GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Dechlorosoma suillum PS

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate Dsui_3227 Dsui_3227 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>FitnessBrowser__PS:Dsui_3227
          Length = 560

 Score =  594 bits (1532), Expect = e-174
 Identities = 310/608 (50%), Positives = 402/608 (66%), Gaps = 61/608 (10%)

Query: 40  SMPVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMF 99
           S P ++YRPFA    P++L +R WP RVI   P+W + DLRDGNQ+L +PM+  +K RMF
Sbjct: 3   SNPSSKYRPFA----PVQLADRQWPSRVITTPPMWMSTDLRDGNQSLFEPMNVEKKMRMF 58

Query: 100 DLLVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACS 159
             L ++G+KEIEV FPSASQTDF+FVR +IE G IP DVTI+VLTQ R  LI RT ++  
Sbjct: 59  KTLCQVGFKEIEVAFPSASQTDFNFVRSLIEDGHIPQDVTIEVLTQAREHLIRRTMESIK 118

Query: 160 GAPRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPES 219
           GAPRAIVH YN+TS   R  VF  ++AEV A+A +      + AA+ P T+   EYSPE+
Sbjct: 119 GAPRAIVHVYNATSQPFRDFVFGMSKAEVVAMAVEAVTLIKQLAAEMPETEVVLEYSPET 178

Query: 220 YTGTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRES 279
           +T TEL++A +VCDAV      TP+  +I NLP TVEM TPN+YAD IEWM R+LA R+S
Sbjct: 179 FTATELDFALEVCDAVTAAWGATPDNKVILNLPTTVEMATPNIYADQIEWMHRHLARRDS 238

Query: 280 VILSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQ 339
           VILSLHPHNDRGTAVAAAELG  AGADR+EGCLFGNGERTGNV +VT+ LN++++GV P 
Sbjct: 239 VILSLHPHNDRGTAVAAAELGLMAGADRVEGCLFGNGERTGNVDIVTVALNMYTQGVHPG 298

Query: 340 IDFSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADC 399
           +DFS+I+ + RTVE+CNQLP+H RHPY GDLV+TAFSGSHQDAI KG  A K DA     
Sbjct: 299 LDFSDINAVARTVEHCNQLPIHPRHPYVGDLVFTAFSGSHQDAIKKGFSAQKADAP---- 354

Query: 400 DVDDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQ 459
                 W VPYLPIDP DVGR+Y++VIRVNSQSGKGG+AY+++T++G+ +PRRLQ+EFS 
Sbjct: 355 ------WNVPYLPIDPADVGRSYDSVIRVNSQSGKGGIAYLLETEYGVVMPRRLQVEFSG 408

Query: 460 VIQKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVK 519
           V+Q+ A+     G E++  ++W  F   YL PV P+     H+    + G    I  +V 
Sbjct: 409 VVQQHAD---SHGSELTAADIWQLFCRTYLEPVAPVHYREHHL---FEHGSAQGIRLSVD 462

Query: 520 INGVETEISGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSA---GDDAQAAAYVEASVT 576
           I+G    +SG GNGP+ A +HAL   G  V V  Y E +M+    G +A+A A+VE +  
Sbjct: 463 IDGTAHLLSGEGNGPIDAAIHALRGAGMQVQVRSYEERSMAPSQDGGEARACAFVEMA-- 520

Query: 577 IASPAQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVV 636
                                                  +  +GVGI  +I TASL+A+V
Sbjct: 521 ------------------------------------CDGREFYGVGIDGNIVTASLKAIV 544

Query: 637 SAVNRAAR 644
           S +NR+ +
Sbjct: 545 SGLNRSGQ 552


Lambda     K      H
   0.317    0.133    0.399 

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: 922
Number of extensions: 33
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: 644
Length of database: 560
Length adjustment: 37
Effective length of query: 607
Effective length of database: 523
Effective search space:   317461
Effective search space used:   317461
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 Dsui_3227 Dsui_3227 (2-isopropylmalate synthase)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.3313.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3313.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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