GapMind for catabolism of small carbon sources

 

Alignments for a candidate for tdcB in Pseudomonas fluorescens FW300-N2C3

Align L-threonine dehydratase biosynthetic IlvA; EC 4.3.1.19; Threonine deaminase (uncharacterized)
to candidate AO356_27710 AO356_27710 threonine dehydratase

Query= curated2:P37946
         (422 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_27710
          Length = 333

 Score =  230 bits (586), Expect = 5e-65
 Identities = 133/331 (40%), Positives = 193/331 (58%), Gaps = 9/331 (2%)

Query: 7   ENSLIQ--VKHILKAHQNVKDVVIHTPLQRNDRLSERYECNIYLKREDLQVVRSFKLRGA 64
           E +L++  VK IL A   V ++ + TPLQ    LSE     I LKREDLQ   SFK+RGA
Sbjct: 7   EQTLLEHYVKKILAAP--VYELAVRTPLQAAPALSEALGNRILLKREDLQPTFSFKIRGA 64

Query: 65  YHKMKQLSSEQTENGVVCASAGNHAQGVAFSCKHLGIHGKIFMPSTTPRQKVSQVELFGK 124
           Y+K+  L+ EQ   GV+ ASAGNHAQGVA + + LGI  +I MP TTP+ KV  V   G 
Sbjct: 65  YNKLVHLTPEQRARGVITASAGNHAQGVALAARELGISARIVMPVTTPQLKVLGVRNRGA 124

Query: 125 GFIDIILTGDTFDDVYKSAAECCEAESRTFIHPFDDPDVMAGQGTLAVEILNDIDTEPHF 184
              + +L GD+F      A E  E   R F+ PFDDPDV+AGQGT+A+EIL         
Sbjct: 125 ---EALLHGDSFPFALAHALELAEQTGREFVSPFDDPDVIAGQGTVAMEILRQHPGRLDA 181

Query: 185 LFASVGGGGLLSGVGTYLKNVSPDTKVIAVEPAGAASYFESNKAGHVVTLDKIDKFVDGA 244
           +F  VGGGGL++G+  Y+K + P+ ++I VE   +A    +  AG  VTL ++  F DG 
Sbjct: 182 IFVPVGGGGLIAGIAAYVKYLRPEVRIIGVESQHSACLQAALAAGERVTLPEVGTFADGV 241

Query: 245 AVKKIGEETFRTLETVVDDILLVPEGKVCTSILELYNECAVVAEPAGALSVAALDLY--K 302
           AV +IG          VD+++ V   ++C +I ++Y++   + EP+GAL+VA +  Y   
Sbjct: 242 AVAQIGAHGLDICRFCVDEVMTVSNDQLCAAIKDIYDDTRSITEPSGALAVAGIKQYVAH 301

Query: 303 DQIKGKNVVCVVSGGNNDIGRMQEMKERSLI 333
              +G+ +V + SG N +   ++ + ER+ +
Sbjct: 302 TGARGETLVAIDSGANINFDSLRHVAERAAV 332


Lambda     K      H
   0.318    0.137    0.397 

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: 329
Number of extensions: 15
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: 422
Length of database: 333
Length adjustment: 30
Effective length of query: 392
Effective length of database: 303
Effective search space:   118776
Effective search space used:   118776
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: 50 (23.9 bits)

Align candidate AO356_27710 AO356_27710 (threonine dehydratase)
to HMM TIGR01124 (ilvA: threonine ammonia-lyase, biosynthetic (EC 4.3.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.29986.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29986.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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