GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Shewanella loihica PV-4

Align dihydroxyacid dehydratase (characterized)
to candidate 5207771 Shew_0292 dihydroxy-acid dehydratase (RefSeq)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__PV4:5207771
          Length = 616

 Score =  957 bits (2475), Expect = 0.0
 Identities = 476/614 (77%), Positives = 534/614 (86%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           M K RSAT+T GRNMAGARALWRATG+ D+DFGKPI+A+ NSFTQFVPGHVHL+D+G LV
Sbjct: 1   MAKLRSATSTQGRNMAGARALWRATGVKDSDFGKPIVAIANSFTQFVPGHVHLKDMGSLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A  IE AGG+AKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADA+VCIS
Sbjct: 61  AGAIEEAGGIAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADALVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMA+LRLNIPV+FVSGGPMEAGKTKLSD++IKLDLVDAM+  AD +VSD  
Sbjct: 121 NCDKITPGMLMAALRLNIPVVFVSGGPMEAGKTKLSDKLIKLDLVDAMVAAADDRVSDED 180

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
           S+++ERSACPTCGSCSGMFTANSMNCLTEALGLS PGNGSLLATH+DR++LFL AG+R++
Sbjct: 181 SEKIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSLLATHSDRRELFLEAGRRVM 240

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
            L  RYY  +DESALPRNIAS  AFENAM LDIAMGGS+NTVLHLLAAAQEA++DFTM+D
Sbjct: 241 ALANRYYRDDDESALPRNIASFKAFENAMALDIAMGGSSNTVLHLLAAAQEAKVDFTMAD 300

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           ID+LSR+VP LCKVAPST KYHMEDVHRAGGV+GILGELDRAGLL+ DV +V G  L   
Sbjct: 301 IDRLSRQVPHLCKVAPSTPKYHMEDVHRAGGVMGILGELDRAGLLHTDVSHVAGENLKAV 360

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           L QYD++ TQD+AV+  + AGPAGI TT+AFSQ CRW +LD DR  GCIR+ E A+S++G
Sbjct: 361 LVQYDLVQTQDEAVQQFYAAGPAGIPTTKAFSQSCRWPSLDVDRQEGCIRTREFAFSQEG 420

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVL GN A +GCIVKTAGVD++   F G A+VYESQDDAV  ILGG+VVAGDVVVIRY
Sbjct: 421 GLAVLSGNIAADGCIVKTAGVDEANHTFVGHARVYESQDDAVAGILGGEVVAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPTS+LKS GLG +CALITDGRFSGGTSGLSIGHVSPEAA+GG+I L
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGTSCALITDGRFSGGTSGLSIGHVSPEAAAGGTIAL 540

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAYASLA 600
           +E GD I IDIP R I L VSD  L  RR+A  ARG +AW P NRER VS AL+AYA LA
Sbjct: 541 VETGDRIEIDIPARSITLAVSDEVLETRRQAMQARGKQAWKPVNRERSVSLALKAYAMLA 600

Query: 601 TSADKGAVRDKSKL 614
           TSADKGAVRD SKL
Sbjct: 601 TSADKGAVRDVSKL 614


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: 1246
Number of extensions: 39
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 5207771 Shew_0292 (dihydroxy-acid dehydratase (RefSeq))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.20608.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20608.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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