Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate RR42_RS17175 RR42_RS17175 ornithine carbamoyltransferase
Query= reanno::HerbieS:HSERO_RS07185 (304 letters) >FitnessBrowser__Cup4G11:RR42_RS17175 Length = 307 Score = 457 bits (1177), Expect = e-133 Identities = 222/303 (73%), Positives = 253/303 (83%), Gaps = 1/303 (0%) Query: 2 AIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFE 61 +IKHYLQFSD T DEYEY+++R+R++K KFKNYE H L DRTL M+FEKNSTRTRLSFE Sbjct: 5 SIKHYLQFSDLTPDEYEYLLDRARILKTKFKNYETWHPLHDRTLSMIFEKNSTRTRLSFE 64 Query: 62 AGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVP 121 AG+HQ+GG A++LNTRDSQLGRGEP+EDAAQV+SRM D+IMIRT+GQEIIERFA HSRVP Sbjct: 65 AGIHQLGGHAVFLNTRDSQLGRGEPIEDAAQVISRMVDIIMIRTFGQEIIERFAAHSRVP 124 Query: 122 VINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVS 181 VINGLTNE HPCQVLADVFTYIE GSI+GK VAW+GDANNM Y+W+QAAE GF + S Sbjct: 125 VINGLTNEYHPCQVLADVFTYIEQRGSIRGKTVAWIGDANNMAYTWIQAAERLGFTFHFS 184 Query: 182 TPKGYDIDPAQVSPGNKNYT-FFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240 P GY +DPA V + F DP ACQ ADLVTTDVWTSMG+EAEN+AR +AF W Sbjct: 185 APPGYQLDPAMVPATAAHLVKVFDDPLTACQGADLVTTDVWTSMGYEAENDARKRAFQNW 244 Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300 +V A M RA DALFMHCLPAHRGEEV A VIDGP+SVVWEEAENRLHVQKAL+EYL+ Sbjct: 245 MVTTAMMDRAGDDALFMHCLPAHRGEEVEAAVIDGPKSVVWEEAENRLHVQKALMEYLLC 304 Query: 301 GRF 303 GR+ Sbjct: 305 GRY 307 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: 383 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: 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 RR42_RS17175 RR42_RS17175 (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.carbon/TIGR00658.hmm # target sequence database: /tmp/gapView.25904.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.3e-110 354.0 0.0 3.8e-110 353.8 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS17175 RR42_RS17175 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS17175 RR42_RS17175 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 353.8 0.0 3.8e-110 3.8e-110 1 303 [. 7 303 .. 7 304 .. 0.98 Alignments for each domain: == domain 1 score: 353.8 bits; conditional E-value: 3.8e-110 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 +h+l++ dl+++e ++ll++a+ lk++ k+ ++ + l+ +tl++iFek+stRtR+sfe+++ +lG++++ lcl|FitnessBrowser__Cup4G11:RR42_RS17175 7 KHYLQFSDLTPDEYEYLLDRARILKTKFKNYETWHPLHDRTLSMIFEKNSTRTRLSFEAGIHQLGGHAV 75 799***************************9999*********************************** PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +ln+ ++qlgr+e+i+D a+v+sr+vd+i++R++ +e++e +a ++ vPvingLt++ hPcq+laD++t lcl|FitnessBrowser__Cup4G11:RR42_RS17175 76 FLNTRDSQLGRGEPIEDAAQVISRMVDIIMIRTFGQEIIERFAAHSRVPVINGLTNEYHPCQVLADVFT 144 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 +e+ g++ + +++++GDann+a + + aa lG++++ ++P+g++ ++++v + +++ lcl|FitnessBrowser__Cup4G11:RR42_RS17175 145 YIEQRGSIRGKTVAWIGDANNMAYTWIQAAERLGFTFHFSAPPGYQLDPAMVPATA------AHLVKVF 207 **************************************************998763......35799** PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +dp a ++ad++ tDvw+smG e+++++r ++++++ v++ +++ a +++ f+hCLPa+rGeev v lcl|FitnessBrowser__Cup4G11:RR42_RS17175 208 DDPLTACQGADLVTTDVWTSMGYEAENDARKRAFQNWMVTTAMMDRAGDDALFMHCLPAHRGEEVEAAV 276 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s+v++eaenRlh+qka++++ll lcl|FitnessBrowser__Cup4G11:RR42_RS17175 277 IDGPKSVVWEEAENRLHVQKALMEYLL 303 ***********************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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 10.07 // [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