Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8 (865 letters) >FitnessBrowser__SynE:Synpcc7942_0903 Length = 861 Score = 1146 bits (2964), Expect = 0.0 Identities = 580/858 (67%), Positives = 688/858 (80%), Gaps = 16/858 (1%) Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60 MLE YR+ AER A G+ P PLDA Q AAL ELL+ PPVGEE LL LL +RVPPGVD+A Sbjct: 1 MLEAYRQAAAEREALGVPPLPLDADQTAALCELLQAPPVGEEATLLHLLRDRVPPGVDQA 60 Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALD--DAKLAPIAAKA 118 AYVKA FL+A+A G+TTSPL+ P +A+ELLGTM GGYN+ LID L D +A A A Sbjct: 61 AYVKATFLSAIAHGETTSPLIMPVEAVELLGTMIGGYNVAALIDLLKSADVAIATAAVAA 120 Query: 119 LSHTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETN 178 LS TLL++D + DV A+ N YA+QV++SWA AEWF S+P L E ITVT+FKV GETN Sbjct: 121 LSKTLLVYDAYNDVVALAET-NAYAQQVLESWAKAEWFTSKPTLPEAITVTIFKVPGETN 179 Query: 179 TDDLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGD 238 TDDLSPA A +RPDIPLHAQAML+ + G ++ I L++KGYPLAYVGD Sbjct: 180 TDDLSPATHATTRPDIPLHAQAMLETR----------LPGSLETIPVLKEKGYPLAYVGD 229 Query: 239 VVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDV 298 VVGTGSSRKSA NSVLW +G+DIP VPNKR GG+ LGGKIAPIFFNT ED+GALPIE DV Sbjct: 230 VVGTGSSRKSAINSVLWHIGEDIPFVPNKRSGGIILGGKIAPIFFNTAEDSGALPIECDV 289 Query: 299 SNLNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAR 358 S L+ G V+ +YPY+G +++ E G +L+TF LK D ++DEVRAGGRIPL+IGR LT K R Sbjct: 290 SALDTGMVVTIYPYEGVIKD-EAGTVLSTFSLKPDTILDEVRAGGRIPLLIGRSLTDKVR 348 Query: 359 EALGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTG 418 LGLP SDVF + + A++ +GF+LAQKMVGRACG+ G+RPG CEP MT+VGSQDTTG Sbjct: 349 SQLGLPVSDVFVRPQPPADTGKGFTLAQKMVGRACGLPGVRPGTSCEPIMTTVGSQDTTG 408 Query: 419 PMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGV 478 PMTRDE+K+LACLGFSADLVMQSFCHTAAYPKPVD+ TH TLPDFI RGGV+L+PGDG+ Sbjct: 409 PMTRDEMKELACLGFSADLVMQSFCHTAAYPKPVDIKTHKTLPDFIAQRGGVALKPGDGI 468 Query: 479 IHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG 538 IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAA G MPLDMPESVLVRF G Sbjct: 469 IHSWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAAAIGAMPLDMPESVLVRFTG 528 Query: 539 KMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDA 598 +QPGITLRD+V+AIP AI+QGLLTV K+ K N+FSGRI+EIEGLPDLK+EQAFELTDA Sbjct: 529 SLQPGITLRDVVNAIPYQAIQQGLLTVSKENKVNVFSGRIMEIEGLPDLKLEQAFELTDA 588 Query: 599 SAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLL 658 +AERS AG TIKL+++ + EYL SN+ L+K MIA GY D RTL RRI+ ME WLA+PQLL Sbjct: 589 TAERSCAGSTIKLSEDTVAEYLRSNVALMKNMIARGYEDSRTLARRIRQMEDWLANPQLL 648 Query: 659 EADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFR 718 AD DAEYAAVI+I+L ++ EPIL PNDPD+ + LS+V G+ I E+FIGSCMTNIGH+R Sbjct: 649 SADEDAEYAAVIEINLDELTEPILACPNDPDNVKKLSEVAGDPIHEIFIGSCMTNIGHYR 708 Query: 719 AAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQAR 778 AA K+L+ +GQ+ RLW+ PPTRMD +L EEGYYS F +GAR+E+PGCSLCMGNQAR Sbjct: 709 AAAKVLEG-EGQVGGRLWICPPTRMDEDRLKEEGYYSTFAAAGARLEVPGCSLCMGNQAR 767 Query: 779 VADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQ-VDKTA 837 VAD TV STSTRNF NR+G GA V+L SAELAAV AL+G++PT EEY A+ ++ A Sbjct: 768 VADNTTVFSTSTRNFNNRMGKGAQVYLGSAELAAVCALLGRIPTLEEYLKVAAEKINPFA 827 Query: 838 VDTYRYLNFDQLSQYTEK 855 D Y+YLNFDQL + E+ Sbjct: 828 ADLYQYLNFDQLEGFAEE 845 Lambda K H 0.317 0.136 0.400 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: 1908 Number of extensions: 74 Number of successful extensions: 7 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: 865 Length of database: 861 Length adjustment: 42 Effective length of query: 823 Effective length of database: 819 Effective search space: 674037 Effective search space used: 674037 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 Synpcc7942_0903 Synpcc7942_0903 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase)
to HMM TIGR00117 (acnB: aconitate hydratase 2 (EC 4.2.1.3))
# 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/TIGR00117.hmm # target sequence database: /tmp/gapView.10289.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00117 [M=844] Accession: TIGR00117 Description: acnB: aconitate hydratase 2 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 1578.0 0.0 0 1577.8 0.0 1.0 1 lcl|FitnessBrowser__SynE:Synpcc7942_0903 Synpcc7942_0903 bifunctional aco Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SynE:Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehyd # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 1577.8 0.0 0 0 1 843 [. 1 843 [. 1 844 [. 1.00 Alignments for each domain: == domain 1 score: 1577.8 bits; conditional E-value: 0 TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69 +le+yr+ aer+a+g++plpl+a+q+aal+ell+ +p +ee+ ll+ll+drvppgvd+aayvka fl+ lcl|FitnessBrowser__SynE:Synpcc7942_0903 1 MLEAYRQAAAEREALGVPPLPLDADQTAALCELLQAPPVGEEATLLHLLRDRVPPGVDQAAYVKATFLS 69 79******************************************************************* PP TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138 aia+ge +spli + eavellgtm+ggynv +li++l+s d ia+aa alsktllv+da++dv +l+ lcl|FitnessBrowser__SynE:Synpcc7942_0903 70 AIAHGETTSPLIMPVEAVELLGTMIGGYNVAALIDLLKSADVAIATAAVAALSKTLLVYDAYNDVVALA 138 ********************************************************************* PP TIGR00117 139 ktneyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknki 207 +tn+ya+qvleswa+aewf k++l+e itvt+fkv+getntddlspa++a+trpdiplha+aml++++ lcl|FitnessBrowser__SynE:Synpcc7942_0903 139 ETNAYAQQVLESWAKAEWFTSKPTLPEAITVTIFKVPGETNTDDLSPATHATTRPDIPLHAQAMLETRL 207 ********************************************************************* PP TIGR00117 208 eeieqrikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffnt 276 ++ +++i lk+kg+p+ayvgdvvgtgssrksa+nsvlw++g+dipfvpnkr+gg++lggkiapiffnt lcl|FitnessBrowser__SynE:Synpcc7942_0903 208 PGSLETIPVLKEKGYPLAYVGDVVGTGSSRKSAINSVLWHIGEDIPFVPNKRSGGIILGGKIAPIFFNT 276 ********************************************************************* PP TIGR00117 277 aedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltd 345 aedsgalpie+dv+ l++g v++iypy+g i+ +++ v++tf lkp+t+ldevraggripl+igr+ltd lcl|FitnessBrowser__SynE:Synpcc7942_0903 277 AEDSGALPIECDVSALDTGMVVTIYPYEGVIKDEAGTVLSTFSLKPDTILDEVRAGGRIPLLIGRSLTD 345 ********************************************************************* PP TIGR00117 346 karealglsesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrde 414 k r lgl+ s+vf++++ pa+++kgftlaqk+vg+acg+ g+rpgt+cep++ttvgsqdttg+mtrde lcl|FitnessBrowser__SynE:Synpcc7942_0903 346 KVRSQLGLPVSDVFVRPQPPADTGKGFTLAQKMVGRACGLPGVRPGTSCEPIMTTVGSQDTTGPMTRDE 414 ********************************************************************* PP TIGR00117 415 lkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvg 483 +kela+lgf+adlv+qsfchtaaypkpvd+kthktlpdfi+qrggval+pgdg+ihswlnrmllpdtvg lcl|FitnessBrowser__SynE:Synpcc7942_0903 415 MKELACLGFSADLVMQSFCHTAAYPKPVDIKTHKTLPDFIAQRGGVALKPGDGIIHSWLNRMLLPDTVG 483 ********************************************************************* PP TIGR00117 484 tggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkgl 552 tggdshtrfplgisfpagsglvafaaa+g mpldmpesvlvrf+g lqpgitlrd+vnaipy ai++gl lcl|FitnessBrowser__SynE:Synpcc7942_0903 484 TGGDSHTRFPLGISFPAGSGLVAFAAAIGAMPLDMPESVLVRFTGSLQPGITLRDVVNAIPYQAIQQGL 552 ********************************************************************* PP TIGR00117 553 ltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemi 621 ltv k++kvnvf+gri+eieglpdlk+eqafeltda+aers+ag+tikl++++v+eyl+sn+ l+k+mi lcl|FitnessBrowser__SynE:Synpcc7942_0903 553 LTVSKENKVNVFSGRIMEIEGLPDLKLEQAFELTDATAERSCAGSTIKLSEDTVAEYLRSNVALMKNMI 621 ********************************************************************* PP TIGR00117 622 aegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagd 690 a+gyed rtl rri +me+wlanp+ll+ad daeyaaviei+l+e++epila+pndpd+vk+lsevagd lcl|FitnessBrowser__SynE:Synpcc7942_0903 622 ARGYEDSRTLARRIRQMEDWLANPQLLSADEDAEYAAVIEINLDELTEPILACPNDPDNVKKLSEVAGD 690 ********************************************************************* PP TIGR00117 691 aidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcs 759 i+e+figscmtnigh+raa+k+le++++v +rlw++pptrmde++l+eegyy+ f+aagar+evpgcs lcl|FitnessBrowser__SynE:Synpcc7942_0903 691 PIHEIFIGSCMTNIGHYRAAAKVLEGEGQVGGRLWICPPTRMDEDRLKEEGYYSTFAAAGARLEVPGCS 759 ********************************************************************* PP TIGR00117 760 lcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakd 828 lcmgnqarv+d++tvfststrnf+nr+gkga+vylgsaelaav+allg+ipt eeyl++ +ek++++ lcl|FitnessBrowser__SynE:Synpcc7942_0903 760 LCMGNQARVADNTTVFSTSTRNFNNRMGKGAQVYLGSAELAAVCALLGRIPTLEEYLKVAAEKINPFAA 828 ********************************************************************* PP TIGR00117 829 klyrylnfnelenfe 843 +ly+ylnf++le f lcl|FitnessBrowser__SynE:Synpcc7942_0903 829 DLYQYLNFDQLEGFA 843 ************996 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (844 nodes) Target sequences: 1 (861 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 0.01s 00:00:00.06 Elapsed: 00:00:00.05 # Mc/sec: 12.94 // [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