GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Dinoroseobacter shibae DFL-12

Align Putative branched-chain-amino-acid aminotransferase; BCAT; EC 2.6.1.42; Transaminase B (uncharacterized)
to candidate 3609919 Dshi_3301 branched-chain amino acid aminotransferase (RefSeq)

Query= curated2:O27481
         (306 letters)



>FitnessBrowser__Dino:3609919
          Length = 289

 Score =  214 bits (545), Expect = 2e-60
 Identities = 116/294 (39%), Positives = 175/294 (59%), Gaps = 14/294 (4%)

Query: 4   EASGKIWLNGEMVEWEEATVHVLSHVVHYGSSVFEGIRCYRNSKGSAIFRLREHVKRLFD 63
           +  G IW++G++V+W  A VH+L+H +HY SSVFEG R Y       IF  R H +RL  
Sbjct: 7   DRDGTIWMDGKLVDWRAANVHILTHAMHYASSVFEGERAYNGK----IFESRRHSERLHF 62

Query: 64  SAKIYRMDIPYTQEQICDAIVETVRENGLEECYIRPVVFRGYG-EMGVHPVNCPVDVAVA 122
           SA    ++IP+T ++I  A  E ++ NGL + Y+R V +RG G +MGV     PV +A+A
Sbjct: 63  SAGELDIEIPFTVDEIEAAKYEVMKVNGLSDAYVRAVAWRGAGPDMGVASARNPVHLAIA 122

Query: 123 AWEWGAYLGAEALEVGVDAGVSTWRRMAPNTMPNMAKAGGNYLNSQLAKMEAVRHGYDEA 182
            WEWG+Y G +A   G    ++ W+R +P T+P  AKA G Y+    +K  A   G  +A
Sbjct: 123 CWEWGSYYG-DAKTRGAKLDIAKWKRPSPETIPVHAKAAGLYMICTTSKHAAEAKGCSDA 181

Query: 183 IMLDYHGYISEGSGENIFLVSEGEIYTPPVSSSLLRGITRDSVIKIARTEGVTVHEEPIT 242
           + +DY GY++E +G NIF V +GE++TP      L GITR +VI + R + V VHE  I 
Sbjct: 182 LFMDYRGYVAEATGANIFFVKDGEVHTPD-PDCFLNGITRQTVIGMLRDKQVKVHERHIM 240

Query: 243 REMLYIADEAFFTGTAAEITPIRSVD--GIEIGAGRRGPVTKLLQDEFFRIIRA 294
            E L   ++ + TGTAAE+TP+  +     E+GA     +T+ + + + +++RA
Sbjct: 241 PEELEGFEQCWLTGTAAEVTPVGQIGTYNFEVGA-----LTRDIAESYEQLVRA 289


Lambda     K      H
   0.320    0.136    0.414 

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: 286
Number of extensions: 16
Number of successful extensions: 5
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: 306
Length of database: 289
Length adjustment: 26
Effective length of query: 280
Effective length of database: 263
Effective search space:    73640
Effective search space used:    73640
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: 48 (23.1 bits)

Align candidate 3609919 Dshi_3301 (branched-chain amino acid aminotransferase (RefSeq))
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.17994.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17994.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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