GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Bacteroides thetaiotaomicron VPI-5482

Align Triosephosphate isomerase; TIM; Triose-phosphate isomerase; EC 5.3.1.1 (characterized)
to candidate 353455 BT3929 triosephosphate isomerase (NCBI ptt file)

Query= SwissProt::P29613
         (247 letters)



>FitnessBrowser__Btheta:353455
          Length = 252

 Score =  224 bits (572), Expect = 1e-63
 Identities = 122/248 (49%), Positives = 166/248 (66%), Gaps = 5/248 (2%)

Query: 3   RKFCVGGNWKMNGDQKSIAEIAKTLSSAALD--PNTEVVIGCPAIYLMYARNLLPC-ELG 59
           RK  V GNWKMN   +    +AK L+ A  +  PN +V+I  P I+L     L+   ++G
Sbjct: 2   RKNIVAGNWKMNKTLQEGIALAKELNEALANEKPNCDVIICTPFIHLASVTPLVDAAKIG 61

Query: 60  LAGQNAYKVAKGAFTGEISPAMLKDIGADWVILGHSERRAIFGESDALIAEKAEHALAEG 119
           +  +N    A GA+TGE+S  M+   GA +VILGHSERRA +GE+ A++ EK + ALA G
Sbjct: 62  VGAENCADKASGAYTGEVSAEMVASTGAKYVILGHSERRAYYGETVAILEEKVKLALANG 121

Query: 120 LKVIACIGETLEEREAGKTNEVVARQM-CAYAQKIKDWKNVVVAYEPVWAIGTGQTATPD 178
           L  I CIGE LEEREA K NEVVA QM   ++   +D+  +++AYEPVWAIGTG+TA+P+
Sbjct: 122 LTPIFCIGEVLEEREANKQNEVVAAQMESVFSLSAEDFSKIILAYEPVWAIGTGKTASPE 181

Query: 179 QAQEVHAFLRQWLSDNISKEVSASLRIQYGGSVTAANAKELAKKPDIDGFLVGGASLK-P 237
           QAQE+HAF+R  ++D   KE++ +  I YGGS   +NAKEL   PD+DG L+GGA+LK  
Sbjct: 182 QAQEIHAFIRSIVADKYGKEIADNTSILYGGSCKPSNAKELFSNPDVDGGLIGGAALKVS 241

Query: 238 EFVDIINA 245
           +F  II+A
Sbjct: 242 DFKGIIDA 249


Lambda     K      H
   0.316    0.132    0.388 

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: 196
Number of extensions: 9
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: 247
Length of database: 252
Length adjustment: 24
Effective length of query: 223
Effective length of database: 228
Effective search space:    50844
Effective search space used:    50844
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: 46 (22.3 bits)

Align candidate 353455 BT3929 (triosephosphate isomerase (NCBI ptt file))
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.6271.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6271.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.