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 RR42_RS11270 RR42_RS11270 aconitate hydratase
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__Cup4G11:RR42_RS11270 Length = 865 Score = 1496 bits (3872), Expect = 0.0 Identities = 740/870 (85%), Positives = 800/870 (91%), Gaps = 6/870 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ANRKPLPGT+LD+FD RAAV+AIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSL Q Sbjct: 1 MNTANRKPLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLKQ 60 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 ++ RK++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA QGGDP VNPVVP QL+VDH Sbjct: 61 IIERKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPVMVNPVVPTQLVVDH 120 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVECGGFDPDAFAKNRAIEDRRNEDRF FI+WTK+AFKNVDVIPPGNGI+HQINLE+M Sbjct: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFDFINWTKKAFKNVDVIPPGNGILHQINLERM 180 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPV+ +GVA+PDT VGTDSHTP VDALGVIAIGVGGLEAE+VMLGRASWMRLPDI+GV Sbjct: 181 SPVVQVKDGVAFPDTLVGTDSHTPMVDALGVIAIGVGGLEAESVMLGRASWMRLPDIIGV 240 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK QPGITATD VLALTEFLRKEKVV +YLEF GEG + LTLGDRATISNMAPE+G+ Sbjct: 241 ELTGKPQPGITATDTVLALTEFLRKEKVVSSYLEFFGEGTTHLTLGDRATISNMAPEFGS 300 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+IDEQTI YL+LTGR D +KLVETYA+ AGLWADSLKNAEY RVL+FDLS+VVR Sbjct: 301 TAAMFYIDEQTIKYLKLTGRDDALVKLVETYAKEAGLWADSLKNAEYPRVLRFDLSTVVR 360 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 N+AGPSNPHKR+PTS LA RGI+ + GLMPDGAVIIAA+TSCTNT+NPRN+ Sbjct: 361 NIAGPSNPHKRVPTSELAARGIS-----GKVENEPGLMPDGAVIIAAVTSCTNTNNPRNM 415 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 +AA LLARNAN GL RKPWVKSSLAPGSKAV LYLEEANLLP+LE+LGFG+VA+ACT+C Sbjct: 416 VAAGLLARNANKLGLTRKPWVKSSLAPGSKAVTLYLEEANLLPELEQLGFGVVAYACTSC 475 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGALDP IQ+E++DRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI Sbjct: 476 NGMSGALDPVIQKEVVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 535 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKDVLGTD DGKPV LKDIWPSDEEIDA+VA SVKP QFRKVYEPMFA+TA +GE Sbjct: 536 RFDIEKDVLGTDADGKPVTLKDIWPSDEEIDAVVAASVKPAQFRKVYEPMFAVTADTGEK 595 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 SPLYDWR STYIRRPPYWEGALAGER L +RPLAVLGDNITTDHLSPSNAIML+SAA Sbjct: 596 ASPLYDWREMSTYIRRPPYWEGALAGERALTGMRPLAVLGDNITTDHLSPSNAIMLDSAA 655 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720 GEYLA+MGLPEEDFNSYATHRGDHLTAQRATFANPTL NEM VVDG+VK GSLARIEPEG Sbjct: 656 GEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANPTLKNEMVVVDGKVKPGSLARIEPEG 715 Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780 KV RMWEAIETYM RKQPLI++AGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN Sbjct: 716 KVTRMWEAIETYMARKQPLIVVAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 775 Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840 L+GMGVLPLEFKPGVNR TLG+DGTETYDVIG+R PR LTLV++RKNGERVEVPVTCRL Sbjct: 776 LVGMGVLPLEFKPGVNRATLGIDGTETYDVIGDRTPRCDLTLVMHRKNGERVEVPVTCRL 835 Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESSRATA 869 D+ EEVSIYEAGGVL FAQDFLESS+A A Sbjct: 836 DTAEEVSIYEAGGVLQRFAQDFLESSKAAA 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: 2304 Number of extensions: 93 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 RR42_RS11270 RR42_RS11270 (aconitate hydratase)
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.9852.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 1804.4 0.0 0 1804.3 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS11270 RR42_RS11270 aconitate hydratase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS11270 RR42_RS11270 aconitate hydratase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1804.3 0.0 0 0 1 858 [] 2 859 .. 2 859 .. 1.00 Alignments for each domain: == domain 1 score: 1804.3 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldf 69 nt+ rk+lpgt+ld+fd+raav+ai+pgaydklpytsrvlaenlvrr+dp+tl++slkq+ierk+eldf lcl|FitnessBrowser__Cup4G11:RR42_RS11270 2 NTANRKPLPGTQLDFFDTRAAVDAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLKQIIERKQELDF 70 7899***************************************************************** PP TIGR02333 70 pwyparvvchdilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknra 138 pw+parvvchdilgqtalvdlaglrdaia++ggdp vnpvv+tql+vdhslave+ggfdpdaf+knra lcl|FitnessBrowser__Cup4G11:RR42_RS11270 71 PWFPARVVCHDILGQTALVDLAGLRDAIAAQGGDPVMVNPVVPTQLVVDHSLAVECGGFDPDAFAKNRA 139 ********************************************************************* PP TIGR02333 139 iedrrnedrfhfinwtkkafknvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvda 207 iedrrnedrf finwtkkafknvdvip+gngi+hqinle+mspvvqvk+gvafpdtlvgtdshtp vda lcl|FitnessBrowser__Cup4G11:RR42_RS11270 140 IEDRRNEDRFDFINWTKKAFKNVDVIPPGNGILHQINLERMSPVVQVKDGVAFPDTLVGTDSHTPMVDA 208 ********************************************************************* PP TIGR02333 208 lgviaigvggleaetvmlgraslmrlpdivgveltgkrqpgitatdivlalteflrkekvvsayleffg 276 lgviaigvggleae+vmlgras+mrlpdi+gveltgk qpgitatd vlalteflrkekvvs+yleffg lcl|FitnessBrowser__Cup4G11:RR42_RS11270 209 LGVIAIGVGGLEAESVMLGRASWMRLPDIIGVELTGKPQPGITATDTVLALTEFLRKEKVVSSYLEFFG 277 ********************************************************************* PP TIGR02333 277 egakaltlgdratisnmtpeygataamfaideqtidylkltgreeeqvklvetyakaaglwadslkkav 345 eg+ ltlgdratisnm+pe+g+taamf+ideqti+ylkltgr+++ vklvetyak aglwadslk+a+ lcl|FitnessBrowser__Cup4G11:RR42_RS11270 278 EGTTHLTLGDRATISNMAPEFGSTAAMFYIDEQTIKYLKLTGRDDALVKLVETYAKEAGLWADSLKNAE 346 ********************************************************************* PP TIGR02333 346 yervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpdgaviiaaitsctntsnprn 414 y+rvl+fdls+vvrn+agpsnph+r++ts+laa+gi+++ve+e+ glmpdgaviiaa+tsctnt nprn lcl|FitnessBrowser__Cup4G11:RR42_RS11270 347 YPRVLRFDLSTVVRNIAGPSNPHKRVPTSELAARGISGKVENEP-GLMPDGAVIIAAVTSCTNTNNPRN 414 ********************************************.************************ PP TIGR02333 415 vvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafacttcngmsgald 483 +vaagllarnanklgl+rkpwvksslapgsk+v lyleea+ll+ele+lgfg+va+act+cngmsgald lcl|FitnessBrowser__Cup4G11:RR42_RS11270 415 MVAAGLLARNANKLGLTRKPWVKSSLAPGSKAVTLYLEEANLLPELEQLGFGVVAYACTSCNGMSGALD 483 ********************************************************************* PP TIGR02333 484 pviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgke 552 pviq+e++drdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+dadgk+ lcl|FitnessBrowser__Cup4G11:RR42_RS11270 484 PVIQKEVVDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGTDADGKP 552 ********************************************************************* PP TIGR02333 553 irlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalag 620 + lkdiwpsdeeidavvaa+vkp qfrkvy+pmf++ d+++k+splydwr mstyirrppywegalag lcl|FitnessBrowser__Cup4G11:RR42_RS11270 553 VTLKDIWPSDEEIDAVVAASVKPAQFRKVYEPMFAVTaDTGEKASPLYDWREMSTYIRRPPYWEGALAG 621 ***********************************999******************************* PP TIGR02333 621 ertlkgmrplavlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanp 689 er+l gmrplavlgdnittdhlspsnai+ldsaageylakmglpeedfnsyathrgdhltaqratfanp lcl|FitnessBrowser__Cup4G11:RR42_RS11270 622 ERALTGMRPLAVLGDNITTDHLSPSNAIMLDSAAGEYLAKMGLPEEDFNSYATHRGDHLTAQRATFANP 690 ********************************************************************* PP TIGR02333 690 klfnemvkedgkvkqgslariepegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlag 758 l+nemv +dgkvk gslariepegkvtrmweaietym rkqpli++agadygqgssrdwaakgvrlag lcl|FitnessBrowser__Cup4G11:RR42_RS11270 691 TLKNEMVVVDGKVKPGSLARIEPEGKVTRMWEAIETYMARKQPLIVVAGADYGQGSSRDWAAKGVRLAG 759 ********************************************************************* PP TIGR02333 759 veaivaegferihrtnlvgmgvlplefkpgtnrktlaldgtevydvvgeitpradltlvvtrkngekle 827 veaivaegferihrtnlvgmgvlplefkpg+nr+tl++dgte+ydv+g++tpr+dltlv++rknge++e lcl|FitnessBrowser__Cup4G11:RR42_RS11270 760 VEAIVAEGFERIHRTNLVGMGVLPLEFKPGVNRATLGIDGTETYDVIGDRTPRCDLTLVMHRKNGERVE 828 ********************************************************************* PP TIGR02333 828 vpvtcrldtaeevsvyeaggvlqrfaqdfle 858 vpvtcrldtaeevs+yeaggvlqrfaqdfle lcl|FitnessBrowser__Cup4G11:RR42_RS11270 829 VPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 859 *****************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (865 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: 00:00:00.08 # Mc/sec: 9.07 // [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