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 BWI76_RS04910 BWI76_RS04910 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8
(865 letters)
>FitnessBrowser__Koxy:BWI76_RS04910
Length = 872
Score = 1679 bits (4347), Expect = 0.0
Identities = 835/865 (96%), Positives = 853/865 (98%)
Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
+LEEYRKHVAERAA+GIVPKPLDATQMAALVELLK PP GEEEFLLDLLINRVPPGVDEA
Sbjct: 8 VLEEYRKHVAERAAEGIVPKPLDATQMAALVELLKNPPAGEEEFLLDLLINRVPPGVDEA 67
Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFLAA+AKGD TSPLV+ EKA+ELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS
Sbjct: 68 AYVKAGFLAAIAKGDATSPLVTREKAVELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 127
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRP LA+KITVTVFKVTGETNTD
Sbjct: 128 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPQLADKITVTVFKVTGETNTD 187
Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
DLSPAPDAWSRPDIPLHA AMLKNAREGI+PDQPG VGPIKQIEALQ+KG+PLAYVGDVV
Sbjct: 188 DLSPAPDAWSRPDIPLHALAMLKNAREGIDPDQPGAVGPIKQIEALQQKGFPLAYVGDVV 247
Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGL LGGKIAPIFFNTMEDAGALPIEVDV+N
Sbjct: 248 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLVLGGKIAPIFFNTMEDAGALPIEVDVNN 307
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
LNMGDVIDVYP+KGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA
Sbjct: 308 LNMGDVIDVYPFKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 367
Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLPHS+VFRQAKDVAESSRG+SLAQKMVGRACGV G+RPGAYCEPKMTSVGSQDTTGPM
Sbjct: 368 LGLPHSEVFRQAKDVAESSRGYSLAQKMVGRACGVAGVRPGAYCEPKMTSVGSQDTTGPM 427
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFS+DLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 428 TRDELKDLACLGFSSDLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 487
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 488 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 547
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA
Sbjct: 548 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 607
Query: 601 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLEA 660
ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERR+QGMEKWLA+P+LLE
Sbjct: 608 ERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRVQGMEKWLAEPELLEG 667
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA
Sbjct: 668 DADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAA 727
Query: 721 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA
Sbjct: 728 GKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 787
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA DT
Sbjct: 788 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAADT 847
Query: 841 YRYLNFDQLSQYTEKADGVIFQTAV 865
YRYLNFDQL QYTEKADGVIFQTAV
Sbjct: 848 YRYLNFDQLGQYTEKADGVIFQTAV 872
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: 2366
Number of extensions: 73
Number of successful extensions: 1
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: 872
Length adjustment: 42
Effective length of query: 823
Effective length of database: 830
Effective search space: 683090
Effective search space used: 683090
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 BWI76_RS04910 BWI76_RS04910 (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.77988.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 1684.1 0.0 0 1683.8 0.0 1.0 1 FitnessBrowser__Koxy:BWI76_RS04910
Domain annotation for each sequence (and alignments):
>> FitnessBrowser__Koxy:BWI76_RS04910
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1683.8 0.0 0 0 1 844 [] 8 861 .. 8 861 .. 1.00
Alignments for each domain:
== domain 1 score: 1683.8 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75
+leeyrkhvaeraaegi p+pl+a q+aalvellkn+p++eeefll+lli+rvppgvdeaayvkagflaaiakg+
FitnessBrowser__Koxy:BWI76_RS04910 8 VLEEYRKHVAERAAEGIVPKPLDATQMAALVELLKNPPAGEEEFLLDLLINRVPPGVDEAAYVKAGFLAAIAKGD 82
69************************************************************************* PP
TIGR00117 76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
++spl++ e+avellgtm+ggyn++pli+al+ d+++a++aakals+tll+fd+f+dvee++k+ neyakqv++
FitnessBrowser__Koxy:BWI76_RS04910 83 ATSPLVTREKAVELLGTMQGGYNIHPLIDALD--DAKLAPIAAKALSHTLLMFDNFYDVEEKAKAgNEYAKQVMQ 155
********************************..*******************************9********* PP
TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
swa+aewfl +++la+kitvtvfkv+getntddlspapda++rpdiplhalamlkn++e+i++ +i
FitnessBrowser__Koxy:BWI76_RS04910 156 SWADAEWFLSRPQLADKITVTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIDPdqpgavgpikQI 230
*************************************************************9999********** PP
TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
+al+qkg+p+ayvgdvvgtgssrksatnsvlwf+g+dip vpnkr+gglvlggkiapiffnt+ed+galpievdv
FitnessBrowser__Koxy:BWI76_RS04910 231 EALQQKGFPLAYVGDVVGTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLVLGGKIAPIFFNTMEDAGALPIEVDV 305
*************************************************************************** PP
TIGR00117 290 kdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkak 363
++ln+gdvi++yp+kge++n+et e++atf+lk+++l+devraggripliigrglt+karealgl++sevf++ak
FitnessBrowser__Koxy:BWI76_RS04910 306 NNLNMGDVIDVYPFKGEVRNHETgELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREALGLPHSEVFRQAK 380
**********************99*************************************************** PP
TIGR00117 364 apaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaay 438
++aes++g++laqk+vg+acgv g+rpg+ycepk+t+vgsqdttg+mtrdelk+la+lgf++dlv+qsfchtaay
FitnessBrowser__Koxy:BWI76_RS04910 381 DVAESSRGYSLAQKMVGRACGVAGVRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSSDLVMQSFCHTAAY 455
*************************************************************************** PP
TIGR00117 439 pkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgv 513
pkpvdv th+tlpdfi++rggv+lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgv
FitnessBrowser__Koxy:BWI76_RS04910 456 PKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGV 530
*************************************************************************** PP
TIGR00117 514 mpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltda 588
mpldmpesvlvrfkg++qpgitlrdlv+aip+yaik+glltvekkgk+n+f+grileieglpdlkveqafeltda
FitnessBrowser__Koxy:BWI76_RS04910 531 MPLDMPESVLVRFKGKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDA 605
*************************************************************************** PP
TIGR00117 589 saersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieid 663
saersaagctiklnkep++eyl snivllk+miaegy+d+rtl+rr+++mekwla+pelle+dadaeyaavi+id
FitnessBrowser__Koxy:BWI76_RS04910 606 SAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRVQGMEKWLAEPELLEGDADAEYAAVIDID 680
*************************************************************************** PP
TIGR00117 664 laeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqql 737
la+ikepil+apndpdd++lls+v+g++idevfigscmtnighfraagk+l+++k ++++rlwv+pptrmd++ql
FitnessBrowser__Koxy:BWI76_RS04910 681 LADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHFRAAGKLLDNHKgQLPTRLWVAPPTRMDAAQL 755
******************************************************99******************* PP
TIGR00117 738 ieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptk 812
+eegyy++fg++gar+e+pgcslcmgnqarv+dgatv+ststrnf+nrlg+ga+v+l+saelaavaal+gk+pt+
FitnessBrowser__Koxy:BWI76_RS04910 756 TEEGYYSVFGKSGARIEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTP 830
*************************************************************************** PP
TIGR00117 813 eeylalvsekvesakdklyrylnfnelenfee 844
eey+++v++++++a d +yrylnf++l +++e
FitnessBrowser__Koxy:BWI76_RS04910 831 EEYQTYVAQVDKTAAD-TYRYLNFDQLGQYTE 861
***************9.************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (872 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.02
# Mc/sec: 28.94
//
[ok]
This GapMind analysis is from Apr 09 2024. 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