GapMind for catabolism of small carbon sources

 

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

Align arginine deiminase (EC 3.5.3.6) (characterized)
to candidate PfGW456L13_1874 Arginine deiminase (EC 3.5.3.6)

Query= BRENDA::P13981
         (418 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1874
          Length = 418

 Score =  718 bits (1853), Expect = 0.0
 Identities = 343/418 (82%), Positives = 380/418 (90%)

Query: 1   MSTEKTKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVT 60
           M+TEK K GVHSEAGKLRKVMVCSPGLAHQRLTP+NCDELLFDDV+WV QAKRDHFDFVT
Sbjct: 1   MTTEKVKYGVHSEAGKLRKVMVCSPGLAHQRLTPNNCDELLFDDVLWVAQAKRDHFDFVT 60

Query: 61  KMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLA 120
           KMRER IDVLEMHNLLT+ +  PEAL WIL+RK+TA+SVGLGL +E  SWL SLEPRK+A
Sbjct: 61  KMRERNIDVLEMHNLLTDIVAIPEALDWILERKVTANSVGLGLINETSSWLRSLEPRKIA 120

Query: 121 EYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPM 180
           E+LIGGV+ DDLP+S G   ++M+R++LG+SSF+LPPLPNTQFTRDTTCWIYGGVTLNPM
Sbjct: 121 EFLIGGVSGDDLPSSFGGKAIEMFRDFLGNSSFILPPLPNTQFTRDTTCWIYGGVTLNPM 180

Query: 181 YWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGM 240
           YWPARRQETLLTTAIYKFHPEF  A+FEIWYGDPD DHG+STLEGGDVMPIGNGVVLIGM
Sbjct: 181 YWPARRQETLLTTAIYKFHPEFTKADFEIWYGDPDLDHGNSTLEGGDVMPIGNGVVLIGM 240

Query: 241 GERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKE 300
           GERSSRQAI Q+A +LF   A E+VIVAGLPKSRAAMHLDTVFSFCDRDLVT+FPEVV +
Sbjct: 241 GERSSRQAIAQLAVNLFKNKAVEKVIVAGLPKSRAAMHLDTVFSFCDRDLVTIFPEVVNQ 300

Query: 301 IVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNN 360
           IV F+LRPD S   G++IRREE +FL+ VA++L LK LRVVETGGNSFAAEREQWDDGNN
Sbjct: 301 IVAFTLRPDESKAGGIDIRREETSFLDTVAQALNLKALRVVETGGNSFAAEREQWDDGNN 360

Query: 361 VVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPIDY 418
           VV +EPGVV+GYDRNTYTNTLLRKAGVEVITISA ELGRGRGGGHCMTCPI+RDPIDY
Sbjct: 361 VVAVEPGVVIGYDRNTYTNTLLRKAGVEVITISAGELGRGRGGGHCMTCPIIRDPIDY 418


Lambda     K      H
   0.319    0.137    0.414 

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: 672
Number of extensions: 14
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: 418
Length of database: 418
Length adjustment: 32
Effective length of query: 386
Effective length of database: 386
Effective search space:   148996
Effective search space used:   148996
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 PfGW456L13_1874 (Arginine deiminase (EC 3.5.3.6))
to HMM TIGR01078 (arcA: arginine deiminase (EC 3.5.3.6))

Software error:

../bin/blast/fastacmd -i /tmp/list.25544.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25544.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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