Align Aconitate hydratase B; ACN; Aconitase; (2R,3S)-2-methylisocitrate dehydratase; (2S,3R)-3-hydroxybutane-1,2,3-tricarboxylate dehydratase; 2-methyl-cis-aconitate hydratase; Iron-responsive protein-like; IRP-like; RNA-binding protein; EC 4.2.1.3; EC 4.2.1.99 (characterized)
to candidate WP_025165718.1 TMS3_RS13040 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= SwissProt::Q8ZRS8
(865 letters)
>NCBI__GCF_000498575.2:WP_025165718.1
Length = 869
Score = 1359 bits (3517), Expect = 0.0
Identities = 659/859 (76%), Positives = 753/859 (87%), Gaps = 3/859 (0%)
Query: 1 MLEEYRKHVAERAAQGIVPKPLDATQMAALVELLKTPPVGEEEFLLDLLINRVPPGVDEA 60
MLE YRKHVAERAAQGIVP+PL+A Q A L+ELLK PP GE+ FLLDL+ NRVPPGVDEA
Sbjct: 1 MLEAYRKHVAERAAQGIVPQPLNAEQTAGLIELLKNPPAGEQAFLLDLITNRVPPGVDEA 60
Query: 61 AYVKAGFLAAVAKGDTTSPLVSPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL+A+AKG+ TSPL+S + A+ELLGTMQGGYNI +++ LDD++LA + A+ L
Sbjct: 61 AYVKAGFLSAIAKGEATSPLISKQHAVELLGTMQGGYNIATMVELLDDSELAGVTAEQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLSRPPLAEKITVTVFKVTGETNTD 180
HTLLMFD F+DV EKAK GN +A+ V+QSWAD EWF +RP LA+KI++ VFKVTGETNTD
Sbjct: 121 HTLLMFDAFHDVAEKAKNGNAHAQGVLQSWADGEWFKNRPTLADKISLRVFKVTGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHAQAMLKNAREGIEPDQPGVVGPIKQIEALQKKGYPLAYVGDVV 240
DLSPAPDAWSRPDIPLHA AMLK AR+GI PD+ GV GP+KQIE ++ +G+P+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKMARDGIVPDEQGVTGPMKQIETMRGEGFPIAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPNVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDD+PNVPNKR GG C G KIAPIF+NTMEDAGALPIE DVSN
Sbjct: 241 GTGSSRKSATNSVLWFFGDDVPNVPNKRAGGFCFGNKIAPIFYNTMEDAGALPIEFDVSN 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
++MGDVID+YP+ G+V H T E+L TFE+KT VL+DEVRAGGRIPLIIGRGLT KAR
Sbjct: 301 MHMGDVIDLYPHAGKVCKHGTDEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAE 360
Query: 361 LGLPHSDVFRQAKDVAESSRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGL +D+F+ + A S++GF+LAQKMVG+ACG+ +G+RPG YCEPKMT+VGSQDTT
Sbjct: 361 LGLGPTDLFKLPEPPAASTKGFTLAQKMVGKACGLAEGQGVRPGTYCEPKMTTVGSQDTT 420
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVTTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKP+DVTTHHTLPDFI RGGVSLRPGDG
Sbjct: 421 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDG 480
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
+IHSWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPES+LVRFK
Sbjct: 481 IIHSWLNRMLLPDTVGTGGDSHTRFPMGISFPAGSGLVAFAAATGVMPLDMPESILVRFK 540
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
GK+QPG+TLRDLVHAIP YAI++GLLTVEKKGK N FSGRILEIEGL +L VEQAFEL+D
Sbjct: 541 GKLQPGVTLRDLVHAIPYYAIQKGLLTVEKKGKVNAFSGRILEIEGLDELTVEQAFELSD 600
Query: 598 ASAERSAAGCTIKLNKEPIVEYLTSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLADPQL 657
ASAERSAAGCTIKL ++ I EYL SNI LL+WMI+EGYGD RT+ERR Q ME WLA+PQL
Sbjct: 601 ASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMISEGYGDARTMERRAQAMEAWLANPQL 660
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARLLSDVQGEKIDEVFIGSCMTNIGHF 717
+ AD DAEYA +I+IDLA+I EPILCAPNDPDDARLLS V GEKIDEVFIGSCMTNIGHF
Sbjct: 661 MSADKDAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHF 720
Query: 718 RAAGKLLDNHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGKLL+ G LPTRLW++PPT+MD QLTEEGYY ++GK+GAR+E+PGCSLCMGNQA
Sbjct: 721 RAAGKLLEKVDGSLPTRLWLSPPTKMDQHQLTEEGYYEIYGKAGARLEMPGCSLCMGNQA 780
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
RV ATVVSTSTRNFPNRLG GANV+LASAELAAVA++IGKLPT EEY Y +D A
Sbjct: 781 RVEAKATVVSTSTRNFPNRLGDGANVYLASAELAAVASIIGKLPTVEEYMVYAKDIDSMA 840
Query: 838 VDTYRYLNFDQLSQYTEKA 856
D YRYL+FDQ++++ E A
Sbjct: 841 ADVYRYLSFDQIAEFREAA 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: 2207
Number of extensions: 85
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: 869
Length adjustment: 42
Effective length of query: 823
Effective length of database: 827
Effective search space: 680621
Effective search space used: 680621
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_025165718.1 TMS3_RS13040 (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.2769241.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 1515.9 0.0 0 1515.7 0.0 1.0 1 NCBI__GCF_000498575.2:WP_025165718.1
Domain annotation for each sequence (and alignments):
>> NCBI__GCF_000498575.2:WP_025165718.1
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1515.7 0.0 0 0 1 844 [] 1 857 [. 1 857 [. 0.99
Alignments for each domain:
== domain 1 score: 1515.7 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagflaaiak 73
+le+yrkhvaeraa+gi p+plna+q+a l+ellkn+p++e++fll+l+++rvppgvdeaayvkagfl+aiak
NCBI__GCF_000498575.2:WP_025165718.1 1 MLEAYRKHVAERAAQGIVPQPLNAEQTAGLIELLKNPPAGEQAFLLDLITNRVPPGVDEAAYVKAGFLSAIAK 73
79*********************************************************************** PP
TIGR00117 74 gevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveelskt.neyak 145
ge++splis ++avellgtm+ggyn+ +++e+l+ d+++a ++a+ l++tll+fdaf+dv+e++k n++a+
NCBI__GCF_000498575.2:WP_025165718.1 74 GEATSPLISKQHAVELLGTMQGGYNIATMVELLD--DSELAGVTAEQLKHTLLMFDAFHDVAEKAKNgNAHAQ 144
**********************************..*****************************999***** PP
TIGR00117 146 qvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknkieeieq...... 212
vl+swa++ewf n+++la+ki+ vfkv+getntddlspapda++rpdiplhalamlk ++++i +
NCBI__GCF_000498575.2:WP_025165718.1 145 GVLQSWADGEWFKNRPTLADKISLRVFKVTGETNTDDLSPAPDAWSRPDIPLHALAMLKMARDGIVPdeqgvt 217
****************************************************************999999*** PP
TIGR00117 213 ....rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvlggkiapiffntaedsg 281
+i++++ g+p+ayvgdvvgtgssrksatnsvlwf+g+d+p vpnkragg+++g kiapif+nt+ed+g
NCBI__GCF_000498575.2:WP_025165718.1 218 gpmkQIETMRGEGFPIAYVGDVVGTGSSRKSATNSVLWFFGDDVPNVPNKRAGGFCFGNKIAPIFYNTMEDAG 290
************************************************************************* PP
TIGR00117 282 alpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevraggripliigrgltdkarealgl 353
alpie dv+++++gdvi++yp+ g++ ++ t ev++tf++k+ +lldevraggripliigrglt+kar lgl
NCBI__GCF_000498575.2:WP_025165718.1 291 ALPIEFDVSNMHMGDVIDLYPHAGKVCKHGTdEVLTTFEMKTPVLLDEVRAGGRIPLIIGRGLTEKARAELGL 363
*****************************9999**************************************** PP
TIGR00117 354 sesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvttvgsqdttgamtrdelkelaslgf 423
+++++fk ++ pa s+kgftlaqk+vgkacg+ +g+rpgtycepk+ttvgsqdttg+mtrdelk+la+lgf
NCBI__GCF_000498575.2:WP_025165718.1 364 GPTDLFKLPEPPAASTKGFTLAQKMVGKACGLaegQGVRPGTYCEPKMTTVGSQDTTGPMTRDELKDLACLGF 436
*******************************86668************************************* PP
TIGR00117 424 dadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihswlnrmllpdtvgtggdshtrfplgi 496
+adlv+qsfchtaaypkp+dv th+tlpdfi +rggv+lrpgdg+ihswlnrmllpdtvgtggdshtrfp+gi
NCBI__GCF_000498575.2:WP_025165718.1 437 SADLVMQSFCHTAAYPKPIDVTTHHTLPDFIRTRGGVSLRPGDGIIHSWLNRMLLPDTVGTGGDSHTRFPMGI 509
************************************************************************* PP
TIGR00117 497 sfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlvnaipyyaikkglltvekkgkvnvfngril 569
sfpagsglvafaaatgvmpldmpes+lvrfkg+lqpg+tlrdlv+aipyyai+kglltvekkgkvn f+gril
NCBI__GCF_000498575.2:WP_025165718.1 510 SFPAGSGLVAFAAATGVMPLDMPESILVRFKGKLQPGVTLRDLVHAIPYYAIQKGLLTVEKKGKVNAFSGRIL 582
************************************************************************* PP
TIGR00117 570 eieglpdlkveqafeltdasaersaagctiklnkepvieylksnivllkemiaegyedkrtlkrridamekwl 642
eiegl +l veqafel+dasaersaagctikl +++++eyl+sni ll++mi+egy+d+rt++rr +ame+wl
NCBI__GCF_000498575.2:WP_025165718.1 583 EIEGLDELTVEQAFELSDASAERSAAGCTIKLPEKAIAEYLQSNITLLRWMISEGYGDARTMERRAQAMEAWL 655
************************************************************************* PP
TIGR00117 643 anpelleadadaeyaavieidlaeikepilaapndpddvkllsevagdaidevfigscmtnighfraagkile 715
anp+l++ad daeya++ieidlaei+epil+apndpdd++lls vag++idevfigscmtnighfraagk+le
NCBI__GCF_000498575.2:WP_025165718.1 656 ANPQLMSADKDAEYAEIIEIDLAEINEPILCAPNDPDDARLLSSVAGEKIDEVFIGSCMTNIGHFRAAGKLLE 728
************************************************************************9 PP
TIGR00117 716 aak.tvkarlwvvpptrmdeqqlieegyyaifgaagartevpgcslcmgnqarvedgatvfststrnfdnrlg 787
+ + ++++rlw+ ppt+md++ql+eegyy i+g+agar+e+pgcslcmgnqarve +atv+ststrnf+nrlg
NCBI__GCF_000498575.2:WP_025165718.1 729 KVDgSLPTRLWLSPPTKMDQHQLTEEGYYEIYGKAGARLEMPGCSLCMGNQARVEAKATVVSTSTRNFPNRLG 801
987799******************************************************************* PP
TIGR00117 788 kgakvylgsaelaavaallgkiptkeeylalvsekvesakdklyrylnfnelenfee 844
ga+vyl+saelaava+++gk+pt+eey+ + + + a d +yryl f+++ +f+e
NCBI__GCF_000498575.2:WP_025165718.1 802 DGANVYLASAELAAVASIIGKLPTVEEYMVYAKDIDSMAAD-VYRYLSFDQIAEFRE 857
*****************************998888777777.************985 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (869 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.03
# Mc/sec: 22.82
//
[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