GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acs in Pseudomonas putida KT2440

Align Acetyl-coenzyme A synthetase (EC 6.2.1.1) (characterized)
to candidate PP_4702 PP_4702 acetyl-CoA synthetase

Query= reanno::pseudo3_N2E3:AO353_03060
         (651 letters)



>FitnessBrowser__Putida:PP_4702
          Length = 644

 Score =  861 bits (2224), Expect = 0.0
 Identities = 408/637 (64%), Positives = 491/637 (77%), Gaps = 4/637 (0%)

Query: 7   YPVRPEVAANTLTDEATYKAMYQQSVVNPDGFWREQAKRLDWIKPFTTVKQTSFDDHHVD 66
           YP    V+ +       Y+ +Y+QSV +PD FW EQAKRLDWIKP+++V+Q   D H   
Sbjct: 7   YPQALAVSQSAALTPEDYRRLYRQSVEDPDTFWAEQAKRLDWIKPWSSVQQC--DLHTGK 64

Query: 67  IKWFADGTLNVSYNCLDRHLAERGDQIAIIWEGDDPAESRNITYRELHEQVCKFANALRG 126
            +WF    LNVSYNC+DRHLA+RG+Q A++WEGDDP +S+ ITYRELH QVC+ ANA++ 
Sbjct: 65  ARWFDGAQLNVSYNCIDRHLAQRGEQTALLWEGDDPKDSKAITYRELHRQVCRLANAMKA 124

Query: 127 QDVHRGDVVTIYMPMIPEAVVAMLACTRIGAIHSVVFGGFSPEALAGRIIDCKSKVVITA 186
           + V +GD V+IYMPMIPEA  AMLACTRIGAIHSVVFGGFSP+AL  RI+D   + VITA
Sbjct: 125 RGVKKGDRVSIYMPMIPEAAFAMLACTRIGAIHSVVFGGFSPDALRDRILDADCRTVITA 184

Query: 187 DEGLRAGKKISLKANVDDALTNPETSSIQKVIVCKRTGGNIKWNQHRDIWYEDLMKVAGT 246
           DEG+R GK+I LK NVD AL +    ++  V+V +RTGG++ W + RD+WY +  K AG 
Sbjct: 185 DEGVRGGKRIPLKQNVDKALAS--CPAVSSVLVVRRTGGDVAWTEGRDLWYHEATKDAGD 242

Query: 247 VCAPKEMGAEEALFILYTSGSTGKPKGVQHTTGGYLLYAALTHERVFDYRPGEIYWCTAD 306
            C P+ M AE+ LFILYTSGSTGKPKGV HTTGGYLL A +T + VFDYR GE++WCTAD
Sbjct: 243 DCPPEPMEAEDPLFILYTSGSTGKPKGVLHTTGGYLLQATMTFKVVFDYRDGEVFWCTAD 302

Query: 307 VGWVTGHTYIVYGPLANGATTLLFEGVPNYPDITRVAKIIDKHKVNILYTAPTAIRAMMA 366
           VGWVTGH+YIVYGPLANGA +L+FEGVPNYPD +R  +++DKH+VNI YTAPTA+RA+M 
Sbjct: 303 VGWVTGHSYIVYGPLANGAISLMFEGVPNYPDTSRFWQVVDKHQVNIFYTAPTALRALMR 362

Query: 367 QGTAAVEGADGSSLRLLGSVGEPINPEAWEWYYKNVGQSRCPIVDTWWQTETGATLMSPL 426
           +G+A ++     SLRLLGSVGEPINPEAWEWY++ VGQ RCPIVDTWWQTETG  +++PL
Sbjct: 363 EGSAPLQSTSRKSLRLLGSVGEPINPEAWEWYFEEVGQKRCPIVDTWWQTETGGIMLTPL 422

Query: 427 PGAHGLKPGSAARPFFGVVPALVDNLGNIIEGVAEGNLVILDSWPGQARTLYGDHDRFVD 486
           PG   LKPG A +P FGV P L+D  G +IEG   G L I  SWPGQ R++YGDH R VD
Sbjct: 423 PGTQSLKPGCATQPMFGVQPVLLDEKGKLIEGPGAGVLAIKASWPGQIRSVYGDHQRMVD 482

Query: 487 TYFKTFRGMYFTGDGARRDADGYWWITGRVDDVLNVSGHRMGTAEIESAMVAHPKVAEAA 546
           TYFK   G YFTGDGARRDADG +WITGR+DDV+NVSGHR+GTAE+ESA+V H  VAEAA
Sbjct: 483 TYFKPLPGYYFTGDGARRDADGDYWITGRIDDVINVSGHRIGTAEVESALVLHDSVAEAA 542

Query: 547 VVGVPHDIKGQGIYVYVTLNGGEEPSEALRLELKNWVRKEIGPIASPDVIQWAPGLPKTR 606
           VVG PHD+KGQG+Y +VT   G  P + L+ EL   V KEIG  A P++IQWAP LPKTR
Sbjct: 543 VVGYPHDLKGQGVYAFVTTMNGVTPDDTLKAELLALVSKEIGSFAKPELIQWAPALPKTR 602

Query: 607 SGKIMRRILRKIATGEYDGLGDISTLADPGVVQHLID 643
           SGKIMRRILRKIA  E + LGD STLADP VVQ LID
Sbjct: 603 SGKIMRRILRKIACNELENLGDTSTLADPSVVQGLID 639


Lambda     K      H
   0.319    0.136    0.425 

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: 1451
Number of extensions: 70
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: 644
Length adjustment: 38
Effective length of query: 613
Effective length of database: 606
Effective search space:   371478
Effective search space used:   371478
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 (21.7 bits)
S2: 54 (25.4 bits)

Align candidate PP_4702 PP_4702 (acetyl-CoA synthetase)
to HMM TIGR02188 (acs: acetate--CoA ligase (EC 6.2.1.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.29770.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29770.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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