GapMind for catabolism of small carbon sources

 

Alignments for a candidate for fba in Shewanella amazonensis SB2B

Align fructose-bisphosphate aldolase (EC 4.1.2.13) (characterized)
to candidate 6938653 Sama_2756 fructose-1,6-bisphosphate aldolase (RefSeq)

Query= BRENDA::Q602L6
         (354 letters)



>FitnessBrowser__SB2B:6938653
          Length = 355

 Score =  504 bits (1297), Expect = e-147
 Identities = 249/351 (70%), Positives = 284/351 (80%)

Query: 1   MALISLRQLLDHAAEHGYGLPAFNVNNMEQIKAIMEAASAVDAPVILQGSAGARTYAGEP 60
           MALISLRQLLDHAAEHGYG+PAFNVNN+EQ++AIM+AA A D+PVI+Q SAGAR YA   
Sbjct: 1   MALISLRQLLDHAAEHGYGVPAFNVNNLEQMRAIMQAAEATDSPVIVQASAGARKYARPQ 60

Query: 61  FLRHLVRAAIEMYPHIPVCMHQDHGASPAVCIRSIQSGFSSVMMDGSLLEDMKTPASYAY 120
           FL++L+ AA+E YP IPVC+HQDHG  P VC RSIQ G SSVMMDGSL+ D KTPASY Y
Sbjct: 61  FLKYLMNAALEQYPDIPVCIHQDHGTHPDVCQRSIQLGMSSVMMDGSLMSDGKTPASYDY 120

Query: 121 NVETTRKVVEMAHACGVSVEGELGCLGSLETGRAGKEDGHGAEGELDHSLLLTDPDEAAD 180
           NV+ TRK V  AHACGVSVEGE+GCLGSLETG AG+EDG GA G L H  LLT  +EAA 
Sbjct: 121 NVDVTRKTVAFAHACGVSVEGEIGCLGSLETGTAGEEDGIGAVGVLSHDQLLTTAEEAAR 180

Query: 181 FVRQTQVDALAIAIGTSHGAYKFTRKPTGQVLRIDRVKAIHQRIPTIHLVMHGSSSVPEE 240
           FV  T VDALAIAIGTSHGAYKF+RKPTG VLRIDR+K IH RIP  HLVMHGSSSVP+ 
Sbjct: 181 FVADTHVDALAIAIGTSHGAYKFSRKPTGDVLRIDRIKEIHARIPNTHLVMHGSSSVPQY 240

Query: 241 WAQMINDYGGDIGQTYGVPVEEIVEGIRHGVRKVNIDTDLRIASYGAMRRFMVEDRKNFD 300
           W ++IN YGG+I +TYGVP+EEIVEGI+HGVRKVNIDTDLR+AS GA+R+F+ E+   FD
Sbjct: 241 WLEIINQYGGEIPETYGVPLEEIVEGIKHGVRKVNIDTDLRLASTGAVRKFLAENPSEFD 300

Query: 301 PRKLYKAAQTAMTAICRARYEAFGAAGQAAKIKPLRLEDMSLAYAQGKLDP 351
           PRK  KA+  AM  IC  RYEAFG AG A+KIKPL L+ M   Y  G+LDP
Sbjct: 301 PRKFLKASMEAMADICTERYEAFGCAGMASKIKPLSLQAMYKRYQTGELDP 351


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: 486
Number of extensions: 18
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: 355
Length adjustment: 29
Effective length of query: 325
Effective length of database: 326
Effective search space:   105950
Effective search space used:   105950
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 6938653 Sama_2756 (fructose-1,6-bisphosphate aldolase (RefSeq))
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.25873.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25873.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.