GapMind for catabolism of small carbon sources

 

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

Align Ribokinase (EC 2.7.1.15) (characterized)
to candidate H281DRAFT_05229 H281DRAFT_05229 ribokinase

Query= reanno::pseudo3_N2E3:AO353_20835
         (305 letters)



>FitnessBrowser__Burk376:H281DRAFT_05229
          Length = 307

 Score =  368 bits (945), Expect = e-107
 Identities = 200/299 (66%), Positives = 232/299 (77%), Gaps = 1/299 (0%)

Query: 3   AKVVVVGSLNMDLVTRAQRLPHAGETLHGESFATVSGGKGANQAVASARLGAQVSMIGCV 62
           A+V VVGSLNMDLV RA RLPH GETL G +FA V+GGKG NQAVA+ARLGAQVSM+GCV
Sbjct: 8   ARVAVVGSLNMDLVARAPRLPHPGETLAGRTFAQVAGGKGGNQAVAAARLGAQVSMLGCV 67

Query: 63  GDDAYGEQLRAALLAEQIDCQALTSVEGSSGVALIVVDDNSQNAIVIVAGANGQLTPGMV 122
           G DA G QLRA L AE IDC A+ +   ++GVALIVVDD SQNAIVIVAG+NG++TP  +
Sbjct: 68  GADANGAQLRAGLEAEGIDCAAVETGREATGVALIVVDDASQNAIVIVAGSNGEVTPETI 127

Query: 123 AGFDAVLAAADVIICQLEVPMHTVGYVLKRGRELGKTVILNPAPATSPLPADWYSSIDYL 182
           A  +AVLAAADV+ICQLE P+ TV   L   R LGKTVILNPAPAT PLPA+W   IDYL
Sbjct: 128 ARHEAVLAAADVVICQLETPLDTVQAALATARRLGKTVILNPAPATGPLPAEWLPLIDYL 187

Query: 183 IPNESEASALSGLPVDSLESAELAASRLIAAGAGKVIITLGPQGSLFA-NGQSCEHFPAP 241
           IPNE EA+ L+GLPV S E A  AA+ L AAGA  V++TLGP+G   A  G +   + AP
Sbjct: 188 IPNELEAATLTGLPVGSPEEAATAAAVLRAAGARNVLVTLGPRGVQAALEGAAPALYDAP 247

Query: 242 KVKSVDTTAAGDTFVGGFAAALAAGKSEVEAIRFGQVAAALSVTRAGAQPSIPSLSDVQ 300
           KVK++DTTAAGDTF+GGFAA LA G S   AIRF Q AAALSVTRAGAQPSIP+ ++V+
Sbjct: 248 KVKAIDTTAAGDTFIGGFAAQLAQGASVDAAIRFAQRAAALSVTRAGAQPSIPTWTEVE 306


Lambda     K      H
   0.315    0.130    0.363 

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: 323
Number of extensions: 11
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: 305
Length of database: 307
Length adjustment: 27
Effective length of query: 278
Effective length of database: 280
Effective search space:    77840
Effective search space used:    77840
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate H281DRAFT_05229 H281DRAFT_05229 (ribokinase)
to HMM TIGR02152 (rbsK: ribokinase (EC 2.7.1.15))

Software error:

../bin/blast/fastacmd -i /tmp/list.1932.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1932.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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