GapMind for catabolism of small carbon sources

 

Alignments for a candidate for L-LDH in Desulfovibrio vulgaris Hildenborough

Align L-lactate dehydrogenase (EC 1.1.1.27) (characterized)
to candidate 209544 DVU0600 L-lactate dehydrogenase

Query= BRENDA::B1A4R6
         (311 letters)



>MicrobesOnline__882:209544
          Length = 309

 Score =  286 bits (733), Expect = 3e-82
 Identities = 139/302 (46%), Positives = 210/302 (69%)

Query: 1   MSKISVIGSGFVGATTAYTLALSGIAKTIVLIDINKDKAEGDALDISHGVPFISPVEVYA 60
           M++I+VIG G VG   AY  A+  +A  IVLID N  +AEG+++D++  +  + PV++ +
Sbjct: 1   MNRIAVIGVGNVGMAFAYAAAIKRLANDIVLIDANAARAEGESMDLADAMALVGPVQIRS 60

Query: 61  GDYGDTVGSDIIIITAGAAQKPGETRLDLVKKNTMIFKDIVAKLIKVNDTAIYLIVTNPV 120
           G Y    G+ I+++TAGA Q PG++RLDLV+ N  I +DI+  +++  D  +Y++ TNPV
Sbjct: 61  GGYEQCEGARIVVVTAGAKQMPGQSRLDLVRVNAGITRDILTAVMQYADDPLYIMATNPV 120

Query: 121 DILTYVTYKISGLPYGRVLGSGTVLDSARFRYLLSKHCNIDPRNIHGYIIGEHGDSELAA 180
           D+LT+V   ++G+  GRV+GSGTVLDSARFR  +++   +D R +H +I+GEHGDSE+A 
Sbjct: 121 DVLTHVARTVTGVAPGRVIGSGTVLDSARFRGHVAEILGVDVRGVHAHIVGEHGDSEVAL 180

Query: 181 WSITNIAGIPIDNYCNLCGKVCEKDFREEIFNNVVRAAYTIIEKKGATYYAVALAVRRIV 240
           WS  N++GIP+   C   G   +  FRE+   +V  AAY II +KGAT Y + +++ RIV
Sbjct: 181 WSRANVSGIPVAEMCARRGIAYDAAFREKALGHVRHAAYEIIGRKGATGYGIGMSLCRIV 240

Query: 241 EAILRDENSILTVSSPLTGQYGVTDVALSLPSVVGRNGIVNILELPLSQEEIAAFRRSAE 300
           EAIL DE+S+LTVS P+ G YG+ DV+LSLP V+G +GI  +L+ P++++E AA   SA 
Sbjct: 241 EAILHDEHSVLTVSCPVAGHYGLGDVSLSLPCVIGSDGIEEVLDAPIAEDEQAALAASAR 300

Query: 301 II 302
           ++
Sbjct: 301 VL 302


Lambda     K      H
   0.319    0.138    0.391 

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: 280
Number of extensions: 6
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: 311
Length of database: 309
Length adjustment: 27
Effective length of query: 284
Effective length of database: 282
Effective search space:    80088
Effective search space used:    80088
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 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate 209544 DVU0600 (L-lactate dehydrogenase)
to HMM TIGR01771 (L-lactate dehydrogenase (EC 1.1.1.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.23641.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23641.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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