Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate AZOBR_RS03120 AZOBR_RS03120 ornithine cyclodeaminase
Query= SwissProt::P09773 (354 letters) >FitnessBrowser__azobra:AZOBR_RS03120 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 Apr 09 2024. The underlying query database was built on Apr 09 2024.
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:
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