Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate 3609708 Dshi_3091 aspartate carbamoyltransferase (RefSeq)
Query= curated2:A8LE44 (317 letters) >FitnessBrowser__Dino:3609708 Length = 316 Score = 103 bits (257), Expect = 5e-27 Identities = 98/316 (31%), Positives = 143/316 (45%), Gaps = 25/316 (7%) Query: 1 MTARHFLLDTDLTSSEQAALLDLADQLKATRRDRKPARRPLEGRSVALIFEKPSTRTRLS 60 + ARH L L E LLDLAD+ R L+G + +F + STRT+ S Sbjct: 3 LRARHLLGIEHLAPDEIVTLLDLADRYADLNRRPDKHGDALDGLTQINMFFENSTRTQAS 62 Query: 61 FDVAVAELGGHPIVIDSGSSQLGRGETIEDTAAVL-SRYVDAIVIRTFAQDRVDRMAAAA 119 F++A LG + ++ +S + +GET+ DTA L + + D +V+R V+ +A Sbjct: 63 FEIAGKRLGADVMNMEVRASSIKKGETLIDTAMTLNAMHPDLLVVRHPHSGAVNLLAEKV 122 Query: 120 TVPVINALSD-HTHPCQALADLQTIREIRGRLAGVTLAYLGDGNNVAHS------LLLAG 172 V+NA H HP QAL D TIR +G+L + +A GD +AHS +LL G Sbjct: 123 NCAVLNAGDGRHEHPTQALLDALTIRRAKGKLHRLNVAICGD---IAHSRVARSNILLLG 179 Query: 173 ALAGLRVHVASPPGYEPIEQVVRHANEIGAVTGGEALVTHDALEAAAGADVLYTDVWASM 232 + R+ + P P E E+G V D G DV+ Sbjct: 180 KMEN-RIRLVGPRTLMPAE-----IAELGVE------VYEDMKAGLDGVDVVMMLRLQKE 227 Query: 233 GQDTE-SDSRALVFQPYRLDEKVVEAASPDAIVMHCLPAHREMEISAAVLDG-PRSVVFD 290 D S + Y LD + + A PDAIVMH P +R +EI + D RSV+ + Sbjct: 228 RMDGGFIPSEREYYHRYGLDAEKLAYAKPDAIVMHPGPMNRGVEIDGTLADDINRSVIQE 287 Query: 291 QAENRLHAQKALLSFL 306 Q E + + A + L Sbjct: 288 QVEMGVAVRMAAMDLL 303 Lambda K H 0.318 0.132 0.371 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: 235 Number of extensions: 11 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: 317 Length of database: 316 Length adjustment: 27 Effective length of query: 290 Effective length of database: 289 Effective search space: 83810 Effective search space used: 83810 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