GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Dinoroseobacter shibae DFL-12

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 3610172 Dshi_3553 acetate--CoA ligase (RefSeq)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Dino:3610172
          Length = 658

 Score =  841 bits (2172), Expect = 0.0
 Identities = 399/630 (63%), Positives = 490/630 (77%), Gaps = 5/630 (0%)

Query: 19  INPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVSIKWYEDGTLNLA 78
           I+  +Y  MY  S++ P+ FWGE G+ LDWIKPY KVK+TSFA  +V ++W+EDGTLN+A
Sbjct: 26  IDSSKYSEMYAASVSDPEGFWGEHGRSLDWIKPYTKVKDTSFAHDDVHVRWFEDGTLNVA 85

Query: 79  ANCLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLLELGIKKGDVVAI 137
           ANC+DRHL   GD+TAII+E DD A  ++HI+Y+ELHR VC+ +N L +LG++KGD V +
Sbjct: 86  ANCIDRHLATRGDQTAIIFEPDDPAEPAQHITYRELHRQVCKLSNVLEDLGVRKGDRVIL 145

Query: 138 YMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVITSDEGVRAGRSIP 197
           YMPM+PEAA AMLACARIGA+HS++F GFSP+A++ RI  +++RL+IT+D   R GR  P
Sbjct: 146 YMPMIPEAAYAMLACARIGAIHSIVFAGFSPDALSARINGADARLLITADYAPRGGRQTP 205

Query: 198 LKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQASDQHQAEEMNAED 257
           LK N D AL +        ++V+KRTGG+  W +GRD  +H+L+ +A +     E+ AE 
Sbjct: 206 LKSNADAALLHTR--DDVKMLVVKRTGGQTTWVDGRDFDYHELMLEADEVQHPVEVEAEH 263

Query: 258 PLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTADVGWVTGHSYLL 317
           PLFILYTSGSTG+PKGV+H++GGYL+YAA+T KYVFD H GD+YWCTADVGWVTGHSY++
Sbjct: 264 PLFILYTSGSTGQPKGVVHSSGGYLLYAAMTQKYVFDVHEGDVYWCTADVGWVTGHSYIV 323

Query: 318 YGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTDR 377
           YGPLA G TT+MFEGVP +P  +R  QV DKH+V   YTAPTAIRALMA+G + +E  D 
Sbjct: 324 YGPLANGGTTVMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTAIRALMAKGPEFVETCDL 383

Query: 378 SSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITPLPGATELKAGSA 437
           SSLR+LG+VGEPINPEAW WY   +G  +CP+VDTWWQTETGG ++TPLPGA   K GSA
Sbjct: 384 SSLRVLGTVGEPINPEAWNWYNDLVGKGRCPIVDTWWQTETGGHLLTPLPGAIATKPGSA 443

Query: 438 TRPFFGVQPALVDNEGNP--LEGATEGSLVITDSWPGQARTLFGDHERFEQTYFSTFKNM 495
           T PFFGVQP ++D        E   EG L + DSWPGQ RT++GDHERF +TYFS +K  
Sbjct: 444 TLPFFGVQPVVLDPHSGAEITETECEGVLCLKDSWPGQMRTVYGDHERFVKTYFSDYKGY 503

Query: 496 YFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHNIK 555
           YFSGDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH K+AEAAVVG PH+IK
Sbjct: 504 YFSGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHAKVAEAAVVGYPHDIK 563

Query: 556 GQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRIL 615
           GQ IY YVTL +GEEPS EL  E+R WVR EIGP+A PD++ W   LPKTRSGKIMRRIL
Sbjct: 564 GQGIYCYVTLMNGEEPSEELRKELRTWVRTEIGPIAAPDLIQWAPGLPKTRSGKIMRRIL 623

Query: 616 RKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           RKIA  D   LGDTSTLADP VVE L+E +
Sbjct: 624 RKIAEDDFGALGDTSTLADPSVVEDLIENR 653


Lambda     K      H
   0.317    0.135    0.421 

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: 1413
Number of extensions: 63
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: 652
Length of database: 658
Length adjustment: 38
Effective length of query: 614
Effective length of database: 620
Effective search space:   380680
Effective search space used:   380680
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate 3610172 Dshi_3553 (acetate--CoA ligase (RefSeq))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.8910.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8910.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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