GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvE in Azospirillum brasilense Sp245

Align Branched-chain amino acid aminotransferase (EC 2.6.1.42) (characterized)
to candidate AZOBR_RS16425 AZOBR_RS16425 branched-chain amino acid aminotransferase

Query= reanno::psRCH2:GFF445
         (307 letters)



>FitnessBrowser__azobra:AZOBR_RS16425
          Length = 290

 Score =  242 bits (618), Expect = 7e-69
 Identities = 130/290 (44%), Positives = 176/290 (60%), Gaps = 7/290 (2%)

Query: 5   DRDGVIWYDGELVQWRDATTHVLTHTLHYGMGVFEGVRAYNTPDGTAIFRLQAHTDRLFD 64
           DRDGVIWYDG LV WRDA  HVL+H LHY   VFEG R YN   GT +F+L  H++RL  
Sbjct: 8   DRDGVIWYDGALVPWRDANLHVLSHGLHYASCVFEGERVYN---GT-VFKLTEHSERLAA 63

Query: 65  SAHIMNMPMPYSKEEINEATRAAVRENNLESAYIRPMVFYGSEGMGLRASGLKVHVIVAA 124
           SA I+   +PYS  EI+ AT   V+      AY+RP+ + GSE MG+ A   ++HV +A 
Sbjct: 64  SARILGFELPYSVAEIDAATNETVKAMGFTDAYVRPVAWRGSEMMGVAAQASRIHVAIAV 123

Query: 125 WHWGAYMGDEALELGIKVRTSSFTRHHVNITMTRAKSNGAYINSMLALQEAISGGADEAL 184
           W W +Y   EA   GIK+  S + R   ++  T +K+ G Y+   L+  EA + G  +AL
Sbjct: 124 WQWPSYFSPEAKMAGIKLTWSRWRRPAPDMAPTASKAAGLYMICTLSKHEAEAEGYQDAL 183

Query: 185 MLDPEGYVAEGSGENIFIIKDGVIYTPEVTACLNGITRGTVLTLAAEHGLKIVEKRITRD 244
           MLD  GY+AE +G N+F++ DG I+TP+    L+GITR TV+ LA   G++++E+ I  D
Sbjct: 184 MLDYRGYLAEATGANLFLVMDGKIHTPKPDCFLDGITRRTVIDLAKARGIEVIERHIQPD 243

Query: 245 EVYIADEAFFTGTAAEVTPIREVDGRAIGIGRRGPITEKLQKAYFDLVTG 294
           E+    E F TGTAAEVTP+ ++       GR   + E L K Y  LV G
Sbjct: 244 ELANTQEVFLTGTAAEVTPVGQIGDHRFTPGR---VCETLVKDYDALVRG 290


Lambda     K      H
   0.319    0.135    0.400 

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: 266
Number of extensions: 6
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: 307
Length of database: 290
Length adjustment: 27
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 AZOBR_RS16425 AZOBR_RS16425 (branched-chain amino acid aminotransferase)
to HMM TIGR01122 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.11193.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11193.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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