GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Dyella japonica UNC79MFTsu3.2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate N515DRAFT_3177 N515DRAFT_3177 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Dyella79:N515DRAFT_3177
          Length = 606

 Score =  749 bits (1934), Expect = 0.0
 Identities = 376/599 (62%), Positives = 455/599 (75%), Gaps = 2/599 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           +HP V EVT RL  RSR TR AYLA I  A + G  R +L C N AHG A CG  DK +L
Sbjct: 5   LHPVVAEVTARLRERSRDTRAAYLARIAAAGTGGTHRERLSCGNLAHGFAACGPHDKAAL 64

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R  +  N+ IV+SYNDMLSAHQPYE +PE I++  RE G   Q AGG PAMCDGVTQG  
Sbjct: 65  REGHTPNLGIVTSYNDMLSAHQPYERYPELIRRIARESGITAQVAGGVPAMCDGVTQGRE 124

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR++IA++TAV+LSH+MFD  L LGICDKIVPGL++GAL FGHLP IFVPGGP
Sbjct: 125 GMELSLFSRDLIAMATAVSLSHDMFDGTLYLGICDKIVPGLLIGALSFGHLPGIFVPGGP 184

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSGI+N++K+ VRQ YAEGKA R ELLE+E  +YH+PGTCTFYGTAN+NQ+LME+MGLH
Sbjct: 185 MPSGITNEQKSKVRQAYAEGKANRAELLEAEAAAYHAPGTCTFYGTANSNQMLMEIMGLH 244

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFV P TPLRDALT EA  +V  L+    N  PIG IVDER+++N ++ LHATGGS
Sbjct: 245 LPGASFVAPDTPLRDALTAEAVHRVAALSAHGDNHLPIGHIVDERAIINGVIGLHATGGS 304

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNH LH+ A+A+AAGIQL W D   LS VVP L+ VYPNG AD+N F  AGGMAFLI +L
Sbjct: 305 TNHLLHLVAMARAAGIQLRWDDFDALSSVVPLLARVYPNGYADVNQFHDAGGMAFLIDQL 364

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLD-NGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           L AGLLH DV TV G GL  Y Q P LD +G L W     ES +  +LR +A  F  +GG
Sbjct: 365 LGAGLLHGDVRTVFGTGLDGYAQVPSLDASGALQWTPVAKESGNRGVLRGMAEPFRADGG 424

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           LR++ GNLGR V+KVS+V    Q++EAPAVVF DQ ++  AF+ GEL +DF+AV+RFQGP
Sbjct: 425 LRMLAGNLGRAVIKVSSVPDDRQVIEAPAVVFHDQDEVRKAFERGELNRDFIAVVRFQGP 484

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           R+ GMPELHK+TP L VLQDRG+++AL+TDGRMSGASG++PAAIHV+PEAQ  GA+AR+R
Sbjct: 485 RAIGMPELHKLTPTLAVLQDRGYRIALLTDGRMSGASGRVPAAIHVTPEAQAQGAIARIR 544

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKG-LLGNNVGSGRELFGFMRMAFSSAEQGA 597
           DGD+IR+D  +GTL++ VDA EFA+R PA   L  ++ G GRELFG  R A + A+ GA
Sbjct: 545 DGDLIRLDATRGTLDVLVDASEFASRAPATADLSSHHSGMGRELFGLFRQAAAEADLGA 603


Lambda     K      H
   0.318    0.134    0.386 

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: 1137
Number of extensions: 60
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: 608
Length of database: 606
Length adjustment: 37
Effective length of query: 571
Effective length of database: 569
Effective search space:   324899
Effective search space used:   324899
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 (21.7 bits)
S2: 53 (25.0 bits)

Align candidate N515DRAFT_3177 N515DRAFT_3177 (6-phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.13210.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13210.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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