Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate 6936061 Sama_0258 ornithine carbamoyltransferase (RefSeq)
Query= SwissProt::Q9K4Y9 (301 letters) >FitnessBrowser__SB2B:6936061 Length = 301 Score = 400 bits (1029), Expect = e-116 Identities = 186/300 (62%), Positives = 249/300 (83%) Query: 1 MENLLSVKDLSKQQILDLLALAKAVKANPAEYSQALAGKSIVTIYEKPSLRTRVTFDIGI 60 M++L+S+K+L+++Q+LDLL LAK +KA+PA+YS+ALAGKS+V ++EKPSLRTRV+FDIGI Sbjct: 1 MKHLISIKELTQKQMLDLLTLAKEIKADPAKYSRALAGKSVVMLFEKPSLRTRVSFDIGI 60 Query: 61 HKLGGHAVYLDAQNGAIGERETVKDFAANISRWADAIVARVVSHKTLEGLVEHGSVPVVN 120 +KLGGH +YLD QNGA+G+RE+VKDFA+N+S WADAIVAR +H+T+EGL ++G VPV+N Sbjct: 61 NKLGGHCLYLDQQNGALGKRESVKDFASNLSCWADAIVARTFAHETVEGLAKYGRVPVIN 120 Query: 121 SLCDLYHPCQALADFLTISEHYEDVSKVKLAYVGEGNNVTHSLMLTGAILGAEVTAVCPR 180 +L DLYHPCQ LADFL+++E ++D+SKV+LAYVG+GNNV+HSLM A+LGA +T +CP Sbjct: 121 ALSDLYHPCQGLADFLSLAEKFDDLSKVRLAYVGDGNNVSHSLMYGAALLGATMTVICPP 180 Query: 181 GSSPDAQIVKQAMALAEISGGKINVTDNLDDIVDYDVIYGDTWVSMGDDTPLAQVKEKYM 240 G PD V+QA +A GGK+ +T +++ I +D +Y DTW+SMGD+T L +K K+ Sbjct: 181 GHFPDGFEVQQAQQIAAAHGGKLVLTSDINAIEGHDAVYTDTWISMGDNTALTDIKAKFA 240 Query: 241 PYQINKALLMRTGIKHVLHCQPAHRELEITSEVMDGEHSLIFDQAENRMHAQNAVLLTLL 300 PYQ+NKAL+ + G + +HC PAHR LE+T EVMDGE SLI DQAENRMHAQNAVL+TLL Sbjct: 241 PYQVNKALMNKAGASYFMHCLPAHRGLEVTDEVMDGEGSLILDQAENRMHAQNAVLVTLL 300 Lambda K H 0.317 0.133 0.379 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: 272 Number of extensions: 2 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: 301 Length of database: 301 Length adjustment: 27 Effective length of query: 274 Effective length of database: 274 Effective search space: 75076 Effective search space used: 75076 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: 48 (23.1 bits)
Align candidate 6936061 Sama_0258 (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.5584.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.8e-109 349.9 0.0 6.5e-109 349.7 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6936061 Sama_0258 ornithine carbamoyltra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6936061 Sama_0258 ornithine carbamoyltransferase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 349.7 0.0 6.5e-109 6.5e-109 1 303 [. 2 300 .. 2 301 .] 0.98 Alignments for each domain: == domain 1 score: 349.7 bits; conditional E-value: 6.5e-109 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 +hl+s+++l+++++ +ll lak++k++ k ++ l gk++ ++Fek+s RtRvsf++++ +lG++ lyl++++ lcl|FitnessBrowser__SB2B:6936061 2 KHLISIKELTQKQMLDLLTLAKEIKADPAK--YSRALAGKSVVMLFEKPSLRTRVSFDIGINKLGGHCLYLDQQNGA 76 7*************************9988..6889***************************************** PP TIGR00658 78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyv 154 lg++es+kD a ls + daiv+R+++he+ve laky vPvin+L+dl hPcq laD+l + ek+++l++v+l+yv lcl|FitnessBrowser__SB2B:6936061 77 LGKRESVKDFASNLSCWADAIVARTFAHETVEGLAKYGRVPVINALSDLYHPCQGLADFLSLAEKFDDLSKVRLAYV 153 ***************************************************************************** PP TIGR00658 155 GDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGee 231 GD+nnv +sl+ +aa+lG +++v +P+g p+ v++a++ia+++ggkl lt+d+ +a+++ d +ytD+w+smG++ lcl|FitnessBrowser__SB2B:6936061 154 GDGNNVSHSLMYGAALLGATMTVICPPGHFPDGFEVQQAQQIAAAHGGKLVLTSDI-NAIEGHDAVYTDTWISMGDN 229 *******************************************************7.69****************** PP TIGR00658 232 ekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 ++ + + + pyqvn+ l++ a + f+hCLPa+rG evtdev++ge s++ d+aenR+haq avl++ll lcl|FitnessBrowser__SB2B:6936061 230 TALTDIKAKFAPYQVNKALMNKAGAS-YFMHCLPAHRGLEVTDEVMDGEGSLILDQAENRMHAQNAVLVTLL 300 **********************9876.59***************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (301 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 8.73 // [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