Align N-succinylornithine carbamoyltransferase (EC 2.1.3.11) (characterized)
to candidate Ga0059261_3206 Ga0059261_3206 ornithine carbamoyltransferase
Query= BRENDA::Q8A1E9 (318 letters) >FitnessBrowser__Korea:Ga0059261_3206 Length = 307 Score = 94.4 bits (233), Expect = 3e-24 Identities = 86/280 (30%), Positives = 127/280 (45%), Gaps = 32/280 (11%) Query: 37 KTLMMIFFNSSLRTRLSTQKAALNLGMNVMVLDINQGAWKLETERGVIMDGDKPEHLLEA 96 +TL M+F +S RTR+S + A LG + +VLD A + RG E + + Sbjct: 48 RTLAMVFEKNSTRTRVSFEMAIRQLGGSAVVLD----AATSQLGRG--------ETVADT 95 Query: 97 IPVMGCYCDIIGVRSFARFEDRDFDYQETILNQFIQYSGRPVFSMEAATRHPLQSFADLI 156 V+ YCD I VR+ D +L + QY+ PV + HP Q ADL Sbjct: 96 ARVLSGYCDAIMVRT---------DDHAKLL-EMAQYATVPVINGLTDDSHPCQIMADLQ 145 Query: 157 TIEEYKKTARPKVVMTWAPHPRPLPQAVPNSFAEWMNATDYDFVITHPEGYELAPQFV-- 214 TI E K A P + + W V S E +D V P+ + L + + Sbjct: 146 TILESGK-ALPGLKVAWLGDGNN----VLASIVEAAGLMHFDVVAACPQSFALPEEAMAL 200 Query: 215 --GNAKVEYDQMKAFEGADFIYAKNWAAYTGDNYGQILSKDREWTVSDRQMAVTN-NAFF 271 G A+ D ++A GAD + W + + L+ + V++ MA + +A F Sbjct: 201 GKGRARTVNDPVEAVAGADVVVTDTWISMGQAHADVKLAALAPYQVTEALMAQASPDAKF 260 Query: 272 MHCLPVRRNMIVTDDVIESPQSIVIPEAANREISATVVLK 311 +HCLP R VTD VI+ PQS++ PEA NR + VL+ Sbjct: 261 LHCLPAHRGEEVTDAVIDGPQSLIWPEAENRLHAQKAVLR 300 Lambda K H 0.322 0.136 0.406 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: 9 Number of successful extensions: 4 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: 307 Length adjustment: 27 Effective length of query: 291 Effective length of database: 280 Effective search space: 81480 Effective search space used: 81480 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