GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Herbaspirillum seropedicae SmR1

Align 3-oxoadipate enol-lactonase (EC 3.1.1.24) (characterized)
to candidate HSERO_RS19935 HSERO_RS19935 hydrolase

Query= BRENDA::Q13KT2
         (263 letters)



>FitnessBrowser__HerbieS:HSERO_RS19935
          Length = 420

 Score =  154 bits (388), Expect = 4e-42
 Identities = 93/254 (36%), Positives = 126/254 (49%), Gaps = 5/254 (1%)

Query: 11  LHYRIDGERHGNAP--WIVLSNSLGTDLSMWAPQVAALSKHFRVLRYDTRGHGHSEAPKG 68
           LHY +   R+G AP   +VLS++LGTDL MW      L+   RV+ YD RGHG SE   G
Sbjct: 164 LHYTVREPRNGKAPRHTVVLSHALGTDLMMWDGLANQLAADCRVIAYDHRGHGSSEKADG 223

Query: 69  PYTIEQLTGDVLGLMDTLKIARANFCGLSMGGLTGVALAARHADRIERVALCNTAARI-- 126
            Y++  L  D   L+  L      + GLSMGG+ G  LA RH   +  + L NT +    
Sbjct: 224 LYSMADLADDAARLLRELDSGPVVWVGLSMGGMVGQELALRHPGLVRALVLANTTSAYPD 283

Query: 127 GSPEVWVPRAVKARTEGMHALADAVLPRWFTADYMEREPVVLAMIRDVFVHTDKEGYASN 186
            + E W  R    R EG+  +ADAV+ R+F   +   +   +A  R   V TD  GY   
Sbjct: 284 AAREAWQQRIATVRAEGIEVIADAVMGRYFHEGFRSAQAATVARYRQRLVTTDAVGYVGC 343

Query: 187 CEAIDAADLRPEAPGIKVPALVISGTHDLAATPAQGRELAQAIAGARY-VELDASHISNI 245
           C A+   D       I+VP LVI+G  D     A  + L   I+GAR  V   ASH+S +
Sbjct: 344 CHAVGTVDTAARLGSIRVPTLVIAGELDQGTPVAMAQALVDGISGARLAVIAGASHVSAV 403

Query: 246 ERADAFTKTVVDFL 259
           E+   F + V  F+
Sbjct: 404 EQPALFAELVCGFI 417


Lambda     K      H
   0.320    0.134    0.402 

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: 293
Number of extensions: 18
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: 263
Length of database: 420
Length adjustment: 28
Effective length of query: 235
Effective length of database: 392
Effective search space:    92120
Effective search space used:    92120
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_RS19935 HSERO_RS19935 (hydrolase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

Software error:

../bin/blast/fastacmd -i /tmp/list.10010.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10010.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.