GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Cupriavidus basilensis 4G11

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate RR42_RS24175 RR42_RS24175 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Cup4G11:RR42_RS24175
          Length = 469

 Score =  604 bits (1557), Expect = e-177
 Identities = 300/468 (64%), Positives = 360/468 (76%), Gaps = 3/468 (0%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           MAKTLY+KL+D H V+  E+ T LLYIDRHL++EVTSPQAF+GLR    PV +     A 
Sbjct: 1   MAKTLYDKLWDDHAVHVEEDGTTLLYIDRHLLNEVTSPQAFEGLRMSEHPVWRISANLAV 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
            DHNV T  +       ++++Q+  L  NC  FG+  + +N   QGIVHV+GPEQG TLP
Sbjct: 61  SDHNVPTTNRSQGIADPVSKLQVDTLDANCDSFGITQFKMNDHRQGIVHVIGPEQGATLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           GMT+VCGDSHT+THGAFGALA GIGTSEVEHV+ATQTL   +   M ++V+GK   G TA
Sbjct: 121 GMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVMATQTLLGKKTMNMLVKVEGKLPRGCTA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGK G+AGGTG+ +EF G AIRDL++EGRMT+CNMAIE GA+AGLVA D+ T 
Sbjct: 181 KDIVLAIIGKIGTAGGTGNTIEFAGSAIRDLTVEGRMTVCNMAIEAGARAGLVAVDDVTL 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
            Y KGR +AP+G ++D AV YW+TL +D GA FD VV L+AEEI PQVTWGT+P  VIS+
Sbjct: 241 EYFKGRPYAPQGVEWDQAVGYWRTLHSDAGAKFDLVVELRAEEIRPQVTWGTSPEMVISI 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
            D +PDP    DP +R + E+AL YMGL+P +P+  + IDKVFIGSCTNSRI+D+RAAA 
Sbjct: 301 EDRVPDPDKEKDPNKRTAMERALEYMGLQPNVPVESINIDKVFIGSCTNSRIDDMRAAAW 360

Query: 361 IAK--GRKVAPGVQ-ALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDR 417
           + +  GRKVA  V+ ALVVPGSG VK QAE EGLD++F  AGFEWR PGCSMCLAMN DR
Sbjct: 361 VVQKLGRKVASNVKLALVVPGSGLVKEQAEREGLDEVFKAAGFEWREPGCSMCLAMNADR 420

Query: 418 LNPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
           L PGERCASTSNRNFEGRQG GGRTHLVSPAMAAAAA+ GHF D+R +
Sbjct: 421 LEPGERCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAIEGHFVDVRKL 468


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: 735
Number of extensions: 21
Number of successful extensions: 2
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: 469
Length adjustment: 33
Effective length of query: 433
Effective length of database: 436
Effective search space:   188788
Effective search space used:   188788
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 RR42_RS24175 RR42_RS24175 (isopropylmalate isomerase)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.2419.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2419.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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