Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate WP_011777328.1 MVAN_RS00025 6-phosphogluconate dehydrogenase (decarboxylating)
Query= BRENDA::Q2RIZ2 (298 letters) >NCBI__GCF_000015305.1:WP_011777328.1 Length = 297 Score = 268 bits (686), Expect = 9e-77 Identities = 136/301 (45%), Positives = 184/301 (61%), Gaps = 13/301 (4%) Query: 1 MHIGLVGLGRMGLNLALNMLDHGHEVRGYARTKATVDKAAAQGIKGAYSLEELAGQLKTP 60 M +GL+GLG+MG N+ + D GH+V G+ D A SL +LA +L P Sbjct: 1 MQLGLIGLGKMGFNMRARLRDGGHDVVGFDPRPEVSDVA---------SLADLAARLSAP 51 Query: 61 RLVWLMIPAGKAVDEVIEQLAPLLAPGDIIVDGGNSHYRDTLRRYKFLKEKGIHLVDSGT 120 R+VW+M+P+G D I +LA +L+PGD+++DGGNS Y + R L EKGI +D+G Sbjct: 52 RVVWVMVPSGTVTDSTISELAGVLSPGDLVIDGGNSRYTEDGRHANLLAEKGIAFIDAGV 111 Query: 121 SGGVEGARHGACCMVGAEDEVFAYLEPLFKDITVPG----GYLHTGPPGSGHYVKMVHNG 176 SGG+ G G MVG D A P+F+ + PG G++H GP G+GH+ KMVHNG Sbjct: 112 SGGIWGLTEGYGLMVGGSDADVARAMPIFETLRPPGPLEDGFVHVGPVGAGHFAKMVHNG 171 Query: 177 IEYGMMQAIGEGMEVLAGAPFKLDLKEVARVWRHGSVIRGWLMDLMEKALAKDNTLDGIK 236 IEY +M A EG E+LA D + V + W +G+V+R WL L+ KAL +D +L I Sbjct: 172 IEYALMTAYAEGYEMLAAEDLVKDPQAVYQAWTNGTVVRSWLQQLLAKALKEDPSLSDIS 231 Query: 237 DIAYSSGEGLWTIEEALRLKVPAPVITAALLMRYRSEQEESFATKVVAALRHEFGGHDVA 296 SGEG WT+EEA+RL+VP P I A+L R+ S Q+ES K VAALR++FGGH V Sbjct: 232 GYTEDSGEGRWTVEEAIRLRVPVPGIAASLFARFLSRQDESPTMKAVAALRNQFGGHAVK 291 Query: 297 R 297 R Sbjct: 292 R 292 Lambda K H 0.320 0.139 0.415 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: 318 Number of extensions: 13 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: 298 Length of database: 297 Length adjustment: 26 Effective length of query: 272 Effective length of database: 271 Effective search space: 73712 Effective search space used: 73712 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 48 (23.1 bits)
Align candidate WP_011777328.1 MVAN_RS00025 (6-phosphogluconate dehydrogenase (decarboxylating))
to HMM TIGR00872 (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/TIGR00872.hmm # target sequence database: /tmp/gapView.25231.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00872 [M=299] Accession: TIGR00872 Description: gnd_rel: 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-104 335.9 0.0 1.4e-104 335.5 0.0 1.2 1 lcl|NCBI__GCF_000015305.1:WP_011777328.1 MVAN_RS00025 6-phosphogluconate Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000015305.1:WP_011777328.1 MVAN_RS00025 6-phosphogluconate dehydrogenase (decarboxylating) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.5 0.0 1.4e-104 1.4e-104 1 297 [. 1 292 [. 1 294 [. 0.97 Alignments for each domain: == domain 1 score: 335.5 bits; conditional E-value: 1.4e-104 TIGR00872 1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvmvpa 69 m+lgliGlG+mG n+ rl ++gh+vvg+d ++ +va+l +l rlsaprvvwvmvp lcl|NCBI__GCF_000015305.1:WP_011777328.1 1 MQLGLIGLGKMGFNMRARLRDGGHDVVGFDPRPEVS---------DVASLADLAARLSAPRVVWVMVPS 60 9*****************************998764.........5899******************** PP TIGR00872 70 g.ivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGGd 137 g ++d+ + ela +l+ Gd+vidgGns y ++ r+ ++l ekgi ++d+G+sGG++G +Gy lm+GG lcl|NCBI__GCF_000015305.1:WP_011777328.1 61 GtVTDSTISELAGVLSPGDLVIDGGNSRYTEDGRHANLLAEKGIAFIDAGVSGGIWGLTEGYGLMVGGS 129 98999**************************************************************** PP TIGR00872 138 eeafkkaeplfkdva...veekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlknsqfdfdlee 203 + ++a p+f+ + + e+G++++G+ G+Ghf+kmvhnGiey lm a aeG+e+l + d + lcl|NCBI__GCF_000015305.1:WP_011777328.1 130 DADVARAMPIFETLRppgPLEDGFVHVGPVGAGHFAKMVHNGIEYALMTAYAEGYEMLAAEDLVKDPQA 198 999********98752125689*********************************************** PP TIGR00872 204 varvyrrGsvirsflldltakaleesadleeveGrvedsGeGrwtvkaavdlgvpapvlatslqerfas 272 v + +++G+v+rs+l +l+akal+e++ l +++G+ edsGeGrwtv++a+ l vp+p +a sl rf s lcl|NCBI__GCF_000015305.1:WP_011777328.1 199 VYQAWTNGTVVRSWLQQLLAKALKEDPSLSDISGYTEDSGEGRWTVEEAIRLRVPVPGIAASLFARFLS 267 ********************************************************************* PP TIGR00872 273 rekddfankvlaalrkefGghaekk 297 r+++ + k++aalr++fGgha+k+ lcl|NCBI__GCF_000015305.1:WP_011777328.1 268 RQDESPTMKAVAALRNQFGGHAVKR 292 **********************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (297 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: 00:00:00.01 # Mc/sec: 7.52 // [ok]
This GapMind analysis is from Sep 24 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