GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 in Pseudomonas fluorescens GW456-L13

Align β-ketoadipyl-CoA thiolase (EC 2.3.1.174; EC 2.3.1.223) (characterized)
to candidate PfGW456L13_2430 Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2430
          Length = 403

 Score =  694 bits (1790), Expect = 0.0
 Identities = 348/401 (86%), Positives = 375/401 (93%)

Query: 1   MNEALIIDAVRTPIGRYAGALASVRADDLGAIPLKALIARHPQLDWSAVDDVIYGCANQA 60
           MN+ALIIDAVRTPIGRYAG L+SVRADDLGA+PL+ L+ RHPQ+DW+ VDDVIYGCANQA
Sbjct: 1   MNDALIIDAVRTPIGRYAGVLSSVRADDLGAVPLRELLRRHPQVDWNTVDDVIYGCANQA 60

Query: 61  GEDNRNVARMAALLAGLPVSVPGTTLNRLCGSGLDAVGSAARALRCGEAGLMLAGGVESM 120
           GEDNRNVARM+ALLAGLPVSVPGTTLNRLCGSGLDA+G+AARA+R GE GLML GGVESM
Sbjct: 61  GEDNRNVARMSALLAGLPVSVPGTTLNRLCGSGLDAIGTAARAIRSGETGLMLVGGVESM 120

Query: 121 SRAPFVMGKSEQAFGRSAEIFDTTIGWRFVNKLMQQGFGIDSMPETAENVAAQFNISRAD 180
           SRAP VMGK+EQAF R+AE+FDTTIGWRFVN LM++ +GIDSMPETAENVA QFNISRAD
Sbjct: 121 SRAPLVMGKAEQAFSRTAEVFDTTIGWRFVNPLMKKTYGIDSMPETAENVAEQFNISRAD 180

Query: 181 QDAFALRSQHKAAAAIANGRLAKEIVAVEIAQRKGPAKIVEHDEHPRGDTTLEQLAKLGT 240
           QDAFALRSQ +AAAA A+GRLAKEIVAVEI QRKGPAK+VEHDEHPRGDTTLEQLAKLGT
Sbjct: 181 QDAFALRSQQRAAAAQASGRLAKEIVAVEIPQRKGPAKVVEHDEHPRGDTTLEQLAKLGT 240

Query: 241 PFRQGGSVTAGNASGVNDGACALLLASSEAAQRHGLKARARVVGMATAGVEPRIMGIGPV 300
           PFR+GGS+TAGNASGVNDGACALLLAS E A+R GL AR RVV MATAGVEPRIMGIGPV
Sbjct: 241 PFREGGSITAGNASGVNDGACALLLASPEVAKRQGLTARGRVVAMATAGVEPRIMGIGPV 300

Query: 301 PATRKVLELTGLALADMDVIELNEAFAAQGLAVLRELGLADDDERVNPNGGAIALGHPLG 360
           PATRKVLE+  L+LADMDVIELNEAFAAQGLAVLRELGL+D D RVNPNGGAIALGHPLG
Sbjct: 301 PATRKVLEVANLSLADMDVIELNEAFAAQGLAVLRELGLSDTDPRVNPNGGAIALGHPLG 360

Query: 361 MSGARLVTTALHELEERQGRYALCTMCIGVGQGIALIIERI 401
           MSGARLVTTALHELEER GRYALCTMCIGVGQGIALIIER+
Sbjct: 361 MSGARLVTTALHELEERNGRYALCTMCIGVGQGIALIIERL 401


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: 639
Number of extensions: 16
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: 403
Length adjustment: 31
Effective length of query: 370
Effective length of database: 372
Effective search space:   137640
Effective search space used:   137640
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 PfGW456L13_2430 (Acetyl-CoA acetyltransferase (EC 2.3.1.9) @ Beta-ketoadipyl CoA thiolase (EC 2.3.1.-))
to HMM TIGR02430 (pcaF: 3-oxoadipyl-CoA thiolase (EC 2.3.1.174))

Software error:

../bin/blast/fastacmd -i /tmp/list.4531.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4531.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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