Alignments for a candidate for edd in Marivita geojedonensis DPG-138

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Marivita geojedonensis DPG-138

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_085637224.1 MGEO_RS10995 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>NCBI__GCF_002115805.1:WP_085637224.1
          Length = 603

 Score =  680 bits (1754), Expect = 0.0
 Identities = 342/598 (57%), Positives = 438/598 (73%), Gaps = 4/598 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  +  VTER+  RS  +R  Y+  +R AA++GP+R  L C N AH  A  G +D+  L
Sbjct: 5   LNDTIKRVTERVQERSETSRGRYMDRMRQAAAEGPRRAHLSCGNQAHAYAAMG-QDQDKL 63

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
               + N+ IV++YNDMLSAHQP+E +P+ I+ A R  G   Q AGG PAMCDGVTQG+ 
Sbjct: 64  ATERSPNIGIVTAYNDMLSAHQPFEKYPDIIRNAARAAGGTAQVAGGVPAMCDGVTQGQV 123

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+VIAL+  VALSHN FD+AL LG+CDKIVPGL++ A  FG+LP IF+P GP
Sbjct: 124 GMELSLFSRDVIALAAGVALSHNTFDSALYLGVCDKIVPGLVIAAGTFGYLPGIFIPAGP 183

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SG+ N EKA VRQ++A G+  R+EL+++EM SYHSPGTCTFYGTAN+NQ+LME MGLH
Sbjct: 184 MRSGLPNDEKAKVRQKFAAGEVGRDELMKAEMASYHSPGTCTFYGTANSNQMLMEFMGLH 243

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNP TPLR+ALT    ++   +T+   ++ P+ +++DE++ VN IV L ATGGS
Sbjct: 244 LPGSSFVNPGTPLREALTVAGTERALEITQLGNDYRPVCDVLDEKAFVNGIVGLMATGGS 303

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  LH+PA+A+AAG++L  +D  D+S V P ++ VYPNG AD+NHF AAGG+ F+I EL
Sbjct: 304 TNLVLHLPAMARAAGVELRLEDFEDISSVTPLMAKVYPNGLADVNHFHAAGGLGFMIGEL 363

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+ GLLHE+V TVAG GL  YTQEP + +G++V+  G  E+ ++ ILRP +  F P GGL
Sbjct: 364 LKNGLLHEEVKTVAGDGLHLYTQEPKVADGRVVYGPGAGETQNDRILRPASDPFQPTGGL 423

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           + + GNLG+G+MK SAVA +  ++EA A VF DQ+D+  AFK GE  +D V V+RFQGP 
Sbjct: 424 KQLAGNLGKGMMKTSAVAPERHVIEAKARVFHDQEDVKTAFKNGEFTEDTVVVVRFQGPS 483

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELH +TP L VLQDRG KVALVTDGRMSGASGK+P+AIHVSPEA  GG LARVRD
Sbjct: 484 SNGMPELHSLTPTLAVLQDRGLKVALVTDGRMSGASGKVPSAIHVSPEAAKGGPLARVRD 543

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKG-LLGNNVGSGRELFGFMRMAFSSAEQGA 597
           GD++RVD V G ++    A++F  REPA   L GN  G GRELF   R     AE GA
Sbjct: 544 GDVLRVDAVSGKIDCL--AEDFDQREPATADLSGNGHGVGRELFAAFRENVGLAEFGA 599


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: 1129
Number of extensions: 48
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: 603
Length adjustment: 37
Effective length of query: 571
Effective length of database: 566
Effective search space:   323186
Effective search space used:   323186
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_085637224.1 MGEO_RS10995 (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.3870735.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
   2.2e-287  940.1   0.4   2.5e-287  940.0   0.4    1.0  1  NCBI__GCF_002115805.1:WP_085637224.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_002115805.1:WP_085637224.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  940.0   0.4  2.5e-287  2.5e-287       3     599 ..       8     601 ..       6     603 .] 0.99

  Alignments for each domain:
  == domain 1  score: 940.0 bits;  conditional E-value: 2.5e-287
                             TIGR01196   3 rlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                            ++++ter++ers++ r +y++++r+a+ +g+ r++l+cgn ah++aa+ ++ + +l++e+ +n++i+taynd
  NCBI__GCF_002115805.1:WP_085637224.1   8 TIKRVTERVQERSETSRGRYMDRMRQAAAEGPRRAHLSCGNQAHAYAAMGQD-QDKLATERSPNIGIVTAYND 79 
                                           5899*********************************************975.56899*************** PP

                             TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgal 148
                                           mlsahqpf++ypd+i++a++ a+++aqvagGvpamcdGvtqG+ Gmelsl+srdvial+++++lshn fd+al
  NCBI__GCF_002115805.1:WP_085637224.1  80 MLSAHQPFEKYPDIIRNAARAAGGTAQVAGGVPAMCDGVTQGQVGMELSLFSRDVIALAAGVALSHNTFDSAL 152
                                           ************************************************************************* PP

                             TIGR01196 149 flGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtct 221
                                           +lGvcdkivpGl+iaa +fG lp++f+paGpm sGl+n+ekakvrq fa G v+r+el+k+emasyh+pGtct
  NCBI__GCF_002115805.1:WP_085637224.1 153 YLGVCDKIVPGLVIAAGTFGYLPGIFIPAGPMRSGLPNDEKAKVRQKFAAGEVGRDELMKAEMASYHSPGTCT 225
                                           ************************************************************************* PP

                             TIGR01196 222 fyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgll 294
                                           fyGtansnqml+e+mGlhlpg+sfvnp tplr+alt + ++r+ ++t+ ++++ p+++++dek++vn++vgl+
  NCBI__GCF_002115805.1:WP_085637224.1 226 FYGTANSNQMLMEFMGLHLPGSSFVNPGTPLREALTVAGTERALEITQLGNDYRPVCDVLDEKAFVNGIVGLM 298
                                           ************************************************************************* PP

                             TIGR01196 295 atGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhe 367
                                           atGGstn  lhl a+araaG+ l  +d++++s++ pl+a+vypnG advnhf+aaGGl+f+i ellk+Gllhe
  NCBI__GCF_002115805.1:WP_085637224.1 299 ATGGSTNLVLHLPAMARAAGVELRLEDFEDISSVTPLMAKVYPNGLADVNHFHAAGGLGFMIGELLKNGLLHE 371
                                           ************************************************************************* PP

                             TIGR01196 368 dvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkees 440
                                           +v+tvag Gl+ yt+ep++ dg+++y ++a ++ ++ ilr++++pf+++GGlk l GnlG++++k+sav++e 
  NCBI__GCF_002115805.1:WP_085637224.1 372 EVKTVAGDGLHLYTQEPKVADGRVVYGPGAGETQNDRILRPASDPFQPTGGLKQLAGNLGKGMMKTSAVAPER 444
                                           ************************************************************************* PP

                             TIGR01196 441 rvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsG 513
                                           +viea+a+vf+dq+++++afk+ge+  d v+vvrfqGp +nGmpelh lt++l vlqdrg kvalvtdGr+sG
  NCBI__GCF_002115805.1:WP_085637224.1 445 HVIEAKARVFHDQEDVKTAFKNGEFTEDTVVVVRFQGPSSNGMPELHSLTPTLAVLQDRGLKVALVTDGRMSG 517
                                           ************************************************************************* PP

                             TIGR01196 514 asGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaal 586
                                           asGkvp+aihv+pea++gG+la++rdGd++r+dav+g+++ l +d++   re+++ dl+ n  G+Grelfaa+
  NCBI__GCF_002115805.1:WP_085637224.1 518 ASGKVPSAIHVSPEAAKGGPLARVRDGDVLRVDAVSGKIDCLAEDFD--QREPATADLSGNGHGVGRELFAAF 588
                                           ********************************************975..79999******************* PP

                             TIGR01196 587 rekvssaeeGass 599
                                           re+v+ ae Ga +
  NCBI__GCF_002115805.1:WP_085637224.1 589 RENVGLAEFGAGV 601
                                           *********9976 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (603 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: 33.97
//
[ok]

This GapMind analysis is from Sep 24 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 2024 update 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