GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Shewanella oneidensis MR-1

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 199482 SO0287 3-dehydroquinate synthase (NCBI ptt file)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__MR1:199482
          Length = 359

 Score =  429 bits (1104), Expect = e-125
 Identities = 216/358 (60%), Positives = 271/358 (75%), Gaps = 2/358 (0%)

Query: 2   ERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQAG 61
           ++I V LGERSYPI I   L ++  +       +++++VTNET+APLYL +V+  +   G
Sbjct: 3   QQIQVDLGERSYPIYIGQSLMSDSETLSRYLLKKRILIVTNETVAPLYLKQVQDTMASFG 62

Query: 62  VNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQRG 121
             + SVIL DGEQ+K L  LD++FTALLQ+ +GRD+ LVALGGGV+GD+TGFAAA YQRG
Sbjct: 63  -EISSVILSDGEQFKDLTHLDSIFTALLQRNYGRDSVLVALGGGVIGDMTGFAAACYQRG 121

Query: 122 VRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELASG 181
           + FIQ+PTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQP  V++D +CL+TLP RE A+G
Sbjct: 122 IDFIQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPQIVIIDTECLQTLPAREFAAG 181

Query: 182 LAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLRA 241
           +AEVIKYGI+ D  FF WLE N+ AL  LD  A+ Y I RCCE+KA+VV+ DE E G+RA
Sbjct: 182 MAEVIKYGIMWDADFFQWLENNVQALKSLDTQALVYAISRCCEIKADVVSQDETEQGVRA 241

Query: 242 LLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRAG 301
           LLNLGHTFGHAIEAEMGYGNWLHGEAVAAG V+AA+T++ LG    +   RI+ LL+   
Sbjct: 242 LLNLGHTFGHAIEAEMGYGNWLHGEAVAAGTVLAAQTAKSLGLIDESIVCRIVQLLQAFD 301

Query: 302 LPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVSHELVLNAIADC 359
           LPV  P  M  ++++ HM RDKKVL G++RL+LP AIG++EV S V  E  L  +  C
Sbjct: 302 LPVKAPESMDFESFIQHMRRDKKVLGGQIRLVLPTAIGRAEVFSQVP-ESTLEQVICC 358


Lambda     K      H
   0.320    0.136    0.392 

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: 328
Number of extensions: 5
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: 362
Length of database: 359
Length adjustment: 29
Effective length of query: 333
Effective length of database: 330
Effective search space:   109890
Effective search space used:   109890
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: 49 (23.5 bits)

Align candidate 199482 SO0287 (3-dehydroquinate synthase (NCBI ptt file))
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.1813.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1813.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.