Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate PP_1079 PP_1079 Ornithine carbamoyltransferase
Query= SwissProt::Q02047 (306 letters) >FitnessBrowser__Putida:PP_1079 Length = 306 Score = 497 bits (1280), Expect = e-145 Identities = 247/306 (80%), Positives = 271/306 (88%) Query: 1 MNARHFLSMMDYTPDELLGLIRRGVELKDLRIRGELFEPLKNRVLGMIFEKSSTRTRLSF 60 M+ARHFLS++D+T DELLG+IR G+ELKDLR RG LFEPLKNRVLGMIFEKSSTRTR+SF Sbjct: 1 MSARHFLSLLDFTTDELLGVIRHGIELKDLRKRGVLFEPLKNRVLGMIFEKSSTRTRVSF 60 Query: 61 EAGMIQLGGQAIFLSHRDTQLGRGEPIADSAKVMSRMLDAVMIRTYAHSNLTEFAANSRV 120 EAGMIQLGGQAIFLS RDTQLGRGEPI DSA V+S M+D VMIRT+AHS LTEFAA SRV Sbjct: 61 EAGMIQLGGQAIFLSPRDTQLGRGEPIGDSAIVLSSMVDVVMIRTHAHSTLTEFAAKSRV 120 Query: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180 PVINGLSD+ HPCQLLADMQTF+EHRGSI+GKTV WIGDG NMCNSYIEAA QFDFQLR+ Sbjct: 121 PVINGLSDESHPCQLLADMQTFVEHRGSIQGKTVTWIGDGFNMCNSYIEAARQFDFQLRI 180 Query: 181 ACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAPF 240 ACP GYEP+ F+AL G+RV I+RD + AV AHLV TDVWTSMGQEEETARR+A FAP+ Sbjct: 181 ACPEGYEPDQRFMALGGDRVQIIRDAREAVRDAHLVVTDVWTSMGQEEETARRLAHFAPY 240 Query: 241 QVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLVA 300 QVTR LDLA DVLFMHCLPAHRGEEIS DLLDD RSVAWD+AENRLHAQKALLEFLV Sbjct: 241 QVTRELLDLAAPDVLFMHCLPAHRGEEISQDLLDDPRSVAWDEAENRLHAQKALLEFLVE 300 Query: 301 PSHQRA 306 P++ A Sbjct: 301 PAYHHA 306 Lambda K H 0.322 0.135 0.397 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: 354 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: 306 Length of database: 306 Length adjustment: 27 Effective length of query: 279 Effective length of database: 279 Effective search space: 77841 Effective search space used: 77841 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 PP_1079 PP_1079 (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.32724.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-115 371.6 0.0 1.6e-115 371.4 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_1079 PP_1079 Ornithine carbamoyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1079 PP_1079 Ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 371.4 0.0 1.6e-115 1.6e-115 1 303 [. 4 299 .. 4 300 .. 0.98 Alignments for each domain: == domain 1 score: 371.4 bits; conditional E-value: 1.6e-115 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 rh+lslld++++el ++ + +lk +k+g+ + lk++ l++iFek+stRtRvsfe+++++lG+q+++l++ + lcl|FitnessBrowser__Putida:PP_1079 4 RHFLSLLDFTTDELLGVIRHGIELKDLRKRGVLFEPLKNRVLGMIFEKSSTRTRVSFEAGMIQLGGQAIFLSPRD 78 8************************************************************************** PP TIGR00658 76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevk 150 +qlgr+e+i D a vls++vd++++R+++h++++e+a ++ vPvingL+d++hPcq+laD++t e+ g++++ + lcl|FitnessBrowser__Putida:PP_1079 79 TQLGRGEPIGDSAIVLSSMVDVVMIRTHAHSTLTEFAAKSRVPVINGLSDESHPCQLLADMQTFVEHRGSIQGKT 153 *************************************************************************** PP TIGR00658 151 lvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvw 225 ++++GD+ n++ns + aa ++ +++++a+Peg+ep+++ + g ++++++d +av+da++++tDvw lcl|FitnessBrowser__Putida:PP_1079 154 VTWIGDGFNMCNSYIEAARQFDFQLRIACPEGYEPDQRFMAL-------GGDRVQIIRDAREAVRDAHLVVTDVW 221 ************************************887655.......589*********************** PP TIGR00658 226 vsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlk 300 +smG+ee+++ rl+ + pyqv++ell+la p+v f+hCLPa+rGee++++ l+ ++s+ +deaenRlhaqka+l+ lcl|FitnessBrowser__Putida:PP_1079 222 TSMGQEEETARRLAHFAPYQVTRELLDLAAPDVLFMHCLPAHRGEEISQDLLDDPRSVAWDEAENRLHAQKALLE 296 **************************************************************************9 PP TIGR00658 301 all 303 +l+ lcl|FitnessBrowser__Putida:PP_1079 297 FLV 299 987 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.14 // [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