Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_092053351.1 BQ4888_RS02750 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_900111775.1:WP_092053351.1 Length = 361 Score = 338 bits (867), Expect = 2e-97 Identities = 181/340 (53%), Positives = 234/340 (68%), Gaps = 5/340 (1%) Query: 83 VDLGTRSYPIYIGAGLLDQ-PDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPNV 141 V LG RSYPI+IG G+LD+ + L +RV VVTN TV Y ++ + L G Sbjct: 6 VGLGERSYPIWIGEGILDRLAEALDAVAFPRRVAVVTNPTVFGHYGERVLRLLEGGGYRP 65 Query: 142 TVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRGV 201 TV + LPDGEQ+K ++ L K++D + DR +ALGGGVIGDM G+AAA+Y+RG+ Sbjct: 66 TV--IELPDGEQYKTLQYLEKIYDSLLTGGFDRHSGLLALGGGVIGDMTGFAAATYVRGI 123 Query: 202 NFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASGL 261 F QIPTT+++QVDSSVGGKT +NHPLGKNMIGAFYQP+ V ID TL TLP RE A+G+ Sbjct: 124 PFAQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPRHVHIDVATLKTLPAREFAAGM 183 Query: 262 AEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRAT 321 AEVIKYG+IRD EFF W ++ LL P A YA+K SC+ KADVV +DEKES VRA Sbjct: 184 AEVIKYGVIRDREFFAWLAKHRTELLELRPDALIYAVKSSCQIKADVVEEDEKESSVRAI 243 Query: 322 LNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAKL 381 LN GHTFGHAVET GYG + HGEAVA G +A ++SR LG+ ++ V +++ ++ L Sbjct: 244 LNFGHTFGHAVETLSGYGAYSHGEAVAIGMGVAAELSRLLGFGSEADVDQIRSLMSGFDL 303 Query: 382 PTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNC 421 P PP +++ + + M DKKV DGKLR +L G +G+C Sbjct: 304 PLDPP-AHSLDAYLAAMGRDKKVHDGKLRFVLNHG-IGDC 341 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: 403 Number of extensions: 14 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: 442 Length of database: 361 Length adjustment: 31 Effective length of query: 411 Effective length of database: 330 Effective search space: 135630 Effective search space used: 135630 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 WP_092053351.1 BQ4888_RS02750 (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.1684.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.5e-121 391.8 0.0 1.8e-121 391.5 0.0 1.0 1 lcl|NCBI__GCF_900111775.1:WP_092053351.1 BQ4888_RS02750 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900111775.1:WP_092053351.1 BQ4888_RS02750 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 391.5 0.0 1.8e-121 1.8e-121 1 335 [. 13 347 .. 13 356 .. 0.97 Alignments for each domain: == domain 1 score: 391.5 bits; conditional E-value: 1.8e-121 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++ +geg+l++l+e+l+ + +++ v+t+ +v +++e+++++l+ g++ +v+ +pdge++K+l+ lcl|NCBI__GCF_900111775.1:WP_092053351.1 13 YPIWIGEGILDRLAEALDAvaFPRRVAVVTNPTVFGHYGERVLRLLEGGGYRPTVIELPDGEQYKTLQY 81 6799**************96555********************************************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++k++d ll+ +++r+s l+a+GGGv+gD++GF+Aaty+RGi++ q+PTtll++vDssvGGKt++n+pl lcl|NCBI__GCF_900111775.1:WP_092053351.1 82 LEKIYDSLLTGGFDRHSGLLALGGGVIGDMTGFAAATYVRGIPFAQIPTTLLSQVDSSVGGKTAVNHPL 150 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGafyqP+ V id+++l+tlp re+++GmaEviK+g+i d+e+f++l k+ +ll+l +al lcl|NCBI__GCF_900111775.1:WP_092053351.1 151 GKNMIGAFYQPRHVHIDVATLKTLPAREFAAGMAEVIKYGVIRDREFFAWLAKHRTELLELRP-DALIY 218 ********************************************************9998755.***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 ++k+s+++Ka+vVeeDekes++Ra+LNfGHt+gHa+E+l++y+ +sHGeaVaiGm v+a+ls+ lg+ + lcl|NCBI__GCF_900111775.1:WP_092053351.1 219 AVKSSCQIKADVVEEDEKESSVRAILNFGHTFGHAVETLSGYGaYSHGEAVAIGMGVAAELSRLLGFGS 287 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevt 335 + +++++++l++ + lp + + +s++++l+a+ +DKK +++k+++vl + iG++ l+ ++ lcl|NCBI__GCF_900111775.1:WP_092053351.1 288 EADVDQIRSLMSGFDLPLDPPA-HSLDAYLAAMGRDKKVHDGKLRFVLNHGIGDCGLH-DIA 347 *********************7.********************************998.544 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (361 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: 7.80 // [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