Alignments for a candidate for gnd in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Alignments for a candidate for gnd in Pseudomonas fluorescens GW456-L13

Align phosphogluconate dehydrogenase (NAD+-dependent, decarboxylating) (EC 1.1.1.343) (characterized)
to candidate PfGW456L13_3001 6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)

Query= BRENDA::G5EBD7
         (332 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001
          Length = 326

 Score =  420 bits (1079), Expect = e-122
 Identities = 207/331 (62%), Positives = 251/331 (75%), Gaps = 10/331 (3%)

Query: 1   MRIGIIGLGRMGGNIAVRLTRHGHDVVVHDRTSEVTTSVVGRCEAGRATPADTLADMAKL 60
           M++GIIGLGRMGGNIA RL  +GH  VV+DR +    ++      G       + D+  L
Sbjct: 1   MQLGIIGLGRMGGNIARRLMLNGHTTVVYDRNTAFVEALATEGSTG-------VTDLPAL 53

Query: 61  LEG-DEHRVVWVMLPAGAITEDCVQQLGGLLGRGDIIIDGGNTYYKDDVRRSAELAEKGI 119
           + G    R VWVMLPAGA TE+ +  L  LL  GD IIDGGNT+YKDD+RR+  L+EKG+
Sbjct: 54  VAGLARPRAVWVMLPAGAPTEETIDTLSTLLDAGDTIIDGGNTFYKDDIRRAKTLSEKGL 113

Query: 120 SYVDVGTSGGVWGLERGYCMMFGGTKETAEYIDPILSALAPGIGDVPRTPGRDEAGHDPR 179
            Y+DVGTSGGVWGLERGYCMM GG  ET + +DP+ + LAPG+GD+PRT  +D    D R
Sbjct: 114 HYIDVGTSGGVWGLERGYCMMIGGDAETVKRLDPLFATLAPGLGDIPRT--KDRKSDDDR 171

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

Query: 240 AEVWRRGSVVSSWLLDLTAEALTRSETLNEFSGEVADSGEGRWTIEAAIEEDVPAPVMTA 299
           AEVWRRGSVVSSWLLDLTA+AL     L+ FSG VADSGEG+WTIEAA+E+ VP PV++ 
Sbjct: 232 AEVWRRGSVVSSWLLDLTADALASDPKLDGFSGSVADSGEGQWTIEAAMEQAVPVPVLSN 291

Query: 300 ALFTRFRSRSGNNFAEKILSAQRFGFGGHVE 330
           +LF+R+RSR    F +KILSAQRFGFGGHVE
Sbjct: 292 SLFSRYRSRGQGTFGDKILSAQRFGFGGHVE 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: 401
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: 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 PfGW456L13_3001 (6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44))
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.23384.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-123  395.7   0.0   7.2e-123  395.5   0.0    1.0  1  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001  6-phosphogluconate dehydrogenase


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001  6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.4
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  395.5   0.0  7.2e-123  7.2e-123       1     298 [.       1     325 [.       1     326 [] 0.98

  Alignments for each domain:
  == domain 1  score: 395.5 bits;  conditional E-value: 7.2e-123
                                               TIGR00872   1 mklgliGlGrmGaniakrlakrghevvgydrdqdaveelkedraegvanlkellk 55 
                                                             m+lg+iGlGrmG nia+rl+ +gh  v+ydr+ + ve+l+ ++++gv++l  l+ 
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001   1 MQLGIIGLGRMGGNIARRLMLNGHTTVVYDRNTAFVEALATEGSTGVTDLPALVA 55 
                                                             9****************************************************** PP

                                               TIGR00872  56 rlsaprvvwvmvpag.ivdavleelapllekGdividgGnsyykdslrrekelke 109
                                                              l  pr vwvm+pag  +++ ++ l+ ll++Gd++idgGn++ykd++rr k l e
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001  56 GLARPRAVWVMLPAGaPTEETIDTLSTLLDAGDTIIDGGNTFYKDDIRRAKTLSE 110
                                                             ***************66899*********************************** PP

                                               TIGR00872 110 kgihlldvGtsGGvlGkerGyclmiGGdeeafkkaeplfk............... 149
                                                             kg+h++dvGtsGGv+G erGyc+miGGd e+ k+ +plf+               
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001 111 KGLHYIDVGTSGGVWGLERGYCMMIGGDAETVKRLDPLFAtlapglgdiprtkdr 165
                                                             ******************************************************* PP

                                               TIGR00872 150 ..dvaveekGylylGeaGsGhfvkmvhnGieyGlmaalaeGlevlkns....... 195
                                                               d    e+Gy+++G+aGsGhfvkm+hnGieyG+m+a+aeG+++lk         
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001 166 ksDDDRAERGYIHAGPAGSGHFVKMIHNGIEYGMMQAFAEGFDILKTKnseslpq 220
                                                             *98888999************************************97777***** PP

                                               TIGR00872 196 ..qfdfdleevarvyrrGsvirsflldltakaleesadleeveGrvedsGeGrwt 248
                                                               +fd ++ ++a+v+rrGsv+ s+lldlta al+ +++l+ ++G v dsGeG+wt
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001 221 dqRFDLNVADIAEVWRRGSVVSSWLLDLTADALASDPKLDGFSGSVADSGEGQWT 275
                                                             *99**************************************************** PP

                                               TIGR00872 249 vkaavdlgvpapvlatslqerfasrekddfankvlaalrkefGghaekkk 298
                                                             ++aa+++ vp+pvl++sl +r++sr + +f +k+l+a r  fGgh e  k
  lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3001 276 IEAAMEQAVPVPVLSNSLFSRYRSRGQGTFGDKILSAQRFGFGGHVETSK 325
                                                             *********************************************98765 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: 9.26
//
[ok]

This GapMind analysis is from Sep 17 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