GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Magnetospirillum magneticum AMB-1

Align phosphoserine phosphatase (EC 3.1.3.3) (characterized)
to candidate WP_011385839.1 AMB_RS17605 phosphoserine phosphatase SerB

Query= BRENDA::Q58989
         (211 letters)



>NCBI__GCF_000009985.1:WP_011385839.1
          Length = 298

 Score =  157 bits (396), Expect = 3e-43
 Identities = 83/205 (40%), Positives = 128/205 (62%)

Query: 3   KKKKLILFDFDSTLVNNETIDEIAREAGVEEEVKKITKEAMEGKLNFEQSLRKRVSLLKD 62
           ++K L++ D DST+V  ET+DE+A  AG+++ + +IT  AM G++ FE +LR+RV LLKD
Sbjct: 82  RRKMLLVADMDSTMVIGETLDELADFAGLKDHIARITARAMNGEIGFEAALRERVGLLKD 141

Query: 63  LPIEKVEKAIKRITPTEGAEETIKELKNRGYVVAVVSGGFDIAVNKIKEKLGLDYAFANR 122
           LP E ++K   RI  T GA + ++ +   G    +VSGGF    +K+++  G     AN 
Sbjct: 142 LPEECLQKTWDRIEFTPGAHKLVRTMVKHGAHAVLVSGGFKFFTSKVRDACGFHRDIANE 201

Query: 123 LIVKDGKLTGDVEGEVLKENAKGEILEKIAKIEGINLEDTVAVGDGANDISMFKKAGLKI 182
           LIV++G+LTG V   ++   AK   L  ++   GI  E  V+VGDGAND+ M + AGL +
Sbjct: 202 LIVENGRLTGQVGDTIIGREAKLATLNAVSAELGITPELAVSVGDGANDLDMLRAAGLGV 261

Query: 183 AFCAKPILKEKADICIEKRDLREIL 207
           AF AKP++  +A + ++  DL  +L
Sbjct: 262 AFHAKPVVAAEARVRVDHGDLVTLL 286


Lambda     K      H
   0.314    0.136    0.358 

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: 167
Number of extensions: 8
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: 211
Length of database: 298
Length adjustment: 24
Effective length of query: 187
Effective length of database: 274
Effective search space:    51238
Effective search space used:    51238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 46 (22.3 bits)

Align candidate WP_011385839.1 AMB_RS17605 (phosphoserine phosphatase SerB)
to HMM TIGR00338 (serB: phosphoserine phosphatase SerB (EC 3.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.15783.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15783.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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