GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gli in Dinoroseobacter shibae DFL-12

Align D-galactarolactone cycloisomerase (EC 5.5.1.27) (characterized)
to candidate 3607183 Dshi_0604 amidohydrolase 2 (RefSeq)

Query= BRENDA::A9CEQ7
         (292 letters)



>FitnessBrowser__Dino:3607183
          Length = 286

 Score =  144 bits (363), Expect = 2e-39
 Identities = 86/274 (31%), Positives = 131/274 (47%), Gaps = 6/274 (2%)

Query: 13  PNPAFPRGAVDTQMHMYLP--GYPALPGGPGLPPGALPGPEDYRRLMQWLGIDRVIITQG 70
           P    P GA D   H+ +P   +P +      PP A      Y+ L   LGI+R +I Q 
Sbjct: 15  PKRPLPPGATDCHSHVIVPEADHPFVANRSYTPPPATLA--QYKALHARLGIERAVIVQP 72

Query: 71  NAHQRDNGNTLACVAEMGEAAHAVVIIDATTTEKDMEKLTAAGTVGARIMDLPGGAVNLS 130
           + +  DN  TL  +A  G     + ++DA  + +D++ + AAG  GARI  L  G + L 
Sbjct: 73  SVYGTDNSVTLEAIAGYGPGCRGIAVVDADVSMRDLQAMNAAGIRGARINMLFSGGIGLD 132

Query: 131 ELDAVDERAHAADWMVAVQFDGNGLLDHLPRLQKIRSRWVFDHHGKFFKGIRTDGPEMAA 190
           +L+ +  R    DW   +  DG  L D   RL  +    V DH G        D P   A
Sbjct: 133 DLEPLARRIADLDWHFQLLIDGPTLADLEARLANLPVPVVIDHMGHMQTHDGLDQPGFRA 192

Query: 191 LLKLIDRGNLWFKFAGVYESSRKSWPYADVAAFSRVIAAHAPERIVWGTNWPHNSVRETA 250
           L +L+ RGN W K +G Y  S +   + DV  F++ + +   E +VWGT+WPH ++ +  
Sbjct: 193 LRRLVVRGNTWVKLSGNYRMSSQRPRFEDVVPFAQALISDNSEHMVWGTDWPHPAMLD-- 250

Query: 251 AYPDDARLAELTLGWLPDEAARHRALVENPEALF 284
             PDD  L +    ++  +  + R LV+NP  L+
Sbjct: 251 FMPDDGSLVDALDAYVTSQDQKQRILVDNPATLY 284


Lambda     K      H
   0.319    0.136    0.426 

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: 236
Number of extensions: 12
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: 292
Length of database: 286
Length adjustment: 26
Effective length of query: 266
Effective length of database: 260
Effective search space:    69160
Effective search space used:    69160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 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