GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Sphingomonas koreensis DSMZ 15582

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate Ga0059261_0837 Ga0059261_0837 3-hydroxyacyl-CoA dehydrogenase

Query= BRENDA::O87873
         (258 letters)



>FitnessBrowser__Korea:Ga0059261_0837
          Length = 676

 Score = 85.5 bits (210), Expect = 3e-21
 Identities = 66/217 (30%), Positives = 97/217 (44%), Gaps = 17/217 (7%)

Query: 13  ERDGSLLRLRLARPKANIVDAAMIAAMRQALGEHLQAPALRAVLLDAEGPHFSFGASVDE 72
           ER G +L +    P  N + AA+   +  A+ E     +L+A ++  +G  F  GA + E
Sbjct: 8   ERQGDILVITSNNPPVNALGAAVRQGLDAAIKELAGDDSLKAAVIRCDGRTFFAGADITE 67

Query: 73  HMPDQCAQMLKSLHGLVREMLDSPVPILVALRGQCLGGGLEVAAAGNLLFAAPDAKFGQP 132
                    L  L  L+     S  P++ A+ G  LGGG EVA A +   A P AKFG P
Sbjct: 68  FGKPMQEPSLPVLVDLIEA---SEKPVVAAVHGTALGGGCEVALACHYRIAVPSAKFGLP 124

Query: 133 EIRLGVFAPAASCLLPPRVGQA-CAEDLLWSGRSIDGAEGHRIGLIDVLAEDPEAAALRW 191
           E++LG+   A      PRVG    A +L   G  +  +     GL+D LA +        
Sbjct: 125 EVKLGILPGAGGTQRLPRVGGVEFALELATKGDPVSASAAKDAGLVDRLAGEDS------ 178

Query: 192 FDEHIARLSASSLRFAVRAARCDSVPRIKQKLDTVEA 228
                  L+A ++ +A   A    +PR  +K  TVEA
Sbjct: 179 -------LTADAIAYANEIAAARPLPRTSEKPVTVEA 208


Lambda     K      H
   0.321    0.135    0.402 

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: 352
Number of extensions: 13
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: 258
Length of database: 676
Length adjustment: 31
Effective length of query: 227
Effective length of database: 645
Effective search space:   146415
Effective search space used:   146415
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 (21.9 bits)
S2: 50 (23.9 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