Align N-succinylornithine carbamoyltransferase (EC 2.1.3.11) (characterized)
to candidate WP_057687254.1 ABB28_RS15390 acetylornithine carbamoyltransferase
Query= reanno::Cola:Echvi_3849 (313 letters) >NCBI__GCF_001431535.1:WP_057687254.1 Length = 336 Score = 199 bits (506), Expect = 8e-56 Identities = 120/328 (36%), Positives = 182/328 (55%), Gaps = 24/328 (7%) Query: 5 TQFENKSLADQLIQKALEYKKAPLSDNNLGRGKRIGLLFLNPSLRTRVSTQIAASNLGME 64 TQ ++S D L+ +A +K+ L D +GK I L+F NPS+RTR S ++ A LG Sbjct: 9 TQDWSRSELDALLTQAALFKRNKLGDQL--KGKSIALVFFNPSMRTRTSFELGAFQLGAH 66 Query: 65 SIVLNMDKESWALEMEDGVIMNQGKAEHIRDAAGVLGSYFDILALRAFPSLTNKDEDSED 124 ++VL K++W +E G +M+ EHI + A VLG Y D++A+RAFP + D ED Sbjct: 67 AVVLQPGKDAWPIEFNLGTVMDGDTEEHIAEVAKVLGRYCDMIAVRAFPKFVDWSVDRED 126 Query: 125 FILHQFAKHSGLPLISLESAIRHPLQSLADMVTIQEH---KQKEKPKVVLTWAPHIKAIP 181 +L FAK+S +P+I++E+ I HP Q LA + +QEH + K VLTW H K + Sbjct: 127 TVLKSFAKYSPVPVINMET-ITHPCQELAHAMALQEHFGTQDLRGKKYVLTWTYHPKPLN 185 Query: 182 HAVANSFAEWSIGCGHDVTITHP-EGYELDERFTQGA-----------TIEHDQDKALAN 229 AVANS + G DVT+ P Y LDER+ A + HD + A Sbjct: 186 TAVANSALTIATRMGMDVTLLCPTPDYILDERYMGWAEQNVAENGGSLQVSHDIESAYTG 245 Query: 230 ADFVYVKNWSAFNEYGK------ILCTDESWMLNEQKLSQAPNAKVMHCLPVRRNVELSD 283 AD VY K+W A +G I + ++++EQK++ N HCLP+RRNV+ +D Sbjct: 246 ADVVYAKSWGALPFFGNWEPEKPIRDQYKHFIVDEQKMALTNNGVFSHCLPLRRNVKATD 305 Query: 284 EILDGPRSLVQHQAKNRVFAAQAALSEL 311 ++D P+ + ++A+NR+ +A ++ L Sbjct: 306 AVMDSPQCIAINEAENRLHVQKAIMAAL 333 Lambda K H 0.317 0.132 0.384 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: 288 Number of extensions: 8 Number of successful extensions: 5 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: 313 Length of database: 336 Length adjustment: 28 Effective length of query: 285 Effective length of database: 308 Effective search space: 87780 Effective search space used: 87780 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 (21.7 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