Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate SMa0695 SMa0695 ornithine carbamoyltransferase
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__Smeli:SMa0695 Length = 334 Score = 488 bits (1257), Expect = e-143 Identities = 230/335 (68%), Positives = 284/335 (84%), Gaps = 1/335 (0%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 M+FN+ NR+LL++ ++ RE RYL+DL+RDLKRAKY TEQ+HLK K I LIFEKTSTRT Sbjct: 1 MSFNLRNRSLLTVQDYTPREFRYLVDLARDLKRAKYARTEQEHLKGKEICLIFEKTSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 RCAFEVA DQGANVTY+DP SQIGHKES KDTARVLGRMYDAIEYRG Q VE LAK Sbjct: 61 RCAFEVACSDQGANVTYLDPAGSQIGHKESFKDTARVLGRMYDAIEYRGASQAGVETLAK 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 +AGVPV+NGLTDEYHPTQM+ADV+TMREHSDKP+ +I YAY+GD R+NMG+SLL++G + Sbjct: 121 YAGVPVYNGLTDEYHPTQMIADVMTMREHSDKPISEIKYAYIGDTRSNMGHSLLIVGCLM 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRI P++LWP +E+ K+ +SGA+L +T++P+EAV+GVDF+HTDVWVSMGEP Sbjct: 181 GMDVRICGPRSLWPSEEYQTIAKRLKAQSGARLMITDNPREAVEGVDFIHTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 E W ERI+ L PYQVN E+M A+GNP+ KFMHCLPA+H++ET +GKQI++ Y +++G+ Sbjct: 241 KEVWKERIQLLTPYQVNAELMAASGNPQTKFMHCLPAYHDTETTIGKQISDDY-GMSDGL 299 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLAD 335 EVT++VFES NIAFEQAENRMHTIKA+LV+TL D Sbjct: 300 EVTDEVFESQANIAFEQAENRMHTIKALLVATLGD 334 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: 412 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: 336 Length of database: 334 Length adjustment: 28 Effective length of query: 308 Effective length of database: 306 Effective search space: 94248 Effective search space used: 94248 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 SMa0695 SMa0695 (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.448.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-129 418.1 0.0 1.1e-129 417.9 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMa0695 SMa0695 ornithine carbamoyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMa0695 SMa0695 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 417.9 0.0 1.1e-129 1.1e-129 1 303 [. 8 332 .. 8 333 .. 0.99 Alignments for each domain: == domain 1 score: 417.9 bits; conditional E-value: 1.1e-129 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeel 76 r+ll+++d++++e+++l++la++lk++k++ +e+++lkgk++ liFek+stRtR++feva ++Ga+v+yl++ + lcl|FitnessBrowser__Smeli:SMa0695 8 RSLLTVQDYTPREFRYLVDLARDLKRAKYARTEQEHLKGKEICLIFEKTSTRTRCAFEVACSDQGANVTYLDPAGS 83 789************************************************************************* PP TIGR00658 77 qlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkevkl 151 q+g+kes+kDtarvl+r++dai +R+ ++ ve+lakya+vPv+ngLtd+ hP+q++aD++t++e+ + ++e+k+ lcl|FitnessBrowser__Smeli:SMa0695 84 QIGHKESFKDTARVLGRMYDAIEYRGASQAGVETLAKYAGVPVYNGLTDEYHPTQMIADVMTMREHSDkPISEIKY 159 ********************************************************************99****** PP TIGR00658 152 vyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwv 226 +y+GD+ n+++sll+ + ++G+dv++++P+ l+p++e+ + ak++ +++g++l +t++p +av+++d+i+tDvwv lcl|FitnessBrowser__Smeli:SMa0695 160 AYIGDTrSNMGHSLLIVGCLMGMDVRICGPRSLWPSEEYQTIAKRLKAQSGARLMITDNPREAVEGVDFIHTDVWV 235 ******9********************************************************************* PP TIGR00658 227 smGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr..................Geevtdevlegeas 282 smGe +e ++er++ll pyqvn el++ + +p++kf+hCLPa + G evtdev+e++a+ lcl|FitnessBrowser__Smeli:SMa0695 236 SMGEpKEVWKERIQLLTPYQVNAELMAASgNPQTKFMHCLPAYHdtettigkqisddygmsdGLEVTDEVFESQAN 311 ****9999********************99********************************************** PP TIGR00658 283 ivfdeaenRlhaqkavlkall 303 i f++aenR+h++ka+l+a+l lcl|FitnessBrowser__Smeli:SMa0695 312 IAFEQAENRMHTIKALLVATL 332 *****************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (334 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: 9.30 // [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