Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF835 Psest_0849 6-phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__psRCH2:GFF835 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.30041.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: 0.04u 0.01s 00:00:00.05 Elapsed: 00:00:00.04 # Mc/sec: 7.39 // [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