GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Pseudomonas fluorescens FW300-N2C3

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate AO356_06550 AO356_06550 2-isopropylmalate synthase

Query= BRENDA::P9WQB3
         (644 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_06550
          Length = 559

 Score =  588 bits (1515), Expect = e-172
 Identities = 312/604 (51%), Positives = 405/604 (67%), Gaps = 63/604 (10%)

Query: 42  PVNRYRPFAEEVEPIRLRNRTWPDRVIDRAPLWCAVDLRDGNQALIDPMSPARKRRMFDL 101
           P ++YR F      I L +RTWP + I  AP+WC+ DLRDGNQ+LI+PM   +K R +  
Sbjct: 7   PSSKYRAFPT----INLPDRTWPSKTITAAPIWCSSDLRDGNQSLIEPMDAVKKLRFWKT 62

Query: 102 LVRMGYKEIEVGFPSASQTDFDFVREIIEQGAIPDDVTIQVLTQCRPELIERTFQACSGA 161
           LV +G KEIE  FP+ASQTDFDFVR +IE+G IPDD TIQVLTQ R +LI RTF++  GA
Sbjct: 63  LVAVGVKEIEASFPAASQTDFDFVRTLIEEGHIPDDTTIQVLTQAREDLIARTFESLRGA 122

Query: 162 PRAIVHFYNSTSILQRRVVFRANRAEVQAIATDGARKCVEQAAKYPGTQWRFEYSPESYT 221
            +AIVH YN+T    RR+VF  ++  V+ IA + A+  V+ AA+ P TQW+FEYSPE+++
Sbjct: 123 KKAIVHLYNATCPSFRRIVFNQDKEGVKEIAVNAAKLFVKYAAQQPETQWQFEYSPETFS 182

Query: 222 GTELEYAKQVCDAVGEVIAPTPERPIIFNLPATVEMTTPNVYADSIEWMSRNLANRESVI 281
            TELE+AK+VCDAV EV  PTPER +I NLPATVE+ TPN+YAD IEW  RN+  R+SV+
Sbjct: 183 ATELEFAKEVCDAVIEVWNPTPERKVILNLPATVEVATPNIYADQIEWFHRNITRRDSVL 242

Query: 282 LSLHPHNDRGTAVAAAELGFAAGADRIEGCLFGNGERTGNVCLVTLGLNLFSRGVDPQID 341
           +SLH HNDRGT VAA ELG  AGADR+EGCLFGNGERTGNV LVT+ LNL+++G++P++D
Sbjct: 243 ISLHTHNDRGTGVAATELGLMAGADRVEGCLFGNGERTGNVDLVTVALNLYTQGINPELD 302

Query: 342 FSNIDEIRRTVEYCNQLPVHERHPYGGDLVYTAFSGSHQDAINKGLDAMKLDADAADCDV 401
           FS+ID +R+ VE CNQ+PVH RHPY GDLV+TAFSGSHQDAI KG    K          
Sbjct: 303 FSDIDGVRKVVEECNQIPVHPRHPYVGDLVHTAFSGSHQDAIRKGFAQQK---------- 352

Query: 402 DDMLWQVPYLPIDPRDVGRTYEAVIRVNSQSGKGGVAYIMKTDHGLSLPRRLQIEFSQVI 461
            D LW+VPYLPIDP D+GR+YEAVIRVNSQSGKGG+AY+++ ++G+SLPRR+QIEFSQV+
Sbjct: 353 PDTLWEVPYLPIDPADIGRSYEAVIRVNSQSGKGGIAYLLEQEYGISLPRRMQIEFSQVV 412

Query: 462 QKIAEGTAGEGGEVSPKEMWDAFAEEYLAPVRPLERIRQHVDAADDDGGTTSITATVKIN 521
           Q+    T   G E++ +++      EYL    P   +   +    ++ G +++   V   
Sbjct: 413 QR---ETDRLGLEMTAQQIHGLLQREYLQANTPYALVSHRL---QEENGNSAVEVEVASK 466

Query: 522 GV-ETEI--SGSGNGPLAAFVHALADVGFDVAVLDYYEHAMSAGDDAQAAAYVEASVTIA 578
           G  ET +   G GNG L A V   A +   V ++DY EHA+ AG +A+AAAY+E  V   
Sbjct: 467 GQGETNLHWRGKGNGALEALV---AGLPIPVEIMDYNEHAIGAGTNAKAAAYIELRVN-- 521

Query: 579 SPAQPGEAGRHASDPVTIASPAQPGEAGRHASDPVTSKTVWGVGIAPSITTASLRAVVSA 638
                GE                              + V GVGI  +ITTAS +A+ SA
Sbjct: 522 -----GE------------------------------RAVHGVGIDENITTASFKALFSA 546

Query: 639 VNRA 642
           +NR+
Sbjct: 547 LNRS 550


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: 895
Number of extensions: 41
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 644
Length of database: 559
Length adjustment: 37
Effective length of query: 607
Effective length of database: 522
Effective search space:   316854
Effective search space used:   316854
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 AO356_06550 AO356_06550 (2-isopropylmalate synthase)
to HMM TIGR00970 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.29072.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29072.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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