Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_011778653.1 MVAN_RS07025 ornithine carbamoyltransferase
Query= SwissProt::P08308 (336 letters) >NCBI__GCF_000015305.1:WP_011778653.1 Length = 334 Score = 519 bits (1336), Expect = e-152 Identities = 253/334 (75%), Positives = 288/334 (86%) Query: 1 MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60 MAFN NR+LLSL+HH+ R+L YLLDLSRDLKRAKY+G +Q L KNIALIFEKTSTRT Sbjct: 1 MAFNNRNRSLLSLVHHTERDLHYLLDLSRDLKRAKYSGLGRQSLAGKNIALIFEKTSTRT 60 Query: 61 RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120 RCAFEVAA+D+GA+VTYIDP SSQIGHKESMKDTARVLGRMYDAIEYRG Q VEELA Sbjct: 61 RCAFEVAAHDEGAHVTYIDPASSQIGHKESMKDTARVLGRMYDAIEYRGASQSTVEELAA 120 Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180 +AGVPVFNGLTDE+HPTQMLADVLTM EH KPL DI++A++GD RNN+ NSLLL+ AKL Sbjct: 121 YAGVPVFNGLTDEFHPTQMLADVLTMTEHCPKPLTDIAFAFVGDGRNNVANSLLLVAAKL 180 Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240 GMDVRI AP LWPH++ V+ C++FA SGA+L +T++P +AV GVDF++TDVWVSMGEP Sbjct: 181 GMDVRIGAPPDLWPHEDHVSMCEEFAAASGARLLITDEPAKAVHGVDFIYTDVWVSMGEP 240 Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300 VE WGERI ELLP+QVN +M A GNPR KFMHCLPAFHN ETKVG QIA QYP+LA GI Sbjct: 241 VETWGERIDELLPFQVNDTLMAAAGNPRVKFMHCLPAFHNCETKVGAQIAAQYPHLAGGI 300 Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTLA 334 EVT+ VFESP NIAFEQAENRMHTIKA+LVS L+ Sbjct: 301 EVTDAVFESPANIAFEQAENRMHTIKAVLVSALS 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: 430 Number of extensions: 9 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: 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 WP_011778653.1 MVAN_RS07025 (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.14575.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-131 423.0 0.0 3.5e-131 422.9 0.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011778653.1 MVAN_RS07025 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011778653.1 MVAN_RS07025 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 422.9 0.0 3.5e-131 3.5e-131 1 303 [. 8 333 .. 8 334 .] 0.99 Alignments for each domain: == domain 1 score: 422.9 bits; conditional E-value: 3.5e-131 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 r+llsl++++e++l++ll+l+++lk++k++g ++ l gk++aliFek+stRtR++fevaa ++Ga+v+ lcl|NCBI__GCF_000015305.1:WP_011778653.1 8 RSLLSLVHHTERDLHYLLDLSRDLKRAKYSGLGRQSLAGKNIALIFEKTSTRTRCAFEVAAHDEGAHVT 76 78******************************************************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 y+++ ++q+g+kes+kDtarvl+r++dai +R+ ++++veela ya+vPv+ngLtd++hP+q+laD+lt lcl|NCBI__GCF_000015305.1:WP_011778653.1 77 YIDPASSQIGHKESMKDTARVLGRMYDAIEYRGASQSTVEELAAYAGVPVFNGLTDEFHPTQMLADVLT 145 ********************************************************************* PP TIGR00658 139 ikeklg.klkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkle 205 ++e++ l ++ +++vGD+ nnvanslll aaklG+dv++ +P++l+p+++ v++++++a+++g++l lcl|NCBI__GCF_000015305.1:WP_011778653.1 146 MTEHCPkPLTDIAFAFVGDGrNNVANSLLLVAAKLGMDVRIGAPPDLWPHEDHVSMCEEFAAASGARLL 214 ******99************************************************************* PP TIGR00658 206 ltedpkkavkdadviytDvwvsmGe.eekkeerlkllkpyqvneellela.kpevkflhCLPavr.... 268 +t++p+kav+++d+iytDvwvsmGe e++ er++ l p+qvn+ l++ a +p vkf+hCLPa++ lcl|NCBI__GCF_000015305.1:WP_011778653.1 215 ITDEPAKAVHGVDFIYTDVWVSMGEpVETWGERIDELLPFQVNDTLMAAAgNPRVKFMHCLPAFHncet 283 *************************999***************************************** PP TIGR00658 269 ...............GeevtdevlegeasivfdeaenRlhaqkavlkall 303 G evtd v+e++a+i f++aenR+h++kavl+ l lcl|NCBI__GCF_000015305.1:WP_011778653.1 284 kvgaqiaaqyphlagGIEVTDAVFESPANIAFEQAENRMHTIKAVLVSAL 333 **********************************************9776 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: 7.48 // [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