GapMind for catabolism of small carbon sources

 

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

Align Phenylacetate-coenzyme A ligase; Phenylacetyl-CoA ligase; PA-CoA ligase; EC 6.2.1.30 (characterized)
to candidate PfGW456L13_2428 Phenylacetate-coenzyme A ligase (EC 6.2.1.30) PaaF

Query= SwissProt::O33469
         (439 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2428
          Length = 441

 Score =  752 bits (1941), Expect = 0.0
 Identities = 364/426 (85%), Positives = 394/426 (92%)

Query: 11  LLDPMETASVDALRQHQLERLRWSLKHAYDNVPLYRQRFAECGAHPDDLTCLEDLAKFPF 70
           +LDP+ETAS+D LRQHQLERLRWSL HAY+NVPLYRQRF   G HPDD+  L+DLAKFPF
Sbjct: 13  VLDPLETASIDELRQHQLERLRWSLNHAYNNVPLYRQRFDALGVHPDDIKSLDDLAKFPF 72

Query: 71  TGKNDLRDNYPYGMFAVPQEEVVRLHASSGTTGKPTVVGYTQNDINTWANVVARSIRAAG 130
           T K+DLRDNYPYGMFAVP  ++VRLHASSGTTGKPTVVGYTQNDI+TWANVVARSIRAAG
Sbjct: 73  TTKSDLRDNYPYGMFAVPMHDIVRLHASSGTTGKPTVVGYTQNDIDTWANVVARSIRAAG 132

Query: 131 GRKGDKVHVSYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIRDFQPDIIMVTP 190
           G +GDKVH+SYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLI+DFQPDIIMVTP
Sbjct: 133 GHRGDKVHISYGYGLFTGGLGAHYGAERLGCTVIPMSGGQTEKQVQLIKDFQPDIIMVTP 192

Query: 191 SYMLNLADEIERQGIDPHDLKLRLGIFGAEPWTDELRRSIEQRLGINALDIYGLSEIMGP 250
           SYMLN+ADEIERQGIDPH L LRLGIFGAEPWT ELR +IE R+GI ALDIYGLSEIMGP
Sbjct: 193 SYMLNIADEIERQGIDPHKLALRLGIFGAEPWTAELRSAIEARMGITALDIYGLSEIMGP 252

Query: 251 GVAMECIETKDGPTIWEDHFYPEIIDPVTGEVLPDGQLGELVFTSLSKEALPMVRYRTRD 310
           GVAMEC ETKDGPTIWEDHFYPEIIDPVTGEVLPDGQ+GELVFTSLSKEALPM+RYRTRD
Sbjct: 253 GVAMECAETKDGPTIWEDHFYPEIIDPVTGEVLPDGQMGELVFTSLSKEALPMIRYRTRD 312

Query: 311 LTRLLPGTARPMRRIGKITGRSDDMLIIRGVNVFPTQIEEQVLKIKQLSEMYEIHLYRNG 370
           LTRLLPGTARPMRRI KITGRSDDMLIIRGVNVFPTQIEEQVLK+KQL+E YEIHLYRNG
Sbjct: 313 LTRLLPGTARPMRRIDKITGRSDDMLIIRGVNVFPTQIEEQVLKVKQLAECYEIHLYRNG 372

Query: 371 NLDSVEVHVELRAECQHLDEGQRKLVIGELSKQIKTYIGISTQVHLQACGTLKRSEGKAC 430
           NLDSV+VHVEL+AE QHL + Q+K V GELS+ IKTYIGIS+++ LQ   ++KRSEGKAC
Sbjct: 373 NLDSVDVHVELKAEHQHLGDEQQKAVCGELSRHIKTYIGISSRIVLQPFHSIKRSEGKAC 432

Query: 431 HVYDKR 436
           HV DKR
Sbjct: 433 HVVDKR 438


Lambda     K      H
   0.320    0.138    0.415 

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: 788
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: 439
Length of database: 441
Length adjustment: 32
Effective length of query: 407
Effective length of database: 409
Effective search space:   166463
Effective search space used:   166463
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: 51 (24.3 bits)

Align candidate PfGW456L13_2428 (Phenylacetate-coenzyme A ligase (EC 6.2.1.30) PaaF)
to HMM TIGR02155 (paaF: phenylacetate-CoA ligase (EC 6.2.1.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.22011.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22011.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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