GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapA in Pseudomonas putida KT2440

Align 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7) (characterized)
to candidate PP_1237 PP_1237 4-hydroxy-tetrahydrodipicolinate synthase

Query= BRENDA::Q9I4W3
         (292 letters)



>FitnessBrowser__Putida:PP_1237
          Length = 295

 Score =  448 bits (1152), Expect = e-131
 Identities = 228/294 (77%), Positives = 254/294 (86%), Gaps = 3/294 (1%)

Query: 1   MIAGSMVALVTPFDAQGRLDWDSLAKLVDFHLQEGTNAIVAVGTTGESATLDVEEHIQVI 60
           MIAGSMVALVTP DAQGR+DW SL KLVDFHL+ GT+AIVAVGTTGESATLDVEEHI VI
Sbjct: 1   MIAGSMVALVTPMDAQGRVDWGSLDKLVDFHLENGTHAIVAVGTTGESATLDVEEHILVI 60

Query: 61  RRVVDQVKGR---IPVIAGTGANSTREAVALTEAAKSGGADACLLVTPYYNKPTQEGMYQ 117
           + VV++VK     IPVIAGTGANST EAV LT+ AK+ GADACLLV PYYNKPTQEG+YQ
Sbjct: 61  KHVVERVKRSAKPIPVIAGTGANSTAEAVHLTQNAKNAGADACLLVVPYYNKPTQEGLYQ 120

Query: 118 HFRHIAEAVAIPQILYNVPGRTSCDMLPETVERLSKVPNIIGIKEATGDLQRAKEVIERV 177
           HF+HIAEAV IPQILYNVPGRTSCDM  ETV RLS VPNIIGIKEATGDL RAK +++ V
Sbjct: 121 HFKHIAEAVDIPQILYNVPGRTSCDMQAETVIRLSTVPNIIGIKEATGDLARAKAILDGV 180

Query: 178 GKDFLVYSGDDATAVELMLLGGKGNISVTANVAPRAMSDLCAAAMRGDAAAARAINDRLM 237
            KDF+V SGDD TAVEL+L+GGKGNISVTANVAPR M+DLC AA+ G+A  ARAIN++LM
Sbjct: 181 SKDFIVMSGDDPTAVELILMGGKGNISVTANVAPREMADLCEAALEGNAEKARAINEKLM 240

Query: 238 PLHKALFIESNPIPVKWALHEMGLIPEGIRLPLTWLSPRCHEPLRQAMRQTGVL 291
           PLHK LF ESNPIPVKWAL EMGL+ +GIRLPLTWLS  CHE +R A+RQ+GVL
Sbjct: 241 PLHKDLFCESNPIPVKWALVEMGLMQKGIRLPLTWLSEGCHEKVRTALRQSGVL 294


Lambda     K      H
   0.319    0.134    0.393 

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: 329
Number of extensions: 7
Number of successful extensions: 2
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: 292
Length of database: 295
Length adjustment: 26
Effective length of query: 266
Effective length of database: 269
Effective search space:    71554
Effective search space used:    71554
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 PP_1237 PP_1237 (4-hydroxy-tetrahydrodipicolinate synthase)
to HMM TIGR00674 (dapA: 4-hydroxy-tetrahydrodipicolinate synthase (EC 4.3.3.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.3311.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3311.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.