Align 3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54) (characterized)
to candidate WP_025275001.1 HALAL_RS0116200 3-deoxy-7-phosphoheptulonate synthase class II
Query= BRENDA::O68903 (455 letters) >NCBI__GCF_000527155.1:WP_025275001.1 Length = 460 Score = 592 bits (1526), Expect = e-174 Identities = 289/439 (65%), Positives = 336/439 (76%), Gaps = 4/439 (0%) Query: 16 RSRLDDALGRPAAQQPEWPDADLARRVRAVLESVPPITVPAEIDRLRENLAAVARGEAFM 75 R LD G P Q P W D V VLE VPPI P E+ RLR A V G AF+ Sbjct: 25 RFGLDYWRGLPRKQMPPWKDYSEVEAVSGVLEGVPPIVAPYEVKRLRNLFAEVCEGRAFL 84 Query: 76 LQGGDCAETFADNTEPHIRANVRTLLQMAVVLTYGASLPVVKIGRIAGQYAKPRSSGTDA 135 +QGGDCAETF NTE H+ AN+RTLLQMAVVLTYGASLPVVK+GR+AGQY+KPRS+ DA Sbjct: 85 VQGGDCAETFLSNTESHVLANIRTLLQMAVVLTYGASLPVVKVGRVAGQYSKPRSNDLDA 144 Query: 136 LGLPSYRGDIVNSLVPTPEARVADPGRMIRAYANAGAAMNLLRAMTTAGMADLHRLHDWN 195 L LP YRGD+ NSL P +ARV DP RMIRAYAN+ A+MN+LRA G+ADL +HDWN Sbjct: 145 LDLPVYRGDMFNSLEPNADARVCDPQRMIRAYANSAASMNMLRAYLGGGLADLQSVHDWN 204 Query: 196 KDFVRTSPAGERYEALAAEIDRGLRFMSACGVNDSSLHTTEIFASHEALLLDYERALLRL 255 KDFVR+SPAGERYEA+ EIDR + FM ACGV DS+LHT E+FASHE L ++Y+RAL Sbjct: 205 KDFVRSSPAGERYEAIGREIDRAMAFMQACGVQDSALHTAEVFASHEMLAIEYDRAL--- 261 Query: 256 DTRGDEPKLYDLSSHFLWIGERTKQLDGAHIAFAELLANPIGLKIGPSTTPEMAVEYVER 315 TR + + Y LS H LW GERT+Q+DGAHI F ++NP+G KIGP+ TPE VE + Sbjct: 262 -TRVFDGEAYGLSGHMLWSGERTRQIDGAHIDFLSRVSNPVGCKIGPTATPEEVVELCHK 320 Query: 316 LDPHNQPGRLTLIIRMGNGKVRDVLPAIVEKVTASGHKVIWQCDPMHGNTHESSTGYKTR 375 L+PHN PG+L L+ RMG KVRDVL I+EKV ASG KV+WQCDPMHGNT E+ G+KTR Sbjct: 321 LNPHNLPGKLVLVSRMGQAKVRDVLTPIIEKVEASGRKVVWQCDPMHGNTFEAKGGFKTR 380 Query: 376 HFDRIVDEVQGFFEVHRRLGTHPGGIHIELTGEDVTECLGGAQEISDTDLAGRYETACDP 435 FD +VDEV GFFEVHR LGTHPGGIHIELTG++VTEC+GGAQEI + +L+ RYETACDP Sbjct: 381 AFDHVVDEVLGFFEVHRELGTHPGGIHIELTGDNVTECVGGAQEIQEEELSDRYETACDP 440 Query: 436 RLNTQQSLELAFLVAEMLR 454 RLNTQQSLELAFLVAEMLR Sbjct: 441 RLNTQQSLELAFLVAEMLR 459 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: 601 Number of extensions: 19 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: 455 Length of database: 460 Length adjustment: 33 Effective length of query: 422 Effective length of database: 427 Effective search space: 180194 Effective search space used: 180194 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_025275001.1 HALAL_RS0116200 (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.20588.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-199 649.1 0.0 1.6e-199 648.9 0.0 1.0 1 lcl|NCBI__GCF_000527155.1:WP_025275001.1 HALAL_RS0116200 3-deoxy-7-phosph Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000527155.1:WP_025275001.1 HALAL_RS0116200 3-deoxy-7-phosphoheptulonate synthase class II # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 648.9 0.0 1.6e-199 1.6e-199 4 440 .. 29 459 .. 26 460 .] 0.99 Alignments for each domain: == domain 1 score: 648.9 bits; conditional E-value: 1.6e-199 TIGR01358 4 eswrskpaaqlPeyPdaealeavldtleslPPlvlageilklkeklaevakGeafllqgGdcaesfkev 72 + wr p +q+P + d +++eav le +PP+v + e+++l++ +aev +G+afl+qgGdcae+f ++ lcl|NCBI__GCF_000527155.1:WP_025275001.1 29 DYWRGLPRKQMPPWKDYSEVEAVSGVLEGVPPIVAPYEVKRLRNLFAEVCEGRAFLVQGGDCAETFLSN 97 67******************************************************************* PP TIGR01358 73 eadnirdklrvllqmavvltygaslPvvkvgriaGqyakPrsepieakdgvtlpsyrGdvingaafdea 141 +++++ ++r+llqmavvltygaslPvvkvgr+aGqy+kPrs++++a d lp+yrGd+ n+ +++++ lcl|NCBI__GCF_000527155.1:WP_025275001.1 98 TESHVLANIRTLLQMAVVLTYGASLPVVKVGRVAGQYSKPRSNDLDALD---LPVYRGDMFNSLEPNAD 163 **********************************************999...***************** PP TIGR01358 142 arvpdperlvrayaksaatlnllraltsgGyadlkkvheWnlefvkkspagaryeklaeeidealrfms 210 arv dp+r++raya+saa++n+lra+ gG+adl+ vh+Wn++fv++spag+rye++ +eid+a+ fm+ lcl|NCBI__GCF_000527155.1:WP_025275001.1 164 ARVCDPQRMIRAYANSAASMNMLRAYLGGGLADLQSVHDWNKDFVRSSPAGERYEAIGREIDRAMAFMQ 232 ********************************************************************* PP TIGR01358 211 avgvaeaealkrvelytsheallldyeealtrvdskegqlfdlsahllWiGertrqldgahveflrgvk 279 a+gv+++ l+++e+++she l ++y++altrv + + + ls+h+lW Gertrq+dgah++fl++v+ lcl|NCBI__GCF_000527155.1:WP_025275001.1 233 ACGVQDSA-LHTAEVFASHEMLAIEYDRALTRVFDG--EAYGLSGHMLWSGERTRQIDGAHIDFLSRVS 298 ****9998.************************875..67***************************** PP TIGR01358 280 nPigikvgpsmeadellklievldPenePGrltlisrlGaekiaeklPelleavkaaGravvWvtdpmh 348 nP+g k+gp+ +++e+++l+++l+P+n PG+l+l+sr+G +k+++ l +++e+v+a+Gr+vvW++dpmh lcl|NCBI__GCF_000527155.1:WP_025275001.1 299 NPVGCKIGPTATPEEVVELCHKLNPHNLPGKLVLVSRMGQAKVRDVLTPIIEKVEASGRKVVWQCDPMH 367 ********************************************************************* PP TIGR01358 349 GntleaasGyktrrfddilsevkeffevhkaeGthpGGvhleltGedvteclGGareitetdlasryet 417 Gnt+ea +G+ktr fd++++ev +ffevh+++GthpGG+h+eltG++vtec+GGa+ei+e++l++ryet lcl|NCBI__GCF_000527155.1:WP_025275001.1 368 GNTFEAKGGFKTRAFDHVVDEVLGFFEVHRELGTHPGGIHIELTGDNVTECVGGAQEIQEEELSDRYET 436 ********************************************************************* PP TIGR01358 418 acdPrlnaeqslelaflvaeklr 440 acdPrln++qslelaflvae+lr lcl|NCBI__GCF_000527155.1:WP_025275001.1 437 ACDPRLNTQQSLELAFLVAEMLR 459 *********************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (443 nodes) Target sequences: 1 (460 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: 11.82 // [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