Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate Pf6N2E2_2470 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54)
Query= BRENDA::P00888 (356 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 Length = 358 Score = 415 bits (1066), Expect = e-120 Identities = 206/350 (58%), Positives = 259/350 (74%), Gaps = 1/350 (0%) Query: 6 LNNVHITDEQVLMTPEQLKAAFPLSLQQEAQIADSRKSISDIIAGRDPRLLVVCGPCSIH 65 +N++++ + L+TP+QLK PLS + R+ I +I+ G D RL VV GPCSIH Sbjct: 6 INDLNVASNETLITPDQLKRDIPLSDAALRTVTKGREVIRNILDGTDHRLFVVIGPCSIH 65 Query: 66 DPETALEYARRFKALAAEVSDSLYLVMRVYFEKPRTTVGWKGLINDPHMDGSFDVEAGLQ 125 D + A EYA R K LAAEVSD+LYLVMRVYFEKPRTTVGWKGLINDP++D SF ++ GL Sbjct: 66 DIKAAHEYAERLKVLAAEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLH 125 Query: 126 IARKLLLELVNMGLPLATEALDPNSPQYLGDLFSWSAIGARTTESQTHREMASGLSMPVG 185 I R+LLL+L MGLP ATEALDP SPQYL DL SWSAIGARTTESQTHREMASGLS VG Sbjct: 126 IGRQLLLDLAEMGLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVG 185 Query: 186 FKNGTDGSLATAINAMRAAAQPHRFVGINQAGQVALLQTQGNPDGHVILRGGKA-PNYSP 244 FKNGTDG L AINA+++ + PHRF+GINQ G V+++ T+GN GHV+LRGG PNY Sbjct: 186 FKNGTDGGLTVAINALQSVSSPHRFLGINQEGGVSIVTTKGNAYGHVVLRGGNGKPNYDS 245 Query: 245 ADVAQCEKEMEQAGLRPSLMVDCSHGNSNKDYRRQPAVAESVVAQIKDGNRSIIGLMIES 304 VA CE+ + +A ++P++MVDCSH NSNKD QP V E+V QI +GN+SIIGLM+ES Sbjct: 246 VSVALCEQALNKAKIKPNIMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVES 305 Query: 305 NIHEGNQSSEQPRSEMKYGVSVTDACISWEMTDALLREIHQDLNGQLTAR 354 +++ G Q+ + ++++YGVS+TDACI W T+ LR +H L L R Sbjct: 306 HLNWGCQAIPKDLADLQYGVSITDACIDWSATENTLRSMHAKLKDVLPKR 355 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: 411 Number of extensions: 10 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: 358 Length adjustment: 29 Effective length of query: 327 Effective length of database: 329 Effective search space: 107583 Effective search space used: 107583 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 Pf6N2E2_2470 (2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha (EC 2.5.1.54))
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.3006.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-153 495.8 0.0 2.9e-153 495.6 0.0 1.0 1 lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 2-keto-3-deoxy-D-arabino-heptulo Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 2-keto-3-deoxy-D-arabino-heptulosonate-7- phosphate synthase I alpha ( # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 495.6 0.0 2.9e-153 2.9e-153 2 339 .. 8 349 .. 7 352 .. 0.98 Alignments for each domain: == domain 1 score: 495.6 bits; conditional E-value: 2.9e-153 TIGR00034 2 dlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaal 65 dl++++ + l+tP++lk+ +pl+ +a +v+k r+ i +il+G d+rl+vviGPcsihd +aa lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 8 DLNVASNETLITPDQLKRDIPLSDAALRTVTKGREVIRNILDGTDHRLFVVIGPCSIHDIKAAH 71 7889999********************************************************* PP TIGR00034 66 eyakrlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlv 129 eya+rlk la++++d l++vmrvyfekPrttvGWkGlindP+l++sf++++Gl+i r+llldl+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 72 EYAERLKVLAAEVSDTLYLVMRVYFEKPRTTVGWKGLINDPYLDDSFKIQDGLHIGRQLLLDLA 135 **************************************************************** PP TIGR00034 130 elglplatelldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaid 193 e+glp+ate+ld+ispqyl dl+sw+aiGarttesq+hre+asgls +vgfkngtdG+l vai+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 136 EMGLPTATEALDPISPQYLQDLISWSAIGARTTESQTHREMASGLSSAVGFKNGTDGGLTVAIN 199 **************************************************************** PP TIGR00034 194 airaaaaehlflsvtkaGqvaivetkGnedghiilrGGkk.pnydaedvaevkeelekaglkee 256 a+++ +++h+fl+++++G v+iv+tkGn +gh++lrGG+ pnyd+ +va +++ l+ka+ k++ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 200 ALQSVSSPHRFLGINQEGGVSIVTTKGNAYGHVVLRGGNGkPNYDSVSVALCEQALNKAKIKPN 263 **************************************988*********************** PP TIGR00034 257 lmidfshgnsnkdykrqlevaesvveqiaeGekaiiGvmiesnleeGnqsl...keelkyGksv 317 +m+d+sh+nsnkd q+ v+e+v++qi eG+++iiG+m+es+l+ G q + ++l+yG+s+ lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 264 IMVDCSHANSNKDPALQPLVMENVANQILEGNQSIIGLMVESHLNWGCQAIpkdLADLQYGVSI 327 ***************************************************53234689***** PP TIGR00034 318 tdacigwedteallrklaeavk 339 tdaci+w te+ lr +++++k lcl|FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2470 328 TDACIDWSATENTLRSMHAKLK 349 *****************99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (358 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: 10.34 // [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