GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pseudomonas putida KT2440

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PP_3280 PP_3280 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase

Query= metacyc::MONOMER-15952
         (401 letters)



>FitnessBrowser__Putida:PP_3280
          Length = 406

 Score =  703 bits (1815), Expect = 0.0
 Identities = 353/399 (88%), Positives = 377/399 (94%)

Query: 3   EALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQAGE 62
           +ALIIDAVRTPIGRYAGAL+SVRADDL AIPLKALI RHP+LDW A+DDVI+GCANQAGE
Sbjct: 8   DALIIDAVRTPIGRYAGALSSVRADDLAAIPLKALIQRHPELDWKAIDDVIFGCANQAGE 67

Query: 63  DNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESMSR 122
           DNRNVA MA+LLAGLP+ VPGTT+NRLCGSGLDA+G+AARALRCGEAGLMLAGGVESMSR
Sbjct: 68  DNRNVAHMASLLAGLPLEVPGTTINRLCGSGLDAIGNAARALRCGEAGLMLAGGVESMSR 127

Query: 123 APFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRADQD 182
           APFVMGKSEQAFGR+AE+FDTTIGWRFVN LM+  +GIDSMPETAENVA QF ISRADQD
Sbjct: 128 APFVMGKSEQAFGRAAELFDTTIGWRFVNPLMKAAYGIDSMPETAENVAEQFGISRADQD 187

Query: 183 AFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGTPF 242
           AFALRSQHKAAAA A GRLA+EIV VEI QRKGPAK+VEHDEHPRGDTTLEQLA+LGTPF
Sbjct: 188 AFALRSQHKAAAAQARGRLAREIVPVEIPQRKGPAKVVEHDEHPRGDTTLEQLARLGTPF 247

Query: 243 RQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPVPA 302
           R+GGSVTAGNASGVNDGACALLLASS AA+RHGLKAR R+VGMA AGVEPR+MGIGPVPA
Sbjct: 248 REGGSVTAGNASGVNDGACALLLASSAAARRHGLKARGRIVGMAVAGVEPRLMGIGPVPA 307

Query: 303 TRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLGMS 362
           TRKVL LTGLALAD+DVIELNEAFAAQGLAVLRELGLADDD RVN NGGAIALGHPLGMS
Sbjct: 308 TRKVLALTGLALADLDVIELNEAFAAQGLAVLRELGLADDDPRVNRNGGAIALGHPLGMS 367

Query: 363 GARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           GARLVTTALHELEE  GRYALCTMCIGVGQGIA+IIER+
Sbjct: 368 GARLVTTALHELEETAGRYALCTMCIGVGQGIAMIIERL 406


Lambda     K      H
   0.319    0.134    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: 665
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: 401
Length of database: 406
Length adjustment: 31
Effective length of query: 370
Effective length of database: 375
Effective search space:   138750
Effective search space used:   138750
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 PP_3280 PP_3280 (3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase)
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.14574.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14574.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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