Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate AO356_29450 AO356_29450 ornithine cyclodeaminase
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_29450 Length = 351 Score = 408 bits (1049), Expect = e-118 Identities = 208/334 (62%), Positives = 258/334 (77%), Gaps = 1/334 (0%) Query: 1 MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPV 60 MT FIDV + L +G+ I E+A + D+ RW FDKS R A+HS GVIELMP Sbjct: 1 MTLFIDVDHAARLFAKVGIRRAIREMADYIEADYSRWAQFDKSPRTANHSANGVIELMPT 60 Query: 61 ADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMA 120 D +Y+FKYVNGHP N NL TVMAFGVLADV SGYP LLSELT+ TA+RTAATS + Sbjct: 61 DDGQQYSFKYVNGHPDNGRSNLLTVMAFGVLADVHSGYPTLLSELTLTTAVRTAATSALV 120 Query: 121 AQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGL 180 A++LARP+A MA+IGNGAQSEFQALAFH+ L I+E+ +D D A+ KL NL + L Sbjct: 121 AKSLARPDASSMAIIGNGAQSEFQALAFHEMLAIKELRIFDIDRDASLKLKRNLSAFPDL 180 Query: 181 TIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVL 240 + ASS EAVKG DI+TTVTADKAYATI+TP+M+EPGMH+NAVGGDCPGKTELHA++L Sbjct: 181 EVILASSAQEAVKGADIVTTVTADKAYATILTPEMIEPGMHINAVGGDCPGKTELHAEIL 240 Query: 241 RNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALED 300 RNARV VE+EPQTRIEG+IQQL ADFPVV+ +R+++G +GR++D+QVTVFDSVGFALED Sbjct: 241 RNARVIVEFEPQTRIEGDIQQLEADFPVVEFFRIVQGAIQGRENDAQVTVFDSVGFALED 300 Query: 301 YTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLF 334 ++ LRY+L A++ +G +I LVP + KDL+ Sbjct: 301 FSSLRYMLDLAQEHAIGERIHLVP-TPANIKDLY 333 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: 341 Number of extensions: 12 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: 350 Length of database: 351 Length adjustment: 29 Effective length of query: 321 Effective length of database: 322 Effective search space: 103362 Effective search space used: 103362 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