GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas fluorescens GW456-L13

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PfGW456L13_1517 Acetyl-coenzyme A synthetase (EC 6.2.1.1)

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



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1517
          Length = 645

 Score =  815 bits (2104), Expect = 0.0
 Identities = 400/641 (62%), Positives = 481/641 (75%), Gaps = 7/641 (1%)

Query: 5   SLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKR-LDWIKPFTTVKQTSFDDH 63
           S +P    V  +    +  Y+ +Y+QSV +P  FW EQA R LDW  P+ TV++ +    
Sbjct: 5   STFPKADAVRRAAQLSQDDYQRLYRQSVEHPSTFWAEQATRFLDWSAPWETVQRYNLKTG 64

Query: 64  HVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKFANA 123
             +  WFA   LNVSYNC+DRHL +RGDQ+AIIWEGDDP++S +ITY++LHE VC+ AN 
Sbjct: 65  --EASWFAGAQLNVSYNCIDRHLEKRGDQVAIIWEGDDPADSTSITYKKLHENVCRLANV 122

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

Query: 184 ITADEGVRAGKKIPLKANVDDALTN-PETSSIQKVIVCKRTAGNIKWNQHRDIWYEDLMK 242
           ITADEGVR GK + LK NVD AL + P+ SS   V+V +RT G + W + RDI Y+  ++
Sbjct: 183 ITADEGVRGGKVVSLKQNVDKALQSCPDVSS---VLVVERTKGLVNWVEGRDIKYQQALR 239

Query: 243 VAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEVYW 302
            A   C P+ M AE+ LFILYTSGSTGKPKGV HTT GYLL AA+T + V DY+  EV+W
Sbjct: 240 EASADCPPEPMDAEDPLFILYTSGSTGKPKGVLHTTGGYLLQAAMTFKYVLDYRDDEVFW 299

Query: 303 CTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTAIR 362
           CTADVGWVTGHSYIVYGPLANGATTL+FEGVPNYP  +R  +VIDKHKV+I YTAPTA+R
Sbjct: 300 CTADVGWVTGHSYIVYGPLANGATTLIFEGVPNYPSTSRFWQVIDKHKVNIFYTAPTALR 359

Query: 363 AMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGGVL 422
           A+M  G   ++    +S+RLLG+VGEPINPEAW+WY+  VG+ERCPIVDTWWQTETGG++
Sbjct: 360 ALMREGPEPLKQTSRASVRLLGTVGEPINPEAWEWYFHEVGEERCPIVDTWWQTETGGIM 419

Query: 423 ISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGDHD 482
           +SPL  A  +KPG AT+P FGV P L+D  G  I+GA  G L I  SWP Q R++Y D  
Sbjct: 420 LSPLVSAQRIKPGCATQPMFGVQPVLLDEQGKEIKGAGSGVLAIKSSWPAQIRSVYRDPQ 479

Query: 483 RFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHPKV 542
           R VDTYFK + G YFTGDGARRDEDG YWITGR+DDV+NVSGHR+GTAE+ESA+V H  +
Sbjct: 480 RMVDTYFKPYPGYYFTGDGARRDEDGDYWITGRIDDVINVSGHRIGTAEVESALVLHENI 539

Query: 543 AEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAPGL 602
           AEAA VG PHDIKGQGIYV+VT   G ET++ L+ EL   V KEIG  A PD+IQWAP L
Sbjct: 540 AEAAAVGYPHDIKGQGIYVFVTPMNGVETNDELKKELLALVSKEIGSFAKPDLIQWAPAL 599

Query: 603 PKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIE 643
           PKTRSGKIMRRILRKIA  E D LGD STLADP VV  LI+
Sbjct: 600 PKTRSGKIMRRILRKIACNELDNLGDTSTLADPSVVQGLID 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: 1339
Number of extensions: 73
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 PfGW456L13_1517 (Acetyl-coenzyme A synthetase (EC 6.2.1.1))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.25871.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25871.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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