Alignments for a candidate for gnd in Dyella japonica UNC79MFTsu3.2

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Dyella japonica UNC79MFTsu3.2

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate N515DRAFT_2625 N515DRAFT_2625 6-phosphogluconate dehydrogenase

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__Dyella79:N515DRAFT_2625
          Length = 301

 Score =  293 bits (749), Expect = 5e-84
 Identities = 155/328 (47%), Positives = 204/328 (62%), Gaps = 32/328 (9%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M IG+IGLGRMG N+A RL R GH +V  D  +    ++    E   A  A +LAD+   
Sbjct: 1   MNIGMIGLGRMGANMAQRLLRGGHQIVGFDPQAAARKAL----EDKGAGSAPSLADLVAA 56

Query: 61  LEGDEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGIS 120
           L     R +W+M+PAGA T+  +  L  LLG GD +IDGGN++YKD +RR+    E+GI+
Sbjct: 57  LPAP--RTLWLMVPAGAPTDASLDTLLPLLGEGDTVIDGGNSFYKDTLRRAQRFGERGIA 114

Query: 121 YVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPRA 180
           Y+D GTSGG+WGL+ GY +M GG     E + P+   LAP                   +
Sbjct: 115 YIDCGTSGGIWGLDEGYSLMIGGDAAAVERLRPVFETLAPA------------------S 156

Query: 181 EQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMKSKNSPILAEKDRFELNMGDIA 240
           +QG+   GP G+GHF KMVHNGIEYG+MQA+AEGF I+K K          FEL++  IA
Sbjct: 157 DQGWSRVGPVGAGHFTKMVHNGIEYGLMQAYAEGFSILKHKTE--------FELDLHRIA 208

Query: 241 EVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAAIEEDVPAPVMTAA 300
           EVWR GSVV SWLLDLTA+AL ++  +   +  V DSGEGRWT++ AIE +VP PV+  +
Sbjct: 209 EVWRHGSVVRSWLLDLTADALKKNPEMAGIAPYVPDSGEGRWTVDEAIELNVPTPVIAQS 268

Query: 301 LFTRFRSRSGNNFAEKILSAQRFGFGGH 328
           L  R RSR   +FA+K+LS+ R  FGGH
Sbjct: 269 LIERLRSRDKESFADKLLSSMRNEFGGH 296


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: 340
Number of extensions: 19
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: 301
Length adjustment: 27
Effective length of query: 305
Effective length of database: 274
Effective search space:    83570
Effective search space used:    83570
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: 48 (23.1 bits)

Align candidate N515DRAFT_2625 N515DRAFT_2625 (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.21437.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                    -----------
     2e-121  390.8   0.0   2.3e-121  390.6   0.0    1.0  1  lcl|FitnessBrowser__Dyella79:N515DRAFT_2625  N515DRAFT_2625 6-phosphogluconat


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dyella79:N515DRAFT_2625  N515DRAFT_2625 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  390.6   0.0  2.3e-121  2.3e-121       1     294 [.       1     297 [.       1     301 [] 0.98

  Alignments for each domain:
  == domain 1  score: 390.6 bits;  conditional E-value: 2.3e-121
                                    TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvm 66 
                                                  m++g+iGlGrmGan+a+rl  +gh++vg+d + +a+++l++++a    +l +l+  l+apr++w+m
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2625   1 MNIGMIGLGRMGANMAQRLLRGGHQIVGFDPQAAARKALEDKGAGSAPSLADLVAALPAPRTLWLM 66 
                                                  89**************************************9999999******************* PP

                                    TIGR00872  67 vpag.ivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyc 131
                                                  vpag  +da l+ l pll +Gd+vidgGns+ykd lrr +++ e+gi ++d+GtsGG++G ++Gy+
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2625  67 VPAGaPTDASLDTLLPLLGEGDTVIDGGNSFYKDTLRRAQRFGERGIAYIDCGTSGGIWGLDEGYS 132
                                                  ****7799********************************************************** PP

                                    TIGR00872 132 lmiGGdeeafkkaeplfkdvav.eekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlk.ns 195
                                                  lmiGGd  a ++  p+f+ +a+ +++G+  +G+ G+Ghf kmvhnGieyGlm+a aeG+ +lk ++
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2625 133 LMIGGDAAAVERLRPVFETLAPaSDQGWSRVGPVGAGHFTKMVHNGIEYGLMQAYAEGFSILKhKT 198
                                                  ********************97479*************************************8468 PP

                                    TIGR00872 196 qfdfdleevarvyrrGsvirsflldltakaleesadleeveGrvedsGeGrwtvkaavdlgvpapv 261
                                                  +f+ dl+++a+v+r+Gsv+rs+lldlta al+++++++ +  +v dsGeGrwtv +a++l+vp+pv
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2625 199 EFELDLHRIAEVWRHGSVVRSWLLDLTADALKKNPEMAGIAPYVPDSGEGRWTVDEAIELNVPTPV 264
                                                  9***************************************************************** PP

                                    TIGR00872 262 latslqerfasrekddfankvlaalrkefGgha 294
                                                  +a+sl er +sr+k+ fa+k l+ +r+efGgh 
  lcl|FitnessBrowser__Dyella79:N515DRAFT_2625 265 IAQSLIERLRSRDKESFADKLLSSMRNEFGGHP 297
                                                  ********************************6 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: 9.78
//
[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