Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_010961323.1 MCA_RS10185 ornithine carbamoyltransferase
Query= SwissProt::P11724 (305 letters) >NCBI__GCF_000008325.1:WP_010961323.1 Length = 298 Score = 388 bits (997), Expect = e-113 Identities = 197/299 (65%), Positives = 227/299 (75%), Gaps = 3/299 (1%) Query: 1 MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSF 60 M RHF++ D S E LI R DL+ R YEPLK++VLGMVFEK+STRTR+SF Sbjct: 1 MKPRHFVTLRDLSSAEFRALIARAI---DLKARKEPYEPLKNKVLGMVFEKSSTRTRVSF 57 Query: 61 EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKV 120 E GM Q GG +IFLSPRDTQLGRGEPI DSARV+SRM+D +M+RT AH T+ FA +S+V Sbjct: 58 EVGMAQFGGSSIFLSPRDTQLGRGEPIEDSARVLSRMVDCIMLRTHAHRTVEIFAEYSRV 117 Query: 121 PVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRV 180 PVINGL+D HPCQLLADMQT+ EHRG I GKTVAWIGDGNNMC +Y+ AA DF+LR+ Sbjct: 118 PVINGLTDRFHPCQLLADMQTYFEHRGDIAGKTVAWIGDGNNMCQTYVHAAGLLDFRLRI 177 Query: 181 ACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240 ACP GYEP+AE V AG + V D R AV GA LV TDVWASMGQE E R FR Y Sbjct: 178 ACPPGYEPEAELVEAAGKCVEVGHDVRTAVNGADLVVTDVWASMGQESEQTERTGAFRDY 237 Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLI 299 QVNAAL+ A D LFMHCLPAHRGEE+S E+L+ P+SV WD+AENRLHAQKALLE L+ Sbjct: 238 QVNAALMALAHADALFMHCLPAHRGEEVSAEVLEGPQSVVWDEAENRLHAQKALLEFLL 296 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: 331 Number of extensions: 9 Number of successful extensions: 2 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: 298 Length adjustment: 27 Effective length of query: 278 Effective length of database: 271 Effective search space: 75338 Effective search space used: 75338 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_010961323.1 MCA_RS10185 (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.21725.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-121 390.1 0.0 3.7e-121 389.9 0.0 1.0 1 lcl|NCBI__GCF_000008325.1:WP_010961323.1 MCA_RS10185 ornithine carbamoylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000008325.1:WP_010961323.1 MCA_RS10185 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 389.9 0.0 3.7e-121 3.7e-121 1 303 [. 4 296 .. 4 297 .. 0.98 Alignments for each domain: == domain 1 score: 389.9 bits; conditional E-value: 3.7e-121 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 rh+++l dls++e++ l+ +a +lk++k+ + lk+k l+++Fek+stRtRvsfev+++++G+ ++ lcl|NCBI__GCF_000008325.1:WP_010961323.1 4 RHFVTLRDLSSAEFRALIARAIDLKARKEP---YEPLKNKVLGMVFEKSSTRTRVSFEVGMAQFGGSSI 69 8************************99887...789********************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l++ ++qlgr+e+i+D arvlsr+vd+i++R+++h++ve +a+y+ vPvingLtd +hPcq+laD++t lcl|NCBI__GCF_000008325.1:WP_010961323.1 70 FLSPRDTQLGRGEPIEDSARVLSRMVDCIMLRTHAHRTVEIFAEYSRVPVINGLTDRFHPCQLLADMQT 138 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 e+ g++ + +++++GD+nn++++ + aa +l + +++a+P+g+epeae+v+ a g +e+ lcl|NCBI__GCF_000008325.1:WP_010961323.1 139 YFEHRGDIAGKTVAWIGDGNNMCQTYVHAAGLLDFRLRIACPPGYEPEAELVEAA-------GKCVEVG 200 ****************************************************999.......558999* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +d+ av++ad+++tDvw+smG+e+++ er ++++yqvn l++la+ ++ f+hCLPa+rGeev+ ev lcl|NCBI__GCF_000008325.1:WP_010961323.1 201 HDVRTAVNGADLVVTDVWASMGQESEQTERTGAFRDYQVNAALMALAHADALFMHCLPAHRGEEVSAEV 269 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 leg++s+v+deaenRlhaqka+l++ll lcl|NCBI__GCF_000008325.1:WP_010961323.1 270 LEGPQSVVWDEAENRLHAQKALLEFLL 296 ************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (298 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.93 // [ok]
This GapMind analysis is from Sep 24 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