GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sinorhizobium meliloti 1021

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate SMc01035 SMc01035 dihydrolipoamide dehydrogenase

Query= BRENDA::P50970
         (466 letters)



>FitnessBrowser__Smeli:SMc01035
          Length = 481

 Score =  513 bits (1321), Expect = e-150
 Identities = 264/480 (55%), Positives = 334/480 (69%), Gaps = 15/480 (3%)

Query: 1   MADHFDLIVLGGGPGGYVAAIRAAQLNLKVALVERVHLGGICLNWGCIPTKSLLRSAEVY 60
           MA+++D+IV+G GPGGYV AIR+AQL LK A+VER HLGGICLNWGCIPTK+LLRSAE+ 
Sbjct: 1   MAENYDVIVVGSGPGGYVTAIRSAQLGLKTAIVEREHLGGICLNWGCIPTKALLRSAEIL 60

Query: 61  HEMQNAEAYGLT-SFKPDFDLDKIIARSREVATRLASGVKTLLRKNKVEVISGVGQLTGN 119
               +A+ YGLT   K   ++  ++ARSR V+ RL  GV  L++KNKV+VI G  +LT  
Sbjct: 61  DHANHAKNYGLTLEGKITANVKDVVARSRGVSARLNGGVAFLMKKNKVDVIWGEAKLTKP 120

Query: 120 QQMLVETTEGE--------------EKILEAKDIIIATGARARQLPNVHSDGKHIWTYHH 165
            +++V                    E    AK II+ATGAR R LP +  DGK IWTY  
Sbjct: 121 GEIVVGAPSKPAVQPQNPVPKGVKGEGTYTAKHIIVATGARPRALPGIEPDGKLIWTYFE 180

Query: 166 ALKPPAMPKKLLVIGSGAIGIEFASFYADFGAEVSIVEHAPQILPMEDAEVSAYVAKAFK 225
           A+KP   PK LLV+GSGAIGIEFASFY   G +V++VE  PQI+P+EDAE+SA+  K  +
Sbjct: 181 AMKPEEFPKSLLVMGSGAIGIEFASFYRSMGVDVTVVELLPQIMPVEDAEISAFARKQLE 240

Query: 226 KRGIRILTQSALQNLTPDDEGVTAEIAGADGKVTKERFSHAIVAIGVVANVENIGLDKLG 285
           KRG++I+T + +  +      VTA +   DGKVT  +    I A+GV  N+EN+GL+ LG
Sbjct: 241 KRGLKIITDAKVTKVEKGANDVTAHVETKDGKVTPIKADRLISAVGVQGNIENLGLEALG 300

Query: 286 IKLDRGFIAVDGFGRTNVDHVWAIGDVAGAPCLAHKASHQGVIAAEAIAGCDHVHPLNTQ 345
           +K DRG I  DG+G+TNV  ++AIGDVAG P LAHKA H+GVI  E IAG   VH L+  
Sbjct: 301 VKTDRGCIVTDGYGKTNVAGIYAIGDVAGPPMLAHKAEHEGVICVEKIAGVPGVHALDKG 360

Query: 346 NIPGCTYARPQVASVGLTEEKARQQGYNVKIGNFPFIANGKAIAQGATDGFVKTVFDADS 405
            IPGCTY  PQVASVGLTE KA++ G ++++G + F ANGKAIA G   G +KT+FD  +
Sbjct: 361 KIPGCTYCDPQVASVGLTEAKAKELGRDIRVGRYSFGANGKAIALGEDQGLIKTIFDKKT 420

Query: 406 GALLGAHMVGAEVTEMIQGYTVARTLETTEAEIMETIFPHPTLSEAMHESVLAAYGRALH 465
           G L+GAHMVGAEVTE+IQG+ VA  LETTE E+M T+FPHPTLSE M ESVL AYGR L+
Sbjct: 421 GELIGAHMVGAEVTELIQGFVVAMNLETTEEELMHTVFPHPTLSEMMKESVLDAYGRVLN 480


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: 721
Number of extensions: 31
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: 466
Length of database: 481
Length adjustment: 33
Effective length of query: 433
Effective length of database: 448
Effective search space:   193984
Effective search space used:   193984
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 SMc01035 SMc01035 (dihydrolipoamide dehydrogenase)
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.18472.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18472.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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