GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dch in Novosphingobium barchaimii LL02

Align cyclohexa-1,5-dienecarbonyl-CoA hydratase (EC 4.2.1.100) (characterized)
to candidate WP_059151871.1 V474_RS12920 enoyl-CoA hydratase

Query= BRENDA::D3RXI0
         (252 letters)



>NCBI__GCF_001046635.1:WP_059151871.1
          Length = 255

 Score =  108 bits (269), Expect = 1e-28
 Identities = 75/248 (30%), Positives = 124/248 (50%), Gaps = 7/248 (2%)

Query: 10  KDERVARIKIANPPV-NVLDMETMKEIISAIDEVEGVDVI---VFSGEG-KSFSAGAEIK 64
           +++ +A I +  P   N L  E  + + +A    E  D +   + +G G K+F AG ++K
Sbjct: 10  REDGIAVITLNRPEQRNALTAEVREGLRAAWARFEADDALRIAILTGSGDKAFCAGGDLK 69

Query: 65  EHFPDKAPEMIRWFTQLIDKVLRCKAITVAAVKGFALGGGFELAIACDFVLASKNAKLGV 124
           E          R    L    +     T+AAV G A  GG+ +A ACD  +AS  AK  +
Sbjct: 70  EMVETGMAVPPRDMYALPYDTIELSKPTIAAVNGVAFAGGWMIAQACDLCVASTAAKFAI 129

Query: 125 PEITLAHYPPVAIALLPRMIGWKNAYELILTGEAITAERAFEIGLVNKVFEDENFEESVN 184
            E+ +    P A  L+  MIG +   E++LTG+ I A RA+EIGLVN++ +     ++  
Sbjct: 130 TEVKVGRGSPWAAPLI-HMIGQRIFMEIVLTGKPIDAARAYEIGLVNRLAQPGAVLDAAI 188

Query: 185 DFVNSLLEKSSVALRLTKKALLFSTEKEYLSLFDVINDVYLSQLVKSEDAVEGLKAFLEK 244
           +    +LE + ++++  ++ ++ STE    +        +      S+DA EG +AF EK
Sbjct: 189 ELAREVLEGAPLSVKAARETVMLSTEMGRSAALAAARSAH-EHTYNSQDAQEGPRAFAEK 247

Query: 245 RKPEWKGR 252
           R+P W GR
Sbjct: 248 RRPVWSGR 255


Lambda     K      H
   0.318    0.136    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: 137
Number of extensions: 7
Number of successful extensions: 3
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: 252
Length of database: 255
Length adjustment: 24
Effective length of query: 228
Effective length of database: 231
Effective search space:    52668
Effective search space used:    52668
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: 41 (21.7 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