GapMind for catabolism of small carbon sources

 

Alignments for a candidate for araB in Echinicola vietnamensis KMM 6221, DSM 17526

Align Ribulokinase (EC 2.7.1.16) (characterized)
to candidate Echvi_0515 Echvi_0515 L-ribulokinase

Query= reanno::Cola:Echvi_0515
         (562 letters)



>FitnessBrowser__Cola:Echvi_0515
          Length = 562

 Score = 1131 bits (2926), Expect = 0.0
 Identities = 562/562 (100%), Positives = 562/562 (100%)

Query: 1   MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL 60
           MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL
Sbjct: 1   MNDKFVIGLDYGSDSVRAVIVNTGNGEVKGSHVFWYPRWKAGKYCDPVNNQFRQHPLDHL 60

Query: 61  EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW 120
           EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW
Sbjct: 61  EGLEETIREVIKESGVPADQIKGICVDTTGSSPMAVDQQGKPLALSPEFAENPNAMMVLW 120

Query: 121 KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME 180
           KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME
Sbjct: 121 KDHTAIKEADEINELARTWGGEDYTKYEGGIYSSEWFWAKILHVIREDDAVAQAAYSWME 180

Query: 181 HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT 240
           HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT
Sbjct: 181 HCDVITAELIGADNPLDVKRSRCAAGHKALWHESWDGLPPKEFLSKLDPRLADLRDRLYT 240

Query: 241 ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI 300
           ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI
Sbjct: 241 ETFTSDLPAGNLSAEWAKKLGLSTDTVIAVGTFDAHAGAVGGEVTENTLVKVMGTSTCDI 300

Query: 301 MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS 360
           MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS
Sbjct: 301 MVATHEAIGDNLVKGICGQVDGSVIPGTVGLEAGQSGFGDVLAWFKHLVVKPTAALIRAS 360

Query: 361 NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM 420
           NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM
Sbjct: 361 NVLDEEKKEALIHEIDSQLLIKLSEEAIQIPLSETAPVALDWVNGRRTPDANQALKGAVM 420

Query: 421 GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV 480
           GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV
Sbjct: 421 GLNMGTDAARVFKALVESICFGSKKIVDRFREEGVAIDTVIGMGGVAKKSKLVMQTMADV 480

Query: 481 LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL 540
           LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL
Sbjct: 481 LNMPIKIATSDQAPALGAAMYASVAAGIHPTTEAAIAAMTNGFDKVYEPIPENVEVYKAL 540

Query: 541 YAKYAEFGAFVEGQTSPVLADQ 562
           YAKYAEFGAFVEGQTSPVLADQ
Sbjct: 541 YAKYAEFGAFVEGQTSPVLADQ 562


Lambda     K      H
   0.316    0.133    0.398 

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: 1233
Number of extensions: 26
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: 562
Length of database: 562
Length adjustment: 36
Effective length of query: 526
Effective length of database: 526
Effective search space:   276676
Effective search space used:   276676
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate Echvi_0515 Echvi_0515 (L-ribulokinase)
to HMM TIGR01234 (araB: ribulokinase (EC 2.7.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.17167.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17167.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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