Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_010961708.1 MCA_RS12190 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_000008325.1:WP_010961708.1
Length = 858
Score = 1319 bits (3413), Expect = 0.0
Identities = 643/856 (75%), Positives = 742/856 (86%), Gaps = 7/856 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
ML +YR+HVAERAA+G+ PKPL A Q AALVELLK+PPAGEE FLLDLL+NRVP GVDEA
Sbjct: 1 MLTQYREHVAERAAQGLVPKPLTAEQTAALVELLKSPPAGEEAFLLDLLSNRVPAGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFLAA+A+GEA SP+++P +A ELLGTM GGYN+ PLI+ LD ++LAP+AA LS
Sbjct: 61 AYVKAGFLAAVARGEAVSPIVSPRRATELLGTMLGGYNVAPLIELLDHSELAPVAAHGLS 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD F+DV+ KA+AGN +A+ V+++WADAEWF +RP + KLTVTVFKV GETNTD
Sbjct: 121 RTLLMFDAFHDVQVKAEAGNVHAQAVLRAWADAEWFTSRPEVPGKLTVTVFKVPGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPA DAWSRPDIPLHA +MLK REGI + QI L+ KGFP+AYVGDVV
Sbjct: 181 DLSPAQDAWSRPDIPLHAKSMLKVPREGIHDAEA-------QIAELKTKGFPVAYVGDVV 233
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNS+LW++G+DIPHVPNKR GG+C+GGKIAPIFFNT+ED+GALPIE DV+
Sbjct: 234 GTGSSRKSATNSLLWYIGEDIPHVPNKRQGGVCIGGKIAPIFFNTLEDSGALPIECDVTA 293
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ GDVID++PY+G +RNHE+G L F LKT++L+DEVRAGGRI LIIGRGLT +AR+
Sbjct: 294 MQTGDVIDIHPYEGVLRNHESGVELCRFTLKTEILLDEVRAGGRINLIIGRGLTDRARKV 353
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGLP S+VFR+ + E+ +G++LAQK+VG+ACGV GIRPG YCEP MT+VGSQDTTGPM
Sbjct: 354 LGLPPSEVFRRPRAPIETGKGYTLAQKIVGKACGVAGIRPGTYCEPAMTTVGSQDTTGPM 413
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADLV+QSFCHTAAYPKPVDV THHTLPDFIMNRGGVSLRPGDG+IH
Sbjct: 414 TRDELKDLACLGFSADLVLQSFCHTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIH 473
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKG+M
Sbjct: 474 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGEM 533
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIP A+++GLLTVEK+GKKN+FSGRILEIEGLPDLKVEQAFEL DASA
Sbjct: 534 QPGITLRDLVHAIPYVALQRGLLTVEKQGKKNVFSGRILEIEGLPDLKVEQAFELADASA 593
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAA CTIKL++ PI EYL+SNI LL+WMIAEGYGD RTL RRI ME WLA+P+LLEA
Sbjct: 594 ERSAAACTIKLDRAPIEEYLHSNITLLRWMIAEGYGDARTLRRRIAAMEAWLADPQLLEA 653
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
D DAEYA VI+IDL I EP+LC PNDPDD +PLS V G IDEVF+GSCMTNIGHFRAA
Sbjct: 654 DPDAEYAEVIEIDLDQITEPLLCCPNDPDDVKPLSQVAGTHIDEVFLGSCMTNIGHFRAA 713
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
G+LL+A PTRLW+APPTRMD AQLTEEGYY+ +GK+GAR E+PGCSLCMGNQARVA
Sbjct: 714 GRLLEAFGKPTPTRLWIAPPTRMDQAQLTEEGYYATYGKAGARTEMPGCSLCMGNQARVA 773
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
D ATVVSTSTRNFPNRLG GA VFLASAELAAV +++G++P+ EEY Y ++++ A DT
Sbjct: 774 DNATVVSTSTRNFPNRLGAGARVFLASAELAAVCSILGRIPSLEEYMAYAGKIEEKAADT 833
Query: 841 YRYLNFNQLSQYTEKA 856
YRYLNF++ Y E+A
Sbjct: 834 YRYLNFDRTPAYAERA 849
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: 2025
Number of extensions: 69
Number of successful extensions: 2
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: 858
Length adjustment: 42
Effective length of query: 823
Effective length of database: 816
Effective search space: 671568
Effective search space used: 671568
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_010961708.1 MCA_RS12190 (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.608012.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 1537.8 0.0 0 1537.6 0.0 1.0 1 NCBI__GCF_000008325.1:WP_010961708.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000008325.1:WP_010961708.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1537.6 0.0 0 0 1 842 [. 1 845 [. 1 847 [. 0.99
Alignments for each domain:
== domain 1 score: 1537.6 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73
+l +yr hvaeraa+g+ p+pl a+q+aalvellk +p++ee+fll+ll +rvp gvdeaayvkagflaa+a+
NCBI__GCF_000008325.1:WP_010961708.1 1 MLTQYREHVAERAAQGLVPKPLTAEQTAALVELLKSPPAGEEAFLLDLLSNRVPAGVDEAAYVKAGFLAAVAR 73
799********************************************************************** PP
TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145
ge+ sp +s+++a+ellgtmlggynv plie+l+ +++a++aa+ ls+tll+fdaf+dv+ ++++ n +a+
NCBI__GCF_000008325.1:WP_010961708.1 74 GEAVSPIVSPRRATELLGTMLGGYNVAPLIELLD--HSELAPVAAHGLSRTLLMFDAFHDVQVKAEAgNVHAQ 144
**********************************..899***************************99***** PP
TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq...rik 215
vl +wa+aewf ++e++ k+tvtvfkv+getntddlspa da++rpdiplha++mlk +e+i++ +i+
NCBI__GCF_000008325.1:WP_010961708.1 145 AVLRAWADAEWFTSRPEVPGKLTVTVFKVPGETNTDDLSPAQDAWSRPDIPLHAKSMLKVPREGIHDaeaQIA 217
***********************************************************98887654444*** PP
TIGR00117 216 alkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievd 288
+lk+kg+pvayvgdvvgtgssrksatns+lw++g+dip+vpnkr gg+++ggkiapiffnt+edsgalpie+d
NCBI__GCF_000008325.1:WP_010961708.1 218 ELKTKGFPVAYVGDVVGTGSSRKSATNSLLWYIGEDIPHVPNKRQGGVCIGGKIAPIFFNTLEDSGALPIECD 290
************************************************************************* PP
TIGR00117 289 vkdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealglsesevfk 360
v +++gdvi+i+py+g ++n+e+ ++ f lk+e+lldevraggri liigrgltd+ar++lgl++sevf+
NCBI__GCF_000008325.1:WP_010961708.1 291 VTAMQTGDVIDIHPYEGVLRNHESgVELCRFTLKTEILLDEVRAGGRINLIIGRGLTDRARKVLGLPPSEVFR 363
***********************956699******************************************** PP
TIGR00117 361 kakapaesakgftlaqklvgkacgvkgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfc 433
+++ap e++kg+tlaqk+vgkacgv girpgtycep +ttvgsqdttg+mtrdelk+la+lgf+adlvlqsfc
NCBI__GCF_000008325.1:WP_010961708.1 364 RPRAPIETGKGYTLAQKIVGKACGVAGIRPGTYCEPAMTTVGSQDTTGPMTRDELKDLACLGFSADLVLQSFC 436
************************************************************************* PP
TIGR00117 434 htaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglva 506
htaaypkpvdv+th+tlpdfi++rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglva
NCBI__GCF_000008325.1:WP_010961708.1 437 HTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVA 509
************************************************************************* PP
TIGR00117 507 faaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkv 579
faaatgvmpldmpesvlvrfkge+qpgitlrdlv+aipy+a+++glltvek+gk+nvf+grileieglpdlkv
NCBI__GCF_000008325.1:WP_010961708.1 510 FAAATGVMPLDMPESVLVRFKGEMQPGITLRDLVHAIPYVALQRGLLTVEKQGKKNVFSGRILEIEGLPDLKV 582
************************************************************************* PP
TIGR00117 580 eqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleada 652
eqafel+dasaersaa+ctikl++ p+ eyl+sni ll++miaegy+d+rtl+rri+ame+wla+p+llead
NCBI__GCF_000008325.1:WP_010961708.1 583 EQAFELADASAERSAAACTIKLDRAPIEEYLHSNITLLRWMIAEGYGDARTLRRRIAAMEAWLADPQLLEADP 655
************************************************************************* PP
TIGR00117 653 daeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarl 724
daeya+vieidl++i+ep+l++pndpddvk+ls+vag idevf+gscmtnighfraag++lea + ++++rl
NCBI__GCF_000008325.1:WP_010961708.1 656 DAEYAEVIEIDLDQITEPLLCCPNDPDDVKPLSQVAGTHIDEVFLGSCMTNIGHFRAAGRLLEAFGkPTPTRL 728
****************************************************************97699**** PP
TIGR00117 725 wvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsa 797
w++pptrmd++ql+eegyya +g+agarte+pgcslcmgnqarv+d+atv+ststrnf+nrlg ga+v+l+sa
NCBI__GCF_000008325.1:WP_010961708.1 729 WIAPPTRMDQAQLTEEGYYATYGKAGARTEMPGCSLCMGNQARVADNATVVSTSTRNFPNRLGAGARVFLASA 801
************************************************************************* PP
TIGR00117 798 elaavaallgkiptkeeylalvsekvesakdklyrylnfnelenf 842
elaav+++lg+ip+ eey+a+ + e a d +yrylnf++ +
NCBI__GCF_000008325.1:WP_010961708.1 802 ELAAVCSILGRIPSLEEYMAYAGKIEEKAAD-TYRYLNFDRTPAY 845
*********************9999888888.*******987666 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (858 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.02
# Mc/sec: 28.84
//
[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