GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Burkholderia phytofirmans PsJN

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate BPHYT_RS28515 BPHYT_RS28515 mannonate dehydratase

Query= metacyc::MONOMER-17955
         (360 letters)



>FitnessBrowser__BFirm:BPHYT_RS28515
          Length = 350

 Score =  399 bits (1025), Expect = e-116
 Identities = 195/353 (55%), Positives = 248/353 (70%), Gaps = 12/353 (3%)

Query: 3   LVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLKLE 62
           + FRWYG+  D V L  IRQIPG+ GVV A++D+PVGEVWP + I  LKE +E  GL LE
Sbjct: 1   MTFRWYGDT-DPVPLAYIRQIPGMVGVVSAIYDVPVGEVWPIDRIRSLKEKIEAHGLTLE 59

Query: 63  VIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKKLP 122
           VIESV VHEDIKLG PTRD  I NY +T+RNL   GVKVVCYNFMPVFDW RT L   LP
Sbjct: 60  VIESVPVHEDIKLGKPTRDTLIVNYGQTLRNLGACGVKVVCYNFMPVFDWTRTSLEMPLP 119

Query: 123 DGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWD-RLEKLRETFELYKNVDEEK 181
           DGS T+ +D + I          R  + S+G  LPGW+   R E+L+     Y+ +DE  
Sbjct: 120 DGSTTLAFDTQAI----------RELDVSEGIQLPGWDASYRPEQLKALLRDYEALDEAG 169

Query: 182 LFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPYNG 241
           L+ NL YFL  +IPV +E  +K+AIHPDDPP  IFGLPRI+ N+ +++R+L  VD P NG
Sbjct: 170 LWANLDYFLRAIIPVAKEAGIKMAIHPDDPPRPIFGLPRIVKNRADLQRVLDIVDDPANG 229

Query: 242 ITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHDLF 301
           +T C GSLGA+ +N+IP ++R FG  GRIHFAH+RN++      F+ET+H S  GS D+ 
Sbjct: 230 LTLCSGSLGADLQNDIPALVREFGARGRIHFAHLRNVQTNAAGDFHETSHRSADGSLDMA 289

Query: 302 EVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDK 354
           E++KA+ + G+EGY RPDHGR+IWGE  R GYGL+DRALGA Y+ G+WE + K
Sbjct: 290 EIVKAYFETGFEGYARPDHGRMIWGETGRAGYGLFDRALGAVYLNGIWEGLAK 342


Lambda     K      H
   0.322    0.142    0.448 

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: 467
Number of extensions: 20
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: 360
Length of database: 350
Length adjustment: 29
Effective length of query: 331
Effective length of database: 321
Effective search space:   106251
Effective search space used:   106251
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: 49 (23.5 bits)

Align candidate BPHYT_RS28515 BPHYT_RS28515 (mannonate dehydratase)
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.17795.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17795.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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