GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Caulobacter crescentus NA1000

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate CCNA_03322 CCNA_03322 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>FitnessBrowser__Caulo:CCNA_03322
          Length = 526

 Score =  378 bits (971), Expect = e-109
 Identities = 214/528 (40%), Positives = 322/528 (60%), Gaps = 13/528 (2%)

Query: 5   PVVLIAEELSPATVDAL---GPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAV 61
           P VLIA++LSPA V+     G  F+I+   G  + EL+  I D D I +RS  K+D + +
Sbjct: 4   PRVLIADKLSPAAVEIFKNRGLAFDIK--TGLSKDELIAVIGDYDGIAIRSGAKLDKDVI 61

Query: 62  AAAKKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQA 121
           AAA KL+V+ARAG+G+DNVD+ AAT  G++V+N P  N +T AE A  ++ A AR IP A
Sbjct: 62  AAANKLRVIARAGIGVDNVDIPAATAKGIVVMNTPFGNSITTAEHAIAMMFALARQIPAA 121

Query: 122 NAALKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAA 181
           + + + G+W+++++ GVEL  KTLG++G G IG +VA R     MKVVAYDP++ P RA 
Sbjct: 122 DVSTQGGKWEKNRFMGVELYAKTLGLIGAGNIGGIVADRALGLKMKVVAYDPFLSPERAV 181

Query: 182 QMGVKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEA 241
           +MGV+ + LDELL  +D IT+H P T +T  ++  E L K K  V IVN ARGG+VDE A
Sbjct: 182 EMGVEKVELDELLARADVITLHTPLTDKTRNILSAENLAKTKKGVMIVNCARGGLVDEAA 241

Query: 242 LYSALKEGRVAGAGLDVYAKEPCTDSPLFEFDQVVATPHLGASTDEAQEKAGIAVAKSVR 301
           L   L EG V GA  DV+  EP  ++PLF  D+VVATPHLGAST+EAQE   + VA+ V 
Sbjct: 242 LRKLLDEGHVGGAAFDVFTVEPAKENPLFGSDKVVATPHLGASTNEAQENVALQVAEQVS 301

Query: 302 LALAGELVPDAVNVQGGVIAED---VKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEIT 358
             L    V +A+N    + AE+   +KP + LAE++G     +       +D+   GE++
Sbjct: 302 DYLLTGAVTNALN-SPSITAEEAPKLKPFVALAEKIGAFAGQMVDFGVKAIDIAYEGEVS 360

Query: 359 QHDVKVLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEHRNVVIVRGT 418
             +VK +  +AL GV + ++ E ++ V+AP  A+ERG+ V  +    SP + +++ V  T
Sbjct: 361 NLNVKPMTSAALAGVLKPMLAE-INMVSAPAIAKERGITVSESRQEVSPTYDSLMRVTIT 419

Query: 419 LSDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGEA 478
              G+       +AG     +IV +   ++D A +  M+ +   D+PG +G +G ++GEA
Sbjct: 420 TEKGKRAFAGTVIAG---APRIVEVKGMELDAAFSPAMLYVNNLDKPGFIGALGMLLGEA 476

Query: 479 GLNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSV 526
           G+NIA   + R +   +A+A++ VD    +G+LA++ A      AR++
Sbjct: 477 GVNIATFNLGRVSADEDAIALVGVDQAPDAGLLAKIQALPHVKEARAL 524


Lambda     K      H
   0.315    0.133    0.362 

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: 740
Number of extensions: 39
Number of successful extensions: 6
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: 529
Length of database: 526
Length adjustment: 35
Effective length of query: 494
Effective length of database: 491
Effective search space:   242554
Effective search space used:   242554
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_03322 CCNA_03322 (D-3-phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

Software error:

../bin/blast/fastacmd -i /tmp/list.30298.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30298.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.