Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 7023199 Shewana3_0433 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__ANA3:7023199
Length = 890
Score = 1442 bits (3734), Expect = 0.0
Identities = 704/865 (81%), Positives = 784/865 (90%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YRKHVAERAAEG+ PKPLDA+Q+A LV+L++NPPAGEE +LDLL NR+PPGVDEA
Sbjct: 26 VLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAVILDLLENRIPPGVDEA 85
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKA FL A+AKG A SP+L+ E+A ELLGTMQGGYNI PLI LD+ LAP+AAKALS
Sbjct: 86 AYVKAAFLDAVAKGAATSPILSAERATELLGTMQGGYNIEPLIAQLDNPALAPLAAKALS 145
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD+F+DV EK +AGN YAKQV+++WA+A+W+L+RP LA+K+T+TVFKV+GETNTD
Sbjct: 146 HTLLMFDSFHDVVEKMEAGNAYAKQVVEAWANADWYLSRPKLADKVTLTVFKVSGETNTD 205
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKNAR+GIEPD PG VGPIK++E L+ KGFPL YVGDVV
Sbjct: 206 DLSPAPDAWSRPDIPLHALAMLKNARDGIEPDVPGSVGPIKKLEELKTKGFPLVYVGDVV 265
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWFMGDDIP VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS
Sbjct: 266 GTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 325
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ MGDVID+YPY G+V+ H T E+++ F LKTDVL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 326 MEMGDVIDIYPYAGQVKRHGTEEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARSV 385
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP SDVF + +D+A+S +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 386 LGLPASDVFVRPQDIADSGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 445
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 446 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 505
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM
Sbjct: 506 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 565
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIPL AI+ GLLTVEKKGK NIFSGR+LEIEGL LKVEQAFEL+DASA
Sbjct: 566 QPGITLRDLVHAIPLKAIEMGLLTVEKKGKINIFSGRVLEIEGLETLKVEQAFELSDASA 625
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKL+KEPIIEYLNSNI +LKWMIAEGYGDRRT+ERRI+GME+WLANPEL+ A
Sbjct: 626 ERSAAGCTIKLDKEPIIEYLNSNITMLKWMIAEGYGDRRTIERRIKGMEEWLANPELMSA 685
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
D DAEYAAVI+IDL +IKEPILCAPNDPDDA LS+V +IDEVF+GSCMTNIGHFRA
Sbjct: 686 DKDAEYAAVIEIDLNEIKEPILCAPNDPDDAVLLSSVAQTQIDEVFVGSCMTNIGHFRAT 745
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GK+LD LPTRLW+APPT+MD QLTEEGYY +FG+ GARIEIPGCSLCMGNQARVA
Sbjct: 746 GKMLDKFAKTLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPGCSLCMGNQARVA 805
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
+GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LPT EEYQ Y ++D TA DT
Sbjct: 806 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAADT 865
Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
YRYLNF+Q+ YT+KA VIFQ+AV
Sbjct: 866 YRYLNFDQIDSYTKKASQVIFQSAV 890
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: 2153
Number of extensions: 74
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: 890
Length adjustment: 43
Effective length of query: 822
Effective length of database: 847
Effective search space: 696234
Effective search space used: 696234
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 7023199 Shewana3_0433 (bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq))
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.30800.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 1575.7 0.0 0 1575.5 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7023199 Shewana3_0433 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__ANA3:7023199 Shewana3_0433 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (Re
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1575.5 0.0 0 0 1 843 [. 26 878 .. 26 879 .. 0.99
Alignments for each domain:
== domain 1 score: 1575.5 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevk 77
+le+yrkhvaeraaeg+ p+pl+a+qva+lv+l++n+p++ee+ +l+ll +r+ppgvdeaayvka fl a+akg ++
lcl|FitnessBrowser__ANA3:7023199 26 VLEAYRKHVAERAAEGVVPKPLDAHQVAELVKLVQNPPAGEEAVILDLLENRIPPGVDEAAYVKAAFLDAVAKGAAT 102
69*************************************************************************** PP
TIGR00117 78 splisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswae 153
sp +sae+a+ellgtm+ggyn+epli +l+ + +a+ aakals+tll+fd+f+dv e+ ++ n+yakqv+e+wa+
lcl|FitnessBrowser__ANA3:7023199 103 SPILSAERATELLGTMQGGYNIEPLIAQLD--NPALAPLAAKALSHTLLMFDSFHDVVEKMEAgNAYAKQVVEAWAN 177
******************************..899**********************9999988************* PP
TIGR00117 154 aewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqk 220
a+w+l +++la+k+t tvfkv+getntddlspapda++rpdiplhalamlkn++++ie+ ++++lk+k
lcl|FitnessBrowser__ANA3:7023199 178 ADWYLSRPKLADKVTLTVFKVSGETNTDDLSPAPDAWSRPDIPLHALAMLKNARDGIEPdvpgsvgpikKLEELKTK 254
***************************************************************************** PP
TIGR00117 221 gvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdv 297
g+p+ yvgdvvgtgssrksatnsvlwf+g+dipfvpnkragg++lggkiapiffnt+ed+galpie dv+++++gdv
lcl|FitnessBrowser__ANA3:7023199 255 GFPLVYVGDVVGTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSKMEMGDV 331
***************************************************************************** PP
TIGR00117 298 ikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgft 373
i+iypy g+++ + t ev++ f lk+++lldevraggripliigrgltdkar +lgl+ s+vf+++++ a+s+kg+t
lcl|FitnessBrowser__ANA3:7023199 332 IDIYPYAGQVKRHGTeEVISEFSLKTDVLLDEVRAGGRIPLIIGRGLTDKARSVLGLPASDVFVRPQDIADSGKGYT 408
*************9989************************************************************ PP
TIGR00117 374 laqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktl 450
laqk+vgkacgv g+rpg ycepk+t+vgsqdttg+mtrdelk+la+lgf+adl++qsfchtaaypkpvdv+th+tl
lcl|FitnessBrowser__ANA3:7023199 409 LAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTL 485
***************************************************************************** PP
TIGR00117 451 pdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfk 527
pdfi++rggv+lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfk
lcl|FitnessBrowser__ANA3:7023199 486 PDFIMNRGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 562
***************************************************************************** PP
TIGR00117 528 gelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnke 604
g++qpgitlrdlv+aip+ ai+ glltvekkgk+n+f+gr+leiegl lkveqafel+dasaersaagctikl+ke
lcl|FitnessBrowser__ANA3:7023199 563 GKMQPGITLRDLVHAIPLKAIEMGLLTVEKKGKINIFSGRVLEIEGLETLKVEQAFELSDASAERSAAGCTIKLDKE 639
***************************************************************************** PP
TIGR00117 605 pvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddv 681
p+ieyl+sni +lk+miaegy+d+rt++rri++me+wlanpel++ad daeyaavieidl+eikepil+apndpdd+
lcl|FitnessBrowser__ANA3:7023199 640 PIIEYLNSNITMLKWMIAEGYGDRRTIERRIKGMEEWLANPELMSADKDAEYAAVIEIDLNEIKEPILCAPNDPDDA 716
***************************************************************************** PP
TIGR00117 682 kllsevagdaidevfigscmtnighfraagkilea.aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpg 757
lls va +idevf+gscmtnighfra+gk+l++ akt+++rlw++ppt+md++ql+eegyy+ifg+ gar+e+pg
lcl|FitnessBrowser__ANA3:7023199 717 VLLSSVAQTQIDEVFVGSCMTNIGHFRATGKMLDKfAKTLPTRLWIAPPTKMDKDQLTEEGYYGIFGRVGARIEIPG 793
*********************************983569************************************** PP
TIGR00117 758 cslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyryl 834
cslcmgnqarv++gatv+ststrnf+nrlg+ga+vyl+saelaavaallg++pt+eey+++ e +++a d +yryl
lcl|FitnessBrowser__ANA3:7023199 794 CSLCMGNQARVAEGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPTVEEYQEYAKELDATAAD-TYRYL 869
*******************************************************************9999.***** PP
TIGR00117 835 nfnelenfe 843
nf++++ ++
lcl|FitnessBrowser__ANA3:7023199 870 NFDQIDSYT 878
******997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (890 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: 0.06u 0.04s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 7.78
//
[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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.
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