GapMind for catabolism of small carbon sources

 

Alignments for a candidate for LRA6 in Dinoroseobacter shibae DFL-12

Align L-2,4-diketo-3-deoxyrhamnonate hydrolase; 2,4-dioxopentanoate hydrolase (characterized)
to candidate 3609154 Dshi_2542 5-oxopent-3-ene-1,2,5-tricarboxylate decarboxylase (RefSeq)

Query= reanno::Smeli:SM_b21112
         (281 letters)



>FitnessBrowser__Dino:3609154
          Length = 308

 Score =  186 bits (471), Expect = 7e-52
 Identities = 98/226 (43%), Positives = 132/226 (58%), Gaps = 7/226 (3%)

Query: 60  NPRLGPCVAGTGKFICIGLNYSDHAAETGAT------VPPEPIIFMKATSAIVGPNDD-L 112
           NP L P         C+G NY++H AE          +   P+ F K  +A+VG   D L
Sbjct: 81  NPFLAPLHTPRKNIFCVGRNYAEHIAEGERAQNAKIGITEHPVYFTKPATAVVGHGGDVL 140

Query: 113 VLPRGSEKTDWEVELGIVIGKTAKYVSEAEALDYVAGYCTVHDVSERAFQTERHGQWTKG 172
           + P  SEK D+EVEL +VIG T + + +  A  +V GY  ++D++ R  Q    GQ+ KG
Sbjct: 141 IFPSVSEKIDYEVELAVVIGTTGRDIPKDRAFAHVFGYTILNDITARDVQRRHGGQYFKG 200

Query: 173 KSCDTFGPTGPWLVTKDEVADPQDLAMWLKVNGETMQDGSTKTMVYGAAHLVSYLSQFMS 232
           KS D   P GPW+VT DE+ DPQDL++ L VNGE  Q+G T  M++    L++ LS+ ++
Sbjct: 201 KSLDGSCPIGPWIVTADEITDPQDLSISLSVNGELRQNGWTHDMIFDIPTLIASLSEGLT 260

Query: 233 LRPGDIISTGTPPGVGMGMKPPRYLKAGDVVELGIEGLGSQKQRVR 278
           L PGDII+TGTP GVG  M PP+YLK GD V   I  +G  K  VR
Sbjct: 261 LEPGDIIATGTPSGVGYAMDPPQYLKPGDTVICDIANIGQLKNTVR 306


Lambda     K      H
   0.315    0.136    0.408 

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: 293
Number of extensions: 16
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: 281
Length of database: 308
Length adjustment: 26
Effective length of query: 255
Effective length of database: 282
Effective search space:    71910
Effective search space used:    71910
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: 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