Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_011308421.1 MBAR_RS18595 ornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_000195895.1:WP_011308421.1 Length = 302 Score = 333 bits (853), Expect = 4e-96 Identities = 167/303 (55%), Positives = 217/303 (71%), Gaps = 4/303 (1%) Query: 8 RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67 +D+L + D + EEI+ +LE+A LK +K G+P L+ K+L MIF+K STRTRVSFEVA Sbjct: 3 KDVLSITDLSKEEIYELLESAMDLKEKRKAGEPTEYLKNKSLGMIFEKASTRTRVSFEVA 62 Query: 68 MAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYASVPVI 127 M GGH+LYLN++D+Q+ RGETI DTAR LS Y+ IMARV H+ VE LAKY+++PVI Sbjct: 63 MTDFGGHSLYLNSRDIQIGRGETIEDTARTLSGYLHGIMARVMSHETVEKLAKYSTIPVI 122 Query: 128 NGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVVATP 187 N LSD HPCQ L D+MTI E K + +K +VGDGNNV +S ++ +G + VA P Sbjct: 123 NALSDREHPCQILGDFMTIMEYKDKFEDLKFAWVGDGNNVCNSALLGSAIVGMEFAVACP 182 Query: 188 EGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEERRKI 247 +GYEP + + + A GG F + DP AVKDAD+IYTDVW SMG EAE E+R K Sbjct: 183 KGYEPKPEFL----EKAKSLGGKFTVTDDPKVAVKDADIIYTDVWVSMGDEAEQEKRLKE 238 Query: 248 FRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLA 307 F FQVN +L+ AKPD + MHCLPA RG E+TD+V+D PNSV+++EAENRLHAQKA++ Sbjct: 239 FATFQVNTELLGVAKPDVIVMHCLPARRGLEITDEVMDGPNSVIFEEAENRLHAQKALIL 298 Query: 308 LLL 310 L+ Sbjct: 299 KLM 301 Lambda K H 0.319 0.134 0.400 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: 292 Number of extensions: 9 Number of successful extensions: 2 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: 317 Length of database: 302 Length adjustment: 27 Effective length of query: 290 Effective length of database: 275 Effective search space: 79750 Effective search space used: 79750 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 (21.7 bits) S2: 48 (23.1 bits)
Align candidate WP_011308421.1 MBAR_RS18595 (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.aa/TIGR00658.hmm # target sequence database: /tmp/gapView.22239.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-137 441.9 0.0 6.5e-137 441.7 0.0 1.0 1 lcl|NCBI__GCF_000195895.1:WP_011308421.1 MBAR_RS18595 ornithine carbamoyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195895.1:WP_011308421.1 MBAR_RS18595 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 441.7 0.0 6.5e-137 6.5e-137 1 303 [. 3 301 .. 3 302 .] 0.99 Alignments for each domain: == domain 1 score: 441.7 bits; conditional E-value: 6.5e-137 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 +++ls++dls+ee+ elle a +lk+++k+g+ +++lk+k+l++iFek+stRtRvsfeva++++G+++l lcl|NCBI__GCF_000195895.1:WP_011308421.1 3 KDVLSITDLSKEEIYELLESAMDLKEKRKAGEPTEYLKNKSLGMIFEKASTRTRVSFEVAMTDFGGHSL 71 689****************************************************************** PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 yln+ ++q+gr+e+i+Dtar+ls y+++i++Rv++he+ve+laky+++Pvin+L+d ehPcqil D++t lcl|NCBI__GCF_000195895.1:WP_011308421.1 72 YLNSRDIQIGRGETIEDTARTLSGYLHGIMARVMSHETVEKLAKYSTIPVINALSDREHPCQILGDFMT 140 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 i+e+++k++++k+++vGD+nnv+ns ll++a +G+++ va+P+g+ep++e ++kak ggk+++t lcl|NCBI__GCF_000195895.1:WP_011308421.1 141 IMEYKDKFEDLKFAWVGDGNNVCNSALLGSAIVGMEFAVACPKGYEPKPEFLEKAK----SLGGKFTVT 205 ******************************************************95....58******* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 +dpk avkdad+iytDvwvsmG+e+++e+rlk + +qvn+ell +akp+v+++hCLPa rG e+tdev lcl|NCBI__GCF_000195895.1:WP_011308421.1 206 DDPKVAVKDADIIYTDVWVSMGDEAEQEKRLKEFATFQVNTELLGVAKPDVIVMHCLPARRGLEITDEV 274 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s++f+eaenRlhaqka++ l+ lcl|NCBI__GCF_000195895.1:WP_011308421.1 275 MDGPNSVIFEEAENRLHAQKALILKLM 301 **********************98876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (302 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: 11.37 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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