Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 7025921 Shewana3_3070 aspartate carbamoyltransferase (RefSeq)
Query= BRENDA::Q51742 (315 letters) >FitnessBrowser__ANA3:7025921 Length = 339 Score = 114 bits (286), Expect = 3e-30 Identities = 100/320 (31%), Positives = 151/320 (47%), Gaps = 22/320 (6%) Query: 7 GRDLLCLQDYTAEEIWTILETAKMFKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEV 66 G +L + + I TI A + K ++LEG L +F +PSTRTRVSF Sbjct: 6 GSHILSVNQLDLDSIQTIFNVAHRMMPYALREKRTKVLEGAILGNLFFEPSTRTRVSFGC 65 Query: 67 AMAHLGGHALYLNAQ-DLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYATVP 125 A LGGH L +GE++ DTARVLS Y D I R D V++ A+ + VP Sbjct: 66 AFNLLGGHVRETTGMASSSLSKGESLYDTARVLSTYSDVIAMRHPDSYSVKEFAEGSRVP 125 Query: 126 VINGLSDFS--HPCQALADYMTIWEKKG----TIKGVKVVYVGD--GNNVAHSL--MIAG 175 VING D S HP QAL D TI ++ G I G+ + VGD HSL ++ Sbjct: 126 VING-GDGSNEHPTQALLDLFTIQKELGHAGRGIDGMHIAMVGDLKFGRTVHSLSRLLCM 184 Query: 176 TKLGADVVVATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASM 235 K + +++ E PD + + +G S ++ + AD++Y Sbjct: 185 YKNISFTLISPTELAMPD-----YVISDIENAGHSIKITDQLEGHLDKADILYL-TRIQE 238 Query: 236 GQEAEAEERRKIFRPFQVNKDL-VKHAKPDYMFMHCLPAH---RGEEVTDDVIDSPNSVV 291 + EE K F++N+ + +H K + + MH LP + E+ +D+ PN + Sbjct: 239 ERFPSQEEANKYRGKFRLNRSIYTQHCKSNTVIMHPLPRDSRAQANELDNDLNSHPNLAI 298 Query: 292 WDQAENRLHAQKAVLALVMG 311 + QA+N L + A+ AL +G Sbjct: 299 FRQADNGLLIRMALFALTLG 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: 230 Number of extensions: 14 Number of successful extensions: 4 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: 339 Length adjustment: 28 Effective length of query: 287 Effective length of database: 311 Effective search space: 89257 Effective search space used: 89257 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 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