GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pta in Dinoroseobacter shibae DFL-12

Align phosphate acetyltransferase (EC 2.3.1.8) (characterized)
to candidate 3608428 Dshi_1825 phosphate acetyltransferase (RefSeq)

Query= BRENDA::Q5LMK3
         (337 letters)



>FitnessBrowser__Dino:3608428
          Length = 341

 Score =  333 bits (855), Expect = 3e-96
 Identities = 183/327 (55%), Positives = 223/327 (68%), Gaps = 1/327 (0%)

Query: 6   PIDLLLSDPPARRATVALSEGSDPRVVAGALAAHSAGIADVILVGQAAEIRAAL-KAQGA 64
           P+ ++L++       +ALSEG DPRVVA A+ A    +A V+LVG  A I A L +A GA
Sbjct: 3   PLQMILANAARSDRKIALSEGEDPRVVAAAVQARKQRVARVVLVGDRATIVARLAEAGGA 62

Query: 65  PADSLTIHDPDSSPLTAEFAAAYYGLRRHKGVSEAAALAAVRTPLVYAAMLVRGDHAVGT 124
             D + +HDP      AE AA Y+ LR+HKGV+EA A AA+  P VYAA+LVR  HA GT
Sbjct: 63  ELDGIDVHDPREDLHRAEMAATYHQLRKHKGVTEADAEAAILNPHVYAALLVRLGHADGT 122

Query: 125 VGGAVATTSDVVRTAIQVIGAAPGAAMVSSFFLMYPPEAATAHARAMLYSDSGLVIDPSV 184
           +GGA ATT+++VRTAIQVIG APGA MVSSFFLM   +        ++++D+GLVIDP+ 
Sbjct: 123 LGGATATTAEIVRTAIQVIGTAPGAKMVSSFFLMLLCKDHHEKKGGLVFADAGLVIDPTA 182

Query: 185 AELAAIAAASAASCRALLRAEPKIAMLSFSTKGSARHPHVSKVTDALARLRADHPDLDAD 244
           AE+A I  ASAAS   L    P++AMLSFST+GSA    VSKV +A    R   P++  D
Sbjct: 183 AEMAEIGRASAASLVQLTGETPRVAMLSFSTRGSASGDKVSKVVEATEIFRQLAPEVTVD 242

Query: 245 GELQFDAAFVPSVGASKAPGSDVAGQANVMIFPNLDAGNIGYKITQRLGGYTAIGPVLQG 304
           GELQFDAAFVP V  +KAP S + G ANV +FPNLD GNI YKI QR+GG  AIGP+LQG
Sbjct: 243 GELQFDAAFVPEVATAKAPDSAIGGSANVFVFPNLDTGNIAYKIAQRIGGAVAIGPILQG 302

Query: 305 LAKPANDLSRGCVAGDVTQMIAVTVLQ 331
           LA PANDLSRGC A DV  MIA T  Q
Sbjct: 303 LALPANDLSRGCSAEDVLHMIATTAAQ 329


Lambda     K      H
   0.317    0.130    0.362 

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: 268
Number of extensions: 12
Number of successful extensions: 3
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: 337
Length of database: 341
Length adjustment: 28
Effective length of query: 309
Effective length of database: 313
Effective search space:    96717
Effective search space used:    96717
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: 49 (23.5 bits)

Align candidate 3608428 Dshi_1825 (phosphate acetyltransferase (RefSeq))
to HMM TIGR00651 (pta: phosphate acetyltransferase (EC 2.3.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.27732.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27732.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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