Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate WP_012173008.1 AZC_RS23015 3-dehydroquinate synthase
Query= BRENDA::Q3M4V2 (363 letters) >NCBI__GCF_000010525.1:WP_012173008.1 Length = 377 Score = 270 bits (689), Expect = 6e-77 Identities = 156/364 (42%), Positives = 222/364 (60%), Gaps = 8/364 (2%) Query: 5 INVNLPTQSYEIAIAPASLDQIGQSLAGLKLGKKVLLVSNPTIFKHFGKVAVDSLEAAGF 64 + V L ++Y+I I P L Q G +A L+ G +V +V++ + + A SL AAG Sbjct: 14 VRVELGQRAYDILIGPGLLAQAGARIAALRPGARVAIVTDRNVAERHLGTAEASLAAAGI 73 Query: 65 QVASYCLPAGERYKTLNSIQKLYDIALENRLERSSTMVALGGGVIGDMTGFAAATWLRGI 124 ++ + GE K+ +Q++ + + R+ER ++ALGGGV+GD+ GFAA+ RG+ Sbjct: 74 DHSAIVVEPGEATKSYAGLQQVTEGLIAARIERRDLVLALGGGVVGDLAGFAASVVRRGL 133 Query: 125 NVVQVPTTLLAMVDSAIGGKTGVNHPHGKNLIGAFHQPRFVLIDPQVLKTLPVREFRAGM 184 + VQ PTTLL+ VDS++GGKTG+N P GKNLIGAFHQP VL D L TLP RE RAG Sbjct: 134 DFVQAPTTLLSQVDSSVGGKTGINSPQGKNLIGAFHQPVLVLADTAALDTLPARELRAGY 193 Query: 185 AEVIKYGVIWDAELFNQLEQSKRLDQLRYIKPELMDAILTRSCQAKADVVGKDEKEGGLR 244 AEV KYG++ DA LF+ LE + R + + ++A+ SC AKA +V +DE E G R Sbjct: 194 AEVAKYGLLGDARLFDWLEGAWR--DIVTGDAQRVEAV-AASCLAKAAIVARDETETGDR 250 Query: 245 AILNYGHTVGHAVESLTNY-RLLKHGEAVGIGMVAAGQIAVNLGLWQQADADRQNALIEK 303 A+LN GHT GHA+E+ Y + L HGEAV IGM A + LGL DA R +E Sbjct: 251 ALLNLGHTFGHALEAGAGYSQRLLHGEAVSIGMCLAFAYSARLGLCAGQDAVRAQRHLEA 310 Query: 304 AGLPTKL---PAGL-DIEGIIEALQLDKKVKDGKVRFVLPTQIGVVTVTDEVTSDHIRQV 359 GLPT++ P L D +G++ + DKKV G++ F+L IG + ++V +D +R Sbjct: 311 VGLPTRIADVPGELPDTDGLMRLIAQDKKVSRGRLTFILARGIGEAFIAEDVDADSVRAF 370 Query: 360 LQQM 363 L++M Sbjct: 371 LEEM 374 Lambda K H 0.319 0.136 0.388 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: 334 Number of extensions: 12 Number of successful extensions: 4 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: 363 Length of database: 377 Length adjustment: 30 Effective length of query: 333 Effective length of database: 347 Effective search space: 115551 Effective search space used: 115551 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate WP_012173008.1 AZC_RS23015 (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.25604.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.2e-109 350.8 0.0 4.8e-109 350.6 0.0 1.0 1 lcl|NCBI__GCF_000010525.1:WP_012173008.1 AZC_RS23015 3-dehydroquinate syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000010525.1:WP_012173008.1 AZC_RS23015 3-dehydroquinate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 350.6 0.0 4.8e-109 4.8e-109 1 340 [. 23 368 .. 23 372 .. 0.96 Alignments for each domain: == domain 1 score: 350.6 bits; conditional E-value: 4.8e-109 TIGR01357 1 ykvkvgegllkklveelae.ka.sklvvitdeeveklvaekleealkslgvevlvlvvpdgeesKslet 67 y++ +g gll+++ + +a + ++ ++td++v++ + + e+ l+++g+ + +vv++ge +Ks + lcl|NCBI__GCF_000010525.1:WP_012173008.1 23 YDILIGPGLLAQAGARIAAlRPgARVAIVTDRNVAERHLGTAEASLAAAGIDHSAIVVEPGEATKSYAG 91 6899***********999963369********************************************* PP TIGR01357 68 vaklldqlleeklerksvlvaiGGGvvgDlaGFvAatylRGirlvqvPTtllamvDssvGGKtginlpl 136 ++++++ l+++ +er+++++a+GGGvvgDlaGF+A++ RG+++vq PTtll++vDssvGGKtgin p+ lcl|NCBI__GCF_000010525.1:WP_012173008.1 92 LQQVTEGLIAARIERRDLVLALGGGVVGDLAGFAASVVRRGLDFVQAPTTLLSQVDSSVGGKTGINSPQ 160 ********************************************************************* PP TIGR01357 137 gkNliGafyqPkaVlidlkvletlperelreGmaEviKhgliadaelfeelekneklllklaelealee 205 gkNliGaf+qP +Vl d++ l tlp relr+G+aEv K+gl+ da+lf++le ++++++ ++ e lcl|NCBI__GCF_000010525.1:WP_012173008.1 161 GKNLIGAFHQPVLVLADTAALDTLPARELRAGYAEVAKYGLLGDARLFDWLEGAWRDIVT--GDAQRVE 227 *******************************************************98885..4578999 PP TIGR01357 206 likrsievKaevVeeDekesglRalLNfGHtlgHaiEallkyk..lsHGeaVaiGmvveaklseklgll 272 +++ s+ Ka +V++De+e+g RalLN+GHt+gHa+Ea ++y+ l HGeaV+iGm +++ +s +lgl+ lcl|NCBI__GCF_000010525.1:WP_012173008.1 228 AVAASCLAKAAIVARDETETGDRALLNLGHTFGHALEAGAGYSqrLLHGEAVSIGMCLAFAYSARLGLC 296 *****************************************9999************************ PP TIGR01357 273 kaellerlvallkklglptklkk....klsveellkallkDKKnegskiklvlleeiGkaalasevtee 337 +++ r ++ l+++glpt++ + +++ l++ + +DKK ++++++++l++ iG+a++a++v+++ lcl|NCBI__GCF_000010525.1:WP_012173008.1 297 AGQDAVRAQRHLEAVGLPTRIADvpgeLPDTDGLMRLIAQDKKVSRGRLTFILARGIGEAFIAEDVDAD 365 ***********************99987899********************************999777 PP TIGR01357 338 ell 340 + lcl|NCBI__GCF_000010525.1:WP_012173008.1 366 SVR 368 655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (344 nodes) Target sequences: 1 (377 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: 11.53 // [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