Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate SM_b21494 SM_b21494 ornithine cyclodeaminase
Query= SwissProt::P09773 (354 letters) >FitnessBrowser__Smeli:SM_b21494 Length = 355 Score = 495 bits (1274), Expect = e-145 Identities = 240/337 (71%), Positives = 285/337 (84%) Query: 9 IVPFISVENMMDLAVSTGIENFLVQLAGYIEEDFRRWESFDKIPRIASHSRDGVIELMPT 68 +VPF+SV+NMM L GIE L +L IE DFRRWESFDK PR+ASHSRDGVIELMPT Sbjct: 11 MVPFVSVDNMMRLVHHLGIETVLAELTDTIEADFRRWESFDKTPRVASHSRDGVIELMPT 70 Query: 69 SDGTLYGFKYVNGHPKNTKSGRQTVTAFGVLSDVDSGYPLLLSEMTILTALRTAATSAIA 128 SDG +Y FKYVNGHPKNT G QTVTAFG+L++V +GYP LL+EMTILTALRTAATSA+A Sbjct: 71 SDGRVYSFKYVNGHPKNTAEGLQTVTAFGLLAEVSTGYPALLTEMTILTALRTAATSAMA 130 Query: 129 AKYLARKDSRTMALIGNGAQSEFQALAFKALIGVDRIRLYDIDPEATARCSRNLQRFGFQ 188 A++LA K +RTMA+IGNGAQ+EFQALA KA+ G+D IRLYDIDP AT + +RNL G + Sbjct: 131 ARHLAPKGARTMAMIGNGAQAEFQALAMKAVCGIDTIRLYDIDPRATEKAARNLDGSGLK 190 Query: 189 IEACTSAEQAVEGADIITTATADKHNATILSDNMIGPGVHINGVGGDCPGKTEMHRDILL 248 I +C SA++A+EGA+I+TT TADK ATIL+DNM+G GVHIN +GGDCPGKTE+HRDIL Sbjct: 191 ILSCRSAQEAIEGAEIVTTCTADKQFATILTDNMVGAGVHINAIGGDCPGKTELHRDILQ 250 Query: 249 RSDIFVEFPPQTRIEGEIQQLAPDHPVTELWRVMTGQDVGRKSDKQITLFDSVGFAIEDF 308 RSD+FVE+PPQTRIEGEIQQ+APD PVTELW+V+TG+ GR+ +QITLFDSVGFAIEDF Sbjct: 251 RSDVFVEYPPQTRIEGEIQQMAPDFPVTELWKVVTGEAQGRRDGRQITLFDSVGFAIEDF 310 Query: 309 SALRYVRDRVEGSSHSSPLDLLADPDEPRDLFGMLLR 345 SALRYVR R+ G+ LD++ADPD+PRDLFGMLLR Sbjct: 311 SALRYVRARLPGTDFYQNLDMIADPDDPRDLFGMLLR 347 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: 396 Number of extensions: 10 Number of successful extensions: 1 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: 355 Length adjustment: 29 Effective length of query: 325 Effective length of database: 326 Effective search space: 105950 Effective search space used: 105950 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.
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