Alignments for a candidate for gnd in Pseudomonas fluorescens FW300-N2C3

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Pseudomonas fluorescens FW300-N2C3

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate AO356_27855 AO356_27855 6-phosphogluconate dehydrogenase

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27855
          Length = 326

 Score =  428 bits (1100), Expect = e-124
 Identities = 212/331 (64%), Positives = 257/331 (77%), Gaps = 10/331 (3%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M++GIIGLGRMGGNIA RL  +GH  VV+DR +    ++       R   A  +AD+  L
Sbjct: 1   MQLGIIGLGRMGGNIARRLMLNGHATVVYDRNAAFVENL-------RQEGATGVADLQAL 53

Query: 61  LEG-DEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGI 119
           + G ++ R VWVMLPAGA TED +  L  LL  GD+IIDGGNTYYKDD+RR+  L+EKG+
Sbjct: 54  VAGLEKPRAVWVMLPAGAPTEDTINVLSELLEPGDVIIDGGNTYYKDDIRRAQALSEKGL 113

Query: 120 SYVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPR 179
           SY+DVGTSGGVWGLERGYCMM GG  E  + +DP+  +LAPG+GD+PRT  RD    D R
Sbjct: 114 SYIDVGTSGGVWGLERGYCMMIGGEAEVVKRLDPLFDSLAPGMGDIPRT--RDRKSDDDR 171

Query: 180 AEQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMKSKNSPILAEKDRFELNMGDI 239
           AE+GY+H GPAGSGHFVKM+HNGIEYGMMQAFAEGFDI+K+K+S  L  + RF+LN+ DI
Sbjct: 172 AERGYIHAGPAGSGHFVKMIHNGIEYGMMQAFAEGFDILKTKSSESLPAEQRFDLNVADI 231

Query: 240 AEVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAAIEEDVPAPVMTA 299
           AEVWRRGSVVSSWLLDLTA+AL     L+ FSGEVADSGEGRWTIEAAIE+ VP PV+++
Sbjct: 232 AEVWRRGSVVSSWLLDLTADALASDPKLDGFSGEVADSGEGRWTIEAAIEQAVPVPVLSS 291

Query: 300 ALFTRFRSRSGNNFAEKILSAQRFGFGGHVE 330
           +LF RFRSR  + + +K+LSA RFGFGGHVE
Sbjct: 292 SLFARFRSRQQSTYGDKMLSAMRFGFGGHVE 322


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: 399
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: 326
Length adjustment: 28
Effective length of query: 304
Effective length of database: 298
Effective search space:    90592
Effective search space used:    90592
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 AO356_27855 AO356_27855 (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.19421.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                       -----------
   2.9e-123  396.8   0.0   3.3e-123  396.7   0.0    1.0  1  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855  AO356_27855 6-phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855  AO356_27855 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  396.7   0.0  3.3e-123  3.3e-123       1     298 [.       1     325 [.       1     326 [] 0.98

  Alignments for each domain:
  == domain 1  score: 396.7 bits;  conditional E-value: 3.3e-123
                                       TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvv 63 
                                                     m+lg+iGlGrmG nia+rl+ +gh  v+ydr+ + ve+l++++a+gva+l+ l+  l+ pr v
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855   1 MQLGIIGLGRMGGNIARRLMLNGHATVVYDRNAAFVENLRQEGATGVADLQALVAGLEKPRAV 63 
                                                     9************************************************************** PP

                                       TIGR00872  64 wvmvpag.ivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlG 125
                                                     wvm+pag  +++ ++ l++lle Gd++idgGn+yykd++rr + l ekg+ ++dvGtsGGv+G
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855  64 WVMLPAGaPTEDTINVLSELLEPGDVIIDGGNTYYKDDIRRAQALSEKGLSYIDVGTSGGVWG 126
                                                     *******668899************************************************** PP

                                       TIGR00872 126 kerGyclmiGGdeeafkkaeplfk.................dvaveekGylylGeaGsGhfvk 171
                                                      erGyc+miGG+ e+ k+ +plf                  d    e+Gy+++G+aGsGhfvk
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855 127 LERGYCMMIGGEAEVVKRLDPLFDslapgmgdiprtrdrksDDDRAERGYIHAGPAGSGHFVK 189
                                                     ****************************************98888999*************** PP

                                       TIGR00872 172 mvhnGieyGlmaalaeGlevlkns.........qfdfdleevarvyrrGsvirsflldltaka 225
                                                     m+hnGieyG+m+a+aeG+++lk           +fd ++ ++a+v+rrGsv+ s+lldlta a
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855 190 MIHNGIEYGMMQAFAEGFDILKTKsseslpaeqRFDLNVADIAEVWRRGSVVSSWLLDLTADA 252
                                                     *********************98779******99***************************** PP

                                       TIGR00872 226 leesadleeveGrvedsGeGrwtvkaavdlgvpapvlatslqerfasrekddfankvlaalrk 288
                                                     l+ +++l+ ++G v dsGeGrwt++aa+++ vp+pvl+ sl  rf+sr++ ++ +k+l+a+r 
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855 253 LASDPKLDGFSGEVADSGEGRWTIEAAIEQAVPVPVLSSSLFARFRSRQQSTYGDKMLSAMRF 315
                                                     *************************************************************** PP

                                       TIGR00872 289 efGghaekkk 298
                                                      fGgh e +k
  lcl|FitnessBrowser__pseudo5_N2C3_1:AO356_27855 316 GFGGHVETPK 325
                                                     *****99876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (326 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: 9.50
//
[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