GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Shewanella loihica PV-4

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate 5209348 Shew_1822 aconitate hydratase (RefSeq)

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__PV4:5209348
          Length = 862

 Score = 1477 bits (3824), Expect = 0.0
 Identities = 728/861 (84%), Positives = 791/861 (91%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MN+ +RKPLPG+ALDYFDTR A+EA++ GAY KLPYT++VLAENLVRRCEPE+L  +L Q
Sbjct: 1   MNSLHRKPLPGSALDYFDTRAAVEALSAGAYDKLPYTAKVLAENLVRRCEPELLNDALSQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +I+ K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDP++VNPVVPTQLIVDH
Sbjct: 61  LIDRKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE+ GF+KDAF KNRAIEDRRNEDRFHFINWT+ AFKN+DVI  GNGIMHQINLE+M
Sbjct: 121 SLAVEHAGFEKDAFEKNRAIEDRRNEDRFHFINWTKTAFKNVDVIQPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPVI AR+GVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGR SYMRLPDI+GV
Sbjct: 181 SPVIQARDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRPSYMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGK Q GITATDIVLALTEFLR +KVVS+YLEFFGEGA  LTLGDRATISNMTPEFGA
Sbjct: 241 ELTGKRQSGITATDIVLALTEFLRQEKVVSAYLEFFGEGAADLTLGDRATISNMTPEFGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           +A MFYIDQQT+DYLT+TGR++EQVKLVE YAKT GLW+D LK A Y R L FDLSSVVR
Sbjct: 301 SAGMFYIDQQTIDYLTITGRDSEQVKLVENYAKTTGLWADSLKDAEYERVLTFDLSSVVR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
            IAGPSNPH RV TSELA++GI+G VE +  LMPDGAVIIAAITSCTNTSNPRNVIAAGL
Sbjct: 361 NIAGPSNPHRRVATSELASQGIAGVVEQDDKLMPDGAVIIAAITSCTNTSNPRNVIAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           LA+ AN  GL RKPWVKTS APGSK  +LYL++A LLPELE LGFGIVGFACTTCNGMSG
Sbjct: 421 LAKKANELGLVRKPWVKTSFAPGSKVAELYLKDAGLLPELEQLGFGIVGFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           KD+LG D  G+P+RL +IWPSD EIDA++ ASVKP+QFR +Y PMFDL+VDYG+ V+PLY
Sbjct: 541 KDILGHDDKGEPIRLKDIWPSDEEIDAIVKASVKPQQFRDIYTPMFDLAVDYGEDVNPLY 600

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
           DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAI+  SAAGEYL 
Sbjct: 601 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILASSAAGEYLA 660

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEGIVTRM 724
           KMGLPE DFNSYATHRGDHLTAQRATFANPKL NEMA+VDG+VKQGSL R+EPEG V RM
Sbjct: 661 KMGLPEVDFNSYATHRGDHLTAQRATFANPKLINEMALVDGEVKQGSLTRLEPEGEVMRM 720

Query: 725 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 784
           WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG
Sbjct: 721 WEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMG 780

Query: 785 VLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEE 844
           VLPLEFKAGENR TYGIDG+E FDVIG   PRADLTV+ITR+NGERVEVPV CRLDTA+E
Sbjct: 781 VLPLEFKAGENRHTYGIDGSETFDVIGEPTPRADLTVVITRQNGERVEVPVICRLDTADE 840

Query: 845 VSIYEAGGVLQRFAQDFLESN 865
           V +Y+AGGVLQRFAQDFLE+N
Sbjct: 841 VLVYQAGGVLQRFAQDFLEAN 861


Lambda     K      H
   0.318    0.136    0.397 

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: 2250
Number of extensions: 104
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: 867
Length of database: 862
Length adjustment: 42
Effective length of query: 825
Effective length of database: 820
Effective search space:   676500
Effective search space used:   676500
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 5209348 Shew_1822 (aconitate hydratase (RefSeq))
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.18663.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18663.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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