Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_068174008.1 HTA01S_RS17420 ornithine carbamoyltransferase
Query= reanno::HerbieS:HSERO_RS07185 (304 letters) >NCBI__GCF_001592305.1:WP_068174008.1 Length = 315 Score = 406 bits (1044), Expect = e-118 Identities = 200/315 (63%), Positives = 242/315 (76%), Gaps = 11/315 (3%) Query: 1 MAIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLAD--RTLVMVFEKNSTRTRL 58 M I+HYLQF D + DEY Y++ R+ IK KFK E H AD RTL M+FEK STRTR+ Sbjct: 1 MNIRHYLQFKDLSADEYAYLLTRAAFIKAKFKAVEKHQPFADPDRTLAMIFEKASTRTRV 60 Query: 59 SFEAGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHS 118 SFEAGM+Q+GG+ ++L T DSQLGR EP+ED+A+V+SRM D++MIRT+ Q IERFA HS Sbjct: 61 SFEAGMYQLGGSVVHLTTGDSQLGRAEPIEDSAKVISRMVDLVMIRTFEQSKIERFAAHS 120 Query: 119 RVPVINGLTNEQHPCQVLADVFTYIEHH--------GSIQGKIVAWVGDANNMLYSWLQA 170 RVPVINGLTNE HPCQ+LAD+FT +E+ +++GK+V WVGD NNM +WLQA Sbjct: 121 RVPVINGLTNEFHPCQILADLFTMVEYRPAASGNPLDALKGKVVTWVGDGNNMANTWLQA 180 Query: 171 AEVFGFHVNVSTPKGYDIDPAQVSPGNKN-YTFFADPADACQDADLVTTDVWTSMGFEAE 229 AE+ GF V+VSTP GY++DP N Y F DP +AC+ ADLVTTDVWTSMG+EAE Sbjct: 181 AELLGFTVHVSTPSGYEVDPKLAGVSNPACYKVFKDPKEACKGADLVTTDVWTSMGYEAE 240 Query: 230 NNARLKAFDGWIVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLH 289 N R AF W VD+A MA AK DALFMHCLPAHRGEEV+AEVIDGPQSVVW+EAENR+H Sbjct: 241 NEVRRAAFAQWCVDEAMMAVAKPDALFMHCLPAHRGEEVSAEVIDGPQSVVWDEAENRMH 300 Query: 290 VQKALLEYLVHGRFD 304 VQKAL+EYL+ GR + Sbjct: 301 VQKALMEYLLLGRLN 315 Lambda K H 0.321 0.135 0.409 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: 347 Number of extensions: 10 Number of successful extensions: 4 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: 304 Length of database: 315 Length adjustment: 27 Effective length of query: 277 Effective length of database: 288 Effective search space: 79776 Effective search space used: 79776 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 (21.9 bits) S2: 48 (23.1 bits)
Align candidate WP_068174008.1 HTA01S_RS17420 (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.3368069.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-111 358.9 0.0 1.2e-111 358.7 0.0 1.0 1 NCBI__GCF_001592305.1:WP_068174008.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001592305.1:WP_068174008.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.7 0.0 1.2e-111 1.2e-111 1 303 [. 4 310 .. 4 311 .. 0.94 Alignments for each domain: == domain 1 score: 358.7 bits; conditional E-value: 1.2e-111 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklk..gktlaliFekrstRtRvsfevaayelGaqvlyl 71 rh+l+++dls +e +ll +a+ +k++ k+ ++++ + +tla+iFek+stRtRvsfe+++y+lG+ v++l NCBI__GCF_001592305.1:WP_068174008.1 4 RHYLQFKDLSADEYAYLLTRAAFIKAKFKAVEKHQPFAdpDRTLAMIFEKASTRTRVSFEAGMYQLGGSVVHL 76 89****************************999**9973469******************************* PP TIGR00658 72 nkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklg 144 + ++qlgr e+i+D a+v+sr+vd +++R+++++++e +a ++ vPvingLt+++hPcqilaDl+t+ e+ NCBI__GCF_001592305.1:WP_068174008.1 77 TTGDSQLGRAEPIEDSAKVISRMVDLVMIRTFEQSKIERFAAHSRVPVINGLTNEFHPCQILADLFTMVEYRP 149 **********************************************************************975 PP TIGR00658 145 klkev........klvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelted 209 + ++ +++vGD+nn+an+ l aa +lG++v+v+tP g+e ++++ + n + ++ +d NCBI__GCF_001592305.1:WP_068174008.1 150 AASGNpldalkgkVVTWVGDGNNMANTWLQAAELLGFTVHVSTPSGYEVDPKLAGVS------NPACYKVFKD 216 3322222333554799************************************98776......568999**** PP TIGR00658 210 pkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeas 282 pk+a k+ad++ tDvw+smG e+++e r +++ ++ v+e ++++akp++ f+hCLPa+rGeev+ ev++g++s NCBI__GCF_001592305.1:WP_068174008.1 217 PKEACKGADLVTTDVWTSMGYEAENEVRRAAFAQWCVDEAMMAVAKPDALFMHCLPAHRGEEVSAEVIDGPQS 289 ************************************************************************* PP TIGR00658 283 ivfdeaenRlhaqkavlkall 303 +v+deaenR+h+qka++++ll NCBI__GCF_001592305.1:WP_068174008.1 290 VVWDEAENRMHVQKALMEYLL 310 *****************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (315 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: 16.67 // [ok]
This GapMind analysis is from Apr 09 2024. 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