Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate AZOBR_RS03220 AZOBR_RS03220 3-dehydroquinate synthase
Query= SwissProt::U3KRF2 (445 letters) >FitnessBrowser__azobra:AZOBR_RS03220 Length = 378 Score = 289 bits (740), Expect = 9e-83 Identities = 167/360 (46%), Positives = 227/360 (63%), Gaps = 11/360 (3%) Query: 81 PTIVD---VDLGDRSYPIYIGSGLLDQPD-LLQRHVHGKRVLVVTNSTVAPIYLDKVVGA 136 PT +D +DLG RSY I +G +LD + GK +VVT+ VAP +L + Sbjct: 7 PTAIDTVRLDLGPRSYDILVGDRVLDGAGPRIAAITRGKAPIVVTDENVAPRHLPTLERT 66 Query: 137 LTNGNPNVSVESVILPDGEKYKNMDTLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYA 196 L + + ++++LP GEK K++ ++ D + ++R +ALGGGVIGD+ G+A Sbjct: 67 LRDAGIEPT-QAIVLPAGEKTKDIAHFERLMDAVLARGIERSAVLLALGGGVIGDITGFA 125 Query: 197 AASFLRGVNFIQIPTTVMAQVDSSVGGKTGINHRLGKNLIGAFYQPQCVLIDTDTLNTLP 256 AAS LRG++FIQ+PTT+++QVDSSVGGKTGIN GKNLIGAF+QP+ V+ DT TL+TLP Sbjct: 126 AASALRGIDFIQVPTTLLSQVDSSVGGKTGINSPHGKNLIGAFHQPRLVIADTATLDTLP 185 Query: 257 DRELASGLAEVVKYGLIRDANFFEWQEKNMPALMARDPSALAYAIKRSCENKAEVVSLDE 316 RE+ +G AEVVKYGLIR FF W E+N ++A D A +A+ SC KA +V +DE Sbjct: 186 RREVLAGYAEVVKYGLIRLPGFFAWLEENGERVVAGDSDARRHAVTESCRAKAAIVGVDE 245 Query: 317 KESGLRATLNLGHTFGHAIETGFGYG-QWLHGEAVAAGMVMAVDMSYRLGWIDESIVNRA 375 +ESG RA LNLGHTFGHA+E G+G + LHGEAV+ GMV+A D+S RLG + +A Sbjct: 246 RESGDRALLNLGHTFGHALEAATGFGSRLLHGEAVSIGMVLAFDLSVRLGLCPAADAEKA 305 Query: 376 HNILQQAKLPTAPPETMTVEM----FKSVMAVDKKVADGLLRLILLKGPLGNCVFTGDYD 431 L + LP P + VE MA DKKV DG + +L++ LG+ D D Sbjct: 306 RAHLARVGLPVRPTDVPGVEWDIDGLILSMAKDKKVKDGRITFVLVRA-LGDAFTQRDVD 364 Lambda K H 0.318 0.133 0.385 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: 398 Number of extensions: 13 Number of successful extensions: 4 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: 445 Length of database: 378 Length adjustment: 31 Effective length of query: 414 Effective length of database: 347 Effective search space: 143658 Effective search space used: 143658 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate AZOBR_RS03220 AZOBR_RS03220 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))
# 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/TIGR01357.hmm # target sequence database: /tmp/gapView.8830.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01357 [M=344] Accession: TIGR01357 Description: aroB: 3-dehydroquinate synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-111 357.8 0.0 3.9e-111 357.5 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS03220 AZOBR_RS03220 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS03220 AZOBR_RS03220 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 357.5 0.0 3.9e-111 3.9e-111 1 336 [. 22 365 .. 22 372 .. 0.95 Alignments for each domain: == domain 1 score: 357.5 bits; conditional E-value: 3.9e-111 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgve.vlvlvvpdgeesKsle 66 y++ vg+ +l+ + +a + + +v+tde+v+ + +le++l+++g+e ++ +v+p+ge++K+++ lcl|FitnessBrowser__azobra:AZOBR_RS03220 22 YDILVGDRVLDGAGPRIAAitRGKAPIVVTDENVAPRHLPTLERTLRDAGIEpTQAIVLPAGEKTKDIA 90 68999999999999999987455999***********************7652778899********** PP TIGR01357 67 tvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135 ++++l+d++l++++er+ vl+a+GGGv+gD++GF+Aa+ lRGi+++qvPTtll++vDssvGGKtgin p lcl|FitnessBrowser__azobra:AZOBR_RS03220 91 HFERLMDAVLARGIERSAVLLALGGGVIGDITGFAAASALRGIDFIQVPTTLLSQVDSSVGGKTGINSP 159 ********************************************************************* PP TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleale 204 +gkNliGaf+qP++V+ d+++l tlp+re+ +G+aEv+K+gli +f++le+n + ++ + +a + lcl|FitnessBrowser__azobra:AZOBR_RS03220 160 HGKNLIGAFHQPRLVIADTATLDTLPRREVLAGYAEVVKYGLIRLPGFFAWLEENGERVVAG-DSDARR 227 ********************************************************988875.559*** PP TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271 +++++s++ Ka +V De+esg RalLN+GHt+gHa+Ea+++++ l HGeaV+iGmv+++ ls +lgl lcl|FitnessBrowser__azobra:AZOBR_RS03220 228 HAVTESCRAKAAIVGVDERESGDRALLNLGHTFGHALEAATGFGsrLLHGEAVSIGMVLAFDLSVRLGL 296 ******************************************9999*********************** PP TIGR01357 272 lkaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevte 336 ++a ++e+ +a l ++glp++ ++ +++++ l+ ++ kDKK ++++i++vl++++G+a+++++v+ lcl|FitnessBrowser__azobra:AZOBR_RS03220 297 CPAADAEKARAHLARVGLPVRPTDvpgvEWDIDGLILSMAKDKKVKDGRITFVLVRALGDAFTQRDVDP 365 **********************99999***********************************9987754 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (378 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: 00:00:00.01 # Mc/sec: 7.91 // [ok]
This GapMind analysis is from Apr 09 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