GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvA in Cupriavidus basilensis 4G11

Align Threonine dehydratase 1 biosynthetic, chloroplastic; SlTD1; Threonine deaminase 1; EC 4.3.1.19 (characterized)
to candidate RR42_RS02315 RR42_RS02315 threonine dehydratase

Query= SwissProt::A0FKE6
         (606 letters)



>FitnessBrowser__Cup4G11:RR42_RS02315
          Length = 508

 Score =  512 bits (1319), Expect = e-149
 Identities = 266/503 (52%), Positives = 354/503 (70%), Gaps = 5/503 (0%)

Query: 107 EYLTNILSSKVYDVAYETPLQKAPKLSERLGVNVWLKREDLQPVFSFKIRGAYNMMAKLP 166
           +YL  IL++KVYDVA ET L  A  LS R G  VW KRED QPVFSFK+RGAYN MA L 
Sbjct: 6   DYLRKILTAKVYDVAQETDLTYANLLSARTGNKVWFKREDTQPVFSFKLRGAYNKMASLS 65

Query: 167 KEQLEKGVICSSAGNHAQGVALSAQRLGCDAVIVMPVTTPDIKWKSVKRLGAT---VVLV 223
            E+L++GVI +SAGNHAQGVALSA RL C A+I MPVTTP +K  +V+  G     +VL 
Sbjct: 66  PEELKRGVIAASAGNHAQGVALSAARLKCKALIAMPVTTPQVKIDAVRERGGEWVEIVLH 125

Query: 224 GDSYDEAQAYAKKRAESEGRTFIPPFDHPDVIVGQGTVGMEINRQLKDNIHAIFVPVGGG 283
           GDSY +A  +A    +    TFI PFD P+VI GQGT+ MEI RQ    +HA+FV +GGG
Sbjct: 126 GDSYSDAYNHAAVLEKKHKLTFIHPFDDPEVIAGQGTIAMEILRQHPGPLHAVFVAIGGG 185

Query: 284 GLIAGIAAYLKRVAPDIKIIGVEPLDANALALSLHHGQRVMLDQVGGFADGVAVKVVGEE 343
           GLI+GIA+Y+K V P+IK+IGV+ +D++A+  S+  G+RV L +VG F+DG AVK+VG+E
Sbjct: 186 GLISGIASYIKAVRPEIKVIGVQTVDSDAMKRSVDAGKRVELKEVGLFSDGTAVKLVGKE 245

Query: 344 TYRLCEELIDGVVLVGRDAICASIKDMFEEKRSILEPAGALALAGAEAYCKYYGLKGENV 403
           T+R+  EL+D ++LV  DAICA +KD+F++ RSILEPAGA+A+AG + Y +   LKG+++
Sbjct: 246 TFRITRELVDEIILVDTDAICAGLKDVFQDTRSILEPAGAMAVAGLKLYAEREKLKGQHL 305

Query: 404 VAITSGANMNFDRLRLVTELADVGRQREAVLATFMPEDPGSFKKFAEMVGPMNITEFKYR 463
           VAI  GANMNFDRLR V E A+VG  REAV A  +PE+ GSFK+F E +G  N+TEF YR
Sbjct: 306 VAIACGANMNFDRLRFVAERAEVGEAREAVFAVSIPEERGSFKRFCEQLGTRNVTEFNYR 365

Query: 464 YNSDKERALVLYSVGLHTILELEGMVERMESADLQTINLTDNDLVKDHLRHLMGGRTNV- 522
             +DK  A +   V + +  E E +          T++L++++L K H+R+++GG + + 
Sbjct: 366 I-ADKSMAHIFVGVQIASRAENEKIAAGFRRHGFDTLDLSNDELAKQHIRYMVGGHSPLA 424

Query: 523 HNELLCRFTFPEKPGALMKFLDAFSPRWNISLFHYRAQGDTGANVLVGIQVPPDEVVEFE 582
           H+ELL RF FPE+PGALM+FL + SP WNISLFHYR QG   +N+LVGIQVP +E   F 
Sbjct: 425 HDELLYRFEFPERPGALMRFLSSMSPNWNISLFHYRNQGGDTSNILVGIQVPKNEKRAFR 484

Query: 583 GRADSLGYEYAMESLNEAYQLIM 605
               +LGY +  E+ N  Y+L +
Sbjct: 485 DFLATLGYVHWEETENPVYKLFL 507


Lambda     K      H
   0.318    0.136    0.393 

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: 704
Number of extensions: 31
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: 606
Length of database: 508
Length adjustment: 36
Effective length of query: 570
Effective length of database: 472
Effective search space:   269040
Effective search space used:   269040
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate RR42_RS02315 RR42_RS02315 (threonine dehydratase)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.32312.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32312.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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