GapMind for catabolism of small carbon sources

 

Alignments for a candidate for iolG in Pseudomonas fluorescens FW300-N2E2

Align inositol 2-dehydrogenase (EC 1.1.1.18) (characterized)
to candidate Pf6N2E2_1002 Myo-inositol 2-dehydrogenase (EC 1.1.1.18)

Query= BRENDA::O68965
         (330 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1002
          Length = 333

 Score =  279 bits (713), Expect = 8e-80
 Identities = 150/330 (45%), Positives = 206/330 (62%), Gaps = 4/330 (1%)

Query: 3   VRFGLLGAGRIGKVHAKAVSGNADARLVAVADAFPAAAEAIAGAYGCEVRT--IDAIEAA 60
           +R  +LGAGRIGK+HA  V+ N   +LV +AD +     A+A   GCE       AIE  
Sbjct: 2   LRIAVLGAGRIGKIHAANVATNPRTKLVVIADPWKEGVNALAMQLGCEAAYDYASAIERT 61

Query: 61  ADIDAVVICTPTDTHADLIERFARAGKAIFCEKPIDLDAERVRACLKVVSDTKAKLMVGF 120
            D+DAV I TPT+ H +L+ +  R GK + CEKPID+D ER +A +  +     ++M+ F
Sbjct: 62  -DVDAVFIGTPTEFHIELMLQAVRLGKPVICEKPIDMDYERAKAAVDELERLNGRVMLAF 120

Query: 121 NRRFDPHFMAVRKAIDDGRIGEVEMVTITSRDPSAPPVDYIKRSGGIFRDMTIHDFDMAR 180
           NRRFDP ++ +R+AIDDG IG V  V ITSRDP+     Y++ SGGIFRDMTIHDFDMAR
Sbjct: 121 NRRFDPDYLRLRRAIDDGEIGVVRQVIITSRDPALAARAYLETSGGIFRDMTIHDFDMAR 180

Query: 181 FLLGEEPVSVTATAAVLIDKAIGDAGDYDSVSVILQTASGKQAIISNSRRATYGYDQRIE 240
            LLGEEPV V A  + L+D  +    DYDSV V+++TASG+Q  I+  R A YG+DQR+E
Sbjct: 181 SLLGEEPVEVFAVGSRLVDPTLESIPDYDSVMVLMRTASGRQCHINCCREAVYGFDQRLE 240

Query: 241 VHGSKGAVAAENQRPVSIEIATGDGY-TRPPLHDFFMTRYTEAYANEIESFIAAIEKGAE 299
           V GSKG +  EN R  S+     +      PL +FF+ R+ ++Y  E+ SF+ A+E  + 
Sbjct: 241 VSGSKGMLLNENHRTNSVRRYGAEATDVADPLLNFFLERHADSYKIELNSFLDAVENNSP 300

Query: 300 IAPSGNDGLAALALADAAVRSVAEKRQISI 329
           +  +  DGL AL LA+ A  S    + + +
Sbjct: 301 MPATPRDGLRALRLANCASESAETGKVVRV 330


Lambda     K      H
   0.320    0.134    0.379 

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: 301
Number of extensions: 9
Number of successful extensions: 3
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: 330
Length of database: 333
Length adjustment: 28
Effective length of query: 302
Effective length of database: 305
Effective search space:    92110
Effective search space used:    92110
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 Pf6N2E2_1002 (Myo-inositol 2-dehydrogenase (EC 1.1.1.18))
to HMM TIGR04380 (iolG: inositol 2-dehydrogenase (EC 1.1.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.16769.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16769.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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