GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Herbaspirillum seropedicae SmR1

Align Dihydrolipoyl dehydrogenase; Dihydrolipoamide dehydrogenase; E3 component of 2-oxoglutarate dehydrogenase complex; EC 1.8.1.4 (characterized)
to candidate HSERO_RS14875 HSERO_RS14875 dihydrolipoamide dehydrogenase

Query= SwissProt::P14218
         (478 letters)



>FitnessBrowser__HerbieS:HSERO_RS14875
          Length = 475

 Score =  514 bits (1325), Expect = e-150
 Identities = 270/476 (56%), Positives = 338/476 (71%), Gaps = 7/476 (1%)

Query: 1   MSQKFDVVVIGAGPGGYVAAIRAAQLGLKTACIEKYIGKEGKVALGGTCLNVGCIPSKAL 60
           MS+ FDVVVIG GPGGY+AAIRAAQLG  TACI+++  ++G  A GGTC NVGCIPSKAL
Sbjct: 1   MSKNFDVVVIGGGPGGYIAAIRAAQLGFNTACIDEWKNEKGGPAPGGTCTNVGCIPSKAL 60

Query: 61  LDSSYKYHEAKEAFKVHGIEAKGVTIDVPAMVARKANIVKNLTGGIATLFKANGVTSFEG 120
           L SS  Y  A   F  HGIE KG+ +++  M+ RK  +VK    GI  LFK N V+ F G
Sbjct: 61  LQSSEHYEHASHGFAEHGIEVKGLGLNLEKMLGRKNTVVKQNNDGILYLFKKNKVSFFHG 120

Query: 121 HGKLLANK----QVEVTGLDGKTQVLEAENVIIASGSRPVEIPPAPLSDDIIVDSTGALE 176
            G  +       +++V G   +T  + A++VI+A+GS    +P A   + +I+ +TGAL 
Sbjct: 121 RGSFVKGDANGYEIKVAGAAEET--ITAKHVIVATGSNARALPGAEFDEKLILSNTGALS 178

Query: 177 FQAVPKKLGVIGAGVIGLELGSVWARLGAEVTVLEALDKFLPAADEQIAKEALKVLTKQG 236
              VPKKLGVIGAGVIGLE+GSVW RLGAEVTVLEAL  FL A DEQIAKEA K+LTKQG
Sbjct: 179 ITEVPKKLGVIGAGVIGLEMGSVWRRLGAEVTVLEALPTFLGAVDEQIAKEAQKLLTKQG 238

Query: 237 LNIRLGARVTASEVKKKQVTVTFTDANGEQKE-TFDKLIVAVGRRPVTTDLLAADSGVTL 295
           L + LG ++ A +  K  V+V +TDA G+     FDKLIV++GR P T  L A   G+ L
Sbjct: 239 LAVNLGVKIGAIKAGKNSVSVEYTDAKGDAHTGEFDKLIVSIGRTPNTIGLNAEGVGLKL 298

Query: 296 DERGFIYVDDHCKTSVPGVFAIGDVVRGAMLAHKASEEGVMVAERIAGHKAQMNYDLIPS 355
           DERGFI VD  CKT++P V+A+GDVVRG MLAHKA EEGV VAERIAG    +N++ IP 
Sbjct: 299 DERGFIAVDGDCKTNLPNVWAVGDVVRGPMLAHKAEEEGVAVAERIAGQHGHVNFNTIPW 358

Query: 356 VIYTHPEIAWVGKTEQTLKAEGVEVNVGTFPFAASGRAMAANDTTGLVKVIADAKTDRVL 415
           VIYT PEIAWVGKTEQ LKAEGV+   GTFPF A+GRA A  DT+G+VK +ADAKTD +L
Sbjct: 359 VIYTSPEIAWVGKTEQQLKAEGVQYKAGTFPFLANGRARALGDTSGMVKFLADAKTDEIL 418

Query: 416 GVHVIGPSAAELVQQGAIGMEFGTSAEDLGMMVFSHPTLSEALHEAALAVNGHAIH 471
           GVH++GP A+EL+ +  + MEF  S+ED+  +  +HP+LSEA  EAALAV+  A++
Sbjct: 419 GVHIVGPMASELISEAVVAMEFRASSEDIARICHAHPSLSEATKEAALAVDKRALN 474


Lambda     K      H
   0.316    0.134    0.375 

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: 682
Number of extensions: 33
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: 478
Length of database: 475
Length adjustment: 33
Effective length of query: 445
Effective length of database: 442
Effective search space:   196690
Effective search space used:   196690
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate HSERO_RS14875 HSERO_RS14875 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.14236.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14236.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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