Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_057508721.1 ABB28_RS11280 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_001431535.1:WP_057508721.1 Length = 370 Score = 291 bits (745), Expect = 2e-83 Identities = 171/356 (48%), Positives = 217/356 (60%), Gaps = 7/356 (1%) Query: 9 GERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAGVN--VDS 66 GE Y ITI G + + G V+LV++ +APLYL VR L QA + + Sbjct: 13 GEHPYSITIGPGQLADGHALARHVRGRHVLLVSDSEVAPLYLAGVRAALLQARPDLLIGE 72 Query: 67 VILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRGVRFIQ 126 +LP GE K+LA AL RD ++ALGGGVVGDL+GFAAA + RGV +Q Sbjct: 73 HVLPAGEASKTLAEFGRAIEALAALGATRDACVLALGGGVVGDLSGFAAACWMRGVDCVQ 132 Query: 127 VPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASGLAEVI 186 +PTTLL+ VDSSVGGKTAV+ GKN++GAF+ P +V+ D L TLP REL +GLAEV+ Sbjct: 133 LPTTLLAMVDSSVGGKTAVDIAAGKNLVGAFHPPRAVIADTQVLSTLPVRELRAGLAEVV 192 Query: 187 KYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRALLNLG 246 KYG + D FF+WL+ + L D +A I R C KA +VA D E G RALLNLG Sbjct: 193 KYGALGDPEFFDWLQRHAQGLSAGDSALLAEAIARSCAHKAAIVARDPLEKGERALLNLG 252 Query: 247 HTFGHAIEAEMGYG-----NWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAG 301 HTFGHAIE E GY HGEAVA GMV+AAR S L + +A+ R++ LL+ Sbjct: 253 HTFGHAIETEQGYAAPGRDALNHGEAVAVGMVLAARLSTALDRAPAADADRLVALLQSLQ 312 Query: 302 LPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIA 357 LPV P ++ QA L M DKK +AG +RL+L IGK+EV + V E VL +A Sbjct: 313 LPVAIPAGLAPQALLERMRLDKKNVAGRLRLVLWRGIGKAEVVADVHDEAVLAVLA 368 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: 331 Number of extensions: 14 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_057508721.1 ABB28_RS11280 (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.19563.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.6e-110 354.8 0.0 2.9e-110 354.7 0.0 1.0 1 lcl|NCBI__GCF_001431535.1:WP_057508721.1 ABB28_RS11280 3-dehydroquinate s Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_001431535.1:WP_057508721.1 ABB28_RS11280 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 354.7 0.0 2.9e-110 2.9e-110 2 341 .. 18 365 .. 17 368 .. 0.94 Alignments for each domain: == domain 1 score: 354.7 bits; conditional E-value: 2.9e-110 TIGR01357 2 kvkvgegllkklveelae.kasklvvitdeeveklvaekleealksl..gvevlvlvvpdgeesKslet 67 ++++g g l+ + ++ + +++++++d+ev+ l+ + +++al ++ + ++v+p+ge sK+l++ lcl|NCBI__GCF_001431535.1:WP_057508721.1 18 SITIGPGQLADGHALARHvRGRHVLLVSDSEVAPLYLAGVRAALLQArpDLLIGEHVLPAGEASKTLAE 86 67788877775555555545699*************99999998887344555679************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 + + +++l++ +++r+ +++a+GGGvvgDl GF+Aa ++RG+++vq+PTtllamvDssvGGKt+++ + lcl|NCBI__GCF_001431535.1:WP_057508721.1 87 FGRAIEALAALGATRDACVLALGGGVVGDLSGFAAACWMRGVDCVQLPTTLLAMVDSSVGGKTAVDIAA 155 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNl+Gaf+ P+aV+ d++vl+tlp relr+G+aEv+K+g++ d e+f++l+++++ l+ + + l+e lcl|NCBI__GCF_001431535.1:WP_057508721.1 156 GKNLVGAFHPPRAVIADTQVLSTLPVRELRAGLAEVVKYGALGDPEFFDWLQRHAQGLSAG-DSALLAE 223 *******************************************************988865.66***** PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk......lsHGeaVaiGmvveaklsek 268 +i+rs+ Ka +V++D+ e+g RalLN+GHt+gHaiE++ +y l+HGeaVa+Gmv++a+ls + lcl|NCBI__GCF_001431535.1:WP_057508721.1 224 AIARSCAHKAAIVARDPLEKGERALLNLGHTFGHAIETEQGYAapgrdaLNHGEAVAVGMVLAARLSTA 292 *****************************************988888999******************* PP TIGR01357 269 lgllkaellerlvallkklglptklkkklsveellkallkDKKnegskiklvlleeiGkaalasevtee 337 l ++a +++rlvall++l+lp+ ++ l+ ++ll+ + DKKn +++++lvl + iGka++ +v +e lcl|NCBI__GCF_001431535.1:WP_057508721.1 293 LDRAPAADADRLVALLQSLQLPVAIPAGLAPQALLERMRLDKKNVAGRLRLVLWRGIGKAEVVADVHDE 361 ***************************************************************999999 PP TIGR01357 338 elle 341 ++l+ lcl|NCBI__GCF_001431535.1:WP_057508721.1 362 AVLA 365 8876 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 8.99 // [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