GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Marinobacter adhaerens HP15

Align 2-methylcitrate dehydratase (2-methyl-trans-aconitate forming) (EC 4.2.1.117) (characterized)
to candidate GFF1973 HP15_1930 aconitate hydratase 1

Query= BRENDA::Q8EJW3
         (867 letters)



>FitnessBrowser__Marino:GFF1973
          Length = 865

 Score = 1402 bits (3628), Expect = 0.0
 Identities = 687/861 (79%), Positives = 765/861 (88%), Gaps = 1/861 (0%)

Query: 5   MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64
           MNT+YRK LPGT LDYFDTR+A+E I  GAY KLPYTS++LAE LVRRC+PE+LT SLKQ
Sbjct: 1   MNTEYRKSLPGTDLDYFDTRQAVEDIQAGAYDKLPYTSKILAEQLVRRCDPEVLTDSLKQ 60

Query: 65  IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124
           +IE K++LDFPW+PARVVCHDILGQTALVDLAGLRDAIA KGGDPA+VNPVVPTQLIVDH
Sbjct: 61  LIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQLIVDH 120

Query: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184
           SLAVE+ GF+KDAF KNR IEDRRN+DRFHFINWT+ AFKN+DVIP GNGIMHQINLE+M
Sbjct: 121 SLAVEHAGFEKDAFEKNREIEDRRNDDRFHFINWTKTAFKNVDVIPPGNGIMHQINLEKM 180

Query: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244
           SPV+  R+GVAFPDT VGTDSHTP VDALGVI++GVGGLEAESVMLGRAS MRLPDI+GV
Sbjct: 181 SPVVQNRDGVAFPDTCVGTDSHTPMVDALGVISVGVGGLEAESVMLGRASMMRLPDIVGV 240

Query: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304
           ELTGK QPGIT+TD+VLA+TEFLR +KVV +YLEF+GEGA++L++GDRATISNMTPE+GA
Sbjct: 241 ELTGKLQPGITSTDMVLAITEFLRKEKVVGAYLEFYGEGADSLSVGDRATISNMTPEYGA 300

Query: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364
           TAAMFYID QT+DYL LTGRE +QV LVE +AK  GLW+D +K A Y R L FDLS V R
Sbjct: 301 TAAMFYIDGQTIDYLKLTGREDDQVALVEKFAKETGLWADSMKNAEYERVLKFDLSKVTR 360

Query: 365 TIAGPSNPHARVPTSELAARGISGEVENEPGLMPDGAVIIAAITSCTNTSNPRNVIAAGL 424
           T+AGPSNPHA +PTSELAARGI+GE E E G MPDGA IIAAITSCTNTSNPRN++AAGL
Sbjct: 361 TLAGPSNPHAHLPTSELAARGIAGEWEQEEGKMPDGACIIAAITSCTNTSNPRNMVAAGL 420

Query: 425 LARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTCNGMSG 484
           +ARNAN  GLTRKPWVKTSLAPGSK V++YLEEA LLPELE LGFG+V FACTTCNGMSG
Sbjct: 421 IARNANKLGLTRKPWVKTSLAPGSKTVKMYLEEAKLLPELEQLGFGVVAFACTTCNGMSG 480

Query: 485 ALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 544
           ALDP I QE++DRDL++TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE
Sbjct: 481 ALDPKIAQEIMDRDLFSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIE 540

Query: 545 KDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDKVSPLY 604
           KD LG D+DG PV L +IWP DAEIDA++ +SVKPEQFR  Y PMFD++ D     +PLY
Sbjct: 541 KDALGYDQDGNPVTLKDIWPDDAEIDAIVKSSVKPEQFRSTYIPMFDITRDAQANTNPLY 600

Query: 605 DWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAAGEYLH 664
            WRPQSTYIRRPPYWEG + GE+TLKGMRPLAVL DNITTDHLSPSNAIMM+SAAGEYLH
Sbjct: 601 KWRPQSTYIRRPPYWEGGMVGEKTLKGMRPLAVLPDNITTDHLSPSNAIMMNSAAGEYLH 660

Query: 665 KMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMA-IVDGKVKQGSLARIEPEGIVTR 723
           KMG+PEEDFNSYATHRGDHLTAQRATFANPKL NEM    +G VKQGSLARIEPEG V R
Sbjct: 661 KMGVPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRDENGNVKQGSLARIEPEGKVVR 720

Query: 724 MWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGM 783
           MWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGV LAGVEAIVAEGFERIHRTNL+GM
Sbjct: 721 MWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRTNLIGM 780

Query: 784 GVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAE 843
           GV+PL+F+ G  R T GIDGTE +DV G+ APRA+LT++I RKNG    +PV CRLDTAE
Sbjct: 781 GVMPLQFEEGTTRKTLGIDGTETYDVEGTPAPRAELTLVIHRKNGSTERIPVVCRLDTAE 840

Query: 844 EVSIYEAGGVLQRFAQDFLES 864
           EVSIY AGGVLQRFA+DFL+S
Sbjct: 841 EVSIYSAGGVLQRFAEDFLQS 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: 2211
Number of extensions: 93
Number of successful extensions: 2
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: 865
Length adjustment: 42
Effective length of query: 825
Effective length of database: 823
Effective search space:   678975
Effective search space used:   678975
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 GFF1973 HP15_1930 (aconitate hydratase 1)
to HMM TIGR01341 (acnA: aconitate hydratase 1 (EC 4.2.1.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.30136.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30136.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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