Align Ornithine cyclodeaminase; OCD; EC 4.3.1.12 (characterized)
to candidate WP_011951896.1 SWIT_RS05355 ornithine cyclodeaminase
Query= SwissProt::P09773 (354 letters) >NCBI__GCF_000016765.1:WP_011951896.1 Length = 346 Score = 497 bits (1280), Expect = e-145 Identities = 239/343 (69%), Positives = 286/343 (83%) Query: 7 LNIVPFISVENMMDLAVSTGIENFLVQLAGYIEEDFRRWESFDKIPRIASHSRDGVIELM 66 LN VPF+SV++MM + + G+E LV+LA Y+E+DFRRW+ FDK PR+ASHSR+GVIELM Sbjct: 3 LNTVPFVSVDHMMRIVLDIGVERVLVELADYVEDDFRRWDCFDKTPRVASHSREGVIELM 62 Query: 67 PTSDGTLYGFKYVNGHPKNTKSGRQTVTAFGVLSDVDSGYPLLLSEMTILTALRTAATSA 126 PTSDG +YGFKYVNGHP N + G QTVTAFGVL+ VDSGYPL+LSEMT+LTALRTAATSA Sbjct: 63 PTSDGEVYGFKYVNGHPSNMQRGLQTVTAFGVLAAVDSGYPLMLSEMTLLTALRTAATSA 122 Query: 127 IAAKYLARKDSRTMALIGNGAQSEFQALAFKALIGVDRIRLYDIDPEATARCSRNLQRFG 186 +AA++LA D+ MA+IGNGAQ+EFQALAFKA++G+ I LYDIDP AT +C NL+ G Sbjct: 123 VAARHLAPADAHRMAIIGNGAQAEFQALAFKAILGITEISLYDIDPAATRKCVGNLRSHG 182 Query: 187 FQIEACTSAEQAVEGADIITTATADKHNATILSDNMIGPGVHINGVGGDCPGKTEMHRDI 246 F I SAE+AV+GA I+TT TADK ATIL+DNMIG GVHIN +GGDCPGKTE+HRDI Sbjct: 183 FDIRVANSAEEAVQGAQIVTTVTADKQYATILTDNMIGSGVHINAIGGDCPGKTELHRDI 242 Query: 247 LLRSDIFVEFPPQTRIEGEIQQLAPDHPVTELWRVMTGQDVGRKSDKQITLFDSVGFAIE 306 LLRS IFVEF PQTRIEGEIQQLAPDHPV+ELW V+ G+ GR S QITLFDSVGFAIE Sbjct: 243 LLRSSIFVEFTPQTRIEGEIQQLAPDHPVSELWEVIAGRAEGRTSPDQITLFDSVGFAIE 302 Query: 307 DFSALRYVRDRVEGSSHSSPLDLLADPDEPRDLFGMLLRRQAF 349 DF+ALRY+RDR+ + H LD++ADPD+PRDLFGML+R + + Sbjct: 303 DFAALRYLRDRLADTRHFVELDMIADPDDPRDLFGMLMRAREY 345 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: 400 Number of extensions: 6 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: 346 Length adjustment: 29 Effective length of query: 325 Effective length of database: 317 Effective search space: 103025 Effective search space used: 103025 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 Jul 25 2024. The underlying query database was built on Jul 25 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