GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Cupriavidus basilensis 4G11

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate RR42_RS10690 RR42_RS10690 3-oxoadipate enol-lactonase

Query= reanno::pseudo3_N2E3:AO353_17230
         (266 letters)



>FitnessBrowser__Cup4G11:RR42_RS10690
          Length = 259

 Score =  288 bits (738), Expect = 6e-83
 Identities = 143/258 (55%), Positives = 181/258 (70%), Gaps = 3/258 (1%)

Query: 3   FVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGRSL 62
           F +     L Y+LDG +  PVLVL+NSLGTNL MW+ QI AF KHFRVLR+DTRGHG+S 
Sbjct: 3   FAEFPGVRLHYRLDGDDTLPVLVLANSLGTNLDMWNPQIEAFAKHFRVLRYDTRGHGQSS 62

Query: 63  VTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNTAA 122
           VTPGPY+I QLG DV+ALLDAL I+RAHFCGLSMGG+ G WL +N   R  K+V+CNTAA
Sbjct: 63  VTPGPYTIPQLGEDVIALLDALKIDRAHFCGLSMGGITGMWLALNHAGRFDKVVLCNTAA 122

Query: 123 KIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQ 182
            IG    W  R   V RDG   + ++ +A + +W TP +A   PA+ + +  ML+AT   
Sbjct: 123 YIGPAENWTNRAAAVERDG---VGSIANAVVDKWLTPGYAAGQPALVQLLQAMLSATDAA 179

Query: 183 GYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYAAH 242
           GYAANC AVRD+D R+ +A IT PTLVIAG+ D  TPP  G+++ +++ GA YAE  AAH
Sbjct: 180 GYAANCRAVRDSDLRDAVAGITRPTLVIAGSGDIPTPPHDGQYLAQKIPGARYAELDAAH 239

Query: 243 LSNVQAGSAFSDRVLSFL 260
           LSN++    F+D VL FL
Sbjct: 240 LSNLEQVEGFTDAVLEFL 257


Lambda     K      H
   0.321    0.136    0.410 

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: 272
Number of extensions: 12
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: 266
Length of database: 259
Length adjustment: 25
Effective length of query: 241
Effective length of database: 234
Effective search space:    56394
Effective search space used:    56394
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 (21.9 bits)
S2: 47 (22.7 bits)

Align candidate RR42_RS10690 RR42_RS10690 (3-oxoadipate enol-lactonase)
to HMM TIGR02427 (pcaD: 3-oxoadipate enol-lactonase (EC 3.1.1.24))

Software error:

../bin/blast/fastacmd -i /tmp/list.17803.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17803.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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