GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Shewanella oneidensis MR-1

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate 201881 SO2743 acetyl-coenzyme A synthetase (NCBI ptt file)

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



>FitnessBrowser__MR1:201881
          Length = 650

 Score =  986 bits (2548), Expect = 0.0
 Identities = 456/649 (70%), Positives = 540/649 (83%)

Query: 1   MSAASLYPVRPEVAASTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSF 60
           MS+ SLY V   +AA+ L +   YK MYQ+S+VNP+GFWRE  KR+DWIKP+T +K+T+F
Sbjct: 1   MSSQSLYKVSGNIAANALVNNDQYKTMYQESIVNPEGFWREHGKRIDWIKPYTKIKKTTF 60

Query: 61  DDHHVDIKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPSESRNITYRELHEEVCKF 120
           DDH++ I WF DGTLN S NCLDRHLA   D++AIIWEGD+ +E R ITY ELH +VCKF
Sbjct: 61  DDHNLSINWFYDGTLNASANCLDRHLAAHSDRVAIIWEGDNANEQRKITYGELHTQVCKF 120

Query: 121 ANALRGQDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKS 180
           ANALR Q V RGD+VTIYMPM+PEA VAMLAC RIGA+HSVVFGGFSP+++A R+ID KS
Sbjct: 121 ANALRSQGVRRGDIVTIYMPMVPEAAVAMLACARIGAVHSVVFGGFSPDSIASRVIDGKS 180

Query: 181 KVVITADEGVRAGKKIPLKANVDDALTNPETSSIQKVIVCKRTAGNIKWNQHRDIWYEDL 240
           K+VIT+DEG+R G+ IPLK N+DDAL +P+ +S++KVIV KRT G I W + RD+W+  L
Sbjct: 181 KIVITSDEGMRGGRAIPLKRNIDDALKHPDVTSVEKVIVLKRTGGKIDWVEGRDVWWHSL 240

Query: 241 MKVAGTVCAPKEMGAEEALFILYTSGSTGKPKGVQHTTAGYLLYAALTHERVFDYKPGEV 300
           ++ A   CA +EMGAE+ LF+LYTSGSTG PKGV HTT GY++YA++THE VFDYKPGE+
Sbjct: 241 VETASEHCAVEEMGAEDPLFLLYTSGSTGNPKGVLHTTGGYMVYASMTHEYVFDYKPGEI 300

Query: 301 YWCTADVGWVTGHSYIVYGPLANGATTLLFEGVPNYPDITRVAKVIDKHKVSILYTAPTA 360
           YWCTADVGW+TGHSY+VYGPLANGAT L+ EGVPN+P   R+ ++ID+HKV+ILYTAPT 
Sbjct: 301 YWCTADVGWITGHSYMVYGPLANGATVLIHEGVPNHPSPARLGEMIDRHKVNILYTAPTL 360

Query: 361 IRAMMASGTAAVEGADGSSLRLLGSVGEPINPEAWDWYYKNVGKERCPIVDTWWQTETGG 420
           IRA+MA G    +  +GSSLR++GSVGEPINPEAW WY++ +G E CPIVDTWWQTETGG
Sbjct: 361 IRALMAEGKQHFDKYNGSSLRIMGSVGEPINPEAWRWYHEVIGHEHCPIVDTWWQTETGG 420

Query: 421 VLISPLPGATALKPGSATRPFFGVVPALVDNLGNLIEGAAEGNLVILDSWPGQARTLYGD 480
           +LI+PLPGAT  KPGSATRPFFGV PALVDN+GN++EGA EGNLV+LDSWPGQ RT+YGD
Sbjct: 421 ILITPLPGATDTKPGSATRPFFGVQPALVDNMGNILEGATEGNLVLLDSWPGQMRTVYGD 480

Query: 481 HDRFVDTYFKTFSGMYFTGDGARRDEDGYYWITGRVDDVLNVSGHRMGTAEIESAMVAHP 540
           H+RFV TYFKTF GMYFTGDGARRDEDGYYWITGRVDDV+NVSGHR+GTAE+ESA+V+H 
Sbjct: 481 HERFVLTYFKTFRGMYFTGDGARRDEDGYYWITGRVDDVINVSGHRLGTAEVESALVSHE 540

Query: 541 KVAEAAVVGVPHDIKGQGIYVYVTLNAGEETSEALRLELKNWVRKEIGPIASPDVIQWAP 600
            VAEAAVVG PHDIKGQGIY YVTL  G E SE LR EL+ WVRKEIG +A+PD+IQWA 
Sbjct: 541 LVAEAAVVGYPHDIKGQGIYAYVTLTRGTEESEELRQELRQWVRKEIGALATPDLIQWAT 600

Query: 601 GLPKTRSGKIMRRILRKIATAEYDGLGDISTLADPGVVAHLIETHKTMN 649
           GLPKTRSGKIMRR LRKIA  E   LGD STLADP V+  LIET    N
Sbjct: 601 GLPKTRSGKIMRRFLRKIAANEVTNLGDASTLADPAVIETLIETRLNRN 649


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: 1457
Number of extensions: 51
Number of successful extensions: 1
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: 650
Length adjustment: 38
Effective length of query: 613
Effective length of database: 612
Effective search space:   375156
Effective search space used:   375156
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 201881 SO2743 (acetyl-coenzyme A synthetase (NCBI ptt file))
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.24279.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24279.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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