GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Brevibacterium jeotgali SJ5-8

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_101588181.1 BJEO58_RS03580 2,3-dehydroadipyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_900169175.1:WP_101588181.1
          Length = 251

 Score =  191 bits (485), Expect = 1e-53
 Identities = 106/248 (42%), Positives = 148/248 (59%), Gaps = 3/248 (1%)

Query: 12  GNLFWITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFN 71
           G +  +TL+RP  LNAL+  L+ +L  A++ AES   +R I++TG  KAFCAGADITQ  
Sbjct: 5   GGVRVLTLDRPKALNALSVDLVAQLTAALTDAESTDSVRAIVLTGSDKAFCAGADITQIP 64

Query: 72  QLTPAEAW-KFSKKGREIMDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLG 130
           Q+  A    K +  G  +   I  L+KPTIA + G A GGG E+ALACD+ IA E AQ G
Sbjct: 65  QMQKAAPLDKLAFDG--LFSTIARLNKPTIAAVRGMAFGGGCEIALACDMAIAGESAQFG 122

Query: 131 LPEINLGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQE 190
           +PE+ LG+ PG GGTQRL   +GK +A+ M++TG+ +    AE  GLV  VV   ++   
Sbjct: 123 VPEVKLGVLPGAGGTQRLVHALGKAKAMRMLLTGEPVTATWAESAGLVAEVVADVDVLDT 182

Query: 191 TRKLAEKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLE 250
              + E IA  +P+++ L  +      +  L  GL LE   + ++  TED  EG+SAF E
Sbjct: 183 AVGIGETIAGNAPLAVRLTADAARHAEELGLSRGLDLERRNFLLLLGTEDAAEGISAFAE 242

Query: 251 KREPTFKG 258
           +R   FKG
Sbjct: 243 RRTADFKG 250


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: 150
Number of extensions: 7
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: 251
Length adjustment: 24
Effective length of query: 235
Effective length of database: 227
Effective search space:    53345
Effective search space used:    53345
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