Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 3609708 Dshi_3091 aspartate carbamoyltransferase (RefSeq)
Query= curated2:Q8TKT5 (302 letters) >FitnessBrowser__Dino:3609708 Length = 316 Score = 90.1 bits (222), Expect = 6e-23 Identities = 99/310 (31%), Positives = 140/310 (45%), Gaps = 20/310 (6%) Query: 3 RDVLSITDLSKEEIYELLESA---ADLKAKR-KAGESTEYLKNKSLGMIFEKSSTRTRVS 58 R +L I L+ +EI LL+ A ADL + K G++ + L + M FE +STRT+ S Sbjct: 6 RHLLGIEHLAPDEIVTLLDLADRYADLNRRPDKHGDALDGLTQ--INMFFE-NSTRTQAS 62 Query: 59 FEVAMTDFGGHALYLNSRDIQVGRGETIEDTARTLSGYLHGLMARVMSHD-TVEKLAKYS 117 FE+A G + + R + +GET+ DTA TL+ L+ H V LA+ Sbjct: 63 FEIAGKRLGADVMNMEVRASSIKKGETLIDTAMTLNAMHPDLLVVRHPHSGAVNLLAEKV 122 Query: 118 TMPVINALSDR-EHPCQILGDFMTIMEFKKKFEGLKFAWVGD--GNNVCNSALLGSAIMG 174 V+NA R EHP Q L D +TI K K L A GD + V S +L M Sbjct: 123 NCAVLNAGDGRHEHPTQALLDALTIRRAKGKLHRLNVAICGDIAHSRVARSNILLLGKME 182 Query: 175 MEFAVACPKGYEPKAEFLEQAKALGGKFTITDDPKVAAKDADII-YTDVWVSMGDEAEQE 233 + P+ P AE E LG + +D K D++ + D Sbjct: 183 NRIRLVGPRTLMP-AEIAE----LG--VEVYEDMKAGLDGVDVVMMLRLQKERMDGGFIP 235 Query: 234 KRLREFASFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPN-SVIFEEAENRLHA 292 + + ++ E L AKPD IVMH P RG+EI + D N SVI E+ E + Sbjct: 236 SEREYYHRYGLDAEKLAYAKPDAIVMHPGPMNRGVEIDGTLADDINRSVIQEQVEMGVAV 295 Query: 293 QKALILKLMR 302 + A + L R Sbjct: 296 RMAAMDLLAR 305 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: 204 Number of extensions: 7 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: 316 Length adjustment: 27 Effective length of query: 275 Effective length of database: 289 Effective search space: 79475 Effective search space used: 79475 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 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