Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate PP_1010 PP_1010 phosphogluconate dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Putida:PP_1010 Length = 608 Score = 1056 bits (2732), Expect = 0.0 Identities = 528/608 (86%), Positives = 566/608 (93%) Query: 1 MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60 MHPR+LEVT+RLV RSRATRE YL LIRGAAS+GP R LQCANFAHGVAGCGSEDK +L Sbjct: 1 MHPRILEVTQRLVERSRATRERYLQLIRGAASEGPMRASLQCANFAHGVAGCGSEDKQTL 60 Query: 61 RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120 R+MNAANVAIVS+YNDMLSAHQPY HFPEQIK+ALRE+GSVGQFAGG PAMCDGVTQGE Sbjct: 61 RLMNAANVAIVSAYNDMLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEP 120 Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 GMEL++ SREVIA+STAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP Sbjct: 121 GMELAIASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180 Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 M SGISNK+KADVRQRYAEGKA+REELLESEM SYHSPGTCTFYGTANTNQL+MEVMGLH Sbjct: 181 MVSGISNKQKADVRQRYAEGKASREELLESEMNSYHSPGTCTFYGTANTNQLVMEVMGLH 240 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300 LPGASFVNPYTPLRDALT EAAQQVTR+TK SG+F P+GEIVDE++LVNSIVALHATGGS Sbjct: 241 LPGASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGGS 300 Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 TNHTLH+PAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL Sbjct: 301 TNHTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360 Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420 L+AGLLHEDVNTVAG GL RYTQEPFLDNGKLVWR+GP SLDE+ILRPV+R FS EGGL Sbjct: 361 LDAGLLHEDVNTVAGHGLRRYTQEPFLDNGKLVWREGPQHSLDESILRPVSRPFSAEGGL 420 Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480 RVMEGNLGRGVMKVSAVA +HQ+VEAPA VFQDQQ LADAFKAGELE+DFVAV+RFQGPR Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQVVEAPARVFQDQQSLADAFKAGELERDFVAVVRFQGPR 480 Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540 NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGKIPAAIHV PEA GG LARVRD Sbjct: 481 CNGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKIPAAIHVCPEAYDGGPLARVRD 540 Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600 GDI+RVDGV+GTL + V A+E A+RE GN++G GRELFGFMRMAFS AEQGASAF Sbjct: 541 GDIVRVDGVEGTLRIMVSAEELASRELPPAPQGNDLGCGRELFGFMRMAFSPAEQGASAF 600 Query: 601 TSALENLK 608 TSALE+LK Sbjct: 601 TSALEHLK 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: 1306 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 PP_1010 PP_1010 (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.27678.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 1049.0 0.1 0 1048.8 0.1 1.0 1 lcl|FitnessBrowser__Putida:PP_1010 PP_1010 phosphogluconate dehydra Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_1010 PP_1010 phosphogluconate dehydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1048.8 0.1 0 0 1 601 [] 2 601 .. 2 601 .. 1.00 Alignments for each domain: == domain 1 score: 1048.8 bits; conditional E-value: 0 TIGR01196 1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 h+r++e+t+r++ers++tre+yl+ ir a+++g++r++l c+n+ahgva + ++k++l+ ++ +n+ai++aynd lcl|FitnessBrowser__Putida:PP_1010 2 HPRILEVTQRLVERSRATRERYLQLIRGAASEGPMRASLQCANFAHGVAGCGSEDKQTLRLMNAANVAIVSAYND 76 79************************************************************************* PP TIGR01196 76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150 mlsahqp+ ++p++ik+al+e ++v+q agGvpamcdGvtqGe+Gmel+++sr+via+sta++lshnmfd+al+l lcl|FitnessBrowser__Putida:PP_1010 77 MLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEPGMELAIASREVIAMSTAVALSHNMFDAALML 151 *************************************************************************** PP TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225 G+cdkivpGl+++al fGhlp++fvp+Gpm+sG++nk+ka vrq +aeGk++reell+sem+syh+pGtctfyGt lcl|FitnessBrowser__Putida:PP_1010 152 GICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISNKQKADVRQRYAEGKASREELLESEMNSYHSPGTCTFYGT 226 *************************************************************************** PP TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300 an+nq+++e+mGlhlpgasfvnp+tplrdalt+eaa++++r+t +g+++pl+e++dek++vn++v+l+atGGst lcl|FitnessBrowser__Putida:PP_1010 227 ANTNQLVMEVMGLHLPGASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGGST 301 *************************************************************************** PP TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375 nhtlh+ aia+aaGi+l+w+d+ +ls++vp+l +vypnGkad+nhf+aaGG++flirell++Gllhedv+tvag+ lcl|FitnessBrowser__Putida:PP_1010 302 NHTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLDAGLLHEDVNTVAGH 376 *************************************************************************** PP TIGR01196 376 GlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivf 450 Glrryt+epfl++gkl++re++++slde+ilr+v++pfsaeGGl++++GnlGr+v+kvsav++e++v+eapa+vf lcl|FitnessBrowser__Putida:PP_1010 377 GLRRYTQEPFLDNGKLVWREGPQHSLDESILRPVSRPFSAEGGLRVMEGNLGRGVMKVSAVAPEHQVVEAPARVF 451 *************************************************************************** PP TIGR01196 451 kdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvt 525 +dq++l++afkagelerd+vavvrfqGp++nGmpelhklt++lGvlqdrg+kvalvtdGr+sGasGk+paaihv+ lcl|FitnessBrowser__Putida:PP_1010 452 QDQQSLADAFKAGELERDFVAVVRFQGPRCNGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKIPAAIHVC 526 *************************************************************************** PP TIGR01196 526 pealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600 pea++gG+la++rdGd++r+d+v+g l+++v el++re ++++ n+lG+Grelf ++r + s ae+Gas++ lcl|FitnessBrowser__Putida:PP_1010 527 PEAYDGGPLARVRDGDIVRVDGVEGTLRIMVSAEELASRE-LPPAPQGNDLGCGRELFGFMRMAFSPAEQGASAF 600 ***************************************9.6899***************************998 PP TIGR01196 601 t 601 t lcl|FitnessBrowser__Putida:PP_1010 601 T 601 6 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 0.01s 00:00:00.04 Elapsed: 00:00:00.03 # Mc/sec: 11.51 // [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