Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate 201784 SO2646 phospho-2-dehydro-3-deoxyheptonate aldolase, trp-sensitive (NCBI ptt file)
Query= ecocyc::AROH-MONOMER (348 letters) >FitnessBrowser__MR1:201784 Length = 354 Score = 449 bits (1155), Expect = e-131 Identities = 218/341 (63%), Positives = 267/341 (78%) Query: 3 RTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPCSI 62 +TDELRT+ + +++PA+LA YP+T A ++ RR +E I+ GED+RLLVIIGPCSI Sbjct: 4 KTDELRTSLLAKVISPAQLASEYPLTQDAADYLVQQRREVEAIIMGEDQRLLVIIGPCSI 63 Query: 63 HDLTAAMEYATRLQSLRNQYQSRLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNHGL 122 HD AA++YA RL L + + L I+MR YFEKPRT+VGWKGLISDPDL+GS+ N GL Sbjct: 64 HDTQAALDYARRLAVLHQELKDDLCILMRVYFEKPRTIVGWKGLISDPDLDGSFEPNKGL 123 Query: 123 ELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSCPV 182 +AR+LL Q+ EL +P ATEFLDMV GQ+IADLI+WGAIGARTTESQ+HREMASALSCPV Sbjct: 124 RIARQLLQQITELKLPIATEFLDMVNGQYIADLITWGAIGARTTESQVHREMASALSCPV 183 Query: 183 GFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQMTIYQTSGNPYGHIIMRGGKKPNYHA 242 GFKNGTDGN IAVDA+RAA+ H+F SPDK+G M++Y+T GNPYGHII+RGGKKPNY Sbjct: 184 GFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGAMSVYRTHGNPYGHIILRGGKKPNYFE 243 Query: 243 DDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMAES 302 DI A L ++ +VVDFSHGN +K H +QL V E+I Q+R GSTAIAGIMAES Sbjct: 244 QDIEQARLKLESVNVTPRVVVDFSHGNSEKNHLKQLVVAENIMAQMRAGSTAIAGIMAES 303 Query: 303 FLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASA 343 FL+EG QK++ QPL YGQSITD CL W D+E+L+ LASA Sbjct: 304 FLQEGNQKVIEGQPLCYGQSITDACLHWADSEKLLRDLASA 344 Lambda K H 0.320 0.135 0.399 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: 395 Number of extensions: 5 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: 348 Length of database: 354 Length adjustment: 29 Effective length of query: 319 Effective length of database: 325 Effective search space: 103675 Effective search space used: 103675 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 (21.8 bits) S2: 49 (23.5 bits)
Align candidate 201784 SO2646 (phospho-2-dehydro-3-deoxyheptonate aldolase, trp-sensitive (NCBI ptt file))
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.27435.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-162 523.4 0.0 1.1e-161 523.2 0.0 1.0 1 lcl|FitnessBrowser__MR1:201784 SO2646 phospho-2-dehydro-3-deoxy Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:201784 SO2646 phospho-2-dehydro-3-deoxyheptonate aldolase, trp-sensitive (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 523.2 0.0 1.1e-161 1.1e-161 1 342 [] 6 349 .. 6 349 .. 0.99 Alignments for each domain: == domain 1 score: 523.2 bits; conditional E-value: 1.1e-161 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyakrlkklaeklk 79 d+lr+ + ++++P++l++++plt++aa+ + ++r+e++ i+ G+d+rllv+iGPcsihd +aal+ya+rl+ l ++lk lcl|FitnessBrowser__MR1:201784 6 DELRTSLLAKVISPAQLASEYPLTQDAADYLVQQRREVEAIIMGEDQRLLVIIGPCSIHDTQAALDYARRLAVLHQELK 84 68999999*********************************************************************** PP TIGR00034 80 ddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplatelldtispqyladllswgaiG 158 ddl i+mrvyfekPrt+vGWkGli+dPdl++sf+ nkGlriar+ll +++el lp+ate+ld++ +qy+adl++wgaiG lcl|FitnessBrowser__MR1:201784 85 DDLCILMRVYFEKPRTIVGWKGLISDPDLDGSFEPNKGLRIARQLLQQITELKLPIATEFLDMVNGQYIADLITWGAIG 163 ******************************************************************************* PP TIGR00034 159 arttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsvtkaGqvaivetkGnedghiilrGGkkpnyd 237 arttesqvhre+as+ls+pvgfkngtdG++++a+da+raa+ +h+f s++k+G++++++t+Gn++ghiilrGGkkpny lcl|FitnessBrowser__MR1:201784 164 ARTTESQVHREMASALSCPVGFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGAMSVYRTHGNPYGHIILRGGKKPNYF 242 ******************************************************************************* PP TIGR00034 238 aedvaevkeelekaglkeelmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyG 314 ++d+++++ +le ++ ++++++dfshgns+k++ +ql vae++++q++ G++ai+G+m es+l+eGnq++ +++l yG lcl|FitnessBrowser__MR1:201784 243 EQDIEQARLKLESVNVTPRVVVDFSHGNSEKNHLKQLVVAENIMAQMRAGSTAIAGIMAESFLQEGNQKVieGQPLCYG 321 *********************************************************************988899**** PP TIGR00034 315 ksvtdacigwedteallrklaeavkerr 342 +s+tdac++w d+e+llr+la+a ++rr lcl|FitnessBrowser__MR1:201784 322 QSITDACLHWADSEKLLRDLASASRDRR 349 **********************999885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (354 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 11.63 // [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