GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Magnetospirillum magneticum AMB-1

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate WP_011384718.1 AMB_RS11730 dihydrolipoyl dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>NCBI__GCF_000009985.1:WP_011384718.1
          Length = 462

 Score =  543 bits (1398), Expect = e-159
 Identities = 277/464 (59%), Positives = 346/464 (74%), Gaps = 9/464 (1%)

Query: 5   FDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVYHEMQ 64
           FD+IV+GGGPGGYVAAIRAAQL +  ALVER HLGGICLNWGCIPTK+LLRSAE+Y  MQ
Sbjct: 6   FDIIVIGGGPGGYVAAIRAAQLGMNTALVEREHLGGICLNWGCIPTKALLRSAEIYRNMQ 65

Query: 65  NAEAYGLTSFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGNQQMLV 124
           +AE+YGL++    FDL KI+ARSR V+ +L  GVK LL+KNKV VI G  +L G  ++ +
Sbjct: 66  HAESYGLSAPGATFDLAKIVARSRGVSAQLQGGVKHLLKKNKVTVIEGTAKLAGGSKVAI 125

Query: 125 ETTEGEEKILEAKDIIIATGARARQLPNVHSDGKHIWTYHHALKPPAMPKKLLVIGSGAI 184
           E     +  + A  II+ATGARAR LP    DGK IWTY  AL P  MPK+LLVIGSGAI
Sbjct: 126 EG----KPTISAPHIILATGARARILPGFEPDGKFIWTYKEALVPDTMPKRLLVIGSGAI 181

Query: 185 GIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFKKRGIRILTQSALQNLTPD- 243
           GIEFASF+   GA+V++ E   ++LP+EDAE+SA   K+F+K+G++IL  + ++ L  + 
Sbjct: 182 GIEFASFFNALGAQVTVAEAMDRVLPVEDAEISAMAQKSFEKQGMKILAGANIKGLKKNA 241

Query: 244 -DEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLGIKLDRGFIAVDGFGRTN 302
            D  VT E  G   +VT +R    I AIG+V NVEN+GL+    K++R  +  D + RT 
Sbjct: 242 VDVTVTIEAGGKTHEVTVDRI---ITAIGIVGNVENVGLEATKAKVERTHVITDEYCRTG 298

Query: 303 VDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQNIPGCTYARPQVASVGL 362
              ++AIGD+AGAP LAHKASH+ +I  E I G   VHPL+ + IPGCTY  PQVASVGL
Sbjct: 299 EPGLYAIGDIAGAPWLAHKASHEAIICVEKIKGLPDVHPLDMRKIPGCTYCHPQVASVGL 358

Query: 363 TEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADSGALLGAHMVGAEVTEMI 422
           +E KA+++GY VK+G FPF+ANGKAIA G T+G +KTVFDA +G LLGAHM+GAEVTE+I
Sbjct: 359 SEAKAKEKGYAVKVGRFPFMANGKAIALGETEGMIKTVFDAKTGELLGAHMIGAEVTELI 418

Query: 423 QGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALHF 466
           QGY VA+TLETTEAE+M T+F HPTLSE MHESVL AYGRA+HF
Sbjct: 419 QGYVVAKTLETTEAELMHTVFAHPTLSEMMHESVLDAYGRAVHF 462


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: 696
Number of extensions: 32
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: 466
Length of database: 462
Length adjustment: 33
Effective length of query: 433
Effective length of database: 429
Effective search space:   185757
Effective search space used:   185757
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 WP_011384718.1 AMB_RS11730 (dihydrolipoyl dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.29492.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29492.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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