Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_012470140.1 GLOV_RS10335 aspartate carbamoyltransferase catalytic subunit
Query= curated2:P18186 (319 letters) >NCBI__GCF_000020385.1:WP_012470140.1 Length = 310 Score = 131 bits (330), Expect = 2e-35 Identities = 99/308 (32%), Positives = 159/308 (51%), Gaps = 26/308 (8%) Query: 12 KDLLTLKDLSEEDINALLAEAGELKQN-----KIQPIFHGKTLAMIFEKSSTRTRVSFEA 66 KD++ L+DLS+E+I L++ A +++ K P GKT+ +F +SSTRTR SFE Sbjct: 6 KDIIALRDLSKEEIELLISTAENMREVNSRDIKKVPTLRGKTIINLFYESSTRTRTSFEI 65 Query: 67 GMAQLGGSALFLSQKDLQLGRGETVADTA-KVLSGYVDAIMIRTFEHEKVEELAKEADIP 125 +L + ++ + +GET+ADTA +L+ D I++R L+K+ Sbjct: 66 AGKRLSADTVNIAPSNSSATKGETLADTALNLLAMKPDIIVMRHAVSGSHYFLSKKVGCS 125 Query: 126 VIN-GLTDKYHPCQALADLLTIKEIKGKLKGVKVAYIGD--GNNVAHSLMIGCAKMGCDI 182 +IN G HP Q L D+LTIK+ G+L G+KVA +GD + VA S + G KMG I Sbjct: 126 IINAGDGAHEHPSQGLLDMLTIKDKFGRLDGLKVAMVGDITHSRVARSNIQGLTKMGSSI 185 Query: 183 SIASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQEAEEQ 242 +A P ++ +VT+ EA++DADV+ + + QE + + Sbjct: 186 FLAGP----------PTMMPPGVEQLGNVTVCGTMKEAIQDADVV---IMLRIQQERQGK 232 Query: 243 ERLAVFAPYQ----VNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQAENR 298 + Y +N V AKPD +H P +R E+++ ++DG S + +Q EN Sbjct: 233 TLMPNTREYSRYFGLNPENVKWAKPDAMVMHPGPINRGVEMSSYVVDGNQSHILKQVENG 292 Query: 299 LHVQKALL 306 + V+ A+L Sbjct: 293 VAVRMAML 300 Lambda K H 0.315 0.131 0.361 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: 229 Number of extensions: 15 Number of successful extensions: 5 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: 319 Length of database: 310 Length adjustment: 27 Effective length of query: 292 Effective length of database: 283 Effective search space: 82636 Effective search space used: 82636 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.5 bits) S2: 48 (23.1 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