Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Ac3H11_1333 Ornithine carbamoyltransferase (EC 2.1.3.3)
Query= reanno::HerbieS:HSERO_RS07185 (304 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1333 Length = 328 Score = 418 bits (1074), Expect = e-121 Identities = 201/314 (64%), Positives = 247/314 (78%), Gaps = 14/314 (4%) Query: 3 IKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEA 62 +KHYLQF+D DEY Y+ ER+ +IK+KFK Y+ HH L DRTL M+FEK STRTR+SFEA Sbjct: 13 LKHYLQFTDLNADEYAYLFERAALIKKKFKAYDKHHPLVDRTLAMIFEKASTRTRVSFEA 72 Query: 63 GMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPV 122 GM+Q+GG+ ++L T DSQLGR EP+ED+A+V+SRM D++MIRTY Q IERFA +SRVPV Sbjct: 73 GMYQLGGSVVHLTTGDSQLGRAEPIEDSAKVISRMTDLVMIRTYEQAKIERFAANSRVPV 132 Query: 123 INGLTNEQHPCQVLADVFTYIEHHG----------SIQGKIVAWVGDANNMLYSWLQAAE 172 INGLTNE HPCQ+LAD+FT+IEH G ++GK VAWVGD NNM +W+QAA Sbjct: 133 INGLTNEYHPCQILADIFTFIEHRGPKDGTGNLTDCLKGKTVAWVGDGNNMANTWVQAAS 192 Query: 173 VFGFHVNVSTPKGYDIDPAQVSPGN----KNYTFFADPADACQDADLVTTDVWTSMGFEA 228 + GF V+VSTP+GY+ID + + +Y FF++P +AC+ ADLVTTDVWTSMG+EA Sbjct: 193 LLGFKVHVSTPRGYEIDEKLAAGAHGISADSYQFFSNPMEACRGADLVTTDVWTSMGYEA 252 Query: 229 ENNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRL 288 EN AR KAF W VD MA A+ DALFMHCLPAHRGEEV A+VIDGPQSVVW+EAENR+ Sbjct: 253 ENEARKKAFADWCVDTEMMAAAQPDALFMHCLPAHRGEEVEADVIDGPQSVVWDEAENRM 312 Query: 289 HVQKALLEYLVHGR 302 HVQKAL+EYL+ GR Sbjct: 313 HVQKALMEYLLLGR 326 Lambda K H 0.321 0.135 0.409 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: 374 Number of extensions: 14 Number of successful extensions: 3 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: 304 Length of database: 328 Length adjustment: 27 Effective length of query: 277 Effective length of database: 301 Effective search space: 83377 Effective search space used: 83377 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 Ac3H11_1333 (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.carbon/TIGR00658.hmm # target sequence database: /tmp/gapView.14383.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.2e-113 362.7 0.0 8.4e-113 362.5 0.0 1.0 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 Ornithine carbamoyltransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 Ornithine carbamoyltransferase (EC 2.1.3.3) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.5 0.0 8.4e-113 8.4e-113 1 303 [. 14 323 .. 14 324 .. 0.97 Alignments for each domain: == domain 1 score: 362.5 bits; conditional E-value: 8.4e-113 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaay 62 +h+l+++dl+ +e +l e+a+ +kk+ k+ +++ l +tla+iFek+stRtRvsfe+++y lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 14 KHYLQFTDLNADEYAYLFERAALIKKKFKAYDKHHPLVDRTLAMIFEKASTRTRVSFEAGMY 75 799*********************************************************** PP TIGR00658 63 elGaqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLt 124 +lG+ v++l + ++qlgr e+i+D a+v+sr+ d +++R+y++ ++e +a ++ vPvingLt lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 76 QLGGSVVHLTTGDSQLGRAEPIEDSAKVISRMTDLVMIRTYEQAKIERFAANSRVPVINGLT 137 ************************************************************** PP TIGR00658 125 dlehPcqilaDlltikeklgklkev..........klvyvGDannvanslllaaaklGldvv 176 ++ hPcqilaD++t +e+ g ++ ++++vGD+nn+an+ + aa +lG++v+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 138 NEYHPCQILADIFTFIEHRGPKDGTgnltdclkgkTVAWVGDGNNMANTWVQAASLLGFKVH 199 ******************99777767778889998*************************** PP TIGR00658 177 vatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeerl 238 v+tP+g+e ++++ a+ i+++ + ++ ++p +a ++ad++ tDvw+smG e+++e+r lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 200 VSTPRGYEIDEKLAAGAHGISAD---SYQFFSNPMEACRGADLVTTDVWTSMGYEAENEARK 258 *****************998765...6899******************************** PP TIGR00658 239 kllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlk 300 k++ ++ v++e+++ a+p++ f+hCLPa+rGeev +v++g++s+v+deaenR+h+qka+++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 259 KAFADWCVDTEMMAAAQPDALFMHCLPAHRGEEVEADVIDGPQSVVWDEAENRMHVQKALME 320 *************************************************************9 PP TIGR00658 301 all 303 +ll lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_1333 321 YLL 323 987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (328 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: 9.16 // [ok]
This GapMind analysis is from Sep 17 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