GapMind for Amino acid biosynthesis

 

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

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate 201554 SO2410 phosphoserine aminotransferase (NCBI ptt file)

Query= CharProtDB::CH_002572
         (362 letters)



>FitnessBrowser__MR1:201554
          Length = 367

 Score =  410 bits (1053), Expect = e-119
 Identities = 212/364 (58%), Positives = 270/364 (74%), Gaps = 5/364 (1%)

Query: 1   MAQIFNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDL 60
           ++ I+NF +GPAMLPA V+K+AQQEL DWNGLG SVMEVSHRGKEFI + ++AE D R+L
Sbjct: 3   VSAIYNFCAGPAMLPAAVMKKAQQELLDWNGLGVSVMEVSHRGKEFIALTKQAEADLREL 62

Query: 61  LNVPSNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFD 120
           +++P NY VLF HGGGRGQF+AV  N LG++  A Y+ +G W+++A+ EA+K       D
Sbjct: 63  MHIPQNYHVLFMHGGGRGQFSAVVNNFLGNQGRALYLVSGQWSSAALAEAQKLAGDAQID 122

Query: 121 AKVTVDG---LRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSS 177
           +   V+    L AV      ++  +  Y+HYCPNET+DGI I +  D    +V  AD SS
Sbjct: 123 SLNIVEKHNCLNAVVLPDLHKIDADYRYVHYCPNETVDGIEIFDELDSPWPIV--ADLSS 180

Query: 178 TILSRPIDVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSM 237
           TI+SR IDVSRYG+IYAGAQKNIGP+GL+IVIVR+D+L   ++   SI+DY +  ++ SM
Sbjct: 181 TIMSREIDVSRYGLIYAGAQKNIGPSGLSIVIVRDDMLTLPSLPQSSIMDYRLAVEHDSM 240

Query: 238 FNTPPTFAWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSR 297
           FNTPPTFAWYL+  VF WLK+ GGVA + KINQQKA++LY  ID + FY+N V  ANRS+
Sbjct: 241 FNTPPTFAWYLAAEVFAWLKSIGGVASIAKINQQKAQMLYACIDANPFYKNGVVAANRSQ 300

Query: 298 MNVPFQLADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEF 357
           MNV FQLAD +LD  FL+E+ A GL ALKGHR+VGGMRAS+YNAMPLEGV AL  FM EF
Sbjct: 301 MNVTFQLADESLDGAFLKEAEAVGLVALKGHRIVGGMRASLYNAMPLEGVAALVTFMNEF 360

Query: 358 ERRH 361
             +H
Sbjct: 361 AAKH 364


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: 386
Number of extensions: 7
Number of successful extensions: 3
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: 367
Length adjustment: 29
Effective length of query: 333
Effective length of database: 338
Effective search space:   112554
Effective search space used:   112554
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: 49 (23.5 bits)

Align candidate 201554 SO2410 (phosphoserine aminotransferase (NCBI ptt file))
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))

Software error:

../bin/blast/fastacmd -i /tmp/list.30224.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30224.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.