GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Pseudomonas putida KT2440

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate PP_4960 PP_4960 Fructose-bisphosphate aldolase

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__Putida:PP_4960
          Length = 354

 Score =  523 bits (1346), Expect = e-153
 Identities = 257/349 (73%), Positives = 290/349 (83%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALIS+RQ+LDHAAE GYG+PAFNVNN+EQ++AIMEAA   D+PVI+Q SAGAR YAG P
Sbjct: 1   MALISMRQMLDHAAEFGYGVPAFNVNNLEQMRAIMEAADKTDSPVIVQASAGARKYAGAP 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FLRHL+ AAIE +PHIPVCMHQDHG SP VC RSIQ GFSSVMMDGSL ED KTP  Y Y
Sbjct: 61  FLRHLILAAIEEFPHIPVCMHQDHGTSPDVCQRSIQLGFSSVMMDGSLGEDGKTPTDYEY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV  T++ V MAHACGVSVEGELGCLGSLETG AG+EDG GAEG LDHS +LTDP+EAAD
Sbjct: 121 NVRVTQQTVAMAHACGVSVEGELGCLGSLETGMAGEEDGIGAEGVLDHSQMLTDPEEAAD 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV++TQVDALAIAIGTSHGAYKFT+ PTG VL IDR+K IH+RIP  HLVMHGSSSVP+E
Sbjct: 181 FVKKTQVDALAIAIGTSHGAYKFTKPPTGDVLAIDRIKEIHKRIPNTHLVMHGSSSVPQE 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W  +IN YGGDI +TYGVPVEEIVEGI+HGVRKVNIDTDLR+AS GAMRR M ++   FD
Sbjct: 241 WLAIINQYGGDIKETYGVPVEEIVEGIKHGVRKVNIDTDLRLASTGAMRRLMAQNPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKL 349
           PRK +     AM  +C ARYEAFG AG A+KIKP+ LE M   Y +G+L
Sbjct: 301 PRKFFGETIKAMRDVCIARYEAFGTAGNASKIKPISLEGMYQRYLKGEL 349


Lambda     K      H
   0.320    0.134    0.391 

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: 494
Number of extensions: 17
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: 354
Length of database: 354
Length adjustment: 29
Effective length of query: 325
Effective length of database: 325
Effective search space:   105625
Effective search space used:   105625
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: 49 (23.5 bits)

Align candidate PP_4960 PP_4960 (Fructose-bisphosphate aldolase)
to HMM TIGR01521 (fba: fructose-bisphosphate aldolase, class II, Calvin cycle subtype (EC 4.1.2.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.10551.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10551.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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