Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate WP_245257982.1 RVAN_RS11965 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >NCBI__GCF_000166055.1:WP_245257982.1 Length = 312 Score = 358 bits (919), Expect = e-104 Identities = 179/300 (59%), Positives = 220/300 (73%), Gaps = 3/300 (1%) Query: 4 RHFTDLSTVSEGDLRFMLDDAVVRKARLK---AGERTRPLEGKVLAMIFDKPSTRTRVSF 60 RHF D+ LR +LD+A K +K A + + EGKVLAM+F+K STRTRVSF Sbjct: 9 RHFLDIDDYDFDTLRLILDNARALKKLIKTSPASDWPKVAEGKVLAMLFEKSSTRTRVSF 68 Query: 61 DVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATV 120 DV MRQLGGETI+L +MQLGR ETIADTA+VLSRYVDAIM+R TSH+ L+EL E++ V Sbjct: 69 DVAMRQLGGETIVLNRNDMQLGRGETIADTARVLSRYVDAIMMRCTSHEALIELAEHSAV 128 Query: 121 PVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNV 180 PVINGL+D +HPCQ++ADIMT EEH+G VA +AW GD NNV S + A+ RF F + + Sbjct: 129 PVINGLSDRSHPCQILADIMTLEEHKGDVAPLKVAWIGDFNNVTASWVHAAVRFGFAMTL 188 Query: 181 AVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFS 240 A P+ +P + +DW+ GG++ P AV ADCVVTD WVSMGQE+ A + + Sbjct: 189 ATPKLLQPPRSFLDWANDEGGRITVVEDPAVAVAGADCVVTDVWVSMGQENVAERETLLA 248 Query: 241 PYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWC 300 PYQVNA LM A +A+FMHCLPAHRG EVTD+VIDGP SVVFDEAENRLHAQ+A+LAWC Sbjct: 249 PYQVNAALMEKADKNAIFMHCLPAHRGREVTDDVIDGPQSVVFDEAENRLHAQRAILAWC 308 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: 336 Number of extensions: 13 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: 303 Length of database: 312 Length adjustment: 27 Effective length of query: 276 Effective length of database: 285 Effective search space: 78660 Effective search space used: 78660 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_245257982.1 RVAN_RS11965 (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.1179627.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-120 388.0 0.0 1.6e-120 387.8 0.0 1.0 1 NCBI__GCF_000166055.1:WP_245257982.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000166055.1:WP_245257982.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 387.8 0.0 1.6e-120 1.6e-120 1 303 [. 9 309 .. 9 310 .. 0.97 Alignments for each domain: == domain 1 score: 387.8 bits; conditional E-value: 1.6e-120 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgke...ekklkgktlaliFekrstRtRvsfevaayelGaqvly 70 rh+l++ d++ + l+ +l+ a+ lkk k++ k +gk la++Fek+stRtRvsf+va+ +lG+++++ NCBI__GCF_000166055.1:WP_245257982.1 9 RHFLDIDDYDFDTLRLILDNARALKKLIKTSPAsdwPKVAEGKVLAMLFEKSSTRTRVSFDVAMRQLGGETIV 81 8************************9877755444468899******************************** PP TIGR00658 71 lnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikekl 143 ln++++qlgr+e+i+Dtarvlsryvdai++R ++he + ela++++vPvingL+d +hPcqilaD++t++e++ NCBI__GCF_000166055.1:WP_245257982.1 82 LNRNDMQLGRGETIADTARVLSRYVDAIMMRCTSHEALIELAEHSAVPVINGLSDRSHPCQILADIMTLEEHK 154 ************************************************************************* PP TIGR00658 144 gklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkd 216 g++ +k++++GD nnv+ s + aa+ +G+ +++atP+ l+p + +++a +++gg+++++edp+ av++ NCBI__GCF_000166055.1:WP_245257982.1 155 GDVAPLKVAWIGDFNNVTASWVHAAVRFGFAMTLATPKLLQPPRSFLDWA----NDEGGRITVVEDPAVAVAG 223 ************************************************99....669**************** PP TIGR00658 217 adviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeae 289 ad ++tDvwvsmG+e+ + er ll pyqvn l+e a+++++f+hCLPa+rG+evtd+v++g++s+vfdeae NCBI__GCF_000166055.1:WP_245257982.1 224 ADCVVTDVWVSMGQENVA-ERETLLAPYQVNAALMEKADKNAIFMHCLPAHRGREVTDDVIDGPQSVVFDEAE 295 **************9987.899*************************************************** PP TIGR00658 290 nRlhaqkavlkall 303 nRlhaq+a+l++++ NCBI__GCF_000166055.1:WP_245257982.1 296 NRLHAQRAILAWCF 309 **********9876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (312 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: 17.79 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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