Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_090447774.1 BLS63_RS21135 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_900100495.1:WP_090447774.1
Length = 866
Score = 1369 bits (3544), Expect = 0.0
Identities = 667/856 (77%), Positives = 753/856 (87%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR HVA RA +G+ P L+A Q A LVELLKNPPAGEEE LLDL+TNRVPPGVDEA
Sbjct: 1 MLEAYRNHVAARAEQGLPPLALNAEQTAGLVELLKNPPAGEEEVLLDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKG A SPLL+ +A+ELLGTMQGGYNI L++ LDDA+L +AA+ L
Sbjct: 61 AYVKAGFLSAVAKGAAGSPLLSKTRAVELLGTMQGGYNIATLVELLDDAELGSVAAEQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DV EKAKAGN +AK V+QSWAD EWF RPA+AEK +++VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKAGNAHAKAVLQSWADGEWFTKRPAIAEKYSLSVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLK AR+GIEP+Q G +GP+KQI A++ KGFP+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIEPEQQGAIGPLKQIAAIKAKGFPVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDDIP+VPNKR GG C G KIAPIF+NTMEDAGALPIE DV+N
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCFGNKIAPIFYNTMEDAGALPIEFDVAN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
L MGDVIDVYPY G+V H + +++ FELKT+VL+DEVRAGGRIPLI+GRGLT KAR
Sbjct: 301 LEMGDVIDVYPYAGKVCKHGSDQVITRFELKTEVLLDEVRAGGRIPLIVGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGL S++F + A+S +GF+LAQKMVG+ACGV G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLGVSELFNKPVAPADSGKGFTLAQKMVGKACGVTGVRPGTYCEPKMTTVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDF+ +RGGVSL+PGDG+IH
Sbjct: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFMRSRGGVSLKPGDGIIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK+
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKL 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPGITLRDLVHAIP YAI++GLLTVEKKGK N FSGRILEIEGL +L VEQAFEL+DASA
Sbjct: 541 QPGITLRDLVHAIPYYAIQKGLLTVEKKGKINAFSGRILEIEGLDELTVEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTIKL ++ I EYL SNI LL+WMI EGYGD RTLERR Q ME WLANP+L+ A
Sbjct: 601 ERSAAGCTIKLPEKAIAEYLQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPQLMSA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
DADAEYA V++IDLA+I +PILCAPNDPDDAR LS+VQGEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DADAEYAEVVEIDLAEINQPILCAPNDPDDARLLSSVQGEKIDEVFIGSCMTNIGHFRAA 720
Query: 721 GKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARVA 780
GKLLD KG +PTRLW++PPT+MDA QLTEEGYY ++GK+GAR+E+PGCSLCMGNQARVA
Sbjct: 721 GKLLDKVKGGIPTRLWLSPPTKMDAHQLTEEGYYGIYGKAGARMEMPGCSLCMGNQARVA 780
Query: 781 DGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVDT 840
ATVVSTSTRNFPNRLG GANV+LASAELAAVAA+ GKLPT EEY Y +D A D
Sbjct: 781 ANATVVSTSTRNFPNRLGDGANVYLASAELAAVAAITGKLPTVEEYMAYAKDIDSMAADV 840
Query: 841 YRYLNFNQLSQYTEKA 856
YRYL+F+Q++++ E A
Sbjct: 841 YRYLSFDQIAEFREAA 856
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: 2127
Number of extensions: 76
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: 866
Length adjustment: 42
Effective length of query: 823
Effective length of database: 824
Effective search space: 678152
Effective search space used: 678152
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_090447774.1 BLS63_RS21135 (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.9234.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 1541.9 0.0 0 1541.8 0.0 1.0 1 lcl|NCBI__GCF_900100495.1:WP_090447774.1 BLS63_RS21135 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_900100495.1:WP_090447774.1 BLS63_RS21135 bifunctional aconitate hydratase 2/2-methylisocitrate dehydra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1541.8 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1541.8 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr+hva ra++g++pl lna+q+a lvellkn+p++eee ll+l+++rvppgvdeaayvkagfl+
lcl|NCBI__GCF_900100495.1:WP_090447774.1 1 MLEAYRNHVAARAEQGLPPLALNAEQTAGLVELLKNPPAGEEEVLLDLITNRVPPGVDEAAYVKAGFLS 69
79******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
a+akg + spl+s +avellgtm+ggyn+ +l+e+l+ d+++ ++aa+ l++tll+fdaf+dv+e++
lcl|NCBI__GCF_900100495.1:WP_090447774.1 70 AVAKGAAGSPLLSKTRAVELLGTMQGGYNIATLVELLD--DAELGSVAAEQLKHTLLMFDAFHDVAEKA 136
**************************************..***************************** PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
k+ n++ak vl+swa++ewf ++++aek + +vfkv+getntddlspapda++rpdiplhalamlk +
lcl|NCBI__GCF_900100495.1:WP_090447774.1 137 KAgNAHAKAVLQSWADGEWFTKRPAIAEKYSLSVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKMA 205
**9****************************************************************** PP
TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
+++ie+ +i+a+k kg+pvayvgdvvgtgssrksatnsvlwf+g+dip+vpnkragg+++
lcl|NCBI__GCF_900100495.1:WP_090447774.1 206 RDGIEPeqqgaigplkQIAAIKAKGFPVAYVGDVVGTGSSRKSATNSVLWFFGDDIPYVPNKRAGGFCF 274
****9999************************************************************* PP
TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevragg 333
g kiapif+nt+ed+galpie dv +l++gdvi++ypy g++ ++ + +v++ f+lk+e+lldevragg
lcl|NCBI__GCF_900100495.1:WP_090447774.1 275 GNKIAPIFYNTMEDAGALPIEFDVANLEMGDVIDVYPYAGKVCKHGSdQVITRFELKTEVLLDEVRAGG 343
********************************************998799******************* PP
TIGR00117 334 ripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvg 402
ripli+grglt+kar lgl+ se+f+k+ apa+s+kgftlaqk+vgkacgv g+rpgtycepk+ttvg
lcl|NCBI__GCF_900100495.1:WP_090447774.1 344 RIPLIVGRGLTEKARAELGLGVSELFNKPVAPADSGKGFTLAQKMVGKACGVTGVRPGTYCEPKMTTVG 412
********************************************************************* PP
TIGR00117 403 sqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihs 471
sqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdv+th+tlpdf+ +rggv+l+pgdg+ihs
lcl|NCBI__GCF_900100495.1:WP_090447774.1 413 SQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFMRSRGGVSLKPGDGIIHS 481
********************************************************************* PP
TIGR00117 472 wlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlv 540
wlnrmllpdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg+lqpgitlrdlv
lcl|NCBI__GCF_900100495.1:WP_090447774.1 482 WLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKLQPGITLRDLV 550
********************************************************************* PP
TIGR00117 541 naipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepviey 609
+aipyyai+kglltvekkgk+n f+grileiegl +l veqafel+dasaersaagctikl +++++ey
lcl|NCBI__GCF_900100495.1:WP_090447774.1 551 HAIPYYAIQKGLLTVEKKGKINAFSGRILEIEGLDELTVEQAFELSDASAERSAAGCTIKLPEKAIAEY 619
********************************************************************* PP
TIGR00117 610 lksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndp 678
l+sni ll++mi egy+d+rtl+rr +ame+wlanp+l++adadaeya+v+eidlaei++pil+apndp
lcl|NCBI__GCF_900100495.1:WP_090447774.1 620 LQSNITLLRWMIGEGYGDARTLERRAQAMEAWLANPQLMSADADAEYAEVVEIDLAEINQPILCAPNDP 688
********************************************************************* PP
TIGR00117 679 ddvkllsevagdaidevfigscmtnighfraagkileaak.tvkarlwvvpptrmdeqqlieegyyaif 746
dd++lls v+g++idevfigscmtnighfraagk+l++ k +++rlw+ ppt+md++ql+eegyy+i+
lcl|NCBI__GCF_900100495.1:WP_090447774.1 689 DDARLLSSVQGEKIDEVFIGSCMTNIGHFRAAGKLLDKVKgGIPTRLWLSPPTKMDAHQLTEEGYYGIY 757
*************************************99879*************************** PP
TIGR00117 747 gaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkeey 815
g+agar+e+pgcslcmgnqarv+ +atv+ststrnf+nrlg ga+vyl+saelaavaa+ gk+pt+eey
lcl|NCBI__GCF_900100495.1:WP_090447774.1 758 GKAGARMEMPGCSLCMGNQARVAANATVVSTSTRNFPNRLGDGANVYLASAELAAVAAITGKLPTVEEY 826
********************************************************************* PP
TIGR00117 816 lalvsekvesakdklyrylnfnelenfee 844
+a+ + + a d +yryl f+++ +f+e
lcl|NCBI__GCF_900100495.1:WP_090447774.1 827 MAYAKDIDSMAAD-VYRYLSFDQIAEFRE 854
***9888877777.************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (866 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: 00:00:00.06
# Mc/sec: 11.11
//
[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