Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_041441734.1 TCUR_RS13035 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::O68903 (455 letters) >NCBI__GCF_000024385.1:WP_041441734.1 Length = 440 Score = 550 bits (1416), Expect = e-161 Identities = 267/432 (61%), Positives = 327/432 (75%), Gaps = 5/432 (1%) Query: 26 PAAQQPEWPDADLARRVRAVLESVPPITVPAEIDRLRENLAAVARGEAFMLQGGDCAETF 85 PA QQPEW D + R V A L PP+ E D+L+E LA VARGEAF+LQGGDCAETF Sbjct: 8 PAVQQPEWDDPEEVRAVTAELAKAPPLVFAGECDQLKERLAEVARGEAFVLQGGDCAETF 67 Query: 86 ADNTEPHIRANVRTLLQMAVVLTYGASLPVVKIGRIAGQYAKPRSSGT---DALGLPSYR 142 A +T +R ++TLLQMAVVLTY S+PVVKIGR+AGQ+AKPRS D + LPSYR Sbjct: 68 AGSTADAVRNKLKTLLQMAVVLTYAGSVPVVKIGRMAGQFAKPRSKPVEVRDGVTLPSYR 127 Query: 143 GDIVNSLVPTPEARVADPGRMIRAYANAGAAMNLLRAMTTAGMADLHRLHDWNKDFVRTS 202 GD VN TPEAR +DP R+++AY + +NL RA T G ADL ++H WN+DFV +S Sbjct: 128 GDAVNGAEFTPEARRSDPRRLLQAYHCSAVTLNLCRAFTKGGYADLRQVHAWNQDFVASS 187 Query: 203 PAGERYEALAAEIDRGLRFMSACGVNDSSLHTTEIFASHEALLLDYERALLRLDTRGDEP 262 PAG+RYE LA EIDR L FM ACG + H+ E ++SHEALLL+YERAL R+D+R P Sbjct: 188 PAGQRYERLAGEIDRALAFMKACGADPEEFHSVEFYSSHEALLLEYERALTRIDSRTGLP 247 Query: 263 KLYDLSSHFLWIGERTKQLDGAHIAFAELLANPIGLKIGPSTTPEMAVEYVERLDPHNQP 322 YD+S+HFLWIGERT+ LDGAH+ FA + NPIG+K+GP+TTP+ A+ +ERL+P +P Sbjct: 248 --YDVSAHFLWIGERTRALDGAHVEFASRIRNPIGVKLGPTTTPDDALALIERLNPDGEP 305 Query: 323 GRLTLIIRMGNGKVRDVLPAIVEKVTASGHKVIWQCDPMHGNTHESSTGYKTRHFDRIVD 382 GRLT I RMG G++R+VLP +VEKV+ SG V+W CDPMHGNT E+ +G+KTR FD ++D Sbjct: 306 GRLTFITRMGAGRIREVLPPLVEKVSQSGGPVVWMCDPMHGNTFEAPSGHKTRRFDDVLD 365 Query: 383 EVQGFFEVHRRLGTHPGGIHIELTGEDVTECLGGAQEISDTDLAGRYETACDPRLNTQQS 442 EV GFFEVHR LGTHPGGIHIE TG+DVTEC+GG QEI + DL RYETACDPRLN QS Sbjct: 366 EVAGFFEVHRSLGTHPGGIHIEFTGDDVTECVGGGQEIVEEDLHQRYETACDPRLNRSQS 425 Query: 443 LELAFLVAEMLR 454 L+LAF+VAEM R Sbjct: 426 LDLAFIVAEMYR 437 Lambda K H 0.319 0.135 0.404 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: 622 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: 455 Length of database: 440 Length adjustment: 33 Effective length of query: 422 Effective length of database: 407 Effective search space: 171754 Effective search space used: 171754 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: 51 (24.3 bits)
Align candidate WP_041441734.1 TCUR_RS13035 (3-deoxy-7-phosphoheptulonate synthase class II)
to HMM TIGR01358 (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/TIGR01358.hmm # target sequence database: /tmp/gapView.14247.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01358 [M=443] Accession: TIGR01358 Description: DAHP_synth_II: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.1e-227 740.2 0.0 3.5e-227 740.1 0.0 1.0 1 lcl|NCBI__GCF_000024385.1:WP_041441734.1 TCUR_RS13035 3-deoxy-7-phosphohe Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000024385.1:WP_041441734.1 TCUR_RS13035 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 740.1 0.0 3.5e-227 3.5e-227 4 441 .. 2 438 .. 1 440 [] 0.99 Alignments for each domain: == domain 1 score: 740.1 bits; conditional E-value: 3.5e-227 TIGR01358 4 eswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 ++wr+ pa+q+Pe+ d e+++av+++l++ PPlv+age+++lke+laeva+Geaf+lqgGdcae+f lcl|NCBI__GCF_000024385.1:WP_041441734.1 2 DAWRALPAVQQPEWDDPEEVRAVTAELAKAPPLVFAGECDQLKERLAEVARGEAFVLQGGDCAETFAGS 70 79******************************************************************* PP TIGR01358 73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdea 141 +ad +r+kl++llqmavvlty++s+Pvvk+gr+aGq+akPrs+p+e++dgvtlpsyrGd +nga+f+ + lcl|NCBI__GCF_000024385.1:WP_041441734.1 71 TADAVRNKLKTLLQMAVVLTYAGSVPVVKIGRMAGQFAKPRSKPVEVRDGVTLPSYRGDAVNGAEFTPE 139 ********************************************************************* PP TIGR01358 142 arvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfms 210 ar+ dp+rl++ay+ sa+tlnl ra+t+gGyadl++vh+Wn++fv +spag+rye+la eid+al fm+ lcl|NCBI__GCF_000024385.1:WP_041441734.1 140 ARRSDPRRLLQAYHCSAVTLNLCRAFTKGGYADLRQVHAWNQDFVASSPAGQRYERLAGEIDRALAFMK 208 ********************************************************************* PP TIGR01358 211 avgvaeaealkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvk 279 a+g +++e ++ ve+y+shealll+ye+altr ds++g +d+sah+lWiGertr ldgahvef+++++ lcl|NCBI__GCF_000024385.1:WP_041441734.1 209 ACGADPEE-FHSVEFYSSHEALLLEYERALTRIDSRTGLPYDVSAHFLWIGERTRALDGAHVEFASRIR 276 ******99.************************************************************ PP TIGR01358 280 nPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmh 348 nPig+k+gp++++d++l lie+l+P+ ePGrlt+i+r+Ga +i+e lP+l+e+v ++G vvW++dpmh lcl|NCBI__GCF_000024385.1:WP_041441734.1 277 NPIGVKLGPTTTPDDALALIERLNPDGEPGRLTFITRMGAGRIREVLPPLVEKVSQSGGPVVWMCDPMH 345 ********************************************************************* PP TIGR01358 349 GntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryet 417 Gnt+ea+sG+ktrrfdd+l+ev++ffevh+++GthpGG+h+e+tG+dvtec+GG++ei+e+dl++ryet lcl|NCBI__GCF_000024385.1:WP_041441734.1 346 GNTFEAPSGHKTRRFDDVLDEVAGFFEVHRSLGTHPGGIHIEFTGDDVTECVGGGQEIVEEDLHQRYET 414 ********************************************************************* PP TIGR01358 418 acdPrlnaeqslelaflvaeklre 441 acdPrln++qsl+laf+vae++r lcl|NCBI__GCF_000024385.1:WP_041441734.1 415 ACDPRLNRSQSLDLAFIVAEMYRG 438 *********************995 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (440 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: 00:00:00.02 # Mc/sec: 8.54 // [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