GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Shewanella oneidensis MR-1

Align threonine ammonia-lyase (EC 4.3.1.19) (characterized)
to candidate 203422 SO4344 threonine dehydratase (NCBI ptt file)

Query= BRENDA::P04968
         (514 letters)



>FitnessBrowser__MR1:203422
          Length = 545

 Score =  598 bits (1542), Expect = e-175
 Identities = 303/523 (57%), Positives = 389/523 (74%), Gaps = 12/523 (2%)

Query: 2   ADSQPLSGAPEGAE-------YLRAVLRAPVYEAAQVTPLQKMEKLSSRLDNVILVKRED 54
           A+SQP   +P   E       YL+ +L + VY+ A+VTPL  + KLS+RL   + +KRED
Sbjct: 12  AESQPAQASPASVEKSQLAQHYLQKILLSSVYDVAKVTPLSSLNKLSARLGCQVFLKRED 71

Query: 55  RQPVHSFKLRGAYAMMAGLTEEQKAHGVITASAGNHAQGVAFSSARLGVKALIVMPTATA 114
            QPVHSFKLRGAY  +A L++ +   GV+ ASAGNHAQGVA S+A  GV A+IVMP  T 
Sbjct: 72  MQPVHSFKLRGAYNRIAQLSQAECQRGVVCASAGNHAQGVAMSAASRGVDAVIVMPETTP 131

Query: 115 DIKVDAVRGFGGEVLLHGANFDEAKAKAIELSQQQGFTWVPPFDHPMVIAGQGTLALELL 174
           DIKVDAVR  GG V+LHG  FD+A   A+ ++QQ+G  ++ PFD   VIAGQGT+A E+L
Sbjct: 132 DIKVDAVRRLGGNVVLHGQAFDQANGFAMTMAQQEGRVYIAPFDDEAVIAGQGTIAQEML 191

Query: 175 QQDAHLDRVFVPVGGGGLAAGVAVLIKQLMPQIKVIAVEAEDSACLKAALDAGHPVDLPR 234
           QQ   L+ +FVPVGGGGL AG+A   K +MPQ+K++ VE ED+ACLKAA++AG PV L +
Sbjct: 192 QQQRDLEVIFVPVGGGGLIAGIAAYYKAVMPQVKIVGVEPEDAACLKAAMEAGEPVTLSQ 251

Query: 235 VGLFAEGVAVKRIGDETFRLCQEYLDDIITVDSDAICAAMKDLFEDVRAVAEPSGALALA 294
           VGLFA+GVAVKRIG E FR+ +  +D ++TV SD ICAA+KD+FED RA+AEP+GAL+LA
Sbjct: 252 VGLFADGVAVKRIGTEPFRVAKLCVDAVVTVTSDEICAAVKDIFEDTRAIAEPAGALSLA 311

Query: 295 GMKKYIALH----NIRGERLAHILSGANVNFHGLRYVSERCELGEQREALLAVTIPEEKG 350
           G+KKY++ +    + RGE++A ILSGANVNFH LRYVSERCELGEQ+EA+LAV +PE  G
Sbjct: 312 GLKKYVSTNATGESGRGEKVAAILSGANVNFHSLRYVSERCELGEQKEAVLAVKVPERPG 371

Query: 351 SFLKFCQLLGGRSVTEFNYRFADAKNACIFVGVRLSRGLEERKEILQMLNDGGYSVVDLS 410
           SFL+FC+LL  R +TEFNYRF+    A +F G+RL++G  E ++I+  L D G+ V DLS
Sbjct: 372 SFLRFCELLEKRVMTEFNYRFSSRDMAVVFAGIRLTKGHGELEQIINTLEDNGFEVQDLS 431

Query: 411 DDEMAKLHVRYMVGGRPSHPLQERLYSFEFPESPGALLRFLNTLGTYWNISLFHYRSHGT 470
            DE AKLHVRYMVGG P  PL+ERL+SFEFPE PGALL+FL TL + WNISLFHYR+HG 
Sbjct: 432 GDETAKLHVRYMVGGHPPEPLEERLFSFEFPEHPGALLKFLTTLQSKWNISLFHYRNHGA 491

Query: 471 DYGRVLAAFELGDHEP-DFETRLNELGYDCHDETNNPAFRFFL 512
            +GRVLA FE+   +   F+  L ELG+   +ET +PA++ FL
Sbjct: 492 AFGRVLAGFEVPASDALPFQQFLTELGFVYQEETQSPAYQLFL 534


Lambda     K      H
   0.321    0.138    0.403 

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: 776
Number of extensions: 25
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: 514
Length of database: 545
Length adjustment: 35
Effective length of query: 479
Effective length of database: 510
Effective search space:   244290
Effective search space used:   244290
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: 52 (24.6 bits)

Align candidate 203422 SO4344 (threonine dehydratase (NCBI ptt file))
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.4371.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4371.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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