GapMind for catabolism of small carbon sources

 

Alignments for a candidate for edd in Herbaspirillum seropedicae SmR1

Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate HSERO_RS05520 HSERO_RS05520 phosphogluconate dehydratase

Query= BRENDA::Q1PAG1
         (608 letters)



>FitnessBrowser__HerbieS:HSERO_RS05520
          Length = 623

 Score =  746 bits (1925), Expect = 0.0
 Identities = 367/608 (60%), Positives = 462/608 (75%), Gaps = 8/608 (1%)

Query: 1   MHPRVLEVTERLVARSRATREAYLALIRGAASDGPQRGKLQCANFAHGVAGCGSEDKHSL 60
           ++  +  VT+R+  RSR  R AYL  +  A   G QRG L C N AHG A   + DK  L
Sbjct: 3   LNATLASVTQRIAERSRPYRTAYLERLEAARRKGAQRGALACTNLAHGFAAFPANDKLKL 62

Query: 61  RMMNAANVAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEA 120
           +   A ++AIVS+YNDMLSAHQP+E FP+ IK A RE G+V QFAGG+PAMCDGVTQG+A
Sbjct: 63  KEDKAPSLAIVSAYNDMLSAHQPFERFPQIIKDAAREAGAVAQFAGGSPAMCDGVTQGQA 122

Query: 121 GMELSLPSREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGP 180
           GMELSL SR+ IA++TA+ALSHNMFDAAL LG+CDKIVPGL++GAL FGHLP +FVP GP
Sbjct: 123 GMELSLFSRDAIAMATAIALSHNMFDAALYLGVCDKIVPGLLIGALHFGHLPAVFVPAGP 182

Query: 181 MPSGISNKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240
           M SG+SN +K  +RQ Y  GK  R ELLE+E KSYH  GTCTFYGTAN+NQ+LME MGLH
Sbjct: 183 MTSGMSNSDKVKIRQLYTAGKIGRAELLEAESKSYHGAGTCTFYGTANSNQMLMEAMGLH 242

Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQSGNFTPIGEIVDERSLVNSIVALHATGGS 300
           LPGA+F+ P TPLRDALT  AA+Q  ++T     +TP+G ++DE+S+VN+IVALHATGGS
Sbjct: 243 LPGAAFITPNTPLRDALTAAAAKQAAKITDLGTQYTPVGRMIDEKSIVNAIVALHATGGS 302

Query: 301 TNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMAFLIREL 360
           TNHTLH+ AIA+AAGI + W D   LS VVP ++ +YPNG AD+NHF AAGG  F++REL
Sbjct: 303 TNHTLHLVAIAKAAGIVIDWDDFDKLSAVVPLITKIYPNGTADVNHFHAAGGTGFVLREL 362

Query: 361 LEAGLLHEDVNTVAGRGLSRYTQEPFL----DNGK---LVWRDGPIESLDENILRPVARA 413
           ++AGL+H+DV T+ G+GL ++ +EP L    +NG+   + W D P +S DE +L  VA+ 
Sbjct: 363 IDAGLMHDDVTTILGQGLRQHCKEPMLAAEGENGRPGIVTWHDAPAQSGDEGVLGTVAKP 422

Query: 414 FSPEGGLRVMEGNLGRGVMKVSAVALQHQIVEAPAVVFQDQQDLADAFKAGELEKDFVAV 473
           F+ +GGL++++GNLGR V+K+SAV  +H++VEAPAVVF  Q+    AFKAG+L++DFVAV
Sbjct: 423 FAADGGLKLLQGNLGRAVIKISAVKPEHRVVEAPAVVFHSQEAFMAAFKAGQLDRDFVAV 482

Query: 474 MRFQGPRSNGMPELHKMTPFLGVLQDRGFKVALVTDGRMSGASGKIPAAIHVSPEAQVGG 533
           + FQGPR+NGMPELH +TP LG+LQD+G  VALVTDGRMSGASGK+PAAIHV+PE   GG
Sbjct: 483 ITFQGPRANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLGGG 542

Query: 534 ALARVRDGDIIRVDGVKGTLELKVDADEFAAR-EPAKGLLGNNVGSGRELFGFMRMAFSS 592
            L RVRDGDIIR+D   GTLE KVDA E+AAR + +  L GN  G GRELF   R A  +
Sbjct: 543 PLGRVRDGDIIRLDAEAGTLEAKVDATEWAARSQDSSDLSGNQHGMGRELFSLFRNAVGT 602

Query: 593 AEQGASAF 600
           AE+G + F
Sbjct: 603 AEEGGATF 610


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: 1134
Number of extensions: 52
Number of successful extensions: 3
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: 623
Length adjustment: 37
Effective length of query: 571
Effective length of database: 586
Effective search space:   334606
Effective search space used:   334606
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 HSERO_RS05520 HSERO_RS05520 (phosphogluconate dehydratase)
to HMM TIGR01196 (edd: phosphogluconate dehydratase (EC 4.2.1.12))

Software error:

../bin/blast/fastacmd -i /tmp/list.2733.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2733.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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