GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Dechlorosoma suillum PS

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate Dsui_3201 Dsui_3201 3-isopropylmalate dehydratase, large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__PS:Dsui_3201
          Length = 468

 Score =  593 bits (1530), Expect = e-174
 Identities = 298/467 (63%), Positives = 355/467 (76%), Gaps = 2/467 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           M +TLY+KL+  HVV+E  + T L+YIDRHLVHEVTSPQAF+GL+  GR   +     AT
Sbjct: 1   MPQTLYDKLWQNHVVHEEADGTALIYIDRHLVHEVTSPQAFEGLKLAGRKPWRVSSIVAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELY-DLNHPYQGIVHVMGPEQGVTL 119
            DHN  T   +      ++R Q++ L  N +E G   Y       QGIVHV+GPE G TL
Sbjct: 61  ADHNTPTDHWEEGIKDPISRQQVETLDANIREVGALAYWPFKDMRQGIVHVVGPENGATL 120

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMT+VCGDSHT+THGAF  +A GIGTSEVEHV+ATQ L Q ++K+M I V+GK   G+T
Sbjct: 121 PGMTVVCGDSHTSTHGAFACMAHGIGTSEVEHVMATQCLIQKKSKSMLIRVEGKLGKGVT 180

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD+ LAIIGK G+AGGTG+ +EF G AIR LSMEGRMTLCNMAIE GA+ G VA D+TT
Sbjct: 181 GKDVALAIIGKIGTAGGTGYAIEFGGSAIRGLSMEGRMTLCNMAIEAGARMGFVAVDDTT 240

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
            NY+K R  +PKG+ +D AVAYW+TL++DEGA FD  V L+AEEI PQVTWGT+P  V+ 
Sbjct: 241 INYLKDRPFSPKGETWDKAVAYWRTLKSDEGARFDCTVDLKAEEIQPQVTWGTSPEMVVP 300

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           +   +PDPA  ADPV+R   E+AL YMGL P + + ++AIDKVFIGSCTNSRIEDLR AA
Sbjct: 301 IGATVPDPAKEADPVKREGMERALQYMGLTPNLEIKKIAIDKVFIGSCTNSRIEDLREAA 360

Query: 360 EIAKGRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
            + +GR+ A  V+ ALVVPGSG VK QAEAEGLDKIF+ AGFEWR PGCSMCLAMN DRL
Sbjct: 361 AVVRGRQKAANVKLALVVPGSGLVKRQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRL 420

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAA + GHFAD+R+I
Sbjct: 421 EPGERCASTSNRNFEGRQGPGGRTHLVSPAMAAAAGIAGHFADVRDI 467


Lambda     K      H
   0.317    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: 738
Number of extensions: 27
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 Dsui_3201 Dsui_3201 (3-isopropylmalate dehydratase, large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.7719.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.7719.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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