Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate Pf1N1B4_616 Ornithine carbamoyltransferase (EC 2.1.3.3)
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 Length = 336 Score = 601 bits (1550), Expect = e-177 Identities = 292/336 (86%), Positives = 317/336 (94%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 MAFNM NR+LLSLMHH+TREL YLLDLSRDLKRAKYTGTE+ HL+ KNIALIFEKTSTRT Sbjct: 1 MAFNMRNRSLLSLMHHTTRELNYLLDLSRDLKRAKYTGTERPHLQGKNIALIFEKTSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 RCAFEVAA+DQGA+VTYIDP SSQIGHKESMKDTARVLGRM+DAIEYRGF+QEIVEELAK Sbjct: 61 RCAFEVAAHDQGAHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAK 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 FAGVPVFNGLT E+HPTQM+AD LTMREHSDKPLHDISYAYLGDAR NMGNSLL+IGAKL Sbjct: 121 FAGVPVFNGLTAEFHPTQMIADTLTMREHSDKPLHDISYAYLGDARYNMGNSLLMIGAKL 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRIAAPKALWPH +F+ QCK FAEESGA++T+TEDPKEAVK VDF+HTD+WVSMGEP Sbjct: 181 GMDVRIAAPKALWPHQDFIDQCKAFAEESGARITITEDPKEAVKDVDFIHTDIWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 VEAW ERI++LLPYQVN E+MKA+GNPR KFMHCLPAFHNSETKVGK IA +YP+LANG+ Sbjct: 241 VEAWDERIEQLLPYQVNAEMMKASGNPRVKFMHCLPAFHNSETKVGKDIAARYPHLANGV 300 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLADI 336 EVTEDVFESP NIAFEQAENRMHTIKAILVS LADI Sbjct: 301 EVTEDVFESPANIAFEQAENRMHTIKAILVSALADI 336 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: 490 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: 336 Length of database: 336 Length adjustment: 28 Effective length of query: 308 Effective length of database: 308 Effective search space: 94864 Effective search space used: 94864 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 Pf1N1B4_616 (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.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.3061.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-133 429.0 0.0 5.2e-133 428.9 0.0 1.0 1 lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 Ornithine carbamoyltransferase ( Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 Ornithine carbamoyltransferase (EC 2.1.3.3) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 428.9 0.0 5.2e-133 5.2e-133 1 303 [. 8 333 .. 8 334 .. 0.99 Alignments for each domain: == domain 1 score: 428.9 bits; conditional E-value: 5.2e-133 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelG 65 r+llsl++++++el++ll+l+++lk++k++g+e+ +l+gk++aliFek+stRtR++fevaa ++G lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 8 RSLLSLMHHTTRELNYLLDLSRDLKRAKYTGTERPHLQGKNIALIFEKTSTRTRCAFEVAAHDQG 72 78*************************************************************** PP TIGR00658 66 aqvlylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPc 130 a+v+y+++ ++q+g+kes+kDtarvl+r++dai +R++++e+veelak+a+vPv+ngLt ++hP+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 73 AHVTYIDPVSSQIGHKESMKDTARVLGRMFDAIEYRGFEQEIVEELAKFAGVPVFNGLTAEFHPT 137 ***************************************************************** PP TIGR00658 131 qilaDlltikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkka 193 q++aD lt++e+ + l++++++y+GDa n++nsll+++aklG+dv++a+P++l+p+++ ++++ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 138 QMIADTLTMREHSDkPLHDISYAYLGDArYNMGNSLLMIGAKLGMDVRIAAPKALWPHQDFIDQC 202 **************99************99*********************************** PP TIGR00658 194 kkiakenggkleltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kp 256 k++a+e+g+++++tedpk+avkd+d+i+tD+wvsmGe e+++er+++l pyqvn e+++ + +p lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 203 KAFAEESGARITITEDPKEAVKDVDFIHTDIWVSMGEpVEAWDERIEQLLPYQVNAEMMKASgNP 267 *************************************9999********************99** PP TIGR00658 257 evkflhCLPavr...................GeevtdevlegeasivfdeaenRlhaqkavlkal 302 vkf+hCLPa++ G evt++v+e++a+i f++aenR+h++ka+l+ lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 268 RVKFMHCLPAFHnsetkvgkdiaaryphlanGVEVTEDVFESPANIAFEQAENRMHTIKAILVSA 332 *************************************************************9976 PP TIGR00658 303 l 303 l lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_616 333 L 333 6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (336 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: 11.04 // [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