GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Desulfovibrio vulgaris Hildenborough

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 206126 DVU0701 malate synthase G

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



>MicrobesOnline__882:206126
          Length = 729

 Score =  873 bits (2255), Expect = 0.0
 Identities = 421/728 (57%), Positives = 538/728 (73%), Gaps = 6/728 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT R++ GGL VA+ L+  +  E +PGTG+  + FWAG + ++  L P+NR LLA+RD++
Sbjct: 1   MTGRIREGGLAVAEPLHRCIEREILPGTGISPSIFWAGLEELVGTLGPRNRELLARRDNM 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           QA IDAWH+   G+ HDA AY+ FL++I YLLP  +D    T+ VD E+A +AGPQLVVP
Sbjct: 61  QAAIDAWHKEHQGRPHDAAAYRRFLEDIRYLLPAPQDLAVETQGVDPEVATIAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISEADGASKGPGYNEIRGNKVIAYARNFLNEAA 180
           + N R+ALNA NARWGSLYDALYG+D I+++DGA++G  YN +RG KV+AYA  FL+   
Sbjct: 121 VTNPRYALNAVNARWGSLYDALYGSDVIADSDGAARGAAYNPLRGAKVVAYAAAFLDRTF 180

Query: 181 PLETGSHVDSTGYRIEGG----KLVVSLKDGSTTGLKNPAQLQGFQGEASAPIAVLLKNN 236
           PL    H D   Y + G     KL     DG+ TGL +P    G+ G    P  VLL+NN
Sbjct: 181 PLAGARHADVVRYELTGPPVGRKLSALCADGTVTGLLHPDAFAGYTG-GERPTTVLLRNN 239

Query: 237 GIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLM 296
           G+H E+Q D   P+G    AG+KD+++ESA+TTI+DCEDS+A VDA+DK + YRN LGL 
Sbjct: 240 GLHVELQFDRRHPVGAAHPAGLKDVVLESAVTTILDCEDSVATVDAEDKALAYRNLLGLF 299

Query: 297 KGDLVEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKE 356
           +GDL    +KGG+ + R +  DR YT A G     L GRSL+ +RNVG LMT DA+LD  
Sbjct: 300 RGDLETSFDKGGRSVFRRLAADRTYT-APGGAAYALPGRSLMLVRNVGLLMTTDAVLDAA 358

Query: 357 GNEVPEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVE 416
           G E+PEGI+DGL T+ I +H+L G    +N+  GS+YIVKPK+HGPEEVAF  E F R+E
Sbjct: 359 GQEIPEGILDGLVTACIGLHDLRGAGRHRNSGAGSVYIVKPKLHGPEEVAFVCEQFRRIE 418

Query: 417 DVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPM 476
           D+LG+ RNTLK+G+MDEERRTT+NL  CI+ A +R++FINTGFLDRTGDEIHT MEAGP+
Sbjct: 419 DILGMARNTLKMGVMDEERRTTLNLAECIRVASQRIIFINTGFLDRTGDEIHTCMEAGPV 478

Query: 477 VRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGA 536
           VRK  MKA++W+ AYE+ NVD GLA G  GKAQIGKGMW  PD +A M+  K  HP AGA
Sbjct: 479 VRKNDMKAQRWMLAYEDWNVDTGLAAGFGGKAQIGKGMWPKPDRLAEMVATKGAHPRAGA 538

Query: 537 NTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPLAQDTNWSEEEKRNE 596
           N AWVPSPTAATLHA+HYH++DV ARQ ELA   +AS+DD+L +PL  +   S  E R E
Sbjct: 539 NCAWVPSPTAATLHALHYHEVDVFARQRELAGCHRASLDDLLALPLMGEARPSPAEVREE 598

Query: 597 LDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKDQ 656
           L+NN+Q ILGY+VRWVE G+GCSKVPDI+D+ LMEDRATLRISSQH+ANW+RHG+ T+D+
Sbjct: 599 LENNAQSILGYVVRWVEMGIGCSKVPDIHDVGLMEDRATLRISSQHIANWLRHGICTEDE 658

Query: 657 VVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHRR 716
           V + + RMA VVDRQN+ +P YRPM+ D  +SVAF+AA +LV EG +QPNGYTEP+LH R
Sbjct: 659 VRDVMLRMATVVDRQNKDEPGYRPMSADPGSSVAFRAACDLVFEGARQPNGYTEPILHAR 718

Query: 717 RREFKAKN 724
           RRE KA++
Sbjct: 719 RREVKARS 726


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: 1384
Number of extensions: 55
Number of successful extensions: 5
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: 729
Length adjustment: 40
Effective length of query: 686
Effective length of database: 689
Effective search space:   472654
Effective search space used:   472654
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 206126 DVU0701 (malate synthase G)
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.32106.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32106.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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