GapMind for Amino acid biosynthesis

 

Alignments for a candidate for DAPtransferase in Desulfovibrio vulgaris Hildenborough

Align LL-diaminopimelate aminotransferase (EC 2.6.1.83) (characterized)
to candidate 207114 DVU1655 aminotransferase, classes I and II

Query= BRENDA::O66630
         (387 letters)



>MicrobesOnline__882:207114
          Length = 388

 Score =  479 bits (1232), Expect = e-140
 Identities = 237/385 (61%), Positives = 290/385 (75%), Gaps = 1/385 (0%)

Query: 2   FEFSDRLKVLPPYLFAELDRKKQEKIEQGVDVIDLGVGDPDMPTPKPIVEAAKKALENPE 61
           F+ +DRL  LPPYLFA +D+ K E   +GVD+I LG+GDPDM TP  I+EA K+A+  P 
Sbjct: 4   FKLADRLATLPPYLFAGIDKVKAEVAARGVDIISLGIGDPDMATPGFIIEAMKEAIARPA 63

Query: 62  NHKYPSYVGKYEFRKAVADWYKRRFDVDLDPNTEVITLIGSKEGIAHFPLAFVNPGDIVL 121
           NH+YPSYVG   FR+ VA+WY RRF V LDP TEVI LIGSKEGIAHFP AF+NPGD+VL
Sbjct: 64  NHQYPSYVGMLAFRQEVANWYDRRFGVSLDPATEVIGLIGSKEGIAHFPFAFINPGDLVL 123

Query: 122 CPDPAYPVYRIGAIFAGGTPYTVPLKEENNFLPDLDSIPEDVAKKAKIIWINYPNNPTSA 181
              P YPVY I   FAGG    VPL EEN+FLPDLD+IPED  K+AK+I++NYPNNPT+A
Sbjct: 124 VCTPNYPVYHIATGFAGGEVQFVPLLEENDFLPDLDAIPEDTWKRAKMIFVNYPNNPTAA 183

Query: 182 PPTLEFYKKLVDWAKEYNVIIASDNAYSEIYTGQE-KPPSILQVPGAKDVAIEFHSLSKT 240
              L FY+KLVD  + ++VIIA D AY+EIY  ++ +PPSIL VPGAKDVAIEFHSLSKT
Sbjct: 184 TAPLGFYEKLVDICRRFDVIIAHDTAYTEIYYDEDNRPPSILSVPGAKDVAIEFHSLSKT 243

Query: 241 YNMTGWRIGMAVGNKELVAGLGKVKTNVDSGQFGAVQDAGIVALNLPEEEVEKIRDVYRE 300
           YNMTGWR+GMAVGN  LVAGLGK+K N+DSG F AVQ+A IVAL   ++   ++R +YR+
Sbjct: 244 YNMTGWRVGMAVGNPTLVAGLGKIKENMDSGIFQAVQEASIVALRDGDDFCRELRGIYRQ 303

Query: 301 RKKIMTEALEKIGLEIYRSDYTFYLWIKVPEGYTSAEFVGRLIDEAGIVCTPGNGFGEYG 360
           R+  +  AL K G++      TFY+W +VP+G+TSA+FV R++ E G+V TPGNGFG  G
Sbjct: 304 RRDTVINALHKAGIQCRVPQATFYVWARVPQGHTSADFVTRVLQETGVVVTPGNGFGTPG 363

Query: 361 EGYFRISLTVPTERLLEAAERIKNL 385
           EG+FRISLTV   RL EA  RI  L
Sbjct: 364 EGFFRISLTVDNARLEEAVSRIAKL 388


Lambda     K      H
   0.317    0.139    0.413 

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: 508
Number of extensions: 20
Number of successful extensions: 3
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: 387
Length of database: 388
Length adjustment: 30
Effective length of query: 357
Effective length of database: 358
Effective search space:   127806
Effective search space used:   127806
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate 207114 DVU1655 (aminotransferase, classes I and II)
to HMM TIGR03540 (LL-diaminopimelate aminotransferase (EC 2.6.1.83))

Software error:

../bin/blast/fastacmd -i /tmp/list.2405.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2405.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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