GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Shewanella amazonensis SB2B

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate 6936140 Sama_0337 isopropylmalate isomerase large subunit (RefSeq)

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__SB2B:6936140
          Length = 470

 Score =  696 bits (1797), Expect = 0.0
 Identities = 342/463 (73%), Positives = 389/463 (84%)

Query: 1   MAKTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFAT 60
           MAKTLYEK++DAH+V E   E P++Y+DRHLVHEVTSPQAF GL+  GRP+R   KTFAT
Sbjct: 1   MAKTLYEKVWDAHLVVEPAGEAPIIYVDRHLVHEVTSPQAFSGLKMAGRPLRAVEKTFAT 60

Query: 61  MDHNVSTQTKDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLP 120
           MDHN ST++  + A   MAR Q++ L  NC++F V LYD++HP QGIVHVMGPE G+TLP
Sbjct: 61  MDHNTSTKSASLTALSPMARTQVETLADNCRDFNVRLYDIHHPNQGIVHVMGPELGITLP 120

Query: 121 GMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITA 180
           G  IVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTL+Q +AKTMKIEV+GK A GITA
Sbjct: 121 GTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRGKVADGITA 180

Query: 181 KDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTF 240
           KDIVLAIIGK G  GGTG+VVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAG+VAPDETTF
Sbjct: 181 KDIVLAIIGKIGMDGGTGYVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGMVAPDETTF 240

Query: 241 NYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISV 300
            Y++GR  APKG  +  A+A W+ L TD  A FD  V L+A  I+PQ+TWGTNPGQV+++
Sbjct: 241 AYLEGREFAPKGDAWQQALADWRELHTDADAVFDAEVVLEAAAIAPQLTWGTNPGQVVAI 300

Query: 301 NDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360
           +  +P+PA   +PV R S EKALAY+ L PG P+T++AI+KVFIGSCTNSRIEDLRAAA 
Sbjct: 301 DGVVPNPADETNPVVRTSMEKALAYVDLTPGTPMTDIAINKVFIGSCTNSRIEDLRAAAA 360

Query: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420
            AKGRKVA GV A+VVPGSG VK QAEAEGLDKIF+EAGFEWRLPGCSMCLAMN+DRL  
Sbjct: 361 QAKGRKVASGVTAIVVPGSGQVKLQAEAEGLDKIFLEAGFEWRLPGCSMCLAMNDDRLEA 420

Query: 421 GERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIR 463
           G+RCASTSNRNFEGRQGRG RTHLVSPAMAAAAAV GHF DIR
Sbjct: 421 GDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAVAGHFVDIR 463


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: 796
Number of extensions: 21
Number of successful extensions: 1
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: 470
Length adjustment: 33
Effective length of query: 433
Effective length of database: 437
Effective search space:   189221
Effective search space used:   189221
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 6936140 Sama_0337 (isopropylmalate isomerase large subunit (RefSeq))
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.12770.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12770.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.