GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prpB in Herbaspirillum seropedicae SmR1

Align 2-methylcitrate lyase (EC 4.1.3.30) (characterized)
to candidate HSERO_RS15660 HSERO_RS15660 2-methylisocitrate lyase

Query= metacyc::MONOMER-13636
         (302 letters)



>FitnessBrowser__HerbieS:HSERO_RS15660
          Length = 296

 Score =  495 bits (1274), Expect = e-145
 Identities = 249/292 (85%), Positives = 270/292 (92%)

Query: 11  SAGARFRQALADEHPLQVVGTINANHALLAKRAGYRAIYLSGGGVAAGSLGLPDLGISNL 70
           SAGA FR+A+ +E PLQV+G INANHALLAKRAG+RAIYLSGGGVAAGSLGLPDLGISNL
Sbjct: 5   SAGAAFRKAVQEESPLQVIGAINANHALLAKRAGFRAIYLSGGGVAAGSLGLPDLGISNL 64

Query: 71  DDVLTDIRRITDVCDTPLLVDVDTGFGASAFNVARTTKSLIKFGAAAMHIEDQVGAKRCG 130
           DDVLTD+RRITDVCD PLLVDVDTGFGASAFNVART KS+IKFGAAAMHIEDQVGAKRCG
Sbjct: 65  DDVLTDVRRITDVCDLPLLVDVDTGFGASAFNVARTVKSMIKFGAAAMHIEDQVGAKRCG 124

Query: 131 HRPNKEIVTQGEMVDRIRAAVDARTDENFVIMARTDALAVEGLDKAIERAVACAEAGADA 190
           HRPNKEIV++ EMVDRI+AAVDARTDENFVIMARTDALAVEGLD AIERAVAC EAGAD 
Sbjct: 125 HRPNKEIVSKQEMVDRIKAAVDARTDENFVIMARTDALAVEGLDAAIERAVACVEAGADM 184

Query: 191 IFPEAMTDLAMYRKFVDAVKVPVLANITEFGATPLFTTEELGGAGVSMVLYPLSAFRAMN 250
           IFPEA+TDLAMY++F +AVKVP+LANITEFG+TPLFT +EL GA V +VLYPLSAFRAMN
Sbjct: 185 IFPEAITDLAMYKQFANAVKVPILANITEFGSTPLFTVDELKGADVGLVLYPLSAFRAMN 244

Query: 251 KAAENVYAAIRRDGTQKNVVDTMQTRAELYESIGYHDFEQKLDALFAQGKGK 302
           KAAENVY AIRRDGTQKNVVDTMQTR ELY+ I YH +EQ+LDALFAQ K K
Sbjct: 245 KAAENVYQAIRRDGTQKNVVDTMQTRMELYDRIDYHSYEQRLDALFAQQKNK 296


Lambda     K      H
   0.320    0.134    0.376 

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: 364
Number of extensions: 6
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: 302
Length of database: 296
Length adjustment: 27
Effective length of query: 275
Effective length of database: 269
Effective search space:    73975
Effective search space used:    73975
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: 48 (23.1 bits)

Align candidate HSERO_RS15660 HSERO_RS15660 (2-methylisocitrate lyase)
to HMM TIGR02317 (prpB: methylisocitrate lyase (EC 4.1.3.30))

Software error:

../bin/blast/fastacmd -i /tmp/list.28747.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28747.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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