Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate WP_029132271.1 A3GO_RS0103790 3-dehydroquinate synthase
Query= SwissProt::Q8RU74 (442 letters) >NCBI__GCF_000428045.1:WP_029132271.1 Length = 366 Score = 428 bits (1100), Expect = e-124 Identities = 210/364 (57%), Positives = 269/364 (73%), Gaps = 5/364 (1%) Query: 79 TVVEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGN 138 +++ VDL RSYPIYIG L+ + + HIHG++VLVV+NTTVAPLYL+ SAL Sbjct: 6 SILNVDLAERSYPIYIGTNLIGDSAVYRPHIHGQQVLVVSNTTVAPLYLEAVKSALQ--- 62 Query: 139 PNVTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYL 198 V++VILPDGEQ K + ++ D +E+R DRRCT + LGGGV+GDM G+AAA Y Sbjct: 63 -GYQVQTVILPDGEQHKTLAVWQQIIDSLLENRFDRRCTVIGLGGGVVGDMAGFAAACYQ 121 Query: 199 RGVNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELA 258 RGV FIQ+PTT++AQVDSSVGGKTG+NHPLGKNMIGAFYQPQCV+ D TL+TL +R+L+ Sbjct: 122 RGVYFIQVPTTLLAQVDSSVGGKTGVNHPLGKNMIGAFYQPQCVIADIQTLSTLDNRQLS 181 Query: 259 SGLAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGV 318 +GLAEVIKYGLI D +FF W EQN+ L+ARD YAI+RSC +KA VV+ DE+E+G Sbjct: 182 AGLAEVIKYGLIGDPDFFAWLEQNVDGLMARDQALLAYAIERSCSDKASVVAADEREAGN 241 Query: 319 RATLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQ 378 RA LNLGHTFGHA+ETG+GYG+WLHGEAV AG MA D+SRRLGWI +S R+ ++ + Sbjct: 242 RALLNLGHTFGHAIETGMGYGEWLHGEAVGAGICMAADLSRRLGWITESDQARIASLIVR 301 Query: 379 AKLPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438 A+LP PP + E F +M+VDKKV K+RL+L++ LG V T D+D L TL Sbjct: 302 AELPIYPPNNINAEQFMQLMSVDKKVLAQKIRLVLMR-RLGYSVVTDDFDPDLLKVTLNE 360 Query: 439 FSKS 442 + ++ Sbjct: 361 YGRT 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: 433 Number of extensions: 10 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: 442 Length of database: 366 Length adjustment: 31 Effective length of query: 411 Effective length of database: 335 Effective search space: 137685 Effective search space used: 137685 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_029132271.1 A3GO_RS0103790 (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.10182.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.9e-119 383.2 0.0 7e-119 383.0 0.0 1.0 1 lcl|NCBI__GCF_000428045.1:WP_029132271.1 A3GO_RS0103790 3-dehydroquinate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000428045.1:WP_029132271.1 A3GO_RS0103790 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 383.0 0.0 7e-119 7e-119 1 335 [. 17 350 .. 17 358 .. 0.95 Alignments for each domain: == domain 1 score: 383.0 bits; conditional E-value: 7e-119 TIGR01357 1 ykvkvgegllk.klveelae.kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g++l+ ++v + + ++++v+++ +v+ l+ e +++al+ g++v+++++pdge++K+l++ lcl|NCBI__GCF_000428045.1:WP_029132271.1 17 YPIYIGTNLIGdSAVYR-PHiHGQQVLVVSNTTVAPLYLEAVKSALQ--GYQVQTVILPDGEQHKTLAV 82 67999999999444443.333669**********************6..7******************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++++d lle+ ++r+ +++++GGGvvgD+aGF+Aa y+RG+ ++qvPTtlla+vDssvGGKtg+n+pl lcl|NCBI__GCF_000428045.1:WP_029132271.1 83 WQQIIDSLLENRFDRRCTVIGLGGGVVGDMAGFAAACYQRGVYFIQVPTTLLAQVDSSVGGKTGVNHPL 151 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkN+iGafyqP+ V+ d+++l+tl++r+l++G+aEviK+gli d ++f++le+n + l + +++ l+ lcl|NCBI__GCF_000428045.1:WP_029132271.1 152 GKNMIGAFYQPQCVIADIQTLSTLDNRQLSAGLAEVIKYGLIGDPDFFAWLEQNVDGLMAR-DQALLAY 219 *******************************************************987765.569**** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk.lsHGeaVaiGmvveaklseklgllk 273 +i+rs++ Ka+vV++De+e+g RalLN+GHt+gHaiE+ ++y+ + HGeaV G+ ++a ls++lg + lcl|NCBI__GCF_000428045.1:WP_029132271.1 220 AIERSCSDKASVVAADEREAGNRALLNLGHTFGHAIETGMGYGeWLHGEAVGAGICMAADLSRRLGWIT 288 ********************************************************************* PP TIGR01357 274 aellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevt 335 +++ r+++l+ +++lp+ ++++++e++++ ++ DKK ++ki+lvl++++G +++++++ lcl|NCBI__GCF_000428045.1:WP_029132271.1 289 ESDQARIASLIVRAELPIYPPNNINAEQFMQLMSVDKKVLAQKIRLVLMRRLGYSVVTDDFD 350 *****************************************************999887775 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (366 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: 8.75 // [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