GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aacS in Magnetospirillum magneticum AMB-1

Align acetoacetate-CoA ligase (EC 6.2.1.16) (characterized)
to candidate WP_011383023.1 AMB_RS03000 acetoacetate--CoA ligase

Query= BRENDA::Q9Z3R3
         (650 letters)



>NCBI__GCF_000009985.1:WP_011383023.1
          Length = 652

 Score =  811 bits (2096), Expect = 0.0
 Identities = 406/648 (62%), Positives = 487/648 (75%), Gaps = 6/648 (0%)

Query: 7   LWVPDREIVERSPMAEFIDWCGERFGRSFADYDAFHDWSVSERGAFWTAVWEHCKVIGES 66
           LW P +E  E S +A F+     RF     DY     WSV     FW+ VW+   +IG+ 
Sbjct: 5   LWQPSKERAEASALARFMRRADARFQVGATDYAGLWRWSVDRPDQFWSLVWDEVGIIGDR 64

Query: 67  GEKALV--DGDRMLDARFFPEARLNFAENLLRKTGSGDALIFRGEDKVSYRLTWDELRAL 124
            +  +V  D  RM  AR+FPEARLNFAENLLR+   GDAL+F GEDKV  RL++ ELRAL
Sbjct: 65  PDGGVVVDDAGRMPGARWFPEARLNFAENLLRRDDGGDALVFWGEDKVKRRLSFAELRAL 124

Query: 125 VSRLQQALRAQGIGAGDRVAAMMPNMPETIALMLATASVGAIWSSCSPDFGEQGVLDRFG 184
           VSRLQQAL A G+G GDRVA  MPNMPE++A MLA AS+GAIWSS SPDFG QGVLDRFG
Sbjct: 125 VSRLQQALSAAGVGKGDRVAGYMPNMPESVAFMLAVASLGAIWSSASPDFGVQGVLDRFG 184

Query: 185 QIAPKLFIVCDGYWYNGKRQDVDSKVRAVAKSLGA--PTVIVPYAGDSAALAPTVEGGVT 242
           QIAPK+ +  +GY+Y+GK  D   K+ A+   + +    V+VPY  ++A L+  V+  V 
Sbjct: 185 QIAPKVLVAAEGYFYSGKAHDCLEKLAAIVPGIPSLERVVVVPYTREAADLSG-VDKAVH 243

Query: 243 LADFIAGFQAGPLVFERLPFGHPLYILFSSGTTGVPKCIVHSAGGTLLQHLKEHRFHCGL 302
           L DF+A F A  + F RLPF HPLYI++SSGTTG PKCIVHSAGG+L+Q LKEHR HC +
Sbjct: 244 LGDFLAPFPAKAVEFLRLPFDHPLYIMYSSGTTGAPKCIVHSAGGSLIQQLKEHRLHCDV 303

Query: 303 RDGERLFYFTTCGWMMWNWLASGLAVGATLCLYDGSPFCPDGNVLFDYAAAERFAVFGTS 362
           R  +R+FYFTTCGWMMWNWL +GL   ATL LYDG+P    GN+LFD+A AE   +FGTS
Sbjct: 304 RKDDRVFYFTTCGWMMWNWLVAGLGAEATLLLYDGNPSHLGGNILFDFADAEGMTLFGTS 363

Query: 363 AKYIDAVRKGGFTPARTHDLSSLRLMTSTGSPLSPEGFSFVYEGIKPDVQLASISGGTDI 422
           AK+IDA+ K G  P +TH L+++R + STGS L+PEGF +VY  +K DVQLASISGGTDI
Sbjct: 364 AKWIDAIAKSGLEPIKTHSLATVRTICSTGSVLAPEGFDYVYAKVKADVQLASISGGTDI 423

Query: 423 VSCFVLGNPLKPVWRGEIQGPGLGLAVDVWNDEGKPVRGEKGELVCTRAFPSMPVMFWND 482
           +SCF+LGNPL PV+RGEIQ  GLG+ V+V+++ G+ + G KGELVCTRAFPSMPV FWND
Sbjct: 424 ISCFMLGNPLVPVYRGEIQCRGLGMKVEVFDENGQSLAGSKGELVCTRAFPSMPVGFWND 483

Query: 483 PDGAKYRAAYFDRFDNVWCHGDFAEWTPH-GGIVIHGRSDATLNPGGVRIGTAEIYNQVE 541
            DGAKYRAAYF++F  +W HGD+ E  P  GGI++ GRSDATLNPGGVRIGTAEIY QVE
Sbjct: 484 DDGAKYRAAYFEKFPGIWTHGDWVELNPETGGIIVFGRSDATLNPGGVRIGTAEIYRQVE 543

Query: 542 QMDEVAEALCIGQDWEDDVRVVLFVRLARGVELTEALTREIKNRIRSGASPRHVPAKIIA 601
           Q+D+V E+L IGQDW+ DVRVVLFVRL  GV L+  L   IK RIR   +PRHVPAK++ 
Sbjct: 544 QIDDVLESLVIGQDWQADVRVVLFVRLRDGVTLSPELETRIKKRIRDNTTPRHVPAKVVQ 603

Query: 602 VADIPRTKSGKIVELAVRDVVHGRPVKNKEALANPEALDLFAGLEELK 649
           VADIPRTKSGKIVELAVRDVVHGR VKNKEALANPEALDLFAG  EL+
Sbjct: 604 VADIPRTKSGKIVELAVRDVVHGRAVKNKEALANPEALDLFAGRAELE 651


Lambda     K      H
   0.322    0.139    0.441 

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: 1441
Number of extensions: 65
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: 650
Length of database: 652
Length adjustment: 38
Effective length of query: 612
Effective length of database: 614
Effective search space:   375768
Effective search space used:   375768
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 (21.9 bits)
S2: 54 (25.4 bits)

Align candidate WP_011383023.1 AMB_RS03000 (acetoacetate--CoA ligase)
to HMM TIGR01217 (acetoacetate-CoA ligase (EC 6.2.1.16))

Software error:

../bin/blast/fastacmd -i /tmp/list.25285.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25285.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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