Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_011780513.1 MVAN_RS16605 ornithine carbamoyltransferase
Query= SwissProt::A0QYS8 (307 letters) >NCBI__GCF_000015305.1:WP_011780513.1 Length = 307 Score = 535 bits (1378), Expect = e-157 Identities = 268/306 (87%), Positives = 279/306 (91%) Query: 1 MIRHFLRDDDLSPEEQAEVLTLAADLKKTPFSRRPLEGPRGVAVIFEKNSTRTRFSFEMG 60 M RHFLRDDDLSPEEQAEVL LAADLKK FSRRPLEGPRGVAVIFEKNSTRTRFSFEMG Sbjct: 1 MTRHFLRDDDLSPEEQAEVLALAADLKKDRFSRRPLEGPRGVAVIFEKNSTRTRFSFEMG 60 Query: 61 IAQLGGHAIVVDGRSTQLGREETLEDTGAVLSRYVDAIVWRTFAQERLTAMASGASVPIV 120 IA+LGGHA+VVDGRSTQLGREETLEDTG VLSRYVDAIVWRTFAQERLTAMASG++VPI+ Sbjct: 61 IAELGGHAVVVDGRSTQLGREETLEDTGQVLSRYVDAIVWRTFAQERLTAMASGSTVPII 120 Query: 121 NALSDEFHPCQVLADLQTLAERKGKLAGLRMTYFGDGANNMAHSLMLGGVTAGVHVTIAA 180 NALSDEFHPCQVLADLQTLAERKG L GLR+TYFGDGANNMAHSLMLGGVTAG+HVTIAA Sbjct: 121 NALSDEFHPCQVLADLQTLAERKGDLKGLRLTYFGDGANNMAHSLMLGGVTAGIHVTIAA 180 Query: 181 PDGFEPDPRFVDAARRRAAETGATVALTKDAKAGADGADVLVTDTWTSMGQENDGLDRVR 240 P GFEP P FV AA RA TGATV LT D ADG DVLVTDTWTSMGQENDGLDRVR Sbjct: 181 PRGFEPHPMFVAAAETRAHRTGATVTLTDDPVRAADGVDVLVTDTWTSMGQENDGLDRVR 240 Query: 241 PFRPFQVNADLLELADPAAVVLHCLPAHRGHEITDEVIDGPQSAVFDEAENRLHAQKALL 300 PFRPFQVNAD+L AD AVVLHCLPAHRGHEITD+VIDGPQSAV+DEAENRLHAQKALL Sbjct: 241 PFRPFQVNADMLAHADSEAVVLHCLPAHRGHEITDDVIDGPQSAVWDEAENRLHAQKALL 300 Query: 301 VWLLEK 306 WLLE+ Sbjct: 301 AWLLER 306 Lambda K H 0.319 0.135 0.393 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: 432 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: 307 Length of database: 307 Length adjustment: 27 Effective length of query: 280 Effective length of database: 280 Effective search space: 78400 Effective search space used: 78400 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_011780513.1 MVAN_RS16605 (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.20286.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.8e-119 383.3 0.0 4.3e-119 383.2 0.0 1.0 1 lcl|NCBI__GCF_000015305.1:WP_011780513.1 MVAN_RS16605 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011780513.1 MVAN_RS16605 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.2 0.0 4.3e-119 4.3e-119 1 303 [. 3 304 .. 3 305 .. 0.98 Alignments for each domain: == domain 1 score: 383.2 bits; conditional E-value: 4.3e-119 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkg.ktlaliFekrstRtRvsfevaayelGaqv 68 rh+l dls+ee e+l la++lkk++ + ++ l+g + +a+iFek+stRtR sfe++++elG+++ lcl|NCBI__GCF_000015305.1:WP_011780513.1 3 RHFLRDDDLSPEEQAEVLALAADLKKDRFS---RRPLEGpRGVAVIFEKNSTRTRFSFEMGIAELGGHA 68 799999*********************999...678888578*************************** PP TIGR00658 69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDll 137 ++++ ++qlgr+e+++Dt +vlsryvdaiv R++++e ++++a+ ++vP+in+L+d++hPcq+laDl+ lcl|NCBI__GCF_000015305.1:WP_011780513.1 69 VVVDGRSTQLGREETLEDTGQVLSRYVDAIVWRTFAQERLTAMASGSTVPIINALSDEFHPCQVLADLQ 137 ********************************************************************* PP TIGR00658 138 tikeklgklkevklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkle 205 t+ e++g+lk+++l+y GD+ nn+a+sl+l++++ G++v++a+P+g+ep++ v a+ a+++g++++ lcl|NCBI__GCF_000015305.1:WP_011780513.1 138 TLAERKGDLKGLRLTYFGDGaNNMAHSLMLGGVTAGIHVTIAAPRGFEPHPMFVAAAETRAHRTGATVT 206 ********************9************************************************ PP TIGR00658 206 ltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtd 274 lt+dp++a+ ++dv++tD+w+smG+e++ +r++ ++p+qvn ++l++a++e+++lhCLPa+rG+e+td lcl|NCBI__GCF_000015305.1:WP_011780513.1 207 LTDDPVRAADGVDVLVTDTWTSMGQENDGLDRVRPFRPFQVNADMLAHADSEAVVLHCLPAHRGHEITD 275 ********************************************************************* PP TIGR00658 275 evlegeasivfdeaenRlhaqkavlkall 303 +v++g++s v+deaenRlhaqka+l++ll lcl|NCBI__GCF_000015305.1:WP_011780513.1 276 DVIDGPQSAVWDEAENRLHAQKALLAWLL 304 **************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (307 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: 6.59 // [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