GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Pedobacter sp. GW460-11-11-14-LB5

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate CA265_RS05155 CA265_RS05155 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Pedo557:CA265_RS05155
          Length = 462

 Score =  462 bits (1189), Expect = e-134
 Identities = 234/462 (50%), Positives = 321/462 (69%), Gaps = 2/462 (0%)

Query: 4   HFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEM 63
           ++D+IVLG GPGGYVAAIRA+QL LKVA+VER  LGGICLNWGCIPTK+LL+SA+V+  +
Sbjct: 2   NYDVIVLGSGPGGYVAAIRASQLGLKVAIVERESLGGICLNWGCIPTKALLKSAQVFEYI 61

Query: 64  QNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQML 123
            +A  YG+T+     D   ++ RSR VA  ++ GV+ L++KNK++VI G G++    ++ 
Sbjct: 62  NHAADYGITTAGATADFAAVVKRSRGVADGMSKGVQFLMKKNKIDVIMGTGKVKPGNKLE 121

Query: 124 VETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGA 183
           V+  +G ++ L AK+IIIATGAR+R+LPN+  DGK I  Y  A+  P +PK ++V+GSGA
Sbjct: 122 VKGADGSQQELSAKNIIIATGARSRELPNLKQDGKKIIGYRQAMVLPELPKSMVVVGSGA 181

Query: 184 IGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPD 243
           IG+EFA FYA  G +V+IVE    ++P+ED +VS  + ++ KK GI ++T ++++++   
Sbjct: 182 IGVEFAYFYATMGTKVTIVEFMDNVVPVEDEDVSKQLLRSLKKVGIDVMTSASVESVDTS 241

Query: 244 DEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTNV 303
             G    +  A G  T E     + A G+VAN+ENIGL++ GIK ++G I  D F  T+V
Sbjct: 242 GAGCKVSVKTASGMQTIEA-DIVLSAAGIVANIENIGLEETGIKTEKGKIVTDEFYNTSV 300

Query: 304 DHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGLT 363
              +AIGDV G   LAH AS +G+I  E IAG  H  PL+  NIPGCTY  P++ASVG T
Sbjct: 301 KGYYAIGDVVGGQALAHVASAEGIICVEKIAG-QHAEPLDYNNIPGCTYCTPEIASVGYT 359

Query: 364 EEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMIQ 423
           E+ A+  GY +KIG FPF A+GKA A GA DGFVK +FDA  G LLGAHM+GA VTEMI 
Sbjct: 360 EKAAKAAGYELKIGKFPFSASGKASAAGAKDGFVKLIFDAKYGELLGAHMIGANVTEMIA 419

Query: 424 GYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
              VAR LETT  E+++++ PHPT+SEA+ E+   AYG  +H
Sbjct: 420 EIVVARKLETTGHEMIKSVHPHPTMSEAIMEAAADAYGEVIH 461


Lambda     K      H
   0.319    0.135    0.393 

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: 601
Number of extensions: 21
Number of successful extensions: 4
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: 466
Length of database: 462
Length adjustment: 33
Effective length of query: 433
Effective length of database: 429
Effective search space:   185757
Effective search space used:   185757
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 CA265_RS05155 CA265_RS05155 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.26256.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26256.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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