GapMind for Amino acid biosynthesis

 

Alignments for a candidate for asp-kinase in Pedobacter sp. GW460-11-11-14-LB5

Align aspartate kinase (EC 2.7.2.4) (characterized)
to candidate CA265_RS09655 CA265_RS09655 aspartate kinase

Query= BRENDA::Q9S702
         (559 letters)



>FitnessBrowser__Pedo557:CA265_RS09655
          Length = 437

 Score =  233 bits (593), Expect = 1e-65
 Identities = 170/470 (36%), Positives = 257/470 (54%), Gaps = 50/470 (10%)

Query: 86  VMKFGGSSVASAERMIQVAKLILSFPDEKPVVVLSAMAKTTNKLL------MAGEK---A 136
           ++KFGG+SV S ERM ++  +I   P+E+ +VVLSA++ TTN L+      +AG+K   +
Sbjct: 3   ILKFGGTSVGSPERMTKLLDIIN--PNEEQIVVLSAVSGTTNSLVEIANYFLAGDKKKGS 60

Query: 137 VCCGVTNVDTIEELSYIKELHIRTAHELGVETAVIAEHLEGLEQLLKGVAMMKELTLRSR 196
            C  V N+    +   ++ L      E G E  VI  H   L  L   +      T    
Sbjct: 61  EC--VENLYQKYKTFVVELLPAAEFQEQGNE--VIDYHFGFLAGLANDI-----FTSIEE 111

Query: 197 DYLVSFGECMSTRLFAAYLNKIGHKARQYDAFEIGIITTDDFTNADILEATYPAVSKKL- 255
             +++ GE +ST L+  YL  IG  +    A +   + TD+    DI     P  +K L 
Sbjct: 112 KVVLAQGELLSTTLYHIYLKSIGVPSVLLPALDF--MKTDEDNEPDI-----PFTTKHLT 164

Query: 256 -LGDWSKENALPVVTGFLGKGWRSCAVTTLGRGGSDLTATTIGKALGLREIQVWKDVDGV 314
            L +  K+N L +  G++ +      V  L RGGSD TA+ +G A+   E+Q+W D+DG+
Sbjct: 165 PLLEQHKDNKLFITQGYICRNSFG-EVDNLRRGGSDYTASLLGAAILAEEVQIWTDIDGM 223

Query: 315 LTCDPNIYCGAQPVPHLTFDEAAELAYFGAQVLHPLSMRPAREGNIPVRVKNSYNPTAPG 374
              DP I  G +P+  L+FDEAAELAYFGA++LHP S+ PA++  IPVR+ N+  P+A G
Sbjct: 224 HNNDPRIVKGTKPIAQLSFDEAAELAYFGAKILHPQSVFPAQKYKIPVRLLNTMEPSAAG 283

Query: 375 TVITRSRDMSKAVLTSIVLKRNVTMLDITSTRMLGQYGFLAKVFSTFEKLGISVDVVATS 434
           T+IT   D  +  + SI  K  +T + I S+RML  YGFL +VF  FE+    +D++ TS
Sbjct: 284 TLIT--HDSERGKIKSIAAKDGITAIRIQSSRMLLAYGFLRRVFEVFERYKTPIDMITTS 341

Query: 435 EVSISLTLDPSKFCSRELIQHELDQVVEELEKIAVVNLLRHRSIISLIGNVQRSSFILEK 494
           EV++SLT+D +           L Q++EELE    V +  + SI+ ++G+     F  EK
Sbjct: 342 EVAVSLTIDETA---------HLPQIIEELESFGTVEVDTNHSIVCVVGD-----FGSEK 387

Query: 495 -GF--RVLR-TNGINVQMISQGASKVNISLIVNDDEAEHCVKALHSAFFE 540
            GF  RVL     I ++MIS G S  N+SL++  +     +++LH+  FE
Sbjct: 388 HGFASRVLEGLKHIPIRMISYGGSNYNVSLLILSEYKTEALRSLHNRLFE 437


Lambda     K      H
   0.319    0.133    0.375 

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: 475
Number of extensions: 21
Number of successful extensions: 7
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: 559
Length of database: 437
Length adjustment: 34
Effective length of query: 525
Effective length of database: 403
Effective search space:   211575
Effective search space used:   211575
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 CA265_RS09655 CA265_RS09655 (aspartate kinase)
to HMM TIGR00657 (aspartate kinase (EC 2.7.2.4))

Software error:

../bin/blast/fastacmd -i /tmp/list.31810.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31810.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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