Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 208411 DVU2901 aspartate carbamoyltransferase
Query= curated2:Q7V8G9 (318 letters) >MicrobesOnline__882:208411 Length = 317 Score = 95.1 bits (235), Expect = 2e-24 Identities = 91/308 (29%), Positives = 141/308 (45%), Gaps = 27/308 (8%) Query: 18 RDFLSCADFTAEQTVALLELSRQLKSGDRRI-----DLGNRVLGLIFTKASTRTRVSFQV 72 +D L + ++ + LL+ + Q +RR L + + L F + STRT+ SF V Sbjct: 12 KDLLDVDQLSKDELLHLLDTAAQFHEINRRPVKKVPTLKGKSVILFFAEPSTRTKTSFDV 71 Query: 73 AMARLGGQTVDLNPQVTQLGRGEPLEDTARVLSRF-CDVMAVRTFAQQELLDYAHWASIP 131 A RL T L + L +GE L+DTA L DV+ +R + A + Sbjct: 72 AGKRLSADTFSLAKSGSSLQKGESLKDTALTLEAMNPDVLVIRHSSSGAARFLAERLACG 131 Query: 132 VLNALTDLE-HPCQAMADFLTIQEALG-SLTGQTLAYVGD--GNNVSHSLMLCGALLGVN 187 V+NA HP QA+ D ++++ G + G+TL +GD + V+ S + LGV Sbjct: 132 VVNAGDGWHAHPTQALLDCYSLRQVWGDTFEGRTLCILGDIAHSRVARSNVKLLTSLGVR 191 Query: 188 VRIGCPQGFEPLPEVIDQARNLAVADARIEVMTDPVDAVRGAQALYTDVWASMGQEQEQS 247 VR+ P+ P V + +EV TD AVR A A+ + + E++Q+ Sbjct: 192 VRLCAPRTLLP----------AGVGNWPVEVFTDLDAAVRDADAV---MCLRLQLERQQA 238 Query: 248 ----QREEAFRGFCLNEDLLAHADPNAIVLHCLPAHRGEEISSGVMEGEASRIFDQAENR 303 E +CL L A P A VLH P +RG EI+S + + AS + DQ Sbjct: 239 GLLPDLREYSNRYCLTPRRLELAKPEAKVLHPGPMNRGLEIASSIADAPASLVLDQVAAG 298 Query: 304 LHVQQALL 311 + + A+L Sbjct: 299 VATRMAIL 306 Lambda K H 0.321 0.135 0.391 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: 207 Number of extensions: 21 Number of successful extensions: 2 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: 318 Length of database: 317 Length adjustment: 27 Effective length of query: 291 Effective length of database: 290 Effective search space: 84390 Effective search space used: 84390 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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