GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Klebsiella michiganensis M5al

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate BWI76_RS13135 BWI76_RS13135 3-oxoadipyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__Koxy:BWI76_RS13135
          Length = 401

 Score =  654 bits (1688), Expect = 0.0
 Identities = 333/401 (83%), Positives = 361/401 (90%)

Query: 1   MREAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           MR+AFICDGIRTPIGRYGGAL+S+RADDLAAIPLRELL RNP+ D   IDDVILGCANQA
Sbjct: 1   MRDAFICDGIRTPIGRYGGALASMRADDLAAIPLRELLSRNPKFDPASIDDVILGCANQA 60

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
           GEDNRNVA MATLLAG P +V GTT+NRLCGSGLDA+GFAARAIKAG+ DL+IAGGVESM
Sbjct: 61  GEDNRNVAHMATLLAGYPHTVPGTTVNRLCGSGLDAIGFAARAIKAGEADLMIAGGVESM 120

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISRED 180
           SRAPFVMGKA++A+ RQAE+FDTTIGWRFVNPLM Q+FGTDSMPETAENVAELL ISR D
Sbjct: 121 SRAPFVMGKASAAYQRQAELFDTTIGWRFVNPLMQQRFGTDSMPETAENVAELLNISRAD 180

Query: 181 QDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKA 240
           QD+FA RSQQR+A+AQ  GILA+EIVPV +   KG V+ +  DEH R ETTLEQL  LK 
Sbjct: 181 QDAFAYRSQQRSARAQRDGILAQEIVPVPIIGGKGAVSTVYEDEHPRAETTLEQLSRLKT 240

Query: 241 PFRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPV 300
           PFR  GV+TAGNASGVNDGAAALIIAS Q A AQGLTPRARIVAMATAGVEP+LMGLGPV
Sbjct: 241 PFRKGGVVTAGNASGVNDGAAALIIASSQQAIAQGLTPRARIVAMATAGVEPKLMGLGPV 300

Query: 301 PATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLG 360
           PA R+VLERAGLSI DMD+IELNEAFAAQALGVLR+LGL DDAPHVNPNGGAIALGHPLG
Sbjct: 301 PAVRKVLERAGLSIKDMDLIELNEAFAAQALGVLRQLGLADDAPHVNPNGGAIALGHPLG 360

Query: 361 MSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           MSGARLAL+AS EL RR+GRYALCTMCIGVGQGIAMILERV
Sbjct: 361 MSGARLALSASLELQRRSGRYALCTMCIGVGQGIAMILERV 401


Lambda     K      H
   0.319    0.135    0.384 

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: 599
Number of extensions: 8
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: 401
Length of database: 401
Length adjustment: 31
Effective length of query: 370
Effective length of database: 370
Effective search space:   136900
Effective search space used:   136900
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: 50 (23.9 bits)

Align candidate BWI76_RS13135 BWI76_RS13135 (3-oxoadipyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.30144.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30144.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.