GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Shewanella sp. ANA-3

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate 7023985 Shewana3_1193 pyrroline-5-carboxylate reductase (RefSeq)

Query= SwissProt::P22008
         (273 letters)



>FitnessBrowser__ANA3:7023985
          Length = 272

 Score =  210 bits (534), Expect = 3e-59
 Identities = 117/269 (43%), Positives = 167/269 (62%), Gaps = 1/269 (0%)

Query: 1   MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60
           MS  +I FIGAGNM  S+I GL   G PAA ++A++P   +   +A +F + V + N  A
Sbjct: 1   MSQQKICFIGAGNMTRSIISGLIRSGYPAALVQATNPSQGKLDALAADFGVRVSQDNFSA 60

Query: 61  VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120
             DADV+VLSVKPQ M+ VCQAL       +L+++IAAGI       +L Q   +VR MP
Sbjct: 61  AQDADVIVLSVKPQLMEQVCQALQGIDMSNKLVITIAAGIKAERYSQYLAQSITLVRTMP 120

Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180
           NTP  +  G +GLYA   +S AQ   A +L+S+ G  +W+++E++I+ V A++GS PAYF
Sbjct: 121 NTPMQIGVGMTGLYAPQPLSDAQQAIAERLMSSGGEIVWVNEESEINQVIALAGSSPAYF 180

Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSS-EVEPAELRRRVTSPNGTTEA 239
           FLLM++M DAG+++G+    A  L  Q ALGAA MA  + E+    LR  VTS  GTT  
Sbjct: 181 FLLMESMIDAGKQMGMDEAKARSLVQQAALGAAMMAKQNPELTLGNLRENVTSKGGTTAQ 240

Query: 240 AIKSFQANGFEALVEQALNAASQRSAELA 268
           AI +F+A     +V+ A+    +R+ E+A
Sbjct: 241 AIATFEAADLRGVVKNAMENCIKRAEEMA 269


Lambda     K      H
   0.315    0.127    0.348 

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: 160
Number of extensions: 8
Number of successful extensions: 2
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: 273
Length of database: 272
Length adjustment: 25
Effective length of query: 248
Effective length of database: 247
Effective search space:    61256
Effective search space used:    61256
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 (21.6 bits)
S2: 47 (22.7 bits)

Align candidate 7023985 Shewana3_1193 (pyrroline-5-carboxylate reductase (RefSeq))
to HMM TIGR00112 (proC: pyrroline-5-carboxylate reductase (EC 1.5.1.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.16792.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16792.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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