Alignments for a candidate for gnd in Trichormus variabilis ATCC 29413

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Trichormus variabilis ATCC 29413

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate WP_011316750.1 AVA_RS28690 decarboxylating 6-phosphogluconate dehydrogenase

Query= BRENDA::G5EBD7
         (332 letters)



>NCBI__GCF_000204075.1:WP_011316750.1
          Length = 337

 Score =  341 bits (875), Expect = 1e-98
 Identities = 178/345 (51%), Positives = 229/345 (66%), Gaps = 22/345 (6%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M +G+IGLGRMG N+A RLT+ GH V+ + R  +    +V      R      +    +L
Sbjct: 1   MELGMIGLGRMGANMAHRLTQAGHTVIGYTRQPQKAEVLVQEGAIARG-----VTSFVEL 55

Query: 61  LEG-DEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGI 119
           +E     R VW+MLPA  + +  +Q L   L   DIIIDGGN+YY DD+RR+ +L  KGI
Sbjct: 56  IEALTPPRTVWLMLPAATV-DATLQTLIPFLDADDIIIDGGNSYYIDDIRRADQLKVKGI 114

Query: 120 SYVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPR 179
            Y+D GTSGG+WG ERGYC+M GG     +Y+DPI +ALAPG+   PRTPGR+  G    
Sbjct: 115 EYIDCGTSGGIWGAERGYCLMIGGALAVVKYLDPIFAALAPGVSAAPRTPGRELMGGT-- 172

Query: 180 AEQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMKSKN------------SPIL- 226
           AEQGYLHCG  G+GHFVKMVHNGIEYG+M A+AEG +I+   N            +P+  
Sbjct: 173 AEQGYLHCGSHGAGHFVKMVHNGIEYGIMAAYAEGLNILHHANIGKQLHQVDAETAPLRN 232

Query: 227 AEKDRFELNMGDIAEVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEA 286
            E  +++ N+ DIAEVWRRGSV+SSWLLDL A AL +   L +F G V+DSGEGRWT+ A
Sbjct: 233 PEFYQYDFNLADIAEVWRRGSVISSWLLDLIAMALVKDPDLTDFGGRVSDSGEGRWTLMA 292

Query: 287 AIEEDVPAPVMTAALFTRFRSRSGNNFAEKILSAQRFGFGGHVEK 331
           AIEE VP PV++ AL+TRF SR  + FA K++SA R+ FGGH+EK
Sbjct: 293 AIEEAVPTPVLSTALYTRFSSRGQSEFANKLISALRYEFGGHLEK 337


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: 355
Number of extensions: 14
Number of successful extensions: 5
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: 337
Length adjustment: 28
Effective length of query: 304
Effective length of database: 309
Effective search space:    93936
Effective search space used:    93936
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 WP_011316750.1 AVA_RS28690 (decarboxylating 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.25908.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   6.4e-126  405.6   0.0   7.2e-126  405.4   0.0    1.0  1  lcl|NCBI__GCF_000204075.1:WP_011316750.1  AVA_RS28690 decarboxylating 6-ph


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_000204075.1:WP_011316750.1  AVA_RS28690 decarboxylating 6-phosphogluconate dehydrogenase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  405.4   0.0  7.2e-126  7.2e-126       1     296 [.       1     337 []       1     337 [] 0.97

  Alignments for each domain:
  == domain 1  score: 405.4 bits;  conditional E-value: 7.2e-126
                                 TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedr..aegvanlkellkrlsaprvvwvmv 67 
                                               m+lg+iGlGrmGan+a+rl++ gh v+gy r+++  e l +++  a gv++  el++ l++pr+vw+m+
  lcl|NCBI__GCF_000204075.1:WP_011316750.1   1 MELGMIGLGRMGANMAHRLTQAGHTVIGYTRQPQKAEVLVQEGaiARGVTSFVELIEALTPPRTVWLML 69 
                                               89*******************************999999876511679********************* PP

                                 TIGR00872  68 pagivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGG 136
                                               pa+ vda l+ l p+l++ di+idgGnsyy d++rr  +lk kgi+++d+GtsGG++G+erGyclmiGG
  lcl|NCBI__GCF_000204075.1:WP_011316750.1  70 PAATVDATLQTLIPFLDADDIIIDGGNSYYIDDIRRADQLKVKGIEYIDCGTSGGIWGAERGYCLMIGG 138
                                               ********************************************************************* PP

                                 TIGR00872 137 deeafkkaeplfk.................dvaveekGylylGeaGsGhfvkmvhnGieyGlmaalaeG 188
                                                  + k  +p+f+                    + e+Gyl++G+ G+GhfvkmvhnGieyG+maa aeG
  lcl|NCBI__GCF_000204075.1:WP_011316750.1 139 ALAVVKYLDPIFAalapgvsaaprtpgrelMGGTAEQGYLHCGSHGAGHFVKMVHNGIEYGIMAAYAEG 207
                                               ****************************764467899******************************** PP

                                 TIGR00872 189 levlkns......................qfdfdleevarvyrrGsvirsflldltakaleesadleev 235
                                               l++l+++                      q+df+l ++a+v+rrGsvi s+lldl+a al +++dl ++
  lcl|NCBI__GCF_000204075.1:WP_011316750.1 208 LNILHHAnigkqlhqvdaetaplrnpefyQYDFNLADIAEVWRRGSVISSWLLDLIAMALVKDPDLTDF 276
                                               ********************************************************************* PP

                                 TIGR00872 236 eGrvedsGeGrwtvkaavdlgvpapvlatslqerfasrekddfankvlaalrkefGghaek 296
                                                Grv+dsGeGrwt  aa+++ vp+pvl+t+l++rf+sr + +fank ++alr+efGgh ek
  lcl|NCBI__GCF_000204075.1:WP_011316750.1 277 GGRVSDSGEGRWTLMAAIEEAVPTPVLSTALYTRFSSRGQSEFANKLISALRYEFGGHLEK 337
                                               **********************************************************876 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (337 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 0.00s 00:00:00.00 Elapsed: 00:00:00.00
# Mc/sec: 10.29
//
[ok]

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

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