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 3607991 Dshi_1399 acetate--CoA ligase (RefSeq)

Query= SwissProt::P27550
         (652 letters)



>FitnessBrowser__Dino:3607991
          Length = 653

 Score =  842 bits (2176), Expect = 0.0
 Identities = 401/642 (62%), Positives = 494/642 (76%), Gaps = 5/642 (0%)

Query: 7   HTIPANIADRCLINPQQYEAMYQQSINVPDTFWGEQGKILDWIKPYQKVKNTSFAPGNVS 66
           +T  A+      I+  +Y  MY  S++ P+ FWGE G+ LDWIKPY KVK+TSFA  +V 
Sbjct: 9   YTPSADFVKNAHIDSSKYSEMYAASVSDPEGFWGEHGRSLDWIKPYTKVKDTSFAHDDVH 68

Query: 67  IKWYEDGTLNLAANCLDRHLQENGDRTAIIWEGDD-ASQSKHISYKELHRDVCRFANTLL 125
           ++W+EDGTLN+AANC+DRHL   GD+TAII+E DD A  ++HI+Y+ELHR VC+ +N L 
Sbjct: 69  VRWFEDGTLNVAANCIDRHLATRGDQTAIIFEPDDPAEPAQHITYRELHRQVCKLSNVLE 128

Query: 126 ELGIKKGDVVAIYMPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSNSRLVIT 185
           +LG++KGD V +YMPM+PEAA AMLACARIGA+HS++F GFSP+A++ RI  +++RL+IT
Sbjct: 129 DLGVRKGDRVILYMPMIPEAAYAMLACARIGAIHSIVFAGFSPDALSARINGADARLLIT 188

Query: 186 SDEGVRAGRSIPLKKNVDDALKNPNVTSVEHVVVLKRTGGKIDWQEGRDLWWHDLVEQAS 245
           +D   R GR  PLK N D AL +        ++V+KRTGG+  W +GRD  +H+L+ +A 
Sbjct: 189 ADYAPRGGRQTPLKSNADAALLHTR--DDVKMLVVKRTGGQTTWVDGRDFDYHELMLEAD 246

Query: 246 DQHQAEEMNAEDPLFILYTSGSTGKPKGVLHTTGGYLVYAALTFKYVFDYHPGDIYWCTA 305
           +     E+ AE PLFILYTSGSTG+PKGV+H++GGYL+YAA+T KYVFD H GD+YWCTA
Sbjct: 247 EVQHPVEVEAEHPLFILYTSGSTGQPKGVVHSSGGYLLYAAMTQKYVFDVHEGDVYWCTA 306

Query: 306 DVGWVTGHSYLLYGPLACGATTLMFEGVPNWPTPARMAQVVDKHQVNILYTAPTAIRALM 365
           DVGWVTGHSY++YGPLA G TT+MFEGVP +P  +R  QV DKH+V   YTAPTAIRALM
Sbjct: 307 DVGWVTGHSYIVYGPLANGGTTVMFEGVPTYPDASRFWQVCDKHKVTQFYTAPTAIRALM 366

Query: 366 AEGDKAIEGTDRSSLRILGSVGEPINPEAWEWYWKKIGNEKCPVVDTWWQTETGGFMITP 425
           A+G + +E  D SSLR+LG+VGEPINPEAW WY   +G  +CP+VDTWWQTETGG ++TP
Sbjct: 367 AKGPEFVETCDLSSLRVLGTVGEPINPEAWNWYNDLVGKGRCPIVDTWWQTETGGHLLTP 426

Query: 426 LPGATELKAGSATRPFFGVQPALVDNEGNP--LEGATEGSLVITDSWPGQARTLFGDHER 483
           LPGA   K GSAT PFFGVQP ++D        E   EG L + DSWPGQ RT++GDHER
Sbjct: 427 LPGAIATKPGSATLPFFGVQPVVLDPHSGAEITETECEGVLCLKDSWPGQMRTVYGDHER 486

Query: 484 FEQTYFSTFKNMYFSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIA 543
           F +TYFS +K  YFSGDG RRD DGYYWITGRVDDV+NVSGHR+GTAE+ESALVAH K+A
Sbjct: 487 FVKTYFSDYKGYYFSGDGCRRDADGYYWITGRVDDVINVSGHRMGTAEVESALVAHAKVA 546

Query: 544 EAAVVGIPHNIKGQAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLP 603
           EAAVVG PH+IKGQ IY YVTL +GEEPS EL  E+R WVR EIGP+A PD++ W   LP
Sbjct: 547 EAAVVGYPHDIKGQGIYCYVTLMNGEEPSEELRKELRTWVRTEIGPIAAPDLIQWAPGLP 606

Query: 604 KTRSGKIMRRILRKIAAGDTSNLGDTSTLADPGVVEKLLEEK 645
           KTRSGKIMRRILRKIA  D   LGDTSTLADP VVE L+E +
Sbjct: 607 KTRSGKIMRRILRKIAEDDFGALGDTSTLADPSVVEDLIENR 648


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: 1427
Number of extensions: 66
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: 653
Length adjustment: 38
Effective length of query: 614
Effective length of database: 615
Effective search space:   377610
Effective search space used:   377610
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 3607991 Dshi_1399 (acetate--CoA ligase (RefSeq))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.8560.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8560.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.