Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_029001555.1 H537_RS0134720 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000430725.1:WP_029001555.1 Length = 375 Score = 428 bits (1100), Expect = e-124 Identities = 217/352 (61%), Positives = 258/352 (73%), Gaps = 5/352 (1%) Query: 4 QNDDLRIKEIKELLPPVALLEKFPATENAANT-VAHARKAIHKILKGNDDRLLVVIGPCS 62 Q DD RI++I L PP L+ FP V R+ I +IL G DDRLLV++GPCS Sbjct: 24 QTDDARIEDITPLPPPEHLIRFFPIRNTPVEALVTQTRQRIGQILHGQDDRLLVIMGPCS 83 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IHDP AA EYA RL+ R D LE+VMRVYFEKPRTTVGWKGLINDP++D SF+I++G Sbjct: 84 IHDPAAALEYARRLMEQRRRYADTLEVVMRVYFEKPRTTVGWKGLINDPYLDESFRIDEG 143 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 LR AR+LL++IN GLPAA EFLD+I+PQY+ DL++WGAIGARTTESQVHRELASG+S P Sbjct: 144 LRFARQLLVEINRLGLPAASEFLDVISPQYIGDLIAWGAIGARTTESQVHRELASGISAP 203 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYS 242 +GFKNGTDG IK+AIDAI AA PH FLSV K G A V T GN DCH+ILRGGK PNY Sbjct: 204 IGFKNGTDGNIKIAIDAIQAASRPHHFLSVHKNGQVATVQTKGNPDCHVILRGGKAPNYD 263 Query: 243 AKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVE 302 A HVA L AGL +M+DFSHANSSK+ ++Q+DV DV QI G ++I GVMVE Sbjct: 264 ADHVAAACRDLQAAGLDTSLMVDFSHANSSKKHERQVDVARDVAAQIRSGGRSIFGVMVE 323 Query: 303 SHLVEGNQSLESGE----PLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350 SHL G Q G+ L YG+SITDACIGW+D+ +L +L+ AVKARRG Sbjct: 324 SHLQPGAQKFTPGKDDASKLVYGQSITDACIGWDDSLTVLEELSAAVKARRG 375 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: 403 Number of extensions: 8 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: 350 Length of database: 375 Length adjustment: 29 Effective length of query: 321 Effective length of database: 346 Effective search space: 111066 Effective search space used: 111066 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 WP_029001555.1 H537_RS0134720 (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.9143.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.4e-165 534.4 0.0 5.1e-165 534.2 0.0 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029001555.1 H537_RS0134720 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029001555.1 H537_RS0134720 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 534.2 0.0 5.1e-165 5.1e-165 1 342 [] 26 374 .. 26 374 .. 0.97 Alignments for each domain: == domain 1 score: 534.2 bits; conditional E-value: 5.1e-165 TIGR00034 1 ddlrivkidelltPeelkakfpltek.aaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleya 68 dd ri++i +l +Pe+l++ fp+ ++ +++ v+++r++i +il+G+ddrllv++GPcsihdp aaleya lcl|NCBI__GCF_000430725.1:WP_029001555.1 26 DDARIEDITPLPPPEHLIRFFPIRNTpVEALVTQTRQRIGQILHGQDDRLLVIMGPCSIHDPAAALEYA 94 799********************987256789************************************* PP TIGR00034 69 krlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplat 137 +rl + + ++ d le+vmrvyfekPrttvGWkGlindP+l+esf++++Glr ar+ll++++ lglp+a+ lcl|NCBI__GCF_000430725.1:WP_029001555.1 95 RRLMEQRRRYADTLEVVMRVYFEKPRTTVGWKGLINDPYLDESFRIDEGLRFARQLLVEINRLGLPAAS 163 ********************************************************************* PP TIGR00034 138 elldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlfls 206 e+ld+ispqy++dl++wgaiGarttesqvhrelasg+s p+gfkngtdG++k+aidai+aa+++h+fls lcl|NCBI__GCF_000430725.1:WP_029001555.1 164 EFLDVISPQYIGDLIAWGAIGARTTESQVHRELASGISAPIGFKNGTDGNIKIAIDAIQAASRPHHFLS 232 ********************************************************************* PP TIGR00034 207 vtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 v+k+Gqva v+tkGn+d+h+ilrGGk+pnyda++va+++++l++agl +lm+dfsh+ns+k+++rq++ lcl|NCBI__GCF_000430725.1:WP_029001555.1 233 VHKNGQVATVQTKGNPDCHVILRGGKAPNYDADHVAAACRDLQAAGLDTSLMVDFSHANSSKKHERQVD 301 ********************************************************************* PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl...k...eelkyGksvtdacigwedteallrklaeav 338 va++v++qi++G ++i+Gvm+es+l+ G+q+ k ++l+yG+s+tdacigw+d+ ++l++l++av lcl|NCBI__GCF_000430725.1:WP_029001555.1 302 VARDVAAQIRSGGRSIFGVMVESHLQPGAQKFtpgKddaSKLVYGQSITDACIGWDDSLTVLEELSAAV 370 ******************************974431333679*************************** PP TIGR00034 339 kerr 342 k+rr lcl|NCBI__GCF_000430725.1:WP_029001555.1 371 KARR 374 *996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (375 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: 7.26 // [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