GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolC in Burkholderia phytofirmans PsJN

Align 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92); possible 5-dehydro-2-deoxyphosphogluconate aldolase DUF2090 (EC 4.1.2.29) (characterized)
to candidate BPHYT_RS13910 BPHYT_RS13910 5-dehydro-2-deoxygluconokinase

Query= reanno::BFirm:BPHYT_RS13910
         (681 letters)



>FitnessBrowser__BFirm:BPHYT_RS13910
          Length = 681

 Score = 1360 bits (3519), Expect = 0.0
 Identities = 681/681 (100%), Positives = 681/681 (100%)

Query: 1   MDQSITSSGVTSASAPATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLG 60
           MDQSITSSGVTSASAPATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLG
Sbjct: 1   MDQSITSSGVTSASAPATGSRFAPGRSRDIVCLGRLAVDLYAQQVGARLEDVSSFAKYLG 60

Query: 61  GSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVLLG 120
           GSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVLLG
Sbjct: 61  GSSANIAFGCARLGLASSMLARVGNDHMGRFLTETLTKEGCDVSHVRIDQERLTALVLLG 120

Query: 121 LKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALDYA 180
           LKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALDYA
Sbjct: 121 LKDRDTFPLIFYRENCADMAVDEADFDEAYIASSKALLITGTHFSTEQVNRTSRRALDYA 180

Query: 181 RRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFRIA 240
           RRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFRIA
Sbjct: 181 RRNQVRTVLDIDYRPVLWGLTGKADGETRFVASEGVTAHLQRILPLFDLVIGTEEEFRIA 240

Query: 241 GGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVLGA 300
           GGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVLGA
Sbjct: 241 GGKTELVDALAMVRAVTPATLVLKRGPMGCQIIDGAVPASLDDLPIHGGVEVEVLNVLGA 300

Query: 301 GDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKADPQ 360
           GDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKADPQ
Sbjct: 301 GDAFASGFLSGWLRDQPLEACARIANASGALVVSRHGCAPAMPTPAELDYFLREAKADPQ 360

Query: 361 RMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGLFV 420
           RMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGLFV
Sbjct: 361 RMRRPDRDATLARLHRVSPARKQWDEVLGFAFDHRNQFFELAQQTGADDARIARLKGLFV 420

Query: 421 EAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRSIG 480
           EAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRSIG
Sbjct: 421 EAVAQTESALGLQNRIGVLIDDRYGQDALNAATGRGWWIGRPVELPGSVPLVFDHGRSIG 480

Query: 481 TTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHAHL 540
           TTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHAHL
Sbjct: 481 TTLIPWPQEHIVKCLVQFHPDEPIEQRLEQEAQLRALYDATQASGHELLLEVIPPKHAHL 540

Query: 541 PQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSAAV 600
           PQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSAAV
Sbjct: 541 PQAPDTVYRALKRLYNIGIYPEWWKLEPMDAAQWRNVDALIAERDPYCRGVVLLGLSAAV 600

Query: 601 EQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASWRA 660
           EQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASWRA
Sbjct: 601 EQLDEGFRAAAQSATCRGFTVGRTIFHEPSHAWLAGEIGDDELIGRVRRTFETLIASWRA 660

Query: 661 TRGASAAQSSAPKPVHQEQAA 681
           TRGASAAQSSAPKPVHQEQAA
Sbjct: 661 TRGASAAQSSAPKPVHQEQAA 681


Lambda     K      H
   0.321    0.136    0.409 

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: 1619
Number of extensions: 39
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: 681
Length of database: 681
Length adjustment: 39
Effective length of query: 642
Effective length of database: 642
Effective search space:   412164
Effective search space used:   412164
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: 54 (25.4 bits)

Align candidate BPHYT_RS13910 BPHYT_RS13910 (5-dehydro-2-deoxygluconokinase)
to HMM TIGR04382 (iolC: 5-dehydro-2-deoxygluconokinase (EC 2.7.1.92))

Software error:

../bin/blast/fastacmd -i /tmp/list.26630.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26630.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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