Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_038210512.1 Q392_RS17510 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000745855.1:WP_038210512.1 Length = 374 Score = 427 bits (1099), Expect = e-124 Identities = 219/352 (62%), Positives = 256/352 (72%), Gaps = 5/352 (1%) Query: 4 QNDDLRIKEIKELLPPVALLEKFPATENAANT-VAHARKAIHKILKGNDDRLLVVIGPCS 62 Q DD RIK+I L PP L+ FP T + R++IH I+ G DDRLLV++GPCS Sbjct: 23 QTDDQRIKDINVLPPPEHLIRFFPIRGTPVETLIGQTRRSIHNIMAGKDDRLLVIMGPCS 82 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IHDP AA EY RL A R++ LEIVMRVYFEKPRTTVGWKGLINDP++D S++I++G Sbjct: 83 IHDPAAAVEYGRRLKAERDKYAGTLEIVMRVYFEKPRTTVGWKGLINDPYLDESYRIDEG 142 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 LRIAR+LL+DIN GLPAA EFLD+I+PQY+ DL+SWGAIGARTTESQVHRELASGLS P Sbjct: 143 LRIARQLLIDINRVGLPAASEFLDVISPQYIGDLISWGAIGARTTESQVHRELASGLSAP 202 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYS 242 +GFKNGTDG I++A DAI AA H FLSV K G AIV T GN DCH+ILRGGK PNY Sbjct: 203 IGFKNGTDGNIRIATDAIQAAARGHHFLSVHKNGQVAIVQTKGNKDCHVILRGGKAPNYD 262 Query: 243 AKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVE 302 A V + L A LP +M+D SHANSSKQ KQMDV D+ QIAGG + + GVMVE Sbjct: 263 AASVEAACKDLEAAKLPPTLMVDCSHANSSKQHGKQMDVARDIAGQIAGGSRRVFGVMVE 322 Query: 303 SHLVEGNQSLESGE----PLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350 SHL G Q G+ L YGKSITDAC+GW+D+ LL L+ AVK RRG Sbjct: 323 SHLQPGAQKFTPGKDSIAALEYGKSITDACLGWDDSRELLETLSQAVKQRRG 374 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: 418 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: 350 Length of database: 374 Length adjustment: 29 Effective length of query: 321 Effective length of database: 345 Effective search space: 110745 Effective search space used: 110745 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_038210512.1 Q392_RS17510 (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.5028.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-165 536.4 0.0 1.3e-165 536.2 0.0 1.0 1 lcl|NCBI__GCF_000745855.1:WP_038210512.1 Q392_RS17510 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000745855.1:WP_038210512.1 Q392_RS17510 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 536.2 0.0 1.3e-165 1.3e-165 1 342 [] 25 373 .. 25 373 .. 0.97 Alignments for each domain: == domain 1 score: 536.2 bits; conditional E-value: 1.3e-165 TIGR00034 1 ddlrivkidelltPeelkakfpltek.aaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleya 68 dd ri++i+ l +Pe+l++ fp+ + +++ + ++r++i++i+aGkddrllv++GPcsihdp aa+ey lcl|NCBI__GCF_000745855.1:WP_038210512.1 25 DDQRIKDINVLPPPEHLIRFFPIRGTpVETLIGQTRRSIHNIMAGKDDRLLVIMGPCSIHDPAAAVEYG 93 799********************8761566688************************************ PP TIGR00034 69 krlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplat 137 +rlk+ ++k+ leivmrvyfekPrttvGWkGlindP+l+es+++++Glriar+ll+d++ +glp+a+ lcl|NCBI__GCF_000745855.1:WP_038210512.1 94 RRLKAERDKYAGTLEIVMRVYFEKPRTTVGWKGLINDPYLDESYRIDEGLRIARQLLIDINRVGLPAAS 162 ********************************************************************* PP TIGR00034 138 elldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlfls 206 e+ld+ispqy++dl+swgaiGarttesqvhrelasgls p+gfkngtdG++++a dai+aaa+ h+fls lcl|NCBI__GCF_000745855.1:WP_038210512.1 163 EFLDVISPQYIGDLISWGAIGARTTESQVHRELASGLSAPIGFKNGTDGNIRIATDAIQAAARGHHFLS 231 ********************************************************************* PP TIGR00034 207 vtkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqle 275 v+k+Gqvaiv+tkGn+d+h+ilrGGk+pnyda++v++++++le+a+l ++lm+d+sh+ns+k++ +q++ lcl|NCBI__GCF_000745855.1:WP_038210512.1 232 VHKNGQVAIVQTKGNKDCHVILRGGKAPNYDAASVEAACKDLEAAKLPPTLMVDCSHANSSKQHGKQMD 300 ********************************************************************* PP TIGR00034 276 vaesvveqiaeGekaiiGvmiesnleeGnqsl..k....eelkyGksvtdacigwedteallrklaeav 338 va++++ qia G++ ++Gvm+es+l+ G+q+ + ++l+yGks+tdac+gw+d+ +ll+ l++av lcl|NCBI__GCF_000745855.1:WP_038210512.1 301 VARDIAGQIAGGSRRVFGVMVESHLQPGAQKFtpGkdsiAALEYGKSITDACLGWDDSRELLETLSQAV 369 ******************************9744222225799************************** PP TIGR00034 339 kerr 342 k+rr lcl|NCBI__GCF_000745855.1:WP_038210512.1 370 KQRR 373 *996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (374 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.07 // [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