Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_089137031.1 CES79_RS09540 ornithine carbamoyltransferase
Query= SwissProt::Q8G998 (343 letters) >NCBI__GCF_002217945.1:WP_089137031.1 Length = 342 Score = 587 bits (1514), Expect = e-172 Identities = 286/341 (83%), Positives = 312/341 (91%) Query: 3 KDFRQNVFQGRSVLAEKDFSAAELEYLIDFGLHLKALKKAGIPHHYLEGKNIALLFEKSS 62 K+F+ +VFQGRSVLAEKDFSAAEL YLIDFGLHLKALKKAG+PHHYLEGKNIALLFEK+S Sbjct: 2 KEFKNSVFQGRSVLAEKDFSAAELNYLIDFGLHLKALKKAGVPHHYLEGKNIALLFEKNS 61 Query: 63 TRTRSAFTTASIDLGAHPEYLGQNDIQLGKKESTSDTAKVLGSMFDGIEFRGFKQSDAEI 122 TRTRSAFTTA+IDLGAHPE+LG NDIQLGKKES DTAKVLGSMFDGIEFRGF Q E Sbjct: 62 TRTRSAFTTAAIDLGAHPEFLGANDIQLGKKESVEDTAKVLGSMFDGIEFRGFSQKVVEQ 121 Query: 123 LARDSGVPVWNGLTDEWHPTQMLADFMTVKENFGKLQGLTLTFMGDGRNNVANSLLVTGA 182 LA SGVPVWNGLTDEWHPTQMLADFMTVKENFG L+GLTLT+MGDGRNN+ANSLLVTGA Sbjct: 122 LAEFSGVPVWNGLTDEWHPTQMLADFMTVKENFGHLKGLTLTYMGDGRNNMANSLLVTGA 181 Query: 183 ILGVNIHIVAPKALFPTEETQNIAKGFAEKSGAKLVITDDLDEGLKGSNVVYTDVWVSMG 242 ILGVNIHIVAP L P +E Q++A GFA+ SGAKL+ITDDLDEGLKGSN+VYTDVWVSMG Sbjct: 182 ILGVNIHIVAPNELHPAQEIQDLANGFAKDSGAKLLITDDLDEGLKGSNIVYTDVWVSMG 241 Query: 243 ESNWEERVKELTPYQVNMEAMKKTGTPDDQLIFMHCLPAFHNTDTQYGKEIKEKYGITEM 302 E+NW+ER+ L PYQVNM A+KKT TPDDQLI MHCLPAFH+T T YGKEI+EKYG+TEM Sbjct: 242 ENNWQERINLLKPYQVNMAALKKTDTPDDQLIVMHCLPAFHDTTTDYGKEIQEKYGLTEM 301 Query: 303 EVTDEVFTSKYARQFEEAENRMHSIKAMMAATLGNLFIPRV 343 E+TDEVF SKYARQFEEAENRMHSIKAMMAATLG+LFIP+V Sbjct: 302 EITDEVFRSKYARQFEEAENRMHSIKAMMAATLGDLFIPKV 342 Lambda K H 0.317 0.133 0.383 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: 536 Number of extensions: 16 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: 343 Length of database: 342 Length adjustment: 29 Effective length of query: 314 Effective length of database: 313 Effective search space: 98282 Effective search space used: 98282 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 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_089137031.1 CES79_RS09540 (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.3698508.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.3e-119 382.9 0.0 6e-119 382.7 0.0 1.0 1 NCBI__GCF_002217945.1:WP_089137031.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_002217945.1:WP_089137031.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 382.7 0.0 6e-119 6e-119 2 303 .. 13 334 .. 12 335 .. 0.98 Alignments for each domain: == domain 1 score: 382.7 bits; conditional E-value: 6e-119 TIGR00658 2 hllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnke 74 ++l+ +d+s +el++l++ + +lk+ kk+g+ +++l+gk++al+Fek+stRtR +f++aa++lGa++ +l+++ NCBI__GCF_002217945.1:WP_089137031.1 13 SVLAEKDFSAAELNYLIDFGLHLKALKKAGVPHHYLEGKNIALLFEKNSTRTRSAFTTAAIDLGAHPEFLGAN 85 677889******************************************************************* PP TIGR00658 75 elqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklk 147 ++qlg+kes++Dta+vl++++d+i +R+++++ ve+la++++vPv+ngLtd+ hP+q+laD++t+ke++g+lk NCBI__GCF_002217945.1:WP_089137031.1 86 DIQLGKKESVEDTAKVLGSMFDGIEFRGFSQKVVEQLAEFSGVPVWNGLTDEWHPTQMLADFMTVKENFGHLK 158 ************************************************************************* PP TIGR00658 148 evklvyvGDa.nnvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219 +++l+y+GD+ nn+ansll+++a lG+++++++P++l+p +ei + a+ +ak++g+kl +t+d ++++k++++ NCBI__GCF_002217945.1:WP_089137031.1 159 GLTLTYMGDGrNNMANSLLVTGAILGVNIHIVAPNELHPAQEIQDLANGFAKDSGAKLLITDDLDEGLKGSNI 231 ************************************************************************* PP TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellela...kpevkflhCLPavr.................Geev 272 +ytDvwvsmGe+ +++er++llkpyqvn+ l+ + +++ +++hCLPa++ +e+ NCBI__GCF_002217945.1:WP_089137031.1 232 VYTDVWVSMGEN-NWQERINLLKPYQVNMAALKKTdtpDDQLIVMHCLPAFHdtttdygkeiqekygltEMEI 303 **********75.689****************9986567899************************9999*** PP TIGR00658 273 tdevlegeasivfdeaenRlhaqkavlkall 303 tdev+ ++ + f+eaenR+h++ka+++a+l NCBI__GCF_002217945.1:WP_089137031.1 304 TDEVFRSKYARQFEEAENRMHSIKAMMAATL 334 ****************************998 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (342 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 13.53 // [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