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 199538 SO0343 aconitate hydratase 1 (NCBI ptt file)
Query= SwissProt::Q937N8 (869 letters) >FitnessBrowser__MR1:199538 Length = 867 Score = 1447 bits (3747), Expect = 0.0 Identities = 722/866 (83%), Positives = 783/866 (90%), Gaps = 6/866 (0%) Query: 1 MNSANRKPLPGTKLDYFDARAAVEAIQPGAYDKLPYTSRVLAENLVRRCDPATLTDSLLQ 60 MN+ RKPLPGT LDYFD R A+EAI PGAY KLPYTSRVLAENLVRRC+P LT SL Q Sbjct: 5 MNTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQ 64 Query: 61 LVGRKRDLDFPWFPARVVCHDILGQTALVDLAGLRDAIADQGGDPAKVNPVVPVQLIVDH 120 ++ K++LDFPWFPARVVCHDILGQTALVDLAGLRDAIA +GGDPA+VNPVVP QLIVDH Sbjct: 65 IIESKQELDFPWFPARVVCHDILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDH 124 Query: 121 SLAVECGGFDPDAFAKNRAIEDRRNEDRFHFIDWTKQAFKNVDVIPPGNGIMHQINLEKM 180 SLAVE GGFD DAFAKNRAIEDRRNEDRFHFI+WT++AFKN+DVIP GNGIMHQINLE+M Sbjct: 125 SLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAFKNIDVIPQGNGIMHQINLERM 184 Query: 181 SPVIHADNGVAYPDTCVGTDSHTPHVDALGVIAIGVGGLEAENVMLGRASWMRLPDIVGV 240 SPVIHA NGVA+PDT VGTDSHTPHVDALGVIAIGVGGLEAE+VMLGRAS+MRLPDI+GV Sbjct: 185 SPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDIIGV 244 Query: 241 ELTGKRQPGITATDIVLALTEFLRKEKVVGAYLEFRGEGASSLTLGDRATISNMAPEYGA 300 ELTGK QPGITATDIVLALTEFLR +KVV +YLEF GEGA +LTLGDRATISNM PE+GA Sbjct: 245 ELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGA 304 Query: 301 TAAMFFIDEQTIDYLRLTGRTDEQLKLVETYARTAGLWADSLKNAEYERVLKFDLSSVVR 360 TAAMF+ID+QT+DYL LTGR EQ+KLVETYA+TAGLW+D LK A Y R L FDLSSVVR Sbjct: 305 TAAMFYIDQQTLDYLTLTGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVR 364 Query: 361 NMAGPSNPHKRLPTSALAERGIAVDLDKASAQEAEGLMPDGAVIIAAITSCTNTSNPRNV 420 +AGPSNPH R+PTS LA RGI+ +++ GLMPDGAVIIAAITSCTNTSNPRNV Sbjct: 365 TIAGPSNPHARVPTSELAARGISGEVENEP-----GLMPDGAVIIAAITSCTNTSNPRNV 419 Query: 421 IAAALLARNANARGLARKPWVKSSLAPGSKAVELYLEEANLLPDLEKLGFGIVAFACTTC 480 IAA LLARNANA+GL RKPWVK+SLAPGSKAV+LYLEEANLLP+LE LGFGIV FACTTC Sbjct: 420 IAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTTC 479 Query: 481 NGMSGALDPKIQQEIIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 540 NGMSGALDP IQQE+IDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI Sbjct: 480 NGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTI 539 Query: 541 RFDIEKDVLGTDQDGKPVYLKDIWPSDEEIDAIVAKSVKPEQFRKVYEPMFAITAASGES 600 RFDIEKDVLG D+DGKPV L +IWPSD EIDA++A SVKPEQFRKVYEPMF ++ G+ Sbjct: 540 RFDIEKDVLGLDKDGKPVRLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSVDYGDK 599 Query: 601 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKALRPLAVLGDNITTDHLSPSNAIMLNSAA 660 VSPLYDWRPQSTYIRRPPYWEGALAGERTLK +RPLAVLGDNITTDHLSPSNAIM++SAA Sbjct: 600 VSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLAVLGDNITTDHLSPSNAIMMDSAA 659 Query: 661 GEYLARMGLPEEDFNSYATHRGDHLTAQRATFANPTLINEMAVVDGQVKKGSLARIEPEG 720 GEYL +MGLPEEDFNSYATHRGDHLTAQRATFANP L NEMA+VDG+VK+GSLARIEPEG Sbjct: 660 GEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARIEPEG 719 Query: 721 KVVRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEVIVAEGFERIHRTN 780 V RMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVE IVAEGFERIHRTN Sbjct: 720 IVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTN 779 Query: 781 LIGMGVLPLEFKPGVNRLTLGLDGTETYDVIGERQPRATLTLVVNRKNGERVEVPVTCRL 840 L+GMGVLPLEFK G NR T G+DGTE +DVIG PRA LT+++ RKNGERVEVPVTCRL Sbjct: 780 LVGMGVLPLEFKAGENRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRL 839 Query: 841 DSDEEVSIYEAGGVL-HFAQDFLESS 865 D+ EEVSIYEAGGVL FAQDFLES+ Sbjct: 840 DTAEEVSIYEAGGVLQRFAQDFLESN 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: 2213 Number of extensions: 88 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: 867 Length adjustment: 42 Effective length of query: 827 Effective length of database: 825 Effective search space: 682275 Effective search space used: 682275 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 199538 SO0343 (aconitate hydratase 1 (NCBI ptt file))
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.20829.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 1873.1 0.0 0 1873.0 0.0 1.0 1 lcl|FitnessBrowser__MR1:199538 SO0343 aconitate hydratase 1 (NC Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:199538 SO0343 aconitate hydratase 1 (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1873.0 0.0 0 0 1 858 [] 6 863 .. 6 863 .. 1.00 Alignments for each domain: == domain 1 score: 1873.0 bits; conditional E-value: 0 TIGR02333 1 ntkyrkalpgtdldyfdaraaveaikpgaydklpytsrvlaenlvrrvdpetleaslkqlierkreldfpwyparvvch 79 nt+yrk+lpgt+ldyfd+r+a+eai+pgay+klpytsrvlaenlvrr++pe+l+aslkq+ie+k+eldfpw+parvvch lcl|FitnessBrowser__MR1:199538 6 NTQYRKPLPGTALDYFDTREAIEAIAPGAYAKLPYTSRVLAENLVRRCEPEMLTASLKQIIESKQELDFPWFPARVVCH 84 89***************************************************************************** PP TIGR02333 80 dilgqtalvdlaglrdaiaekggdpaqvnpvvetqlivdhslaveyggfdpdafeknraiedrrnedrfhfinwtkkaf 158 dilgqtalvdlaglrdaia+kggdpaqvnpvv+tqlivdhslaveyggfd+daf+knraiedrrnedrfhfinwt+kaf lcl|FitnessBrowser__MR1:199538 85 DILGQTALVDLAGLRDAIAAKGGDPAQVNPVVPTQLIVDHSLAVEYGGFDKDAFAKNRAIEDRRNEDRFHFINWTQKAF 163 ******************************************************************************* PP TIGR02333 159 knvdvipagngimhqinlekmspvvqvkegvafpdtlvgtdshtphvdalgviaigvggleaetvmlgraslmrlpdiv 237 kn+dvip+gngimhqinle+mspv+++++gvafpdtlvgtdshtphvdalgviaigvggleae+vmlgras+mrlpdi+ lcl|FitnessBrowser__MR1:199538 164 KNIDVIPQGNGIMHQINLERMSPVIHARNGVAFPDTLVGTDSHTPHVDALGVIAIGVGGLEAESVMLGRASYMRLPDII 242 ******************************************************************************* PP TIGR02333 238 gveltgkrqpgitatdivlalteflrkekvvsayleffgegakaltlgdratisnmtpeygataamfaideqtidylkl 316 gveltgk qpgitatdivlalteflr++kvvs+yleffgega+altlgdratisnmtpe+gataamf+id+qt+dyl+l lcl|FitnessBrowser__MR1:199538 243 GVELTGKPQPGITATDIVLALTEFLRAQKVVSSYLEFFGEGAEALTLGDRATISNMTPEFGATAAMFYIDQQTLDYLTL 321 ******************************************************************************* PP TIGR02333 317 tgreeeqvklvetyakaaglwadslkkavyervlkfdlssvvrnlagpsnpharlatsdlaakgiakeveeeaeglmpd 395 tgre+eqvklvetyak+aglw+d+lk+avy+r+l+fdlssvvr++agpsnphar++ts+laa+gi++eve+e+ glmpd lcl|FitnessBrowser__MR1:199538 322 TGREAEQVKLVETYAKTAGLWSDDLKQAVYPRTLHFDLSSVVRTIAGPSNPHARVPTSELAARGISGEVENEP-GLMPD 399 *************************************************************************.***** PP TIGR02333 396 gaviiaaitsctntsnprnvvaagllarnanklglkrkpwvksslapgskvvklyleeagllkeleklgfgivafactt 474 gaviiaaitsctntsnprnv+aagllarnan++gl+rkpwvk+slapgsk+v+lyleea+ll+ele+lgfgiv+factt lcl|FitnessBrowser__MR1:199538 400 GAVIIAAITSCTNTSNPRNVIAAGLLARNANAKGLTRKPWVKTSLAPGSKAVQLYLEEANLLPELESLGFGIVGFACTT 478 ******************************************************************************* PP TIGR02333 475 cngmsgaldpviqqeiidrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlgvdadgkei 553 cngmsgaldpviqqe+idrdlyatavlsgnrnfdgrihpyakqaflaspplvvayaiagtirfdiekdvlg+d+dgk++ lcl|FitnessBrowser__MR1:199538 479 CNGMSGALDPVIQQEVIDRDLYATAVLSGNRNFDGRIHPYAKQAFLASPPLVVAYAIAGTIRFDIEKDVLGLDKDGKPV 557 ******************************************************************************* PP TIGR02333 554 rlkdiwpsdeeidavvaaavkpeqfrkvyipmfdle.daqkkvsplydwrpmstyirrppywegalagertlkgmrpla 631 rl++iwpsd+eidav+aa+vkpeqfrkvy+pmfdl+ d+++kvsplydwrp+styirrppywegalagertlkgmrpla lcl|FitnessBrowser__MR1:199538 558 RLINIWPSDAEIDAVIAASVKPEQFRKVYEPMFDLSvDYGDKVSPLYDWRPQSTYIRRPPYWEGALAGERTLKGMRPLA 636 ******************************************************************************* PP TIGR02333 632 vlgdnittdhlspsnailldsaageylakmglpeedfnsyathrgdhltaqratfanpklfnemvkedgkvkqgslari 710 vlgdnittdhlspsnai++dsaageyl+kmglpeedfnsyathrgdhltaqratfanpkl+nem+++dgkvkqgslari lcl|FitnessBrowser__MR1:199538 637 VLGDNITTDHLSPSNAIMMDSAAGEYLHKMGLPEEDFNSYATHRGDHLTAQRATFANPKLKNEMAIVDGKVKQGSLARI 715 ******************************************************************************* PP TIGR02333 711 epegkvtrmweaietymnrkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefkpgt 789 epeg+vtrmweaietym+rkqpliiiagadygqgssrdwaakgvrlagveaivaegferihrtnlvgmgvlplefk+g+ lcl|FitnessBrowser__MR1:199538 716 EPEGIVTRMWEAIETYMDRKQPLIIIAGADYGQGSSRDWAAKGVRLAGVEAIVAEGFERIHRTNLVGMGVLPLEFKAGE 794 ******************************************************************************* PP TIGR02333 790 nrktlaldgtevydvvgeitpradltlvvtrkngeklevpvtcrldtaeevsvyeaggvlqrfaqdfle 858 nr+t+++dgtev+dv+g+i+pradlt+++trknge++evpvtcrldtaeevs+yeaggvlqrfaqdfle lcl|FitnessBrowser__MR1:199538 795 NRATYGIDGTEVFDVIGSIAPRADLTVIITRKNGERVEVPVTCRLDTAEEVSIYEAGGVLQRFAQDFLE 863 *******************************************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (858 nodes) Target sequences: 1 (867 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 0.03s 00:00:00.08 Elapsed: 00:00:00.08 # Mc/sec: 8.53 // [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