GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Sphingomonas koreensis DSMZ 15582

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate Ga0059261_2979 Ga0059261_2979 malate synthase (EC 2.3.3.9)

Query= reanno::psRCH2:GFF353
         (726 letters)



>FitnessBrowser__Korea:Ga0059261_2979
          Length = 700

 Score =  827 bits (2137), Expect = 0.0
 Identities = 433/724 (59%), Positives = 523/724 (72%), Gaps = 26/724 (3%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT  V   GL VA+ L  FV    +PG G+DA  FW+GA ++    AP+NRALL  RD L
Sbjct: 1   MTAYVTRAGLSVAEPLARFVEERVLPGPGIDADVFWSGAAAIFARFAPRNRALLDTRDSL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QAQIDAW      +A D  A ++FL+ IGYL+ +   F  TT +VD EIA MAGPQLVVP
Sbjct: 61  QAQIDAWCAEDPARAADPAAQEAFLRGIGYLVDQPGAFTVTTADVDAEIATMAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
            +NARF LNAANARWGSLYDA YGTDA+    GA++  GY+  RG +VIA A+ FL+EA 
Sbjct: 121 ALNARFVLNAANARWGSLYDAFYGTDALP---GAARAGGYDAERGAQVIAAAKAFLDEAV 177

Query: 181 PLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNNGIHF 240
           PL     VD       GG L           L +P QL G +G++     +L ++NG+H 
Sbjct: 178 PLAGMKWVD-----FAGGDLP----------LADPGQLVGTRGDS-----LLFRHNGLHI 217

Query: 241 EIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLMKGDL 300
           E+ ID  S IG+TD AG+ D+L+E+ALTTI+D EDSIAAVDADDK   Y NWLGLM+GDL
Sbjct: 218 EVVIDRDSTIGRTDPAGIADVLLEAALTTIVDLEDSIAAVDADDKVAAYSNWLGLMRGDL 277

Query: 301 VEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKEGNEV 360
           VE  +KGGK +TR +  DRVY +   + +L L GRSLLF+RNVGHLMTN A+L  +G+E 
Sbjct: 278 VETFDKGGKTLTRRLAEDRVYQRPFAS-DLVLPGRSLLFVRNVGHLMTNPAVLI-DGDEA 335

Query: 361 PEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVEDVLG 420
           PEGI+D + TS IA+H+L G  + +N+RTGS+YIVKPKMHGP+E AF  +LF  VED+LG
Sbjct: 336 PEGILDAIVTSTIALHDLKGLGTHRNSRTGSVYIVKPKMHGPDEAAFTNDLFDAVEDLLG 395

Query: 421 LPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPMVRKA 480
           L R+T+KVG+MDEERRT+ NL ACI   + R+ FINTGFLDRTGDEIH+SM AGPM+ KA
Sbjct: 396 LDRHTIKVGVMDEERRTSANLAACIHAVKGRIAFINTGFLDRTGDEIHSSMRAGPMIPKA 455

Query: 481 AMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGANTAW 540
            MKA  WI AYE+ NV +GLA GL G+AQIGKGMWA PD MA MLE KVGHP +GANTAW
Sbjct: 456 EMKASSWIKAYEDRNVRIGLAHGLSGRAQIGKGMWAAPDRMAEMLEVKVGHPQSGANTAW 515

Query: 541 VPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPL-AQDTNWSEEEKRNELDN 599
           VPSPTAATLHAMHYH +DV ARQ E+A      +  +LTIP+ A   NW+ E+   ELDN
Sbjct: 516 VPSPTAATLHAMHYHTVDVFARQREIAGETVPGLAPLLTIPVAAPGRNWTPEDVARELDN 575

Query: 600 NSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQVVE 659
           N+QGILGY+VRW++QGVGCSKVPDINDI LMEDRATLRISSQH+ANW+ HGV T   V  
Sbjct: 576 NAQGILGYVVRWIDQGVGCSKVPDINDIGLMEDRATLRISSQHMANWLLHGVATAADVDA 635

Query: 660 SLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRRRRE 719
           +L RMA  VD QN GDPLYRPMA +   S+AFQAA  LV +G  QPNGYTEP+LHR R E
Sbjct: 636 ALVRMAAKVDAQNAGDPLYRPMAGNEAASLAFQAARALVFDGVAQPNGYTEPLLHRFRAE 695

Query: 720 FKAK 723
            KA+
Sbjct: 696 AKAR 699


Lambda     K      H
   0.316    0.133    0.386 

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: 1403
Number of extensions: 47
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: 726
Length of database: 700
Length adjustment: 39
Effective length of query: 687
Effective length of database: 661
Effective search space:   454107
Effective search space used:   454107
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: 55 (25.8 bits)

Align candidate Ga0059261_2979 Ga0059261_2979 (malate synthase (EC 2.3.3.9))
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.11265.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11265.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.