Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate GFF294 PGA1_c03060 aspartate carbamoyltransferase PyrB
Query= curated2:Q8TKT5 (302 letters) >FitnessBrowser__Phaeo:GFF294 Length = 331 Score = 86.3 bits (212), Expect = 9e-22 Identities = 90/310 (29%), Positives = 136/310 (43%), Gaps = 18/310 (5%) Query: 2 KRDVLSITDLSKEEIYELLESAADL-KAKRKAGESTEYLKNKSLGMIFEKSSTRTRVSFE 60 +R +L I L EI +L+ A + R+ + L + +F ++STRT+ SFE Sbjct: 15 QRHLLGIEPLKPHEITAILDLADSYAELNRRPDKHANALSGLTQVNMFFENSTRTQASFE 74 Query: 61 VAMTDFGGHALYLNSRDIQVGRGETIEDTARTLSGYLHGLMARVMSHD-TVEKLAKYSTM 119 +A G + + + + +GET+ DTA TL+ L+ H V+ LA+ Sbjct: 75 IAGKRLGADVMNMAMQASSIKKGETLIDTAMTLNAMHPDLLVVRHPHSGAVDLLAQKVNC 134 Query: 120 PVINALSDR-EHPCQILGDFMTIMEFKKKFEGLKFAWVGD--GNNVCNSALLGSAIMGME 176 V+NA R EHP Q L D +TI K + L A GD + V S L+ M Sbjct: 135 AVLNAGDGRHEHPTQALLDALTIRRAKGRLHRLNIAICGDVAHSRVARSNLILLGKMENR 194 Query: 177 FAVACPKGYEPK--AEFLEQAKALGGKFTITDDPKVAAKDADIIYT-DVWVSMGDEAEQE 233 + P P A+F + I DD + KD D++ + D Sbjct: 195 IRLIGPPTLVPGHFADFGAE---------IYDDMREGLKDVDVVMMLRLQKERMDGGFIP 245 Query: 234 KRLREFASFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPN-SVIFEEAENRLHA 292 + + ++ E L +AKPD IVMH P RG+EI + D N SVI E+ E + Sbjct: 246 SEREYYHRYGLDAEKLALAKPDAIVMHPGPMNRGVEIDGTLADDINRSVIQEQVEMGVAV 305 Query: 293 QKALILKLMR 302 + A + L R Sbjct: 306 RMAAMDLLAR 315 Lambda K H 0.318 0.134 0.378 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: 9 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: 302 Length of database: 331 Length adjustment: 27 Effective length of query: 275 Effective length of database: 304 Effective search space: 83600 Effective search space used: 83600 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 (21.7 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