GapMind for catabolism of small carbon sources

 

Alignments for a candidate for praD in Cupriavidus basilensis 4G11

Align 2-oxo-3-hexenedioate decarboxylase (EC 4.1.1.77) (characterized)
to candidate RR42_RS32640 RR42_RS32640 4-oxalocrotonate decarboxylase

Query= metacyc::MONOMER-14737
         (262 letters)



>FitnessBrowser__Cup4G11:RR42_RS32640
          Length = 262

 Score =  370 bits (950), Expect = e-107
 Identities = 180/262 (68%), Positives = 216/262 (82%)

Query: 1   MKLDKNTLAQLAEHLENAELKAHDVTKITDDHPDMDWDDAYAIQDLIRARKESRGHKTLG 60
           M L ++T  QLAEHLE AEL    V KITD HP+MDW+DAYAIQD IRARK++RG +  G
Sbjct: 1   MNLTQDTTRQLAEHLETAELNREPVRKITDTHPEMDWEDAYAIQDAIRARKQARGTRIAG 60

Query: 61  LKCGLTSYAKMKQMGVDTPVFGFVSDYMACAEGSDIKTSELIHPKVEAEICVVTKAPLKG 120
           LK GLTS+AKM+QMGV  PV+GF++DY AC +G  I T+ LIHPKVEAEI  V K PLKG
Sbjct: 61  LKMGLTSFAKMRQMGVTDPVYGFLTDYGACMDGGAIDTASLIHPKVEAEIAFVLKHPLKG 120

Query: 121 PGCHVGAVMAAIDFVIPGVEIIDSRYRDFKFDLKSVIADNTSASRFVIGGRARRVEDLDL 180
           PGCH+G V+AA DFV+P VE+IDSRY +F+FDLKSVIADNTS++RFV+GG  R  E +DL
Sbjct: 121 PGCHIGDVLAATDFVLPAVEVIDSRYENFRFDLKSVIADNTSSARFVVGGTHRSAEGIDL 180

Query: 181 RTLGVVLEKNGQIVAMAAGAAVMGHPAAAIAALANHLGARGQEIPTGSFIMTGGVTEAIA 240
           + LGVVLEKNG++VA AAGAAV+GHPA+++A LAN LGARG+E+P G+FIMTGGVTEAIA
Sbjct: 181 KNLGVVLEKNGEVVATAAGAAVLGHPASSVAMLANMLGARGRELPAGTFIMTGGVTEAIA 240

Query: 241 VQAGDSVNVRFQDLGTVGMRFV 262
           V AGDS+ VR+Q LGTV MRFV
Sbjct: 241 VAAGDSITVRYQHLGTVSMRFV 262


Lambda     K      H
   0.320    0.135    0.391 

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: 241
Number of extensions: 6
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: 262
Length of database: 262
Length adjustment: 25
Effective length of query: 237
Effective length of database: 237
Effective search space:    56169
Effective search space used:    56169
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.7 bits)

Align candidate RR42_RS32640 RR42_RS32640 (4-oxalocrotonate decarboxylase)
to HMM TIGR03218 (dmpH: 4-oxalocrotonate decarboxylase (EC 4.1.1.77))

Software error:

../bin/blast/fastacmd -i /tmp/list.8548.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8548.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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