Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate WP_092481664.1 BM299_RS00285 decarboxylating 6-phosphogluconate dehydrogenase
Query= BRENDA::Q2RIZ2 (298 letters) >NCBI__GCF_900115975.1:WP_092481664.1 Length = 301 Score = 411 bits (1056), Expect = e-119 Identities = 197/298 (66%), Positives = 237/298 (79%) Query: 1 MHIGLVGLGRMGLNLALNMLDHGHEVRGYARTKATVDKAAAQGIKGAYSLEELAGQLKTP 60 M +GL+GLG+MG NLALNM DHGH V GY R+ V KA A+GI G YSL++L +L Sbjct: 1 MQVGLIGLGKMGFNLALNMKDHGHRVIGYNRSPGAVKKAEAEGIAGVYSLDKLVEKLAPR 60 Query: 61 RLVWLMIPAGKAVDEVIEQLAPLLAPGDIIVDGGNSHYRDTLRRYKFLKEKGIHLVDSGT 120 R++WLM+PAGK VD+ IE+L PLL DII+DGGNS+Y+DTL RY+ L+EKGI VD GT Sbjct: 61 RVLWLMVPAGKPVDDTIEKLIPLLDEHDIIIDGGNSNYKDTLARYRKLREKGIDFVDVGT 120 Query: 121 SGGVEGARHGACCMVGAEDEVFAYLEPLFKDITVPGGYLHTGPPGSGHYVKMVHNGIEYG 180 SGG EGAR+GAC M+GAED VF+YLEPLF+DI V GGYLHTGP GSGH+VKMVHNG+EYG Sbjct: 121 SGGTEGARYGACTMIGAEDSVFSYLEPLFRDICVEGGYLHTGPSGSGHFVKMVHNGVEYG 180 Query: 181 MMQAIGEGMEVLAGAPFKLDLKEVARVWRHGSVIRGWLMDLMEKALAKDNTLDGIKDIAY 240 MMQAIGEG E+L + F L+ +E+ARVW HGSVIR WLM+L EKA A D L+ IK + + Sbjct: 181 MMQAIGEGFEILEKSLFDLNYREIARVWNHGSVIRSWLMELTEKAFAGDPKLEKIKGVIH 240 Query: 241 SSGEGLWTIEEALRLKVPAPVITAALLMRYRSEQEESFATKVVAALRHEFGGHDVARK 298 SSGEGLWT++EAL L+VP PVI AL MRYRSEQE++F+ KVVAALR+ FGGH V K Sbjct: 241 SSGEGLWTVQEALELQVPVPVIAQALFMRYRSEQEDTFSGKVVAALRNRFGGHAVEEK 298 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: 397 Number of extensions: 13 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: 298 Length of database: 301 Length adjustment: 27 Effective length of query: 271 Effective length of database: 274 Effective search space: 74254 Effective search space used: 74254 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_092481664.1 BM299_RS00285 (decarboxylating 6-phosphogluconate dehydrogenase)
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.83771.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-130 421.1 0.3 1.3e-130 420.9 0.3 1.0 1 NCBI__GCF_900115975.1:WP_092481664.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_900115975.1:WP_092481664.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 420.9 0.3 1.3e-130 1.3e-130 1 298 [. 1 298 [. 1 299 [. 0.99 Alignments for each domain: == domain 1 score: 420.9 bits; conditional E-value: 1.3e-130 TIGR00872 1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvmvpag.iv 72 m++gliGlG+mG n+a ++++ gh v+gy+r++ av+++++++ gv +l +l+++l + rv+w+mvpag v NCBI__GCF_900115975.1:WP_092481664.1 1 MQVGLIGLGKMGFNLALNMKDHGHRVIGYNRSPGAVKKAEAEGIAGVYSLDKLVEKLAPRRVLWLMVPAGkPV 73 99********************************************************************99* PP TIGR00872 73 davleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGGdeeafkkae 145 d+ +e+l pll++ di+idgGns ykd l r+++l+ekgi+++dvGtsGG +G++ G+c miG ++ +f e NCBI__GCF_900115975.1:WP_092481664.1 74 DDTIEKLIPLLDEHDIIIDGGNSNYKDTLARYRKLREKGIDFVDVGTSGGTEGARYGACTMIGAEDSVFSYLE 146 ************************************************************************* PP TIGR00872 146 plfkdvaveekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlknsqfdfdleevarvyrrGsvirsfl 218 plf+d+ ve Gyl++G++GsGhfvkmvhnG+eyG+m+a++eG+e+l++s fd +++e+arv+++Gsvirs+l NCBI__GCF_900115975.1:WP_092481664.1 147 PLFRDICVEG-GYLHTGPSGSGHFVKMVHNGVEYGMMQAIGEGFEILEKSLFDLNYREIARVWNHGSVIRSWL 218 ********99.************************************************************** PP TIGR00872 219 ldltakaleesadleeveGrvedsGeGrwtvkaavdlgvpapvlatslqerfasrekddfankvlaalrkefG 291 ++lt+ka++ +++le+++G++++sGeG wtv++a++l+vp+pv+a++l +r++s ++d+f++kv+aalr++fG NCBI__GCF_900115975.1:WP_092481664.1 219 MELTEKAFAGDPKLEKIKGVIHSSGEGLWTVQEALELQVPVPVIAQALFMRYRSEQEDTFSGKVVAALRNRFG 291 ************************************************************************* PP TIGR00872 292 ghaekkk 298 gha+++k NCBI__GCF_900115975.1:WP_092481664.1 292 GHAVEEK 298 ***9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (299 nodes) Target sequences: 1 (301 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: 0.00u 0.01s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 13.63 // [ok]
This GapMind analysis is from Apr 09 2024. 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