GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Desulfovibrio vulgaris Hildenborough

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate 208900 DVU3373 dihydroxy-acid dehydratase

Query= BRENDA::Q97UB2
         (558 letters)



>MicrobesOnline__882:208900
          Length = 554

 Score =  459 bits (1180), Expect = e-133
 Identities = 242/555 (43%), Positives = 347/555 (62%), Gaps = 4/555 (0%)

Query: 5   LNSPSRYHGIYNAPHRAFLRSVGLTDEEIGKPLVAIATAWSEAGPCNFHTLALARVAKEG 64
           + S    HG+  APHR+ L ++GLT EE+ +PLV +  A +E  P + H   +A   K G
Sbjct: 1   MRSKKMTHGLEKAPHRSLLHALGLTREELARPLVGVVNAANEVVPGHIHLDDIAEAVKAG 60

Query: 65  TKEAGLSPLAFPTMVVNDNIGMGSEGMRYSLVSRDLIADMVEAQFNAHAFDGLVGIGGCD 124
            + AG +PL FP + V D + M  EGMR+SL SR+LIAD +E    AH FD LV I  CD
Sbjct: 61  VRAAGGTPLEFPAIAVCDGLAMNHEGMRFSLPSRELIADSIEIMATAHPFDALVFIPNCD 120

Query: 125 KTTPGILMAMARLNVPSIYIYGGSAEPGYFMGKRLTIEDVHEAIGAYLAKRITENELYEI 184
           K+ PG+LMAM RL+VPS+ + GG    G  +  R  +  V E +G      +TE EL E+
Sbjct: 121 KSVPGMLMAMLRLDVPSVMVSGGPMLAGATLAGRADLITVFEGVGRVQRGDMTEAELDEL 180

Query: 185 EKRAHPTLGTCSGLFTANTMGSMSEALGMALPGSASPTATSSRRVMYVKETGKALGSLIE 244
            + A P  G+C+G+FTAN+M  ++E +G+ALPG+ +  A ++ R+   K  G  +  ++E
Sbjct: 181 VEGACPGCGSCAGMFTANSMNCLAETIGLALPGNGTTPAVTAARIRLAKHAGMKVMEMLE 240

Query: 245 NGIKSREILTFEAFENAITTLMAMGGSTNAVLHLLAIAYEAGVKLTLDDFNRISKRTPYI 304
             I+ R+I+T +A  NA+   MA+G STN VLHL A+  EAG+ LTLD F+++S++TP +
Sbjct: 241 RNIRPRDIVTEKAVANAVAVDMALGCSTNTVLHLPAVFAEAGLDLTLDIFDKVSRKTPNL 300

Query: 305 ASMKPGGDYVMADLDEVGGVPVVLKKLLDAGLLHGDVLTVTGKTMKQNLEQYKYPNVPHS 364
             + P G + + DL   GG+P V+ +L   GL+    +TVTG+T+ +NL+      V  +
Sbjct: 301 CKLSPAGHHHIQDLHAAGGIPAVMAELDRIGLIDRSAMTVTGRTVGENLDALG-AKVRDA 359

Query: 365 HIVRDVKNPIKPRGGIVILKGSLAPEGAVIK--VAATNVVKFEGKAKVYNSEDDAFKGVQ 422
            ++R V  P  P+GGI ILKGSLAP GAV+K    A  ++  E  A+V++SE+ A + + 
Sbjct: 360 DVIRPVDAPYSPQGGIAILKGSLAPGGAVVKQSAVAPEMMVREAVARVFDSEEAACEAIM 419

Query: 423 SGEVSEGEVVIIRYEGPKGAPGMPEMLRVTAAIMGAGLN-NVALVTDGRFSGATRGPMVG 481
            G +  G+ ++IRYEGPKG PGM EML  T+AI G GL  +VAL+TDGRFSG TRG  +G
Sbjct: 420 GGRIKAGDAIVIRYEGPKGGPGMREMLTPTSAIAGMGLGADVALITDGRFSGGTRGAAIG 479

Query: 482 HVAPEAMVGGPIAIVEDGDTIVIDVESERLDLKLSEEEIKNRLKRWSPPSPRYKSGLLAK 541
           HV+PEA  GGPI +V++GD I ID+ +  LDL + E+E+  R   + P      S LL +
Sbjct: 480 HVSPEAAEGGPIGLVQEGDRIRIDIPARALDLLVDEDELARRRAAFVPVEKEITSPLLRR 539

Query: 542 YASLVSQASMGAVTR 556
           YA +VS A+ GA  R
Sbjct: 540 YARMVSSAATGARQR 554


Lambda     K      H
   0.316    0.134    0.383 

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: 843
Number of extensions: 43
Number of successful extensions: 4
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: 558
Length of database: 554
Length adjustment: 36
Effective length of query: 522
Effective length of database: 518
Effective search space:   270396
Effective search space used:   270396
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate 208900 DVU3373 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.8532.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8532.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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