Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12)
Query= SwissProt::P21909 (607 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Length = 589 Score = 661 bits (1706), Expect = 0.0 Identities = 331/598 (55%), Positives = 436/598 (72%), Gaps = 16/598 (2%) Query: 4 LHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVDRPNLSCSNLAHGFAAMNG-DKPAL 62 +H V +VT R+++RS +TR AYL + + + + C+NLAH +AA+ G +K + Sbjct: 1 MHPVVARVTERIVQRSADTRGAYLAGVDAMIARKPAQDRMGCANLAHAYAALPGSEKFKV 60 Query: 63 RDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQP 122 NIGVVT+YNDMLSAH+PY YP ++ A + GATVQVAGGVPAMCDGVTQG P Sbjct: 61 TVEKAPNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVPAMCDGVTQGTP 120 Query: 123 GMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPSGP 182 GME SLFSRD IA+AT+V+LSH +F+GA LLG+CDKIVPGLL+GAL +GHLP + VP+GP Sbjct: 121 GMELSLFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAGP 180 Query: 183 MTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLH 242 M TG+ NK+K ++R+ YAQG +G+ ELL E+A YH+ GTCTFYGTAN+NQM++E +GLH Sbjct: 181 MGTGLSNKDKAKVREQYAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQMLLEAMGLH 240 Query: 243 MPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGS 302 +PG+AF +PGT R+A TR A+ V ++G + + P+GK++DE+ IVNA+ LLATGGS Sbjct: 241 VPGAAFESPGTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAALLATGGS 300 Query: 303 TNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKEL 362 TNH +H AIAR+AG++++W DF +LS VVPL+AR+YPNG D+N+FQ AGG ++++EL Sbjct: 301 TNHLIHWVAIARSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGPPWILREL 360 Query: 363 LSANLLNRDVTTIAKGGIEEYAK-APALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGG 421 L+ ++ DV ++ GGI + K APA++ GD ++LRPVS PF+ GG Sbjct: 361 LAGGFMHPDVMSVNVGGIADGGKSAPAVS-------------GDTSVLRPVSAPFSPTGG 407 Query: 422 LRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGP 481 LRLL+G LGRA+ K SAV IEAP RVF Q+ + AF AG++N+D++ VVRFQGP Sbjct: 408 LRLLQGRLGRAVIKVSAVPEDRHIIEAPARVFDSQEALLAAFSAGDVNQDMVAVVRFQGP 467 Query: 482 RANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLR 541 +ANGMPELHKLTP L VLQ+ G+KVALVTDGRMSGA+GKVP A+HV+PEAL GG + K+R Sbjct: 468 QANGMPELHKLTPPLAVLQNQGFKVALVTDGRMSGASGKVPAAIHVTPEALAGGPLAKVR 527 Query: 542 DGDIVRISVEEGKLEALVPADEWNAR-PHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598 DGDIVR+ G L+ LV W AR P + G GRELF FR++A AE GA Sbjct: 528 DGDIVRVDAVAGTLDVLVDEATWAARTPSPYSAPAQTGFGRELFTNFRRHAGGAEQGA 585 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: 1114 Number of extensions: 48 Number of successful extensions: 4 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: 589 Length adjustment: 37 Effective length of query: 570 Effective length of database: 552 Effective search space: 314640 Effective search space used: 314640 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 Ac3H11_2082 (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.19524.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-270 882.9 0.2 8.7e-270 882.0 0.2 1.4 1 lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Phosphogluconate dehydratase (EC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 882.0 0.2 8.7e-270 8.7e-270 1 599 [. 2 587 .. 2 589 .] 0.98 Alignments for each domain: == domain 1 score: 882.0 bits; conditional E-value: 8.7e-270 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelkse 62 h+ +a++teri++rs++tr +yl+ + + + + + ++gc+nlah++aal+ sek +++ e lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 2 HPVVARVTERIVQRSADTRGAYLAGVDAMIARKPAQDRMGCANLAHAYAALPGSEKFKVTVE 63 67799********************************************************* PP TIGR01196 63 krknlaiitayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmels 124 k +n++++tayndmlsahqp+++yp+++++++ +++a+ qvagGvpamcdGvtqG +Gmels lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 64 KAPNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVPAMCDGVTQGTPGMELS 125 ************************************************************** PP TIGR01196 125 llsrdvialstaiglshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlen 186 l+srd ia++ta++lsh++fdgal+lGvcdkivpGlli+al +Ghlp+vfvpaGpm +Gl+n lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 126 LFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAGPMGTGLSN 187 ************************************************************** PP TIGR01196 187 kekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnp 248 k+kakvr+++a+G v+r+ell++e+a+yh+pGtctfyGtansnqml+e mGlh+pga+f p lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 188 KDKAKVREQYAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQMLLEAMGLHVPGAAFESP 249 ************************************************************** PP TIGR01196 249 ntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaia 310 t+ r+a+tr+a + + + ++ +++p+++l+de++ivna+ +llatGGstnh +h vaia lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 250 GTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAALLATGGSTNHLIHWVAIA 311 ************************************************************** PP TIGR01196 311 raaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetv 372 r+aGi+++w d++els++vpllarvypnG advn+f+aaGG + ++rell G++h dv +v lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 312 RSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGPPWILRELLAGGFMHPDVMSV 373 ************************************************************** PP TIGR01196 373 agkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvs 434 G+ + a+ s d+++lr+v+ pfs++GGl+ll+G lGravikvs lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 374 NVGGIADG------------GKSAPAVSGDTSVLRPVSAPFSPTGGLRLLQGRLGRAVIKVS 423 99998653............36899************************************* PP TIGR01196 435 avkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvl 496 av e+ ++ieapa+vf++q+ llaaf ag++++d+vavvrfqGp+anGmpelhklt++l vl lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 424 AVPEDRHIIEAPARVFDSQEALLAAFSAGDVNQDMVAVVRFQGPQANGMPELHKLTPPLAVL 485 ************************************************************** PP TIGR01196 497 qdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvdd 558 q++gfkvalvtdGr+sGasGkvpaaihvtpeal+gG+lak+rdGd++r+dav+g l+vlvd+ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 486 QNQGFKVALVTDGRMSGASGKVPAAIHVTPEALAGGPLAKVRDGDIVRVDAVAGTLDVLVDE 547 ************************************************************** PP TIGR01196 559 aelkareleeldlednelGlGrelfaalrekvssaeeGass 599 a ++ar+++ + ++ G Grelf+++r+++++ae+Ga++ lcl|FitnessBrowser__acidovorax_3H11:Ac3H11_2082 548 ATWAARTPS-PYSAPAQTGFGRELFTNFRRHAGGAEQGACT 587 *******65.55667899*********************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (589 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: 0.10u 0.02s 00:00:00.12 Elapsed: 00:00:00.10 # Mc/sec: 3.29 // [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