Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate 206531 DVU1096 ornithine carbamoyltransferase
Query= SwissProt::P11724 (305 letters) >MicrobesOnline__882:206531 Length = 300 Score = 297 bits (760), Expect = 2e-85 Identities = 145/296 (48%), Positives = 202/296 (68%), Gaps = 6/296 (2%) Query: 4 RHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSFEAG 63 +HF D E ++ R E+KD RG L+ +V ++FEKASTRTR+SFE Sbjct: 3 KHFTRIRDLGFEGAWKVLERAKEMKDTGYRG---RTLEGKVATLIFEKASTRTRISFEVA 59 Query: 64 MIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKVPVI 123 + LGG IF++P ++QLGR EP+ D+ARV+SR D +++RTF A + E A+ +PV+ Sbjct: 60 VRHLGGTTIFMTPAESQLGRSEPLRDTARVISRYTDCMIVRTFGQAKIDELASFGSIPVV 119 Query: 124 NGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRVACP 183 N L+D+ HPCQ+++D+ T +E + VAWIGDGNNM NS+IEAA+ F F+L +A P Sbjct: 120 NALTDEGHPCQVMSDVLTMYERTPDLSQVRVAWIGDGNNMANSWIEAAMYFPFELFMAFP 179 Query: 184 EGYEPKAEFVAL---AGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240 EGYEP + + L AG ++ + RDP A+ GAH V+TDVWASMGQE+E R A F+ + Sbjct: 180 EGYEPDRQLLGLALEAGAKIFLTRDPHMAIDGAHYVNTDVWASMGQEEEQKRREAAFKGF 239 Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLE 296 ++ AL+ A D FMHCLPAHRGEE+++E+++ P S+ WDQAENRLH QKA+LE Sbjct: 240 CIDGALMGRAHPDAKFMHCLPAHRGEEVTDEVMESPASIVWDQAENRLHMQKAILE 295 Lambda K H 0.322 0.136 0.404 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: 259 Number of extensions: 9 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: 305 Length of database: 300 Length adjustment: 27 Effective length of query: 278 Effective length of database: 273 Effective search space: 75894 Effective search space used: 75894 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate 206531 DVU1096 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR00658.hmm # target sequence database: /tmp/gapView.2304.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00658 [M=304] Accession: TIGR00658 Description: orni_carb_tr: ornithine carbamoyltransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.5e-113 362.7 0.0 8.5e-113 362.5 0.0 1.0 1 lcl|MicrobesOnline__882:206531 DVU1096 ornithine carbamoyltrans Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:206531 DVU1096 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.5 0.0 8.5e-113 8.5e-113 1 303 [. 3 298 .. 3 299 .. 0.98 Alignments for each domain: == domain 1 score: 362.5 bits; conditional E-value: 8.5e-113 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelqlg 79 +h+ + dl e +++le+ak++k + ++ ++l+gk +liFek+stRtR+sfeva+ +lG+ ++++ + e+qlg lcl|MicrobesOnline__882:206531 3 KHFTRIRDLGFEGAWKVLERAKEMKDTGYR---GRTLEGKVATLIFEKASTRTRISFEVAVRHLGGTTIFMTPAESQLG 78 79999********************99999...589******************************************* PP TIGR00658 80 rkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyvGDan 158 r e+++Dtarv+sry d+++vR++ + ++ ela++ s+Pv+n+Ltd+ hPcq+++D+lt++e++ +l++v+++++GD+n lcl|MicrobesOnline__882:206531 79 RSEPLRDTARVISRYTDCMIVRTFGQAKIDELASFGSIPVVNALTDEGHPCQVMSDVLTMYERTPDLSQVRVAWIGDGN 157 ******************************************************************************* PP TIGR00658 159 nvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeer 237 n+ans + aa+ + +++ +a Peg+ep+ +++ a e g+k+ lt+dp+ a+ +a+ + tDvw+smG+ee+++ r lcl|MicrobesOnline__882:206531 158 NMANSWIEAAMYFPFELFMAFPEGYEPDRQLLGLA----LEAGAKIFLTRDPHMAIDGAHYVNTDVWASMGQEEEQKRR 232 *******************************9887....569************************************* PP TIGR00658 238 lkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 +++k++ ++ l+ a+p++kf+hCLPa+rGeevtdev+e++asiv+d+aenRlh qka+l++++ lcl|MicrobesOnline__882:206531 233 EAAFKGFCIDGALMGRAHPDAKFMHCLPAHRGEEVTDEVMESPASIVWDQAENRLHMQKAILEWVF 298 **************************************************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (300 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 9.45 // [ok]
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