Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_002719990.1 RSPH17029_RS07475 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_000015985.1:WP_002719990.1 Length = 370 Score = 278 bits (710), Expect = 2e-79 Identities = 163/364 (44%), Positives = 223/364 (61%), Gaps = 7/364 (1%) Query: 1 MERIVVTLGERSYPITIASGLFNEP-ASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQ 59 ++ + V LG R+Y + I GL A PL +V ++T+ET+A L+LD R L + Sbjct: 3 VDAVRVELGARAYEVRIGPGLIARAGAEIAPLLRRPKVAILTDETVAGLHLDPFRQALAE 62 Query: 60 AGVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQ 119 AG+ ++ LP GE K LL++ R +VALGGGV+GDL GFAAA + Sbjct: 63 AGIASSALALPAGEATKGWPQFARAVEWLLEEKVERRDVVVALGGGVIGDLAGFAAAVLR 122 Query: 120 RGVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELA 179 RGVRF+QVPTTLL+QVDSSVGGKT +N GKN++GAF+QP+ V+ D+ L+TLPPR+ Sbjct: 123 RGVRFVQVPTTLLAQVDSSVGGKTGINTAQGKNLVGAFHQPSLVLADIGVLETLPPRDFR 182 Query: 180 SGLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGL 239 +G EV+KYG++ D F+ WLEE L D A +RR E+KAE+VA DE E G Sbjct: 183 AGYGEVVKYGLLGDADFYEWLEE-AGPRLAADTEARQRAVRRSVEMKAEIVARDETEEGD 241 Query: 240 RALLNLGHTFGHAIEAEMGYGN-WLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLK 298 RALLNLGHTF HA+E GY + LHGE VA G +A S+RLG + R+ L+ Sbjct: 242 RALLNLGHTFCHALEKATGYSDRLLHGEGVAIGCALAFELSQRLGLCAQEAPSRLRAHLR 301 Query: 299 RAGLPV---NGPREM-SAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLN 354 G+ V + P ++ SA+A L M +DKKV+ G++R IL IG++ V V ++V Sbjct: 302 AMGMKVDLRDIPGDLPSAEALLALMAQDKKVVDGKLRFILARGIGQAFVADDVPGDVVRT 361 Query: 355 AIAD 358 + D Sbjct: 362 LLED 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: 287 Number of extensions: 7 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: 370 Length adjustment: 30 Effective length of query: 332 Effective length of database: 340 Effective search space: 112880 Effective search space used: 112880 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_002719990.1 RSPH17029_RS07475 (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.31269.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-112 362.6 0.0 1.3e-112 362.4 0.0 1.0 1 lcl|NCBI__GCF_000015985.1:WP_002719990.1 RSPH17029_RS07475 3-dehydroquina Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015985.1:WP_002719990.1 RSPH17029_RS07475 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 362.4 0.0 1.3e-112 1.3e-112 1 338 [. 15 358 .. 15 364 .. 0.96 Alignments for each domain: == domain 1 score: 362.4 bits; conditional E-value: 1.3e-112 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y+v +g gl++++ +e+a ++ k+ ++tde+v+ l+ + +++al+++g++ l +p+ge +K + + lcl|NCBI__GCF_000015985.1:WP_002719990.1 15 YEVRIGPGLIARAGAEIAPllRRPKVAILTDETVAGLHLDPFRQALAEAGIASSALALPAGEATKGWPQ 83 6899*******9999*999876699******************************************** PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 +a+ +++lleek+er++v+va+GGGv+gDlaGF+Aa+ RG+r+vqvPTtlla+vDssvGGKtgin+++ lcl|NCBI__GCF_000015985.1:WP_002719990.1 84 FARAVEWLLEEKVERRDVVVALGGGVIGDLAGFAAAVLRRGVRFVQVPTTLLAQVDSSVGGKTGINTAQ 152 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNl+Gaf+qP++Vl d+ vletlp r +r+G++Ev+K+gl+ da+++e+le+ l a++ea ++ lcl|NCBI__GCF_000015985.1:WP_002719990.1 153 GKNLVGAFHQPSLVLADIGVLETLPPRDFRAGYGEVVKYGLLGDADFYEWLEEAGPRLA--ADTEARQR 219 *****************************************************998666..4669**** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgll 272 +++rs+e+Kae+V++De+e+g RalLN+GHt+ Ha+E++++y+ l HGe VaiG +++++ls++lgl+ lcl|NCBI__GCF_000015985.1:WP_002719990.1 220 AVRRSVEMKAEIVARDETEEGDRALLNLGHTFCHALEKATGYSdrLLHGEGVAIGCALAFELSQRLGLC 288 ******************************************999************************ PP TIGR01357 273 kaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevtee 337 +e +rl+a l+++g++++l++ s+e+ll+ + +DKK ++k++++l++ iG+a++a++v+ + lcl|NCBI__GCF_000015985.1:WP_002719990.1 289 AQEAPSRLRAHLRAMGMKVDLRDipgdLPSAEALLALMAQDKKVVDGKLRFILARGIGQAFVADDVPGD 357 **********************999977899*******************************9988766 PP TIGR01357 338 e 338 lcl|NCBI__GCF_000015985.1:WP_002719990.1 358 V 358 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (370 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: 0.02u 0.00s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 7.90 // [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