Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate H281DRAFT_01349 H281DRAFT_01349 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase
Query= BRENDA::Q9K169 (351 letters) >FitnessBrowser__Burk376:H281DRAFT_01349 Length = 372 Score = 405 bits (1041), Expect = e-118 Identities = 202/346 (58%), Positives = 257/346 (74%), Gaps = 5/346 (1%) Query: 8 DDIKIKEVKELLPPIAHLYELPISKEASGLVHRTRQEISDLVHGRDKRLLVIIGPCSIHD 67 DD++I V+ L+ P ELP+ LV +TR EI+D++H RD RL++I+GPCSIHD Sbjct: 26 DDVRIGAVRPLISPALLQDELPVPATVQSLVEKTRAEIADVLHERDDRLVMIVGPCSIHD 85 Query: 68 PKAALEYAERLLKLRKQYENELLIVMRVYFEKPRTTVGWKGLINDPHLDGTFDINFGLRQ 127 A+EYA +L Y+++LLIVMRVYFEKPRTTVGWKG INDP LDG+F IN GLR+ Sbjct: 86 HDQAIEYAHKLKAAADAYKDDLLIVMRVYFEKPRTTVGWKGYINDPRLDGSFRINEGLRR 145 Query: 128 ARSLLLSLNNMGMPASTEFLDMITPQYYADLISWGAIGARTTESQVHRELASGLSCPVGF 187 AR LLL +N +G+P +TEFLD+++PQY ADLI+WGAIGARTTESQ HR+LASGLSCP+GF Sbjct: 146 ARQLLLDINGLGLPTATEFLDLLSPQYIADLIAWGAIGARTTESQSHRQLASGLSCPIGF 205 Query: 188 KNGTDGNLKIAIDAIGAASHSHHFLSVTKAGHSAIVHTGGNPDCHVILRGGKE-PNYDAE 246 KNGTDG ++IA DAI AA SH F+ +TK G +AI T GN D HVILRGGK+ PNYD+ Sbjct: 206 KNGTDGGVQIAADAIVAARASHAFMGMTKMGMAAIFETRGNDDAHVILRGGKKGPNYDSA 265 Query: 247 HVSEAAEQLRAAGVTDKLMIDCSHANSRKDYTRQMEVAQDIAAQLEQDGGNIMGVMVESH 306 V+ + L++AG+ +++MIDCSHANS K + RQ++V Q++A QL I+GVM+ESH Sbjct: 266 SVAASCAALKSAGLREQVMIDCSHANSGKSHLRQLDVVQNVAQQLSAQERRIIGVMLESH 325 Query: 307 LVEGRQD----KPEVYGKSITDACIGWGATEELLALLAGANKKRMA 348 L EGRQD +P YG SITDAC+ W TE +L LA A +KR A Sbjct: 326 LEEGRQDLKAGEPLRYGVSITDACVSWAQTEPVLETLADATRKRRA 371 Lambda K H 0.318 0.135 0.396 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: 380 Number of extensions: 15 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: 351 Length of database: 372 Length adjustment: 29 Effective length of query: 322 Effective length of database: 343 Effective search space: 110446 Effective search space used: 110446 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 H281DRAFT_01349 H281DRAFT_01349 (3-deoxy-D-arabinoheptulosonate-7-phosphate 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.26564.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-158 510.3 0.0 1.1e-157 510.1 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_01349 H281DRAFT_01349 3-deoxy-D-arabin Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_01349 H281DRAFT_01349 3-deoxy-D-arabinoheptulosonate-7-phosphate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 510.1 0.0 1.1e-157 1.1e-157 1 342 [] 26 370 .. 26 370 .. 0.99 Alignments for each domain: == domain 1 score: 510.1 bits; conditional E-value: 1.1e-157 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaale 66 dd+ri ++ +l++P+ l+ + p+ +++++ v+k+r eiad+l+ +ddrl++++GPcsihd a+e lcl|FitnessBrowser__Burk376:H281DRAFT_01349 26 DDVRIGAVRPLISPALLQDELPVPATVQSLVEKTRAEIADVLHERDDRLVMIVGPCSIHDHDQAIE 91 799*************************************************************** PP TIGR00034 67 yakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelg 132 ya++lk+ a+ +kddl ivmrvyfekPrttvGWkG indP l++sf++n+Glr ar+llld++ lg lcl|FitnessBrowser__Burk376:H281DRAFT_01349 92 YAHKLKAAADAYKDDLLIVMRVYFEKPRTTVGWKGYINDPRLDGSFRINEGLRRARQLLLDINGLG 157 ****************************************************************** PP TIGR00034 133 lplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaa 198 lp+ate+ld spqy+adl++wgaiGarttesq hr+lasgls+p+gfkngtdG++++a dai aa lcl|FitnessBrowser__Burk376:H281DRAFT_01349 158 LPTATEFLDLLSPQYIADLIAWGAIGARTTESQSHRQLASGLSCPIGFKNGTDGGVQIAADAIVAA 223 ****************************************************************** PP TIGR00034 199 aaehlflsvtkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkeelmidfsh 263 +a+h f+++tk G +ai et+Gn+d+h+ilrGGkk pnyd+++va+ ++ l+ agl+e++mid+sh lcl|FitnessBrowser__Burk376:H281DRAFT_01349 224 RASHAFMGMTKMGMAAIFETRGNDDAHVILRGGKKgPNYDSASVAASCAALKSAGLREQVMIDCSH 289 ****************************************************************** PP TIGR00034 264 gnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedt 327 +ns k + rql+v+++v++q++ e+ iiGvm+es+leeG+q+l +e+l yG+s+tdac++w +t lcl|FitnessBrowser__Burk376:H281DRAFT_01349 290 ANSGKSHLRQLDVVQNVAQQLSAQERRIIGVMLESHLEEGRQDLkaGEPLRYGVSITDACVSWAQT 355 *******************************************966789***************** PP TIGR00034 328 eallrklaeavkerr 342 e +l+ la+a ++rr lcl|FitnessBrowser__Burk376:H281DRAFT_01349 356 EPVLETLADATRKRR 370 **********99986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (372 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: 9.49 // [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