Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_022948417.1 H035_RS0107730 3-deoxy-7-phosphoheptulonate synthase
Query= BRENDA::C3TIE2 (350 letters) >NCBI__GCF_000421465.1:WP_022948417.1 Length = 356 Score = 469 bits (1207), Expect = e-137 Identities = 228/348 (65%), Positives = 279/348 (80%) Query: 3 YQNDDLRIKEIKELLPPVALLEKFPATENAANTVAHARKAIHKILKGNDDRLLVVIGPCS 62 Y+ D+LRI+EI+E+ PP L ++ P T+ A+ + AR+ IH IL G+D RLLV++GPCS Sbjct: 5 YRTDNLRIQEIQEVSPPQQLHDELPLTDRASRSTFEARQTIHNILNGDDKRLLVIMGPCS 64 Query: 63 IHDPVAAKEYATRLLALREELKDELEIVMRVYFEKPRTTVGWKGLINDPHMDNSFQINDG 122 IHDP AA++YA+RL+ +E L ++L IVMRVYFEKPRT VGWKGLINDP +D SF IN G Sbjct: 65 IHDPDAARDYASRLVKWKESLAEDLVIVMRVYFEKPRTRVGWKGLINDPGLDESFNINKG 124 Query: 123 LRIARKLLLDINDSGLPAAGEFLDMITPQYLADLMSWGAIGARTTESQVHRELASGLSCP 182 LR+ARKLL DIN+ GLPAA E+LD+ITPQY++DL+SWGAIGARTTESQVHRELASGLSCP Sbjct: 125 LRVARKLLSDINEMGLPAATEYLDLITPQYVSDLISWGAIGARTTESQVHRELASGLSCP 184 Query: 183 VGFKNGTDGTIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYS 242 VGFKN TDGT++VA+DAI +A PH FLS+TK GHSAI T GN DCH+ILRGG+ PNY Sbjct: 185 VGFKNATDGTVQVAVDAIASAQRPHHFLSLTKAGHSAIFATRGNEDCHLILRGGRRPNYD 244 Query: 243 AKHVAEVKEGLNKAGLPAQVMIDFSHANSSKQFKKQMDVCADVCQQIAGGEKAIIGVMVE 302 A+ V + E L +AGLP ++MIDFSH NS KQFK+QM V DV QQI G++ IIGVMVE Sbjct: 245 AESVNQAAETLEQAGLPGRLMIDFSHGNSFKQFKRQMLVAEDVSQQINAGDERIIGVMVE 304 Query: 303 SHLVEGNQSLESGEPLAYGKSITDACIGWEDTDALLRQLANAVKARRG 350 SHL EG Q L+ G+PL YGKSITDAC+GW D++ +L LA AV+ RRG Sbjct: 305 SHLKEGRQDLKPGQPLEYGKSITDACLGWGDSERVLEMLAQAVRKRRG 352 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: 417 Number of extensions: 11 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: 350 Length of database: 356 Length adjustment: 29 Effective length of query: 321 Effective length of database: 327 Effective search space: 104967 Effective search space used: 104967 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_022948417.1 H035_RS0107730 (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.5432.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.6e-168 545.8 0.0 1.8e-168 545.6 0.0 1.0 1 lcl|NCBI__GCF_000421465.1:WP_022948417.1 H035_RS0107730 3-deoxy-7-phospho Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000421465.1:WP_022948417.1 H035_RS0107730 3-deoxy-7-phosphoheptulonate synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 545.6 0.0 1.8e-168 1.8e-168 1 342 [] 8 351 .. 8 351 .. 0.99 Alignments for each domain: == domain 1 score: 545.6 bits; conditional E-value: 1.8e-168 TIGR00034 1 ddlrivkidelltPeelkakfpltekaaekvaksrkeiadilaGkddrllvviGPcsihdpeaaleyak 69 d+lri++i+e+ +P++l+ + plt +a + ++r++i++il+G+d+rllv++GPcsihdp aa +ya+ lcl|NCBI__GCF_000421465.1:WP_022948417.1 8 DNLRIQEIQEVSPPQQLHDELPLTDRASRSTFEARQTIHNILNGDDKRLLVIMGPCSIHDPDAARDYAS 76 789****************************************************************** PP TIGR00034 70 rlkklaeklkddleivmrvyfekPrttvGWkGlindPdlnesfdvnkGlriarkllldlvelglplate 138 rl k +e l +dl ivmrvyfekPrt vGWkGlindP l+esf++nkGlr+arkll d++e+glp+ate lcl|NCBI__GCF_000421465.1:WP_022948417.1 77 RLVKWKESLAEDLVIVMRVYFEKPRTRVGWKGLINDPGLDESFNINKGLRVARKLLSDINEMGLPAATE 145 ********************************************************************* PP TIGR00034 139 lldtispqyladllswgaiGarttesqvhrelasglslpvgfkngtdGslkvaidairaaaaehlflsv 207 +ld i+pqy++dl+swgaiGarttesqvhrelasgls+pvgfkn+tdG+++va+dai +a+++h+fls lcl|NCBI__GCF_000421465.1:WP_022948417.1 146 YLDLITPQYVSDLISWGAIGARTTESQVHRELASGLSCPVGFKNATDGTVQVAVDAIASAQRPHHFLSL 214 ********************************************************************* PP TIGR00034 208 tkaGqvaivetkGnedghiilrGGkkpnydaedvaevkeelekaglkeelmidfshgnsnkdykrqlev 276 tkaG++ai t+Gned+h+ilrGG++pnydae+v+++ e+le+agl +lmidfshgns k++krq+ v lcl|NCBI__GCF_000421465.1:WP_022948417.1 215 TKAGHSAIFATRGNEDCHLILRGGRRPNYDAESVNQAAETLEQAGLPGRLMIDFSHGNSFKQFKRQMLV 283 ********************************************************************* PP TIGR00034 277 aesvveqiaeGekaiiGvmiesnleeGnqsl..keelkyGksvtdacigwedteallrklaeavkerr 342 ae+v++qi+ G++ iiGvm+es+l+eG+q+l +++l+yGks+tdac+gw d+e++l+ la+av++rr lcl|NCBI__GCF_000421465.1:WP_022948417.1 284 AEDVSQQINAGDERIIGVMVESHLKEGRQDLkpGQPLEYGKSITDACLGWGDSERVLEMLAQAVRKRR 351 *******************************7789******************************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (342 nodes) Target sequences: 1 (356 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.36 // [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