Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_011914098.1 PST_RS15060 ornithine carbamoyltransferase
Query= SwissProt::P11724 (305 letters) >NCBI__GCF_000013785.1:WP_011914098.1 Length = 306 Score = 514 bits (1323), Expect = e-150 Identities = 250/304 (82%), Positives = 278/304 (91%) Query: 1 MSVRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSF 60 MS RHFLS MD +P+EL L+RRG ELKDLR RGVL+EPLK+RVLGM+FEKASTRTRLSF Sbjct: 1 MSARHFLSLMDCTPQELNSLVRRGIELKDLRKRGVLFEPLKNRVLGMIFEKASTRTRLSF 60 Query: 61 EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKV 120 EAGMIQLGGQAIFLSPRDTQLGRGEPI DSA VMSRMLD VMIRTFAH+TLT+FAA+S V Sbjct: 61 EAGMIQLGGQAIFLSPRDTQLGRGEPISDSAIVMSRMLDAVMIRTFAHSTLTDFAANSSV 120 Query: 121 PVINGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRV 180 PVINGLSDDLHPCQL+ADMQT+HEHRGSI GKTVAWIGDGNNMCN+YIEAA++FDF+L+V Sbjct: 121 PVINGLSDDLHPCQLMADMQTYHEHRGSIAGKTVAWIGDGNNMCNTYIEAAIQFDFRLKV 180 Query: 181 ACPEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPY 240 ACPEGYEP AE +A AG+R++V+RDPREA AGA+L+STDVWASMGQEDE AAR+A FRPY Sbjct: 181 ACPEGYEPDAELLARAGERVQVLRDPREAAAGANLISTDVWASMGQEDEVAARLATFRPY 240 Query: 241 QVNAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLIE 300 QVN ALLD AA DVLFMHCLPAHRGEEIS +LLDDPRS AWDQAENRLH QKALLE L+E Sbjct: 241 QVNRALLDCAAADVLFMHCLPAHRGEEISHDLLDDPRSAAWDQAENRLHVQKALLEFLVE 300 Query: 301 HAHY 304 A++ Sbjct: 301 PAYH 304 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: 359 Number of extensions: 8 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: 306 Length adjustment: 27 Effective length of query: 278 Effective length of database: 279 Effective search space: 77562 Effective search space used: 77562 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_011914098.1 PST_RS15060 (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.692290.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-117 377.0 0.0 3.7e-117 376.8 0.0 1.0 1 NCBI__GCF_000013785.1:WP_011914098.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000013785.1:WP_011914098.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 376.8 0.0 3.7e-117 3.7e-117 1 303 [. 4 299 .. 4 300 .. 0.99 Alignments for each domain: == domain 1 score: 376.8 bits; conditional E-value: 3.7e-117 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 rh+lsl+d +++el++l+ ++ +lk +k+g+ + lk++ l++iFek+stRtR+sfe+++++lG+q+++l++ NCBI__GCF_000013785.1:WP_011914098.1 4 RHFLSLMDCTPQELNSLVRRGIELKDLRKRGVLFEPLKNRVLGMIFEKASTRTRLSFEAGMIQLGGQAIFLSP 76 8************************************************************************ PP TIGR00658 74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146 ++qlgr+e+i+D a v+sr++da+++R+++h++++++a ++svPvingL+d hPcq++aD++t +e+ g++ NCBI__GCF_000013785.1:WP_011914098.1 77 RDTQLGRGEPISDSAIVMSRMLDAVMIRTFAHSTLTDFAANSSVPVINGLSDDLHPCQLMADMQTYHEHRGSI 149 ************************************************************************* PP TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219 + +++++GD+nn++n+ + aa ++ + ++va+Peg+ep+ae++ +a g ++++++dp +a+++a++ NCBI__GCF_000013785.1:WP_011914098.1 150 AGKTVAWIGDGNNMCNTYIEAAIQFDFRLKVACPEGYEPDAELLARA-------GERVQVLRDPREAAAGANL 215 ******************************************99988.......77***************** PP TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292 i tDvw+smG+e++ ++rl+ ++pyqvn+ ll++a +v f+hCLPa+rGee++++ l+ ++s +d+aenRl NCBI__GCF_000013785.1:WP_011914098.1 216 ISTDVWASMGQEDEVAARLATFRPYQVNRALLDCAAADVLFMHCLPAHRGEEISHDLLDDPRSAAWDQAENRL 288 ************************************************************************* PP TIGR00658 293 haqkavlkall 303 h+qka+l++l+ NCBI__GCF_000013785.1:WP_011914098.1 289 HVQKALLEFLV 299 *******9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (306 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 15.82 // [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