Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate YP_004140716.1 Mesci_1508 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000185905.1:YP_004140716.1 Length = 378 Score = 268 bits (684), Expect = 3e-76 Identities = 158/350 (45%), Positives = 208/350 (59%), Gaps = 10/350 (2%) Query: 74 SSQAPTVVEVDLGTRSYPIYIGAGLLDQPDL-LQRHIHGKRVLVVTNTTVAPLYLDKTIS 132 S +AP VVEV LG R+Y I IG+GLL + + R + G R VVT+ VA +L + Sbjct: 2 SIEAPVVVEVGLGDRTYDILIGSGLLARAGAEIARRLPGTRAAVVTDANVAAAHLGALKA 61 Query: 133 ALTDGNPNVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGY 192 +L G V + LP GE+ K+ L +V D + ++L+R +A GGGVIGD+ G+ Sbjct: 62 SLETGGIQTAV--ITLPPGEKTKSFAHLEEVVDGVLAAKLERGDIVIAFGGGVIGDLAGF 119 Query: 193 AAASYLRGVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTL 252 AA RG+NF+QIPT+++AQVDSSVGGKTGIN P GKN++G F+QP+ VL DT L+TL Sbjct: 120 AAGIVRRGMNFVQIPTSLLAQVDSSVGGKTGINSPRGKNLVGVFHQPKLVLADTGVLDTL 179 Query: 253 PDRELASGLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQD 312 P RE +G AE+ KYGLI EFF W E+N + A P AI +C KADVV++D Sbjct: 180 PIREFRAGYAELAKYGLIDRPEFFAWLEKNWVQVFAGGPER-AQAIAEACRAKADVVARD 238 Query: 313 EKESGVRATLNLGHTFGHAVETGVGY--GQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQ 370 E E+G RA LNLGHTFGHA+E Y + +HGE VA G +A S RL Sbjct: 239 EFETGDRALLNLGHTFGHALEAATQYDGSRLVHGEGVAIGMALAYRFSSRLNLASPDDAA 298 Query: 371 RVQKILQQAKLP----TSPPETMTVEMFKSIMAVDKKVADGKLRLILLKG 416 RV+ L+ LP P + E + + DKKV+ G L IL +G Sbjct: 299 RVEAHLRAVGLPWRIADIPGDLPDAEALLAFITQDKKVSRGALTFILTRG 348 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: 380 Number of extensions: 16 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: 378 Length adjustment: 31 Effective length of query: 411 Effective length of database: 347 Effective search space: 142617 Effective search space used: 142617 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 YP_004140716.1 Mesci_1508 (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.31263.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-107 346.0 0.0 1.4e-107 345.8 0.0 1.0 1 lcl|NCBI__GCF_000185905.1:YP_004140716.1 Mesci_1508 3-dehydroquinate synt Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000185905.1:YP_004140716.1 Mesci_1508 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 345.8 0.0 1.4e-107 1.4e-107 1 341 [. 18 365 .. 18 368 .. 0.97 Alignments for each domain: == domain 1 score: 345.8 bits; conditional E-value: 1.4e-107 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++ +g+gll+++ +e+a+ +++ v+td +v++ + l++ l++ g+++ v+++p+ge++Ks+++ lcl|NCBI__GCF_000185905.1:YP_004140716.1 18 YDILIGSGLLARAGAEIARrlPGTRAAVVTDANVAAAHLGALKASLETGGIQTAVITLPPGEKTKSFAH 86 6899*******99999998644499******************************************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +++++d +l++kler ++++a+GGGv+gDlaGF+A + RG+++vq+PT+lla+vDssvGGKtgin p+ lcl|NCBI__GCF_000185905.1:YP_004140716.1 87 LEEVVDGVLAAKLERGDIVIAFGGGVIGDLAGFAAGIVRRGMNFVQIPTSLLAQVDSSVGGKTGINSPR 155 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNl+G f+qPk+Vl d+ vl tlp re+r+G+aE+ K+gli e+f++lekn+ ++ a ++ lcl|NCBI__GCF_000185905.1:YP_004140716.1 156 GKNLVGVFHQPKLVLADTGVLDTLPIREFRAGYAELAKYGLIDRPEFFAWLEKNWVQVF--AGGPERAQ 222 *******************************************************9877..467999** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk...lsHGeaVaiGmvveaklseklgl 271 +i+++++ Ka+vV++De e+g RalLN+GHt+gHa+Ea+++y+ l HGe VaiGm+++ ++s +l l lcl|NCBI__GCF_000185905.1:YP_004140716.1 223 AIAEACRAKADVVARDEFETGDRALLNLGHTFGHALEAATQYDgsrLVHGEGVAIGMALAYRFSSRLNL 291 ******************************************9999*********************** PP TIGR01357 272 lkaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevte 336 ++++++ r++a l+++glp ++ + ++e+ll+++++DKK +++ ++++l + +G+a++a++v++ lcl|NCBI__GCF_000185905.1:YP_004140716.1 292 ASPDDAARVEAHLRAVGLPWRIADipgdLPDAEALLAFITQDKKVSRGALTFILTRGVGQAFIAKDVPA 360 ***********************99998789***********************************999 PP TIGR01357 337 eelle 341 +e+l+ lcl|NCBI__GCF_000185905.1:YP_004140716.1 361 SEVLS 365 98876 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.42 // [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