Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate GFF2253 HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__Marino:GFF2253
Length = 864
Score = 1269 bits (3284), Expect = 0.0
Identities = 620/859 (72%), Positives = 720/859 (83%), Gaps = 4/859 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR+HVAER A GI PKPL+A Q AALV+LLKNPPAGEE+ L+ LL NRVPPGVDEA
Sbjct: 1 MLEAYREHVAEREALGIPPKPLNAEQTAALVDLLKNPPAGEEDTLVYLLENRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKA FL AI KGEA SPLL A++LLG MQGGYNI L+D LDD++LA +A + L
Sbjct: 61 AYVKAAFLTAIVKGEASSPLLDKPTAVKLLGMMQGGYNIATLVDLLDDSELAELAGEQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD F DV+EK AGN A+ V++SWA+ EWF N+ + E + VFKVTGETNTD
Sbjct: 121 RTLLMFDAFNDVKEKMDAGNPVARAVIESWANGEWFTNKKKVPESTKMVVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHA A K R+G++P++PGV GP+ QI+ ++ KG P+A+VGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHARAAYKMERDGLKPEEPGVTGPMSQIDEIKAKGLPVAFVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDDIP VPNKR GG+C+G K+APIFFNTMEDAGAL E V +
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPGVPNKRAGGVCIGNKVAPIFFNTMEDAGALVFEAPVDD 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+NMGDVI++ PY G++ N E GE ++ F+ K+DV++DEV+AGGRIPLIIGRGLT KAR A
Sbjct: 301 MNMGDVIEIRPYDGKILN-EAGETISEFKFKSDVILDEVQAGGRIPLIIGRGLTAKARTA 359
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LG+ +D+FR KD +GF+LAQKMVG+ACG+ KG+RP YCEP MT+VGSQDTT
Sbjct: 360 LGMGATDLFRLPKDPEAGTKGFTLAQKMVGKACGLEEGKGVRPNTYCEPHMTTVGSQDTT 419
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV HT+PDFI RGGVSLRPGDG
Sbjct: 420 GPMTRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVEMQHTMPDFIRTRGGVSLRPGDG 479
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 480 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 539
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
G+MQPGITLRDLVHAIPLY IKQG+LTVEKKGK N FSGRILEIEGL L VEQAFEL+D
Sbjct: 540 GEMQPGITLRDLVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELSD 599
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAAGCTI L+++ + EYL SNI +L+WMIAEGYGD RTLERR Q ME+WLA+P+L
Sbjct: 600 ASAERSAAGCTINLSEDSVAEYLRSNITMLRWMIAEGYGDPRTLERRAQQMEEWLADPKL 659
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
+ AD DAEYA VI+IDLADIKEPI+C PNDPDDA+ LS V G+K+DEVFIGSCMTNIGHF
Sbjct: 660 MRADKDAEYAHVIEIDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMTNIGHF 719
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ HKG L TRLW++PPT+MD AQL EEGY++ +G +G R E+PGCSLCMGNQA
Sbjct: 720 RAAGKLLEQHKGPLSTRLWMSPPTKMDQAQLMEEGYFNTYGTAGVRTEMPGCSLCMGNQA 779
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RVA +TV+STSTRNFPNRLG GANV+L SAELAAV A++GKLP+P EY Y ++ +
Sbjct: 780 RVAPKSTVLSTSTRNFPNRLGDGANVYLTSAELAAVGAVLGKLPSPAEYMEYAKDLNSMS 839
Query: 838 VDTYRYLNFNQLSQYTEKA 856
+ Y+YLNF+Q+ YT+KA
Sbjct: 840 KEIYKYLNFDQMENYTKKA 858
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: 2088
Number of extensions: 72
Number of successful extensions: 3
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: 864
Length adjustment: 42
Effective length of query: 823
Effective length of database: 822
Effective search space: 676506
Effective search space used: 676506
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 GFF2253 HP15_2203 (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.7999.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 1467.3 0.0 0 1467.1 0.0 1.0 1 lcl|FitnessBrowser__Marino:GFF2253 HP15_2203 bifunctional aconitate
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__Marino:GFF2253 HP15_2203 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1467.1 0.0 0 0 1 843 [. 1 855 [. 1 856 [. 0.99
Alignments for each domain:
== domain 1 score: 1467.1 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiakge 75
+le+yr hvaer+a+gi+p+plna+q+aalv+llkn+p++ee+ l+ ll +rvppgvdeaayvka fl+ai kge
lcl|FitnessBrowser__Marino:GFF2253 1 MLEAYREHVAEREALGIPPKPLNAEQTAALVDLLKNPPAGEEDTLVYLLENRVPPGVDEAAYVKAAFLTAIVKGE 75
79************************************************************************* PP
TIGR00117 76 vksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyakqvle 149
+ spl+ av+llg m+ggyn+ +l+++l+ d+++a+ a + l++tll+fdaf+dv+e+ ++ n +a+ v+e
lcl|FitnessBrowser__Marino:GFF2253 76 ASSPLLDKPTAVKLLGMMQGGYNIATLVDLLD--DSELAELAGEQLKRTLLMFDAFNDVKEKMDAgNPVARAVIE 148
********************************..****************************9999********* PP
TIGR00117 150 swaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq..........ri 214
swa++ewf nk++++e +++vfkv+getntddlspapda++rpdiplha+a k ++++ ++ +i
lcl|FitnessBrowser__Marino:GFF2253 149 SWANGEWFTNKKKVPESTKMVVFKVTGETNTDDLSPAPDAWSRPDIPLHARAAYKMERDGLKPeepgvtgpmsQI 223
***********************************************************9999999********* PP
TIGR00117 215 kalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsgalpievdv 289
+++k kg pva+vgdvvgtgssrksatnsvlwf+g+dip vpnkragg+++g k+apiffnt+ed+gal e+ v
lcl|FitnessBrowser__Marino:GFF2253 224 DEIKAKGLPVAFVGDVVGTGSSRKSATNSVLWFFGDDIPGVPNKRAGGVCIGNKVAPIFFNTMEDAGALVFEAPV 298
*************************************************************************** PP
TIGR00117 290 kdlnegdvikiypykgeitnketevvatfklkpetlldevraggripliigrgltdkarealglsesevfkkaka 364
+d+n+gdvi+i py+g+i n+++e+++ fk+k++++ldev+aggripliigrglt kar alg++ +++f+ +k+
lcl|FitnessBrowser__Marino:GFF2253 299 DDMNMGDVIEIRPYDGKILNEAGETISEFKFKSDVILDEVQAGGRIPLIIGRGLTAKARTALGMGATDLFRLPKD 373
*************************************************************************** PP
TIGR00117 365 paesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgfdadlvlqsfchta 436
p+ +kgftlaqk+vgkacg+ kg+rp tycep++ttvgsqdttg+mtrdelk+la+lgf+adlv+qsfchta
lcl|FitnessBrowser__Marino:GFF2253 374 PEAGTKGFTLAQKMVGKACGLeegKGVRPNTYCEPHMTTVGSQDTTGPMTRDELKDLACLGFQADLVMQSFCHTA 448
********************86668************************************************** PP
TIGR00117 437 aypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaat 511
aypkpvdv++ +t+pdfi +rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaat
lcl|FitnessBrowser__Marino:GFF2253 449 AYPKPVDVEMQHTMPDFIRTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAAT 523
*************************************************************************** PP
TIGR00117 512 gvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafelt 586
gvmpldmpesvlvrfkge+qpgitlrdlv+aip+y ik+g+ltvekkgk+n f+grileiegl l veqafel+
lcl|FitnessBrowser__Marino:GFF2253 524 GVMPLDMPESVLVRFKGEMQPGITLRDLVHAIPLYGIKQGMLTVEKKGKINEFSGRILEIEGLEHLTVEQAFELS 598
*************************************************************************** PP
TIGR00117 587 dasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavie 661
dasaersaagcti+l++++v+eyl+sni +l++miaegy+d rtl+rr ++me+wla+p+l+ ad daeya vie
lcl|FitnessBrowser__Marino:GFF2253 599 DASAERSAAGCTINLSEDSVAEYLRSNITMLRWMIAEGYGDPRTLERRAQQMEEWLADPKLMRADKDAEYAHVIE 673
*************************************************************************** PP
TIGR00117 662 idlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeq 735
idla+ikepi+++pndpdd+k lsevagd++devfigscmtnighfraagk+le++k ++ +rlw+ ppt+md++
lcl|FitnessBrowser__Marino:GFF2253 674 IDLADIKEPIVCCPNDPDDAKFLSEVAGDKVDEVFIGSCMTNIGHFRAAGKLLEQHKgPLSTRLWMSPPTKMDQA 748
********************************************************999**************** PP
TIGR00117 736 qlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkip 810
ql+eegy++ +g+ag rte+pgcslcmgnqarv+ ++tv+ststrnf+nrlg ga+vyl+saelaav a+lgk+p
lcl|FitnessBrowser__Marino:GFF2253 749 QLMEEGYFNTYGTAGVRTEMPGCSLCMGNQARVAPKSTVLSTSTRNFPNRLGDGANVYLTSAELAAVGAVLGKLP 823
*************************************************************************** PP
TIGR00117 811 tkeeylalvsekvesakdklyrylnfnelenfe 843
++ ey+++ + ++s+ +++y+ylnf+++en++
lcl|FitnessBrowser__Marino:GFF2253 824 SPAEYMEYAKD-LNSMSKEIYKYLNFDQMENYT 855
*******9665.6677777*************8 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (864 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: 12.90
//
[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