Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 6936653 Sama_0840 aspartate carbamoyltransferase (RefSeq)
Query= BRENDA::O93656 (317 letters) >FitnessBrowser__SB2B:6936653 Length = 339 Score = 112 bits (280), Expect = 1e-29 Identities = 99/325 (30%), Positives = 155/325 (47%), Gaps = 22/325 (6%) Query: 2 VVSLKGRDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTR 61 + KG +L + + + I TI A+ + + K R+L+G L +F +PSTRTR Sbjct: 1 MTQFKGSHILSVNQFNLDSIHTIFNVAERMAPYALREKRTRVLDGAILGNLFFEPSTRTR 60 Query: 62 VSFEVAMAHLGGH-ALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAK 120 VSF A LGG A + L +GE++ DTARVLS Y D I R D V + A+ Sbjct: 61 VSFGCAFNLLGGRVAETVGMASSSLSKGESLYDTARVLSTYSDVIAMRHPDAYSVREFAE 120 Query: 121 YASVPVIN-GLSDFSHPCQALADYMTIWEKKG----TIKGVKVVYVGD--GNNVAHSL-- 171 + VPVIN G HP QAL D TI ++ +I G+ + VGD HSL Sbjct: 121 GSRVPVINGGDGPNEHPTQALLDLFTIQKELSHAGMSIDGMHIAMVGDLKFGRTVHSLSR 180 Query: 172 MIAGTKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKD-ADVIYTD 230 ++ K + +++ E PD + E+ G + D ++ D AD++Y Sbjct: 181 LLCLYKNVSFTLISPKELAMPDYVIAD------IENAGHKVTITDQLEGNLDKADILYL- 233 Query: 231 VWASMGQEAEAEERRKIFRPFQVNKDL-VKHAKPDYMFMHCLPAH---RGEEVTDDVIDS 286 + +E K F++N+ + +H K + + MH LP + E+ +D+ Sbjct: 234 TRIQEERFPSQDEANKYRGKFRLNRSIYTQHCKSNTVIMHPLPRDSRAQANELDNDLNSH 293 Query: 287 PNSVVWDEAENRLHAQKAVLALLLG 311 PN ++ +A+N L + A+ AL LG Sbjct: 294 PNLAIFRQADNGLLIRMALFALTLG 318 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: 227 Number of extensions: 15 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: 339 Length adjustment: 28 Effective length of query: 289 Effective length of database: 311 Effective search space: 89879 Effective search space used: 89879 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