GapMind for catabolism of small carbon sources

 

Aligments 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)



>lcl|FitnessBrowser__Koxy:BWI76_RS18100 BWI76_RS18100
           phosphogluconate dehydratase
          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.9512.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  lcl|FitnessBrowser__Koxy:BWI76_RS18100  BWI76_RS18100 phosphogluconate d


Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Koxy:BWI76_RS18100  BWI76_RS18100 phosphogluconate dehydratase
   #    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 hsrlaeiteriierskktrekylekirsaktkgklrstlgcgnlahgvaalsesekvelksekrknlaiit 71 
                                             +s+++++t+riiers++tre+yl++i++akt +++r++l+cgnlahg+aa++ ++k++lks+ r+n+aiit
  lcl|FitnessBrowser__Koxy:BWI76_RS18100   2 NSEMLRVTNRIIERSRDTREAYLARINQAKTDTVHRAQLACGNLAHGFAACQADDKASLKSMLRNNIAIIT 72 
                                             57899****************************************************************** PP

                               TIGR01196  72 ayndmlsahqpfkeypdlikkalqeanavaqvagGvpamcdGvtqGedGmelsllsrdvialstaiglshn 142
                                             +yndmlsahqp+++ypd+i+kal+ anav+qvagGvpamcdGvtqG+dGmelsllsr+via+s+aiglshn
  lcl|FitnessBrowser__Koxy:BWI76_RS18100  73 SYNDMLSAHQPYERYPDIIRKALHSANAVGQVAGGVPAMCDGVTQGQDGMELSLLSREVIAMSAAIGLSHN 143
                                             *********************************************************************** PP

                               TIGR01196 143 mfdgalflGvcdkivpGlliaalsfGhlpavfvpaGpmasGlenkekakvrqlfaeGkvdreellksemas 213
                                             mfdgal+lGvcdkivpGl++aalsfGhlp++f+p+GpmasGl nkek+++rql+aeGkvdr++ll+se+as
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 144 MFDGALYLGVCDKIVPGLAMAALSFGHLPSIFIPSGPMASGLANKEKVRIRQLYAEGKVDRMALLESEAAS 214
                                             *********************************************************************** PP

                               TIGR01196 214 yhapGtctfyGtansnqmlvelmGlhlpgasfvnpntplrdaltreaakrlarltakngevlplaelidek 284
                                             yhapGtctfyGtan+nqm+ve+mG++lpg+sfv+p++plr+alt++aa++++rlt++++e++pl+++ dek
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 215 YHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDAPLREALTAAAARQVTRLTGNGNEWMPLGKMFDEK 285
                                             *********************************************************************** PP

                               TIGR01196 285 sivnalvgllatGGstnhtlhlvaiaraaGiilnwddlselsdlvpllarvypnGkadvnhfeaaGGlsfl 355
                                             ++vn++v+llatGGstnht+hlva+araaGii+nwdd+s+lsd+vpllar+ypnG ad+nhf+aaGG+++l
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 286 VVVNGIVALLATGGSTNHTMHLVAMARAAGIIINWDDFSDLSDVVPLLARLYPNGPADINHFQAAGGVPVL 356
                                             *********************************************************************** PP

                               TIGR01196 356 irellkeGllhedvetvagkGlrrytkepfledgkleyreaaeksldedilrkvdkpfsaeGGlkllkGnl 426
                                             +rellk Gllhedv+tvag Gl+ryt+ep+l++g+l++re+a + lde++++++dkpfs +GG+k+l+Gnl
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 357 VRELLKGGLLHEDVHTVAGFGLSRYTMEPWLNNGELDWREGAAAPLDEAVIATFDKPFSRHGGTKVLSGNL 427
                                             *********************************************************************** PP

                               TIGR01196 427 GravikvsavkeesrvieapaivfkdqaellaafkagelerdlvavvrfqGpkanGmpelhklttvlGvlq 497
                                             Grav+k+sav  e+++ieapa+vf++q+++l+af+ag l++d+v+vvr+qGpkanGmpelhkl+++lGvl+
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 428 GRAVMKTSAVPVENQIIEAPAVVFESQHDVLPAFEAGLLDKDCVVVVRHQGPKANGMPELHKLMPPLGVLL 498
                                             *********************************************************************** PP

                               TIGR01196 498 drgfkvalvtdGrlsGasGkvpaaihvtpealegGalakirdGdlirldavngelevlvddaelkarelee 568
                                             dr fk+alvtdGrlsGasGkvp+aihvtpea++gG lak+rdGd+ir+++++gel++ vddael+ar++++
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 499 DRRFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLRVDDAELAARQPHI 569
                                             *********************************************************************** PP

                               TIGR01196 569 ldlednelGlGrelfaalrekvssaeeGasslt 601
                                             +dl+ +++G+Gre+f alrek+s+ae+Ga+++t
  lcl|FitnessBrowser__Koxy:BWI76_RS18100 570 PDLSGSRVGTGREMFGALREKLSGAEQGATCIT 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.04
# Mc/sec: 7.73
//
[ok]

This GapMind analysis is from Sep 17 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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