GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Burkholderia phytofirmans PsJN

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 BPHYT_RS30145 BPHYT_RS30145 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__BFirm:BPHYT_RS30145
          Length = 865

 Score = 1460 bits (3780), Expect = 0.0
 Identities = 725/870 (83%), Positives = 790/870 (90%), Gaps = 6/870 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+ANRK LPGT+LD+FD RAAV+AIQPGAYDKLPYTSRVLAENLVRRCDP TLT SL Q
Sbjct: 1   MNTANRKRLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPVTLTASLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           ++ RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA VNPVVP QL+VDH
Sbjct: 61  IIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPALVNPVVPTQLVVDH 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 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASYMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK   GITATD+VL+LTEFLRKEKVVGAYLEF G G + LTLGDRATI+NMAPE+GA
Sbjct: 241 ELTGKPAEGITATDVVLSLTEFLRKEKVVGAYLEFYGTGTAKLTLGDRATIANMAPEFGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF IDEQTI YL+LTGR DE +K VETYA+  GLWADSL NAEYERVLKFDLS+VVR
Sbjct: 301 TAAMFSIDEQTIKYLKLTGRDDELVKRVETYAKKTGLWADSLVNAEYERVLKFDLSTVVR 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++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPVIQKEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKDVLG D DG+ V LKDIWP+D EIDAIVA SVKPEQFRKVYEPMFA++  +GE 
Sbjct: 536 RFDIEKDVLGIDADGQAVTLKDIWPTDAEIDAIVASSVKPEQFRKVYEPMFAVSVDTGEK 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
             PLY+WRP STYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAI+ +SA+
Sbjct: 596 ADPLYNWRPMSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAILADSAS 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM + DG+VK GSLARIEPEG
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVLEDGKVKAGSLARIEPEG 715

Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780
           KV RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAG E IVAEGFERIHRTN
Sbjct: 716 KVTRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGAEAIVAEGFERIHRTN 775

Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840
           L+GMGVLPLEFKPGVNRLTL +DGTET+DVIGER+PRA LTLV++RKNGERVEVPVTCRL
Sbjct: 776 LVGMGVLPLEFKPGVNRLTLAIDGTETFDVIGERKPRADLTLVIHRKNGERVEVPVTCRL 835

Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869
           D+ EEVSIYEAGGVL  FAQDFLESS+  A
Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKKAA 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: 2239
Number of extensions: 85
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 BPHYT_RS30145 BPHYT_RS30145 (aconitate hydratase)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.11228.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.11228.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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