Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate Dsui_3249 Dsui_3249 ornithine carbamoyltransferase
Query= reanno::HerbieS:HSERO_RS07185 (304 letters) >FitnessBrowser__PS:Dsui_3249 Length = 307 Score = 432 bits (1112), Expect = e-126 Identities = 208/302 (68%), Positives = 249/302 (82%), Gaps = 1/302 (0%) Query: 2 AIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFE 61 +IKH+LQF DFT +E++Y+ R+R IK +FKNY+ + L DRTLVM+FEK STRTRLSFE Sbjct: 3 SIKHFLQFKDFTREEFDYLFARTRWIKDQFKNYKQYWPLTDRTLVMIFEKASTRTRLSFE 62 Query: 62 AGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVP 121 AGM Q+GG+AIYLNTRDSQLGRGEPVEDAAQV+SRM D++MIRT+ QEIIERFA +SRVP Sbjct: 63 AGMQQLGGSAIYLNTRDSQLGRGEPVEDAAQVISRMSDIVMIRTFEQEIIERFAANSRVP 122 Query: 122 VINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVS 181 VINGLTNE HPCQ++AD+FTYIEH G IQGK VAW+GD+NN+ +WLQAAEV F+V+VS Sbjct: 123 VINGLTNEYHPCQIMADIFTYIEHRGPIQGKTVAWIGDSNNVCNTWLQAAEVLDFNVHVS 182 Query: 182 TPKGYDIDPAQVS-PGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240 TP GY+++ + G N+ F+DP +A + AD+VTTDVWTSMGFEAEN RLK F W Sbjct: 183 TPPGYEVEAERAGLYGTANFEQFSDPMEAAKGADIVTTDVWTSMGFEAENEERLKDFADW 242 Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300 VD M AK DA+F+HCLPAHRGEEV AEVIDGPQS VW+EAENRLH QKAL+EYL+ Sbjct: 243 QVDGDMMRIAKSDAIFLHCLPAHRGEEVTAEVIDGPQSAVWDEAENRLHTQKALMEYLLL 302 Query: 301 GR 302 GR Sbjct: 303 GR 304 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: 371 Number of extensions: 15 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: 304 Length of database: 307 Length adjustment: 27 Effective length of query: 277 Effective length of database: 280 Effective search space: 77560 Effective search space used: 77560 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 Dsui_3249 Dsui_3249 (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.26078.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-114 367.0 0.0 4.3e-114 366.7 0.0 1.0 1 lcl|FitnessBrowser__PS:Dsui_3249 Dsui_3249 ornithine carbamoyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_3249 Dsui_3249 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 366.7 0.0 4.3e-114 4.3e-114 1 303 [. 5 301 .. 5 302 .. 0.97 Alignments for each domain: == domain 1 score: 366.7 bits; conditional E-value: 4.3e-114 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 +h+l+++d+++ee+ +l +++ +k + k+ k+ l+ +tl +iFek+stRtR+sfe+++ +lG+ ++yln+ ++q lcl|FitnessBrowser__PS:Dsui_3249 5 KHFLQFKDFTREEFDYLFARTRWIKDQFKNYKQYWPLTDRTLVMIFEKASTRTRLSFEAGMQQLGGSAIYLNTRDSQ 81 79*************************************************************************** PP TIGR00658 78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyv 154 lgr+e+++D a+v+sr+ d++++R++++e++e +a ++ vPvingLt++ hPcqi+aD++t +e+ g +++ +++++ lcl|FitnessBrowser__PS:Dsui_3249 82 LGRGEPVEDAAQVISRMSDIVMIRTFEQEIIERFAANSRVPVINGLTNEYHPCQIMADIFTYIEHRGPIQGKTVAWI 158 ***************************************************************************** PP TIGR00658 155 GDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGee 231 GD+nnv+n+ l aa l ++v+v+tP+g+e eae +++e +dp +a+k+ad++ tDvw+smG e lcl|FitnessBrowser__PS:Dsui_3249 159 GDSNNVCNTWLQAAEVLDFNVHVSTPPGYEVEAERAGL------YGTANFEQFSDPMEAAKGADIVTTDVWTSMGFE 229 ******************************99864333......34599**************************** PP TIGR00658 232 ekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 +++eerlk + ++qv+ +++++ak++++flhCLPa+rGeevt ev++g++s v+deaenRlh+qka++++ll lcl|FitnessBrowser__PS:Dsui_3249 230 AENEERLKDFADWQVDGDMMRIAKSDAIFLHCLPAHRGEEVTAEVIDGPQSAVWDEAENRLHTQKALMEYLL 301 ********************************************************************9987 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.66 // [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