Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_012707659.1 NGR_RS16730 aspartate carbamoyltransferase catalytic subunit
Query= curated2:O27495 (301 letters) >NCBI__GCF_000018545.1:WP_012707659.1 Length = 313 Score = 108 bits (270), Expect = 2e-28 Identities = 99/312 (31%), Positives = 154/312 (49%), Gaps = 29/312 (9%) Query: 2 KHLLSVCDM--DNVVDLLDLADD-YKEGKIREK---ILRGKTLAMIFEKSSTRTRVSFEV 55 +HLL + + ++ LLD AD+ K + REK LRG T +F ++STRT+ SFE+ Sbjct: 7 RHLLGIKGLTEQDITLLLDRADEAVKISRQREKKTSSLRGLTQINLFFEASTRTQSSFEL 66 Query: 56 GAFQMGAQPLYLSASDLQLGRGEPIADTARTLSR-YVDGIMIRAISHSDVVELAGEASVP 114 ++GA + +S + + +GE + DTA TL+ + D +++R S LA + S Sbjct: 67 AGKRLGADVMNMSVGNSSVKKGETLIDTAMTLNAMHPDVLVVRHSSAGAAALLAQKVSCS 126 Query: 115 VIN-GLTDLEHPCQALADMQTIREKLGGFDGRLVFV-GD--GNNVCHSLLLITATLGMDM 170 V+N G EHP QAL D TIR G +V + GD + V S +L+ +G + Sbjct: 127 VVNAGDGQHEHPTQALLDALTIRRAKGKLSRIIVAICGDVLHSRVARSNILLLNQMGARV 186 Query: 171 DVACPPGYEPDPGIREMAGKIADETGSRIRVIHDPSEAVRGADVVYTDVWVSMGYEDEAE 230 V P P GI +M + V +E ++ ADVV + + + E A Sbjct: 187 RVVAPATLLP-AGIEQMGAE----------VYRSMAEGLKDADVV---MMLRLQRERMAG 232 Query: 231 DRL----EVFRPYQVNMELMELAAPEAIFMHCLPAVRGQETTAEVIDGPHSVVWDQAENR 286 + E F Y ++ E ++ A +A+ MH P RG E +EV DGP SV+ Q E Sbjct: 233 SFVPSVREYFHYYGLDAETLKAAKDDALVMHPGPMNRGVEIASEVADGPQSVIEQQVEMG 292 Query: 287 LHAQKAIMHWLM 298 + + A+M L+ Sbjct: 293 VAVRMAVMETLL 304 Lambda K H 0.320 0.137 0.405 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: 217 Number of extensions: 9 Number of successful extensions: 3 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: 301 Length of database: 313 Length adjustment: 27 Effective length of query: 274 Effective length of database: 286 Effective search space: 78364 Effective search space used: 78364 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 Sep 17 2021.
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