GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Magnetospirillum magneticum AMB-1

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate WP_011384224.1 AMB_RS09205 triose-phosphate isomerase

Query= SwissProt::Q8L1Z5
         (254 letters)



>NCBI__GCF_000009985.1:WP_011384224.1
          Length = 251

 Score =  227 bits (578), Expect = 2e-64
 Identities = 119/248 (47%), Positives = 159/248 (64%), Gaps = 7/248 (2%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLF---EALICVPATLLSRAFDILGGEN 62
           R  IAGNWKMNG      +  A+A G++  L       + L+C P TL++   D L G  
Sbjct: 5   RKLIAGNWKMNGLK---ADGLALAKGLADKLASASPNCDMLVCPPFTLIAPVADALAGSK 61

Query: 63  ILLGGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWR 122
           + +GGQ+CH    G +TGD S  ML + G  + I+GHSERRT + E+D +V+AK  AA  
Sbjct: 62  LAVGGQDCHAKTSGAHTGDTSPAMLADLGCKYAIVGHSERRTDHAETDNVVKAKAAAALS 121

Query: 123 AGLVALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATS 182
           AGLVA++C+GETL +R + + ++V   QL GSLP+GA A N +IAYEPVWA+GTG  AT 
Sbjct: 122 AGLVAIVCIGETLAQRDAGQTIEVNRSQLNGSLPEGANAANTVIAYEPVWAIGTGRVATP 181

Query: 183 ADVAEVHAFIHHKMHSRFG-DEGAKIRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKA 241
           A   EVHA I  ++    G +E  K+R+LYGGS+KP NA ELL+   V+G LIGGA+LK 
Sbjct: 182 AQAQEVHAAIRAELARLVGAEEAGKMRILYGGSMKPDNAKELLALPDVDGGLIGGAALKV 241

Query: 242 IDFLTICD 249
            DF  I +
Sbjct: 242 ADFWAIAE 249


Lambda     K      H
   0.320    0.137    0.403 

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: 224
Number of extensions: 11
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: 254
Length of database: 251
Length adjustment: 24
Effective length of query: 230
Effective length of database: 227
Effective search space:    52210
Effective search space used:    52210
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: 46 (22.3 bits)

Align candidate WP_011384224.1 AMB_RS09205 (triose-phosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.10575.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10575.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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