GapMind for Amino acid biosynthesis

 

Alignments for a candidate for leuA in Synechococcus elongatus PCC 7942

Align 2-isopropylmalate synthase (EC 2.3.3.13) (characterized)
to candidate Synpcc7942_1410 Synpcc7942_1410 2-isopropylmalate synthase

Query= BRENDA::Q30DX9
         (623 letters)



>FitnessBrowser__SynE:Synpcc7942_1410
          Length = 540

 Score =  498 bits (1282), Expect = e-145
 Identities = 283/539 (52%), Positives = 363/539 (67%), Gaps = 32/539 (5%)

Query: 76  SDPNYVRVFDTTLRDGEQSPGATLTSKEKLDIARQLAKLGVDVIEAGFPAASKDDFEAVK 135
           S  + + +FDTTLRDGEQSPGA+L  +EKL IARQLA+L VD+IEAGF  AS  DFEAV+
Sbjct: 5   SSNDRILIFDTTLRDGEQSPGASLNLEEKLAIARQLARLNVDIIEAGFAFASPGDFEAVQ 64

Query: 136 TIAGTVGNAVDGDGYVPVICGLSRCNKRDIETAWEAVKYAKRPRIHTFIATSDIHLEYKL 195
            IA  VG     DG  P IC L+R  ++DI+ A EA+  A + RIHTFIATSDIHLEYKL
Sbjct: 65  RIAAEVGTP---DG--PTICSLARATRQDIKAAAEALAPAAKGRIHTFIATSDIHLEYKL 119

Query: 196 KKSKDEVIEIARNMVKFARSLGCEDVEFSPEDAGRSEREFLYQILGEVIKAGATTLNIPD 255
           KK++ EV+ +   MV +A SL  +DVEFSPEDAGRS+ EFLY+ L   I AGA T+NIPD
Sbjct: 120 KKTRAEVLAVIPEMVGYAASL-VDDVEFSPEDAGRSDPEFLYECLEAAIAAGAKTINIPD 178

Query: 256 TVGITLPSEFGQLIADIKANTPGIENVIISTHCQNDLGLSTANTLSGAHSGARQVEVTIN 315
           TVG T PSEFG LI  IK N   I+  IIS H  NDLGL+ AN L    +GARQ+E TIN
Sbjct: 179 TVGYTTPSEFGALIGGIKQNVCNIDQAIISVHGHNDLGLAVANFLEAVKNGARQLECTIN 238

Query: 316 GIGERAGNASLEEVVMAIKCRGDH---VLG------GLYTGIDTRHIVMTSKMVEDYTGM 366
           GIGERAGNA+LEE+VMA+  R  +    LG         T ++TR I  TS++V + TGM
Sbjct: 239 GIGERAGNAALEELVMALHVRRQYFNPFLGRAADSEAPLTQVNTREIYKTSRLVSNLTGM 298

Query: 367 QTQPHKAIVGANAFAHESGIHQDGMLKHKGTYEIICPEEIGLERSNDAGIVLGKLSGRHA 426
             QP+KAIVGANAFAHESGIHQDG+LK+K TYEI+  E IGL  +    I LGKLSGR+A
Sbjct: 299 LVQPNKAIVGANAFAHESGIHQDGVLKNKLTYEIVDAETIGLSTNR---ITLGKLSGRNA 355

Query: 427 LKDRLTELGYVLDDEQLSSIFWRFKSVAERKKRVTDADIIALVSDEVFQPEALWKLLDIQ 486
            + RL ELGY L ++ L+  F RFK +A++K+ VTD D+ A+V+DE  Q   L+KL  +Q
Sbjct: 356 FRTRLQELGYDLGEDDLNRAFLRFKELADKKREVTDRDLEAIVNDETQQAPELFKLELVQ 415

Query: 487 ITCGTLGLSTATVKLADADGKEHVACSMGTGPVDSAYKAVDLIVKEPATLLEYSMNAVTE 546
           ++ G     TATV L   +G+E    ++GTGPVD+ Y+A++ +V  P  L+E+S+ +VT 
Sbjct: 416 VSAGDHARPTATVTLRTPEGEELTDAAIGTGPVDAIYRAINRVVNIPNELIEFSVKSVTA 475

Query: 547 GIDAIATTRVLIRGNNNYSTTNAITGEEVQRTFSGTGAGMDIVVSSVKAYVGALNKMLD 605
           GIDAI    + +R  +              R FSG  A  DI+V+S +AY+ ALN++ +
Sbjct: 476 GIDAIGEVTIRLRHED--------------RIFSGHSANTDILVASAQAYIHALNRLAE 520


Lambda     K      H
   0.316    0.133    0.379 

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: 707
Number of extensions: 26
Number of successful extensions: 6
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: 623
Length of database: 540
Length adjustment: 36
Effective length of query: 587
Effective length of database: 504
Effective search space:   295848
Effective search space used:   295848
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 (21.6 bits)
S2: 53 (25.0 bits)

Align candidate Synpcc7942_1410 Synpcc7942_1410 (2-isopropylmalate synthase)
to HMM TIGR00973 (leuA: 2-isopropylmalate synthase (EC 2.3.3.13))

Software error:

../bin/blast/fastacmd -i /tmp/list.9348.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9348.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.