Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_012470543.1 GLOV_RS12365 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_000020385.1:WP_012470543.1 Length = 350 Score = 404 bits (1039), Expect = e-117 Identities = 192/342 (56%), Positives = 253/342 (73%), Gaps = 1/342 (0%) Query: 7 NNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHD 66 NN+ ++ ++ P L+ FP+S ++ SR+ I +I+ RD RL+VV GPCSIHD Sbjct: 5 NNLKVSGITPIIAPADLRQVFPMSDTGREFVSRSREKIKEILQRRDRRLMVVVGPCSIHD 64 Query: 67 PETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQI 126 E A++YA+R AL+ V D L LVMRVYFEKPRTTVGWKGLINDP MDGS ++ GL I Sbjct: 65 TEAAVDYAKRLSALSRRVDDQLMLVMRVYFEKPRTTVGWKGLINDPGMDGSHNISKGLGI 124 Query: 127 ARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGF 186 AR LL L ++ +P+A E LDP +P+Y+ DL SW AIGARTTESQTHRE+ASGLS P+GF Sbjct: 125 ARGLLCRLTDLEVPVANEMLDPITPEYVADLISWGAIGARTTESQTHRELASGLSFPIGF 184 Query: 187 KNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPA 245 KNGTDG+L AI+AM ++ PH F+GIN+ G+ +++QT GNPD H++LRGG + PNY P Sbjct: 185 KNGTDGNLQIAIDAMISSRAPHSFLGINREGRASIIQTTGNPDVHIVLRGGSRKPNYLPE 244 Query: 246 DVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESN 305 D+ E+ +++ GL P++MVDCSHGNSNKDYR+QP V E ++ Q+ GN+SI GLMIESN Sbjct: 245 DITHTEESLKKNGLAPTIMVDCSHGNSNKDYRKQPEVLEQIIDQVVAGNQSISGLMIESN 304 Query: 306 IHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDL 347 + EGNQ S++KYGVS+TDACI+W+ T+ +L E H L Sbjct: 305 LEEGNQKVPADHSQLKYGVSITDACINWDTTEKILLEAHARL 346 Lambda K H 0.316 0.131 0.378 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: 400 Number of extensions: 9 Number of successful extensions: 2 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: 356 Length of database: 350 Length adjustment: 29 Effective length of query: 327 Effective length of database: 321 Effective search space: 104967 Effective search space used: 104967 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 49 (23.5 bits)
Align candidate WP_012470543.1 GLOV_RS12365 (3-deoxy-7-phosphoheptulonate synthase)
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))
# 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/TIGR00034.hmm # target sequence database: /tmp/gapView.13391.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00034 [M=342] Accession: TIGR00034 Description: aroFGH: 3-deoxy-7-phosphoheptulonate 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.9e-157 507.0 0.0 1.1e-156 506.8 0.0 1.0 1 lcl|NCBI__GCF_000020385.1:WP_012470543.1 GLOV_RS12365 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000020385.1:WP_012470543.1 GLOV_RS12365 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 506.8 0.0 1.1e-156 1.1e-156 2 341 .. 6 349 .. 5 350 .] 0.98 Alignments for each domain: == domain 1 score: 506.8 bits; conditional E-value: 1.1e-156 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 +l++ i ++++P++l++ fp++ + e v +sr++i++il+ +d rl+vv+GPcsihd eaa++yakr lcl|NCBI__GCF_000020385.1:WP_012470543.1 6 NLKVSGITPIIAPADLRQVFPMSDTGREFVSRSREKIKEILQRRDRRLMVVVGPCSIHDTEAAVDYAKR 74 688999*************************************************************** PP TIGR00034 71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139 l +l+ +++d+l +vmrvyfekPrttvGWkGlindP +++s+++ kGl iar ll l++l++p+a+e+ lcl|NCBI__GCF_000020385.1:WP_012470543.1 75 LSALSRRVDDQLMLVMRVYFEKPRTTVGWKGLINDPGMDGSHNISKGLGIARGLLCRLTDLEVPVANEM 143 ********************************************************************* PP TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208 ld+i+p y+adl+swgaiGarttesq+hrelasgls+p+gfkngtdG+l++aida+ +++a+h fl+++ lcl|NCBI__GCF_000020385.1:WP_012470543.1 144 LDPITPEYVADLISWGAIGARTTESQTHRELASGLSFPIGFKNGTDGNLQIAIDAMISSRAPHSFLGIN 212 ********************************************************************* PP TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 ++G+++i++t+Gn+d hi+lrGG + pny +ed+ +++e+l+k gl +++m+d+shgnsnkdy++q+ev lcl|NCBI__GCF_000020385.1:WP_012470543.1 213 REGRASIIQTTGNPDVHIVLRGGSRkPNYLPEDITHTEESLKKNGLAPTIMVDCSHGNSNKDYRKQPEV 281 ***********************988******************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavker 341 e++++q+ G+++i G+miesnleeGnq++ +++lkyG+s+tdaci+w++te++l + ++ +++r lcl|NCBI__GCF_000020385.1:WP_012470543.1 282 LEQIIDQVVAGNQSISGLMIESNLEEGNQKVpadHSQLKYGVSITDACINWDTTEKILLEAHARLQKR 349 ******************************9877789*********************9999988877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (350 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 11.08 // [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