GapMind for catabolism of small carbon sources

 

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

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate PfGW456L13_1089 L-serine dehydratase (EC 4.3.1.17)

Query= reanno::pseudo3_N2E3:AO353_15500
         (458 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1089
          Length = 458

 Score =  718 bits (1854), Expect = 0.0
 Identities = 358/458 (78%), Positives = 399/458 (87%)

Query: 1   MAISVFDLFKVGIGPSSSHTVGPMRAAATFAQALFDQGLLEQTRRVEVRLYGSLSATGVG 60
           MAISVFDLFK+GIGPSSSHTVGPMRAAA F Q L ++GLLEQ RRVEV+L+GSLSATG+G
Sbjct: 1   MAISVFDLFKIGIGPSSSHTVGPMRAAALFVQGLRERGLLEQVRRVEVQLFGSLSATGIG 60

Query: 61  HATDRACVMGLMGEWPDSIDPSCIGPRIQQLRESGELLLAGRRSIAFDWQRDLLLLDESL 120
           H +D A +MGLMGEWPD+IDPS IG  I  LRE+  LLL GR  + F W RD+ L+DE+L
Sbjct: 61  HGSDNAVIMGLMGEWPDAIDPSQIGICIANLRETDTLLLDGRLPVPFIWGRDMRLIDENL 120

Query: 121 PYHPNAMSLTAFGESGQLWEQTYYSVGGGFIVEAAEAESGVPASSDVVLPYEFSSAVELL 180
           P+HPNAM+L   G+ G+L   TYYSVGGGF+V+ A+A SGV      VLPY+FSSA ELL
Sbjct: 121 PFHPNAMTLIVEGDDGELHRDTYYSVGGGFVVDEAQASSGVVDLDSTVLPYDFSSAAELL 180

Query: 181 SLCNQHGLRVSELMMANERAWRSDAEIRSGLLHIWSVMRECVEQGLRHEGILPGGLDVPR 240
            LC +H LRV+ELMMANER WRS+ EIRSGL+ +W  M++CVEQGL+HEGILPGGL+V R
Sbjct: 181 ELCKKHNLRVAELMMANERVWRSEDEIRSGLMKLWRAMQDCVEQGLKHEGILPGGLNVRR 240

Query: 241 RAAKLHRSLLEIGKPNVISSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300
           RAAKLHRSL E+ KPNVI STLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV
Sbjct: 241 RAAKLHRSLQELNKPNVIGSTLSAMEWVNLFALAVNEENAAGGRMVTAPTNGAAGIIPAV 300

Query: 301 LHYYMKFNPDASDDDVVAFFLAAASVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAD 360
           LHY+MKF+   +D +VV +FL AA+VGILCKKNASISGAEVGCQGEVGSACAMAAAGLA+
Sbjct: 301 LHYFMKFSEAVTDANVVDYFLGAAAVGILCKKNASISGAEVGCQGEVGSACAMAAAGLAE 360

Query: 361 VLGATPEQLENAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINATQMALRGDGK 420
           +LGATPEQL NAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINA QMALRGDG+
Sbjct: 361 ILGATPEQLCNAAEIGLEHNLGLTCDPVGGLVQVPCIERNAIAAVKAINAAQMALRGDGQ 420

Query: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSWVEC 458
           HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVS VEC
Sbjct: 421 HFISLDRVIRTMRDTGADMHDKYKETSRGGLAVSAVEC 458


Lambda     K      H
   0.319    0.134    0.399 

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: 687
Number of extensions: 25
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: 458
Length of database: 458
Length adjustment: 33
Effective length of query: 425
Effective length of database: 425
Effective search space:   180625
Effective search space used:   180625
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: 51 (24.3 bits)

Align candidate PfGW456L13_1089 (L-serine dehydratase (EC 4.3.1.17))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.14302.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14302.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.