GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas simiae WCS417

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate GFF4676 PS417_23925 acetyl-CoA synthetase

Query= reanno::pseudo5_N2C3_1:AO356_18695
         (651 letters)



>FitnessBrowser__WCS417:GFF4676
          Length = 645

 Score =  816 bits (2107), Expect = 0.0
 Identities = 398/640 (62%), Positives = 476/640 (74%), Gaps = 5/640 (0%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  YK +Y+QS+  PD FW EQAK  LDWI P+ TV+++  +  
Sbjct: 5   STFPTADAVRRAAQLSQEDYKRLYRQSIEQPDTFWAEQAKGFLDWITPWHTVQRSDINTG 64

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
                WFA G LNVSYNC+DRHLA+R +Q A IWEGDDP++S  ITYR+LH+ V + AN 
Sbjct: 65  AAH--WFAGGQLNVSYNCIDRHLAQRAEQPAFIWEGDDPAKSCKITYRQLHQNVSRLANV 122

Query: 124 LRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVV 183
           L+ + V +GD V IYMPMIPEA  AMLACTRIGA+HSVVFGGFSP+AL  RI D   + V
Sbjct: 123 LKSRGVKKGDRVCIYMPMIPEAAYAMLACTRIGAVHSVVFGGFSPDALRDRIQDADCRTV 182

Query: 184 ITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMKV 243
           ITADEGVR GK + LK NVD AL +    ++  V+V +RT   + W++ RD+ Y+  +  
Sbjct: 183 ITADEGVRGGKPVALKQNVDKALAS--CPNVSTVLVVERTGATVNWSEGRDLKYQQALDA 240

Query: 244 AGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYWC 303
           A   C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+ GEV+WC
Sbjct: 241 ASDNCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDGEVFWC 300

Query: 304 TADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIRA 363
           TADVGWVTGHSYIVYGPLANGAT+L+FEGVP+YPD +R  +VIDKHKV+I YTAPTA+RA
Sbjct: 301 TADVGWVTGHSYIVYGPLANGATSLMFEGVPSYPDSSRFWQVIDKHKVNIFYTAPTALRA 360

Query: 364 MMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVLI 423
           +M  G A +E    +SLRLLGSVGEPINPEAWDWY+  VG++RCPIVDTWWQTETGG+++
Sbjct: 361 LMREGHAPLESTSRASLRLLGSVGEPINPEAWDWYFNAVGEQRCPIVDTWWQTETGGIML 420

Query: 424 SPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHDR 483
           SPL  A  +KPG AT+P FGV P L+D  G    GA  G L I  SWPGQ R++YGD  R
Sbjct: 421 SPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEFSGAGSGVLAIKASWPGQIRSVYGDPQR 480

Query: 484 FVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVA 543
            +DTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  VA
Sbjct: 481 MIDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHDLVA 540

Query: 544 EAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGLP 603
           EAAVVG PHD+KGQGIY +VT   G E  +AL+  L   V KEIG  A P++IQWAP LP
Sbjct: 541 EAAVVGYPHDVKGQGIYAFVTPMNGVEPDDALKRHLLELVSKEIGSFAKPELIQWAPALP 600

Query: 604 KTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           KTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 601 KTRSGKIMRRILRKIACNELDSLGDTSTLADPSVVEGLID 640


Lambda     K      H
   0.318    0.135    0.418 

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: 1340
Number of extensions: 63
Number of successful extensions: 3
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: 651
Length of database: 645
Length adjustment: 38
Effective length of query: 613
Effective length of database: 607
Effective search space:   372091
Effective search space used:   372091
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 GFF4676 PS417_23925 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.15160.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15160.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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