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 3607827 Dshi_1235 xylulokinase (RefSeq)

Query= reanno::Smeli:SMc03164
         (484 letters)



>FitnessBrowser__Dino:3607827
          Length = 480

 Score =  351 bits (901), Expect = e-101
 Identities = 202/482 (41%), Positives = 261/482 (54%), Gaps = 10/482 (2%)

Query: 1   MYLGLDLGTSGVKAMLMDGEQRIIGSASGALDVDRPHPGWSEQDPADWIRAAEEAIARLR 60
           M+LGLD+GTS VK ++ DG  R++G+AS  L V  P PG SEQDP  W R      A L 
Sbjct: 1   MFLGLDIGTSAVKGLVWDGA-RVLGAASAPLKVQVPVPGASEQDPEAWWRGILAVCAEL- 58

Query: 61  ETHAQALAAVRGIGLSGQMHGATLLDEGDAVLRPCILWNDTRSFREAAALDGDPQFRALT 120
            +     A V  IGLSGQMHGA  L    AVLRP ILWND R+ REAA +   P   A  
Sbjct: 59  -SAQPGWAEVSAIGLSGQMHGAVCLGPDGAVLRPAILWNDNRAVREAAEMAALPGLAARV 117

Query: 121 GNIVFPGFTAPKLAWVRENEPEIFARVRWVLLPKDYLRLWLTGEHMSEMSDSAGTSWLDT 180
           G    PGF APKLAW+   EPE+ A    V+  KD++ + L G  ++E S++AGT WLD 
Sbjct: 118 GVPPMPGFPAPKLAWLARTEPELHAATTMVMQAKDWVGMRLHGRAVTEYSEAAGTLWLDQ 177

Query: 181 GKRKWSASLLAATHLEERQMPDLVEGTDAAGTLRPELAARWGMGPGVVVAGGAGDNAASA 240
             R W    LA + LE  QMP L  GTD AG L    AA  G+ PGV V  G GD    A
Sbjct: 178 AARDWDREALAFSGLERAQMPALGAGTDLAGPLSAAAAAALGLKPGVPVIRGGGDAMVGA 237

Query: 241 CGMGTVGEGQAFVSLGTSGVLFAANASYLPNPESAVHAFCHALPNTWHQMGVILSATDAL 300
            G+G V  GQA +SLGTSG    A+ ++ PNP   VH+F H +P  + QM  +L+    +
Sbjct: 238 AGIGVVAPGQAMISLGTSGQYLVASEAHRPNPAGLVHSFAHCVPGAYIQMAAMLNGAAPM 297

Query: 301 NWHSGVTGRSAAEL--TSELGESLKAPGSVTFLPYLSGERTPHNDATIRGVFAGLGHESS 358
            W +GV GRS  +L   +E  +    P    FLPYL+GERTPH D   R  F GL H S 
Sbjct: 298 AWLAGVLGRSVPDLLAAAETADPAHVP---LFLPYLTGERTPHGDPEARAGFEGLSHGSG 354

Query: 359 RAVLTQAVLEGVSFAIRDSLEALRAAGTKLKRVTAIGGGSRSRYWLSSIATALNLPVDLP 418
              + +AV++ ++++  D+   L  AG +     AIGGG+RS   L ++A  L +PV  P
Sbjct: 355 PGEMMRAVVDAIAYSFADAQAVLGEAGVRAASPLAIGGGARSDLVLQTLADVLEVPVQRP 414

Query: 419 ADGDFGAAFGAARLGLIAATGADPAAVCTAPETAETIAPEASLVPAYEDAYQRYRRLYPA 478
           A  D G A GAA+L  + +     A +   PE      P  S    +     RYR LY  
Sbjct: 415 ASADLGPALGAAKLAAVGSGAMPAARLADPPEIGAVFHPRPS--ARHGARLARYRALYSE 472

Query: 479 IK 480
           ++
Sbjct: 473 LR 474


Lambda     K      H
   0.317    0.132    0.401 

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: 657
Number of extensions: 34
Number of successful extensions: 4
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: 484
Length of database: 480
Length adjustment: 34
Effective length of query: 450
Effective length of database: 446
Effective search space:   200700
Effective search space used:   200700
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 3607827 Dshi_1235 (xylulokinase (RefSeq))
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.2310.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2310.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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