Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_046009440.1 OLEAN_RS12135 ornithine carbamoyltransferase
Query= SwissProt::P08308 (336 letters) >NCBI__GCF_000967895.1:WP_046009440.1 Length = 333 Score = 460 bits (1184), Expect = e-134 Identities = 225/335 (67%), Positives = 278/335 (82%), Gaps = 2/335 (0%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 M+FN+ NRN L L+ + R++ +LLDLSRDLKRAKY+G EQQ LK KNI LIFEK+STRT Sbjct: 1 MSFNLRNRNFLKLLDFNQRDVNFLLDLSRDLKRAKYSGMEQQSLKGKNICLIFEKSSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 CAFEVA++DQGA +TY+ P+ SQIG KESMKDTARVLGRM+DAIEYRGF Q++VEELA+ Sbjct: 61 LCAFEVASFDQGAQITYLGPSGSQIGKKESMKDTARVLGRMFDAIEYRGFGQKVVEELAQ 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 +AGVPV+NGLTDE+HPTQMLAD+LTMREHS KPL DISYAY+GDA +NMG+SL++ G + Sbjct: 121 YAGVPVYNGLTDEFHPTQMLADLLTMREHSKKPLSDISYAYVGDAHSNMGHSLMIAGCLM 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRIAAPK+LWP +EF+ ++ + G KLT+TEDPKEAVKG DF+HTDVWVSMGEP Sbjct: 181 GMDVRIAAPKSLWPSEEFLKPARELEKLYGGKLTITEDPKEAVKGCDFIHTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 W ERIK L PY+V+ E+M+ATG KFMHCLPAFHN +T VG+ I +++ LA + Sbjct: 241 DAVWEERIKLLTPYRVDSELMQATGISTTKFMHCLPAFHNRDTIVGEDIFQKF-GLAE-M 298 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLAD 335 EV+++VFES I FEQAENR+HTIKA+LV+TL + Sbjct: 299 EVSDEVFESVAGIQFEQAENRLHTIKAMLVATLGN 333 Lambda K H 0.318 0.133 0.387 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: 377 Number of extensions: 7 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: 336 Length of database: 333 Length adjustment: 28 Effective length of query: 308 Effective length of database: 305 Effective search space: 93940 Effective search space used: 93940 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_046009440.1 OLEAN_RS12135 (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.7690.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-125 403.9 0.0 2.3e-125 403.7 0.0 1.0 1 lcl|NCBI__GCF_000967895.1:WP_046009440.1 OLEAN_RS12135 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000967895.1:WP_046009440.1 OLEAN_RS12135 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 403.7 0.0 2.3e-125 2.3e-125 1 303 [. 8 331 .. 8 332 .. 0.99 Alignments for each domain: == domain 1 score: 403.7 bits; conditional E-value: 2.3e-125 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 r++l+lld+++++++ ll+l+++lk++k++g+e++ lkgk++ liFek+stRt ++feva +++Gaq + lcl|NCBI__GCF_000967895.1:WP_046009440.1 8 RNFLKLLDFNQRDVNFLLDLSRDLKRAKYSGMEQQSLKGKNICLIFEKSSTRTLCAFEVASFDQGAQIT 76 789****************************************************************** PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 yl+++ +q+g+kes+kDtarvl+r++dai +R++ ++ veela+ya+vPv+ngLtd++hP+q+laDllt lcl|NCBI__GCF_000967895.1:WP_046009440.1 77 YLGPSGSQIGKKESMKDTARVLGRMFDAIEYRGFGQKVVEELAQYAGVPVYNGLTDEFHPTQMLADLLT 145 ********************************************************************* PP TIGR00658 139 ikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkle 205 ++e+ + l++++++yvGDa n+++sl++a+ ++G+dv++a+P+ l+p++e +k a+++ k +ggkl+ lcl|NCBI__GCF_000967895.1:WP_046009440.1 146 MREHSKkPLSDISYAYVGDAhSNMGHSLMIAGCLMGMDVRIAAPKSLWPSEEFLKPARELEKLYGGKLT 214 ****9989************99*********************************************** PP TIGR00658 206 ltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr.... 268 +tedpk+avk+ d+i+tDvwvsmGe ++ +eer+kll py v++el++ + + +kf+hCLPa++ lcl|NCBI__GCF_000967895.1:WP_046009440.1 215 ITEDPKEAVKGCDFIHTDVWVSMGEpDAVWEERIKLLTPYRVDSELMQATgISTTKFMHCLPAFHnrdt 283 *************************9999*********************8999*************** PP TIGR00658 269 .............GeevtdevlegeasivfdeaenRlhaqkavlkall 303 +ev+dev+e+ a i f++aenRlh++ka+l+a+l lcl|NCBI__GCF_000967895.1:WP_046009440.1 284 ivgedifqkfglaEMEVSDEVFESVAGIQFEQAENRLHTIKAMLVATL 331 **********9999******************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (333 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.56 // [ok]
This GapMind analysis is from Sep 24 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