Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 18270 b4245 aspartate carbamoyltransferase catalytic subunit (NCBI)
Query= curated2:A1ATU5 (305 letters) >FitnessBrowser__Keio:18270 Length = 311 Score = 91.7 bits (226), Expect = 2e-23 Identities = 98/323 (30%), Positives = 149/323 (46%), Gaps = 48/323 (14%) Query: 3 RHFLSLHDYTKEELDRLLALAIELKQEQKQGGEHHLLKGKTLAMIFDKSSTRTRISFEVG 62 +H +S++D ++++L+ +LA A +LK + LLK K +A F ++STRTR+SFE Sbjct: 8 KHIISINDLSRDDLNLVLATAAKLKANPQP----ELLKHKVIASCFFEASTRTRLSFETS 63 Query: 63 IYQLGGH--GLFISTGTSQMGRGEPLKDTARVLSRYCDGIMIRTFGQEIVDELAA--YAT 118 +++LG G S TS +GE L DT V+S Y D I++R QE LA Sbjct: 64 MHRLGASVVGFSDSANTSLGKKGETLADTISVISTYVDAIVMR-HPQEGAARLATEFSGN 122 Query: 119 VPVIN-GLTDLFHPCQIMADVMTVMEHKGGYAGLKFAWVGDGNNMANTWIEAAAIFGFD- 176 VPV+N G HP Q + D+ T+ E +G L A VGD A+ FD Sbjct: 123 VPVLNAGDGSNQHPTQTLLDLFTIQETQGRLDNLHVAMVGDLKYGRTVHSLTQALAKFDG 182 Query: 177 --------LALACPQGYEP--DAKVMAWAAERAPGRVTLTAD-------PKEAVSGAHVI 219 ALA PQ D K +AW+ + V D KE + + Sbjct: 183 NRFYFIAPDALAMPQYILDMLDEKGIAWSLHSSIEEVMAEVDILYMTRVQKERLDPSEYA 242 Query: 220 NTDVWASMGMEAEQKVREQAFGGFCLDDALAGLAHPDHIVLHCLPAHRGEEISDSVIEGS 279 N V A + A L +A A + VLH LP R +EI+ V + Sbjct: 243 N--VKAQFVLRASD-----------LHNAKANMK-----VLHPLP--RVDEIATDVDKTP 282 Query: 280 NSRVWDEAENRLHAQKAIMATLM 302 ++ + +A N + A++A++A ++ Sbjct: 283 HAWYFQQAGNGIFARQALLALVL 305 Lambda K H 0.320 0.135 0.409 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: 203 Number of extensions: 13 Number of successful extensions: 3 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: 305 Length of database: 311 Length adjustment: 27 Effective length of query: 278 Effective length of database: 284 Effective search space: 78952 Effective search space used: 78952 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: 48 (23.1 bits)
This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 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