Alignments for a candidate for edd in Klebsiella michiganensis M5al

GapMind for catabolism of small carbon sources

Alignments for a candidate for edd in Klebsiella michiganensis M5al

Align phosphogluconate dehydratase (characterized)
to candidate BWI76_RS18100 BWI76_RS18100 phosphogluconate dehydratase

Query= CharProtDB::CH_024239
         (603 letters)



>FitnessBrowser__Koxy:BWI76_RS18100
          Length = 603

 Score = 1118 bits (2892), Expect = 0.0
 Identities = 554/603 (91%), Positives = 581/603 (96%)

Query: 1   MNPQLLRVTNRIIERSRETRSAYLARIEQAKTSTVHRSQLACGNLAHGFAACQPEDKASL 60
           MN ++LRVTNRIIERSR+TR AYLARI QAKT TVHR+QLACGNLAHGFAACQ +DKASL
Sbjct: 1   MNSEMLRVTNRIIERSRDTREAYLARINQAKTDTVHRAQLACGNLAHGFAACQADDKASL 60

Query: 61  KSMLRNNIAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQD 120
           KSMLRNNIAIITSYNDMLSAHQPYE YP+IIRKALH ANAVGQVAGGVPAMCDGVTQGQD
Sbjct: 61  KSMLRNNIAIITSYNDMLSAHQPYERYPDIIRKALHSANAVGQVAGGVPAMCDGVTQGQD 120

Query: 121 GMELSLLSREVIAMSAAVGLSHNMFDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGP 180
           GMELSLLSREVIAMSAA+GLSHNMFDGAL+LGVCDKIVPGL MAALSFGHLP++F+PSGP
Sbjct: 121 GMELSLLSREVIAMSAAIGLSHNMFDGALYLGVCDKIVPGLAMAALSFGHLPSIFIPSGP 180

Query: 181 MASGLPNKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240
           MASGL NKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ
Sbjct: 181 MASGLANKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQ 240

Query: 241 LPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGS 300
           LPGSSFVHPD+PLR+ALTAAAARQVTR+TGNGNEWMP+GKM DEKVVVNGIVALLATGGS
Sbjct: 241 LPGSSFVHPDAPLREALTAAAARQVTRLTGNGNEWMPLGKMFDEKVVVNGIVALLATGGS 300

Query: 301 TNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVREL 360
           TNHTMHLVAMARAAGI INWDDFSDLSDVVPL+ARLYPNGPADINHFQAAGGVPVLVREL
Sbjct: 301 TNHTMHLVAMARAAGIIINWDDFSDLSDVVPLLARLYPNGPADINHFQAAGGVPVLVREL 360

Query: 361 LKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGT 420
           LK GLLHEDV+TVAGFGLSRYT+EPWLNNGELDWREGA   LD  VIA+F++PFS HGGT
Sbjct: 361 LKGGLLHEDVHTVAGFGLSRYTMEPWLNNGELDWREGAAAPLDEAVIATFDKPFSRHGGT 420

Query: 421 KVLSGNLGRAVMKTSAVPVENQVIEAPAVVFESQHDVMPAFEAGLLDRDCVVVVRHQGPK 480
           KVLSGNLGRAVMKTSAVPVENQ+IEAPAVVFESQHDV+PAFEAGLLD+DCVVVVRHQGPK
Sbjct: 421 KVLSGNLGRAVMKTSAVPVENQIIEAPAVVFESQHDVLPAFEAGLLDKDCVVVVRHQGPK 480

Query: 481 ANGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540
           ANGMPELHKLMPPLGVLLDR FKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD
Sbjct: 481 ANGMPELHKLMPPLGVLLDRRFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRD 540

Query: 541 GDIIRVNGQTGELTLLVDEAELAAREPHIPDLSASRVGTGRELFSALREKLSGAEQGATC 600
           GDIIRVNGQTGELTL VD+AELAAR+PHIPDLS SRVGTGRE+F ALREKLSGAEQGATC
Sbjct: 541 GDIIRVNGQTGELTLRVDDAELAARQPHIPDLSGSRVGTGREMFGALREKLSGAEQGATC 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: 1328
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 BWI76_RS18100 BWI76_RS18100 (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.4076623.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 1094.8   0.3          0 1094.7   0.3    1.0  1  FitnessBrowser__Koxy:BWI76_RS18100  


Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Koxy:BWI76_RS18100  
   #    score  bias  c-Evalue  i-Evalue hmmfrom  hmm to    alifrom  ali to    envfrom  env to     acc
 ---   ------ ----- --------- --------- ------- -------    ------- -------    ------- -------    ----
   1 ! 1094.7   0.3         0         0       1     601 []       2     602 ..       2     602 .. 1.00

  Alignments for each domain:
  == domain 1  score: 1094.7 bits;  conditional E-value: 0
                           TIGR01196   1 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiitaynd 75 
                                         +s+++++t+riiers++tre+yl++i++akt +++r++l+cgnlahg+aa++ ++k++lks+ r+n+aiit+ynd
  FitnessBrowser__Koxy:BWI76_RS18100   2 NSEMLRVTNRIIERSRDTREAYLARINQAKTDTVHRAQLACGNLAHGFAACQADDKASLKSMLRNNIAIITSYND 76 
                                         57899********************************************************************** PP

                           TIGR01196  76 mlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshnmfdgalfl 150
                                         mlsahqp+++ypd+i+kal+ anav+qvagGvpamcdGvtqG+dGmelsllsr+via+s+aiglshnmfdgal+l
  FitnessBrowser__Koxy:BWI76_RS18100  77 MLSAHQPYERYPDIIRKALHSANAVGQVAGGVPAMCDGVTQGQDGMELSLLSREVIAMSAAIGLSHNMFDGALYL 151
                                         *************************************************************************** PP

                           TIGR01196 151 GvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemasyhapGtctfyGt 225
                                         GvcdkivpGl++aalsfGhlp++f+p+GpmasGl nkek+++rql+aeGkvdr++ll+se+asyhapGtctfyGt
  FitnessBrowser__Koxy:BWI76_RS18100 152 GVCDKIVPGLAMAALSFGHLPSIFIPSGPMASGLANKEKVRIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGT 226
                                         *************************************************************************** PP

                           TIGR01196 226 ansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelideksivnalvgllatGGst 300
                                         an+nqm+ve+mG++lpg+sfv+p++plr+alt++aa++++rlt++++e++pl+++ dek++vn++v+llatGGst
  FitnessBrowser__Koxy:BWI76_RS18100 227 ANTNQMVVEFMGMQLPGSSFVHPDAPLREALTAAAARQVTRLTGNGNEWMPLGKMFDEKVVVNGIVALLATGGST 301
                                         *************************************************************************** PP

                           TIGR01196 301 nhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsflirellkeGllhedvetvagk 375
                                         nht+hlva+araaGii+nwdd+s+lsd+vpllar+ypnG ad+nhf+aaGG+++l+rellk Gllhedv+tvag 
  FitnessBrowser__Koxy:BWI76_RS18100 302 NHTMHLVAMARAAGIIINWDDFSDLSDVVPLLARLYPNGPADINHFQAAGGVPVLVRELLKGGLLHEDVHTVAGF 376
                                         *************************************************************************** PP

                           TIGR01196 376 GlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnlGravikvsavkeesrvieapaivf 450
                                         Gl+ryt+ep+l++g+l++re+a + lde++++++dkpfs +GG+k+l+GnlGrav+k+sav  e+++ieapa+vf
  FitnessBrowser__Koxy:BWI76_RS18100 377 GLSRYTMEPWLNNGELDWREGAAAPLDEAVIATFDKPFSRHGGTKVLSGNLGRAVMKTSAVPVENQIIEAPAVVF 451
                                         *************************************************************************** PP

                           TIGR01196 451 kdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlqdrgfkvalvtdGrlsGasGkvpaaihvt 525
                                         ++q+++l+af+ag l++d+v+vvr+qGpkanGmpelhkl+++lGvl+dr fk+alvtdGrlsGasGkvp+aihvt
  FitnessBrowser__Koxy:BWI76_RS18100 452 ESQHDVLPAFEAGLLDKDCVVVVRHQGPKANGMPELHKLMPPLGVLLDRRFKIALVTDGRLSGASGKVPSAIHVT 526
                                         *************************************************************************** PP

                           TIGR01196 526 pealegGalakirdGdlirldavngelevlvddaelkareleeldlednelGlGrelfaalrekvssaeeGassl 600
                                         pea++gG lak+rdGd+ir+++++gel++ vddael+ar+++++dl+ +++G+Gre+f alrek+s+ae+Ga+++
  FitnessBrowser__Koxy:BWI76_RS18100 527 PEAYDGGLLAKVRDGDIIRVNGQTGELTLRVDDAELAARQPHIPDLSGSRVGTGREMFGALREKLSGAEQGATCI 601
                                         *************************************************************************98 PP

                           TIGR01196 601 t 601
                                         t
  FitnessBrowser__Koxy:BWI76_RS18100 602 T 602
                                         6 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 0.01s 00:00:00.02 Elapsed: 00:00:00.01
# Mc/sec: 23.76
//
[ok]

This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
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