Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_051378098.1 H566_RS23155 aspartate carbamoyltransferase catalytic subunit
Query= curated2:A0LUC1 (312 letters) >NCBI__GCF_000482785.1:WP_051378098.1 Length = 315 Score = 85.1 bits (209), Expect = 2e-21 Identities = 94/310 (30%), Positives = 138/310 (44%), Gaps = 22/310 (7%) Query: 2 IRHFLADDDLTPSEQAAVLDEAARLKK--DRYAAR-PLTGPRSVAVVFEKPSTRTRVSFE 58 ++H L + L +LD AA +R + PL +SV +F + STRTR +FE Sbjct: 12 LKHLLTTEGLPQRIIENILDTAASFVSVGERDVKKVPLLRGKSVFNLFFENSTRTRTTFE 71 Query: 59 VAITELGGQPVVLDAVGSQLGRGEPIEDTARVLSRYVAAI-VLRTFGHDRITTLARYAT- 116 +A L + L+ S +GE + DT LS A + V+R +A++ Sbjct: 72 IAAKRLSADVLNLNINASSTSKGESLLDTIANLSAMQADMFVVRHASSGAPYLIAQHVAP 131 Query: 117 -VPVVNALSDAY-HPCQALADLLTIRERKGGLDGVRLAYVGD--GNNVACSLLVAGAMAG 172 V V+NA + HP Q L D+ TIR K +R+A VGD + VA S + A G Sbjct: 132 HVSVINAGDGRHAHPTQGLLDMYTIRHFKKDFTKLRVAVVGDVLHSRVARSDIHALTTLG 191 Query: 173 L-HVTVASPAGYQPPPAVVARAAEIGEQTGGRVEVVDDPRTAARNADVLYT-DVWTSMGQ 230 + V V P P EQ G V V D + DV+ + Q Sbjct: 192 VPEVRVIGPRTLLPNGL---------EQLG--VHVFHDMDEGLKGVDVIMMLRLQNERMQ 240 Query: 231 EEETAARRRAFAGFTVDDDLLALAADDAIVLHCLPAHRGEEITASVLEGPQSAIFDQAEN 290 + + F + + + LALAA DAIV+H P +RG EI ++V +G QS I Q Sbjct: 241 GALLPSAQEYFKNYGLTPERLALAAPDAIVMHPGPMNRGVEIDSTVADGAQSVILSQVTF 300 Query: 291 RLHTAKALLS 300 + A++S Sbjct: 301 GIAVRMAVMS 310 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: 192 Number of extensions: 7 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: 312 Length of database: 315 Length adjustment: 27 Effective length of query: 285 Effective length of database: 288 Effective search space: 82080 Effective search space used: 82080 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