GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuC in Sinorhizobium meliloti 1021

Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33 (characterized)
to candidate SMc03823 SMc03823 isopropylmalate isomerase large subunit

Query= CharProtDB::CH_024771
         (466 letters)



>FitnessBrowser__Smeli:SMc03823
          Length = 469

 Score =  633 bits (1632), Expect = 0.0
 Identities = 313/465 (67%), Positives = 368/465 (79%), Gaps = 1/465 (0%)

Query: 3   KTLYEKLFDAHVVYEAENETPLLYIDRHLVHEVTSPQAFDGLRAHGRPVRQPGKTFATMD 62
           +TLY+K++D H+V   ++ T LLYIDRHLVHEVTSPQAF+GLR  GR VR P KT A +D
Sbjct: 5   RTLYDKIWDDHLVDSQDDGTCLLYIDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTLAVVD 64

Query: 63  HNVSTQT-KDINACGEMARIQMQELIKNCKEFGVELYDLNHPYQGIVHVMGPEQGVTLPG 121
           HNV T   + +    E +RIQ++ L +N  +FGVE Y  N   QGIVH++GPEQG TLPG
Sbjct: 65  HNVPTSPDRHLGIKNEESRIQVEALARNAADFGVEYYSENDKRQGIVHIVGPEQGFTLPG 124

Query: 122 MTIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVQGKAAPGITAK 181
           MTIVCGDSHT+THGAFGALA GIGTSEVEHVLATQTL Q +AK M + V G+  PG+TAK
Sbjct: 125 MTIVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQTLIQKKAKNMLVRVDGQLPPGVTAK 184

Query: 182 DIVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDETTFN 241
           DI+LAIIG+ G+AGGTGHV+EF GEAIR LSMEGRMT+CNM IE GA+AGL+APDETTF 
Sbjct: 185 DIILAIIGEIGTAGGTGHVIEFAGEAIRSLSMEGRMTVCNMTIEGGARAGLIAPDETTFE 244

Query: 242 YVKGRLHAPKGKDFDDAVAYWKTLQTDEGATFDTVVTLQAEEISPQVTWGTNPGQVISVN 301
           Y+K +  APKG+ +D AV YWKTL TDEGA +D VV L A  + P V+WG++P  V+SV 
Sbjct: 245 YIKDKPRAPKGEAWDRAVEYWKTLHTDEGAHYDRVVVLDAANLPPIVSWGSSPEDVVSVQ 304

Query: 302 DNIPDPASFADPVERASAEKALAYMGLKPGIPLTEVAIDKVFIGSCTNSRIEDLRAAAEI 361
             +P+P    D  +R S  +AL YMGLKPG  +T++AID+VFIGSCTN RIEDLRA AE+
Sbjct: 305 GVVPNPDDIQDETKRTSKWRALDYMGLKPGTKITDIAIDRVFIGSCTNGRIEDLRAVAEV 364

Query: 362 AKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNPG 421
            +GRKVAP V A++VPGSG VK QAEAEGLDKIF EAGF+WR PGCSMCLAMN+DRL PG
Sbjct: 365 VEGRKVAPTVSAMIVPGSGLVKEQAEAEGLDKIFKEAGFDWREPGCSMCLAMNDDRLKPG 424

Query: 422 ERCASTSNRNFEGRQGRGGRTHLVSPAMAAAAAVTGHFADIRNIK 466
           ERCASTSNRNFEGRQG  GRTHL+SPAMAAAAAV GHF DIR  K
Sbjct: 425 ERCASTSNRNFEGRQGFKGRTHLLSPAMAAAAAVAGHFVDIREWK 469


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: 26
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 SMc03823 SMc03823 (isopropylmalate isomerase large subunit)
to HMM TIGR00170 (leuC: 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33))

Software error:

../bin/blast/fastacmd -i /tmp/list.5816.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5816.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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