GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ans in Escherichia coli BW25113

Align asparaginase (EC 3.5.1.1) (characterized)
to candidate 17036 b2957 periplasmic L-asparaginase II (NCBI)

Query= BRENDA::P00805
         (348 letters)



>FitnessBrowser__Keio:17036
          Length = 348

 Score =  687 bits (1773), Expect = 0.0
 Identities = 348/348 (100%), Positives = 348/348 (100%)

Query: 1   MEFFKKTALAALVMGFSGAALALPNITILATGGTIAGGGDSATKSNYTVGKVGVENLVNA 60
           MEFFKKTALAALVMGFSGAALALPNITILATGGTIAGGGDSATKSNYTVGKVGVENLVNA
Sbjct: 1   MEFFKKTALAALVMGFSGAALALPNITILATGGTIAGGGDSATKSNYTVGKVGVENLVNA 60

Query: 61  VPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTDTMEETAYF 120
           VPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTDTMEETAYF
Sbjct: 61  VPQLKDIANVKGEQVVNIGSQDMNDNVWLTLAKKINTDCDKTDGFVITHGTDTMEETAYF 120

Query: 121 LDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGR 180
           LDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGR
Sbjct: 121 LDLTVKCDKPVVMVGAMRPSTSMSADGPFNLYNAVVTAADKASANRGVLVVMNDTVLDGR 180

Query: 181 DVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVY 240
           DVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVY
Sbjct: 181 DVTKTNTTDVATFKSVNYGPLGYIHNGKIDYQRTPARKHTSDTPFDVSKLNELPKVGIVY 240

Query: 241 NYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGAT 300
           NYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGAT
Sbjct: 241 NYANASDLPAKALVDAGYDGIVSAGVGNGNLYKSVFDTLATAAKTGTAVVRSSRVPTGAT 300

Query: 301 TQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 348
           TQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY
Sbjct: 301 TQDAEVDDAKYGFVASGTLNPQKARVLLQLALTQTKDPQQIQQIFNQY 348


Lambda     K      H
   0.314    0.130    0.368 

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: 566
Number of extensions: 9
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: 348
Length of database: 348
Length adjustment: 29
Effective length of query: 319
Effective length of database: 319
Effective search space:   101761
Effective search space used:   101761
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 49 (23.5 bits)

Align candidate 17036 b2957 (periplasmic L-asparaginase II (NCBI))
to HMM TIGR00520 (L-asparaginase, type II (EC 3.5.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.30345.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30345.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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