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.17721.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: 00:00:00.03
# Mc/sec: 10.07
//
[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:

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