GapMind for catabolism of small carbon sources

 

Alignments for a candidate for xylA in Dyella japonica UNC79MFTsu3.2

Align Xylose isomerase (EC 5.3.1.5) (characterized)
to candidate N515DRAFT_3229 N515DRAFT_3229 D-xylose isomerase (EC 5.3.1.5)

Query= reanno::BFirm:BPHYT_RS32825
         (440 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3229
          Length = 438

 Score =  680 bits (1755), Expect = 0.0
 Identities = 313/437 (71%), Positives = 372/437 (85%)

Query: 1   MSYFEHIPEIRYEGPQSDNPLAYRHYDKSKKVLGKTLEEHLRIAVCYWHTFVWPGVDIFG 60
           MSYFEH+  IRY G ++D+PLA+RHYD S+ +LGK ++EHLR+AVCYWH+FVWPG+D+FG
Sbjct: 1   MSYFEHVAPIRYAGAKTDDPLAFRHYDPSRVILGKRMDEHLRLAVCYWHSFVWPGMDMFG 60

Query: 61  QGTFRRPWQQAGDAMERAQQKADSAFEFFSKLGTPYYTFHDTDVSPEGSNLKEYSENFLR 120
            GTF+RPWQQAGD M +A  KAD+AF+FF +LG P+YTFHDTDV+PEG+NL EYS NF  
Sbjct: 61  AGTFQRPWQQAGDLMAQAHAKADAAFDFFQRLGAPFYTFHDTDVAPEGANLAEYSRNFAA 120

Query: 121 ITDYLARKQESTGIKLLWGTANLFSHPRYAAGAATSPDPEVFAFAATQVRHALDATQRLG 180
           + D L  KQ  TG+KLLWGTANLFSHPRYAAGAA+SP PEVFA+AA+QV HA+ AT RLG
Sbjct: 121 MVDVLEAKQAQTGMKLLWGTANLFSHPRYAAGAASSPQPEVFAYAASQVFHAMGATHRLG 180

Query: 181 GDNYVLWGGREGYDTLLNTDLVRERDQLARFLHMVVDHAHKIGFKGSLLIEPKPQEPTKH 240
           G NYVLWGGREGYDTLLNTDL RER QL RF  MVV+H HK+GF+G++LIEPKPQEPTKH
Sbjct: 181 GANYVLWGGREGYDTLLNTDLRRERAQLGRFFQMVVEHKHKLGFQGTILIEPKPQEPTKH 240

Query: 241 QYDYDVATVHGFLLQHGLDKEIRVNIEANHATLAGHSFHHEIATAYALGIFGSVDANRGD 300
           QYDYD ATV+GFL + GL++E++VN+EANHATLAGHSFHHE+ATA +LG+FGS+DANRGD
Sbjct: 241 QYDYDTATVYGFLKEFGLEREVKVNLEANHATLAGHSFHHEVATAISLGVFGSIDANRGD 300

Query: 301 PQNGWDTDQFPNSVEELTLAFYEILKHGGFTTGGMNFDSKVRRQSVDPEDLFYGHIGAID 360
           PQNGWDTDQFPNSVEELTL  YEIL+ GGFTTGG NFD+KVRRQSVD  DLF+GH+GAID
Sbjct: 301 PQNGWDTDQFPNSVEELTLVMYEILQAGGFTTGGFNFDTKVRRQSVDAADLFHGHVGAID 360

Query: 361 NLALAVERAAVLIENDRLDQFKRQRYSGWDAEFGRKISSGDYSLSALAEEAMARGLNPQH 420
            LALA+ERAA +I++DRL  FK QRY+GWDA  G++I  G Y+L ALA+EA  R L P H
Sbjct: 361 ALALALERAAKMIDDDRLAAFKAQRYAGWDAGLGQQILDGGYTLQALADEAAKRDLRPGH 420

Query: 421 ASGHQELMENIVNQAIY 437
            SG QE +EN+VN+ IY
Sbjct: 421 VSGQQERLENLVNRYIY 437


Lambda     K      H
   0.319    0.136    0.414 

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: 755
Number of extensions: 20
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: 440
Length of database: 438
Length adjustment: 32
Effective length of query: 408
Effective length of database: 406
Effective search space:   165648
Effective search space used:   165648
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate N515DRAFT_3229 N515DRAFT_3229 (D-xylose isomerase (EC 5.3.1.5))
to HMM TIGR02630 (xylA: xylose isomerase (EC 5.3.1.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.13140.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.13140.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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