GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araB in Klebsiella michiganensis M5al

Align ribulokinase; EC 2.7.1.16 (characterized)
to candidate BWI76_RS04590 BWI76_RS04590 ribulokinase

Query= CharProtDB::CH_002149
         (566 letters)



>FitnessBrowser__Koxy:BWI76_RS04590
          Length = 569

 Score = 1024 bits (2648), Expect = 0.0
 Identities = 495/560 (88%), Positives = 523/560 (93%)

Query: 1   MAIAIGLDFGSDSVRALAVDCATGEEIATSVEWYPRWQKGQFCDAPNNQFRHHPRDYIES 60
           MAIAIGLDFGSDSVRALAV+CATGEE+A SVEWYPRWQ+G FCD PNNQFRHHPRDYIES
Sbjct: 1   MAIAIGLDFGSDSVRALAVECATGEELAASVEWYPRWQEGLFCDGPNNQFRHHPRDYIES 60

Query: 61  MEAALKTVLAELSVEQRAAVVGIGVDSTGSTPAPIDADGNVLALRPEFAENPNAMFVLWK 120
           MEAALK+VLA LS EQRAAVVGIGVDSTGSTPAPIDADGNVLALR EFA NPNAMFVLWK
Sbjct: 61  MEAALKSVLASLSAEQRAAVVGIGVDSTGSTPAPIDADGNVLALRDEFASNPNAMFVLWK 120

Query: 121 DHTAVEEAEEITRLCHAPGNVDYSRYIGGIYSSEWFWAKILHVTRQDSAVAQSAASWIEL 180
           DHT+VEEAEEITRLCH PG  DYSRYIGGIYSSEWFWAKILHVTRQDSAVA++AASWIEL
Sbjct: 121 DHTSVEEAEEITRLCHQPGKEDYSRYIGGIYSSEWFWAKILHVTRQDSAVAEAAASWIEL 180

Query: 181 CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPASFFDELDPILNRHLPSPLFT 240
           CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPA FFDELDPI+N++L  P+F+
Sbjct: 181 CDWVPALLSGTTRPQDIRRGRCSAGHKSLWHESWGGLPPAGFFDELDPIINQNLAYPMFS 240

Query: 241 DTWTADIPVGTLCPEWAQRLGLPESVVISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI 300
           +TWTAD+PVGTL  EWA RLGLP++V ISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI
Sbjct: 241 ETWTADVPVGTLTAEWAARLGLPQTVAISGGAFDCHMGAVGAGAQPNALVKVIGTSTCDI 300

Query: 301 LIADKQSVGERAVKGICGQVDGSVVPGFIGLEAGQSAFGDIYAWFGRVLGWPLEQLAAQH 360
           LIADKQSVGER VKGICGQVDGSVVP FIG+EAGQSAFGDIYAWFGR+LGWPLEQLA  H
Sbjct: 301 LIADKQSVGERTVKGICGQVDGSVVPDFIGMEAGQSAFGDIYAWFGRILGWPLEQLAQAH 360

Query: 361 PELKTQINASQKQLLPALTEAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA 420
           PELK QI ASQKQLLPALT+AWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA
Sbjct: 361 PELKEQIKASQKQLLPALTDAWAKNPSLDHLPVVLDWFNGRRTPNANQRLKGVITDLNLA 420

Query: 421 TDAPLLFGGLIAATAFGARAIMECFTDQGIAVNNVMALGGIARKNQVIMQACCDVLNRPL 480
           TDAP LFGGLIAATAFGARAIMECFTDQGI VNNVMALGGIARKN VIMQACCDVLNRPL
Sbjct: 421 TDAPALFGGLIAATAFGARAIMECFTDQGIPVNNVMALGGIARKNPVIMQACCDVLNRPL 480

Query: 481 QIVASDQCCALGAAIFAAVAAKVHADIPSAQQKMASAVEKTLQPCSEQAQRFEQLYRRYQ 540
           QIVASDQCCALGAAIFAAVAA V+ DIP+AQ+ MAS VE TLQP   QAQRFEQLY+RYQ
Sbjct: 481 QIVASDQCCALGAAIFAAVAAGVYRDIPAAQENMASQVESTLQPRPAQAQRFEQLYQRYQ 540

Query: 541 QWAMSAEQHYLPTSAPAQAA 560
           QW++SAEQ YLP++A A+ A
Sbjct: 541 QWSLSAEQRYLPSTAKAETA 560


Lambda     K      H
   0.320    0.133    0.419 

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: 1185
Number of extensions: 39
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: 566
Length of database: 569
Length adjustment: 36
Effective length of query: 530
Effective length of database: 533
Effective search space:   282490
Effective search space used:   282490
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: 53 (25.0 bits)

Align candidate BWI76_RS04590 BWI76_RS04590 (ribulokinase)
to HMM TIGR01234 (araB: ribulokinase (EC 2.7.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.25567.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25567.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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