GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Escherichia coli BW25113

Align dihydroxyacid dehydratase (characterized)
to candidate 1937120 b3771 dihydroxy-acid dehydratase (NCBI)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__Keio:1937120
          Length = 616

 Score = 1220 bits (3156), Expect = 0.0
 Identities = 616/616 (100%), Positives = 616/616 (100%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV
Sbjct: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ
Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV
Sbjct: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD
Sbjct: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT
Sbjct: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG
Sbjct: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY
Sbjct: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL
Sbjct: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA 600
           IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA
Sbjct: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA 600

Query: 601 TSADKGAVRDKSKLGG 616
           TSADKGAVRDKSKLGG
Sbjct: 601 TSADKGAVRDKSKLGG 616


Lambda     K      H
   0.317    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: 1470
Number of extensions: 43
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: 616
Length of database: 616
Length adjustment: 37
Effective length of query: 579
Effective length of database: 579
Effective search space:   335241
Effective search space used:   335241
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 1937120 b3771 (dihydroxy-acid dehydratase (NCBI))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.3277.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3277.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.