GapMind for Amino acid biosynthesis

 

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

Align branched-chain-amino-acid transaminase (EC 2.6.1.42) (characterized)
to candidate 353418 BT3892 branched-chain amino acid aminotransferase (NCBI ptt file)

Query= BRENDA::Q7BPX6
         (340 letters)



>FitnessBrowser__Btheta:353418
          Length = 339

 Score =  333 bits (855), Expect = 3e-96
 Identities = 173/338 (51%), Positives = 228/338 (67%), Gaps = 4/338 (1%)

Query: 5   LDWENLGFSYRNLPFRYIARFKDGKWSAGELTGDNQLHISESSPALHYGQQGFEGLKAYR 64
           +DW NL F Y    +     F++G W   E++ D  L++  ++  LHYGQ+ FEGLKA+R
Sbjct: 4   IDWANLSFGYMKTDYNVRINFRNGAWGELEVSSDEHLNLHMAATCLHYGQEAFEGLKAFR 63

Query: 65  TKDGSIQLFRPDQNAARLQKTARRLCMAEVSTEMFIDAVKQVVKANKDFVPPYGTGATLY 124
            KDG +++FR ++NAARLQ T + + MAE+ TE F +A+ +VVK N+ F+PPY TGA+LY
Sbjct: 64  GKDGKVRIFRLEENAARLQSTCQGILMAELPTERFKEAILKVVKLNERFIPPYETGASLY 123

Query: 125 LRPLLIGVGDVIGVKPADEYIFKVFAMPVGSYFKGGLAPSKFVISREYDRAAPLGTGGAK 184
           +RPLLIG    +GV PA+EY+F VF  PVG YFKGG + + +VI RE+DRAAP GTG  K
Sbjct: 124 IRPLLIGTSAQVGVHPAEEYMFVVFVTPVGPYFKGGFSTNPYVIIREFDRAAPHGTGIYK 183

Query: 185 VGGNYAASLQAEVGAKASGYADAIYLDPSTHTKIEEVGAANFFGITADNEFITPLSPSIL 244
           VGGNYAASL+A   A   GY+   YLD      I+E GAANFFGI  DN +ITP S SIL
Sbjct: 184 VGGNYAASLRANKKAHDLGYSCEFYLDAKEKKYIDECGAANFFGI-KDNTYITPKSSSIL 242

Query: 245 PSITKYSLLYLAEHRLGLKAIEGEVYAKDLGKFVEAGACGTAAIISPIGRIDDGED--SY 302
           PSIT  SL+ LAE  +G+K     +  ++L  F EAGACGTAA+ISPI RIDD E+  SY
Sbjct: 243 PSITNKSLMQLAED-MGIKVERRPIPEEELETFEEAGACGTAAVISPIQRIDDLENGKSY 301

Query: 303 IFHSETEVGPTVKRLYDELVGIQFGDVEAPEGWIVKVD 340
           +   + + GP   +LY++L GIQ+GD     GW+  V+
Sbjct: 302 VISKDGKPGPICTKLYNKLRGIQYGDEPDTHGWVTIVE 339


Lambda     K      H
   0.318    0.138    0.407 

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: 350
Number of extensions: 20
Number of successful extensions: 4
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: 340
Length of database: 339
Length adjustment: 28
Effective length of query: 312
Effective length of database: 311
Effective search space:    97032
Effective search space used:    97032
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 (21.7 bits)
S2: 49 (23.5 bits)

Align candidate 353418 BT3892 (branched-chain amino acid aminotransferase (NCBI ptt file))
to HMM TIGR01123 (ilvE: branched-chain amino acid aminotransferase (EC 2.6.1.42))

Software error:

../bin/blast/fastacmd -i /tmp/list.19106.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19106.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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