Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate RR42_RS03960 RR42_RS03960 ornithine cyclodeaminase
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__Cup4G11:RR42_RS03960 Length = 358 Score = 401 bits (1030), Expect = e-116 Identities = 203/334 (60%), Positives = 250/334 (74%), Gaps = 1/334 (0%) Query: 1 MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPV 60 MT F+D ++ LV GVA I ++A +R DF RW+AFDKSAR+A+HS GVIELMPV Sbjct: 6 MTRFLDAADVAALVRATGVANTIAQMAHHIRQDFVRWEAFDKSARLATHSVDGVIELMPV 65 Query: 61 ADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMA 120 +D +YAFKYVNGHP N + TVMAFGVLA+V SG+P+LL +LT+ATALRTAATS +A Sbjct: 66 SDAVQYAFKYVNGHPRNAQNAMPTVMAFGVLAEVASGFPLLLCDLTLATALRTAATSALA 125 Query: 121 AQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGL 180 AQ +ARP A +ALIGNGAQ+EFQALAFH +GI EI AYD DP ATA+L NL+ GL Sbjct: 126 AQVMARPGAATLALIGNGAQAEFQALAFHAMVGIREIRAYDIDPAATARLARNLQGVPGL 185 Query: 181 TIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVL 240 + SV AV+G DII+T+TADK ATI+TPD++ PG+H+NAVGGDCPGKTELH +L Sbjct: 186 KVAAVDSVRTAVQGADIISTITADKTRATILTPDLVAPGVHINAVGGDCPGKTELHPQIL 245 Query: 241 RNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALED 300 R AR+ VEY PQTRIEGEIQQLPAD PV +LW +L G GR QVTVFDSVGFALED Sbjct: 246 RQARIVVEYAPQTRIEGEIQQLPADTPVTELWEILSGRVAGRTETGQVTVFDSVGFALED 305 Query: 301 YTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLF 334 Y+ LR++ A + G+ ++LV DP++L+ Sbjct: 306 YSALRWLHAAAHAQHRGSHVELVA-TPPDPRNLY 338 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: 355 Number of extensions: 9 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: 358 Length adjustment: 29 Effective length of query: 321 Effective length of database: 329 Effective search space: 105609 Effective search space used: 105609 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