GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylB in Dyella japonica UNC79MFTsu3.2

Align xylulokinase; EC 2.7.1.17 (characterized)
to candidate N515DRAFT_3230 N515DRAFT_3230 xylulokinase

Query= CharProtDB::CH_003784
         (484 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3230
          Length = 490

 Score =  561 bits (1445), Expect = e-164
 Identities = 290/491 (59%), Positives = 348/491 (70%), Gaps = 11/491 (2%)

Query: 1   MYIGIDLGTSGVKVILLNEQGEVVAAQTEKLTVSRPHPLWSEQDPEQWWQATDRAMKAL- 59
           M++G+DLGTS VK +L++  G V A  ++ LTVS P P WSEQDP  WW+A   A+  L 
Sbjct: 1   MFLGLDLGTSAVKAVLVDAAGAVRAVASQPLTVSHPRPRWSEQDPVDWWRAAVAAIDELL 60

Query: 60  ----GDQHSLQDVKALGIAGQMHGATLLDAQQRVLRPAILWNDGRCAQECTLLEARVPQS 115
                D      V A+G++GQMHGATLLD   RVLRPAILWNDGR   +C  +E  +P  
Sbjct: 61  QAAARDGIPASRVAAIGLSGQMHGATLLDRSDRVLRPAILWNDGRSDAQCRWMET-LPDF 119

Query: 116 RVITGNLMMPGFTAPKLLWVQRHEPEIFRQIDKVLLPKDYLRLRMTGEFASDMSDAAGTM 175
             ITGNL MPGFTAPKL WV+ HEP +F  + KVLLPKDYLRL +TG++ASD+SDAAGT+
Sbjct: 120 HAITGNLAMPGFTAPKLAWVREHEPSVFDAVAKVLLPKDYLRLCLTGDYASDVSDAAGTL 179

Query: 176 WLDVAKRDWSDVMLQACDLSRDQMPALYEGSEITGALLPEVAKAWGMATVPVVAGGGDNA 235
           WLDV KR WSD ML AC LSR+QMP ++EGSE  G L  E+A+ WGMA VPV AGGGDNA
Sbjct: 180 WLDVGKRQWSDPMLAACGLSREQMPGVHEGSESAGRLRAELAERWGMARVPVAAGGGDNA 239

Query: 236 AGAVGVGMVDANQAMLSLGTSGVYFAVSEGFLSKPESAVHSFCHALPQRWHLMSVMLSAA 295
           AGAVG G+V   QAMLSLGTSGVYFAVS+GFLS+PE AVHSFCHALP  WHLMSVML+AA
Sbjct: 240 AGAVGAGIVRHGQAMLSLGTSGVYFAVSDGFLSRPEQAVHSFCHALPGTWHLMSVMLNAA 299

Query: 296 SCLDWAAKLTGLSNVPALIAAAQQADESAEPVWFLPYLSGERTPHNNPQAKGVFFGLTHQ 355
           SCLD+ A+LTG ++V A++A AQ A    +   FLPYL+GERTPHN+  A G F GL   
Sbjct: 300 SCLDYTARLTGHADVGAMLAEAQAAPRRDDGPLFLPYLTGERTPHNDVHATGSFTGLQAD 359

Query: 356 HGPNELARAVLEGVGYALADGMDVVHACGIKPQSVTLIGGGARSEYWRQMLADISGQQLD 415
               +LA A LEGVG  L DG++ V A G++   V +IGGG RS YW QMLADI+G+ L+
Sbjct: 360 TTRADLANATLEGVGLGLLDGIEAVDAAGLRADRVAVIGGGTRSAYWLQMLADIAGRPLE 419

Query: 416 YRTGGDVGPALGAARLAQIAANPEKSLIELLPQLPLEQSHLPDAQRYAAY----QPR-RE 470
            R GGDVG ALGAARLA +AA P   + E+    PL   +LPDA R+A Y    QPR R+
Sbjct: 420 LRAGGDVGAALGAARLAHLAAEPGARIDEVCAMPPLVSEYLPDAARHAYYREHRQPRFRD 479

Query: 471 TFRRLYQQLLP 481
           T+RRL     P
Sbjct: 480 TYRRLRTATTP 490


Lambda     K      H
   0.319    0.134    0.409 

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: 677
Number of extensions: 26
Number of successful extensions: 3
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: 490
Length adjustment: 34
Effective length of query: 450
Effective length of database: 456
Effective search space:   205200
Effective search space used:   205200
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: 52 (24.6 bits)

Align candidate N515DRAFT_3230 N515DRAFT_3230 (xylulokinase)
to HMM TIGR01312 (xylB: xylulokinase (EC 2.7.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.20251.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20251.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.