GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Pseudomonas simiae WCS417

Align Aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF1478 PS417_07515 aconitate hydratase

Query= reanno::Marino:GFF3491
         (919 letters)



>FitnessBrowser__WCS417:GFF1478
          Length = 913

 Score = 1325 bits (3428), Expect = 0.0
 Identities = 657/912 (72%), Positives = 752/912 (82%), Gaps = 5/912 (0%)

Query: 7   SKDSLNTLSSLDAGGKTFHYYSLPKAADTLGDLNRLPFSLKVLMENLLRNEDGTTVDRSH 66
           S DSL TL +L+   KT+HY+SLP+AA +LGDL++LP SLKVL+ENLLR ED  TV  + 
Sbjct: 3   SLDSLRTLKTLEIDSKTYHYFSLPEAAKSLGDLDKLPMSLKVLLENLLRWEDNKTVTGAD 62

Query: 67  IDAMVQWMKDRHSDTEIQFRPARVLMQDFTGVPGVVDLAAMREAVQAAGKDPAMINPLSP 126
           + A+  W+K+R SD EIQ+RPARVLMQDFTGVP VVDLAAMR AV  AG DP  INPLSP
Sbjct: 63  LKAIAAWLKERQSDREIQYRPARVLMQDFTGVPAVVDLAAMRAAVAKAGGDPQRINPLSP 122

Query: 127 VDLVIDHSVMVDKFGDASSFKDNVAIEMERNQERYEFLRWGQQAFDNFRVVPPGTGICHQ 186
           VDLVIDHSVMVDKFG   +F+ NV IEM+RN ERY FLRWGQ AFDNF VVPPGTGICHQ
Sbjct: 123 VDLVIDHSVMVDKFGTTGAFEQNVDIEMQRNGERYAFLRWGQSAFDNFSVVPPGTGICHQ 182

Query: 187 VNLEYLGKTVWQKDQDGKTIAYPDTLVGTDSHTTMINGLGILGWGVGGIEAEAAMLGQPV 246
           VNLEYLG+TVW KD+DG+T A+PDTLVGTDSHTTMINGLG+LGWGVGGIEAEAAMLGQPV
Sbjct: 183 VNLEYLGRTVWTKDEDGRTYAFPDTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPV 242

Query: 247 SMLIPEVVGFKITGKLREGITATDLVLTVTEMLRKKGVVGKFVEFYGDGLKDMPVADRAT 306
           SMLIPEV+GFK+TGKL+EGITATDLVLTVT+MLRKKGVVGKFVEFYGDGL D+P+ADRAT
Sbjct: 243 SMLIPEVIGFKLTGKLKEGITATDLVLTVTQMLRKKGVVGKFVEFYGDGLADLPLADRAT 302

Query: 307 IANMAPEYGATCGFFPVDEQTIKYMRLTGREEEQLELVEAYAKAQGLWREPGHEPVYTDN 366
           IANMAPEYGATCGFFPVDE T+ Y+RL+GR  E ++LVEAY KAQGLWR  G EPV+TD+
Sbjct: 303 IANMAPEYGATCGFFPVDEVTLDYLRLSGRPTETVKLVEAYTKAQGLWRNAGQEPVFTDS 362

Query: 367 LELDMGEVEASLAGPKRPQDRVALKNMKSSFELLMETAEGPAENREANLESEGGQ-TAVG 425
           L LDMG VEASLAGPKRPQDRVAL N+  +F   ++    P    E  LESEGG   AVG
Sbjct: 363 LALDMGSVEASLAGPKRPQDRVALPNVGQAFSDFLDLQFKPTNKEEGRLESEGGGGVAVG 422

Query: 426 VDDSYKHHASQPLEMNGEKSRLDPGAVVIAAITSCTNTSNPSVMMAAGLIAQKAVQKGLS 485
             D          E +G+  RL  GAVVIAAITSCTNTSNPSVMMAAGL+A+KAV+KGL+
Sbjct: 423 NADLV---GETDYEYDGQTYRLKNGAVVIAAITSCTNTSNPSVMMAAGLLAKKAVEKGLT 479

Query: 486 TKPWVKTSLAPGSKVVTDYLKVGGFQDDLDKLGFNLVGYGCTTCIGNSGPLPDAVEKAIS 545
            KPWVKTSLAPGSKVVTDY K  G    LDKLGF+LVGYGCTTCIGNSGPLP+ +EKAI 
Sbjct: 480 RKPWVKTSLAPGSKVVTDYYKAAGLTQYLDKLGFDLVGYGCTTCIGNSGPLPEPIEKAIQ 539

Query: 546 DGDLTVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGNVRLDLSQDPLGNDKDGN 605
             DL VASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAG VR+D+S +PLGND+ G+
Sbjct: 540 KADLAVASVLSGNRNFEGRVHPLVKTNWLASPPLVVAYALAGTVRIDISSEPLGNDQHGH 599

Query: 606 PVYLKDLWPSQQEIAEAVEKVKTDMFRKEYAEVFDGDATWKSIKVPESKVYEWSDKSTYI 665
           PVYLKD+WP+ QEIA+AV +V T MF KEYAEVF GD  W++I+VP++  Y W   STYI
Sbjct: 600 PVYLKDIWPTSQEIADAVAQVTTGMFHKEYAEVFAGDEQWQAIEVPQAATYVWQKDSTYI 659

Query: 666 QHPPFFEGLKEEPDAIDDIKDANILALLGDSVTTDHISPAGSFKPDTPAGKYLQEHGVEP 725
           QHPPFF+ +      I D+K AN+LALLGDSVTTDHISPAG+ K D+PAG+YL+E GVEP
Sbjct: 660 QHPPFFDDIAGPLPVIKDVKGANVLALLGDSVTTDHISPAGNIKTDSPAGRYLREQGVEP 719

Query: 726 KDFNSYGSRRGNHEVMMRGTFANVRIRNEMLDGVEGGYTKFVPTGEQMAIYDAAMKYQEK 785
           +DFNSYGSRRGNHEVMMRGTFAN+RIRNEML G EGG T ++PTGE+M IYDA+MKYQ  
Sbjct: 720 RDFNSYGSRRGNHEVMMRGTFANIRIRNEMLGGEEGGNTLYIPTGEKMPIYDASMKYQAS 779

Query: 786 GTPLVVIAGKEYGTGSSRDWAAKGTRLLGVKAVVAESYERIHRSNLIGMGVMPLQFPEGT 845
           GTPLVV+AG+EYGTGSSRDWAAKGT LLGVKAV+AES+ERIHRSNL+GMGV+PLQF    
Sbjct: 780 GTPLVVVAGQEYGTGSSRDWAAKGTNLLGVKAVIAESFERIHRSNLVGMGVLPLQFKLDQ 839

Query: 846 DRKSLKLTGEETISIEGLSG-EIKPGQTLKMTVKYKDGSTETCELKSRIDTANEAVYFKH 904
           +RKSLKLTG+E I I GL+  EI P   L + +  +DGS+E  E+  RIDT NE  YFK 
Sbjct: 840 NRKSLKLTGKEKIDILGLTDVEIVPRMNLTLVITREDGSSEKVEVLCRIDTLNEVEYFKS 899

Query: 905 GGILHYVVREML 916
           GGILHYV+R+++
Sbjct: 900 GGILHYVLRQLI 911


Lambda     K      H
   0.315    0.134    0.390 

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: 2370
Number of extensions: 100
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: 919
Length of database: 913
Length adjustment: 43
Effective length of query: 876
Effective length of database: 870
Effective search space:   762120
Effective search space used:   762120
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: 42 (22.0 bits)
S2: 57 (26.6 bits)

Align candidate GFF1478 PS417_07515 (aconitate hydratase)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.19829.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19829.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.