GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aspA in Pseudomonas putida KT2440

Align aspartate ammonia-lyase (EC 4.3.1.1) (characterized)
to candidate PP_5338 PP_5338 aspartate ammonia-lyase

Query= BRENDA::Q9HTD7
         (474 letters)



>FitnessBrowser__Putida:PP_5338
          Length = 478

 Score =  831 bits (2147), Expect = 0.0
 Identities = 425/474 (89%), Positives = 444/474 (93%)

Query: 1   MSPVASSRIEKDLLGTLEVPADAYYGIQTLRAVNNFRLSGVPLSHYPKLVVALAMVKQAA 60
           MS  AS R+EKDLLGTLEVPADAYYGIQTLRA NNF LSGVPLSHYPKLVVALAMVKQAA
Sbjct: 5   MSSAASFRVEKDLLGTLEVPADAYYGIQTLRAANNFHLSGVPLSHYPKLVVALAMVKQAA 64

Query: 61  ADANRQLGHLPEDKHAAISEACARLIRGDFHEQFVVDMIQGGAGTSTNMNANEVIANIAL 120
           ADANR+LGHL + KHAAIS ACARLI+GDFH+QFVVDMIQGGAGTSTNMNANEVIAN+AL
Sbjct: 65  ADANRELGHLSDAKHAAISAACARLIKGDFHDQFVVDMIQGGAGTSTNMNANEVIANVAL 124

Query: 121 EAMGHTKGEYKYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDTLLASLDSLIQAFAAKGV 180
           EAMGH KGEY+YLHPNNDVNMAQSTNDAYPTAIRLGLLLGHD LLASLDSLIQAFAAKG 
Sbjct: 125 EAMGHQKGEYQYLHPNNDVNMAQSTNDAYPTAIRLGLLLGHDALLASLDSLIQAFAAKGK 184

Query: 181 EFAGVLKMGRTQLQDAVPMTLGQEFHAFATTLGEDLDRLRRLAPELLTEVNLGGTAIGTG 240
           EF  VLKMGRTQLQDAVPMTLGQEF AFATT+ EDL RLR LAPELLTE+NLGGTAIGTG
Sbjct: 185 EFDHVLKMGRTQLQDAVPMTLGQEFRAFATTMTEDLQRLRSLAPELLTEINLGGTAIGTG 244

Query: 241 INADPGYQKLAVERLAAISGQPLKPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 300
           INADPGYQ LAV+RLA ISG PL PAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL
Sbjct: 245 INADPGYQALAVQRLATISGHPLVPAADLIEATSDMGAFVLFSGMLKRTAVKLSKICNDL 304

Query: 301 RLLSSGPRTGINEINLPPRQPGSSIMPGKVNPVIPEAVNQVAFEVIGNDLALTLAAEGGQ 360
           RLLSSGPRTGINEINLP RQPGSSIMPGKVNPVIPEAVNQVAF ++GNDLALT+AAEGGQ
Sbjct: 305 RLLSSGPRTGINEINLPARQPGSSIMPGKVNPVIPEAVNQVAFAIMGNDLALTVAAEGGQ 364

Query: 361 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCITGITANVERCHELVEHSIGLVTALNPY 420
           LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCI GITAN +RC ELVEHSIGLVTALNPY
Sbjct: 365 LQLNVMEPLIAYKIFDSIRLLQRAMDMLREHCIVGITANEQRCRELVEHSIGLVTALNPY 424

Query: 421 IGYENSTRIAKTALESGRGVLELVREEKLLDEATLADILLPENMIAPRLIPLRA 474
           IGYEN+TRIA+ ALESGRGVLELVREEKLLD+A L DIL PENMIAPRL+PL+A
Sbjct: 425 IGYENATRIARVALESGRGVLELVREEKLLDDAMLDDILRPENMIAPRLVPLKA 478


Lambda     K      H
   0.318    0.135    0.380 

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: 810
Number of extensions: 21
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: 474
Length of database: 478
Length adjustment: 33
Effective length of query: 441
Effective length of database: 445
Effective search space:   196245
Effective search space used:   196245
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate PP_5338 PP_5338 (aspartate ammonia-lyase)
to HMM TIGR00839 (aspA: aspartate ammonia-lyase (EC 4.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.19180.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19180.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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