Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF2220 HP15_2174 6-phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Marino:GFF2220 Length = 610 Score = 775 bits (2001), Expect = 0.0 Identities = 380/601 (63%), Positives = 472/601 (78%), Gaps = 1/601 (0%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 MHP V +VT+R++ RS TR+ YL + + P R L C N AHG A C DK +L Sbjct: 5 MHPTVDKVTQRIIERSHPTRQDYLNRMNALKAQSPHRSSLSCGNLAHGFAACNQGDKDTL 64 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 + MN ANVA+V++YNDMLSAHQPYE FP+ I++A R MGSV Q AGGTPAMCDGVTQG+ Sbjct: 65 KFMNKANVAMVTAYNDMLSAHQPYEKFPDIIREAARGMGSVAQVAGGTPAMCDGVTQGQP 124 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMELSL SR+ IA+STAVALSHNMFDA L+LGICDKIVPGL++G+L FG+LPTI +P GP Sbjct: 125 GMELSLFSRDTIAMSTAVALSHNMFDATLLLGICDKIVPGLLIGSLSFGYLPTILLPAGP 184 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 MPSG+ NKEK +RQ YAEGK +EELLE+E KSYHSPGTCTFYGTAN+NQLL+EVMGLH Sbjct: 185 MPSGLPNKEKQRIRQLYAEGKVGKEELLEAESKSYHSPGTCTFYGTANSNQLLVEVMGLH 244 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 +PG++FVNP TPLRD LT A +QV RL+K G +G++VDE+S+VN++VAL TGGS Sbjct: 245 MPGSAFVNPNTPLRDELTRAATEQVIRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGS 304 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TNHT+H AIA+AAGI + W D A+LS VVP+++ +YPNG+ D+N F AGG FLIREL Sbjct: 305 TNHTIHWIAIARAAGIIIDWNDYAELSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIREL 364 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 L G +H DVNTV G GL RYT+ P L + +LVW+ P +SL ++L PVA F+P+GGL Sbjct: 365 LSGGYVHNDVNTVVGYGLERYTEMPELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGL 424 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 RV++GNLGRGV+KVSAVA +H+ VEAPAVVF DQ +L AF+AG+L++D + ++RFQGP+ Sbjct: 425 RVLDGNLGRGVIKVSAVAPEHRKVEAPAVVFNDQNELKAAFEAGDLDRDCIVIVRFQGPK 484 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 SNGMPELHK+TP+LGVLQDRGFKV LVTDGRMSGASGK+PAAIHV PEA GG LA+V++ Sbjct: 485 SNGMPELHKLTPYLGVLQDRGFKVGLVTDGRMSGASGKVPAAIHVYPEALDGGPLAKVKN 544 Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKG-LLGNNVGSGRELFGFMRMAFSSAEQGASA 599 GD++ +D G L +++D EFA RE K L G + G GRELFG+MR A S+ E+GAS Sbjct: 545 GDMVCLDAESGVLAIRLDDQEFAGRESEKADLTGYHHGYGRELFGWMRRAASNPEEGASF 604 Query: 600 F 600 F Sbjct: 605 F 605 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: 1099 Number of extensions: 44 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: 608 Length of database: 610 Length adjustment: 37 Effective length of query: 571 Effective length of database: 573 Effective search space: 327183 Effective search space used: 327183 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 GFF2220 HP15_2174 (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.10834.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.6e-298 974.7 0.0 8.6e-298 974.5 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF2220 HP15_2174 6-phosphogluconate deh Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Marino:GFF2220 HP15_2174 6-phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 974.5 0.0 8.6e-298 8.6e-298 1 600 [. 6 605 .. 6 606 .. 0.99 Alignments for each domain: == domain 1 score: 974.5 bits; conditional E-value: 8.6e-298 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 h+ + ++t+riiers++tr+ yl+++++ k ++++rs+l+cgnlahg+aa+++ +k +lk ++++n+a++taynd lcl|FitnessBrowser__Marino:GFF2220 6 HPTVDKVTQRIIERSHPTRQDYLNRMNALKAQSPHRSSLSCGNLAHGFAACNQGDKDTLKFMNKANVAMVTAYND 80 68899********************************************************************** PP TIGR01196 76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150 mlsahqp++++pd+i++a++ ++vaqvagG+pamcdGvtqG++Gmelsl+srd ia+sta++lshnmfd++l+l lcl|FitnessBrowser__Marino:GFF2220 81 MLSAHQPYEKFPDIIREAARGMGSVAQVAGGTPAMCDGVTQGQPGMELSLFSRDTIAMSTAVALSHNMFDATLLL 155 *************************************************************************** PP TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225 G+cdkivpGlli++lsfG lp++++paGpm+sGl+nkek ++rql+aeGkv++eell++e++syh+pGtctfyGt lcl|FitnessBrowser__Marino:GFF2220 156 GICDKIVPGLLIGSLSFGYLPTILLPAGPMPSGLPNKEKQRIRQLYAEGKVGKEELLEAESKSYHSPGTCTFYGT 230 *************************************************************************** PP TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300 ansnq+lve+mGlh+pg++fvnpntplrd+ltr+a++++ rl g l l++++deksivnalv+ll tGGst lcl|FitnessBrowser__Marino:GFF2220 231 ANSNQLLVEVMGLHMPGSAFVNPNTPLRDELTRAATEQVIRLSKPHGGELGLGDMVDEKSIVNALVALLVTGGST 305 ******************************************99999999************************* PP TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375 nht+h +aiaraaGii++w+d els++vp ++r+ypnG+ dvn+f+ aGG +flirell+ G +h+dv+tv+g lcl|FitnessBrowser__Marino:GFF2220 306 NHTIHWIAIARAAGIIIDWNDYAELSSVVPSMTRIYPNGQEDVNAFHEAGGTPFLIRELLSGGYVHNDVNTVVGY 380 *************************************************************************** PP TIGR01196 376 GlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivf 450 Gl+ryt+ p l+d++l++++a+eksl d+l +v +pf+++GGl++l+GnlGr+vikvsav++e+r++eapa+vf lcl|FitnessBrowser__Marino:GFF2220 381 GLERYTEMPELSDEQLVWKPAPEKSLRPDVLSPVAEPFAPDGGLRVLDGNLGRGVIKVSAVAPEHRKVEAPAVVF 455 *************************************************************************** PP TIGR01196 451 kdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvt 525 +dq+el+aaf+ag+l+rd++++vrfqGpk+nGmpelhklt+ lGvlqdrgfkv lvtdGr+sGasGkvpaaihv lcl|FitnessBrowser__Marino:GFF2220 456 NDQNELKAAFEAGDLDRDCIVIVRFQGPKSNGMPELHKLTPYLGVLQDRGFKVGLVTDGRMSGASGKVPAAIHVY 530 *************************************************************************** PP TIGR01196 526 pealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600 peal+gG+lak+++Gd++ lda +g l + dd e++ re e+ dl + G Grelf +r+++s eeGas + lcl|FitnessBrowser__Marino:GFF2220 531 PEALDGGPLAKVKNGDMVCLDAESGVLAIRLDDQEFAGRESEKADLTGYHHGYGRELFGWMRRAASNPEEGASFF 605 ***********************************************************************9866 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (601 nodes) Target sequences: 1 (610 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 10.47 // [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