Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate PP_4998 PP_4998 Aspartate carbamoyltransferase
Query= BRENDA::Q51742 (315 letters) >FitnessBrowser__Putida:PP_4998 Length = 334 Score = 106 bits (264), Expect = 9e-28 Identities = 98/318 (30%), Positives = 147/318 (46%), Gaps = 28/318 (8%) Query: 8 RDLLCLQDYTAEEIWTILETAKMF-KIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEV 66 R L L E + IL+TA F ++ + K LL GKT+ +F + STRTR +FE+ Sbjct: 19 RHFLSLDGLPRELLTEILDTADSFLEVGARAVKKVPLLRGKTVCNVFFENSTRTRTTFEL 78 Query: 67 AMAHLGGHALYLNAQDLQLRRGETIADTARVL-SRYVDAIMARVYDHKDVEDLAKYA--T 123 A L + LN +GET+ DT R L + D + R D +A++ Sbjct: 79 AAQRLSADVISLNVSTSSTSKGETLFDTLRNLEAMAADMFVVRHSDSGAAHFIAEHVCPE 138 Query: 124 VPVINGLSD-FSHPCQALADYMTIWEKKGTIKGVKVVYVGD--GNNVAHSLMIAGTKLGA 180 V VING +HP Q + D +TI KG+ + + V VGD + VA S M+A LG Sbjct: 139 VAVINGGDGRHAHPTQGMLDMLTIRRHKGSFENLSVAIVGDILHSRVARSDMLALKALGC 198 Query: 181 DVVVATPEGYEPDEKVI--KWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQE 238 PD +VI K E G ++ D + +KD DV+ + + +E Sbjct: 199 -----------PDIRVIGPKTLIPIGIEQYG-VKVYTDLAEGLKDVDVV---IMLRLQRE 243 Query: 239 AEA----EERRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDQ 294 A + +R F + + AKPD + MH P +RG E+ V D +SV+ +Q Sbjct: 244 RMAGGLLPSEGEFYRLFGLTTARLAGAKPDAIVMHPGPINRGVEIESAVADGKHSVILNQ 303 Query: 295 AENRLHAQKAVLALVMGG 312 + + AVL++ M G Sbjct: 304 VTYGIAVRMAVLSMAMSG 321 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: 219 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: 315 Length of database: 334 Length adjustment: 28 Effective length of query: 287 Effective length of database: 306 Effective search space: 87822 Effective search space used: 87822 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