GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Phaeobacter inhibens BS107

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Phaeo:GFF2757
          Length = 607

 Score =  699 bits (1805), Expect = 0.0
 Identities = 349/606 (57%), Positives = 453/606 (74%), Gaps = 5/606 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  V +VT+R++ARS   R AYL  +R A   GP R  L C+  AH  A  G ED+  L
Sbjct: 3   LNQTVRDVTDRIIARSAKPRAAYLDRMRAAKGKGPARAHLSCSGQAHAYAATG-EDQMPL 61

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
               A ++ IV++YNDMLSAHQP+E +P++I+ A+R +G   Q AGG PAMCDGVTQGEA
Sbjct: 62  AEGTAGHLGIVTAYNDMLSAHQPFETYPQRIRDAVRRVGGTAQVAGGVPAMCDGVTQGEA 121

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+ IA++T +ALSHN+FDA + LG+CDKIVPGL++GA  FGHLP +F+P GP
Sbjct: 122 GMELSLFSRDTIAMATGIALSHNVFDATVYLGVCDKIVPGLVIGAQVFGHLPAVFLPAGP 181

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISN +KA VRQ++A G+  R+ELL+SEM +YH PGTCTFYGTANTNQ+LME MGLH
Sbjct: 182 MTSGISNDDKAKVRQKFAAGEIGRDELLKSEMAAYHGPGTCTFYGTANTNQMLMEFMGLH 241

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPG+SFVNP T +R ALT E A++   L+    ++TP+ +I+DER+ VN IV L  TGGS
Sbjct: 242 LPGSSFVNPGTDMRAALTEEGARRALALSALGNDYTPVCDILDERAYVNGIVGLMTTGGS 301

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TN  +H+ A+A+A GI L WQD ++LS+VVP L+ VYPNG AD+NHF AAGG+ ++I +L
Sbjct: 302 TNLLIHLIAMARAGGIILDWQDFSELSDVVPLLARVYPNGLADVNHFHAAGGLGYVIGQL 361

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L +G LH D  TVAG GL  YT EPFL +  LVW+ G  ESL++ I+RP +  F P GGL
Sbjct: 362 LNSGHLHSDTRTVAGSGLESYTAEPFLSDDGLVWKPGAAESLNDKIIRPASAPFQPTGGL 421

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEK-DFVAVMRFQGP 479
             + GNLG GVMK+SAVA +H++VEAPA VF DQ+++  AFKAGEL+K D + V+RFQGP
Sbjct: 422 ARLSGNLGTGVMKISAVAPEHRMVEAPARVFHDQEEVKAAFKAGELDKGDMIIVVRFQGP 481

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELH MTPFLG++Q RG KVALVTDGRMSGASGKIP+AIHV PEA  GG ++++R
Sbjct: 482 KANGMPELHSMTPFLGIMQGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGGPISKLR 541

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREP-AKGLLGNNVGSGRELFGFMRMAFSSAEQGAS 598
           DGD++RVD + GTLE+K  A+ F  R+P    L     G+GRE+F   R A +SA+ GA+
Sbjct: 542 DGDMVRVDALTGTLEVK--AEGFDDRDPVVADLSAYQHGTGREMFALFRNAVTSADTGAT 599

Query: 599 AFTSAL 604
            F++ +
Sbjct: 600 VFSTLI 605


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: 1079
Number of extensions: 43
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: 608
Length of database: 607
Length adjustment: 37
Effective length of query: 571
Effective length of database: 570
Effective search space:   325470
Effective search space used:   325470
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 GFF2757 PGA1_c28000 (phosphogluconate dehydratase Edd)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.376.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.376.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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