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 N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming)
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__Dyella79:N515DRAFT_0029 Length = 869 Score = 1511 bits (3912), Expect = 0.0 Identities = 756/873 (86%), Positives = 808/873 (92%), Gaps = 11/873 (1%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ R+ L GT LDYFDARAAVEAIQPGAYD LPYTSRVLAENLVRRCDPA L +SL Q Sbjct: 1 MNTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 ++ RKR+ DFPWFPARVVCHDILGQTALVDLAGLRDAIAD+GGDPAKVNPVVPVQLIVDH Sbjct: 61 IIERKRERDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVECGGFDP+AFA+NRAIEDRRNEDRFHFI+WT+QAF+NVDVIPPGNGIMHQINLEKM Sbjct: 121 SLAVECGGFDPNAFARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKM 180 Query: 181 SPVIHADN-----GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 235 SPVI + GVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP Sbjct: 181 SPVIQVQHDDQGKGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLP 240 Query: 236 DIVGVELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMA 295 DI+GVELTGKRQPGITATDIVLALTEFLR+EKVVGAYLEFRGEGA+SLTLGDRATISNMA Sbjct: 241 DIIGVELTGKRQPGITATDIVLALTEFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMA 300 Query: 296 PEYGATAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDL 355 PEYGATAAMFFID+QT+DYLRLTGR+DEQ++LVETYA+ AGLWAD+L A+YER L FDL Sbjct: 301 PEYGATAAMFFIDDQTLDYLRLTGRSDEQVRLVETYAKAAGLWADTLAAAQYERTLSFDL 360 Query: 356 SSVVRNMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTS 415 SSVVRNMAGPSNPHKRLPT+ LA RGIA QE G MPDGAVIIAAITSCTNTS Sbjct: 361 SSVVRNMAGPSNPHKRLPTADLAARGIA-----GQWQEQPGQMPDGAVIIAAITSCTNTS 415 Query: 416 NPRNVIAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAF 475 NPRNVIAAALLARNANARGL RKPWVKSSLAPGSKAVELYL+EANLLP+LEKLGFGIVAF Sbjct: 416 NPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLLPELEKLGFGIVAF 475 Query: 476 ACTTCNGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535 ACTTCNGMSGALDP IQQEI++RDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA Sbjct: 476 ACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYA 535 Query: 536 IAGTIRFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITA 595 IAGTIRFDIE+DVLG D +G+PV LKDIWPSDEEID IVA SVKPEQFRKVYEPMFA T Sbjct: 536 IAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFARTG 595 Query: 596 ASGESVSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIM 655 SG +PLYDWR QSTYIRRPPYWEGALAGERTLK +R LAVLGDNITTDHLSPSNAIM Sbjct: 596 RSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIM 655 Query: 656 LNSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLAR 715 +SAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTL+NEMAVVDG+VKKGSLAR Sbjct: 656 ADSAAGEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLAR 715 Query: 716 IEPEGKVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFER 775 +EPEGKV+RMWEAIETYM+RKQPLI+IAGADYGQGSSRDWAAKGVRLAGVE I AEGFER Sbjct: 716 VEPEGKVMRMWEAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFER 775 Query: 776 IHRTNLIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVP 835 IHRTNLIGMGVLPLEF+PG +R TLG+DGTET+DV G R PRA LTLV++R+NGERVEVP Sbjct: 776 IHRTNLIGMGVLPLEFQPGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVP 835 Query: 836 VTCRLDSDEEVSIYEAGGVL-HFAQDFLESSRA 867 VTCRLD+ EEVSIYEAGGVL FAQDFLE+++A Sbjct: 836 VTCRLDTAEEVSIYEAGGVLQRFAQDFLEAAQA 868 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: 2239 Number of extensions: 86 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 N515DRAFT_0029 N515DRAFT_0029 (aconitase /2-methylcitrate dehydratase (trans-methylaconitate-forming))
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.18939.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 1793.1 0.2 0 1792.9 0.2 1.0 1 lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 N515DRAFT_0029 aconitase /2-meth Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 N515DRAFT_0029 aconitase /2-methylcitrate dehydratase (trans-methylaconi # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1792.9 0.2 0 0 1 858 [] 2 864 .. 2 864 .. 0.99 Alignments for each domain: == domain 1 score: 1792.9 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkre 66 nt yr++l gt+ldyfdaraaveai+pgayd+lpytsrvlaenlvrr+dp+ l +slkq+ierkre lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 2 NTVYRQSLLGTSLDYFDARAAVEAIQPGAYDTLPYTSRVLAENLVRRCDPAILAESLKQIIERKRE 67 899*************************************************************** PP TIGR02333 67 ldfpwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpda 132 dfpw+parvvchdilgqtalvdlaglrdaia++ggdpa+vnpvv++qlivdhslave+ggfdp+a lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 68 RDFPWFPARVVCHDILGQTALVDLAGLRDAIADRGGDPAKVNPVVPVQLIVDHSLAVECGGFDPNA 133 ****************************************************************** PP TIGR02333 133 feknraiedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvk.....egvafpd 193 f++nraiedrrnedrfhfi+wt++af+nvdvip+gngimhqinlekmspv+qv+ +gva+pd lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 134 FARNRAIEDRRNEDRFHFIEWTRQAFENVDVIPPGNGIMHQINLEKMSPVIQVQhddqgKGVAYPD 199 ****************************************************974444469***** PP TIGR02333 194 tlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalt 259 t+vgtdshtphvdalgviaigvggleae+vmlgras+mrlpdi+gveltgkrqpgitatdivlalt lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 200 TCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIIGVELTGKRQPGITATDIVLALT 265 ****************************************************************** PP TIGR02333 260 eflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvk 325 eflr+ekvv+aylef gega +ltlgdratisnm+peygataamf+id+qt+dyl+ltgr +eqv+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 266 EFLRQEKVVGAYLEFRGEGAASLTLGDRATISNMAPEYGATAAMFFIDDQTLDYLRLTGRSDEQVR 331 ****************************************************************** PP TIGR02333 326 lvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeg 391 lvetyakaaglwad+l a+yer+l+fdlssvvrn+agpsnph+rl+t+dlaa+gia++++e++ g lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 332 LVETYAKAAGLWADTLAAAQYERTLSFDLSSVVRNMAGPSNPHKRLPTADLAARGIAGQWQEQP-G 396 ****************************************************************.* PP TIGR02333 392 lmpdgaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagll 457 +mpdgaviiaaitsctntsnprnv+aa+llarnan++gl rkpwvksslapgsk+v+lyl+ea+ll lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 397 QMPDGAVIIAAITSCTNTSNPRNVIAAALLARNANARGLVRKPWVKSSLAPGSKAVELYLKEANLL 462 ****************************************************************** PP TIGR02333 458 keleklgfgivafacttcngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflasp 523 +eleklgfgivafacttcngmsgaldp+iqqei++rdlyatavlsgnrnfdgrihpyakqaflasp lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 463 PELEKLGFGIVAFACTTCNGMSGALDPAIQQEIVERDLYATAVLSGNRNFDGRIHPYAKQAFLASP 528 ****************************************************************** PP TIGR02333 524 plvvayaiagtirfdiekdvlgvdadgkeirlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle 589 plvvayaiagtirfdie+dvlg+da+g+++ lkdiwpsdeeid++vaa+vkpeqfrkvy+pmf+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 529 PLVVAYAIAGTIRFDIEQDVLGIDANGQPVTLKDIWPSDEEIDTIVAASVKPEQFRKVYEPMFART 594 ***************************************************************987 PP TIGR02333 590 .daqkkvsplydwrpmstyirrppywegalagertlkgmrplavlgdnittdhlspsnailldsaa 654 ++++++plydwr +styirrppywegalagertlkgmr lavlgdnittdhlspsnai++dsaa lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 595 gRSGTRAAPLYDWRAQSTYIRRPPYWEGALAGERTLKGMRALAVLGDNITTDHLSPSNAIMADSAA 660 6999************************************************************** PP TIGR02333 655 geylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslariepegkvtrmw 720 geyla+mglpeedfnsyathrgdhltaqratfanp l nem+ +dg+vk+gslar+epegkv+rmw lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLLNEMAVVDGEVKKGSLARVEPEGKVMRMW 726 ****************************************************************** PP TIGR02333 721 eaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefk 786 eaietym+rkqpli+iagadygqgssrdwaakgvrlagveai aegferihrtnl+gmgvlplef+ lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 727 EAIETYMERKQPLIVIAGADYGQGSSRDWAAKGVRLAGVEAIAAEGFERIHRTNLIGMGVLPLEFQ 792 ****************************************************************** PP TIGR02333 787 pgtnrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrf 852 pgt+rktl++dgte++dv g++tpra+ltlv++r+nge++evpvtcrldtaeevs+yeaggvlqrf lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 793 PGTDRKTLGIDGTETFDVTGARTPRAQLTLVIHRRNGERVEVPVTCRLDTAEEVSIYEAGGVLQRF 858 ****************************************************************** PP TIGR02333 853 aqdfle 858 aqdfle lcl|FitnessBrowser__Dyella79:N515DRAFT_0029 859 AQDFLE 864 ****97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (869 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: 0.05u 0.02s 00:00:00.07 Elapsed: 00:00:00.05 # Mc/sec: 12.87 // [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