GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaD in Pseudomonas simiae WCS417

Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate GFF1325 PS417_06735 3-oxoadipate enol-lactonase

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



>FitnessBrowser__WCS417:GFF1325
          Length = 263

 Score =  458 bits (1178), Expect = e-134
 Identities = 226/261 (86%), Positives = 243/261 (93%)

Query: 1   VGFVQLADGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKHFRVLRFDTRGHGR 60
           + FVQLA+GEL YQLDGPE APVLVLSNSLGT+LHMWD+QIPAFT+HFRVLRFDTRGHG+
Sbjct: 1   MAFVQLAEGELHYQLDGPEGAPVLVLSNSLGTDLHMWDLQIPAFTQHFRVLRFDTRGHGK 60

Query: 61  SLVTPGPYSIEQLGRDVLALLDALNIERAHFCGLSMGGLIGQWLGINAGERLHKLVVCNT 120
           SLVTPGPYSIEQLG+DV+ALLDAL+I+RAHFCGLSMGGLIGQWLGINAG+RL +LVVCNT
Sbjct: 61  SLVTPGPYSIEQLGQDVIALLDALDIQRAHFCGLSMGGLIGQWLGINAGQRLQRLVVCNT 120

Query: 121 AAKIGDPSVWNPRIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATS 180
           AAKIG P VWNPRIE VLRDG AAMVALRDASIARWFT DFA ANP  AKQITDMLAATS
Sbjct: 121 AAKIGTPEVWNPRIEMVLRDGAAAMVALRDASIARWFTADFAAANPYQAKQITDMLAATS 180

Query: 181 PQGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPSGGRFIQERVRGAEYAEFYA 240
           P+GYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPP+G  FIQ  V+GAEYAEFYA
Sbjct: 181 PEGYAANCAAVRDADFREQLASITVPTLVIAGTEDAVTPPAGSHFIQNHVQGAEYAEFYA 240

Query: 241 AHLSNVQAGSAFSDRVLSFLL 261
           AHLSNVQAG+AFSD V+ FLL
Sbjct: 241 AHLSNVQAGAAFSDCVIEFLL 261


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: 358
Number of extensions: 5
Number of successful extensions: 1
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: 263
Length adjustment: 25
Effective length of query: 241
Effective length of database: 238
Effective search space:    57358
Effective search space used:    57358
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 GFF1325 PS417_06735 (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.5504.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5504.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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