Alignments for a candidate for edd in Phyllobacterium brassicacearum STM 196

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Phyllobacterium brassicacearum STM 196

Align phosphogluconate dehydratase (characterized)
to candidate WP_106709318.1 CU102_RS02320 phosphogluconate dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>NCBI__GCF_003010955.1:WP_106709318.1
          Length = 607

 Score =  743 bits (1918), Expect = 0.0
 Identities = 371/595 (62%), Positives = 457/595 (76%), Gaps = 3/595 (0%)

Query: 8   VTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASLKSMLRNN 67
           +T+RI E+S+ TR  YL  + +A +    RS LAC NLAHGFAAC P DKA+L   +  N
Sbjct: 10  ITHRICEQSKPTRDVYLDHLREAASRKPKRSALACANLAHGFAACSPSDKAALAGDVVPN 69

Query: 68  IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGMELSLL 127
           + IITSYNDMLSAHQP+E YP++I+ A  EA  V QVAGGVPAMCDGVTQGQ GMELSL 
Sbjct: 70  LGIITSYNDMLSAHQPFETYPQLIKAAAKEAGGVAQVAGGVPAMCDGVTQGQPGMELSLF 129

Query: 128 SREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPN 187
           SR+VIAM+ A+GLSH+MFD A++LGVCDKIVPGL + AL+FGHLPAVF+P+GPM +GLPN
Sbjct: 130 SRDVIAMATAIGLSHDMFDAAVYLGVCDKIVPGLVIGALTFGHLPAVFIPAGPMTTGLPN 189

Query: 188 KEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFV 247
            EK + RQLYAEGKV R ALLESE+ SYH PGTCTFYGTAN+NQM++E MG+ +PGSSF+
Sbjct: 190 DEKAKTRQLYAEGKVGREALLESESKSYHGPGTCTFYGTANSNQMLMEIMGLHMPGSSFI 249

Query: 248 HPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHL 307
           +P +PLRDALT  AA++   +T  GNE+ P+G+MIDE+ +VNG+V L ATGGSTNHTMHL
Sbjct: 250 NPGTPLRDALTREAAKRALAITALGNEYTPVGEMIDERSIVNGVVGLHATGGSTNHTMHL 309

Query: 308 VAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLH 367
           VAMA AAGI++ W D SDLSDVVPL+AR+YPNG AD+NHF AAGG+  ++RELL  GLLH
Sbjct: 310 VAMAAAAGIKLTWQDISDLSDVVPLLARVYPNGLADVNHFHAAGGMGYIIRELLDGGLLH 369

Query: 368 EDVNTV--AGFGLSRYTLEPWL-NNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLS 424
           EDV TV   G GL  YT+EP L  NG +     A +S D  V+++ +QPF   GG K+L 
Sbjct: 370 EDVKTVWGGGDGLRAYTIEPKLGENGTVVREPVAAESADKKVLSTCKQPFQVTGGLKMLK 429

Query: 425 GNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPKANGM 484
           GNLG AV+KTSAV  +  +IEAPA+VF+SQ  +  AF+AG LDRD V VVR QGP+ANGM
Sbjct: 430 GNLGTAVIKTSAVKADRHIIEAPAIVFDSQAALQDAFKAGKLDRDFVAVVRFQGPRANGM 489

Query: 485 PELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDII 544
           PELHKL P LGVL DR   +ALVTDGR+SGASGKVP+AIHVTPEA DGG++ K+ DGD++
Sbjct: 490 PELHKLTPALGVLQDRGHMVALVTDGRMSGASGKVPAAIHVTPEALDGGIIGKIHDGDVV 549

Query: 545 RVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGAT 599
           R++ + G L +L D   LAAR     D++ +  G GRELF+A R  +  AE GA+
Sbjct: 550 RLDAEIGTLDVLEDPDVLAARPTPEVDINHNSYGMGRELFAAFRNVVGKAENGAS 604


Lambda     K      H
   0.318    0.134    0.392 

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: 49
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: 603
Length of database: 607
Length adjustment: 37
Effective length of query: 566
Effective length of database: 570
Effective search space:   322620
Effective search space used:   322620
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_106709318.1 CU102_RS02320 (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.1525750.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 1038.1   0.9          0 1037.9   0.9    1.0  1  NCBI__GCF_003010955.1:WP_106709318.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_003010955.1:WP_106709318.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1037.9   0.9         0         0       3     600 ..       6     606 ..       4     607 .] 0.99

  Alignments for each domain:
  == domain 1  score: 1037.9 bits;  conditional E-value: 0
                             TIGR01196   3 rlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                           r+++it+ri e+sk+tr+ yl+++r+a+++ ++rs+l+c+nlahg+aa+s+s+k++l+ + ++nl+iit+ynd
  NCBI__GCF_003010955.1:WP_106709318.1   6 RVKSITHRICEQSKPTRDVYLDHLREAASRKPKRSALACANLAHGFAACSPSDKAALAGDVVPNLGIITSYND 78 
                                           7999********************************************************************* PP

                             TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgal 148
                                           mlsahqpf++yp+lik a++ea++vaqvagGvpamcdGvtqG++Gmelsl+srdvia++taiglsh+mfd+a+
  NCBI__GCF_003010955.1:WP_106709318.1  79 MLSAHQPFETYPQLIKAAAKEAGGVAQVAGGVPAMCDGVTQGQPGMELSLFSRDVIAMATAIGLSHDMFDAAV 151
                                           ************************************************************************* PP

                             TIGR01196 149 flGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtct 221
                                           +lGvcdkivpGl+i+al+fGhlpavf+paGpm++Gl+n+ekak+rql+aeGkv+re+ll+se++syh+pGtct
  NCBI__GCF_003010955.1:WP_106709318.1 152 YLGVCDKIVPGLVIGALTFGHLPAVFIPAGPMTTGLPNDEKAKTRQLYAEGKVGREALLESESKSYHGPGTCT 224
                                           ************************************************************************* PP

                             TIGR01196 222 fyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgll 294
                                           fyGtansnqml+e+mGlh+pg+sf+np tplrdaltreaakr+ ++ta ++e++p++e+ide+sivn++vgl+
  NCBI__GCF_003010955.1:WP_106709318.1 225 FYGTANSNQMLMEIMGLHMPGSSFINPGTPLRDALTREAAKRALAITALGNEYTPVGEMIDERSIVNGVVGLH 297
                                           ************************************************************************* PP

                             TIGR01196 295 atGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhe 367
                                           atGGstnht+hlva+a aaGi l+w+d+s+lsd+vpllarvypnG advnhf+aaGG++++irell+ Gllhe
  NCBI__GCF_003010955.1:WP_106709318.1 298 ATGGSTNHTMHLVAMAAAAGIKLTWQDISDLSDVVPLLARVYPNGLADVNHFHAAGGMGYIIRELLDGGLLHE 370
                                           ************************************************************************* PP

                             TIGR01196 368 dvetvag..kGlrrytkepfled.gkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437
                                           dv+tv g   Glr+yt+ep+l + g +++++ a +s+d+++l + ++pf+ +GGlk+lkGnlG avik+savk
  NCBI__GCF_003010955.1:WP_106709318.1 371 DVKTVWGggDGLRAYTIEPKLGEnGTVVREPVAAESADKKVLSTCKQPFQVTGGLKMLKGNLGTAVIKTSAVK 443
                                           *****987799**********764899999999**************************************** PP

                             TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510
                                            + ++ieapaivf++qa l++afkag+l+rd+vavvrfqGp+anGmpelhklt++lGvlqdrg+ valvtdGr
  NCBI__GCF_003010955.1:WP_106709318.1 444 ADRHIIEAPAIVFDSQAALQDAFKAGKLDRDFVAVVRFQGPRANGMPELHKLTPALGVLQDRGHMVALVTDGR 516
                                           ************************************************************************* PP

                             TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583
                                           +sGasGkvpaaihvtpeal+gG + ki+dGd++rlda  g l+vl+d   l+ar + e+d+++n++G+Grelf
  NCBI__GCF_003010955.1:WP_106709318.1 517 MSGASGKVPAAIHVTPEALDGGIIGKIHDGDVVRLDAEIGTLDVLEDPDVLAARPTPEVDINHNSYGMGRELF 589
                                           ************************************************************************* PP

                             TIGR01196 584 aalrekvssaeeGassl 600
                                           aa+r+ v+ ae+Gas++
  NCBI__GCF_003010955.1:WP_106709318.1 590 AAFRNVVGKAENGASVF 606
                                           **************998 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (607 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01
# Mc/sec: 24.39
//
[ok]

This GapMind analysis is from Sep 24 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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SQLite3 databases

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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