Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate WP_057508242.1 ABB28_RS08620 aspartate carbamoyltransferase catalytic subunit
Query= curated2:Q6AR58 (303 letters) >NCBI__GCF_001431535.1:WP_057508242.1 Length = 316 Score = 101 bits (251), Expect = 3e-26 Identities = 96/318 (30%), Positives = 148/318 (46%), Gaps = 33/318 (10%) Query: 4 HLSSLGDFTGEEIASLIARAIELKEERSRGIRHQQ--LAGKSVALIFEKPSTRTRVSFES 61 HL +L E + L+ RA ++++ + +++ LAG +V +F +PSTRTR SF+ Sbjct: 14 HLLTLQGLPRETLLQLLDRAGQIRDAAVGRVGNKRAVLAGSAVCTLFFEPSTRTRSSFQL 73 Query: 62 AMYGLGGQVLFLSGRDTQLSRSEPLKDMARVMSRY-VDGIVVRTFGQEVVNELAQYAT-- 118 A LG VL + + E D R + V G VVR V LA A Sbjct: 74 AAQRLGADVLNFDASTSSTRKGETATDTLRNLEAMGVRGFVVRHPDDGAVAALAAAAGEG 133 Query: 119 VPVINALTDLH-HPCQILSDIMTVIEKKGA-IQDLKIVWVGD--GNNMANSWIQAAAKLG 174 +INA HP Q L D++T+ + KG+ +K+V VGD + +A + + A LG Sbjct: 134 TALINAGDGRSSHPTQGLLDMLTLRQAKGSDFSKMKVVIVGDVKHSRVARTDLHALRTLG 193 Query: 175 FELILAC-PEGYDPDAEILAAA--------QAEGAKPITLLRDPQTAVLGADVINVDVFA 225 I C P+ PD + L EGA + +LR L + + + Sbjct: 194 VGEIRVCGPQSLLPDDDTLKGCVVGQDFDEMLEGADALMMLR------LQRERMEEGLVP 247 Query: 226 SMGQESEQDERLKIFASYQVNAEMMAKAADDAIVLHCLPAHRGEEITEDVLEGPQCVAFD 285 S+ Q +Q Y ++A +A+A DA VLH P +RG E+T++V +GPQ Sbjct: 248 SLEQYHQQ---------YGLHAARLARAGKDAAVLHPGPINRGVEVTDEVADGPQSWVLR 298 Query: 286 EAENKMHMHKAILERFLG 303 + N + + A+LE LG Sbjct: 299 QVANGVAVRMAVLETLLG 316 Lambda K H 0.319 0.134 0.381 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: 210 Number of extensions: 13 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: 303 Length of database: 316 Length adjustment: 27 Effective length of query: 276 Effective length of database: 289 Effective search space: 79764 Effective search space used: 79764 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 (21.7 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