GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Paraburkholderia bryophila 376MFSha3.1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate H281DRAFT_04278 H281DRAFT_04278 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Burk376:H281DRAFT_04278
          Length = 641

 Score =  759 bits (1960), Expect = 0.0
 Identities = 376/601 (62%), Positives = 470/601 (78%), Gaps = 2/601 (0%)

Query: 2   HPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSLR 61
           H ++L+VT+R+V RS+ TREAYLA I  A    P RG L CAN AHG AG    DK  ++
Sbjct: 5   HSQLLKVTQRVVERSKPTREAYLARIHEAQGRFPARGALSCANLAHGFAGLEGNDKLVIK 64

Query: 62  MMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAG 121
            +   NV IVSSYN+MLSAH PY+++P+ IK+A RE G V QFAGG PAMCDG+TQG AG
Sbjct: 65  QIREPNVGIVSSYNEMLSAHAPYKNYPDIIKQAARENGGVAQFAGGVPAMCDGITQGNAG 124

Query: 122 MELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPM 181
           MELSL SREVIA+STAVAL+HNMFDAAL LGICDKIVPGL++GAL+FGHLPTIFVP GPM
Sbjct: 125 MELSLFSREVIAMSTAVALTHNMFDAALCLGICDKIVPGLLIGALQFGHLPTIFVPAGPM 184

Query: 182 PSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHL 241
            SG+SN +KA  RQ++A G+  R+ LLE+E  +YH  GTCTFYGTAN+NQ+LME+MGLHL
Sbjct: 185 TSGLSNDDKAKTRQQFATGQCGRDALLEAEAAAYHGHGTCTFYGTANSNQMLMEIMGLHL 244

Query: 242 PGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGST 301
           PG++FV+P+TPLRDALT +AA++V  LT + G++ PIG ++DE+++VN IVAL ATGGST
Sbjct: 245 PGSAFVHPHTPLRDALTAQAARRVLDLTVERGHYMPIGHVIDEKAIVNGIVALLATGGST 304

Query: 302 NHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRELL 361
           NHTLH+ AIA+AAGI + W D   LS+ VP L+ +YPNGKAD+NHF AAGG+AFL+R LL
Sbjct: 305 NHTLHLVAIARAAGIVIDWDDFDTLSQAVPLLAKIYPNGKADVNHFHAAGGVAFLVRNLL 364

Query: 362 EAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGLR 421
           E GLLHEDVNTVAG+GL  YT+EP L +GKL W  G   S D  +LR +   F  +GGLR
Sbjct: 365 EGGLLHEDVNTVAGKGLHHYTEEPKLLDGKLQWVPGVQASEDTAVLRGIKEPFQADGGLR 424

Query: 422 VMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRS 481
           +M+G LGRGV+K+SAVA QH+ V+APA+VF  Q+ + +AF  GEL++DF+AV+RFQG R+
Sbjct: 425 LMQGKLGRGVIKISAVAQQHRKVKAPAIVFDSQEAVQEAFDNGELKRDFIAVVRFQGARA 484

Query: 482 NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDG 541
           NGMPELH++TP LGVLQD+GF VALVTDGRMSGASGK+PA IH+SPEA + G + +VR G
Sbjct: 485 NGMPELHRLTPLLGVLQDQGFHVALVTDGRMSGASGKVPAVIHLSPEALLQGPIGKVRSG 544

Query: 542 DIIRVDGVKGTLELKVDADEFAAREPAKGL--LGNNVGSGRELFGFMRMAFSSAEQGASA 599
           D++ +D   G L++++D  E+AAR  A  L    N VG GRELFG  R A + AEQGAS 
Sbjct: 545 DMLVIDAEAGVLDIEIDPAEWAARPNAVPLHQAENEVGFGRELFGVFRAAAAPAEQGASV 604

Query: 600 F 600
           F
Sbjct: 605 F 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: 1192
Number of extensions: 49
Number of successful extensions: 2
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: 641
Length adjustment: 37
Effective length of query: 571
Effective length of database: 604
Effective search space:   344884
Effective search space used:   344884
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: 54 (25.4 bits)

Align candidate H281DRAFT_04278 H281DRAFT_04278 (6-phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.21431.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21431.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.