Align Ornithine carbamoyltransferase 1, anabolic; OTCase 1; Ornithine carbamoyltransferase 1, phaseolotoxin-sensitive; SOCT; EC 2.1.3.3 (characterized)
to candidate WP_086510014.1 BZY95_RS11205 ornithine carbamoyltransferase
Query= SwissProt::Q02047 (306 letters) >NCBI__GCF_002151265.1:WP_086510014.1 Length = 306 Score = 400 bits (1027), Expect = e-116 Identities = 196/300 (65%), Positives = 239/300 (79%), Gaps = 1/300 (0%) Query: 1 MNARHFLSMMDYTPDELLGLIRRGVELKD-LRIRGELFEPLKNRVLGMIFEKSSTRTRLS 59 M RHFL+++D +PDEL LI+R + +K+ LR +G ++ P NR L MIFEKSSTRTR+S Sbjct: 1 MATRHFLTLLDLSPDELHYLIQRAITIKNRLRAQGPVYAPFTNRTLAMIFEKSSTRTRVS 60 Query: 60 FEAGMIQLGGQAIFLSHRDTQLGRGEPIADSAKVMSRMLDAVMIRTYAHSNLTEFAANSR 119 FE M GG A+FLS RDTQLGRGEPI D+A+V++ M+D VMIRT++H+ L +AA S Sbjct: 61 FETAMAHFGGHALFLSPRDTQLGRGEPIEDTARVLAEMVDIVMIRTFSHAGLETYAAASS 120 Query: 120 VPVINGLSDDLHPCQLLADMQTFLEHRGSIKGKTVAWIGDGNNMCNSYIEAAIQFDFQLR 179 VPVIN LSDD HPCQLLAD+ T+ E RGS++G+T WIGDGNNMC+S+I AA QFDFQLR Sbjct: 121 VPVINALSDDYHPCQLLADVMTWTELRGSVRGRTAVWIGDGNNMCHSWINAARQFDFQLR 180 Query: 180 VACPAGYEPNPEFLALAGERVTIVRDPKAAVAGAHLVSTDVWTSMGQEEETARRMALFAP 239 + CP GYEP + LA AG+RVT++RDP AAVAGA LV+TDVW SMGQEEE A+R A FA Sbjct: 181 ICCPEGYEPRQDILAAAGDRVTLLRDPAAAVAGADLVTTDVWASMGQEEEQAKREADFAG 240 Query: 240 FQVTRASLDLAEKDVLFMHCLPAHRGEEISVDLLDDSRSVAWDQAENRLHAQKALLEFLV 299 FQV+ A LDLA+ DVLF+HCLPAHRGEEIS LLDD R+V W +A NRLHAQKAL+EFL+ Sbjct: 241 FQVSEALLDLAKPDVLFLHCLPAHRGEEISETLLDDPRAVVWQEAGNRLHAQKALIEFLL 300 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: 315 Number of extensions: 10 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: 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 WP_086510014.1 BZY95_RS11205 (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.12203.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-115 370.3 0.0 4.1e-115 370.1 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086510014.1 BZY95_RS11205 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086510014.1 BZY95_RS11205 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 370.1 0.0 4.1e-115 4.1e-115 1 303 [. 4 300 .. 4 301 .. 0.98 Alignments for each domain: == domain 1 score: 370.1 bits; conditional E-value: 4.1e-115 TIGR00658 1 rhllslldlseeelkellelakklkkekkk.gkeekklkgktlaliFekrstRtRvsfevaayelGaqv 68 rh+l+lldls++el++l+++a ++k++ ++ g + ++++tla+iFek+stRtRvsfe+a++++G+++ lcl|NCBI__GCF_002151265.1:WP_086510014.1 4 RHFLTLLDLSPDELHYLIQRAITIKNRLRAqGPVYAPFTNRTLAMIFEKSSTRTRVSFETAMAHFGGHA 72 8************************997761556899******************************** PP TIGR00658 69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDll 137 l+l++ ++qlgr+e+i+Dtarvl +vd++++R+++h +e+ a +svPvin+L+d hPcq+laD++ lcl|NCBI__GCF_002151265.1:WP_086510014.1 73 LFLSPRDTQLGRGEPIEDTARVLAEMVDIVMIRTFSHAGLETYAAASSVPVINALSDDYHPCQLLADVM 141 ********************************************************************* PP TIGR00658 138 tikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklel 206 t +e g++ + + v++GD+nn+++s + aa ++ +++++++Peg+ep+++i+ a g +++l lcl|NCBI__GCF_002151265.1:WP_086510014.1 142 TWTELRGSVRGRTAVWIGDGNNMCHSWINAARQFDFQLRICCPEGYEPRQDILAAA-------GDRVTL 203 ***************************************************99887.......88**** PP TIGR00658 207 tedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtde 275 ++dp+ av++ad++ tDvw+smG+ee++++r + + ++qv+e ll+lakp+v flhCLPa+rGee+++ lcl|NCBI__GCF_002151265.1:WP_086510014.1 204 LRDPAAAVAGADLVTTDVWASMGQEEEQAKREADFAGFQVSEALLDLAKPDVLFLHCLPAHRGEEISET 272 ********************************************************************* PP TIGR00658 276 vlegeasivfdeaenRlhaqkavlkall 303 l+ ++ +v++ea nRlhaqka++++ll lcl|NCBI__GCF_002151265.1:WP_086510014.1 273 LLDDPRAVVWQEAGNRLHAQKALIEFLL 300 ************************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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.04 // [ok]
This GapMind analysis is from Apr 10 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