GapMind for Amino acid biosynthesis

 

Alignments for a candidate for trpE in Dinoroseobacter shibae DFL-12

Align anthranilate synthase (EC 4.1.3.27) (characterized)
to candidate 3608396 Dshi_1796 anthranilate synthase component I (RefSeq)

Query= BRENDA::P20580
         (492 letters)



>FitnessBrowser__Dino:3608396
          Length = 509

 Score =  415 bits (1067), Expect = e-120
 Identities = 246/480 (51%), Positives = 307/480 (63%), Gaps = 26/480 (5%)

Query: 25  ADFDTPLSIYLKLADA-PNSYLLESVQGGEKWGRYSIIGLPCRTVLRVYDHQVRISIDGV 83
           AD DTP+S+ LKLA A  +S++LESV GGE  GRYS++GL    +        RI+    
Sbjct: 28  ADLDTPVSLMLKLAGARKDSFMLESVTGGEVRGRYSVVGLKPDLIWECRGTGARIN---- 83

Query: 84  ETERFDC-------ADPLAFVEEFKARYQVPTVPGLPRFDGGLVGYFGYDCVRYVEKRLA 136
            + RFD         DPLA +    A  ++     LP    GL GY GYD +R VE    
Sbjct: 84  RSARFDAEAFEDIPGDPLAALRALIAESRIEMPDELPAIAAGLFGYLGYDMIRLVEHLPN 143

Query: 137 TCPNPDPLGNPDILLMVSDAVVVFDNLAGKIHAI--VLAD------PSEENAYERGQARL 188
              NPDPLG PD +L+    V V D + G++  +  V A+       S   AY +   R+
Sbjct: 144 V--NPDPLGLPDAVLVRPSVVAVLDGVKGEVTVVSPVWANGSAGGGQSARAAYAQAAERV 201

Query: 189 EELLERL-RQPITPRRGLDLEAAQGREPAFRASFTREDYENAVGRIKDYILAGDCMQVVP 247
            + +  L R  +  RR L  EAA+  EP   ++F   DY  AV R KDYI AGD  QVVP
Sbjct: 202 MDAVRDLERSAMAERRDLG-EAAELGEPV--SNFAHADYLAAVERAKDYIRAGDIFQVVP 258

Query: 248 SQRMSIEFKAAPIDLYRALRCFNPTPYMYFFNFGDFHVVGSSPEVLVRVEDGLVTVRPIA 307
           SQR S  F   P  LYR+LR  NP+P+M++FNFG F +VG+SPE+LVRV    VT+RPIA
Sbjct: 259 SQRWSQAFPLPPFALYRSLRRTNPSPFMFYFNFGGFQIVGASPEILVRVFGREVTIRPIA 318

Query: 308 GTRPRGINEEADLALEQDLLSDAKEIAEHLMLIDLGRNDVGRVSDIGAVKVTEKMVIERY 367
           GTRPRG     D ALE DLL+DAKE AEHLML+DLGRNDVGRV+ IG V+ TE+ +IERY
Sbjct: 319 GTRPRGATPAEDDALEADLLADAKECAEHLMLLDLGRNDVGRVAKIGTVRPTEQFIIERY 378

Query: 368 SNVMHIVSNVTGQLREGLSAMDALRAILPAGTLSGAPKIRAMEIIDELEPVKRGVYGGAV 427
           S+VMHIVSNV G+L E   A+ AL A LPAGT+SGAPK+RAMEIIDELEP KRGVYGG  
Sbjct: 379 SHVMHIVSNVVGELSEEHDALSALLAGLPAGTVSGAPKVRAMEIIDELEPEKRGVYGGGC 438

Query: 428 GYLAWNGNMDTAIAIRTAVIKNGELHVQAGGGIVADSVPALEWEETINKRRAMFRAVALA 487
           GY A NG+MD  IA+RTAV+K+  L++QAGGG+V DS P  E++ET+NK +A+  A   A
Sbjct: 439 GYFAANGDMDMCIALRTAVVKDETLYIQAGGGVVYDSDPEAEFQETVNKAKAIRMAAQQA 498


Lambda     K      H
   0.321    0.139    0.408 

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: 687
Number of extensions: 36
Number of successful extensions: 5
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: 492
Length of database: 509
Length adjustment: 34
Effective length of query: 458
Effective length of database: 475
Effective search space:   217550
Effective search space used:   217550
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: 52 (24.6 bits)

Align candidate 3608396 Dshi_1796 (anthranilate synthase component I (RefSeq))
to HMM TIGR00564 (trpE: anthranilate synthase component I (EC 4.1.3.27))

Software error:

../bin/blast/fastacmd -i /tmp/list.10511.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10511.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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