Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_013420185.1 RVAN_RS13050 3-dehydroquinate synthase
Query= BRENDA::P07639 (362 letters) >NCBI__GCF_000166055.1:WP_013420185.1 Length = 378 Score = 282 bits (722), Expect = 9e-81 Identities = 168/360 (46%), Positives = 221/360 (61%), Gaps = 11/360 (3%) Query: 3 RIVVTLGERSYPITIASGLFNEPASFLP-LKSGEQVMLVTNETLAPLYLDKVRGVLEQAG 61 R+ V LGERSYPI I +GL FL G + +V +E + Y +++ L AG Sbjct: 10 RVDVELGERSYPILIGNGLIAGAPQFLAETLPGTRFAIVADEAVRA-YAEQLEAGLAGAG 68 Query: 62 VNVD-SVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120 + + +V +P GE KS A L+ V ALL RD +VALGGGV+GDL GFAAA+ +R Sbjct: 69 LLLGPTVYVPSGEASKSFASLERVTAALLDLGVERDHAVVALGGGVIGDLAGFAAATLKR 128 Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180 GVR +QVPTTLL+QVDSSVGGKT ++ GKN++GAF+QP+ V++DLD LKTLPPRE + Sbjct: 129 GVRVVQVPTTLLAQVDSSVGGKTGIDTQHGKNLVGAFHQPSLVLIDLDTLKTLPPREFRA 188 Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240 G AEV KYG + D FF WLE+N A+ LD + + +KAE+V+ DE+E G R Sbjct: 189 GYAEVAKYGALGDSVFFRWLEDNAAAIFELDTYPLTDAVETSVRMKAEIVSRDEKEAGDR 248 Query: 241 ALLNLGHTFGHAIEAEMGY-GNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKR 299 ALLNLGHTFGHA+EA GY G+ LHGEAVA GMV+AAR SE G + ++R+ L Sbjct: 249 ALLNLGHTFGHAVEAWAGYSGDVLHGEAVALGMVLAARFSEAEGFCAHTVSRRLEDHLAE 308 Query: 300 AGLPVNGP-------REMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELV 352 G R + M +DKKV G+M L+L IG + V V+ + + Sbjct: 309 VGFATTFSELRQRLGRAPTLDELTGFMEQDKKVKDGKMNLVLLSGIGNAFVAKDVARDKI 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: 309 Number of extensions: 11 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: 378 Length adjustment: 30 Effective length of query: 332 Effective length of database: 348 Effective search space: 115536 Effective search space used: 115536 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_013420185.1 RVAN_RS13050 (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.21389.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-111 358.5 0.0 2.3e-111 358.3 0.0 1.0 1 lcl|NCBI__GCF_000166055.1:WP_013420185.1 RVAN_RS13050 3-dehydroquinate sy Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000166055.1:WP_013420185.1 RVAN_RS13050 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 358.3 0.0 2.3e-111 2.3e-111 1 340 [. 20 369 .. 20 373 .. 0.93 Alignments for each domain: == domain 1 score: 358.3 bits; conditional E-value: 2.3e-111 TIGR01357 1 ykvkvgegllkklveelae..kasklvvitdeeveklvaekleealkslgvev.lvlvvpdgeesKsle 66 y++ +g+gl++ + + lae ++ ++ de+v++ +ae+le+ l+ +g + ++ vp+ge sKs++ lcl|NCBI__GCF_000166055.1:WP_013420185.1 20 YPILIGNGLIAGAPQFLAEtlPGTRFAIVADEAVRA-YAEQLEAGLAGAGLLLgPTVYVPSGEASKSFA 87 578899999998888888753337777777777776.779999999888655426899*********** PP TIGR01357 67 tvaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlp 135 ++++++ +ll+ ++er++++va+GGGv+gDlaGF+Aat +RG+r+vqvPTtlla+vDssvGGKtgi+++ lcl|NCBI__GCF_000166055.1:WP_013420185.1 88 SLERVTAALLDLGVERDHAVVALGGGVIGDLAGFAAATLKRGVRVVQVPTTLLAQVDSSVGGKTGIDTQ 156 ********************************************************************* PP TIGR01357 136 lgkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaeleale 204 +gkNl+Gaf+qP++Vlidl++l+tlp re+r+G+aEv K+g++ d+ +f++le+n++++ +l ++ l+ lcl|NCBI__GCF_000166055.1:WP_013420185.1 157 HGKNLVGAFHQPSLVLIDLDTLKTLPPREFRAGYAEVAKYGALGDSVFFRWLEDNAAAIFEL-DTYPLT 224 *********************************************************99986.559*** PP TIGR01357 205 elikrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgl 271 ++++ s+++Kae+V++Deke+g RalLN+GHt+gHa+Ea ++y+ + HGeaVa+Gmv++a++se+ g+ lcl|NCBI__GCF_000166055.1:WP_013420185.1 225 DAVETSVRMKAEIVSRDEKEAGDRALLNLGHTFGHAVEAWAGYSgdVLHGEAVALGMVLAARFSEAEGF 293 *******************************************999*********************** PP TIGR01357 272 lkaellerlvallkklglptklkk.......klsveellkallkDKKnegskiklvlleeiGkaalase 333 + +++++rl++ l ++g t++++ +++el+ ++ +DKK +++k++lvll+ iG+a++a++ lcl|NCBI__GCF_000166055.1:WP_013420185.1 294 CAHTVSRRLEDHLAEVGFATTFSElrqrlgrAPTLDELTGFMEQDKKVKDGKMNLVLLSGIGNAFVAKD 362 **********************999999999899*********************************99 PP TIGR01357 334 vteeell 340 v ++++ lcl|NCBI__GCF_000166055.1:WP_013420185.1 363 VARDKIR 369 9777665 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: 8.04 // [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