GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Pseudomonas simiae WCS417

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF390 PS417_01985 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__WCS417:GFF390
          Length = 366

 Score =  431 bits (1107), Expect = e-125
 Identities = 224/358 (62%), Positives = 270/358 (75%), Gaps = 5/358 (1%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           ++VDLG RSYPI+IG GLLDQP+LL  HI G++V +++N TVAPLYL++   +L      
Sbjct: 4   LKVDLGERSYPIHIGEGLLDQPELLAPHIAGRQVAIISNETVAPLYLERLSRSLAA---- 59

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
            +V SVILPDGE  KN ETL  +FD  + +R DRR T +ALGGGVIGDM G+AAA Y RG
Sbjct: 60  YSVISVILPDGEAHKNWETLQLIFDGLLTARHDRRTTVIALGGGVIGDMAGFAAACYQRG 119

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           V+FIQ+PTT+++QVDSSVGGKTGINHPLGKNM+GAFYQPQ VLIDT TLNTLP REL++G
Sbjct: 120 VDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPQAVLIDTTTLNTLPPRELSAG 179

Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320
           LAEVIKYGLI D  F  W E+++  L   D  A T AI RSC  KA VV+ DE+ESGVRA
Sbjct: 180 LAEVIKYGLICDEPFLTWLEEHVDALRNLDQAALTEAISRSCAAKALVVNADERESGVRA 239

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
           TLNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS+RLGWI      R  ++ Q+A 
Sbjct: 240 TLNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSQRLGWISAQERDRGIRLFQRAG 299

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438
           LP  PPE MT   F   MA+DKKV DG+LRL+LL+  +G  V T DY ++ L  TL A
Sbjct: 300 LPVIPPEEMTEADFLEHMAIDKKVIDGRLRLVLLR-HMGEAVVTDDYPKEILQATLGA 356


Lambda     K      H
   0.318    0.133    0.385 

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: 409
Number of extensions: 9
Number of successful extensions: 2
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: 442
Length of database: 366
Length adjustment: 31
Effective length of query: 411
Effective length of database: 335
Effective search space:   137685
Effective search space used:   137685
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: 50 (23.9 bits)

Align candidate GFF390 PS417_01985 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.22574.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22574.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.