GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tpi in Dyella japonica UNC79MFTsu3.2

Align triose-phosphate isomerase (EC 5.3.1.1) (characterized)
to candidate N515DRAFT_1376 N515DRAFT_1376 triosephosphate isomerase

Query= BRENDA::P0A858
         (255 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1376
          Length = 249

 Score =  253 bits (646), Expect = 3e-72
 Identities = 136/250 (54%), Positives = 170/250 (68%), Gaps = 3/250 (1%)

Query: 1   MRHPLVMGNWKLNGSRHMVHELVSNLRKELAGVAGCAVAIAPPEMYIDMAKREAEGSHIM 60
           MR  LV GNWK++GSR M   L S++   +   A     + PP  YI     +  GS + 
Sbjct: 1   MRKKLVAGNWKMHGSRSMAAALASDIAAGMP--ASVDAVVFPPFPYIAELAAQHAGSGLG 58

Query: 61  LGAQNVDLNLS-GAFTGETSAAMLKDIGAQYIIIGHSERRTYHKESDELIAKKFAVLKEQ 119
            G Q+V  +   GA+TGE SA+ML+D+GAQ+ ++GHSERR YH ESDEL+A+KFA  +  
Sbjct: 59  FGGQDVSEHEGQGAYTGEVSASMLQDVGAQWTLVGHSERRQYHHESDELVARKFAAARAG 118

Query: 120 GLTPVLCIGETEAENEAGKTEEVCARQIDAVLKTQGAAAFEGAVIAYEPVWAIGTGKSAT 179
           GLTPVLC+GET A+ EAG+TE V ARQ+ AVL   G A+F+ AVIAYEPVWAIGTG++AT
Sbjct: 119 GLTPVLCVGETLAQREAGETEAVIARQLLAVLALNGVASFDTAVIAYEPVWAIGTGRTAT 178

Query: 180 PAQAQAVHKFIRDHIAKVDANIAEQVIIQYGGSVNASNAAELFAQPDIDGALVGGASLKA 239
           P QAQ VH FIR  +A+ DA IA    + YGGSV  +NAAELFAQ D+DG LVGGA L +
Sbjct: 179 PEQAQQVHGFIRSQLAREDAMIARLTRLLYGGSVKPANAAELFAQADVDGGLVGGACLTS 238

Query: 240 DAFAVIVKAA 249
             F  I  AA
Sbjct: 239 ADFLAICAAA 248


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: 196
Number of extensions: 5
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: 249
Length adjustment: 24
Effective length of query: 231
Effective length of database: 225
Effective search space:    51975
Effective search space used:    51975
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 N515DRAFT_1376 N515DRAFT_1376 (triosephosphate isomerase)
to HMM TIGR00419 (tpiA: triose-phosphate isomerase (EC 5.3.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.18393.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18393.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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