GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Erythrobacter marinus HWDM-33

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_047094365.1 AAV99_RS12275 enoyl-CoA hydratase/isomerase family protein

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_001013305.1:WP_047094365.1
          Length = 252

 Score =  119 bits (298), Expect = 6e-32
 Identities = 78/252 (30%), Positives = 123/252 (48%), Gaps = 11/252 (4%)

Query: 11  EGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGK--GKAFCAGADIT 68
           +G +  + ++R DK NA N  + E +   + QA +DP +R ++I     G  FCAGADI 
Sbjct: 8   DGPVAHLLIDRLDKRNAFNMAMWEAMPGLLEQARADPAVRTLVIRSAQPGGVFCAGADIK 67

Query: 69  QFNQLTPAEAWKFSKKG--REIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEE 126
           +        AW  + +     +   +  L+ PT+A + G  +GGG  +A+ACD+R+A ++
Sbjct: 68  EMLLHKDDGAWLAANQAAINRVQHDLARLTLPTVAFVEGDCVGGGCGIAIACDLRVATDK 127

Query: 127 AQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLAN 186
           A+ G+    LGI       + LT ++G G+A  M+ TG  +   +A++ GLV  +     
Sbjct: 128 ARFGITPGKLGIVYPLHDVKLLTDLVGPGQAKRMLFTGGLLDAAEAQRIGLVEMIA---- 183

Query: 187 LEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVS 246
                R L   I   SP S+  IK  V R LD          ++ +   F   D  EG +
Sbjct: 184 --DSPRGLLNDILSASPHSIREIKMFVRRVLDGQTGDDDQTLAI-FTDAFMRGDFAEGAA 240

Query: 247 AFLEKREPTFKG 258
           AF  KR+P F G
Sbjct: 241 AFAGKRKPDFNG 252


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: 134
Number of extensions: 6
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: 252
Length adjustment: 24
Effective length of query: 235
Effective length of database: 228
Effective search space:    53580
Effective search space used:    53580
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