GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Sphingomonas koreensis DSMZ 15582

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate Ga0059261_0220 Ga0059261_0220 L-serine dehydratase, iron-sulfur-dependent, single chain form

Query= reanno::Cup4G11:RR42_RS20080
         (458 letters)



>FitnessBrowser__Korea:Ga0059261_0220
          Length = 463

 Score =  483 bits (1244), Expect = e-141
 Identities = 253/456 (55%), Positives = 312/456 (68%), Gaps = 9/456 (1%)

Query: 3   VSVFDLFKVGIGPSSSHTVGPMRAALMFAQGLARDGLLPQVASVRVELYGSLGATGRGHG 62
           + + DLF +GIGPSSSHTVGPMRAA  F++     G+     SV  EL+GSL  TG+GH 
Sbjct: 17  IGLADLFTIGIGPSSSHTVGPMRAAHAFSEAALDRGI---PVSVSCELFGSLALTGKGHA 73

Query: 63  TDKGVILGLLGEAPDTIDPDTIDVRLAALRASRTLSLLGTHPVPFVEKEHIVFYRREAMA 122
           TD  VILGL G  P+++DPD +   +A +++ + LSL G   VPFVE  H++F     + 
Sbjct: 74  TDTAVILGLAGHQPESVDPDAVASIVATIQSEQKLSLGGQVIVPFVEGRHLIFRSDRFLP 133

Query: 123 EHPNGMKFHAFNAGGERIREGRYLSVGGGFIITAGAANTHILEADQQLPHPFRSGRAMLE 182
            HPNGM+F A    GE   E  + S+GGG ++  G        ++  LP  F SG  +L 
Sbjct: 134 AHPNGMRFVAHYPDGEPY-ETFWYSIGGGAVVEGGCEAPR---SNVTLPMNFSSGAELLA 189

Query: 183 MAAASKKSIARLMMENECVWRSEAEVNAGLLQIWAVMQACVARGCRTDGELPGPFKVKRR 242
           +A     +IA ++  NE  WR + E +A L  + A M AC+ RG R +GELPG  KVKRR
Sbjct: 190 VAEEKGVTIADIVRANEAAWRDDTETDAFLDSLRAAMSACIERGMRGEGELPGGLKVKRR 249

Query: 243 AHDLFRNLTEHAERALADPLSVIDWVNLYAIAVNEENAAGGRVVTAPTNGAAGIIPAVLH 302
           A DL   L     R+  DP  V DWV+L+A+AVNEENAAGGRVVTAPTNGAAG+IPAVL 
Sbjct: 250 ARDLHNKLLARGPRS--DPSLVFDWVSLWALAVNEENAAGGRVVTAPTNGAAGVIPAVLR 307

Query: 303 YYDRFVPGANPQGVIDFLLTAGAIGMLYKLNASISGAEVGCQGEVGVACSMAAGALAAVM 362
           YY+ F     P G   FLLT  AIG LYK  ASIS AE+GCQGEVGVACSMAA  LAA +
Sbjct: 308 YYETFCASPTPAGARTFLLTTAAIGFLYKKRASISAAEMGCQGEVGVACSMAAAGLAAAL 367

Query: 363 GGTPEQVENAAEIGMEHNLGLTCDPVGGLVQIPCIERNAMASVKAVNAARMALRGDGMHY 422
           G T  Q+ENAAEIGMEHNLGLTCDP+GGLVQIPCIERN M ++KA+NAA +A+ GDG H 
Sbjct: 368 GATNAQIENAAEIGMEHNLGLTCDPIGGLVQIPCIERNTMGAIKAINAAYLAMHGDGSHV 427

Query: 423 VSLDSVIKTMRETGADMKTKYKETARGGLAVNIVEC 458
           VSLD+VI+TMR+TG DM++KYKETA+GGLAVN+V C
Sbjct: 428 VSLDAVIETMRQTGEDMRSKYKETAQGGLAVNVVAC 463


Lambda     K      H
   0.320    0.136    0.400 

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: 639
Number of extensions: 23
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: 458
Length of database: 463
Length adjustment: 33
Effective length of query: 425
Effective length of database: 430
Effective search space:   182750
Effective search space used:   182750
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: 51 (24.3 bits)

Align candidate Ga0059261_0220 Ga0059261_0220 (L-serine dehydratase, iron-sulfur-dependent, single chain form)
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.25954.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25954.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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