GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Pseudomonas simiae WCS417

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate GFF1476 PS417_07505 cysteine synthase

Query= BRENDA::P0ABK5
         (323 letters)



>FitnessBrowser__WCS417:GFF1476
          Length = 324

 Score =  442 bits (1138), Expect = e-129
 Identities = 229/324 (70%), Positives = 264/324 (81%), Gaps = 3/324 (0%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIG--NGRILAKVESRNPSFSVKCRIGANMIWDAEKRGV 58
           MS+IF DN+ +IG+TPLV++NRI      ILAK+E RNP +SVKCRIGANMIWDAE  G 
Sbjct: 1   MSRIFADNAHSIGNTPLVQINRIAPRGVTILAKIEGRNPGYSVKCRIGANMIWDAESTGK 60

Query: 59  LKPGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAK 118
           LKPG+ +VEPTSGNTGI LA+VAAARGYKL LTMP +MSIERRK+LKALGA LVLTE AK
Sbjct: 61  LKPGMTIVEPTSGNTGIGLAFVAAARGYKLLLTMPASMSIERRKVLKALGAELVLTEPAK 120

Query: 119 GMKGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGT 178
           GMKGAI+KA EIVAS+P  Y +  QF NPANP IHEKTTGPEIW DTDG VDV +AGVGT
Sbjct: 121 GMKGAIEKAGEIVASDPATYFMPAQFENPANPAIHEKTTGPEIWNDTDGAVDVLVAGVGT 180

Query: 179 GGTLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPAN 238
           GGT+TGVSRYIK   GK  ++SVAVEP  SPVI QALAGEEIKP PHKIQGIGAGF+P N
Sbjct: 181 GGTITGVSRYIKNIAGK-PILSVAVEPIVSPVITQALAGEEIKPSPHKIQGIGAGFVPKN 239

Query: 239 LDLKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVI 298
           LDL +VD+V  +T++E+ + A RLM+EEGIL GIS GAA+A A++L E      K IVVI
Sbjct: 240 LDLSMVDRVELVTDDESKAMALRLMQEEGILCGISCGAAMAVAVRLAEKPEMQGKTIVVI 299

Query: 299 LPSSGERYLSTALFADLFTEKELQ 322
           LP SGERYLS+ LF+DLFTE+E Q
Sbjct: 300 LPDSGERYLSSMLFSDLFTEQENQ 323


Lambda     K      H
   0.313    0.133    0.368 

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: 405
Number of extensions: 18
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: 323
Length of database: 324
Length adjustment: 28
Effective length of query: 295
Effective length of database: 296
Effective search space:    87320
Effective search space used:    87320
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate GFF1476 PS417_07505 (cysteine synthase)
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

Software error:

../bin/blast/fastacmd -i /tmp/list.5079.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5079.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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