GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Pseudomonas fluorescens FW300-N2E2

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate Pf6N2E2_805 Xylulose kinase (EC 2.7.1.17)

Query= reanno::pseudo6_N2E2:Pf6N2E2_805
         (495 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_805
          Length = 495

 Score =  991 bits (2563), Expect = 0.0
 Identities = 495/495 (100%), Positives = 495/495 (100%)

Query: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ
Sbjct: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120
           ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL
Sbjct: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG
Sbjct: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240
           DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA
Sbjct: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300
           VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL
Sbjct: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360
           PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS
Sbjct: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420
           LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA
Sbjct: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420

Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA 480
           DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA
Sbjct: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA 480

Query: 481 SQQAYERYRQHVATL 495
           SQQAYERYRQHVATL
Sbjct: 481 SQQAYERYRQHVATL 495


Lambda     K      H
   0.318    0.133    0.402 

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: 1070
Number of extensions: 32
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: 495
Length of database: 495
Length adjustment: 34
Effective length of query: 461
Effective length of database: 461
Effective search space:   212521
Effective search space used:   212521
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: 52 (24.6 bits)

Align candidate Pf6N2E2_805 (Xylulose kinase (EC 2.7.1.17))
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.3733.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3733.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.