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_RS01530 RR42_RS01530 isopropylmalate isomerase

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Cup4G11:RR42_RS01530
          Length = 472

 Score =  476 bits (1226), Expect = e-139
 Identities = 242/464 (52%), Positives = 310/464 (66%), Gaps = 1/464 (0%)

Query: 4   TLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMDH 63
           T Y KL D+H V   + +  LLY D HL++E TSPQAF GL A GR V  PG+  A +DH
Sbjct: 5   TYYRKLVDSHTVAALDADHVLLYADLHLMNEYTSPQAFAGLAAQGRGVPSPGQQVAVVDH 64

Query: 64  NVSTQTKDINACGEMAR-IQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPGM 122
            + T  +      + A  +Q + L +NC + G+ L+D +   QGI HV+ PE G+  PGM
Sbjct: 65  IIPTHAESPRRIQDPASALQARNLKRNCDQHGIPLFDTDDALQGIEHVIAPEHGMIRPGM 124

Query: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAKD 182
            ++CGDSHT T+GA GAL FGIGTSEVEHVLATQTL    A  M+I V G    G TAKD
Sbjct: 125 VVLCGDSHTTTYGALGALGFGIGTSEVEHVLATQTLVYRVAMDMRIRVDGVLPCGATAKD 184

Query: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFNY 242
           ++L II +  + G  G+VVEF G AI  LS+E RMTLCNM +E GA+  L+APD     Y
Sbjct: 185 MILHIISRISAQGARGYVVEFTGSAIAALSIEARMTLCNMTVEAGARGALIAPDAAAIEY 244

Query: 243 VKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVND 302
           V  R         + A+A W+ L +D  A FD+ +   A  ++P V+WGT+P Q I ++ 
Sbjct: 245 VLARAADIDATLRERALACWRALHSDADARFDSELVFDASNVAPYVSWGTSPDQAIPIDA 304

Query: 303 NIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEIA 362
            +P      D   R++A KAL Y+GL+ G  L  + + +VFIGSCTN RIEDLRA A I 
Sbjct: 305 CVPPVEDAIDDTARSAAAKALDYIGLQAGATLEGLPVQRVFIGSCTNGRIEDLRAVAAIV 364

Query: 363 KGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPGE 422
           +GRKVA GV+A+VVPGSG V+ QAE EG+ ++ ++AGFEWR PGCSMCLAMN+D L PGE
Sbjct: 365 RGRKVAAGVRAMVVPGSGAVRQQAEDEGIAQVLLDAGFEWRKPGCSMCLAMNDDVLAPGE 424

Query: 423 RCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           RCAST+NRNFEGRQGR GRTHL+SPAMAAAAA+TG   D+R ++
Sbjct: 425 RCASTTNRNFEGRQGRAGRTHLMSPAMAAAAALTGCITDVRRLE 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: 710
Number of extensions: 22
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 RR42_RS01530 RR42_RS01530 (isopropylmalate isomerase)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.13993.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13993.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.