GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Echinicola vietnamensis KMM 6221, DSM 17526

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Echvi_4069 Echvi_4069 Enoyl-CoA hydratase/carnithine racemase

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__Cola:Echvi_4069
          Length = 261

 Score =  214 bits (544), Expect = 2e-60
 Identities = 114/260 (43%), Positives = 168/260 (64%), Gaps = 3/260 (1%)

Query: 2   EFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KA 60
           E   I ++ +  + ++T+NR  KLNA+N   LEEL    ++   +  IR +++TG G KA
Sbjct: 3   ESTNILSENKDGILYLTINRESKLNAINFDTLEELKNIFNEVSDNKSIRGVVLTGSGEKA 62

Query: 61  FCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDI 120
           F AGADI++  +L    A KFS+ G+E+   IE+  KP IA++NG+ALGGG EL++AC +
Sbjct: 63  FVAGADISEIAELNELNARKFSENGQEVFSLIESCHKPVIAVVNGFALGGGCELSMACHM 122

Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180
           RIA   A+ G PE+NLGI PGYGGTQRLT +IG+ +A E++MTGD +   +A+  GLVN 
Sbjct: 123 RIATSNAKFGQPEVNLGIIPGYGGTQRLTFLIGRTKANELLMTGDMVDAAEAKALGLVNY 182

Query: 181 VVPL-ANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239
           V    A   Q+  ++ +KI  K+P+S+ +I + VN  + S   +G  +E+  +     +E
Sbjct: 183 VTQTKAEAIQKAEEILQKIMTKAPLSIGMIIDCVN-AVYSNDENGYLIEANSFARCVKSE 241

Query: 240 DKKEGVSAFLEKREPTFKGK 259
           D  EG SAFLEKR+P FKG+
Sbjct: 242 DYSEGTSAFLEKRKPNFKGE 261


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: 148
Number of extensions: 9
Number of successful extensions: 4
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: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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