GapMind for catabolism of small carbon sources

 

Alignments for a candidate for PRO3 in Shewanella amazonensis SB2B

Align Pyrroline-5-carboxylate reductase; P5C reductase; P5CR; PCA reductase; EC 1.5.1.2 (characterized)
to candidate 6938359 Sama_2478 pyrroline-5-carboxylate reductase (RefSeq)

Query= SwissProt::P22008
         (273 letters)



>FitnessBrowser__SB2B:6938359
          Length = 271

 Score =  200 bits (508), Expect = 3e-56
 Identities = 112/269 (41%), Positives = 166/269 (61%), Gaps = 2/269 (0%)

Query: 1   MSTPRIAFIGAGNMAASLIGGLRAQGVPAAQIRASDPGAEQRAKIAGEFAIDVVESNAEA 60
           M   +I FIGAGNM+ ++IGGL   G  A+ I A++P   +   +A ++ I+  + N  +
Sbjct: 1   MQNKKICFIGAGNMSRAIIGGLIKSGYSASLITATNPSLPKLDALAADYGINTSQDNVPS 60

Query: 61  VADADVVVLSVKPQAMKAVCQALAPALKPEQLIVSIAAGIPCASLEAWLGQPRPVVRCMP 120
            + ADV+VLSVKPQ M+AVC++LA  +  ++L+++IAAGIP      + G+   ++R MP
Sbjct: 61  ASAADVIVLSVKPQLMQAVCESLAGVVD-DKLLITIAAGIPENRYHDYFGKQVKLIRTMP 119

Query: 121 NTPALLRQGASGLYANAQVSAAQCEQAGQLLSAVGIALWLDDEAQIDAVTAVSGSGPAYF 180
           NTP  L  G +GLYA A +       A  L+ A G  +W+++E+ ID V A++GS PAYF
Sbjct: 120 NTPMQLGLGMTGLYAPAGMPDEDKAFAESLMRACGDIVWVNEESGIDKVIALAGSSPAYF 179

Query: 181 FLLMQAMTDAGEKLGLSRETASRLTLQTALGAAQMALSSE-VEPAELRRRVTSPNGTTEA 239
           FL ++AM +AG ++GL    A  L  Q A+GAA M   +  + PAELR  VTS  GTT  
Sbjct: 180 FLFIEAMIEAGVEMGLPEADARTLAQQAAVGAAAMVKQNPGLTPAELRANVTSKGGTTAE 239

Query: 240 AIKSFQANGFEALVEQALNAASQRSAELA 268
           AI +F+A G   LV+ A+    +R+ E+A
Sbjct: 240 AIATFEAGGLRTLVKDAMGNCIKRAEEMA 268


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: 188
Number of extensions: 7
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: 273
Length of database: 271
Length adjustment: 25
Effective length of query: 248
Effective length of database: 246
Effective search space:    61008
Effective search space used:    61008
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 6938359 Sama_2478 (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.29684.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29684.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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