Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate 3607382 Dshi_0796 ornithine carbamoyltransferase (RefSeq)
Query= BRENDA::Q98BB6 (303 letters) >FitnessBrowser__Dino:3607382 Length = 308 Score = 356 bits (913), Expect = e-103 Identities = 179/305 (58%), Positives = 219/305 (71%), Gaps = 7/305 (2%) Query: 5 HFTDLSTVSEGDLRFMLDDA----VVRKARLK-AGERTRPLEGKVLAMIFDKPSTRTRVS 59 HF D+ T DLR MLD R R K A + +PL G ++A+IF+KPSTRTRVS Sbjct: 3 HFLDIHTTDPADLRAMLDRGRAMKTARAGRPKGASDDDQPLAGHMVALIFEKPSTRTRVS 62 Query: 60 FDVGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENAT 119 FD+G+RQ+GG+T++L+G +MQLG ETIADTA+VLSRYVD IMIRT LLE+ E+A+ Sbjct: 63 FDLGVRQMGGQTMVLSGADMQLGHGETIADTARVLSRYVDLIMIRTFEETTLLEMAEHAS 122 Query: 120 VPVINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLN 179 VPVINGLT+ THPCQ+MAD+MT+EEHRGP+AGK + W GDGNNV S L A+ +F F++ Sbjct: 123 VPVINGLTNRTHPCQIMADVMTYEEHRGPIAGKKVVWCGDGNNVCASFLHAAGQFGFDMT 182 Query: 180 VAVPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSM--GQEHRARGHN 237 P +P + + ++A G + R P AV AD VV D WVSM Q + R HN Sbjct: 183 FTGPPTLDPEAEFVAGARAKGVTVEIERDPAVAVQGADLVVADTWVSMHDSQTTKERRHN 242 Query: 238 VFSPYQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVL 297 PYQV+ LM AKPDALFMHCLPAHRGEEVT EV+DGPHSV+FDEAENRLHAQKAV+ Sbjct: 243 QLRPYQVDRALMEKAKPDALFMHCLPAHRGEEVTSEVMDGPHSVIFDEAENRLHAQKAVM 302 Query: 298 AWCLG 302 WCLG Sbjct: 303 RWCLG 307 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: 340 Number of extensions: 14 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: 308 Length adjustment: 27 Effective length of query: 276 Effective length of database: 281 Effective search space: 77556 Effective search space used: 77556 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 3607382 Dshi_0796 (ornithine carbamoyltransferase (RefSeq))
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.462697.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-116 374.4 0.0 2.3e-116 374.2 0.0 1.0 1 FitnessBrowser__Dino:3607382 Domain annotation for each sequence (and alignments): >> FitnessBrowser__Dino:3607382 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 374.2 0.0 2.3e-116 2.3e-116 2 303 .. 3 306 .. 2 307 .. 0.96 Alignments for each domain: == domain 1 score: 374.2 bits; conditional E-value: 2.3e-116 TIGR00658 2 hllslldlseeelkellelakklkkekkkgke.....ekklkgktlaliFekrstRtRvsfevaayelGaqvlylnkeelq 77 h+l+++ ++++l+ +l++++ +k+++ + ++ l g+ +aliFek+stRtRvsf+ ++ ++G+q+++l+ ++q FitnessBrowser__Dino:3607382 3 HFLDIHTTDPADLRAMLDRGRAMKTARAGRPKgasddDQPLAGHMVALIFEKPSTRTRVSFDLGVRQMGGQTMVLSGADMQ 83 9***********************9887544445566999***************************************** PP TIGR00658 78 lgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDlltikeklgklkevklvyvGDan 158 lg++e+i+Dtarvlsryvd i++R+++++++ e+a++asvPvingLt+ +hPcqi+aD++t +e+ g + + k+v+ GD+n FitnessBrowser__Dino:3607382 84 LGHGETIADTARVLSRYVDLIMIRTFEETTLLEMAEHASVPVINGLTNRTHPCQIMADVMTYEEHRGPIAGKKVVWCGDGN 164 ********************************************************************************* PP TIGR00658 159 nvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggkleltedpkkavkdadviytDvwvsmGe.eekkeerl 238 nv+ s+l aa ++G+d++ ++P+ l+peae v a+ ++g ++e+ +dp+ av++ad+++ D+wvsm + +++ke r FitnessBrowser__Dino:3607382 165 NVCASFLHAAGQFGFDMTFTGPPTLDPEAEFVAGAR----AKGVTVEIERDPAVAVQGADLVVADTWVSMHDsQTTKERRH 241 ********************************9995....59*****************************9566777788 PP TIGR00658 239 kllkpyqvneellelakpevkflhCLPavrGeevtdevlegeasivfdeaenRlhaqkavlkall 303 ++l+pyqv++ l+e akp++ f+hCLPa+rGeevt ev++g++s++fdeaenRlhaqkav+ ++l FitnessBrowser__Dino:3607382 242 NQLRPYQVDRALMEKAKPDALFMHCLPAHRGEEVTSEVMDGPHSVIFDEAENRLHAQKAVMRWCL 306 9************************************************************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (308 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: 00:00:00.00 # Mc/sec: 12.54 // [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