Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq)
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Dino:3608367 Length = 601 Score = 689 bits (1779), Expect = 0.0 Identities = 348/594 (58%), Positives = 437/594 (73%), Gaps = 4/594 (0%) Query: 5 VLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMN 64 + +VT R+ ARS R YL +R AA DGP+R L C N AH A G DK +L Sbjct: 7 ISDVTARIEARSAEARSTYLDRMRRAAEDGPRRAHLSCGNQAHAYAAMGG-DKEALVAER 65 Query: 65 AANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMEL 124 +AN+ IV++YNDMLSAHQP++ +P++IK+A R G+ Q AGG PAMCDGVTQG+ GMEL Sbjct: 66 SANIGIVTAYNDMLSAHQPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGMEL 125 Query: 125 SLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG 184 SL SR+VIAL+T VALSHN FDAA LG+CDKIVPGL++ A FG+LP +FVP GPM SG Sbjct: 126 SLFSRDVIALATGVALSHNTFDAAAYLGVCDKIVPGLVIAAATFGYLPGVFVPAGPMVSG 185 Query: 185 ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGA 244 + N +KA VRQ++A G+ R++L+E+EM SYH PGTCTFYGTAN+NQ+LME MGLHLPGA Sbjct: 186 LPNDQKAKVRQQFAAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGLHLPGA 245 Query: 245 SFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHT 304 SFVNP TPLR+ALT AA+++ +T+ + P+ +I+D ++ VN IV L ATGGSTN Sbjct: 246 SFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGGSTNLV 305 Query: 305 LHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAG 364 +H+PA+A+AAG+ L QD AD+SE P ++ VYPNG AD+NHF AAGG+A++I ELL G Sbjct: 306 IHLPAMARAAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGELLSEG 365 Query: 365 LLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVME 424 LLH D T+AG GL+ Y +EP L +G L W DGP SL+ ILRP + F+P GGL+ ++ Sbjct: 366 LLHPDTKTIAGDGLADYAREPKLIDGVLRWEDGPRRSLNAKILRPASDGFAPSGGLKELK 425 Query: 425 GNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGM 484 GNLGRGVMKVSAVA + ++EA A VF+DQ + DAFKAGE +D V ++RFQGP++NGM Sbjct: 426 GNLGRGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAGEFTEDTVVIVRFQGPKANGM 485 Query: 485 PELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDII 544 PELH +TP L VLQDRG KVALVTDGRMSGASGK+PAAIHV+PEA GG +A+VR GD++ Sbjct: 486 PELHALTPVLAVLQDRGLKVALVTDGRMSGASGKVPAAIHVAPEALDGGLMAKVRTGDLV 545 Query: 545 RVDGVKGTLELKVDADEFAAREPA-KGLLGNNVGSGRELFGFMRMAFSSAEQGA 597 RVD V G LE+ E R PA L GN+ G GRELF R A GA Sbjct: 546 RVDAVAGVLEVLEPGVE--DRAPAMPDLSGNSHGIGRELFDVFRTTVGPASTGA 597 Lambda K H 0.318 0.134 0.386 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: 1081 Number of extensions: 44 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: 608 Length of database: 601 Length adjustment: 37 Effective length of query: 571 Effective length of database: 564 Effective search space: 322044 Effective search space used: 322044 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 3608367 Dshi_1769 (6-phosphogluconate dehydratase (RefSeq))
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.18772.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.8e-287 939.8 1.5 3.1e-287 939.6 1.5 1.0 1 lcl|FitnessBrowser__Dino:3608367 Dshi_1769 6-phosphogluconate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dino:3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 939.6 1.5 3.1e-287 3.1e-287 4 599 .. 7 599 .. 4 601 .] 0.99 Alignments for each domain: == domain 1 score: 939.6 bits; conditional E-value: 3.1e-287 TIGR01196 4 laeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmlsah 80 + ++t+ri +rs++ r++yl+++r a++ g+ r++l+cgn ah++aa+ +k +l e+ +n++i+tayndmlsah lcl|FitnessBrowser__Dino:3608367 7 ISDVTARIEARSAEARSTYLDRMRRAAEDGPRRAHLSCGNQAHAYAAMGG-DKEALVAERSANIGIVTAYNDMLSAH 82 679*********************************************86.78999********************* PP TIGR01196 81 qpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkiv 157 qpfk+ypd ik+a+++a+a+aqvagGvpamcdGvtqG+ Gmelsl+srdvial+t+++lshn fd+a +lGvcdkiv lcl|FitnessBrowser__Dino:3608367 83 QPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGMELSLFSRDVIALATGVALSHNTFDAAAYLGVCDKIV 159 ***************************************************************************** PP TIGR01196 158 pGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlve 234 pGl+iaa++fG lp+vfvpaGpm+sGl+n++kakvrq+fa G ++r++l+++emasyh+pGtctfyGtansnqml+e lcl|FitnessBrowser__Dino:3608367 160 PGLVIAAATFGYLPGVFVPAGPMVSGLPNDQKAKVRQQFAAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLME 236 ***************************************************************************** PP TIGR01196 235 lmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiar 311 +mGlhlpgasfvnp tplr+alt++aa+rla++t+ ++e+ p+++++d k++vn++vgl+atGGstn +hl a+ar lcl|FitnessBrowser__Dino:3608367 237 FMGLHLPGASFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGGSTNLVIHLPAMAR 313 ***************************************************************************** PP TIGR01196 312 aaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfled 388 aaG+il+ +d+ ++s+ pl+arvypnG advnhf+aaGGl+++i ell+eGllh d++t+ag Gl y++ep+l d lcl|FitnessBrowser__Dino:3608367 314 AAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGELLSEGLLHPDTKTIAGDGLADYAREPKLID 390 ***************************************************************************** PP TIGR01196 389 gkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagel 465 g l++++++ +sl+ +ilr++++ f+++GGlk lkGnlGr+v+kvsav++e +viea+a+vf+dq +++afkage+ lcl|FitnessBrowser__Dino:3608367 391 GVLRWEDGPRRSLNAKILRPASDGFAPSGGLKELKGNLGRGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAGEF 467 ***************************************************************************** PP TIGR01196 466 erdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdl 542 d v++vrfqGpkanGmpelh lt+vl vlqdrg kvalvtdGr+sGasGkvpaaihv+peal+gG +ak+r+Gdl lcl|FitnessBrowser__Dino:3608367 468 TEDTVVIVRFQGPKANGMPELHALTPVLAVLQDRGLKVALVTDGRMSGASGKVPAAIHVAPEALDGGLMAKVRTGDL 544 ***************************************************************************** PP TIGR01196 543 irldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599 +r+dav+g levl+ +e r ++++dl+ n+ G+Grelf +r++v+ a +Ga + lcl|FitnessBrowser__Dino:3608367 545 VRVDAVAGVLEVLEPGVE--DRAPAMPDLSGNSHGIGRELFDVFRTTVGPASTGAGV 599 *************88766..67788*****************************976 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (601 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: 00:00:00.03 # Mc/sec: 10.67 // [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