GapMind for catabolism of small carbon sources

 

Alignments for a candidate for hutG' in Pseudomonas fluorescens FW300-N2C3

Align N-formylglutamate deformylase (EC 3.5.1.68) (characterized)
to candidate AO356_09590 AO356_09590 N-formylglutamate deformylase

Query= reanno::pseudo5_N2C3_1:AO356_09590
         (267 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_09590
          Length = 267

 Score =  551 bits (1419), Expect = e-162
 Identities = 267/267 (100%), Positives = 267/267 (100%)

Query: 1   VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGAS 60
           VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGAS
Sbjct: 1   VEKVLNFKQGRVPLLVSMPHAGLRLTPAVKAGLIPEAQSLPDTDWHIPQLYEFANELGAS 60

Query: 61  TLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQV 120
           TLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQV
Sbjct: 61  TLAAEYSRFVVDLNRPSDDKPMYVGATTGLYPATLFDGVPLFREGLEPSAEERATYLQQV 120

Query: 121 WMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLA 180
           WMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLA
Sbjct: 121 WMPYHQALRQELARLKAEFGYALLFDAHSIRSVIPHLFDGKLPDFNLGTFNGASCDPTLA 180

Query: 181 SQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRP 240
           SQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRP
Sbjct: 181 SQLEAICARHGQFTHVLNGRFKGGHITRHYGNPAEDIHAVQLELCQSTYMEEFEPFNYRP 240

Query: 241 DLAAPTQVVLRELLEGFLAWGQKTYKH 267
           DLAAPTQVVLRELLEGFLAWGQKTYKH
Sbjct: 241 DLAAPTQVVLRELLEGFLAWGQKTYKH 267


Lambda     K      H
   0.321    0.138    0.425 

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: 439
Number of extensions: 9
Number of successful extensions: 1
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: 267
Length of database: 267
Length adjustment: 25
Effective length of query: 242
Effective length of database: 242
Effective search space:    58564
Effective search space used:    58564
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: 47 (22.7 bits)

Align candidate AO356_09590 AO356_09590 (N-formylglutamate deformylase)
to HMM TIGR02017 (hutG: N-formylglutamate deformylase (EC 3.5.1.68))

Software error:

../bin/blast/fastacmd -i /tmp/list.25184.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25184.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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