GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hpcD in Marinobacter algicola DG893

Align 3-hydroxypropionyl-CoA dehydratase (EC 4.2.1.116) (characterized)
to candidate WP_007155005.1 MDG893_RS16740 2,3-dehydroadipyl-CoA hydratase

Query= BRENDA::A4YI89
         (259 letters)



>NCBI__GCF_000170835.1:WP_007155005.1
          Length = 257

 Score =  199 bits (505), Expect = 6e-56
 Identities = 110/244 (45%), Positives = 152/244 (62%), Gaps = 4/244 (1%)

Query: 17  ITLNRPDKLNALNAKLLEELDRAVSQAESDPEIRVIIITGKGKAFCAGADITQFNQLTPA 76
           +TLNRPD LNALN  LL  L +A+  AE+DPE+R I+ITG  KAF AGADI   N++   
Sbjct: 17  LTLNRPDVLNALNTDLLNNLSKALDDAEADPEVRAIVITGNQKAFAAGADI---NEMAAR 73

Query: 77  EAWKFSKKGREI-MDKIEALSKPTIAMINGYALGGGLELALACDIRIAAEEAQLGLPEIN 135
           +     +  R    ++I   +KP IA +NG+ALGGG ELA+  DI IA E A+ G PEIN
Sbjct: 74  DLVGILEDPRVAHWERIARFTKPIIAAVNGFALGGGCELAMHADILIAGENARFGQPEIN 133

Query: 136 LGIYPGYGGTQRLTRVIGKGRALEMMMTGDRIPGKDAEKYGLVNRVVPLANLEQETRKLA 195
           LGI PG GGTQRLTR +G+  A+ M +TG++I    A + GLV+ +       +   ++ 
Sbjct: 134 LGIMPGAGGTQRLTRKVGEALAMHMALTGEQINATRALQAGLVSEISQPELTVERAIEIG 193

Query: 196 EKIAKKSPISLALIKEVVNRGLDSPLLSGLALESVGWGVVFSTEDKKEGVSAFLEKREPT 255
           + IA+K+PI++ L KE V +  D  L  GL  E   + ++  T D++EG+ AF EKR P 
Sbjct: 194 QTIARKAPIAVRLTKESVRKADDMSLSDGLRFERHAFTLLAGTADRQEGLDAFREKRSPR 253

Query: 256 FKGK 259
           F G+
Sbjct: 254 FNGQ 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: 141
Number of extensions: 6
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 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