GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Stenotrophomonas chelatiphaga DSM 21508

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_057507562.1 ABB28_RS04910 enoyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_001431535.1:WP_057507562.1
          Length = 265

 Score =  146 bits (369), Expect = 4e-40
 Identities = 90/253 (35%), Positives = 137/253 (54%), Gaps = 2/253 (0%)

Query: 6   IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAG 64
           ++ + +G++  ITL+ P   +      L  L   V+   +D  I  ++I+G+G K F AG
Sbjct: 12  LKVEADGHVAVITLHNPPA-HTWTVHSLAALRDLVAALNADRSIYALVISGEGEKFFSAG 70

Query: 65  ADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAA 124
           AD+ QF       A + +++  E  + +      +IA INGYA+GGGLE ALACD+RI  
Sbjct: 71  ADLNQFASGDRGAAREAARRFGEAFEALSGFRGVSIAAINGYAMGGGLECALACDLRIIE 130

Query: 125 EEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPL 184
           E AQ+ LPE  +G+ P  GGTQ L R++G+G A  M++ G+RI    A + GL  +    
Sbjct: 131 EHAQVALPEATVGLLPCAGGTQNLPRLVGEGWAKRMILLGERIDADTAVRIGLAEQKAGK 190

Query: 185 ANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEG 244
              +    + A+K  K+SP S+A  K +V         + L  E   +  +F + D+ EG
Sbjct: 191 GEAKALALEWAKKAGKQSPTSIAACKTLVQSTRTGTHAAALVAEREAFVDLFDSADQVEG 250

Query: 245 VSAFLEKREPTFK 257
           VSAFLEKR   +K
Sbjct: 251 VSAFLEKRSAQWK 263


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: 135
Number of extensions: 7
Number of successful extensions: 1
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: 265
Length adjustment: 25
Effective length of query: 234
Effective length of database: 240
Effective search space:    56160
Effective search space used:    56160
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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