GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Synechococcus elongatus PCC 7942

Align phosphoglycerate dehydrogenase (EC 1.1.1.95) (characterized)
to candidate Synpcc7942_1501 Synpcc7942_1501 D-3-phosphoglycerate dehydrogenase

Query= BRENDA::Q9Z564
         (529 letters)



>FitnessBrowser__SynE:Synpcc7942_1501
          Length = 546

 Score =  394 bits (1013), Expect = e-114
 Identities = 217/531 (40%), Positives = 333/531 (62%), Gaps = 10/531 (1%)

Query: 5   PVVLIAEELSPATVDALGPDFEIRHCNGADRAELLPAIADVDAILVRSATKVDAEAVAAA 64
           P VL+++ +    +D L    ++    G   +EL   I + DA+++RS T+V AE + A 
Sbjct: 19  PKVLVSDPIDQVGLDILSQVAQVDVKTGLSPSELAQIIGEYDALMLRSGTRVTAEVIEAG 78

Query: 65  KKLKVVARAGVGLDNVDVSAATKAGVMVVNAPTSNIVTAAELACGLIVATARNIPQANAA 124
           +KL+++ RAGVG+DNVDV AAT+ G++VVN+P  N + AAE    ++++ +R+IP ANA+
Sbjct: 79  QKLRIIGRAGVGVDNVDVPAATRRGIVVVNSPEGNTIAAAEHTLAMMLSLSRHIPDANAS 138

Query: 125 LKNGEWKRSKYTGVELAEKTLGVVGLGRIGALVAQRMSAFGMKVVAYDPYVQPARAAQMG 184
            K+G W R  + G E+ +KTLGVVGLG+IG+ VA    A GMK++AYDP++   RA Q+G
Sbjct: 139 TKSGGWDRKSFVGTEVYKKTLGVVGLGKIGSHVATVAKAMGMKLLAYDPFISAERAEQIG 198

Query: 185 VKVLSLDELLEVSDFITVHLPKTPETLGLIGDEALRKVKPSVRIVNAARGGIVDEEALYS 244
            +++ LD L + +D+IT+H+PKTPET  LI  E L K+KP+ RI+N ARGG+++E+AL  
Sbjct: 199 ARLVELDILFQEADYITLHIPKTPETANLINAETLAKMKPTTRIINCARGGVINEQALAD 258

Query: 245 ALKEGRVAGAGLDVYAKEPC-TDSPLFEFDQ-VVATPHLGASTDEAQEKAGIAVAKSVRL 302
           A+  G++ GA LDVY +EP   DSPL    + ++ TPHLGAST EAQ    + VA+ +R 
Sbjct: 259 AIAAGKIGGAALDVYDQEPLQADSPLRALGKNLILTPHLGASTTEAQVNVAVDVAEQIRD 318

Query: 303 ALAGELVPDAVNVQG--GVIAEDVKPGLPLAERLGRIFTALAGEVAVRLDVEVYGEITQH 360
            L G     AVN+ G    I E ++P L LAE LG + + +AG    +L V + GE+   
Sbjct: 319 VLLGLPARSAVNIPGLYPDILEKLRPYLQLAETLGNLLSQVAGGRLEQLTVRLQGELAAQ 378

Query: 361 DVKVLELSALKGVFEDVVDETVSYVNAPLFAQERGVEVRLTTSSESPEH---RNVVIVRG 417
             + + ++ALKG+    + E V+YVNA + A+ERG+ + + T  ES         + +  
Sbjct: 379 QSQPIVVAALKGLLTQALRERVNYVNAMIEAKERGIRI-IETRDESVRDDYAGGSLQLVA 437

Query: 418 TLSDGEEVSVSGTLAGPKHLQKIVAIGEYDVDLALADHMVVLRYEDRPGVVGTVGRIIGE 477
           T S+GE   V G L G   + +I  + E+ V++  + +M+  R+ D PG++G +G ++G 
Sbjct: 438 TGSNGEH-RVMGALLGDGEI-RITNVDEFPVNVPPSRYMLFTRHRDMPGIIGKIGSLLGS 495

Query: 478 AGLNIAGMQVARATVGGEALAVLTVDDTVPSGVLAEVAAEIGATSARSVNL 528
             +NIA MQV R  V G+A+ VL++DD +P G+LAE+    G + A +V L
Sbjct: 496 FNVNIASMQVGRRIVRGDAVMVLSLDDPLPEGILAEITKVAGISDAYTVVL 546


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: 754
Number of extensions: 24
Number of successful extensions: 5
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: 546
Length adjustment: 35
Effective length of query: 494
Effective length of database: 511
Effective search space:   252434
Effective search space used:   252434
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 Synpcc7942_1501 Synpcc7942_1501 (D-3-phosphoglycerate dehydrogenase)
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

Software error:

../bin/blast/fastacmd -i /tmp/list.10382.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10382.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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