Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_006746647.1 THITH_RS16710 aspartate carbamoyltransferase
Query= BRENDA::Q48296 (295 letters) >NCBI__GCF_000227685.2:WP_006746647.1 Length = 358 Score = 81.6 bits (200), Expect = 2e-20 Identities = 81/322 (25%), Positives = 141/322 (43%), Gaps = 47/322 (14%) Query: 3 HLVDINDVESEEIEQLLDLAASMKENPGEFSGVMDNKSLVMLFAKPSTRTRLSFETGMTQ 62 H+V + + QL LAA + P + K L+ F +PSTRTRLSFE+ + Sbjct: 45 HVVSSRQFDRATLIQLFRLAAQYEATPALMHLPLTGKILISAFYEPSTRTRLSFESAWHR 104 Query: 63 LGGHGI-FFEMGSSQLSRGEPISDVSQVMSRYEDAIMARLFEHDEMMELAENADVPVV-- 119 LGG + + S+ +++GE + D++++ + Y D I+ R E + ++ E +P+V Sbjct: 105 LGGAIMSITDPKSTGMAKGESLVDIAEMFNNYGDVIVLRSSEDQAVYQMLEGLRIPIVNA 164 Query: 120 -NGLTDFLHPCQALTDMFTMQE------KDRLDTLAFVGDG-------NNVAHSLMQASA 165 NG+ + HP QAL D++T+ + + +D A + G SL+ Sbjct: 165 GNGIDE--HPTQALADVYTLAKWRPDLFRGEVDLQARIRVGIIGVPSRMRTVRSLLLMLG 222 Query: 166 KMGVDCRIATPEGMEPD-------EEIQD-----RVSDANVTVTNDPYEAVDGATAVYGD 213 + R E + EE++ RV D V + A A GD Sbjct: 223 RFPEAIREVVIISREDENFDAGQREELEAAGLVLRVVDQLDPVLPELDVVYINAIAWVGD 282 Query: 214 VFVSMGEEEQREEKLAEFDGFQIDQDLMDAARDDAIFMHCLPAHRGEEVTAEVADGPQSV 273 F S+G G + ++ + AI +H P RG+E+ ++ D P + Sbjct: 283 TFESLG------------TGLHLTRN--SPLKPGAIILH--PLARGDELATDLDDTPHNW 326 Query: 274 IFDQAENRMHVQKAIVHTLVNQ 295 F QA + V+ A++ ++V + Sbjct: 327 YFAQARGAVFVRMALLTSVVRR 348 Lambda K H 0.316 0.132 0.369 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: 252 Number of extensions: 16 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 295 Length of database: 358 Length adjustment: 28 Effective length of query: 267 Effective length of database: 330 Effective search space: 88110 Effective search space used: 88110 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 (21.6 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Apr 10 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