Alignments for a candidate for leuC in Caulobacter crescentus NA1000

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate CCNA_00196 CCNA_00196 3-isopropylmalate dehydratase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Caulo:CCNA_00196
          Length = 479

 Score =  594 bits (1531), Expect = e-174
 Identities = 297/471 (63%), Positives = 359/471 (76%), Gaps = 9/471 (1%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+K++DAHVV EA  E  +LYID HL+HEVT+PQAF GLRA GR VR+P +T A  D
Sbjct: 4   KTLYDKIWDAHVVSEAGGEA-ILYIDLHLIHEVTTPQAFAGLRAAGRKVRRPDRTLAVAD 62

Query: 63  HNVSTQTKDINA---CGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HN+ T+ + +       E AR+Q++ L +N  + G+E + +     GIVHV+GPEQG T 
Sbjct: 63  HNIPTEGQALGVDAVADEEARLQLKTLARNVADNGIEFFPMGDIRNGIVHVVGPEQGRTQ 122

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGMTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL+Q +AK M + V G+  PG+T
Sbjct: 123 PGMTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLRQKKAKNMLVRVDGQLPPGVT 182

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD+ LA+IG+ G+AGGTG+V+EF GEAI  LSMEGRMTLCN+ IE GAKAGLVAPD+ T
Sbjct: 183 GKDVALAVIGEIGTAGGTGYVIEFAGEAIAGLSMEGRMTLCNLTIEGGAKAGLVAPDDKT 242

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
           F Y++G+  APKG  +D A+++WKT  TDE A FD  V +    + P VTWGT+P  VI 
Sbjct: 243 FAYIQGKPAAPKGAAWDMALSHWKTFFTDEDAVFDRTVVIDGSALVPMVTWGTSPEDVIP 302

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           V  N+PDP SFA P +RA+A +AL YMGLK G P++E  ID+VFIGSCTNSRIED+RAAA
Sbjct: 303 VTGNVPDPESFATPDKRAAAHRALDYMGLKAGQPISEARIDRVFIGSCTNSRIEDMRAAA 362

Query: 360 EIAK-----GRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMN 414
            + +     GR VAP V+A+VVPGSG VK QAE EGLD IF  AGF+WR PGCSMCLAMN
Sbjct: 363 AVVQEAFLHGRLVAPHVKAMVVPGSGLVKEQAEEEGLDAIFKAAGFDWREPGCSMCLAMN 422

Query: 415 NDRLNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
            D+L P ERCASTSNRNFEGRQGR GRTHLVSPAMAAAAA+ GH  D+R +
Sbjct: 423 PDKLAPQERCASTSNRNFEGRQGRAGRTHLVSPAMAAAAAIAGHLVDVRTL 473


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: 774
Number of extensions: 33
Number of successful extensions: 4
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: 479
Length adjustment: 33
Effective length of query: 433
Effective length of database: 446
Effective search space:   193118
Effective search space used:   193118
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 CCNA_00196 CCNA_00196 (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.22103.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.22103.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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