GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Haloterrigena daqingensis JX313

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_076581564.1 BB347_RS11510 enoyl-CoA hydratase/isomerase family protein

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_001971705.1:WP_076581564.1
          Length = 261

 Score =  183 bits (464), Expect = 4e-51
 Identities = 107/260 (41%), Positives = 154/260 (59%), Gaps = 12/260 (4%)

Query: 5   TIETKKEGNLFWITLNRPDKLNALNAKLLEELDRAVS--QAESDPEI--RVIIITGKGKA 60
           T+E  ++  +  +TLNRPD LNAL+ +L E++  ++   + ++D EI  RV++++G    
Sbjct: 9   TVEFDEDTGVGRVTLNRPDALNALSGQLREDIVESLRLLEEQNDDEIALRVVVVSGAAGN 68

Query: 61  FCAGADITQFNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDI 120
           FCAGADIT+F   +P          R     I     P IA I GY LGGGLE A+ACD 
Sbjct: 69  FCAGADITEFEDASPG-----GSPERTHYQFIMDFPVPVIAKIEGYCLGGGLETAMACDF 123

Query: 121 RIAAEEAQLGLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNR 180
           R A E+A+LGLPE++LGI PG GG Q ++ + G   A E+ MTGD I    A++ G+VNR
Sbjct: 124 RFADEDARLGLPEVDLGIIPGAGGVQYISELAGPAAAKEIAMTGDHISATRADELGIVNR 183

Query: 181 VVPLANLEQETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTED 240
           V    +L++ T+K AEKIA K P+++  IK        + L  G+  ++  +  + +TED
Sbjct: 184 VPD--DLDEATQKFAEKIASKPPLAIQTIKNSARISTQTSLKEGIDYDNKVFEPLLATED 241

Query: 241 KKEGVSAFLE-KREPTFKGK 259
            KEG  AF E   EP FKG+
Sbjct: 242 HKEGARAFAEDDYEPEFKGR 261


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: 163
Number of extensions: 8
Number of successful extensions: 4
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: 261
Length adjustment: 24
Effective length of query: 235
Effective length of database: 237
Effective search space:    55695
Effective search space used:    55695
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