Alignments for a candidate for gnd in Paraburkholderia bryophila 376MFSha3.1

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Paraburkholderia bryophila 376MFSha3.1

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate H281DRAFT_02800 H281DRAFT_02800 6-phosphogluconate dehydrogenase (decarboxylating)

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__Burk376:H281DRAFT_02800
          Length = 345

 Score =  335 bits (859), Expect = 1e-96
 Identities = 176/344 (51%), Positives = 231/344 (67%), Gaps = 22/344 (6%)

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

Query: 61  LEGDEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGIS 120
           LE  + R VW+M+PA A+ +  + +L  LL  GDI+IDGGN+YY DD+RR A+LAE+ + 
Sbjct: 57  LE--KPRAVWLMVPA-AVVDGTLDKLLPLLEPGDIVIDGGNSYYHDDIRRGAQLAERKLH 113

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

Query: 181 EQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMK------------SKNSPILA- 227
           EQG+LHCGP G+GHFVKMVHNGIEYG+M A+AEG +I++            ++ SP+   
Sbjct: 172 EQGFLHCGPIGAGHFVKMVHNGIEYGLMAAYAEGLNILRHADAGKHARDADAETSPLRRP 231

Query: 228 EKDRFELNMGDIAEVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAA 287
           E  +++LN+ DIAEVWRRGSV+ SWLLDL A +L     L  ++G V+DSGEGRWT+ AA
Sbjct: 232 ELYQYDLNLADIAEVWRRGSVIGSWLLDLIAGSLVGDADLKNYAGRVSDSGEGRWTMAAA 291

Query: 288 IEEDVPAPVMTAALFTRFRSRSGNNFAEKILSAQRFGFGGHVEK 331
           ++E VPAPV++AALF RF SR   +FA ++LSA R  FGGH EK
Sbjct: 292 VDEGVPAPVLSAALFGRFSSRGEADFANRVLSAMRHDFGGHAEK 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: 389
Number of extensions: 16
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 H281DRAFT_02800 H281DRAFT_02800 (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.27690.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-127  410.9   0.0   1.7e-127  410.7   0.0    1.0  1  lcl|FitnessBrowser__Burk376:H281DRAFT_02800  H281DRAFT_02800 6-phosphoglucona


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Burk376:H281DRAFT_02800  H281DRAFT_02800 6-phosphogluconate dehydrogenase (decarboxylating)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  410.7   0.0  1.7e-127  1.7e-127       1     297 [.       1     336 [.       1     338 [. 0.99

  Alignments for each domain:
  == domain 1  score: 410.7 bits;  conditional E-value: 1.7e-127
                                    TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvm 66 
                                                  m+lg+iGlGrmGa++++rl+k+g ++++yd++++ave+l +++  g  +l++l+ +l+ pr vw+m
  lcl|FitnessBrowser__Burk376:H281DRAFT_02800   1 MQLGMIGLGRMGADMVRRLTKGGQQCIAYDVQPAAVERLGQEGVLGASSLEDLVAKLEKPRAVWLM 66 
                                                  9***************************************************************** PP

                                    TIGR00872  67 vpagivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGycl 132
                                                  vpa++vd  l++l plle GdividgGnsyy+d++rr  +l e+ +h++dvGtsGGv G+erGycl
  lcl|FitnessBrowser__Burk376:H281DRAFT_02800  67 VPAAVVDGTLDKLLPLLEPGDIVIDGGNSYYHDDIRRGAQLAERKLHYVDVGTSGGVAGRERGYCL 132
                                                  ****************************************************************** PP

                                    TIGR00872 133 miGGdeeafkkaeplfk.................dvaveekGylylGeaGsGhfvkmvhnGieyGl 181
                                                  miGG+ e+ ++ ep+f                    ++ e+G+l++G+ G+GhfvkmvhnGieyGl
  lcl|FitnessBrowser__Burk376:H281DRAFT_02800 133 MIGGEAEVVQRLEPIFStlapgaaaapatpgrteGSSTAEQGFLHCGPIGAGHFVKMVHNGIEYGL 198
                                                  ********************************987788999************************* PP

                                    TIGR00872 182 maalaeGlevlkns......................qfdfdleevarvyrrGsvirsflldltaka 225
                                                  maa aeGl++l+++                      q+d +l ++a+v+rrGsvi+s+lldl+a +
  lcl|FitnessBrowser__Burk376:H281DRAFT_02800 199 MAAYAEGLNILRHAdagkhardadaetsplrrpelyQYDLNLADIAEVWRRGSVIGSWLLDLIAGS 264
                                                  ****************************************************************** PP

                                    TIGR00872 226 leesadleeveGrvedsGeGrwtvkaavdlgvpapvlatslqerfasrekddfankvlaalrkefG 291
                                                  l  +adl++  Grv+dsGeGrwt+ aavd+gvpapvl+ +l  rf+sr + dfan+vl+a+r++fG
  lcl|FitnessBrowser__Burk376:H281DRAFT_02800 265 LVGDADLKNYAGRVSDSGEGRWTMAAAVDEGVPAPVLSAALFGRFSSRGEADFANRVLSAMRHDFG 330
                                                  ****************************************************************** PP

                                    TIGR00872 292 ghaekk 297
                                                  ghaek+
  lcl|FitnessBrowser__Burk376:H281DRAFT_02800 331 GHAEKP 336
                                                  ***997 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 10.38
//
[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