Alignments for a candidate for edd in Pseudomonas benzenivorans DSM 8628

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Pseudomonas benzenivorans DSM 8628

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_090447193.1 BLS63_RS18160 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_900100495.1:WP_090447193.1
          Length = 608

 Score = 1031 bits (2665), Expect = 0.0
 Identities = 517/608 (85%), Positives = 558/608 (91%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVT+RL+ARSRATRE YLA+IR AASDGPQRGKLQCANFAHGVAGCGS DK +L
Sbjct: 1   MHPRVLEVTDRLIARSRATRERYLAMIRAAASDGPQRGKLQCANFAHGVAGCGSSDKQTL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R+M+AANVAIVS+YNDMLSAHQPYEHFPEQIK+ALRE+GSVGQFAGG PAMCDGVTQGE 
Sbjct: 61  RLMDAANVAIVSAYNDMLSAHQPYEHFPEQIKQALREIGSVGQFAGGVPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMEL + SREVIA++TAVALSHNMFDAAL LGICDKIVPGL+MGALRFGHLP++FVP GP
Sbjct: 121 GMELGIASREVIAMATAVALSHNMFDAALYLGICDKIVPGLLMGALRFGHLPSLFVPAGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSG+SNKEKADVRQRYAEGKATR+ELLE+EM +YHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MPSGLSNKEKADVRQRYAEGKATRDELLEAEMAAYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNP TPLRDALT EAAQQVTRLT+QSG F P+GEIVDER LVNSIVAL ATGGS
Sbjct: 241 LPGASFVNPNTPLRDALTREAAQQVTRLTRQSGQFMPLGEIVDERCLVNSIVALSATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLHMPAIAQAAGIQLTWQDMADLS V PTL+HVYPNGKADINHFQAAGGMAFLIREL
Sbjct: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSAVTPTLAHVYPNGKADINHFQAAGGMAFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+AGLLHEDVNTVAG GLSRYT+EPFL++G+LVWRDGP +S DE++LRPV R FS EGGL
Sbjct: 361 LDAGLLHEDVNTVAGHGLSRYTREPFLEDGQLVWRDGPRKSHDESVLRPVVRPFSAEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           R+M+GNLGRGVMKVSAV  +HQ+VEAPA VF DQQ LADAFKAGELE+DFVAVMRFQGPR
Sbjct: 421 RLMQGNLGRGVMKVSAVDPEHQLVEAPARVFHDQQALADAFKAGELERDFVAVMRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHV PEA  GG LARVRD
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVCPEAYGGGPLARVRD 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GD+IRVDG  G L+L V+A E AAREPA   L +  G GRELF FMR AFSSAEQGASAF
Sbjct: 541 GDLIRVDGKTGELQLLVEAAELAAREPAVDDLVDAEGCGRELFAFMRQAFSSAEQGASAF 600

Query: 601 TSALENLK 608
           TS+LE+ K
Sbjct: 601 TSSLESRK 608


Lambda     K      H
   0.318    0.134    0.386 

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: 1284
Number of extensions: 50
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: 608
Length of database: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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: 53 (25.0 bits)

Align candidate WP_090447193.1 BLS63_RS18160 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

# 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/TIGR01196.hmm
# target sequence database:        /tmp/gapView.30689.genome.faa
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -

Query:       TIGR01196  [M=601]
Accession:   TIGR01196
Description: edd: phosphogluconate dehydratase
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
    ------- ------ -----    ------- ------ -----   ---- --  --------                                 -----------
          0 1046.0   0.1          0 1045.8   0.1    1.0  1  lcl|NCBI__GCF_900100495.1:WP_090447193.1  BLS63_RS18160 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447193.1  BLS63_RS18160 phosphogluconate dehydratase
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1045.8   0.1         0         0       1     601 []       2     601 ..       2     601 .. 0.99

  Alignments for each domain:
  == domain 1  score: 1045.8 bits;  conditional E-value: 0
                                 TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlai 69 
                                               h+r++e+t+r+i+rs++tre+yl++ir+a++ g++r++l c+n+ahgva +  s+k++l+ +  +n+ai
  lcl|NCBI__GCF_900100495.1:WP_090447193.1   2 HPRVLEVTDRLIARSRATRERYLAMIRAAASDGPQRGKLQCANFAHGVAGCGSSDKQTLRLMDAANVAI 70 
                                               79******************************************************************* PP

                                 TIGR01196  70 itayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaig 138
                                               ++ayndmlsahqp++++p++ik+al+e ++v+q agGvpamcdGvtqGe+Gmel ++sr+via++ta++
  lcl|NCBI__GCF_900100495.1:WP_090447193.1  71 VSAYNDMLSAHQPYEHFPEQIKQALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIASREVIAMATAVA 139
                                               ********************************************************************* PP

                                 TIGR01196 139 lshnmfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreell 207
                                               lshnmfd+al+lG+cdkivpGll++al fGhlp++fvpaGpm+sGl+nkeka vrq +aeGk++r+ell
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 140 LSHNMFDAALYLGICDKIVPGLLMGALRFGHLPSLFVPAGPMPSGLSNKEKADVRQRYAEGKATRDELL 208
                                               ********************************************************************* PP

                                 TIGR01196 208 ksemasyhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlp 276
                                               ++ema+yh+pGtctfyGtan+nq+l+e+mGlhlpgasfvnpntplrdaltreaa++++rlt ++g+++p
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 209 EAEMAAYHSPGTCTFYGTANTNQLLMEVMGLHLPGASFVNPNTPLRDALTREAAQQVTRLTRQSGQFMP 277
                                               ********************************************************************* PP

                                 TIGR01196 277 laelideksivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnh 345
                                               l+e++de+++vn++v+l atGGstnhtlh+ aia+aaGi+l+w+d+ +ls + p+la+vypnGkad+nh
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 278 LGEIVDERCLVNSIVALSATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSAVTPTLAHVYPNGKADINH 346
                                               ********************************************************************* PP

                                 TIGR01196 346 feaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfs 414
                                               f+aaGG++flirell++Gllhedv+tvag+Gl+ryt+epfledg+l++r+++ ks de++lr+v +pfs
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 347 FQAAGGMAFLIRELLDAGLLHEDVNTVAGHGLSRYTREPFLEDGQLVWRDGPRKSHDESVLRPVVRPFS 415
                                               ********************************************************************* PP

                                 TIGR01196 415 aeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGm 483
                                               aeGGl+l++GnlGr+v+kvsav +e++ +eapa+vf+dq+ l++afkagelerd+vav+rfqGp++nGm
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 416 AEGGLRLMQGNLGRGVMKVSAVDPEHQLVEAPARVFHDQQALADAFKAGELERDFVAVMRFQGPRSNGM 484
                                               ********************************************************************* PP

                                 TIGR01196 484 pelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngel 552
                                               pelhk+t++lGvlqdrgfkvalvtdGr+sGasGk+paaihv+pea+ gG+la++rdGdlir+d+++gel
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 485 PELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVCPEAYGGGPLARVRDGDLIRVDGKTGEL 553
                                               ********************************************************************* PP

                                 TIGR01196 553 evlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601
                                               ++lv+ ael+are++  dl d+e G+Grelfa++r++ ssae+Gas++t
  lcl|NCBI__GCF_900100495.1:WP_090447193.1 554 QLLVEAAELAAREPAVDDLVDAE-GCGRELFAFMRQAFSSAEQGASAFT 601
                                               *************9999998865.*********************9986 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (608 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: 0.02u 0.02s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 9.86
//
[ok]

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

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Protein sequences (fasta format)
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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