GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaG in Herbaspirillum seropedicae SmR1

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate HSERO_RS20665 HSERO_RS20665 2,3-dehydroadipyl-CoA hydratase

Query= BRENDA::P77467
         (262 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS20665 HSERO_RS20665
           2,3-dehydroadipyl-CoA hydratase
          Length = 262

 Score =  145 bits (365), Expect = 1e-39
 Identities = 87/250 (34%), Positives = 136/250 (54%), Gaps = 6/250 (2%)

Query: 13  VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAGRGFCAGQDLNDRNVD 72
           V+ LTLNRP   N+  ++   ++   L + E DD++R ++++G  + F AG DLN+  + 
Sbjct: 19  VLHLTLNRPALRNALRNQSLREIVAALARAEEDDSVRVVVISGNEKAFAAGADLNEM-IH 77

Query: 73  PTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAKF 132
               A  L +  + +     R +A+ PKP++ AVNG A GAG  L +  DI IAAR AK 
Sbjct: 78  KDAIATQLDVRAQYW-----RAIARFPKPILAAVNGYALGAGCELLMHADIAIAARGAKI 132

Query: 133 VMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLAD 192
                 +G +P  GGT  L R  G+  AM + L G  +SA+QA + G++ +VVDD+   +
Sbjct: 133 GQPEINVGTLPGAGGTQRLIRTVGKPLAMKMVLSGEFISADQALQAGLVAEVVDDDATLE 192

Query: 193 TAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAFL 252
               LA  +A +    + L K+A+  +    L+  L  ER    L   SAD +EG++AF 
Sbjct: 193 RTLALAHSIAQKSPLAVRLAKEAMLQSFELGLEAGLLFERKSFSLMAASADRQEGIAAFQ 252

Query: 253 AKRSPQFTGK 262
            KR+  F+G+
Sbjct: 253 EKRAAVFSGR 262


Lambda     K      H
   0.321    0.136    0.403 

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: 126
Number of extensions: 7
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: 262
Length of database: 262
Length adjustment: 25
Effective length of query: 237
Effective length of database: 237
Effective search space:    56169
Effective search space used:    56169
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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