GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ocd in Cupriavidus basilensis 4G11

Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate RR42_RS27330 RR42_RS27330 ornithine cyclodeaminase

Query= BRENDA::Q88H32
         (350 letters)



>FitnessBrowser__Cup4G11:RR42_RS27330
          Length = 310

 Score = 97.1 bits (240), Expect = 6e-25
 Identities = 77/233 (33%), Positives = 117/233 (50%), Gaps = 13/233 (5%)

Query: 90  VLADVDSGYPVLLSELTIATALRTAATSLMAAQALARPNARKMALIGNGAQSEFQALAFH 149
           ++   + G P+   +    T LRTAA S++AA+ LARP A  +AL G G Q    A    
Sbjct: 79  LIFSTEDGRPLASFDAGAITRLRTAACSVLAARHLARPGAEVLALFGAGTQGVQHARQLA 138

Query: 150 KHLGIEEIVAYDTDPLATAKLIANLKEYSGLTIRRASSVAEAVKGVDIITTVTADKAYAT 209
             L ++ I+   +DP A A +   L    G+ +  A    +AV   DI+  VTA ++   
Sbjct: 139 AALPLKRILL--SDPYADAAMPERLARQCGIPVDLAEP-DQAVAQADIV--VTASRSTTP 193

Query: 210 IITPDMLEPGMHLNAVGGDCPGKTELHADVL-RNARVFVEYEPQT-RIEGEI-----QQL 262
           + +   L+PG  + A+G   P   EL    L R AR+ VE+ PQ+ R  G+I       L
Sbjct: 194 LFSGHSLKPGAFVAAIGSSLPHTRELDDVALSRAARLVVEWRPQSMREAGDIVLADPAVL 253

Query: 263 PADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALEDYTVLRYVLQQAEKRG 315
           PAD  VV+L  V+ G  + R +D+ + ++ SVG  LED  +  +  +Q E  G
Sbjct: 254 PAD-KVVELADVVTGSVKPRGNDTDILIYKSVGVGLEDVALAGFAYRQIEAAG 305


Lambda     K      H
   0.320    0.134    0.387 

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: 197
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: 350
Length of database: 310
Length adjustment: 28
Effective length of query: 322
Effective length of database: 282
Effective search space:    90804
Effective search space used:    90804
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: 49 (23.5 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