GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Rhodobacter ovatus JA234

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_097028846.1 CRO07_RS01150 2-(1,2-epoxy-1,2-dihydrophenyl)acetyl-CoA isomerase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_900207575.1:WP_097028846.1
          Length = 258

 Score =  135 bits (341), Expect = 6e-37
 Identities = 86/260 (33%), Positives = 136/260 (52%), Gaps = 3/260 (1%)

Query: 1   MEFETIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKA 60
           M + TI  +++  +  +TL RP+ +NAL++ +  EL +AV+QA      RVI++TG+G+ 
Sbjct: 1   MGYRTIRIEEQDGVALVTLCRPEVMNALSSLMRAELLQAVTQAAQ--AARVIVLTGEGRG 58

Query: 61  FCAGADITQFNQLTPAEAWKFSKKGRE-IMDKIEALSKPTIAMINGYALGGGLELALACD 119
           FC+G D+     L   +  +  ++  E ++  I     PT+A +NG A G G  LALACD
Sbjct: 59  FCSGQDLGDAQGLETPDFGRILREEYEPLLRAIATCPIPTLAAVNGPAAGAGANLALACD 118

Query: 120 IRIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVN 179
           + IAA+ A        +G+ P  GGT  L R IG  RA+   +  DRI  + A  +G++ 
Sbjct: 119 VVIAAQSASFIQAFTRIGLIPDAGGTWTLPRQIGLARAMGATLFADRIGAQHAADWGMIY 178

Query: 180 RVVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTE 239
             VP        R  A ++A     +   +K+ +     +     LALE+       ++ 
Sbjct: 179 EAVPDEAFPARWRDRAAQLATGPTTAYRALKQALRASSGNDFNQQLALEADLQASCGTSA 238

Query: 240 DKKEGVSAFLEKREPTFKGK 259
           D +EGV+AFLEKR P F G+
Sbjct: 239 DFREGVAAFLEKRPPRFTGR 258


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: 138
Number of extensions: 5
Number of successful extensions: 3
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: 258
Length adjustment: 24
Effective length of query: 235
Effective length of database: 234
Effective search space:    54990
Effective search space used:    54990
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 24 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