GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Burkholderia phytofirmans PsJN

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate BPHYT_RS12185 BPHYT_RS12185 succinyldiaminopimelate aminotransferase

Query= BRENDA::Q9ZEX3
         (397 letters)



>FitnessBrowser__BFirm:BPHYT_RS12185
          Length = 405

 Score =  474 bits (1220), Expect = e-138
 Identities = 242/403 (60%), Positives = 296/403 (73%), Gaps = 11/403 (2%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MNP LD+L PYPFEKLRAL AD   P+  L  I+  IGEPKH  P  +  A+ A+L GLS
Sbjct: 1   MNPLLDSLQPYPFEKLRALFADV-TPSAGLAHISFGIGEPKHPTPELIRDAVVASLGGLS 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAPDPESEVLPVLGSREALFAFAQTVIDPSAGA-- 118
            YP+T G PALR++I++W++RRY++P  DP ++VLPV GSREALFA AQTV+DP   A  
Sbjct: 60  SYPATIGSPALRESIAKWVTRRYNLPPVDPATQVLPVSGSREALFALAQTVLDPKKNADG 119

Query: 119 ---LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSP 175
              +V+CPNPFYQIYEGAA+LAGA PY+VN+DPAR+F      VP ++W RTQL++VCSP
Sbjct: 120 EPAIVLCPNPFYQIYEGAAILAGAQPYFVNSDPARNFACDYSAVPADIWARTQLLYVCSP 179

Query: 176 GNPAGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYT 235
           GNP G V++L++WR LF LSDR+GFVIA+ ECYSEIY DE  PPLG L+AA +LGR  + 
Sbjct: 180 GNPTGAVLTLDDWRELFALSDRYGFVIASDECYSEIYFDEANPPLGGLEAAHKLGRG-FE 238

Query: 236 NLVAFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRM 295
            LV  SSLSKRSNVPGMRSGFVAGDAA+L  FLLYRTYHG+A+S V  +ASI AW+    
Sbjct: 239 RLVMLSSLSKRSNVPGMRSGFVAGDAAILKDFLLYRTYHGAALSTVFQSASIVAWNDETH 298

Query: 296 CRKT-AQYRAKFEAVLPILQNVLDVRAPQASFYLWAG---TPGSDTAFARELYGRTGVTV 351
            R+  A+Y  KF  V P+L  VLDVR P A+FYLWA    T  +DT FA+ LY    VTV
Sbjct: 299 VRENRAKYVQKFSTVTPMLAEVLDVRLPDAAFYLWADVSRTGLTDTEFAQRLYADYNVTV 358

Query: 352 LPGSLLAREAHNANPGQGRIRIALVAPLDQCVQAAERIAHFAR 394
           LPGS LAR AH  NPG+  +R+ALVA +D+C Q A+RI  F R
Sbjct: 359 LPGSFLARTAHGVNPGRNFVRMALVAGVDECTQGAQRIVDFCR 401


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: 564
Number of extensions: 21
Number of successful extensions: 6
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: 405
Length adjustment: 31
Effective length of query: 366
Effective length of database: 374
Effective search space:   136884
Effective search space used:   136884
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 BPHYT_RS12185 BPHYT_RS12185 (succinyldiaminopimelate aminotransferase)
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.20454.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20454.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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