Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF835 Psest_0849 6-phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >lcl|FitnessBrowser__psRCH2:GFF835 Psest_0849 6-phosphogluconate dehydratase Length = 608 Score = 952 bits (2462), Expect = 0.0 Identities = 471/608 (77%), Positives = 536/608 (88%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 MHP V+EVTERL+ RSR TREAYLA+IRGAAS GP R QCANFAHGVAGCG++DK L Sbjct: 1 MHPVVVEVTERLIQRSRPTREAYLAMIRGAASAGPARNGAQCANFAHGVAGCGTQDKQRL 60 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 R+ +AANVAIV++YNDMLSAHQPYE +PE++++ALR++GSVGQ AGG PAMCDGVTQGE Sbjct: 61 RLPDAANVAIVTAYNDMLSAHQPYEGYPERLRQALRDVGSVGQVAGGVPAMCDGVTQGEP 120 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMEL++ SREVIA+STAVALSHN+FDAAL+LGICDKIVPGL++GALRFGHLP +FVP GP Sbjct: 121 GMELAIASREVIAMSTAVALSHNLFDAALLLGICDKIVPGLLIGALRFGHLPAVFVPAGP 180 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 MPSG++NK+KA VRQRYAEGKA+R+ELL +EM++YHSPGTCTFYGTANTNQ+LMEVMGLH Sbjct: 181 MPSGLANKDKAAVRQRYAEGKASRDELLAAEMQAYHSPGTCTFYGTANTNQMLMEVMGLH 240 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPG+SFVNP TPLRDALT EAA+QVTRLT Q G FTP+GE+VDER LVN+IVALHATGGS Sbjct: 241 LPGSSFVNPGTPLRDALTAEAARQVTRLTPQGGCFTPLGELVDERVLVNAIVALHATGGS 300 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TNHTLHMPAIAQAAGIQLTWQDMADLS VVPTL+ VYPNG ADINHF AAGG+A L+REL Sbjct: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSAVVPTLARVYPNGPADINHFHAAGGVAVLVREL 360 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 L AGLLHEDV+TV GRGLSRYTQEPFL+ G+L WR+G SLDE++LRPVAR FS EGGL Sbjct: 361 LAAGLLHEDVHTVMGRGLSRYTQEPFLEGGRLTWREGAAASLDESLLRPVARPFSAEGGL 420 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 RVM GNLGRGVMKVSAVA +H++VEAPA VF DQ +L +AFKAGELE+D VAV+RFQGPR Sbjct: 421 RVMSGNLGRGVMKVSAVAPEHRVVEAPARVFADQLELVEAFKAGELERDVVAVVRFQGPR 480 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 +NGMPELHK+TP+LG+LQDRGFKVALVTDGRMSGASGK+PAAIHV PEA GG LARVRD Sbjct: 481 ANGMPELHKLTPYLGLLQDRGFKVALVTDGRMSGASGKVPAAIHVCPEAIDGGPLARVRD 540 Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600 GD++RVDG G LE+ VDA E A R P + G GRELFGFMR AFSSAEQGAS F Sbjct: 541 GDLLRVDGQAGVLEVLVDAAELAGRSPVAAPAASVQGCGRELFGFMRSAFSSAEQGASVF 600 Query: 601 TSALENLK 608 T+ LE L+ Sbjct: 601 TAGLEALR 608 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: 1284 Number of extensions: 55 Number of successful extensions: 1 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: 608 Length adjustment: 37 Effective length of query: 571 Effective length of database: 571 Effective search space: 326041 Effective search space used: 326041 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 GFF835 Psest_0849 (6-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.27353.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1023.9 0.2 0 1023.7 0.2 1.0 1 lcl|FitnessBrowser__psRCH2:GFF835 Psest_0849 6-phosphogluconate de Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__psRCH2:GFF835 Psest_0849 6-phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1023.7 0.2 0 0 1 601 [] 2 601 .. 2 601 .. 0.99 Alignments for each domain: == domain 1 score: 1023.7 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndm 76 h+ ++e+ter+i+rs++tre+yl++ir a++ g+ r+ c+n+ahgva + ++k+ l+ +n+ai+tayndm lcl|FitnessBrowser__psRCH2:GFF835 2 HPVVVEVTERLIQRSRPTREAYLAMIRGAASAGPARNGAQCANFAHGVAGCGTQDKQRLRLPDAANVAIVTAYNDM 77 67799*********************************************************************** PP TIGR01196 77 lsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGv 152 lsahqp++ yp+ +++al++ ++v+qvagGvpamcdGvtqGe+Gmel+++sr+via+sta++lshn+fd+al+lG+ lcl|FitnessBrowser__psRCH2:GFF835 78 LSAHQPYEGYPERLRQALRDVGSVGQVAGGVPAMCDGVTQGEPGMELAIASREVIAMSTAVALSHNLFDAALLLGI 153 **************************************************************************** PP TIGR01196 153 cdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtans 228 cdkivpGlli+al fGhlpavfvpaGpm+sGl nk+ka+vrq +aeGk++r+ell++em++yh+pGtctfyGtan+ lcl|FitnessBrowser__psRCH2:GFF835 154 CDKIVPGLLIGALRFGHLPAVFVPAGPMPSGLANKDKAAVRQRYAEGKASRDELLAAEMQAYHSPGTCTFYGTANT 229 **************************************************************************** PP TIGR01196 229 nqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtl 304 nqml+e+mGlhlpg+sfvnp tplrdalt+eaa++++rlt+++g ++pl+el+de+++vna+v+l+atGGstnhtl lcl|FitnessBrowser__psRCH2:GFF835 230 NQMLMEVMGLHLPGSSFVNPGTPLRDALTAEAARQVTRLTPQGGCFTPLGELVDERVLVNAIVALHATGGSTNHTL 305 **************************************************************************** PP TIGR01196 305 hlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrry 380 h+ aia+aaGi+l+w+d+ +ls +vp+larvypnG ad+nhf+aaGG+++l+rell +Gllhedv+tv+g+Gl+ry lcl|FitnessBrowser__psRCH2:GFF835 306 HMPAIAQAAGIQLTWQDMADLSAVVPTLARVYPNGPADINHFHAAGGVAVLVRELLAAGLLHEDVHTVMGRGLSRY 381 **************************************************************************** PP TIGR01196 381 tkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqael 456 t+epfle g+l++re+a +slde++lr+v +pfsaeGGl++++GnlGr+v+kvsav++e+rv+eapa+vf dq el lcl|FitnessBrowser__psRCH2:GFF835 382 TQEPFLEGGRLTWREGAAASLDESLLRPVARPFSAEGGLRVMSGNLGRGVMKVSAVAPEHRVVEAPARVFADQLEL 457 **************************************************************************** PP TIGR01196 457 laafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegG 532 ++afkagelerd+vavvrfqGp+anGmpelhklt+ lG+lqdrgfkvalvtdGr+sGasGkvpaaihv+pea++gG lcl|FitnessBrowser__psRCH2:GFF835 458 VEAFKAGELERDVVAVVRFQGPRANGMPELHKLTPYLGLLQDRGFKVALVTDGRMSGASGKVPAAIHVCPEAIDGG 533 **************************************************************************** PP TIGR01196 533 alakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601 +la++rdGdl+r+d+++g levlvd ael+ r++ ++ ++ +G+Grelf ++r++ ssae+Gas++t lcl|FitnessBrowser__psRCH2:GFF835 534 PLARVRDGDLLRVDGQAGVLEVLVDAAELAGRSP-VAAPAASVQGCGRELFGFMRSAFSSAEQGASVFT 601 ********************************96.56789999***********************986 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: 0.03u 0.02s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 8.31 // [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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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