GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Pseudomonas fluorescens FW300-N2E2

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate Pf6N2E2_2521 Phosphoserine aminotransferase (EC 2.6.1.52)

Query= CharProtDB::CH_002572
         (362 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_2521
          Length = 363

 Score =  406 bits (1043), Expect = e-118
 Identities = 202/358 (56%), Positives = 252/358 (70%), Gaps = 2/358 (0%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           +NF +GPA LP  VLK+AQ EL DW+G G SVME+SHR  EF+ +A +AE+D RDLLN+P
Sbjct: 8   YNFCAGPAALPEAVLKRAQGELLDWHGKGLSVMEMSHRSDEFVSIATKAEQDLRDLLNIP 67

Query: 65  SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124
           SNYKVLF  GG   QFA +PLN+L +   ADY+D G W+  AI+EA +Y   NV      
Sbjct: 68  SNYKVLFLQGGASQQFAQIPLNLLPESGKADYIDTGIWSQKAIEEASRYGHVNVAATAKP 127

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
            D   A+    EW LS +AAY+HY PNETI G+  +  P+ G DV + AD SS ILSRP+
Sbjct: 128 YDYF-AIPGQNEWNLSKDAAYVHYAPNETIGGLEFNWIPETG-DVPLVADMSSDILSRPV 185

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           D+SR+G+IYAGAQKNIGP+G+ + I+REDLLG+A   CP++L+Y +  DNGSM+NTPPT 
Sbjct: 186 DISRFGMIYAGAQKNIGPSGILVSIIREDLLGRARSLCPTMLNYKVAADNGSMYNTPPTL 245

Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           AWYLSGLVF+WLK  GGV  + K+N+ K   LY  ID S  Y N + K +RS MNVPF+L
Sbjct: 246 AWYLSGLVFEWLKEQGGVEAIGKLNEVKQRTLYDFIDASGLYSNPINKTDRSWMNVPFRL 305

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           AD  LDK FL  +   GL  LKGHR VGGMRASIYNA+ +  V AL  +M EFE+ HG
Sbjct: 306 ADDRLDKPFLAGADERGLLNLKGHRSVGGMRASIYNAVDINAVNALIAYMAEFEKEHG 363


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: 11
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: 363
Length adjustment: 29
Effective length of query: 333
Effective length of database: 334
Effective search space:   111222
Effective search space used:   111222
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 Pf6N2E2_2521 (Phosphoserine aminotransferase (EC 2.6.1.52))
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))

Software error:

../bin/blast/fastacmd -i /tmp/list.27850.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27850.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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