Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_005455410.1 SACCYDRAFT_RS08520 ornithine carbamoyltransferase
Query= curated2:A0LUC1 (312 letters) >NCBI__GCF_000244975.1:WP_005455410.1 Length = 306 Score = 188 bits (478), Expect = 1e-52 Identities = 113/303 (37%), Positives = 163/303 (53%), Gaps = 3/303 (0%) Query: 2 IRHFLADDDLTPSEQAAVLDEAARLKKDRYAARPLTGPRSVAVVFEKPSTRTRVSFEVAI 61 ++H ++ DDLT ++ A ++D AR R + R V + F STRTR SF Sbjct: 3 VKHLVSIDDLTDTDLADLVDSGARFAAAPDDPRKVLSGRVVGLYFRLTSTRTRTSFWSGA 62 Query: 62 TELGGQPVVLDAVGSQLGRGEPIEDTARVLSRYVAAIVLRTFG-HDRITTLARYATVPVV 120 LG V D Q GE EDT RV S + +V RT G + + + A + + V+ Sbjct: 63 LRLGAGVVNFDPGSLQTATGETTEDTGRVFSSMLDVLVARTGGAPEEMRSWASWNRMSVI 122 Query: 121 NALSDAYHPCQALADLLTIRERKGGLDGVRLAYVGDGNNVACSLLVA-GAMAGLHVTVAS 179 NA+S HP QAL DL+T+R G L G+R+ Y+G+GNN A ++ +A + GL + + + Sbjct: 123 NAMSGPEHPTQALTDLITLRAHFGDLRGLRVVYLGEGNNTAAAVALAFSRIPGLELELRT 182 Query: 180 PAGYQPPPAVVARAAEIGEQTGGRVEVVDDPRTAARNADVLYTDVWTSMGQEEETAARRR 239 P GY P ++ +AA E++G RV V R + D YT W + G + R Sbjct: 183 PPGYGVDPVIMEKAARSAERSGARVREVHHMRDLPGDVDAFYTTRWQTTGTSKPDPDWRA 242 Query: 240 AFAGFTVDDDLLALAADDAIVLHCLPAHRGEEITASVLEGPQSAIFDQAENRLHTAKALL 299 FA F V + L + A+ LH LPAHRGEE+TA VL+GP S FDQA N++ A A+L Sbjct: 243 RFAPFQVTEGLWE-RSPKAVFLHDLPAHRGEEVTAEVLDGPASLAFDQAANKMACAMAVL 301 Query: 300 SFL 302 ++ Sbjct: 302 DWI 304 Lambda K H 0.319 0.134 0.385 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: 229 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: 312 Length of database: 306 Length adjustment: 27 Effective length of query: 285 Effective length of database: 279 Effective search space: 79515 Effective search space used: 79515 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 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