GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Escherichia coli BW25113

Align phosphogluconate dehydratase (characterized)
to candidate 15969 b1851 phosphogluconate dehydratase (NCBI)

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__Keio:15969
          Length = 603

 Score = 1198 bits (3099), Expect = 0.0
 Identities = 603/603 (100%), Positives = 603/603 (100%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL
Sbjct: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD
Sbjct: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP
Sbjct: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ
Sbjct: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS
Sbjct: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300

Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360
           TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL
Sbjct: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360

Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420
           LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT
Sbjct: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK
Sbjct: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480

Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540
           ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD
Sbjct: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600
           GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC
Sbjct: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600

Query: 601 ITF 603
           ITF
Sbjct: 601 ITF 603


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: 1363
Number of extensions: 41
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: 603
Length of database: 603
Length adjustment: 37
Effective length of query: 566
Effective length of database: 566
Effective search space:   320356
Effective search space used:   320356
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 15969 b1851 (phosphogluconate dehydratase (NCBI))
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.1352520.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 1130.4   0.2          0 1130.2   0.2    1.0  1  lcl|FitnessBrowser__Keio:15969  b1851 phosphogluconate dehydrata


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Keio:15969  b1851 phosphogluconate dehydratase (NCBI)
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1130.2   0.2         0         0       1     601 []       2     602 ..       2     602 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1130.2 bits;  conditional E-value: 0
                       TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitayndmlsa 79 
                                     +++l+++t+riiers++tr++yl++i++akt++++rs+l+cgnlahg+aa+++++k++lks+ r+n+aiit+yndmlsa
  lcl|FitnessBrowser__Keio:15969   2 NPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASLKSMLRNNIAIITSYNDMLSA 80 
                                     589**************************************************************************** PP

                       TIGR01196  80 hqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalflGvcdkivp 158
                                     hqp+++yp++i+kal+eanav+qvagGvpamcdGvtqG+dGmelsllsr+via+s+a+glshnmfdgalflGvcdkivp
  lcl|FitnessBrowser__Keio:15969  81 HQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVP 159
                                     ******************************************************************************* PP

                       TIGR01196 159 GlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGtansnqmlvelmG 237
                                     Gl++aalsfGhlpavfvp+GpmasGl+nkek+++rql+aeGkvdr++ll+se+asyhapGtctfyGtan+nqm+ve+mG
  lcl|FitnessBrowser__Keio:15969 160 GLTMAALSFGHLPAVFVPSGPMASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMG 238
                                     ******************************************************************************* PP

                       TIGR01196 238 lhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGstnhtlhlvaiaraaGii 316
                                     ++lpg+sfv+p++plrdalt++aa++++r+t++++e++p++++idek++vn++v+llatGGstnht+hlva+araaGi+
  lcl|FitnessBrowser__Keio:15969 239 MQLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIQ 317
                                     ******************************************************************************* PP

                       TIGR01196 317 lnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagkGlrrytkepfledgkleyre 395
                                     +nwdd+s+lsd+vpl+ar+ypnG ad+nhf+aaGG+++l+rellk+Gllhedv+tvag Gl+ryt ep+l++g+l++re
  lcl|FitnessBrowser__Keio:15969 318 INWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWRE 396
                                     ******************************************************************************* PP

                       TIGR01196 396 aaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvr 474
                                     +aeksld+++++++++pfs++GG+k+l+GnlGrav+k+sav  e++vieapa+vf++q+++++af+ag l+rd+v+vvr
  lcl|FitnessBrowser__Keio:15969 397 GAEKSLDSNVIASFEQPFSHHGGTKVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVR 475
                                     ******************************************************************************* PP

                       TIGR01196 475 fqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngele 553
                                     +qGpkanGmpelhkl+++lGvl+dr+fk+alvtdGrlsGasGkvp+aihvtpea++gG lak+rdGd+ir+++++gel+
  lcl|FitnessBrowser__Keio:15969 476 HQGPKANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELT 554
                                     ******************************************************************************* PP

                       TIGR01196 554 vlvddaelkareleeldlednelGlGrelfaalrekvssaeeGasslt 601
                                     +lvd+ael+are++++dl+++++G+Grelf+alrek+s+ae+Ga+++t
  lcl|FitnessBrowser__Keio:15969 555 LLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATCIT 602
                                     *********************************************986 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.00
# Mc/sec: 36.53
//
[ok]

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

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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