GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lpd in Sphingomonas koreensis DSMZ 15582

Align dihydrolipoyl dehydrogenase (EC 1.8.1.4) (characterized)
to candidate Ga0059261_1343 Ga0059261_1343 dihydrolipoamide dehydrogenase (EC 1.8.1.4)

Query= BRENDA::A0A0H2ZHZ0
         (467 letters)



>FitnessBrowser__Korea:Ga0059261_1343
          Length = 464

 Score =  513 bits (1321), Expect = e-150
 Identities = 261/463 (56%), Positives = 345/463 (74%), Gaps = 12/463 (2%)

Query: 5   YDVIVIGAGPGGYNAAIRAGQLGLKVACVEGRETLGGTCLNVGCMPSKALLHASELYAAA 64
           +DV+VIG+GPGGY AAIRA QLGLK AC EGRETLGGTCLNVGC+PSKALLHASELY  A
Sbjct: 6   FDVLVIGSGPGGYVAAIRAAQLGLKTACAEGRETLGGTCLNVGCIPSKALLHASELYEEA 65

Query: 65  SGGEFARLGIRVSP-ELDLAQMMKQKDESVAALTRGVEFLFRKHKVQWIKGWARLQGEGR 123
           + G  A+LG+++   ELDL  M  Q+ ++V  LT G+EFLF+K+KV+W+KG+A   G+  
Sbjct: 66  ASGALAKLGVKLGKVELDLDAMHAQRLDAVKGLTGGIEFLFKKNKVEWLKGYATFTGKDS 125

Query: 124 VGVALADGGHAQLEARDIVIATGSEPAPLPGVPVDNQRILDSTGALELAEVPRHLVVIGA 183
           V V     G  ++ A++IVIATGS   PLPGV +D + ++DSTGALELA+VP HLVVIG 
Sbjct: 126 VKV-----GDREVRAKNIVIATGSSVTPLPGVEIDQKIVVDSTGALELAKVPEHLVVIGG 180

Query: 184 GVIGLELGSVWRRLGAQVTVLEYLERICPGLDGETARTLQRALTRQGMRFRLGTRV--VA 241
           GVIGLELGSVWRR+GA+VTV+EYL++I PG D +  +   R   +QG+ F+ GT+V  VA
Sbjct: 181 GVIGLELGSVWRRVGAKVTVVEYLDQILPGFDADVRKEAARLFKKQGIEFKTGTKVTGVA 240

Query: 242 ARSGEQGVELDLQPAAGGATESLQADYVLVAIGRRPYTEGLGLETVGLASDRRGMLE-NQ 300
            + G+    + ++PAAGGA E+++AD VLVAIGR+P T+GLGL+  GL  ++RG +E + 
Sbjct: 241 VKGGK--ATITVEPAAGGAAETIEADNVLVAIGRKPNTDGLGLDAAGLTVNQRGQIETDH 298

Query: 301 GQRSAAPGVWVIGDVTSGPMLAHKAEEEAIVCIERIAGHAAEMNAEVIPSVIYTQPEVAS 360
             +++ PG+W IGDV  GPMLAHKAE+E I   E IAG    +N +VIPSV+YT PE+A 
Sbjct: 299 SFKTSVPGIWAIGDVIPGPMLAHKAEDEGIAVAENIAGLTGIVNHDVIPSVVYTMPEIAG 358

Query: 361 VGLGEEQLQAARREYKVGRFPFSANSRAKINHESEGFIKILSDARSDQVLGVHMIGPGVS 420
           VGL EE  + A+ E KVG+FP + NSRAK NHE +GF+K+++DA++D+VLGV +I     
Sbjct: 359 VGLTEEAAK-AKGEVKVGKFPMAGNSRAKTNHEPDGFVKVIADAKTDRVLGVWIITSVAG 417

Query: 421 EMIGEACVAMEFSASAEDLALTCHPHPTRSEALRQAAMDVHGR 463
            MI +A  AMEF A++ED+A TCH HPT SEA+++AAM V G+
Sbjct: 418 TMIAQAAQAMEFGATSEDIAYTCHAHPTHSEAIKEAAMAVTGK 460


Lambda     K      H
   0.318    0.135    0.390 

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: 689
Number of extensions: 29
Number of successful extensions: 5
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: 467
Length of database: 464
Length adjustment: 33
Effective length of query: 434
Effective length of database: 431
Effective search space:   187054
Effective search space used:   187054
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate Ga0059261_1343 Ga0059261_1343 (dihydrolipoamide dehydrogenase (EC 1.8.1.4))
to HMM TIGR01350 (lpdA: dihydrolipoyl dehydrogenase (EC 1.8.1.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.29013.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29013.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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