GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas simiae WCS417

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF4432 PS417_22690 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__WCS417:GFF4432
          Length = 608

 Score = 1115 bits (2883), Expect = 0.0
 Identities = 560/608 (92%), Positives = 586/608 (96%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPRVLEVTERL+ARSRATREAYLALIRGAA DGP RGKLQCANFAHGVAGCG+EDK+SL
Sbjct: 1   MHPRVLEVTERLIARSRATREAYLALIRGAAIDGPMRGKLQCANFAHGVAGCGTEDKNSL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALRE+GSVGQFAGGTPAMCDGVTQGE 
Sbjct: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREVGSVGQFAGGTPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SREVIA+STAVALSHNMFDAALMLGICDKIVPGLMMGALR+GHLP IFVPGGP
Sbjct: 121 GMELSLLSREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRYGHLPMIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           MPSGISNK+KADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH
Sbjct: 181 MPSGISNKQKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNPYTPLRDALT EAA QVTRLTK +G+F PIGEIVDE+S+VNSI+AL+ATGGS
Sbjct: 241 LPGASFVNPYTPLRDALTREAAHQVTRLTKANGSFMPIGEIVDEKSIVNSIIALNATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLHMPAIA +AGI LTW DMADLSEVVPTLSHVYPNGKADINHFQAAGGM+FLIREL
Sbjct: 301 TNHTLHMPAIAMSAGIILTWDDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           LEAGLLHEDVNTVAG+GLSRYTQEPFL +G+L+WR+GPIESLDE ILRPVARAFSPEGGL
Sbjct: 361 LEAGLLHEDVNTVAGKGLSRYTQEPFLVDGELIWREGPIESLDETILRPVARAFSPEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVA +HQIVEAPAVVFQDQQDLADAFKAG+LEKDFVAVMRFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQIVEAPAVVFQDQQDLADAFKAGQLEKDFVAVMRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
           SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHV+PEAQ GG LARVRD
Sbjct: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVNPEAQSGGPLARVRD 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDIIRVDGVKGTLELKVDA+EFAAR PA GLLGNNVG+GRELF FMR+A SSAEQGASAF
Sbjct: 541 GDIIRVDGVKGTLELKVDAEEFAARAPATGLLGNNVGAGRELFAFMRLAASSAEQGASAF 600

Query: 601 TSALENLK 608
           TSALE LK
Sbjct: 601 TSALETLK 608


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: 1338
Number of extensions: 46
Number of successful extensions: 1
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: 608
Length adjustment: 37
Effective length of query: 571
Effective length of database: 571
Effective search space:   326041
Effective search space used:   326041
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 GFF4432 PS417_22690 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.20604.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20604.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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