GapMind for Amino acid biosynthesis

 

Alignments for a candidate for prs in Pseudomonas stutzeri RCH2

Align Ribose-phosphate pyrophosphokinase; RPPK; EC 2.7.6.1; 5-phospho-D-ribosyl alpha-1-diphosphate; Phosphoribosyl diphosphate synthase; Phosphoribosyl pyrophosphate synthase; P-Rib-PP synthase; PRPP synthase; PRPPase (uncharacterized)
to candidate GFF2178 Psest_2222 ribose-phosphate pyrophosphokinase

Query= curated2:Q9PQV0
         (330 letters)



>FitnessBrowser__psRCH2:GFF2178
          Length = 317

 Score =  145 bits (365), Expect = 2e-39
 Identities = 92/289 (31%), Positives = 148/289 (51%), Gaps = 16/289 (5%)

Query: 4   NDDILLFSLSNSHQLANKIANLLKIELSPIRIDKFADGELIVAPQVPVRGRRVIIIQST- 62
           N   LLF+L  + + A ++A  + +EL+ I    F DGE       PV GR+V +  +  
Sbjct: 3   NHPPLLFALQGTQEYAARVARHMGLELAEIEERAFEDGEHKSRALTPVEGRKVAVFHALY 62

Query: 63  ---SKPVNDSLMELLIAIDSIKRASAKAISVVIPYYGYARQDRKAKPREPITARLVAKMI 119
               + VND L  LL    ++K A A+ + VV PY  YAR++R+ + ++PI  R VA + 
Sbjct: 63  GDDERSVNDKLCRLLFFCGALKDAGARHVQVVAPYLCYARKERRTQFQDPIITRYVAALF 122

Query: 120 ESAGATSVLTWDIHSLQT-QGFFDIPFDSLEAVWVLMKHYFSAYKDSSNITIVSPDYGGV 178
           E+     + T ++H+L      F IP   +E+  +   H F+     + +  VSPD GG 
Sbjct: 123 EACRVDRLTTLEVHNLAAFDNAFRIPTRHIESAELFAAH-FAQLSADAELVAVSPDAGGA 181

Query: 179 KRA----REISIATGATLAIVDKRRSGKNQVEINNVL-GDVKDRDCVIVDDMIDTGGTIL 233
           KRA    R +   TG ++      +   N +    +L GDV+DR  +IVDD+I TGGT+L
Sbjct: 182 KRAESFRRALQQHTGRSVGSAYMEKYRSNDIVTGTMLVGDVRDRIAIIVDDLISTGGTLL 241

Query: 234 GAAKIVREKGAKSITIIATHGLFNNNARQHFQQAIKDRIINKICIADTI 282
            A +  R+ GA+ +   A HGLF         + ++  + +++ I DT+
Sbjct: 242 RAGEACRKAGARQVHAAAAHGLFTGG-----PELLESPVFDQLVITDTV 285


Lambda     K      H
   0.319    0.135    0.378 

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: 221
Number of extensions: 11
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: 330
Length of database: 317
Length adjustment: 28
Effective length of query: 302
Effective length of database: 289
Effective search space:    87278
Effective search space used:    87278
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: 48 (23.1 bits)

Align candidate GFF2178 Psest_2222 (ribose-phosphate pyrophosphokinase)
to HMM TIGR01251 (prs: ribose-phosphate diphosphokinase (EC 2.7.6.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.4041.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4041.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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