GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas stutzeri RCH2

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 GFF2274 Psest_2319 aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__psRCH2:GFF2274
          Length = 867

 Score = 1433 bits (3710), Expect = 0.0
 Identities = 712/866 (82%), Positives = 781/866 (90%), Gaps = 6/866 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+ +RKPLPGT LDYFD R A+EAIQPG+YDKLPYTSRVLAE LVRRC+P  LTDSL Q
Sbjct: 1   MNTEHRKPLPGTGLDYFDTREAIEAIQPGSYDKLPYTSRVLAEQLVRRCEPEALTDSLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA+QGGDPAKVNPVVP QLIVDH
Sbjct: 61  IIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEQGGDPAKVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE  GFDPDAF KNRA+E+RRNEDRFHFI+WTK AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVEFAGFDPDAFEKNRAVEERRNEDRFHFIEWTKTAFKNVDVIPAGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI A  GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE VMLG  S MRLPDIVGV
Sbjct: 181 SPVIQARGGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAETVMLGLPSMMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
            LTGKRQPGITATDIVLALTEFLRKE+VVGA++EF GEGA SLT+GDRATISNM PEYGA
Sbjct: 241 RLTGKRQPGITATDIVLALTEFLRKERVVGAWVEFFGEGADSLTIGDRATISNMCPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TA+MF+ID+QTIDYL+LTGR  EQ+ LVE YA+  GLWA +L+ AEYERVL+FDLSSVVR
Sbjct: 301 TASMFYIDQQTIDYLKLTGREPEQVALVEQYAKETGLWATALEGAEYERVLEFDLSSVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDK---ASAQEAEGLMPDGAVIIAAITSCTNTSNP 417
           NMAGPSNPHKRLPTSAL ERGIA D DK   A A+EAEGL+PDGAVIIAAITSCTNTSNP
Sbjct: 361 NMAGPSNPHKRLPTSALHERGIA-DEDKLAAARAEEAEGLLPDGAVIIAAITSCTNTSNP 419

Query: 418 RNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFAC 477
           RNV+AA LLA+ AN  GL RKPWVK+S APGSK  +LYLEEA LL +LEKLGFGIVA+AC
Sbjct: 420 RNVVAAGLLAKKANELGLVRKPWVKTSFAPGSKVAKLYLEEAGLLSELEKLGFGIVAYAC 479

Query: 478 TTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA 537
           TTCNGMSGALDP IQQEII+RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA
Sbjct: 480 TTCNGMSGALDPVIQQEIIERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIA 539

Query: 538 GTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAAS 597
           GT+RFDIE+DVLGTD++G P+ LKD+WPSDEEIDAIVA SVKPEQF+++Y PMF +    
Sbjct: 540 GTVRFDIEQDVLGTDKNGNPITLKDLWPSDEEIDAIVASSVKPEQFKQIYIPMFDLGTIE 599

Query: 598 GESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLN 657
            E+ SPLYDWRP STYIRRPPYWEGALAGERTLK +RPLA+L DNITTDHLSPSNAI+L+
Sbjct: 600 -EAKSPLYDWRPMSTYIRRPPYWEGALAGERTLKGMRPLAILPDNITTDHLSPSNAILLD 658

Query: 658 SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIE 717
           SAAGEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L+NEMAVVDG+ +KGSLAR+E
Sbjct: 659 SAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPQLVNEMAVVDGKAQKGSLARVE 718

Query: 718 PEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 777
           PEGKV+RMWEAIETYM+RKQ LII+AGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH
Sbjct: 719 PEGKVMRMWEAIETYMNRKQNLIIVAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIH 778

Query: 778 RTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVT 837
           RTNL+GMGVLP+EFKPG  RLTLGLDGTET+D+ GE  PR  LTLV++  +GE   VPVT
Sbjct: 779 RTNLVGMGVLPVEFKPGTTRLTLGLDGTETFDIEGELSPRCDLTLVIHHMSGEETRVPVT 838

Query: 838 CRLDSDEEVSIYEAGGVL-HFAQDFL 862
           CRLD+  EVS+Y+AGGVL  FA+DFL
Sbjct: 839 CRLDTAAEVSVYQAGGVLQRFAKDFL 864


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: 2244
Number of extensions: 74
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: 869
Length of database: 867
Length adjustment: 42
Effective length of query: 827
Effective length of database: 825
Effective search space:   682275
Effective search space used:   682275
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 GFF2274 Psest_2319 (aconitate hydratase 1/2-methylisocitrate dehydratase, Fe/S-dependent)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.10878.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.10878.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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