GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Shewanella amazonensis SB2B

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 6937208 Sama_1378 enoyl-CoA hydratase (RefSeq)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__SB2B:6937208
          Length = 257

 Score =  167 bits (422), Expect = 3e-46
 Identities = 100/250 (40%), Positives = 142/250 (56%), Gaps = 2/250 (0%)

Query: 11  EGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADITQ 69
           EGN   +T++ P   N    + L EL   V +   + EI  +++TG+G K F AGAD+  
Sbjct: 9   EGNTAILTISNPPA-NTWTRESLNELKEKVLELNDNNEIYALVLTGEGEKFFSAGADLKL 67

Query: 70  FNQLTPAEAWKFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQL 129
           F       A   +K   E  + + A    +IA INGYA+GGGLE+ALACDIRIA  +A +
Sbjct: 68  FADGDKGNAATMAKAFGEAFETLSAFRGVSIAAINGYAMGGGLEVALACDIRIAEIQAVM 127

Query: 130 GLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQ 189
            LPE  +G+ P  GGTQ LT ++G+G A  M++ G+RI    A   GLV  VV       
Sbjct: 128 ALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERIDATKALNLGLVEEVVEKGESLS 187

Query: 190 ETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFL 249
               LA K+AK+SP ++A+ K+++  G + P    L LE   +  +F TED+ EGV+AFL
Sbjct: 188 AAIALAAKVAKQSPSAVAVCKKLIQSGRNMPRTQALPLERELFVGLFDTEDQAEGVNAFL 247

Query: 250 EKREPTFKGK 259
           EKR   +K +
Sbjct: 248 EKRAAQWKNR 257


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: 135
Number of extensions: 5
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: 259
Length of database: 257
Length adjustment: 24
Effective length of query: 235
Effective length of database: 233
Effective search space:    54755
Effective search space used:    54755
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 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