GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Phaeobacter inhibens BS107

Align Aconitate hydratase A; ACN; 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 GFF1856 PGA1_c18830 aconitate hydratase AcnA

Query= SwissProt::P70920
         (906 letters)



>FitnessBrowser__Phaeo:GFF1856
          Length = 895

 Score = 1095 bits (2831), Expect = 0.0
 Identities = 549/903 (60%), Positives = 690/903 (76%), Gaps = 19/903 (2%)

Query: 5   DSFKCKKTLKVGAKTYVYYSLPTAEKNGLKGISKLPYSMKVLLENLLRNEDGR-SVKKAD 63
           D+ K ++ L  G K+  YYS+P A + GL   +KLP ++KV+LEN+LR EDG  SV   D
Sbjct: 8   DNAKTRRKLSAGGKSISYYSIPAATEAGLGDFAKLPAALKVVLENMLRFEDGGFSVSTDD 67

Query: 64  IVAVSKWLRKKSLE-HEIAFRPARVLMQDFTGVPAVVDLAAMRNAMQKLGGDAEKINPLV 122
           I A ++W         EIA+RPARVLMQDFTGVPAVVDLAAMR+ ++ LGGDA+KINPL 
Sbjct: 68  IKAFAEWGANGGKNPREIAYRPARVLMQDFTGVPAVVDLAAMRDGIKALGGDAQKINPLN 127

Query: 123 PVDLVIDHSVIVNFFGDNKAFAKNVTEEYKQNQERYEFLKWGQAAFSNFSVVPPGTGICH 182
           PVDLVIDHSV+++ FG+ +AF  NV  EY++N ERY+FLKWGQ AF+NF VVPPGTGICH
Sbjct: 128 PVDLVIDHSVMIDEFGNPRAFQMNVDREYERNMERYQFLKWGQGAFNNFRVVPPGTGICH 187

Query: 183 QVNLEYLSQTVWTKKEKMTVGKKTGTFEVAYPDSLVGTDSHTTMVNGLAVLGWGVGGIEA 242
           QVNLEYL+QT+W+ +++       G   VAYPD+LVGTDSHTTMVNG AVLGWGVGGIEA
Sbjct: 188 QVNLEYLAQTIWSDEDQ------NGDM-VAYPDTLVGTDSHTTMVNGAAVLGWGVGGIEA 240

Query: 243 EACMLGQPLSMLLPNVVGFKLKGAMKEGVTATDLVLTVTQMLRKLGVVGKFVEFFGPGLD 302
           EA MLGQP+SML+P V+GF+L GAM EG T TDLVL V +MLR  GVVGKFVEF+G GLD
Sbjct: 241 EAAMLGQPISMLIPEVIGFELTGAMVEGTTGTDLVLKVVEMLRAKGVVGKFVEFYGKGLD 300

Query: 303 HLSVADKATIANMAPEYGATCGFFPVDAAAIDYLKTSGRAAPRVALVQAYAKAQGLFRTA 362
            L +AD+ATIANMAPEYGATCGFFP+D   I YL+ +GR   R+ALV+AYAK  G +R A
Sbjct: 301 TLPLADRATIANMAPEYGATCGFFPIDDETIRYLRNTGRDEDRIALVEAYAKENGFWRDA 360

Query: 363 KSADPVFTETLTLDLADVVPSMAGPKRPEGRIALPSVAEGFSVALANEYKKTEEPAKRFA 422
             A P++T+TL+LD+  +VP+++GPKRP+  +AL      F   +   +K+     K  A
Sbjct: 361 DYA-PIYTDTLSLDMGTIVPAISGPKRPQDYVALTGAKAAFQKEMEETFKRPM--GKEIA 417

Query: 423 VEGKKYEIGHGDVVIAAITSCTNTSNPSVLIGAGLLARNAAAKGLKAKPWVKTSLAPGSQ 482
           V+G+ Y +  G VVIA+ITSCTNTSNP V+IGAGL+AR AAA GL  KPWVKTSLAPGSQ
Sbjct: 418 VKGEDYTMESGKVVIASITSCTNTSNPYVMIGAGLVARKAAALGLDRKPWVKTSLAPGSQ 477

Query: 483 VVAAYLADSGLQAHLDKVGFNLVGFGCTTCIGNSGPLPEEISKSINDNGIVAAAVLSGNR 542
           VV+AYL  + LQ  LDK+GFNLVG+GCTTCIGNSGP+ +E+S +I +  +VA +VLSGNR
Sbjct: 478 VVSAYLEAANLQEDLDKIGFNLVGYGCTTCIGNSGPIQQELSDAIAEGDLVATSVLSGNR 537

Query: 543 NFEGRVSPDVQANYLASPPLVVAHALAGSVTKNLAVEPLGEGKDGKPVYLKDIWPTSKEI 602
           NFEGR+SPDV+ANYLASPPLVVA+ALAG++  +LA +P+ + KDG  VYLKDIWP+ KEI
Sbjct: 538 NFEGRISPDVRANYLASPPLVVAYALAGTMDIDLATDPIAQDKDGNDVYLKDIWPSQKEI 597

Query: 603 NAFMKKFVTASIFKKKYADVFKGDTNWRKIKTVESETYRWNMSSTYVQNPPYFEGMKKEP 662
              ++  VT   F  KYADVFKGD  W+ ++T ++ETY W  +STY+QNPPYF+GM  EP
Sbjct: 598 ADLVEATVTREAFLSKYADVFKGDEKWQAVETTDAETYDWPAASTYIQNPPYFQGMGTEP 657

Query: 663 EPVTDIVEARILAMFGDKITTDHISPAGSIKLTSPAGKYLSEHQVRPADFNQYGTRRGNH 722
             +++I +A+ L + GD +TTDHISPAGS   T+PAG+YL + QV+P +FN YG+RRGNH
Sbjct: 658 GTISNIKDAKPLLILGDMVTTDHISPAGSFATTTPAGQYLLDRQVQPREFNSYGSRRGNH 717

Query: 723 EVMMRGTFANIRIKNFMLKGADGNIPEGGLTKHWPDGEQMSIYDAAMKYQQEQVPLVVFA 782
           E+MMRGTFANIRIKN ML G      EGG TK  PDGEQ S+Y+A+M YQ++ +PLVVF 
Sbjct: 718 EIMMRGTFANIRIKNEMLDGV-----EGGYTK-GPDGEQTSVYEASMAYQEQGIPLVVFG 771

Query: 783 GAEYGNGSSRDWAAKGTRLLGVRAVICQSFERIHRSNLVGMGVLPLTFEEGTSWSSLGLK 842
           G +YG GSSRDWAAKGT LLGV+AVI +SFERIHRSNLVGMGV+P  F  G +  SL L 
Sbjct: 772 GEQYGAGSSRDWAAKGTALLGVKAVIAESFERIHRSNLVGMGVIPFEFTGGDTRKSLNLT 831

Query: 843 GDEKVTLRGLVGDLKPRQKLTAEIVSGDGSLQRVSLLCRIDTLDELDYYRNGGILHYVLR 902
           GDE V++ GL   +KP+++++ +I  GDG+ + ++L CRIDT  E++Y  +GG+LHYVLR
Sbjct: 832 GDETVSIHGL-DTIKPQEEVSCDITYGDGTTKTITLKCRIDTAPEIEYIEHGGVLHYVLR 890

Query: 903 KLA 905
            LA
Sbjct: 891 NLA 893


Lambda     K      H
   0.317    0.134    0.393 

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: 2161
Number of extensions: 112
Number of successful extensions: 8
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: 906
Length of database: 895
Length adjustment: 43
Effective length of query: 863
Effective length of database: 852
Effective search space:   735276
Effective search space used:   735276
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 (21.6 bits)
S2: 56 (26.2 bits)

Align candidate GFF1856 PGA1_c18830 (aconitate hydratase AcnA)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.20357.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20357.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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