Alignments for a candidate for gnd in Pseudomonas simiae WCS417

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Pseudomonas simiae WCS417

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate GFF2440 PS417_12445 6-phosphogluconate dehydrogenase

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__WCS417:GFF2440
          Length = 327

 Score =  427 bits (1098), Expect = e-124
 Identities = 216/330 (65%), Positives = 253/330 (76%), Gaps = 7/330 (2%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M++GIIGLGRMGGNIA RL  +GH  VV+DR       V G  E G    AD  A +A L
Sbjct: 1   MQLGIIGLGRMGGNIARRLMLNGHTTVVYDRNEAF---VKGLSEEGATGVADLKALVAGL 57

Query: 61  LEGDEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGIS 120
               + R VWVMLPAGA TED + +L  LL  GD IIDGGNT YKDDVRR+  LAEKG+ 
Sbjct: 58  ---QKPRTVWVMLPAGAPTEDTINELSTLLEDGDAIIDGGNTNYKDDVRRAKALAEKGLH 114

Query: 121 YVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPRA 180
           YVDVGTSGGVWGLERGYCMM GG  ET + +DPI  +LAPG+G++PRT  R ++  DPRA
Sbjct: 115 YVDVGTSGGVWGLERGYCMMIGGDAETVQRLDPIFKSLAPGLGNIPRTKDRSDSA-DPRA 173

Query: 181 EQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMKSKNSPILAEKDRFELNMGDIA 240
           EQGY+H GPAGSGHFVKM+HNGIEYGMMQAFAEGFDI+K+KNS  L E  RF+LN+ DIA
Sbjct: 174 EQGYIHAGPAGSGHFVKMIHNGIEYGMMQAFAEGFDILKTKNSENLPEDQRFDLNVADIA 233

Query: 241 EVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAAIEEDVPAPVMTAA 300
           EVWRRGSVVSSWLLDLTA+AL     L+ +SG VADSGEGRWTIEAA+E+ VP PV++ +
Sbjct: 234 EVWRRGSVVSSWLLDLTADALATDPKLDGYSGSVADSGEGRWTIEAAMEQAVPVPVLSTS 293

Query: 301 LFTRFRSRSGNNFAEKILSAQRFGFGGHVE 330
           LF RFRSR  + + +K+LSA RFGFGGH+E
Sbjct: 294 LFARFRSRQQSTYGDKMLSAMRFGFGGHLE 323


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: 381
Number of extensions: 23
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: 332
Length of database: 327
Length adjustment: 28
Effective length of query: 304
Effective length of database: 299
Effective search space:    90896
Effective search space used:    90896
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 GFF2440 PS417_12445 (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.31442.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                           -----------
   5.3e-124  399.3   0.1   5.9e-124  399.1   0.1    1.0  1  lcl|FitnessBrowser__WCS417:GFF2440  PS417_12445 6-phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__WCS417:GFF2440  PS417_12445 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  399.1   0.1  5.9e-124  5.9e-124       1     298 [.       1     326 [.       1     327 [] 0.97

  Alignments for each domain:
  == domain 1  score: 399.1 bits;  conditional E-value: 5.9e-124
                           TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvmvpag.ivda 74 
                                         m+lg+iGlGrmG nia+rl+ +gh  v+ydr+++ v+ l e++a+gva+lk l+  l+ pr+vwvm+pag  +++
  lcl|FitnessBrowser__WCS417:GFF2440   1 MQLGIIGLGRMGGNIARRLMLNGHTTVVYDRNEAFVKGLSEEGATGVADLKALVAGLQKPRTVWVMLPAGaPTED 75 
                                         9*********************************************************************66889 PP

                           TIGR00872  75 vleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGGdeeafkkaeplfk 149
                                          ++el+ lle Gd +idgGn+ ykd++rr k l ekg+h++dvGtsGGv+G erGyc+miGGd e+ ++ +p+fk
  lcl|FitnessBrowser__WCS417:GFF2440  76 TINELSTLLEDGDAIIDGGNTNYKDDVRRAKALAEKGLHYVDVGTSGGVWGLERGYCMMIGGDAETVQRLDPIFK 150
                                         *************************************************************************** PP

                           TIGR00872 150 ................dva..veekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlkns.........qf 197
                                                         d a    e+Gy+++G+aGsGhfvkm+hnGieyG+m+a+aeG+++lk           +f
  lcl|FitnessBrowser__WCS417:GFF2440 151 slapglgniprtkdrsDSAdpRAEQGYIHAGPAGSGHFVKMIHNGIEYGMMQAFAEGFDILKTKnsenlpedqRF 225
                                         ***************9555225789************************************97778******99* PP

                           TIGR00872 198 dfdleevarvyrrGsvirsflldltakaleesadleeveGrvedsGeGrwtvkaavdlgvpapvlatslqerfas 272
                                         d ++ ++a+v+rrGsv+ s+lldlta al+ +++l+  +G v dsGeGrwt++aa+++ vp+pvl+tsl  rf+s
  lcl|FitnessBrowser__WCS417:GFF2440 226 DLNVADIAEVWRRGSVVSSWLLDLTADALATDPKLDGYSGSVADSGEGRWTIEAAMEQAVPVPVLSTSLFARFRS 300
                                         *************************************************************************** PP

                           TIGR00872 273 rekddfankvlaalrkefGghaekkk 298
                                         r++ ++ +k+l+a+r  fGgh e  k
  lcl|FitnessBrowser__WCS417:GFF2440 301 RQQSTYGDKMLSAMRFGFGGHLETSK 326
                                         *********************88655 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (327 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: 7.40
//
[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