GapMind for catabolism of small carbon sources

 

Alignments for a candidate for speB in Pseudomonas fluorescens GW456-L13

Align Agmatinase; Agmatine ureohydrolase; AUH; EC 3.5.3.11 (characterized)
to candidate PfGW456L13_2989 Agmatinase (EC 3.5.3.11)

Query= SwissProt::Q7X3P1
         (306 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2989
          Length = 319

 Score =  322 bits (826), Expect = 6e-93
 Identities = 158/280 (56%), Positives = 204/280 (72%), Gaps = 6/280 (2%)

Query: 31  YSSD---ADWVITGVPFDMATSGRAGTRHGPGAIRQISTNLAWEGHRWPWHFDMRERLKV 87
           YS D    D  ++GVPFD ATS R G R GP  IR  S  +AWE H WPW FD  + L V
Sbjct: 36  YSRDLRGVDVAVSGVPFDTATSNRPGARFGPRGIRAASAGIAWERH-WPWTFDPFDHLAV 94

Query: 88  VDCGDLVFNFGDAQDMSDKLQAHTEKLLAAGKRCLTFGGDHFVTLPLLRAHAKHFGKMAL 147
           +D GD  F++G  Q   + ++AH E +L AG   LTFGGDHF+T PLL+AHA+  G ++L
Sbjct: 95  IDYGDCDFDYGSPQSTPEMIEAHAEHILNAGTAMLTFGGDHFITYPLLKAHARKHGALSL 154

Query: 148 VHFDAHTDTYAN--GSKFDHGTMFYHAPNEGLIDPQHSVQIGIRTEHDTNNGFTVLDAAQ 205
           +HFDAH+DT+ +  G + DHGTMF+HA  EGL+DP  SVQIG+RT +D + GF VLDA Q
Sbjct: 155 IHFDAHSDTWPDEEGKRIDHGTMFWHAAREGLVDPSRSVQIGLRTTNDDHQGFEVLDARQ 214

Query: 206 VNDRGVDDLVAQIKEIVGSLPVYLTFDIDCLDPAFAPGTGTPVVGGLTTDKALKMLRALQ 265
           V+ RG + +V  I+  VG  PVYLTFDIDCLDPAFAPGTGTPV GGL+T +AL++L  L+
Sbjct: 215 VHRRGCEAIVEAIRARVGDNPVYLTFDIDCLDPAFAPGTGTPVCGGLSTVQALEILGGLR 274

Query: 266 PLNIVGMDLVEVSPAYDQSDITALAGATIALDMLYLQAAK 305
            +N+VGMD+VEV+PAYD ++IT+LA AT+A++ML L AA+
Sbjct: 275 GINLVGMDVVEVAPAYDSAEITSLAAATLAMEMLCLYAAR 314


Lambda     K      H
   0.321    0.138    0.426 

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: 341
Number of extensions: 16
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: 306
Length of database: 319
Length adjustment: 27
Effective length of query: 279
Effective length of database: 292
Effective search space:    81468
Effective search space used:    81468
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 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate PfGW456L13_2989 (Agmatinase (EC 3.5.3.11))
to HMM TIGR01230 (speB: agmatinase (EC 3.5.3.11))

Software error:

../bin/blast/fastacmd -i /tmp/list.1966.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1966.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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