Align ornithine cyclodeaminase (EC 4.3.1.12) (characterized)
to candidate Pf1N1B4_4977 Ornithine cyclodeaminase (EC 4.3.1.12)
Query= BRENDA::Q88H32 (350 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4977 Length = 341 Score = 422 bits (1085), Expect = e-123 Identities = 214/341 (62%), Positives = 265/341 (77%), Gaps = 1/341 (0%) Query: 1 MTYFIDVPTMSDLVHDIGVAPFIGELAAALRDDFKRWQAFDKSARVASHSEVGVIELMPV 60 MT FIDV + L IG+ I E+A ++ D+ RW FDKS R A+HS+ GVIELMP Sbjct: 1 MTLFIDVDHAATLFRKIGIGNAIREMALYIKADYCRWADFDKSPRTANHSDSGVIELMPT 60 Query: 61 ADKSRYAFKYVNGHPANTARNLHTVMAFGVLADVDSGYPVLLSELTIATALRTAATSLMA 120 D +Y+FKYVNGHPAN + NL TVMAFGVLADVDSGYP +LSELT+ TA+RTAATS + Sbjct: 61 DDGKQYSFKYVNGHPANASNNLLTVMAFGVLADVDSGYPTVLSELTLTTAVRTAATSALV 120 Query: 121 AQALARPNARKMALIGNGAQSEFQALAFHKHLGIEEIVAYDTDPLATAKLIANLKEYSGL 180 AQ+LAR + +MA+IGNGAQSEFQA+AF++ LGI E+ +D D A+ KL NL+ Y+G+ Sbjct: 121 AQSLARKGSTRMAIIGNGAQSEFQAIAFYEMLGINEVRIFDIDSAASLKLKQNLESYTGI 180 Query: 181 TIRRASSVAEAVKGVDIITTVTADKAYATIITPDMLEPGMHLNAVGGDCPGKTELHADVL 240 + A+SV EAVKGVDIITTVTADKAYATI+TPDM+EPGMH+NAVGGDCPGKTELHAD+L Sbjct: 181 NVTVAASVHEAVKGVDIITTVTADKAYATILTPDMIEPGMHINAVGGDCPGKTELHADIL 240 Query: 241 RNARVFVEYEPQTRIEGEIQQLPADFPVVDLWRVLRGETEGRQSDSQVTVFDSVGFALED 300 RNAR+ VE+EPQTRIEG+IQQL AD PV++ +R++R GR+SD+QVTVFDSVGFALED Sbjct: 241 RNARIIVEFEPQTRIEGDIQQLNADHPVIEYFRIVRDNEPGRESDTQVTVFDSVGFALED 300 Query: 301 YTVLRYVLQQAEKRGMGTKIDLVPWVEDDPKDLFSHTRGRA 341 ++ LRY+ QA K +G KI LVP + K+L+ G A Sbjct: 301 FSSLRYLHDQAGKYAIGEKIHLVP-TPANIKNLYQLIEGNA 340 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: 348 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: 350 Length of database: 341 Length adjustment: 29 Effective length of query: 321 Effective length of database: 312 Effective search space: 100152 Effective search space used: 100152 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