Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_011156071.1 TX73_RS02610 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_000195775.1:WP_011156071.1 Length = 381 Score = 271 bits (692), Expect = 3e-77 Identities = 160/354 (45%), Positives = 214/354 (60%), Gaps = 11/354 (3%) Query: 4 IVVTLGERSYPITIASGLFNEPASFLP-LKSGEQVMLVTNETLAPLYLDKVRGVLEQAGV 62 + V LG+R+Y I I + + L+ G + +VT+ T+A +L + VL+QAG+ Sbjct: 13 VEVALGDRAYEIVIGRDVIASLGERIAKLRPGARTAIVTDRTVAKTWLKRTEEVLDQAGI 72 Query: 63 NVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRGV 122 SVI+ +GE KS A L+ V AL+ R+ ++ALGGGV+GDL GF+A+ +RGV Sbjct: 73 AHASVIVGEGESSKSYAGLEQVCEALIAAKIERNDLVIALGGGVIGDLAGFSASLLRRGV 132 Query: 123 RFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASGL 182 F+QVPT+LL+QVDSSVGGKT +N P GKN+IG F+QP V+ D L TL PR+ +G Sbjct: 133 DFVQVPTSLLAQVDSSVGGKTGINSPQGKNLIGTFHQPVLVLADTAILDTLSPRQFRAGY 192 Query: 183 AEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRAL 242 AEV KYG + D AFF WLE N A L G A + + C KA +VA DERETG RAL Sbjct: 193 AEVAKYGALGDEAFFAWLEAN-HAELFSGGAAREHAVATSCRAKAAIVARDERETGDRAL 251 Query: 243 LNLGHTFGHAIEAEMGYGNWL-HGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAG 301 LNLGHTFGHA+EA G+ + L HGE VA GMV+AA S G + + +R+ L G Sbjct: 252 LNLGHTFGHALEAATGFSDRLFHGEGVAIGMVLAAEFSAERGMMPATDAERLAKHLAEVG 311 Query: 302 LP-----VNGPRE---MSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGV 347 LP + G + A + M +DKKV GE+ IL IG++ + S V Sbjct: 312 LPTRLQDIAGFTQEGLADADRLMALMAQDKKVKRGELTFILMEGIGRAVIASKV 365 Lambda K H 0.320 0.136 0.392 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: 301 Number of extensions: 12 Number of successful extensions: 3 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: 362 Length of database: 381 Length adjustment: 30 Effective length of query: 332 Effective length of database: 351 Effective search space: 116532 Effective search space used: 116532 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: 49 (23.5 bits)
Align candidate WP_011156071.1 TX73_RS02610 (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.7825.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-113 365.5 0.0 1.8e-113 365.2 0.0 1.0 1 lcl|NCBI__GCF_000195775.1:WP_011156071.1 TX73_RS02610 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000195775.1:WP_011156071.1 TX73_RS02610 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 365.2 0.0 1.8e-113 1.8e-113 1 336 [. 22 367 .. 22 374 .. 0.97 Alignments for each domain: == domain 1 score: 365.2 bits; conditional E-value: 1.8e-113 TIGR01357 1 ykvkvgegllkklveelae.ka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++++g++++++l e +a+ + ++ ++td++v+k+ ++ ee+l ++g+++ ++v +ge+sKs + lcl|NCBI__GCF_000195775.1:WP_011156071.1 22 YEIVIGRDVIASLGERIAKlRPgARTAIVTDRTVAKTWLKRTEEVLDQAGIAHASVIVGEGESSKSYAG 90 689****************73369********************************************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++++ ++l+++k+er+++++a+GGGv+gDlaGF A+ RG+++vqvPT+lla+vDssvGGKtgin p+ lcl|NCBI__GCF_000195775.1:WP_011156071.1 91 LEQVCEALIAAKIERNDLVIALGGGVIGDLAGFSASLLRRGVDFVQVPTSLLAQVDSSVGGKTGINSPQ 159 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNliG+f+qP +Vl d+++l tl+ r++r+G+aEv K+g++ d+++f++le n+++l + +a e+ lcl|NCBI__GCF_000195775.1:WP_011156071.1 160 GKNLIGTFHQPVLVLADTAILDTLSPRQFRAGYAEVAKYGALGDEAFFAWLEANHAELFS--GGAAREH 226 *****************************************************9997774..6799*** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgll 272 +++ s++ Ka +V++De+e+g RalLN+GHt+gHa+Ea+++++ l HGe VaiGmv++a++s + g++ lcl|NCBI__GCF_000195775.1:WP_011156071.1 227 AVATSCRAKAAIVARDERETGDRALLNLGHTFGHALEAATGFSdrLFHGEGVAIGMVLAAEFSAERGMM 295 *****************************************9999************************ PP TIGR01357 273 kaellerlvallkklglptklkk........klsveellkallkDKKnegskiklvlleeiGkaalase 333 +a+++erl++ l ++glpt+l++ +++ l++ + +DKK ++++++++l+e iG+a++as+ lcl|NCBI__GCF_000195775.1:WP_011156071.1 296 PATDAERLAKHLAEVGLPTRLQDiagftqegLADADRLMALMAQDKKVKRGELTFILMEGIGRAVIASK 364 *****************************9999********************************9988 PP TIGR01357 334 vte 336 v lcl|NCBI__GCF_000195775.1:WP_011156071.1 365 VEP 367 754 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (381 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: 8.89 // [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