GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Pseudomonas putida KT2440

Align phosphoserine aminotransferase; EC 2.6.1.52 (characterized)
to candidate PP_1768 PP_1768 phosphoserine aminotransferase

Query= CharProtDB::CH_002572
         (362 letters)



>FitnessBrowser__Putida:PP_1768
          Length = 361

 Score =  413 bits (1062), Expect = e-120
 Identities = 206/358 (57%), Positives = 259/358 (72%), Gaps = 2/358 (0%)

Query: 5   FNFSSGPAMLPAEVLKQAQQELRDWNGLGTSVMEVSHRGKEFIQVAEEAEKDFRDLLNVP 64
           FNF +GPA LP  VL++AQ E+ DW G G SVME+SHR  +++ +AE+AE+D RDLL+VP
Sbjct: 6   FNFCAGPAALPDAVLQRAQAEMLDWRGKGLSVMEMSHRSDDYVAIAEKAEQDLRDLLSVP 65

Query: 65  SNYKVLFCHGGGRGQFAAVPLNILGDKTTADYVDAGYWAASAIKEAKKYCTPNVFDAKVT 124
           SNYKVLF  GG   QFA +PLN+L +  TADY++ G W+  AI+EA+++   NV      
Sbjct: 66  SNYKVLFLQGGASQQFAEIPLNLLPENGTADYIETGIWSKKAIEEARRFGNVNVAATAKP 125

Query: 125 VDGLRAVKPMREWQLSDNAAYMHYCPNETIDGIAIDETPDFGADVVVAADFSSTILSRPI 184
            D L A+    EW L+ NAAY+HY  NETI G+  D  P  G DV +  D SS ILSRPI
Sbjct: 126 YDYL-AIPGQNEWNLTKNAAYVHYASNETIGGLQFDWVPQTG-DVPLVVDMSSDILSRPI 183

Query: 185 DVSRYGVIYAGAQKNIGPAGLTIVIVREDLLGKANIACPSILDYSILNDNGSMFNTPPTF 244
           DVS++G+IYAGAQKNIGP+GL +VIVREDLLG A  +CP++LDY +  DNGSM+NTP T+
Sbjct: 184 DVSQFGLIYAGAQKNIGPSGLVVVIVREDLLGHARSSCPTMLDYKVSADNGSMYNTPATY 243

Query: 245 AWYLSGLVFKWLKANGGVAEMDKINQQKAELLYGVIDNSDFYRNDVAKANRSRMNVPFQL 304
           +WYLSGLVF+WLK  GGV  M++ N+ K + LYG ID S+FY N ++   RS MNVPF+L
Sbjct: 244 SWYLSGLVFEWLKEQGGVEAMEQRNRAKKDRLYGFIDRSEFYTNPISVNARSWMNVPFRL 303

Query: 305 ADSALDKLFLEESFAAGLHALKGHRVVGGMRASIYNAMPLEGVKALTDFMVEFERRHG 362
           AD  LDK FL  + A GL  LKGHR VGGMRASIYNA+ LE V+AL  +M EFE+ HG
Sbjct: 304 ADERLDKAFLAGADARGLLNLKGHRSVGGMRASIYNALGLEAVEALVGYMAEFEKEHG 361


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: 410
Number of extensions: 13
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: 361
Length adjustment: 29
Effective length of query: 333
Effective length of database: 332
Effective search space:   110556
Effective search space used:   110556
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 PP_1768 PP_1768 (phosphoserine aminotransferase)
to HMM TIGR01364 (serC: phosphoserine transaminase (EC 2.6.1.52))

Software error:

../bin/blast/fastacmd -i /tmp/list.30650.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30650.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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