GapMind for catabolism of small carbon sources

 

Alignments for a candidate for uxuA in Paraburkholderia bryophila 376MFSha3.1

Align D-mannonate dehydratase (EC 4.2.1.8) (characterized)
to candidate H281DRAFT_02953 H281DRAFT_02953 D-mannonate dehydratase (EC 4.2.1.8)

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



>FitnessBrowser__Burk376:H281DRAFT_02953
          Length = 353

 Score =  400 bits (1028), Expect = e-116
 Identities = 195/355 (54%), Positives = 250/355 (70%), Gaps = 12/355 (3%)

Query: 1   MKLVFRWYGEKHDTVTLEQIRQIPGVEGVVGALFDIPVGEVWPFEEIMKLKETVEKAGLK 60
           +K+ FRWYG+  D V L  IRQIPG+ GVV A++D+PVG+VWP + I  LKE +E  GL 
Sbjct: 1   LKMTFRWYGDA-DPVPLAYIRQIPGMVGVVSAVYDVPVGDVWPVDTIRSLKEKIEAHGLT 59

Query: 61  LEVIESVNVHEDIKLGLPTRDRYIENYKKTIRNLAKAGVKVVCYNFMPVFDWMRTDLHKK 120
           L+VIESV VHEDIKLG PTRD  I NY +T+RNL   GVKVVCYNFMPVFDW RT L   
Sbjct: 60  LDVIESVPVHEDIKLGKPTRDTLIANYGQTLRNLGACGVKVVCYNFMPVFDWTRTSLEMP 119

Query: 121 LPDGSETMEYDHRLIEGVTPDELIKRVKEGSQGFVLPGWEWD-RLEKLRETFELYKNVDE 179
           LPDGS T+ +D + I          R  + SQG  LPGW+   R E+L+     Y+ +DE
Sbjct: 120 LPDGSTTLAFDTQAI----------RELDVSQGIQLPGWDASYRPEQLKALLREYEALDE 169

Query: 180 EKLFENLVYFLERVIPVCEECDVKLAIHPDDPPWSIFGLPRIITNKENIERMLKAVDSPY 239
             L+ NL YFL  +IPV +E  +K+AIHPDDPP  IFGLPRI+ N+ +++R+L  VD P 
Sbjct: 170 AGLWANLDYFLRAIIPVAKEAGIKMAIHPDDPPRPIFGLPRIVKNRADLQRVLAIVDDPA 229

Query: 240 NGITFCMGSLGANPENNIPEMIRYFGKMGRIHFAHVRNLKFTGEKSFYETAHPSFCGSHD 299
           NG+T C GSLGA+ +N+IP ++R FG  GRIHFAH+RN++      F+ET+H S  GS D
Sbjct: 230 NGLTLCSGSLGADLQNDIPALVREFGARGRIHFAHLRNVQTNAAGDFHETSHRSADGSLD 289

Query: 300 LFEVMKAFHDIGYEGYIRPDHGRLIWGEKARPGYGLYDRALGATYILGLWEAIDK 354
           + E++KA+ + G+EGY RPDHGR+IWGE  R GYGL+DRALGA Y+ G+WE + K
Sbjct: 290 MAEIVKAYFETGFEGYARPDHGRMIWGETGRAGYGLFDRALGAVYLNGIWEGLAK 344


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: 468
Number of extensions: 21
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: 360
Length of database: 353
Length adjustment: 29
Effective length of query: 331
Effective length of database: 324
Effective search space:   107244
Effective search space used:   107244
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 H281DRAFT_02953 H281DRAFT_02953 (D-mannonate dehydratase (EC 4.2.1.8))
to HMM TIGR00695 (uxuA: mannonate dehydratase (EC 4.2.1.8))

Software error:

../bin/blast/fastacmd -i /tmp/list.28463.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28463.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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