GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Desulfovibrio vulgaris Miyazaki F

Align Acetyl-coenzyme A synthetase; AcCoA synthetase; Acs; Acetate--CoA ligase; Acyl-activating enzyme; EC 6.2.1.1 (characterized)
to candidate 8501039 DvMF_1775 acetate/CoA ligase (RefSeq)

Query= SwissProt::Q8ZKF6
         (652 letters)



>FitnessBrowser__Miya:8501039
          Length = 667

 Score =  748 bits (1932), Expect = 0.0
 Identities = 370/627 (59%), Positives = 468/627 (74%), Gaps = 10/627 (1%)

Query: 22  EQYETKYKQSINDPDTFWGEQGK-ILDWITPYQKVKNTSFAPGNVSIKWYEDGTLNLAAN 80
           ++Y    +++  DP+ FWG++ + +LDW TP+ KV +         I+W++  TLN+A N
Sbjct: 38  DEYLAHRERADKDPEGFWGDRARQLLDWFTPWDKVMDADM--NEPRIEWFKGATLNVAYN 95

Query: 81  CLDRHLQENGDRT--AIIWEGDDTSQSKHISYRELHRDVCRFANTLLDLGIKKGDVVAIY 138
           CLDRHL  NG R   AIIW+G+     + ++Y+ L+ +VCRFA+ L  LG++KGD VA+Y
Sbjct: 96  CLDRHLV-NGRRNKAAIIWQGEPEDDVRVLTYQMLYDEVCRFASVLQGLGVQKGDRVALY 154

Query: 139 MPMVPEAAVAMLACARIGAVHSVIFGGFSPEAVAGRIIDSSSRLVITADEGVRAGRSIPL 198
           MPM+PE AVAMLACARIGAVHS++F GFS  ++  RI D  +++V+TAD  +RAGRSIPL
Sbjct: 155 MPMIPELAVAMLACARIGAVHSIVFAGFSAVSLQNRIQDCEAKVVVTADAVLRAGRSIPL 214

Query: 199 KKNVDDALKNPNVTSVEHVIVLKRTGSDIDWQEGRDLWWRD-LIEKASPEHQPEA-MNAE 256
           K NVD+ALK+    SVE V+V+ R  S+   +EGRD+WW + + ++      P A M++E
Sbjct: 215 KVNVDEALKD--CPSVERVVVVDRAHSNCAMREGRDMWWHEAMADRTLDTSCPCAKMDSE 272

Query: 257 DPLFILYTSGSTGKPKGVLHTTGGYLVYAATTFKYVFDYHPGDIYWCTADVGWVTGHSYL 316
           D LFILYTSGSTGKPKGV+HTTGGYL YAA T ++VFD H  D+YWCTAD+GW+TGHSY+
Sbjct: 273 DMLFILYTSGSTGKPKGVVHTTGGYLAYAAHTTQWVFDLHDDDVYWCTADIGWITGHSYI 332

Query: 317 LYGPLACGATTLMFEGVPNWPTPARMCQVVDKHQVNILYTAPTAIRALMAEGDKAIEGTD 376
           +YGPLA G TTLMFEGVP+WP P R   +V+K +VNI YTAPT IRALM EG    +  D
Sbjct: 333 VYGPLALGGTTLMFEGVPSWPGPDRFWHIVEKFRVNIFYTAPTVIRALMREGAHWTQKHD 392

Query: 377 RSSLRILGSVGEPINPEAWEWYWKKIGKEKCPVVDTWWQTETGGFMITPLPGAIELKAGS 436
            SSLR+LGSVGEPINPEAW WY + IG  + P+VDTWWQTETGG MI+ LP A  LK GS
Sbjct: 393 LSSLRVLGSVGEPINPEAWMWYHEHIGHSRLPIVDTWWQTETGGIMISALPYATTLKPGS 452

Query: 437 ATRPFFGVQPALVDNEGHPQEGATEGNLVITDSWPGQARTLFGDHERFEQTYFSTFKNMY 496
           AT P  G+  A+V  +G P      G+LV+   WPG  R +FG  ER++ TYF  F  MY
Sbjct: 453 ATMPLPGIDAAVVKADGTPCGPNEGGHLVVRKPWPGMLRGVFGSPERYKSTYFERFPGMY 512

Query: 497 FSGDGARRDEDGYYWITGRVDDVLNVSGHRLGTAEIESALVAHPKIAEAAVVGIPHAIKG 556
            SGDGAR DEDGY W+ GR+DDV+NVSGHR+GTAE+ESALV+HP +AEAAVVG+PHAIKG
Sbjct: 513 ESGDGARTDEDGYTWVMGRLDDVINVSGHRMGTAEVESALVSHPAVAEAAVVGMPHAIKG 572

Query: 557 QAIYAYVTLNHGEEPSPELYAEVRNWVRKEIGPLATPDVLHWTDSLPKTRSGKIMRRILR 616
           +AIYAYVTL+ G E + EL A +R WVRKEIGP+ATP+V+ + + LPKTRSGKIMRRILR
Sbjct: 573 EAIYAYVTLSAGTEETEELRAALRTWVRKEIGPIATPEVIQFAEGLPKTRSGKIMRRILR 632

Query: 617 KIAAGDTSNLGDTSTLADPGVVEKLLE 643
           KIA+G  S+ GDTSTLADPGVV+ L+E
Sbjct: 633 KIASGAGSDFGDTSTLADPGVVQDLIE 659


Lambda     K      H
   0.317    0.135    0.423 

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: 1442
Number of extensions: 62
Number of successful extensions: 6
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: 667
Length adjustment: 38
Effective length of query: 614
Effective length of database: 629
Effective search space:   386206
Effective search space used:   386206
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 8501039 DvMF_1775 (acetate/CoA ligase (RefSeq))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.13165.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13165.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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