Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate RR42_RS23515 RR42_RS23515 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__Cup4G11:RR42_RS23515
Length = 861
Score = 1280 bits (3312), Expect = 0.0
Identities = 637/862 (73%), Positives = 731/862 (84%), Gaps = 6/862 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR HVAERAA GI P PL A Q A L+ELLK+PPAGEE+ L+DL+T+RVP GVD+A
Sbjct: 1 MLENYRAHVAERAALGIPPLPLTAKQTAELIELLKSPPAGEEQVLVDLITHRVPAGVDDA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA +LAA+A G+ L++ KA ELLGTM GGYNI PLI+ LDDA++ P+AA+AL
Sbjct: 61 AKVKASYLAAVALGKEACALISRAKAAELLGTMLGGYNISPLIELLDDAEIGPVAAEALK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD F+DV+EKA GN AK V+QSWADAEWF +RP + + LTVTVFKVTGETNTD
Sbjct: 121 KTLLMFDAFHDVKEKADKGNAIAKSVLQSWADAEWFTSRPEVPQSLTVTVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDA +RPDIPLHALAMLKNAR GI P++ G GP+K IE+L++KG +AYVGDVV
Sbjct: 181 DLSPAPDATTRPDIPLHALAMLKNARPGITPEEDGKRGPVKFIESLKEKGNLVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF G+DIP VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS
Sbjct: 241 GTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ MGDV+++ PY G+ + G+++A F +K+DVL DEVRAGGRIPLI+GRGLT KAREA
Sbjct: 301 MEMGDVVELRPYDGKALKN--GQVIAEFTVKSDVLFDEVRAGGRIPLIVGRGLTAKAREA 358
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGL S +FR + A++ RGF+LAQKMVGRACG+ KGIRPG YCEPKMTSVGSQDTT
Sbjct: 359 LGLAPSTLFRLPHNPADTGRGFTLAQKMVGRACGLPEGKGIRPGTYCEPKMTSVGSQDTT 418
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDV THHTLP FI RGG+SLRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPQFISTRGGISLRPGDG 478
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GKMQPG+TLRDLV+AIPLYAIK GLLTV K+GKKNIFSGR+LEIEGLPDLKVEQAFEL+D
Sbjct: 539 GKMQPGVTLRDLVNAIPLYAIKSGLLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSD 598
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGC+++LNKEPIIEY+NSNI LLKWMIAEGY D R+L RRIQ ME WLA+P+L
Sbjct: 599 ASAERSAAGCSVRLNKEPIIEYINSNITLLKWMIAEGYQDPRSLSRRIQAMEAWLADPKL 658
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
LE DADAEYAAVI+IDLAD+ EPI+ PNDPDD + LS V G KIDEVFIGSCMTNIGHF
Sbjct: 659 LEPDADAEYAAVIEIDLADVHEPIVACPNDPDDVKTLSEVAGAKIDEVFIGSCMTNIGHF 718
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAA KLL+ K +P +LWVAPPT+MDA QLTEEG+Y VFG +GAR E+PGCSLCMGNQA
Sbjct: 719 RAASKLLEG-KRDIPVKLWVAPPTKMDAKQLTEEGHYGVFGTAGARTEMPGCSLCMGNQA 777
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
+V +GATV+STSTRNFPNRLG NV+L SAELAA+ + +G++PT EEY + + +
Sbjct: 778 QVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEEYMSDMGVLATNG 837
Query: 838 VDTYRYLNFNQLSQYTEKADGV 859
Y+YLNF+++ + AD V
Sbjct: 838 DQIYKYLNFDKIEDFKGVADTV 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: 2045
Number of extensions: 73
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 RR42_RS23515 RR42_RS23515 (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.26679.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 1518.9 0.0 0 1518.7 0.0 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS23515 RR42_RS23515 bifunctional aconit
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Cup4G11:RR42_RS23515 RR42_RS23515 bifunctional aconitate hydratase 2/2-methylisocitrate dehydrat
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1518.7 0.0 0 0 1 843 [. 1 853 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1518.7 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr hvaeraa+gi+plpl akq+a+l+ellk +p++ee+ l++l+++rvp gvd+aa+vka +la
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 1 MLENYRAHVAERAALGIPPLPLTAKQTAELIELLKSPPAGEEQVLVDLITHRVPAGVDDAAKVKASYLA 69
79******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
a+a g+ ++lis +a ellgtmlggyn+ plie+l+ d++i ++aa+al+ktll+fdaf+dv+e++
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 70 AVALGKEACALISRAKAAELLGTMLGGYNISPLIELLD--DAEIGPVAAEALKKTLLMFDAFHDVKEKA 136
**************************************..****************************9 PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
+ n++ak vl+swa+aewf ++e+++ +tvtvfkv+getntddlspapda+trpdiplhalamlkn+
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 137 DKgNAIAKSVLQSWADAEWFTSRPEVPQSLTVTVFKVTGETNTDDLSPAPDATTRPDIPLHALAMLKNA 205
888****************************************************************** PP
TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
+++i + i++lk+kg vayvgdvvgtgssrksatnsvlwf g+dipfvpnkr gg++l
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 206 RPGITPeedgkrgpvkFIESLKEKGNLVAYVGDVVGTGSSRKSATNSVLWFTGEDIPFVPNKRFGGVCL 274
****99999*****999**************************************************** PP
TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggr 334
g kiapif+nt+ed+galpie dv+++++gdv+++ py+g+ k+++v+a f +k+++l+devraggr
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 275 GSKIAPIFYNTMEDAGALPIELDVSQMEMGDVVELRPYDGKAL-KNGQVIAEFTVKSDVLFDEVRAGGR 342
*****************************************75.566********************** PP
TIGR00117 335 ipliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvtt 400
ipli+grglt karealgl++s +f+ +++pa++++gftlaqk+vg+acg+ kgirpgtycepk+t+
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 343 IPLIVGRGLTAKAREALGLAPSTLFRLPHNPADTGRGFTLAQKMVGRACGLpegKGIRPGTYCEPKMTS 411
**************************************************87779************** PP
TIGR00117 401 vgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdvkth+tlp+fis+rgg++lrpgdgvi
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 412 VGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVKTHHTLPQFISTRGGISLRPGDGVI 480
********************************************************************* PP
TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
hswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg++qpg+tlrd
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 481 HSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKMQPGVTLRD 549
********************************************************************* PP
TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvi 607
lvnaip+yaik glltv k+gk+n+f+gr+leieglpdlkveqafel+dasaersaagc ++lnkep+i
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 550 LVNAIPLYAIKSGLLTVAKQGKKNIFSGRVLEIEGLPDLKVEQAFELSDASAERSAAGCSVRLNKEPII 618
********************************************************************* PP
TIGR00117 608 eylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
ey++sni llk+miaegy+d r+l rri+ame+wla+p+lle+dadaeyaavieidla+++epi+a+pn
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 619 EYINSNITLLKWMIAEGYQDPRSLSRRIQAMEAWLADPKLLEPDADAEYAAVIEIDLADVHEPIVACPN 687
********************************************************************* PP
TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyai 745
dpddvk+lsevag +idevfigscmtnighfraa+k+le++++++ +lwv+ppt+md++ql+eeg y++
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 688 DPDDVKTLSEVAGAKIDEVFIGSCMTNIGHFRAASKLLEGKRDIPVKLWVAPPTKMDAKQLTEEGHYGV 756
********************************************************************* PP
TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
fg+agarte+pgcslcmgnqa+v++gatv+ststrnf+nrlgk ++vylgsaelaa+++ lg+iptkee
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 757 FGTAGARTEMPGCSLCMGNQAQVREGATVMSTSTRNFPNRLGKNTNVYLGSAELAAICSRLGRIPTKEE 825
********************************************************************* PP
TIGR00117 815 ylalvsekvesakdklyrylnfnelenfe 843
y++ + +++++ d++y+ylnf+++e+f+
lcl|FitnessBrowser__Cup4G11:RR42_RS23515 826 YMSDMG-VLATNGDQIYKYLNFDKIEDFK 853
**9875.889999**************97 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: 0.07u 0.03s 00:00:00.10 Elapsed: 00:00:00.09
# Mc/sec: 7.70
//
[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