GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Klebsiella michiganensis M5al

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate BWI76_RS14145 BWI76_RS14145 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Koxy:BWI76_RS14145
          Length = 465

 Score =  520 bits (1338), Expect = e-152
 Identities = 259/465 (55%), Positives = 334/465 (71%), Gaps = 1/465 (0%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           M D +D++++GGGPGGYVAAIRA QL L+ ALVE+ HLGGICLNWGCIPTK+LL  AEV 
Sbjct: 1   MHDKYDVLIIGGGPGGYVAAIRAGQLGLRTALVEKQHLGGICLNWGCIPTKALLHGAEVA 60

Query: 61  HEMQNAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQ 120
           H + +A+  G +  +  FDL K++  SR V+ +L  GV+ LL+KN V VI+G  +L G  
Sbjct: 61  HTIAHADRLGFSLSEVSFDLQKLVQFSRAVSQQLTGGVEYLLKKNGVTVIAGTARLRGKG 120

Query: 121 QMLVETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIG 180
           Q+ V   +GEE+   A  +I+ATGAR R LP V  DG+ IWTY  AL+P  +P+ LL+IG
Sbjct: 121 QVTVADPQGEERDYRADHVILATGARPRALPGVEPDGERIWTYFEALQPERLPESLLIIG 180

Query: 181 SGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNL 240
           SGAIG+EFAS Y D G+ V++VE A QILP+EDAEVSA V K+F++RGI + +Q+ L  +
Sbjct: 181 SGAIGVEFASLYNDLGSNVTLVEQAAQILPVEDAEVSATVRKSFERRGIHVHSQTLLTQV 240

Query: 241 TPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGR 300
              D GV   +     + T E     ++A GV  NVE +GL+ LG++LDRGFI  D   R
Sbjct: 241 KRTDTGVRCALKTTGAEQTLE-VERVLLAAGVQPNVEGLGLEALGVELDRGFIKTDAACR 299

Query: 301 TNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASV 360
           TNV  ++AIGDVAG PCLAHKASH+GVI  E +AG + V PLN   +PGCTYARPQVAS+
Sbjct: 300 TNVFGLYAIGDVAGPPCLAHKASHEGVICVETLAGVEGVRPLNCDYVPGCTYARPQVASL 359

Query: 361 GLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTE 420
           GLTE KAR+ G  +K+G F +  NGKA+A G T+GFVKT+FDA++G LLGAHMVG +VTE
Sbjct: 360 GLTEAKARETGRPIKVGKFAYQGNGKALASGETEGFVKTIFDAETGELLGAHMVGEQVTE 419

Query: 421 MIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
            IQG+ +A  LE T+  ++  IF HPTLSEAMHES+LAA G+ LH
Sbjct: 420 QIQGFGIAHHLEATDESLLSMIFAHPTLSEAMHESILAASGQPLH 464


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: 643
Number of extensions: 24
Number of successful extensions: 2
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: 465
Length adjustment: 33
Effective length of query: 433
Effective length of database: 432
Effective search space:   187056
Effective search space used:   187056
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 BWI76_RS14145 BWI76_RS14145 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.3381.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3381.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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