GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Pseudomonas fluorescens FW300-N2E3

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate AO353_05590 AO353_05590 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__pseudo3_N2E3:AO353_05590
          Length = 251

 Score =  234 bits (598), Expect = 1e-66
 Identities = 126/250 (50%), Positives = 163/250 (65%), Gaps = 2/250 (0%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR P+V GNWK++G+R  V EL++ LR  LA  +G  VA+ PP +YI+      EG+ I 
Sbjct: 1   MRRPMVAGNWKMHGTRASVAELINGLR-HLALPSGVEVAVFPPCLYINQVIDGLEGTSIS 59

Query: 61  LGAQNVDLN-LSGAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
           +GAQN  +  + GA TGE + + L D G   ++IGHSERR    E DE + +KFA  +  
Sbjct: 60  VGAQNSAVEAMQGALTGEIAPSQLVDSGCSLVLIGHSERRQIIGERDETLIRKFAAAQAC 119

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GL PVLCIGET  + EAGKT EV   Q+ +++   G   F  AVIAYEPVWAIGTG +A+
Sbjct: 120 GLIPVLCIGETLEQREAGKTLEVVGHQLGSIIDELGVGVFAKAVIAYEPVWAIGTGLTAS 179

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
           P QAQ VH  IR  +A  ++ +A+ V + YGGSV A+NA ELF  PDIDG L+GGASL A
Sbjct: 180 PQQAQDVHAAIRAQLAAENSEVAQGVRLLYGGSVKAANAVELFGMPDIDGGLIGGASLNA 239

Query: 240 DAFAVIVKAA 249
           D F  I +AA
Sbjct: 240 DEFGAICRAA 249


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: 176
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: 255
Length of database: 251
Length adjustment: 24
Effective length of query: 231
Effective length of database: 227
Effective search space:    52437
Effective search space used:    52437
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 AO353_05590 AO353_05590 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.19298.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19298.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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