GapMind for catabolism of small carbon sources

 

Aligments for a candidate for ocd in Azospirillum brasilense Sp245

Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate AZOBR_RS03120 AZOBR_RS03120 ornithine cyclodeaminase

Query= SwissProt::P09773
         (354 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS03120 AZOBR_RS03120 ornithine
           cyclodeaminase
          Length = 318

 Score =  116 bits (290), Expect = 9e-31
 Identities = 88/267 (32%), Positives = 125/267 (46%), Gaps = 10/267 (3%)

Query: 60  DGVIELMPTSD-GTLYGFKYVNGHPKNTKSGRQTVTAFGVLSDVDSGYPLLLSEMTILTA 118
           DG + LMP        G K V   P N       V    +L D  +G P  + + T LT 
Sbjct: 47  DGTLLLMPAWQVNQSIGVKVVTVFPDNGAKDLPAVQGLYLLMDGKTGMPQAVLDGTALTK 106

Query: 119 LRTAATSAIAAKYLARKDSRTMALIGNGAQSEFQALAFKALIGVDRIRLYDIDPEATARC 178
            RTAA SA+AA YLAR DS  + ++G GA +     AF  ++ +  + ++    E   + 
Sbjct: 107 RRTAAASALAASYLARPDSERLLMVGTGALAPELIEAFATVLPIKHVLVWGRSLEKAKKV 166

Query: 179 SRNLQRFGFQIEACTSAEQAVEGADIITTATADKHNATILSDNMIGPGVHINGVGGDCPG 238
           +    R  F+IEA    E AV GA +I+ AT  K    ++    + PG H++ VGG  P 
Sbjct: 167 ASRFHRPKFRIEATADLEGAVRGAQVISCATLAKE--PLIRGEWLQPGAHLDLVGGFTPE 224

Query: 239 KTEMHRDILLRSDIFVEFPPQTRIE-GEIQQ------LAPDHPVTELWRVMTGQDVGRKS 291
             E   D + RS +FV+       E G+I Q      L       +L+ +  GQ  GR+ 
Sbjct: 225 MREADDDCIRRSRVFVDTREGACKEAGDIVQPMKAGILTDADIAGDLYDLTRGQRAGRRF 284

Query: 292 DKQITLFDSVGFAIEDFSALRYVRDRV 318
             QITLF SVG A+ED  A +   + V
Sbjct: 285 YDQITLFKSVGTALEDLCAAQLAVEMV 311


Lambda     K      H
   0.320    0.137    0.396 

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: 239
Number of extensions: 14
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: 354
Length of database: 318
Length adjustment: 28
Effective length of query: 326
Effective length of database: 290
Effective search space:    94540
Effective search space used:    94540
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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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