GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Pseudomonas stutzeri RCH2

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate GFF1853 Psest_1892 6-phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__psRCH2:GFF1853
          Length = 609

 Score =  977 bits (2526), Expect = 0.0
 Identities = 482/609 (79%), Positives = 545/609 (89%), Gaps = 1/609 (0%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGS-EDKHS 59
           MHPRVLEVTERLV RSR TRE YLA++  AAS+GPQRG LQCANFAHGVAGC S +DK S
Sbjct: 1   MHPRVLEVTERLVERSRKTRERYLAMMAAAASEGPQRGGLQCANFAHGVAGCNSPQDKQS 60

Query: 60  LRMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGE 119
           LR+MNA NVAIVS+YNDMLSAHQPYEHFPE I++ALRE+GSVGQFAGG PAMCDGVTQGE
Sbjct: 61  LRLMNAVNVAIVSAYNDMLSAHQPYEHFPEMIRQALREIGSVGQFAGGVPAMCDGVTQGE 120

Query: 120 AGMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGG 179
           AGME+SL SREVIA+STAVALSHNMFDAALMLGICDKIVPGLM+GALRFGHLPTIFVPGG
Sbjct: 121 AGMEMSLASREVIAMSTAVALSHNMFDAALMLGICDKIVPGLMIGALRFGHLPTIFVPGG 180

Query: 180 PMPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGL 239
           PMPSGI NK KA+VRQRYAEGKA+REELLESEMKSYHSPGTCTFYGTANTNQ++ME+MGL
Sbjct: 181 PMPSGIPNKAKAEVRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQVVMEIMGL 240

Query: 240 HLPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGG 299
           HLPG+SFVNPYTPLRDALT EAAQQVTRLT Q+GN+TP+ ++VDE+S+VNS+VAL+ATGG
Sbjct: 241 HLPGSSFVNPYTPLRDALTREAAQQVTRLTHQAGNYTPLCQVVDEKSIVNSVVALNATGG 300

Query: 300 STNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIRE 359
           STNHTLH+PA A+AAGIQLTW+DMADLSEVVPTL+ VYPNG+AD+NHF A GG+ F++R 
Sbjct: 301 STNHTLHIPAFARAAGIQLTWKDMADLSEVVPTLAKVYPNGQADVNHFHACGGVPFMVRT 360

Query: 360 LLEAGLLHEDVNTVAGRGLSRYTQEPFLDNGKLVWRDGPIESLDENILRPVARAFSPEGG 419
           LL+AGLLHEDV+TV G+GL RY QEPFLD  +LVWRDGP +SLDE+ILRP  R FSPEGG
Sbjct: 361 LLDAGLLHEDVHTVVGKGLRRYIQEPFLDGDRLVWRDGPTQSLDESILRPAERPFSPEGG 420

Query: 420 LRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAVMRFQGP 479
           LRV+EGNLGRGV K+SAVA +H++VEAPA VF DQ +LA AFKAGELE+DF+AV+RFQGP
Sbjct: 421 LRVLEGNLGRGVTKISAVAPEHRVVEAPARVFIDQSELAAAFKAGELERDFIAVVRFQGP 480

Query: 480 RSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVR 539
           ++NGMPELHK+TPFLGVLQDRG+KVALVTDGRMSGASGK+PAAIHV PEA  GG LARVR
Sbjct: 481 KANGMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVCPEALDGGPLARVR 540

Query: 540 DGDIIRVDGVKGTLELKVDADEFAAREPAKGLLGNNVGSGRELFGFMRMAFSSAEQGASA 599
           DGDI+RVDG  G L   VD  E+ AREPA       +G GRELF FMR +FS+AEQGASA
Sbjct: 541 DGDILRVDGESGELLALVDPVEWGAREPAIRPEDVGIGCGRELFAFMRASFSTAEQGASA 600

Query: 600 FTSALENLK 608
           FT +LE L+
Sbjct: 601 FTESLEALR 609


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: 1230
Number of extensions: 43
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: 609
Length adjustment: 37
Effective length of query: 571
Effective length of database: 572
Effective search space:   326612
Effective search space used:   326612
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 GFF1853 Psest_1892 (6-phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.8943.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8943.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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