GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Marinobacter adhaerens HP15

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate GFF1877 HP15_1834 protein containing 3-isopropylmalate dehydratase, large subunit region domain

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Marino:GFF1877
          Length = 472

 Score =  597 bits (1540), Expect = e-175
 Identities = 295/467 (63%), Positives = 358/467 (76%), Gaps = 4/467 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           KTLY+KL+D H+V + ++ + L+YIDR L+HEVTSPQAF+GLR  GR   +     AT D
Sbjct: 4   KTLYDKLWDDHLVKQRDDGSALIYIDRQLLHEVTSPQAFEGLRLAGRKPWRIDANIATPD 63

Query: 63  HNVSTQTKDINACG---EMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTL 119
           HNV T  +D    G    ++RIQ++ L KNC EFG+  + +    QGIVHV+GPEQG TL
Sbjct: 64  HNVPTTDRDRGVEGIVDPVSRIQVETLDKNCDEFGILEFKIKDQRQGIVHVIGPEQGATL 123

Query: 120 PGMTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGIT 179
           PGM+IVCGDSHT+THGAFG LA GIGTSEVEHVLATQ L Q + K M ++V GK  PG+T
Sbjct: 124 PGMSIVCGDSHTSTHGAFGCLAHGIGTSEVEHVLATQCLVQQKMKNMLVKVNGKLGPGVT 183

Query: 180 AKDIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETT 239
            KD+VLAIIGK G+AGGTGH +EF GEAIR LSMEGRMT+CNM+IE GA+ G+VA D+TT
Sbjct: 184 GKDVVLAIIGKIGTAGGTGHAIEFGGEAIRGLSMEGRMTICNMSIEAGARVGMVAVDDTT 243

Query: 240 FNYVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVIS 299
             YV+ R   PKG+ +D AV YW+TL +D  A FD +V L+  EI PQV+WGT+P  V  
Sbjct: 244 IEYVRNRPFGPKGEQWDAAVEYWRTLHSDSDAVFDKIVELEGSEIQPQVSWGTSPEMVAG 303

Query: 300 VNDNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAA 359
           ++  +PDP   ADP++R    +AL YMGL+P + +T++ +D+VFIGSCTNSRIEDLR AA
Sbjct: 304 IDGKVPDPEQEADPIKREGIVRALKYMGLQPNMAITDIKLDRVFIGSCTNSRIEDLREAA 363

Query: 360 EIAKGRKVAPGV-QALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRL 418
            + KGRKV+P + QA+VVPGSG VKAQAE EGLDKIFIEAG EWR PGCSMCLAMN D+L
Sbjct: 364 AVVKGRKVSPILKQAMVVPGSGLVKAQAEQEGLDKIFIEAGLEWRDPGCSMCLAMNADKL 423

Query: 419 NPGERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNI 465
             GE CASTSNRNFEGRQG GGRTHLVSPAMAAAAAVTGHF D+R +
Sbjct: 424 GQGEHCASTSNRNFEGRQGFGGRTHLVSPAMAAAAAVTGHFVDVREL 470


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: 759
Number of extensions: 24
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: 472
Length adjustment: 33
Effective length of query: 433
Effective length of database: 439
Effective search space:   190087
Effective search space used:   190087
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 GFF1877 HP15_1834 (protein containing 3-isopropylmalate dehydratase, large subunit region domain)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.18052.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18052.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.