GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Dechlorosoma suillum PS

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate Dsui_2708 Dsui_2708 succinyldiaminopimelate transaminase

Query= BRENDA::Q9ZEX3
         (397 letters)



>FitnessBrowser__PS:Dsui_2708
          Length = 401

 Score =  465 bits (1197), Expect = e-136
 Identities = 240/397 (60%), Positives = 286/397 (72%), Gaps = 5/397 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP L  L PYPFEKLR L      P  D   I LSIGEP+HA P  + +A+ ANL GL+
Sbjct: 1   MNPFLAKLQPYPFEKLRQLFQGV-TPNPDYQEIKLSIGEPQHATPGFIKEALTANLGGLA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAG--A 118
            YP+++G PALRQAI+ W+ RRY +   +P++E+LPV GSREALFAFAQTVIDPS G   
Sbjct: 60  NYPTSQGTPALRQAIAAWMERRYGLAGVNPDTEILPVNGSREALFAFAQTVIDPSRGYVP 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LVV PNPFYQIYEGAA LAGA PY++N  P  DF L    + +  W R QL++VCSPGNP
Sbjct: 120 LVVSPNPFYQIYEGAAYLAGAEPYFLNTLPENDFSLELEALSEADWARVQLLYVCSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G V+ LE+W+ LF LSD++GFVIA+ ECYSEIY DE  PPLG LQAA++LGR  +  LV
Sbjct: 180 TGKVLDLEDWKKLFALSDKYGFVIASDECYSEIYFDEAKPPLGGLQAAKQLGRG-FERLV 238

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCRK 298
            FSSLSKRSNVPG+RSGFVAGDAA+L +FLLYRTYHG AM+P V AAS  AW+     R+
Sbjct: 239 MFSSLSKRSNVPGLRSGFVAGDAAVLKKFLLYRTYHGGAMNPAVQAASAIAWNEEAHARE 298

Query: 299 T-AQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
              QY+ KF+AV PI+ +VL    P ASFYLWA TP +DT FAR L     V VLPGS L
Sbjct: 299 NRRQYKEKFDAVTPIVASVLQTGLPDASFYLWARTPIADTEFARRLLADYNVVVLPGSYL 358

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFAR 394
           AREA   NPG+  +RIALVAPL  C++AAERI  F +
Sbjct: 359 AREARGVNPGENFVRIALVAPLADCLEAAERIRLFVQ 395


Lambda     K      H
   0.321    0.135    0.412 

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: 578
Number of extensions: 25
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: 397
Length of database: 401
Length adjustment: 31
Effective length of query: 366
Effective length of database: 370
Effective search space:   135420
Effective search space used:   135420
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate Dsui_2708 Dsui_2708 (succinyldiaminopimelate transaminase)
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.14504.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14504.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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