GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Cronobacter condimenti 1330

Align phosphogluconate dehydratase (characterized)
to candidate WP_007677916.1 BN137_RS04825 phosphogluconate dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>NCBI__GCF_000319285.1:WP_007677916.1
          Length = 603

 Score = 1077 bits (2784), Expect = 0.0
 Identities = 532/603 (88%), Positives = 566/603 (93%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           M+P+LLRVT RI ERSR TR AYLARIE+AK+ TVHR+ LACGNLAHGFAACQP+DKA+L
Sbjct: 1   MHPKLLRVTKRITERSRATREAYLARIEEAKSQTVHRASLACGNLAHGFAACQPDDKAAL 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           KSMLRNNI IITSYNDMLSAHQPYE+YP+ IR ALH   AV QVAGGVPAMCDGVTQGQD
Sbjct: 61  KSMLRNNIGIITSYNDMLSAHQPYENYPQQIRDALHSVGAVAQVAGGVPAMCDGVTQGQD 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAMSAAVGLSHNMFDGAL+LGVCDKIVPGL MAALSFGHLP VF+PSGP
Sbjct: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALYLGVCDKIVPGLVMAALSFGHLPGVFIPSGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           M+SGLPNKEKVRIRQLYAEGKVDR ALLESEAASYH PGTCTFYGTANTNQMV+EFMGMQ
Sbjct: 181 MSSGLPNKEKVRIRQLYAEGKVDRAALLESEAASYHEPGTCTFYGTANTNQMVIEFMGMQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFVHPD+PLR ALTAAAARQVTR+TGNGN+WMP+G+++DEKVVVNGIVALLATGGS
Sbjct: 241 LPGSSFVHPDAPLRHALTAAAARQVTRLTGNGNDWMPLGRLVDEKVVVNGIVALLATGGS 300

Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360
           TNHTMHLVAMARAAGI INWDDFS+LS+ VPL+ARLYPNGPADINHFQAAGGVPVL+REL
Sbjct: 301 TNHTMHLVAMARAAGIIINWDDFSELSEAVPLLARLYPNGPADINHFQAAGGVPVLMREL 360

Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420
           LK GLLHEDVNTVAGFGL+RYT EPWLNNGEL WR+GA  SLD  +IA+ ++PFS HGGT
Sbjct: 361 LKGGLLHEDVNTVAGFGLTRYTQEPWLNNGELAWRDGAAASLDDAIIATVDKPFSQHGGT 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           KVLSGNLGRAVMKTSAVPVENQV+EAPAVVFESQHDV+PAFEAGLLDRDCVVVVRHQGPK
Sbjct: 421 KVLSGNLGRAVMKTSAVPVENQVVEAPAVVFESQHDVLPAFEAGLLDRDCVVVVRHQGPK 480

Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540
           ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD
Sbjct: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600
           GDIIRVNGQTGELTLLVD+A L+ RE   PDLSA RVGTGRELF ALREKLSGAEQGATC
Sbjct: 541 GDIIRVNGQTGELTLLVDDATLSQREAFHPDLSAQRVGTGRELFGALREKLSGAEQGATC 600

Query: 601 ITF 603
           I F
Sbjct: 601 IDF 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: 1284
Number of extensions: 46
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 WP_007677916.1 BN137_RS04825 (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.2345268.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 1095.3   0.1          0 1095.1   0.1    1.0  1  NCBI__GCF_000319285.1:WP_007677916.1  


Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000319285.1:WP_007677916.1  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1095.1   0.1         0         0       1     600 [.       2     601 ..       2     602 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1095.1 bits;  conditional E-value: 0
                             TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitay 73 
                                           h++l+++t+ri+ers++tre+yl++i++ak+++++r++l+cgnlahg+aa+++++k++lks+ r+n++iit+y
  NCBI__GCF_000319285.1:WP_007677916.1   2 HPKLLRVTKRITERSRATREAYLARIEEAKSQTVHRASLACGNLAHGFAACQPDDKAALKSMLRNNIGIITSY 74 
                                           79*********************************************************************** PP

                             TIGR01196  74 ndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdg 146
                                           ndmlsahqp+++yp++i++al+  +avaqvagGvpamcdGvtqG+dGmelsllsr+via+s+a+glshnmfdg
  NCBI__GCF_000319285.1:WP_007677916.1  75 NDMLSAHQPYENYPQQIRDALHSVGAVAQVAGGVPAMCDGVTQGQDGMELSLLSREVIAMSAAVGLSHNMFDG 147
                                           ************************************************************************* PP

                             TIGR01196 147 alflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGt 219
                                           al+lGvcdkivpGl++aalsfGhlp+vf+p+Gpm+sGl+nkek+++rql+aeGkvdr +ll+se+asyh+pGt
  NCBI__GCF_000319285.1:WP_007677916.1 148 ALYLGVCDKIVPGLVMAALSFGHLPGVFIPSGPMSSGLPNKEKVRIRQLYAEGKVDRAALLESEAASYHEPGT 220
                                           ************************************************************************* PP

                             TIGR01196 220 ctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvg 292
                                           ctfyGtan+nqm++e+mG++lpg+sfv+p++plr+alt++aa++++rlt+++++++pl++l+dek++vn++v+
  NCBI__GCF_000319285.1:WP_007677916.1 221 CTFYGTANTNQMVIEFMGMQLPGSSFVHPDAPLRHALTAAAARQVTRLTGNGNDWMPLGRLVDEKVVVNGIVA 293
                                           ************************************************************************* PP

                             TIGR01196 293 llatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGll 365
                                           llatGGstnht+hlva+araaGii+nwdd+sels+ vpllar+ypnG ad+nhf+aaGG+++l+rellk Gll
  NCBI__GCF_000319285.1:WP_007677916.1 294 LLATGGSTNHTMHLVAMARAAGIIINWDDFSELSEAVPLLARLYPNGPADINHFQAAGGVPVLMRELLKGGLL 366
                                           ************************************************************************* PP

                             TIGR01196 366 hedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavke 438
                                           hedv+tvag Gl ryt+ep+l++g+l +r++a +sld++i+++vdkpfs++GG+k+l+GnlGrav+k+sav  
  NCBI__GCF_000319285.1:WP_007677916.1 367 HEDVNTVAGFGLTRYTQEPWLNNGELAWRDGAAASLDDAIIATVDKPFSQHGGTKVLSGNLGRAVMKTSAVPV 439
                                           ************************************************************************* PP

                             TIGR01196 439 esrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrl 511
                                           e++v+eapa+vf++q+++l+af+ag l+rd+v+vvr+qGpkanGmpelhkl+++lGvl+dr+fk+alvtdGrl
  NCBI__GCF_000319285.1:WP_007677916.1 440 ENQVVEAPAVVFESQHDVLPAFEAGLLDRDCVVVVRHQGPKANGMPELHKLMPPLGVLLDRCFKIALVTDGRL 512
                                           ************************************************************************* PP

                             TIGR01196 512 sGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfa 584
                                           sGasGkvp+aihvtpea++gG lak+rdGd+ir+++++gel++lvdda l  re  ++dl+++++G+Grelf 
  NCBI__GCF_000319285.1:WP_007677916.1 513 SGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDDATLSQREAFHPDLSAQRVGTGRELFG 585
                                           ************************************************************************* PP

                             TIGR01196 585 alrekvssaeeGassl 600
                                           alrek+s+ae+Ga+++
  NCBI__GCF_000319285.1:WP_007677916.1 586 ALREKLSGAEQGATCI 601
                                           *************997 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 0.00s 00:00:00.00 Elapsed: 00:00:00.01
# Mc/sec: 31.86
//
[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