GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align acetate-CoA ligase (EC 6.2.1.1) (characterized)
to candidate 8502070 DvMF_2783 acetate/CoA ligase (RefSeq)

Query= BRENDA::Q2XNL6
         (634 letters)



>FitnessBrowser__Miya:8502070
          Length = 651

 Score =  713 bits (1840), Expect = 0.0
 Identities = 347/641 (54%), Positives = 458/641 (71%), Gaps = 17/641 (2%)

Query: 8   LLEEKRVFKPHYTVVEEAHIKNWE---AELEKGKDHENYWAEKAERLEWFRKWDRVLDES 64
           LL E+RVF+P   VV  A +   +   A      D + YW E AE LEWFR+WD V D S
Sbjct: 11  LLREERVFRPLPQVVAGAVVNPQDVARARARAAADPDGYWEEAAEELEWFRRWDAVHDGS 70

Query: 65  NRPFYRWFVNGKINMTYNAVDRWLDTDKRNQVAILYVNERGDERKLTYYELYREVSRTAN 124
           N PF+RWF   + N+ +NA+DR ++T  +N++A+++  E GD R  TYY+LYREV+R AN
Sbjct: 71  NAPFHRWFTGARCNIVHNALDRHIETGTKNRLALIWEGESGDTRSFTYYQLYREVNRLAN 130

Query: 125 ALKSLGIKKGDAVALYLPMCPELVVSMLACAKIGAVHSVIYSGLSVGALVERLNDARAKI 184
           AL+ LG+ KGD V +Y+P  PE V +MLA AKIGAVHS ++ G S  +L +R+ DAR  +
Sbjct: 131 ALRGLGVGKGDRVIIYMPPLPETVFAMLAAAKIGAVHSTVFGGFSARSLRDRMEDARPAV 190

Query: 185 IITADGTYRRGGVIKLKPIVDEAILQCPT-----IETTVVVKHTDIDIEMSDISGREMLF 239
           I+T DG YR G VI LKPI DEA+   P      +   VVV    ++  M++  GR++ +
Sbjct: 191 IVTVDGFYRNGRVIPLKPIADEAVATLPPDLAAGVRHMVVVHRAHVETPMTE--GRDIWY 248

Query: 240 DKLIEGEGDRCDAEEMDAEDPLFILYTSGSTGKPKGVLHTTGGYMVGVASTLEMTFDIHN 299
              + G+      E MD+ DPLF+LYTSG+TGKPKG +H  GGYMVGV  T+   FD+  
Sbjct: 249 HDAVRGQHHEALTEIMDSTDPLFLLYTSGTTGKPKGHVHAHGGYMVGVHRTMRWVFDVKP 308

Query: 300 GDLWWCTADIGWITGHSYVVYGPLLLGTTTLLYEGAPDYPDPGVWWSIVEKYGVTKFYTA 359
            D++WCTA+ GWITGHSYVVYGPL+ GTTT+LYEG P YP+PG  WS+VE+ G+T  YTA
Sbjct: 309 TDIFWCTAEPGWITGHSYVVYGPLMAGTTTVLYEGHPLYPEPGRVWSMVERLGITILYTA 368

Query: 360 PTAIRHLMRFGDKHPKRYNLESLKILGTVGEPINPEAWMWYYRNIGREKCPIIDTWWQTE 419
           PT +R LMR G +H  R++L +L++LGTVGEPI+PEAW+W++R++GR +CP++DTWWQTE
Sbjct: 369 PTLVRMLMRHGAQHVARHDLTTLRLLGTVGEPISPEAWLWFHRHVGRGRCPVLDTWWQTE 428

Query: 420 TGMHLIAPLPVTPLKPGSVTKPLPGIEADVVDENGDPVPLGKGGFLVIRKPWPAMFRTLF 479
           TGM +++PLPV+ LKPGSVT+PLPGIEADVVDE+G PV  G GG LV+++PWPAM   ++
Sbjct: 429 TGMIMLSPLPVSLLKPGSVTRPLPGIEADVVDEHGKPVGPGHGGLLVLQRPWPAMSCGVY 488

Query: 480 NDEQRYIDVYWKQIPGGVYTAGDMARKDEDGYFWIQGRSDDVLNIAGHRIGTAEVESVFV 539
           ND++ Y  +YW++ PG  Y  GD+AR+DEDGYFWIQGR+DDVL IAGHRIGTAE+E+   
Sbjct: 489 NDDESYRRLYWERFPGW-YCTGDVARRDEDGYFWIQGRADDVLLIAGHRIGTAEMEAALA 547

Query: 540 AHPAVAEAAVIGKADPIKGEVIKAFLILKKGH-----KLNA-ALIEELKRHLRHELGPVA 593
           +H +VAE AVIG  D ++GEV KAF++L   H      +NA  L  EL  H+R ELGPVA
Sbjct: 548 SHRSVAECAVIGVPDALRGEVAKAFVVLVDDHPPLGTMVNADELAAELVEHVRRELGPVA 607

Query: 594 VVGEMVQVDSLPKTRSGKIMRRILRAREEGEDLGDTSTLEE 634
           V+ E+   + LP+ RSGKIMRR+LR+ E G D GD STLE+
Sbjct: 608 VIREVSFREGLPRNRSGKIMRRVLRSEELGRDTGDLSTLED 648


Lambda     K      H
   0.319    0.138    0.428 

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: 1378
Number of extensions: 68
Number of successful extensions: 4
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: 634
Length of database: 651
Length adjustment: 38
Effective length of query: 596
Effective length of database: 613
Effective search space:   365348
Effective search space used:   365348
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 8502070 DvMF_2783 (acetate/CoA ligase (RefSeq))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.9888.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9888.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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