GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Shewanella amazonensis SB2B

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate 6936772 Sama_0957 Triose-phosphate isomerase (RefSeq)

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__SB2B:6936772
          Length = 260

 Score =  243 bits (620), Expect = 3e-69
 Identities = 121/259 (46%), Positives = 170/259 (65%), Gaps = 8/259 (3%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAE----- 55
           +R P+V GNWK+NGS  +  EL      +L   +   V + PP +Y++  ++  E     
Sbjct: 3   LRRPMVAGNWKMNGSAALAQELFKKFAVKLQNDSA-EVVLCPPTIYLESVRQLLEANKEA 61

Query: 56  --GSHIMLGAQNVDLNLSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKF 113
             G  + +GAQN+  +  GA+TGE S  MLKD G +Y+I+GHSERR  + E+ +++A+KF
Sbjct: 62  LNGCLVRMGAQNLSQHDFGAYTGEISGQMLKDSGCRYVIVGHSERRRMYGETSDIVAEKF 121

Query: 114 AVLKEQGLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIG 173
           A  ++ GLTP+LC+GE+    EA +T EV A ++D V++  G  AF+ A+IAYEP+WA+G
Sbjct: 122 AAAQKHGLTPILCVGESGPAREARRTFEVIAEELDVVIEKNGTMAFDNAIIAYEPLWAVG 181

Query: 174 TGKSATPAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVG 233
           TGKSATP QAQ VH FIR  +++V   I E V I YGGSV  SNAA+LFAQPD+DG L+G
Sbjct: 182 TGKSATPEQAQEVHAFIRRRLSEVSPFIGENVRILYGGSVTPSNAADLFAQPDVDGGLIG 241

Query: 234 GASLKADAFAVIVKAAEAA 252
           GASL +  F  +   A +A
Sbjct: 242 GASLNSTEFLTLCSIAMSA 260


Lambda     K      H
   0.316    0.130    0.366 

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: 194
Number of extensions: 6
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: 255
Length of database: 260
Length adjustment: 24
Effective length of query: 231
Effective length of database: 236
Effective search space:    54516
Effective search space used:    54516
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 6936772 Sama_0957 (Triose-phosphate isomerase (RefSeq))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.22262.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22262.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.