GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas putida KT2440

Align Aconitate hydratase A; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; Iron-responsive protein-like; IRP-like; Probable 2-methyl-cis-aconitate hydratase; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate PP_2336 PP_2336 aconitate hydratase 1

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Putida:PP_2336
          Length = 862

 Score = 1459 bits (3777), Expect = 0.0
 Identities = 739/867 (85%), Positives = 782/867 (90%), Gaps = 8/867 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A RK LPGT LDYFDARAAVEAI+PGAYD LPYTSRVLAENLVRRCDPATL  SL Q
Sbjct: 1   MNTAYRKHLPGTDLDYFDARAAVEAIKPGAYDGLPYTSRVLAENLVRRCDPATLDASLSQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPA+VNPVVPVQLIVDH
Sbjct: 61  LIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADKGGDPAQVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDP AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVI PGNGIMHQINLEKM
Sbjct: 121 SLAVECGGFDPQAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIQPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+H+D GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP+IVGV
Sbjct: 181 SPVVHSDRGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPEIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK  P ITATD+VLALTEFLRK+KVVGAYLEF GEGA +LTLGDRATISNMAPEYGA
Sbjct: 241 ELTGKLAPNITATDLVLALTEFLRKQKVVGAYLEFHGEGARALTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF ID+QTIDYLRLTGR ++Q+KLVETYA+  GLWADSL  A YER L FDLSSVVR
Sbjct: 301 TAAMFAIDQQTIDYLRLTGREEQQVKLVETYAKATGLWADSLGGAVYERTLSFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           NMAGPSNPH R+ TS LA +GIA      S +E  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NMAGPSNPHARVATSDLAAKGIA-----GSWEEVPGQMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA L+ARNAN  GL RKPWVKSSLAPGSKAV+LYLEEA L  +LE+LGFGIVAFACTTC
Sbjct: 416 IAAGLIARNANKLGLTRKPWVKSSLAPGSKAVQLYLEEAGLEKELEQLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG   DGK + LKDIWPSDEEIDA+V  +VKPEQFRKVY PMFAI    G  
Sbjct: 536 RFDIEKDVLGV-VDGKEIRLKDIWPSDEEIDAVVRAAVKPEQFRKVYIPMFAIEEDRGPK 594

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           V+PLYDWRP STYIRRPPYWEGALAGERTL+ +RPLAVL DNITTDHLSPSNAIML+SAA
Sbjct: 595 VAPLYDWRPMSTYIRRPPYWEGALAGERTLRGMRPLAVLPDNITTDHLSPSNAIMLDSAA 654

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG VK+GSLARIEPE
Sbjct: 655 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRNDDGSVKQGSLARIEPE 714

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV RMWEAIETYM RKQPLII+AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 715 GKVTRMWEAIETYMQRKQPLIIVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 774

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NL+GMGVLPLEFKPG +R TLGLDG+ETYDV+G R PRATLTLVV R NGE +EVPVTCR
Sbjct: 775 NLVGMGVLPLEFKPGTDRKTLGLDGSETYDVLGARTPRATLTLVVTRANGECLEVPVTCR 834

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
           LD+ EEVSIYEAGGVL  FAQDFLE++
Sbjct: 835 LDTAEEVSIYEAGGVLQRFAQDFLEAT 861


Lambda     K      H
   0.318    0.135    0.398 

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: 2240
Number of extensions: 88
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: 869
Length of database: 862
Length adjustment: 42
Effective length of query: 827
Effective length of database: 820
Effective search space:   678140
Effective search space used:   678140
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: 56 (26.2 bits)

Align candidate PP_2336 PP_2336 (aconitate hydratase 1)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.24216.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24216.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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