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 AO353_00890 AO353_00890 Fe/S-dependent 2-methylisocitrate dehydratase AcnD
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__pseudo3_N2E3:AO353_00890 Length = 864 Score = 1449 bits (3752), Expect = 0.0 Identities = 729/868 (83%), Positives = 782/868 (90%), Gaps = 6/868 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RK LPG+ LDYFD RAAVEAIQPGAYD LPYTSRVLAENLVRRCDPATLT+SL Q Sbjct: 1 MNTDFRKSLPGSHLDYFDTRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 + RKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDPA+VNPVVP QLIVDH Sbjct: 61 FIERKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVE GGFDP+AF KNRAIEDRRNEDRFHFI+WTK+AFKNVDVIPPGNGIMHQINLEKM Sbjct: 121 SLAVERGGFDPEAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVI +GVA+PDTCVGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRASWMRLP+ VGV Sbjct: 181 SPVIQVRDGVAFPDTCVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK QPGITATD+VLALTEFLRK+KVVGA+LEF GEGAS+LTLGDRATISNMAPEYGA Sbjct: 241 ELTGKLQPGITATDMVLALTEFLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGA 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+ID+QTIDYL+LTGR DEQ++LVE YA+T GLWADSLK A+YER L FDLSSVVR Sbjct: 301 TAAMFYIDQQTIDYLKLTGREDEQVQLVENYAKTTGLWADSLKGAQYERGLTFDLSSVVR 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 NMAGPSNPH R+ TS LA +GI+ D + G MPDGAVIIAAITSCTNTSNPRNV Sbjct: 361 NMAGPSNPHARVATSDLAAQGISGQWD-----DVPGQMPDGAVIIAAITSCTNTSNPRNV 415 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 IAA LLARNAN GL RKPWVKSSLAPGSK V LYL+EA L +LE+LGFG+VAFACTTC Sbjct: 416 IAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAGLTSELEQLGFGVVAFACTTC 475 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGALDP IQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI Sbjct: 476 NGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKDVLG DGK + LKDIWPSDEEIDA+V SVKPEQFR+VY PMFAI +G Sbjct: 536 RFDIEKDVLGLSADGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPMFAIHEDTGPK 595 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 V PLYDWR STYIRRPPYWEGALAG R LK +RPLAVL DNITTDHLSPSNAIML+SAA Sbjct: 596 VKPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIMLDSAA 655 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720 GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANP L NEM +G+VK+GSLAR+EPEG Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 715 Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780 +V+RMWEAIETYM+RKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE I AEGFERIHRTN Sbjct: 716 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTN 775 Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840 L+GMGVLPLEFKPG +R TLG+DGTET+DVIGER PRATLTLV+ RKNGE+V VPVTCRL Sbjct: 776 LVGMGVLPLEFKPGTDRKTLGIDGTETFDVIGERTPRATLTLVITRKNGEQVSVPVTCRL 835 Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRA 867 D+ EEVSIYEAGGVL FAQDFLES+ A Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESAVA 863 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: 2203 Number of extensions: 79 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: 864 Length adjustment: 42 Effective length of query: 827 Effective length of database: 822 Effective search space: 679794 Effective search space used: 679794 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 AO353_00890 AO353_00890 (Fe/S-dependent 2-methylisocitrate dehydratase AcnD)
to HMM TIGR02333 (acnD: 2-methylisocitrate dehydratase, Fe/S-dependent (EC 4.2.1.99))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR02333.hmm # target sequence database: /tmp/gapView.5879.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR02333 [M=858] Accession: TIGR02333 Description: 2met_isocit_dHY: 2-methylisocitrate dehydratase, Fe/S-dependent Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 0 1840.6 0.0 0 1840.4 0.0 1.0 1 lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 AO353_00890 Fe/S-dependent 2-met Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 AO353_00890 Fe/S-dependent 2-methylisocitrate dehydratase AcnD # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1840.4 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00 Alignments for each domain: == domain 1 score: 1840.4 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkr 65 nt +rk+lpg++ldyfd+raaveai+pgayd+lpytsrvlaenlvrr+dp+tl++slkq+ierkr lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 2 NTDFRKSLPGSHLDYFDTRAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPATLTESLKQFIERKR 66 799************************************************************** PP TIGR02333 66 eldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdp 130 +ldfpw+parvvchdilgqtalvdlaglrdaia +ggdpaqvnpvv+tqlivdhslave ggfdp lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 67 DLDFPWFPARVVCHDILGQTALVDLAGLRDAIALQGGDPAQVNPVVPTQLIVDHSLAVERGGFDP 131 ***************************************************************** PP TIGR02333 131 dafeknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtl 195 +afeknraiedrrnedrfhfinwtkkafknvdvip+gngimhqinlekmspv+qv++gvafpdt+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 132 EAFEKNRAIEDRRNEDRFHFINWTKKAFKNVDVIPPGNGIMHQINLEKMSPVIQVRDGVAFPDTC 196 ***************************************************************** PP TIGR02333 196 vgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalte 260 vgtdshtphvdalgviaigvggleae+vmlgras+mrlp+ vgveltgk qpgitatd+vlalte lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 197 VGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASWMRLPESVGVELTGKLQPGITATDMVLALTE 261 ***************************************************************** PP TIGR02333 261 flrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvk 325 flrk+kvv+a+leffgega altlgdratisnm+peygataamf+id+qtidylkltgre+eqv+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 262 FLRKQKVVGAWLEFFGEGASALTLGDRATISNMAPEYGATAAMFYIDQQTIDYLKLTGREDEQVQ 326 ***************************************************************** PP TIGR02333 326 lvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeae 390 lve yak++glwadslk a+yer l+fdlssvvrn+agpsnphar+atsdlaa+gi++++++++ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 327 LVENYAKTTGLWADSLKGAQYERGLTFDLSSVVRNMAGPSNPHARVATSDLAAQGISGQWDDVP- 390 ****************************************************************. PP TIGR02333 391 glmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeag 455 g+mpdgaviiaaitsctntsnprnv+aagllarnanklgl+rkpwvksslapgsk+v lyl+eag lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 391 GQMPDGAVIIAAITSCTNTSNPRNVIAAGLLARNANKLGLTRKPWVKSSLAPGSKTVALYLDEAG 455 ***************************************************************** PP TIGR02333 456 llkeleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqafl 520 l +ele+lgfg+vafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqafl lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 456 LTSELEQLGFGVVAFACTTCNGMSGALDPVIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFL 520 ***************************************************************** PP TIGR02333 521 aspplvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipm 585 aspplvvayaiagtirfdiekdvlg+ adgkeirlkdiwpsdeeidavv+a+vkpeqfr+vyipm lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 521 ASPPLVVAYAIAGTIRFDIEKDVLGLSADGKEIRLKDIWPSDEEIDAVVKASVKPEQFRQVYIPM 585 ***************************************************************** PP TIGR02333 586 fdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnail 649 f+++ d++ kv plydwr mstyirrppywegalag r lkgmrplavl+dnittdhlspsnai+ lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 586 FAIHeDTGPKVKPLYDWREMSTYIRRPPYWEGALAGARPLKGMRPLAVLPDNITTDHLSPSNAIM 650 ***989*********************************************************** PP TIGR02333 650 ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepeg 714 ldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemv+e+gkvkqgslar+epeg lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 651 LDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPKLFNEMVQENGKVKQGSLARVEPEG 715 ***************************************************************** PP TIGR02333 715 kvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmg 779 +v+rmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveai aegferihrtnlvgmg lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 716 QVMRMWEAIETYMERKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLVGMG 780 ***************************************************************** PP TIGR02333 780 vlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvye 844 vlplefkpgt+rktl++dgte++dv+ge+tpra+ltlv+trknge++ vpvtcrldtaeevs+ye lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 781 VLPLEFKPGTDRKTLGIDGTETFDVIGERTPRATLTLVITRKNGEQVSVPVTCRLDTAEEVSIYE 845 ***************************************************************** PP TIGR02333 845 aggvlqrfaqdfle 858 aggvlqrfaqdfle lcl|FitnessBrowser__pseudo3_N2E3:AO353_00890 846 AGGVLQRFAQDFLE 859 ************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (864 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.06u 0.03s 00:00:00.09 Elapsed: 00:00:00.08 # Mc/sec: 8.67 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory