GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Pseudomonas fluorescens FW300-N1B4

Align dihydroxyacid dehydratase (characterized)
to candidate Pf1N1B4_2303 Dihydroxy-acid dehydratase (EC 4.2.1.9)

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2303
          Length = 613

 Score =  917 bits (2370), Expect = 0.0
 Identities = 460/617 (74%), Positives = 521/617 (84%), Gaps = 6/617 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS T+THGRNMAGARALWRATGM D DF KPIIA+ NSFTQFVPGHVHL+DLG+LV
Sbjct: 1   MPDYRSKTSTHGRNMAGARALWRATGMKDDDFKKPIIAIANSFTQFVPGHVHLKDLGQLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IE AGGVAKEFNTIAVDDGIAMGH GMLYSLPSRE+IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIERAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAIVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLSDQIIKLDLVDAMIQGADPKVSDSQ 180
           NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKL+     LDLVDAM+  AD   SD +
Sbjct: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKTKLASH--GLDLVDAMVIAADSSASDEK 178

Query: 181 SDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAGKRIV 240
             + ERSACPTCGSCSGMFTANSMNCL EALGL+ PGNGS LATH+DR+QLFL AG+ IV
Sbjct: 179 VAEYERSACPTCGSCSGMFTANSMNCLVEALGLALPGNGSTLATHSDREQLFLQAGRTIV 238

Query: 241 ELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDFTMSD 300
           EL KRYY +NDES LPRNIA+  AFENAMTLDIAMGGSTNT+LHLLAAAQEAEIDF + D
Sbjct: 239 ELCKRYYGENDESVLPRNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDFDLRD 298

Query: 301 IDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLTLPQT 360
           ID+LSR VPQLCKVAP+ QKYHMEDVHRAGG+  ILG L R GLL+ D+  V   ++ + 
Sbjct: 299 IDRLSRHVPQLCKVAPNIQKYHMEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKSMAEG 358

Query: 361 LEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAYSKDG 420
           + ++D+  T D+AV + F+AGPAGI T  AFSQ  RW+TLDDDR NGCIRS+EHAYSK+G
Sbjct: 359 IAKWDITQTTDEAVHHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSKEG 418

Query: 421 GLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVVVIRY 480
           GLAVLYGN A +GC+VKTAGVD+SI  F G AK++ESQD AV  IL  +V AGD+V+IRY
Sbjct: 419 GLAVLYGNIALDGCVVKTAGVDESIHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRY 478

Query: 481 EGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGGSIGL 540
           EGPKGGPGMQEMLYPTS+LKS GLGKACAL+TDGRFSGGTSGLSIGH SPEAA+GG+IGL
Sbjct: 479 EGPKGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGL 538

Query: 541 IEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTP-KNRERQVSFALRAYASL 599
           ++DGD + IDIPNR I L +SD E+AARR  QD +G   W P + R R+V+ AL+AYA L
Sbjct: 539 VQDGDKVLIDIPNRSINLLISDEEMAARRAEQDKKG---WKPVEVRPRKVTTALKAYALL 595

Query: 600 ATSADKGAVRDKSKLGG 616
           ATSADKGAVR+K+ L G
Sbjct: 596 ATSADKGAVRNKAMLDG 612


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: 1208
Number of extensions: 42
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: 616
Length of database: 613
Length adjustment: 37
Effective length of query: 579
Effective length of database: 576
Effective search space:   333504
Effective search space used:   333504
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 Pf1N1B4_2303 (Dihydroxy-acid dehydratase (EC 4.2.1.9))
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.1158.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1158.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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