++ L+   D   T   VN
Sbjct: 289 LTPHIGGSTMEAQANIGTEVSQKLIEYSDNGSTMGAVN 326


Lambda     K      H
   0.317    0.131    0.366 

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: 262
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: 321
Length of database: 415
Length adjustment: 30
Effective length of query: 291
Effective length of database: 385
Effective search space:   112035
Effective search space used:   112035
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: 49 (23.5 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