GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serA in Dinoroseobacter shibae DFL-12

Align phosphoglycerate dehydrogenase; EC 1.1.1.95 (characterized)
to candidate 3609936 Dshi_3318 D-3-phosphoglycerate dehydrogenase (RefSeq)

Query= CharProtDB::CH_004924
         (525 letters)



>FitnessBrowser__Dino:3609936
          Length = 531

 Score =  413 bits (1062), Expect = e-120
 Identities = 218/513 (42%), Positives = 320/513 (62%), Gaps = 9/513 (1%)

Query: 3   RVLVSDKMSNDGLQPL----IESDFIEIVQKNVADAEDELHTFDALLVRSATKVTEDLFN 58
           +VLVSDK+S   +Q      IE DF   + K+     + +  +D L +RSATKVTE L  
Sbjct: 4   KVLVSDKLSETAVQIFRDRGIEVDFEPSLGKDKDKLAEVIGKYDGLAIRSATKVTEKLLA 63

Query: 59  KMTSLKIVGRAGVGVDNIDIDEATKHGVIVINAPNGNTISTAEHTFAMISSLMRHIPQAN 118
              +LK+VGRAG+G DN+D   A+K GVIV+N P GN I+TAEH  AM+ ++ R IP+A+
Sbjct: 64  HADNLKVVGRAGIGTDNVDKVAASKKGVIVMNTPFGNMITTAEHAIAMMFAVARQIPEAS 123

Query: 119 ISVKSREWNRTAYVGSELYGKTLGIVGLGRIGSEIAQRRGAFGMTVHVFDPFLTEERAKK 178
            S  + +W ++ ++G EL  KTLG++G G IG  + +R     M V  +DPFL+EERA K
Sbjct: 124 ASTHAGKWEKSKFMGVELTAKTLGVIGAGNIGGIVCERALGLKMKVIAYDPFLSEERADK 183

Query: 179 IGVNSRTFEEVLESADIITVHTPLTKETKGLLNKETIAKTKKGVRLINCARGGIIDEAAL 238
           +GV     + +L  AD IT+H PLT +T+ +L++E + KTKKGVR+INCARGG++DE AL
Sbjct: 184 LGVEKVDLDTLLARADFITLHVPLTDQTRNILSREALEKTKKGVRIINCARGGLVDEQAL 243

Query: 239 LEALENGHVAGAALDVFEVEPPVDNKLVDHPLVIATPHLGASTKEAQLNVAAQVSEEVLQ 298
            + L++GHVAGAA DVF  EP  +N L   P V+ TPHLGAST EAQ NVA QV+E++  
Sbjct: 244 ADLLKSGHVAGAAFDVFAEEPATENPLFGLPNVVCTPHLGASTTEAQENVALQVAEQMSN 303

Query: 299 FAKGLPVMSAINLPAMTKDEFAKIKPYHQIAGKIGSLVSQCMKEPVQDVAIQYEGTIAKL 358
           +     V +A+N+P++T +E   + P+ ++AG +G+ V Q   EP+  + I Y GT+AK+
Sbjct: 304 YLLSGAVENALNMPSVTAEEAKTMGPWVKLAGHLGTFVGQLTDEPIDSIEILYNGTVAKM 363

Query: 359 ETSFITKALLSGFLKPRVDSTVNEVNAGGVAKERGISFSEKISSSESGYDNCISVKVTGD 418
               +  A+++G ++   +  VN V+A  +AKERGI  S         +D  + + V  D
Sbjct: 364 NLEALNCAVIAGIMQ-ATNPDVNMVSAPVIAKERGIGLSTTTQDKSGVFDGYVKLTVKTD 422

Query: 419 RSTFTVTATYIPHFGERIVEINGFNIDFYPTGHLVYIQHQDTTGVIGRVGRILGDNDINI 478
           + T ++  T       R ++I G NID     H++Y  ++DT G+IG +G ILG+N +NI
Sbjct: 423 QRTRSIAGTVFSDGKPRFIQIKGINIDAEIGEHMLYTTNKDTPGMIGTLGGILGENQVNI 482

Query: 479 ATMQVGRKEKGGEAIMMLSFD----RHLEDKIV 507
           A   +GR E  G+AI ML  D    R ++DK++
Sbjct: 483 ANFTLGRNETNGDAIAMLYLDAPLPRDVQDKLI 515


Lambda     K      H
   0.317    0.134    0.374 

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: 639
Number of extensions: 26
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 525
Length of database: 531
Length adjustment: 35
Effective length of query: 490
Effective length of database: 496
Effective search space:   243040
Effective search space used:   243040
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 3609936 Dshi_3318 (D-3-phosphoglycerate dehydrogenase (RefSeq))
to HMM TIGR01327 (serA: phosphoglycerate dehydrogenase (EC 1.1.1.95))

Software error:

../bin/blast/fastacmd -i /tmp/list.7339.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7339.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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