Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate SMc01360 SMc01360 aspartate carbamoyltransferase catalytic subunit
Query= curated2:P18186 (319 letters) >FitnessBrowser__Smeli:SMc01360 Length = 313 Score = 115 bits (289), Expect = 1e-30 Identities = 94/316 (29%), Positives = 150/316 (47%), Gaps = 35/316 (11%) Query: 12 KDLLTLKDLSEEDINALLAEAGEL-----KQNKIQPIFHGKTLAMIFEKSSTRTRVSFEA 66 + LL +K L+E+DI LL A E ++ K G T +F ++STRT+ SFE Sbjct: 7 RHLLGIKGLTEQDITLLLDRADEAVKISRQREKKTSSLRGLTQINLFFEASTRTQSSFEL 66 Query: 67 GMAQLGGSALFLSQKDLQLGRGETVADTAKVLSG-YVDAIMIRTFEHEKVEELAKEADIP 125 +LG + +S + + +GET+ DTA L+ + D +++R LA++ Sbjct: 67 AGKRLGADVMNMSVGNSSVKKGETLIDTAMTLNAMHPDVLVVRHSSAGAASLLAQKVSCS 126 Query: 126 VINGLTDKY-HPCQALADLLTIKEIKGKLKGVKVAYIGD--GNNVAHSLMIGCAKMGCDI 182 V+N ++ HP QAL D LTI+ KGKL + VA GD + VA S ++ +MG + Sbjct: 127 VVNAGDGQHEHPTQALLDALTIRRAKGKLSRIIVAICGDVLHSRVARSNILLLNQMGARV 186 Query: 183 SIASPKGYEVLDEAAEAAKTYALQSGSSVTLTDDPIEAVKDADVIYSDVFTSMGQEAEEQ 242 + +P A A+ Y + E +KDADV+ M + + Sbjct: 187 RVVAPATLLPAGIAEMGAEVYHSMA-----------EGLKDADVV-------MMLRLQRE 228 Query: 243 ERLAVFAP--------YQVNAALVSHAKPDYTFLHCLPAHREEEVTAEIIDGPNSAVFQQ 294 F P Y ++A + AK D +H P +R E+ +EI DGP S + QQ Sbjct: 229 RMAGSFVPSVREYFHYYGLDAEKLKVAKDDALVMHPGPMNRGVEIASEIADGPQSVIEQQ 288 Query: 295 AENRLHVQKALLKAIL 310 E + V+ A+++ +L Sbjct: 289 VEMGVAVRMAVMETLL 304 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: 228 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: 319 Length of database: 313 Length adjustment: 27 Effective length of query: 292 Effective length of database: 286 Effective search space: 83512 Effective search space used: 83512 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 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