Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (uncharacterized)
to candidate HSERO_RS02330 HSERO_RS02330 aspartate carbamoyltransferase
Query= curated2:Q97ZM1 (307 letters) >FitnessBrowser__HerbieS:HSERO_RS02330 Length = 319 Score = 69.3 bits (168), Expect = 1e-16 Identities = 88/288 (30%), Positives = 131/288 (45%), Gaps = 36/288 (12%) Query: 36 KVPNSLSGKRVALLFEKPSTRTRVSTELAVSLLGGIPIVLNKQDLQWSRGELIEDTGRVL 95 KVP + GK V LF + STRTR + E+A L I LN Q S+GE + DT L Sbjct: 46 KVP-LMRGKSVFNLFFENSTRTRTTFEIASKRLSADVINLNIQASSTSKGESLLDTIDNL 104 Query: 96 GRVVNGI--------GARVLNHLTLVKLKESSGVPVFNLLSDL-SHPLQALADLMTIR-- 144 + + GA L L+ K+S V V N +HP Q L D+ TIR Sbjct: 105 AAMHADMFVVRHAQSGAPFLIAKHLIDTKQSH-VHVVNAGDGRHAHPTQGLLDMYTIRHY 163 Query: 145 -ERFGNNLVKIAFVGDG-SDNVLLSLMAIVAKLGL-ELHVATPKELKPRDDLYKIISEIA 201 + F N +++A VGD V S + + LG+ E+ P+ L P Sbjct: 164 KKDFTN--LRVAIVGDILHSRVARSDIHALTTLGVPEVRAIGPRTLLPSG---------L 212 Query: 202 EDTGSVIEFHEDPYEAVRGVHVVYTDVWVSMGQENIA----EQKKRMLQNYRVTADLMKY 257 E G V FH + E ++ V V+ + + + E ++ + ++Y +T + + Sbjct: 213 EQMG-VRVFH-NMEEGLKDVDVI---IMLRLQNERMSGALLPSAQEFFKSYGLTPERLAL 267 Query: 258 AVKDAIFMHCLPANRGEEVDPEVIDGSKSAVWDQAENRLYTTMAVFSL 305 A DAI MH P NRG E+D V DG+++ + Q + MAV S+ Sbjct: 268 AKPDAIVMHPGPMNRGVEIDSAVADGAQAVILPQVTFGIAVRMAVMSI 315 Lambda K H 0.320 0.137 0.389 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: 205 Number of extensions: 10 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: 307 Length of database: 319 Length adjustment: 27 Effective length of query: 280 Effective length of database: 292 Effective search space: 81760 Effective search space used: 81760 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 Sep 17 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