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.28740.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 0.03s 00:00:00.09 Elapsed: 00:00:00.08
# Mc/sec: 8.70
//
[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