Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_018232268.1 THITHI_RS0106510 ornithine carbamoyltransferase
Query= SwissProt::P11724 (305 letters) >NCBI__GCF_000378965.1:WP_018232268.1 Length = 300 Score = 402 bits (1034), Expect = e-117 Identities = 200/299 (66%), Positives = 233/299 (77%) Query: 1 MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSF 60 M+VRHFLS +D S EEL GLI R ELK L G +E L+ +VLGM+FEK+STRTR+SF Sbjct: 1 MTVRHFLSLLDLSTEELRGLIARAIELKRLHRSGTEHESLRGKVLGMIFEKSSTRTRVSF 60 Query: 61 EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKV 120 E GMIQLGGQA+FLSPRDTQLGRGEPI D+ARV+SRM+DGVMIRT+ H + FAAHS+V Sbjct: 61 EVGMIQLGGQALFLSPRDTQLGRGEPIEDTARVLSRMVDGVMIRTYEHEKIERFAAHSRV 120 Query: 121 PVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRV 180 PVINGL+D HPCQLLAD+QT+ EHRG I G+ V ++GDGNNMCNSYI AA F LR Sbjct: 121 PVINGLTDLEHPCQLLADLQTWFEHRGDITGRVVTYVGDGNNMCNSYINAAQLLGFTLRA 180 Query: 181 ACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240 ACPEGY+P E V AGD + VVRDP EAV A LV TDVWASMGQEDE AR F Y Sbjct: 181 ACPEGYDPDPELVRAAGDAVSVVRDPAEAVRNADLVVTDVWASMGQEDEQTARRQAFTDY 240 Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLI 299 V++AL+ A + LFMHCLPAHR EE+S E+L+ P+SV WD+AENRLHAQKALLE L+ Sbjct: 241 VVDSALMKRANPEALFMHCLPAHREEEVSTEVLEGPQSVVWDEAENRLHAQKALLEFLL 299 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: 317 Number of extensions: 4 Number of successful extensions: 1 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 WP_018232268.1 THITHI_RS0106510 (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.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.1919.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.5e-126 406.4 0.0 3.9e-126 406.3 0.0 1.0 1 lcl|NCBI__GCF_000378965.1:WP_018232268.1 THITHI_RS0106510 ornithine carba Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000378965.1:WP_018232268.1 THITHI_RS0106510 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 406.3 0.0 3.9e-126 3.9e-126 1 303 [. 4 299 .. 4 300 .] 0.99 Alignments for each domain: == domain 1 score: 406.3 bits; conditional E-value: 3.9e-126 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 rh+lslldls+eel+ l+ +a +lk+ +++g+e++ l+gk l++iFek+stRtRvsfev++++lG+q+l lcl|NCBI__GCF_000378965.1:WP_018232268.1 4 RHFLSLLDLSTEELRGLIARAIELKRLHRSGTEHESLRGKVLGMIFEKSSTRTRVSFEVGMIQLGGQAL 72 8******************************************************************** PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l++ ++qlgr+e+i+Dtarvlsr+vd++++R+y+he++e +a ++ vPvingLtdlehPcq+laDl+t lcl|NCBI__GCF_000378965.1:WP_018232268.1 73 FLSPRDTQLGRGEPIEDTARVLSRMVDGVMIRTYEHEKIERFAAHSRVPVINGLTDLEHPCQLLADLQT 141 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 e+ g++ + ++yvGD+nn++ns + aa +lG++++ a+Peg++p++e+v+ a g ++++ lcl|NCBI__GCF_000378965.1:WP_018232268.1 142 WFEHRGDITGRVVTYVGDGNNMCNSYINAAQLLGFTLRAACPEGYDPDPELVRAA-------GDAVSVV 203 ****************************************************998.......779**** PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +dp++av++ad+++tDvw+smG+e+++ +r +++ +y v++ l++ a+pe+ f+hCLPa+r eev+ ev lcl|NCBI__GCF_000378965.1:WP_018232268.1 204 RDPAEAVRNADLVVTDVWASMGQEDEQTARRQAFTDYVVDSALMKRANPEALFMHCLPAHREEEVSTEV 272 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 leg++s+v+deaenRlhaqka+l++ll lcl|NCBI__GCF_000378965.1:WP_018232268.1 273 LEGPQSVVWDEAENRLHAQKALLEFLL 299 ************************998 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: 00:00:00.01 # Mc/sec: 7.14 // [ok]
This GapMind analysis is from Apr 10 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