Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_115185091.1 AFK65_RS03735 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_001277175.1:WP_115185091.1
Length = 865
Score = 1637 bits (4240), Expect = 0.0
Identities = 812/865 (93%), Positives = 843/865 (97%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLEEYRKHVAERAAEGI KPLDA QMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA
Sbjct: 1 MLEEYRKHVAERAAEGIVAKPLDATQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFLAA+AKGEA SPL+TPEKA+ELLGTMQGGYNIHPLI+ALD+ LAPIAAKALS
Sbjct: 61 AYVKAGFLAAVAKGEATSPLVTPEKAVELLGTMQGGYNIHPLIEALDNDTLAPIAAKALS 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFDNFYDVEEKAKAGN YAKQ+MQSWADAEWFL+RPALA+K+TVTVFKVTGETNTD
Sbjct: 121 HTLLMFDNFYDVEEKAKAGNAYAKQIMQSWADAEWFLSRPALADKITVTVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPG VGPIKQIEALQQKGFPLAYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGSVGPIKQIEALQQKGFPLAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWFMGDDIP+VPNKRGGG+ LGGKIAPIFFNTMEDAGALPIEVDVSN
Sbjct: 241 GTGSSRKSATNSVLWFMGDDIPYVPNKRGGGVVLGGKIAPIFFNTMEDAGALPIEVDVSN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
LNMGDVID+YPY GEVRNHETGELLA FELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA
Sbjct: 301 LNMGDVIDIYPYSGEVRNHETGELLANFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLPHSDVFR AKDVAES+RG+SLAQKMVGRACGV G+RPGAYCEPKMTSVGSQDTTGPM
Sbjct: 361 LGLPHSDVFRHAKDVAESNRGYSLAQKMVGRACGVAGVRPGAYCEPKMTSVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLPDFIMNRGGVSLRPGDGVIH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG++
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGQL 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIP YAI+QGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA
Sbjct: 541 QPGITLRDLVHAIPYYAIQQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLA+P+LLEA
Sbjct: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQLLEA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEYAAVI+IDL +IKEPILCAPNDPDDAR LS V G+KIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAAVIEIDLNEIKEPILCAPNDPDDARLLSDVTGDKIDEVFIGSCMTNIGHFRAA 720
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GKLLD HKGQLPTRLW+APPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA
Sbjct: 721 GKLLDTHKGQLPTRLWMAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
DGATVVSTSTRNFPNRLGTGANV+LASAELAAVAALIG+LPTP+EYQ +++QVDKTAVDT
Sbjct: 781 DGATVVSTSTRNFPNRLGTGANVYLASAELAAVAALIGRLPTPDEYQQFMSQVDKTAVDT 840
Query: 841 YRYLNFNQLSQYTEKADGVIFQTAV 865
YRYLNF+QL QYTEKADGVIFQTAV
Sbjct: 841 YRYLNFDQLDQYTEKADGVIFQTAV 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: 2289
Number of extensions: 69
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 WP_115185091.1 AFK65_RS03735 (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.3654980.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 1675.6 0.0 0 1675.4 0.0 1.0 1 NCBI__GCF_001277175.1:WP_115185091.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001277175.1:WP_115185091.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1675.4 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 1.00
Alignments for each domain:
== domain 1 score: 1675.4 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73
+leeyrkhvaeraaegi +pl+a q+aalvellkn+p++eeefll+ll++rvppgvdeaayvkagflaa+ak
NCBI__GCF_001277175.1:WP_115185091.1 1 MLEEYRKHVAERAAEGIVAKPLDATQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEAAYVKAGFLAAVAK 73
79*********************************************************************** PP
TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145
ge++spl+++e+avellgtm+ggyn++plieal+ + +a++aakals+tll+fd+f+dvee++k+ n+yak
NCBI__GCF_001277175.1:WP_115185091.1 74 GEATSPLVTPEKAVELLGTMQGGYNIHPLIEALD--NDTLAPIAAKALSHTLLMFDNFYDVEEKAKAgNAYAK 144
**********************************..778****************************9***** PP
TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq...... 212
q+++swa+aewfl +++la+kitvtvfkv+getntddlspapda++rpdiplhalamlkn++e+ie+
NCBI__GCF_001277175.1:WP_115185091.1 145 QIMQSWADAEWFLSRPALADKITVTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNAREGIEPdqpgsv 217
******************************************************************99***** PP
TIGR00117 213 ....rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsg 281
+i+al+qkg+p+ayvgdvvgtgssrksatnsvlwf+g+dip+vpnkr+gg+vlggkiapiffnt+ed+g
NCBI__GCF_001277175.1:WP_115185091.1 218 gpikQIEALQQKGFPLAYVGDVVGTGSSRKSATNSVLWFMGDDIPYVPNKRGGGVVLGGKIAPIFFNTMEDAG 290
************************************************************************* PP
TIGR00117 282 alpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealgl 353
alpievdv++ln+gdvi+iypy ge++n+et e++a f+lk+++l+devraggripliigrglt+karealgl
NCBI__GCF_001277175.1:WP_115185091.1 291 ALPIEVDVSNLNMGDVIDIYPYSGEVRNHETgELLANFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREALGL 363
******************************99***************************************** PP
TIGR00117 354 sesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdad 426
++s+vf++ak++aes++g++laqk+vg+acgv g+rpg+ycepk+t+vgsqdttg+mtrdelk+la+lgf+ad
NCBI__GCF_001277175.1:WP_115185091.1 364 PHSDVFRHAKDVAESNRGYSLAQKMVGRACGVAGVRPGAYCEPKMTSVGSQDTTGPMTRDELKDLACLGFSAD 436
************************************************************************* PP
TIGR00117 427 lvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfp 499
lv+qsfchtaaypkpvdv th+tlpdfi++rggv+lrpgdgvihswlnrmllpdtvgtggdshtrfp+gisfp
NCBI__GCF_001277175.1:WP_115185091.1 437 LVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGISFP 509
************************************************************************* PP
TIGR00117 500 agsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileie 572
agsglvafaaatgvmpldmpesvlvrfkg+lqpgitlrdlv+aipyyai++glltvekkgk+n+f+grileie
NCBI__GCF_001277175.1:WP_115185091.1 510 AGSGLVAFAAATGVMPLDMPESVLVRFKGQLQPGITLRDLVHAIPYYAIQQGLLTVEKKGKKNIFSGRILEIE 582
************************************************************************* PP
TIGR00117 573 glpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanp 645
glpdlkveqafeltdasaersaagctiklnkep+ieyl+snivllk+miaegy+d+rtl+rri++mekwla+p
NCBI__GCF_001277175.1:WP_115185091.1 583 GLPDLKVEQAFELTDASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADP 655
************************************************************************* PP
TIGR00117 646 elleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak 718
+lleadadaeyaavieidl+eikepil+apndpdd++lls+v+gd+idevfigscmtnighfraagk+l+++k
NCBI__GCF_001277175.1:WP_115185091.1 656 QLLEADADAEYAAVIEIDLNEIKEPILCAPNDPDDARLLSDVTGDKIDEVFIGSCMTNIGHFRAAGKLLDTHK 728
************************************************************************9 PP
TIGR00117 719 .tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkga 790
++++rlw++pptrmd++ql+eegyy++fg++gar+e+pgcslcmgnqarv+dgatv+ststrnf+nrlg+ga
NCBI__GCF_001277175.1:WP_115185091.1 729 gQLPTRLWMAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVADGATVVSTSTRNFPNRLGTGA 801
9************************************************************************ PP
TIGR00117 791 kvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfee 844
+vyl+saelaavaal+g++pt++ey++++s+++++a+d +yrylnf++l++++e
NCBI__GCF_001277175.1:WP_115185091.1 802 NVYLASAELAAVAALIGRLPTPDEYQQFMSQVDKTAVD-TYRYLNFDQLDQYTE 854
**************************************.*************85 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: 0.03u 0.01s 00:00:00.04 Elapsed: 00:00:00.03
# Mc/sec: 20.18
//
[ok]
This GapMind analysis is from Sep 24 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