GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas putida KT2440

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate PP_1010 PP_1010 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__Putida:PP_1010
          Length = 608

 Score = 1056 bits (2732), Expect = 0.0
 Identities = 528/608 (86%), Positives = 566/608 (93%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           MHPR+LEVT+RLV RSRATRE YL LIRGAAS+GP R  LQCANFAHGVAGCGSEDK +L
Sbjct: 1   MHPRILEVTQRLVERSRATRERYLQLIRGAASEGPMRASLQCANFAHGVAGCGSEDKQTL 60

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           R+MNAANVAIVS+YNDMLSAHQPY HFPEQIK+ALRE+GSVGQFAGG PAMCDGVTQGE 
Sbjct: 61  RLMNAANVAIVSAYNDMLSAHQPYLHFPEQIKQALREVGSVGQFAGGVPAMCDGVTQGEP 120

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMEL++ SREVIA+STAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP
Sbjct: 121 GMELAIASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SGISNK+KADVRQRYAEGKA+REELLESEM SYHSPGTCTFYGTANTNQL+MEVMGLH
Sbjct: 181 MVSGISNKQKADVRQRYAEGKASREELLESEMNSYHSPGTCTFYGTANTNQLVMEVMGLH 240

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGASFVNPYTPLRDALT EAAQQVTR+TK SG+F P+GEIVDE++LVNSIVALHATGGS
Sbjct: 241 LPGASFVNPYTPLRDALTAEAAQQVTRMTKASGSFMPLGEIVDEKALVNSIVALHATGGS 300

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLH+PAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL
Sbjct: 301 TNHTLHIPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGGL 420
           L+AGLLHEDVNTVAG GL RYTQEPFLDNGKLVWR+GP  SLDE+ILRPV+R FS EGGL
Sbjct: 361 LDAGLLHEDVNTVAGHGLRRYTQEPFLDNGKLVWREGPQHSLDESILRPVSRPFSAEGGL 420

Query: 421 RVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPR 480
           RVMEGNLGRGVMKVSAVA +HQ+VEAPA VFQDQQ LADAFKAGELE+DFVAV+RFQGPR
Sbjct: 421 RVMEGNLGRGVMKVSAVAPEHQVVEAPARVFQDQQSLADAFKAGELERDFVAVVRFQGPR 480

Query: 481 SNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRD 540
            NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGKIPAAIHV PEA  GG LARVRD
Sbjct: 481 CNGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKIPAAIHVCPEAYDGGPLARVRD 540

Query: 541 GDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASAF 600
           GDI+RVDGV+GTL + V A+E A+RE      GN++G GRELFGFMRMAFS AEQGASAF
Sbjct: 541 GDIVRVDGVEGTLRIMVSAEELASRELPPAPQGNDLGCGRELFGFMRMAFSPAEQGASAF 600

Query: 601 TSALENLK 608
           TSALE+LK
Sbjct: 601 TSALEHLK 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: 1306
Number of extensions: 55
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 PP_1010 PP_1010 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.5008.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5008.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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