Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate WP_011606298.1 FRAAL_RS22690 ornithine carbamoyltransferase
Query= SwissProt::A0QYS8 (307 letters) >NCBI__GCF_000058485.1:WP_011606298.1 Length = 342 Score = 327 bits (838), Expect = 2e-94 Identities = 172/305 (56%), Positives = 214/305 (70%), Gaps = 4/305 (1%) Query: 3 RHFLRDDDLSPEEQAEVLTLAADLKKTPFSRRPLEGP---RGVAVIFEKNSTRTRFSFEM 59 RHFL D DL+ EQA +L +A LK P + P R VA++FEK STRTR SF++ Sbjct: 4 RHFLLDTDLTSAEQAGILDVADQLKARRRDPGPADRPLAGRSVALLFEKPSTRTRLSFDV 63 Query: 60 GIAQLGGHAIVVDGRSTQLGREETLEDTGAVLSRYVDAIVWRTFAQERLTAMASGASVPI 119 G+A+LGGH IV+D ++ LGR ET+EDT AVLSRYVDAIV RTFAQ+RL +A+ ASVP+ Sbjct: 64 GVAELGGHPIVIDATTSHLGRGETIEDTAAVLSRYVDAIVVRTFAQQRLERLAAAASVPV 123 Query: 120 VNALSDEFHPCQVLADLQTLAERKGKLAGLRMTYFGDGANNMAHSLMLGGVTAGVHVTIA 179 VNALSD HPCQ LADLQT+ ER+G+LAGL +TY GDG NN+AHSL+L G AG+ V +A Sbjct: 124 VNALSDHAHPCQALADLQTIRERRGRLAGLTLTYLGDG-NNVAHSLLLAGALAGMRVHVA 182 Query: 180 APDGFEPDPRFVDAARRRAAETGATVALTKDAKAGADGADVLVTDTWTSMGQENDGLDRV 239 +P G+EP + V A A TG + DA A GADVL TD W SMGQE++ R Sbjct: 183 SPPGYEPFEQVVRHANEIGATTGGEALVMHDALEAAAGADVLYTDVWASMGQEDESDSRS 242 Query: 240 RPFRPFQVNADLLELADPAAVVLHCLPAHRGHEITDEVIDGPQSAVFDEAENRLHAQKAL 299 F+P++++ +E A P +V+HCLPAHR EI V+DGP S VFD+AENRLHAQKAL Sbjct: 243 LVFQPYRLDEKAVEAARPDVLVMHCLPAHRDLEIAASVLDGPHSVVFDQAENRLHAQKAL 302 Query: 300 LVWLL 304 L LL Sbjct: 303 LSLLL 307 Lambda K H 0.319 0.135 0.393 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: 308 Number of extensions: 10 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: 307 Length of database: 342 Length adjustment: 28 Effective length of query: 279 Effective length of database: 314 Effective search space: 87606 Effective search space used: 87606 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_011606298.1 FRAAL_RS22690 (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.1133.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-120 388.2 0.0 1.4e-120 388.0 0.0 1.0 1 lcl|NCBI__GCF_000058485.1:WP_011606298.1 FRAAL_RS22690 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000058485.1:WP_011606298.1 FRAAL_RS22690 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 388.0 0.0 1.4e-120 1.4e-120 1 303 [. 4 307 .. 4 308 .. 0.98 Alignments for each domain: == domain 1 score: 388.0 bits; conditional E-value: 1.4e-120 TIGR00658 1 rhllslldlseeelkellelakklkkekkkg.keekklkgktlaliFekrstRtRvsfevaayelGaqv 68 rh+l +dl+++e +l++a++lk++++ ++ l g+++al+Fek+stRtR+sf+v+++elG+++ lcl|NCBI__GCF_000058485.1:WP_011606298.1 4 RHFLLDTDLTSAEQAGILDVADQLKARRRDPgPADRPLAGRSVALLFEKPSTRTRLSFDVGVAELGGHP 72 7899999******************999885156899******************************** PP TIGR00658 69 lylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDll 137 +++++ ++lgr+e+i+Dta vlsryvdaivvR+++++ +e la asvPv+n+L+d++hPcq+laDl+ lcl|NCBI__GCF_000058485.1:WP_011606298.1 73 IVIDATTSHLGRGETIEDTAAVLSRYVDAIVVRTFAQQRLERLAAAASVPVVNALSDHAHPCQALADLQ 141 ********************************************************************* PP TIGR00658 138 tikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklel 206 ti+e+ g+l +++l+y+GD+nnva+sllla+a+ G+ v+va+P+g+ep +++v++a++i + +gg+ + lcl|NCBI__GCF_000058485.1:WP_011606298.1 142 TIRERRGRLAGLTLTYLGDGNNVAHSLLLAGALAGMRVHVASPPGYEPFEQVVRHANEIGATTGGEALV 210 ********************************************************************* PP TIGR00658 207 tedpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtde 275 ++d +a+++adv+ytDvw+smG+e++ ++r +++py ++e+ +e a p+v ++hCLPa+r e++ lcl|NCBI__GCF_000058485.1:WP_011606298.1 211 MHDALEAAAGADVLYTDVWASMGQEDESDSRSLVFQPYRLDEKAVEAARPDVLVMHCLPAHRDLEIAAS 279 ********************************************************************* PP TIGR00658 276 vlegeasivfdeaenRlhaqkavlkall 303 vl+g++s+vfd+aenRlhaqka+l++ll lcl|NCBI__GCF_000058485.1:WP_011606298.1 280 VLDGPHSVVFDQAENRLHAQKALLSLLL 307 ************************9987 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 9.62 // [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