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