GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glcB in Desulfovibrio vulgaris Miyazaki F

Align Malate synthase G (EC 2.3.3.9) (characterized)
to candidate 8501453 DvMF_2183 malate synthase G (RefSeq)

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



>FitnessBrowser__Miya:8501453
          Length = 731

 Score =  930 bits (2404), Expect = 0.0
 Identities = 460/731 (62%), Positives = 558/731 (76%), Gaps = 6/731 (0%)

Query: 1   MTERVQVGGLQVAKVLYDFVNNEAIPGTGVDAAAFWAGADSVIHDLAPKNRALLAKRDDL 60
           MT+RVQVGGLQ+A  LYD +  +  PGTGVD   FW   ++++  +A +NRALLAKR +L
Sbjct: 1   MTQRVQVGGLQIAAPLYDVIVRDIAPGTGVDPDRFWTALENMVETMADRNRALLAKRAEL 60

Query: 61  QAQIDAWHQARAGQAHDAVAYKSFLQEIGYLLPEAEDFQATTENVDEEIARMAGPQLVVP 120
           Q  IDAWH+ R G  HD  AY++FL+ IGYL+PE  DF  TTE VD EIA +AGPQLVVP
Sbjct: 61  QDAIDAWHRERRGTPHDGAAYEAFLRSIGYLVPEGPDFAVTTEGVDPEIALVAGPQLVVP 120

Query: 121 IMNARFALNAANARWGSLYDALYGTDAISE---ADGASKGPGYNEIRGNKVIAYARNFLN 177
           I NAR+ALNAANARWGSLYDALYGTD I E     GA +G  YN  RG  V+A A  FL+
Sbjct: 121 ITNARYALNAANARWGSLYDALYGTDVIPEDPARGGAPRGGAYNPARGALVVARAAAFLD 180

Query: 178 EAAPLETGSHVDSTGYRIEGGKLVVSLKDGSTTGLKNPAQLQGFQGE-ASAPIAVLLKNN 236
           EA PL TGSH D+  Y + GGKL V LKDG+ TGL +PA+  G  G+ A    AVLL+N+
Sbjct: 181 EAFPLATGSHADAARYDVRGGKLAVILKDGAETGLADPARFVGHAGDPAGGNGAVLLRNH 240

Query: 237 GIHFEIQIDPASPIGQTDAAGVKDILMESALTTIMDCEDSIAAVDADDKTVVYRNWLGLM 296
           G+H EI+ID    IG+  AAGV+D++ME+A+TTI+DCEDS+A VD  DK + YRN LGL 
Sbjct: 241 GLHAEIRIDREHAIGRGHAAGVRDVVMEAAMTTILDCEDSVAVVDGADKALAYRNMLGLF 300

Query: 297 KGDLVEELEKGGKRITRAMNPDRVYTKADGNGELTLHGRSLLFIRNVGHLMTNDAILDKE 356
           +GDL  E  KGG+ + R +NPDR YT  DG    +L GRSLL +R VGHLMT DA+L + 
Sbjct: 301 RGDLSAEFPKGGRSVLRTLNPDREYTGPDG-AAFSLPGRSLLLVRTVGHLMTTDAVLARS 359

Query: 357 GNEVPEGIMDGLFTSLIAVHNLNGNTSRKNTRTGSMYIVKPKMHGPEEVAFATELFGRVE 416
           G E+PEG++D + T+ IA+H+L G +S +N+RTG +YIVKPK HGPEEVAF  ELF   E
Sbjct: 360 GEEIPEGMLDTMATAYIALHDLRGTSSVRNSRTGGVYIVKPKQHGPEEVAFTVELFRMAE 419

Query: 417 DVLGLPRNTLKVGIMDEERRTTINLKACIKEARERVVFINTGFLDRTGDEIHTSMEAGPM 476
           D LG+PRNTLK+GIMDEERRTT+NLK CI+ A ERV+FINTGFLDRTGDEIHT MEAGP+
Sbjct: 420 DALGMPRNTLKIGIMDEERRTTVNLKECIRAAAERVIFINTGFLDRTGDEIHTCMEAGPV 479

Query: 477 VRKAAMKAEKWISAYENNNVDVGLACGLQGKAQIGKGMWAMPDLMAAMLEQKVGHPMAGA 536
           VRK AM+ E+WI AYE+ NVD GLACGL G+AQ+GKGMWA PD+M  M+E K+GHP AGA
Sbjct: 480 VRKNAMRGERWIIAYEDWNVDTGLACGLAGRAQVGKGMWAKPDMMREMVETKIGHPRAGA 539

Query: 537 NTAWVPSPTAATLHAMHYHKIDVQARQVELAKREKASIDDILTIPL-AQDTNWSEEEKRN 595
           N AWVPSPTAATLHAMHYH +DV A Q  LA + +A++ D+LT+PL    +  + +E   
Sbjct: 540 NCAWVPSPTAATLHAMHYHAVDVAAVQKTLAGQRRATLADLLTLPLMGPASRPTPQEVEE 599

Query: 596 ELDNNSQGILGYMVRWVEQGVGCSKVPDINDIALMEDRATLRISSQHVANWMRHGVVTKD 655
           EL NN+Q ILGY+VRWVEQG+GCSKVPDI D+ LMEDRATLRISSQH+ANW+ HG+ T+D
Sbjct: 600 ELANNAQSILGYVVRWVEQGIGCSKVPDITDVGLMEDRATLRISSQHIANWLHHGICTRD 659

Query: 656 QVVESLKRMAPVVDRQNQGDPLYRPMAPDFDNSVAFQAALELVLEGTKQPNGYTEPVLHR 715
           QVV  LKRMA VVDRQN GDP YRPM+ DFD SVAFQAA +LVL G +QP+GYTEP+LH 
Sbjct: 660 QVVAVLKRMAAVVDRQNAGDPAYRPMSADFDASVAFQAACDLVLLGREQPSGYTEPILHA 719

Query: 716 RRREFKAKNGL 726
           RR+E KAK G+
Sbjct: 720 RRQEAKAKFGI 730


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: 1424
Number of extensions: 47
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: 731
Length adjustment: 40
Effective length of query: 686
Effective length of database: 691
Effective search space:   474026
Effective search space used:   474026
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 8501453 DvMF_2183 (malate synthase G (RefSeq))
to HMM TIGR01345 (glcB: malate synthase G (EC 2.3.3.9))

Software error:

../bin/blast/fastacmd -i /tmp/list.5628.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.5628.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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