GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gnd in Desulfoscipio geothermicus DSM 3669

Align phosphogluconate dehydrogenase (NADP+-dependent, decarboxylating) (EC 1.1.1.44) (characterized)
to candidate WP_092481664.1 BM299_RS00285 decarboxylating 6-phosphogluconate dehydrogenase

Query= BRENDA::Q2RIZ2
         (298 letters)



>NCBI__GCF_900115975.1:WP_092481664.1
          Length = 301

 Score =  411 bits (1056), Expect = e-119
 Identities = 197/298 (66%), Positives = 237/298 (79%)

Query: 1   MHIGLVGLGRMGLNLALNMLDHGHEVRGYARTKATVDKAAAQGIKGAYSLEELAGQLKTP 60
           M +GL+GLG+MG NLALNM DHGH V GY R+   V KA A+GI G YSL++L  +L   
Sbjct: 1   MQVGLIGLGKMGFNLALNMKDHGHRVIGYNRSPGAVKKAEAEGIAGVYSLDKLVEKLAPR 60

Query: 61  RLVWLMIPAGKAVDEVIEQLAPLLAPGDIIVDGGNSHYRDTLRRYKFLKEKGIHLVDSGT 120
           R++WLM+PAGK VD+ IE+L PLL   DII+DGGNS+Y+DTL RY+ L+EKGI  VD GT
Sbjct: 61  RVLWLMVPAGKPVDDTIEKLIPLLDEHDIIIDGGNSNYKDTLARYRKLREKGIDFVDVGT 120

Query: 121 SGGVEGARHGACCMVGAEDEVFAYLEPLFKDITVPGGYLHTGPPGSGHYVKMVHNGIEYG 180
           SGG EGAR+GAC M+GAED VF+YLEPLF+DI V GGYLHTGP GSGH+VKMVHNG+EYG
Sbjct: 121 SGGTEGARYGACTMIGAEDSVFSYLEPLFRDICVEGGYLHTGPSGSGHFVKMVHNGVEYG 180

Query: 181 MMQAIGEGMEVLAGAPFKLDLKEVARVWRHGSVIRGWLMDLMEKALAKDNTLDGIKDIAY 240
           MMQAIGEG E+L  + F L+ +E+ARVW HGSVIR WLM+L EKA A D  L+ IK + +
Sbjct: 181 MMQAIGEGFEILEKSLFDLNYREIARVWNHGSVIRSWLMELTEKAFAGDPKLEKIKGVIH 240

Query: 241 SSGEGLWTIEEALRLKVPAPVITAALLMRYRSEQEESFATKVVAALRHEFGGHDVARK 298
           SSGEGLWT++EAL L+VP PVI  AL MRYRSEQE++F+ KVVAALR+ FGGH V  K
Sbjct: 241 SSGEGLWTVQEALELQVPVPVIAQALFMRYRSEQEDTFSGKVVAALRNRFGGHAVEEK 298


Lambda     K      H
   0.320    0.139    0.415 

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: 397
Number of extensions: 13
Number of successful extensions: 1
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: 298
Length of database: 301
Length adjustment: 27
Effective length of query: 271
Effective length of database: 274
Effective search space:    74254
Effective search space used:    74254
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate WP_092481664.1 BM299_RS00285 (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.83771.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   1.1e-130  421.1   0.3   1.3e-130  420.9   0.3    1.0  1  NCBI__GCF_900115975.1:WP_092481664.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_900115975.1:WP_092481664.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  420.9   0.3  1.3e-130  1.3e-130       1     298 [.       1     298 [.       1     299 [. 0.99

  Alignments for each domain:
  == domain 1  score: 420.9 bits;  conditional E-value: 1.3e-130
                             TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvmvpag.iv 72 
                                           m++gliGlG+mG n+a ++++ gh v+gy+r++ av+++++++  gv +l +l+++l + rv+w+mvpag  v
  NCBI__GCF_900115975.1:WP_092481664.1   1 MQVGLIGLGKMGFNLALNMKDHGHRVIGYNRSPGAVKKAEAEGIAGVYSLDKLVEKLAPRRVLWLMVPAGkPV 73 
                                           99********************************************************************99* PP

                             TIGR00872  73 davleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGGdeeafkkae 145
                                           d+ +e+l pll++ di+idgGns ykd l r+++l+ekgi+++dvGtsGG +G++ G+c miG ++ +f   e
  NCBI__GCF_900115975.1:WP_092481664.1  74 DDTIEKLIPLLDEHDIIIDGGNSNYKDTLARYRKLREKGIDFVDVGTSGGTEGARYGACTMIGAEDSVFSYLE 146
                                           ************************************************************************* PP

                             TIGR00872 146 plfkdvaveekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlknsqfdfdleevarvyrrGsvirsfl 218
                                           plf+d+ ve  Gyl++G++GsGhfvkmvhnG+eyG+m+a++eG+e+l++s fd +++e+arv+++Gsvirs+l
  NCBI__GCF_900115975.1:WP_092481664.1 147 PLFRDICVEG-GYLHTGPSGSGHFVKMVHNGVEYGMMQAIGEGFEILEKSLFDLNYREIARVWNHGSVIRSWL 218
                                           ********99.************************************************************** PP

                             TIGR00872 219 ldltakaleesadleeveGrvedsGeGrwtvkaavdlgvpapvlatslqerfasrekddfankvlaalrkefG 291
                                           ++lt+ka++ +++le+++G++++sGeG wtv++a++l+vp+pv+a++l +r++s ++d+f++kv+aalr++fG
  NCBI__GCF_900115975.1:WP_092481664.1 219 MELTEKAFAGDPKLEKIKGVIHSSGEGLWTVQEALELQVPVPVIAQALFMRYRSEQEDTFSGKVVAALRNRFG 291
                                           ************************************************************************* PP

                             TIGR00872 292 ghaekkk 298
                                           gha+++k
  NCBI__GCF_900115975.1:WP_092481664.1 292 GHAVEEK 298
                                           ***9987 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: 13.63
//
[ok]

This GapMind analysis is from Apr 09 2024. 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:

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:

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:

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:

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