GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaF in Synechococcus elongatus PCC 7942

Align trans-2,3-dehydroadipyl-CoA hydratase (EC 4.2.1.17) (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase

Query= reanno::BFirm:BPHYT_RS17335
         (258 letters)



>FitnessBrowser__SynE:Synpcc7942_0597
          Length = 279

 Score =  118 bits (296), Expect = 1e-31
 Identities = 89/263 (33%), Positives = 125/263 (47%), Gaps = 10/263 (3%)

Query: 3   YENILVETRGR-VGLVTLNRPKALNALNDALMDELGAALREFDADDAIGAIVVTGS---- 57
           YE+I  E     +  +T+NRP   NA     + EL  A  +   D AIG I++TG+    
Sbjct: 12  YEDIRYEKCAEGIAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGPHT 71

Query: 58  --EKAFAAGADIGMMSTYTYMDV--YKGDYITRNWETVRSIRKPIIAAVAGFALGGGCEL 113
               AF AG D  +     Y+D        +      +R+I K +IA VAG+A+GGG  L
Sbjct: 72  DGRYAFCAGGDQSVRGAGGYIDEEGLPRLNVLDLQRLIRTIPKVVIALVAGYAIGGGHVL 131

Query: 114 AMMCDIIFAADTAKFGQPEIKLGIMPGAGGTQRLPRAVSKAKAMDLCLTARFMDAAEAER 173
            ++CD+  AAD A FGQ   K+G   G  G   L R V + KA ++    R   A EA +
Sbjct: 132 HILCDLTIAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQYGAKEALQ 191

Query: 174 AGLVSRVIPAASLVDEAIAAAATIAEFPSPAVMMVKESVNRAYETTLAEGVHFERRLFHS 233
            GLV+ V+P   L  E I  A  I E    A+  +K + N   +  +A          H 
Sbjct: 192 MGLVNTVVPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELD-GMAGIQELAGHATHL 250

Query: 234 LFATEDQKEGMAAFVEKRKPVFK 256
            + TE+  EG  AF+EKR P F+
Sbjct: 251 YYLTEEGSEGKQAFLEKRSPDFR 273


Lambda     K      H
   0.321    0.134    0.380 

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: 155
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: 258
Length of database: 279
Length adjustment: 25
Effective length of query: 233
Effective length of database: 254
Effective search space:    59182
Effective search space used:    59182
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 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