GapMind for catabolism of small carbon sources

 

Alignments for a candidate for deoC in Herbaspirillum seropedicae SmR1

Align deoxyribose-phosphate aldolase (EC 4.1.2.4) (characterized)
to candidate HSERO_RS05120 HSERO_RS05120 deoxyribose-phosphate aldolase

Query= BRENDA::Q9Y315
         (318 letters)



>FitnessBrowser__HerbieS:HSERO_RS05120
          Length = 343

 Score =  357 bits (915), Expect = e-103
 Identities = 183/303 (60%), Positives = 231/303 (76%), Gaps = 2/303 (0%)

Query: 11  DLSWISKIQVNHPAVLRRAEQIQARRTVKKEWQAAWLLKAVTFIDLTTLSGDDTSSNIQR 70
           D +    +++N  A  +R   ++ RR+VKK+ QAAWLLKA+T IDLTTLSGDDT   ++R
Sbjct: 38  DAAAFEHLRINLSAAEKRVATLKGRRSVKKDAQAAWLLKAITCIDLTTLSGDDTPQRVRR 97

Query: 71  LCYKAKYPIREDLLKALNMHDKGITTAAVCVYPARVCDAVKALKAAGCNIPVASVAAGFP 130
           LC KA  P+R DLL+AL M D+G+TT AVCVY   V  AV AL+  G  IPVA+V+ GFP
Sbjct: 98  LCAKAANPLRADLLEALGMQDRGLTTGAVCVYHRFVKTAVDALEGKG--IPVAAVSTGFP 155

Query: 131 AGQTHLKTRLEEIRLAVEDGATEIDVVINRSLVLTGQWEALYDEIRQFRKACGEAHLKTI 190
           AG      +L+EI  +V DGA EID+VI R  VLTG WEALY E+R FR+ACGEAH+K I
Sbjct: 156 AGLNPHALKLKEIEASVRDGAAEIDIVITREHVLTGNWEALYREMRDFRQACGEAHVKAI 215

Query: 191 LATGELGTLTNVYKASMIAMMAGSDFIKTSTGKETVNATFPVAIVMLRAIRDFFWKTGNK 250
           LATGEL TL NV KASM+ MMAG+DFIKTSTGKE+VNAT  V++VMLR IR +   TG K
Sbjct: 216 LATGELKTLRNVAKASMVCMMAGADFIKTSTGKESVNATPLVSLVMLRMIRQYQEMTGIK 275

Query: 251 IGFKPAGGIRSAKDSLAWLSLVKEELGDEWLKPELFRIGASTLLSDIERQIYHHVTGRYA 310
           +G+KPAGG+ +AKD L +  L+KEELG +WL+P+LFR+GAS+LL+DIERQ+ HHVTGRY+
Sbjct: 276 VGYKPAGGVATAKDVLEYQVLMKEELGHDWLQPDLFRVGASSLLADIERQLEHHVTGRYS 335

Query: 311 AYH 313
           A++
Sbjct: 336 AFN 338


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: 342
Number of extensions: 10
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: 343
Length adjustment: 28
Effective length of query: 290
Effective length of database: 315
Effective search space:    91350
Effective search space used:    91350
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 HSERO_RS05120 HSERO_RS05120 (deoxyribose-phosphate aldolase)
to HMM TIGR00126 (deoC: deoxyribose-phosphate aldolase (EC 4.1.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.13882.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13882.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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