GapMind for catabolism of small carbon sources

 

Alignments for a candidate for badI in Synechococcus elongatus PCC 7942

Align BadI (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase

Query= metacyc::MONOMER-892
         (260 letters)



>FitnessBrowser__SynE:Synpcc7942_0597
          Length = 279

 Score =  240 bits (612), Expect = 3e-68
 Identities = 130/265 (49%), Positives = 168/265 (63%), Gaps = 8/265 (3%)

Query: 2   QFEDLIYE-IRNGVAWIIINRPDKMNAFRGTTCDELIKALYKAGYDKDVGAIVLAGAGDR 60
           ++ED+ YE    G+A I INRP K NAFR  T  EL  A   A  D  +G I+L GAG  
Sbjct: 11  EYEDIRYEKCAEGIAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGPH 70

Query: 61  -----AFCTGGDQSTHD--GNYDGRGTVGLPMEELHTAIRDVPKPVIARVQGYAIGGGNV 113
                AFC GGDQS     G  D  G   L + +L   IR +PK VIA V GYAIGGG+V
Sbjct: 71  TDGRYAFCAGGDQSVRGAGGYIDEEGLPRLNVLDLQRLIRTIPKVVIALVAGYAIGGGHV 130

Query: 114 LATICDLTICSEKAIFGQVGPKMGSVDPGYGTAFLARVVGEKKAREIWYMCKRYSGKEAE 173
           L  +CDLTI ++ A+FGQ GPK+GS D G+G ++LAR+VG+KKAREIW++C++Y  KEA 
Sbjct: 131 LHILCDLTIAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQYGAKEAL 190

Query: 174 AMGLANLCVPHDELDAEVQKWGEELCERSPTALAIAKRSFNMDTAHQAGIAGMGMYALKL 233
            MGL N  VP +EL+AE  +W  E+ E+SP A+   K +FN +    AGI  +  +A  L
Sbjct: 191 QMGLVNTVVPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELDGMAGIQELAGHATHL 250

Query: 234 YYDTDESREGVKALQEKRKPEFRKY 258
           YY T+E  EG +A  EKR P+FR+Y
Sbjct: 251 YYLTEEGSEGKQAFLEKRSPDFRQY 275


Lambda     K      H
   0.319    0.138    0.418 

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: 14
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: 260
Length of database: 279
Length adjustment: 25
Effective length of query: 235
Effective length of database: 254
Effective search space:    59690
Effective search space used:    59690
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 (21.7 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