GapMind for Amino acid biosynthesis

 

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

Align acetolactate synthase (subunit 2/2) (EC 2.2.1.6) (characterized)
to candidate Pf1N1B4_2878 Acetolactate synthase large subunit (EC 2.2.1.6)

Query= BRENDA::P00893
         (574 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_2878
          Length = 566

 Score =  749 bits (1933), Expect = 0.0
 Identities = 359/568 (63%), Positives = 444/568 (78%), Gaps = 4/568 (0%)

Query: 9   MVVRSLIDQGVKQVFGYPGGAVLDIYDALHTVGGIDHVLVRHEQAAVHMADGLARATGEV 68
           M+VR L D+GVK ++GYPGGA+L +YDAL     + H+LVRHEQAA HMADG ARATG+ 
Sbjct: 1   MLVRFLRDEGVKYIYGYPGGALLHVYDALFKEPEVTHILVRHEQAATHMADGYARATGKA 60

Query: 69  GVVLVTSGPGATNAITGIATAYMDSIPLVVLSGQVATSLIGYDAFQECDMVGISRPVVKH 128
           GVVLVTSGPGATNAITGIATAYMDSIP+V++SGQV ++++G DAFQE DM+GISRP+VKH
Sbjct: 61  GVVLVTSGPGATNAITGIATAYMDSIPMVIISGQVPSTMVGTDAFQETDMIGISRPIVKH 120

Query: 129 SFLVKQTEDIPQVLKKAFWLAASGRPGPVVVDLPKDILNPANKLPYVWPESVSMRSYNPT 188
           SF++K   +IP+V+KKAF+LA SGRPGPVVVD+PKD+ NPA K  Y++P+   +RSY+P 
Sbjct: 121 SFMIKHASEIPEVMKKAFYLAQSGRPGPVVVDIPKDMTNPAEKFEYIFPKKAKLRSYSPA 180

Query: 189 TTGHKGQIKRALQTLVAAKKPVVYVGGGAITAGCHQQLKETVEALNLPVVCSLMGLGAFP 248
             GH GQI++A + L+AAK+PV+Y GGG I  G    L E  + LNLPV  +LMGLGA+P
Sbjct: 181 VRGHSGQIRKAAEMLLAAKRPVLYSGGGVILGGGSAPLTELAKMLNLPVTNTLMGLGAYP 240

Query: 249 ATHRQALGMLGMHGTYEANMTMHNADVIFAVGVRFDDRTTNNLAKYCPNATVLHIDIDPT 308
            T RQ +GMLGMHG+Y AN+ MH+ADVI AVG RFDDR  N  AK+CPNA ++HIDIDP 
Sbjct: 241 GTDRQFIGMLGMHGSYTANLAMHHADVILAVGARFDDRVINGPAKFCPNAKIIHIDIDPA 300

Query: 309 SISKTVTADIPIVGDARQVLEQMLELLSQESAHQPLDEIRDWWQQIEQWRA-RQCLKYDT 367
           SISKT+ AD+PIVG    VL +M+ +L +       + +  WW+Q+++WR  R    YD 
Sbjct: 301 SISKTIKADVPIVGPVESVLTEMVAILKEIGETPNKESVASWWKQVDEWRGDRGLFPYDK 360

Query: 368 -HSEKIKPQAVIETLWRLTKGDAYVTSDVGQHQMFAALYYPFDKPRRWINSGGLGTMGFG 426
                IKPQ VIETL  +TKGDA+VTSDVGQHQMFAA YY F+KP RWINSGGLGTMGFG
Sbjct: 361 GDGSVIKPQTVIETLCEVTKGDAFVTSDVGQHQMFAAQYYTFNKPNRWINSGGLGTMGFG 420

Query: 427 LPAALGVKMALPEETVVCVTGDGSIQMNIQELSTALQYELPVLVVNLNNRYLGMVKQWQD 486
           LPAA+G+K++ P++ V CVTG+GSIQMNIQELST LQY LPV +V LNN  LGMV+QWQD
Sbjct: 421 LPAAMGIKLSFPDDDVACVTGEGSIQMNIQELSTCLQYGLPVKIVILNNGVLGMVRQWQD 480

Query: 487 MIYSGRHSQSYMQSLPDFVRLAEAYGHVGIQISHPHELESKLSEALEQVRNNRLVFVDVT 546
           M Y  RHS SYM+SLPDFV+LAEAYGHVG++I+   +L+SK+ EA      +RLV +D++
Sbjct: 481 MSYGSRHSHSYMESLPDFVKLAEAYGHVGVRITESKDLKSKMEEAF--AMKDRLVVIDIS 538

Query: 547 VDGSEHVYPMQIRGGGMDEMWLSKTERT 574
           VD SEHVYPMQI+ G M +MWLSKTERT
Sbjct: 539 VDTSEHVYPMQIKDGSMRDMWLSKTERT 566


Lambda     K      H
   0.319    0.135    0.403 

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: 1015
Number of extensions: 32
Number of successful extensions: 3
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: 574
Length of database: 566
Length adjustment: 36
Effective length of query: 538
Effective length of database: 530
Effective search space:   285140
Effective search space used:   285140
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 53 (25.0 bits)

Align candidate Pf1N1B4_2878 (Acetolactate synthase large subunit (EC 2.2.1.6))
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

Software error:

../bin/blast/fastacmd -i /tmp/list.11171.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11171.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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