Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate WP_086509646.1 BZY95_RS09205 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>NCBI__GCF_002151265.1:WP_086509646.1
Length = 867
Score = 1370 bits (3547), Expect = 0.0
Identities = 671/861 (77%), Positives = 752/861 (87%), Gaps = 1/861 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
MLE YR+HV ERAAEG+ PKPL+A Q AALVELLKNPPAGEEEF+LDLLTNR+PPGVDEA
Sbjct: 1 MLEAYRQHVEERAAEGVPPKPLNAEQAAALVELLKNPPAGEEEFVLDLLTNRIPPGVDEA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
AYVKAGFL AI KGEA+SPL+ A++LLGTMQGGYNI L++ LDDA+LA A + L
Sbjct: 61 AYVKAGFLTAITKGEAQSPLVDKVHAVKLLGTMQGGYNIATLVELLDDAELAKEAGEQLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
HTLLMFD F+DVEE+AKAGN AK VMQSWA+AEWFL++PALAEK+T+TVFKV GETNTD
Sbjct: 121 HTLLMFDAFHDVEERAKAGNAVAKDVMQSWAEAEWFLSKPALAEKITLTVFKVPGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHA AMLKN REGI P+ PG GP+KQIE ++ KG+P+AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHANAMLKNEREGIVPEVPGTTGPLKQIEEVKAKGYPVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLWF GDDIP+VPNKR GG C GGKIAPIFFNTMEDAGALP+E+DVS
Sbjct: 241 GTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCFGGKIAPIFFNTMEDAGALPVEMDVSK 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
L MGDVIDVYPY+G+V H T E+L TFELKT V++DEVRAGGRIPLIIGRGLT KARE+
Sbjct: 301 LEMGDVIDVYPYEGKVCKHGTDEVLTTFELKTQVILDEVRAGGRIPLIIGRGLTGKARES 360
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGVKGIRPGAYCEPKMTSVGSQDTTGPM 420
LGL SDVFR + ++ +GF+LAQKMVG+ACG+ G+RPG YCEPKMT+VGSQDTTGPM
Sbjct: 361 LGLAPSDVFRLPEQPKDTGKGFTLAQKMVGKACGMAGVRPGMYCEPKMTTVGSQDTTGPM 420
Query: 421 TRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDGVIH 480
TRDELKDLACLGF ADLVMQSFCHTAAYPKPVDV THHTLPDFIMNRGGVSLRPGDG+IH
Sbjct: 421 TRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIH 480
Query: 481 SWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKM 540
SWLNRMLLPDTVGTGGDSHTRFP+GISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGK
Sbjct: 481 SWLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKR 540
Query: 541 QPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTDASA 600
QPG+TLRDLVHAIP YAIKQGLLTV K GKKN FSGR+LEIEGL DL VEQAFEL+DASA
Sbjct: 541 QPGVTLRDLVHAIPYYAIKQGLLTVAKAGKKNAFSGRVLEIEGLEDLTVEQAFELSDASA 600
Query: 601 ERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPELLEA 660
ERSAAGCTI L + + EYL SNI LLKWMIA GYGD+RT+ERRI ME+WLANP L+ A
Sbjct: 601 ERSAAGCTITLGEASVTEYLKSNITLLKWMIANGYGDKRTIERRILAMEEWLANPSLMRA 660
Query: 661 DADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHFRAA 720
D DAEYA VI+IDL ++KEP+LCAPNDPDDAR LS V GEKIDEVFIGSCMTNIGHFRAA
Sbjct: 661 DKDAEYAEVIEIDLDELKEPVLCAPNDPDDARLLSEVAGEKIDEVFIGSCMTNIGHFRAA 720
Query: 721 GKLLDAH-KGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQARV 779
GKLL+ G L TRLW+APPT+MD QLTEEGYY ++G++GAR+E+PGCSLCMGNQARV
Sbjct: 721 GKLLEKQPAGSLKTRLWLAPPTKMDQHQLTEEGYYGIYGRAGARMEMPGCSLCMGNQARV 780
Query: 780 ADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTAVD 839
A +TVVSTSTRNFPNRLG GANV+LASAELAAVAA+ G+LP+ EEYQ Y+ + D A +
Sbjct: 781 AAKSTVVSTSTRNFPNRLGDGANVYLASAELAAVAAVEGRLPSVEEYQRYMGEFDAMAGE 840
Query: 840 TYRYLNFNQLSQYTEKADGVI 860
YRY+NF+++ +Y A VI
Sbjct: 841 IYRYMNFHEIEEYQNAASNVI 861
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: 2191
Number of extensions: 73
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: 867
Length adjustment: 42
Effective length of query: 823
Effective length of database: 825
Effective search space: 678975
Effective search space used: 678975
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_086509646.1 BZY95_RS09205 (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.3050.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 1560.0 0.0 0 1559.8 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086509646.1 BZY95_RS09205 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|NCBI__GCF_002151265.1:WP_086509646.1 BZY95_RS09205 bifunctional aconitate hydratase 2/2-methylisocitrate dehydra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1559.8 0.0 0 0 1 843 [. 1 854 [. 1 855 [. 0.99
Alignments for each domain:
== domain 1 score: 1559.8 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr+hv eraaeg++p+plna+q aalvellkn+p++eeef+l+ll++r+ppgvdeaayvkagfl+
lcl|NCBI__GCF_002151265.1:WP_086509646.1 1 MLEAYRQHVEERAAEGVPPKPLNAEQAAALVELLKNPPAGEEEFVLDLLTNRIPPGVDEAAYVKAGFLT 69
79******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
ai+kge++spl+ +av+llgtm+ggyn+ +l+e+l+ d+++ak+a + l++tll+fdaf+dvee +
lcl|NCBI__GCF_002151265.1:WP_086509646.1 70 AITKGEAQSPLVDKVHAVKLLGTMQGGYNIATLVELLD--DAELAKEAGEQLKHTLLMFDAFHDVEERA 136
**************************************..***************************** PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
k+ n++ak+v++swaeaewfl k++laekit tvfkv+getntddlspapda++rpdiplha amlkn+
lcl|NCBI__GCF_002151265.1:WP_086509646.1 137 KAgNAVAKDVMQSWAEAEWFLSKPALAEKITLTVFKVPGETNTDDLSPAPDAWSRPDIPLHANAMLKNE 205
**9****************************************************************** PP
TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
+e+i + +i+++k kg+pvayvgdvvgtgssrksatnsvlwf+g+dip vpnkragg+++
lcl|NCBI__GCF_002151265.1:WP_086509646.1 206 REGIVPevpgttgplkQIEEVKAKGYPVAYVGDVVGTGSSRKSATNSVLWFFGDDIPNVPNKRAGGFCF 274
****999************************************************************** PP
TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnket.evvatfklkpetlldevragg 333
ggkiapiffnt+ed+galp+e+dv++l++gdvi++ypy+g++ ++ t ev++tf+lk++++ldevragg
lcl|NCBI__GCF_002151265.1:WP_086509646.1 275 GGKIAPIFFNTMEDAGALPVEMDVSKLEMGDVIDVYPYEGKVCKHGTdEVLTTFELKTQVILDEVRAGG 343
*********************************************9999******************** PP
TIGR00117 334 ripliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgvkgirpgtycepkvttvg 402
ripliigrglt kare lgl++s+vf+ +++p++++kgftlaqk+vgkacg+ g+rpg ycepk+ttvg
lcl|NCBI__GCF_002151265.1:WP_086509646.1 344 RIPLIIGRGLTGKARESLGLAPSDVFRLPEQPKDTGKGFTLAQKMVGKACGMAGVRPGMYCEPKMTTVG 412
********************************************************************* PP
TIGR00117 403 sqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvihs 471
sqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypkpvdv+th+tlpdfi++rggv+lrpgdg+ihs
lcl|NCBI__GCF_002151265.1:WP_086509646.1 413 SQDTTGPMTRDELKDLACLGFQADLVMQSFCHTAAYPKPVDVETHHTLPDFIMNRGGVSLRPGDGIIHS 481
********************************************************************* PP
TIGR00117 472 wlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrdlv 540
wlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkg+ qpg+tlrdlv
lcl|NCBI__GCF_002151265.1:WP_086509646.1 482 WLNRMLLPDTVGTGGDSHTRFPLGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGKRQPGVTLRDLV 550
********************************************************************* PP
TIGR00117 541 naipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepviey 609
+aipyyaik+glltv k gk+n f+gr+leiegl dl veqafel+dasaersaagcti l + +v ey
lcl|NCBI__GCF_002151265.1:WP_086509646.1 551 HAIPYYAIKQGLLTVAKAGKKNAFSGRVLEIEGLEDLTVEQAFELSDASAERSAAGCTITLGEASVTEY 619
********************************************************************* PP
TIGR00117 610 lksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapndp 678
lksni llk+mia+gy+dkrt++rri ame+wlanp+l+ ad daeya+vieidl+e+kep+l+apndp
lcl|NCBI__GCF_002151265.1:WP_086509646.1 620 LKSNITLLKWMIANGYGDKRTIERRILAMEEWLANPSLMRADKDAEYAEVIEIDLDELKEPVLCAPNDP 688
********************************************************************* PP
TIGR00117 679 ddvkllsevagdaidevfigscmtnighfraagkileaak..tvkarlwvvpptrmdeqqlieegyyai 745
dd++llsevag++idevfigscmtnighfraagk+le+++ ++k+rlw++ppt+md++ql+eegyy+i
lcl|NCBI__GCF_002151265.1:WP_086509646.1 689 DDARLLSEVAGEKIDEVFIGSCMTNIGHFRAAGKLLEKQPagSLKTRLWLAPPTKMDQHQLTEEGYYGI 757
************************************99775699************************* PP
TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
+g+agar+e+pgcslcmgnqarv+ ++tv+ststrnf+nrlg ga+vyl+saelaavaa+ g++p++ee
lcl|NCBI__GCF_002151265.1:WP_086509646.1 758 YGRAGARMEMPGCSLCMGNQARVAAKSTVVSTSTRNFPNRLGDGANVYLASAELAAVAAVEGRLPSVEE 826
********************************************************************* PP
TIGR00117 815 ylalvsekvesakdklyrylnfnelenfe 843
y+ ++ e ++ +++yry+nf e+e+++
lcl|NCBI__GCF_002151265.1:WP_086509646.1 827 YQRYMGEFDAM-AGEIYRYMNFHEIEEYQ 854
******98765.567************97 PP
Internal pipeline statistics summary:
-------------------------------------
Query model(s): 1 (844 nodes)
Target sequences: 1 (867 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: 12.54
//
[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