GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Cupriavidus basilensis 4G11

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate RR42_RS04455 RR42_RS04455 MFS transporter

Query= CharProtDB::CH_002572
         (362 letters)



>FitnessBrowser__Cup4G11:RR42_RS04455
          Length = 386

 Score =  362 bits (929), Expect = e-105
 Identities = 186/365 (50%), Positives = 247/365 (67%), Gaps = 9/365 (2%)

Query: 3   QIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLN 62
           +++NFS GPA LP EVL QA  E+  W+G G SVME+SHR +EF  +  EA  + R+LL 
Sbjct: 20  RVYNFSPGPAALPTEVLLQAADEMLSWHGSGVSVMEMSHRSREFESIQAEALANLRELLQ 79

Query: 63  VPSNYKVLFCHGGGRGQFAAVPLNIL----GDKTTADYVDAGYWAASAIKEAKKYCTPNV 118
           VP N+++LF  GG  G+   VPLN++     D+  AD+V  G W+  + +EA++Y   N+
Sbjct: 80  VPKNFRILFLQGGAIGENGIVPLNLMRRVNADRPKADFVVTGTWSVKSEQEARRYGEVNI 139

Query: 119 FDAKVTVDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFG----ADVVVAAD 174
             A  T      +  + +W+LSD+AAY+H C NETI G+   + PD G       VV AD
Sbjct: 140 A-ATSTAQKFARIPDVADWKLSDDAAYVHLCTNETIVGVEFQDVPDIGQHRDGGPVVVAD 198

Query: 175 FSSTILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDN 234
            SS ILSRP+D SR  V Y GAQKNIGPAGLTIVIVREDLLG A+  CPS  ++ ++ ++
Sbjct: 199 VSSHILSRPVDWSRVQVAYGGAQKNIGPAGLTIVIVREDLLGHAHPLCPSAFNWRLVAEH 258

Query: 235 GSMFNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKAN 294
            SM+NTPPT++ Y++GLVFKWLKA GGV  +++ N  K+  LY  +D S FYRN++   +
Sbjct: 259 DSMYNTPPTYSIYIAGLVFKWLKAQGGVGAIEQRNIAKSHALYEFLDQSAFYRNEIDPGS 318

Query: 295 RSRMNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFM 354
           RSRMNVPF LAD + +  FL  + A GL  LKGH+ VGGMRAS+YNAMP+EGV AL ++M
Sbjct: 319 RSRMNVPFFLADESRNDAFLAGARANGLVQLKGHKSVGGMRASLYNAMPIEGVAALIEYM 378

Query: 355 VEFER 359
            EFER
Sbjct: 379 REFER 383


Lambda     K      H
   0.319    0.136    0.405 

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: 417
Number of extensions: 12
Number of successful extensions: 4
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: 362
Length of database: 386
Length adjustment: 30
Effective length of query: 332
Effective length of database: 356
Effective search space:   118192
Effective search space used:   118192
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: 50 (23.9 bits)

Align candidate RR42_RS04455 RR42_RS04455 (MFS transporter)
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))

Software error:

../bin/blast/fastacmd -i /tmp/list.16911.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16911.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.