GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Erythrobacter gangjinensis K7-2

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate WP_047007750.1 AAW01_RS12290 phosphogluconate dehydratase

Query= SwissProt::P21909
         (607 letters)



>NCBI__GCF_001010925.1:WP_047007750.1
          Length = 604

 Score =  760 bits (1963), Expect = 0.0
 Identities = 377/608 (62%), Positives = 468/608 (76%), Gaps = 5/608 (0%)

Query: 1   MTDLHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVDRPNLSCSNLAHGFAAMNGDKP 60
           M++LH T+ +VT R+IE+S+++R+AYL LI  E +   +R  +SCSNLAH FA    D+ 
Sbjct: 1   MSNLHPTIARVTDRIIEKSKDSRRAYLYLIDREADNQPERSQVSCSNLAHAFAGAEEDQE 60

Query: 61  ALRDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQG 120
           AL+     NIG+VTSYNDMLSAH+PY RYPE++K++AREVGAT QVAGG PAMCDGVTQG
Sbjct: 61  ALKTNRGPNIGIVTSYNDMLSAHQPYGRYPERLKIYAREVGATAQVAGGTPAMCDGVTQG 120

Query: 121 QPGMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPS 180
           + GME SLFSRDVIAL+T V+LSH M++G  LLGICDKIVPGLLMGALRFGHLP + VPS
Sbjct: 121 ETGMELSLFSRDVIALSTGVALSHAMYDGMLLLGICDKIVPGLLMGALRFGHLPAVFVPS 180

Query: 181 GPMTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLG 240
           GPM +G+ NKEK R+RQLYA+GK  + ELL+ E   YH+ GTCTF+GTAN+NQM+ME++G
Sbjct: 181 GPMPSGVSNKEKQRVRQLYAEGKATRAELLESELGSYHSPGTCTFFGTANSNQMMMEMMG 240

Query: 241 LHMPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATG 300
           LH+PG+AF  PGT +RQAL RAAV RV  +G  G+D+RPLG  +DEK+IVNA VGLLATG
Sbjct: 241 LHVPGAAFFQPGTKIRQALDRAAVQRVTAMGRNGNDFRPLGHCVDEKAIVNAAVGLLATG 300

Query: 301 GSTNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIK 360
           GSTNH +HIPA ARAAGV ++W D  +LS  VPL+AR+YPNG  D N F  AGGM +VIK
Sbjct: 301 GSTNHAIHIPAFARAAGVQIDWTDLSELSGAVPLLARVYPNGSGDTNHFHEAGGMGFVIK 360

Query: 361 ELLSANLLNRDVTTIAK-GGIEEYAKAPALNDAGELVWKPAGEPGDDTILRPVSNPFAKD 419
           EL SA L + DV  + +  G+E+Y + P L+D   L W+  GE GDDT+LRP S+PF  D
Sbjct: 361 ELTSAGLAHADVIGVGETRGMEQYGQEPWLDD-DMLSWRDVGESGDDTMLRPASDPFQPD 419

Query: 420 GGLRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQ 479
           GG+RL++GNLGRA +K+SAV+ + WTIEAP RVF  Q  V + FK GEL++DV+VVVRFQ
Sbjct: 420 GGMRLVQGNLGRACFKSSAVEKERWTIEAPCRVFQTQAAVNECFKKGELDRDVVVVVRFQ 479

Query: 480 GPRANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGK 539
           GPRANGMPELHKLTPALGVLQD GY+VALVTDGRMSGA+GKVP A+H SPEALGGG +  
Sbjct: 480 GPRANGMPELHKLTPALGVLQDRGYRVALVTDGRMSGASGKVPSAIHCSPEALGGGPLSL 539

Query: 540 LRDGDIVRISVEEGKLEALVPADEWNARPHAEKPAFRPGTGRELFDIFRQNAAKAEDGAV 599
           L+DGD+V++  E G+L       +  +R  A  PA   GTGRE+F +FR  A +AE G  
Sbjct: 540 LQDGDVVKVCAETGELSTTA---DLGSRTPAPDPAPESGTGREIFAMFRNFADEAERGGS 596

Query: 600 AIYAGAGI 607
           A+ A  G+
Sbjct: 597 AMLATGGL 604


Lambda     K      H
   0.318    0.136    0.403 

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: 1210
Number of extensions: 52
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: 607
Length of database: 604
Length adjustment: 37
Effective length of query: 570
Effective length of database: 567
Effective search space:   323190
Effective search space used:   323190
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_047007750.1 AAW01_RS12290 (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.4152163.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
    ------- ------ -----    ------- ------ -----   ---- --  --------                             -----------
     1e-268  878.5   0.0   1.2e-268  878.2   0.0    1.0  1  NCBI__GCF_001010925.1:WP_047007750.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001010925.1:WP_047007750.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 !  878.2   0.0  1.2e-268  1.2e-268       1     600 [.       5     598 ..       5     599 .. 0.97

  Alignments for each domain:
  == domain 1  score: 878.2 bits;  conditional E-value: 1.2e-268
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h+ +a++t+riie+sk+ r++yl  i   +++ + rs+++c+nlah++a  + +++ +lk+++ +n++i+t+y
  NCBI__GCF_001010925.1:WP_047007750.1   5 HPTIARVTDRIIEKSKDSRRAYLYLIDREADNQPERSQVSCSNLAHAFAGAE-EDQEALKTNRGPNIGIVTSY 76 
                                           7899********************************************9875.56789*************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahqp+ +yp+ +k  ++e +a+aqvagG+pamcdGvtqGe Gmelsl+srdvialst+++lsh m+dg
  NCBI__GCF_001010925.1:WP_047007750.1  77 NDMLSAHQPYGRYPERLKIYAREVGATAQVAGGTPAMCDGVTQGETGMELSLFSRDVIALSTGVALSHAMYDG 149
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                            l+lG+cdkivpGll++al fGhlpavfvp+Gpm+sG++nkek +vrql+aeGk++r ell+se  syh+pGt
  NCBI__GCF_001010925.1:WP_047007750.1 150 MLLLGICDKIVPGLLMGALRFGHLPAVFVPSGPMPSGVSNKEKQRVRQLYAEGKATRAELLESELGSYHSPGT 222
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctf+Gtansnqm++e+mGlh+pga+f +p t++r+al r+a +r++++  +++++ pl++ +dek+ivna vg
  NCBI__GCF_001010925.1:WP_047007750.1 223 CTFFGTANSNQMMMEMMGLHVPGAAFFQPGTKIRQALDRAAVQRVTAMGRNGNDFRPLGHCVDEKAIVNAAVG 295
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           llatGGstnh++h+ a+araaG++++w dlsels  vpllarvypnG+ d nhf+ aGG++f+i+el ++Gl 
  NCBI__GCF_001010925.1:WP_047007750.1 296 LLATGGSTNHAIHIPAFARAAGVQIDWTDLSELSGAVPLLARVYPNGSGDTNHFHEAGGMGFVIKELTSAGLA 368
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvag.kGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavk 437
                                           h dv  v + +G+++y +ep+l+d+ l++r+   +s d+ +lr++++pf+++GG++l++GnlGra +k sav+
  NCBI__GCF_001010925.1:WP_047007750.1 369 HADVIGVGEtRGMEQYGQEPWLDDDMLSWRDVG-ESGDDTMLRPASDPFQPDGGMRLVQGNLGRACFKSSAVE 440
                                           ******98769*******************976.58999********************************** PP

                             TIGR01196 438 eesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGr 510
                                           +e   ieap++vf++qa +++ fk+gel+rd+v+vvrfqGp+anGmpelhklt++lGvlqdrg++valvtdGr
  NCBI__GCF_001010925.1:WP_047007750.1 441 KERWTIEAPCRVFQTQAAVNECFKKGELDRDVVVVVRFQGPRANGMPELHKLTPALGVLQDRGYRVALVTDGR 513
                                           ************************************************************************* PP

                             TIGR01196 511 lsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelf 583
                                           +sGasGkvp+aih +peal gG+l  ++dGd++++ a +gel+     a+l +r++  +d+ ++e G+Gre+f
  NCBI__GCF_001010925.1:WP_047007750.1 514 MSGASGKVPSAIHCSPEALGGGPLSLLQDGDVVKVCAETGELST---TADLGSRTP-APDP-APESGTGREIF 581
                                           *****************************************875...567888884.4554.7899******* PP

                             TIGR01196 584 aalrekvssaeeGassl 600
                                           a++r+ ++ ae+G+s++
  NCBI__GCF_001010925.1:WP_047007750.1 582 AMFRNFADEAERGGSAM 598
                                           *************9875 PP



Internal pipeline statistics summary:
-------------------------------------
Query model(s):                            1  (601 nodes)
Target sequences:                          1  (604 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: 23.43
//
[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:

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:

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:

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:

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