GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Bacteroides thetaiotaomicron VPI-5482

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate 349837 BT0309 Dihydrolipoamide dehydrogenase (NCBI ptt file)

Query= BRENDA::Q8VPK7
         (567 letters)



>FitnessBrowser__Btheta:349837
          Length = 447

 Score =  298 bits (762), Expect = 4e-85
 Identities = 180/451 (39%), Positives = 259/451 (57%), Gaps = 14/451 (3%)

Query: 112 FDIVVIGGGPAGYVAAIKAAQFGGKVALVEKSELGGTCLNRGCIPTKTYLHNAEIIENIG 171
           FDI +IGGGPAGY AA +A   G +  L EK  +GG CLN GCIPTKT L++A+I+++I 
Sbjct: 3   FDIAIIGGGPAGYTAAERAGANGLRAVLFEKKAIGGVCLNEGCIPTKTLLYSAKILDSIK 62

Query: 172 HAANRGIVIENPNFTVDMEKLLETKSKVVNTLVGGVAGLLRSYGVTVHKGIGTITKDKNV 231
            A+  GI  E+P+F  D+ K++  K K V  L GGV   + SYGVT+ +    I  ++N 
Sbjct: 63  SASKYGISAESPSF--DLTKIMSRKEKTVKMLTGGVKMTVNSYGVTIVEKEAFIEGEENG 120

Query: 232 LVN---GSELLETKKIILAGGSKVNKINVPGMESPLVMTSDDILEMNEVPESLVIIGGGV 288
           L+      E  E K +++  GS      +PG+      TS + LE+ E+PE+LV+IGGGV
Sbjct: 121 LIRIICDGERYEVKYLLVCTGSDTVIPPIPGLSEVSYWTSKEALEIKELPETLVVIGGGV 180

Query: 289 VGIELGQAFMTFGSKVTVIEMMDRIVPAMDVEVSKNLRLILERKGMTILTGTKLQEIIEE 348
           +G+E    F + G KV V+EMM  I+  MD E S  LR+   ++G+T    TK+ E+  +
Sbjct: 181 IGMEFASFFNSMGVKVHVVEMMPEILGVMDKETSSMLRMEYAKRGVTFYLNTKVIEVKPD 240

Query: 349 NGQLRIKVEGKDDII-ASKALLSIGRMPDLEGIG--EVEFELDRGCIKVTEYMETSVPGI 405
              + I+ +GK   I   K LLS+GR  ++  +G  ++  EL R  +KV EY++TS PG+
Sbjct: 241 G--VVIEKDGKASTIKTEKILLSVGRKANITNVGLDKLNIELHRNGVKVDEYLQTSHPGV 298

Query: 406 YAPGDINGTKMLAHAAFRMGEVSAENALKGNHAVAKLNLTPAAIYTLPEVAAVGLTEEQ- 464
           YA GDI G  +LAH A R  EV A N + G       N  P  +YT PEVA VG TEE+ 
Sbjct: 299 YACGDITGYSLLAHTAIREAEV-AINHILGVEDRMNYNSVPGVVYTNPEVAGVGKTEEEL 357

Query: 465 AREKYDVAIGKFNFAANGRAIA-SDAAQGFVKVIADKKYGEILGVHIIGPAAAELINEAS 523
            ++     + K   A +GR +A ++   G  K+I D+    I+G H++G  A+ELI  A 
Sbjct: 358 TKQGIPYRVTKLPMAYSGRFVAENEQVNGICKLILDEA-DHIIGCHMLGNPASELIVIAG 416

Query: 524 SIIEMEITVEEMLKTIHGHPTYSEVMYEAFA 554
             I+   TVEE  K +  HPT  E+ +E  +
Sbjct: 417 IAIQKGYTVEEFQKNVFPHPTVGEIYHEVLS 447


Lambda     K      H
   0.314    0.135    0.370 

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: 622
Number of extensions: 32
Number of successful extensions: 8
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: 567
Length of database: 447
Length adjustment: 34
Effective length of query: 533
Effective length of database: 413
Effective search space:   220129
Effective search space used:   220129
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: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate 349837 BT0309 (Dihydrolipoamide dehydrogenase (NCBI ptt file))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.13287.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13287.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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