GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisD in Pseudomonas putida KT2440

Align histidinol dehydrogenase (EC 1.1.1.23) (characterized)
to candidate PP_0966 PP_0966 Histidinol dehydrogenase

Query= BRENDA::Q8G2R2
         (430 letters)



>FitnessBrowser__Putida:PP_0966
          Length = 441

 Score =  395 bits (1016), Expect = e-114
 Identities = 208/428 (48%), Positives = 285/428 (66%), Gaps = 1/428 (0%)

Query: 2   VTTLRQTDPDFEQKFAAFLSGKREVSEDVDRAVREIVDRVRREGDSALLDYSRRFDRIDL 61
           +  L   DPDF +     LS +    + V++ V +I+  VR  GD+AL+++++RFD +D 
Sbjct: 7   IARLNAADPDFARHLDHLLSWESVSDDAVNQRVLDIIKAVRERGDAALVEFTQRFDGVDA 66

Query: 62  EKTG-IAVTEAEIDAAFDAAPASTVEALKLARDRIEKHHARQLPKDDRYTDALGVELGSR 120
           +    + +  A ++ A         EAL+ A +R+  +H RQ     +YT+A G  LG +
Sbjct: 67  KSIDDLILDRARLELALTRITPVQREALEKAANRVRIYHERQKQDSWQYTEADGTVLGQK 126

Query: 121 WTAIEAVGLYVPGGTASYPSSVLMNAMPAKVAGVDRIVMVVPAPDGNLNPLVLVAARLAG 180
            T ++  GLYVPGG ASYPSSVLMNA+PAKVAGV  +VMVVP P G +N LVL AA +AG
Sbjct: 127 VTPLDRAGLYVPGGKASYPSSVLMNAIPAKVAGVTEVVMVVPTPRGEVNELVLAAACIAG 186

Query: 181 VSEIYRVGGAQAIAALAYGTETIRPVAKIVGPGNAYVAAAKRIVFGTVGIDMIAGPSEVL 240
           V  ++ VGGAQA+AALAYGTE++  V KIVGPGN YVA AKR VFG VGIDMIAGPSE+L
Sbjct: 187 VDRVFTVGGAQAVAALAYGTESVPQVDKIVGPGNIYVATAKRHVFGQVGIDMIAGPSEIL 246

Query: 241 IVADKDNNPDWIAADLLAQAEHDTAAQSILMTNDEAFAHAVEEAVERQLHTLARTETASA 300
           +V D   +PDWIA DL +QAEHD  AQ+IL++ D AF   V  ++++ + T+ R +    
Sbjct: 247 VVCDGQTDPDWIAMDLFSQAEHDEDAQAILVSPDAAFLDRVAASIDKLMPTMERADIIEK 306

Query: 301 SWRDFGAVILVKDFEDAIPLANRIAAEHLEIAVADAEAFVPRIRNAGSIFIGGYTPEVIG 360
           S    GA+I V+D + A+ +ANRIA EHLE++VAD +A++P IR+AG+IF+G +T E +G
Sbjct: 307 SINGRGALIQVRDMQQAMDVANRIAPEHLELSVADPQAWLPHIRHAGAIFMGRHTSEALG 366

Query: 361 DYVGGCNHVLPTARSARFSSGLSVLDYMKRTSLLKLGSEQLRALGPAAIEIARAEGLDAH 420
           DY  G NHVLPT+ +ARFSS L V D+ KR+S++    +    LG  A  +AR E L AH
Sbjct: 367 DYCAGPNHVLPTSGTARFSSPLGVYDFQKRSSIIFCSEQGASELGHTASVLARGESLTAH 426

Query: 421 AQSVAIRL 428
           A+S   R+
Sbjct: 427 ARSAEYRI 434


Lambda     K      H
   0.318    0.134    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: 485
Number of extensions: 21
Number of successful extensions: 2
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: 430
Length of database: 441
Length adjustment: 32
Effective length of query: 398
Effective length of database: 409
Effective search space:   162782
Effective search space used:   162782
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate PP_0966 PP_0966 (Histidinol dehydrogenase)
to HMM TIGR00069 (hisD: histidinol dehydrogenase (EC 1.1.1.23))

Software error:

../bin/blast/fastacmd -i /tmp/list.19421.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19421.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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