Align Ornithine carbamoyltransferase, anabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_024850654.1 N745_RS0102980 ornithine carbamoyltransferase
Query= SwissProt::P11724 (305 letters) >NCBI__GCF_000526715.1:WP_024850654.1 Length = 300 Score = 382 bits (982), Expect = e-111 Identities = 182/297 (61%), Positives = 227/297 (76%) Query: 3 VRHFLSFMDYSPEELIGLIRRGSELKDLRNRGVLYEPLKSRVLGMVFEKASTRTRLSFEA 62 +RHFL+ D++P+EL L+ R +ELK ++ G +YEPLK++ L M+FEK+STRTRLSFE Sbjct: 1 MRHFLTLKDFTPDELHKLLIRATELKAMQKAGEIYEPLKNQTLAMIFEKSSTRTRLSFEI 60 Query: 63 GMIQLGGQAIFLSPRDTQLGRGEPIGDSARVMSRMLDGVMIRTFAHATLTEFAAHSKVPV 122 GM QLGG A+F+SP TQLGRGEPI DSA+V+S M DG+MIRTF H + FA +S VPV Sbjct: 61 GMTQLGGHALFMSPDATQLGRGEPIEDSAKVISSMADGIMIRTFGHDIVETFAQYSSVPV 120 Query: 123 INGLSDDLHPCQLLADMQTFHEHRGSIQGKTVAWIGDGNNMCNSYIEAALKFDFQLRVAC 182 IN L+DD HPCQLLADMQT++EHRGSIQGKTV W+GDGNNMC+SYI AA ++ F+LR+A Sbjct: 121 INALTDDFHPCQLLADMQTYYEHRGSIQGKTVLWVGDGNNMCHSYINAAAQYGFKLRIAA 180 Query: 183 PEGYEPKAEFVALAGDRLRVVRDPREAVAGAHLVSTDVWASMGQEDEAAARIALFRPYQV 242 PEGY+P ++ V D + V RDP EA +V TDVWASMGQE+E R F+ +QV Sbjct: 181 PEGYDPNSDLVKAHADIVEVFRDPMEAAENVDVVVTDVWASMGQEEEQKKREKAFKSFQV 240 Query: 243 NAALLDGAADDVLFMHCLPAHRGEEISEELLDDPRSVAWDQAENRLHAQKALLELLI 299 N L+ A +D LFMHCLPAHRGEE+ ++D P SV WD+AENRLHAQKALLE L+ Sbjct: 241 NQDLMQRADNDALFMHCLPAHRGEEVCTSVIDAPDSVVWDEAENRLHAQKALLEFLM 297 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: 301 Number of extensions: 6 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_024850654.1 N745_RS0102980 (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.458018.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-125 403.8 0.0 2.6e-125 403.6 0.0 1.0 1 NCBI__GCF_000526715.1:WP_024850654.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000526715.1:WP_024850654.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.6 0.0 2.6e-125 2.6e-125 1 303 [. 2 297 .. 2 298 .. 0.99 Alignments for each domain: == domain 1 score: 403.6 bits; conditional E-value: 2.6e-125 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 rh+l+l+d++++el++ll +a++lk+ +k+g+ + lk++tla+iFek+stRtR+sfe+++++lG+++l++++ NCBI__GCF_000526715.1:WP_024850654.1 2 RHFLTLKDFTPDELHKLLIRATELKAMQKAGEIYEPLKNQTLAMIFEKSSTRTRLSFEIGMTQLGGHALFMSP 74 8************************************************************************ PP TIGR00658 74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146 + +qlgr+e+i+D a+v+s++ d+i++R++ h++ve++a+y+svPvin+Ltd +hPcq+laD++t +e+ g++ NCBI__GCF_000526715.1:WP_024850654.1 75 DATQLGRGEPIEDSAKVISSMADGIMIRTFGHDIVETFAQYSSVPVINALTDDFHPCQLLADMQTYYEHRGSI 147 ************************************************************************* PP TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219 ++ ++ +vGD+nn+++s + aaa+ G+++++a+Peg++p++++vk + +e+ +dp +a++++dv NCBI__GCF_000526715.1:WP_024850654.1 148 QGKTVLWVGDGNNMCHSYINAAAQYGFKLRIAAPEGYDPNSDLVKAHAD-------IVEVFRDPMEAAENVDV 213 *******************************************987755.......589************** PP TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292 ++tDvw+smG+ee++++r k++k +qvn++l++ a++++ f+hCLPa+rGeev v++ + s+v+deaenRl NCBI__GCF_000526715.1:WP_024850654.1 214 VVTDVWASMGQEEEQKKREKAFKSFQVNQDLMQRADNDALFMHCLPAHRGEEVCTSVIDAPDSVVWDEAENRL 286 ************************************************************************* PP TIGR00658 293 haqkavlkall 303 haqka+l++l+ NCBI__GCF_000526715.1:WP_024850654.1 287 HAQKALLEFLM 297 ********987 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: 15.54 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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