Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate H281DRAFT_03046 H281DRAFT_03046 6-phosphogluconate dehydrogenase (decarboxylating)
Query= BRENDA::P00350 (468 letters) >FitnessBrowser__Burk376:H281DRAFT_03046 Length = 469 Score = 689 bits (1779), Expect = 0.0 Identities = 344/468 (73%), Positives = 400/468 (85%), Gaps = 2/468 (0%) Query: 1 MSKQQIGVVGMAVMGRNLALNIESRGYTVSIFNRSREKTEEVIAENPGKKLVPYYTVKEF 60 M KQ IGVVG+AVMGRNLALNIESRG+ VS++NRSREKT+E+IAE P KKLVP +T++EF Sbjct: 1 MGKQAIGVVGLAVMGRNLALNIESRGHAVSVYNRSREKTDELIAEYPDKKLVPAFTLEEF 60 Query: 61 VESLETPRRILLMVKAGAGTDAAIDSLKPYLDKGDIIIDGGNTFFQDTIRRNRELSAEGF 120 VESLE PRRILLMVKAG TDA I SLKP L+KGDI+IDGGNT F DTIRRN+EL+ G Sbjct: 61 VESLEKPRRILLMVKAGEPTDATIASLKPLLEKGDILIDGGNTHFTDTIRRNQELAKAGL 120 Query: 121 NFIGTGVSGGEEGALKGPSIMPGGQKEAYELVAPILTKIAAVAEDGEPCVTYIGADGAGH 180 +FIGTGVSGGEEGALKGPSIMPGGQ++AY+LVAPILT+IAA A DGEPCV Y+G DGAGH Sbjct: 121 HFIGTGVSGGEEGALKGPSIMPGGQRDAYDLVAPILTEIAAKAPDGEPCVAYMGPDGAGH 180 Query: 181 YVKMVHNGIEYGDMQLIAEAYSLLKGGLNLTNEELAQTFTEWNNGELSSYLIDITKDIFT 240 +VKMVHNGIEYGDMQLIAE+Y++LK + L+NEEL + +TEWN GEL SYLI+IT IF+ Sbjct: 181 FVKMVHNGIEYGDMQLIAESYAVLKQVVGLSNEELGKVYTEWNQGELDSYLIEITSKIFS 240 Query: 241 KKDED-GNYLVDVILDEAANKGTGKWTSQSALDLGEPLSLITESVFARYISSLKDQRVAA 299 KKDE+ G LVDVILD AA KGTGKWTSQ+ALDLG PL LITE+VFAR +SSLKDQRVAA Sbjct: 241 KKDEETGKDLVDVILDRAAQKGTGKWTSQNALDLGAPLPLITEAVFARVLSSLKDQRVAA 300 Query: 300 SKVLSGPQAQPAGDKAE-FIEKVRRALYLGKIVSYAQGFSQLRAASEEYNWDLNYGEIAK 358 SKVL GP A+P G + E FIE VRRALY K++SYAQGF+QLRAASEEY WDL++G IAK Sbjct: 301 SKVLDGPSAKPLGAEREAFIESVRRALYFSKVISYAQGFAQLRAASEEYKWDLDFGTIAK 360 Query: 359 IFRAGCIIRAQFLQKITDAYAENPQIANLLLAPYFKQIADDYQQALRDVVAYAVQNGIPV 418 IFRAGCIIRA+FLQKITDAY + IANLLL PYF+ IA +YQ ALR+VV A+ G+PV Sbjct: 361 IFRAGCIIRARFLQKITDAYTKEKTIANLLLDPYFRDIASNYQSALREVVVAAINAGVPV 420 Query: 419 PTFSAAVAYYDSYRAAVLPANLIQAQRDYFGAHTYKRIDKEGVFHTEW 466 P F++AVAY+D+YR+ LPANL+QAQRD+FGAHT++RIDK G FH W Sbjct: 421 PAFASAVAYFDAYRSERLPANLVQAQRDFFGAHTFERIDKPGSFHANW 468 Lambda K H 0.317 0.135 0.385 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: 753 Number of extensions: 25 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: 468 Length of database: 469 Length adjustment: 33 Effective length of query: 435 Effective length of database: 436 Effective search space: 189660 Effective search space used: 189660 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 (21.6 bits) S2: 51 (24.3 bits)
Align candidate H281DRAFT_03046 H281DRAFT_03046 (6-phosphogluconate dehydrogenase (decarboxylating))
to HMM TIGR00873 (gnd: 6-phosphogluconate dehydrogenase (decarboxylating) (EC 1.1.1.44))
# 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/TIGR00873.hmm # target sequence database: /tmp/gapView.12078.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00873 [M=467] Accession: TIGR00873 Description: gnd: 6-phosphogluconate dehydrogenase (decarboxylating) 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8.4e-227 739.4 0.0 9.6e-227 739.2 0.0 1.0 1 lcl|FitnessBrowser__Burk376:H281DRAFT_03046 H281DRAFT_03046 6-phosphoglucona Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Burk376:H281DRAFT_03046 H281DRAFT_03046 6-phosphogluconate dehydrogenase (decarboxylating) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 739.2 0.0 9.6e-227 9.6e-227 2 466 .. 6 469 .] 5 469 .] 0.99 Alignments for each domain: == domain 1 score: 739.2 bits; conditional E-value: 9.6e-227 TIGR00873 2 iGliGlavmGknlvlniadkGfsvavynrtkektdellkeeakgkklvgaesieefvkslekPrki 67 iG++GlavmG+nl+lni+++G+ v+vynr++ektdel++e +kklv+a ++eefv+slekPr+i lcl|FitnessBrowser__Burk376:H281DRAFT_03046 6 IGVVGLAVMGRNLALNIESRGHAVSVYNRSREKTDELIAE-YPDKKLVPAFTLEEFVESLEKPRRI 70 9***************************************.78999******************** PP TIGR00873 68 lllvkaGaavdavieellpllekgdiiidGGnslykdterrekelkekgilfvGvGvsGGeeGark 133 ll+vkaG+++da+i++l+pllekgdi+idGGn++++dt+rr++el+++g++f+G+GvsGGeeGa+k lcl|FitnessBrowser__Burk376:H281DRAFT_03046 71 LLMVKAGEPTDATIASLKPLLEKGDILIDGGNTHFTDTIRRNQELAKAGLHFIGTGVSGGEEGALK 136 ****************************************************************** PP TIGR00873 134 GPslmpGGskeayelvepilqkiaakve.gepcceyiGedGaGhyvkmvhnGieygdmqliaeaye 198 GPs+mpGG+++ay+lv+pil++iaak+ gepc+ y+G+dGaGh+vkmvhnGieygdmqliae+y lcl|FitnessBrowser__Burk376:H281DRAFT_03046 137 GPSIMPGGQRDAYDLVAPILTEIAAKAPdGEPCVAYMGPDGAGHFVKMVHNGIEYGDMQLIAESYA 202 **************************977************************************* PP TIGR00873 199 llkealklsaeeiaevfeeWnegeldsylieitadilkkkded.GkplvdkildaagqkGtGkWta 263 +lk++++ls+ee+ +v++eWn+geldsylieit++i++kkde+ Gk lvd+ild+a+qkGtGkWt+ lcl|FitnessBrowser__Burk376:H281DRAFT_03046 203 VLKQVVGLSNEELGKVYTEWNQGELDSYLIEITSKIFSKKDEEtGKDLVDVILDRAAQKGTGKWTS 268 *****************************************999********************** PP TIGR00873 264 idaldlGvPvtlitesvfarvlsslkeervaaskllsgplaeekaedkeefiedvrealyaskivs 329 ++aldlG P+ lite+vfarvlsslk++rvaask+l gp+a+ + ++e+fie+vr+aly sk++s lcl|FitnessBrowser__Burk376:H281DRAFT_03046 269 QNALDLGAPLPLITEAVFARVLSSLKDQRVAASKVLDGPSAKPLGAEREAFIESVRRALYFSKVIS 334 ****************************************************************** PP TIGR00873 330 yaqGfallkeaskeygwdlnlgeialiwrgGciirskfldkikkafeenpelenlllaeyfkdalk 395 yaqGfa+l++as+ey wdl++g+ia+i+r+Gciir++fl+ki++a+++++ ++nlll++yf+d+ + lcl|FitnessBrowser__Burk376:H281DRAFT_03046 335 YAQGFAQLRAASEEYKWDLDFGTIAKIFRAGCIIRARFLQKITDAYTKEKTIANLLLDPYFRDIAS 400 ****************************************************************** PP TIGR00873 396 kaqkglrkvvakaielgipvPalsaalsfydgyrtarlpanllqaqrdyfGahtyertdkprgeff 461 ++q++lr+vv+ ai++g+pvPa+++a++++d+yr++rlpanl+qaqrd+fGaht+er+dkp+ f lcl|FitnessBrowser__Burk376:H281DRAFT_03046 401 NYQSALREVVVAAINAGVPVPAFASAVAYFDAYRSERLPANLVQAQRDFFGAHTFERIDKPG--SF 464 **************************************************************..9* PP TIGR00873 462 hteWl 466 h++W+ lcl|FitnessBrowser__Burk376:H281DRAFT_03046 465 HANWS 469 ****6 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (467 nodes) Target sequences: 1 (469 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02 # Mc/sec: 9.20 // [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