GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvD in Sinorhizobium meliloti 1021

Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (characterized)
to candidate SMc04045 SMc04045 dihydroxy-acid dehydratase

Query= SwissProt::P55186
         (617 letters)



>FitnessBrowser__Smeli:SMc04045
          Length = 612

 Score =  976 bits (2522), Expect = 0.0
 Identities = 490/612 (80%), Positives = 537/612 (87%), Gaps = 4/612 (0%)

Query: 1   MPPYRSRTTTHGRNMAGARGLWRATGMKDEDFGKPIIAVANSFTQFVPGHVHLKDLGQLV 60
           MP YRSRTTTHGRNMAGARGLWRATGMKD DFGKPIIAV NSFTQFVPGHVHLKDLGQLV
Sbjct: 1   MPAYRSRTTTHGRNMAGARGLWRATGMKDSDFGKPIIAVVNSFTQFVPGHVHLKDLGQLV 60

Query: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHGGMLYSLPSRDLIADSVEYMVNAHCADAIVCIS 120
           AREIEAAGGVAKEFNTIAVDDGIAMGH GMLYSLPSR++IADSVEYMVNAHCADA+VCIS
Sbjct: 61  AREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCIS 120

Query: 121 NCDKITPGMLMAAMRLNIPVVFVSGGPMEAGKVTVKGKIRALDLVDAMVVAADDSYSDEE 180
           NCDKITPGMLMAA+RLNIP VFVSGGPMEAGKV + GK  ALDLVDAMV AADD  SDE+
Sbjct: 121 NCDKITPGMLMAALRLNIPAVFVSGGPMEAGKVVLHGKTHALDLVDAMVAAADDKVSDED 180

Query: 181 VEAIEKAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSVLATHADREALFKEAGRVVV 240
           V+ IE++ACPTCGSCSGMFTANSMNCLTEALGLSLPGNGS LATHADR+ LF EAG ++V
Sbjct: 181 VQIIERSACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHADRKRLFVEAGHLIV 240

Query: 241 DLCQRWYEQEDATALPRGIATRAAFENAMSLDIAMGGSTNTVLHLLAAAHEGGIDFSMAD 300
           DL +R+YEQED   LPR IAT+ AFENAM+LDIAMGGSTNTVLH+LAAA+EG IDF+M D
Sbjct: 241 DLARRYYEQEDERVLPRNIATKQAFENAMALDIAMGGSTNTVLHILAAAYEGEIDFTMDD 300

Query: 301 IDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVMAILGELERGGLIDASQPTVHAPTMGEA 360
           IDRLSR VPCLSKVAPAK+DVHMEDVHRAGG+M+ILGEL++GGLI+   PTVHA T+G+A
Sbjct: 301 IDRLSRKVPCLSKVAPAKADVHMEDVHRAGGIMSILGELDKGGLINRDCPTVHAETLGDA 360

Query: 361 LARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQAARWEELDLDRENGVIRSVEHPFSKDG 420
           + RWDI RT+S    +FF+AAPGG PTQVAFSQ ARW+ELD DRENGVIRSVEHPFSKDG
Sbjct: 361 IDRWDITRTSSDTVRKFFRAAPGGIPTQVAFSQEARWDELDTDRENGVIRSVEHPFSKDG 420

Query: 421 GLAVLFGNLAPEGCIVKTAGVDESILTFRGTARVFESQDAAVSGILGGQVKAGEVVVIRY 480
           GLAVL GN+A +GCIVKTAGVDESIL F G ARVFESQDAAV GIL  ++KAG+VVVIRY
Sbjct: 421 GLAVLKGNIALDGCIVKTAGVDESILKFSGPARVFESQDAAVKGILANEIKAGDVVVIRY 480

Query: 481 EGPKGGPGMQEMLYPTTYLKSKGLGAACALVTDGRFSGGTSGLSIGHVSPEAGEGGLIAL 540
           EGPKGGPGMQEMLYPT+YLKSKGLG ACAL+TDGRFSGGTSGLSIGHVSPEA  GG I L
Sbjct: 481 EGPKGGPGMQEMLYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHVSPEAANGGTIGL 540

Query: 541 VETGDPILIDIPTRGITLEVSDAVLAARREAQLARGKDAWTPL-NRKRDLTPALRAYAAM 599
           V  GD I IDIP R I+L V +A LAARR  Q A+G   W P+  RKR +T AL+AYAA 
Sbjct: 541 VREGDMIDIDIPNRTISLRVDEAELAARRTEQDAKG---WKPVEQRKRRVTTALKAYAAF 597

Query: 600 TTNAARGAVRDV 611
            T+A RGAVRD+
Sbjct: 598 ATSADRGAVRDL 609


Lambda     K      H
   0.318    0.134    0.395 

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: 1296
Number of extensions: 39
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: 617
Length of database: 612
Length adjustment: 37
Effective length of query: 580
Effective length of database: 575
Effective search space:   333500
Effective search space used:   333500
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 SMc04045 SMc04045 (dihydroxy-acid dehydratase)
to HMM TIGR00110 (ilvD: dihydroxy-acid dehydratase (EC 4.2.1.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.1639.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1639.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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