GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Acidovorax sp. GW101-3H11

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate Ac3H11_2775 Enoyl-CoA hydratase (EC 4.2.1.17)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2775
          Length = 279

 Score =  197 bits (501), Expect = 2e-55
 Identities = 109/257 (42%), Positives = 156/257 (60%), Gaps = 4/257 (1%)

Query: 6   IETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAG 64
           +E ++ G + WI LNRPD++NA+N  +   +  A+++ +SDP +RVI+I G G + FCAG
Sbjct: 24  VEVERRGGVGWIVLNRPDQINAINDDIRRGVPAALAELDSDPSVRVIVIRGAGARGFCAG 83

Query: 65  ADITQFNQL-TPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIA 123
           ADI +     T  +  +  +K R I + ++   KP IA I+GY +GGG+ELALACD+R A
Sbjct: 84  ADIKERRAAETSVQVRRRMQKSRWI-EALDRTEKPVIAAIHGYCMGGGMELALACDLRFA 142

Query: 124 AEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVP 183
           A +A   LPE  LG+ PG GGTQRL  V+G GRAL++++TGDR+  + A   GL+ R+  
Sbjct: 143 ASDAVFALPETGLGLIPGGGGTQRLGAVVGPGRALDLLLTGDRVDARRAFDIGLITRMAD 202

Query: 184 LA-NLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKK 242
            A +L  E   LAE+IA+K P +    K+         L SGL LE   + ++    D K
Sbjct: 203 SADSLLAEVTALAERIAQKPPTATLFAKQAARAACHLDLKSGLDLELDLFAMLVPMNDVK 262

Query: 243 EGVSAFLEKREPTFKGK 259
           E   AF EKR P F G+
Sbjct: 263 EAALAFREKRAPCFSGE 279


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: 165
Number of extensions: 5
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: 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