Align ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate AZOBR_RS19030 AZOBR_RS19030 ornithine carbamoyltransferase
Query= BRENDA::Q98BB6 (303 letters) >FitnessBrowser__azobra:AZOBR_RS19030 Length = 304 Score = 357 bits (916), Expect = e-103 Identities = 180/302 (59%), Positives = 216/302 (71%), Gaps = 2/302 (0%) Query: 2 SVRHFTDLSTVSEGDLRFMLDDAVVRKARLKAGERTRPLEGKVLAMIFDKPSTRTRVSFD 61 +VRHF D+ + + LR +L A K + A G+ LAMIF+KPSTRTRVSF+ Sbjct: 3 AVRHFLDIDRLDKATLRQILAMAATIKKDIPAYRSL--FAGRTLAMIFEKPSTRTRVSFE 60 Query: 62 VGMRQLGGETIMLTGTEMQLGRSETIADTAKVLSRYVDAIMIRTTSHDRLLELTENATVP 121 VGMRQLGG+ ++L +MQLGR ETI DTA+VLSRYVDA+M+RT +R+ EL E A+VP Sbjct: 61 VGMRQLGGDVVVLKPDDMQLGRGETIGDTARVLSRYVDAVMVRTMGEERVHELAEFASVP 120 Query: 122 VINGLTDDTHPCQLMADIMTFEEHRGPVAGKTIAWTGDGNNVLHSLLEASARFRFNLNVA 181 +INGLTD +HPCQ+MAD+MTFEEHRGP+ G+T+AW GD NNV S + + R + + Sbjct: 121 IINGLTDQSHPCQIMADVMTFEEHRGPIEGRTVAWIGDVNNVAVSWVHVAVRLGVEIRLG 180 Query: 182 VPEGSEPAQKHIDWSKAHGGKLHFTRSPEEAVDQADCVVTDCWVSMGQEHRARGHNVFSP 241 PE PA + +DW K GG++ T SPEEAV ADCVVTD W SM V P Sbjct: 181 CPEIYGPAPELLDWVKREGGRITVTTSPEEAVRGADCVVTDAWASMHNTDVDERAAVLGP 240 Query: 242 YQVNAKLMAHAKPDALFMHCLPAHRGEEVTDEVIDGPHSVVFDEAENRLHAQKAVLAWCL 301 YQVN LMA A PDALFMHCLPAHRGEEVTD VIDG HSVV+DEAENRLHAQKA+LAWCL Sbjct: 241 YQVNEALMALAAPDALFMHCLPAHRGEEVTDGVIDGRHSVVWDEAENRLHAQKAILAWCL 300 Query: 302 GA 303 GA Sbjct: 301 GA 302 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: 361 Number of extensions: 14 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: 304 Length adjustment: 27 Effective length of query: 276 Effective length of database: 277 Effective search space: 76452 Effective search space used: 76452 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 AZOBR_RS19030 AZOBR_RS19030 (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.24308.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-117 377.9 0.0 1.9e-117 377.7 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS19030 AZOBR_RS19030 ornithine carbamoy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS19030 AZOBR_RS19030 ornithine carbamoyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 377.7 0.0 1.9e-117 1.9e-117 1 303 [. 5 300 .. 5 301 .. 0.98 Alignments for each domain: == domain 1 score: 377.7 bits; conditional E-value: 1.9e-117 TIGR00658 1 rhllslldlseeelkellelakklkkekkkgkeekklkgktlaliFekrstRtRvsfevaayelGaqvl 69 rh+l++ l+++ l+++l +a+++kk+ + ++ + g+tla+iFek+stRtRvsfev++ +lG+ v+ lcl|FitnessBrowser__azobra:AZOBR_RS19030 5 RHFLDIDRLDKATLRQILAMAATIKKDIPA--YRSLFAGRTLAMIFEKPSTRTRVSFEVGMRQLGGDVV 71 8*************************9988..6889********************************* PP TIGR00658 70 ylnkeelqlgrkesikDtarvlsryvdaivvRvykhedveelakyasvPvingLtdlehPcqilaDllt 138 +l+++++qlgr+e+i Dtarvlsryvda++vR++ +e v+ela++asvP+ingLtd++hPcqi+aD++t lcl|FitnessBrowser__azobra:AZOBR_RS19030 72 VLKPDDMQLGRGETIGDTARVLSRYVDAVMVRTMGEERVHELAEFASVPIINGLTDQSHPCQIMADVMT 140 ********************************************************************* PP TIGR00658 139 ikeklgklkevklvyvGDannvanslllaaaklGldvvvatPeglepeaeivkkakkiakenggklelt 207 +e+ g +++ +++++GD nnva s + a+ lG+++++ +Pe + p +e++++ k++gg++++t lcl|FitnessBrowser__azobra:AZOBR_RS19030 141 FEEHRGPIEGRTVAWIGDVNNVAVSWVHVAVRLGVEIRLGCPEIYGPAPELLDWV----KREGGRITVT 205 ****************************************************998....67******** PP TIGR00658 208 edpkkavkdadviytDvwvsmGeeekkeerlkllkpyqvneellelakpevkflhCLPavrGeevtdev 276 p++av++ad ++tD w+sm + + +er ++l pyqvne l++la p++ f+hCLPa+rGeevtd v lcl|FitnessBrowser__azobra:AZOBR_RS19030 206 TSPEEAVRGADCVVTDAWASMHNTD-VDERAAVLGPYQVNEALMALAAPDALFMHCLPAHRGEEVTDGV 273 *********************8765.669**************************************** PP TIGR00658 277 legeasivfdeaenRlhaqkavlkall 303 ++g++s+v+deaenRlhaqka+l+++l lcl|FitnessBrowser__azobra:AZOBR_RS19030 274 IDGRHSVVWDEAENRLHAQKAILAWCL 300 ***********************9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (304 nodes) Target sequences: 1 (304 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: 11.46 // [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