GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Dinoroseobacter shibae DFL-12

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 3608572 Dshi_1966 dihydrolipoamide dehydrogenase (RefSeq)

Query= BRENDA::Q0KBV8
         (594 letters)



>FitnessBrowser__Dino:3608572
          Length = 580

 Score =  691 bits (1783), Expect = 0.0
 Identities = 356/591 (60%), Positives = 433/591 (73%), Gaps = 14/591 (2%)

Query: 4   IEVKVPDIGDFDAVEVIEVLVKAGDTVEVEQSLIVLESDKASMDVPSSAAGKVVEVKVKV 63
           +++KVPDIGDF  V V+ +LV  GDTV  E  LI LESDKA+M+VPS AAG V E+KV  
Sbjct: 1   MDIKVPDIGDFTDVPVVSILVAVGDTVAEEDPLIELESDKATMEVPSPAAGVVKEIKVAE 60

Query: 64  GDKVGQGAVICTIEAQQAAAAPAPAQAPAPAQAPAPAAAAPAPAPAAASHSGGADIQCEM 123
           GD V +G VI   E+  A  AP  A      +APA AAAAP    A  + +G  D+  E+
Sbjct: 61  GDNVSEGTVIMVFESSGAEEAPKGAD-----EAPA-AAAAPEAVAATGTATGPGDVHGEV 114

Query: 124 LVLGAGPGGYSAAFRAADLGMNTVLVERYSTLGGVCLNVGCIPSKALLHNAAVIDEAKAL 183
           +VLG+GPGGY+AAFRAADLG   VL+ERY +LGGVCLNVGCIPSKALLH A VI EA+ +
Sbjct: 115 VVLGSGPGGYTAAFRAADLGKKVVLIERYPSLGGVCLNVGCIPSKALLHVAKVITEAEEM 174

Query: 184 AAHGILFGEAKIDLDGLRHYKNQVVGKLTGGLAGMAKARKVQVVRGIGNFLDPHHMEVEL 243
            AHG+ FG+ K+DLD LR +K+ V+G+LTGGL+G+AK RKV+VV G G F  P+ + VE 
Sbjct: 175 GAHGVSFGKPKVDLDELRAFKDSVIGQLTGGLSGLAKGRKVEVVTGYGKFTGPNMIAVEG 234

Query: 244 TEGEGKRSTGKKTVIRFEKAIIAAGSQAVKLPFIPEDPRIVDSTGALELPEVPNKMLVIG 303
            +G         T + F++ IIAAGS+ V LPF+PED RI+DSTGALEL ++P +ML++G
Sbjct: 235 EDGV--------TTVSFDQCIIAAGSEPVNLPFLPEDDRIIDSTGALELKDIPKRMLILG 286

Query: 304 GGIIGLEMATVYSTLGADIDVVEMLDGLMNGADRDLVKVWEKKNKDRFGKVMLKTKTVGV 363
           GGIIGLEMA VY  LG+DI VVE +D LM GAD+D+VK   K+ + R+  ++LKTK  GV
Sbjct: 287 GGIIGLEMACVYDALGSDITVVEFMDQLMPGADKDIVKPLHKRIEGRYENILLKTKVTGV 346

Query: 364 EAKPDGIYVKFEGEAAPAEPQRYDLVLVSVGRSPNGKRISAEKAGVAVSERGFINVDKQM 423
           EA   G+ V FE          +D VLV+VGR PNG  I AEKAGVAV ERGFI VD Q 
Sbjct: 347 EALKKGLKVTFEDAKGELTTDTFDKVLVAVGRKPNGALIDAEKAGVAVDERGFIAVDSQQ 406

Query: 424 RTNVPHIFAIGDIVGQPMLAHKAVHEAHVAAEAAHGEKAYFDAKQIPSVAFTDPEVAWAG 483
           RT V HIFAIGD+VGQPMLAHKAVHE  VAAE   G   +FDA+ IPSVA+TDPEVAW G
Sbjct: 407 RTGVAHIFAIGDLVGQPMLAHKAVHEGKVAAEVCAGHNRHFDARLIPSVAYTDPEVAWCG 466

Query: 484 LTEDECKEKGIKYSKGVFPWAASGRAIANGRDEGFTKLIFDEETHRVIGGGIVGTHAGDL 543
           +TE + K KGI Y KGVFPWAASGR+++NGR EG TKL+FD E  RVIG  IVGT+AGDL
Sbjct: 467 VTETDAKAKGIAYEKGVFPWAASGRSLSNGRSEGITKLLFDPEDDRVIGACIVGTNAGDL 526

Query: 544 ISEVCLAIEMGADAVDIGKTIHPHPTLGESIGMAAEIYEGTCTDVPPPRKR 594
           ISEV LAIEMGADAVD+G TIHPHPTL E++  AAE++EGT TD+ PP+K+
Sbjct: 527 ISEVALAIEMGADAVDLGHTIHPHPTLSETVNFAAEMFEGTITDLMPPKKK 577


Lambda     K      H
   0.316    0.134    0.387 

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: 988
Number of extensions: 52
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: 594
Length of database: 580
Length adjustment: 37
Effective length of query: 557
Effective length of database: 543
Effective search space:   302451
Effective search space used:   302451
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: 53 (25.0 bits)

Align candidate 3608572 Dshi_1966 (dihydrolipoamide dehydrogenase (RefSeq))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.19331.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19331.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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