GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Billgrantia desiderata SP1

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 WP_086511660.1 BZY95_RS20065 Fe/S-dependent 2-methylisocitrate dehydratase AcnD

Query= SwissProt::Q937N8
         (869 letters)



>NCBI__GCF_002151265.1:WP_086511660.1
          Length = 869

 Score = 1401 bits (3627), Expect = 0.0
 Identities = 700/866 (80%), Positives = 764/866 (88%), Gaps = 3/866 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RKPLPGT+LDYFD R AVE IQPGAYD LPYTSRVLAE LVRRC+P  LTD+L Q
Sbjct: 1   MNTQYRKPLPGTELDYFDVREAVEEIQPGAYDTLPYTSRVLAEQLVRRCEPELLTDALKQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ R+RDLDFPW+PARVVCHDILGQTALVDLAGLRDAIA++GGDP+KVNPVVP QLIVDH
Sbjct: 61  LIERRRDLDFPWYPARVVCHDILGQTALVDLAGLRDAIAEKGGDPSKVNPVVPTQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGG DPDAFAKNRAIEDRRNEDRFHFIDWT+ AFKNVDVIP GNGIMHQINLEKM
Sbjct: 121 SLAVECGGDDPDAFAKNRAIEDRRNEDRFHFIDWTRTAFKNVDVIPAGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVI A +GVAYPDTCVGTDSHTPH+D LGVIAIGVGGLEAE VMLGR S MRLPDIVGV
Sbjct: 181 SPVIQARDGVAYPDTCVGTDSHTPHIDCLGVIAIGVGGLEAETVMLGRPSMMRLPDIVGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTGKRQ GITATDIVLA+TEFLR+E+VVGAYLEF GEGA SLT+GDRATISNM PEYGA
Sbjct: 241 ELTGKRQSGITATDIVLAITEFLRQERVVGAYLEFFGEGADSLTIGDRATISNMTPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF+ID+QT+DYL +TGR  EQ+ LVE YA+T GLWADSLKN +YERVL FDLS+V R
Sbjct: 301 TAAMFYIDQQTLDYLAITGREPEQVALVENYAKTVGLWADSLKNVQYERVLTFDLSTVER 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
           N+AGPSNPH+RLPTSALAERGIAV+L+ A A+E  G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 NLAGPSNPHRRLPTSALAERGIAVNLELALAEEKAGRMPDGAVIIAAITSCTNTSNPRNV 420

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           +AA LLA+ AN  GL RKPWVKSS APGSK   LYLEEA LLP+LEKLGFGIVA+ACTTC
Sbjct: 421 VAAGLLAKKANELGLVRKPWVKSSFAPGSKVARLYLEEAGLLPELEKLGFGIVAYACTTC 480

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGAL P+IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGT+
Sbjct: 481 NGMSGALRPEIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTV 540

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIEKD LG D+ G PV LKD+WPSDEEIDAIV + VKPEQF++VY PMF +     ++
Sbjct: 541 RFDIEKDALGYDKAGNPVTLKDLWPSDEEIDAIVGEYVKPEQFKQVYIPMFNLDEVE-QA 599

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
            SPLYDWRPQSTYIRRPPYWEG +A ER LK +RPLA+L DNITTDHLSPSNAI+L+SAA
Sbjct: 600 KSPLYDWRPQSTYIRRPPYWEGNMARERGLKGMRPLAILPDNITTDHLSPSNAILLDSAA 659

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVD-GQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRAT ANP L NEM   + G+V +GSLARIEPE
Sbjct: 660 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATLANPKLFNEMVRDEKGEVIQGSLARIEPE 719

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV RMWEAIETYM+R QPLI+IAGADYGQGSSRDWAAKGV LAGVE IVAEGFERIHRT
Sbjct: 720 GKVTRMWEAIETYMERGQPLIVIAGADYGQGSSRDWAAKGVALAGVEAIVAEGFERIHRT 779

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NL+GMGV+PL+F+ G  R TL LDGTETYDV G+  P ATLTLV++R  G    VPV CR
Sbjct: 780 NLVGMGVMPLQFQEGTTRHTLKLDGTETYDVEGKPAPGATLTLVIHRAGGNSERVPVLCR 839

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLES 864
           LD+ EEVS+Y AGGVL  FAQDFLES
Sbjct: 840 LDTAEEVSVYSAGGVLQRFAQDFLES 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: 2179
Number of extensions: 80
Number of successful extensions: 4
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: 869
Length adjustment: 42
Effective length of query: 827
Effective length of database: 827
Effective search space:   683929
Effective search space used:   683929
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 WP_086511660.1 BZY95_RS20065 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.24389.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.24389.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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