GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroB in Shewanella amazonensis SB2B

Align 3-dehydroquinate synthase (EC 4.2.3.4) (characterized)
to candidate 6939274 Sama_3367 3-dehydroquinate synthase (RefSeq)

Query= BRENDA::P07639
         (362 letters)



>FitnessBrowser__SB2B:6939274
          Length = 359

 Score =  438 bits (1127), Expect = e-128
 Identities = 221/348 (63%), Positives = 263/348 (75%)

Query: 1   MERIVVTLGERSYPITIASGLFNEPASFLPLKSGEQVMLVTNETLAPLYLDKVRGVLEQA 60
           M++I V L  RSYPI I   LF +   F P+ SG++V++V+NET+APLYLDK+   L   
Sbjct: 1   MKQIQVDLANRSYPIHIGPNLFEDQELFAPVVSGKKVLVVSNETIAPLYLDKISATLSAR 60

Query: 61  GVNVDSVILPDGEQYKSLAVLDTVFTALLQKPHGRDTTLVALGGGVVGDLTGFAAASYQR 120
              V SVILPDGEQYK+L  L+ +F ALL+    RD  LVALGGGV+GD+TGFAAA YQR
Sbjct: 61  AAQVASVILPDGEQYKTLDYLNEIFDALLEGNFARDCVLVALGGGVIGDMTGFAAACYQR 120

Query: 121 GVRFIQVPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPASVVVDLDCLKTLPPRELAS 180
           GV FIQ+PTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQP  VV+D++CLKTLP RE A+
Sbjct: 121 GVDFIQIPTTLLSQVDSSVGGKTAVNHPLGKNMIGAFYQPKLVVIDINCLKTLPAREFAA 180

Query: 181 GLAEVIKYGIILDGAFFNWLEENLDALLRLDGPAMAYCIRRCCELKAEVVAADERETGLR 240
           G+AEVIKYGII D   F WLE+N+ AL  LD  A+ + I RCCE+KAEVV+ DE E G+R
Sbjct: 181 GMAEVIKYGIIRDSELFTWLEQNVSALKALDQDAIIHVIARCCEIKAEVVSEDETEQGVR 240

Query: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVMAARTSERLGQFSSAETQRIITLLKRA 300
           ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMV+AA+TS  LG    +   RI  L++  
Sbjct: 241 ALLNLGHTFGHAIEAEMGYGNWLHGEAVAAGMVLAAQTSVTLGLIDKSILCRIAALIQAF 300

Query: 301 GLPVNGPREMSAQAYLPHMLRDKKVLAGEMRLILPLAIGKSEVRSGVS 348
            LPV  P  M   +++ HM RDKKVL G++RL+LPL IG +EV S  S
Sbjct: 301 DLPVQAPESMDFNSFIKHMRRDKKVLGGQLRLVLPLGIGAAEVSSQAS 348


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: 334
Number of extensions: 7
Number of successful extensions: 1
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 6939274 Sama_3367 (3-dehydroquinate synthase (RefSeq))
to HMM TIGR01357 (aroB: 3-dehydroquinate synthase (EC 4.2.3.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.10125.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10125.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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