Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate Ga0059261_0354 Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12)
Query= SwissProt::P21909 (607 letters) >FitnessBrowser__Korea:Ga0059261_0354 Length = 608 Score = 777 bits (2007), Expect = 0.0 Identities = 383/607 (63%), Positives = 474/607 (78%), Gaps = 3/607 (0%) Query: 1 MTDLHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVD-RPNLSCSNLAHGFAAMNGDK 59 +T+L + VT R+IERS++ R AY L+ +RE G R L C+NLAH +A + + Sbjct: 1 VTNLLPEIAAVTDRIIERSKKRRAAYNALMTAQREAGSSSRGRLGCANLAHAYAGTDEQR 60 Query: 60 PALRDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQ 119 ++ NRMNIG+VT+YNDMLSAH PYYRYPEQMK++A E GAT QVAGGVPAMCDGVTQ Sbjct: 61 DVMKPANRMNIGIVTAYNDMLSAHAPYYRYPEQMKIWALEAGATAQVAGGVPAMCDGVTQ 120 Query: 120 GQPGMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVP 179 G GME SLFSRD IA++T+V+LSH FEGAALLGICDKIVPGLLMGALRFGHLP +L+P Sbjct: 121 GYAGMELSLFSRDTIAMSTAVALSHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIP 180 Query: 180 SGPMTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVL 239 G M TGI NKEK R+R+LYA+GK ++ELLD E A YH +GTCTFYGTAN+NQM++E + Sbjct: 181 GGAMPTGIANKEKARVRELYAEGKASREELLDSEIAAYHGKGTCTFYGTANSNQMMVEAM 240 Query: 240 GLHMPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLAT 299 GLHMPG+AF+ PGT LRQALTRAAV R+ E+GW +DYRP+G+I+DE++IVNA V LLAT Sbjct: 241 GLHMPGAAFIHPGTKLRQALTRAAVQRLPEIGWDSNDYRPIGEIVDERAIVNAAVVLLAT 300 Query: 300 GGSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVI 359 GGSTNH +H+PAIAR AGV+++W+DF LS VVPL+AR+YPNG D+N F++AGG +VI Sbjct: 301 GGSTNHLIHLPAIARCAGVLIDWDDFDRLSRVVPLLARVYPNGSADVNGFEDAGGPTFVI 360 Query: 360 KELLSANLLNRDVTTIAKGGIEEYAKAPALNDAGELVWKPAG-EPGDDTILRPVSNPFAK 418 +EL+ +L+ D T+A + +Y + P L D LVWK G + GDD+ILR + PF++ Sbjct: 361 RELIKGGVLHGDTLTVAGDSLADYVRRPVLED-DTLVWKDHGAKSGDDSILRTIDAPFSE 419 Query: 419 DGGLRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRF 478 +GG R+L GNLGRA K SAV+ WTIEAP RVF+ Q +VQ AFKAGEL++DV+VVVRF Sbjct: 420 EGGFRILSGNLGRACIKVSAVERDRWTIEAPCRVFATQQEVQDAFKAGELDRDVVVVVRF 479 Query: 479 QGPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIG 538 QGPRANGMPELHKLTP LGVLQ+ G++VALVTDGRMSGA+GKVP A+H+SPEA+GGG IG Sbjct: 480 QGPRANGMPELHKLTPPLGVLQNKGFRVALVTDGRMSGASGKVPAAIHLSPEAIGGGPIG 539 Query: 539 KLRDGDIVRISVEEGKLEALVPADEWNARPHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598 KLRDGD+VR+ EEG L+ALV EW AR A P GTGRELF + R A++AE G Sbjct: 540 KLRDGDVVRLCAEEGILQALVEPAEWEARELAAAPPPDLGTGRELFAMMRAGASEAEAGG 599 Query: 599 VAIYAGA 605 A+ A A Sbjct: 600 SAMLAAA 606 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: 1161 Number of extensions: 46 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: 607 Length of database: 608 Length adjustment: 37 Effective length of query: 570 Effective length of database: 571 Effective search space: 325470 Effective search space used: 325470 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 Ga0059261_0354 Ga0059261_0354 (6-phosphogluconate dehydratase (EC 4.2.1.12))
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.18009.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.7e-274 896.1 0.0 5.5e-274 895.9 0.0 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0354 Ga0059261_0354 6-phosphogluconat Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0354 Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 895.9 0.0 5.5e-274 5.5e-274 3 600 .. 7 602 .. 5 603 .. 0.98 Alignments for each domain: == domain 1 score: 895.9 bits; conditional E-value: 5.5e-274 TIGR01196 3 rlaeiteriierskktrekylekirsaktkgk.lrstlgcgnlahgvaalsesekvelksekrknlaii 70 ++a++t+riierskk r +y + +++ ++ g r++lgc+nlah++a +e+ + +k +r n++i+ lcl|FitnessBrowser__Korea:Ga0059261_0354 7 EIAAVTDRIIERSKKRRAAYNALMTAQREAGSsSRGRLGCANLAHAYAGTDEQ-RDVMKPANRMNIGIV 74 7899****************99998888777516778***********98766.567999********* PP TIGR01196 71 tayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaigl 139 tayndmlsah p+ +yp+++k + ea+a+aqvagGvpamcdGvtqG++Gmelsl+srd ia+sta++l lcl|FitnessBrowser__Korea:Ga0059261_0354 75 TAYNDMLSAHAPYYRYPEQMKIWALEAGATAQVAGGVPAMCDGVTQGYAGMELSLFSRDTIAMSTAVAL 143 ********************************************************************* PP TIGR01196 140 shnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellk 208 shn f+ga +lG+cdkivpGll++al fGhlp v++p+G m++G+ nkeka+vr+l+aeGk++reell+ lcl|FitnessBrowser__Korea:Ga0059261_0354 144 SHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIPGGAMPTGIANKEKARVRELYAEGKASREELLD 212 ********************************************************************* PP TIGR01196 209 semasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlpl 277 se+a+yh+ GtctfyGtansnqm+ve mGlh+pga+f++p t+lr+altr+a +rl ++ +++++ p+ lcl|FitnessBrowser__Korea:Ga0059261_0354 213 SEIAAYHGKGTCTFYGTANSNQMMVEAMGLHMPGAAFIHPGTKLRQALTRAAVQRLPEIGWDSNDYRPI 281 ********************************************************************* PP TIGR01196 278 aelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhf 346 +e++de++ivna v llatGGstnh +hl aiar+aG++++wdd++ ls +vpllarvypnG+advn f lcl|FitnessBrowser__Korea:Ga0059261_0354 282 GEIVDERAIVNAAVVLLATGGSTNHLIHLPAIARCAGVLIDWDDFDRLSRVVPLLARVYPNGSADVNGF 350 ********************************************************************* PP TIGR01196 347 eaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsa 415 e aGG +f+irel+k G+lh d+ tvag l y + p+led+ l++++ ks d++ilr++d pfs+ lcl|FitnessBrowser__Korea:Ga0059261_0354 351 EDAGGPTFVIRELIKGGVLHGDTLTVAGDSLADYVRRPVLEDDTLVWKDHGAKSGDDSILRTIDAPFSE 419 ********************************************************************* PP TIGR01196 416 eGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmp 484 eGG ++l+GnlGra ikvsav+ + ieap++vf +q+e+++afkagel+rd+v+vvrfqGp+anGmp lcl|FitnessBrowser__Korea:Ga0059261_0354 420 EGGFRILSGNLGRACIKVSAVERDRWTIEAPCRVFATQQEVQDAFKAGELDRDVVVVVRFQGPRANGMP 488 ********************************************************************* PP TIGR01196 485 elhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngele 553 elhklt++lGvlq++gf+valvtdGr+sGasGkvpaaih++pea+ gG++ k+rdGd++rl a +g l+ lcl|FitnessBrowser__Korea:Ga0059261_0354 489 ELHKLTPPLGVLQNKGFRVALVTDGRMSGASGKVPAAIHLSPEAIGGGPIGKLRDGDVVRLCAEEGILQ 557 ********************************************************************* PP TIGR01196 554 vlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600 lv+ ae++arel+ ++lG+Grelfa++r +s ae G+s++ lcl|FitnessBrowser__Korea:Ga0059261_0354 558 ALVEPAEWEARELAAA--PPPDLGTGRELFAMMRAGASEAEAGGSAM 602 ************7654..5688*********************9875 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (608 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: 00:00:00.02 # Mc/sec: 12.49 // [ok]
This GapMind analysis is from Sep 17 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