Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate 3607012 Dshi_0433 ornithine carbamoyltransferase (RefSeq)
Query= SwissProt::P08308 (336 letters) >FitnessBrowser__Dino:3607012 Length = 333 Score = 439 bits (1129), Expect = e-128 Identities = 213/333 (63%), Positives = 268/333 (80%), Gaps = 2/333 (0%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 MAFN+ NR+ L+L + E+ +LL LS DLK AKY GTE L+ K IALIFEK STRT Sbjct: 1 MAFNLKNRHFLTLRGFTPEEIGFLLKLSADLKSAKYAGTEVPTLRGKEIALIFEKDSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 R FEVAA+DQGA VTY+ P+ + +G KE++KDTARVLGR+YDAIEYRGF QEIV+ELA Sbjct: 61 RVGFEVAAHDQGATVTYLGPSGTHLGKKETVKDTARVLGRVYDAIEYRGFGQEIVQELAD 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 +AGVPV+NGLTDE+HPTQ+LAD LTM+EH +KPL +++Y ++GDA NNMG+SLL+ GAK+ Sbjct: 121 WAGVPVYNGLTDEFHPTQILADFLTMQEHCEKPLREVAYCFMGDAGNNMGDSLLIGGAKM 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVR+ AP++LWP + + AE +GA++TLTED +AVKGVDFV+TDVWVSMGEP Sbjct: 181 GMDVRLCAPRSLWPVQSIQDEARAIAEHTGARVTLTEDVDKAVKGVDFVYTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 VE W ERI L+PYQVN ++M TGNPR +FMHCLPAFHN+ET+VG I +++ + Sbjct: 241 VEKWAERIDLLMPYQVNADVMARTGNPRVRFMHCLPAFHNAETEVGCDIQDKFG--LEAM 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: 396 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: 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 3607012 Dshi_0433 (ornithine carbamoyltransferase (RefSeq))
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.5463.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-130 420.2 0.0 2.6e-130 420.0 0.0 1.0 1 lcl|FitnessBrowser__Dino:3607012 Dshi_0433 ornithine carbamoyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3607012 Dshi_0433 ornithine carbamoyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.0 0.0 2.6e-130 2.6e-130 1 303 [. 8 331 .. 8 332 .. 0.99 Alignments for each domain: == domain 1 score: 420.0 bits; conditional E-value: 2.6e-130 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 rh+l+l +++ee+ ll+l+++lk++k++g+e +l+gk++aliFek+stRtRv fevaa ++Ga v+yl+++ ++ lcl|FitnessBrowser__Dino:3607012 8 RHFLTLRGFTPEEIGFLLKLSADLKSAKYAGTEVPTLRGKEIALIFEKDSTRTRVGFEVAAHDQGATVTYLGPSGTH 84 8**************************************************************************** PP TIGR00658 78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg.klkevklvy 153 lg+ke++kDtarvl+r++dai +R++ +e+v+ela+ a+vPv+ngLtd++hP+qilaD+lt++e+++ l ev + + lcl|FitnessBrowser__Dino:3607012 85 LGKKETVKDTARVLGRVYDAIEYRGFGQEIVQELADWAGVPVYNGLTDEFHPTQILADFLTMQEHCEkPLREVAYCF 161 *******************************************************************99******** PP TIGR00658 154 vGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmG 229 +GDa nn+++sll+++ak+G+dv++++P+ l+p ++i ++a++ia+++g++++lted++kavk++d++ytDvwvsmG lcl|FitnessBrowser__Dino:3607012 162 MGDAgNNMGDSLLIGGAKMGMDVRLCAPRSLWPVQSIQDEARAIAEHTGARVTLTEDVDKAVKGVDFVYTDVWVSMG 238 ***99************************************************************************ PP TIGR00658 230 e.eekkeerlkllkpyqvneellela.kpevkflhCLPavr.................Geevtdevlegeasivfde 287 e ek++er++ll pyqvn ++++ + +p v f+hCLPa++ +evt+ev+e++asivfd+ lcl|FitnessBrowser__Dino:3607012 239 EpVEKWAERIDLLMPYQVNADVMARTgNPRVRFMHCLPAFHnaetevgcdiqdkfgleAMEVTEEVFESPASIVFDQ 315 *999**********************9****************************9999****************** PP TIGR00658 288 aenRlhaqkavlkall 303 aenR+h++kavl+a+l lcl|FitnessBrowser__Dino:3607012 316 AENRMHTIKAVLVATL 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.32 // [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