GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Shewanella oneidensis MR-1

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate 200845 SO1680 enoyl-CoA hydratase/isomerase family protein (NCBI ptt file)

Query= BRENDA::A4YI89
         (259 letters)



>FitnessBrowser__MR1:200845
          Length = 257

 Score =  159 bits (403), Expect = 4e-44
 Identities = 94/250 (37%), Positives = 139/250 (55%), Gaps = 2/250 (0%)

Query: 11  EGNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKG-KAFCAGADITQ 69
           EG+   +T+N P   N   A+ L+ L   V +  ++ +I  +++TG+G K F AGAD+  
Sbjct: 9   EGHTAILTMNNPPA-NTWTAQSLQALKAKVLELNANKDIYALVLTGEGNKFFSAGADLKL 67

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

Query: 130 GLPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQ 189
            LPE  +G+ P  GGTQ LT ++G+G A  M++ G+R+    A    LV  VV       
Sbjct: 128 ALPEATVGLLPCAGGTQNLTALVGEGWAKRMILCGERVNAAQALNLRLVEEVVETGEALN 187

Query: 190 ETRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFL 249
               LA K+A +SP S+   K ++  G   P    L +E   +  +F TED+ EGV+AFL
Sbjct: 188 AAIALAAKVANQSPSSVTACKTLIQAGRQMPRSQALPIEHELFVGLFDTEDQAEGVNAFL 247

Query: 250 EKREPTFKGK 259
           EKR+  +K +
Sbjct: 248 EKRKADWKNR 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: 115
Number of extensions: 4
Number of successful extensions: 1
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