Align N-succinylornithine carbamoyltransferase (EC 2.1.3.11) (characterized)
to candidate WP_011308421.1 MBAR_RS18595 ornithine carbamoyltransferase
Query= reanno::Cola:Echvi_3849 (313 letters) >NCBI__GCF_000195895.1:WP_011308421.1 Length = 302 Score = 118 bits (295), Expect = 2e-31 Identities = 87/290 (30%), Positives = 138/290 (47%), Gaps = 38/290 (13%) Query: 35 RGKRIGLLFLNPSLRTRVSTQIAASNLGMESIVLNMDKESWALEMEDGVIMNQGKAEHIR 94 + K +G++F S RTRVS ++A ++ G S+ LN + G+ E I Sbjct: 40 KNKSLGMIFEKASTRTRVSFEVAMTDFGGHSLYLNSRD------------IQIGRGETIE 87 Query: 95 DAAGVLGSYFDILALRAFPSLTNKDEDSEDFILHQFAKHSGLPLISLESAIRHPLQSLAD 154 D A L Y + R T + + AK+S +P+I+ S HP Q L D Sbjct: 88 DTARTLSGYLHGIMARVMSHET----------VEKLAKYSTIPVINALSDREHPCQILGD 137 Query: 155 MVTIQEHKQKEKPKVVLTWAPHIKAIPHAVANSFAEWSIGCGHDVTITHPEGYELDERFT 214 +TI E+K K + + W + V NS S G + + P+GYE F Sbjct: 138 FMTIMEYKDKFED-LKFAWVGD----GNNVCNSALLGSAIVGMEFAVACPKGYEPKPEFL 192 Query: 215 QGA-------TIEHDQDKALANADFVYVKNWSAFN---EYGKILCTDESWMLNEQKLSQA 264 + A T+ D A+ +AD +Y W + E K L ++ +N + L A Sbjct: 193 EKAKSLGGKFTVTDDPKVAVKDADIIYTDVWVSMGDEAEQEKRLKEFATFQVNTELLGVA 252 Query: 265 -PNAKVMHCLPVRRNVELSDEILDGPRSLVQHQAKNRVFAAQAALSELLK 313 P+ VMHCLP RR +E++DE++DGP S++ +A+NR+ A +A + +L+K Sbjct: 253 KPDVIVMHCLPARRGLEITDEVMDGPNSVIFEEAENRLHAQKALILKLMK 302 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: 207 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: 313 Length of database: 302 Length adjustment: 27 Effective length of query: 286 Effective length of database: 275 Effective search space: 78650 Effective search space used: 78650 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