GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Dinoroseobacter shibae DFL-12

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate 3608604 Dshi_1997 xylulokinase (RefSeq)

Query= reanno::Dino:3608604
         (480 letters)



>FitnessBrowser__Dino:3608604
          Length = 480

 Score =  965 bits (2494), Expect = 0.0
 Identities = 480/480 (100%), Positives = 480/480 (100%)

Query: 1   MYLGLDLGTSGLKAVLIDENQALVAEATAPLEVARPHPGWSEQMPCDWLAATEAAMAALG 60
           MYLGLDLGTSGLKAVLIDENQALVAEATAPLEVARPHPGWSEQMPCDWLAATEAAMAALG
Sbjct: 1   MYLGLDLGTSGLKAVLIDENQALVAEATAPLEVARPHPGWSEQMPCDWLAATEAAMAALG 60

Query: 61  ARADLSGVRAIGLSGQMHGATLLDASHEVLRPCILWNDTRAAAEAAALDADPAFRSVTGN 120
           ARADLSGVRAIGLSGQMHGATLLDASHEVLRPCILWNDTRAAAEAAALDADPAFRSVTGN
Sbjct: 61  ARADLSGVRAIGLSGQMHGATLLDASHEVLRPCILWNDTRAAAEAAALDADPAFRSVTGN 120

Query: 121 IVFPGFTAPKLAWVRAHEPDVFDRTALVLLPKDYLRLWLTGEAVAEMSDAAGTSWLDTGA 180
           IVFPGFTAPKLAWVRAHEPDVFDRTALVLLPKDYLRLWLTGEAVAEMSDAAGTSWLDTGA
Sbjct: 121 IVFPGFTAPKLAWVRAHEPDVFDRTALVLLPKDYLRLWLTGEAVAEMSDAAGTSWLDTGA 180

Query: 181 RDWSAPLLAATGLSRDHMPRLVEGSEVSGTLRDSLADAWGLPRGVPVAGGGGDNAASGIG 240
           RDWSAPLLAATGLSRDHMPRLVEGSEVSGTLRDSLADAWGLPRGVPVAGGGGDNAASGIG
Sbjct: 181 RDWSAPLLAATGLSRDHMPRLVEGSEVSGTLRDSLADAWGLPRGVPVAGGGGDNAASGIG 240

Query: 241 MGVVRAGDGFVSLGTSGVLFAACDAYAPDPATAVHTFCHALPETWHQMGVILAATDALNW 300
           MGVVRAGDGFVSLGTSGVLFAACDAYAPDPATAVHTFCHALPETWHQMGVILAATDALNW
Sbjct: 241 MGVVRAGDGFVSLGTSGVLFAACDAYAPDPATAVHTFCHALPETWHQMGVILAATDALNW 300

Query: 301 FARTCGTDAATLTGGLGPLQAPGRPVFLPYLGGERTPHNDAAIRGAFARIDHAADRDALA 360
           FARTCGTDAATLTGGLGPLQAPGRPVFLPYLGGERTPHNDAAIRGAFARIDHAADRDALA
Sbjct: 301 FARTCGTDAATLTGGLGPLQAPGRPVFLPYLGGERTPHNDAAIRGAFARIDHAADRDALA 360

Query: 361 RAVLEGVAFAFRDSFDALAATGTRLERLVAVGGGAKSDTWVRMIATLIGLPIDLPQAGDY 420
           RAVLEGVAFAFRDSFDALAATGTRLERLVAVGGGAKSDTWVRMIATLIGLPIDLPQAGDY
Sbjct: 361 RAVLEGVAFAFRDSFDALAATGTRLERLVAVGGGAKSDTWVRMIATLIGLPIDLPQAGDY 420

Query: 421 GGAFGAARLGMMAATGQGAALATRPPIARSLDPVPALADAFGEAHATYRATYTALKGLDR 480
           GGAFGAARLGMMAATGQGAALATRPPIARSLDPVPALADAFGEAHATYRATYTALKGLDR
Sbjct: 421 GGAFGAARLGMMAATGQGAALATRPPIARSLDPVPALADAFGEAHATYRATYTALKGLDR 480


Lambda     K      H
   0.320    0.135    0.418 

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: 997
Number of extensions: 38
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: 480
Length of database: 480
Length adjustment: 34
Effective length of query: 446
Effective length of database: 446
Effective search space:   198916
Effective search space used:   198916
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: 51 (24.3 bits)

Align candidate 3608604 Dshi_1997 (xylulokinase (RefSeq))
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.16217.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16217.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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