GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Psychromonas ingrahamii 37

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_157035422.1 PING_RS03450 2,3-dehydroadipyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000015285.1:WP_157035422.1
          Length = 244

 Score =  167 bits (424), Expect = 1e-46
 Identities = 94/237 (39%), Positives = 142/237 (59%), Gaps = 4/237 (1%)

Query: 23  DKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPAEAWKFS 82
           +K NAL+   L EL   + +AE    I  +++TG  + F AGAD+ +       + W   
Sbjct: 10  EKRNALSNDCLNELAGVLDKAEQQNHIAAVVLTGGQRCFAAGADLNELATQGAIDTWLNP 69

Query: 83  KKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEINLGIYPGY 142
           +   E+  ++   SKP +A +NGYALG GLEL L CDI I+ ++A  GLPEI LG+ PG 
Sbjct: 70  RP--ELWARLNKFSKPLLAAVNGYALGAGLELVLLCDIAISGQKALFGLPEITLGLIPGA 127

Query: 143 GGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVV-PLANLEQETRKLAEKIAKK 201
           GGTQRL R +GK    +M++TG  I  + A + GL++ VV P   LE+ T  +AE IAK+
Sbjct: 128 GGTQRLARTVGKSLTNQMVLTGLPITAERALQAGLISEVVIPELTLER-TIIIAETIAKR 186

Query: 202 SPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKREPTFKG 258
           +P+++   K+ + +  +S L  GL  E   +  + ++ D+KEG+ AF  KR+PT+KG
Sbjct: 187 APLAIKAAKQSLQQVPNSSLDQGLKFERQLFVTLAASNDRKEGIDAFFNKRQPTYKG 243


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: 147
Number of extensions: 5
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: 259
Length of database: 244
Length adjustment: 24
Effective length of query: 235
Effective length of database: 220
Effective search space:    51700
Effective search space used:    51700
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: 46 (22.3 bits)

This GapMind analysis is from Sep 24 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