Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate HSERO_RS07185 HSERO_RS07185 ornithine carbamoyltransferase
Query= reanno::HerbieS:HSERO_RS07185 (304 letters) >FitnessBrowser__HerbieS:HSERO_RS07185 Length = 304 Score = 624 bits (1610), Expect = 0.0 Identities = 304/304 (100%), Positives = 304/304 (100%) Query: 1 MAIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSF 60 MAIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSF Sbjct: 1 MAIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSF 60 Query: 61 EAGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRV 120 EAGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRV Sbjct: 61 EAGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRV 120 Query: 121 PVINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNV 180 PVINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNV Sbjct: 121 PVINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNV 180 Query: 181 STPKGYDIDPAQVSPGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240 STPKGYDIDPAQVSPGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW Sbjct: 181 STPKGYDIDPAQVSPGNKNYTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240 Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH Sbjct: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300 Query: 301 GRFD 304 GRFD Sbjct: 301 GRFD 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: 496 Number of extensions: 7 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: 304 Length of database: 304 Length adjustment: 27 Effective length of query: 277 Effective length of database: 277 Effective search space: 76729 Effective search space used: 76729 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 HSERO_RS07185 HSERO_RS07185 (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.32696.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-110 353.4 0.0 5.8e-110 353.2 0.0 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS07185 HSERO_RS07185 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS07185 HSERO_RS07185 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.2 0.0 5.8e-110 5.8e-110 1 303 [. 4 299 .. 4 300 .. 0.98 Alignments for each domain: == domain 1 score: 353.2 bits; conditional E-value: 5.8e-110 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqv 68 +h+l++ d++ +e ++++e+++ +k++ k+ + +++l +tl ++Fek+stRtR+sfe+++ ++G+ + lcl|FitnessBrowser__HerbieS:HSERO_RS07185 4 KHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEAGMHQMGGAA 71 799***************************************************************** PP TIGR00658 69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDl 136 +yln+ ++qlgr+e+++D a+v+sr+ d+i++R+y +e++e +ak++ vPvingLt+++hPcq+laD+ lcl|FitnessBrowser__HerbieS:HSERO_RS07185 72 IYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPVINGLTNEQHPCQVLADV 139 ******************************************************************** PP TIGR00658 137 ltikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkl 204 +t +e+ g++++ +++vGDann+ s l aa +G++v+v+tP+g++ +++ v+ +k + lcl|FitnessBrowser__HerbieS:HSERO_RS07185 140 FTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVSTPKGYDIDPAQVSPGNK-------NY 200 ***************************************************99988866.......78 PP TIGR00658 205 eltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeev 272 ++ dp++a +dad++ tDvw+smG e+++++rlk++ ++ v++ ++ ak+++ f+hCLPa+rGeev lcl|FitnessBrowser__HerbieS:HSERO_RS07185 201 TFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEV 268 9******************************************************************* PP TIGR00658 273 tdevlegeasivfdeaenRlhaqkavlkall 303 + ev++g++s+v++eaenRlh+qka+l++l+ lcl|FitnessBrowser__HerbieS:HSERO_RS07185 269 AAEVIDGPQSVVWEEAENRLHVQKALLEYLV 299 ***************************9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (304 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: 7.59 // [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