Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_011382764.1 AMB_RS01610 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >NCBI__GCF_000009985.1:WP_011382764.1 Length = 305 Score = 341 bits (874), Expect = 1e-98 Identities = 172/298 (57%), Positives = 210/298 (70%), Gaps = 4/298 (1%) Query: 4 RHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSFDVG 63 RHF DL LR +LD + K + PL GK+LAMIF+KPSTRTRVSF+VG Sbjct: 11 RHFLDLDGFDTATLRHILDLGLAYK---QGKGPKAPLAGKMLAMIFEKPSTRTRVSFEVG 67 Query: 64 MRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVPVI 123 M+QLGG+ IML + QLGR ETIADTA+VLSR+VDA+MIRT ++L EL + A VPVI Sbjct: 68 MKQLGGDVIMLAAGDTQLGRGETIADTARVLSRFVDAVMIRTNLPEKLTELAKYADVPVI 127 Query: 124 NGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVAVP 183 NGLTD +HPCQ+MAD+MTFEEHRG + GK +AW GDGNNV S + A+ F + +A P Sbjct: 128 NGLTDQSHPCQVMADVMTFEEHRGSLKGKVVAWVGDGNNVAASWIHAAGHFGCEIRLACP 187 Query: 184 EGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSPYQ 243 + P++ +DW++A G + T P EAV A V+TD WVSMG + R H + PYQ Sbjct: 188 DSLMPSRAAVDWARAKGASVVLTTHPAEAVAGAHLVLTDTWVSMGCQDSNR-HELLEPYQ 246 Query: 244 VNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCL 301 VN LMA A PDALFMHCLPAHRGEEVTD V+DG SVV+DEAENR+H QK +L WCL Sbjct: 247 VNEALMAKAAPDALFMHCLPAHRGEEVTDPVMDGIQSVVWDEAENRMHVQKGILTWCL 304 Lambda K H 0.320 0.133 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: 343 Number of extensions: 11 Number of successful extensions: 3 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: 303 Length of database: 305 Length adjustment: 27 Effective length of query: 276 Effective length of database: 278 Effective search space: 76728 Effective search space used: 76728 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_011382764.1 AMB_RS01610 (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.10778.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.3e-115 371.7 0.0 1.5e-115 371.5 0.0 1.0 1 lcl|NCBI__GCF_000009985.1:WP_011382764.1 AMB_RS01610 ornithine carbamoylt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000009985.1:WP_011382764.1 AMB_RS01610 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 371.5 0.0 1.5e-115 1.5e-115 1 303 [. 11 304 .. 11 305 .] 0.98 Alignments for each domain: == domain 1 score: 371.5 bits; conditional E-value: 1.5e-115 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 rh+l+l ++++ l+++l+l+ +k+ k ++ l gk la+iFek+stRtRvsfev++ +lG+ v+ lcl|NCBI__GCF_000009985.1:WP_011382764.1 11 RHFLDLDGFDTATLRHILDLGLAYKQGKGP---KAPLAGKMLAMIFEKPSTRTRVSFEVGMKQLGGDVI 76 8*************************9988...689********************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l + ++qlgr+e+i+Dtarvlsr+vda+++R++ e+++elakya vPvingLtd++hPcq++aD++t lcl|NCBI__GCF_000009985.1:WP_011382764.1 77 MLAAGDTQLGRGETIADTARVLSRFVDAVMIRTNLPEKLTELAKYADVPVINGLTDQSHPCQVMADVMT 145 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 +e+ g+lk+ +++vGD+nnva s + aa +G ++++a+P+ l p+ + v++a++ +g+++ lt lcl|NCBI__GCF_000009985.1:WP_011382764.1 146 FEEHRGSLKGKVVAWVGDGNNVAASWIHAAGHFGCEIRLACPDSLMPSRAAVDWARA----KGASVVLT 210 *****************************************************9965....9******* PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 p++av++a+++ tD+wvsmG ++++ r +ll+pyqvne l++ a p++ f+hCLPa+rGeevtd v lcl|NCBI__GCF_000009985.1:WP_011382764.1 211 THPAEAVAGAHLVLTDTWVSMGCQDSN--RHELLEPYQVNEALMAKAAPDALFMHCLPAHRGEEVTDPV 277 **********************99887..999************************************* PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g +s+v+deaenR+h+qk++l+++l lcl|NCBI__GCF_000009985.1:WP_011382764.1 278 MDGIQSVVWDEAENRMHVQKGILTWCL 304 ***********************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (305 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 10.01 // [ok]
This GapMind analysis is from Sep 17 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