Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate 8499267 DvMF_0046 ornithine carbamoyltransferase (RefSeq)
Query= SwissProt::P11724 (305 letters) >FitnessBrowser__Miya:8499267 Length = 300 Score = 295 bits (754), Expect = 1e-84 Identities = 147/296 (49%), Positives = 204/296 (68%), Gaps = 6/296 (2%) Query: 4 RHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSFEAG 63 RHF D E L++R E+KD +RG + E K+ +L +FEKASTRTR+SFE Sbjct: 3 RHFTRIRDLGYEGAWKLLQRAKEMKDTAHRGKIMEG-KTAIL--IFEKASTRTRVSFEMA 59 Query: 64 MIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKVPVI 123 + LGG IF++P ++QLGR EP+ D+ARV+SR D +++RTF + +TE A + +PVI Sbjct: 60 VRHLGGSTIFMTPAESQLGRSEPLRDTARVLSRYADCMVVRTFGQSKITELAEYGSIPVI 119 Query: 124 NGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRVACP 183 N L+D+ HPCQ++ D+ T +E + VAW+GDGNNM NS+IEAA+ F F+L +A P Sbjct: 120 NALTDEGHPCQVMGDVLTMYERTPDLSTVRVAWVGDGNNMANSWIEAAVYFPFELFMAFP 179 Query: 184 EGYEPKAEFVAL---AGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240 EGYEP + + AG ++ + DPR AV GAH V+TDVWASMGQE+E R A F+ Y Sbjct: 180 EGYEPDRDLLGYALNAGAKIFLTHDPRMAVEGAHYVNTDVWASMGQEEEQKKREAAFKGY 239 Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLE 296 ++ ++ AA D FMHCLPAHRGEE+++E+++ P S+ +DQAENRLH QKA+LE Sbjct: 240 CIDTEMMALAAPDAKFMHCLPAHRGEEVTDEVMESPASIIFDQAENRLHIQKAILE 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: 258 Number of extensions: 13 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 8499267 DvMF_0046 (ornithine carbamoyltransferase (RefSeq))
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.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.9685.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.9e-117 376.4 0.0 5.5e-117 376.2 0.0 1.0 1 lcl|FitnessBrowser__Miya:8499267 DvMF_0046 ornithine carbamoyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8499267 DvMF_0046 ornithine carbamoyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.2 0.0 5.5e-117 5.5e-117 1 303 [. 3 298 .. 3 299 .. 0.98 Alignments for each domain: == domain 1 score: 376.2 bits; conditional E-value: 5.5e-117 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 rh+ + dl e ++ll++ak++k + ++ k+++gkt liFek+stRtRvsfe+a+ +lG+ ++++ + e+q lcl|FitnessBrowser__Miya:8499267 3 RHFTRIRDLGYEGAWKLLQRAKEMKDTAHR---GKIMEGKTAILIFEKASTRTRVSFEMAVRHLGGSTIFMTPAESQ 76 7999**********************9999...5899**************************************** PP TIGR00658 78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyv 154 lgr e+++Dtarvlsry d++vvR++ +++++ela+y s+Pvin+Ltd+ hPcq++ D+lt++e++ +l+ v++++v lcl|FitnessBrowser__Miya:8499267 77 LGRSEPLRDTARVLSRYADCMVVRTFGQSKITELAEYGSIPVINALTDEGHPCQVMGDVLTMYERTPDLSTVRVAWV 153 ***************************************************************************** PP TIGR00658 155 GDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGee 231 GD+nn+ans + aa+ + +++ +a Peg+ep+ +++ a + g+k+ lt+dp av++a+ + tDvw+smG+e lcl|FitnessBrowser__Miya:8499267 154 GDGNNMANSWIEAAVYFPFELFMAFPEGYEPDRDLLGYAL----NAGAKIFLTHDPRMAVEGAHYVNTDVWASMGQE 226 ************************************9985....59******************************* PP TIGR00658 232 ekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 e++++r +++k+y +++e+++la p++kf+hCLPa+rGeevtdev+e++asi+fd+aenRlh qka+l++ + lcl|FitnessBrowser__Miya:8499267 227 EEQKKREAAFKGYCIDTEMMALAAPDAKFMHCLPAHRGEEVTDEVMESPASIIFDQAENRLHIQKAILEWAF 298 ********************************************************************9876 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.74 // [ok]
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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