GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Phaeobacter inhibens BS107

Align Triosephosphate isomerase; TIM; TPI; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate GFF2032 PGA1_c20650 triosephosphate isomerase TpiA

Query= SwissProt::Q8L1Z5
         (254 letters)



>FitnessBrowser__Phaeo:GFF2032
          Length = 250

 Score =  246 bits (629), Expect = 2e-70
 Identities = 131/243 (53%), Positives = 163/243 (67%), Gaps = 4/243 (1%)

Query: 6   RPFIAGNWKMNGTGESLGELRAIAAGISSDLGRLFEALICVPATLLSRAFDILGGENILL 65
           R   AGNWKMNGT  +L EL  +A    S      E LIC PATLL RA ++     + +
Sbjct: 3   RKLAAGNWKMNGTASALTELGNLAYSCKSAKA---EVLICPPATLLYRAANVCVDSKVSI 59

Query: 66  GGQNCHFDDYGPYTGDISAFMLKEAGASHVIIGHSERRTVYQESDAIVRAKVQAAWRAGL 125
           G Q+CH   YG +TGD+SA ML +AGA+ VI+GHSERR  + E+D  VRAK + A  AGL
Sbjct: 60  GAQDCHDATYGAHTGDLSAEMLHDAGATAVILGHSERRADHDETDETVRAKAKTAIAAGL 119

Query: 126 VALICVGETLEERKSNKVLDVLTRQLEGSLPDGATAENIIIAYEPVWAVGTGNTATSADV 185
            A+ICVGETL +R++ K LDV+  QL GSLPD A+   +++AYEPVWA+GTG   T   +
Sbjct: 120 TAIICVGETLNDREAGKTLDVVRAQLAGSLPDDASGTTVVVAYEPVWAIGTGKVPTVEQI 179

Query: 186 AEVHAFIHHKMHSRFGDEGAK-IRLLYGGSVKPSNAFELLSTAHVNGALIGGASLKAIDF 244
           AEVH  +   +  RFG E A  IRLLYGGSVK SNA E+ + AHV+GAL+GGASLKA DF
Sbjct: 180 AEVHNDMRASLVKRFGGETANAIRLLYGGSVKASNAKEIFAVAHVDGALVGGASLKAADF 239

Query: 245 LTI 247
             I
Sbjct: 240 API 242


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: 232
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: 254
Length of database: 250
Length adjustment: 24
Effective length of query: 230
Effective length of database: 226
Effective search space:    51980
Effective search space used:    51980
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 GFF2032 PGA1_c20650 (triosephosphate isomerase TpiA)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.29653.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29653.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.