Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_092482997.1 BM299_RS08240 ornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_900115975.1:WP_092482997.1 Length = 315 Score = 378 bits (970), Expect = e-109 Identities = 190/307 (61%), Positives = 231/307 (75%) Query: 4 SLKGRDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVS 63 +LKGRDLL L D+TP EI IL+ A LK QK G+PH LL+G TLAMIFQK STRTRVS Sbjct: 7 NLKGRDLLSLHDFTPGEIQFILDYAADLKQKQKNGEPHELLKGLTLAMIFQKSSTRTRVS 66 Query: 64 FEVAMAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYAS 123 FEV M LGGHALYLNA DLQL RGE+IADT RVL RY D IM R + DVE+LA+ AS Sbjct: 67 FEVGMYQLGGHALYLNANDLQLGRGESIADTGRVLGRYADGIMIRTFAQGDVEELAECAS 126 Query: 124 VPVINGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVV 183 +PVINGL+D HPCQ LAD +T+ E KG + G+K+ YVGDGNNV HSL+ K G + Sbjct: 127 IPVINGLTDLLHPCQILADLLTVQEHKGRLAGLKLAYVGDGNNVCHSLLYGCAKTGMHIS 186 Query: 184 VATPEGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEE 243 VA+PEG+ P E+++ A +AA +G + DP +AV ADV+ TDVWASMGQE+E + Sbjct: 187 VASPEGFLPREEIVATARYDAAATGAEVTVTTDPAEAVSGADVVVTDVWASMGQESEQQA 246 Query: 244 RRKIFRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQK 303 R ++F P+QVN+ LV A DY+F+HCLPAHRGEEV +VID P+SVV+DEAENRLHAQK Sbjct: 247 RMRVFAPYQVNEQLVAKAASDYIFLHCLPAHRGEEVAAEVIDGPHSVVFDEAENRLHAQK 306 Query: 304 AVLALLL 310 AVL+LL+ Sbjct: 307 AVLSLLM 313 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: 307 Number of extensions: 11 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: 317 Length of database: 315 Length adjustment: 27 Effective length of query: 290 Effective length of database: 288 Effective search space: 83520 Effective search space used: 83520 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_092482997.1 BM299_RS08240 (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.26937.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-140 453.7 0.0 1.6e-140 453.6 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092482997.1 BM299_RS08240 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092482997.1 BM299_RS08240 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 453.6 0.0 1.6e-140 1.6e-140 1 303 [. 11 313 .. 11 314 .. 0.99 Alignments for each domain: == domain 1 score: 453.6 bits; conditional E-value: 1.6e-140 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 r+llsl+d+++ e++ +l++a++lk+++k+g+ ++ lkg tla+iF+k+stRtRvsfev++y+lG+++l lcl|NCBI__GCF_900115975.1:WP_092482997.1 11 RDLLSLHDFTPGEIQFILDYAADLKQKQKNGEPHELLKGLTLAMIFQKSSTRTRVSFEVGMYQLGGHAL 79 79******************************************************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 yln+++lqlgr+esi+Dt rvl+ry d+i++R++++ dveela+ as+PvingLtdl hPcqilaDllt lcl|NCBI__GCF_900115975.1:WP_092482997.1 80 YLNANDLQLGRGESIADTGRVLGRYADGIMIRTFAQGDVEELAECASIPVINGLTDLLHPCQILADLLT 148 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 ++e++g+l ++kl+yvGD+nnv++sll ++ak+G++++va+Peg+ p++eiv +a+ a+++g+++++t lcl|NCBI__GCF_900115975.1:WP_092482997.1 149 VQEHKGRLAGLKLAYVGDGNNVCHSLLYGCAKTGMHISVASPEGFLPREEIVATARYDAAATGAEVTVT 217 ********************************************************************* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 dp++av++adv++tDvw+smG+e+++++r++++ pyqvne+l++ a ++++flhCLPa+rGeev+ ev lcl|NCBI__GCF_900115975.1:WP_092482997.1 218 TDPAEAVSGADVVVTDVWASMGQESEQQARMRVFAPYQVNEQLVAKAASDYIFLHCLPAHRGEEVAAEV 286 ********************************************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s+vfdeaenRlhaqkavl++l+ lcl|NCBI__GCF_900115975.1:WP_092482997.1 287 IDGPHSVVFDEAENRLHAQKAVLSLLM 313 ***********************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 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 10.11 // [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