GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Herbaspirillum seropedicae SmR1

Align dihydroxyacid dehydratase (characterized)
to candidate HSERO_RS02650 HSERO_RS02650 dihydroxy-acid dehydratase

Query= CharProtDB::CH_024768
         (616 letters)



>FitnessBrowser__HerbieS:HSERO_RS02650
          Length = 620

 Score =  905 bits (2339), Expect = 0.0
 Identities = 451/618 (72%), Positives = 519/618 (83%), Gaps = 4/618 (0%)

Query: 1   MPKYRSATTTHGRNMAGARALWRATGMTDADFGKPIIAVVNSFTQFVPGHVHLRDLGKLV 60
           MP YRS TTT GRNMAGARALWRATGM D DF KPIIAVVNSFTQFVPGHVHL+DLG+LV
Sbjct: 1   MPTYRSYTTTQGRNMAGARALWRATGMKDGDFTKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AEQIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRELIADSVEYMVNAHCADAMVCIS 120
           A +IEAAGGVAKEFNTIAVDD    G   MLYSLPSR+LIADSVEYMVNAHCADAMVCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDSGTHGDARMLYSLPSRDLIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMASLRLNIPVIFVSGGPMEAGKT----KLSDQIIKLDLVDAMIQGADPKV 176
           NCDKITPGMLMA++RLNIPV+FVSGGPMEAGK         ++IKLDLVDAMIQ  D  +
Sbjct: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVIKTVNTDKKVIKLDLVDAMIQAGDKNI 180

Query: 177 SDSQSDQVERSACPTCGSCSGMFTANSMNCLTEALGLSQPGNGSLLATHADRKQLFLNAG 236
           SD+   +VERSACPTCGSCSGMFTANSMNCLTE LGLS PGNG+++ATHADRK+LFL AG
Sbjct: 181 SDADVAEVERSACPTCGSCSGMFTANSMNCLTEVLGLSLPGNGTIVATHADRKELFLRAG 240

Query: 237 KRIVELTKRYYEQNDESALPRNIASKAAFENAMTLDIAMGGSTNTVLHLLAAAQEAEIDF 296
           + IVEL KR+YEQ+D S LPRNI +K  +ENAMTLD++MGGSTNTVLHLLAAA EA+++F
Sbjct: 241 RLIVELAKRHYEQDDYSILPRNICTKETWENAMTLDVSMGGSTNTVLHLLAAAHEAKVEF 300

Query: 297 TMSDIDKLSRKVPQLCKVAPSTQKYHMEDVHRAGGVIGILGELDRAGLLNRDVKNVLGLT 356
           TM+DID++SR+VP LCKVAP T KYH+EDVHRAGG+I ILGEL RAGLL+     V   T
Sbjct: 301 TMADIDRISRRVPCLCKVAPMTNKYHIEDVHRAGGIISILGELARAGLLDTSRPTVHSKT 360

Query: 357 LPQTLEQYDVMLTQDDAVKNMFRAGPAGIRTTQAFSQDCRWDTLDDDRANGCIRSLEHAY 416
           L + +E++D+ ++ D AV  +FRA P G+ T  AFSQ+ R++  D DRANGCIR  EHAY
Sbjct: 361 LGEAIEKFDIRVSSDPAVHKLFRAAPGGVPTQVAFSQEERFEANDLDRANGCIRDREHAY 420

Query: 417 SKDGGLAVLYGNFAENGCIVKTAGVDDSILKFTGPAKVYESQDDAVEAILGGKVVAGDVV 476
           S+DGGLAVLYGN AE GCIVKTAGVD+SILKF+G A+V+ESQD AVE ILG KV AGDVV
Sbjct: 421 SQDGGLAVLYGNIAEKGCIVKTAGVDESILKFSGTARVFESQDAAVEGILGDKVKAGDVV 480

Query: 477 VIRYEGPKGGPGMQEMLYPTSFLKSMGLGKACALITDGRFSGGTSGLSIGHVSPEAASGG 536
           ++RYEGPKGGPGMQEMLYPTS++KS GLGKACAL TDGRFSGG+SGL IGH SPEAA GG
Sbjct: 481 IVRYEGPKGGPGMQEMLYPTSYIKSKGLGKACALFTDGRFSGGSSGLVIGHASPEAAEGG 540

Query: 537 SIGLIEDGDLIAIDIPNRGIQLQVSDAELAARREAQDARGDKAWTPKNRERQVSFALRAY 596
           +IGL+E+GD+I IDIPNR I L++S  +LA RR A +ARGD AW P NR+R VS AL+AY
Sbjct: 541 AIGLVEEGDMIDIDIPNRTINLRISSDDLAKRRTAMEARGDAAWQPGNRQRVVSQALQAY 600

Query: 597 ASLATSADKGAVRDKSKL 614
           A+L TSAD+GAVRD S+L
Sbjct: 601 AALTTSADRGAVRDLSQL 618


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: 1202
Number of extensions: 38
Number of successful extensions: 2
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: 620
Length adjustment: 37
Effective length of query: 579
Effective length of database: 583
Effective search space:   337557
Effective search space used:   337557
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 HSERO_RS02650 HSERO_RS02650 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.1532.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1532.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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