GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Desulfovibrio vulgaris Miyazaki F

Align dihydroxy-acid dehydratase (EC 4.2.1.9) (characterized)
to candidate 8501301 DvMF_2034 dihydroxy-acid dehydratase (RefSeq)

Query= BRENDA::Q97UB2
         (558 letters)



>FitnessBrowser__Miya:8501301
          Length = 555

 Score =  456 bits (1173), Expect = e-132
 Identities = 244/555 (43%), Positives = 345/555 (62%), Gaps = 4/555 (0%)

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

Query: 65  TKEAGLSPLAFPTMVVNDNIGMGSEGMRYSLVSRDLIADMVEAQFNAHAFDGLVGIGGCD 124
            + AG +P+ FP + V D + M  EGM +SL SR++IAD +E    AH FD LV I  CD
Sbjct: 61  VRAAGGTPMEFPAIAVCDGLAMNHEGMHFSLPSREIIADSIEIMATAHPFDALVFIPNCD 120

Query: 125 KTTPGILMAMARLNVPSIYIYGGSAEPGYFMGKRLTIEDVHEAIGAYLAKRITENELYEI 184
           K+ PG+LMAM R+++PSI + GG    G  +  R  +  V EA+G      +T  EL E+
Sbjct: 121 KSVPGMLMAMLRMDIPSIMVSGGPMLAGGTLAGRTDLISVFEAVGRVQRGDMTMAELDEM 180

Query: 185 EKRAHPTLGTCSGLFTANTMGSMSEALGMALPGSASPTATSSRRVMYVKETGKALGSLIE 244
            + A P  G+C+G+FTANTM  M+E +G+ALPG+ +  A ++ RV   K  G  +  L+E
Sbjct: 181 TETACPGCGSCAGMFTANTMNCMAETMGLALPGNGTIPAVTAARVRLAKHAGMKVMELLE 240

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

Query: 305 ASMKPGGDYVMADLDEVGGVPVVLKKLLDAGLLHGDVLTVTGKTMKQNLEQYKYPNVPHS 364
             + P G + + DL   GG+P V+ +L   GL+   V+TVTGKT+ +NL +     V + 
Sbjct: 301 CKLSPAGHHHIQDLHAAGGIPAVMAELTRKGLVDTSVMTVTGKTLAENLAELN-ARVLNP 359

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

Query: 423 SGEVSEGEVVIIRYEGPKGAPGMPEMLRVTAAIMGAGLN-NVALVTDGRFSGATRGPMVG 481
            G++++G+ +IIRYEGP+G PGM EML  TAAI G GL  +VAL+TDGRFSG TRG  +G
Sbjct: 420 GGKINKGDAIIIRYEGPRGGPGMREMLSPTAAIAGMGLGADVALITDGRFSGGTRGAAIG 479

Query: 482 HVAPEAMVGGPIAIVEDGDTIVIDVESERLDLKLSEEEIKNRLKRWSPPSPRYKSGLLAK 541
           HV+PEA  GG I +V +GD I+ID+ + RLDL + E E+  R + + P      S LL +
Sbjct: 480 HVSPEAADGGNIGLVREGDHILIDIPARRLDLLVDEAELAARRETFVPLEKPVTSPLLRR 539

Query: 542 YASLVSQASMGAVTR 556
           YA  V+ A+ GA+ R
Sbjct: 540 YARQVTSAATGAMYR 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: 826
Number of extensions: 39
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: 555
Length adjustment: 36
Effective length of query: 522
Effective length of database: 519
Effective search space:   270918
Effective search space used:   270918
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 8501301 DvMF_2034 (dihydroxy-acid dehydratase (RefSeq))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.32176.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32176.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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