Align aconitate hydratase (EC 4.2.1.3) (characterized)
to candidate AZOBR_RS17090 AZOBR_RS17090 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= BRENDA::P36683
(865 letters)
>FitnessBrowser__azobra:AZOBR_RS17090
Length = 861
Score = 1256 bits (3251), Expect = 0.0
Identities = 628/862 (72%), Positives = 720/862 (83%), Gaps = 6/862 (0%)
Query: 1 MLEEYRKHVAERAAEGIAPKPLDANQMAALVELLKNPPAGEEEFLLDLLTNRVPPGVDEA 60
+LE YR+HVAERAA GI PL A Q LV+LL NPP GEE FL+DL+T+RVP GVD+A
Sbjct: 1 VLEAYRQHVAERAALGIPALPLSAKQTEELVDLLLNPPQGEEAFLVDLITHRVPAGVDDA 60
Query: 61 AYVKAGFLAAIAKGEAKSPLLTPEKAIELLGTMQGGYNIHPLIDALDDAKLAPIAAKALS 120
A VKA FLA++AKG SPL++ KA ELLGTM GG+NI PLID L DA+ AA L
Sbjct: 61 AKVKAAFLASLAKGNETSPLISKVKATELLGTMLGGFNIKPLIDLLGDAECGEAAAAGLK 120
Query: 121 HTLLMFDNFYDVEEKAKAGNEYAKQVMQSWADAEWFLNRPALAEKLTVTVFKVTGETNTD 180
TLLMFD F+DV+E A GN AK V+QSWADAEWF +RP + LT+T+FKV+GETNTD
Sbjct: 121 TTLLMFDYFHDVKELADKGNANAKAVIQSWADAEWFTSRPEVPASLTLTIFKVSGETNTD 180
Query: 181 DLSPAPDAWSRPDIPLHALAMLKNAREGIEPDQPGVVGPIKQIEALQQKGFPLAYVGDVV 240
DLSPAPDAWSRPDIPLHALAMLKN R GI P+ GV GPIKQ+E L+ KG +AYVGDVV
Sbjct: 181 DLSPAPDAWSRPDIPLHALAMLKNPRPGIVPEDAGVRGPIKQLEDLKAKGNLVAYVGDVV 240
Query: 241 GTGSSRKSATNSVLWFMGDDIPHVPNKRGGGLCLGGKIAPIFFNTMEDAGALPIEVDVSN 300
GTGSSRKSATNSVLW+ G+DIP+VPNKR GG+CLG KIAPIF+NTMEDAGALPIE+DVS
Sbjct: 241 GTGSSRKSATNSVLWWTGEDIPYVPNKRFGGVCLGSKIAPIFYNTMEDAGALPIELDVSQ 300
Query: 301 LNMGDVIDVYPYKGEVRNHETGELLATFELKTDVLIDEVRAGGRIPLIIGRGLTTKAREA 360
+ GD +++ PY+G+ + G ++A F +K+DV+ DEVRAGGRIPLIIGRGLT +AREA
Sbjct: 301 METGDTVELRPYEGKALKN--GAVIAEFTVKSDVIFDEVRAGGRIPLIIGRGLTARAREA 358
Query: 361 LGLPHSDVFRQAKDVAESDRGFSLAQKMVGRACGV---KGIRPGAYCEPKMTSVGSQDTT 417
LGL S +FR +S +GF+LAQKMVGRA G+ +G+RPG YCEPKMT+VGSQDTT
Sbjct: 359 LGLAPSTLFRLPSSPVDSGKGFTLAQKMVGRAVGLPEGQGVRPGTYCEPKMTTVGSQDTT 418
Query: 418 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKPVDVNTHHTLPDFIMNRGGVSLRPGDG 477
GPMTRDELKDLACLGFSADLVMQSFCHTAAYPK VDV TH LP FI RGGV+LRPGDG
Sbjct: 419 GPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVKTHRELPTFISTRGGVALRPGDG 478
Query: 478 VIHSWLNRMLLPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 537
VIHSWLNR+L+PDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK
Sbjct: 479 VIHSWLNRLLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFK 538
Query: 538 GKMQPGITLRDLVHAIPLYAIKQGLLTVEKKGKKNIFSGRILEIEGLPDLKVEQAFELTD 597
G +QPG+TLRDLV+AIPLYAI+QGLLTVEKKGKKNIFSGRILEIEGLP+LKVEQAFEL+D
Sbjct: 539 GALQPGVTLRDLVNAIPLYAIRQGLLTVEKKGKKNIFSGRILEIEGLPELKVEQAFELSD 598
Query: 598 ASAERSAAGCTIKLNKEPIIEYLNSNIVLLKWMIAEGYGDRRTLERRIQGMEKWLANPEL 657
ASAERSAA CT++LNKEPIIEY+ SNI L+KWMIA GY D RTL RRI+ ME W+ANP L
Sbjct: 599 ASAERSAAACTVRLNKEPIIEYMRSNITLMKWMIANGYEDARTLGRRIKAMEDWIANPSL 658
Query: 658 LEADADAEYAAVIDIDLADIKEPILCAPNDPDDARPLSAVQGEKIDEVFIGSCMTNIGHF 717
LE DADAEYAAVIDIDLADIKEPI+ PNDPDD + LS V G+KIDEVFIGSCMTNIGHF
Sbjct: 659 LEPDADAEYAAVIDIDLADIKEPIVACPNDPDDVKLLSEVAGDKIDEVFIGSCMTNIGHF 718
Query: 718 RAAGKLLDAHKGQLPTRLWVAPPTRMDAAQLTEEGYYSVFGKSGARIEIPGCSLCMGNQA 777
RAAGK+LD K +PTRLW+APPT+MDA LTEEGYY V GKSGAR+E+PGCSLCMGNQA
Sbjct: 719 RAAGKILDG-KTDIPTRLWIAPPTKMDAQILTEEGYYGVLGKSGARMEMPGCSLCMGNQA 777
Query: 778 RVADGATVVSTSTRNFPNRLGTGANVFLASAELAAVAALIGKLPTPEEYQTYVAQVDKTA 837
++ G+T +STSTRNFPNRLG V+L SAEL+AVAAL+GKLPTP EY V+ V++ A
Sbjct: 778 QIRKGSTAISTSTRNFPNRLGIDTRVYLGSAELSAVAALLGKLPTPAEYLEQVSVVNQKA 837
Query: 838 VDTYRYLNFNQLSQYTEKADGV 859
D YRY+NF+Q+ ++ + AD V
Sbjct: 838 GDIYRYMNFDQIKEFQDVADTV 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: 2064
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 AZOBR_RS17090 AZOBR_RS17090 (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.25804.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 1489.8 0.0 0 1489.6 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS17090 AZOBR_RS17090 bifunctional aconi
Domain annotation for each sequence (and alignments):
>> lcl|FitnessBrowser__azobra:AZOBR_RS17090 AZOBR_RS17090 bifunctional aconitate hydratase 2/2-methylisocitrate dehydra
# score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc
--- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ----
1 ! 1489.6 0.0 0 0 1 844 [] 1 854 [. 1 854 [. 0.99
Alignments for each domain:
== domain 1 score: 1489.6 bits; conditional E-value: 0
TIGR00117 1 lleeyrkhvaeraaegiaplplnakqvaalvellkndpeaeeefllellidrvppgvdeaayvkagfla 69
+le+yr+hvaeraa+gi+ lpl akq+++lv+ll n+p++ee+fl++l+++rvp gvd+aa+vka fla
lcl|FitnessBrowser__azobra:AZOBR_RS17090 1 VLEAYRQHVAERAALGIPALPLSAKQTEELVDLLLNPPQGEEAFLVDLITHRVPAGVDDAAKVKAAFLA 69
69******************************************************************* PP
TIGR00117 70 aiakgevksplisaeeavellgtmlggynvepliealeskdkniakaaakalsktllvfdafddveels 138
++akg+ +splis +a+ellgtmlgg+n++pli++l d++ +aaa l++tll+fd f+dv+el+
lcl|FitnessBrowser__azobra:AZOBR_RS17090 70 SLAKGNETSPLISKVKATELLGTMLGGFNIKPLIDLLG--DAECGEAAAAGLKTTLLMFDYFHDVKELA 136
*************************************9..****************************9 PP
TIGR00117 139 kt.neyakqvleswaeaewflnkeelaekitvtvfkvdgetntddlspapdaftrpdiplhalamlknk 206
+ n+ ak v++swa+aewf ++e++ +t t+fkv+getntddlspapda++rpdiplhalamlkn
lcl|FitnessBrowser__azobra:AZOBR_RS17090 137 DKgNANAKAVIQSWADAEWFTSRPEVPASLTLTIFKVSGETNTDDLSPAPDAWSRPDIPLHALAMLKNP 205
988****************************************************************** PP
TIGR00117 207 ieeieq..........rikalkqkgvpvayvgdvvgtgssrksatnsvlwflgkdipfvpnkragglvl 265
+++i + ++++lk kg vayvgdvvgtgssrksatnsvlw+ g+dip+vpnkr gg++l
lcl|FitnessBrowser__azobra:AZOBR_RS17090 206 RPGIVPedagvrgpikQLEDLKAKGNLVAYVGDVVGTGSSRKSATNSVLWWTGEDIPYVPNKRFGGVCL 274
****9999************************************************************* PP
TIGR00117 266 ggkiapiffntaedsgalpievdvkdlnegdvikiypykgeitnketevvatfklkpetlldevraggr 334
g kiapif+nt+ed+galpie dv+++++gd +++ py+g+ k++ v+a f +k+++++devraggr
lcl|FitnessBrowser__azobra:AZOBR_RS17090 275 GSKIAPIFYNTMEDAGALPIELDVSQMETGDTVELRPYEGKAL-KNGAVIAEFTVKSDVIFDEVRAGGR 342
*****************************************75.5569********************* PP
TIGR00117 335 ipliigrgltdkarealglsesevfkkakapaesakgftlaqklvgkacgv...kgirpgtycepkvtt 400
ipliigrglt +arealgl++s +f+ +++p +s+kgftlaqk+vg+a g+ +g+rpgtycepk+tt
lcl|FitnessBrowser__azobra:AZOBR_RS17090 343 IPLIIGRGLTARAREALGLAPSTLFRLPSSPVDSGKGFTLAQKMVGRAVGLpegQGVRPGTYCEPKMTT 411
**************************************************87669************** PP
TIGR00117 401 vgsqdttgamtrdelkelaslgfdadlvlqsfchtaaypkpvdvkthktlpdfisqrggvalrpgdgvi 469
vgsqdttg+mtrdelk+la+lgf+adlv+qsfchtaaypk vdvkth++lp fis+rggvalrpgdgvi
lcl|FitnessBrowser__azobra:AZOBR_RS17090 412 VGSQDTTGPMTRDELKDLACLGFSADLVMQSFCHTAAYPKLVDVKTHRELPTFISTRGGVALRPGDGVI 480
********************************************************************* PP
TIGR00117 470 hswlnrmllpdtvgtggdshtrfplgisfpagsglvafaaatgvmpldmpesvlvrfkgelqpgitlrd 538
hswlnr+l+pdtvgtggdshtrfp+gisfpagsglvafaaatgvmpldmpesvlvrfkg lqpg+tlrd
lcl|FitnessBrowser__azobra:AZOBR_RS17090 481 HSWLNRLLMPDTVGTGGDSHTRFPIGISFPAGSGLVAFAAATGVMPLDMPESVLVRFKGALQPGVTLRD 549
********************************************************************* PP
TIGR00117 539 lvnaipyyaikkglltvekkgkvnvfngrileieglpdlkveqafeltdasaersaagctiklnkepvi 607
lvnaip+yai++glltvekkgk+n+f+grileieglp+lkveqafel+dasaersaa+ct++lnkep+i
lcl|FitnessBrowser__azobra:AZOBR_RS17090 550 LVNAIPLYAIRQGLLTVEKKGKKNIFSGRILEIEGLPELKVEQAFELSDASAERSAAACTVRLNKEPII 618
********************************************************************* PP
TIGR00117 608 eylksnivllkemiaegyedkrtlkrridamekwlanpelleadadaeyaavieidlaeikepilaapn 676
ey++sni l+k+mia+gyed+rtl rri+ame+w+anp+lle+dadaeyaavi+idla+ikepi+a+pn
lcl|FitnessBrowser__azobra:AZOBR_RS17090 619 EYMRSNITLMKWMIANGYEDARTLGRRIKAMEDWIANPSLLEPDADAEYAAVIDIDLADIKEPIVACPN 687
********************************************************************* PP
TIGR00117 677 dpddvkllsevagdaidevfigscmtnighfraagkileaaktvkarlwvvpptrmdeqqlieegyyai 745
dpddvkllsevagd+idevfigscmtnighfraagkil++++++++rlw++ppt+md+q l+eegyy++
lcl|FitnessBrowser__azobra:AZOBR_RS17090 688 DPDDVKLLSEVAGDKIDEVFIGSCMTNIGHFRAAGKILDGKTDIPTRLWIAPPTKMDAQILTEEGYYGV 756
********************************************************************* PP
TIGR00117 746 fgaagartevpgcslcmgnqarvedgatvfststrnfdnrlgkgakvylgsaelaavaallgkiptkee 814
+g++gar+e+pgcslcmgnqa+++ g+t +ststrnf+nrlg ++vylgsael+avaallgk+pt+ e
lcl|FitnessBrowser__azobra:AZOBR_RS17090 757 LGKSGARMEMPGCSLCMGNQAQIRKGSTAISTSTRNFPNRLGIDTRVYLGSAELSAVAALLGKLPTPAE 825
********************************************************************* PP
TIGR00117 815 ylalvsekvesakdklyrylnfnelenfee 844
yl+ vs + + a d +yry+nf+++++f++
lcl|FitnessBrowser__azobra:AZOBR_RS17090 826 YLEQVSVVNQKAGD-IYRYMNFDQIKEFQD 854
******88877776.************985 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: 0.04u 0.02s 00:00:00.06 Elapsed: 00:00:00.06
# Mc/sec: 11.98
//
[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