Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_011736409.1 PPRO_RS12595 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::P00888 (356 letters) >NCBI__GCF_000015045.1:WP_011736409.1 Length = 350 Score = 379 bits (972), Expect = e-110 Identities = 186/342 (54%), Positives = 244/342 (71%), Gaps = 1/342 (0%) Query: 7 NNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIHD 66 NN++++ ++ P +L+ FPLS + ++ SR I DI+ D RL+VV GPCSIHD Sbjct: 5 NNLNVSAITPIIAPAELRQVFPLSAKDRDFVSRSRGQIKDILQRNDRRLMVVVGPCSIHD 64 Query: 67 PETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQI 126 E A EYARR L+ VSD L LVMRVYFEKPRTT+GWKGLINDP M+ + + GL I Sbjct: 65 TEAAKEYARRLADLSRRVSDQLLLVMRVYFEKPRTTIGWKGLINDPDMNHTHLISKGLGI 124 Query: 127 ARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVGF 186 AR LL + + +P+A E LDP +P+Y+ D+ SW AIGARTTESQTHREMASGLS PVGF Sbjct: 125 ARGLLGWITALEVPVANEMLDPITPEYVADMISWGAIGARTTESQTHREMASGLSFPVGF 184 Query: 187 KNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGG-KAPNYSPA 245 KNGTDG+L A++AM+AA PH F+GIN+ G+ +++QT GNPD H++LRGG + NY Sbjct: 185 KNGTDGNLQIAMDAMKAAQHPHSFLGINREGRTSIIQTTGNPDVHIVLRGGSRKSNYHAE 244 Query: 246 DVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIESN 305 D+ E+ +E+ L P++MVDCSHGNSNKDY+RQ V + +V Q+ DGN SI G+M+ES Sbjct: 245 DIRLVEECLEKNQLFPTIMVDCSHGNSNKDYQRQALVLDDIVQQVVDGNNSISGVMLESF 304 Query: 306 IHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDL 347 + GNQ S++KYGVS+TDACI WE T+ +L + H L Sbjct: 305 LSAGNQKIPTDTSQLKYGVSITDACIDWETTERILLDAHAKL 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: 383 Number of extensions: 17 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_011736409.1 PPRO_RS12595 (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.13717.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-155 503.0 0.0 1.8e-155 502.9 0.0 1.0 1 lcl|NCBI__GCF_000015045.1:WP_011736409.1 PPRO_RS12595 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015045.1:WP_011736409.1 PPRO_RS12595 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 502.9 0.0 1.8e-155 1.8e-155 2 342 .] 6 350 .] 5 350 .] 0.98 Alignments for each domain: == domain 1 score: 502.9 bits; conditional E-value: 1.8e-155 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakr 70 +l++ +i ++++P+el++ fpl++k + v +sr +i+dil+ +d rl+vv+GPcsihd eaa+eya+r lcl|NCBI__GCF_000015045.1:WP_011736409.1 6 NLNVSAITPIIAPAELRQVFPLSAKDRDFVSRSRGQIKDILQRNDRRLMVVVGPCSIHDTEAAKEYARR 74 688999*************************************************************** PP TIGR00034 71 lkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatel 139 l++l+ +++d+l +vmrvyfekPrtt+GWkGlindPd+n+++ + kGl iar ll ++ l++p+a+e+ lcl|NCBI__GCF_000015045.1:WP_011736409.1 75 LADLSRRVSDQLLLVMRVYFEKPRTTIGWKGLINDPDMNHTHLISKGLGIARGLLGWITALEVPVANEM 143 ********************************************************************* PP TIGR00034 140 ldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvt 208 ld+i+p y+ad++swgaiGarttesq+hre+asgls+pvgfkngtdG+l++a+da++aa+++h fl+++ lcl|NCBI__GCF_000015045.1:WP_011736409.1 144 LDPITPEYVADMISWGAIGARTTESQTHREMASGLSFPVGFKNGTDGNLQIAMDAMKAAQHPHSFLGIN 212 ********************************************************************* PP TIGR00034 209 kaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 ++G+++i++t+Gn+d hi+lrGG + +ny+aed+ v+e lek +l +++m+d+shgnsnkdy+rq v lcl|NCBI__GCF_000015045.1:WP_011736409.1 213 REGRTSIIQTTGNPDVHIVLRGGSRkSNYHAEDIRLVEECLEKNQLFPTIMVDCSHGNSNKDYQRQALV 281 ***********************988******************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksvtdacigwedteallrklaeavkerr 342 +++v+q+ +G+++i Gvm+es+l+ Gnq++ +++lkyG+s+tdaci+we+te++l + ++++kerr lcl|NCBI__GCF_000015045.1:WP_011736409.1 282 LDDIVQQVVDGNNSISGVMLESFLSAGNQKIptdTSQLKYGVSITDACIDWETTERILLDAHAKLKERR 350 ******************************9876789**********************9999999986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.70 // [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