Align N-succinylornithine carbamoyltransferase; EC 2.1.3.11 (characterized, see rationale)
to candidate Synpcc7942_2514 Synpcc7942_2514 ornithine carbamoyltransferase
Query= uniprot:L0G4Z0_ECHVK (313 letters) >FitnessBrowser__SynE:Synpcc7942_2514 Length = 305 Score = 104 bits (260), Expect = 2e-27 Identities = 87/290 (30%), Positives = 136/290 (46%), Gaps = 41/290 (14%) Query: 37 KRIGLLFLNPSLRTRVSTQIAASNLGMESIVLNMDKESWALEMEDGVIMNQGKAEHIRDA 96 K +GL+F S RTRVS A +G + + LN + + G+ E I D Sbjct: 40 KTLGLIFSKSSTRTRVSFSAAIMQMGGQVLDLNPN------------VTQVGRGEPIADT 87 Query: 97 AGVLGSYFDILALRAFPSLTNKDEDSEDFILHQFAKHSGLPLISLESAIRHPLQSLADMV 156 A VL Y D LA+R F L ++A ++ +P+I+ + HP Q LAD+ Sbjct: 88 ARVLSRYLDALAIRTFAQQD----------LEEYAHYADIPVINALTDDYHPCQILADLQ 137 Query: 157 TIQEHKQKEKPKVVLTWAPHIKAIPHAVANSFAEWSIGCGHDVTITHPEGYELDERFTQG 216 TIQE+ + + + LT+ + H++ A+ G +V I P Y+ ER Sbjct: 138 TIQENFGQWQD-LTLTYLGDGNNVAHSLLLGCAQ----VGMNVRIACPPDYQPQERIVAK 192 Query: 217 AT----------IEHDQDKALANADFVYVKNWSAFNEYGKILCTDES---WMLNEQKLSQ 263 A I HD A A +Y W++ + + ++ + LN+ L + Sbjct: 193 AQQIAGDRAKVEILHDPIAASQGAHVLYTDVWASMGQEEEAQARVKAFTPYQLNQALLEK 252 Query: 264 A-PNAKVMHCLPVRRNVELSDEILDGPRSLVQHQAKNRVFAAQAALSELL 312 A P A V+HCLP R E++ E+L+G +S V QA+NR+ A +A L+ LL Sbjct: 253 ADPAAIVLHCLPAHREEEITAEVLEGSQSRVWDQAENRLHAQKAVLALLL 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: 182 Number of extensions: 8 Number of successful extensions: 4 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: 305 Length adjustment: 27 Effective length of query: 286 Effective length of database: 278 Effective search space: 79508 Effective search space used: 79508 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 Aug 03 2021. The underlying query database was built on Aug 03 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