Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_053935988.1 WG78_RS01390 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_001294205.1:WP_053935988.1
Length = 861
Score = 1271 bits (3288), Expect = 0.0
Identities = 633/862 (73%), Positives = 724/862 (83%), Gaps = 6/862 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR+HVAERAA GI P PL A Q AALVELL+NPPAGEE FLLDL+T+RVPPGVD+A
Sbjct: 1 MLESYRQHVAERAALGIPPLPLTAQQTAALVELLQNPPAGEESFLLDLITHRVPPGVDDA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA FLAA+A+G+ L++ A+ELL TM GG+NI P+ID L DA++ +AA+ L
Sbjct: 61 AKVKAAFLAAVAQGKDSCALISRAHAVELLATMLGGFNIKPMIDLLGDAEVGAVAAEGLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD F+DV+ A +GN AK V+QSWADAEWF +RP + + +T+TVFKVTGETNTD
Sbjct: 121 KTLLMFDYFHDVKALADSGNANAKAVLQSWADAEWFTSRPEVPQSVTLTVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKN R+GI P++ G GPIK ++ L KG +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNTRDGITPEEDGKRGPIKFLQDLAAKGHAVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLW+ G+DIP+VPNKR GG CLGGKIAPIFFNT ED+GALPIEVDVS
Sbjct: 241 GTGSSRKSATNSVLWWTGEDIPYVPNKRFGGYCLGGKIAPIFFNTQEDSGALPIEVDVSQ 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
LNMGDVI++ PY G+++ + G +++ F++K+DVL DEVRAGGRI LIIGRGLT KAREA
Sbjct: 301 LNMGDVIELLPYAGQIKKN--GAVVSEFKVKSDVLFDEVRAGGRINLIIGRGLTAKAREA 358
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGLP S +FR S +GF+ AQKMVGRA G+ +G+RPG YCEP+MTSVGSQDTT
Sbjct: 359 LGLPVSTLFRLPTAPVTSTKGFTQAQKMVGRAVGLPEGQGVRPGTYCEPRMTSVGSQDTT 418
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THH LP+FI NRGGVSLRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHELPEFIRNRGGVSLRPGDG 478
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAF AATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFGAATGVMPLDMPESVLVRFK 538
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
G++QPGITLRDLV+AIPLYAIK GLLTV K GK NIFSGRILEIEGLP LKVEQAFELTD
Sbjct: 539 GELQPGITLRDLVNAIPLYAIKAGLLTVAKAGKTNIFSGRILEIEGLPKLKVEQAFELTD 598
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGC+++L+KEPIIEYLNSNI LLK MIA GYGD +TL RR+ ME WLANP L
Sbjct: 599 ASAERSAAGCSVRLDKEPIIEYLNSNITLLKSMIANGYGDAKTLARRVNAMEAWLANPNL 658
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
+E DADAEYAAVI+IDLAD+KEPIL PNDPDD + LS V G IDEVFIGSCMTNIGHF
Sbjct: 659 IEPDADAEYAAVIEIDLADVKEPILACPNDPDDVKVLSEVAGTHIDEVFIGSCMTNIGHF 718
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ K +P +LW+APPT+MDA QLTEEGYY FG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAAGKLLEG-KRDIPVKLWIAPPTKMDAQQLTEEGYYGTFGTAGARTEMPGCSLCMGNQA 777
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
+V +GATVVSTSTRNFPNRLG NVFL+SAELAA+A+ +G++PT EY + +++
Sbjct: 778 QVREGATVVSTSTRNFPNRLGKNTNVFLSSAELAAIASRLGRIPTVAEYMADIGVINEKG 837
Query: 838 VDTYRYLNFNQLSQYTEKADGV 859
+ YRYLNFNQ+ Y +AD V
Sbjct: 838 AEVYRYLNFNQIETYQAEADTV 859
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: 1975
Number of extensions: 77
Number of successful extensions: 4
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: 861
Length adjustment: 42
Effective length of query: 823
Effective length of database: 819
Effective search space: 674037
Effective search space used: 674037
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_053935988.1 WG78_RS01390 (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.3096947.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 1499.6 0.0 0 1499.3 0.0 1.0 1 NCBI__GCF_001294205.1:WP_053935988.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_001294205.1:WP_053935988.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1499.3 0.0 0 0 1 843 [. 1 853 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1499.3 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73
+le yr+hvaeraa+gi+plpl a+q+aalvell+n+p++ee fll+l+++rvppgvd+aa+vka flaa+a+
NCBI__GCF_001294205.1:WP_053935988.1 1 MLESYRQHVAERAALGIPPLPLTAQQTAALVELLQNPPAGEESFLLDLITHRVPPGVDDAAKVKAAFLAAVAQ 73
79*********************************************************************** PP
TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145
g+ ++lis +avell tmlgg+n++p+i++l d+++ +aa+ l+ktll+fd f+dv++l+++ n+ ak
NCBI__GCF_001294205.1:WP_053935988.1 74 GKDSCALISRAHAVELLATMLGGFNIKPMIDLLG--DAEVGAVAAEGLKKTLLMFDYFHDVKALADSgNANAK 144
*********************************9..******************************99***** PP
TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq...... 212
vl+swa+aewf ++e+++ +t tvfkv+getntddlspapda++rpdiplhalamlkn +++i +
NCBI__GCF_001294205.1:WP_053935988.1 145 AVLQSWADAEWFTSRPEVPQSVTLTVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKNTRDGITPeedgkr 217
****************************************************************9999999*9 PP
TIGR00117 213 ....rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsg 281
+++l kg+ vayvgdvvgtgssrksatnsvlw+ g+dip+vpnkr gg++lggkiapiffnt edsg
NCBI__GCF_001294205.1:WP_053935988.1 218 gpikFLQDLAAKGHAVAYVGDVVGTGSSRKSATNSVLWWTGEDIPYVPNKRFGGYCLGGKIAPIFFNTQEDSG 290
9887789999*************************************************************** PP
TIGR00117 282 alpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealgls 354
alpievdv++ln+gdvi++ py g+i+++ vv+ fk+k+++l+devraggri liigrglt karealgl+
NCBI__GCF_001294205.1:WP_053935988.1 291 ALPIEVDVSQLNMGDVIELLPYAGQIKKNG-AVVSEFKVKSDVLFDEVRAGGRINLIIGRGLTAKAREALGLP 362
**************************9876.9***************************************** PP
TIGR00117 355 esevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfd 424
s +f+ ++ap s+kgft aqk+vg+a g+ +g+rpgtycep++t+vgsqdttg+mtrdelk+la+lgf+
NCBI__GCF_001294205.1:WP_053935988.1 363 VSTLFRLPTAPVTSTKGFTQAQKMVGRAVGLpegQGVRPGTYCEPRMTSVGSQDTTGPMTRDELKDLACLGFS 435
******************************87669************************************** PP
TIGR00117 425 adlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgis 497
adlv+qsfchtaaypkpvdvkth++lp+fi +rggv+lrpgdgvihswlnrmllpdtvgtggdshtrfp+gis
NCBI__GCF_001294205.1:WP_053935988.1 436 ADLVMQSFCHTAAYPKPVDVKTHHELPEFIRNRGGVSLRPGDGVIHSWLNRMLLPDTVGTGGDSHTRFPIGIS 508
************************************************************************* PP
TIGR00117 498 fpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrile 570
fpagsglvaf aatgvmpldmpesvlvrfkgelqpgitlrdlvnaip+yaik glltv k gk n+f+grile
NCBI__GCF_001294205.1:WP_053935988.1 509 FPAGSGLVAFGAATGVMPLDMPESVLVRFKGELQPGITLRDLVNAIPLYAIKAGLLTVAKAGKTNIFSGRILE 581
************************************************************************* PP
TIGR00117 571 ieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwla 643
ieglp lkveqafeltdasaersaagc ++l+kep+ieyl+sni llk mia+gy+d++tl rr++ame+wla
NCBI__GCF_001294205.1:WP_053935988.1 582 IEGLPKLKVEQAFELTDASAERSAAGCSVRLDKEPIIEYLNSNITLLKSMIANGYGDAKTLARRVNAMEAWLA 654
************************************************************************* PP
TIGR00117 644 npelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkilea 716
np+l+e+dadaeyaavieidla++kepila+pndpddvk+lsevag idevfigscmtnighfraagk+le+
NCBI__GCF_001294205.1:WP_053935988.1 655 NPNLIEPDADAEYAAVIEIDLADVKEPILACPNDPDDVKVLSEVAGTHIDEVFIGSCMTNIGHFRAAGKLLEG 727
************************************************************************* PP
TIGR00117 717 aktvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkg 789
+++++ +lw++ppt+md+qql+eegyy+ fg+agarte+pgcslcmgnqa+v++gatv+ststrnf+nrlgk
NCBI__GCF_001294205.1:WP_053935988.1 728 KRDIPVKLWIAPPTKMDAQQLTEEGYYGTFGTAGARTEMPGCSLCMGNQAQVREGATVVSTSTRNFPNRLGKN 800
************************************************************************* PP
TIGR00117 790 akvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfe 843
++v+l+saelaa+a+ lg+ipt+ ey+a + e ++yrylnfn++e ++
NCBI__GCF_001294205.1:WP_053935988.1 801 TNVFLSSAELAAIASRLGRIPTVAEYMADIGVINEKG-AEVYRYLNFNQIETYQ 853
****************************998766655.55***********997 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (861 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: 20.48
//
[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