GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Acidovorax sp. GW101-3H11

Align Phosphogluconate dehydratase; 6-phosphogluconate dehydratase; EC 4.2.1.12 (characterized)
to candidate Ac3H11_2082 Phosphogluconate dehydratase (EC 4.2.1.12)

Query= SwissProt::P21909
         (607 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2082
          Length = 589

 Score =  661 bits (1706), Expect = 0.0
 Identities = 331/598 (55%), Positives = 436/598 (72%), Gaps = 16/598 (2%)

Query: 4   LHSTVEKVTARVIERSRETRKAYLDLIQYEREKGVDRPNLSCSNLAHGFAAMNG-DKPAL 62
           +H  V +VT R+++RS +TR AYL  +     +   +  + C+NLAH +AA+ G +K  +
Sbjct: 1   MHPVVARVTERIVQRSADTRGAYLAGVDAMIARKPAQDRMGCANLAHAYAALPGSEKFKV 60

Query: 63  RDFNRMNIGVVTSYNDMLSAHEPYYRYPEQMKVFAREVGATVQVAGGVPAMCDGVTQGQP 122
                 NIGVVT+YNDMLSAH+PY  YP  ++  A + GATVQVAGGVPAMCDGVTQG P
Sbjct: 61  TVEKAPNIGVVTAYNDMLSAHQPYQSYPAVLRDEAAKQGATVQVAGGVPAMCDGVTQGTP 120

Query: 123 GMEESLFSRDVIALATSVSLSHGMFEGAALLGICDKIVPGLLMGALRFGHLPTILVPSGP 182
           GME SLFSRD IA+AT+V+LSH +F+GA LLG+CDKIVPGLL+GAL +GHLP + VP+GP
Sbjct: 121 GMELSLFSRDAIAMATAVALSHDVFDGALLLGVCDKIVPGLLIGALHYGHLPCVFVPAGP 180

Query: 183 MTTGIPNKEKIRIRQLYAQGKIGQKELLDMEAACYHAEGTCTFYGTANTNQMVMEVLGLH 242
           M TG+ NK+K ++R+ YAQG +G+ ELL  E+A YH+ GTCTFYGTAN+NQM++E +GLH
Sbjct: 181 MGTGLSNKDKAKVREQYAQGLVGRDELLQAESAAYHSPGTCTFYGTANSNQMLLEAMGLH 240

Query: 243 MPGSAFVTPGTPLRQALTRAAVHRVAELGWKGDDYRPLGKIIDEKSIVNAIVGLLATGGS 302
           +PG+AF +PGT  R+A TR A+  V ++G +   + P+GK++DE+ IVNA+  LLATGGS
Sbjct: 241 VPGAAFESPGTEAREAFTRQALRTVLDIGKRSKRFTPIGKLVDERCIVNAMAALLATGGS 300

Query: 303 TNHTMHIPAIARAAGVIVNWNDFHDLSEVVPLIARIYPNGPRDINEFQNAGGMAYVIKEL 362
           TNH +H  AIAR+AG++++W DF +LS VVPL+AR+YPNG  D+N+FQ AGG  ++++EL
Sbjct: 301 TNHLIHWVAIARSAGILIDWTDFDELSSVVPLLARVYPNGDADVNQFQAAGGPPWILREL 360

Query: 363 LSANLLNRDVTTIAKGGIEEYAK-APALNDAGELVWKPAGEPGDDTILRPVSNPFAKDGG 421
           L+   ++ DV ++  GGI +  K APA++             GD ++LRPVS PF+  GG
Sbjct: 361 LAGGFMHPDVMSVNVGGIADGGKSAPAVS-------------GDTSVLRPVSAPFSPTGG 407

Query: 422 LRLLEGNLGRAMYKASAVDPKFWTIEAPVRVFSDQDDVQKAFKAGELNKDVIVVVRFQGP 481
           LRLL+G LGRA+ K SAV      IEAP RVF  Q+ +  AF AG++N+D++ VVRFQGP
Sbjct: 408 LRLLQGRLGRAVIKVSAVPEDRHIIEAPARVFDSQEALLAAFSAGDVNQDMVAVVRFQGP 467

Query: 482 RANGMPELHKLTPALGVLQDNGYKVALVTDGRMSGATGKVPVALHVSPEALGGGAIGKLR 541
           +ANGMPELHKLTP L VLQ+ G+KVALVTDGRMSGA+GKVP A+HV+PEAL GG + K+R
Sbjct: 468 QANGMPELHKLTPPLAVLQNQGFKVALVTDGRMSGASGKVPAAIHVTPEALAGGPLAKVR 527

Query: 542 DGDIVRISVEEGKLEALVPADEWNAR-PHAEKPAFRPGTGRELFDIFRQNAAKAEDGA 598
           DGDIVR+    G L+ LV    W AR P       + G GRELF  FR++A  AE GA
Sbjct: 528 DGDIVRVDAVAGTLDVLVDEATWAARTPSPYSAPAQTGFGRELFTNFRRHAGGAEQGA 585


Lambda     K      H
   0.318    0.136    0.403 

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: 1114
Number of extensions: 48
Number of successful extensions: 4
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: 607
Length of database: 589
Length adjustment: 37
Effective length of query: 570
Effective length of database: 552
Effective search space:   314640
Effective search space used:   314640
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 Ac3H11_2082 (Phosphogluconate dehydratase (EC 4.2.1.12))
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.2843.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2843.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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