Alignments for a candidate for gnd in Cupriavidus basilensis 4G11

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Cupriavidus basilensis 4G11

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate RR42_RS27085 RR42_RS27085 hypothetical protein

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__Cup4G11:RR42_RS27085
          Length = 322

 Score =  406 bits (1044), Expect = e-118
 Identities = 198/330 (60%), Positives = 249/330 (75%), Gaps = 8/330 (2%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M++GIIGLGRMG NIA RL R  H+VVV++R+++   ++      G  +    + ++A  
Sbjct: 1   MQLGIIGLGRMGANIARRLLRAQHEVVVYNRSADKVQALAADGAVGVTSIEALVGELAA- 59

Query: 61  LEGDEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGIS 120
                 R +WVMLPAG  TE  +  L  LL  GD+IIDGGNT+YKDD+RR+ ELA + + 
Sbjct: 60  -----PRAIWVMLPAGDTTEQMIATLADLLEPGDVIIDGGNTFYKDDIRRAGELAARQLH 114

Query: 121 YVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPRA 180
           YVDVGTSGGVWGLERGYC+M GG +E    +DP+   LAPG GD+PRTPGR+ A  + RA
Sbjct: 115 YVDVGTSGGVWGLERGYCLMIGGRQEVVGRLDPLFDTLAPGYGDIPRTPGRNPA--NDRA 172

Query: 181 EQGYLHCGPAGSGHFVKMVHNGIEYGMMQAFAEGFDIMKSKNSPILAEKDRFELNMGDIA 240
           E+GY+H GPAG+GHFVKMVHNGIEYG+MQA+AEGFDI+K+K +  L E +RF L++ DIA
Sbjct: 173 ERGYIHAGPAGAGHFVKMVHNGIEYGLMQAYAEGFDILKTKAAESLPEAERFALDLADIA 232

Query: 241 EVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAAIEEDVPAPVMTAA 300
           EVWRRGSVVSSWLLDLTA+AL     L+ FSGEVADSGEGRWTI+AA+E+ VP PV+ +A
Sbjct: 233 EVWRRGSVVSSWLLDLTAQALASDVKLSRFSGEVADSGEGRWTIDAAVEQAVPVPVLASA 292

Query: 301 LFTRFRSRSGNNFAEKILSAQRFGFGGHVE 330
           LF RFRSR  + + E++LSA RFGFGGHVE
Sbjct: 293 LFARFRSRQDHTYGERLLSAMRFGFGGHVE 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: 392
Number of extensions: 14
Number of successful extensions: 2
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: 322
Length adjustment: 28
Effective length of query: 304
Effective length of database: 294
Effective search space:    89376
Effective search space used:    89376
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 RR42_RS27085 RR42_RS27085 (hypothetical protein)
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.30871.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
   1.7e-119  384.5   0.0   1.9e-119  384.3   0.0    1.0  1  lcl|FitnessBrowser__Cup4G11:RR42_RS27085  RR42_RS27085 hypothetical protei


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS27085  RR42_RS27085 hypothetical protein
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  384.3   0.0  1.9e-119  1.9e-119       1     294 [.       1     321 [.       1     322 [] 0.98

  Alignments for each domain:
  == domain 1  score: 384.3 bits;  conditional E-value: 1.9e-119
                                 TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellkrlsaprvvwvmvpa 69 
                                               m+lg+iGlGrmGania+rl   +hevv+y+r+ d v++l++d+a+gv++++ l+ +l apr +wvm+pa
  lcl|FitnessBrowser__Cup4G11:RR42_RS27085   1 MQLGIIGLGRMGANIARRLLRAQHEVVVYNRSADKVQALAADGAVGVTSIEALVGELAAPRAIWVMLPA 69 
                                               9******************************************************************** PP

                                 TIGR00872  70 g.ivdavleelapllekGdividgGnsyykdslrrekelkekgihlldvGtsGGvlGkerGyclmiGGd 137
                                               g  +++++  la+lle Gd++idgGn++ykd++rr  el  +++h++dvGtsGGv+G erGyclmiGG 
  lcl|FitnessBrowser__Cup4G11:RR42_RS27085  70 GdTTEQMIATLADLLEPGDVIIDGGNTFYKDDIRRAGELAARQLHYVDVGTSGGVWGLERGYCLMIGGR 138
                                               *88999*************************************************************** PP

                                 TIGR00872 138 eeafkkaeplfk.................dvaveekGylylGeaGsGhfvkmvhnGieyGlmaalaeGl 189
                                               +e+  + +plf                       e+Gy+++G+aG+GhfvkmvhnGieyGlm+a aeG+
  lcl|FitnessBrowser__Cup4G11:RR42_RS27085 139 QEVVGRLDPLFDtlapgygdiprtpgrnpANDRAERGYIHAGPAGAGHFVKMVHNGIEYGLMQAYAEGF 207
                                               ***************************875556789********************************* PP

                                 TIGR00872 190 evlkns.........qfdfdleevarvyrrGsvirsflldltakaleesadleeveGrvedsGeGrwtv 249
                                               ++lk           +f  dl ++a+v+rrGsv+ s+lldlta+al+ + +l  ++G v dsGeGrwt+
  lcl|FitnessBrowser__Cup4G11:RR42_RS27085 208 DILKTKaaeslpeaeRFALDLADIAEVWRRGSVVSSWLLDLTAQALASDVKLSRFSGEVADSGEGRWTI 276
                                               ***98889************************************************************* PP

                                 TIGR00872 250 kaavdlgvpapvlatslqerfasrekddfankvlaalrkefGgha 294
                                                aav++ vp+pvla +l  rf+sr++ ++ ++ l+a+r  fGgh 
  lcl|FitnessBrowser__Cup4G11:RR42_RS27085 277 DAAVEQAVPVPVLASALFARFRSRQDHTYGERLLSAMRFGFGGHV 321
                                               ********************************************6 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (299 nodes)
Target sequences:                          1  (322 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: 00:00:00.01
# Mc/sec: 8.41
//
[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