Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate 5207682 Shew_0204 ornithine carbamoyltransferase (RefSeq)
Query= SwissProt::Q9K4Y9 (301 letters) >FitnessBrowser__PV4:5207682 Length = 301 Score = 389 bits (1000), Expect = e-113 Identities = 180/300 (60%), Positives = 242/300 (80%) Query: 1 MENLLSVKDLSKQQILDLLALAKAVKANPAEYSQALAGKSIVTIYEKPSLRTRVTFDIGI 60 M +LLS+K+L++QQ++DLLALAK +KANP +Y +AL GKS+V ++EKPSLRTRV+FDIGI Sbjct: 1 MNHLLSIKELTQQQLIDLLALAKTIKANPEDYRKALDGKSVVMLFEKPSLRTRVSFDIGI 60 Query: 61 HKLGGHAVYLDAQNGAIGERETVKDFAANISRWADAIVARVVSHKTLEGLVEHGSVPVVN 120 +KLGGH +YLD QNGA+G+RE V DFAANIS WADAIVAR +H T+E L EHG+VPV+N Sbjct: 61 NKLGGHCLYLDQQNGALGKREPVSDFAANISCWADAIVARTFAHSTIEQLAEHGTVPVIN 120 Query: 121 SLCDLYHPCQALADFLTISEHYEDVSKVKLAYVGEGNNVTHSLMLTGAILGAEVTAVCPR 180 +L D+YHPCQ LADFLT++E ++DVSKVKLAYVG+GNNVTHSLM A+LGA++T +CP+ Sbjct: 121 ALSDMYHPCQGLADFLTLAEQFDDVSKVKLAYVGDGNNVTHSLMYGAALLGAKMTVICPQ 180 Query: 181 GSSPDAQIVKQAMALAEISGGKINVTDNLDDIVDYDVIYGDTWVSMGDDTPLAQVKEKYM 240 G PD ++V +A A+AE GG++ ++ +++ I +D IY DTW+SMGD L ++K K+ Sbjct: 181 GHFPDGKVVLEAQAIAEAHGGELVLSSDVEAIAGHDAIYTDTWISMGDKASLDEIKAKFA 240 Query: 241 PYQINKALLMRTGIKHVLHCQPAHRELEITSEVMDGEHSLIFDQAENRMHAQNAVLLTLL 300 PY ++ ++ + G K +HC PA+R +E+ +EV+DG SLI QAENRMHAQNAVL+TLL Sbjct: 241 PYHVDTDMMNKAGAKFFMHCLPAYRGVEVAAEVVDGAGSLILQQAENRMHAQNAVLVTLL 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: 261 Number of extensions: 6 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 5207682 Shew_0204 (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.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.454032.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-104 335.8 0.0 1.2e-104 335.7 0.0 1.0 1 FitnessBrowser__PV4:5207682 Domain annotation for each sequence (and alignments): >> FitnessBrowser__PV4:5207682 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.7 0.0 1.2e-104 1.2e-104 2 303 .. 3 300 .. 2 301 .] 0.98 Alignments for each domain: == domain 1 score: 335.7 bits; conditional E-value: 1.2e-104 TIGR00658 2 hllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelqlgrkes 83 hlls+++l++++l +ll lak++k++ + +k l gk++ ++Fek+s RtRvsf++++ +lG++ lyl++++ lg++e+ FitnessBrowser__PV4:5207682 3 HLLSIKELTQQQLIDLLALAKTIKANPED--YRKALDGKSVVMLFEKPSLRTRVSFDIGINKLGGHCLYLDQQNGALGKREP 82 9************************9998..6889*********************************************** PP TIGR00658 84 ikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyvGDannvansll 165 ++D a +s + daiv+R+++h+++e+la++ +vPvin+L+d+ hPcq laD+lt+ e+++++++vkl+yvGD+nnv++sl+ FitnessBrowser__PV4:5207682 83 VSDFAANISCWADAIVARTFAHSTIEQLAEHGTVPVINALSDMYHPCQGLADFLTLAEQFDDVSKVKLAYVGDGNNVTHSLM 164 ********************************************************************************** PP TIGR00658 166 laaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvn 247 +aa+lG +++v +P+g p+ ++v +a++ia+++gg+l l +d+ +a+++ d iytD+w+smG++++ +e + + py v+ FitnessBrowser__PV4:5207682 165 YGAALLGAKMTVICPQGHFPDGKVVLEAQAIAEAHGGELVLSSDV-EAIAGHDAIYTDTWISMGDKASLDEIKAKFAPYHVD 245 ***************************************999996.79********************************** PP TIGR00658 248 eellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 +++++ a + f+hCLPa rG ev+ ev++g+ s++ ++aenR+haq avl++ll FitnessBrowser__PV4:5207682 246 TDMMNKAGAK-FFMHCLPAYRGVEVAAEVVDGAGSLILQQAENRMHAQNAVLVTLL 300 *****99765.69***************************************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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 19.15 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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