GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Synechococcus elongatus PCC 7942

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Synpcc7942_0597 Synpcc7942_0597 naphthoate synthase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__SynE:Synpcc7942_0597
          Length = 279

 Score =  130 bits (327), Expect = 3e-35
 Identities = 96/271 (35%), Positives = 138/271 (50%), Gaps = 23/271 (8%)

Query: 2   EFETIETKK--EGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGK 59
           E+E I  +K  EG +  IT+NRP K NA   K + EL  A   A  D  I VI++TG G 
Sbjct: 11  EYEDIRYEKCAEG-IAKITINRPHKRNAFRPKTVVELYDAFCDAREDIAIGVILLTGAGP 69

Query: 60  ------AFCAGADITQFNQLTPAEAWKFSKKGR------EIMDKIEALSKPTIAMINGYA 107
                 AFCAG D     Q          ++G       ++   I  + K  IA++ GYA
Sbjct: 70  HTDGRYAFCAGGD-----QSVRGAGGYIDEEGLPRLNVLDLQRLIRTIPKVVIALVAGYA 124

Query: 108 LGGGLELALACDIRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRI 167
           +GGG  L + CD+ IAA+ A  G     +G + G  G   L R++G+ +A E+     + 
Sbjct: 125 IGGGHVLHILCDLTIAADNAVFGQTGPKVGSFDGGFGASYLARLVGQKKAREIWFLCRQY 184

Query: 168 PGKDAEKYGLVNRVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGL-A 226
             K+A + GLVN VVP+  LE E  + A +I +KSPI++  +K   N  LD   ++G+  
Sbjct: 185 GAKEALQMGLVNTVVPVEELEAEGIRWALEILEKSPIAIRCLKAAFNAELDG--MAGIQE 242

Query: 227 LESVGWGVVFSTEDKKEGVSAFLEKREPTFK 257
           L      + + TE+  EG  AFLEKR P F+
Sbjct: 243 LAGHATHLYYLTEEGSEGKQAFLEKRSPDFR 273


Lambda     K      H
   0.315    0.135    0.382 

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: 128
Number of extensions: 7
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: 259
Length of database: 279
Length adjustment: 25
Effective length of query: 234
Effective length of database: 254
Effective search space:    59436
Effective search space used:    59436
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: 42 (22.0 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