Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_043745147.1 AMB_RS18300 aspartate carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_000009985.1:WP_043745147.1 Length = 317 Score = 112 bits (280), Expect = 1e-29 Identities = 93/309 (30%), Positives = 149/309 (48%), Gaps = 18/309 (5%) Query: 8 RDLLCLQDYTPEEIWTILETAK-MLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEV 66 R LL +Q P EI ++L+ A+ ++ + K LL G+T+ +F + STRTR SFE+ Sbjct: 9 RHLLGIQGLAPSEITSLLDLAEGYVEQNRSSDKRKNLLRGRTVINLFYENSTRTRTSFEL 68 Query: 67 AMAHLGGHALYLNAQDLQLRRGETIADTARVL-SRYVDAIMARVYDHKDVEDLAKYASVP 125 A LG + + + +++GET+ DTA L + ++D ++ R D V+ L++ + Sbjct: 69 AGKRLGADVINMQSAGSSVQKGETLIDTAMTLNAMHLDVLVVRHPDSGAVKLLSEKVNCA 128 Query: 126 VIN-GLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTKLGADV 182 VIN G HP QAL D +TI +KG + G+ V GD + VA S + +GA V Sbjct: 129 VINGGDGSHEHPTQALLDALTIRRRKGKLSGLNVAICGDVRHSRVARSNIYLLNAMGAHV 188 Query: 183 VVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVI-YTDVWASMGQEAEA 241 + P P + E+ HD K + D DVI + Sbjct: 189 RLIGPRTLLP-----------SGLDRMGVEVFHDMRKGLADVDVIMMLRIQNERMSGNFI 237 Query: 242 EERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDS-PNSVVWDEAENRLH 300 R+ F F ++++ + AKPD + MH P +RG E+ DV D S++ + E + Sbjct: 238 PSIREYFHFFGLDREKLGIAKPDAVIMHPGPMNRGVEIDSDVADDVERSLIRSQVEMGVA 297 Query: 301 AQKAVLALL 309 + A L +L Sbjct: 298 VRMACLDML 306 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: 213 Number of extensions: 11 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: 317 Length of database: 317 Length adjustment: 27 Effective length of query: 290 Effective length of database: 290 Effective search space: 84100 Effective search space used: 84100 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 (21.7 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