GapMind for catabolism of small carbon sources

 

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

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate H281DRAFT_01118 H281DRAFT_01118 deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>FitnessBrowser__Burk376:H281DRAFT_01118
          Length = 337

 Score =  370 bits (951), Expect = e-107
 Identities = 187/314 (59%), Positives = 238/314 (75%), Gaps = 2/314 (0%)

Query: 5   NRGTELDLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDT 64
           N G   D SW+  +++N  AV RR   +  RRTVKK+ QAAWLLKAVT IDLTTLSGDDT
Sbjct: 26  NPGMPFDASWLDGLRINQSAVERRTATLATRRTVKKDAQAAWLLKAVTCIDLTTLSGDDT 85

Query: 65  SSNIQRLCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVAS 124
              ++RLC KA+ P+R DLL+AL M  + +TT AVCVY   V  AV ALK +G  IPVA+
Sbjct: 86  EGRVRRLCAKARQPVRADLLEALGMTPQRVTTGAVCVYHRFVAAAVDALKGSG--IPVAA 143

Query: 125 VAAGFPAGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGE 184
           V+ GFPAG      +L+EI  +V DGA EID+V+ R  VLTG W+ALYDE+R+FR ACG 
Sbjct: 144 VSTGFPAGLIPHPLKLKEIEASVADGAAEIDIVVTREYVLTGNWQALYDEVREFRAACGP 203

Query: 185 AHLKTILATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFF 244
           AHLK ILATG++ TL+N+ +ASM+ MMAG+DFIKTSTGKE VNAT  V++VM+R IR++ 
Sbjct: 204 AHLKAILATGDIRTLSNIARASMVCMMAGADFIKTSTGKEGVNATLDVSLVMVRMIREYH 263

Query: 245 WKTGNKIGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHH 304
            +TG  IGFKPAGG+ SAK  L++  L+KEELG  WL+PELFRIGAS+LL+DIERQ+ HH
Sbjct: 264 ERTGVPIGFKPAGGVSSAKSVLSYQILMKEELGRAWLEPELFRIGASSLLADIERQLEHH 323

Query: 305 VTGRYAAYHDLPMS 318
           V+GRY+A++  P++
Sbjct: 324 VSGRYSAFNRHPVA 337


Lambda     K      H
   0.320    0.133    0.397 

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: 336
Number of extensions: 9
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: 318
Length of database: 337
Length adjustment: 28
Effective length of query: 290
Effective length of database: 309
Effective search space:    89610
Effective search space used:    89610
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 H281DRAFT_01118 H281DRAFT_01118 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.3050.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3050.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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