GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Paraburkholderia bryophila 376MFSha3.1

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 H281DRAFT_02981 H281DRAFT_02981 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Burk376:H281DRAFT_02981
          Length = 865

 Score = 1449 bits (3752), Expect = 0.0
 Identities = 718/870 (82%), Positives = 790/870 (90%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+A RK LPGT+LD+FDARAAV+AIQ GAYDKLPYTSRVLAENLVRRCDP TL  SL Q
Sbjct: 1   MNTAYRKRLPGTQLDFFDARAAVDAIQAGAYDKLPYTSRVLAENLVRRCDPVTLVASLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           +V RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA VNPVVP QL+VDH
Sbjct: 61  IVERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPAMVNPVVPTQLVVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AF+NVDVIPPGNGI+HQINLE+M
Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKRAFRNVDVIPPGNGILHQINLERM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+  ++GVA+PDT VGTDSHTP VDALGVIAIGVGGLEAE+VMLGRAS+MRLPDIVGV
Sbjct: 181 SPVVQVNDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           +LTGK   GITATD+VL+LTEFLRKEKVVGAYLEF GEG + LTLGDRATI+NMAPE+GA
Sbjct: 241 KLTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFFGEGTAKLTLGDRATIANMAPEFGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+IDEQTI YL+LTGR DE +KLVETYA+ AGLWADSL +AEYERVLKFDLS+VVR
Sbjct: 301 TAAMFYIDEQTIKYLKLTGRDDELVKLVETYAKEAGLWADSLTHAEYERVLKFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            +AGPSNPH+RLP S LA RGI+        +   GLMPDGAVIIAAITSCTNT+NPRN+
Sbjct: 361 TLAGPSNPHRRLPVSELAARGIS-----GKVENEPGLMPDGAVIIAAITSCTNTNNPRNM 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN RGL RKPW K+SLAPGSKAV LYLEEA LLP+LE+LGFG+VA+ACT+C
Sbjct: 416 IAAGLLARNANRRGLTRKPWAKTSLAPGSKAVTLYLEEAGLLPELEQLGFGVVAYACTSC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDP IQ+EI++RDLYATAVLSGNRNFDGRIHP+AKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPAIQKEIVERDLYATAVLSGNRNFDGRIHPFAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG D DG  V LKDIWPSDEEIDAIVA SVKPEQFRKVYEPMFA++  + E 
Sbjct: 536 RFDIEKDVLGVDADGNNVTLKDIWPSDEEIDAIVASSVKPEQFRKVYEPMFAVSVDTQEK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
            +PLYDWRP STYIRRPPYWEGALAGERTL+ +R LAVLGDNITTDHLSPSNAI+ +SAA
Sbjct: 596 ANPLYDWRPMSTYIRRPPYWEGALAGERTLQGMRALAVLGDNITTDHLSPSNAILPDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM + DG+VK GS ARIEPEG
Sbjct: 656 GEYLTKMGLPEEDFNSYATHRGDHLTAQRATFANPTLRNEMVIEDGKVKAGSFARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           K+ RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAG E IVAEGFERIHRTN
Sbjct: 716 KITRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPGVNR+TL +DGTET+DVIGER+PR  LTLV++R++GERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRITLAIDGTETFDVIGERKPRTDLTLVIHRRSGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EE+SIYEAGGVL  FAQDFLESS+A A
Sbjct: 836 DTAEELSIYEAGGVLQRFAQDFLESSKAAA 865


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: 2221
Number of extensions: 82
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: 865
Length adjustment: 42
Effective length of query: 827
Effective length of database: 823
Effective search space:   680621
Effective search space used:   680621
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 H281DRAFT_02981 H281DRAFT_02981 (aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming))
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.14170.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14170.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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