GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Pseudomonas putida KT2440

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate PP_5078 PP_5078 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__Putida:PP_5078
          Length = 365

 Score =  436 bits (1121), Expect = e-127
 Identities = 227/358 (63%), Positives = 269/358 (75%), Gaps = 5/358 (1%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           ++VDLG RSYPIYIG GLLDQP+LL  HI G++V +V+N TVAPLYL++   AL      
Sbjct: 4   LKVDLGERSYPIYIGEGLLDQPELLAPHIAGRQVAIVSNETVAPLYLERLSKALGA---- 59

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
            +V  V+LPDGE  KN ETL  +FD  + +R DRR T VALGGGVIGDM G+AAA Y RG
Sbjct: 60  YSVLPVVLPDGEAHKNWETLQLIFDGLLTARHDRRTTVVALGGGVIGDMAGFAAACYQRG 119

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           V+FIQ+PTT+++QVDSSVGGKTGINHPLGKNM+GAFYQP+ VLIDT +L TLP REL++G
Sbjct: 120 VDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMVGAFYQPKAVLIDTTSLKTLPARELSAG 179

Query: 261 LAEVIKYGLIRDAEFFEWQEQNMPLLLARDPTAFTYAIKRSCENKADVVSQDEKESGVRA 320
           LAEVIKYGLI D  F  W E NM  L A D  A T AI+RSC  KA VV  DE+ESG+RA
Sbjct: 180 LAEVIKYGLICDKPFLAWLEDNMQALRALDSAALTEAIRRSCAAKAAVVGADERESGLRA 239

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
           TLNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS RLGWID +   R  ++LQ A 
Sbjct: 240 TLNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSMRLGWIDQAERDRGIRLLQDAG 299

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438
           LP  PP+ MT   F   MAVDKKV DG+LRL+LL+  +G  V T DY ++ L  TL A
Sbjct: 300 LPVVPPQEMTPAHFMEHMAVDKKVLDGRLRLVLLR-QMGEAVVTDDYSKEILQATLSA 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: 411
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: 365
Length adjustment: 31
Effective length of query: 411
Effective length of database: 334
Effective search space:   137274
Effective search space used:   137274
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 PP_5078 PP_5078 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.7269.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7269.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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