GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaG in Dyella japonica UNC79MFTsu3.2

Align 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase (EC 5.3.3.18) (characterized)
to candidate N515DRAFT_1164 N515DRAFT_1164 enoyl-CoA hydratase

Query= BRENDA::P77467
         (262 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1164
          Length = 260

 Score =  140 bits (354), Expect = 2e-38
 Identities = 89/251 (35%), Positives = 128/251 (50%), Gaps = 5/251 (1%)

Query: 13  VMTLTLNRPERLNSFNDEMHAQLAECLKQVERDDTIRCLLLTGAG-RGFCAGQDLNDRNV 71
           V  +T+NRP++LN+ N +   +L     Q  +DD +R ++L GAG + F AG D+ + N 
Sbjct: 14  VRIITVNRPDKLNALNRDTLNELTLAFAQAAQDDAVRTVVLAGAGDKAFVAGADIAEMN- 72

Query: 72  DPTGPAPDLGMSVERFYNPLVRRLAKLPKPVICAVNGVAAGAGATLALGGDIVIAARSAK 131
              G  P       R    L+  + +L KPV+  + G A G G  LA+   + +A+  A+
Sbjct: 73  ---GYTPVQAQGFSRAGQRLMSSIERLGKPVVARIQGFALGGGMELAMACHLRVASEKAR 129

Query: 132 FVMAFSKLGLIPDCGGTWLLPRVAGRARAMGLALLGNQLSAEQAHEWGMIWQVVDDETLA 191
           F      LGLIP  GGT  L R+AGR  A+ L L G  + A++A+E G++ +VV  E L 
Sbjct: 130 FGQPEINLGLIPGFGGTQRLLRLAGRGAALELCLTGAMVGAQRAYELGVVNRVVAPEALD 189

Query: 192 DTAQQLARHLATQPTFGLGLIKQAINSAETNTLDTQLDLERDYQRLAGRSADYREGVSAF 251
           +T   LA  LA         I  AI       LD  L+ E     LA  + D REG +AF
Sbjct: 190 ETVDALADQLAASAPLAAAGILDAILQGGEMALDQGLEFETQAFALAFSTEDMREGTTAF 249

Query: 252 LAKRSPQFTGK 262
           L KR  +F G+
Sbjct: 250 LEKRKAEFKGR 260


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: 144
Number of extensions: 11
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: 260
Length adjustment: 25
Effective length of query: 237
Effective length of database: 235
Effective search space:    55695
Effective search space used:    55695
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 (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