Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate 5210998 Shew_3424 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__PV4:5210998
Length = 865
Score = 1438 bits (3723), Expect = 0.0
Identities = 704/865 (81%), Positives = 785/865 (90%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YRKHVAERAAEG+ PKPLDA+Q+A L+EL+KNPPAGEEEF+LDLL NR+PPGVDEA
Sbjct: 1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELIELVKNPPAGEEEFILDLLENRIPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL A+AKGEA SP+L+ +A+ELLGTMQGGYNI PLI LD+ AP+A KALS
Sbjct: 61 AYVKAGFLDAVAKGEATSPILSAARAVELLGTMQGGYNIEPLIAQLDNDVQAPLAVKALS 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
+TLLMFD ++DV EK +AGN +AKQV++SWA+AEWFL+RP LA+K+T+TVFKVTGETNTD
Sbjct: 121 NTLLMFDAYHDVVEKMQAGNAHAKQVVESWANAEWFLSRPKLADKVTLTVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKNAR+GI PD+ GV GPI +IEAL+QKG PL YVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNARDGIVPDEAGVKGPINEIEALKQKGHPLVYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWFMGDDIP VPNKR GG CLGGKIAPIFFNTMEDAGALPIE+DVS
Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSK 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+NMGDVID+YPY+G V+ H + E+++ F+LKTDVL+DEVRAGGRIPLIIGRGLT +ARE
Sbjct: 301 MNMGDVIDIYPYEGVVKLHGSDEVISEFKLKTDVLLDEVRAGGRIPLIIGRGLTDRARET 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP SDVF + +DVA+S +G++LAQKMVG+ACGV G+RPG YCEPKMTSVGSQDTTGPM
Sbjct: 361 LGLPASDVFVRPQDVADSGKGYTLAQKMVGKACGVAGVRPGQYCEPKMTSVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADL MQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 421 TRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPES+LVRFKG+M
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEM 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIP AI+ GLLTVEKKGK N FSGRILEIEGL LKVEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRILEIEGLEKLKVEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKL+KEPIIEYLNSNIV+LKWMIAEGYGDRRT+ERRI ME+WLANPEL+ A
Sbjct: 601 ERSAAGCTIKLDKEPIIEYLNSNIVMLKWMIAEGYGDRRTIERRIAAMEEWLANPELMAA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEYA VI+IDL +IKEPILCAPNDPDDA LS V+ +IDEVF+GSCMTNIGHFRA
Sbjct: 661 DADAEYAEVIEIDLNEIKEPILCAPNDPDDAVLLSQVKDTQIDEVFVGSCMTNIGHFRAT 720
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GK+LD LPTRLW+APPT+MD QLTEEGYY++FG+ GARIEIPGCSLCMGNQARVA
Sbjct: 721 GKMLDKFAKTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQARVA 780
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
+GATVVSTSTRNFPNRLGTGANV+LASAELAAVAAL+G+LP+ EEYQ Y ++D TA DT
Sbjct: 781 EGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSVEEYQEYAKEIDATAADT 840
Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
YRYLNF+Q+ YT+KA VIFQ+AV
Sbjct: 841 YRYLNFDQIDSYTQKAGEVIFQSAV 865
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: 2167
Number of extensions: 77
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: 865
Length adjustment: 42
Effective length of query: 823
Effective length of database: 823
Effective search space: 677329
Effective search space used: 677329
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 5210998 Shew_3424 (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.2670.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 1581.0 0.0 0 1580.8 0.0 1.0 1 lcl|FitnessBrowser__PV4:5210998 Shew_3424 bifunctional aconitate
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__PV4:5210998 Shew_3424 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase (RefSeq)
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1580.8 0.0 0 0 1 843 [. 1 853 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1580.8 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakgevks 78
+le+yrkhvaeraaeg+ p+pl+a+qva+l+el+kn+p++eeef+l+ll +r+ppgvdeaayvkagfl a+akge++s
lcl|FitnessBrowser__PV4:5210998 1 MLEAYRKHVAERAAEGVVPKPLDAHQVAELIELVKNPPAGEEEFILDLLENRIPPGVDEAAYVKAGFLDAVAKGEATS 78
79**************************************************************************** PP
TIGR00117 79 plisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvleswaeae 155
p +sa +avellgtm+ggyn+epli +l+ + a+ a kals+tll+fda++dv e+ ++ n++akqv+eswa+ae
lcl|FitnessBrowser__PV4:5210998 79 PILSAARAVELLGTMQGGYNIEPLIAQLD--NDVQAPLAVKALSNTLLMFDAYHDVVEKMQAgNAHAKQVVESWANAE 154
*****************************..44569*******************99998888*************** PP
TIGR00117 156 wflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........rikalkqkgvp 223
wfl +++la+k+t tvfkv+getntddlspapda++rpdiplhalamlkn++++i + +i+alkqkg+p
lcl|FitnessBrowser__PV4:5210998 155 WFLSRPKLADKVTLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNARDGIVPdeagvkgpinEIEALKQKGHP 232
*******************************************************9999******************* PP
TIGR00117 224 vayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdvkdlnegdvikiy 301
+ yvgdvvgtgssrksatnsvlwf+g+dipfvpnkragg++lggkiapiffnt+ed+galpie dv+++n+gdvi+iy
lcl|FitnessBrowser__PV4:5210998 233 LVYVGDVVGTGSSRKSATNSVLWFMGDDIPFVPNKRAGGFCLGGKIAPIFFNTMEDAGALPIELDVSKMNMGDVIDIY 310
****************************************************************************** PP
TIGR00117 302 pykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfkkakapaesakgftlaqkl 378
py+g ++++ + ev++ fklk+++lldevraggripliigrgltd+are+lgl+ s+vf++++++a+s+kg+tlaqk+
lcl|FitnessBrowser__PV4:5210998 311 PYEGVVKLHGSdEVISEFKLKTDVLLDEVRAGGRIPLIIGRGLTDRARETLGLPASDVFVRPQDVADSGKGYTLAQKM 388
*********9889***************************************************************** PP
TIGR00117 379 vgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisq 456
vgkacgv g+rpg ycepk+t+vgsqdttg+mtrdelk+la+lgf+adl++qsfchtaaypkpvdv+th+tlpdfi++
lcl|FitnessBrowser__PV4:5210998 389 VGKACGVAGVRPGQYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSADLTMQSFCHTAAYPKPVDVNTHHTLPDFIMN 466
****************************************************************************** PP
TIGR00117 457 rggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgi 534
rggv+lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpes+lvrfkge+qpgi
lcl|FitnessBrowser__PV4:5210998 467 RGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESILVRFKGEMQPGI 544
****************************************************************************** PP
TIGR00117 535 tlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvieylks 612
tlrdlv+aip+ ai+ glltvekkgk+n f+grileiegl lkveqafel+dasaersaagctikl+kep+ieyl+s
lcl|FitnessBrowser__PV4:5210998 545 TLRDLVHAIPHKAIEMGLLTVEKKGKINAFSGRILEIEGLEKLKVEQAFELSDASAERSAAGCTIKLDKEPIIEYLNS 622
****************************************************************************** PP
TIGR00117 613 nivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndpddvkllsevagd 690
niv+lk+miaegy+d+rt++rri+ame+wlanpel+ adadaeya+vieidl+eikepil+apndpdd+ lls+v+
lcl|FitnessBrowser__PV4:5210998 623 NIVMLKWMIAEGYGDRRTIERRIAAMEEWLANPELMAADADAEYAEVIEIDLNEIKEPILCAPNDPDDAVLLSQVKDT 700
****************************************************************************** PP
TIGR00117 691 aidevfigscmtnighfraagkilea.aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqar 767
+idevf+gscmtnighfra+gk+l++ akt+++rlw++ppt+md +ql+eegyyaifg+ gar+e+pgcslcmgnqar
lcl|FitnessBrowser__PV4:5210998 701 QIDEVFVGSCMTNIGHFRATGKMLDKfAKTLPTRLWIAPPTKMDRDQLTEEGYYAIFGRVGARIEIPGCSLCMGNQAR 778
************************983569************************************************ PP
TIGR00117 768 vedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
v++gatv+ststrnf+nrlg+ga+vyl+saelaavaallg++p++eey+++ e +++a d +yrylnf++++ ++
lcl|FitnessBrowser__PV4:5210998 779 VAEGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALLGRLPSVEEYQEYAKEIDATAAD-TYRYLNFDQIDSYT 853
**********************************************************999.************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (865 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.05
# Mc/sec: 13.07
//
[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