GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Marinobacter adhaerens HP15

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 GFF1973 HP15_1930 aconitate hydratase 1

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__Marino:GFF1973
          Length = 865

 Score = 1387 bits (3590), Expect = 0.0
 Identities = 692/869 (79%), Positives = 757/869 (87%), Gaps = 7/869 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RK LPGT LDYFD R AVE IQ GAYDKLPYTS++LAE LVRRCDP  LTDSL Q
Sbjct: 1   MNTEYRKSLPGTDLDYFDTRQAVEDIQAGAYDKLPYTSKILAEQLVRRCDPEVLTDSLKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKRDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDPAKVNPVVP QLIVDH
Sbjct: 61  LIERKRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPAKVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVE  GF+ DAF KNR IEDRRN+DRFHFI+WTK AFKNVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVEHAGFEKDAFEKNREIEDRRNDDRFHFINWTKTAFKNVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPV+   +GVA+PDTCVGTDSHTP VDALGVI++GVGGLEAE+VMLGRAS MRLPDIVGV
Sbjct: 181 SPVVQNRDGVAFPDTCVGTDSHTPMVDALGVISVGVGGLEAESVMLGRASMMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGK QPGIT+TD+VLA+TEFLRKEKVVGAYLEF GEGA SL++GDRATISNM PEYGA
Sbjct: 241 ELTGKLQPGITSTDMVLAITEFLRKEKVVGAYLEFYGEGADSLSVGDRATISNMTPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+ID QTIDYL+LTGR D+Q+ LVE +A+  GLWADS+KNAEYERVLKFDLS V R
Sbjct: 301 TAAMFYIDGQTIDYLKLTGREDDQVALVEKFAKETGLWADSMKNAEYERVLKFDLSKVTR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            +AGPSNPH  LPTS LA RGIA        ++ EG MPDGA IIAAITSCTNTSNPRN+
Sbjct: 361 TLAGPSNPHAHLPTSELAARGIA-----GEWEQEEGKMPDGACIIAAITSCTNTSNPRNM 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           +AA L+ARNAN  GL RKPWVK+SLAPGSK V++YLEEA LLP+LE+LGFG+VAFACTTC
Sbjct: 416 VAAGLIARNANKLGLTRKPWVKTSLAPGSKTVKMYLEEAKLLPELEQLGFGVVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDPKI QEI+DRDL++TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIAQEIMDRDLFSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKD LG DQDG PV LKDIWP D EIDAIV  SVKPEQFR  Y PMF IT  +  +
Sbjct: 536 RFDIEKDALGYDQDGNPVTLKDIWPDDAEIDAIVKSSVKPEQFRSTYIPMFDITRDAQAN 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
            +PLY WRPQSTYIRRPPYWEG + GE+TLK +RPLAVL DNITTDHLSPSNAIM+NSAA
Sbjct: 596 TNPLYKWRPQSTYIRRPPYWEGGMVGEKTLKGMRPLAVLPDNITTDHLSPSNAIMMNSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYL +MG+PEEDFNSYATHRGDHLTAQRATFANP L NEM    +G VK+GSLARIEPE
Sbjct: 656 GEYLHKMGVPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVRDENGNVKQGSLARIEPE 715

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKVVRMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGV LAGVE IVAEGFERIHRT
Sbjct: 716 GKVVRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRT 775

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NLIGMGV+PL+F+ G  R TLG+DGTETYDV G   PRA LTLV++RKNG    +PV CR
Sbjct: 776 NLIGMGVMPLQFEEGTTRKTLGIDGTETYDVEGTPAPRAELTLVIHRKNGSTERIPVVCR 835

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESSRA 867
           LD+ EEVSIY AGGVL  FA+DFL+S  A
Sbjct: 836 LDTAEEVSIYSAGGVLQRFAEDFLQSEGA 864


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: 2137
Number of extensions: 83
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 GFF1973 HP15_1930 (aconitate hydratase 1)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.18587.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18587.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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