Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_028322683.1 H567_RS0119505 aspartate carbamoyltransferase catalytic subunit
Query= BRENDA::Q51742 (315 letters) >NCBI__GCF_000422285.1:WP_028322683.1 Length = 319 Score = 141 bits (356), Expect = 2e-38 Identities = 107/320 (33%), Positives = 157/320 (49%), Gaps = 31/320 (9%) Query: 8 RDLLCLQDYTAEEIWTILETAKMFK-IWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEV 66 +DLL + + ++I IL+TA FK I + K L GK++ F + STRTR SFEV Sbjct: 7 KDLLGMGQLSVDDIQLILDTADSFKDISSREIKKVPTLRGKSIVNFFYEASTRTRTSFEV 66 Query: 67 AMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYV-DAIMARVYDHKDVEDLAKYATVP 125 A L L+A + +GET+ DT R L D I+ R LAK Sbjct: 67 AAKRLSADTFSLSASTSSMVKGETLIDTGRNLQAMSPDVIVIRHSSSGAPHLLAKGVKAC 126 Query: 126 VINGLSDFS-HPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTKLGADV 182 V+N + HP QAL D TI E+KG I+G+ + +GD + VA S MI TK+GA V Sbjct: 127 VVNAGDGINEHPTQALLDLYTIRERKGRIRGLNIAIIGDIAHSRVARSNMIGLTKMGARV 186 Query: 183 VVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAE 242 + P P E++ DP +A+ D DV+ M + E Sbjct: 187 TIGGPPTMIP-----------LGMEAFGVEVVPDPREAIGDKDVV-------MMLRIQLE 228 Query: 243 ERRKIFRP--------FQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDQ 294 +R+ P F ++ + +K AKPD + MH P +RG E++ ++ DSP S++ DQ Sbjct: 229 RQRRTLFPSLREYSAAFGLDSEALKSAKPDCVIMHPGPINRGVEISSELADSPASLILDQ 288 Query: 295 AENRLHAQKAVLALVMGGIK 314 N + + A+L L++GG K Sbjct: 289 VANGVAVRMAILYLLIGGSK 308 Lambda K H 0.319 0.134 0.400 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: 195 Number of extensions: 10 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: 315 Length of database: 319 Length adjustment: 27 Effective length of query: 288 Effective length of database: 292 Effective search space: 84096 Effective search space used: 84096 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 (21.8 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