Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 1936874 b2870 hypothetical protein (NCBI)
Query= BRENDA::O93656 (317 letters) >FitnessBrowser__Keio:1936874 Length = 396 Score = 100 bits (248), Expect = 8e-26 Identities = 92/346 (26%), Positives = 152/346 (43%), Gaps = 58/346 (16%) Query: 5 LKGRDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSF 64 L +D L + TP+E+ +L+ A LK + ++ +F+ STRTR S+ Sbjct: 19 LHEKDFLLTWEQTPDELKQVLDVAAALKALRAENISTKVFNSGLGISVFRDNSTRTRFSY 78 Query: 65 EVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMAR---------VYDHK-- 113 A+ LG L+ Q+ GET+ +TA ++S DAI R Y + Sbjct: 79 ASALNLLGLAQQDLDEGKSQIAHGETVRETANMISFCADAIGIRDDMYLGAGNAYMREVG 138 Query: 114 -DVEDLAKYASVP----VINGLSDFSHPCQALADYMTIWEKKGTI---KGVKVVYV---- 161 ++D K +P ++N D HP Q++AD + E G++ KG K+ Sbjct: 139 AALDDGYKQGVLPQRPALVNLQCDIDHPTQSMADLAWLREHFGSLENLKGKKIAMTWAYS 198 Query: 162 ---GDGNNVAHSLMIAGTKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPV 218 G +V ++ T+ G DV +A PEGY+ V++ A+ NA SGGSF + Sbjct: 199 PSYGKPLSVPQGIIGLMTRFGMDVTLAHPEGYDLIPDVVEVAKNNAKASGGSFRQVTSME 258 Query: 219 KAVKDADVIYTDVWASMGQEAEAEERRKIFR----------------------PFQVNKD 256 +A KDAD++Y WA EER ++ R + ++ Sbjct: 259 EAFKDADIVYPKSWAPY---KVMEERTELLRANDHEGLKALEKQCLAQNAQHKDWHCTEE 315 Query: 257 LVKHAKP-DYMFMHCLPAH------RGEEVTDDVIDSPNSVVWDEA 295 +++ + + ++MHCLPA + EVT+ V + + EA Sbjct: 316 MMELTRDGEALYMHCLPADISGVSCKEGEVTEGVFEKYRIATYKEA 361 Lambda K H 0.319 0.134 0.400 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: 288 Number of extensions: 20 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 317 Length of database: 396 Length adjustment: 29 Effective length of query: 288 Effective length of database: 367 Effective search space: 105696 Effective search space used: 105696 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: 49 (23.5 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