Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_073039304.1 BUB04_RS11055 ornithine carbamoyltransferase
Query= BRENDA::O93656 (317 letters) >NCBI__GCF_900129305.1:WP_073039304.1 Length = 307 Score = 318 bits (816), Expect = 8e-92 Identities = 160/303 (52%), Positives = 216/303 (71%), Gaps = 3/303 (0%) Query: 8 RDLLCLQDYTPEEIWTILETAKMLKIWQKIGKPHRLLEGKTLAMIFQKPSTRTRVSFEVA 67 RD L L D +E+ +L+ A LK G +L+ KTL MIF KPSTRTRVSFE A Sbjct: 3 RDFLSLWDVNADELNHLLDLAGRLKAEWAAGTLRPVLQQKTLGMIFSKPSTRTRVSFEAA 62 Query: 68 MAHLGGHALYLNAQDLQLRRGETIADTARVLSRYVDAIMARVYDHKDVEDLAKYASVPVI 127 M LGG+ +++ QD Q+ R E ++DTARVLSRY+ A++ R Y ++VE LA+YAS+PVI Sbjct: 63 MHRLGGNCTFMSVQDTQISRAEPLSDTARVLSRYIHALVVRTYAQEEVETLAQYASIPVI 122 Query: 128 NGLSDFSHPCQALADYMTIWEKKGTIKGVKVVYVGDGNNVAHSLMIAGTKLGADVVVATP 187 NGL+D HPCQ L+D +TI EK+G++ G+ V ++GDGNN+AHS + A +LG + +A P Sbjct: 123 NGLTDLYHPCQVLSDLLTIREKRGSLDGMVVAWIGDGNNMAHSWINASARLGFRLNIACP 182 Query: 188 EGYEPDEKVIKWAEQNAAESGGSFELLHDPVKAVKDADVIYTDVWASMGQEAEAEERRKI 247 EGY P +VI E+ E L DP +AV++ADVI TDVWASMGQE+EA RR + Sbjct: 183 EGYWPSARVI---ERARTEGAAPIRLFDDPRQAVEEADVINTDVWASMGQESEAATRRAL 239 Query: 248 FRPFQVNKDLVKHAKPDYMFMHCLPAHRGEEVTDDVIDSPNSVVWDEAENRLHAQKAVLA 307 F+PFQVN++L+++A M +HCLPAHRGEE+T++V++ P SVV+D+AENRLHAQ A+L Sbjct: 240 FQPFQVNRELLRYAPSHAMVLHCLPAHRGEEITEEVLEGPQSVVFDQAENRLHAQAALLY 299 Query: 308 LLL 310 LL Sbjct: 300 WLL 302 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: 291 Number of extensions: 12 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: 307 Length adjustment: 27 Effective length of query: 290 Effective length of database: 280 Effective search space: 81200 Effective search space used: 81200 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_073039304.1 BUB04_RS11055 (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.1804690.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-126 406.0 0.0 5.5e-126 405.8 0.0 1.0 1 NCBI__GCF_900129305.1:WP_073039304.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900129305.1:WP_073039304.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 405.8 0.0 5.5e-126 5.5e-126 1 303 [. 3 302 .. 3 303 .. 0.99 Alignments for each domain: == domain 1 score: 405.8 bits; conditional E-value: 5.5e-126 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvlylnk 73 r++lsl+d++ +el++ll+la +lk+e +g+ + l++ktl++iF k+stRtRvsfe+a+ +lG++ ++++ NCBI__GCF_900129305.1:WP_073039304.1 3 RDFLSLWDVNADELNHLLDLAGRLKAEWAAGTLRPVLQQKTLGMIFSKPSTRTRVSFEAAMHRLGGNCTFMSV 75 79*********************************************************************** PP TIGR00658 74 eelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgkl 146 +++q++r e+++Dtarvlsry++a+vvR+y++e+ve+la+yas+PvingLtdl hPcq+l+Dllti+ek g+l NCBI__GCF_900129305.1:WP_073039304.1 76 QDTQISRAEPLSDTARVLSRYIHALVVRTYAQEEVETLAQYASIPVINGLTDLYHPCQVLSDLLTIREKRGSL 148 ************************************************************************* PP TIGR00658 147 kevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadv 219 +++ ++++GD+nn+a+s + a+a lG+ +++a+Peg++p+a+++++a+ e + ++l +dp +av++adv NCBI__GCF_900129305.1:WP_073039304.1 149 DGMVVAWIGDGNNMAHSWINASARLGFRLNIACPEGYWPSARVIERART---EGAAPIRLFDDPRQAVEEADV 218 ***********************************************76...77799**************** PP TIGR00658 220 iytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRl 292 i tDvw+smG+e++++ r +l++p+qvn+ell++a +++++lhCLPa+rGee+t+evleg++s+vfd+aenRl NCBI__GCF_900129305.1:WP_073039304.1 219 INTDVWASMGQESEAATRRALFQPFQVNRELLRYAPSHAMVLHCLPAHRGEEITEEVLEGPQSVVFDQAENRL 291 ************************************************************************* PP TIGR00658 293 haqkavlkall 303 haq a+l +ll NCBI__GCF_900129305.1:WP_073039304.1 292 HAQAALLYWLL 302 ******99987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (307 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: 21.24 // [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