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))

Software error:

../bin/blast/fastacmd -i /tmp/list.6906.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6906.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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