Alignments for a candidate for edd in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Dinoroseobacter shibae DFL-12

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate 3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq)

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Dino:3608367
          Length = 601

 Score =  689 bits (1779), Expect = 0.0
 Identities = 348/594 (58%), Positives = 437/594 (73%), Gaps = 4/594 (0%)

Query: 5   VLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLRMMN 64
           + +VT R+ ARS   R  YL  +R AA DGP+R  L C N AH  A  G  DK +L    
Sbjct: 7   ISDVTARIEARSAEARSTYLDRMRRAAEDGPRRAHLSCGNQAHAYAAMGG-DKEALVAER 65

Query: 65  AANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMEL 124
           +AN+ IV++YNDMLSAHQP++ +P++IK+A R  G+  Q AGG PAMCDGVTQG+ GMEL
Sbjct: 66  SANIGIVTAYNDMLSAHQPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGMEL 125

Query: 125 SLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG 184
           SL SR+VIAL+T VALSHN FDAA  LG+CDKIVPGL++ A  FG+LP +FVP GPM SG
Sbjct: 126 SLFSRDVIALATGVALSHNTFDAAAYLGVCDKIVPGLVIAAATFGYLPGVFVPAGPMVSG 185

Query: 185 ISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLPGA 244
           + N +KA VRQ++A G+  R++L+E+EM SYH PGTCTFYGTAN+NQ+LME MGLHLPGA
Sbjct: 186 LPNDQKAKVRQQFAAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGLHLPGA 245

Query: 245 SFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGSTNHT 304
           SFVNP TPLR+ALT  AA+++  +T+    + P+ +I+D ++ VN IV L ATGGSTN  
Sbjct: 246 SFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGGSTNLV 305

Query: 305 LHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELLEAG 364
           +H+PA+A+AAG+ L  QD AD+SE  P ++ VYPNG AD+NHF AAGG+A++I ELL  G
Sbjct: 306 IHLPAMARAAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGELLSEG 365

Query: 365 LLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLRVME 424
           LLH D  T+AG GL+ Y +EP L +G L W DGP  SL+  ILRP +  F+P GGL+ ++
Sbjct: 366 LLHPDTKTIAGDGLADYAREPKLIDGVLRWEDGPRRSLNAKILRPASDGFAPSGGLKELK 425

Query: 425 GNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGM 484
           GNLGRGVMKVSAVA +  ++EA A VF+DQ  + DAFKAGE  +D V ++RFQGP++NGM
Sbjct: 426 GNLGRGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAGEFTEDTVVIVRFQGPKANGM 485

Query: 485 PELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDII 544
           PELH +TP L VLQDRG KVALVTDGRMSGASGK+PAAIHV+PEA  GG +A+VR GD++
Sbjct: 486 PELHALTPVLAVLQDRGLKVALVTDGRMSGASGKVPAAIHVAPEALDGGLMAKVRTGDLV 545

Query: 545 RVDGVKGTLELKVDADEFAAREPA-KGLLGNNVGSGRELFGFMRMAFSSAEQGA 597
           RVD V G LE+     E   R PA   L GN+ G GRELF   R     A  GA
Sbjct: 546 RVDAVAGVLEVLEPGVE--DRAPAMPDLSGNSHGIGRELFDVFRTTVGPASTGA 597


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: 1081
Number of extensions: 44
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: 608
Length of database: 601
Length adjustment: 37
Effective length of query: 571
Effective length of database: 564
Effective search space:   322044
Effective search space used:   322044
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 3608367 Dshi_1769 (6-phosphogluconate dehydratase (RefSeq))
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.29142.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                         -----------
   2.8e-287  939.8   1.5   3.1e-287  939.6   1.5    1.0  1  lcl|FitnessBrowser__Dino:3608367  Dshi_1769 6-phosphogluconate deh


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Dino:3608367  Dshi_1769 6-phosphogluconate dehydratase (RefSeq)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  939.6   1.5  3.1e-287  3.1e-287       4     599 ..       7     599 ..       4     601 .] 0.99

  Alignments for each domain:
  == domain 1  score: 939.6 bits;  conditional E-value: 3.1e-287
                         TIGR01196   4 laeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmlsah 80 
                                       + ++t+ri +rs++ r++yl+++r a++ g+ r++l+cgn ah++aa+   +k +l  e+ +n++i+tayndmlsah
  lcl|FitnessBrowser__Dino:3608367   7 ISDVTARIEARSAEARSTYLDRMRRAAEDGPRRAHLSCGNQAHAYAAMGG-DKEALVAERSANIGIVTAYNDMLSAH 82 
                                       679*********************************************86.78999********************* PP

                         TIGR01196  81 qpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkiv 157
                                       qpfk+ypd ik+a+++a+a+aqvagGvpamcdGvtqG+ Gmelsl+srdvial+t+++lshn fd+a +lGvcdkiv
  lcl|FitnessBrowser__Dino:3608367  83 QPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGMELSLFSRDVIALATGVALSHNTFDAAAYLGVCDKIV 159
                                       ***************************************************************************** PP

                         TIGR01196 158 pGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlve 234
                                       pGl+iaa++fG lp+vfvpaGpm+sGl+n++kakvrq+fa G ++r++l+++emasyh+pGtctfyGtansnqml+e
  lcl|FitnessBrowser__Dino:3608367 160 PGLVIAAATFGYLPGVFVPAGPMVSGLPNDQKAKVRQQFAAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLME 236
                                       ***************************************************************************** PP

                         TIGR01196 235 lmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiar 311
                                       +mGlhlpgasfvnp tplr+alt++aa+rla++t+ ++e+ p+++++d k++vn++vgl+atGGstn  +hl a+ar
  lcl|FitnessBrowser__Dino:3608367 237 FMGLHLPGASFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGGSTNLVIHLPAMAR 313
                                       ***************************************************************************** PP

                         TIGR01196 312 aaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfled 388
                                       aaG+il+ +d+ ++s+  pl+arvypnG advnhf+aaGGl+++i ell+eGllh d++t+ag Gl  y++ep+l d
  lcl|FitnessBrowser__Dino:3608367 314 AAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGELLSEGLLHPDTKTIAGDGLADYAREPKLID 390
                                       ***************************************************************************** PP

                         TIGR01196 389 gkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagel 465
                                       g l++++++ +sl+ +ilr++++ f+++GGlk lkGnlGr+v+kvsav++e +viea+a+vf+dq  +++afkage+
  lcl|FitnessBrowser__Dino:3608367 391 GVLRWEDGPRRSLNAKILRPASDGFAPSGGLKELKGNLGRGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAGEF 467
                                       ***************************************************************************** PP

                         TIGR01196 466 erdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdl 542
                                         d v++vrfqGpkanGmpelh lt+vl vlqdrg kvalvtdGr+sGasGkvpaaihv+peal+gG +ak+r+Gdl
  lcl|FitnessBrowser__Dino:3608367 468 TEDTVVIVRFQGPKANGMPELHALTPVLAVLQDRGLKVALVTDGRMSGASGKVPAAIHVAPEALDGGLMAKVRTGDL 544
                                       ***************************************************************************** PP

                         TIGR01196 543 irldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGass 599
                                       +r+dav+g levl+  +e   r ++++dl+ n+ G+Grelf  +r++v+ a +Ga +
  lcl|FitnessBrowser__Dino:3608367 545 VRVDAVAGVLEVLEPGVE--DRAPAMPDLSGNSHGIGRELFDVFRTTVGPASTGAGV 599
                                       *************88766..67788*****************************976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (601 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 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 11.22
//
[ok]

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

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Steps (tab-delimited)
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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