GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badH in Synechococcus elongatus PCC 7942

Align BadH (characterized)
to candidate Synpcc7942_1573 Synpcc7942_1573 3-oxoacyl-(acyl-carrier protein) reductase

Query= metacyc::MONOMER-893
         (255 letters)



>FitnessBrowser__SynE:Synpcc7942_1573
          Length = 266

 Score =  138 bits (347), Expect = 1e-37
 Identities = 88/266 (33%), Positives = 136/266 (51%), Gaps = 16/266 (6%)

Query: 1   MARLQNKTAVITGGGGGIGGATCRRFAQEGAKIAV-FDLNLDAAEKVAGAIRDAGGTAE- 58
           M +L N+ A++TG   GIG     R A EGA + + +  + + AE+    +  AG     
Sbjct: 1   MGKLDNQIALVTGSSQGIGQEIAIRLASEGASVVIDYRSHPEGAEETRKQVEAAGAQCHL 60

Query: 59  ---------AVRCDIADRTSVDAAIATTTTTLGPVDILVNNAGWDIFKPFTKTEPGEWER 109
                     V+ D+ D T V   +A +    G +DILVNNAG +   PF +    +++ 
Sbjct: 61  AKDHAPEGYVVQADLGDVTQVRNLVAESIKHFGKLDILVNNAGMERRAPFWEVTEADYDM 120

Query: 110 LIAINLTGALHMHHAVLPGMVE-RRHGRIVNIASDAARVGSSGEAVYAACKGGLVAFSKT 168
           ++ +NL GA     A++  ++E +R G+I+NI+S    +     A Y   KGG+   ++ 
Sbjct: 121 VLNVNLKGAFFAAQALVQHLLETKRPGKIINISSVHEELPFPNFASYCLSKGGIKMMTRD 180

Query: 169 LAREHARHGITVNVVCPGPTDTALLADVTSGAANPEKLIEAFTKAIPLGRLGKPDDLAGA 228
           LA E   +GIT+N V PG  +T +  ++ +   NP +L  A    IPL RLGKP D+A  
Sbjct: 181 LAVELGEYGITINNVAPGAIETPINTNLLN---NPTEL-NALLGNIPLKRLGKPKDIASL 236

Query: 229 IAFFGSDDAGFITGQVLSVSGGLTMN 254
           + F  S DA +ITG  +   GGL  N
Sbjct: 237 VLFLASPDADYITGTTIFADGGLLWN 262


Lambda     K      H
   0.318    0.135    0.398 

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: 162
Number of extensions: 8
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: 255
Length of database: 266
Length adjustment: 24
Effective length of query: 231
Effective length of database: 242
Effective search space:    55902
Effective search space used:    55902
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