GapMind for catabolism of small carbon sources

 

Alignments for a candidate for acn in Herbaspirillum seropedicae SmR1

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 HSERO_RS11425 HSERO_RS11425 aconitate hydratase

Query= SwissProt::Q937N8
         (869 letters)



>FitnessBrowser__HerbieS:HSERO_RS11425
          Length = 873

 Score = 1476 bits (3821), Expect = 0.0
 Identities = 739/867 (85%), Positives = 790/867 (91%), Gaps = 7/867 (0%)

Query: 1   MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60
           MN+  RK LPGT+LDYFDARAAVEAI+PGA+D LPYTSRVLAENLVRRCDPATLTDSL Q
Sbjct: 1   MNTQYRKQLPGTRLDYFDARAAVEAIRPGAWDTLPYTSRVLAENLVRRCDPATLTDSLRQ 60

Query: 61  LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120
           L+ RKR+LDFPWFPARVVCHDILGQTALVDLAGLRDAIAD GGDPAKVNPVVPVQLIVDH
Sbjct: 61  LIERKRELDFPWFPARVVCHDILGQTALVDLAGLRDAIADMGGDPAKVNPVVPVQLIVDH 120

Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180
           SLAVECGG DP AF KNRAIEDRRNEDRFHFIDWTK AF+NVDVIPPGNGIMHQINLEKM
Sbjct: 121 SLAVECGGDDPQAFVKNRAIEDRRNEDRFHFIDWTKLAFENVDVIPPGNGIMHQINLEKM 180

Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240
           SPVIHA +GVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDI+GV
Sbjct: 181 SPVIHAKDGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGV 240

Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300
           ELTG+RQPGITATDIVL+LTEFLRK+KVVGAYLEF G+GA+SLTLGDRATISNMAPEYGA
Sbjct: 241 ELTGRRQPGITATDIVLSLTEFLRKQKVVGAYLEFYGDGAASLTLGDRATISNMAPEYGA 300

Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360
           TAAMF ID+QTIDYL+LTGR DEQ+KLVETYA+ AGLW+D+L   EYERVL+FDLS+VVR
Sbjct: 301 TAAMFSIDQQTIDYLKLTGREDEQVKLVETYAKEAGLWSDTLAKVEYERVLRFDLSTVVR 360

Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420
            +AGPSNPHKRLP S LA +GIA        +   G MPDGAVIIAAITSCTNTSNPRNV
Sbjct: 361 TLAGPSNPHKRLPVSELAAQGIA-----GKVENEPGKMPDGAVIIAAITSCTNTSNPRNV 415

Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480
           IAA LLARNAN  GLARKPWVKSSLAPGSKAVELYLEEA L  DLEKLGFGIVAFACTTC
Sbjct: 416 IAAGLLARNANRLGLARKPWVKSSLAPGSKAVELYLEEAGLTADLEKLGFGIVAFACTTC 475

Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540
           NGMSGALDPKIQQEIIDRDLY+TAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI
Sbjct: 476 NGMSGALDPKIQQEIIDRDLYSTAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535

Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600
           RFDIE+DVLG   +G+ + LKDIWPSDEEIDA+V  +VKP+QFR VY PMFA      +S
Sbjct: 536 RFDIEQDVLGVTAEGREIRLKDIWPSDEEIDAVVTAAVKPQQFRNVYTPMFAARVDRSQS 595

Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660
           VSPLYDWRPQSTYIRRPPYWEGALAGERTL  +RPLAVLGDNITTDHLSPSNAI+L+SAA
Sbjct: 596 VSPLYDWRPQSTYIRRPPYWEGALAGERTLSGMRPLAVLGDNITTDHLSPSNAILLDSAA 655

Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMA-VVDGQVKKGSLARIEPE 719
           GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM    DG V++GSLAR+EPE
Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVKKADGSVQQGSLARLEPE 715

Query: 720 GKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRT 779
           GKV+RMWE IETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRT
Sbjct: 716 GKVMRMWETIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRT 775

Query: 780 NLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCR 839
           NLIGMGVLPLEFK G NR T  +DGTETYDVIG+R+PRA LTLV++RKNGERVEVPVTCR
Sbjct: 776 NLIGMGVLPLEFKAGENRNTYAIDGTETYDVIGQRRPRADLTLVIHRKNGERVEVPVTCR 835

Query: 840 LDSDEEVSIYEAGGVL-HFAQDFLESS 865
           LD+ EEVSIYEAGGVL  FAQDFLE+S
Sbjct: 836 LDTAEEVSIYEAGGVLQRFAQDFLEAS 862


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: 2276
Number of extensions: 102
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: 873
Length adjustment: 42
Effective length of query: 827
Effective length of database: 831
Effective search space:   687237
Effective search space used:   687237
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 HSERO_RS11425 HSERO_RS11425 (aconitate hydratase)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))

Software error:

../bin/blast/fastacmd -i /tmp/list.29089.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29089.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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