Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_025763134.1 X939_RS0110055 N-acetylornithine carbamoyltransferase
Query= reanno::HerbieS:HSERO_RS07185 (304 letters) >NCBI__GCF_000566685.1:WP_025763134.1 Length = 316 Score = 123 bits (309), Expect = 5e-33 Identities = 104/328 (31%), Positives = 156/328 (47%), Gaps = 46/328 (14%) Query: 3 IKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEA 62 +KH+L F D T + +I V KR + ++T+ ++F +S RTR+S + Sbjct: 1 MKHFLSFEDVT--DLSQLITSGIVAKRN--PFGDQELGKNKTIGLLFFNSSLRTRISTQK 56 Query: 63 GMHQMGGAAIYLNTRDSQLG------------RGEPVEDAAQVMSRMCDVIMIRTYG--- 107 +G I +N G + E V++AA V+ CD+I IR++ Sbjct: 57 AAQNLGLNVITMNVGQDGWGLEMEEGVVMNGDKAEHVKEAAAVIGSYCDIIGIRSFASLT 116 Query: 108 ------QEII-ERFAKHSRVPVINGLTNEQHPCQVLADVFTYIEHHGSIQGKIV-AWVGD 159 QEI+ ++F K++ VP++N + +HP Q LAD T E + K+V W+ Sbjct: 117 DREKDYQEIVFQQFKKYAGVPIVNLESATRHPLQSLADCITIEEFKLKERPKVVLTWLPH 176 Query: 160 AN-------NMLYSWLQAAEVFGFHVNVSTPKGYDIDPAQVSPGNKNYTFFADPADACQD 212 N W+ A+V + V+ PKGYD+ P V G Y D A + Sbjct: 177 FKPLPQAVANSFCEWMNHADV---ELVVTHPKGYDLSPEFVGKGQVIY----DQNKALEG 229 Query: 213 ADLVTTDVWTSMGFEAENNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEVAAEV 272 AD V W+S FE L + W++ +AKMA + FMHCLP R +VA EV Sbjct: 230 ADFVYGKNWSS--FEPYGQV-LNSDPSWMITEAKMALTD-NGKFMHCLPLRRNMKVADEV 285 Query: 273 IDGPQSVVWEEAENR-LHVQKALLEYLV 299 +DGP+S+V E+A NR Q AL E L+ Sbjct: 286 LDGPRSLVIEQAANREWSAQAALREILI 313 Lambda K H 0.321 0.135 0.409 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: 214 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: 304 Length of database: 316 Length adjustment: 27 Effective length of query: 277 Effective length of database: 289 Effective search space: 80053 Effective search space used: 80053 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 (21.9 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. 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