GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Pseudomonas simiae WCS417

Align Xylulose kinase (EC 2.7.1.17) (characterized)
to candidate GFF2488 PS417_12690 xylulose kinase

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



>FitnessBrowser__WCS417:GFF2488
          Length = 493

 Score =  813 bits (2099), Expect = 0.0
 Identities = 402/495 (81%), Positives = 440/495 (88%), Gaps = 2/495 (0%)

Query: 1   MANQQLFLGIDCGTQGTKALILDATSGQVLGLGAAAHSMISGANGRREQDTQQWLDAFTQ 60
           M  Q LFLGIDCGTQGTKA++LDA+SG+VLGLGAAAH++ISGANGRREQ TQ+WLDAFT+
Sbjct: 1   MTQQNLFLGIDCGTQGTKAIVLDASSGKVLGLGAAAHTLISGANGRREQHTQEWLDAFTE 60

Query: 61  ATHQALAAAGVDGQAILGIGVSGQQHGLVLLDDQGQVLRPAKLWCDTETTPENDRLLAHL 120
           ATH+AL  AGVDGQ ILGIGVSGQQHGLVLLDDQG+VLRPAKLWCDTET PEN+RLL HL
Sbjct: 61  ATHRALQQAGVDGQDILGIGVSGQQHGLVLLDDQGRVLRPAKLWCDTETAPENERLLQHL 120

Query: 121 GGEDGSLERLGVVIAPGYTVSKLLWTREQHPQVFERIASVLLPHDFLNYWLTGRHCSEYG 180
           GGE GSLERLGV IAPGYTVSKLLWTREQHP +F RI  +LLPHD+LNYWLTGR  +EYG
Sbjct: 121 GGESGSLERLGVAIAPGYTVSKLLWTREQHPDIFARITHILLPHDYLNYWLTGRAVAEYG 180

Query: 181 DASGTGYFNVRTRQWDVQLLQHIDPSARLQAALPELIEAHQPVGRILPAIAAHLGINPEA 240
           DASGTGYFNVRTR+WDV LL+HIDPS RL+ ALP+LIEA Q VG ILPAIA  LGINP A
Sbjct: 181 DASGTGYFNVRTREWDVALLKHIDPSGRLENALPQLIEADQSVGTILPAIAERLGINPNA 240

Query: 241 VVASGGGDNMMGAIGTGNIQPGVITMSLGSSGTVYAYAAEPAVSPQPSVATFCSSSGGWL 300
           +V+SGGGDNMMGAIGTGNI PGVITMSLGSSGTVYA+A +P+VSPQ SVATFCSSSGGWL
Sbjct: 241 IVSSGGGDNMMGAIGTGNIAPGVITMSLGSSGTVYAFADQPSVSPQASVATFCSSSGGWL 300

Query: 301 PLICTMNLTNATGAIRELLDLDIDAFNALVAKAPIGAEGVCMLPFLNGERVPALPHATGS 360
           PLICTMNLTNATG IREL DLD+ AFNALV +APIGA+GV MLPFLNGERVPALPHATGS
Sbjct: 301 PLICTMNLTNATGVIRELFDLDLTAFNALVEQAPIGADGVSMLPFLNGERVPALPHATGS 360

Query: 361 LLGLTTTNLTRANLCRAVVEGTTFGLRYGLDLLRANGLQAQSIRLIGGGSKSAQWRQIVA 420
           L GLT TNLTRANLCRAVVEGTTFGLRYGLDLLR  GLQ+QSIRLIGGGSKS  WRQ+VA
Sbjct: 361 LHGLTMTNLTRANLCRAVVEGTTFGLRYGLDLLRQTGLQSQSIRLIGGGSKSPIWRQMVA 420

Query: 421 DTMDTTVICTEQSEAAALGAAIQAAWCHSGSQTGLAELCERCVKLDPSSETRPIAAHVAA 480
           D M+T V+CTEQSEAAALGAAIQAAW  SG    LA LC++CV +DP+S T P+AA V+A
Sbjct: 421 DIMNTEVVCTEQSEAAALGAAIQAAWSQSGE--SLASLCDKCVSVDPASRTLPVAASVSA 478

Query: 481 SQQAYERYRQHVATL 495
            QQAYERY+Q VATL
Sbjct: 479 YQQAYERYQQLVATL 493


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: 901
Number of extensions: 34
Number of successful extensions: 2
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: 493
Length adjustment: 34
Effective length of query: 461
Effective length of database: 459
Effective search space:   211599
Effective search space used:   211599
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 GFF2488 PS417_12690 (xylulose kinase)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.23169.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23169.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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