GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Synechococcus elongatus PCC 7942

Align 3-isopropylmalate dehydratase large subunit 1; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1; EC 4.2.1.33 (characterized)
to candidate Synpcc7942_1898 Synpcc7942_1898 isopropylmalate isomerase large subunit

Query= SwissProt::P15717
         (466 letters)



>FitnessBrowser__SynE:Synpcc7942_1898
          Length = 468

 Score =  493 bits (1269), Expect = e-144
 Identities = 251/462 (54%), Positives = 320/462 (69%), Gaps = 2/462 (0%)

Query: 4   TLYEKLFDAHVVFEAPNETPLLYIDRHLVHEVTSPQAFDGLRAHHRPVRQPGKTFATMDH 63
           TL++K++D H V   P+    L+I  HL+HEVTSPQAF  LR     V+ PG+T AT+DH
Sbjct: 5   TLFDKVWDLHTVATLPSGQTQLFIGLHLIHEVTSPQAFSMLRDRGLTVKFPGRTVATVDH 64

Query: 64  NVSTQTKDINASGEMARIQMQELIKNCNEFGVELYDLNHPYQGIVHVMGPEQGVTLPGMT 123
            V T+ +    +  +A   +  L +NC E G+  Y++    QGIVHV+ PEQG+T PGMT
Sbjct: 65  IVPTENQARPFADSLAEEMIVTLERNCRENGIRFYNIGSGSQGIVHVIAPEQGLTQPGMT 124

Query: 124 IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVTGNAAPGITAKDI 183
           I CGDSHT+THGAFGA+AFGIGTS+V  VLA+QTL   + K  KIEV G   PG+ AKD+
Sbjct: 125 IACGDSHTSTHGAFGAIAFGIGTSQVRDVLASQTLALSKLKVRKIEVNGELQPGVYAKDV 184

Query: 184 VLAIIGKTGSAGGTGHVVEFCGDAIRALSMEGRMTLCNMAIEMGAKAGLVAPDETTFNYV 243
           +L II K G  GG G+  EF G    A+SME RMT+CNMAIE GA+ G V PD+ T++Y+
Sbjct: 185 ILHIIRKLGVKGGVGYAYEFAGSTFAAMSMEERMTVCNMAIEGGARCGYVNPDQITYDYL 244

Query: 244 KGRLHAPKGRDFDEAVEYWKTLKTDDGATFDTVVALRAEEIAPQVTWGTNPGQVISVTDI 303
           +GR  AP+G  +D A+ +W++L+++  A +D VV   A EIAP VTWG  PGQ I +T+ 
Sbjct: 245 QGREFAPQGEAWDRAIAWWESLRSEADAEYDDVVVFDAAEIAPTVTWGITPGQGIGITET 304

Query: 304 IPDPASFSDPVERASAEKALAYMGLQPGVPLTDVAIDKVFIGSCTNSRIEDLRAAAEVAK 363
           IP P S  D  +RA A +A +YM L+PG PL    +D  FIGSCTN R+ DLR AA+VA+
Sbjct: 305 IPTPDSLLDE-DRAVAAEAYSYMDLEPGAPLQGTKVDVCFIGSCTNGRLSDLREAAKVAQ 363

Query: 364 GRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGER 423
           GRKVA G++A VVPGS  VK QAEAEGLD+IF  AGFEWR  GCSMCLAMN D+L   + 
Sbjct: 364 GRKVAAGIKAFVVPGSERVKQQAEAEGLDQIFTAAGFEWRQAGCSMCLAMNPDKLEGRQI 423

Query: 424 CASTSNRNFEGRQG-RGGRTHLVSPAMAAAAAVTGHFADIRS 464
            AS+SNRNF+GRQG   GRT L+SPAM AAAA+ G   D+R+
Sbjct: 424 SASSSNRNFKGRQGSASGRTLLMSPAMVAAAAIAGEVTDVRN 465


Lambda     K      H
   0.318    0.134    0.396 

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: 712
Number of extensions: 29
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: 466
Length of database: 468
Length adjustment: 33
Effective length of query: 433
Effective length of database: 435
Effective search space:   188355
Effective search space used:   188355
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: 51 (24.3 bits)

Align candidate Synpcc7942_1898 Synpcc7942_1898 (isopropylmalate isomerase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.31235.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.31235.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.