Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF4047 HP15_3987 ornithine carbamoyltransferase
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__Marino:GFF4047 Length = 333 Score = 449 bits (1155), Expect = e-131 Identities = 219/333 (65%), Positives = 268/333 (80%), Gaps = 2/333 (0%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 MAFN+ NR+ L+L S RE+ +LL LS DLK AKY GTE L+ K+IALIFEK STRT Sbjct: 1 MAFNLKNRHFLTLRDFSPREIAFLLKLSADLKTAKYAGTEVPKLEGKDIALIFEKNSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 R FEVAA+DQGA VTY+ P + IGHKES+KDTARVLGR+YDAIEYRGF Q +V+ELA+ Sbjct: 61 RVGFEVAAFDQGARVTYLGPTGTHIGHKESVKDTARVLGRVYDAIEYRGFGQSVVDELAQ 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 +AGVPV+NGLT+E+HPTQ+LAD LTM+EH +KPL D++Y ++GDA NNMG+SLL+ GAK+ Sbjct: 121 YAGVPVYNGLTNEFHPTQILADFLTMQEHVEKPLRDVAYVFIGDAANNMGDSLLIGGAKM 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVR+ APKA WP + + A E+GA++T+TED AV GVDFV+TDVWVSMGEP Sbjct: 181 GMDVRLCAPKACWPGQAVQEEAQALAAETGARITITEDVDAAVAGVDFVYTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 E W ERIK L+PYQVN +M TGNPRA+FMHCLPAFHN+ET VGK+I E Y + + Sbjct: 241 KEKWAERIKLLMPYQVNAALMAKTGNPRARFMHCLPAFHNTETVVGKEIQETYG--IDAM 298 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTL 333 EVTE+VFESP +I F+QAENRMHTIKA+LV+TL Sbjct: 299 EVTEEVFESPASIVFDQAENRMHTIKAVLVATL 331 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: 386 Number of extensions: 6 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 GFF4047 HP15_3987 (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.3840.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.1e-133 428.1 0.0 1e-132 427.9 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF4047 HP15_3987 ornithine carbamoyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF4047 HP15_3987 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 427.9 0.0 1e-132 1e-132 1 303 [. 8 331 .. 8 332 .. 0.99 Alignments for each domain: == domain 1 score: 427.9 bits; conditional E-value: 1e-132 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkee 75 rh+l+l d+s++e+ ll+l+++lk++k++g+e kl+gk +aliFek+stRtRv fevaa+++Ga+v+yl++ lcl|FitnessBrowser__Marino:GFF4047 8 RHFLTLRDFSPREIAFLLKLSADLKTAKYAGTEVPKLEGKDIALIFEKNSTRTRVGFEVAAFDQGARVTYLGPTG 82 8************************************************************************** PP TIGR00658 76 lqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkev 149 +++g+kes+kDtarvl+r++dai +R++ ++ v ela+ya+vPv+ngLt+++hP+qilaD+lt++e+++ l +v lcl|FitnessBrowser__Marino:GFF4047 83 THIGHKESVKDTARVLGRVYDAIEYRGFGQSVVDELAQYAGVPVYNGLTNEFHPTQILADFLTMQEHVEkPLRDV 157 *********************************************************************99**** PP TIGR00658 150 klvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytD 223 +v++GDa nn+++sll+++ak+G+dv++++P++++p +++ ++a+++a+e+g+++++ted++ av+++d++ytD lcl|FitnessBrowser__Marino:GFF4047 158 AYVFIGDAaNNMGDSLLIGGAKMGMDVRLCAPKACWPGQAVQEEAQALAAETGARITITEDVDAAVAGVDFVYTD 232 *******99****************************************************************** PP TIGR00658 224 vwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr.................Geevtdevleg 279 vwvsmGe +ek++er+kll pyqvn l++ + +p + f+hCLPa++ +evt+ev+e+ lcl|FitnessBrowser__Marino:GFF4047 233 VWVSMGEpKEKWAERIKLLMPYQVNAALMAKTgNPRARFMHCLPAFHntetvvgkeiqetygidAMEVTEEVFES 307 *******999********************999****************************9999********** PP TIGR00658 280 easivfdeaenRlhaqkavlkall 303 +asivfd+aenR+h++kavl+a+l lcl|FitnessBrowser__Marino:GFF4047 308 PASIVFDQAENRMHTIKAVLVATL 331 *********************998 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.32 // [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