Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_041566425.1 NPUN_RS26215 aspartate carbamoyltransferase catalytic subunit
Query= curated2:P18186 (319 letters) >NCBI__GCF_000020025.1:WP_041566425.1 Length = 342 Score = 80.9 bits (198), Expect = 4e-20 Identities = 87/331 (26%), Positives = 146/331 (44%), Gaps = 45/331 (13%) Query: 14 LLTLKDLSEEDINALLAEAGELKQ-----NKIQPIFHGKTLAMIFEKSSTRTRVSFEAGM 68 +L+L D + + + +L A ++ K P G+ +A +F +SSTRTR SFE Sbjct: 11 ILSLADFTTTEYDTVLQTAASFQEVLSRRTKKVPTLQGQVVANLFFESSTRTRSSFELAA 70 Query: 69 AQLGGSALFLSQKDLQLGRGETVADTAKV-LSGYVDAIMIRTFEHEKVEELAKEAD---- 123 +L L + + +GET+ DTAK L+ D +++R E +A E D Sbjct: 71 KRLSADTLNFAAATSSMTKGETILDTAKTYLAMGTDIMVVRHREAGVPNAIAAEMDRLGV 130 Query: 124 -IPVIN-GLTDKYHPCQALADLLTIKEIKGK-------LKGVKVAYIGD--GNNVAHSLM 172 + V+N G HP QAL DL TI + LKG K+A +GD + VA S + Sbjct: 131 RVSVLNAGDGQHEHPSQALLDLFTICTLIDPASPRLELLKGKKIAIVGDILHSRVARSNI 190 Query: 173 IGCAKMGCDISIASPKGYEVLDEAAEAAKTYALQSGS-SVTLTDDPI-------EAVKDA 224 G ++ +A+P A ++ ++S S P+ A++DA Sbjct: 191 WSLIASGAEVHLAAPPTLLPKLFAEYISEELGVRSQELSSHFPTPPLFLHWQLEPALQDA 250 Query: 225 DVIYSDVFTSMGQEAEEQERLAVFAP--------YQVNAALVSHAKPDYTFLHCLPAHRE 276 D + M +++ A P + + + KP+ LH P +R Sbjct: 251 DFV-------MTLRLQKERMTAHLLPSLREYHQLFGITRTELQLCKPNVKVLHPGPVNRG 303 Query: 277 EEVTAEIIDGPNSAVFQ-QAENRLHVQKALL 306 E+++E++D P ++ Q Q + + V+ ALL Sbjct: 304 VEISSELMDDPEFSLIQSQVTSGIAVRMALL 334 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: 191 Number of extensions: 7 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 319 Length of database: 342 Length adjustment: 28 Effective length of query: 291 Effective length of database: 314 Effective search space: 91374 Effective search space used: 91374 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: 49 (23.5 bits)
This GapMind analysis is from Apr 10 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