Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate CCNA_01463 CCNA_01463 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >FitnessBrowser__Caulo:CCNA_01463 Length = 369 Score = 446 bits (1148), Expect = e-130 Identities = 215/344 (62%), Positives = 268/344 (77%) Query: 6 DDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCSIHD 65 DDLRI++++ L PP ++ + PAT + A V AR+A+H+IL G DDRL+VVIGPCSIHD Sbjct: 17 DDLRIEKLQTLSPPAQVIGEAPATSSVAEIVGGARQAVHQILHGQDDRLVVVIGPCSIHD 76 Query: 66 PVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDGLRI 125 P AA +YA RL A RE ELE++MRVYFEKPRTTVGWKGLINDP +D F+INDGLR+ Sbjct: 77 PKAAIDYARRLAAERERHAGELEVIMRVYFEKPRTTVGWKGLINDPGLDGGFRINDGLRL 136 Query: 126 ARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCPVGF 185 AR++LLD++ GLPAA EFLD+ TPQY+ADL+SWGAIGARTTESQ+HRELASGLSCPVGF Sbjct: 137 ARRVLLDVSAQGLPAACEFLDVTTPQYIADLVSWGAIGARTTESQIHRELASGLSCPVGF 196 Query: 186 KNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 245 KNGT+G +K+A+DA+ AA PH FL+VTK G +AI T+GNGDCH++LRGGK PNY A Sbjct: 197 KNGTNGDVKIAVDAVMAASQPHHFLAVTKEGRAAIATTTGNGDCHLVLRGGKTPNYDAAS 256 Query: 246 VAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVESHL 305 VA E L+KAGLP ++M+D SHANS K + Q V ADVC Q+A G ++GVM+ES+L Sbjct: 257 VAAAAEVLSKAGLPQRLMVDVSHANSGKNHENQPAVIADVCAQVATGASPVMGVMIESNL 316 Query: 306 VEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARR 349 V G Q + G+ L YG+S+TDAC+ WE + LL LA AV+A R Sbjct: 317 VAGRQDIVQGQGLTYGQSVTDACVDWETSVRLLDDLAGAVRAGR 360 Lambda K H 0.317 0.134 0.397 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: 427 Number of extensions: 12 Number of successful extensions: 1 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: 350 Length of database: 369 Length adjustment: 29 Effective length of query: 321 Effective length of database: 340 Effective search space: 109140 Effective search space used: 109140 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 (21.7 bits) S2: 49 (23.5 bits)
Align candidate CCNA_01463 CCNA_01463 (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.23688.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.5e-162 524.0 0.0 7.6e-162 523.8 0.0 1.0 1 lcl|FitnessBrowser__Caulo:CCNA_01463 CCNA_01463 3-deoxy-7-phosphohept Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Caulo:CCNA_01463 CCNA_01463 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 523.8 0.0 7.6e-162 7.6e-162 1 340 [. 17 358 .. 17 360 .. 0.99 Alignments for each domain: == domain 1 score: 523.8 bits; conditional E-value: 7.6e-162 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkk 73 ddlri+k++ l +P++++ + p+t+++ae v +r+++++il+G+ddrl+vviGPcsihdp+aa++ya+rl++ lcl|FitnessBrowser__Caulo:CCNA_01463 17 DDLRIEKLQTLSPPAQVIGEAPATSSVAEIVGGARQAVHQILHGQDDRLVVVIGPCSIHDPKAAIDYARRLAA 89 799********************************************************************** PP TIGR00034 74 laeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispq 146 +e+ +le++mrvyfekPrttvGWkGlindP l++ f++n+Glr+ar++lld+ glp+a+e+ld+ +pq lcl|FitnessBrowser__Caulo:CCNA_01463 90 ERERHAGELEVIMRVYFEKPRTTVGWKGLINDPGLDGGFRINDGLRLARRVLLDVSAQGLPAACEFLDVTTPQ 162 ************************************************************************* PP TIGR00034 147 yladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetk 219 y+adl+swgaiGarttesq+hrelasgls+pvgfkngt+G++k+a+da+ aa+++h+fl+vtk+G++ai +t+ lcl|FitnessBrowser__Caulo:CCNA_01463 163 YIADLVSWGAIGARTTESQIHRELASGLSCPVGFKNGTNGDVKIAVDAVMAASQPHHFLAVTKEGRAAIATTT 235 ************************************************************************* PP TIGR00034 220 GnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaii 292 Gn d+h++lrGGk+pnyda++va++ e l+kagl ++lm+d+sh+ns k++++q++v ++v++q+a+G ++ lcl|FitnessBrowser__Caulo:CCNA_01463 236 GNGDCHLVLRGGKTPNYDAASVAAAAEVLSKAGLPQRLMVDVSHANSGKNHENQPAVIADVCAQVATGASPVM 308 ************************************************************************* PP TIGR00034 293 GvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavke 340 Gvmiesnl+ G+q++ +++l+yG+svtdac++we++ +ll +la av++ lcl|FitnessBrowser__Caulo:CCNA_01463 309 GVMIESNLVAGRQDIvqGQGLTYGQSVTDACVDWETSVRLLDDLAGAVRA 358 **************988899***************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (369 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: 7.66 // [ok]
This GapMind analysis is from Apr 09 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