GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Shewanella oneidensis MR-1

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate 200302 SO1122 gamma-glutamyl phosphate reductase (NCBI ptt file)

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__MR1:200302
          Length = 425

 Score =  474 bits (1219), Expect = e-138
 Identities = 246/416 (59%), Positives = 308/416 (74%)

Query: 2   LEQMGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEA 61
           L+Q+G  AKQASY LA L++ +K  +L+ IAD L   +  IL ANA+DVA A+A GL++A
Sbjct: 10  LQQLGHNAKQASYALANLTASQKADLLDAIADALTENTLAILAANAKDVAAAKAEGLNDA 69

Query: 62  MLDRLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEA 121
           M+DRL L  +RL GI  D+  V  LADPVG+     VLD+GLRL RRRVPLGVIGVIYEA
Sbjct: 70  MIDRLLLNESRLAGIIGDISDVVRLADPVGEEFGSRVLDNGLRLTRRRVPLGVIGVIYEA 129

Query: 122 RPNVTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDR 181
           RPNVTVD+A L LKTGNAVILRGGKET  +N     VI+ A+ S GLP  AVQ ID+ DR
Sbjct: 130 RPNVTVDIAVLALKTGNAVILRGGKETLESNKLISEVIRGAIASQGLPVDAVQLIDSSDR 189

Query: 182 ALVSEMLRMDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKV 241
           ALV+ +L++D+Y+DM++PRGG  L +LC EQ+TIPVI GGIG+CH+YVD++  +  AL+V
Sbjct: 190 ALVTGLLKLDQYVDMIVPRGGQALQRLCAEQATIPVILGGIGICHLYVDKAANLERALEV 249

Query: 242 IVNAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKV 301
           I NAK QRP+ CN ++TLLV+K IA +F+P + + +   GV       + A L      +
Sbjct: 250 IANAKVQRPTVCNALDTLLVDKTIAANFVPQIVEYLHCLGVRFSVCEQSHALLDGLGFDI 309

Query: 302 VAVKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDS 361
                + +  E+LSL L +K+VSD+D AIAHIR H + HS+AILT D+  A  F+NEV+S
Sbjct: 310 ELATEQSFATEWLSLTLGIKVVSDIDAAIAHIRRHSSGHSEAILTDDIHAATHFMNEVNS 369

Query: 362 SAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWIGIGDYTIRA 417
           +AVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKW+  GDYT RA
Sbjct: 370 AAVYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWLAWGDYTSRA 425


Lambda     K      H
   0.317    0.133    0.369 

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: 506
Number of extensions: 13
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: 417
Length of database: 425
Length adjustment: 32
Effective length of query: 385
Effective length of database: 393
Effective search space:   151305
Effective search space used:   151305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 200302 SO1122 (gamma-glutamyl phosphate reductase (NCBI ptt file))
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))

Software error:

../bin/blast/fastacmd -i /tmp/list.12333.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12333.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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