GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Pseudomonas stutzeri RCH2

Align 3-dehydroquinate synthase, chloroplastic; EC 4.2.3.4 (characterized)
to candidate GFF3646 Psest_3713 3-dehydroquinate synthase

Query= SwissProt::Q8RU74
         (442 letters)



>FitnessBrowser__psRCH2:GFF3646
          Length = 367

 Score =  428 bits (1100), Expect = e-124
 Identities = 221/358 (61%), Positives = 269/358 (75%), Gaps = 5/358 (1%)

Query: 81  VEVDLGTRSYPIYIGAGLLDQPDLLQRHIHGKRVLVVTNTTVAPLYLDKTISALTDGNPN 140
           ++VDLG RSYPI+IG  LLD+P+L    I G++V +VTN TVAPLYLD+    L+    N
Sbjct: 4   LQVDLGERSYPIHIGERLLDRPELFSDKIRGRQVAIVTNETVAPLYLDRLTRTLS----N 59

Query: 141 VTVESVILPDGEQFKNMETLMKVFDKAIESRLDRRCTFVALGGGVIGDMCGYAAASYLRG 200
             V  VILPDGE+ KN +TL  +FD  + +R DR  T +ALGGGV+GDM GYAAASY RG
Sbjct: 60  HAVTPVILPDGEEHKNWQTLQLIFDALLGARHDRNTTIIALGGGVVGDMAGYAAASYQRG 119

Query: 201 VNFIQIPTTVMAQVDSSVGGKTGINHPLGKNMIGAFYQPQCVLIDTDTLNTLPDRELASG 260
           V+FIQ+PTT+++QVDSSVGGKTGINHPLGKNMIGAFYQP+ V+IDT TL TLP REL++G
Sbjct: 120 VDFIQVPTTLLSQVDSSVGGKTGINHPLGKNMIGAFYQPRAVVIDTTTLATLPARELSAG 179

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

Query: 321 TLNLGHTFGHAVETGVGYGQWLHGEAVAAGTVMAVDMSRRLGWIDDSLVQRVQKILQQAK 380
            LNLGHTFGHA+ET +GYG WLHGEAVAAGTVMA++MS +LGWI ++   R  ++LQ+A 
Sbjct: 240 ILNLGHTFGHAIETHMGYGVWLHGEAVAAGTVMALEMSCQLGWIGEAERDRAIRLLQRAA 299

Query: 381 LPTSPPETMTVEMFKSIMAVDKKVADGKLRLILLKGSLGNCVFTGDYDQKALDETLRA 438
           LP  PP  M  + F   MAVDKKV DG+LRL+LL+  LG  V TGD+ +  L+ TL A
Sbjct: 300 LPVVPPAQMRPQDFLEHMAVDKKVLDGRLRLVLLR-QLGEAVVTGDFPRDVLETTLNA 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: 430
Number of extensions: 7
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: 367
Length adjustment: 31
Effective length of query: 411
Effective length of database: 336
Effective search space:   138096
Effective search space used:   138096
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 GFF3646 Psest_3713 (3-dehydroquinate synthase)
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.12930.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12930.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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