GapMind for Amino acid biosynthesis

 

Alignments for a candidate for ilvH in Phaeobacter inhibens BS107

Align acetohydroxyacid synthase subunit B (EC 2.2.1.6) (characterized)
to candidate GFF1987 PGA1_c20210 acetolactate synthase isozyme 3 large subunit

Query= metacyc::MONOMER-18810
         (585 letters)



>FitnessBrowser__Phaeo:GFF1987
          Length = 583

 Score =  598 bits (1543), Expect = e-175
 Identities = 310/570 (54%), Positives = 397/570 (69%), Gaps = 6/570 (1%)

Query: 18  EMIGAEILVHALAEEGVEYVWGYPGGAVLYIYDELHKQTKFEHILVRHEQAAVHAADGYA 77
           EM GA+++V AL ++GV+ V+GYPGGAVL IYDE+  Q    HILVRHEQ AVHAA+GYA
Sbjct: 4   EMTGAKMVVQALKDQGVDTVFGYPGGAVLPIYDEIFLQNDIRHILVRHEQGAVHAAEGYA 63

Query: 78  RATGKVGVALVTSGPGVTNAVTGIATAYLDSIPMVVITGNVPTHAIGQDAFQECDTVGIT 137
           R+TGK GV LVTSGPG TNAVTG+  A LDSIP+VV+TG VPT  IG DAFQE DTVGIT
Sbjct: 64  RSTGKPGVVLVTSGPGATNAVTGLTDALLDSIPLVVLTGQVPTFMIGSDAFQEADTVGIT 123

Query: 138 RPIVKHNFLVKDVRDLAATIKKAFFIAATGRPGPVVVDIPKDVSRNACKYEYPKSIDMRS 197
           RP  KHN+LVKD   LA T+ +AF +A  GRPGPV++DIPKDV      Y+ PK      
Sbjct: 124 RPCTKHNWLVKDTEKLAGTLHEAFHVATAGRPGPVLIDIPKDVQFATGTYQDPKPA-ASH 182

Query: 198 YNPVNKGHSGQIRKAVALLQGAERPYIYTGGGVVLA--NASDELRQLAALTGHPVTNTLM 255
           Y P  KG    I + VA ++ A+RP  YTGGGV+ +   AS  LR+L A TG PVT+TLM
Sbjct: 183 YQPPVKGDLEAITELVAAMETAKRPVFYTGGGVINSGPGASQLLRELVAATGIPVTSTLM 242

Query: 256 GLGAFPGTSKQFVGMLGMHGTYEANMAMQNCDVLIAIGARFDDRVIGNPAHFTSQARKII 315
           GLGA+P + K ++GMLGMHG YEANMAM +CD++I IGARFDDR+ G    F+  + K  
Sbjct: 243 GLGAYPASGKNWLGMLGMHGLYEANMAMHDCDLMINIGARFDDRITGRLDAFSPNSTK-A 301

Query: 316 HIDIDPSSISKRVKVDIPIVGNVKDVLQELIAQIKASDIKPKREALAKWWEQIEQWRSVD 375
           HIDIDPSSI+K ++VDIPIVG++  VL++++   K+   K    A+AKW EQI +WR + 
Sbjct: 302 HIDIDPSSINKVIRVDIPIVGDIGHVLEDVLKVWKSRGRKVDSAAIAKWQEQITEWRDIR 361

Query: 376 CLKYDRSSEIIKPQYVVEKIWELTKG-DAFICSDVGQHQMWAAQFYKFDEPRRWINSGGL 434
           CL Y  S   IKPQY +E++  LTK  + +I ++VGQHQMWAAQ+  F++P RW+ SGGL
Sbjct: 362 CLAYTASESTIKPQYALERLEALTKDRNRYITTEVGQHQMWAAQYLGFEDPNRWMTSGGL 421

Query: 435 GTMGVGLPYAMGIKKAFPEKEVVTITGEGSIQMCIQELSTCLQYDTPVKICSLNNGYLGM 494
           GTMG G P ++G++ A P+  V+ + GE S  M +QE+ T +QY  PVK   LNN  LGM
Sbjct: 422 GTMGYGTPASLGVQVAHPDALVINVAGEASWLMNMQEMGTAVQYRLPVKQFILNNERLGM 481

Query: 495 VRQWQEIEYDNRYSHSYMDALPDFVKLAEAYGHVGMRVEKTSDVEPALREAFRLKDRTVF 554
           VRQWQE+ +  RYSHS+ +ALPDFVKLAEA+G  G+  +   D++ A+ E     D  V 
Sbjct: 482 VRQWQELLHGERYSHSWSEALPDFVKLAEAFGAKGIICKDPKDLDDAIMEMLDY-DGPVI 540

Query: 555 LDFQTDPTENVWPMVQAGKGISEMLLGAED 584
            D   +  EN +PM+ +GK  +EMLLG  D
Sbjct: 541 FDCLVEKHENCFPMIPSGKAHNEMLLGEAD 570


Lambda     K      H
   0.319    0.135    0.407 

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: 987
Number of extensions: 40
Number of successful extensions: 6
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: 585
Length of database: 583
Length adjustment: 36
Effective length of query: 549
Effective length of database: 547
Effective search space:   300303
Effective search space used:   300303
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 GFF1987 PGA1_c20210 (acetolactate synthase isozyme 3 large subunit)
to HMM TIGR00118 (ilvB: acetolactate synthase, large subunit, biosynthetic type (EC 2.2.1.6))

Software error:

../bin/blast/fastacmd -i /tmp/list.25849.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25849.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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