Alignments for a candidate for gnd in Burkholderia phytofirmans PsJN

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Burkholderia phytofirmans PsJN

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate BPHYT_RS26220 BPHYT_RS26220 6-phosphogluconate dehydrogenase

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__BFirm:BPHYT_RS26220
          Length = 345

 Score =  332 bits (850), Expect = 1e-95
 Identities = 173/344 (50%), Positives = 230/344 (66%), Gaps = 22/344 (6%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M++G+IGLGRMG ++  RLT+ G   + +D    V  + V + +      A +L D+   
Sbjct: 1   MQLGMIGLGRMGADMVRRLTKGGQQCIAYD----VQPAAVEKLKQDGVPGAASLEDLVAQ 56

Query: 61  LEGDEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGIS 120
           L  D+ R VW+M+PA A+ +  +++L  LL  GDI+IDGGN+YY DD+RR  ELAE+ + 
Sbjct: 57  L--DKPRAVWLMVPA-AVVDMTLEKLVPLLEPGDIVIDGGNSYYHDDIRRGTELAERKLH 113

Query: 121 YVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPRA 180
           YVDVGTSGGV G ERGYC+M GG  E  + ++PI + LAPG G  P TPGR        A
Sbjct: 114 YVDVGTSGGVAGRERGYCLMIGGEPEVVKRLEPIFATLAPGAGSEPATPGR--VAGSSTA 171

Query: 181 EQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMK------------SKNSPILA- 227
           +QG+LHCGP G+GHFVKMVHNGIEYGMM A+AEG +I+             ++ SP+   
Sbjct: 172 DQGFLHCGPQGAGHFVKMVHNGIEYGMMAAYAEGLNILHHADAGKHAREADAETSPLRRP 231

Query: 228 EKDRFELNMGDIAEVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAA 287
           E  +++LN+ D+ EVWRRGSV+SSWLLDL A +L     L  ++G V+DSGEGRWT+ AA
Sbjct: 232 ELYQYDLNLADVTEVWRRGSVISSWLLDLIAGSLVSDVDLKNYAGRVSDSGEGRWTVAAA 291

Query: 288 IEEDVPAPVMTAALFTRFRSRSGNNFAEKILSAQRFGFGGHVEK 331
           I+E VP PV++AALF RF SR   +FA ++LSA R  FGGH EK
Sbjct: 292 IDEGVPTPVLSAALFARFSSRGEADFANRVLSAMRNDFGGHAEK 335


Lambda     K      H
   0.318    0.137    0.413 

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: 378
Number of extensions: 18
Number of successful extensions: 4
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: 332
Length of database: 345
Length adjustment: 28
Effective length of query: 304
Effective length of database: 317
Effective search space:    96368
Effective search space used:    96368
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: 49 (23.5 bits)

Align candidate BPHYT_RS26220 BPHYT_RS26220 (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.28035.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                -----------
   1.5e-129  417.5   0.0   1.7e-129  417.3   0.0    1.0  1  lcl|FitnessBrowser__BFirm:BPHYT_RS26220  BPHYT_RS26220 6-phosphogluconate


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__BFirm:BPHYT_RS26220  BPHYT_RS26220 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  417.3   0.0  1.7e-129  1.7e-129       1     298 [.       1     337 [.       1     338 [. 0.99

  Alignments for each domain:
  == domain 1  score: 417.3 bits;  conditional E-value: 1.7e-129
                                TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvmvpag 70 
                                              m+lg+iGlGrmGa++++rl+k+g ++++yd++++ave+lk+d+  g a+l++l+ +l+ pr vw+mvpa+
  lcl|FitnessBrowser__BFirm:BPHYT_RS26220   1 MQLGMIGLGRMGADMVRRLTKGGQQCIAYDVQPAAVEKLKQDGVPGAASLEDLVAQLDKPRAVWLMVPAA 70 
                                              9********************************************************************* PP

                                TIGR00872  71 ivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGGdeea 140
                                              +vd  le+l plle GdividgGnsyy+d++rr  el e+ +h++dvGtsGGv G+erGyclmiGG+ e+
  lcl|FitnessBrowser__BFirm:BPHYT_RS26220  71 VVDMTLEKLVPLLEPGDIVIDGGNSYYHDDIRRGTELAERKLHYVDVGTSGGVAGRERGYCLMIGGEPEV 140
                                              ********************************************************************** PP

                                TIGR00872 141 fkkaeplfk.................dvaveekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlk 193
                                               k+ ep+f+                   ++ ++G+l++G+ G+GhfvkmvhnGieyG+maa aeGl++l+
  lcl|FitnessBrowser__BFirm:BPHYT_RS26220 141 VKRLEPIFAtlapgagsepatpgrvaGSSTADQGFLHCGPQGAGHFVKMVHNGIEYGMMAAYAEGLNILH 210
                                              ***********************8887778899************************************* PP

                                TIGR00872 194 ns......................qfdfdleevarvyrrGsvirsflldltakaleesadleeveGrved 241
                                              ++                      q+d +l +v++v+rrGsvi s+lldl+a +l  + dl++  Grv+d
  lcl|FitnessBrowser__BFirm:BPHYT_RS26220 211 HAdagkhareadaetsplrrpelyQYDLNLADVTEVWRRGSVISSWLLDLIAGSLVSDVDLKNYAGRVSD 280
                                              ********************************************************************** PP

                                TIGR00872 242 sGeGrwtvkaavdlgvpapvlatslqerfasrekddfankvlaalrkefGghaekkk 298
                                              sGeGrwtv aa+d+gvp+pvl+ +l  rf+sr + dfan+vl+a+r++fGghaek +
  lcl|FitnessBrowser__BFirm:BPHYT_RS26220 281 SGEGRWTVAAAIDEGVPTPVLSAALFARFSSRGEADFANRVLSAMRNDFGGHAEKAA 337
                                              *****************************************************9975 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (345 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: 11.00
//
[ok]

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources