Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_047007750.1 AAW01_RS12290 phosphogluconate dehydratase
Query= SwissProt::P21909 (607 letters) >NCBI__GCF_001010925.1:WP_047007750.1 Length = 604 Score = 760 bits (1963), Expect = 0.0 Identities = 377/608 (62%), Positives = 468/608 (76%), Gaps = 5/608 (0%) Query: 1 MTDLHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVDRPNLSCSNLAHGFAAMNGDKP 60 M++LH T+ +VT R+IE+S+++R+AYL LI E + +R +SCSNLAH FA D+ Sbjct: 1 MSNLHPTIARVTDRIIEKSKDSRRAYLYLIDREADNQPERSQVSCSNLAHAFAGAEEDQE 60 Query: 61 ALRDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQG 120 AL+ NIG+VTSYNDMLSAH+PY RYPE++K++AREVGAT QVAGG PAMCDGVTQG Sbjct: 61 ALKTNRGPNIGIVTSYNDMLSAHQPYGRYPERLKIYAREVGATAQVAGGTPAMCDGVTQG 120 Query: 121 QPGMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPS 180 + GME SLFSRDVIAL+T V+LSH M++G LLGICDKIVPGLLMGALRFGHLP + VPS Sbjct: 121 ETGMELSLFSRDVIALSTGVALSHAMYDGMLLLGICDKIVPGLLMGALRFGHLPAVFVPS 180 Query: 181 GPMTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLG 240 GPM +G+ NKEK R+RQLYA+GK + ELL+ E YH+ GTCTF+GTAN+NQM+ME++G Sbjct: 181 GPMPSGVSNKEKQRVRQLYAEGKATRAELLESELGSYHSPGTCTFFGTANSNQMMMEMMG 240 Query: 241 LHMPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATG 300 LH+PG+AF PGT +RQAL RAAV RV +G G+D+RPLG +DEK+IVNA VGLLATG Sbjct: 241 LHVPGAAFFQPGTKIRQALDRAAVQRVTAMGRNGNDFRPLGHCVDEKAIVNAAVGLLATG 300 Query: 301 GSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIK 360 GSTNH +HIPA ARAAGV ++W D +LS VPL+AR+YPNG D N F AGGM +VIK Sbjct: 301 GSTNHAIHIPAFARAAGVQIDWTDLSELSGAVPLLARVYPNGSGDTNHFHEAGGMGFVIK 360 Query: 361 ELLSANLLNRDVTTIAK-GGIEEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKD 419 EL SA L + DV + + G+E+Y + P L+D L W+ GE GDDT+LRP S+PF D Sbjct: 361 ELTSAGLAHADVIGVGETRGMEQYGQEPWLDD-DMLSWRDVGESGDDTMLRPASDPFQPD 419 Query: 420 GGLRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQ 479 GG+RL++GNLGRA +K+SAV+ + WTIEAP RVF Q V + FK GEL++DV+VVVRFQ Sbjct: 420 GGMRLVQGNLGRACFKSSAVEKERWTIEAPCRVFQTQAAVNECFKKGELDRDVVVVVRFQ 479 Query: 480 GPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGK 539 GPRANGMPELHKLTPALGVLQD GY+VALVTDGRMSGA+GKVP A+H SPEALGGG + Sbjct: 480 GPRANGMPELHKLTPALGVLQDRGYRVALVTDGRMSGASGKVPSAIHCSPEALGGGPLSL 539 Query: 540 LRDGDIVRISVEEGKLEALVPADEWNARPHAEKPAFRPGTGRELFDIFRQNAAKAEDGAV 599 L+DGD+V++ E G+L + +R A PA GTGRE+F +FR A +AE G Sbjct: 540 LQDGDVVKVCAETGELSTTA---DLGSRTPAPDPAPESGTGREIFAMFRNFADEAERGGS 596 Query: 600 AIYAGAGI 607 A+ A G+ Sbjct: 597 AMLATGGL 604 Lambda K H 0.318 0.136 0.403 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: 1210 Number of extensions: 52 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: 607 Length of database: 604 Length adjustment: 37 Effective length of query: 570 Effective length of database: 567 Effective search space: 323190 Effective search space used: 323190 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: 53 (25.0 bits)
Align candidate WP_047007750.1 AAW01_RS12290 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))
# 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.carbon/TIGR01196.hmm # target sequence database: /tmp/gapView.4152163.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01196 [M=601] Accession: TIGR01196 Description: edd: phosphogluconate dehydratase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-268 878.5 0.0 1.2e-268 878.2 0.0 1.0 1 NCBI__GCF_001010925.1:WP_047007750.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_001010925.1:WP_047007750.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 878.2 0.0 1.2e-268 1.2e-268 1 600 [. 5 598 .. 5 599 .. 0.97 Alignments for each domain: == domain 1 score: 878.2 bits; conditional E-value: 1.2e-268 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 h+ +a++t+riie+sk+ r++yl i +++ + rs+++c+nlah++a + +++ +lk+++ +n++i+t+y NCBI__GCF_001010925.1:WP_047007750.1 5 HPTIARVTDRIIEKSKDSRRAYLYLIDREADNQPERSQVSCSNLAHAFAGAE-EDQEALKTNRGPNIGIVTSY 76 7899********************************************9875.56789*************** PP TIGR01196 74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146 ndmlsahqp+ +yp+ +k ++e +a+aqvagG+pamcdGvtqGe Gmelsl+srdvialst+++lsh m+dg NCBI__GCF_001010925.1:WP_047007750.1 77 NDMLSAHQPYGRYPERLKIYAREVGATAQVAGGTPAMCDGVTQGETGMELSLFSRDVIALSTGVALSHAMYDG 149 ************************************************************************* PP TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219 l+lG+cdkivpGll++al fGhlpavfvp+Gpm+sG++nkek +vrql+aeGk++r ell+se syh+pGt NCBI__GCF_001010925.1:WP_047007750.1 150 MLLLGICDKIVPGLLMGALRFGHLPAVFVPSGPMPSGVSNKEKQRVRQLYAEGKATRAELLESELGSYHSPGT 222 ************************************************************************* PP TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292 ctf+Gtansnqm++e+mGlh+pga+f +p t++r+al r+a +r++++ +++++ pl++ +dek+ivna vg NCBI__GCF_001010925.1:WP_047007750.1 223 CTFFGTANSNQMMMEMMGLHVPGAAFFQPGTKIRQALDRAAVQRVTAMGRNGNDFRPLGHCVDEKAIVNAAVG 295 ************************************************************************* PP TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365 llatGGstnh++h+ a+araaG++++w dlsels vpllarvypnG+ d nhf+ aGG++f+i+el ++Gl NCBI__GCF_001010925.1:WP_047007750.1 296 LLATGGSTNHAIHIPAFARAAGVQIDWTDLSELSGAVPLLARVYPNGSGDTNHFHEAGGMGFVIKELTSAGLA 368 ************************************************************************* PP TIGR01196 366 hedvetvag.kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437 h dv v + +G+++y +ep+l+d+ l++r+ +s d+ +lr++++pf+++GG++l++GnlGra +k sav+ NCBI__GCF_001010925.1:WP_047007750.1 369 HADVIGVGEtRGMEQYGQEPWLDDDMLSWRDVG-ESGDDTMLRPASDPFQPDGGMRLVQGNLGRACFKSSAVE 440 ******98769*******************976.58999********************************** PP TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510 +e ieap++vf++qa +++ fk+gel+rd+v+vvrfqGp+anGmpelhklt++lGvlqdrg++valvtdGr NCBI__GCF_001010925.1:WP_047007750.1 441 KERWTIEAPCRVFQTQAAVNECFKKGELDRDVVVVVRFQGPRANGMPELHKLTPALGVLQDRGYRVALVTDGR 513 ************************************************************************* PP TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583 +sGasGkvp+aih +peal gG+l ++dGd++++ a +gel+ a+l +r++ +d+ ++e G+Gre+f NCBI__GCF_001010925.1:WP_047007750.1 514 MSGASGKVPSAIHCSPEALGGGPLSLLQDGDVVKVCAETGELST---TADLGSRTP-APDP-APESGTGREIF 581 *****************************************875...567888884.4554.7899******* PP TIGR01196 584 aalrekvssaeeGassl 600 a++r+ ++ ae+G+s++ NCBI__GCF_001010925.1:WP_047007750.1 582 AMFRNFADEAERGGSAM 598 *************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (604 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: 23.43 // [ok]
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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