Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate Pf1N1B4_762 Ornithine carbamoyltransferase (EC 2.1.3.3)
Query= SwissProt::Q02047 (306 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 Length = 307 Score = 537 bits (1383), Expect = e-157 Identities = 268/306 (87%), Positives = 284/306 (92%) Query: 1 MNARHFLSMMDYTPDELLGLIRRGVELKDLRIRGELFEPLKNRVLGMIFEKSSTRTRLSF 60 M+ARHFLS+MD TP+EL+ +IRRGVELKDLR RG LFEPLKNRVLGMIFEKSSTRTR+SF Sbjct: 2 MSARHFLSLMDCTPEELVSVIRRGVELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRISF 61 Query: 61 EAGMIQLGGQAIFLSHRDTQLGRGEPIADSAKVMSRMLDAVMIRTYAHSNLTEFAANSRV 120 EAGMIQLGGQAIFLS RDTQLGRGEPI D A VMS MLDAVMIRT+AHS LTEFAANSRV Sbjct: 62 EAGMIQLGGQAIFLSPRDTQLGRGEPIGDCAIVMSSMLDAVMIRTFAHSTLTEFAANSRV 121 Query: 121 PVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLRV 180 PVINGLSDDLHPCQLLADMQTFLEHRGSI+GKTVAWIGDGNNMCNSYIEAAIQFDFQLR+ Sbjct: 122 PVINGLSDDLHPCQLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAAIQFDFQLRI 181 Query: 181 ACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAPF 240 ACP GYEPNPEF+A AG+RVTIVRDP+ AV GAHLVSTDVWTSMGQEEETA+R+ LFAPF Sbjct: 182 ACPEGYEPNPEFVAKAGDRVTIVRDPQEAVRGAHLVSTDVWTSMGQEEETAKRLKLFAPF 241 Query: 241 QVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLVA 300 QV RA LDLA DVLFMHCLPAHRGEEIS+DLLDDSRSVAWDQAENRLHAQKALLEFLV Sbjct: 242 QVNRALLDLAAPDVLFMHCLPAHRGEEISLDLLDDSRSVAWDQAENRLHAQKALLEFLVP 301 Query: 301 PSHQRA 306 PS+ A Sbjct: 302 PSYHHA 307 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: 373 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: 306 Length of database: 307 Length adjustment: 27 Effective length of query: 279 Effective length of database: 280 Effective search space: 78120 Effective search space used: 78120 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 Pf1N1B4_762 (Ornithine carbamoyltransferase (EC 2.1.3.3))
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.12783.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-118 380.6 0.0 3e-118 380.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 Ornithine carbamoyltransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 Ornithine carbamoyltransferase (EC 2.1.3.3) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 380.4 0.0 3e-118 3e-118 1 303 [. 5 300 .. 5 301 .. 0.99 Alignments for each domain: == domain 1 score: 380.4 bits; conditional E-value: 3e-118 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelG 65 rh+lsl+d ++eel++++ ++ +lk +++g+ + lk++ l++iFek+stRtR+sfe+++++lG lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 5 RHFLSLMDCTPEELVSVIRRGVELKDLRNRGVLFEPLKNRVLGMIFEKSSTRTRISFEAGMIQLG 69 8**************************************************************** PP TIGR00658 66 aqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPc 130 +q+++l++ ++qlgr+e+i D a v+s+++da+++R+++h++++e+a ++ vPvingL+d hPc lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 70 GQAIFLSPRDTQLGRGEPIGDCAIVMSSMLDAVMIRTFAHSTLTEFAANSRVPVINGLSDDLHPC 134 ***************************************************************** PP TIGR00658 131 qilaDlltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakk 195 q+laD++t e+ g++++ +++++GD+nn++ns + aa ++ +++++a+Peg+ep++e v ka lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 135 QLLADMQTFLEHRGSIQGKTVAWIGDGNNMCNSYIEAAIQFDFQLRIACPEGYEPNPEFVAKA-- 197 **********************************************************99988.. PP TIGR00658 196 iakenggkleltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkf 260 g ++++++dp++av++a+++ tDvw+smG+ee++++rlkl+ p+qvn+ ll+la p+v f lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 198 -----GDRVTIVRDPQEAVRGAHLVSTDVWTSMGQEEETAKRLKLFAPFQVNRALLDLAAPDVLF 257 .....88********************************************************** PP TIGR00658 261 lhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 +hCLPa+rGee++ + l+ ++s+ +d+aenRlhaqka+l++l+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_762 258 MHCLPAHRGEEISLDLLDDSRSVAWDQAENRLHAQKALLEFLV 300 ***************************************9975 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (307 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: 8.45 // [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